Mercurial > hg > orthanc-webviewer
annotate Plugin/ParsedDicomImage.cpp @ 38:fec65ef2c7e9
fix
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Fri, 03 Jul 2015 10:45:51 +0200 |
parents | 111689a2c177 |
children | abdde1dfb3eb |
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" | |
25 #include "../Orthanc/Core/ImageFormats/ImageProcessing.h" | |
26 #include "../Orthanc/Core/ImageFormats/ImageBuffer.h" | |
31 | 27 #include "../Orthanc/Core/ImageFormats/PngReader.h" |
0 | 28 #include "JpegWriter.h" |
29 #include "ViewerToolbox.h" | |
30 | |
31 #include <gdcmImageReader.h> | |
32 #include <gdcmImageChangePlanarConfiguration.h> | |
33 #include <gdcmImageChangePhotometricInterpretation.h> | |
34 #include <boost/lexical_cast.hpp> | |
35 #include <boost/math/special_functions/round.hpp> | |
36 | |
26 | 37 #include "../Orthanc/Resources/ThirdParty/base64/base64.h" |
0 | 38 |
39 | |
40 namespace OrthancPlugins | |
41 { | |
31 | 42 class ParsedDicomImage::PImpl |
0 | 43 { |
31 | 44 private: |
45 OrthancPluginContext* context_; | |
46 std::string instanceId_; | |
0 | 47 gdcm::ImageReader reader_; |
48 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; | |
49 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; | |
50 std::string decoded_; | |
31 | 51 Orthanc::PngReader png_; |
52 bool insidePng_; | |
53 bool isDecoded_; | |
54 | |
55 bool DecodeUsingGdcm() | |
56 { | |
57 // Change photometric interpretation, if required | |
58 { | |
59 const gdcm::Image& image = GetImage(); | |
60 if (image.GetPixelFormat().GetSamplesPerPixel() == 1) | |
61 { | |
62 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
63 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
64 { | |
65 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
66 photometric_->SetInput(image); | |
67 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
68 if (!photometric_->Change() || | |
69 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
70 { | |
71 OrthancPluginLogWarning(context_, "GDCM cannot change the photometric interpretation"); | |
72 return false; | |
73 } | |
74 } | |
75 } | |
76 else | |
77 { | |
78 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
79 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
80 { | |
81 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
82 photometric_->SetInput(image); | |
83 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
84 if (!photometric_->Change() || | |
85 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
86 { | |
87 OrthancPluginLogWarning(context_, "GDCM cannot change the photometric interpretation"); | |
88 return false; | |
89 } | |
90 } | |
91 } | |
92 } | |
93 | |
94 // Possibly convert planar configuration to interleaved | |
95 { | |
96 const gdcm::Image& image = GetImage(); | |
97 if (image.GetPlanarConfiguration() != 0 && | |
98 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
99 { | |
100 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
101 interleaved_->SetInput(image); | |
102 if (!interleaved_->Change() || | |
103 GetImage().GetPlanarConfiguration() != 0) | |
104 { | |
105 OrthancPluginLogWarning(context_, "GDCM cannot change the planar configuration to interleaved"); | |
106 return false; | |
107 } | |
108 } | |
109 } | |
110 | |
111 // Decode the image to the memory buffer | |
112 { | |
113 const gdcm::Image& image = GetImage(); | |
114 decoded_.resize(image.GetBufferLength()); | |
115 | |
116 if (decoded_.size() > 0) | |
117 { | |
118 image.GetBuffer(&decoded_[0]); | |
119 } | |
120 } | |
121 | |
122 return true; | |
123 } | |
124 | |
125 | |
126 bool DecodeUsingOrthanc() | |
127 { | |
128 /** | |
129 * This is a DICOM image that cannot be properly decoded by | |
130 * GDCM. Let's give a try with the Orthanc built-in decoder. | |
131 **/ | |
132 std::string file = "/instances/" + instanceId_; | |
133 | |
134 const gdcm::Image& image = GetImage(); | |
135 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 || | |
136 image.GetPixelFormat().GetSamplesPerPixel() == 4) | |
137 { | |
138 file += "/preview"; | |
139 } | |
140 else | |
141 { | |
142 file += "/image-uint16"; | |
143 } | |
144 | |
145 std::string png; | |
146 if (!GetStringFromOrthanc(png, context_, file)) | |
147 { | |
148 return false; | |
149 } | |
150 else | |
151 { | |
152 try | |
153 { | |
154 png_.ReadFromMemory(png); | |
155 insidePng_ = true; | |
156 return true; | |
157 } | |
158 catch (Orthanc::OrthancException&) | |
159 { | |
160 return false; | |
161 } | |
162 } | |
163 } | |
164 | |
165 | |
166 bool Decode() | |
167 { | |
168 if (isDecoded_) | |
169 { | |
170 return true; | |
171 } | |
172 | |
173 if (DecodeUsingGdcm()) | |
174 { | |
175 isDecoded_ = true; | |
176 return true; | |
177 } | |
178 | |
179 // GDCM cannot decode this image, try and use Orthanc built-in functions | |
180 photometric_.reset(); | |
181 interleaved_.reset(); | |
182 decoded_.clear(); | |
183 | |
184 if (DecodeUsingOrthanc()) | |
185 { | |
186 isDecoded_ = true; | |
187 return true; | |
188 } | |
189 else | |
190 { | |
191 return false; | |
192 } | |
193 } | |
194 | |
195 | |
196 public: | |
197 PImpl(OrthancPluginContext* context, | |
198 const std::string& instanceId) : | |
199 context_(context), | |
200 instanceId_(instanceId), | |
201 insidePng_(false), | |
202 isDecoded_(false) | |
203 { | |
204 } | |
205 | |
206 | |
207 const gdcm::DataSet& GetDataSet() const | |
208 { | |
209 return reader_.GetFile().GetDataSet(); | |
210 } | |
211 | |
0 | 212 |
213 const gdcm::Image& GetImage() const | |
214 { | |
215 if (interleaved_.get() != NULL) | |
216 { | |
217 return interleaved_->GetOutput(); | |
218 } | |
219 | |
220 if (photometric_.get() != NULL) | |
221 { | |
222 return photometric_->GetOutput(); | |
223 } | |
224 | |
225 return reader_.GetImage(); | |
226 } | |
227 | |
228 | |
31 | 229 void Parse(const std::string& dicom) |
230 { | |
231 // Prepare a memory stream over the DICOM instance | |
232 std::stringstream stream(dicom); | |
233 | |
234 // Parse the DICOM instance using GDCM | |
235 reader_.SetStream(stream); | |
236 if (!reader_.Read()) | |
237 { | |
238 throw Orthanc::OrthancException("GDCM cannot extract an image from this DICOM instance"); | |
239 } | |
240 } | |
241 | |
242 | |
243 bool GetAccessor(Orthanc::ImageAccessor& accessor) | |
0 | 244 { |
31 | 245 if (!Decode()) |
246 { | |
247 return false; | |
248 } | |
249 | |
250 if (insidePng_) | |
251 { | |
252 // The image was decoded using Orthanc's built-in REST API | |
253 accessor = png_; | |
254 return true; | |
255 } | |
256 | |
257 const gdcm::Image& image = GetImage(); | |
258 | |
259 size_t size = decoded_.size(); | |
260 void* buffer = (size ? &decoded_[0] : NULL); | |
261 unsigned int height = image.GetRows(); | |
262 unsigned int width = image.GetColumns(); | |
263 | |
264 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
265 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
266 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
267 { | |
268 switch (image.GetPixelFormat()) | |
269 { | |
270 case gdcm::PixelFormat::UINT16: | |
271 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale16, width, height, 2 * width, buffer); | |
272 return true; | |
273 | |
274 case gdcm::PixelFormat::INT16: | |
275 accessor.AssignWritable(Orthanc::PixelFormat_SignedGrayscale16, width, height, 2 * width, buffer); | |
276 return true; | |
277 | |
278 case gdcm::PixelFormat::UINT8: | |
279 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale8, width, height, width, buffer); | |
280 return true; | |
281 | |
282 default: | |
283 return false; | |
284 } | |
285 } | |
286 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
287 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB) | |
288 { | |
289 switch (image.GetPixelFormat()) | |
290 { | |
291 case gdcm::PixelFormat::UINT8: | |
292 accessor.AssignWritable(Orthanc::PixelFormat_RGB24, width, height, 3 * width, buffer); | |
293 return true; | |
294 | |
295 default: | |
296 return false; | |
297 } | |
298 } | |
299 | |
300 return false; | |
0 | 301 } |
302 }; | |
303 | |
304 | |
305 template <typename TargetType, typename SourceType> | |
306 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
307 const Orthanc::ImageAccessor& source, | |
308 SourceType source1, TargetType target1, | |
309 SourceType source2, TargetType target2) | |
310 { | |
311 if (source.GetWidth() != target.GetWidth() || | |
312 source.GetHeight() != target.GetHeight()) | |
313 { | |
314 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
315 } | |
316 | |
317 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
318 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
319 | |
320 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
321 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
322 | |
323 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
324 { | |
325 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
326 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
327 | |
328 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
329 { | |
330 float v = (scale * static_cast<float>(*p)) + offset; | |
331 | |
332 if (v > maxValue) | |
333 { | |
334 *q = std::numeric_limits<TargetType>::max(); | |
335 } | |
336 else if (v < minValue) | |
337 { | |
338 *q = std::numeric_limits<TargetType>::min(); | |
339 } | |
340 else | |
341 { | |
342 *q = static_cast<TargetType>(boost::math::iround(v)); | |
343 } | |
344 } | |
345 } | |
346 } | |
347 | |
348 | |
31 | 349 ParsedDicomImage::ParsedDicomImage(OrthancPluginContext* context, |
350 const std::string& instanceId) : | |
351 pimpl_(new PImpl(context, instanceId)) | |
0 | 352 { |
31 | 353 std::string file = "/instances/" + instanceId + "/file"; |
0 | 354 |
31 | 355 std::string dicom; |
356 if (!GetStringFromOrthanc(dicom, context, file)) | |
0 | 357 { |
31 | 358 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
0 | 359 } |
360 | |
31 | 361 pimpl_->Parse(dicom); |
0 | 362 } |
363 | |
364 | |
365 bool ParsedDicomImage::GetTag(std::string& result, | |
366 uint16_t group, | |
367 uint16_t element, | |
368 bool stripSpaces) | |
369 { | |
370 const gdcm::Tag tag(group, element); | |
371 | |
372 if (pimpl_->GetDataSet().FindDataElement(tag)) | |
373 { | |
374 const gdcm::ByteValue* value = pimpl_->GetDataSet().GetDataElement(tag).GetByteValue(); | |
375 if (value) | |
376 { | |
377 result = std::string(value->GetPointer(), value->GetLength()); | |
378 | |
379 if (stripSpaces) | |
380 { | |
381 result = Orthanc::Toolbox::StripSpaces(result); | |
382 } | |
383 | |
384 return true; | |
385 } | |
386 } | |
387 | |
388 return false; | |
389 } | |
390 | |
391 | |
392 bool ParsedDicomImage::GetCornerstoneMetadata(Json::Value& json) | |
393 { | |
394 using namespace Orthanc; | |
395 | |
396 ImageAccessor accessor; | |
31 | 397 if (!pimpl_->GetAccessor(accessor)) |
0 | 398 { |
399 return false; | |
400 } | |
401 | |
402 float windowCenter, windowWidth; | |
403 | |
404 switch (accessor.GetFormat()) | |
405 { | |
406 case PixelFormat_Grayscale8: | |
407 case PixelFormat_Grayscale16: | |
408 case PixelFormat_SignedGrayscale16: | |
409 { | |
410 int64_t a, b; | |
411 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
412 json["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); | |
413 json["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
414 json["color"] = false; | |
415 | |
416 windowCenter = static_cast<float>(a + b) / 2.0f; | |
417 | |
418 if (a == b) | |
419 { | |
1
828c61fc8253
default window width set to 256
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
420 windowWidth = 256.0f; // Arbitrary value |
0 | 421 } |
422 else | |
423 { | |
424 windowWidth = static_cast<float>(b - a) / 2.0f; | |
425 } | |
426 | |
427 break; | |
428 } | |
429 | |
430 case PixelFormat_RGB24: | |
431 json["minPixelValue"] = 0; | |
432 json["maxPixelValue"] = 255; | |
433 json["color"] = true; | |
434 windowCenter = 127.5f; | |
1
828c61fc8253
default window width set to 256
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
435 windowWidth = 256.0f; |
0 | 436 break; |
437 | |
438 default: | |
439 return false; | |
440 } | |
441 | |
442 const gdcm::Image& image = pimpl_->GetImage(); | |
443 json["slope"] = image.GetSlope(); | |
444 json["intercept"] = image.GetIntercept(); | |
445 json["rows"] = image.GetRows(); | |
446 json["columns"] = image.GetColumns(); | |
447 json["height"] = image.GetRows(); | |
448 json["width"] = image.GetColumns(); | |
449 json["columnPixelSpacing"] = image.GetSpacing(1); | |
450 json["rowPixelSpacing"] = image.GetSpacing(0); | |
451 | |
452 json["windowCenter"] = windowCenter * image.GetSlope() + image.GetIntercept(); | |
453 json["windowWidth"] = windowWidth * image.GetSlope(); | |
454 | |
455 try | |
456 { | |
457 std::string width, center; | |
458 if (GetTag(center, 0x0028, 0x1050 /*DICOM_TAG_WINDOW_CENTER*/) && | |
459 GetTag(width, 0x0028, 0x1051 /*DICOM_TAG_WINDOW_WIDTH*/)) | |
460 { | |
461 float a = boost::lexical_cast<float>(width); | |
462 float b = boost::lexical_cast<float>(center); | |
463 json["windowWidth"] = a; | |
464 json["windowCenter"] = b; | |
465 } | |
466 } | |
467 catch (boost::bad_lexical_cast&) | |
468 { | |
469 } | |
470 | |
471 return true; | |
472 } | |
473 | |
474 | |
475 bool ParsedDicomImage::EncodeUsingDeflate(Json::Value& result, | |
476 uint8_t compressionLevel /* between 0 and 9 */) | |
477 { | |
478 using namespace Orthanc; | |
479 | |
480 ImageAccessor accessor; | |
31 | 481 if (!pimpl_->GetAccessor(accessor)) |
0 | 482 { |
483 return false; | |
484 } | |
485 | |
486 result = Json::objectValue; | |
487 result["Orthanc"] = Json::objectValue; | |
488 if (!GetCornerstoneMetadata(result)) | |
489 { | |
490 return false; | |
491 } | |
492 | |
493 ImageBuffer buffer; | |
494 buffer.SetMinimalPitchForced(true); | |
495 | |
496 ImageAccessor converted; | |
497 | |
498 | |
499 switch (accessor.GetFormat()) | |
500 { | |
501 case Orthanc::PixelFormat_RGB24: | |
502 converted = accessor; | |
503 break; | |
504 | |
505 case Orthanc::PixelFormat_Grayscale8: | |
506 case Orthanc::PixelFormat_Grayscale16: | |
507 buffer.SetFormat(Orthanc::PixelFormat_SignedGrayscale16); | |
508 buffer.SetWidth(accessor.GetWidth()); | |
509 buffer.SetHeight(accessor.GetHeight()); | |
510 converted = buffer.GetAccessor(); | |
511 ImageProcessing::Convert(converted, accessor); | |
512 break; | |
513 | |
514 case Orthanc::PixelFormat_SignedGrayscale16: | |
515 converted = accessor; | |
516 break; | |
517 | |
518 default: | |
519 // Unsupported pixel format | |
520 return false; | |
521 } | |
522 | |
523 // Sanity check: The pitch must be minimal | |
524 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
525 GetBytesPerPixel(converted.GetFormat())); | |
526 result["Orthanc"]["Compression"] = "Deflate"; | |
527 result["sizeInBytes"] = converted.GetSize(); | |
528 | |
529 std::string z; | |
530 if (!CompressUsingDeflate(z, converted.GetConstBuffer(), converted.GetSize(), compressionLevel)) | |
531 { | |
532 return false; | |
533 } | |
534 | |
535 result["Orthanc"]["PixelData"] = base64_encode(z); | |
536 | |
537 return true; | |
538 } | |
539 | |
540 | |
541 | |
542 bool ParsedDicomImage::EncodeUsingJpeg(Json::Value& result, | |
543 uint8_t quality /* between 0 and 100 */) | |
544 { | |
545 using namespace Orthanc; | |
546 | |
547 ImageAccessor accessor; | |
31 | 548 if (!pimpl_->GetAccessor(accessor)) |
0 | 549 { |
550 return false; | |
551 } | |
552 | |
553 result = Json::objectValue; | |
554 result["Orthanc"] = Json::objectValue; | |
555 GetCornerstoneMetadata(result); | |
556 | |
557 ImageBuffer buffer; | |
558 buffer.SetMinimalPitchForced(true); | |
559 | |
560 ImageAccessor converted; | |
561 | |
562 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
563 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
564 { | |
565 result["Orthanc"]["Stretched"] = false; | |
566 converted = accessor; | |
567 } | |
568 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || | |
569 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
570 { | |
571 result["Orthanc"]["Stretched"] = true; | |
572 buffer.SetFormat(Orthanc::PixelFormat_Grayscale8); | |
573 buffer.SetWidth(accessor.GetWidth()); | |
574 buffer.SetHeight(accessor.GetHeight()); | |
575 converted = buffer.GetAccessor(); | |
576 | |
577 int64_t a, b; | |
578 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
579 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
580 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
581 | |
582 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
583 { | |
584 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
585 } | |
586 else | |
587 { | |
588 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
589 } | |
590 } | |
591 else | |
592 { | |
593 return false; | |
594 } | |
595 | |
596 result["Orthanc"]["Compression"] = "Jpeg"; | |
597 result["sizeInBytes"] = converted.GetSize(); | |
598 | |
599 std::string jpeg; | |
600 OrthancPlugins::JpegWriter writer; | |
601 writer.SetQuality(quality); | |
602 writer.WriteToMemory(jpeg, converted); | |
603 result["Orthanc"]["PixelData"] = base64_encode(jpeg); | |
604 return true; | |
605 } | |
26 | 606 } |