Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 2099:bcbc9137a535
refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 07 Oct 2016 11:13:41 +0200 |
parents | d108412411e5 |
children | b9bd52c72ba2 |
rev | line source |
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790 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
1900 | 3 * Copyright (C) 2012-2016 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 "OrthancInitialization.h" |
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84 #include "ServerToolbox.h" |
790 | 85 #include "FromDcmtkBridge.h" |
86 #include "ToDcmtkBridge.h" | |
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87 #include "Internals/DicomFrameIndex.h" |
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88 #include "../Core/Images/JpegReader.h" |
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89 #include "../Core/Images/PngReader.h" |
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90 #include "../Core/Logging.h" |
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91 #include "../Core/OrthancException.h" |
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92 #include "../Core/Toolbox.h" |
790 | 93 #include "../Core/Uuid.h" |
94 | |
95 #include <list> | |
96 #include <limits> | |
97 | |
98 #include <boost/lexical_cast.hpp> | |
99 | |
100 #include <dcmtk/dcmdata/dcchrstr.h> | |
101 #include <dcmtk/dcmdata/dcdicent.h> | |
102 #include <dcmtk/dcmdata/dcdict.h> | |
103 #include <dcmtk/dcmdata/dcfilefo.h> | |
104 #include <dcmtk/dcmdata/dcuid.h> | |
105 #include <dcmtk/dcmdata/dcmetinf.h> | |
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106 #include <dcmtk/dcmdata/dcdeftag.h> |
790 | 107 |
108 #include <dcmtk/dcmdata/dcvrae.h> | |
109 #include <dcmtk/dcmdata/dcvras.h> | |
110 #include <dcmtk/dcmdata/dcvrcs.h> | |
111 #include <dcmtk/dcmdata/dcvrda.h> | |
112 #include <dcmtk/dcmdata/dcvrds.h> | |
113 #include <dcmtk/dcmdata/dcvrdt.h> | |
114 #include <dcmtk/dcmdata/dcvrfd.h> | |
115 #include <dcmtk/dcmdata/dcvrfl.h> | |
116 #include <dcmtk/dcmdata/dcvris.h> | |
117 #include <dcmtk/dcmdata/dcvrlo.h> | |
118 #include <dcmtk/dcmdata/dcvrlt.h> | |
119 #include <dcmtk/dcmdata/dcvrpn.h> | |
120 #include <dcmtk/dcmdata/dcvrsh.h> | |
121 #include <dcmtk/dcmdata/dcvrsl.h> | |
122 #include <dcmtk/dcmdata/dcvrss.h> | |
123 #include <dcmtk/dcmdata/dcvrst.h> | |
124 #include <dcmtk/dcmdata/dcvrtm.h> | |
125 #include <dcmtk/dcmdata/dcvrui.h> | |
126 #include <dcmtk/dcmdata/dcvrul.h> | |
127 #include <dcmtk/dcmdata/dcvrus.h> | |
128 #include <dcmtk/dcmdata/dcvrut.h> | |
129 #include <dcmtk/dcmdata/dcpixel.h> | |
130 #include <dcmtk/dcmdata/dcpixseq.h> | |
131 #include <dcmtk/dcmdata/dcpxitem.h> | |
132 | |
133 | |
134 #include <boost/math/special_functions/round.hpp> | |
135 #include <dcmtk/dcmdata/dcostrmb.h> | |
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136 #include <boost/algorithm/string/predicate.hpp> |
790 | 137 |
138 | |
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139 #if DCMTK_VERSION_NUMBER <= 360 |
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140 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax |
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141 #endif |
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142 |
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143 |
790 | 144 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; |
145 | |
146 | |
147 | |
148 namespace Orthanc | |
149 { | |
794 | 150 struct ParsedDicomFile::PImpl |
151 { | |
152 std::auto_ptr<DcmFileFormat> file_; | |
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153 std::auto_ptr<DicomFrameIndex> frameIndex_; |
794 | 154 }; |
155 | |
156 | |
790 | 157 static void SendPathValueForDictionary(RestApiOutput& output, |
158 DcmItem& dicom) | |
159 { | |
160 Json::Value v = Json::arrayValue; | |
161 | |
162 for (unsigned long i = 0; i < dicom.card(); i++) | |
163 { | |
164 DcmElement* element = dicom.getElement(i); | |
165 if (element) | |
166 { | |
167 char buf[16]; | |
168 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
169 v.append(buf); | |
170 } | |
171 } | |
172 | |
173 output.AnswerJson(v); | |
174 } | |
175 | |
176 static inline uint16_t GetCharValue(char c) | |
177 { | |
178 if (c >= '0' && c <= '9') | |
179 return c - '0'; | |
180 else if (c >= 'a' && c <= 'f') | |
181 return c - 'a' + 10; | |
182 else if (c >= 'A' && c <= 'F') | |
183 return c - 'A' + 10; | |
184 else | |
185 return 0; | |
186 } | |
187 | |
188 static inline uint16_t GetTagValue(const char* c) | |
189 { | |
190 return ((GetCharValue(c[0]) << 12) + | |
191 (GetCharValue(c[1]) << 8) + | |
192 (GetCharValue(c[2]) << 4) + | |
193 GetCharValue(c[3])); | |
194 } | |
195 | |
196 static void ParseTagAndGroup(DcmTagKey& key, | |
197 const std::string& tag) | |
198 { | |
199 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
200 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
201 } | |
202 | |
203 | |
204 static void SendSequence(RestApiOutput& output, | |
205 DcmSequenceOfItems& sequence) | |
206 { | |
207 // This element is a sequence | |
208 Json::Value v = Json::arrayValue; | |
209 | |
210 for (unsigned long i = 0; i < sequence.card(); i++) | |
211 { | |
212 v.append(boost::lexical_cast<std::string>(i)); | |
213 } | |
214 | |
215 output.AnswerJson(v); | |
216 } | |
217 | |
218 | |
219 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
220 E_TransferSyntax transferSyntax) | |
221 { | |
222 DcmPixelSequence* pixelSequence = NULL; | |
223 if (pixelData.getEncapsulatedRepresentation | |
224 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
225 { | |
226 return pixelSequence->card(); | |
227 } | |
228 else | |
229 { | |
230 return 1; | |
231 } | |
232 } | |
233 | |
234 | |
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235 namespace |
790 | 236 { |
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237 class DicomFieldStream : public IHttpStreamAnswer |
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238 { |
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239 private: |
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240 DcmElement& element_; |
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241 uint32_t length_; |
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242 uint32_t offset_; |
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243 std::string chunk_; |
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244 size_t chunkSize_; |
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245 |
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246 public: |
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247 DicomFieldStream(DcmElement& element, |
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248 E_TransferSyntax transferSyntax) : |
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249 element_(element), |
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250 length_(element.getLength(transferSyntax)), |
1616 | 251 offset_(0), |
252 chunkSize_(0) | |
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253 { |
1521 | 254 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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255 chunk_.resize(CHUNK_SIZE); |
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256 } |
790 | 257 |
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258 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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259 bool /*deflateAllowed*/) |
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260 { |
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261 // No support for compression |
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262 return HttpCompression_None; |
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263 } |
790 | 264 |
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265 virtual bool HasContentFilename(std::string& filename) |
790 | 266 { |
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267 return false; |
790 | 268 } |
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269 |
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270 virtual std::string GetContentType() |
790 | 271 { |
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272 return ""; |
790 | 273 } |
274 | |
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275 virtual uint64_t GetContentLength() |
790 | 276 { |
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277 return length_; |
790 | 278 } |
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279 |
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280 virtual bool ReadNextChunk() |
790 | 281 { |
1520 | 282 assert(offset_ <= length_); |
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283 |
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284 if (offset_ == length_) |
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285 { |
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286 return false; |
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287 } |
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288 else |
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289 { |
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290 if (length_ - offset_ < chunk_.size()) |
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291 { |
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292 chunkSize_ = length_ - offset_; |
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293 } |
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294 else |
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295 { |
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296 chunkSize_ = chunk_.size(); |
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297 } |
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298 |
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299 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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300 |
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301 offset_ += chunkSize_; |
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302 |
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303 if (!cond.good()) |
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304 { |
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305 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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306 throw OrthancException(ErrorCode_InternalError); |
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307 } |
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308 |
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309 return true; |
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310 } |
790 | 311 } |
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312 |
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313 virtual const char *GetChunkContent() |
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314 { |
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315 return chunk_.c_str(); |
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316 } |
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317 |
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318 virtual size_t GetChunkSize() |
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319 { |
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320 return chunkSize_; |
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321 } |
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322 }; |
790 | 323 } |
324 | |
325 | |
326 static bool AnswerPixelData(RestApiOutput& output, | |
327 DcmItem& dicom, | |
328 E_TransferSyntax transferSyntax, | |
329 const std::string* blockUri) | |
330 { | |
331 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
332 DICOM_TAG_PIXEL_DATA.GetElement()); | |
333 | |
334 DcmElement *element = NULL; | |
335 if (!dicom.findAndGetElement(k, element).good() || | |
336 element == NULL) | |
337 { | |
338 return false; | |
339 } | |
340 | |
341 try | |
342 { | |
343 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
344 if (blockUri == NULL) | |
345 { | |
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346 // The user asks how many blocks are present in this pixel data |
790 | 347 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); |
348 | |
349 Json::Value result(Json::arrayValue); | |
350 for (unsigned int i = 0; i < blocks; i++) | |
351 { | |
352 result.append(boost::lexical_cast<std::string>(i)); | |
353 } | |
354 | |
355 output.AnswerJson(result); | |
356 return true; | |
357 } | |
358 | |
359 | |
360 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
361 | |
362 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
363 { | |
364 DcmPixelSequence* pixelSequence = NULL; | |
365 if (pixelData.getEncapsulatedRepresentation | |
366 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
367 { | |
368 // This is the case for JPEG transfer syntaxes | |
369 if (block < pixelSequence->card()) | |
370 { | |
371 DcmPixelItem* pixelItem = NULL; | |
372 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
373 { | |
374 if (pixelItem->getLength() == 0) | |
375 { | |
376 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
377 return true; | |
378 } | |
379 | |
380 Uint8* buffer = NULL; | |
381 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
382 { | |
383 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
384 return true; | |
385 } | |
386 } | |
387 } | |
388 } | |
389 else | |
390 { | |
391 // This is the case for raw, uncompressed image buffers | |
392 assert(*blockUri == "0"); | |
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393 DicomFieldStream stream(*element, transferSyntax); |
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394 output.AnswerStream(stream); |
790 | 395 } |
396 } | |
397 } | |
398 catch (boost::bad_lexical_cast&) | |
399 { | |
400 // The URI entered by the user is not a number | |
401 } | |
402 catch (std::bad_cast&) | |
403 { | |
404 // This should never happen | |
405 } | |
406 | |
407 return false; | |
408 } | |
409 | |
410 | |
411 | |
412 static void SendPathValueForLeaf(RestApiOutput& output, | |
413 const std::string& tag, | |
414 DcmItem& dicom, | |
415 E_TransferSyntax transferSyntax) | |
416 { | |
417 DcmTagKey k; | |
418 ParseTagAndGroup(k, tag); | |
419 | |
420 DcmSequenceOfItems* sequence = NULL; | |
421 if (dicom.findAndGetSequence(k, sequence).good() && | |
422 sequence != NULL && | |
423 sequence->getVR() == EVR_SQ) | |
424 { | |
425 SendSequence(output, *sequence); | |
426 return; | |
427 } | |
428 | |
429 DcmElement* element = NULL; | |
430 if (dicom.findAndGetElement(k, element).good() && | |
431 element != NULL && | |
432 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
433 element->getVR() != EVR_SQ) | |
434 { | |
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435 DicomFieldStream stream(*element, transferSyntax); |
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436 output.AnswerStream(stream); |
790 | 437 } |
438 } | |
439 | |
440 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
441 const UriComponents& uri) | |
442 { | |
794 | 443 DcmItem* dicom = pimpl_->file_->getDataset(); |
444 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
790 | 445 |
446 // Special case: Accessing the pixel data | |
447 if (uri.size() == 1 || | |
448 uri.size() == 2) | |
449 { | |
450 DcmTagKey tag; | |
451 ParseTagAndGroup(tag, uri[0]); | |
452 | |
453 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
454 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
455 { | |
456 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
457 return; | |
458 } | |
459 } | |
460 | |
461 // Go down in the tag hierarchy according to the URI | |
462 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
463 { | |
464 size_t index; | |
465 try | |
466 { | |
467 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
468 } | |
469 catch (boost::bad_lexical_cast&) | |
470 { | |
471 return; | |
472 } | |
473 | |
474 DcmTagKey k; | |
475 DcmItem *child = NULL; | |
476 ParseTagAndGroup(k, uri[2 * pos]); | |
477 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
478 child == NULL) | |
479 { | |
480 return; | |
481 } | |
482 | |
483 dicom = child; | |
484 } | |
485 | |
486 // We have reached the end of the URI | |
487 if (uri.size() % 2 == 0) | |
488 { | |
489 SendPathValueForDictionary(output, *dicom); | |
490 } | |
491 else | |
492 { | |
493 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
494 } | |
495 } | |
496 | |
497 | |
498 void ParsedDicomFile::Remove(const DicomTag& tag) | |
499 { | |
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500 InvalidateCache(); |
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501 |
790 | 502 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
794 | 503 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
790 | 504 if (element != NULL) |
505 { | |
506 delete element; | |
507 } | |
508 } | |
509 | |
510 | |
511 | |
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512 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
790 | 513 { |
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514 InvalidateCache(); |
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515 |
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516 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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517 |
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518 // Loop over the dataset to detect its private tags |
790 | 519 typedef std::list<DcmElement*> Tags; |
520 Tags privateTags; | |
521 | |
522 for (unsigned long i = 0; i < dataset.card(); i++) | |
523 { | |
524 DcmElement* element = dataset.getElement(i); | |
525 DcmTag tag(element->getTag()); | |
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526 |
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527 // Is this a private tag? |
1694 | 528 if (tag.isPrivate()) |
790 | 529 { |
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530 bool remove = true; |
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531 |
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532 // Check whether this private tag is to be kept |
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533 if (toKeep != NULL) |
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534 { |
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535 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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536 if (toKeep->find(tmp) != toKeep->end()) |
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537 { |
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538 remove = false; // Keep it |
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539 } |
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540 } |
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541 |
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542 if (remove) |
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543 { |
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544 privateTags.push_back(element); |
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545 } |
790 | 546 } |
547 } | |
548 | |
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549 // Loop over the detected private tags to remove them |
790 | 550 for (Tags::iterator it = privateTags.begin(); |
551 it != privateTags.end(); ++it) | |
552 { | |
553 DcmElement* tmp = dataset.remove(*it); | |
554 if (tmp != NULL) | |
555 { | |
556 delete tmp; | |
557 } | |
558 } | |
559 } | |
560 | |
561 | |
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562 static void InsertInternal(DcmDataset& dicom, |
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563 DcmElement* element) |
790 | 564 { |
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565 OFCondition cond = dicom.insert(element, false, false); |
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566 if (!cond.good()) |
790 | 567 { |
568 // This field already exists | |
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569 delete element; |
790 | 570 throw OrthancException(ErrorCode_InternalError); |
571 } | |
572 } | |
573 | |
574 | |
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575 void ParsedDicomFile::Insert(const DicomTag& tag, |
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576 const Json::Value& value, |
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577 bool decodeDataUriScheme) |
790 | 578 { |
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579 if (pimpl_->file_->getDataset()->tagExists(ToDcmtkBridge::Convert(tag))) |
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580 { |
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581 throw OrthancException(ErrorCode_AlreadyExistingTag); |
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582 } |
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583 |
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584 if (decodeDataUriScheme && |
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585 value.type() == Json::stringValue && |
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586 (tag == DICOM_TAG_ENCAPSULATED_DOCUMENT || |
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587 tag == DICOM_TAG_PIXEL_DATA)) |
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588 { |
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589 if (EmbedContentInternal(value.asString())) |
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590 { |
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591 return; |
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592 } |
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593 } |
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594 |
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595 InvalidateCache(); |
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596 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
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597 InsertInternal(*pimpl_->file_->getDataset(), element.release()); |
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598 } |
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599 |
790 | 600 |
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601 static bool CanReplaceProceed(DcmDataset& dicom, |
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602 const DcmTagKey& tag, |
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603 DicomReplaceMode mode) |
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604 { |
1979 | 605 if (dicom.findAndDeleteElement(tag).good()) |
790 | 606 { |
1979 | 607 // This tag was existing, it has been deleted |
608 return true; | |
609 } | |
610 else | |
611 { | |
612 // This tag was absent, act wrt. the specified "mode" | |
790 | 613 switch (mode) |
614 { | |
615 case DicomReplaceMode_InsertIfAbsent: | |
1979 | 616 return true; |
790 | 617 |
618 case DicomReplaceMode_ThrowIfAbsent: | |
619 throw OrthancException(ErrorCode_InexistentItem); | |
620 | |
621 case DicomReplaceMode_IgnoreIfAbsent: | |
1979 | 622 return false; |
623 | |
624 default: | |
625 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
790 | 626 } |
627 } | |
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628 } |
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629 |
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630 |
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631 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag, |
1695 | 632 const std::string& utf8Value, |
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633 bool decodeDataUriScheme) |
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634 { |
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635 if (tag != DICOM_TAG_SOP_CLASS_UID && |
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636 tag != DICOM_TAG_SOP_INSTANCE_UID) |
790 | 637 { |
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638 return; |
790 | 639 } |
640 | |
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641 std::string binary; |
1695 | 642 const std::string* decoded = &utf8Value; |
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643 |
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644 if (decodeDataUriScheme && |
1695 | 645 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
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646 { |
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647 std::string mime; |
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648 if (!Toolbox::DecodeDataUriScheme(mime, binary, utf8Value)) |
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649 { |
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650 throw OrthancException(ErrorCode_BadFileFormat); |
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651 } |
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652 |
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653 decoded = &binary; |
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654 } |
1695 | 655 else |
656 { | |
657 Encoding encoding = GetEncoding(); | |
658 if (GetEncoding() != Encoding_Utf8) | |
659 { | |
660 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding); | |
661 decoded = &binary; | |
662 } | |
663 } | |
790 | 664 |
665 /** | |
666 * dcmodify will automatically correct 'Media Storage SOP Class | |
667 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
668 * you make changes to the related tags in the dataset ('SOP Class | |
669 * UID' and 'SOP Instance UID') via insert or modify mode | |
670 * options. You can disable this behaviour by using the -nmu | |
671 * option. | |
672 **/ | |
673 | |
674 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
675 { | |
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676 ReplacePlainString(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded); |
790 | 677 } |
678 | |
679 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
680 { | |
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681 ReplacePlainString(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded); |
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682 } |
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683 } |
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684 |
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685 |
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686 void ParsedDicomFile::Replace(const DicomTag& tag, |
1695 | 687 const std::string& utf8Value, |
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688 bool decodeDataUriScheme, |
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689 DicomReplaceMode mode) |
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690 { |
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691 InvalidateCache(); |
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692 |
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693 DcmDataset& dicom = *pimpl_->file_->getDataset(); |
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694 if (CanReplaceProceed(dicom, ToDcmtkBridge::Convert(tag), mode)) |
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695 { |
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696 // Either the tag was previously existing (and now removed), or |
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697 // the replace mode was set to "InsertIfAbsent" |
1979 | 698 |
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699 if (decodeDataUriScheme && |
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700 (tag == DICOM_TAG_ENCAPSULATED_DOCUMENT || |
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701 tag == DICOM_TAG_PIXEL_DATA)) |
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702 { |
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703 if (EmbedContentInternal(utf8Value)) |
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704 { |
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705 return; |
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706 } |
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707 } |
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708 |
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709 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
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710 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, decodeDataUriScheme, GetEncoding()); |
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711 |
1979 | 712 InsertInternal(dicom, element.release()); |
713 UpdateStorageUid(tag, utf8Value, false); | |
714 } | |
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715 } |
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716 |
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717 |
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718 void ParsedDicomFile::Replace(const DicomTag& tag, |
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719 const Json::Value& value, |
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720 bool decodeDataUriScheme, |
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721 DicomReplaceMode mode) |
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722 { |
1924
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723 InvalidateCache(); |
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724 |
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725 DcmDataset& dicom = *pimpl_->file_->getDataset(); |
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726 if (CanReplaceProceed(dicom, ToDcmtkBridge::Convert(tag), mode)) |
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727 { |
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728 // Either the tag was previously existing (and now removed), or |
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729 // the replace mode was set to "InsertIfAbsent" |
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730 |
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731 if (decodeDataUriScheme && |
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732 value.type() == Json::stringValue && |
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733 (tag == DICOM_TAG_ENCAPSULATED_DOCUMENT || |
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734 tag == DICOM_TAG_PIXEL_DATA)) |
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735 { |
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736 if (EmbedContentInternal(value.asString())) |
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737 { |
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738 return; |
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739 } |
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740 } |
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741 |
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|
742 InsertInternal(dicom, FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
1979 | 743 |
744 if (tag == DICOM_TAG_SOP_CLASS_UID || | |
745 tag == DICOM_TAG_SOP_INSTANCE_UID) | |
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746 { |
1979 | 747 if (value.type() != Json::stringValue) |
748 { | |
749 throw OrthancException(ErrorCode_BadParameterType); | |
750 } | |
751 | |
752 UpdateStorageUid(tag, value.asString(), decodeDataUriScheme); | |
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753 } |
790 | 754 } |
755 } | |
756 | |
757 | |
758 void ParsedDicomFile::Answer(RestApiOutput& output) | |
759 { | |
760 std::string serialized; | |
1004
a226e0959d8b
DicomInstanceToStore
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diff
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|
761 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
790 | 762 { |
763 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
764 } | |
765 } | |
766 | |
767 | |
768 | |
769 bool ParsedDicomFile::GetTagValue(std::string& value, | |
770 const DicomTag& tag) | |
771 { | |
772 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
794 | 773 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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Fix replacement and insertion of private DICOM tags
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774 |
1818
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775 if (tag.IsPrivate() || |
1655
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diff
changeset
|
776 FromDcmtkBridge::IsUnknownTag(tag) || |
1556
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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777 tag == DICOM_TAG_PIXEL_DATA || |
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778 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
790 | 779 { |
1307
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Fix replacement and insertion of private DICOM tags
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changeset
|
780 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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Fix replacement and insertion of private DICOM tags
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diff
changeset
|
781 long unsigned int count = 0; |
790 | 782 |
1307
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Fix replacement and insertion of private DICOM tags
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diff
changeset
|
783 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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Fix replacement and insertion of private DICOM tags
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parents:
1288
diff
changeset
|
784 { |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
785 if (count > 0) |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
786 { |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
787 assert(data != NULL); |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
788 value.assign(reinterpret_cast<const char*>(data), count); |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
789 } |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
790 else |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
791 { |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
792 value.clear(); |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
793 } |
790 | 794 |
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
795 return true; |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
796 } |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
797 else |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
798 { |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
799 return false; |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
800 } |
790 | 801 } |
802 else | |
803 { | |
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
804 DcmElement* element = NULL; |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
805 if (!dataset.findAndGetElement(k, element).good() || |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
806 element == NULL) |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
807 { |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
808 return false; |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
809 } |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
810 |
1736
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
811 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement |
1929
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1928
diff
changeset
|
812 (*element, DicomToJsonFlags_Default, |
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1928
diff
changeset
|
813 ORTHANC_MAXIMUM_TAG_LENGTH, GetEncoding())); |
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
814 |
1737
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
815 if (v.get() == NULL || |
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
816 v->IsNull()) |
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
817 { |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
818 value = ""; |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
819 } |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
820 else |
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
821 { |
1737
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
822 // TODO v->IsBinary() |
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
823 value = v->GetContent(); |
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
824 } |
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
825 |
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
826 return true; |
790 | 827 } |
828 } | |
829 | |
830 | |
831 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
832 { | |
833 std::string patientId, studyUid, seriesUid, instanceUid; | |
834 | |
835 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
836 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
837 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
838 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
839 { | |
840 throw OrthancException(ErrorCode_BadFileFormat); | |
841 } | |
842 | |
843 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
844 } | |
845 | |
846 | |
847 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
848 { | |
1004
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
991
diff
changeset
|
849 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
790 | 850 } |
851 | |
852 | |
853 void ParsedDicomFile::SaveToFile(const std::string& path) | |
854 { | |
855 // TODO Avoid using a temporary memory buffer, write directly on disk | |
856 std::string content; | |
857 SaveToMemoryBuffer(content); | |
858 Toolbox::WriteFile(content, path); | |
859 } | |
860 | |
861 | |
1805
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
862 ParsedDicomFile::ParsedDicomFile(bool createIdentifiers) : pimpl_(new PImpl) |
790 | 863 { |
794 | 864 pimpl_->file_.reset(new DcmFileFormat); |
1805
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
865 |
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
866 if (createIdentifiers) |
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
867 { |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
868 ReplacePlainString(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
869 ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
870 ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
871 ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
1805
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
872 } |
790 | 873 } |
874 | |
791 | 875 |
1787
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
876 ParsedDicomFile::ParsedDicomFile(const DicomMap& map) : pimpl_(new PImpl) |
1786
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
877 { |
1787
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
878 std::auto_ptr<DcmDataset> dataset(ToDcmtkBridge::Convert(map)); |
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
879 |
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
880 // NOTE: This implies an unnecessary memory copy of the dataset, but no way to get around |
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
881 // http://support.dcmtk.org/redmine/issues/544 |
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
882 std::auto_ptr<DcmFileFormat> fileFormat(new DcmFileFormat(dataset.get())); |
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
883 |
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
884 pimpl_->file_.reset(fileFormat.release()); |
1786
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
885 } |
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
886 |
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
887 |
1800
30e97a1f4093
callback for handling worklists with plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1788
diff
changeset
|
888 ParsedDicomFile::ParsedDicomFile(const void* content, |
30e97a1f4093
callback for handling worklists with plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1788
diff
changeset
|
889 size_t size) : pimpl_(new PImpl) |
791 | 890 { |
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
891 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(content, size)); |
791 | 892 } |
893 | |
794 | 894 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
791 | 895 { |
896 if (content.size() == 0) | |
897 { | |
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
898 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(NULL, 0)); |
791 | 899 } |
900 else | |
901 { | |
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
902 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(&content[0], content.size())); |
791 | 903 } |
904 } | |
792 | 905 |
906 | |
794 | 907 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
908 pimpl_(new PImpl) | |
792 | 909 { |
794 | 910 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
956
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
911 |
1564
1b7def486e62
creation of DICOM series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1562
diff
changeset
|
912 // Create a new instance-level identifier |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
913 ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
792 | 914 } |
915 | |
916 | |
1788
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
917 ParsedDicomFile::ParsedDicomFile(DcmDataset& dicom) : pimpl_(new PImpl) |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
918 { |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
919 pimpl_->file_.reset(new DcmFileFormat(&dicom)); |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
920 } |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
921 |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
922 |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
923 ParsedDicomFile::ParsedDicomFile(DcmFileFormat& dicom) : pimpl_(new PImpl) |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
924 { |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
925 pimpl_->file_.reset(new DcmFileFormat(dicom)); |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
926 } |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
927 |
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
928 |
792 | 929 ParsedDicomFile::~ParsedDicomFile() |
930 { | |
794 | 931 delete pimpl_; |
792 | 932 } |
933 | |
793 | 934 |
1824
b530c3dfe2a6
refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1818
diff
changeset
|
935 DcmFileFormat& ParsedDicomFile::GetDcmtkObject() const |
793 | 936 { |
1788
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
937 return *pimpl_->file_.get(); |
793 | 938 } |
939 | |
940 | |
941 ParsedDicomFile* ParsedDicomFile::Clone() | |
942 { | |
794 | 943 return new ParsedDicomFile(*this); |
793 | 944 } |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
945 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
946 |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
947 bool ParsedDicomFile::EmbedContentInternal(const std::string& dataUriScheme) |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
948 { |
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1616
diff
changeset
|
949 std::string mime, content; |
1981
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
950 if (!Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme)) |
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
951 { |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
952 return false; |
1981
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
953 } |
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
954 |
1562 | 955 Toolbox::ToLowerCase(mime); |
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
956 |
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
957 if (mime == "image/png" || |
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
958 mime == "image/jpeg") |
1562 | 959 { |
960 EmbedImage(mime, content); | |
961 } | |
962 else if (mime == "application/pdf") | |
963 { | |
964 EmbedPdf(content); | |
965 } | |
966 else | |
967 { | |
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
968 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime; |
1562 | 969 throw OrthancException(ErrorCode_NotImplemented); |
970 } | |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
971 |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
972 return true; |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
973 } |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
974 |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
975 |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
976 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
977 { |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
978 if (!EmbedContentInternal(dataUriScheme)) |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
979 { |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
980 throw OrthancException(ErrorCode_BadFileFormat); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
981 } |
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
982 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
983 |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
984 |
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
985 void ParsedDicomFile::EmbedImage(const std::string& mime, |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
986 const std::string& content) |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
987 { |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
988 if (mime == "image/png") |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
989 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
990 PngReader reader; |
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
991 reader.ReadFromMemory(content); |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
992 EmbedImage(reader); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
993 } |
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
994 else if (mime == "image/jpeg") |
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
995 { |
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
996 JpegReader reader; |
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
997 reader.ReadFromMemory(content); |
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
998 EmbedImage(reader); |
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
999 } |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1000 else |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1001 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1002 throw OrthancException(ErrorCode_NotImplemented); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1003 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1004 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1005 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1006 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1007 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1008 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1009 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1010 accessor.GetFormat() != PixelFormat_Grayscale16 && |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1011 accessor.GetFormat() != PixelFormat_SignedGrayscale16 && |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1012 accessor.GetFormat() != PixelFormat_RGB24 && |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1013 accessor.GetFormat() != PixelFormat_RGBA32) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1014 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1015 throw OrthancException(ErrorCode_NotImplemented); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1016 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1017 |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1018 InvalidateCache(); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1019 |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1020 if (accessor.GetFormat() == PixelFormat_RGBA32) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1021 { |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1022 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
|
1023 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1024 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1025 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1026 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1027 Remove(DICOM_TAG_PIXEL_DATA); |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1028 ReplacePlainString(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1029 ReplacePlainString(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1030 ReplacePlainString(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1031 ReplacePlainString(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1032 |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1033 if (accessor.GetFormat() == PixelFormat_SignedGrayscale16) |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1034 { |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1035 ReplacePlainString(DICOM_TAG_PIXEL_REPRESENTATION, "1"); |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1036 } |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1037 else |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1038 { |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1039 ReplacePlainString(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1040 } |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1041 |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1042 ReplacePlainString(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1043 ReplacePlainString(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1044 |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1045 unsigned int bytesPerPixel = 0; |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1046 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1047 switch (accessor.GetFormat()) |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1048 { |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1049 case PixelFormat_Grayscale8: |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1050 ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "8"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1051 ReplacePlainString(DICOM_TAG_BITS_STORED, "8"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1052 ReplacePlainString(DICOM_TAG_HIGH_BIT, "7"); |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1053 bytesPerPixel = 1; |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1054 break; |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1055 |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1056 case PixelFormat_RGB24: |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1057 case PixelFormat_RGBA32: |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1058 ReplacePlainString(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1059 ReplacePlainString(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1060 ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "8"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1061 ReplacePlainString(DICOM_TAG_BITS_STORED, "8"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1062 ReplacePlainString(DICOM_TAG_HIGH_BIT, "7"); |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1063 bytesPerPixel = 3; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1064 break; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1065 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1066 case PixelFormat_Grayscale16: |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1067 case PixelFormat_SignedGrayscale16: |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1068 ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "16"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1069 ReplacePlainString(DICOM_TAG_BITS_STORED, "16"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1070 ReplacePlainString(DICOM_TAG_HIGH_BIT, "15"); |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1071 bytesPerPixel = 2; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1072 break; |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1073 |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1074 default: |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1075 throw OrthancException(ErrorCode_NotImplemented); |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1076 } |
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1077 |
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1078 assert(bytesPerPixel != 0); |
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1079 |
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1080 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
ecedd89055db
generation of DICOM images from PNG files
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parents:
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|
1081 DICOM_TAG_PIXEL_DATA.GetElement()); |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1082 |
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generation of DICOM images from PNG files
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|
1083 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
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generation of DICOM images from PNG files
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diff
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1084 |
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generation of DICOM images from PNG files
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parents:
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changeset
|
1085 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
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generation of DICOM images from PNG files
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parents:
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diff
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|
1086 Uint8* target = NULL; |
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generation of DICOM images from PNG files
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parents:
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diff
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|
1087 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1088 |
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generation of DICOM images from PNG files
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parents:
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changeset
|
1089 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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generation of DICOM images from PNG files
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diff
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1090 { |
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generation of DICOM images from PNG files
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parents:
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|
1091 switch (accessor.GetFormat()) |
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generation of DICOM images from PNG files
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parents:
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1092 { |
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generation of DICOM images from PNG files
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parents:
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diff
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|
1093 case PixelFormat_RGB24: |
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generation of DICOM images from PNG files
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parents:
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diff
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|
1094 case PixelFormat_Grayscale8: |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
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1095 case PixelFormat_Grayscale16: |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1096 case PixelFormat_SignedGrayscale16: |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1097 { |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1098 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
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1099 target += pitch; |
ecedd89055db
generation of DICOM images from PNG files
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parents:
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diff
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1100 break; |
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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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|
1101 } |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1102 |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1103 case PixelFormat_RGBA32: |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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1104 { |
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generation of DICOM images from PNG files
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parents:
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diff
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1105 // The alpha channel is not supported by the DICOM standard |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1106 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1107 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
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generation of DICOM images from PNG files
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parents:
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diff
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1108 { |
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generation of DICOM images from PNG files
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parents:
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1109 target[0] = source[0]; |
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generation of DICOM images from PNG files
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parents:
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diff
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1110 target[1] = source[1]; |
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generation of DICOM images from PNG files
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parents:
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diff
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1111 target[2] = source[2]; |
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generation of DICOM images from PNG files
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parents:
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diff
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1112 } |
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1113 |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1114 break; |
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generation of DICOM images from PNG files
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parents:
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diff
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1115 } |
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generation of DICOM images from PNG files
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parents:
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changeset
|
1116 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1117 default: |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1118 throw OrthancException(ErrorCode_NotImplemented); |
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diff
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1119 } |
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parents:
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|
1120 } |
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diff
changeset
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1121 |
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changeset
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1122 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
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parents:
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diff
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1123 { |
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1124 throw OrthancException(ErrorCode_InternalError); |
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diff
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1125 } |
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parents:
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diff
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1126 } |
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1127 |
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1128 |
956
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primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1129 Encoding ParsedDicomFile::GetEncoding() const |
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primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1130 { |
1928
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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1131 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset(), |
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1924
diff
changeset
|
1132 Configuration::GetDefaultEncoding()); |
956
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parents:
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diff
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|
1133 } |
1090
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Sebastien Jodogne <s.jodogne@gmail.com>
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1134 |
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1135 |
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1136 void ParsedDicomFile::SetEncoding(Encoding encoding) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1137 { |
1558
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fix encodings of newly created dicom files
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diff
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1138 if (encoding == Encoding_Windows1251) |
1090
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diff
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|
1139 { |
1558
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1140 // This Cyrillic codepage is not officially supported by the |
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parents:
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diff
changeset
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1141 // DICOM standard. Do not set the SpecificCharacterSet tag. |
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parents:
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diff
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|
1142 return; |
1090
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1143 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1144 |
1565
4b23310eb7e8
add tags per instances in a series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1564
diff
changeset
|
1145 std::string s = GetDicomSpecificCharacterSet(encoding); |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1146 ReplacePlainString(DICOM_TAG_SPECIFIC_CHARACTER_SET, s); |
1090
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diff
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|
1147 } |
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diff
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|
1148 |
1686 | 1149 void ParsedDicomFile::ToJson(Json::Value& target, |
1150 DicomToJsonFormat format, | |
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1701
diff
changeset
|
1151 DicomToJsonFlags flags, |
1686 | 1152 unsigned int maxStringLength) |
1160
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1153 { |
1928
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1924
diff
changeset
|
1154 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), |
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1155 format, flags, maxStringLength, |
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1924
diff
changeset
|
1156 Configuration::GetDefaultEncoding()); |
1160
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generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
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1113
diff
changeset
|
1157 } |
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1158 |
d6a93e12b1c1
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diff
changeset
|
1159 |
1831
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1160 void ParsedDicomFile::HeaderToJson(Json::Value& target, |
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1161 DicomToJsonFormat format) |
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"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1162 { |
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
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1827
diff
changeset
|
1163 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getMetaInfo(), format, DicomToJsonFlags_None, 0); |
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
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1827
diff
changeset
|
1164 } |
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
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parents:
1827
diff
changeset
|
1165 |
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1166 |
1555
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1523
diff
changeset
|
1167 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1168 { |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1169 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1170 return pimpl_->file_->getDataset()->tagExists(key); |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1171 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1523
diff
changeset
|
1172 |
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1173 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1174 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1175 { |
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1176 if (pdf.size() < 5 || // (*) |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1177 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1178 { |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1523
diff
changeset
|
1179 LOG(ERROR) << "Not a PDF file"; |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1180 throw OrthancException(ErrorCode_BadFileFormat); |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
1523
diff
changeset
|
1181 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1182 |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1183 InvalidateCache(); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1184 |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1185 ReplacePlainString(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1186 ReplacePlainString(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1187 ReplacePlainString(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1188 ReplacePlainString(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1189 //ReplacePlainString(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1190 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1191 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1192 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1193 size_t s = pdf.size(); |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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|
1194 if (s & 1) |
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Creation of DICOM files with encapsulated PDF
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changeset
|
1195 { |
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Creation of DICOM files with encapsulated PDF
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changeset
|
1196 // 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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diff
changeset
|
1197 s += 1; |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
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1198 } |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1199 |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1200 Uint8* bytes = NULL; |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1201 OFCondition result = element->createUint8Array(s, bytes); |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1202 if (!result.good() || bytes == NULL) |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1203 { |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1204 throw OrthancException(ErrorCode_NotEnoughMemory); |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1205 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1206 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1207 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1208 bytes[s - 1] = 0; |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1209 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1210 memcpy(bytes, pdf.c_str(), pdf.size()); |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1211 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1212 DcmPolymorphOBOW* obj = element.release(); |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1213 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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diff
changeset
|
1214 |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1215 if (!result.good()) |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1216 { |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1217 delete obj; |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1218 throw OrthancException(ErrorCode_NotEnoughMemory); |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1219 } |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1220 } |
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1221 |
1556
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1222 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1223 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1224 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1225 std::string sop, mime; |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1226 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1227 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1228 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1229 sop != UID_EncapsulatedPDFStorage || |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1230 mime != "application/pdf") |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1231 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1232 return false; |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1233 } |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1234 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1235 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1236 { |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1237 return false; |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1238 } |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1239 |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1240 // Strip the possible pad byte at the end of file, because the |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1241 // encapsulated documents must always have an even length. The PDF |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1242 // format expects files to end with %%EOF followed by CR/LF. If |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1243 // the last character of the file is not a CR or LF, we assume it |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1244 // is a pad byte and remove it. |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1245 if (pdf.size() > 0) |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1246 { |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1247 char last = *pdf.rbegin(); |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1248 |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1249 if (last != 10 && last != 13) |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1250 { |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1251 pdf.resize(pdf.size() - 1); |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1252 } |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1253 } |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1254 |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1255 return true; |
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1256 } |
1662
09be34b2f30e
ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1655
diff
changeset
|
1257 |
09be34b2f30e
ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1258 |
09be34b2f30e
ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1259 void ParsedDicomFile::Convert(DicomMap& tags) |
09be34b2f30e
ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1260 { |
1929
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1928
diff
changeset
|
1261 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset(), |
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1928
diff
changeset
|
1262 ORTHANC_MAXIMUM_TAG_LENGTH, |
1928
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1924
diff
changeset
|
1263 Configuration::GetDefaultEncoding()); |
1662
09be34b2f30e
ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1655
diff
changeset
|
1264 } |
1818
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1265 |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1266 |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1267 ParsedDicomFile* ParsedDicomFile::CreateFromJson(const Json::Value& json, |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1268 DicomFromJsonFlags flags) |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1269 { |
2028 | 1270 const bool generateIdentifiers = (flags & DicomFromJsonFlags_GenerateIdentifiers) ? true : false; |
1271 const bool decodeDataUriScheme = (flags & DicomFromJsonFlags_DecodeDataUriScheme) ? true : false; | |
1818
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1272 |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1273 std::auto_ptr<ParsedDicomFile> result(new ParsedDicomFile(generateIdentifiers)); |
1934
72a2fd7fed8b
FromDcmtkBridge::FromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1929
diff
changeset
|
1274 result->SetEncoding(FromDcmtkBridge::ExtractEncoding(json, Configuration::GetDefaultEncoding())); |
1818
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1275 |
1934
72a2fd7fed8b
FromDcmtkBridge::FromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1929
diff
changeset
|
1276 const Json::Value::Members tags = json.getMemberNames(); |
72a2fd7fed8b
FromDcmtkBridge::FromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1929
diff
changeset
|
1277 |
1818
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1278 for (size_t i = 0; i < tags.size(); i++) |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1279 { |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1280 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1281 const Json::Value& value = json[tags[i]]; |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1282 |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1283 if (tag == DICOM_TAG_PIXEL_DATA || |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1284 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1285 { |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1286 if (value.type() != Json::stringValue) |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1287 { |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1288 throw OrthancException(ErrorCode_BadRequest); |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1289 } |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1290 else |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1291 { |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1292 result->EmbedContent(value.asString()); |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1293 } |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1294 } |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1295 else if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1296 { |
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1297 result->Replace(tag, value, decodeDataUriScheme, DicomReplaceMode_InsertIfAbsent); |
1818
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1298 } |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1299 } |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1300 |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1301 return result.release(); |
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
1302 } |
1924
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1303 |
6c73df12ca51
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1304 |
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1305 void ParsedDicomFile::GetRawFrame(std::string& target, |
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1306 std::string& mime, |
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1307 unsigned int frameId) |
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1308 { |
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1309 if (pimpl_->frameIndex_.get() == NULL) |
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1310 { |
1956 | 1311 pimpl_->frameIndex_.reset(new DicomFrameIndex(*pimpl_->file_)); |
1924
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1312 } |
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1313 |
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1314 pimpl_->frameIndex_->GetRawFrame(target, frameId); |
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1315 |
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1316 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); |
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1317 switch (transferSyntax) |
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1318 { |
1946
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1319 case EXS_JPEGProcess1: |
1924
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1320 mime = "image/jpeg"; |
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1321 break; |
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1322 |
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1323 case EXS_JPEG2000LosslessOnly: |
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1324 case EXS_JPEG2000: |
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1325 mime = "image/jp2"; |
2016 | 1326 break; |
1924
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1327 |
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1328 default: |
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1329 mime = "application/octet-stream"; |
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1330 break; |
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1331 } |
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1332 } |
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1333 |
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1334 |
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1335 void ParsedDicomFile::InvalidateCache() |
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1336 { |
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1337 pimpl_->frameIndex_.reset(NULL); |
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1338 } |
1950
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1339 |
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1340 |
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1341 unsigned int ParsedDicomFile::GetFramesCount() const |
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1342 { |
1956 | 1343 return DicomFrameIndex::GetFramesCount(*pimpl_->file_); |
1950
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1344 } |
790 | 1345 } |