Mercurial > hg > orthanc
annotate PalantirServer/FromDcmtkBridge.cpp @ 42:ea48f38afe5f
access to raw images
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 03 Sep 2012 11:34:00 +0200 |
parents | c1097a676eca |
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rev | line source |
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0 | 1 /** |
2 * Palantir - A Lightweight, RESTful DICOM Store | |
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 | |
20 | |
21 #include "FromDcmtkBridge.h" | |
22 | |
23 #include "ToDcmtkBridge.h" | |
24 #include "DicomIntegerPixelAccessor.h" | |
25 #include "../Core/PalantirException.h" | |
26 #include "../Core/PngWriter.h" | |
27 #include "../Core/DicomFormat/DicomString.h" | |
28 #include "../Core/DicomFormat/DicomNullValue.h" | |
29 | |
30 #include <boost/locale.hpp> | |
31 #include <boost/lexical_cast.hpp> | |
32 | |
33 #include <dcmtk/dcmdata/dcdicent.h> | |
34 #include <dcmtk/dcmdata/dcdict.h> | |
35 #include <dcmtk/dcmdata/dcelem.h> | |
36 #include <dcmtk/dcmdata/dcfilefo.h> | |
37 #include <dcmtk/dcmdata/dcistrmb.h> | |
38 #include <dcmtk/dcmdata/dcsequen.h> | |
39 #include <dcmtk/dcmdata/dcvrfd.h> | |
40 #include <dcmtk/dcmdata/dcvrfl.h> | |
41 #include <dcmtk/dcmdata/dcvrsl.h> | |
42 #include <dcmtk/dcmdata/dcvrss.h> | |
43 #include <dcmtk/dcmdata/dcvrul.h> | |
44 #include <dcmtk/dcmdata/dcvrus.h> | |
45 | |
2 | 46 #include <boost/math/special_functions/round.hpp> |
0 | 47 |
48 namespace Palantir | |
49 { | |
50 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) | |
51 { | |
52 target.Clear(); | |
53 for (unsigned long i = 0; i < dataset.card(); i++) | |
54 { | |
55 DcmElement* element = dataset.getElement(i); | |
56 if (element && element->isLeaf()) | |
57 { | |
58 target.SetValue(element->getTag().getGTag(), | |
59 element->getTag().getETag(), | |
60 ConvertLeafElement(*element)); | |
61 } | |
62 } | |
63 } | |
64 | |
65 | |
66 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
67 { | |
68 return DicomTag(element.getGTag(), element.getETag()); | |
69 } | |
70 | |
71 | |
72 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
73 { | |
74 if (!element.isLeaf()) | |
75 { | |
76 throw PalantirException("Only applicable to leaf elements"); | |
77 } | |
78 | |
79 if (element.isaString()) | |
80 { | |
81 char *c; | |
82 if (element.getString(c).good() && | |
83 c != NULL) | |
84 { | |
85 std::string s(c); | |
86 std::string utf8; | |
87 try | |
88 { | |
89 utf8 = boost::locale::conv::to_utf<char>(s, "ISO-8859-1"); // TODO Parameter? | |
90 } | |
2 | 91 catch (std::runtime_error&) |
0 | 92 { |
93 // Bad input string or bad encoding | |
94 utf8 = s; | |
95 } | |
96 | |
97 return new DicomString(utf8); | |
98 } | |
99 else | |
100 { | |
101 return new DicomNullValue; | |
102 } | |
103 } | |
104 | |
105 try | |
106 { | |
107 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
108 switch (element.getVR()) | |
109 { | |
110 | |
111 /** | |
112 * TODO. | |
113 **/ | |
114 | |
115 case EVR_DS: // decimal string | |
116 case EVR_IS: // integer string | |
117 case EVR_OB: // other byte | |
118 case EVR_OF: // other float | |
119 case EVR_OW: // other word | |
120 case EVR_AS: // age string | |
121 case EVR_AT: // attribute tag | |
122 case EVR_DA: // date string | |
123 case EVR_DT: // date time string | |
124 case EVR_TM: // time string | |
125 case EVR_UN: // unknown value representation | |
126 return new DicomNullValue(); | |
127 | |
128 | |
129 /** | |
130 * String types, should never happen at this point because of | |
131 * "element.isaString()". | |
132 **/ | |
133 | |
134 case EVR_AE: // application entity title | |
135 case EVR_CS: // code string | |
136 case EVR_SH: // short string | |
137 case EVR_LO: // long string | |
138 case EVR_ST: // short text | |
139 case EVR_LT: // long text | |
140 case EVR_UT: // unlimited text | |
141 case EVR_PN: // person name | |
142 case EVR_UI: // unique identifier | |
143 return new DicomNullValue(); | |
144 | |
145 | |
146 /** | |
147 * Numerical types | |
148 **/ | |
149 | |
150 case EVR_SL: // signed long | |
151 { | |
152 Sint32 f; | |
153 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) | |
154 { | |
155 return new DicomString(boost::lexical_cast<std::string>(f)); | |
156 } | |
157 else | |
158 { | |
159 return new DicomNullValue(); | |
160 } | |
161 } | |
162 | |
163 case EVR_SS: // signed short | |
164 { | |
165 Sint16 f; | |
166 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) | |
167 { | |
168 return new DicomString(boost::lexical_cast<std::string>(f)); | |
169 } | |
170 else | |
171 { | |
172 return new DicomNullValue(); | |
173 } | |
174 } | |
175 | |
176 case EVR_UL: // unsigned long | |
177 { | |
178 Uint32 f; | |
179 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) | |
180 { | |
181 return new DicomString(boost::lexical_cast<std::string>(f)); | |
182 } | |
183 else | |
184 { | |
185 return new DicomNullValue(); | |
186 } | |
187 } | |
188 | |
189 case EVR_US: // unsigned short | |
190 { | |
191 Uint16 f; | |
192 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) | |
193 { | |
194 return new DicomString(boost::lexical_cast<std::string>(f)); | |
195 } | |
196 else | |
197 { | |
198 return new DicomNullValue(); | |
199 } | |
200 } | |
201 | |
202 case EVR_FL: // float single-precision | |
203 { | |
204 Float32 f; | |
205 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) | |
206 { | |
207 return new DicomString(boost::lexical_cast<std::string>(f)); | |
208 } | |
209 else | |
210 { | |
211 return new DicomNullValue(); | |
212 } | |
213 } | |
214 | |
215 case EVR_FD: // float double-precision | |
216 { | |
217 Float64 f; | |
218 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
219 { | |
220 return new DicomString(boost::lexical_cast<std::string>(f)); | |
221 } | |
222 else | |
223 { | |
224 return new DicomNullValue(); | |
225 } | |
226 } | |
227 | |
228 | |
229 /** | |
230 * Sequence types, should never occur at this point because of | |
231 * "element.isLeaf()". | |
232 **/ | |
233 | |
234 case EVR_SQ: // sequence of items | |
235 return new DicomNullValue; | |
236 | |
237 | |
238 /** | |
239 * Internal to DCMTK. | |
240 **/ | |
241 | |
242 case EVR_ox: // OB or OW depending on context | |
243 case EVR_xs: // SS or US depending on context | |
244 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
245 case EVR_na: // na="not applicable", for data which has no VR | |
246 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
247 case EVR_item: // used internally for items | |
248 case EVR_metainfo: // used internally for meta info datasets | |
249 case EVR_dataset: // used internally for datasets | |
250 case EVR_fileFormat: // used internally for DICOM files | |
251 case EVR_dicomDir: // used internally for DICOMDIR objects | |
252 case EVR_dirRecord: // used internally for DICOMDIR records | |
253 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
254 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
255 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
256 case EVR_PixelData: // used internally for uncompressed pixeld data | |
257 case EVR_OverlayData: // used internally for overlay data | |
258 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
259 return new DicomNullValue; | |
260 | |
261 | |
262 /** | |
263 * Default case. | |
264 **/ | |
265 | |
266 default: | |
267 return new DicomNullValue; | |
268 } | |
269 } | |
270 catch (boost::bad_lexical_cast) | |
271 { | |
272 return new DicomNullValue; | |
273 } | |
274 } | |
275 | |
276 | |
277 static void StoreElement(Json::Value& target, | |
278 DcmElement& element, | |
279 unsigned int maxStringLength); | |
280 | |
281 static void StoreItem(Json::Value& target, | |
282 DcmItem& item, | |
283 unsigned int maxStringLength) | |
284 { | |
285 target = Json::Value(Json::objectValue); | |
286 | |
287 for (unsigned long i = 0; i < item.card(); i++) | |
288 { | |
289 DcmElement* element = item.getElement(i); | |
290 StoreElement(target, *element, maxStringLength); | |
291 } | |
292 } | |
293 | |
294 | |
295 static void StoreElement(Json::Value& target, | |
296 DcmElement& element, | |
297 unsigned int maxStringLength) | |
298 { | |
299 assert(target.type() == Json::objectValue); | |
300 | |
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301 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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302 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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303 const std::string formattedTag = tag.Format(); |
0 | 304 |
305 if (element.isLeaf()) | |
306 { | |
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307 Json::Value value(Json::objectValue); |
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308 value["Name"] = tagName; |
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309 |
0 | 310 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
311 if (v->IsNull()) | |
312 { | |
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313 value["Type"] = "Null"; |
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314 value["Value"] = Json::nullValue; |
0 | 315 } |
316 else | |
317 { | |
318 std::string s = v->AsString(); | |
319 if (maxStringLength == 0 || | |
320 s.size() <= maxStringLength) | |
321 { | |
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322 value["Type"] = "String"; |
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323 value["Value"] = s; |
0 | 324 } |
325 else | |
326 { | |
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327 value["Type"] = "TooLong"; |
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328 value["Value"] = Json::nullValue; |
0 | 329 } |
330 } | |
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331 |
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332 target[formattedTag] = value; |
0 | 333 } |
334 else | |
335 { | |
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336 Json::Value children(Json::arrayValue); |
0 | 337 |
338 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
339 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
340 // etc. are not." The following cast is thus OK. | |
341 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
342 | |
343 for (unsigned long i = 0; i < sequence.card(); i++) | |
344 { | |
345 DcmItem* child = sequence.getItem(i); | |
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346 Json::Value& v = children.append(Json::objectValue); |
0 | 347 StoreItem(v, *child, maxStringLength); |
348 } | |
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349 |
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350 target[formattedTag]["Name"] = tagName; |
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351 target[formattedTag]["Type"] = "Sequence"; |
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352 target[formattedTag]["Value"] = children; |
0 | 353 } |
354 } | |
355 | |
356 | |
357 void FromDcmtkBridge::ToJson(Json::Value& root, | |
358 DcmDataset& dataset, | |
359 unsigned int maxStringLength) | |
360 { | |
361 StoreItem(root, dataset, maxStringLength); | |
362 } | |
363 | |
364 | |
365 | |
366 void FromDcmtkBridge::ToJson(Json::Value& target, | |
367 const std::string& path, | |
368 unsigned int maxStringLength) | |
369 { | |
370 DcmFileFormat dicom; | |
371 if (!dicom.loadFile(path.c_str()).good()) | |
372 { | |
373 throw PalantirException(ErrorCode_BadFileFormat); | |
374 } | |
375 else | |
376 { | |
377 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
378 } | |
379 } | |
380 | |
381 | |
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382 static void ExtractPngImagePreview(std::string& result, |
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383 DicomIntegerPixelAccessor& accessor) |
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384 { |
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385 PngWriter w; |
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386 |
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387 int32_t min, max; |
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388 accessor.GetExtremeValues(min, max); |
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389 |
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390 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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391 if (min != max) |
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392 { |
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393 uint8_t* pixel = &image[0]; |
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394 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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395 { |
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396 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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397 { |
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398 int32_t v = accessor.GetValue(x, y); |
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399 *pixel = static_cast<uint8_t>( |
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400 boost::math::lround(static_cast<float>(v - min) / |
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401 static_cast<float>(max - min) * 255.0f)); |
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402 } |
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403 } |
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404 } |
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405 |
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406 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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407 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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408 } |
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409 |
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410 |
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411 template <typename T> |
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412 static void ExtractPngImageTruncate(std::string& result, |
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413 DicomIntegerPixelAccessor& accessor, |
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414 PixelFormat format) |
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415 { |
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416 PngWriter w; |
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417 |
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418 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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419 T* pixel = &image[0]; |
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420 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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421 { |
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422 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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423 { |
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424 int32_t v = accessor.GetValue(x, y); |
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425 if (v < std::numeric_limits<T>::min()) |
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426 *pixel = std::numeric_limits<T>::min(); |
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427 else if (v > std::numeric_limits<T>::max()) |
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428 *pixel = std::numeric_limits<T>::max(); |
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429 else |
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430 *pixel = static_cast<T>(v); |
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431 } |
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432 } |
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433 |
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434 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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435 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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436 } |
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437 |
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438 |
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439 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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440 DcmDataset& dataset, |
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441 ImageExtractionMode mode) |
0 | 442 { |
443 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
444 | |
445 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
446 | |
447 DicomMap m; | |
448 FromDcmtkBridge::Convert(m, dataset); | |
449 | |
450 DcmElement* e; | |
451 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DicomTag::PIXEL_DATA), e).good() && | |
452 e != NULL) | |
453 { | |
454 Uint8* pixData = NULL; | |
455 if (e->getUint8Array(pixData) == EC_Normal) | |
456 { | |
457 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
458 } | |
459 } | |
460 | |
42
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461 PixelFormat format; |
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462 switch (mode) |
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463 { |
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464 case ImageExtractionMode_Preview: |
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465 case ImageExtractionMode_UInt8: |
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466 format = PixelFormat_Grayscale8; |
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467 break; |
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468 |
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469 case ImageExtractionMode_UInt16: |
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470 format = PixelFormat_Grayscale16; |
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471 break; |
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472 |
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473 default: |
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474 throw PalantirException(ErrorCode_NotImplemented); |
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475 } |
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476 |
0 | 477 if (accessor.get() == NULL || |
478 accessor->GetWidth() == 0 || | |
479 accessor->GetHeight() == 0) | |
480 { | |
42
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481 PngWriter w; |
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482 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
0 | 483 } |
484 else | |
485 { | |
42
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486 switch (mode) |
0 | 487 { |
42
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488 case ImageExtractionMode_Preview: |
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489 ExtractPngImagePreview(result, *accessor); |
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490 break; |
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491 |
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492 case ImageExtractionMode_UInt8: |
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493 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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494 break; |
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495 |
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496 case ImageExtractionMode_UInt16: |
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497 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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498 break; |
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499 |
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500 default: |
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501 throw PalantirException(ErrorCode_NotImplemented); |
0 | 502 } |
503 } | |
504 } | |
505 | |
506 | |
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507 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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508 const std::string& dicomContent, |
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509 ImageExtractionMode mode) |
0 | 510 { |
511 DcmInputBufferStream is; | |
512 if (dicomContent.size() > 0) | |
513 { | |
514 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
515 } | |
516 is.setEos(); | |
517 | |
518 DcmFileFormat dicom; | |
519 if (dicom.read(is).good()) | |
520 { | |
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521 ExtractPngImage(result, *dicom.getDataset(), mode); |
0 | 522 } |
523 else | |
524 { | |
525 throw PalantirException(ErrorCode_BadFileFormat); | |
526 } | |
527 } | |
528 | |
529 | |
530 | |
531 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
532 { | |
533 DcmTagKey tag(t.GetGroup(), t.GetElement()); | |
534 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
535 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
536 | |
537 std::string s("Unknown"); | |
538 if (entry != NULL) | |
539 { | |
540 s = std::string(entry->getTagName()); | |
541 } | |
542 | |
543 dcmDataDict.unlock(); | |
544 return s; | |
545 } | |
546 | |
547 | |
548 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
549 { | |
550 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
551 const DcmDictEntry* entry = dict.findEntry(name); | |
552 | |
553 if (entry == NULL) | |
554 { | |
555 dcmDataDict.unlock(); | |
556 throw PalantirException("Unknown DICOM tag"); | |
557 } | |
558 else | |
559 { | |
560 DcmTagKey key = entry->getKey(); | |
561 DicomTag tag(key.getGroup(), key.getElement()); | |
562 dcmDataDict.unlock(); | |
563 return tag; | |
564 } | |
565 } | |
566 | |
567 | |
568 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
569 { | |
570 for (DicomMap::Map::const_iterator | |
571 it = m.map_.begin(); it != m.map_.end(); it++) | |
572 { | |
573 DicomTag t = it->first; | |
574 std::string s = it->second->AsString(); | |
575 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
576 } | |
577 } | |
578 | |
579 | |
580 void FromDcmtkBridge::ToJson(Json::Value& result, | |
581 const DicomMap& values) | |
582 { | |
583 if (result.type() != Json::objectValue) | |
584 { | |
585 throw PalantirException(ErrorCode_BadParameterType); | |
586 } | |
587 | |
588 result.clear(); | |
589 | |
590 for (DicomMap::Map::const_iterator | |
591 it = values.map_.begin(); it != values.map_.end(); it++) | |
592 { | |
593 result[GetName(it->first)] = it->second->AsString(); | |
594 } | |
595 } | |
596 } |