Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 133:1969ff16457c
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 08 Oct 2012 13:27:49 +0200 |
parents | e759f777cb72 |
children | fe180eae201d |
rev | line source |
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0 | 1 /** |
62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
0 | 3 * Copyright (C) 2012 Medical Physics Department, CHU of Liege, |
4 * Belgium | |
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 * This program is distributed in the hope that it will be useful, but | |
12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
14 * General Public License for more details. | |
15 * | |
16 * You should have received a copy of the GNU General Public License | |
17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
18 **/ | |
19 | |
71 | 20 #ifndef NOMINMAX |
21 #define NOMINMAX | |
22 #endif | |
0 | 23 |
24 #include "FromDcmtkBridge.h" | |
25 | |
26 #include "ToDcmtkBridge.h" | |
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27 #include "../Core/Toolbox.h" |
62 | 28 #include "../Core/OrthancException.h" |
0 | 29 #include "../Core/PngWriter.h" |
30 #include "../Core/DicomFormat/DicomString.h" | |
31 #include "../Core/DicomFormat/DicomNullValue.h" | |
79 | 32 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
0 | 33 |
71 | 34 #include <limits> |
35 | |
0 | 36 #include <boost/lexical_cast.hpp> |
37 | |
38 #include <dcmtk/dcmdata/dcdicent.h> | |
39 #include <dcmtk/dcmdata/dcdict.h> | |
40 #include <dcmtk/dcmdata/dcfilefo.h> | |
41 #include <dcmtk/dcmdata/dcistrmb.h> | |
42 #include <dcmtk/dcmdata/dcvrfd.h> | |
43 #include <dcmtk/dcmdata/dcvrfl.h> | |
44 #include <dcmtk/dcmdata/dcvrsl.h> | |
45 #include <dcmtk/dcmdata/dcvrss.h> | |
46 #include <dcmtk/dcmdata/dcvrul.h> | |
47 #include <dcmtk/dcmdata/dcvrus.h> | |
48 | |
2 | 49 #include <boost/math/special_functions/round.hpp> |
0 | 50 |
62 | 51 namespace Orthanc |
0 | 52 { |
53 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) | |
54 { | |
55 target.Clear(); | |
56 for (unsigned long i = 0; i < dataset.card(); i++) | |
57 { | |
58 DcmElement* element = dataset.getElement(i); | |
59 if (element && element->isLeaf()) | |
60 { | |
61 target.SetValue(element->getTag().getGTag(), | |
62 element->getTag().getETag(), | |
63 ConvertLeafElement(*element)); | |
64 } | |
65 } | |
66 } | |
67 | |
68 | |
69 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
70 { | |
71 return DicomTag(element.getGTag(), element.getETag()); | |
72 } | |
73 | |
74 | |
75 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
76 { | |
77 if (!element.isLeaf()) | |
78 { | |
62 | 79 throw OrthancException("Only applicable to leaf elements"); |
0 | 80 } |
81 | |
82 if (element.isaString()) | |
83 { | |
84 char *c; | |
85 if (element.getString(c).good() && | |
86 c != NULL) | |
87 { | |
88 std::string s(c); | |
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89 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
0 | 90 return new DicomString(utf8); |
91 } | |
92 else | |
93 { | |
94 return new DicomNullValue; | |
95 } | |
96 } | |
97 | |
98 try | |
99 { | |
100 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
101 switch (element.getVR()) | |
102 { | |
103 | |
104 /** | |
105 * TODO. | |
106 **/ | |
107 | |
108 case EVR_DS: // decimal string | |
109 case EVR_IS: // integer string | |
110 case EVR_OB: // other byte | |
111 case EVR_OF: // other float | |
112 case EVR_OW: // other word | |
113 case EVR_AS: // age string | |
114 case EVR_AT: // attribute tag | |
115 case EVR_DA: // date string | |
116 case EVR_DT: // date time string | |
117 case EVR_TM: // time string | |
118 case EVR_UN: // unknown value representation | |
119 return new DicomNullValue(); | |
120 | |
121 | |
122 /** | |
123 * String types, should never happen at this point because of | |
124 * "element.isaString()". | |
125 **/ | |
126 | |
127 case EVR_AE: // application entity title | |
128 case EVR_CS: // code string | |
129 case EVR_SH: // short string | |
130 case EVR_LO: // long string | |
131 case EVR_ST: // short text | |
132 case EVR_LT: // long text | |
133 case EVR_UT: // unlimited text | |
134 case EVR_PN: // person name | |
135 case EVR_UI: // unique identifier | |
136 return new DicomNullValue(); | |
137 | |
138 | |
139 /** | |
140 * Numerical types | |
141 **/ | |
142 | |
143 case EVR_SL: // signed long | |
144 { | |
145 Sint32 f; | |
146 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) | |
147 { | |
148 return new DicomString(boost::lexical_cast<std::string>(f)); | |
149 } | |
150 else | |
151 { | |
152 return new DicomNullValue(); | |
153 } | |
154 } | |
155 | |
156 case EVR_SS: // signed short | |
157 { | |
158 Sint16 f; | |
159 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) | |
160 { | |
161 return new DicomString(boost::lexical_cast<std::string>(f)); | |
162 } | |
163 else | |
164 { | |
165 return new DicomNullValue(); | |
166 } | |
167 } | |
168 | |
169 case EVR_UL: // unsigned long | |
170 { | |
171 Uint32 f; | |
172 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) | |
173 { | |
174 return new DicomString(boost::lexical_cast<std::string>(f)); | |
175 } | |
176 else | |
177 { | |
178 return new DicomNullValue(); | |
179 } | |
180 } | |
181 | |
182 case EVR_US: // unsigned short | |
183 { | |
184 Uint16 f; | |
185 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) | |
186 { | |
187 return new DicomString(boost::lexical_cast<std::string>(f)); | |
188 } | |
189 else | |
190 { | |
191 return new DicomNullValue(); | |
192 } | |
193 } | |
194 | |
195 case EVR_FL: // float single-precision | |
196 { | |
197 Float32 f; | |
198 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) | |
199 { | |
200 return new DicomString(boost::lexical_cast<std::string>(f)); | |
201 } | |
202 else | |
203 { | |
204 return new DicomNullValue(); | |
205 } | |
206 } | |
207 | |
208 case EVR_FD: // float double-precision | |
209 { | |
210 Float64 f; | |
211 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
212 { | |
213 return new DicomString(boost::lexical_cast<std::string>(f)); | |
214 } | |
215 else | |
216 { | |
217 return new DicomNullValue(); | |
218 } | |
219 } | |
220 | |
221 | |
222 /** | |
223 * Sequence types, should never occur at this point because of | |
224 * "element.isLeaf()". | |
225 **/ | |
226 | |
227 case EVR_SQ: // sequence of items | |
228 return new DicomNullValue; | |
229 | |
230 | |
231 /** | |
232 * Internal to DCMTK. | |
233 **/ | |
234 | |
235 case EVR_ox: // OB or OW depending on context | |
236 case EVR_xs: // SS or US depending on context | |
237 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
238 case EVR_na: // na="not applicable", for data which has no VR | |
239 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
240 case EVR_item: // used internally for items | |
241 case EVR_metainfo: // used internally for meta info datasets | |
242 case EVR_dataset: // used internally for datasets | |
243 case EVR_fileFormat: // used internally for DICOM files | |
244 case EVR_dicomDir: // used internally for DICOMDIR objects | |
245 case EVR_dirRecord: // used internally for DICOMDIR records | |
246 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
247 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
248 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
249 case EVR_PixelData: // used internally for uncompressed pixeld data | |
250 case EVR_OverlayData: // used internally for overlay data | |
251 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
252 return new DicomNullValue; | |
253 | |
254 | |
255 /** | |
256 * Default case. | |
257 **/ | |
258 | |
259 default: | |
260 return new DicomNullValue; | |
261 } | |
262 } | |
263 catch (boost::bad_lexical_cast) | |
264 { | |
265 return new DicomNullValue; | |
266 } | |
267 } | |
268 | |
269 | |
270 static void StoreElement(Json::Value& target, | |
271 DcmElement& element, | |
272 unsigned int maxStringLength); | |
273 | |
274 static void StoreItem(Json::Value& target, | |
275 DcmItem& item, | |
276 unsigned int maxStringLength) | |
277 { | |
278 target = Json::Value(Json::objectValue); | |
279 | |
280 for (unsigned long i = 0; i < item.card(); i++) | |
281 { | |
282 DcmElement* element = item.getElement(i); | |
283 StoreElement(target, *element, maxStringLength); | |
284 } | |
285 } | |
286 | |
287 | |
288 static void StoreElement(Json::Value& target, | |
289 DcmElement& element, | |
290 unsigned int maxStringLength) | |
291 { | |
292 assert(target.type() == Json::objectValue); | |
293 | |
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294 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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295 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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296 const std::string formattedTag = tag.Format(); |
0 | 297 |
298 if (element.isLeaf()) | |
299 { | |
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300 Json::Value value(Json::objectValue); |
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301 value["Name"] = tagName; |
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302 |
0 | 303 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
304 if (v->IsNull()) | |
305 { | |
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306 value["Type"] = "Null"; |
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307 value["Value"] = Json::nullValue; |
0 | 308 } |
309 else | |
310 { | |
311 std::string s = v->AsString(); | |
312 if (maxStringLength == 0 || | |
313 s.size() <= maxStringLength) | |
314 { | |
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315 value["Type"] = "String"; |
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316 value["Value"] = s; |
0 | 317 } |
318 else | |
319 { | |
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320 value["Type"] = "TooLong"; |
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321 value["Value"] = Json::nullValue; |
0 | 322 } |
323 } | |
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324 |
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325 target[formattedTag] = value; |
0 | 326 } |
327 else | |
328 { | |
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329 Json::Value children(Json::arrayValue); |
0 | 330 |
331 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
332 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
333 // etc. are not." The following cast is thus OK. | |
334 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
335 | |
336 for (unsigned long i = 0; i < sequence.card(); i++) | |
337 { | |
338 DcmItem* child = sequence.getItem(i); | |
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339 Json::Value& v = children.append(Json::objectValue); |
0 | 340 StoreItem(v, *child, maxStringLength); |
341 } | |
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342 |
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343 target[formattedTag]["Name"] = tagName; |
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344 target[formattedTag]["Type"] = "Sequence"; |
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345 target[formattedTag]["Value"] = children; |
0 | 346 } |
347 } | |
348 | |
349 | |
350 void FromDcmtkBridge::ToJson(Json::Value& root, | |
351 DcmDataset& dataset, | |
352 unsigned int maxStringLength) | |
353 { | |
354 StoreItem(root, dataset, maxStringLength); | |
355 } | |
356 | |
357 | |
358 | |
359 void FromDcmtkBridge::ToJson(Json::Value& target, | |
360 const std::string& path, | |
361 unsigned int maxStringLength) | |
362 { | |
363 DcmFileFormat dicom; | |
364 if (!dicom.loadFile(path.c_str()).good()) | |
365 { | |
62 | 366 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 367 } |
368 else | |
369 { | |
370 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
371 } | |
372 } | |
373 | |
374 | |
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375 static void ExtractPngImagePreview(std::string& result, |
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376 DicomIntegerPixelAccessor& accessor) |
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377 { |
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378 PngWriter w; |
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379 |
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380 int32_t min, max; |
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381 accessor.GetExtremeValues(min, max); |
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382 |
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383 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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384 if (min != max) |
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385 { |
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386 uint8_t* pixel = &image[0]; |
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387 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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388 { |
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389 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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390 { |
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391 int32_t v = accessor.GetValue(x, y); |
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392 *pixel = static_cast<uint8_t>( |
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393 boost::math::lround(static_cast<float>(v - min) / |
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394 static_cast<float>(max - min) * 255.0f)); |
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395 } |
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396 } |
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397 } |
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398 |
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399 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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400 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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401 } |
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402 |
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403 |
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404 template <typename T> |
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405 static void ExtractPngImageTruncate(std::string& result, |
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406 DicomIntegerPixelAccessor& accessor, |
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407 PixelFormat format) |
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408 { |
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409 PngWriter w; |
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410 |
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411 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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412 T* pixel = &image[0]; |
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413 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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414 { |
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415 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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416 { |
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417 int32_t v = accessor.GetValue(x, y); |
73 | 418 if (v < std::numeric_limits<T>::min()) |
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419 *pixel = std::numeric_limits<T>::min(); |
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420 else if (v > std::numeric_limits<T>::max()) |
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421 *pixel = std::numeric_limits<T>::max(); |
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422 else |
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423 *pixel = static_cast<T>(v); |
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424 } |
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425 } |
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426 |
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427 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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428 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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429 } |
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430 |
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431 |
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432 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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433 DcmDataset& dataset, |
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434 unsigned int frame, |
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435 ImageExtractionMode mode) |
0 | 436 { |
437 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
438 | |
439 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
440 | |
441 DicomMap m; | |
442 FromDcmtkBridge::Convert(m, dataset); | |
443 | |
444 DcmElement* e; | |
80 | 445 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
0 | 446 e != NULL) |
447 { | |
448 Uint8* pixData = NULL; | |
449 if (e->getUint8Array(pixData) == EC_Normal) | |
450 { | |
451 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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452 accessor->SetCurrentFrame(frame); |
0 | 453 } |
454 } | |
455 | |
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456 PixelFormat format; |
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457 switch (mode) |
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458 { |
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459 case ImageExtractionMode_Preview: |
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460 case ImageExtractionMode_UInt8: |
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461 format = PixelFormat_Grayscale8; |
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462 break; |
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463 |
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464 case ImageExtractionMode_UInt16: |
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465 format = PixelFormat_Grayscale16; |
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466 break; |
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467 |
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468 default: |
62 | 469 throw OrthancException(ErrorCode_NotImplemented); |
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470 } |
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471 |
0 | 472 if (accessor.get() == NULL || |
473 accessor->GetWidth() == 0 || | |
474 accessor->GetHeight() == 0) | |
475 { | |
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476 PngWriter w; |
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477 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 478 } |
479 else | |
480 { | |
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481 switch (mode) |
0 | 482 { |
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483 case ImageExtractionMode_Preview: |
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484 ExtractPngImagePreview(result, *accessor); |
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485 break; |
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486 |
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487 case ImageExtractionMode_UInt8: |
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488 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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489 break; |
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490 |
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491 case ImageExtractionMode_UInt16: |
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492 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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493 break; |
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494 |
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495 default: |
62 | 496 throw OrthancException(ErrorCode_NotImplemented); |
0 | 497 } |
498 } | |
499 } | |
500 | |
501 | |
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502 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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503 const std::string& dicomContent, |
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504 unsigned int frame, |
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505 ImageExtractionMode mode) |
0 | 506 { |
507 DcmInputBufferStream is; | |
508 if (dicomContent.size() > 0) | |
509 { | |
510 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
511 } | |
512 is.setEos(); | |
513 | |
514 DcmFileFormat dicom; | |
515 if (dicom.read(is).good()) | |
516 { | |
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517 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
0 | 518 } |
519 else | |
520 { | |
62 | 521 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 522 } |
523 } | |
524 | |
525 | |
526 | |
527 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
528 { | |
106 | 529 // Some patches for important tags because of different DICOM |
530 // dictionaries between DCMTK versions | |
531 if (t == DICOM_TAG_PATIENT_NAME) | |
532 return "PatientName"; | |
533 | |
534 if (t == DicomTag(0x0010, 0x0030)) | |
535 return "PatientBirthDate"; | |
536 | |
537 if (t == DicomTag(0x0010, 0x0040)) | |
538 return "PatientSex"; | |
539 | |
540 // End of patches | |
541 | |
0 | 542 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
543 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
544 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
545 | |
546 std::string s("Unknown"); | |
547 if (entry != NULL) | |
548 { | |
549 s = std::string(entry->getTagName()); | |
550 } | |
551 | |
552 dcmDataDict.unlock(); | |
553 return s; | |
554 } | |
555 | |
556 | |
557 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
558 { | |
559 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
560 const DcmDictEntry* entry = dict.findEntry(name); | |
561 | |
562 if (entry == NULL) | |
563 { | |
564 dcmDataDict.unlock(); | |
62 | 565 throw OrthancException("Unknown DICOM tag"); |
0 | 566 } |
567 else | |
568 { | |
569 DcmTagKey key = entry->getKey(); | |
570 DicomTag tag(key.getGroup(), key.getElement()); | |
571 dcmDataDict.unlock(); | |
572 return tag; | |
573 } | |
574 } | |
575 | |
576 | |
577 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
578 { | |
579 for (DicomMap::Map::const_iterator | |
580 it = m.map_.begin(); it != m.map_.end(); it++) | |
581 { | |
582 DicomTag t = it->first; | |
583 std::string s = it->second->AsString(); | |
584 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
585 } | |
586 } | |
587 | |
588 | |
589 void FromDcmtkBridge::ToJson(Json::Value& result, | |
590 const DicomMap& values) | |
591 { | |
592 if (result.type() != Json::objectValue) | |
593 { | |
62 | 594 throw OrthancException(ErrorCode_BadParameterType); |
0 | 595 } |
596 | |
597 result.clear(); | |
598 | |
599 for (DicomMap::Map::const_iterator | |
600 it = values.map_.begin(); it != values.map_.end(); it++) | |
601 { | |
602 result[GetName(it->first)] = it->second->AsString(); | |
603 } | |
604 } | |
605 } |