Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 107:3b45473c0a73
replace boost::locale with iconv for debian
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 04 Oct 2012 11:22:20 +0200 |
parents | 332fec038d52 |
children | e759f777cb72 |
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/dcelem.h> | |
41 #include <dcmtk/dcmdata/dcfilefo.h> | |
42 #include <dcmtk/dcmdata/dcistrmb.h> | |
43 #include <dcmtk/dcmdata/dcsequen.h> | |
44 #include <dcmtk/dcmdata/dcvrfd.h> | |
45 #include <dcmtk/dcmdata/dcvrfl.h> | |
46 #include <dcmtk/dcmdata/dcvrsl.h> | |
47 #include <dcmtk/dcmdata/dcvrss.h> | |
48 #include <dcmtk/dcmdata/dcvrul.h> | |
49 #include <dcmtk/dcmdata/dcvrus.h> | |
50 | |
2 | 51 #include <boost/math/special_functions/round.hpp> |
0 | 52 |
62 | 53 namespace Orthanc |
0 | 54 { |
55 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) | |
56 { | |
57 target.Clear(); | |
58 for (unsigned long i = 0; i < dataset.card(); i++) | |
59 { | |
60 DcmElement* element = dataset.getElement(i); | |
61 if (element && element->isLeaf()) | |
62 { | |
63 target.SetValue(element->getTag().getGTag(), | |
64 element->getTag().getETag(), | |
65 ConvertLeafElement(*element)); | |
66 } | |
67 } | |
68 } | |
69 | |
70 | |
71 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
72 { | |
73 return DicomTag(element.getGTag(), element.getETag()); | |
74 } | |
75 | |
76 | |
77 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
78 { | |
79 if (!element.isLeaf()) | |
80 { | |
62 | 81 throw OrthancException("Only applicable to leaf elements"); |
0 | 82 } |
83 | |
84 if (element.isaString()) | |
85 { | |
86 char *c; | |
87 if (element.getString(c).good() && | |
88 c != NULL) | |
89 { | |
90 std::string s(c); | |
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91 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
0 | 92 return new DicomString(utf8); |
93 } | |
94 else | |
95 { | |
96 return new DicomNullValue; | |
97 } | |
98 } | |
99 | |
100 try | |
101 { | |
102 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
103 switch (element.getVR()) | |
104 { | |
105 | |
106 /** | |
107 * TODO. | |
108 **/ | |
109 | |
110 case EVR_DS: // decimal string | |
111 case EVR_IS: // integer string | |
112 case EVR_OB: // other byte | |
113 case EVR_OF: // other float | |
114 case EVR_OW: // other word | |
115 case EVR_AS: // age string | |
116 case EVR_AT: // attribute tag | |
117 case EVR_DA: // date string | |
118 case EVR_DT: // date time string | |
119 case EVR_TM: // time string | |
120 case EVR_UN: // unknown value representation | |
121 return new DicomNullValue(); | |
122 | |
123 | |
124 /** | |
125 * String types, should never happen at this point because of | |
126 * "element.isaString()". | |
127 **/ | |
128 | |
129 case EVR_AE: // application entity title | |
130 case EVR_CS: // code string | |
131 case EVR_SH: // short string | |
132 case EVR_LO: // long string | |
133 case EVR_ST: // short text | |
134 case EVR_LT: // long text | |
135 case EVR_UT: // unlimited text | |
136 case EVR_PN: // person name | |
137 case EVR_UI: // unique identifier | |
138 return new DicomNullValue(); | |
139 | |
140 | |
141 /** | |
142 * Numerical types | |
143 **/ | |
144 | |
145 case EVR_SL: // signed long | |
146 { | |
147 Sint32 f; | |
148 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) | |
149 { | |
150 return new DicomString(boost::lexical_cast<std::string>(f)); | |
151 } | |
152 else | |
153 { | |
154 return new DicomNullValue(); | |
155 } | |
156 } | |
157 | |
158 case EVR_SS: // signed short | |
159 { | |
160 Sint16 f; | |
161 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) | |
162 { | |
163 return new DicomString(boost::lexical_cast<std::string>(f)); | |
164 } | |
165 else | |
166 { | |
167 return new DicomNullValue(); | |
168 } | |
169 } | |
170 | |
171 case EVR_UL: // unsigned long | |
172 { | |
173 Uint32 f; | |
174 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) | |
175 { | |
176 return new DicomString(boost::lexical_cast<std::string>(f)); | |
177 } | |
178 else | |
179 { | |
180 return new DicomNullValue(); | |
181 } | |
182 } | |
183 | |
184 case EVR_US: // unsigned short | |
185 { | |
186 Uint16 f; | |
187 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) | |
188 { | |
189 return new DicomString(boost::lexical_cast<std::string>(f)); | |
190 } | |
191 else | |
192 { | |
193 return new DicomNullValue(); | |
194 } | |
195 } | |
196 | |
197 case EVR_FL: // float single-precision | |
198 { | |
199 Float32 f; | |
200 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) | |
201 { | |
202 return new DicomString(boost::lexical_cast<std::string>(f)); | |
203 } | |
204 else | |
205 { | |
206 return new DicomNullValue(); | |
207 } | |
208 } | |
209 | |
210 case EVR_FD: // float double-precision | |
211 { | |
212 Float64 f; | |
213 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
214 { | |
215 return new DicomString(boost::lexical_cast<std::string>(f)); | |
216 } | |
217 else | |
218 { | |
219 return new DicomNullValue(); | |
220 } | |
221 } | |
222 | |
223 | |
224 /** | |
225 * Sequence types, should never occur at this point because of | |
226 * "element.isLeaf()". | |
227 **/ | |
228 | |
229 case EVR_SQ: // sequence of items | |
230 return new DicomNullValue; | |
231 | |
232 | |
233 /** | |
234 * Internal to DCMTK. | |
235 **/ | |
236 | |
237 case EVR_ox: // OB or OW depending on context | |
238 case EVR_xs: // SS or US depending on context | |
239 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
240 case EVR_na: // na="not applicable", for data which has no VR | |
241 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
242 case EVR_item: // used internally for items | |
243 case EVR_metainfo: // used internally for meta info datasets | |
244 case EVR_dataset: // used internally for datasets | |
245 case EVR_fileFormat: // used internally for DICOM files | |
246 case EVR_dicomDir: // used internally for DICOMDIR objects | |
247 case EVR_dirRecord: // used internally for DICOMDIR records | |
248 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
249 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
250 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
251 case EVR_PixelData: // used internally for uncompressed pixeld data | |
252 case EVR_OverlayData: // used internally for overlay data | |
253 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
254 return new DicomNullValue; | |
255 | |
256 | |
257 /** | |
258 * Default case. | |
259 **/ | |
260 | |
261 default: | |
262 return new DicomNullValue; | |
263 } | |
264 } | |
265 catch (boost::bad_lexical_cast) | |
266 { | |
267 return new DicomNullValue; | |
268 } | |
269 } | |
270 | |
271 | |
272 static void StoreElement(Json::Value& target, | |
273 DcmElement& element, | |
274 unsigned int maxStringLength); | |
275 | |
276 static void StoreItem(Json::Value& target, | |
277 DcmItem& item, | |
278 unsigned int maxStringLength) | |
279 { | |
280 target = Json::Value(Json::objectValue); | |
281 | |
282 for (unsigned long i = 0; i < item.card(); i++) | |
283 { | |
284 DcmElement* element = item.getElement(i); | |
285 StoreElement(target, *element, maxStringLength); | |
286 } | |
287 } | |
288 | |
289 | |
290 static void StoreElement(Json::Value& target, | |
291 DcmElement& element, | |
292 unsigned int maxStringLength) | |
293 { | |
294 assert(target.type() == Json::objectValue); | |
295 | |
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296 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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297 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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298 const std::string formattedTag = tag.Format(); |
0 | 299 |
300 if (element.isLeaf()) | |
301 { | |
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302 Json::Value value(Json::objectValue); |
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303 value["Name"] = tagName; |
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304 |
0 | 305 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
306 if (v->IsNull()) | |
307 { | |
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308 value["Type"] = "Null"; |
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309 value["Value"] = Json::nullValue; |
0 | 310 } |
311 else | |
312 { | |
313 std::string s = v->AsString(); | |
314 if (maxStringLength == 0 || | |
315 s.size() <= maxStringLength) | |
316 { | |
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317 value["Type"] = "String"; |
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318 value["Value"] = s; |
0 | 319 } |
320 else | |
321 { | |
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322 value["Type"] = "TooLong"; |
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323 value["Value"] = Json::nullValue; |
0 | 324 } |
325 } | |
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326 |
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327 target[formattedTag] = value; |
0 | 328 } |
329 else | |
330 { | |
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331 Json::Value children(Json::arrayValue); |
0 | 332 |
333 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
334 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
335 // etc. are not." The following cast is thus OK. | |
336 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
337 | |
338 for (unsigned long i = 0; i < sequence.card(); i++) | |
339 { | |
340 DcmItem* child = sequence.getItem(i); | |
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341 Json::Value& v = children.append(Json::objectValue); |
0 | 342 StoreItem(v, *child, maxStringLength); |
343 } | |
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344 |
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345 target[formattedTag]["Name"] = tagName; |
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346 target[formattedTag]["Type"] = "Sequence"; |
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347 target[formattedTag]["Value"] = children; |
0 | 348 } |
349 } | |
350 | |
351 | |
352 void FromDcmtkBridge::ToJson(Json::Value& root, | |
353 DcmDataset& dataset, | |
354 unsigned int maxStringLength) | |
355 { | |
356 StoreItem(root, dataset, maxStringLength); | |
357 } | |
358 | |
359 | |
360 | |
361 void FromDcmtkBridge::ToJson(Json::Value& target, | |
362 const std::string& path, | |
363 unsigned int maxStringLength) | |
364 { | |
365 DcmFileFormat dicom; | |
366 if (!dicom.loadFile(path.c_str()).good()) | |
367 { | |
62 | 368 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 369 } |
370 else | |
371 { | |
372 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
373 } | |
374 } | |
375 | |
376 | |
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377 static void ExtractPngImagePreview(std::string& result, |
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378 DicomIntegerPixelAccessor& accessor) |
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379 { |
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380 PngWriter w; |
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381 |
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382 int32_t min, max; |
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383 accessor.GetExtremeValues(min, max); |
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384 |
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385 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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386 if (min != max) |
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387 { |
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388 uint8_t* pixel = &image[0]; |
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389 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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390 { |
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391 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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392 { |
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393 int32_t v = accessor.GetValue(x, y); |
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394 *pixel = static_cast<uint8_t>( |
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395 boost::math::lround(static_cast<float>(v - min) / |
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396 static_cast<float>(max - min) * 255.0f)); |
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397 } |
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398 } |
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399 } |
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400 |
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401 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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402 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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403 } |
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404 |
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405 |
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406 template <typename T> |
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407 static void ExtractPngImageTruncate(std::string& result, |
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408 DicomIntegerPixelAccessor& accessor, |
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409 PixelFormat format) |
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410 { |
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411 PngWriter w; |
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412 |
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413 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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414 T* pixel = &image[0]; |
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415 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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416 { |
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417 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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418 { |
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419 int32_t v = accessor.GetValue(x, y); |
73 | 420 if (v < std::numeric_limits<T>::min()) |
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421 *pixel = std::numeric_limits<T>::min(); |
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422 else if (v > std::numeric_limits<T>::max()) |
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423 *pixel = std::numeric_limits<T>::max(); |
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424 else |
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425 *pixel = static_cast<T>(v); |
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426 } |
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427 } |
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428 |
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429 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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430 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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431 } |
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432 |
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433 |
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434 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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435 DcmDataset& dataset, |
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436 unsigned int frame, |
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437 ImageExtractionMode mode) |
0 | 438 { |
439 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
440 | |
441 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
442 | |
443 DicomMap m; | |
444 FromDcmtkBridge::Convert(m, dataset); | |
445 | |
446 DcmElement* e; | |
80 | 447 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
0 | 448 e != NULL) |
449 { | |
450 Uint8* pixData = NULL; | |
451 if (e->getUint8Array(pixData) == EC_Normal) | |
452 { | |
453 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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454 accessor->SetCurrentFrame(frame); |
0 | 455 } |
456 } | |
457 | |
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458 PixelFormat format; |
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459 switch (mode) |
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460 { |
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461 case ImageExtractionMode_Preview: |
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462 case ImageExtractionMode_UInt8: |
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463 format = PixelFormat_Grayscale8; |
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464 break; |
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465 |
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466 case ImageExtractionMode_UInt16: |
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467 format = PixelFormat_Grayscale16; |
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468 break; |
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469 |
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470 default: |
62 | 471 throw OrthancException(ErrorCode_NotImplemented); |
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472 } |
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473 |
0 | 474 if (accessor.get() == NULL || |
475 accessor->GetWidth() == 0 || | |
476 accessor->GetHeight() == 0) | |
477 { | |
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478 PngWriter w; |
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479 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 480 } |
481 else | |
482 { | |
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483 switch (mode) |
0 | 484 { |
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485 case ImageExtractionMode_Preview: |
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486 ExtractPngImagePreview(result, *accessor); |
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487 break; |
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488 |
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489 case ImageExtractionMode_UInt8: |
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490 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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491 break; |
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492 |
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493 case ImageExtractionMode_UInt16: |
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494 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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495 break; |
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496 |
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497 default: |
62 | 498 throw OrthancException(ErrorCode_NotImplemented); |
0 | 499 } |
500 } | |
501 } | |
502 | |
503 | |
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504 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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505 const std::string& dicomContent, |
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506 unsigned int frame, |
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507 ImageExtractionMode mode) |
0 | 508 { |
509 DcmInputBufferStream is; | |
510 if (dicomContent.size() > 0) | |
511 { | |
512 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
513 } | |
514 is.setEos(); | |
515 | |
516 DcmFileFormat dicom; | |
517 if (dicom.read(is).good()) | |
518 { | |
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519 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
0 | 520 } |
521 else | |
522 { | |
62 | 523 throw OrthancException(ErrorCode_BadFileFormat); |
0 | 524 } |
525 } | |
526 | |
527 | |
528 | |
529 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
530 { | |
106 | 531 // Some patches for important tags because of different DICOM |
532 // dictionaries between DCMTK versions | |
533 if (t == DICOM_TAG_PATIENT_NAME) | |
534 return "PatientName"; | |
535 | |
536 if (t == DicomTag(0x0010, 0x0030)) | |
537 return "PatientBirthDate"; | |
538 | |
539 if (t == DicomTag(0x0010, 0x0040)) | |
540 return "PatientSex"; | |
541 | |
542 // End of patches | |
543 | |
0 | 544 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
545 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
546 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
547 | |
548 std::string s("Unknown"); | |
549 if (entry != NULL) | |
550 { | |
551 s = std::string(entry->getTagName()); | |
552 } | |
553 | |
554 dcmDataDict.unlock(); | |
555 return s; | |
556 } | |
557 | |
558 | |
559 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
560 { | |
561 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
562 const DcmDictEntry* entry = dict.findEntry(name); | |
563 | |
564 if (entry == NULL) | |
565 { | |
566 dcmDataDict.unlock(); | |
62 | 567 throw OrthancException("Unknown DICOM tag"); |
0 | 568 } |
569 else | |
570 { | |
571 DcmTagKey key = entry->getKey(); | |
572 DicomTag tag(key.getGroup(), key.getElement()); | |
573 dcmDataDict.unlock(); | |
574 return tag; | |
575 } | |
576 } | |
577 | |
578 | |
579 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
580 { | |
581 for (DicomMap::Map::const_iterator | |
582 it = m.map_.begin(); it != m.map_.end(); it++) | |
583 { | |
584 DicomTag t = it->first; | |
585 std::string s = it->second->AsString(); | |
586 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
587 } | |
588 } | |
589 | |
590 | |
591 void FromDcmtkBridge::ToJson(Json::Value& result, | |
592 const DicomMap& values) | |
593 { | |
594 if (result.type() != Json::objectValue) | |
595 { | |
62 | 596 throw OrthancException(ErrorCode_BadParameterType); |
0 | 597 } |
598 | |
599 result.clear(); | |
600 | |
601 for (DicomMap::Map::const_iterator | |
602 it = values.map_.begin(); it != values.map_.end(); it++) | |
603 { | |
604 result[GetName(it->first)] = it->second->AsString(); | |
605 } | |
606 } | |
607 } |