Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1519:8bd0d897763f
refactoring: IHttpStreamAnswer
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 11 Aug 2015 13:15:16 +0200 |
| parents | f967bdf8534e |
| children | 4a503a8c7749 |
| rev | line source |
|---|---|
| 790 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
|
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
| 790 | 5 * |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 | |
| 34 /*========================================================================= | |
| 35 | |
| 36 This file is based on portions of the following project: | |
| 37 | |
| 38 Program: GDCM (Grassroots DICOM). A DICOM library | |
| 39 Module: http://gdcm.sourceforge.net/Copyright.html | |
| 40 | |
| 41 Copyright (c) 2006-2011 Mathieu Malaterre | |
| 42 Copyright (c) 1993-2005 CREATIS | |
| 43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
| 44 All rights reserved. | |
| 45 | |
| 46 Redistribution and use in source and binary forms, with or without | |
| 47 modification, are permitted provided that the following conditions are met: | |
| 48 | |
| 49 * Redistributions of source code must retain the above copyright notice, | |
| 50 this list of conditions and the following disclaimer. | |
| 51 | |
| 52 * Redistributions in binary form must reproduce the above copyright notice, | |
| 53 this list of conditions and the following disclaimer in the documentation | |
| 54 and/or other materials provided with the distribution. | |
| 55 | |
| 56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
| 57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
| 58 endorse or promote products derived from this software without specific | |
| 59 prior written permission. | |
| 60 | |
| 61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
| 62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| 63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| 64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
| 65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
| 66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
| 67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
| 68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
| 69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
| 70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| 71 | |
| 72 =========================================================================*/ | |
| 73 | |
| 74 | |
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75 #include "PrecompiledHeadersServer.h" |
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76 |
| 790 | 77 #ifndef NOMINMAX |
| 78 #define NOMINMAX | |
| 79 #endif | |
| 80 | |
| 81 #include "ParsedDicomFile.h" | |
| 82 | |
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83 #include "ServerToolbox.h" |
| 790 | 84 #include "FromDcmtkBridge.h" |
| 85 #include "ToDcmtkBridge.h" | |
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86 #include "Internals/DicomImageDecoder.h" |
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87 #include "../Core/Logging.h" |
| 790 | 88 #include "../Core/Toolbox.h" |
| 89 #include "../Core/OrthancException.h" | |
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90 #include "../Core/ImageFormats/ImageBuffer.h" |
| 799 | 91 #include "../Core/ImageFormats/PngWriter.h" |
| 790 | 92 #include "../Core/Uuid.h" |
| 93 #include "../Core/DicomFormat/DicomString.h" | |
| 94 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 95 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
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96 #include "../Core/ImageFormats/PngReader.h" |
| 790 | 97 |
| 98 #include <list> | |
| 99 #include <limits> | |
| 100 | |
| 101 #include <boost/lexical_cast.hpp> | |
| 102 | |
| 103 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 104 #include <dcmtk/dcmdata/dcdicent.h> | |
| 105 #include <dcmtk/dcmdata/dcdict.h> | |
| 106 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 107 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 108 #include <dcmtk/dcmdata/dcuid.h> | |
| 109 #include <dcmtk/dcmdata/dcmetinf.h> | |
| 110 | |
| 111 #include <dcmtk/dcmdata/dcvrae.h> | |
| 112 #include <dcmtk/dcmdata/dcvras.h> | |
| 113 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 114 #include <dcmtk/dcmdata/dcvrda.h> | |
| 115 #include <dcmtk/dcmdata/dcvrds.h> | |
| 116 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 117 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 118 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 119 #include <dcmtk/dcmdata/dcvris.h> | |
| 120 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 121 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 122 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 123 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 124 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 125 #include <dcmtk/dcmdata/dcvrss.h> | |
| 126 #include <dcmtk/dcmdata/dcvrst.h> | |
| 127 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 128 #include <dcmtk/dcmdata/dcvrui.h> | |
| 129 #include <dcmtk/dcmdata/dcvrul.h> | |
| 130 #include <dcmtk/dcmdata/dcvrus.h> | |
| 131 #include <dcmtk/dcmdata/dcvrut.h> | |
| 132 #include <dcmtk/dcmdata/dcpixel.h> | |
| 133 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 134 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 135 | |
| 136 | |
| 137 #include <boost/math/special_functions/round.hpp> | |
| 138 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 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_; | |
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150 Encoding encoding_; |
| 794 | 151 }; |
| 152 | |
| 153 | |
| 154 // This method can only be called from the constructors! | |
| 790 | 155 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 156 { | |
| 157 DcmInputBufferStream is; | |
| 158 if (size > 0) | |
| 159 { | |
| 160 is.setBuffer(buffer, size); | |
| 161 } | |
| 162 is.setEos(); | |
| 163 | |
| 794 | 164 pimpl_->file_.reset(new DcmFileFormat); |
| 165 pimpl_->file_->transferInit(); | |
| 166 if (!pimpl_->file_->read(is).good()) | |
| 790 | 167 { |
| 794 | 168 delete pimpl_; // Avoid a memory leak due to exception |
| 169 // throwing, as we are in the constructor | |
| 170 | |
| 790 | 171 throw OrthancException(ErrorCode_BadFileFormat); |
| 172 } | |
| 794 | 173 pimpl_->file_->loadAllDataIntoMemory(); |
| 174 pimpl_->file_->transferEnd(); | |
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175 |
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176 pimpl_->encoding_ = FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
| 790 | 177 } |
| 178 | |
| 179 | |
| 180 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 181 DcmItem& dicom) | |
| 182 { | |
| 183 Json::Value v = Json::arrayValue; | |
| 184 | |
| 185 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 186 { | |
| 187 DcmElement* element = dicom.getElement(i); | |
| 188 if (element) | |
| 189 { | |
| 190 char buf[16]; | |
| 191 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 192 v.append(buf); | |
| 193 } | |
| 194 } | |
| 195 | |
| 196 output.AnswerJson(v); | |
| 197 } | |
| 198 | |
| 199 static inline uint16_t GetCharValue(char c) | |
| 200 { | |
| 201 if (c >= '0' && c <= '9') | |
| 202 return c - '0'; | |
| 203 else if (c >= 'a' && c <= 'f') | |
| 204 return c - 'a' + 10; | |
| 205 else if (c >= 'A' && c <= 'F') | |
| 206 return c - 'A' + 10; | |
| 207 else | |
| 208 return 0; | |
| 209 } | |
| 210 | |
| 211 static inline uint16_t GetTagValue(const char* c) | |
| 212 { | |
| 213 return ((GetCharValue(c[0]) << 12) + | |
| 214 (GetCharValue(c[1]) << 8) + | |
| 215 (GetCharValue(c[2]) << 4) + | |
| 216 GetCharValue(c[3])); | |
| 217 } | |
| 218 | |
| 219 static void ParseTagAndGroup(DcmTagKey& key, | |
| 220 const std::string& tag) | |
| 221 { | |
| 222 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 223 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 224 } | |
| 225 | |
| 226 | |
| 227 static void SendSequence(RestApiOutput& output, | |
| 228 DcmSequenceOfItems& sequence) | |
| 229 { | |
| 230 // This element is a sequence | |
| 231 Json::Value v = Json::arrayValue; | |
| 232 | |
| 233 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 234 { | |
| 235 v.append(boost::lexical_cast<std::string>(i)); | |
| 236 } | |
| 237 | |
| 238 output.AnswerJson(v); | |
| 239 } | |
| 240 | |
| 241 | |
| 242 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 243 E_TransferSyntax transferSyntax) | |
| 244 { | |
| 245 DcmPixelSequence* pixelSequence = NULL; | |
| 246 if (pixelData.getEncapsulatedRepresentation | |
| 247 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 248 { | |
| 249 return pixelSequence->card(); | |
| 250 } | |
| 251 else | |
| 252 { | |
| 253 return 1; | |
| 254 } | |
| 255 } | |
| 256 | |
| 257 | |
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258 namespace |
| 790 | 259 { |
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260 class DicomFieldStream : public IHttpStreamAnswer |
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261 { |
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262 private: |
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263 DcmElement& element_; |
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264 uint32_t length_; |
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265 uint32_t offset_; |
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266 std::string chunk_; |
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267 size_t chunkSize_; |
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268 |
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269 public: |
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270 DicomFieldStream(DcmElement& element, |
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271 E_TransferSyntax transferSyntax) : |
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272 element_(element), |
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273 length_(element.getLength(transferSyntax)), |
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274 offset_(0) |
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275 { |
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276 static const size_t CHUNK_SIZE = 64 * 1024; // Use a 64KB chunk |
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277 chunk_.resize(CHUNK_SIZE); |
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278 } |
| 790 | 279 |
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280 virtual HttpCompression GetHttpCompression(bool /*gzipAllowed*/, |
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281 bool /*deflateAllowed*/) |
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282 { |
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283 // No support for compression |
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284 return HttpCompression_None; |
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285 } |
| 790 | 286 |
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287 virtual bool HasContentFilename(std::string& filename) |
| 790 | 288 { |
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289 return false; |
| 790 | 290 } |
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291 |
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292 virtual std::string GetContentType() |
| 790 | 293 { |
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294 return ""; |
| 790 | 295 } |
| 296 | |
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297 virtual uint64_t GetContentLength() |
| 790 | 298 { |
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299 return length_; |
| 790 | 300 } |
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301 |
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302 virtual bool ReadNextChunk() |
| 790 | 303 { |
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304 assert(offset_ < length_); |
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305 |
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306 if (offset_ == length_) |
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307 { |
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308 return false; |
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309 } |
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310 else |
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311 { |
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312 if (length_ - offset_ < chunk_.size()) |
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313 { |
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314 chunkSize_ = length_ - offset_; |
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315 } |
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316 else |
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317 { |
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318 chunkSize_ = chunk_.size(); |
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319 } |
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320 |
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321 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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322 |
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323 offset_ += chunkSize_; |
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324 |
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325 if (!cond.good()) |
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326 { |
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327 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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328 throw OrthancException(ErrorCode_InternalError); |
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329 } |
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330 |
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331 return true; |
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332 } |
| 790 | 333 } |
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334 |
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335 virtual const char *GetChunkContent() |
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336 { |
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337 return chunk_.c_str(); |
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338 } |
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339 |
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340 virtual size_t GetChunkSize() |
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341 { |
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342 return chunkSize_; |
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343 } |
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344 }; |
| 790 | 345 } |
| 346 | |
| 347 | |
| 348 static bool AnswerPixelData(RestApiOutput& output, | |
| 349 DcmItem& dicom, | |
| 350 E_TransferSyntax transferSyntax, | |
| 351 const std::string* blockUri) | |
| 352 { | |
| 353 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 354 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 355 | |
| 356 DcmElement *element = NULL; | |
| 357 if (!dicom.findAndGetElement(k, element).good() || | |
| 358 element == NULL) | |
| 359 { | |
| 360 return false; | |
| 361 } | |
| 362 | |
| 363 try | |
| 364 { | |
| 365 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 366 if (blockUri == NULL) | |
| 367 { | |
| 368 // The user asks how many blocks are presents in this pixel data | |
| 369 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 370 | |
| 371 Json::Value result(Json::arrayValue); | |
| 372 for (unsigned int i = 0; i < blocks; i++) | |
| 373 { | |
| 374 result.append(boost::lexical_cast<std::string>(i)); | |
| 375 } | |
| 376 | |
| 377 output.AnswerJson(result); | |
| 378 return true; | |
| 379 } | |
| 380 | |
| 381 | |
| 382 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 383 | |
| 384 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 385 { | |
| 386 DcmPixelSequence* pixelSequence = NULL; | |
| 387 if (pixelData.getEncapsulatedRepresentation | |
| 388 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 389 { | |
| 390 // This is the case for JPEG transfer syntaxes | |
| 391 if (block < pixelSequence->card()) | |
| 392 { | |
| 393 DcmPixelItem* pixelItem = NULL; | |
| 394 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 395 { | |
| 396 if (pixelItem->getLength() == 0) | |
| 397 { | |
| 398 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 399 return true; | |
| 400 } | |
| 401 | |
| 402 Uint8* buffer = NULL; | |
| 403 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 404 { | |
| 405 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 406 return true; | |
| 407 } | |
| 408 } | |
| 409 } | |
| 410 } | |
| 411 else | |
| 412 { | |
| 413 // This is the case for raw, uncompressed image buffers | |
| 414 assert(*blockUri == "0"); | |
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415 DicomFieldStream stream(*element, transferSyntax); |
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416 output.AnswerStream(stream); |
| 790 | 417 } |
| 418 } | |
| 419 } | |
| 420 catch (boost::bad_lexical_cast&) | |
| 421 { | |
| 422 // The URI entered by the user is not a number | |
| 423 } | |
| 424 catch (std::bad_cast&) | |
| 425 { | |
| 426 // This should never happen | |
| 427 } | |
| 428 | |
| 429 return false; | |
| 430 } | |
| 431 | |
| 432 | |
| 433 | |
| 434 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 435 const std::string& tag, | |
| 436 DcmItem& dicom, | |
| 437 E_TransferSyntax transferSyntax) | |
| 438 { | |
| 439 DcmTagKey k; | |
| 440 ParseTagAndGroup(k, tag); | |
| 441 | |
| 442 DcmSequenceOfItems* sequence = NULL; | |
| 443 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 444 sequence != NULL && | |
| 445 sequence->getVR() == EVR_SQ) | |
| 446 { | |
| 447 SendSequence(output, *sequence); | |
| 448 return; | |
| 449 } | |
| 450 | |
| 451 DcmElement* element = NULL; | |
| 452 if (dicom.findAndGetElement(k, element).good() && | |
| 453 element != NULL && | |
| 454 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 455 element->getVR() != EVR_SQ) | |
| 456 { | |
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457 DicomFieldStream stream(*element, transferSyntax); |
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458 output.AnswerStream(stream); |
| 790 | 459 } |
| 460 } | |
| 461 | |
| 462 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 463 const UriComponents& uri) | |
| 464 { | |
| 794 | 465 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 466 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 467 |
| 468 // Special case: Accessing the pixel data | |
| 469 if (uri.size() == 1 || | |
| 470 uri.size() == 2) | |
| 471 { | |
| 472 DcmTagKey tag; | |
| 473 ParseTagAndGroup(tag, uri[0]); | |
| 474 | |
| 475 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 476 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 477 { | |
| 478 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 479 return; | |
| 480 } | |
| 481 } | |
| 482 | |
| 483 // Go down in the tag hierarchy according to the URI | |
| 484 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 485 { | |
| 486 size_t index; | |
| 487 try | |
| 488 { | |
| 489 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 490 } | |
| 491 catch (boost::bad_lexical_cast&) | |
| 492 { | |
| 493 return; | |
| 494 } | |
| 495 | |
| 496 DcmTagKey k; | |
| 497 DcmItem *child = NULL; | |
| 498 ParseTagAndGroup(k, uri[2 * pos]); | |
| 499 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 500 child == NULL) | |
| 501 { | |
| 502 return; | |
| 503 } | |
| 504 | |
| 505 dicom = child; | |
| 506 } | |
| 507 | |
| 508 // We have reached the end of the URI | |
| 509 if (uri.size() % 2 == 0) | |
| 510 { | |
| 511 SendPathValueForDictionary(output, *dicom); | |
| 512 } | |
| 513 else | |
| 514 { | |
| 515 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 516 } | |
| 517 } | |
| 518 | |
| 519 | |
| 520 | |
| 521 | |
| 522 | |
| 523 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 524 { | |
| 525 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 526 | |
| 527 switch (key.getEVR()) | |
| 528 { | |
| 529 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 530 | |
| 531 /** | |
| 532 * TODO. | |
| 533 **/ | |
| 534 | |
| 535 case EVR_OB: // other byte | |
| 536 case EVR_OF: // other float | |
| 537 case EVR_OW: // other word | |
| 538 case EVR_AT: // attribute tag | |
| 539 throw OrthancException(ErrorCode_NotImplemented); | |
| 540 | |
| 541 case EVR_UN: // unknown value representation | |
| 542 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 543 | |
| 544 | |
| 545 /** | |
| 546 * String types. | |
| 547 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 548 **/ | |
| 549 | |
| 550 case EVR_AS: // age string | |
| 551 return new DcmAgeString(key); | |
| 552 | |
| 553 case EVR_AE: // application entity title | |
| 554 return new DcmApplicationEntity(key); | |
| 555 | |
| 556 case EVR_CS: // code string | |
| 557 return new DcmCodeString(key); | |
| 558 | |
| 559 case EVR_DA: // date string | |
| 560 return new DcmDate(key); | |
| 561 | |
| 562 case EVR_DT: // date time string | |
| 563 return new DcmDateTime(key); | |
| 564 | |
| 565 case EVR_DS: // decimal string | |
| 566 return new DcmDecimalString(key); | |
| 567 | |
| 568 case EVR_IS: // integer string | |
| 569 return new DcmIntegerString(key); | |
| 570 | |
| 571 case EVR_TM: // time string | |
| 572 return new DcmTime(key); | |
| 573 | |
| 574 case EVR_UI: // unique identifier | |
| 575 return new DcmUniqueIdentifier(key); | |
| 576 | |
| 577 case EVR_ST: // short text | |
| 578 return new DcmShortText(key); | |
| 579 | |
| 580 case EVR_LO: // long string | |
| 581 return new DcmLongString(key); | |
| 582 | |
| 583 case EVR_LT: // long text | |
| 584 return new DcmLongText(key); | |
| 585 | |
| 586 case EVR_UT: // unlimited text | |
| 587 return new DcmUnlimitedText(key); | |
| 588 | |
| 589 case EVR_SH: // short string | |
| 590 return new DcmShortString(key); | |
| 591 | |
| 592 case EVR_PN: // person name | |
| 593 return new DcmPersonName(key); | |
| 594 | |
| 595 | |
| 596 /** | |
| 597 * Numerical types | |
| 598 **/ | |
| 599 | |
| 600 case EVR_SL: // signed long | |
| 601 return new DcmSignedLong(key); | |
| 602 | |
| 603 case EVR_SS: // signed short | |
| 604 return new DcmSignedShort(key); | |
| 605 | |
| 606 case EVR_UL: // unsigned long | |
| 607 return new DcmUnsignedLong(key); | |
| 608 | |
| 609 case EVR_US: // unsigned short | |
| 610 return new DcmUnsignedShort(key); | |
| 611 | |
| 612 case EVR_FL: // float single-precision | |
| 613 return new DcmFloatingPointSingle(key); | |
| 614 | |
| 615 case EVR_FD: // float double-precision | |
| 616 return new DcmFloatingPointDouble(key); | |
| 617 | |
| 618 | |
| 619 /** | |
| 620 * Sequence types, should never occur at this point. | |
| 621 **/ | |
| 622 | |
| 623 case EVR_SQ: // sequence of items | |
| 624 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 625 | |
| 626 | |
| 627 /** | |
| 628 * Internal to DCMTK. | |
| 629 **/ | |
| 630 | |
| 631 case EVR_ox: // OB or OW depending on context | |
| 632 case EVR_xs: // SS or US depending on context | |
| 633 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 634 case EVR_na: // na="not applicable", for data which has no VR | |
| 635 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 636 case EVR_item: // used internally for items | |
| 637 case EVR_metainfo: // used internally for meta info datasets | |
| 638 case EVR_dataset: // used internally for datasets | |
| 639 case EVR_fileFormat: // used internally for DICOM files | |
| 640 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 641 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 642 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 643 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 644 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 645 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 646 case EVR_OverlayData: // used internally for overlay data | |
| 647 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 648 default: | |
| 649 break; | |
| 650 } | |
| 651 | |
| 652 throw OrthancException(ErrorCode_InternalError); | |
| 653 } | |
| 654 | |
| 655 | |
| 656 | |
| 657 static void FillElementWithString(DcmElement& element, | |
| 658 const DicomTag& tag, | |
| 659 const std::string& value) | |
| 660 { | |
| 661 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 662 bool ok = false; | |
| 663 | |
| 664 try | |
| 665 { | |
| 666 switch (key.getEVR()) | |
| 667 { | |
| 668 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 669 | |
| 670 /** | |
| 671 * TODO. | |
| 672 **/ | |
| 673 | |
| 674 case EVR_OB: // other byte | |
| 675 case EVR_OF: // other float | |
| 676 case EVR_OW: // other word | |
| 677 case EVR_AT: // attribute tag | |
| 678 throw OrthancException(ErrorCode_NotImplemented); | |
| 679 | |
| 680 case EVR_UN: // unknown value representation | |
| 681 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 682 | |
| 683 | |
| 684 /** | |
| 685 * String types. | |
| 686 **/ | |
| 687 | |
| 688 case EVR_DS: // decimal string | |
| 689 case EVR_IS: // integer string | |
| 690 case EVR_AS: // age string | |
| 691 case EVR_DA: // date string | |
| 692 case EVR_DT: // date time string | |
| 693 case EVR_TM: // time string | |
| 694 case EVR_AE: // application entity title | |
| 695 case EVR_CS: // code string | |
| 696 case EVR_SH: // short string | |
| 697 case EVR_LO: // long string | |
| 698 case EVR_ST: // short text | |
| 699 case EVR_LT: // long text | |
| 700 case EVR_UT: // unlimited text | |
| 701 case EVR_PN: // person name | |
| 702 case EVR_UI: // unique identifier | |
| 703 { | |
| 704 ok = element.putString(value.c_str()).good(); | |
| 705 break; | |
| 706 } | |
| 707 | |
| 708 | |
| 709 /** | |
| 710 * Numerical types | |
| 711 **/ | |
| 712 | |
| 713 case EVR_SL: // signed long | |
| 714 { | |
| 715 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 716 break; | |
| 717 } | |
| 718 | |
| 719 case EVR_SS: // signed short | |
| 720 { | |
| 721 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 722 break; | |
| 723 } | |
| 724 | |
| 725 case EVR_UL: // unsigned long | |
| 726 { | |
| 727 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 728 break; | |
| 729 } | |
| 730 | |
| 731 case EVR_US: // unsigned short | |
| 732 { | |
| 733 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 734 break; | |
| 735 } | |
| 736 | |
| 737 case EVR_FL: // float single-precision | |
| 738 { | |
| 739 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 740 break; | |
| 741 } | |
| 742 | |
| 743 case EVR_FD: // float double-precision | |
| 744 { | |
| 745 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 746 break; | |
| 747 } | |
| 748 | |
| 749 | |
| 750 /** | |
| 751 * Sequence types, should never occur at this point. | |
| 752 **/ | |
| 753 | |
| 754 case EVR_SQ: // sequence of items | |
| 755 { | |
| 756 ok = false; | |
| 757 break; | |
| 758 } | |
| 759 | |
| 760 | |
| 761 /** | |
| 762 * Internal to DCMTK. | |
| 763 **/ | |
| 764 | |
| 765 case EVR_ox: // OB or OW depending on context | |
| 766 case EVR_xs: // SS or US depending on context | |
| 767 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 768 case EVR_na: // na="not applicable", for data which has no VR | |
| 769 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 770 case EVR_item: // used internally for items | |
| 771 case EVR_metainfo: // used internally for meta info datasets | |
| 772 case EVR_dataset: // used internally for datasets | |
| 773 case EVR_fileFormat: // used internally for DICOM files | |
| 774 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 775 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 776 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 777 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 778 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 779 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 780 case EVR_OverlayData: // used internally for overlay data | |
| 781 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 782 default: | |
| 783 break; | |
| 784 } | |
| 785 } | |
| 786 catch (boost::bad_lexical_cast&) | |
| 787 { | |
| 788 ok = false; | |
| 789 } | |
| 790 | |
| 791 if (!ok) | |
| 792 { | |
| 793 throw OrthancException(ErrorCode_InternalError); | |
| 794 } | |
| 795 } | |
| 796 | |
| 797 | |
| 798 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 799 { | |
| 800 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 801 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 802 if (element != NULL) |
| 803 { | |
| 804 delete element; | |
| 805 } | |
| 806 } | |
| 807 | |
| 808 | |
| 809 | |
|
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810 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 811 { |
|
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812 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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813 |
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814 // Loop over the dataset to detect its private tags |
| 790 | 815 typedef std::list<DcmElement*> Tags; |
| 816 Tags privateTags; | |
| 817 | |
| 818 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 819 { | |
| 820 DcmElement* element = dataset.getElement(i); | |
| 821 DcmTag tag(element->getTag()); | |
|
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822 |
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823 // Is this a private tag? |
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824 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 825 { |
|
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826 bool remove = true; |
|
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|
827 |
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828 // Check whether this private tag is to be kept |
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829 if (toKeep != NULL) |
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830 { |
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831 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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832 if (toKeep->find(tmp) != toKeep->end()) |
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833 { |
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834 remove = false; // Keep it |
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835 } |
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836 } |
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837 |
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838 if (remove) |
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839 { |
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840 privateTags.push_back(element); |
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841 } |
| 790 | 842 } |
| 843 } | |
| 844 | |
|
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845 // Loop over the detected private tags to remove them |
| 790 | 846 for (Tags::iterator it = privateTags.begin(); |
| 847 it != privateTags.end(); ++it) | |
| 848 { | |
| 849 DcmElement* tmp = dataset.remove(*it); | |
| 850 if (tmp != NULL) | |
| 851 { | |
| 852 delete tmp; | |
| 853 } | |
| 854 } | |
| 855 } | |
| 856 | |
| 857 | |
| 858 | |
|
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859 |
| 790 | 860 void ParsedDicomFile::Insert(const DicomTag& tag, |
| 861 const std::string& value) | |
| 862 { | |
|
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863 OFCondition cond; |
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864 |
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865 if (FromDcmtkBridge::IsPrivateTag(tag)) |
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866 { |
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867 // This is a private tag |
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868 // http://support.dcmtk.org/redmine/projects/dcmtk/wiki/howto_addprivatedata |
| 790 | 869 |
|
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870 DcmTag key(tag.GetGroup(), tag.GetElement(), EVR_OB); |
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871 cond = pimpl_->file_->getDataset()->putAndInsertUint8Array |
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872 (key, (const Uint8*) value.c_str(), value.size(), false); |
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873 } |
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874 else |
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875 { |
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876 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); |
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877 FillElementWithString(*element, tag, value); |
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878 |
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879 cond = pimpl_->file_->getDataset()->insert(element.release(), false, false); |
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880 } |
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881 |
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|
882 if (!cond.good()) |
| 790 | 883 { |
| 884 // This field already exists | |
| 885 throw OrthancException(ErrorCode_InternalError); | |
| 886 } | |
| 887 } | |
| 888 | |
| 889 | |
| 890 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 891 const std::string& value, | |
| 892 DicomReplaceMode mode) | |
| 893 { | |
| 894 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 895 DcmElement* element = NULL; | |
| 896 | |
| 794 | 897 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 898 element == NULL) |
| 899 { | |
| 900 // This field does not exist, act wrt. the specified "mode" | |
| 901 switch (mode) | |
| 902 { | |
| 903 case DicomReplaceMode_InsertIfAbsent: | |
| 904 Insert(tag, value); | |
| 905 break; | |
| 906 | |
| 907 case DicomReplaceMode_ThrowIfAbsent: | |
| 908 throw OrthancException(ErrorCode_InexistentItem); | |
| 909 | |
| 910 case DicomReplaceMode_IgnoreIfAbsent: | |
| 911 return; | |
| 912 } | |
| 913 } | |
| 914 else | |
| 915 { | |
|
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916 if (FromDcmtkBridge::IsPrivateTag(tag)) |
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917 { |
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918 if (!element->putUint8Array((const Uint8*) value.c_str(), value.size()).good()) |
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919 { |
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920 throw OrthancException(ErrorCode_InternalError); |
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921 } |
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922 } |
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923 else |
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924 { |
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925 FillElementWithString(*element, tag, value); |
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|
926 } |
| 790 | 927 } |
| 928 | |
| 929 | |
| 930 /** | |
| 931 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 932 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 933 * you make changes to the related tags in the dataset ('SOP Class | |
| 934 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 935 * options. You can disable this behaviour by using the -nmu | |
| 936 * option. | |
| 937 **/ | |
| 938 | |
| 939 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 940 { | |
| 941 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 942 } | |
| 943 | |
| 944 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 945 { | |
| 946 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 947 } | |
| 948 } | |
| 949 | |
| 950 | |
| 951 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 952 { | |
| 953 std::string serialized; | |
|
1004
a226e0959d8b
DicomInstanceToStore
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|
954 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 955 { |
| 956 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 957 } | |
| 958 } | |
| 959 | |
| 960 | |
| 961 | |
| 962 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 963 const DicomTag& tag) | |
| 964 { | |
| 965 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 966 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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967 |
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|
968 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 969 { |
|
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970 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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971 long unsigned int count = 0; |
| 790 | 972 |
|
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973 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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974 { |
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975 if (count > 0) |
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976 { |
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977 assert(data != NULL); |
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978 value.assign(reinterpret_cast<const char*>(data), count); |
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979 } |
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980 else |
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981 { |
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|
982 value.clear(); |
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983 } |
| 790 | 984 |
|
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985 return true; |
|
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986 } |
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987 else |
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Fix replacement and insertion of private DICOM tags
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988 { |
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989 return false; |
|
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|
990 } |
| 790 | 991 } |
| 992 else | |
| 993 { | |
|
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994 DcmElement* element = NULL; |
|
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995 if (!dataset.findAndGetElement(k, element).good() || |
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Fix replacement and insertion of private DICOM tags
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|
996 element == NULL) |
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997 { |
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998 return false; |
|
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999 } |
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|
1000 |
|
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1001 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element, pimpl_->encoding_)); |
|
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|
1002 |
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|
1003 if (v.get() == NULL) |
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|
1004 { |
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1005 value = ""; |
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1006 } |
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1007 else |
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1008 { |
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1009 value = v->AsString(); |
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1010 } |
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1011 |
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1012 return true; |
| 790 | 1013 } |
| 1014 } | |
| 1015 | |
| 1016 | |
| 1017 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 1018 { | |
| 1019 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 1020 | |
| 1021 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 1022 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 1023 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 1024 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 1025 { | |
| 1026 throw OrthancException(ErrorCode_BadFileFormat); | |
| 1027 } | |
| 1028 | |
| 1029 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 1030 } | |
| 1031 | |
| 1032 | |
| 1033 template <typename T> | |
| 1034 static void ExtractPngImageTruncate(std::string& result, | |
| 1035 DicomIntegerPixelAccessor& accessor, | |
| 1036 PixelFormat format) | |
| 1037 { | |
|
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1038 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 1039 |
| 1040 PngWriter w; | |
| 1041 | |
|
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1042 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 1043 T* pixel = &image[0]; |
|
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1044 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 1045 { |
|
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1046 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 1047 { |
| 1048 int32_t v = accessor.GetValue(x, y); | |
| 1049 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 1050 *pixel = std::numeric_limits<T>::min(); | |
| 1051 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 1052 *pixel = std::numeric_limits<T>::max(); | |
| 1053 else | |
| 1054 *pixel = static_cast<T>(v); | |
| 1055 } | |
| 1056 } | |
| 1057 | |
|
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1058 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
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1059 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 1060 } |
| 1061 | |
| 1062 | |
| 1063 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 1064 { | |
|
1004
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1065 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 1066 } |
| 1067 | |
| 1068 | |
| 1069 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 1070 { | |
| 1071 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 1072 std::string content; | |
| 1073 SaveToMemoryBuffer(content); | |
| 1074 Toolbox::WriteFile(content, path); | |
| 1075 } | |
| 1076 | |
| 1077 | |
| 794 | 1078 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 1079 { |
| 794 | 1080 pimpl_->file_.reset(new DcmFileFormat); |
|
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1081 pimpl_->encoding_ = Encoding_Ascii; |
| 790 | 1082 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 1083 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 1084 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 1085 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 1086 } | |
| 1087 | |
| 791 | 1088 |
| 794 | 1089 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 1090 { |
| 1091 Setup(content, size); | |
| 1092 } | |
| 1093 | |
| 794 | 1094 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 1095 { |
| 1096 if (content.size() == 0) | |
| 1097 { | |
| 1098 Setup(NULL, 0); | |
| 1099 } | |
| 1100 else | |
| 1101 { | |
| 1102 Setup(&content[0], content.size()); | |
| 1103 } | |
| 1104 } | |
| 792 | 1105 |
| 1106 | |
| 794 | 1107 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1108 pimpl_(new PImpl) | |
| 792 | 1109 { |
| 794 | 1110 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
956
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1111 |
|
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1112 pimpl_->encoding_ = other.pimpl_->encoding_; |
| 792 | 1113 } |
| 1114 | |
| 1115 | |
| 1116 ParsedDicomFile::~ParsedDicomFile() | |
| 1117 { | |
| 794 | 1118 delete pimpl_; |
| 792 | 1119 } |
| 1120 | |
| 793 | 1121 |
| 1122 void* ParsedDicomFile::GetDcmtkObject() | |
| 1123 { | |
| 794 | 1124 return pimpl_->file_.get(); |
| 793 | 1125 } |
| 1126 | |
| 1127 | |
| 1128 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1129 { | |
| 794 | 1130 return new ParsedDicomFile(*this); |
| 793 | 1131 } |
|
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1132 |
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1133 |
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1134 void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) |
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1135 { |
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1136 std::string mime, content; |
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1137 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
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1138 |
|
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1139 std::string decoded; |
|
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1140 Toolbox::DecodeBase64(decoded, content); |
|
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1141 |
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1142 if (mime == "image/png") |
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1143 { |
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1144 PngReader reader; |
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1145 reader.ReadFromMemory(decoded); |
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1146 EmbedImage(reader); |
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1147 } |
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1148 else |
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1149 { |
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1150 throw OrthancException(ErrorCode_NotImplemented); |
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1151 } |
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1152 } |
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1153 |
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1154 |
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1155 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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1156 { |
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1157 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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1158 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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1159 accessor.GetFormat() != PixelFormat_RGB24 && |
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1160 accessor.GetFormat() != PixelFormat_RGBA32) |
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1161 { |
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1162 throw OrthancException(ErrorCode_NotImplemented); |
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1163 } |
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1164 |
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1165 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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1166 { |
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1167 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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1168 } |
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1169 |
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1170 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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1171 |
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1172 Remove(DICOM_TAG_PIXEL_DATA); |
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1173 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
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1174 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
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1175 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
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1176 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
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1177 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
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1178 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
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1179 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
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1180 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
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1181 Replace(DICOM_TAG_BITS_STORED, "8"); |
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1182 Replace(DICOM_TAG_HIGH_BIT, "7"); |
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1183 |
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1184 unsigned int bytesPerPixel = 1; |
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1185 |
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1186 switch (accessor.GetFormat()) |
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1187 { |
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1188 case PixelFormat_RGB24: |
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1189 case PixelFormat_RGBA32: |
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1190 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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1191 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
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1192 bytesPerPixel = 3; |
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1193 break; |
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1194 |
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1195 case PixelFormat_Grayscale8: |
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1196 break; |
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1197 |
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1198 case PixelFormat_Grayscale16: |
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|
1199 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1200 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1201 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1202 bytesPerPixel = 2; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1203 break; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1204 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1205 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1206 throw OrthancException(ErrorCode_NotImplemented); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1207 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1208 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1209 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1210 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1211 |
|
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diff
changeset
|
1212 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1213 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1214 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1215 Uint8* target = NULL; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1216 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1217 |
|
ecedd89055db
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1218 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1219 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1220 switch (accessor.GetFormat()) |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1221 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1222 case PixelFormat_RGB24: |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1223 case PixelFormat_Grayscale8: |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1224 case PixelFormat_Grayscale16: |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1225 case PixelFormat_SignedGrayscale16: |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1226 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1227 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1228 target += pitch; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1229 break; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1230 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1231 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1232 case PixelFormat_RGBA32: |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1233 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1234 // The alpha channel is not supported by the DICOM standard |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1235 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1236 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>
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changeset
|
1237 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1238 target[0] = source[0]; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1239 target[1] = source[1]; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1240 target[2] = source[2]; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1241 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1242 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1243 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1244 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1245 |
|
ecedd89055db
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1246 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1247 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1248 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1249 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1250 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1251 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1252 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1253 throw OrthancException(ErrorCode_InternalError); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1254 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1255 } |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1256 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1257 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1258 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1259 unsigned int frame) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1260 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1261 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1262 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1263 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1264 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1265 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1266 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1267 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1268 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1269 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1270 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1271 unsigned int frame, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1272 ImageExtractionMode mode) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1273 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1274 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1275 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1276 bool ok = false; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1277 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1278 switch (mode) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1279 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1280 case ImageExtractionMode_UInt8: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1281 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1282 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1283 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1284 case ImageExtractionMode_UInt16: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1285 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1286 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1287 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1288 case ImageExtractionMode_Int16: |
|
1015
f009f7c75069
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1289 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1290 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1291 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1292 case ImageExtractionMode_Preview: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1293 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1294 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1295 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1296 default: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1297 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1298 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1299 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1300 if (!ok) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1301 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1302 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1303 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1304 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1305 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1306 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1307 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
87791ebc1f50
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parents:
853
diff
changeset
|
1308 unsigned int frame, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1309 ImageExtractionMode mode) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1310 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1311 ImageBuffer buffer; |
|
87791ebc1f50
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parents:
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diff
changeset
|
1312 ExtractImage(buffer, frame, mode); |
|
87791ebc1f50
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parents:
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diff
changeset
|
1313 |
|
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1314 ImageAccessor accessor(buffer.GetConstAccessor()); |
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1315 PngWriter writer; |
|
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1316 writer.WriteToMemory(result, accessor); |
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1317 } |
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1318 |
|
956
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1319 |
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1320 Encoding ParsedDicomFile::GetEncoding() const |
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1321 { |
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1322 return pimpl_->encoding_; |
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1323 } |
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1324 |
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1325 |
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1326 void ParsedDicomFile::SetEncoding(Encoding encoding) |
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1327 { |
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1328 std::string s; |
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1329 |
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1330 // http://www.dabsoft.ch/dicom/3/C.12.1.1.2/ |
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1331 switch (encoding) |
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1332 { |
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1333 case Encoding_Utf8: |
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1334 case Encoding_Ascii: |
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1335 s = "ISO_IR 192"; |
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1336 break; |
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1337 |
| 1347 | 1338 case Encoding_Windows1251: |
| 1339 // This Cyrillic codepage is not officially supported by the | |
| 1340 // DICOM standard. Do not set the SpecificCharacterSet tag. | |
| 1341 return; | |
| 1342 | |
|
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1343 case Encoding_Latin1: |
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1344 s = "ISO_IR 100"; |
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1345 break; |
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1346 |
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1347 case Encoding_Latin2: |
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1348 s = "ISO_IR 101"; |
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1349 break; |
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1350 |
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1351 case Encoding_Latin3: |
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1352 s = "ISO_IR 109"; |
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1353 break; |
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1354 |
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1355 case Encoding_Latin4: |
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1356 s = "ISO_IR 110"; |
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1357 break; |
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1358 |
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1359 case Encoding_Latin5: |
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1360 s = "ISO_IR 148"; |
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1361 break; |
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1362 |
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1363 case Encoding_Cyrillic: |
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1364 s = "ISO_IR 144"; |
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1365 break; |
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1366 |
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1367 case Encoding_Arabic: |
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1368 s = "ISO_IR 127"; |
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1369 break; |
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1370 |
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1371 case Encoding_Greek: |
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1372 s = "ISO_IR 126"; |
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1373 break; |
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1374 |
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1375 case Encoding_Hebrew: |
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1376 s = "ISO_IR 138"; |
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1377 break; |
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1378 |
| 1091 | 1379 case Encoding_Japanese: |
| 1380 s = "ISO_IR 13"; | |
| 1381 break; | |
| 1382 | |
| 1383 case Encoding_Chinese: | |
| 1384 s = "GB18030"; | |
| 1385 break; | |
|
1090
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1386 |
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1387 case Encoding_Thai: |
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1388 s = "ISO_IR 166"; |
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1389 break; |
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1390 |
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1391 default: |
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1392 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1393 } |
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1394 |
| 1091 | 1395 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
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1396 } |
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1397 |
|
1160
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1398 void ParsedDicomFile::ToJson(Json::Value& target, bool simplify) |
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1399 { |
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1400 if (simplify) |
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1401 { |
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1402 Json::Value tmp; |
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1403 FromDcmtkBridge::ToJson(tmp, *pimpl_->file_->getDataset()); |
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1404 SimplifyTags(target, tmp); |
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1405 } |
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1406 else |
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1407 { |
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1408 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset()); |
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1409 } |
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1410 } |
| 790 | 1411 } |