Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1690:ae09132e4237
FromJson
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 07 Oct 2015 17:42:42 +0200 |
parents | 26083d84d237 |
children | 558b25228a23 |
rev | line source |
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790 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
790 | 5 * |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU General Public License as | |
8 * published by the Free Software Foundation, either version 3 of the | |
9 * License, or (at your option) any later version. | |
10 * | |
11 * In addition, as a special exception, the copyright holders of this | |
12 * program give permission to link the code of its release with the | |
13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
14 * that use the same license as the "OpenSSL" library), and distribute | |
15 * the linked executables. You must obey the GNU General Public License | |
16 * in all respects for all of the code used other than "OpenSSL". If you | |
17 * modify file(s) with this exception, you may extend this exception to | |
18 * your version of the file(s), but you are not obligated to do so. If | |
19 * you do not wish to do so, delete this exception statement from your | |
20 * version. If you delete this exception statement from all source files | |
21 * in the program, then also delete it here. | |
22 * | |
23 * This program is distributed in the hope that it will be useful, but | |
24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
26 * General Public License for more details. | |
27 * | |
28 * You should have received a copy of the GNU General Public License | |
29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
30 **/ | |
31 | |
32 | |
33 | |
34 /*========================================================================= | |
35 | |
36 This file is based on portions of the following project: | |
37 | |
38 Program: GDCM (Grassroots DICOM). A DICOM library | |
39 Module: http://gdcm.sourceforge.net/Copyright.html | |
40 | |
41 Copyright (c) 2006-2011 Mathieu Malaterre | |
42 Copyright (c) 1993-2005 CREATIS | |
43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
44 All rights reserved. | |
45 | |
46 Redistribution and use in source and binary forms, with or without | |
47 modification, are permitted provided that the following conditions are met: | |
48 | |
49 * Redistributions of source code must retain the above copyright notice, | |
50 this list of conditions and the following disclaimer. | |
51 | |
52 * Redistributions in binary form must reproduce the above copyright notice, | |
53 this list of conditions and the following disclaimer in the documentation | |
54 and/or other materials provided with the distribution. | |
55 | |
56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
58 endorse or promote products derived from this software without specific | |
59 prior written permission. | |
60 | |
61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
71 | |
72 =========================================================================*/ | |
73 | |
74 | |
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75 #include "PrecompiledHeadersServer.h" |
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76 |
790 | 77 #ifndef NOMINMAX |
78 #define NOMINMAX | |
79 #endif | |
80 | |
81 #include "ParsedDicomFile.h" | |
82 | |
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83 #include "ServerToolbox.h" |
790 | 84 #include "FromDcmtkBridge.h" |
85 #include "ToDcmtkBridge.h" | |
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86 #include "Internals/DicomImageDecoder.h" |
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87 #include "../Core/Logging.h" |
790 | 88 #include "../Core/Toolbox.h" |
89 #include "../Core/OrthancException.h" | |
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90 #include "../Core/Images/ImageBuffer.h" |
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91 #include "../Core/Images/PngWriter.h" |
790 | 92 #include "../Core/Uuid.h" |
93 #include "../Core/DicomFormat/DicomString.h" | |
94 #include "../Core/DicomFormat/DicomNullValue.h" | |
95 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
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96 #include "../Core/Images/PngReader.h" |
790 | 97 |
98 #include <list> | |
99 #include <limits> | |
100 | |
101 #include <boost/lexical_cast.hpp> | |
102 | |
103 #include <dcmtk/dcmdata/dcchrstr.h> | |
104 #include <dcmtk/dcmdata/dcdicent.h> | |
105 #include <dcmtk/dcmdata/dcdict.h> | |
106 #include <dcmtk/dcmdata/dcfilefo.h> | |
107 #include <dcmtk/dcmdata/dcistrmb.h> | |
108 #include <dcmtk/dcmdata/dcuid.h> | |
109 #include <dcmtk/dcmdata/dcmetinf.h> | |
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110 #include <dcmtk/dcmdata/dcdeftag.h> |
790 | 111 |
112 #include <dcmtk/dcmdata/dcvrae.h> | |
113 #include <dcmtk/dcmdata/dcvras.h> | |
114 #include <dcmtk/dcmdata/dcvrcs.h> | |
115 #include <dcmtk/dcmdata/dcvrda.h> | |
116 #include <dcmtk/dcmdata/dcvrds.h> | |
117 #include <dcmtk/dcmdata/dcvrdt.h> | |
118 #include <dcmtk/dcmdata/dcvrfd.h> | |
119 #include <dcmtk/dcmdata/dcvrfl.h> | |
120 #include <dcmtk/dcmdata/dcvris.h> | |
121 #include <dcmtk/dcmdata/dcvrlo.h> | |
122 #include <dcmtk/dcmdata/dcvrlt.h> | |
123 #include <dcmtk/dcmdata/dcvrpn.h> | |
124 #include <dcmtk/dcmdata/dcvrsh.h> | |
125 #include <dcmtk/dcmdata/dcvrsl.h> | |
126 #include <dcmtk/dcmdata/dcvrss.h> | |
127 #include <dcmtk/dcmdata/dcvrst.h> | |
128 #include <dcmtk/dcmdata/dcvrtm.h> | |
129 #include <dcmtk/dcmdata/dcvrui.h> | |
130 #include <dcmtk/dcmdata/dcvrul.h> | |
131 #include <dcmtk/dcmdata/dcvrus.h> | |
132 #include <dcmtk/dcmdata/dcvrut.h> | |
133 #include <dcmtk/dcmdata/dcpixel.h> | |
134 #include <dcmtk/dcmdata/dcpixseq.h> | |
135 #include <dcmtk/dcmdata/dcpxitem.h> | |
136 | |
137 | |
138 #include <boost/math/special_functions/round.hpp> | |
139 #include <dcmtk/dcmdata/dcostrmb.h> | |
140 | |
141 | |
142 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
143 | |
144 | |
145 | |
146 namespace Orthanc | |
147 { | |
794 | 148 struct ParsedDicomFile::PImpl |
149 { | |
150 std::auto_ptr<DcmFileFormat> file_; | |
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151 Encoding encoding_; |
794 | 152 }; |
153 | |
154 | |
155 // This method can only be called from the constructors! | |
790 | 156 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
157 { | |
158 DcmInputBufferStream is; | |
159 if (size > 0) | |
160 { | |
161 is.setBuffer(buffer, size); | |
162 } | |
163 is.setEos(); | |
164 | |
794 | 165 pimpl_->file_.reset(new DcmFileFormat); |
166 pimpl_->file_->transferInit(); | |
167 if (!pimpl_->file_->read(is).good()) | |
790 | 168 { |
794 | 169 delete pimpl_; // Avoid a memory leak due to exception |
170 // throwing, as we are in the constructor | |
171 | |
790 | 172 throw OrthancException(ErrorCode_BadFileFormat); |
173 } | |
794 | 174 pimpl_->file_->loadAllDataIntoMemory(); |
175 pimpl_->file_->transferEnd(); | |
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176 |
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177 pimpl_->encoding_ = FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
790 | 178 } |
179 | |
180 | |
181 static void SendPathValueForDictionary(RestApiOutput& output, | |
182 DcmItem& dicom) | |
183 { | |
184 Json::Value v = Json::arrayValue; | |
185 | |
186 for (unsigned long i = 0; i < dicom.card(); i++) | |
187 { | |
188 DcmElement* element = dicom.getElement(i); | |
189 if (element) | |
190 { | |
191 char buf[16]; | |
192 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
193 v.append(buf); | |
194 } | |
195 } | |
196 | |
197 output.AnswerJson(v); | |
198 } | |
199 | |
200 static inline uint16_t GetCharValue(char c) | |
201 { | |
202 if (c >= '0' && c <= '9') | |
203 return c - '0'; | |
204 else if (c >= 'a' && c <= 'f') | |
205 return c - 'a' + 10; | |
206 else if (c >= 'A' && c <= 'F') | |
207 return c - 'A' + 10; | |
208 else | |
209 return 0; | |
210 } | |
211 | |
212 static inline uint16_t GetTagValue(const char* c) | |
213 { | |
214 return ((GetCharValue(c[0]) << 12) + | |
215 (GetCharValue(c[1]) << 8) + | |
216 (GetCharValue(c[2]) << 4) + | |
217 GetCharValue(c[3])); | |
218 } | |
219 | |
220 static void ParseTagAndGroup(DcmTagKey& key, | |
221 const std::string& tag) | |
222 { | |
223 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
224 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
225 } | |
226 | |
227 | |
228 static void SendSequence(RestApiOutput& output, | |
229 DcmSequenceOfItems& sequence) | |
230 { | |
231 // This element is a sequence | |
232 Json::Value v = Json::arrayValue; | |
233 | |
234 for (unsigned long i = 0; i < sequence.card(); i++) | |
235 { | |
236 v.append(boost::lexical_cast<std::string>(i)); | |
237 } | |
238 | |
239 output.AnswerJson(v); | |
240 } | |
241 | |
242 | |
243 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
244 E_TransferSyntax transferSyntax) | |
245 { | |
246 DcmPixelSequence* pixelSequence = NULL; | |
247 if (pixelData.getEncapsulatedRepresentation | |
248 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
249 { | |
250 return pixelSequence->card(); | |
251 } | |
252 else | |
253 { | |
254 return 1; | |
255 } | |
256 } | |
257 | |
258 | |
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259 namespace |
790 | 260 { |
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261 class DicomFieldStream : public IHttpStreamAnswer |
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262 { |
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263 private: |
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264 DcmElement& element_; |
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265 uint32_t length_; |
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266 uint32_t offset_; |
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267 std::string chunk_; |
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268 size_t chunkSize_; |
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269 |
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270 public: |
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271 DicomFieldStream(DcmElement& element, |
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272 E_TransferSyntax transferSyntax) : |
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273 element_(element), |
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274 length_(element.getLength(transferSyntax)), |
1616 | 275 offset_(0), |
276 chunkSize_(0) | |
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277 { |
1521 | 278 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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279 chunk_.resize(CHUNK_SIZE); |
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280 } |
790 | 281 |
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282 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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283 bool /*deflateAllowed*/) |
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284 { |
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285 // No support for compression |
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286 return HttpCompression_None; |
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287 } |
790 | 288 |
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289 virtual bool HasContentFilename(std::string& filename) |
790 | 290 { |
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291 return false; |
790 | 292 } |
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293 |
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294 virtual std::string GetContentType() |
790 | 295 { |
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296 return ""; |
790 | 297 } |
298 | |
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299 virtual uint64_t GetContentLength() |
790 | 300 { |
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301 return length_; |
790 | 302 } |
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303 |
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304 virtual bool ReadNextChunk() |
790 | 305 { |
1520 | 306 assert(offset_ <= length_); |
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307 |
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308 if (offset_ == length_) |
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309 { |
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310 return false; |
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311 } |
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312 else |
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313 { |
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314 if (length_ - offset_ < chunk_.size()) |
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315 { |
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316 chunkSize_ = length_ - offset_; |
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317 } |
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318 else |
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319 { |
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320 chunkSize_ = chunk_.size(); |
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321 } |
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322 |
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323 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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324 |
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325 offset_ += chunkSize_; |
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326 |
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327 if (!cond.good()) |
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328 { |
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329 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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330 throw OrthancException(ErrorCode_InternalError); |
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331 } |
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332 |
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333 return true; |
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334 } |
790 | 335 } |
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336 |
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337 virtual const char *GetChunkContent() |
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338 { |
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339 return chunk_.c_str(); |
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340 } |
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341 |
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342 virtual size_t GetChunkSize() |
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343 { |
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344 return chunkSize_; |
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345 } |
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346 }; |
790 | 347 } |
348 | |
349 | |
350 static bool AnswerPixelData(RestApiOutput& output, | |
351 DcmItem& dicom, | |
352 E_TransferSyntax transferSyntax, | |
353 const std::string* blockUri) | |
354 { | |
355 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
356 DICOM_TAG_PIXEL_DATA.GetElement()); | |
357 | |
358 DcmElement *element = NULL; | |
359 if (!dicom.findAndGetElement(k, element).good() || | |
360 element == NULL) | |
361 { | |
362 return false; | |
363 } | |
364 | |
365 try | |
366 { | |
367 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
368 if (blockUri == NULL) | |
369 { | |
370 // The user asks how many blocks are presents in this pixel data | |
371 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
372 | |
373 Json::Value result(Json::arrayValue); | |
374 for (unsigned int i = 0; i < blocks; i++) | |
375 { | |
376 result.append(boost::lexical_cast<std::string>(i)); | |
377 } | |
378 | |
379 output.AnswerJson(result); | |
380 return true; | |
381 } | |
382 | |
383 | |
384 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
385 | |
386 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
387 { | |
388 DcmPixelSequence* pixelSequence = NULL; | |
389 if (pixelData.getEncapsulatedRepresentation | |
390 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
391 { | |
392 // This is the case for JPEG transfer syntaxes | |
393 if (block < pixelSequence->card()) | |
394 { | |
395 DcmPixelItem* pixelItem = NULL; | |
396 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
397 { | |
398 if (pixelItem->getLength() == 0) | |
399 { | |
400 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
401 return true; | |
402 } | |
403 | |
404 Uint8* buffer = NULL; | |
405 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
406 { | |
407 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
408 return true; | |
409 } | |
410 } | |
411 } | |
412 } | |
413 else | |
414 { | |
415 // This is the case for raw, uncompressed image buffers | |
416 assert(*blockUri == "0"); | |
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417 DicomFieldStream stream(*element, transferSyntax); |
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418 output.AnswerStream(stream); |
790 | 419 } |
420 } | |
421 } | |
422 catch (boost::bad_lexical_cast&) | |
423 { | |
424 // The URI entered by the user is not a number | |
425 } | |
426 catch (std::bad_cast&) | |
427 { | |
428 // This should never happen | |
429 } | |
430 | |
431 return false; | |
432 } | |
433 | |
434 | |
435 | |
436 static void SendPathValueForLeaf(RestApiOutput& output, | |
437 const std::string& tag, | |
438 DcmItem& dicom, | |
439 E_TransferSyntax transferSyntax) | |
440 { | |
441 DcmTagKey k; | |
442 ParseTagAndGroup(k, tag); | |
443 | |
444 DcmSequenceOfItems* sequence = NULL; | |
445 if (dicom.findAndGetSequence(k, sequence).good() && | |
446 sequence != NULL && | |
447 sequence->getVR() == EVR_SQ) | |
448 { | |
449 SendSequence(output, *sequence); | |
450 return; | |
451 } | |
452 | |
453 DcmElement* element = NULL; | |
454 if (dicom.findAndGetElement(k, element).good() && | |
455 element != NULL && | |
456 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
457 element->getVR() != EVR_SQ) | |
458 { | |
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459 DicomFieldStream stream(*element, transferSyntax); |
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460 output.AnswerStream(stream); |
790 | 461 } |
462 } | |
463 | |
464 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
465 const UriComponents& uri) | |
466 { | |
794 | 467 DcmItem* dicom = pimpl_->file_->getDataset(); |
468 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
790 | 469 |
470 // Special case: Accessing the pixel data | |
471 if (uri.size() == 1 || | |
472 uri.size() == 2) | |
473 { | |
474 DcmTagKey tag; | |
475 ParseTagAndGroup(tag, uri[0]); | |
476 | |
477 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
478 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
479 { | |
480 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
481 return; | |
482 } | |
483 } | |
484 | |
485 // Go down in the tag hierarchy according to the URI | |
486 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
487 { | |
488 size_t index; | |
489 try | |
490 { | |
491 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
492 } | |
493 catch (boost::bad_lexical_cast&) | |
494 { | |
495 return; | |
496 } | |
497 | |
498 DcmTagKey k; | |
499 DcmItem *child = NULL; | |
500 ParseTagAndGroup(k, uri[2 * pos]); | |
501 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
502 child == NULL) | |
503 { | |
504 return; | |
505 } | |
506 | |
507 dicom = child; | |
508 } | |
509 | |
510 // We have reached the end of the URI | |
511 if (uri.size() % 2 == 0) | |
512 { | |
513 SendPathValueForDictionary(output, *dicom); | |
514 } | |
515 else | |
516 { | |
517 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
518 } | |
519 } | |
520 | |
521 | |
522 void ParsedDicomFile::Remove(const DicomTag& tag) | |
523 { | |
524 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
794 | 525 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
790 | 526 if (element != NULL) |
527 { | |
528 delete element; | |
529 } | |
530 } | |
531 | |
532 | |
533 | |
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534 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
790 | 535 { |
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536 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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537 |
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538 // Loop over the dataset to detect its private tags |
790 | 539 typedef std::list<DcmElement*> Tags; |
540 Tags privateTags; | |
541 | |
542 for (unsigned long i = 0; i < dataset.card(); i++) | |
543 { | |
544 DcmElement* element = dataset.getElement(i); | |
545 DcmTag tag(element->getTag()); | |
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546 |
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547 // Is this a private tag? |
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548 if (FromDcmtkBridge::IsPrivateTag(tag)) |
790 | 549 { |
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550 bool remove = true; |
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551 |
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552 // Check whether this private tag is to be kept |
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553 if (toKeep != NULL) |
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554 { |
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555 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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556 if (toKeep->find(tmp) != toKeep->end()) |
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557 { |
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558 remove = false; // Keep it |
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559 } |
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560 } |
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561 |
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562 if (remove) |
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563 { |
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564 privateTags.push_back(element); |
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565 } |
790 | 566 } |
567 } | |
568 | |
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569 // Loop over the detected private tags to remove them |
790 | 570 for (Tags::iterator it = privateTags.begin(); |
571 it != privateTags.end(); ++it) | |
572 { | |
573 DcmElement* tmp = dataset.remove(*it); | |
574 if (tmp != NULL) | |
575 { | |
576 delete tmp; | |
577 } | |
578 } | |
579 } | |
580 | |
581 | |
582 void ParsedDicomFile::Insert(const DicomTag& tag, | |
583 const std::string& value) | |
584 { | |
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585 OFCondition cond; |
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586 |
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587 if (FromDcmtkBridge::IsPrivateTag(tag) || |
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588 FromDcmtkBridge::IsUnknownTag(tag)) |
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589 { |
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590 // This is a private tag |
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591 // http://support.dcmtk.org/redmine/projects/dcmtk/wiki/howto_addprivatedata |
790 | 592 |
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593 DcmTag key(tag.GetGroup(), tag.GetElement(), EVR_OB); |
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594 cond = pimpl_->file_->getDataset()->putAndInsertUint8Array |
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595 (key, (const Uint8*) value.c_str(), value.size(), false); |
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596 } |
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597 else |
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598 { |
1689 | 599 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
600 FromDcmtkBridge::FillElementWithString(*element, tag, value, false); | |
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601 |
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602 cond = pimpl_->file_->getDataset()->insert(element.release(), false, false); |
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603 } |
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604 |
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605 if (!cond.good()) |
790 | 606 { |
607 // This field already exists | |
608 throw OrthancException(ErrorCode_InternalError); | |
609 } | |
610 } | |
611 | |
612 | |
613 void ParsedDicomFile::Replace(const DicomTag& tag, | |
614 const std::string& value, | |
615 DicomReplaceMode mode) | |
616 { | |
617 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
618 DcmElement* element = NULL; | |
619 | |
794 | 620 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
790 | 621 element == NULL) |
622 { | |
623 // This field does not exist, act wrt. the specified "mode" | |
624 switch (mode) | |
625 { | |
626 case DicomReplaceMode_InsertIfAbsent: | |
627 Insert(tag, value); | |
628 break; | |
629 | |
630 case DicomReplaceMode_ThrowIfAbsent: | |
631 throw OrthancException(ErrorCode_InexistentItem); | |
632 | |
633 case DicomReplaceMode_IgnoreIfAbsent: | |
634 return; | |
635 } | |
636 } | |
637 else | |
638 { | |
1689 | 639 FromDcmtkBridge::FillElementWithString(*element, tag, value, false); |
790 | 640 } |
641 | |
642 | |
643 /** | |
644 * dcmodify will automatically correct 'Media Storage SOP Class | |
645 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
646 * you make changes to the related tags in the dataset ('SOP Class | |
647 * UID' and 'SOP Instance UID') via insert or modify mode | |
648 * options. You can disable this behaviour by using the -nmu | |
649 * option. | |
650 **/ | |
651 | |
652 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
653 { | |
654 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
655 } | |
656 | |
657 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
658 { | |
659 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
660 } | |
661 } | |
662 | |
663 | |
664 void ParsedDicomFile::Answer(RestApiOutput& output) | |
665 { | |
666 std::string serialized; | |
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667 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
790 | 668 { |
669 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
670 } | |
671 } | |
672 | |
673 | |
674 | |
675 bool ParsedDicomFile::GetTagValue(std::string& value, | |
676 const DicomTag& tag) | |
677 { | |
678 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
794 | 679 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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680 |
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681 if (FromDcmtkBridge::IsPrivateTag(tag) || |
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682 FromDcmtkBridge::IsUnknownTag(tag) || |
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683 tag == DICOM_TAG_PIXEL_DATA || |
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684 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
790 | 685 { |
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686 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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687 long unsigned int count = 0; |
790 | 688 |
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689 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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690 { |
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691 if (count > 0) |
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692 { |
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693 assert(data != NULL); |
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694 value.assign(reinterpret_cast<const char*>(data), count); |
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695 } |
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696 else |
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697 { |
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698 value.clear(); |
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699 } |
790 | 700 |
1307
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701 return true; |
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702 } |
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703 else |
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704 { |
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705 return false; |
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706 } |
790 | 707 } |
708 else | |
709 { | |
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710 DcmElement* element = NULL; |
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|
711 if (!dataset.findAndGetElement(k, element).good() || |
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712 element == NULL) |
f796207e3df1
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713 { |
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714 return false; |
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715 } |
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716 |
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diff
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|
717 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element, pimpl_->encoding_)); |
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718 |
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diff
changeset
|
719 if (v.get() == NULL) |
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720 { |
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721 value = ""; |
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722 } |
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723 else |
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724 { |
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725 value = v->AsString(); |
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diff
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|
726 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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727 |
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|
728 return true; |
790 | 729 } |
730 } | |
731 | |
732 | |
733 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
734 { | |
735 std::string patientId, studyUid, seriesUid, instanceUid; | |
736 | |
737 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
738 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
739 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
740 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
741 { | |
742 throw OrthancException(ErrorCode_BadFileFormat); | |
743 } | |
744 | |
745 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
746 } | |
747 | |
748 | |
749 template <typename T> | |
750 static void ExtractPngImageTruncate(std::string& result, | |
751 DicomIntegerPixelAccessor& accessor, | |
752 PixelFormat format) | |
753 { | |
853
839be3022203
DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
831
diff
changeset
|
754 assert(accessor.GetInformation().GetChannelCount() == 1); |
790 | 755 |
756 PngWriter w; | |
757 | |
853
839be3022203
DicomImageInformation
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parents:
831
diff
changeset
|
758 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
790 | 759 T* pixel = &image[0]; |
853
839be3022203
DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
831
diff
changeset
|
760 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
790 | 761 { |
853
839be3022203
DicomImageInformation
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diff
changeset
|
762 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
790 | 763 { |
764 int32_t v = accessor.GetValue(x, y); | |
765 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
766 *pixel = std::numeric_limits<T>::min(); | |
767 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
768 *pixel = std::numeric_limits<T>::max(); | |
769 else | |
770 *pixel = static_cast<T>(v); | |
771 } | |
772 } | |
773 | |
853
839be3022203
DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
831
diff
changeset
|
774 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
839be3022203
DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
831
diff
changeset
|
775 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
790 | 776 } |
777 | |
778 | |
779 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
780 { | |
1004
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
991
diff
changeset
|
781 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
790 | 782 } |
783 | |
784 | |
785 void ParsedDicomFile::SaveToFile(const std::string& path) | |
786 { | |
787 // TODO Avoid using a temporary memory buffer, write directly on disk | |
788 std::string content; | |
789 SaveToMemoryBuffer(content); | |
790 Toolbox::WriteFile(content, path); | |
791 } | |
792 | |
793 | |
794 | 794 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
790 | 795 { |
794 | 796 pimpl_->file_.reset(new DcmFileFormat); |
956
2fd5a163776d
primitives for proper encoding handling
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874
diff
changeset
|
797 pimpl_->encoding_ = Encoding_Ascii; |
790 | 798 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
799 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
800 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
801 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
802 } | |
803 | |
791 | 804 |
794 | 805 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
791 | 806 { |
807 Setup(content, size); | |
808 } | |
809 | |
794 | 810 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
791 | 811 { |
812 if (content.size() == 0) | |
813 { | |
814 Setup(NULL, 0); | |
815 } | |
816 else | |
817 { | |
818 Setup(&content[0], content.size()); | |
819 } | |
820 } | |
792 | 821 |
822 | |
794 | 823 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
824 pimpl_(new PImpl) | |
792 | 825 { |
794 | 826 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
1564
1b7def486e62
creation of DICOM series
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diff
changeset
|
827 pimpl_->encoding_ = other.pimpl_->encoding_; |
956
2fd5a163776d
primitives for proper encoding handling
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874
diff
changeset
|
828 |
1564
1b7def486e62
creation of DICOM series
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parents:
1562
diff
changeset
|
829 // Create a new instance-level identifier |
1b7def486e62
creation of DICOM series
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parents:
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diff
changeset
|
830 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
792 | 831 } |
832 | |
833 | |
834 ParsedDicomFile::~ParsedDicomFile() | |
835 { | |
794 | 836 delete pimpl_; |
792 | 837 } |
838 | |
793 | 839 |
840 void* ParsedDicomFile::GetDcmtkObject() | |
841 { | |
794 | 842 return pimpl_->file_.get(); |
793 | 843 } |
844 | |
845 | |
846 ParsedDicomFile* ParsedDicomFile::Clone() | |
847 { | |
794 | 848 return new ParsedDicomFile(*this); |
793 | 849 } |
800
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generation of DICOM images from PNG files
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diff
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|
850 |
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generation of DICOM images from PNG files
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diff
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|
851 |
1562 | 852 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
800
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generation of DICOM images from PNG files
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diff
changeset
|
853 { |
1641
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Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
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1616
diff
changeset
|
854 std::string mime, content; |
4e56b5a206b7
Support of binary tags encoded using data URI scheme
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1616
diff
changeset
|
855 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
1562 | 856 Toolbox::ToLowerCase(mime); |
1555
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Creation of DICOM files with encapsulated PDF
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diff
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|
857 |
1562 | 858 if (mime == "image/png") |
859 { | |
860 EmbedImage(mime, content); | |
861 } | |
862 else if (mime == "application/pdf") | |
863 { | |
864 EmbedPdf(content); | |
865 } | |
866 else | |
867 { | |
868 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file"; | |
869 throw OrthancException(ErrorCode_NotImplemented); | |
870 } | |
1555
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Creation of DICOM files with encapsulated PDF
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|
871 } |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
872 |
800
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generation of DICOM images from PNG files
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diff
changeset
|
873 |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
874 void ParsedDicomFile::EmbedImage(const std::string& mime, |
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Creation of DICOM files with encapsulated PDF
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875 const std::string& content) |
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Creation of DICOM files with encapsulated PDF
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876 { |
800
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generation of DICOM images from PNG files
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diff
changeset
|
877 if (mime == "image/png") |
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generation of DICOM images from PNG files
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diff
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|
878 { |
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generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
879 PngReader reader; |
1555
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
880 reader.ReadFromMemory(content); |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
881 EmbedImage(reader); |
ecedd89055db
generation of DICOM images from PNG files
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diff
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|
882 } |
ecedd89055db
generation of DICOM images from PNG files
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parents:
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diff
changeset
|
883 else |
ecedd89055db
generation of DICOM images from PNG files
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diff
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|
884 { |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
885 throw OrthancException(ErrorCode_NotImplemented); |
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generation of DICOM images from PNG files
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diff
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|
886 } |
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diff
changeset
|
887 } |
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generation of DICOM images from PNG files
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diff
changeset
|
888 |
ecedd89055db
generation of DICOM images from PNG files
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diff
changeset
|
889 |
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generation of DICOM images from PNG files
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diff
changeset
|
890 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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generation of DICOM images from PNG files
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diff
changeset
|
891 { |
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diff
changeset
|
892 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
ecedd89055db
generation of DICOM images from PNG files
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diff
changeset
|
893 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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generation of DICOM images from PNG files
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diff
changeset
|
894 accessor.GetFormat() != PixelFormat_RGB24 && |
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generation of DICOM images from PNG files
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diff
changeset
|
895 accessor.GetFormat() != PixelFormat_RGBA32) |
ecedd89055db
generation of DICOM images from PNG files
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parents:
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diff
changeset
|
896 { |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
897 throw OrthancException(ErrorCode_NotImplemented); |
ecedd89055db
generation of DICOM images from PNG files
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diff
changeset
|
898 } |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
899 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
900 if (accessor.GetFormat() == PixelFormat_RGBA32) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
901 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
902 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
903 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
904 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
905 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
906 |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
907 Remove(DICOM_TAG_PIXEL_DATA); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
908 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
ecedd89055db
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
909 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
910 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
ecedd89055db
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
911 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
912 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
913 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
914 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
915 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
916 Replace(DICOM_TAG_BITS_STORED, "8"); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
917 Replace(DICOM_TAG_HIGH_BIT, "7"); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
918 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
919 unsigned int bytesPerPixel = 1; |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
920 |
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changeset
|
921 switch (accessor.GetFormat()) |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
922 { |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
923 case PixelFormat_RGB24: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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924 case PixelFormat_RGBA32: |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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925 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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parents:
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926 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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927 bytesPerPixel = 3; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
928 break; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
929 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
930 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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|
931 break; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
932 |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
933 case PixelFormat_Grayscale16: |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
934 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
935 Replace(DICOM_TAG_BITS_STORED, "16"); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
936 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
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|
937 bytesPerPixel = 2; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
938 break; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
939 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
940 default: |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
941 throw OrthancException(ErrorCode_NotImplemented); |
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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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|
942 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
943 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
944 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
945 DICOM_TAG_PIXEL_DATA.GetElement()); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
946 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
947 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
948 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
949 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
ecedd89055db
generation of DICOM images from PNG files
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parents:
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diff
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|
950 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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|
951 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
952 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
953 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
954 { |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
955 switch (accessor.GetFormat()) |
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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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|
956 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
957 case PixelFormat_RGB24: |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
958 case PixelFormat_Grayscale8: |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
959 case PixelFormat_Grayscale16: |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
960 case PixelFormat_SignedGrayscale16: |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
961 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
962 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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963 target += pitch; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
964 break; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
965 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
966 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
967 case PixelFormat_RGBA32: |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
968 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
969 // The alpha channel is not supported by the DICOM standard |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
970 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
971 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
972 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
973 target[0] = source[0]; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
974 target[1] = source[1]; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
975 target[2] = source[2]; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
976 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
977 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
978 break; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
979 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
980 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
981 default: |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
982 throw OrthancException(ErrorCode_NotImplemented); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
983 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
984 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
985 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
986 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
987 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
988 throw OrthancException(ErrorCode_InternalError); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
989 } |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
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|
990 } |
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
991 |
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
992 |
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
993 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
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|
994 unsigned int frame) |
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
995 { |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
996 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
997 |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
998 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
999 { |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1000 throw OrthancException(ErrorCode_BadFileFormat); |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1001 } |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1002 } |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1003 |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1004 |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1005 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1006 unsigned int frame, |
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1007 ImageExtractionMode mode) |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1008 { |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1009 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1010 |
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1011 bool ok = false; |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1012 |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1013 switch (mode) |
87791ebc1f50
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1014 { |
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1015 case ImageExtractionMode_UInt8: |
1015
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1016 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
874
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1017 break; |
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1018 |
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1019 case ImageExtractionMode_UInt16: |
1015
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1020 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
874
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1021 break; |
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1022 |
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1023 case ImageExtractionMode_Int16: |
1015
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1024 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
874
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1025 break; |
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1026 |
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1027 case ImageExtractionMode_Preview: |
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1028 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
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1029 break; |
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1030 |
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1031 default: |
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1032 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1033 } |
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1034 |
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1035 if (!ok) |
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1036 { |
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1037 throw OrthancException(ErrorCode_BadFileFormat); |
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1038 } |
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1039 } |
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1040 |
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1041 |
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1042 void ParsedDicomFile::ExtractPngImage(std::string& result, |
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1043 unsigned int frame, |
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1044 ImageExtractionMode mode) |
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1045 { |
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1046 ImageBuffer buffer; |
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1047 ExtractImage(buffer, frame, mode); |
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1048 |
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1049 ImageAccessor accessor(buffer.GetConstAccessor()); |
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1050 PngWriter writer; |
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1051 writer.WriteToMemory(result, accessor); |
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1052 } |
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1053 |
956
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1054 |
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1055 Encoding ParsedDicomFile::GetEncoding() const |
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1056 { |
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1057 return pimpl_->encoding_; |
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1058 } |
1090
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1059 |
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1060 |
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1061 void ParsedDicomFile::SetEncoding(Encoding encoding) |
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1062 { |
1558
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1063 if (encoding == Encoding_Windows1251) |
1090
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1064 { |
1558
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1065 // This Cyrillic codepage is not officially supported by the |
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1066 // DICOM standard. Do not set the SpecificCharacterSet tag. |
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1067 return; |
1090
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1068 } |
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1069 |
1565
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1070 pimpl_->encoding_ = encoding; |
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1071 |
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1072 std::string s = GetDicomSpecificCharacterSet(encoding); |
1091 | 1073 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
1090
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1074 } |
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1075 |
1686 | 1076 void ParsedDicomFile::ToJson(Json::Value& target, |
1077 DicomToJsonFormat format, | |
1078 unsigned int maxStringLength) | |
1160
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1079 { |
1686 | 1080 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), format, maxStringLength); |
1160
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1081 } |
1555
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1082 |
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1083 |
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1084 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
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1085 { |
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1086 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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1087 return pimpl_->file_->getDataset()->tagExists(key); |
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1088 } |
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1089 |
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1090 |
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1091 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
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1092 { |
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1093 if (pdf.size() < 5 || // (*) |
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1094 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
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1095 { |
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1096 LOG(ERROR) << "Not a PDF file"; |
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1097 throw OrthancException(ErrorCode_BadFileFormat); |
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1098 } |
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1099 |
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1100 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
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1101 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
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1102 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
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1103 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
1566 | 1104 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
1555
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1105 |
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1106 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
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1107 |
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1108 size_t s = pdf.size(); |
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1109 if (s & 1) |
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1110 { |
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1111 // The size of the buffer must be even |
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1112 s += 1; |
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1113 } |
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1114 |
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1115 Uint8* bytes = NULL; |
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1116 OFCondition result = element->createUint8Array(s, bytes); |
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1117 if (!result.good() || bytes == NULL) |
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1118 { |
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1119 throw OrthancException(ErrorCode_NotEnoughMemory); |
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1120 } |
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1121 |
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1122 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
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1123 bytes[s - 1] = 0; |
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1124 |
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1125 memcpy(bytes, pdf.c_str(), pdf.size()); |
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1126 |
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1127 DcmPolymorphOBOW* obj = element.release(); |
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1128 result = pimpl_->file_->getDataset()->insert(obj); |
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1129 |
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1130 if (!result.good()) |
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1131 { |
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1132 delete obj; |
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1133 throw OrthancException(ErrorCode_NotEnoughMemory); |
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1134 } |
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1135 } |
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1136 |
1556
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1137 |
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1138 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
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1139 { |
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1140 std::string sop, mime; |
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1141 |
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1142 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
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1143 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
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1144 sop != UID_EncapsulatedPDFStorage || |
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1145 mime != "application/pdf") |
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1146 { |
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1147 return false; |
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1148 } |
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1149 |
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1150 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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1151 { |
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1152 return false; |
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1153 } |
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1154 |
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1155 // Strip the possible pad byte at the end of file, because the |
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1156 // encapsulated documents must always have an even length. The PDF |
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1157 // format expects files to end with %%EOF followed by CR/LF. If |
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1158 // the last character of the file is not a CR or LF, we assume it |
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1159 // is a pad byte and remove it. |
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1160 if (pdf.size() > 0) |
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1161 { |
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1162 char last = *pdf.rbegin(); |
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1163 |
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1164 if (last != 10 && last != 13) |
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1165 { |
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1166 pdf.resize(pdf.size() - 1); |
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1167 } |
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1168 } |
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1169 |
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1170 return true; |
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1171 } |
1662
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1172 |
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1173 |
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1174 void ParsedDicomFile::Convert(DicomMap& tags) |
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1175 { |
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1176 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset()); |
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1177 } |
790 | 1178 } |