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comparison PalanthirServer/FromDcmtkBridge.cpp @ 45:33d67e1ab173

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 05 Sep 2012 13:24:59 +0200
parents PalantirServer/FromDcmtkBridge.cpp@ea48f38afe5f
children a15e90e5d6fc
comparison
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43:9be852ad33d2 45:33d67e1ab173
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
46 #include <boost/math/special_functions/round.hpp>
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 }
91 catch (std::runtime_error&)
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
301 DicomTag tag(FromDcmtkBridge::GetTag(element));
302 const std::string tagName = FromDcmtkBridge::GetName(tag);
303 const std::string formattedTag = tag.Format();
304
305 if (element.isLeaf())
306 {
307 Json::Value value(Json::objectValue);
308 value["Name"] = tagName;
309
310 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element));
311 if (v->IsNull())
312 {
313 value["Type"] = "Null";
314 value["Value"] = Json::nullValue;
315 }
316 else
317 {
318 std::string s = v->AsString();
319 if (maxStringLength == 0 ||
320 s.size() <= maxStringLength)
321 {
322 value["Type"] = "String";
323 value["Value"] = s;
324 }
325 else
326 {
327 value["Type"] = "TooLong";
328 value["Value"] = Json::nullValue;
329 }
330 }
331
332 target[formattedTag] = value;
333 }
334 else
335 {
336 Json::Value children(Json::arrayValue);
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);
346 Json::Value& v = children.append(Json::objectValue);
347 StoreItem(v, *child, maxStringLength);
348 }
349
350 target[formattedTag]["Name"] = tagName;
351 target[formattedTag]["Type"] = "Sequence";
352 target[formattedTag]["Value"] = children;
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
382 static void ExtractPngImagePreview(std::string& result,
383 DicomIntegerPixelAccessor& accessor)
384 {
385 PngWriter w;
386
387 int32_t min, max;
388 accessor.GetExtremeValues(min, max);
389
390 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0);
391 if (min != max)
392 {
393 uint8_t* pixel = &image[0];
394 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
395 {
396 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
397 {
398 int32_t v = accessor.GetValue(x, y);
399 *pixel = static_cast<uint8_t>(
400 boost::math::lround(static_cast<float>(v - min) /
401 static_cast<float>(max - min) * 255.0f));
402 }
403 }
404 }
405
406 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
407 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]);
408 }
409
410
411 template <typename T>
412 static void ExtractPngImageTruncate(std::string& result,
413 DicomIntegerPixelAccessor& accessor,
414 PixelFormat format)
415 {
416 PngWriter w;
417
418 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0);
419 T* pixel = &image[0];
420 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
421 {
422 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
423 {
424 int32_t v = accessor.GetValue(x, y);
425 if (v < std::numeric_limits<T>::min())
426 *pixel = std::numeric_limits<T>::min();
427 else if (v > std::numeric_limits<T>::max())
428 *pixel = std::numeric_limits<T>::max();
429 else
430 *pixel = static_cast<T>(v);
431 }
432 }
433
434 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
435 accessor.GetWidth() * sizeof(T), format, &image[0]);
436 }
437
438
439 void FromDcmtkBridge::ExtractPngImage(std::string& result,
440 DcmDataset& dataset,
441 ImageExtractionMode mode)
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
461 PixelFormat format;
462 switch (mode)
463 {
464 case ImageExtractionMode_Preview:
465 case ImageExtractionMode_UInt8:
466 format = PixelFormat_Grayscale8;
467 break;
468
469 case ImageExtractionMode_UInt16:
470 format = PixelFormat_Grayscale16;
471 break;
472
473 default:
474 throw PalantirException(ErrorCode_NotImplemented);
475 }
476
477 if (accessor.get() == NULL ||
478 accessor->GetWidth() == 0 ||
479 accessor->GetHeight() == 0)
480 {
481 PngWriter w;
482 w.WriteToMemory(result, 0, 0, 0, format, NULL);
483 }
484 else
485 {
486 switch (mode)
487 {
488 case ImageExtractionMode_Preview:
489 ExtractPngImagePreview(result, *accessor);
490 break;
491
492 case ImageExtractionMode_UInt8:
493 ExtractPngImageTruncate<uint8_t>(result, *accessor, format);
494 break;
495
496 case ImageExtractionMode_UInt16:
497 ExtractPngImageTruncate<uint16_t>(result, *accessor, format);
498 break;
499
500 default:
501 throw PalantirException(ErrorCode_NotImplemented);
502 }
503 }
504 }
505
506
507 void FromDcmtkBridge::ExtractPngImage(std::string& result,
508 const std::string& dicomContent,
509 ImageExtractionMode mode)
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 {
521 ExtractPngImage(result, *dicom.getDataset(), mode);
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 }