Mercurial > hg > orthanc
comparison OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.cpp @ 4044:d25f4c0fa160 framework
splitting code into OrthancFramework and OrthancServer
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 10 Jun 2020 20:30:34 +0200 |
parents | Core/DicomParsing/FromDcmtkBridge.cpp@058b5ade8acd |
children | c02a2d9efbc2 |
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4043:6c6239aec462 | 4044:d25f4c0fa160 |
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1 /** | |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * Copyright (C) 2017-2020 Osimis S.A., Belgium | |
6 * | |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU General Public License as | |
9 * published by the Free Software Foundation, either version 3 of the | |
10 * License, or (at your option) any later version. | |
11 * | |
12 * In addition, as a special exception, the copyright holders of this | |
13 * program give permission to link the code of its release with the | |
14 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
15 * that use the same license as the "OpenSSL" library), and distribute | |
16 * the linked executables. You must obey the GNU General Public License | |
17 * in all respects for all of the code used other than "OpenSSL". If you | |
18 * modify file(s) with this exception, you may extend this exception to | |
19 * your version of the file(s), but you are not obligated to do so. If | |
20 * you do not wish to do so, delete this exception statement from your | |
21 * version. If you delete this exception statement from all source files | |
22 * in the program, then also delete it here. | |
23 * | |
24 * This program is distributed in the hope that it will be useful, but | |
25 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
27 * General Public License for more details. | |
28 * | |
29 * You should have received a copy of the GNU General Public License | |
30 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
31 **/ | |
32 | |
33 | |
34 #include "../PrecompiledHeaders.h" | |
35 | |
36 #ifndef NOMINMAX | |
37 #define NOMINMAX | |
38 #endif | |
39 | |
40 #if !defined(ORTHANC_SANDBOXED) | |
41 # error The macro ORTHANC_SANDBOXED must be defined | |
42 #endif | |
43 | |
44 #if !defined(DCMTK_VERSION_NUMBER) | |
45 # error The macro DCMTK_VERSION_NUMBER must be defined | |
46 #endif | |
47 | |
48 #include "FromDcmtkBridge.h" | |
49 #include "ToDcmtkBridge.h" | |
50 #include "../Compatibility.h" | |
51 #include "../Logging.h" | |
52 #include "../Toolbox.h" | |
53 #include "../OrthancException.h" | |
54 | |
55 #if ORTHANC_SANDBOXED == 0 | |
56 # include "../TemporaryFile.h" | |
57 #endif | |
58 | |
59 #include <list> | |
60 #include <limits> | |
61 | |
62 #include <boost/lexical_cast.hpp> | |
63 #include <boost/filesystem.hpp> | |
64 #include <boost/algorithm/string/predicate.hpp> | |
65 #include <boost/algorithm/string/join.hpp> | |
66 | |
67 #include <dcmtk/dcmdata/dcdeftag.h> | |
68 #include <dcmtk/dcmdata/dcdicent.h> | |
69 #include <dcmtk/dcmdata/dcdict.h> | |
70 #include <dcmtk/dcmdata/dcfilefo.h> | |
71 #include <dcmtk/dcmdata/dcistrmb.h> | |
72 #include <dcmtk/dcmdata/dcostrmb.h> | |
73 #include <dcmtk/dcmdata/dcpixel.h> | |
74 #include <dcmtk/dcmdata/dcuid.h> | |
75 #include <dcmtk/dcmdata/dcxfer.h> | |
76 | |
77 #include <dcmtk/dcmdata/dcvrae.h> | |
78 #include <dcmtk/dcmdata/dcvras.h> | |
79 #include <dcmtk/dcmdata/dcvrat.h> | |
80 #include <dcmtk/dcmdata/dcvrcs.h> | |
81 #include <dcmtk/dcmdata/dcvrda.h> | |
82 #include <dcmtk/dcmdata/dcvrds.h> | |
83 #include <dcmtk/dcmdata/dcvrdt.h> | |
84 #include <dcmtk/dcmdata/dcvrfd.h> | |
85 #include <dcmtk/dcmdata/dcvrfl.h> | |
86 #include <dcmtk/dcmdata/dcvris.h> | |
87 #include <dcmtk/dcmdata/dcvrlo.h> | |
88 #include <dcmtk/dcmdata/dcvrlt.h> | |
89 #include <dcmtk/dcmdata/dcvrpn.h> | |
90 #include <dcmtk/dcmdata/dcvrsh.h> | |
91 #include <dcmtk/dcmdata/dcvrsl.h> | |
92 #include <dcmtk/dcmdata/dcvrss.h> | |
93 #include <dcmtk/dcmdata/dcvrst.h> | |
94 #include <dcmtk/dcmdata/dcvrtm.h> | |
95 #include <dcmtk/dcmdata/dcvrui.h> | |
96 #include <dcmtk/dcmdata/dcvrul.h> | |
97 #include <dcmtk/dcmdata/dcvrus.h> | |
98 #include <dcmtk/dcmdata/dcvrut.h> | |
99 | |
100 #if DCMTK_VERSION_NUMBER >= 361 | |
101 # include <dcmtk/dcmdata/dcvruc.h> | |
102 # include <dcmtk/dcmdata/dcvrur.h> | |
103 #endif | |
104 | |
105 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 | |
106 # include <OrthancFrameworkResources.h> | |
107 #endif | |
108 | |
109 #if ORTHANC_ENABLE_DCMTK_JPEG == 1 | |
110 # include <dcmtk/dcmjpeg/djdecode.h> | |
111 # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
112 # include <dcmtk/dcmjpeg/djencode.h> | |
113 # endif | |
114 #endif | |
115 | |
116 #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1 | |
117 # include <dcmtk/dcmjpls/djdecode.h> | |
118 # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
119 # include <dcmtk/dcmjpls/djencode.h> | |
120 # endif | |
121 #endif | |
122 | |
123 | |
124 #include <dcmtk/dcmdata/dcrledrg.h> | |
125 #if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
126 # include <dcmtk/dcmdata/dcrleerg.h> | |
127 # include <dcmtk/dcmimage/diregist.h> // include to support color images | |
128 #endif | |
129 | |
130 | |
131 namespace Orthanc | |
132 { | |
133 static bool IsBinaryTag(const DcmTag& key) | |
134 { | |
135 return (key.isUnknownVR() || | |
136 key.getEVR() == EVR_OB || | |
137 key.getEVR() == EVR_OW || | |
138 key.getEVR() == EVR_UN || | |
139 key.getEVR() == EVR_ox); | |
140 } | |
141 | |
142 | |
143 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 | |
144 static void LoadEmbeddedDictionary(DcmDataDictionary& dictionary, | |
145 FrameworkResources::FileResourceId resource) | |
146 { | |
147 std::string content; | |
148 FrameworkResources::GetFileResource(content, resource); | |
149 | |
150 #if ORTHANC_SANDBOXED == 0 | |
151 TemporaryFile tmp; | |
152 tmp.Write(content); | |
153 | |
154 if (!dictionary.loadDictionary(tmp.GetPath().c_str())) | |
155 { | |
156 throw OrthancException(ErrorCode_InternalError, | |
157 "Cannot read embedded dictionary. Under Windows, make sure that " | |
158 "your TEMP directory does not contain special characters."); | |
159 } | |
160 #else | |
161 if (!dictionary.loadFromMemory(content)) | |
162 { | |
163 throw OrthancException(ErrorCode_InternalError, | |
164 "Cannot read embedded dictionary. Under Windows, make sure that " | |
165 "your TEMP directory does not contain special characters."); | |
166 } | |
167 #endif | |
168 } | |
169 #endif | |
170 | |
171 | |
172 namespace | |
173 { | |
174 class DictionaryLocker : public boost::noncopyable | |
175 { | |
176 private: | |
177 DcmDataDictionary& dictionary_; | |
178 | |
179 public: | |
180 DictionaryLocker() : dictionary_(dcmDataDict.wrlock()) | |
181 { | |
182 } | |
183 | |
184 ~DictionaryLocker() | |
185 { | |
186 #if DCMTK_VERSION_NUMBER >= 364 | |
187 dcmDataDict.wrunlock(); | |
188 #else | |
189 dcmDataDict.unlock(); | |
190 #endif | |
191 } | |
192 | |
193 DcmDataDictionary& operator*() | |
194 { | |
195 return dictionary_; | |
196 } | |
197 | |
198 DcmDataDictionary* operator->() | |
199 { | |
200 return &dictionary_; | |
201 } | |
202 }; | |
203 | |
204 | |
205 #define DCMTK_TO_CTYPE_CONVERTER(converter, cType, dcmtkType, getter) \ | |
206 \ | |
207 struct converter \ | |
208 { \ | |
209 typedef cType CType; \ | |
210 \ | |
211 static bool Apply(CType& result, \ | |
212 DcmElement& element, \ | |
213 size_t i) \ | |
214 { \ | |
215 return dynamic_cast<dcmtkType&>(element).getter(result, i).good(); \ | |
216 } \ | |
217 }; | |
218 | |
219 DCMTK_TO_CTYPE_CONVERTER(DcmtkToSint32Converter, Sint32, DcmSignedLong, getSint32) | |
220 DCMTK_TO_CTYPE_CONVERTER(DcmtkToSint16Converter, Sint16, DcmSignedShort, getSint16) | |
221 DCMTK_TO_CTYPE_CONVERTER(DcmtkToUint32Converter, Uint32, DcmUnsignedLong, getUint32) | |
222 DCMTK_TO_CTYPE_CONVERTER(DcmtkToUint16Converter, Uint16, DcmUnsignedShort, getUint16) | |
223 DCMTK_TO_CTYPE_CONVERTER(DcmtkToFloat32Converter, Float32, DcmFloatingPointSingle, getFloat32) | |
224 DCMTK_TO_CTYPE_CONVERTER(DcmtkToFloat64Converter, Float64, DcmFloatingPointDouble, getFloat64) | |
225 | |
226 | |
227 template <typename F> | |
228 static DicomValue* ApplyDcmtkToCTypeConverter(DcmElement& element) | |
229 { | |
230 F f; | |
231 typename F::CType value; | |
232 | |
233 if (element.getLength() > sizeof(typename F::CType) | |
234 && (element.getLength() % sizeof(typename F::CType)) == 0) | |
235 { | |
236 size_t count = element.getLength() / sizeof(typename F::CType); | |
237 std::vector<std::string> strings; | |
238 for (size_t i = 0; i < count; i++) { | |
239 if (f.Apply(value, element, i)) { | |
240 strings.push_back(boost::lexical_cast<std::string>(value)); | |
241 } | |
242 } | |
243 return new DicomValue(boost::algorithm::join(strings, "\\"), false); | |
244 } | |
245 else if (f.Apply(value, element, 0)) { | |
246 return new DicomValue(boost::lexical_cast<std::string>(value), false); | |
247 } | |
248 else { | |
249 return new DicomValue; | |
250 } | |
251 } | |
252 | |
253 } | |
254 | |
255 | |
256 void FromDcmtkBridge::InitializeDictionary(bool loadPrivateDictionary) | |
257 { | |
258 LOG(INFO) << "Using DCTMK version: " << DCMTK_VERSION_NUMBER; | |
259 | |
260 { | |
261 DictionaryLocker locker; | |
262 | |
263 locker->clear(); | |
264 | |
265 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 | |
266 LOG(INFO) << "Loading the embedded dictionaries"; | |
267 /** | |
268 * Do not load DICONDE dictionary, it breaks the other tags. The | |
269 * command "strace storescu 2>&1 |grep dic" shows that DICONDE | |
270 * dictionary is not loaded by storescu. | |
271 **/ | |
272 //LoadEmbeddedDictionary(*locker, FrameworkResources::DICTIONARY_DICONDE); | |
273 | |
274 LoadEmbeddedDictionary(*locker, FrameworkResources::DICTIONARY_DICOM); | |
275 | |
276 if (loadPrivateDictionary) | |
277 { | |
278 LOG(INFO) << "Loading the embedded dictionary of private tags"; | |
279 LoadEmbeddedDictionary(*locker, FrameworkResources::DICTIONARY_PRIVATE); | |
280 } | |
281 else | |
282 { | |
283 LOG(INFO) << "The dictionary of private tags has not been loaded"; | |
284 } | |
285 | |
286 #else | |
287 std::vector<std::string> dictionaries; | |
288 | |
289 const char* env = std::getenv(DCM_DICT_ENVIRONMENT_VARIABLE); | |
290 if (env != NULL) | |
291 { | |
292 // This mimics the behavior of DCMTK: | |
293 // https://support.dcmtk.org/docs/file_envvars.html | |
294 #if defined(_WIN32) | |
295 Toolbox::TokenizeString(dictionaries, std::string(env), ';'); | |
296 #else | |
297 Toolbox::TokenizeString(dictionaries, std::string(env), ':'); | |
298 #endif | |
299 } | |
300 else | |
301 { | |
302 boost::filesystem::path base = DCMTK_DICTIONARY_DIR; | |
303 dictionaries.push_back((base / "dicom.dic").string()); | |
304 dictionaries.push_back((base / "private.dic").string()); | |
305 } | |
306 | |
307 for (size_t i = 0; i < dictionaries.size(); i++) | |
308 { | |
309 LOG(WARNING) << "Loading external DICOM dictionary: \"" << dictionaries[i] << "\""; | |
310 | |
311 if (!locker->loadDictionary(dictionaries[i].c_str())) | |
312 { | |
313 throw OrthancException(ErrorCode_InexistentFile); | |
314 } | |
315 } | |
316 | |
317 #endif | |
318 } | |
319 | |
320 /* make sure data dictionary is loaded */ | |
321 if (!dcmDataDict.isDictionaryLoaded()) | |
322 { | |
323 throw OrthancException(ErrorCode_InternalError, | |
324 "No DICOM dictionary loaded, check environment variable: " + | |
325 std::string(DCM_DICT_ENVIRONMENT_VARIABLE)); | |
326 } | |
327 | |
328 { | |
329 // Test the dictionary with a simple DICOM tag | |
330 DcmTag key(0x0010, 0x1030); // This is PatientWeight | |
331 if (key.getEVR() != EVR_DS) | |
332 { | |
333 throw OrthancException(ErrorCode_InternalError, | |
334 "The DICOM dictionary has not been correctly read"); | |
335 } | |
336 } | |
337 } | |
338 | |
339 | |
340 void FromDcmtkBridge::RegisterDictionaryTag(const DicomTag& tag, | |
341 ValueRepresentation vr, | |
342 const std::string& name, | |
343 unsigned int minMultiplicity, | |
344 unsigned int maxMultiplicity, | |
345 const std::string& privateCreator) | |
346 { | |
347 if (minMultiplicity < 1) | |
348 { | |
349 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
350 } | |
351 | |
352 bool arbitrary = false; | |
353 if (maxMultiplicity == 0) | |
354 { | |
355 maxMultiplicity = DcmVariableVM; | |
356 arbitrary = true; | |
357 } | |
358 else if (maxMultiplicity < minMultiplicity) | |
359 { | |
360 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
361 } | |
362 | |
363 DcmEVR evr = ToDcmtkBridge::Convert(vr); | |
364 | |
365 LOG(INFO) << "Registering tag in dictionary: " << tag << " " << (DcmVR(evr).getValidVRName()) << " " | |
366 << name << " (multiplicity: " << minMultiplicity << "-" | |
367 << (arbitrary ? "n" : boost::lexical_cast<std::string>(maxMultiplicity)) << ")"; | |
368 | |
369 std::unique_ptr<DcmDictEntry> entry; | |
370 if (privateCreator.empty()) | |
371 { | |
372 if (tag.GetGroup() % 2 == 1) | |
373 { | |
374 char buf[128]; | |
375 sprintf(buf, "Warning: You are registering a private tag (%04x,%04x), " | |
376 "but no private creator was associated with it", | |
377 tag.GetGroup(), tag.GetElement()); | |
378 LOG(WARNING) << buf; | |
379 } | |
380 | |
381 entry.reset(new DcmDictEntry(tag.GetGroup(), | |
382 tag.GetElement(), | |
383 evr, name.c_str(), | |
384 static_cast<int>(minMultiplicity), | |
385 static_cast<int>(maxMultiplicity), | |
386 NULL /* version */, | |
387 OFTrue /* doCopyString */, | |
388 NULL /* private creator */)); | |
389 } | |
390 else | |
391 { | |
392 // "Private Data Elements have an odd Group Number that is not | |
393 // (0001,eeee), (0003,eeee), (0005,eeee), (0007,eeee), or | |
394 // (FFFF,eeee)." | |
395 if (tag.GetGroup() % 2 == 0 /* even */ || | |
396 tag.GetGroup() == 0x0001 || | |
397 tag.GetGroup() == 0x0003 || | |
398 tag.GetGroup() == 0x0005 || | |
399 tag.GetGroup() == 0x0007 || | |
400 tag.GetGroup() == 0xffff) | |
401 { | |
402 char buf[128]; | |
403 sprintf(buf, "Trying to register private tag (%04x,%04x), but it must have an odd group >= 0x0009", | |
404 tag.GetGroup(), tag.GetElement()); | |
405 throw OrthancException(ErrorCode_ParameterOutOfRange, std::string(buf)); | |
406 } | |
407 | |
408 entry.reset(new DcmDictEntry(tag.GetGroup(), | |
409 tag.GetElement(), | |
410 evr, name.c_str(), | |
411 static_cast<int>(minMultiplicity), | |
412 static_cast<int>(maxMultiplicity), | |
413 "private" /* version */, | |
414 OFTrue /* doCopyString */, | |
415 privateCreator.c_str())); | |
416 } | |
417 | |
418 entry->setGroupRangeRestriction(DcmDictRange_Unspecified); | |
419 entry->setElementRangeRestriction(DcmDictRange_Unspecified); | |
420 | |
421 { | |
422 DictionaryLocker locker; | |
423 | |
424 if (locker->findEntry(name.c_str())) | |
425 { | |
426 throw OrthancException(ErrorCode_AlreadyExistingTag, | |
427 "Cannot register two tags with the same symbolic name \"" + name + "\""); | |
428 } | |
429 | |
430 locker->addEntry(entry.release()); | |
431 } | |
432 } | |
433 | |
434 | |
435 Encoding FromDcmtkBridge::DetectEncoding(bool& hasCodeExtensions, | |
436 DcmItem& dataset, | |
437 Encoding defaultEncoding) | |
438 { | |
439 // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.12.html#sect_C.12.1.1.2 | |
440 | |
441 OFString tmp; | |
442 if (dataset.findAndGetOFStringArray(DCM_SpecificCharacterSet, tmp).good()) | |
443 { | |
444 std::vector<std::string> tokens; | |
445 Toolbox::TokenizeString(tokens, std::string(tmp.c_str()), '\\'); | |
446 | |
447 hasCodeExtensions = (tokens.size() > 1); | |
448 | |
449 for (size_t i = 0; i < tokens.size(); i++) | |
450 { | |
451 std::string characterSet = Toolbox::StripSpaces(tokens[i]); | |
452 | |
453 if (!characterSet.empty()) | |
454 { | |
455 Encoding encoding; | |
456 | |
457 if (GetDicomEncoding(encoding, characterSet.c_str())) | |
458 { | |
459 // The specific character set is supported by the Orthanc core | |
460 return encoding; | |
461 } | |
462 else | |
463 { | |
464 LOG(WARNING) << "Value of Specific Character Set (0008,0005) is not supported: " << characterSet | |
465 << ", fallback to ASCII (remove all special characters)"; | |
466 return Encoding_Ascii; | |
467 } | |
468 } | |
469 } | |
470 } | |
471 else | |
472 { | |
473 hasCodeExtensions = false; | |
474 } | |
475 | |
476 // No specific character set tag: Use the default encoding | |
477 return defaultEncoding; | |
478 } | |
479 | |
480 | |
481 void FromDcmtkBridge::ExtractDicomSummary(DicomMap& target, | |
482 DcmItem& dataset, | |
483 unsigned int maxStringLength, | |
484 Encoding defaultEncoding, | |
485 const std::set<DicomTag>& ignoreTagLength) | |
486 { | |
487 bool hasCodeExtensions; | |
488 Encoding encoding = DetectEncoding(hasCodeExtensions, dataset, defaultEncoding); | |
489 | |
490 target.Clear(); | |
491 for (unsigned long i = 0; i < dataset.card(); i++) | |
492 { | |
493 DcmElement* element = dataset.getElement(i); | |
494 if (element && element->isLeaf()) | |
495 { | |
496 target.SetValueInternal(element->getTag().getGTag(), | |
497 element->getTag().getETag(), | |
498 ConvertLeafElement(*element, DicomToJsonFlags_Default, | |
499 maxStringLength, encoding, hasCodeExtensions, ignoreTagLength)); | |
500 } | |
501 } | |
502 } | |
503 | |
504 | |
505 DicomTag FromDcmtkBridge::Convert(const DcmTag& tag) | |
506 { | |
507 return DicomTag(tag.getGTag(), tag.getETag()); | |
508 } | |
509 | |
510 | |
511 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
512 { | |
513 return DicomTag(element.getGTag(), element.getETag()); | |
514 } | |
515 | |
516 | |
517 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element, | |
518 DicomToJsonFlags flags, | |
519 unsigned int maxStringLength, | |
520 Encoding encoding, | |
521 bool hasCodeExtensions, | |
522 const std::set<DicomTag>& ignoreTagLength) | |
523 { | |
524 if (!element.isLeaf()) | |
525 { | |
526 // This function is only applicable to leaf elements | |
527 throw OrthancException(ErrorCode_BadParameterType); | |
528 } | |
529 | |
530 char *c = NULL; | |
531 if (element.isaString() && | |
532 element.getString(c).good()) | |
533 { | |
534 if (c == NULL) // This case corresponds to the empty string | |
535 { | |
536 return new DicomValue("", false); | |
537 } | |
538 else | |
539 { | |
540 std::string s(c); | |
541 std::string utf8 = Toolbox::ConvertToUtf8(s, encoding, hasCodeExtensions); | |
542 | |
543 if (maxStringLength != 0 && | |
544 utf8.size() > maxStringLength && | |
545 ignoreTagLength.find(GetTag(element)) == ignoreTagLength.end()) | |
546 { | |
547 return new DicomValue; // Too long, create a NULL value | |
548 } | |
549 else | |
550 { | |
551 return new DicomValue(utf8, false); | |
552 } | |
553 } | |
554 } | |
555 | |
556 | |
557 if (element.getVR() == EVR_UN) | |
558 { | |
559 // Unknown value representation: Lookup in the dictionary. This | |
560 // is notably the case for private tags registered with the | |
561 // "Dictionary" configuration option. | |
562 DictionaryLocker locker; | |
563 | |
564 const DcmDictEntry* entry = locker->findEntry(element.getTag().getXTag(), | |
565 element.getTag().getPrivateCreator()); | |
566 if (entry != NULL && | |
567 entry->getVR().isaString()) | |
568 { | |
569 Uint8* data = NULL; | |
570 | |
571 // At (*), we do not try and convert to UTF-8, as nothing says | |
572 // the encoding of the private tag is the same as that of the | |
573 // remaining of the DICOM dataset. Only go for ASCII strings. | |
574 | |
575 if (element.getUint8Array(data) == EC_Normal && | |
576 Toolbox::IsAsciiString(data, element.getLength())) // (*) | |
577 { | |
578 if (data == NULL) | |
579 { | |
580 return new DicomValue("", false); // Empty string | |
581 } | |
582 else if (maxStringLength != 0 && | |
583 element.getLength() > maxStringLength && | |
584 ignoreTagLength.find(GetTag(element)) == ignoreTagLength.end()) | |
585 { | |
586 return new DicomValue; // Too long, create a NULL value | |
587 } | |
588 else | |
589 { | |
590 std::string s(reinterpret_cast<const char*>(data), element.getLength()); | |
591 return new DicomValue(s, false); | |
592 } | |
593 } | |
594 } | |
595 } | |
596 | |
597 | |
598 try | |
599 { | |
600 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
601 switch (element.getVR()) | |
602 { | |
603 | |
604 /** | |
605 * Deal with binary data (including PixelData). | |
606 **/ | |
607 | |
608 case EVR_OB: // other byte | |
609 case EVR_OF: // other float | |
610 case EVR_OW: // other word | |
611 case EVR_UN: // unknown value representation | |
612 case EVR_ox: // OB or OW depending on context | |
613 case EVR_DS: // decimal string | |
614 case EVR_IS: // integer string | |
615 case EVR_AS: // age string | |
616 case EVR_DA: // date string | |
617 case EVR_DT: // date time string | |
618 case EVR_TM: // time string | |
619 case EVR_AE: // application entity title | |
620 case EVR_CS: // code string | |
621 case EVR_SH: // short string | |
622 case EVR_LO: // long string | |
623 case EVR_ST: // short text | |
624 case EVR_LT: // long text | |
625 case EVR_UT: // unlimited text | |
626 case EVR_PN: // person name | |
627 case EVR_UI: // unique identifier | |
628 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
629 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
630 { | |
631 if (!(flags & DicomToJsonFlags_ConvertBinaryToNull)) | |
632 { | |
633 Uint8* data = NULL; | |
634 if (element.getUint8Array(data) == EC_Normal) | |
635 { | |
636 return new DicomValue(reinterpret_cast<const char*>(data), element.getLength(), true); | |
637 } | |
638 } | |
639 | |
640 return new DicomValue; | |
641 } | |
642 | |
643 /** | |
644 * Numeric types | |
645 **/ | |
646 | |
647 case EVR_SL: // signed long | |
648 { | |
649 return ApplyDcmtkToCTypeConverter<DcmtkToSint32Converter>(element); | |
650 } | |
651 | |
652 case EVR_SS: // signed short | |
653 { | |
654 return ApplyDcmtkToCTypeConverter<DcmtkToSint16Converter>(element); | |
655 } | |
656 | |
657 case EVR_UL: // unsigned long | |
658 { | |
659 return ApplyDcmtkToCTypeConverter<DcmtkToUint32Converter>(element); | |
660 } | |
661 | |
662 case EVR_US: // unsigned short | |
663 { | |
664 return ApplyDcmtkToCTypeConverter<DcmtkToUint16Converter>(element); | |
665 } | |
666 | |
667 case EVR_FL: // float single-precision | |
668 { | |
669 return ApplyDcmtkToCTypeConverter<DcmtkToFloat32Converter>(element); | |
670 } | |
671 | |
672 case EVR_FD: // float double-precision | |
673 { | |
674 return ApplyDcmtkToCTypeConverter<DcmtkToFloat64Converter>(element); | |
675 } | |
676 | |
677 | |
678 /** | |
679 * Attribute tag. | |
680 **/ | |
681 | |
682 case EVR_AT: | |
683 { | |
684 DcmTagKey tag; | |
685 if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tag, 0).good()) | |
686 { | |
687 DicomTag t(tag.getGroup(), tag.getElement()); | |
688 return new DicomValue(t.Format(), false); | |
689 } | |
690 else | |
691 { | |
692 return new DicomValue; | |
693 } | |
694 } | |
695 | |
696 | |
697 /** | |
698 * Sequence types, should never occur at this point because of | |
699 * "element.isLeaf()". | |
700 **/ | |
701 | |
702 case EVR_SQ: // sequence of items | |
703 return new DicomValue; | |
704 | |
705 | |
706 /** | |
707 * Internal to DCMTK. | |
708 **/ | |
709 | |
710 case EVR_xs: // SS or US depending on context | |
711 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
712 case EVR_na: // na="not applicable", for data which has no VR | |
713 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
714 case EVR_item: // used internally for items | |
715 case EVR_metainfo: // used internally for meta info datasets | |
716 case EVR_dataset: // used internally for datasets | |
717 case EVR_fileFormat: // used internally for DICOM files | |
718 case EVR_dicomDir: // used internally for DICOMDIR objects | |
719 case EVR_dirRecord: // used internally for DICOMDIR records | |
720 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
721 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
722 case EVR_PixelData: // used internally for uncompressed pixeld data | |
723 case EVR_OverlayData: // used internally for overlay data | |
724 return new DicomValue; | |
725 | |
726 | |
727 /** | |
728 * Default case. | |
729 **/ | |
730 | |
731 default: | |
732 return new DicomValue; | |
733 } | |
734 } | |
735 catch (boost::bad_lexical_cast&) | |
736 { | |
737 return new DicomValue; | |
738 } | |
739 catch (std::bad_cast&) | |
740 { | |
741 return new DicomValue; | |
742 } | |
743 } | |
744 | |
745 | |
746 static Json::Value& PrepareNode(Json::Value& parent, | |
747 DcmElement& element, | |
748 DicomToJsonFormat format) | |
749 { | |
750 assert(parent.type() == Json::objectValue); | |
751 | |
752 DicomTag tag(FromDcmtkBridge::GetTag(element)); | |
753 const std::string formattedTag = tag.Format(); | |
754 | |
755 if (format == DicomToJsonFormat_Short) | |
756 { | |
757 parent[formattedTag] = Json::nullValue; | |
758 return parent[formattedTag]; | |
759 } | |
760 | |
761 // This code gives access to the name of the private tags | |
762 std::string tagName = FromDcmtkBridge::GetTagName(element); | |
763 | |
764 switch (format) | |
765 { | |
766 case DicomToJsonFormat_Human: | |
767 parent[tagName] = Json::nullValue; | |
768 return parent[tagName]; | |
769 | |
770 case DicomToJsonFormat_Full: | |
771 { | |
772 parent[formattedTag] = Json::objectValue; | |
773 Json::Value& node = parent[formattedTag]; | |
774 | |
775 if (element.isLeaf()) | |
776 { | |
777 node["Name"] = tagName; | |
778 | |
779 if (element.getTag().getPrivateCreator() != NULL) | |
780 { | |
781 node["PrivateCreator"] = element.getTag().getPrivateCreator(); | |
782 } | |
783 | |
784 return node; | |
785 } | |
786 else | |
787 { | |
788 node["Name"] = tagName; | |
789 node["Type"] = "Sequence"; | |
790 node["Value"] = Json::nullValue; | |
791 return node["Value"]; | |
792 } | |
793 } | |
794 | |
795 default: | |
796 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
797 } | |
798 } | |
799 | |
800 | |
801 static void LeafValueToJson(Json::Value& target, | |
802 const DicomValue& value, | |
803 DicomToJsonFormat format, | |
804 DicomToJsonFlags flags, | |
805 unsigned int maxStringLength) | |
806 { | |
807 Json::Value* targetValue = NULL; | |
808 Json::Value* targetType = NULL; | |
809 | |
810 switch (format) | |
811 { | |
812 case DicomToJsonFormat_Short: | |
813 case DicomToJsonFormat_Human: | |
814 { | |
815 assert(target.type() == Json::nullValue); | |
816 targetValue = ⌖ | |
817 break; | |
818 } | |
819 | |
820 case DicomToJsonFormat_Full: | |
821 { | |
822 assert(target.type() == Json::objectValue); | |
823 target["Value"] = Json::nullValue; | |
824 target["Type"] = Json::nullValue; | |
825 targetType = &target["Type"]; | |
826 targetValue = &target["Value"]; | |
827 break; | |
828 } | |
829 | |
830 default: | |
831 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
832 } | |
833 | |
834 assert(targetValue != NULL); | |
835 assert(targetValue->type() == Json::nullValue); | |
836 assert(targetType == NULL || targetType->type() == Json::nullValue); | |
837 | |
838 if (value.IsNull()) | |
839 { | |
840 if (targetType != NULL) | |
841 { | |
842 *targetType = "Null"; | |
843 } | |
844 } | |
845 else if (value.IsBinary()) | |
846 { | |
847 if (flags & DicomToJsonFlags_ConvertBinaryToAscii) | |
848 { | |
849 *targetValue = Toolbox::ConvertToAscii(value.GetContent()); | |
850 } | |
851 else | |
852 { | |
853 std::string s; | |
854 value.FormatDataUriScheme(s); | |
855 *targetValue = s; | |
856 } | |
857 | |
858 if (targetType != NULL) | |
859 { | |
860 *targetType = "Binary"; | |
861 } | |
862 } | |
863 else if (maxStringLength == 0 || | |
864 value.GetContent().size() <= maxStringLength) | |
865 { | |
866 *targetValue = value.GetContent(); | |
867 | |
868 if (targetType != NULL) | |
869 { | |
870 *targetType = "String"; | |
871 } | |
872 } | |
873 else | |
874 { | |
875 if (targetType != NULL) | |
876 { | |
877 *targetType = "TooLong"; | |
878 } | |
879 } | |
880 } | |
881 | |
882 | |
883 void FromDcmtkBridge::ElementToJson(Json::Value& parent, | |
884 DcmElement& element, | |
885 DicomToJsonFormat format, | |
886 DicomToJsonFlags flags, | |
887 unsigned int maxStringLength, | |
888 Encoding encoding, | |
889 bool hasCodeExtensions, | |
890 const std::set<DicomTag>& ignoreTagLength) | |
891 { | |
892 if (parent.type() == Json::nullValue) | |
893 { | |
894 parent = Json::objectValue; | |
895 } | |
896 | |
897 assert(parent.type() == Json::objectValue); | |
898 Json::Value& target = PrepareNode(parent, element, format); | |
899 | |
900 if (element.isLeaf()) | |
901 { | |
902 // The "0" below lets "LeafValueToJson()" take care of "TooLong" values | |
903 std::unique_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement | |
904 (element, flags, 0, encoding, hasCodeExtensions, ignoreTagLength)); | |
905 | |
906 if (ignoreTagLength.find(GetTag(element)) == ignoreTagLength.end()) | |
907 { | |
908 LeafValueToJson(target, *v, format, flags, maxStringLength); | |
909 } | |
910 else | |
911 { | |
912 LeafValueToJson(target, *v, format, flags, 0); | |
913 } | |
914 } | |
915 else | |
916 { | |
917 assert(target.type() == Json::nullValue); | |
918 target = Json::arrayValue; | |
919 | |
920 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
921 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
922 // etc. are not." The following dynamic_cast is thus OK. | |
923 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
924 | |
925 for (unsigned long i = 0; i < sequence.card(); i++) | |
926 { | |
927 DcmItem* child = sequence.getItem(i); | |
928 Json::Value& v = target.append(Json::objectValue); | |
929 DatasetToJson(v, *child, format, flags, maxStringLength, encoding, hasCodeExtensions, ignoreTagLength); | |
930 } | |
931 } | |
932 } | |
933 | |
934 | |
935 void FromDcmtkBridge::DatasetToJson(Json::Value& parent, | |
936 DcmItem& item, | |
937 DicomToJsonFormat format, | |
938 DicomToJsonFlags flags, | |
939 unsigned int maxStringLength, | |
940 Encoding encoding, | |
941 bool hasCodeExtensions, | |
942 const std::set<DicomTag>& ignoreTagLength) | |
943 { | |
944 assert(parent.type() == Json::objectValue); | |
945 | |
946 for (unsigned long i = 0; i < item.card(); i++) | |
947 { | |
948 DcmElement* element = item.getElement(i); | |
949 if (element == NULL) | |
950 { | |
951 throw OrthancException(ErrorCode_InternalError); | |
952 } | |
953 | |
954 DicomTag tag(FromDcmtkBridge::Convert(element->getTag())); | |
955 | |
956 /*element->getTag().isPrivate()*/ | |
957 if (tag.IsPrivate() && | |
958 !(flags & DicomToJsonFlags_IncludePrivateTags)) | |
959 { | |
960 continue; | |
961 } | |
962 | |
963 if (!(flags & DicomToJsonFlags_IncludeUnknownTags)) | |
964 { | |
965 DictionaryLocker locker; | |
966 if (locker->findEntry(element->getTag(), element->getTag().getPrivateCreator()) == NULL) | |
967 { | |
968 continue; | |
969 } | |
970 } | |
971 | |
972 if (IsBinaryTag(element->getTag())) | |
973 { | |
974 // This is a binary tag | |
975 if ((tag == DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludePixelData)) || | |
976 (tag != DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludeBinary))) | |
977 { | |
978 continue; | |
979 } | |
980 } | |
981 | |
982 FromDcmtkBridge::ElementToJson(parent, *element, format, flags, | |
983 maxStringLength, encoding, hasCodeExtensions, ignoreTagLength); | |
984 } | |
985 } | |
986 | |
987 | |
988 void FromDcmtkBridge::ExtractDicomAsJson(Json::Value& target, | |
989 DcmDataset& dataset, | |
990 DicomToJsonFormat format, | |
991 DicomToJsonFlags flags, | |
992 unsigned int maxStringLength, | |
993 Encoding defaultEncoding, | |
994 const std::set<DicomTag>& ignoreTagLength) | |
995 { | |
996 bool hasCodeExtensions; | |
997 Encoding encoding = DetectEncoding(hasCodeExtensions, dataset, defaultEncoding); | |
998 | |
999 target = Json::objectValue; | |
1000 DatasetToJson(target, dataset, format, flags, maxStringLength, encoding, hasCodeExtensions, ignoreTagLength); | |
1001 } | |
1002 | |
1003 | |
1004 void FromDcmtkBridge::ExtractHeaderAsJson(Json::Value& target, | |
1005 DcmMetaInfo& dataset, | |
1006 DicomToJsonFormat format, | |
1007 DicomToJsonFlags flags, | |
1008 unsigned int maxStringLength) | |
1009 { | |
1010 std::set<DicomTag> ignoreTagLength; | |
1011 target = Json::objectValue; | |
1012 DatasetToJson(target, dataset, format, flags, maxStringLength, Encoding_Ascii, false, ignoreTagLength); | |
1013 } | |
1014 | |
1015 | |
1016 | |
1017 static std::string GetTagNameInternal(DcmTag& tag) | |
1018 { | |
1019 { | |
1020 // Some patches for important tags because of different DICOM | |
1021 // dictionaries between DCMTK versions | |
1022 DicomTag tmp(tag.getGroup(), tag.getElement()); | |
1023 std::string n = tmp.GetMainTagsName(); | |
1024 if (n.size() != 0) | |
1025 { | |
1026 return n; | |
1027 } | |
1028 // End of patches | |
1029 } | |
1030 | |
1031 #if 0 | |
1032 // This version explicitly calls the dictionary | |
1033 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
1034 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
1035 | |
1036 std::string s(DcmTag_ERROR_TagName); | |
1037 if (entry != NULL) | |
1038 { | |
1039 s = std::string(entry->getTagName()); | |
1040 } | |
1041 | |
1042 dcmDataDict.unlock(); | |
1043 return s; | |
1044 #else | |
1045 const char* name = tag.getTagName(); | |
1046 if (name == NULL) | |
1047 { | |
1048 return DcmTag_ERROR_TagName; | |
1049 } | |
1050 else | |
1051 { | |
1052 return std::string(name); | |
1053 } | |
1054 #endif | |
1055 } | |
1056 | |
1057 | |
1058 std::string FromDcmtkBridge::GetTagName(const DicomTag& t, | |
1059 const std::string& privateCreator) | |
1060 { | |
1061 DcmTag tag(t.GetGroup(), t.GetElement()); | |
1062 | |
1063 if (!privateCreator.empty()) | |
1064 { | |
1065 tag.setPrivateCreator(privateCreator.c_str()); | |
1066 } | |
1067 | |
1068 return GetTagNameInternal(tag); | |
1069 } | |
1070 | |
1071 | |
1072 std::string FromDcmtkBridge::GetTagName(const DcmElement& element) | |
1073 { | |
1074 // Copy the tag to ensure const-correctness of DcmElement. Note | |
1075 // that the private creator information is also copied. | |
1076 DcmTag tag(element.getTag()); | |
1077 | |
1078 return GetTagNameInternal(tag); | |
1079 } | |
1080 | |
1081 | |
1082 | |
1083 DicomTag FromDcmtkBridge::ParseTag(const char* name) | |
1084 { | |
1085 DicomTag parsed(0, 0); | |
1086 if (DicomTag::ParseHexadecimal(parsed, name)) | |
1087 { | |
1088 return parsed; | |
1089 } | |
1090 | |
1091 #if 0 | |
1092 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
1093 const DcmDictEntry* entry = dict.findEntry(name); | |
1094 | |
1095 if (entry == NULL) | |
1096 { | |
1097 dcmDataDict.unlock(); | |
1098 throw OrthancException(ErrorCode_UnknownDicomTag); | |
1099 } | |
1100 else | |
1101 { | |
1102 DcmTagKey key = entry->getKey(); | |
1103 DicomTag tag(key.getGroup(), key.getElement()); | |
1104 dcmDataDict.unlock(); | |
1105 return tag; | |
1106 } | |
1107 #else | |
1108 DcmTag tag; | |
1109 if (DcmTag::findTagFromName(name, tag).good()) | |
1110 { | |
1111 return DicomTag(tag.getGTag(), tag.getETag()); | |
1112 } | |
1113 else | |
1114 { | |
1115 LOG(INFO) << "Unknown DICOM tag: \"" << name << "\""; | |
1116 throw OrthancException(ErrorCode_UnknownDicomTag); | |
1117 } | |
1118 #endif | |
1119 } | |
1120 | |
1121 | |
1122 bool FromDcmtkBridge::IsUnknownTag(const DicomTag& tag) | |
1123 { | |
1124 DcmTag tmp(tag.GetGroup(), tag.GetElement()); | |
1125 return tmp.isUnknownVR(); | |
1126 } | |
1127 | |
1128 | |
1129 void FromDcmtkBridge::ToJson(Json::Value& result, | |
1130 const DicomMap& values, | |
1131 bool simplify) | |
1132 { | |
1133 if (result.type() != Json::objectValue) | |
1134 { | |
1135 throw OrthancException(ErrorCode_BadParameterType); | |
1136 } | |
1137 | |
1138 result.clear(); | |
1139 | |
1140 for (DicomMap::Content::const_iterator | |
1141 it = values.content_.begin(); it != values.content_.end(); ++it) | |
1142 { | |
1143 // TODO Inject PrivateCreator if some is available in the DicomMap? | |
1144 const std::string tagName = GetTagName(it->first, ""); | |
1145 | |
1146 if (simplify) | |
1147 { | |
1148 if (it->second->IsNull()) | |
1149 { | |
1150 result[tagName] = Json::nullValue; | |
1151 } | |
1152 else | |
1153 { | |
1154 // TODO IsBinary | |
1155 result[tagName] = it->second->GetContent(); | |
1156 } | |
1157 } | |
1158 else | |
1159 { | |
1160 Json::Value value = Json::objectValue; | |
1161 | |
1162 value["Name"] = tagName; | |
1163 | |
1164 if (it->second->IsNull()) | |
1165 { | |
1166 value["Type"] = "Null"; | |
1167 value["Value"] = Json::nullValue; | |
1168 } | |
1169 else | |
1170 { | |
1171 // TODO IsBinary | |
1172 value["Type"] = "String"; | |
1173 value["Value"] = it->second->GetContent(); | |
1174 } | |
1175 | |
1176 result[it->first.Format()] = value; | |
1177 } | |
1178 } | |
1179 } | |
1180 | |
1181 | |
1182 std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) | |
1183 { | |
1184 char uid[100]; | |
1185 | |
1186 switch (level) | |
1187 { | |
1188 case ResourceType_Patient: | |
1189 // The "PatientID" field is of type LO (Long String), 64 | |
1190 // Bytes Maximum. An UUID is of length 36, thus it can be used | |
1191 // as a random PatientID. | |
1192 return Toolbox::GenerateUuid(); | |
1193 | |
1194 case ResourceType_Instance: | |
1195 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
1196 | |
1197 case ResourceType_Series: | |
1198 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); | |
1199 | |
1200 case ResourceType_Study: | |
1201 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); | |
1202 | |
1203 default: | |
1204 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
1205 } | |
1206 } | |
1207 | |
1208 | |
1209 | |
1210 static bool SaveToMemoryBufferInternal(std::string& buffer, | |
1211 DcmFileFormat& dicom, | |
1212 E_TransferSyntax xfer) | |
1213 { | |
1214 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
1215 | |
1216 // Create a memory buffer with the proper size | |
1217 { | |
1218 const uint32_t estimatedSize = dicom.calcElementLength(xfer, encodingType); // (*) | |
1219 buffer.resize(estimatedSize); | |
1220 } | |
1221 | |
1222 DcmOutputBufferStream ob(&buffer[0], buffer.size()); | |
1223 | |
1224 // Fill the memory buffer with the meta-header and the dataset | |
1225 dicom.transferInit(); | |
1226 OFCondition c = dicom.write(ob, xfer, encodingType, NULL, | |
1227 /*opt_groupLength*/ EGL_recalcGL, | |
1228 /*opt_paddingType*/ EPD_noChange, | |
1229 /*padlen*/ 0, /*subPadlen*/ 0, /*instanceLength*/ 0, | |
1230 EWM_updateMeta /* creates new SOP instance UID on lossy */); | |
1231 dicom.transferEnd(); | |
1232 | |
1233 if (c.good()) | |
1234 { | |
1235 // The DICOM file is successfully written, truncate the target | |
1236 // buffer if its size was overestimated by (*) | |
1237 ob.flush(); | |
1238 | |
1239 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
1240 if (effectiveSize < buffer.size()) | |
1241 { | |
1242 buffer.resize(effectiveSize); | |
1243 } | |
1244 | |
1245 return true; | |
1246 } | |
1247 else | |
1248 { | |
1249 // Error | |
1250 buffer.clear(); | |
1251 return false; | |
1252 } | |
1253 } | |
1254 | |
1255 | |
1256 bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, | |
1257 DcmDataset& dataSet) | |
1258 { | |
1259 // Determine the transfer syntax which shall be used to write the | |
1260 // information to the file. If not possible, switch to the Little | |
1261 // Endian syntax, with explicit length. | |
1262 | |
1263 // http://support.dcmtk.org/docs/dcxfer_8h-source.html | |
1264 | |
1265 | |
1266 /** | |
1267 * Note that up to Orthanc 0.7.1 (inclusive), the | |
1268 * "EXS_LittleEndianExplicit" was always used to save the DICOM | |
1269 * dataset into memory. We now keep the original transfer syntax | |
1270 * (if available). | |
1271 **/ | |
1272 E_TransferSyntax xfer = dataSet.getCurrentXfer(); | |
1273 if (xfer == EXS_Unknown) | |
1274 { | |
1275 // No information about the original transfer syntax: This is | |
1276 // most probably a DICOM dataset that was read from memory. | |
1277 xfer = EXS_LittleEndianExplicit; | |
1278 } | |
1279 | |
1280 // Create the meta-header information | |
1281 DcmFileFormat ff(&dataSet); | |
1282 ff.validateMetaInfo(xfer); | |
1283 ff.removeInvalidGroups(); | |
1284 | |
1285 return SaveToMemoryBufferInternal(buffer, ff, xfer); | |
1286 } | |
1287 | |
1288 | |
1289 bool FromDcmtkBridge::Transcode(DcmFileFormat& dicom, | |
1290 DicomTransferSyntax syntax, | |
1291 const DcmRepresentationParameter* representation) | |
1292 { | |
1293 E_TransferSyntax xfer; | |
1294 if (!LookupDcmtkTransferSyntax(xfer, syntax)) | |
1295 { | |
1296 throw OrthancException(ErrorCode_InternalError); | |
1297 } | |
1298 else | |
1299 { | |
1300 DicomTransferSyntax sourceSyntax; | |
1301 bool known = LookupOrthancTransferSyntax(sourceSyntax, dicom); | |
1302 | |
1303 if (!dicom.chooseRepresentation(xfer, representation).good() || | |
1304 !dicom.canWriteXfer(xfer) || | |
1305 !dicom.validateMetaInfo(xfer, EWM_updateMeta).good()) | |
1306 { | |
1307 return false; | |
1308 } | |
1309 else | |
1310 { | |
1311 dicom.removeInvalidGroups(); | |
1312 | |
1313 if (known) | |
1314 { | |
1315 LOG(INFO) << "Transcoded an image from transfer syntax " | |
1316 << GetTransferSyntaxUid(sourceSyntax) << " to " | |
1317 << GetTransferSyntaxUid(syntax); | |
1318 } | |
1319 else | |
1320 { | |
1321 LOG(INFO) << "Transcoded an image from unknown transfer syntax to " | |
1322 << GetTransferSyntaxUid(syntax); | |
1323 } | |
1324 | |
1325 return true; | |
1326 } | |
1327 } | |
1328 } | |
1329 | |
1330 | |
1331 ValueRepresentation FromDcmtkBridge::LookupValueRepresentation(const DicomTag& tag) | |
1332 { | |
1333 DcmTag t(tag.GetGroup(), tag.GetElement()); | |
1334 return Convert(t.getEVR()); | |
1335 } | |
1336 | |
1337 ValueRepresentation FromDcmtkBridge::Convert(const DcmEVR vr) | |
1338 { | |
1339 switch (vr) | |
1340 { | |
1341 case EVR_AE: | |
1342 return ValueRepresentation_ApplicationEntity; | |
1343 | |
1344 case EVR_AS: | |
1345 return ValueRepresentation_AgeString; | |
1346 | |
1347 case EVR_AT: | |
1348 return ValueRepresentation_AttributeTag; | |
1349 | |
1350 case EVR_CS: | |
1351 return ValueRepresentation_CodeString; | |
1352 | |
1353 case EVR_DA: | |
1354 return ValueRepresentation_Date; | |
1355 | |
1356 case EVR_DS: | |
1357 return ValueRepresentation_DecimalString; | |
1358 | |
1359 case EVR_DT: | |
1360 return ValueRepresentation_DateTime; | |
1361 | |
1362 case EVR_FL: | |
1363 return ValueRepresentation_FloatingPointSingle; | |
1364 | |
1365 case EVR_FD: | |
1366 return ValueRepresentation_FloatingPointDouble; | |
1367 | |
1368 case EVR_IS: | |
1369 return ValueRepresentation_IntegerString; | |
1370 | |
1371 case EVR_LO: | |
1372 return ValueRepresentation_LongString; | |
1373 | |
1374 case EVR_LT: | |
1375 return ValueRepresentation_LongText; | |
1376 | |
1377 case EVR_OB: | |
1378 return ValueRepresentation_OtherByte; | |
1379 | |
1380 #if DCMTK_VERSION_NUMBER >= 361 | |
1381 case EVR_OD: | |
1382 return ValueRepresentation_OtherDouble; | |
1383 #endif | |
1384 | |
1385 case EVR_OF: | |
1386 return ValueRepresentation_OtherFloat; | |
1387 | |
1388 #if DCMTK_VERSION_NUMBER >= 362 | |
1389 case EVR_OL: | |
1390 return ValueRepresentation_OtherLong; | |
1391 #endif | |
1392 | |
1393 case EVR_OW: | |
1394 return ValueRepresentation_OtherWord; | |
1395 | |
1396 case EVR_PN: | |
1397 return ValueRepresentation_PersonName; | |
1398 | |
1399 case EVR_SH: | |
1400 return ValueRepresentation_ShortString; | |
1401 | |
1402 case EVR_SL: | |
1403 return ValueRepresentation_SignedLong; | |
1404 | |
1405 case EVR_SQ: | |
1406 return ValueRepresentation_Sequence; | |
1407 | |
1408 case EVR_SS: | |
1409 return ValueRepresentation_SignedShort; | |
1410 | |
1411 case EVR_ST: | |
1412 return ValueRepresentation_ShortText; | |
1413 | |
1414 case EVR_TM: | |
1415 return ValueRepresentation_Time; | |
1416 | |
1417 #if DCMTK_VERSION_NUMBER >= 361 | |
1418 case EVR_UC: | |
1419 return ValueRepresentation_UnlimitedCharacters; | |
1420 #endif | |
1421 | |
1422 case EVR_UI: | |
1423 return ValueRepresentation_UniqueIdentifier; | |
1424 | |
1425 case EVR_UL: | |
1426 return ValueRepresentation_UnsignedLong; | |
1427 | |
1428 case EVR_UN: | |
1429 return ValueRepresentation_Unknown; | |
1430 | |
1431 #if DCMTK_VERSION_NUMBER >= 361 | |
1432 case EVR_UR: | |
1433 return ValueRepresentation_UniversalResource; | |
1434 #endif | |
1435 | |
1436 case EVR_US: | |
1437 return ValueRepresentation_UnsignedShort; | |
1438 | |
1439 case EVR_UT: | |
1440 return ValueRepresentation_UnlimitedText; | |
1441 | |
1442 default: | |
1443 return ValueRepresentation_NotSupported; | |
1444 } | |
1445 } | |
1446 | |
1447 | |
1448 DcmElement* FromDcmtkBridge::CreateElementForTag(const DicomTag& tag, | |
1449 const std::string& privateCreator) | |
1450 { | |
1451 if (tag.IsPrivate() && | |
1452 privateCreator.empty()) | |
1453 { | |
1454 // This solves issue 140 (Modifying private tags with REST API | |
1455 // changes VR from LO to UN) | |
1456 // https://bitbucket.org/sjodogne/orthanc/issues/140 | |
1457 LOG(WARNING) << "Private creator should not be empty while creating a private tag: " << tag.Format(); | |
1458 } | |
1459 | |
1460 #if DCMTK_VERSION_NUMBER >= 362 | |
1461 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
1462 if (tag.IsPrivate()) | |
1463 { | |
1464 return DcmItem::newDicomElement(key, privateCreator.c_str()); | |
1465 } | |
1466 else | |
1467 { | |
1468 return DcmItem::newDicomElement(key, NULL); | |
1469 } | |
1470 | |
1471 #else | |
1472 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
1473 if (tag.IsPrivate()) | |
1474 { | |
1475 // https://forum.dcmtk.org/viewtopic.php?t=4527 | |
1476 LOG(WARNING) << "You are using DCMTK <= 3.6.1: All the private tags " | |
1477 "are considered as having a binary value representation"; | |
1478 key.setPrivateCreator(privateCreator.c_str()); | |
1479 return new DcmOtherByteOtherWord(key); | |
1480 } | |
1481 else | |
1482 { | |
1483 return newDicomElement(key); | |
1484 } | |
1485 #endif | |
1486 } | |
1487 | |
1488 | |
1489 | |
1490 void FromDcmtkBridge::FillElementWithString(DcmElement& element, | |
1491 const std::string& utf8Value, | |
1492 bool decodeDataUriScheme, | |
1493 Encoding dicomEncoding) | |
1494 { | |
1495 std::string binary; | |
1496 const std::string* decoded = &utf8Value; | |
1497 | |
1498 if (decodeDataUriScheme && | |
1499 boost::starts_with(utf8Value, URI_SCHEME_PREFIX_BINARY)) | |
1500 { | |
1501 std::string mime; | |
1502 if (!Toolbox::DecodeDataUriScheme(mime, binary, utf8Value)) | |
1503 { | |
1504 throw OrthancException(ErrorCode_BadFileFormat); | |
1505 } | |
1506 | |
1507 decoded = &binary; | |
1508 } | |
1509 else if (dicomEncoding != Encoding_Utf8) | |
1510 { | |
1511 binary = Toolbox::ConvertFromUtf8(utf8Value, dicomEncoding); | |
1512 decoded = &binary; | |
1513 } | |
1514 | |
1515 if (IsBinaryTag(element.getTag())) | |
1516 { | |
1517 bool ok; | |
1518 | |
1519 switch (element.getTag().getEVR()) | |
1520 { | |
1521 case EVR_OW: | |
1522 if (decoded->size() % sizeof(Uint16) != 0) | |
1523 { | |
1524 LOG(ERROR) << "A tag with OW VR must have an even number of bytes"; | |
1525 ok = false; | |
1526 } | |
1527 else | |
1528 { | |
1529 ok = element.putUint16Array((const Uint16*) decoded->c_str(), decoded->size() / sizeof(Uint16)).good(); | |
1530 } | |
1531 | |
1532 break; | |
1533 | |
1534 default: | |
1535 ok = element.putUint8Array((const Uint8*) decoded->c_str(), decoded->size()).good(); | |
1536 break; | |
1537 } | |
1538 | |
1539 if (ok) | |
1540 { | |
1541 return; | |
1542 } | |
1543 else | |
1544 { | |
1545 throw OrthancException(ErrorCode_InternalError); | |
1546 } | |
1547 } | |
1548 | |
1549 bool ok = false; | |
1550 | |
1551 try | |
1552 { | |
1553 switch (element.getTag().getEVR()) | |
1554 { | |
1555 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
1556 | |
1557 /** | |
1558 * TODO. | |
1559 **/ | |
1560 | |
1561 case EVR_OB: // other byte | |
1562 case EVR_OW: // other word | |
1563 case EVR_AT: // attribute tag | |
1564 throw OrthancException(ErrorCode_NotImplemented); | |
1565 | |
1566 case EVR_UN: // unknown value representation | |
1567 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
1568 | |
1569 | |
1570 /** | |
1571 * String types. | |
1572 **/ | |
1573 | |
1574 case EVR_DS: // decimal string | |
1575 case EVR_IS: // integer string | |
1576 case EVR_AS: // age string | |
1577 case EVR_DA: // date string | |
1578 case EVR_DT: // date time string | |
1579 case EVR_TM: // time string | |
1580 case EVR_AE: // application entity title | |
1581 case EVR_CS: // code string | |
1582 case EVR_SH: // short string | |
1583 case EVR_LO: // long string | |
1584 case EVR_ST: // short text | |
1585 case EVR_LT: // long text | |
1586 case EVR_UT: // unlimited text | |
1587 case EVR_PN: // person name | |
1588 case EVR_UI: // unique identifier | |
1589 #if DCMTK_VERSION_NUMBER >= 361 | |
1590 case EVR_UC: // unlimited characters | |
1591 case EVR_UR: // URI/URL | |
1592 #endif | |
1593 { | |
1594 ok = element.putString(decoded->c_str()).good(); | |
1595 break; | |
1596 } | |
1597 | |
1598 | |
1599 /** | |
1600 * Numerical types | |
1601 **/ | |
1602 | |
1603 case EVR_SL: // signed long | |
1604 { | |
1605 ok = element.putSint32(boost::lexical_cast<Sint32>(*decoded)).good(); | |
1606 break; | |
1607 } | |
1608 | |
1609 case EVR_SS: // signed short | |
1610 { | |
1611 ok = element.putSint16(boost::lexical_cast<Sint16>(*decoded)).good(); | |
1612 break; | |
1613 } | |
1614 | |
1615 case EVR_UL: // unsigned long | |
1616 #if DCMTK_VERSION_NUMBER >= 362 | |
1617 case EVR_OL: // other long (requires byte-swapping) | |
1618 #endif | |
1619 { | |
1620 ok = element.putUint32(boost::lexical_cast<Uint32>(*decoded)).good(); | |
1621 break; | |
1622 } | |
1623 | |
1624 case EVR_US: // unsigned short | |
1625 { | |
1626 ok = element.putUint16(boost::lexical_cast<Uint16>(*decoded)).good(); | |
1627 break; | |
1628 } | |
1629 | |
1630 case EVR_FL: // float single-precision | |
1631 case EVR_OF: // other float (requires byte swapping) | |
1632 { | |
1633 ok = element.putFloat32(boost::lexical_cast<float>(*decoded)).good(); | |
1634 break; | |
1635 } | |
1636 | |
1637 case EVR_FD: // float double-precision | |
1638 #if DCMTK_VERSION_NUMBER >= 361 | |
1639 case EVR_OD: // other double (requires byte-swapping) | |
1640 #endif | |
1641 { | |
1642 ok = element.putFloat64(boost::lexical_cast<double>(*decoded)).good(); | |
1643 break; | |
1644 } | |
1645 | |
1646 | |
1647 /** | |
1648 * Sequence types, should never occur at this point. | |
1649 **/ | |
1650 | |
1651 case EVR_SQ: // sequence of items | |
1652 { | |
1653 ok = false; | |
1654 break; | |
1655 } | |
1656 | |
1657 | |
1658 /** | |
1659 * Internal to DCMTK. | |
1660 **/ | |
1661 | |
1662 case EVR_ox: // OB or OW depending on context | |
1663 case EVR_xs: // SS or US depending on context | |
1664 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
1665 case EVR_na: // na="not applicable", for data which has no VR | |
1666 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
1667 case EVR_item: // used internally for items | |
1668 case EVR_metainfo: // used internally for meta info datasets | |
1669 case EVR_dataset: // used internally for datasets | |
1670 case EVR_fileFormat: // used internally for DICOM files | |
1671 case EVR_dicomDir: // used internally for DICOMDIR objects | |
1672 case EVR_dirRecord: // used internally for DICOMDIR records | |
1673 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
1674 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
1675 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
1676 case EVR_PixelData: // used internally for uncompressed pixeld data | |
1677 case EVR_OverlayData: // used internally for overlay data | |
1678 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
1679 default: | |
1680 break; | |
1681 } | |
1682 } | |
1683 catch (boost::bad_lexical_cast&) | |
1684 { | |
1685 ok = false; | |
1686 } | |
1687 | |
1688 if (!ok) | |
1689 { | |
1690 DicomTag tag(element.getTag().getGroup(), element.getTag().getElement()); | |
1691 throw OrthancException(ErrorCode_BadFileFormat, | |
1692 "While creating a DICOM instance, tag (" + tag.Format() + | |
1693 ") has out-of-range value: \"" + (*decoded) + "\""); | |
1694 } | |
1695 } | |
1696 | |
1697 | |
1698 DcmElement* FromDcmtkBridge::FromJson(const DicomTag& tag, | |
1699 const Json::Value& value, | |
1700 bool decodeDataUriScheme, | |
1701 Encoding dicomEncoding, | |
1702 const std::string& privateCreator) | |
1703 { | |
1704 std::unique_ptr<DcmElement> element; | |
1705 | |
1706 switch (value.type()) | |
1707 { | |
1708 case Json::stringValue: | |
1709 element.reset(CreateElementForTag(tag, privateCreator)); | |
1710 FillElementWithString(*element, value.asString(), decodeDataUriScheme, dicomEncoding); | |
1711 break; | |
1712 | |
1713 case Json::nullValue: | |
1714 element.reset(CreateElementForTag(tag, privateCreator)); | |
1715 FillElementWithString(*element, "", decodeDataUriScheme, dicomEncoding); | |
1716 break; | |
1717 | |
1718 case Json::arrayValue: | |
1719 { | |
1720 const char* p = NULL; | |
1721 if (tag.IsPrivate() && | |
1722 !privateCreator.empty()) | |
1723 { | |
1724 p = privateCreator.c_str(); | |
1725 } | |
1726 | |
1727 DcmTag key(tag.GetGroup(), tag.GetElement(), p); | |
1728 if (key.getEVR() != EVR_SQ) | |
1729 { | |
1730 throw OrthancException(ErrorCode_BadParameterType, | |
1731 "Bad Parameter type for tag " + tag.Format()); | |
1732 } | |
1733 | |
1734 DcmSequenceOfItems* sequence = new DcmSequenceOfItems(key); | |
1735 element.reset(sequence); | |
1736 | |
1737 for (Json::Value::ArrayIndex i = 0; i < value.size(); i++) | |
1738 { | |
1739 std::unique_ptr<DcmItem> item(new DcmItem); | |
1740 | |
1741 switch (value[i].type()) | |
1742 { | |
1743 case Json::objectValue: | |
1744 { | |
1745 Json::Value::Members members = value[i].getMemberNames(); | |
1746 for (Json::Value::ArrayIndex j = 0; j < members.size(); j++) | |
1747 { | |
1748 item->insert(FromJson(ParseTag(members[j]), value[i][members[j]], decodeDataUriScheme, dicomEncoding, privateCreator)); | |
1749 } | |
1750 break; | |
1751 } | |
1752 | |
1753 case Json::arrayValue: | |
1754 { | |
1755 // Lua cannot disambiguate between an empty dictionary | |
1756 // and an empty array | |
1757 if (value[i].size() != 0) | |
1758 { | |
1759 throw OrthancException(ErrorCode_BadParameterType); | |
1760 } | |
1761 break; | |
1762 } | |
1763 | |
1764 default: | |
1765 throw OrthancException(ErrorCode_BadParameterType); | |
1766 } | |
1767 | |
1768 sequence->append(item.release()); | |
1769 } | |
1770 | |
1771 break; | |
1772 } | |
1773 | |
1774 default: | |
1775 throw OrthancException(ErrorCode_BadParameterType, "Bad Parameter type for tag " + tag.Format()); | |
1776 } | |
1777 | |
1778 return element.release(); | |
1779 } | |
1780 | |
1781 | |
1782 DcmPixelSequence* FromDcmtkBridge::GetPixelSequence(DcmDataset& dataset) | |
1783 { | |
1784 DcmElement *element = NULL; | |
1785 if (!dataset.findAndGetElement(DCM_PixelData, element).good()) | |
1786 { | |
1787 throw OrthancException(ErrorCode_BadFileFormat); | |
1788 } | |
1789 | |
1790 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
1791 | |
1792 E_TransferSyntax repType; | |
1793 const DcmRepresentationParameter *repParam = NULL; | |
1794 pixelData.getCurrentRepresentationKey(repType, repParam); | |
1795 | |
1796 DcmPixelSequence* pixelSequence = NULL; | |
1797 if (!pixelData.getEncapsulatedRepresentation(repType, repParam, pixelSequence).good()) | |
1798 { | |
1799 return NULL; | |
1800 } | |
1801 else | |
1802 { | |
1803 return pixelSequence; | |
1804 } | |
1805 } | |
1806 | |
1807 | |
1808 Encoding FromDcmtkBridge::ExtractEncoding(const Json::Value& json, | |
1809 Encoding defaultEncoding) | |
1810 { | |
1811 if (json.type() != Json::objectValue) | |
1812 { | |
1813 throw OrthancException(ErrorCode_BadParameterType); | |
1814 } | |
1815 | |
1816 Encoding encoding = defaultEncoding; | |
1817 | |
1818 const Json::Value::Members tags = json.getMemberNames(); | |
1819 | |
1820 // Look for SpecificCharacterSet (0008,0005) in the JSON file | |
1821 for (size_t i = 0; i < tags.size(); i++) | |
1822 { | |
1823 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); | |
1824 if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET) | |
1825 { | |
1826 const Json::Value& value = json[tags[i]]; | |
1827 if (value.type() != Json::stringValue || | |
1828 (value.asString().length() != 0 && | |
1829 !GetDicomEncoding(encoding, value.asCString()))) | |
1830 { | |
1831 throw OrthancException(ErrorCode_BadRequest, | |
1832 "Unknown encoding while creating DICOM from JSON: " + | |
1833 value.toStyledString()); | |
1834 } | |
1835 | |
1836 if (value.asString().length() == 0) | |
1837 { | |
1838 return defaultEncoding; | |
1839 } | |
1840 } | |
1841 } | |
1842 | |
1843 return encoding; | |
1844 } | |
1845 | |
1846 | |
1847 static void SetString(DcmDataset& target, | |
1848 const DcmTag& tag, | |
1849 const std::string& value) | |
1850 { | |
1851 if (!target.putAndInsertString(tag, value.c_str()).good()) | |
1852 { | |
1853 throw OrthancException(ErrorCode_InternalError); | |
1854 } | |
1855 } | |
1856 | |
1857 | |
1858 DcmDataset* FromDcmtkBridge::FromJson(const Json::Value& json, // Encoded using UTF-8 | |
1859 bool generateIdentifiers, | |
1860 bool decodeDataUriScheme, | |
1861 Encoding defaultEncoding, | |
1862 const std::string& privateCreator) | |
1863 { | |
1864 std::unique_ptr<DcmDataset> result(new DcmDataset); | |
1865 Encoding encoding = ExtractEncoding(json, defaultEncoding); | |
1866 | |
1867 SetString(*result, DCM_SpecificCharacterSet, GetDicomSpecificCharacterSet(encoding)); | |
1868 | |
1869 const Json::Value::Members tags = json.getMemberNames(); | |
1870 | |
1871 bool hasPatientId = false; | |
1872 bool hasStudyInstanceUid = false; | |
1873 bool hasSeriesInstanceUid = false; | |
1874 bool hasSopInstanceUid = false; | |
1875 | |
1876 for (size_t i = 0; i < tags.size(); i++) | |
1877 { | |
1878 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); | |
1879 const Json::Value& value = json[tags[i]]; | |
1880 | |
1881 if (tag == DICOM_TAG_PATIENT_ID) | |
1882 { | |
1883 hasPatientId = true; | |
1884 } | |
1885 else if (tag == DICOM_TAG_STUDY_INSTANCE_UID) | |
1886 { | |
1887 hasStudyInstanceUid = true; | |
1888 } | |
1889 else if (tag == DICOM_TAG_SERIES_INSTANCE_UID) | |
1890 { | |
1891 hasSeriesInstanceUid = true; | |
1892 } | |
1893 else if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
1894 { | |
1895 hasSopInstanceUid = true; | |
1896 } | |
1897 | |
1898 if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) | |
1899 { | |
1900 std::unique_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, encoding, privateCreator)); | |
1901 const DcmTagKey& tag = element->getTag(); | |
1902 | |
1903 result->findAndDeleteElement(tag); | |
1904 | |
1905 DcmElement* tmp = element.release(); | |
1906 if (!result->insert(tmp, false, false).good()) | |
1907 { | |
1908 delete tmp; | |
1909 throw OrthancException(ErrorCode_InternalError); | |
1910 } | |
1911 } | |
1912 } | |
1913 | |
1914 if (!hasPatientId && | |
1915 generateIdentifiers) | |
1916 { | |
1917 SetString(*result, DCM_PatientID, GenerateUniqueIdentifier(ResourceType_Patient)); | |
1918 } | |
1919 | |
1920 if (!hasStudyInstanceUid && | |
1921 generateIdentifiers) | |
1922 { | |
1923 SetString(*result, DCM_StudyInstanceUID, GenerateUniqueIdentifier(ResourceType_Study)); | |
1924 } | |
1925 | |
1926 if (!hasSeriesInstanceUid && | |
1927 generateIdentifiers) | |
1928 { | |
1929 SetString(*result, DCM_SeriesInstanceUID, GenerateUniqueIdentifier(ResourceType_Series)); | |
1930 } | |
1931 | |
1932 if (!hasSopInstanceUid && | |
1933 generateIdentifiers) | |
1934 { | |
1935 SetString(*result, DCM_SOPInstanceUID, GenerateUniqueIdentifier(ResourceType_Instance)); | |
1936 } | |
1937 | |
1938 return result.release(); | |
1939 } | |
1940 | |
1941 | |
1942 DcmFileFormat* FromDcmtkBridge::LoadFromMemoryBuffer(const void* buffer, | |
1943 size_t size) | |
1944 { | |
1945 DcmInputBufferStream is; | |
1946 if (size > 0) | |
1947 { | |
1948 is.setBuffer(buffer, size); | |
1949 } | |
1950 is.setEos(); | |
1951 | |
1952 std::unique_ptr<DcmFileFormat> result(new DcmFileFormat); | |
1953 | |
1954 result->transferInit(); | |
1955 | |
1956 /** | |
1957 * New in Orthanc 1.6.0: The "size" is given as an argument to the | |
1958 * "read()" method. This can avoid huge memory consumption if | |
1959 * parsing an invalid DICOM file, which can notably been observed | |
1960 * by executing the integration test "test_upload_compressed" on | |
1961 * valgrind running Orthanc. | |
1962 **/ | |
1963 if (!result->read(is, EXS_Unknown, EGL_noChange, size).good()) | |
1964 { | |
1965 throw OrthancException(ErrorCode_BadFileFormat, | |
1966 "Cannot parse an invalid DICOM file (size: " + | |
1967 boost::lexical_cast<std::string>(size) + " bytes)"); | |
1968 } | |
1969 | |
1970 result->loadAllDataIntoMemory(); | |
1971 result->transferEnd(); | |
1972 | |
1973 return result.release(); | |
1974 } | |
1975 | |
1976 | |
1977 void FromDcmtkBridge::FromJson(DicomMap& target, | |
1978 const Json::Value& source) | |
1979 { | |
1980 if (source.type() != Json::objectValue) | |
1981 { | |
1982 throw OrthancException(ErrorCode_BadFileFormat); | |
1983 } | |
1984 | |
1985 target.Clear(); | |
1986 | |
1987 Json::Value::Members members = source.getMemberNames(); | |
1988 | |
1989 for (size_t i = 0; i < members.size(); i++) | |
1990 { | |
1991 const Json::Value& value = source[members[i]]; | |
1992 | |
1993 if (value.type() != Json::stringValue) | |
1994 { | |
1995 throw OrthancException(ErrorCode_BadFileFormat); | |
1996 } | |
1997 | |
1998 target.SetValue(ParseTag(members[i]), value.asString(), false); | |
1999 } | |
2000 } | |
2001 | |
2002 | |
2003 void FromDcmtkBridge::ChangeStringEncoding(DcmItem& dataset, | |
2004 Encoding source, | |
2005 bool hasSourceCodeExtensions, | |
2006 Encoding target) | |
2007 { | |
2008 // Recursive exploration of a dataset to change the encoding of | |
2009 // each string-like element | |
2010 | |
2011 if (source == target) | |
2012 { | |
2013 return; | |
2014 } | |
2015 | |
2016 for (unsigned long i = 0; i < dataset.card(); i++) | |
2017 { | |
2018 DcmElement* element = dataset.getElement(i); | |
2019 if (element) | |
2020 { | |
2021 if (element->isLeaf()) | |
2022 { | |
2023 char *c = NULL; | |
2024 if (element->isaString() && | |
2025 element->getString(c).good() && | |
2026 c != NULL) | |
2027 { | |
2028 std::string a = Toolbox::ConvertToUtf8(c, source, hasSourceCodeExtensions); | |
2029 std::string b = Toolbox::ConvertFromUtf8(a, target); | |
2030 element->putString(b.c_str()); | |
2031 } | |
2032 } | |
2033 else | |
2034 { | |
2035 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
2036 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
2037 // etc. are not." The following dynamic_cast is thus OK. | |
2038 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(*element); | |
2039 | |
2040 for (unsigned long j = 0; j < sequence.card(); j++) | |
2041 { | |
2042 ChangeStringEncoding(*sequence.getItem(j), source, hasSourceCodeExtensions, target); | |
2043 } | |
2044 } | |
2045 } | |
2046 } | |
2047 } | |
2048 | |
2049 | |
2050 #if ORTHANC_ENABLE_LUA == 1 | |
2051 void FromDcmtkBridge::ExecuteToDicom(DicomMap& target, | |
2052 LuaFunctionCall& call) | |
2053 { | |
2054 Json::Value output; | |
2055 call.ExecuteToJson(output, true /* keep strings */); | |
2056 | |
2057 target.Clear(); | |
2058 | |
2059 if (output.type() == Json::arrayValue && | |
2060 output.size() == 0) | |
2061 { | |
2062 // This case happens for empty tables | |
2063 return; | |
2064 } | |
2065 | |
2066 if (output.type() != Json::objectValue) | |
2067 { | |
2068 throw OrthancException(ErrorCode_LuaBadOutput, | |
2069 "Lua: The script must return a table"); | |
2070 } | |
2071 | |
2072 Json::Value::Members members = output.getMemberNames(); | |
2073 | |
2074 for (size_t i = 0; i < members.size(); i++) | |
2075 { | |
2076 if (output[members[i]].type() != Json::stringValue) | |
2077 { | |
2078 throw OrthancException(ErrorCode_LuaBadOutput, | |
2079 "Lua: The script must return a table " | |
2080 "mapping names of DICOM tags to strings"); | |
2081 } | |
2082 | |
2083 DicomTag tag(ParseTag(members[i])); | |
2084 target.SetValue(tag, output[members[i]].asString(), false); | |
2085 } | |
2086 } | |
2087 #endif | |
2088 | |
2089 | |
2090 void FromDcmtkBridge::ExtractDicomSummary(DicomMap& target, | |
2091 DcmItem& dataset, | |
2092 const std::set<DicomTag>& ignoreTagLength) | |
2093 { | |
2094 ExtractDicomSummary(target, dataset, | |
2095 ORTHANC_MAXIMUM_TAG_LENGTH, | |
2096 GetDefaultDicomEncoding(), ignoreTagLength); | |
2097 } | |
2098 | |
2099 | |
2100 void FromDcmtkBridge::ExtractDicomAsJson(Json::Value& target, | |
2101 DcmDataset& dataset, | |
2102 const std::set<DicomTag>& ignoreTagLength) | |
2103 { | |
2104 ExtractDicomAsJson(target, dataset, | |
2105 DicomToJsonFormat_Full, | |
2106 DicomToJsonFlags_Default, | |
2107 ORTHANC_MAXIMUM_TAG_LENGTH, | |
2108 GetDefaultDicomEncoding(), | |
2109 ignoreTagLength); | |
2110 } | |
2111 | |
2112 | |
2113 void FromDcmtkBridge::InitializeCodecs() | |
2114 { | |
2115 #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1 | |
2116 LOG(INFO) << "Registering JPEG Lossless codecs in DCMTK"; | |
2117 DJLSDecoderRegistration::registerCodecs(); | |
2118 # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
2119 DJLSEncoderRegistration::registerCodecs(); | |
2120 # endif | |
2121 #endif | |
2122 | |
2123 #if ORTHANC_ENABLE_DCMTK_JPEG == 1 | |
2124 LOG(INFO) << "Registering JPEG codecs in DCMTK"; | |
2125 DJDecoderRegistration::registerCodecs(); | |
2126 # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
2127 DJEncoderRegistration::registerCodecs(); | |
2128 # endif | |
2129 #endif | |
2130 | |
2131 LOG(INFO) << "Registering RLE codecs in DCMTK"; | |
2132 DcmRLEDecoderRegistration::registerCodecs(); | |
2133 #if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
2134 DcmRLEEncoderRegistration::registerCodecs(); | |
2135 #endif | |
2136 } | |
2137 | |
2138 | |
2139 void FromDcmtkBridge::FinalizeCodecs() | |
2140 { | |
2141 #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1 | |
2142 // Unregister JPEG-LS codecs | |
2143 DJLSDecoderRegistration::cleanup(); | |
2144 # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
2145 DJLSEncoderRegistration::cleanup(); | |
2146 # endif | |
2147 #endif | |
2148 | |
2149 #if ORTHANC_ENABLE_DCMTK_JPEG == 1 | |
2150 // Unregister JPEG codecs | |
2151 DJDecoderRegistration::cleanup(); | |
2152 # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
2153 DJEncoderRegistration::cleanup(); | |
2154 # endif | |
2155 #endif | |
2156 | |
2157 DcmRLEDecoderRegistration::cleanup(); | |
2158 #if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 | |
2159 DcmRLEEncoderRegistration::cleanup(); | |
2160 #endif | |
2161 } | |
2162 | |
2163 | |
2164 | |
2165 // Forward declaration | |
2166 static void ApplyVisitorToElement(DcmElement& element, | |
2167 ITagVisitor& visitor, | |
2168 const std::vector<DicomTag>& parentTags, | |
2169 const std::vector<size_t>& parentIndexes, | |
2170 Encoding encoding, | |
2171 bool hasCodeExtensions); | |
2172 | |
2173 static void ApplyVisitorToDataset(DcmItem& dataset, | |
2174 ITagVisitor& visitor, | |
2175 const std::vector<DicomTag>& parentTags, | |
2176 const std::vector<size_t>& parentIndexes, | |
2177 Encoding encoding, | |
2178 bool hasCodeExtensions) | |
2179 { | |
2180 assert(parentTags.size() == parentIndexes.size()); | |
2181 | |
2182 for (unsigned long i = 0; i < dataset.card(); i++) | |
2183 { | |
2184 DcmElement* element = dataset.getElement(i); | |
2185 if (element == NULL) | |
2186 { | |
2187 throw OrthancException(ErrorCode_InternalError); | |
2188 } | |
2189 else | |
2190 { | |
2191 ApplyVisitorToElement(*element, visitor, parentTags, parentIndexes, encoding, hasCodeExtensions); | |
2192 } | |
2193 } | |
2194 } | |
2195 | |
2196 | |
2197 static void ApplyVisitorToLeaf(DcmElement& element, | |
2198 ITagVisitor& visitor, | |
2199 const std::vector<DicomTag>& parentTags, | |
2200 const std::vector<size_t>& parentIndexes, | |
2201 const DicomTag& tag, | |
2202 Encoding encoding, | |
2203 bool hasCodeExtensions) | |
2204 { | |
2205 // TODO - Merge this function, that is more recent, with ConvertLeafElement() | |
2206 | |
2207 assert(element.isLeaf()); | |
2208 | |
2209 DcmEVR evr = element.getTag().getEVR(); | |
2210 | |
2211 | |
2212 /** | |
2213 * Fix the EVR for types internal to DCMTK | |
2214 **/ | |
2215 | |
2216 if (evr == EVR_ox) // OB or OW depending on context | |
2217 { | |
2218 evr = EVR_OB; | |
2219 } | |
2220 | |
2221 if (evr == EVR_UNKNOWN || // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
2222 evr == EVR_UNKNOWN2B) // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
2223 { | |
2224 evr = EVR_UN; | |
2225 } | |
2226 | |
2227 const ValueRepresentation vr = FromDcmtkBridge::Convert(evr); | |
2228 | |
2229 | |
2230 /** | |
2231 * Deal with binary data (including PixelData). | |
2232 **/ | |
2233 | |
2234 if (evr == EVR_OB || // other byte | |
2235 evr == EVR_OW || // other word | |
2236 evr == EVR_UN) // unknown value representation | |
2237 { | |
2238 Uint16* data16 = NULL; | |
2239 Uint8* data = NULL; | |
2240 | |
2241 if (evr == EVR_OW && | |
2242 element.getUint16Array(data16) == EC_Normal) | |
2243 { | |
2244 visitor.VisitBinary(parentTags, parentIndexes, tag, vr, data16, element.getLength()); | |
2245 } | |
2246 else if (evr != EVR_OW && | |
2247 element.getUint8Array(data) == EC_Normal) | |
2248 { | |
2249 visitor.VisitBinary(parentTags, parentIndexes, tag, vr, data, element.getLength()); | |
2250 } | |
2251 else | |
2252 { | |
2253 visitor.VisitNotSupported(parentTags, parentIndexes, tag, vr); | |
2254 } | |
2255 | |
2256 return; // We're done | |
2257 } | |
2258 | |
2259 | |
2260 /** | |
2261 * Deal with plain strings (and convert them to UTF-8) | |
2262 **/ | |
2263 | |
2264 char *c = NULL; | |
2265 if (element.isaString() && | |
2266 element.getString(c).good()) | |
2267 { | |
2268 std::string utf8; | |
2269 | |
2270 if (c != NULL) // This case corresponds to the empty string | |
2271 { | |
2272 if (element.getTag() == DCM_SpecificCharacterSet) | |
2273 { | |
2274 utf8.assign(c); | |
2275 } | |
2276 else | |
2277 { | |
2278 std::string s(c); | |
2279 utf8 = Toolbox::ConvertToUtf8(s, encoding, hasCodeExtensions); | |
2280 } | |
2281 } | |
2282 | |
2283 std::string newValue; | |
2284 ITagVisitor::Action action = visitor.VisitString | |
2285 (newValue, parentTags, parentIndexes, tag, vr, utf8); | |
2286 | |
2287 switch (action) | |
2288 { | |
2289 case ITagVisitor::Action_None: | |
2290 break; | |
2291 | |
2292 case ITagVisitor::Action_Replace: | |
2293 { | |
2294 std::string s = Toolbox::ConvertFromUtf8(newValue, encoding); | |
2295 if (element.putString(s.c_str()) != EC_Normal) | |
2296 { | |
2297 throw OrthancException(ErrorCode_InternalError, | |
2298 "Cannot replace value of tag: " + tag.Format()); | |
2299 } | |
2300 | |
2301 break; | |
2302 } | |
2303 | |
2304 default: | |
2305 throw OrthancException(ErrorCode_InternalError); | |
2306 } | |
2307 | |
2308 return; // We're done | |
2309 } | |
2310 | |
2311 | |
2312 try | |
2313 { | |
2314 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
2315 switch (evr) | |
2316 { | |
2317 | |
2318 /** | |
2319 * Plain string values. | |
2320 **/ | |
2321 | |
2322 case EVR_DS: // decimal string | |
2323 case EVR_IS: // integer string | |
2324 case EVR_AS: // age string | |
2325 case EVR_DA: // date string | |
2326 case EVR_DT: // date time string | |
2327 case EVR_TM: // time string | |
2328 case EVR_AE: // application entity title | |
2329 case EVR_CS: // code string | |
2330 case EVR_SH: // short string | |
2331 case EVR_LO: // long string | |
2332 case EVR_ST: // short text | |
2333 case EVR_LT: // long text | |
2334 case EVR_UT: // unlimited text | |
2335 case EVR_PN: // person name | |
2336 case EVR_UI: // unique identifier | |
2337 { | |
2338 Uint8* data = NULL; | |
2339 | |
2340 if (element.getUint8Array(data) == EC_Normal) | |
2341 { | |
2342 const Uint32 length = element.getLength(); | |
2343 Uint32 l = 0; | |
2344 while (l < length && | |
2345 data[l] != 0) | |
2346 { | |
2347 l++; | |
2348 } | |
2349 | |
2350 if (l == length) | |
2351 { | |
2352 // Not a null-terminated plain string | |
2353 visitor.VisitNotSupported(parentTags, parentIndexes, tag, vr); | |
2354 } | |
2355 else | |
2356 { | |
2357 std::string ignored; | |
2358 std::string s(reinterpret_cast<const char*>(data), l); | |
2359 ITagVisitor::Action action = visitor.VisitString | |
2360 (ignored, parentTags, parentIndexes, tag, vr, | |
2361 Toolbox::ConvertToUtf8(s, encoding, hasCodeExtensions)); | |
2362 | |
2363 if (action != ITagVisitor::Action_None) | |
2364 { | |
2365 LOG(WARNING) << "Cannot replace this string tag: " | |
2366 << FromDcmtkBridge::GetTagName(element) | |
2367 << " (" << tag.Format() << ")"; | |
2368 } | |
2369 } | |
2370 } | |
2371 else | |
2372 { | |
2373 visitor.VisitNotSupported(parentTags, parentIndexes, tag, vr); | |
2374 } | |
2375 | |
2376 return; | |
2377 } | |
2378 | |
2379 /** | |
2380 * Numeric types | |
2381 **/ | |
2382 | |
2383 case EVR_SL: // signed long | |
2384 { | |
2385 DcmSignedLong& content = dynamic_cast<DcmSignedLong&>(element); | |
2386 | |
2387 std::vector<int64_t> values; | |
2388 values.reserve(content.getVM()); | |
2389 | |
2390 for (unsigned long i = 0; i < content.getVM(); i++) | |
2391 { | |
2392 Sint32 f; | |
2393 if (content.getSint32(f, i).good()) | |
2394 { | |
2395 values.push_back(f); | |
2396 } | |
2397 } | |
2398 | |
2399 visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); | |
2400 break; | |
2401 } | |
2402 | |
2403 case EVR_SS: // signed short | |
2404 { | |
2405 DcmSignedShort& content = dynamic_cast<DcmSignedShort&>(element); | |
2406 | |
2407 std::vector<int64_t> values; | |
2408 values.reserve(content.getVM()); | |
2409 | |
2410 for (unsigned long i = 0; i < content.getVM(); i++) | |
2411 { | |
2412 Sint16 f; | |
2413 if (content.getSint16(f, i).good()) | |
2414 { | |
2415 values.push_back(f); | |
2416 } | |
2417 } | |
2418 | |
2419 visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); | |
2420 break; | |
2421 } | |
2422 | |
2423 case EVR_UL: // unsigned long | |
2424 #if DCMTK_VERSION_NUMBER >= 362 | |
2425 case EVR_OL: | |
2426 #endif | |
2427 { | |
2428 DcmUnsignedLong& content = dynamic_cast<DcmUnsignedLong&>(element); | |
2429 | |
2430 std::vector<int64_t> values; | |
2431 values.reserve(content.getVM()); | |
2432 | |
2433 for (unsigned long i = 0; i < content.getVM(); i++) | |
2434 { | |
2435 Uint32 f; | |
2436 if (content.getUint32(f, i).good()) | |
2437 { | |
2438 values.push_back(f); | |
2439 } | |
2440 } | |
2441 | |
2442 visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); | |
2443 break; | |
2444 } | |
2445 | |
2446 case EVR_US: // unsigned short | |
2447 { | |
2448 DcmUnsignedShort& content = dynamic_cast<DcmUnsignedShort&>(element); | |
2449 | |
2450 std::vector<int64_t> values; | |
2451 values.reserve(content.getVM()); | |
2452 | |
2453 for (unsigned long i = 0; i < content.getVM(); i++) | |
2454 { | |
2455 Uint16 f; | |
2456 if (content.getUint16(f, i).good()) | |
2457 { | |
2458 values.push_back(f); | |
2459 } | |
2460 } | |
2461 | |
2462 visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); | |
2463 break; | |
2464 } | |
2465 | |
2466 case EVR_FL: // float single-precision | |
2467 case EVR_OF: | |
2468 { | |
2469 DcmFloatingPointSingle& content = dynamic_cast<DcmFloatingPointSingle&>(element); | |
2470 | |
2471 std::vector<double> values; | |
2472 values.reserve(content.getVM()); | |
2473 | |
2474 for (unsigned long i = 0; i < content.getVM(); i++) | |
2475 { | |
2476 Float32 f; | |
2477 if (content.getFloat32(f, i).good()) | |
2478 { | |
2479 values.push_back(f); | |
2480 } | |
2481 } | |
2482 | |
2483 visitor.VisitDoubles(parentTags, parentIndexes, tag, vr, values); | |
2484 break; | |
2485 } | |
2486 | |
2487 case EVR_FD: // float double-precision | |
2488 #if DCMTK_VERSION_NUMBER >= 361 | |
2489 case EVR_OD: | |
2490 #endif | |
2491 { | |
2492 DcmFloatingPointDouble& content = dynamic_cast<DcmFloatingPointDouble&>(element); | |
2493 | |
2494 std::vector<double> values; | |
2495 values.reserve(content.getVM()); | |
2496 | |
2497 for (unsigned long i = 0; i < content.getVM(); i++) | |
2498 { | |
2499 Float64 f; | |
2500 if (content.getFloat64(f, i).good()) | |
2501 { | |
2502 values.push_back(f); | |
2503 } | |
2504 } | |
2505 | |
2506 visitor.VisitDoubles(parentTags, parentIndexes, tag, vr, values); | |
2507 break; | |
2508 } | |
2509 | |
2510 | |
2511 /** | |
2512 * Attribute tag. | |
2513 **/ | |
2514 | |
2515 case EVR_AT: | |
2516 { | |
2517 DcmAttributeTag& content = dynamic_cast<DcmAttributeTag&>(element); | |
2518 | |
2519 std::vector<DicomTag> values; | |
2520 values.reserve(content.getVM()); | |
2521 | |
2522 for (unsigned long i = 0; i < content.getVM(); i++) | |
2523 { | |
2524 DcmTagKey f; | |
2525 if (content.getTagVal(f, i).good()) | |
2526 { | |
2527 DicomTag t(f.getGroup(), f.getElement()); | |
2528 values.push_back(t); | |
2529 } | |
2530 } | |
2531 | |
2532 assert(vr == ValueRepresentation_AttributeTag); | |
2533 visitor.VisitAttributes(parentTags, parentIndexes, tag, values); | |
2534 break; | |
2535 } | |
2536 | |
2537 | |
2538 /** | |
2539 * Sequence types, should never occur at this point because of | |
2540 * "element.isLeaf()". | |
2541 **/ | |
2542 | |
2543 case EVR_SQ: // sequence of items | |
2544 { | |
2545 return; | |
2546 } | |
2547 | |
2548 | |
2549 /** | |
2550 * Internal to DCMTK. | |
2551 **/ | |
2552 | |
2553 case EVR_xs: // SS or US depending on context | |
2554 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
2555 case EVR_na: // na="not applicable", for data which has no VR | |
2556 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
2557 case EVR_item: // used internally for items | |
2558 case EVR_metainfo: // used internally for meta info datasets | |
2559 case EVR_dataset: // used internally for datasets | |
2560 case EVR_fileFormat: // used internally for DICOM files | |
2561 case EVR_dicomDir: // used internally for DICOMDIR objects | |
2562 case EVR_dirRecord: // used internally for DICOMDIR records | |
2563 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
2564 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
2565 case EVR_PixelData: // used internally for uncompressed pixeld data | |
2566 case EVR_OverlayData: // used internally for overlay data | |
2567 { | |
2568 visitor.VisitNotSupported(parentTags, parentIndexes, tag, vr); | |
2569 return; | |
2570 } | |
2571 | |
2572 | |
2573 /** | |
2574 * Default case. | |
2575 **/ | |
2576 | |
2577 default: | |
2578 return; | |
2579 } | |
2580 } | |
2581 catch (boost::bad_lexical_cast&) | |
2582 { | |
2583 return; | |
2584 } | |
2585 catch (std::bad_cast&) | |
2586 { | |
2587 return; | |
2588 } | |
2589 } | |
2590 | |
2591 | |
2592 static void ApplyVisitorToElement(DcmElement& element, | |
2593 ITagVisitor& visitor, | |
2594 const std::vector<DicomTag>& parentTags, | |
2595 const std::vector<size_t>& parentIndexes, | |
2596 Encoding encoding, | |
2597 bool hasCodeExtensions) | |
2598 { | |
2599 assert(parentTags.size() == parentIndexes.size()); | |
2600 | |
2601 DicomTag tag(FromDcmtkBridge::Convert(element.getTag())); | |
2602 | |
2603 if (element.isLeaf()) | |
2604 { | |
2605 ApplyVisitorToLeaf(element, visitor, parentTags, parentIndexes, tag, encoding, hasCodeExtensions); | |
2606 } | |
2607 else | |
2608 { | |
2609 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
2610 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
2611 // etc. are not." The following dynamic_cast is thus OK. | |
2612 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
2613 | |
2614 if (sequence.card() == 0) | |
2615 { | |
2616 visitor.VisitEmptySequence(parentTags, parentIndexes, tag); | |
2617 } | |
2618 else | |
2619 { | |
2620 std::vector<DicomTag> tags = parentTags; | |
2621 std::vector<size_t> indexes = parentIndexes; | |
2622 tags.push_back(tag); | |
2623 indexes.push_back(0); | |
2624 | |
2625 for (unsigned long i = 0; i < sequence.card(); i++) | |
2626 { | |
2627 indexes.back() = static_cast<size_t>(i); | |
2628 DcmItem* child = sequence.getItem(i); | |
2629 ApplyVisitorToDataset(*child, visitor, tags, indexes, encoding, hasCodeExtensions); | |
2630 } | |
2631 } | |
2632 } | |
2633 } | |
2634 | |
2635 | |
2636 void FromDcmtkBridge::Apply(DcmItem& dataset, | |
2637 ITagVisitor& visitor, | |
2638 Encoding defaultEncoding) | |
2639 { | |
2640 std::vector<DicomTag> parentTags; | |
2641 std::vector<size_t> parentIndexes; | |
2642 bool hasCodeExtensions; | |
2643 Encoding encoding = DetectEncoding(hasCodeExtensions, dataset, defaultEncoding); | |
2644 ApplyVisitorToDataset(dataset, visitor, parentTags, parentIndexes, encoding, hasCodeExtensions); | |
2645 } | |
2646 | |
2647 | |
2648 | |
2649 bool FromDcmtkBridge::LookupOrthancTransferSyntax(DicomTransferSyntax& target, | |
2650 DcmFileFormat& dicom) | |
2651 { | |
2652 if (dicom.getDataset() == NULL) | |
2653 { | |
2654 throw OrthancException(ErrorCode_InternalError); | |
2655 } | |
2656 | |
2657 DcmDataset& dataset = *dicom.getDataset(); | |
2658 | |
2659 E_TransferSyntax xfer = dataset.getCurrentXfer(); | |
2660 if (xfer == EXS_Unknown) | |
2661 { | |
2662 dataset.updateOriginalXfer(); | |
2663 xfer = dataset.getOriginalXfer(); | |
2664 if (xfer == EXS_Unknown) | |
2665 { | |
2666 throw OrthancException(ErrorCode_BadFileFormat, | |
2667 "Cannot determine the transfer syntax of the DICOM instance"); | |
2668 } | |
2669 } | |
2670 | |
2671 return FromDcmtkBridge::LookupOrthancTransferSyntax(target, xfer); | |
2672 } | |
2673 } | |
2674 | |
2675 | |
2676 #include "./FromDcmtkBridge_TransferSyntaxes.impl.h" |