Mercurial > hg > orthanc-webviewer
annotate Plugin/ParsedDicomImage.cpp @ 85:581937911d14
merge
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Tue, 13 Oct 2015 17:51:49 +0200 |
parents | abdde1dfb3eb |
children | 02ccb1677e91 |
rev | line source |
---|---|
0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU Affero General Public License | |
8 * as published by the Free Software Foundation, either version 3 of | |
9 * the 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 * Affero General Public License for more details. | |
15 * | |
16 * You should have received a copy of the GNU Affero General Public License | |
17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
18 **/ | |
19 | |
20 | |
21 #include "ParsedDicomImage.h" | |
22 | |
26 | 23 #include "../Orthanc/Core/OrthancException.h" |
24 #include "../Orthanc/Core/Toolbox.h" | |
79 | 25 #include "../Orthanc/Core/Images/ImageProcessing.h" |
26 #include "../Orthanc/Core/Images/ImageBuffer.h" | |
0 | 27 #include "ViewerToolbox.h" |
28 | |
29 #include <gdcmImageReader.h> | |
30 #include <gdcmImageChangePlanarConfiguration.h> | |
31 #include <gdcmImageChangePhotometricInterpretation.h> | |
32 #include <boost/lexical_cast.hpp> | |
33 #include <boost/math/special_functions/round.hpp> | |
34 | |
26 | 35 #include "../Orthanc/Resources/ThirdParty/base64/base64.h" |
0 | 36 |
37 | |
38 namespace OrthancPlugins | |
39 { | |
31 | 40 class ParsedDicomImage::PImpl |
0 | 41 { |
31 | 42 private: |
43 OrthancPluginContext* context_; | |
44 std::string instanceId_; | |
0 | 45 gdcm::ImageReader reader_; |
46 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; | |
47 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; | |
48 std::string decoded_; | |
79 | 49 std::auto_ptr<ImageReader> png_; |
31 | 50 bool isDecoded_; |
51 | |
52 bool DecodeUsingGdcm() | |
53 { | |
54 // Change photometric interpretation, if required | |
55 { | |
56 const gdcm::Image& image = GetImage(); | |
57 if (image.GetPixelFormat().GetSamplesPerPixel() == 1) | |
58 { | |
59 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
60 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
61 { | |
62 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
63 photometric_->SetInput(image); | |
64 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
65 if (!photometric_->Change() || | |
66 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
67 { | |
68 OrthancPluginLogWarning(context_, "GDCM cannot change the photometric interpretation"); | |
69 return false; | |
70 } | |
71 } | |
72 } | |
73 else | |
74 { | |
75 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
76 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
77 { | |
78 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
79 photometric_->SetInput(image); | |
80 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
81 if (!photometric_->Change() || | |
82 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
83 { | |
84 OrthancPluginLogWarning(context_, "GDCM cannot change the photometric interpretation"); | |
85 return false; | |
86 } | |
87 } | |
88 } | |
89 } | |
90 | |
91 // Possibly convert planar configuration to interleaved | |
92 { | |
93 const gdcm::Image& image = GetImage(); | |
94 if (image.GetPlanarConfiguration() != 0 && | |
95 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
96 { | |
97 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
98 interleaved_->SetInput(image); | |
99 if (!interleaved_->Change() || | |
100 GetImage().GetPlanarConfiguration() != 0) | |
101 { | |
102 OrthancPluginLogWarning(context_, "GDCM cannot change the planar configuration to interleaved"); | |
103 return false; | |
104 } | |
105 } | |
106 } | |
107 | |
108 // Decode the image to the memory buffer | |
109 { | |
110 const gdcm::Image& image = GetImage(); | |
111 decoded_.resize(image.GetBufferLength()); | |
112 | |
113 if (decoded_.size() > 0) | |
114 { | |
115 image.GetBuffer(&decoded_[0]); | |
116 } | |
117 } | |
118 | |
119 return true; | |
120 } | |
121 | |
122 | |
123 bool DecodeUsingOrthanc() | |
124 { | |
125 /** | |
126 * This is a DICOM image that cannot be properly decoded by | |
127 * GDCM. Let's give a try with the Orthanc built-in decoder. | |
128 **/ | |
129 std::string file = "/instances/" + instanceId_; | |
130 | |
131 const gdcm::Image& image = GetImage(); | |
132 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 || | |
133 image.GetPixelFormat().GetSamplesPerPixel() == 4) | |
134 { | |
135 file += "/preview"; | |
136 } | |
137 else | |
138 { | |
139 file += "/image-uint16"; | |
140 } | |
141 | |
142 std::string png; | |
143 if (!GetStringFromOrthanc(png, context_, file)) | |
144 { | |
145 return false; | |
146 } | |
147 else | |
148 { | |
149 try | |
150 { | |
79 | 151 png_.reset(new ImageReader(context_, png, OrthancPluginImageFormat_Png)); |
31 | 152 return true; |
153 } | |
154 catch (Orthanc::OrthancException&) | |
155 { | |
156 return false; | |
157 } | |
158 } | |
159 } | |
160 | |
161 | |
162 bool Decode() | |
163 { | |
164 if (isDecoded_) | |
165 { | |
166 return true; | |
167 } | |
168 | |
169 if (DecodeUsingGdcm()) | |
170 { | |
171 isDecoded_ = true; | |
172 return true; | |
173 } | |
174 | |
175 // GDCM cannot decode this image, try and use Orthanc built-in functions | |
176 photometric_.reset(); | |
177 interleaved_.reset(); | |
178 decoded_.clear(); | |
179 | |
180 if (DecodeUsingOrthanc()) | |
181 { | |
182 isDecoded_ = true; | |
183 return true; | |
184 } | |
185 else | |
186 { | |
187 return false; | |
188 } | |
189 } | |
190 | |
191 | |
192 public: | |
193 PImpl(OrthancPluginContext* context, | |
194 const std::string& instanceId) : | |
195 context_(context), | |
196 instanceId_(instanceId), | |
197 isDecoded_(false) | |
198 { | |
199 } | |
200 | |
201 | |
79 | 202 OrthancPluginContext* GetContext() |
203 { | |
204 return context_; | |
205 } | |
206 | |
207 | |
31 | 208 const gdcm::DataSet& GetDataSet() const |
209 { | |
210 return reader_.GetFile().GetDataSet(); | |
211 } | |
212 | |
0 | 213 |
214 const gdcm::Image& GetImage() const | |
215 { | |
216 if (interleaved_.get() != NULL) | |
217 { | |
218 return interleaved_->GetOutput(); | |
219 } | |
220 | |
221 if (photometric_.get() != NULL) | |
222 { | |
223 return photometric_->GetOutput(); | |
224 } | |
225 | |
226 return reader_.GetImage(); | |
227 } | |
228 | |
229 | |
31 | 230 void Parse(const std::string& dicom) |
231 { | |
232 // Prepare a memory stream over the DICOM instance | |
233 std::stringstream stream(dicom); | |
234 | |
235 // Parse the DICOM instance using GDCM | |
236 reader_.SetStream(stream); | |
237 if (!reader_.Read()) | |
238 { | |
79 | 239 OrthancPluginLogError(context_, "GDCM cannot extract an image from this DICOM instance"); |
240 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
31 | 241 } |
242 } | |
243 | |
244 | |
245 bool GetAccessor(Orthanc::ImageAccessor& accessor) | |
0 | 246 { |
31 | 247 if (!Decode()) |
248 { | |
249 return false; | |
250 } | |
251 | |
79 | 252 if (png_.get() != NULL) |
31 | 253 { |
254 // The image was decoded using Orthanc's built-in REST API | |
79 | 255 accessor = png_->GetAccessor(); |
31 | 256 return true; |
257 } | |
258 | |
259 const gdcm::Image& image = GetImage(); | |
260 | |
261 size_t size = decoded_.size(); | |
262 void* buffer = (size ? &decoded_[0] : NULL); | |
263 unsigned int height = image.GetRows(); | |
264 unsigned int width = image.GetColumns(); | |
265 | |
266 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
267 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
268 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
269 { | |
270 switch (image.GetPixelFormat()) | |
271 { | |
272 case gdcm::PixelFormat::UINT16: | |
273 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale16, width, height, 2 * width, buffer); | |
274 return true; | |
275 | |
276 case gdcm::PixelFormat::INT16: | |
277 accessor.AssignWritable(Orthanc::PixelFormat_SignedGrayscale16, width, height, 2 * width, buffer); | |
278 return true; | |
279 | |
280 case gdcm::PixelFormat::UINT8: | |
281 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale8, width, height, width, buffer); | |
282 return true; | |
283 | |
284 default: | |
285 return false; | |
286 } | |
287 } | |
288 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
289 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB) | |
290 { | |
291 switch (image.GetPixelFormat()) | |
292 { | |
293 case gdcm::PixelFormat::UINT8: | |
294 accessor.AssignWritable(Orthanc::PixelFormat_RGB24, width, height, 3 * width, buffer); | |
295 return true; | |
296 | |
297 default: | |
298 return false; | |
299 } | |
300 } | |
301 | |
302 return false; | |
0 | 303 } |
304 }; | |
305 | |
306 | |
307 template <typename TargetType, typename SourceType> | |
308 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
309 const Orthanc::ImageAccessor& source, | |
310 SourceType source1, TargetType target1, | |
311 SourceType source2, TargetType target2) | |
312 { | |
313 if (source.GetWidth() != target.GetWidth() || | |
314 source.GetHeight() != target.GetHeight()) | |
315 { | |
316 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
317 } | |
318 | |
319 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
320 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
321 | |
322 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
323 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
324 | |
325 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
326 { | |
327 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
328 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
329 | |
330 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
331 { | |
332 float v = (scale * static_cast<float>(*p)) + offset; | |
333 | |
334 if (v > maxValue) | |
335 { | |
336 *q = std::numeric_limits<TargetType>::max(); | |
337 } | |
338 else if (v < minValue) | |
339 { | |
340 *q = std::numeric_limits<TargetType>::min(); | |
341 } | |
342 else | |
343 { | |
344 *q = static_cast<TargetType>(boost::math::iround(v)); | |
345 } | |
346 } | |
347 } | |
348 } | |
349 | |
350 | |
31 | 351 ParsedDicomImage::ParsedDicomImage(OrthancPluginContext* context, |
352 const std::string& instanceId) : | |
353 pimpl_(new PImpl(context, instanceId)) | |
0 | 354 { |
31 | 355 std::string file = "/instances/" + instanceId + "/file"; |
0 | 356 |
31 | 357 std::string dicom; |
358 if (!GetStringFromOrthanc(dicom, context, file)) | |
0 | 359 { |
31 | 360 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
0 | 361 } |
362 | |
31 | 363 pimpl_->Parse(dicom); |
0 | 364 } |
365 | |
366 | |
367 bool ParsedDicomImage::GetTag(std::string& result, | |
368 uint16_t group, | |
369 uint16_t element, | |
370 bool stripSpaces) | |
371 { | |
372 const gdcm::Tag tag(group, element); | |
373 | |
374 if (pimpl_->GetDataSet().FindDataElement(tag)) | |
375 { | |
376 const gdcm::ByteValue* value = pimpl_->GetDataSet().GetDataElement(tag).GetByteValue(); | |
377 if (value) | |
378 { | |
379 result = std::string(value->GetPointer(), value->GetLength()); | |
380 | |
381 if (stripSpaces) | |
382 { | |
383 result = Orthanc::Toolbox::StripSpaces(result); | |
384 } | |
385 | |
386 return true; | |
387 } | |
388 } | |
389 | |
390 return false; | |
391 } | |
392 | |
393 | |
394 bool ParsedDicomImage::GetCornerstoneMetadata(Json::Value& json) | |
395 { | |
396 using namespace Orthanc; | |
397 | |
398 ImageAccessor accessor; | |
31 | 399 if (!pimpl_->GetAccessor(accessor)) |
0 | 400 { |
401 return false; | |
402 } | |
403 | |
404 float windowCenter, windowWidth; | |
405 | |
406 switch (accessor.GetFormat()) | |
407 { | |
408 case PixelFormat_Grayscale8: | |
409 case PixelFormat_Grayscale16: | |
410 case PixelFormat_SignedGrayscale16: | |
411 { | |
412 int64_t a, b; | |
413 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
414 json["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); | |
415 json["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
416 json["color"] = false; | |
417 | |
418 windowCenter = static_cast<float>(a + b) / 2.0f; | |
419 | |
420 if (a == b) | |
421 { | |
1
828c61fc8253
default window width set to 256
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
422 windowWidth = 256.0f; // Arbitrary value |
0 | 423 } |
424 else | |
425 { | |
426 windowWidth = static_cast<float>(b - a) / 2.0f; | |
427 } | |
428 | |
429 break; | |
430 } | |
431 | |
432 case PixelFormat_RGB24: | |
433 json["minPixelValue"] = 0; | |
434 json["maxPixelValue"] = 255; | |
435 json["color"] = true; | |
436 windowCenter = 127.5f; | |
1
828c61fc8253
default window width set to 256
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
437 windowWidth = 256.0f; |
0 | 438 break; |
439 | |
440 default: | |
441 return false; | |
442 } | |
443 | |
444 const gdcm::Image& image = pimpl_->GetImage(); | |
445 json["slope"] = image.GetSlope(); | |
446 json["intercept"] = image.GetIntercept(); | |
447 json["rows"] = image.GetRows(); | |
448 json["columns"] = image.GetColumns(); | |
449 json["height"] = image.GetRows(); | |
450 json["width"] = image.GetColumns(); | |
451 json["columnPixelSpacing"] = image.GetSpacing(1); | |
452 json["rowPixelSpacing"] = image.GetSpacing(0); | |
453 | |
454 json["windowCenter"] = windowCenter * image.GetSlope() + image.GetIntercept(); | |
455 json["windowWidth"] = windowWidth * image.GetSlope(); | |
456 | |
457 try | |
458 { | |
459 std::string width, center; | |
460 if (GetTag(center, 0x0028, 0x1050 /*DICOM_TAG_WINDOW_CENTER*/) && | |
461 GetTag(width, 0x0028, 0x1051 /*DICOM_TAG_WINDOW_WIDTH*/)) | |
462 { | |
463 float a = boost::lexical_cast<float>(width); | |
464 float b = boost::lexical_cast<float>(center); | |
465 json["windowWidth"] = a; | |
466 json["windowCenter"] = b; | |
467 } | |
468 } | |
469 catch (boost::bad_lexical_cast&) | |
470 { | |
471 } | |
472 | |
473 return true; | |
474 } | |
475 | |
476 | |
477 bool ParsedDicomImage::EncodeUsingDeflate(Json::Value& result, | |
478 uint8_t compressionLevel /* between 0 and 9 */) | |
479 { | |
480 using namespace Orthanc; | |
481 | |
482 ImageAccessor accessor; | |
31 | 483 if (!pimpl_->GetAccessor(accessor)) |
0 | 484 { |
485 return false; | |
486 } | |
487 | |
488 result = Json::objectValue; | |
489 result["Orthanc"] = Json::objectValue; | |
490 if (!GetCornerstoneMetadata(result)) | |
491 { | |
492 return false; | |
493 } | |
494 | |
495 ImageBuffer buffer; | |
496 buffer.SetMinimalPitchForced(true); | |
497 | |
498 ImageAccessor converted; | |
499 | |
500 | |
501 switch (accessor.GetFormat()) | |
502 { | |
503 case Orthanc::PixelFormat_RGB24: | |
504 converted = accessor; | |
505 break; | |
506 | |
507 case Orthanc::PixelFormat_Grayscale8: | |
508 case Orthanc::PixelFormat_Grayscale16: | |
509 buffer.SetFormat(Orthanc::PixelFormat_SignedGrayscale16); | |
510 buffer.SetWidth(accessor.GetWidth()); | |
511 buffer.SetHeight(accessor.GetHeight()); | |
512 converted = buffer.GetAccessor(); | |
513 ImageProcessing::Convert(converted, accessor); | |
514 break; | |
515 | |
516 case Orthanc::PixelFormat_SignedGrayscale16: | |
517 converted = accessor; | |
518 break; | |
519 | |
520 default: | |
521 // Unsupported pixel format | |
522 return false; | |
523 } | |
524 | |
525 // Sanity check: The pitch must be minimal | |
526 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
527 GetBytesPerPixel(converted.GetFormat())); | |
528 result["Orthanc"]["Compression"] = "Deflate"; | |
529 result["sizeInBytes"] = converted.GetSize(); | |
530 | |
531 std::string z; | |
79 | 532 CompressUsingDeflate(z, pimpl_->GetContext(), converted.GetConstBuffer(), converted.GetSize()); |
0 | 533 |
534 result["Orthanc"]["PixelData"] = base64_encode(z); | |
535 | |
536 return true; | |
537 } | |
538 | |
539 | |
540 | |
541 bool ParsedDicomImage::EncodeUsingJpeg(Json::Value& result, | |
542 uint8_t quality /* between 0 and 100 */) | |
543 { | |
544 using namespace Orthanc; | |
545 | |
546 ImageAccessor accessor; | |
31 | 547 if (!pimpl_->GetAccessor(accessor)) |
0 | 548 { |
549 return false; | |
550 } | |
551 | |
552 result = Json::objectValue; | |
553 result["Orthanc"] = Json::objectValue; | |
554 GetCornerstoneMetadata(result); | |
555 | |
556 ImageBuffer buffer; | |
557 buffer.SetMinimalPitchForced(true); | |
558 | |
559 ImageAccessor converted; | |
560 | |
561 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
562 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
563 { | |
564 result["Orthanc"]["Stretched"] = false; | |
565 converted = accessor; | |
566 } | |
567 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || | |
568 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
569 { | |
570 result["Orthanc"]["Stretched"] = true; | |
571 buffer.SetFormat(Orthanc::PixelFormat_Grayscale8); | |
572 buffer.SetWidth(accessor.GetWidth()); | |
573 buffer.SetHeight(accessor.GetHeight()); | |
574 converted = buffer.GetAccessor(); | |
575 | |
576 int64_t a, b; | |
577 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
578 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
579 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
580 | |
581 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
582 { | |
583 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
584 } | |
585 else | |
586 { | |
587 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
588 } | |
589 } | |
590 else | |
591 { | |
592 return false; | |
593 } | |
594 | |
595 result["Orthanc"]["Compression"] = "Jpeg"; | |
596 result["sizeInBytes"] = converted.GetSize(); | |
597 | |
598 std::string jpeg; | |
79 | 599 WriteJpegToMemory(jpeg, pimpl_->GetContext(), converted, quality); |
600 | |
0 | 601 result["Orthanc"]["PixelData"] = base64_encode(jpeg); |
602 return true; | |
603 } | |
26 | 604 } |