Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1752:c3d8ec63a179 db-changes
cont
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 27 Oct 2015 17:45:05 +0100 |
parents | ec66a16aa398 |
children | 5ad4e4d92ecb |
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/DicomIntegerPixelAccessor.h" | |
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94 #include "../Core/Images/PngReader.h" |
790 | 95 |
96 #include <list> | |
97 #include <limits> | |
98 | |
99 #include <boost/lexical_cast.hpp> | |
100 | |
101 #include <dcmtk/dcmdata/dcchrstr.h> | |
102 #include <dcmtk/dcmdata/dcdicent.h> | |
103 #include <dcmtk/dcmdata/dcdict.h> | |
104 #include <dcmtk/dcmdata/dcfilefo.h> | |
105 #include <dcmtk/dcmdata/dcistrmb.h> | |
106 #include <dcmtk/dcmdata/dcuid.h> | |
107 #include <dcmtk/dcmdata/dcmetinf.h> | |
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108 #include <dcmtk/dcmdata/dcdeftag.h> |
790 | 109 |
110 #include <dcmtk/dcmdata/dcvrae.h> | |
111 #include <dcmtk/dcmdata/dcvras.h> | |
112 #include <dcmtk/dcmdata/dcvrcs.h> | |
113 #include <dcmtk/dcmdata/dcvrda.h> | |
114 #include <dcmtk/dcmdata/dcvrds.h> | |
115 #include <dcmtk/dcmdata/dcvrdt.h> | |
116 #include <dcmtk/dcmdata/dcvrfd.h> | |
117 #include <dcmtk/dcmdata/dcvrfl.h> | |
118 #include <dcmtk/dcmdata/dcvris.h> | |
119 #include <dcmtk/dcmdata/dcvrlo.h> | |
120 #include <dcmtk/dcmdata/dcvrlt.h> | |
121 #include <dcmtk/dcmdata/dcvrpn.h> | |
122 #include <dcmtk/dcmdata/dcvrsh.h> | |
123 #include <dcmtk/dcmdata/dcvrsl.h> | |
124 #include <dcmtk/dcmdata/dcvrss.h> | |
125 #include <dcmtk/dcmdata/dcvrst.h> | |
126 #include <dcmtk/dcmdata/dcvrtm.h> | |
127 #include <dcmtk/dcmdata/dcvrui.h> | |
128 #include <dcmtk/dcmdata/dcvrul.h> | |
129 #include <dcmtk/dcmdata/dcvrus.h> | |
130 #include <dcmtk/dcmdata/dcvrut.h> | |
131 #include <dcmtk/dcmdata/dcpixel.h> | |
132 #include <dcmtk/dcmdata/dcpixseq.h> | |
133 #include <dcmtk/dcmdata/dcpxitem.h> | |
134 | |
135 | |
136 #include <boost/math/special_functions/round.hpp> | |
137 #include <dcmtk/dcmdata/dcostrmb.h> | |
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138 #include <boost/algorithm/string/predicate.hpp> |
790 | 139 |
140 | |
141 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
142 | |
143 | |
144 | |
145 namespace Orthanc | |
146 { | |
794 | 147 struct ParsedDicomFile::PImpl |
148 { | |
149 std::auto_ptr<DcmFileFormat> file_; | |
150 }; | |
151 | |
152 | |
153 // This method can only be called from the constructors! | |
790 | 154 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
155 { | |
156 DcmInputBufferStream is; | |
157 if (size > 0) | |
158 { | |
159 is.setBuffer(buffer, size); | |
160 } | |
161 is.setEos(); | |
162 | |
794 | 163 pimpl_->file_.reset(new DcmFileFormat); |
164 pimpl_->file_->transferInit(); | |
165 if (!pimpl_->file_->read(is).good()) | |
790 | 166 { |
794 | 167 delete pimpl_; // Avoid a memory leak due to exception |
168 // throwing, as we are in the constructor | |
169 | |
790 | 170 throw OrthancException(ErrorCode_BadFileFormat); |
171 } | |
794 | 172 pimpl_->file_->loadAllDataIntoMemory(); |
173 pimpl_->file_->transferEnd(); | |
790 | 174 } |
175 | |
176 | |
177 static void SendPathValueForDictionary(RestApiOutput& output, | |
178 DcmItem& dicom) | |
179 { | |
180 Json::Value v = Json::arrayValue; | |
181 | |
182 for (unsigned long i = 0; i < dicom.card(); i++) | |
183 { | |
184 DcmElement* element = dicom.getElement(i); | |
185 if (element) | |
186 { | |
187 char buf[16]; | |
188 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
189 v.append(buf); | |
190 } | |
191 } | |
192 | |
193 output.AnswerJson(v); | |
194 } | |
195 | |
196 static inline uint16_t GetCharValue(char c) | |
197 { | |
198 if (c >= '0' && c <= '9') | |
199 return c - '0'; | |
200 else if (c >= 'a' && c <= 'f') | |
201 return c - 'a' + 10; | |
202 else if (c >= 'A' && c <= 'F') | |
203 return c - 'A' + 10; | |
204 else | |
205 return 0; | |
206 } | |
207 | |
208 static inline uint16_t GetTagValue(const char* c) | |
209 { | |
210 return ((GetCharValue(c[0]) << 12) + | |
211 (GetCharValue(c[1]) << 8) + | |
212 (GetCharValue(c[2]) << 4) + | |
213 GetCharValue(c[3])); | |
214 } | |
215 | |
216 static void ParseTagAndGroup(DcmTagKey& key, | |
217 const std::string& tag) | |
218 { | |
219 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
220 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
221 } | |
222 | |
223 | |
224 static void SendSequence(RestApiOutput& output, | |
225 DcmSequenceOfItems& sequence) | |
226 { | |
227 // This element is a sequence | |
228 Json::Value v = Json::arrayValue; | |
229 | |
230 for (unsigned long i = 0; i < sequence.card(); i++) | |
231 { | |
232 v.append(boost::lexical_cast<std::string>(i)); | |
233 } | |
234 | |
235 output.AnswerJson(v); | |
236 } | |
237 | |
238 | |
239 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
240 E_TransferSyntax transferSyntax) | |
241 { | |
242 DcmPixelSequence* pixelSequence = NULL; | |
243 if (pixelData.getEncapsulatedRepresentation | |
244 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
245 { | |
246 return pixelSequence->card(); | |
247 } | |
248 else | |
249 { | |
250 return 1; | |
251 } | |
252 } | |
253 | |
254 | |
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255 namespace |
790 | 256 { |
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257 class DicomFieldStream : public IHttpStreamAnswer |
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258 { |
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259 private: |
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260 DcmElement& element_; |
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261 uint32_t length_; |
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262 uint32_t offset_; |
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263 std::string chunk_; |
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264 size_t chunkSize_; |
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265 |
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266 public: |
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267 DicomFieldStream(DcmElement& element, |
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268 E_TransferSyntax transferSyntax) : |
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269 element_(element), |
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270 length_(element.getLength(transferSyntax)), |
1616 | 271 offset_(0), |
272 chunkSize_(0) | |
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273 { |
1521 | 274 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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275 chunk_.resize(CHUNK_SIZE); |
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276 } |
790 | 277 |
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278 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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279 bool /*deflateAllowed*/) |
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280 { |
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281 // No support for compression |
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282 return HttpCompression_None; |
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283 } |
790 | 284 |
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285 virtual bool HasContentFilename(std::string& filename) |
790 | 286 { |
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287 return false; |
790 | 288 } |
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289 |
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290 virtual std::string GetContentType() |
790 | 291 { |
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292 return ""; |
790 | 293 } |
294 | |
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295 virtual uint64_t GetContentLength() |
790 | 296 { |
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297 return length_; |
790 | 298 } |
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299 |
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300 virtual bool ReadNextChunk() |
790 | 301 { |
1520 | 302 assert(offset_ <= length_); |
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303 |
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304 if (offset_ == length_) |
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305 { |
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306 return false; |
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307 } |
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308 else |
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309 { |
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310 if (length_ - offset_ < chunk_.size()) |
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311 { |
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312 chunkSize_ = length_ - offset_; |
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313 } |
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314 else |
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315 { |
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316 chunkSize_ = chunk_.size(); |
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317 } |
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318 |
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319 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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320 |
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321 offset_ += chunkSize_; |
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322 |
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323 if (!cond.good()) |
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324 { |
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325 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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326 throw OrthancException(ErrorCode_InternalError); |
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327 } |
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328 |
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329 return true; |
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330 } |
790 | 331 } |
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332 |
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333 virtual const char *GetChunkContent() |
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334 { |
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335 return chunk_.c_str(); |
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336 } |
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337 |
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338 virtual size_t GetChunkSize() |
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339 { |
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340 return chunkSize_; |
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341 } |
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342 }; |
790 | 343 } |
344 | |
345 | |
346 static bool AnswerPixelData(RestApiOutput& output, | |
347 DcmItem& dicom, | |
348 E_TransferSyntax transferSyntax, | |
349 const std::string* blockUri) | |
350 { | |
351 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
352 DICOM_TAG_PIXEL_DATA.GetElement()); | |
353 | |
354 DcmElement *element = NULL; | |
355 if (!dicom.findAndGetElement(k, element).good() || | |
356 element == NULL) | |
357 { | |
358 return false; | |
359 } | |
360 | |
361 try | |
362 { | |
363 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
364 if (blockUri == NULL) | |
365 { | |
366 // The user asks how many blocks are presents in this pixel data | |
367 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
368 | |
369 Json::Value result(Json::arrayValue); | |
370 for (unsigned int i = 0; i < blocks; i++) | |
371 { | |
372 result.append(boost::lexical_cast<std::string>(i)); | |
373 } | |
374 | |
375 output.AnswerJson(result); | |
376 return true; | |
377 } | |
378 | |
379 | |
380 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
381 | |
382 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
383 { | |
384 DcmPixelSequence* pixelSequence = NULL; | |
385 if (pixelData.getEncapsulatedRepresentation | |
386 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
387 { | |
388 // This is the case for JPEG transfer syntaxes | |
389 if (block < pixelSequence->card()) | |
390 { | |
391 DcmPixelItem* pixelItem = NULL; | |
392 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
393 { | |
394 if (pixelItem->getLength() == 0) | |
395 { | |
396 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
397 return true; | |
398 } | |
399 | |
400 Uint8* buffer = NULL; | |
401 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
402 { | |
403 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
404 return true; | |
405 } | |
406 } | |
407 } | |
408 } | |
409 else | |
410 { | |
411 // This is the case for raw, uncompressed image buffers | |
412 assert(*blockUri == "0"); | |
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413 DicomFieldStream stream(*element, transferSyntax); |
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414 output.AnswerStream(stream); |
790 | 415 } |
416 } | |
417 } | |
418 catch (boost::bad_lexical_cast&) | |
419 { | |
420 // The URI entered by the user is not a number | |
421 } | |
422 catch (std::bad_cast&) | |
423 { | |
424 // This should never happen | |
425 } | |
426 | |
427 return false; | |
428 } | |
429 | |
430 | |
431 | |
432 static void SendPathValueForLeaf(RestApiOutput& output, | |
433 const std::string& tag, | |
434 DcmItem& dicom, | |
435 E_TransferSyntax transferSyntax) | |
436 { | |
437 DcmTagKey k; | |
438 ParseTagAndGroup(k, tag); | |
439 | |
440 DcmSequenceOfItems* sequence = NULL; | |
441 if (dicom.findAndGetSequence(k, sequence).good() && | |
442 sequence != NULL && | |
443 sequence->getVR() == EVR_SQ) | |
444 { | |
445 SendSequence(output, *sequence); | |
446 return; | |
447 } | |
448 | |
449 DcmElement* element = NULL; | |
450 if (dicom.findAndGetElement(k, element).good() && | |
451 element != NULL && | |
452 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
453 element->getVR() != EVR_SQ) | |
454 { | |
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455 DicomFieldStream stream(*element, transferSyntax); |
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456 output.AnswerStream(stream); |
790 | 457 } |
458 } | |
459 | |
460 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
461 const UriComponents& uri) | |
462 { | |
794 | 463 DcmItem* dicom = pimpl_->file_->getDataset(); |
464 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
790 | 465 |
466 // Special case: Accessing the pixel data | |
467 if (uri.size() == 1 || | |
468 uri.size() == 2) | |
469 { | |
470 DcmTagKey tag; | |
471 ParseTagAndGroup(tag, uri[0]); | |
472 | |
473 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
474 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
475 { | |
476 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
477 return; | |
478 } | |
479 } | |
480 | |
481 // Go down in the tag hierarchy according to the URI | |
482 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
483 { | |
484 size_t index; | |
485 try | |
486 { | |
487 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
488 } | |
489 catch (boost::bad_lexical_cast&) | |
490 { | |
491 return; | |
492 } | |
493 | |
494 DcmTagKey k; | |
495 DcmItem *child = NULL; | |
496 ParseTagAndGroup(k, uri[2 * pos]); | |
497 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
498 child == NULL) | |
499 { | |
500 return; | |
501 } | |
502 | |
503 dicom = child; | |
504 } | |
505 | |
506 // We have reached the end of the URI | |
507 if (uri.size() % 2 == 0) | |
508 { | |
509 SendPathValueForDictionary(output, *dicom); | |
510 } | |
511 else | |
512 { | |
513 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
514 } | |
515 } | |
516 | |
517 | |
518 void ParsedDicomFile::Remove(const DicomTag& tag) | |
519 { | |
520 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
794 | 521 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
790 | 522 if (element != NULL) |
523 { | |
524 delete element; | |
525 } | |
526 } | |
527 | |
528 | |
529 | |
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530 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
790 | 531 { |
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532 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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533 |
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534 // Loop over the dataset to detect its private tags |
790 | 535 typedef std::list<DcmElement*> Tags; |
536 Tags privateTags; | |
537 | |
538 for (unsigned long i = 0; i < dataset.card(); i++) | |
539 { | |
540 DcmElement* element = dataset.getElement(i); | |
541 DcmTag tag(element->getTag()); | |
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542 |
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543 // Is this a private tag? |
1694 | 544 if (tag.isPrivate()) |
790 | 545 { |
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546 bool remove = true; |
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547 |
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548 // Check whether this private tag is to be kept |
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549 if (toKeep != NULL) |
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550 { |
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551 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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552 if (toKeep->find(tmp) != toKeep->end()) |
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553 { |
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554 remove = false; // Keep it |
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555 } |
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556 } |
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557 |
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558 if (remove) |
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559 { |
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560 privateTags.push_back(element); |
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561 } |
790 | 562 } |
563 } | |
564 | |
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565 // Loop over the detected private tags to remove them |
790 | 566 for (Tags::iterator it = privateTags.begin(); |
567 it != privateTags.end(); ++it) | |
568 { | |
569 DcmElement* tmp = dataset.remove(*it); | |
570 if (tmp != NULL) | |
571 { | |
572 delete tmp; | |
573 } | |
574 } | |
575 } | |
576 | |
577 | |
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578 static void InsertInternal(DcmDataset& dicom, |
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579 DcmElement* element) |
790 | 580 { |
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581 OFCondition cond = dicom.insert(element, false, false); |
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582 if (!cond.good()) |
790 | 583 { |
584 // This field already exists | |
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585 delete element; |
790 | 586 throw OrthancException(ErrorCode_InternalError); |
587 } | |
588 } | |
589 | |
590 | |
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591 void ParsedDicomFile::Insert(const DicomTag& tag, |
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592 const Json::Value& value, |
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593 bool decodeBinaryTags) |
790 | 594 { |
1695 | 595 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeBinaryTags, GetEncoding())); |
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596 InsertInternal(*pimpl_->file_->getDataset(), element.release()); |
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597 } |
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598 |
790 | 599 |
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600 static void ReplaceInternal(DcmDataset& dicom, |
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601 std::auto_ptr<DcmElement>& element, |
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602 DicomReplaceMode mode) |
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603 { |
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604 const DcmTagKey& tag = element->getTag(); |
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605 |
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606 if (!dicom.findAndDeleteElement(tag).good()) |
790 | 607 { |
608 // This field does not exist, act wrt. the specified "mode" | |
609 switch (mode) | |
610 { | |
611 case DicomReplaceMode_InsertIfAbsent: | |
612 break; | |
613 | |
614 case DicomReplaceMode_ThrowIfAbsent: | |
615 throw OrthancException(ErrorCode_InexistentItem); | |
616 | |
617 case DicomReplaceMode_IgnoreIfAbsent: | |
618 return; | |
619 } | |
620 } | |
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621 |
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622 // Either the tag was not existing, or the replace mode was set to |
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623 // "InsertIfAbsent" |
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624 InsertInternal(dicom, element.release()); |
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625 } |
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626 |
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627 |
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628 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag, |
1695 | 629 const std::string& utf8Value, |
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630 bool decodeBinaryTags) |
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631 { |
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632 if (tag != DICOM_TAG_SOP_CLASS_UID && |
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633 tag != DICOM_TAG_SOP_INSTANCE_UID) |
790 | 634 { |
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635 return; |
790 | 636 } |
637 | |
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638 std::string binary; |
1695 | 639 const std::string* decoded = &utf8Value; |
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640 |
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641 if (decodeBinaryTags && |
1695 | 642 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
1693
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643 { |
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644 std::string mime; |
1695 | 645 Toolbox::DecodeDataUriScheme(mime, binary, utf8Value); |
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646 decoded = &binary; |
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647 } |
1695 | 648 else |
649 { | |
650 Encoding encoding = GetEncoding(); | |
651 if (GetEncoding() != Encoding_Utf8) | |
652 { | |
653 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding); | |
654 decoded = &binary; | |
655 } | |
656 } | |
790 | 657 |
658 /** | |
659 * dcmodify will automatically correct 'Media Storage SOP Class | |
660 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
661 * you make changes to the related tags in the dataset ('SOP Class | |
662 * UID' and 'SOP Instance UID') via insert or modify mode | |
663 * options. You can disable this behaviour by using the -nmu | |
664 * option. | |
665 **/ | |
666 | |
667 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
668 { | |
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669 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
790 | 670 } |
671 | |
672 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
673 { | |
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674 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
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675 } |
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676 } |
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677 |
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678 |
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679 void ParsedDicomFile::Replace(const DicomTag& tag, |
1695 | 680 const std::string& utf8Value, |
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681 DicomReplaceMode mode) |
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682 { |
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683 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
1695 | 684 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, false, GetEncoding()); |
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685 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
1695 | 686 UpdateStorageUid(tag, utf8Value, false); |
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687 } |
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688 |
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689 |
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690 void ParsedDicomFile::Replace(const DicomTag& tag, |
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691 const Json::Value& value, |
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692 bool decodeBinaryTags, |
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693 DicomReplaceMode mode) |
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694 { |
1695 | 695 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeBinaryTags, GetEncoding())); |
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696 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
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697 |
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698 if (tag == DICOM_TAG_SOP_CLASS_UID || |
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699 tag == DICOM_TAG_SOP_INSTANCE_UID) |
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700 { |
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701 if (value.type() != Json::stringValue) |
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702 { |
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703 throw OrthancException(ErrorCode_BadParameterType); |
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704 } |
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705 |
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706 UpdateStorageUid(tag, value.asString(), decodeBinaryTags); |
790 | 707 } |
708 } | |
709 | |
710 | |
711 void ParsedDicomFile::Answer(RestApiOutput& output) | |
712 { | |
713 std::string serialized; | |
1004
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714 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
790 | 715 { |
716 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
717 } | |
718 } | |
719 | |
720 | |
721 | |
722 bool ParsedDicomFile::GetTagValue(std::string& value, | |
723 const DicomTag& tag) | |
724 { | |
725 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
794 | 726 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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727 |
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728 if (FromDcmtkBridge::IsPrivateTag(tag) || |
1655
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729 FromDcmtkBridge::IsUnknownTag(tag) || |
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730 tag == DICOM_TAG_PIXEL_DATA || |
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731 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
790 | 732 { |
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733 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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734 long unsigned int count = 0; |
790 | 735 |
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736 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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737 { |
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738 if (count > 0) |
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739 { |
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740 assert(data != NULL); |
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741 value.assign(reinterpret_cast<const char*>(data), count); |
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742 } |
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743 else |
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744 { |
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745 value.clear(); |
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746 } |
790 | 747 |
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748 return true; |
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749 } |
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750 else |
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751 { |
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752 return false; |
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753 } |
790 | 754 } |
755 else | |
756 { | |
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757 DcmElement* element = NULL; |
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758 if (!dataset.findAndGetElement(k, element).good() || |
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759 element == NULL) |
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760 { |
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761 return false; |
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762 } |
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|
763 |
1736
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diff
changeset
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764 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement |
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765 (*element, DicomToJsonFlags_Default, GetEncoding())); |
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766 |
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767 if (v.get() == NULL || |
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768 v->IsNull()) |
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769 { |
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770 value = ""; |
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771 } |
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772 else |
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773 { |
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774 // TODO v->IsBinary() |
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775 value = v->GetContent(); |
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776 } |
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777 |
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778 return true; |
790 | 779 } |
780 } | |
781 | |
782 | |
783 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
784 { | |
785 std::string patientId, studyUid, seriesUid, instanceUid; | |
786 | |
787 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
788 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
789 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
790 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
791 { | |
792 throw OrthancException(ErrorCode_BadFileFormat); | |
793 } | |
794 | |
795 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
796 } | |
797 | |
798 | |
799 template <typename T> | |
800 static void ExtractPngImageTruncate(std::string& result, | |
801 DicomIntegerPixelAccessor& accessor, | |
802 PixelFormat format) | |
803 { | |
853
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diff
changeset
|
804 assert(accessor.GetInformation().GetChannelCount() == 1); |
790 | 805 |
806 PngWriter w; | |
807 | |
853
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diff
changeset
|
808 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
790 | 809 T* pixel = &image[0]; |
853
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diff
changeset
|
810 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
790 | 811 { |
853
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changeset
|
812 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
790 | 813 { |
814 int32_t v = accessor.GetValue(x, y); | |
815 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
816 *pixel = std::numeric_limits<T>::min(); | |
817 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
818 *pixel = std::numeric_limits<T>::max(); | |
819 else | |
820 *pixel = static_cast<T>(v); | |
821 } | |
822 } | |
823 | |
853
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diff
changeset
|
824 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
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diff
changeset
|
825 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
790 | 826 } |
827 | |
828 | |
829 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
830 { | |
1004
a226e0959d8b
DicomInstanceToStore
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diff
changeset
|
831 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
790 | 832 } |
833 | |
834 | |
835 void ParsedDicomFile::SaveToFile(const std::string& path) | |
836 { | |
837 // TODO Avoid using a temporary memory buffer, write directly on disk | |
838 std::string content; | |
839 SaveToMemoryBuffer(content); | |
840 Toolbox::WriteFile(content, path); | |
841 } | |
842 | |
843 | |
794 | 844 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
790 | 845 { |
794 | 846 pimpl_->file_.reset(new DcmFileFormat); |
790 | 847 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
848 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
849 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
850 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
851 } | |
852 | |
791 | 853 |
794 | 854 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
791 | 855 { |
856 Setup(content, size); | |
857 } | |
858 | |
794 | 859 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
791 | 860 { |
861 if (content.size() == 0) | |
862 { | |
863 Setup(NULL, 0); | |
864 } | |
865 else | |
866 { | |
867 Setup(&content[0], content.size()); | |
868 } | |
869 } | |
792 | 870 |
871 | |
794 | 872 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
873 pimpl_(new PImpl) | |
792 | 874 { |
794 | 875 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
956
2fd5a163776d
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874
diff
changeset
|
876 |
1564
1b7def486e62
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1562
diff
changeset
|
877 // Create a new instance-level identifier |
1b7def486e62
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diff
changeset
|
878 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
792 | 879 } |
880 | |
881 | |
882 ParsedDicomFile::~ParsedDicomFile() | |
883 { | |
794 | 884 delete pimpl_; |
792 | 885 } |
886 | |
793 | 887 |
888 void* ParsedDicomFile::GetDcmtkObject() | |
889 { | |
794 | 890 return pimpl_->file_.get(); |
793 | 891 } |
892 | |
893 | |
894 ParsedDicomFile* ParsedDicomFile::Clone() | |
895 { | |
794 | 896 return new ParsedDicomFile(*this); |
793 | 897 } |
800
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diff
changeset
|
898 |
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|
899 |
1562 | 900 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
800
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diff
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|
901 { |
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
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1616
diff
changeset
|
902 std::string mime, content; |
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Support of binary tags encoded using data URI scheme
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diff
changeset
|
903 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
1562 | 904 Toolbox::ToLowerCase(mime); |
1555
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
905 |
1562 | 906 if (mime == "image/png") |
907 { | |
908 EmbedImage(mime, content); | |
909 } | |
910 else if (mime == "application/pdf") | |
911 { | |
912 EmbedPdf(content); | |
913 } | |
914 else | |
915 { | |
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
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1689
diff
changeset
|
916 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime; |
1562 | 917 throw OrthancException(ErrorCode_NotImplemented); |
918 } | |
1555
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Creation of DICOM files with encapsulated PDF
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diff
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|
919 } |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
920 |
800
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diff
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|
921 |
1555
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
922 void ParsedDicomFile::EmbedImage(const std::string& mime, |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
923 const std::string& content) |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
924 { |
800
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generation of DICOM images from PNG files
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|
925 if (mime == "image/png") |
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|
926 { |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
927 PngReader reader; |
1555
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
928 reader.ReadFromMemory(content); |
800
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generation of DICOM images from PNG files
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|
929 EmbedImage(reader); |
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|
930 } |
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|
931 else |
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diff
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|
932 { |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
933 throw OrthancException(ErrorCode_NotImplemented); |
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|
934 } |
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generation of DICOM images from PNG files
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diff
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|
935 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
936 |
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diff
changeset
|
937 |
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generation of DICOM images from PNG files
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diff
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|
938 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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generation of DICOM images from PNG files
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diff
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|
939 { |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
940 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
941 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
942 accessor.GetFormat() != PixelFormat_RGB24 && |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
943 accessor.GetFormat() != PixelFormat_RGBA32) |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
944 { |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
945 throw OrthancException(ErrorCode_NotImplemented); |
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generation of DICOM images from PNG files
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diff
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|
946 } |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
947 |
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generation of DICOM images from PNG files
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diff
changeset
|
948 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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generation of DICOM images from PNG files
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diff
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|
949 { |
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generation of DICOM images from PNG files
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diff
changeset
|
950 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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generation of DICOM images from PNG files
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diff
changeset
|
951 } |
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diff
changeset
|
952 |
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generation of DICOM images from PNG files
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diff
changeset
|
953 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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diff
changeset
|
954 |
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|
955 Remove(DICOM_TAG_PIXEL_DATA); |
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diff
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|
956 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
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generation of DICOM images from PNG files
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diff
changeset
|
957 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
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generation of DICOM images from PNG files
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diff
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|
958 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
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generation of DICOM images from PNG files
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diff
changeset
|
959 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
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generation of DICOM images from PNG files
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diff
changeset
|
960 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
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generation of DICOM images from PNG files
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diff
changeset
|
961 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
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generation of DICOM images from PNG files
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diff
changeset
|
962 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
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generation of DICOM images from PNG files
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diff
changeset
|
963 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
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generation of DICOM images from PNG files
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diff
changeset
|
964 Replace(DICOM_TAG_BITS_STORED, "8"); |
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generation of DICOM images from PNG files
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diff
changeset
|
965 Replace(DICOM_TAG_HIGH_BIT, "7"); |
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generation of DICOM images from PNG files
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diff
changeset
|
966 |
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generation of DICOM images from PNG files
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diff
changeset
|
967 unsigned int bytesPerPixel = 1; |
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diff
changeset
|
968 |
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generation of DICOM images from PNG files
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diff
changeset
|
969 switch (accessor.GetFormat()) |
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generation of DICOM images from PNG files
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diff
changeset
|
970 { |
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generation of DICOM images from PNG files
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diff
changeset
|
971 case PixelFormat_RGB24: |
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generation of DICOM images from PNG files
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diff
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|
972 case PixelFormat_RGBA32: |
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generation of DICOM images from PNG files
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diff
changeset
|
973 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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generation of DICOM images from PNG files
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diff
changeset
|
974 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
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diff
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|
975 bytesPerPixel = 3; |
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|
976 break; |
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diff
changeset
|
977 |
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generation of DICOM images from PNG files
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changeset
|
978 case PixelFormat_Grayscale8: |
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generation of DICOM images from PNG files
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changeset
|
979 break; |
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generation of DICOM images from PNG files
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diff
changeset
|
980 |
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generation of DICOM images from PNG files
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changeset
|
981 case PixelFormat_Grayscale16: |
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changeset
|
982 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
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changeset
|
983 Replace(DICOM_TAG_BITS_STORED, "16"); |
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|
984 Replace(DICOM_TAG_HIGH_BIT, "15"); |
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|
985 bytesPerPixel = 2; |
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|
986 break; |
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changeset
|
987 |
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changeset
|
988 default: |
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|
989 throw OrthancException(ErrorCode_NotImplemented); |
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changeset
|
990 } |
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changeset
|
991 |
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|
992 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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|
993 DICOM_TAG_PIXEL_DATA.GetElement()); |
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changeset
|
994 |
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|
995 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
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changeset
|
996 |
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changeset
|
997 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
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|
998 Uint8* target = NULL; |
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changeset
|
999 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
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diff
changeset
|
1000 |
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changeset
|
1001 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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changeset
|
1002 { |
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changeset
|
1003 switch (accessor.GetFormat()) |
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changeset
|
1004 { |
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changeset
|
1005 case PixelFormat_RGB24: |
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|
1006 case PixelFormat_Grayscale8: |
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|
1007 case PixelFormat_Grayscale16: |
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|
1008 case PixelFormat_SignedGrayscale16: |
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|
1009 { |
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changeset
|
1010 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
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|
1011 target += pitch; |
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|
1012 break; |
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1013 } |
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1014 |
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1015 case PixelFormat_RGBA32: |
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1016 { |
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|
1017 // The alpha channel is not supported by the DICOM standard |
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1018 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
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|
1019 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
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1020 { |
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1021 target[0] = source[0]; |
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1022 target[1] = source[1]; |
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|
1023 target[2] = source[2]; |
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1024 } |
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1025 |
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1026 break; |
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1027 } |
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1028 |
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1029 default: |
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1030 throw OrthancException(ErrorCode_NotImplemented); |
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1031 } |
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1032 } |
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1033 |
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|
1034 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
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1035 { |
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1036 throw OrthancException(ErrorCode_InternalError); |
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1037 } |
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|
1038 } |
874
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1039 |
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1040 |
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1041 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
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1042 unsigned int frame) |
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|
1043 { |
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1044 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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1045 |
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1046 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
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|
1047 { |
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|
1048 throw OrthancException(ErrorCode_BadFileFormat); |
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1049 } |
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1050 } |
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1051 |
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1052 |
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|
1053 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
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1054 unsigned int frame, |
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|
1055 ImageExtractionMode mode) |
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|
1056 { |
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|
1057 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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|
1058 |
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|
1059 bool ok = false; |
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|
1060 |
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|
1061 switch (mode) |
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|
1062 { |
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|
1063 case ImageExtractionMode_UInt8: |
1015
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1064 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
874
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|
1065 break; |
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|
1066 |
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|
1067 case ImageExtractionMode_UInt16: |
1015
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1068 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
874
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|
1069 break; |
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1070 |
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1071 case ImageExtractionMode_Int16: |
1015
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|
1072 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
874
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|
1073 break; |
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1074 |
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1075 case ImageExtractionMode_Preview: |
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1076 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
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|
1077 break; |
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1078 |
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|
1079 default: |
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1080 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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|
1081 } |
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1082 |
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1083 if (!ok) |
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|
1084 { |
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|
1085 throw OrthancException(ErrorCode_BadFileFormat); |
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1086 } |
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1087 } |
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1088 |
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|
1089 |
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|
1090 void ParsedDicomFile::ExtractPngImage(std::string& result, |
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|
1091 unsigned int frame, |
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|
1092 ImageExtractionMode mode) |
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|
1093 { |
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|
1094 ImageBuffer buffer; |
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|
1095 ExtractImage(buffer, frame, mode); |
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1096 |
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|
1097 ImageAccessor accessor(buffer.GetConstAccessor()); |
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|
1098 PngWriter writer; |
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|
1099 writer.WriteToMemory(result, accessor); |
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1100 } |
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1101 |
956
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1102 |
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1103 Encoding ParsedDicomFile::GetEncoding() const |
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1104 { |
1695 | 1105 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
956
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1106 } |
1090
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1107 |
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1108 |
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1109 void ParsedDicomFile::SetEncoding(Encoding encoding) |
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1110 { |
1558
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1111 if (encoding == Encoding_Windows1251) |
1090
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1112 { |
1558
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1113 // This Cyrillic codepage is not officially supported by the |
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1114 // DICOM standard. Do not set the SpecificCharacterSet tag. |
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|
1115 return; |
1090
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1116 } |
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1117 |
1565
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1118 std::string s = GetDicomSpecificCharacterSet(encoding); |
1091 | 1119 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
1090
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1120 } |
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1121 |
1686 | 1122 void ParsedDicomFile::ToJson(Json::Value& target, |
1123 DicomToJsonFormat format, | |
1735
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1124 DicomToJsonFlags flags, |
1686 | 1125 unsigned int maxStringLength) |
1160
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1126 { |
1735
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1701
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|
1127 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), format, flags, maxStringLength); |
1160
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1128 } |
1555
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1129 |
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1130 |
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1131 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
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1132 { |
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|
1133 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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1134 return pimpl_->file_->getDataset()->tagExists(key); |
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1135 } |
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1136 |
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Creation of DICOM files with encapsulated PDF
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1137 |
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Creation of DICOM files with encapsulated PDF
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1138 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
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Creation of DICOM files with encapsulated PDF
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1139 { |
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Creation of DICOM files with encapsulated PDF
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1140 if (pdf.size() < 5 || // (*) |
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Creation of DICOM files with encapsulated PDF
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1141 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
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Creation of DICOM files with encapsulated PDF
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1142 { |
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Creation of DICOM files with encapsulated PDF
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1143 LOG(ERROR) << "Not a PDF file"; |
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Creation of DICOM files with encapsulated PDF
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1144 throw OrthancException(ErrorCode_BadFileFormat); |
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Creation of DICOM files with encapsulated PDF
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1145 } |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1146 |
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Creation of DICOM files with encapsulated PDF
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1147 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
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Creation of DICOM files with encapsulated PDF
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1148 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
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Creation of DICOM files with encapsulated PDF
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1149 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
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Creation of DICOM files with encapsulated PDF
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1150 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
1566 | 1151 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1152 |
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Creation of DICOM files with encapsulated PDF
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1153 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
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Creation of DICOM files with encapsulated PDF
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1154 |
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Creation of DICOM files with encapsulated PDF
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1155 size_t s = pdf.size(); |
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Creation of DICOM files with encapsulated PDF
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1156 if (s & 1) |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1157 { |
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Creation of DICOM files with encapsulated PDF
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1158 // The size of the buffer must be even |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1159 s += 1; |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1160 } |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1161 |
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Creation of DICOM files with encapsulated PDF
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1162 Uint8* bytes = NULL; |
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Creation of DICOM files with encapsulated PDF
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1163 OFCondition result = element->createUint8Array(s, bytes); |
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Creation of DICOM files with encapsulated PDF
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1164 if (!result.good() || bytes == NULL) |
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Creation of DICOM files with encapsulated PDF
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1165 { |
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Creation of DICOM files with encapsulated PDF
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1166 throw OrthancException(ErrorCode_NotEnoughMemory); |
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Creation of DICOM files with encapsulated PDF
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1167 } |
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Creation of DICOM files with encapsulated PDF
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|
1168 |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1169 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
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Creation of DICOM files with encapsulated PDF
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1170 bytes[s - 1] = 0; |
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Creation of DICOM files with encapsulated PDF
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changeset
|
1171 |
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Creation of DICOM files with encapsulated PDF
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1172 memcpy(bytes, pdf.c_str(), pdf.size()); |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
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1173 |
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Creation of DICOM files with encapsulated PDF
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1174 DcmPolymorphOBOW* obj = element.release(); |
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Creation of DICOM files with encapsulated PDF
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1175 result = pimpl_->file_->getDataset()->insert(obj); |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1176 |
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Creation of DICOM files with encapsulated PDF
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1177 if (!result.good()) |
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Creation of DICOM files with encapsulated PDF
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1178 { |
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Creation of DICOM files with encapsulated PDF
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1179 delete obj; |
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Creation of DICOM files with encapsulated PDF
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1180 throw OrthancException(ErrorCode_NotEnoughMemory); |
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Creation of DICOM files with encapsulated PDF
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1181 } |
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Creation of DICOM files with encapsulated PDF
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1182 } |
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Creation of DICOM files with encapsulated PDF
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1183 |
1556
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1184 |
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1185 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
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1186 { |
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1187 std::string sop, mime; |
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1188 |
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1189 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
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1190 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
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1191 sop != UID_EncapsulatedPDFStorage || |
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1192 mime != "application/pdf") |
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1193 { |
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1194 return false; |
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1195 } |
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1196 |
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1197 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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1198 { |
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1199 return false; |
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1200 } |
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1201 |
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1202 // Strip the possible pad byte at the end of file, because the |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1203 // encapsulated documents must always have an even length. The PDF |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1204 // format expects files to end with %%EOF followed by CR/LF. If |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1205 // the last character of the file is not a CR or LF, we assume it |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1206 // is a pad byte and remove it. |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1207 if (pdf.size() > 0) |
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1208 { |
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1209 char last = *pdf.rbegin(); |
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1210 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1211 if (last != 10 && last != 13) |
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1212 { |
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1213 pdf.resize(pdf.size() - 1); |
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1214 } |
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1215 } |
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1216 |
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1217 return true; |
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1218 } |
1662
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ParsedDicomFile::Convert()
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1219 |
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ParsedDicomFile::Convert()
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1220 |
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ParsedDicomFile::Convert()
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1221 void ParsedDicomFile::Convert(DicomMap& tags) |
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ParsedDicomFile::Convert()
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1222 { |
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ParsedDicomFile::Convert()
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1223 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset()); |
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ParsedDicomFile::Convert()
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1224 } |
790 | 1225 } |