Mercurial > hg > orthanc-webviewer
annotate Plugin/ParsedDicomImage.cpp @ 94:63396b070632
fix mainline version
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 27 Nov 2015 14:43:38 +0100 |
parents | 02ccb1677e91 |
children | a6ba21a083e5 |
rev | line source |
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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> | |
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30 #include <gdcmImageApplyLookupTable.h> |
0 | 31 #include <gdcmImageChangePlanarConfiguration.h> |
32 #include <gdcmImageChangePhotometricInterpretation.h> | |
33 #include <boost/lexical_cast.hpp> | |
34 #include <boost/math/special_functions/round.hpp> | |
35 | |
26 | 36 #include "../Orthanc/Resources/ThirdParty/base64/base64.h" |
0 | 37 |
38 | |
39 namespace OrthancPlugins | |
40 { | |
31 | 41 class ParsedDicomImage::PImpl |
0 | 42 { |
31 | 43 private: |
44 OrthancPluginContext* context_; | |
45 std::string instanceId_; | |
0 | 46 gdcm::ImageReader reader_; |
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47 std::auto_ptr<gdcm::ImageApplyLookupTable> lut_; |
0 | 48 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; |
49 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; | |
50 std::string decoded_; | |
79 | 51 std::auto_ptr<ImageReader> png_; |
31 | 52 bool isDecoded_; |
53 | |
54 bool DecodeUsingGdcm() | |
55 { | |
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56 // Change photometric interpretation or apply LUT, if required |
31 | 57 { |
58 const gdcm::Image& image = GetImage(); | |
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59 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && |
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60 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::PALETTE_COLOR) |
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61 { |
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62 lut_.reset(new gdcm::ImageApplyLookupTable()); |
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63 lut_->SetInput(image); |
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64 if (!lut_->Apply()) |
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65 { |
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66 OrthancPluginLogWarning(context_, "GDCM cannot apply the lookup table"); |
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67 return false; |
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68 } |
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69 } |
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70 else if (image.GetPixelFormat().GetSamplesPerPixel() == 1) |
31 | 71 { |
72 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
73 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
74 { | |
75 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
76 photometric_->SetInput(image); | |
77 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
78 if (!photometric_->Change() || | |
79 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
80 { | |
81 OrthancPluginLogWarning(context_, "GDCM cannot change the photometric interpretation"); | |
82 return false; | |
83 } | |
84 } | |
85 } | |
86 else | |
87 { | |
88 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
89 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
90 { | |
91 photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
92 photometric_->SetInput(image); | |
93 photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
94 if (!photometric_->Change() || | |
95 GetImage().GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
96 { | |
97 OrthancPluginLogWarning(context_, "GDCM cannot change the photometric interpretation"); | |
98 return false; | |
99 } | |
100 } | |
101 } | |
102 } | |
103 | |
104 // Possibly convert planar configuration to interleaved | |
105 { | |
106 const gdcm::Image& image = GetImage(); | |
107 if (image.GetPlanarConfiguration() != 0 && | |
108 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
109 { | |
110 interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
111 interleaved_->SetInput(image); | |
112 if (!interleaved_->Change() || | |
113 GetImage().GetPlanarConfiguration() != 0) | |
114 { | |
115 OrthancPluginLogWarning(context_, "GDCM cannot change the planar configuration to interleaved"); | |
116 return false; | |
117 } | |
118 } | |
119 } | |
120 | |
121 // Decode the image to the memory buffer | |
122 { | |
123 const gdcm::Image& image = GetImage(); | |
124 decoded_.resize(image.GetBufferLength()); | |
125 | |
126 if (decoded_.size() > 0) | |
127 { | |
128 image.GetBuffer(&decoded_[0]); | |
129 } | |
130 } | |
131 | |
132 return true; | |
133 } | |
134 | |
135 | |
136 bool DecodeUsingOrthanc() | |
137 { | |
138 /** | |
139 * This is a DICOM image that cannot be properly decoded by | |
140 * GDCM. Let's give a try with the Orthanc built-in decoder. | |
141 **/ | |
142 std::string file = "/instances/" + instanceId_; | |
143 | |
144 const gdcm::Image& image = GetImage(); | |
145 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 || | |
146 image.GetPixelFormat().GetSamplesPerPixel() == 4) | |
147 { | |
148 file += "/preview"; | |
149 } | |
150 else | |
151 { | |
152 file += "/image-uint16"; | |
153 } | |
154 | |
155 std::string png; | |
156 if (!GetStringFromOrthanc(png, context_, file)) | |
157 { | |
158 return false; | |
159 } | |
160 else | |
161 { | |
162 try | |
163 { | |
79 | 164 png_.reset(new ImageReader(context_, png, OrthancPluginImageFormat_Png)); |
31 | 165 return true; |
166 } | |
167 catch (Orthanc::OrthancException&) | |
168 { | |
169 return false; | |
170 } | |
171 } | |
172 } | |
173 | |
174 | |
175 bool Decode() | |
176 { | |
177 if (isDecoded_) | |
178 { | |
179 return true; | |
180 } | |
181 | |
182 if (DecodeUsingGdcm()) | |
183 { | |
184 isDecoded_ = true; | |
185 return true; | |
186 } | |
187 | |
188 // GDCM cannot decode this image, try and use Orthanc built-in functions | |
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189 lut_.reset(); |
31 | 190 photometric_.reset(); |
191 interleaved_.reset(); | |
192 decoded_.clear(); | |
193 | |
194 if (DecodeUsingOrthanc()) | |
195 { | |
196 isDecoded_ = true; | |
197 return true; | |
198 } | |
199 else | |
200 { | |
201 return false; | |
202 } | |
203 } | |
204 | |
205 | |
206 public: | |
207 PImpl(OrthancPluginContext* context, | |
208 const std::string& instanceId) : | |
209 context_(context), | |
210 instanceId_(instanceId), | |
211 isDecoded_(false) | |
212 { | |
213 } | |
214 | |
215 | |
79 | 216 OrthancPluginContext* GetContext() |
217 { | |
218 return context_; | |
219 } | |
220 | |
221 | |
31 | 222 const gdcm::DataSet& GetDataSet() const |
223 { | |
224 return reader_.GetFile().GetDataSet(); | |
225 } | |
226 | |
0 | 227 |
228 const gdcm::Image& GetImage() const | |
229 { | |
230 if (interleaved_.get() != NULL) | |
231 { | |
232 return interleaved_->GetOutput(); | |
233 } | |
234 | |
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235 if (lut_.get() != NULL) |
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236 { |
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237 return lut_->GetOutput(); |
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238 } |
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239 |
0 | 240 if (photometric_.get() != NULL) |
241 { | |
242 return photometric_->GetOutput(); | |
243 } | |
244 | |
245 return reader_.GetImage(); | |
246 } | |
247 | |
248 | |
31 | 249 void Parse(const std::string& dicom) |
250 { | |
251 // Prepare a memory stream over the DICOM instance | |
252 std::stringstream stream(dicom); | |
253 | |
254 // Parse the DICOM instance using GDCM | |
255 reader_.SetStream(stream); | |
256 if (!reader_.Read()) | |
257 { | |
79 | 258 OrthancPluginLogError(context_, "GDCM cannot extract an image from this DICOM instance"); |
259 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
31 | 260 } |
261 } | |
262 | |
263 | |
264 bool GetAccessor(Orthanc::ImageAccessor& accessor) | |
0 | 265 { |
31 | 266 if (!Decode()) |
267 { | |
268 return false; | |
269 } | |
270 | |
79 | 271 if (png_.get() != NULL) |
31 | 272 { |
273 // The image was decoded using Orthanc's built-in REST API | |
79 | 274 accessor = png_->GetAccessor(); |
31 | 275 return true; |
276 } | |
277 | |
278 const gdcm::Image& image = GetImage(); | |
279 | |
280 size_t size = decoded_.size(); | |
281 void* buffer = (size ? &decoded_[0] : NULL); | |
282 unsigned int height = image.GetRows(); | |
283 unsigned int width = image.GetColumns(); | |
284 | |
285 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
286 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
287 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
288 { | |
289 switch (image.GetPixelFormat()) | |
290 { | |
291 case gdcm::PixelFormat::UINT16: | |
292 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale16, width, height, 2 * width, buffer); | |
293 return true; | |
294 | |
295 case gdcm::PixelFormat::INT16: | |
296 accessor.AssignWritable(Orthanc::PixelFormat_SignedGrayscale16, width, height, 2 * width, buffer); | |
297 return true; | |
298 | |
299 case gdcm::PixelFormat::UINT8: | |
300 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale8, width, height, width, buffer); | |
301 return true; | |
302 | |
303 default: | |
304 return false; | |
305 } | |
306 } | |
307 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
308 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB) | |
309 { | |
310 switch (image.GetPixelFormat()) | |
311 { | |
312 case gdcm::PixelFormat::UINT8: | |
313 accessor.AssignWritable(Orthanc::PixelFormat_RGB24, width, height, 3 * width, buffer); | |
314 return true; | |
315 | |
316 default: | |
317 return false; | |
318 } | |
319 } | |
320 | |
321 return false; | |
0 | 322 } |
323 }; | |
324 | |
325 | |
326 template <typename TargetType, typename SourceType> | |
327 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
328 const Orthanc::ImageAccessor& source, | |
329 SourceType source1, TargetType target1, | |
330 SourceType source2, TargetType target2) | |
331 { | |
332 if (source.GetWidth() != target.GetWidth() || | |
333 source.GetHeight() != target.GetHeight()) | |
334 { | |
335 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
336 } | |
337 | |
338 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
339 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
340 | |
341 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
342 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
343 | |
344 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
345 { | |
346 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
347 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
348 | |
349 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
350 { | |
351 float v = (scale * static_cast<float>(*p)) + offset; | |
352 | |
353 if (v > maxValue) | |
354 { | |
355 *q = std::numeric_limits<TargetType>::max(); | |
356 } | |
357 else if (v < minValue) | |
358 { | |
359 *q = std::numeric_limits<TargetType>::min(); | |
360 } | |
361 else | |
362 { | |
363 *q = static_cast<TargetType>(boost::math::iround(v)); | |
364 } | |
365 } | |
366 } | |
367 } | |
368 | |
369 | |
31 | 370 ParsedDicomImage::ParsedDicomImage(OrthancPluginContext* context, |
371 const std::string& instanceId) : | |
372 pimpl_(new PImpl(context, instanceId)) | |
0 | 373 { |
31 | 374 std::string file = "/instances/" + instanceId + "/file"; |
0 | 375 |
31 | 376 std::string dicom; |
377 if (!GetStringFromOrthanc(dicom, context, file)) | |
0 | 378 { |
31 | 379 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
0 | 380 } |
381 | |
31 | 382 pimpl_->Parse(dicom); |
0 | 383 } |
384 | |
385 | |
386 bool ParsedDicomImage::GetTag(std::string& result, | |
387 uint16_t group, | |
388 uint16_t element, | |
389 bool stripSpaces) | |
390 { | |
391 const gdcm::Tag tag(group, element); | |
392 | |
393 if (pimpl_->GetDataSet().FindDataElement(tag)) | |
394 { | |
395 const gdcm::ByteValue* value = pimpl_->GetDataSet().GetDataElement(tag).GetByteValue(); | |
396 if (value) | |
397 { | |
398 result = std::string(value->GetPointer(), value->GetLength()); | |
399 | |
400 if (stripSpaces) | |
401 { | |
402 result = Orthanc::Toolbox::StripSpaces(result); | |
403 } | |
404 | |
405 return true; | |
406 } | |
407 } | |
408 | |
409 return false; | |
410 } | |
411 | |
412 | |
413 bool ParsedDicomImage::GetCornerstoneMetadata(Json::Value& json) | |
414 { | |
415 using namespace Orthanc; | |
416 | |
417 ImageAccessor accessor; | |
31 | 418 if (!pimpl_->GetAccessor(accessor)) |
0 | 419 { |
420 return false; | |
421 } | |
422 | |
423 float windowCenter, windowWidth; | |
424 | |
425 switch (accessor.GetFormat()) | |
426 { | |
427 case PixelFormat_Grayscale8: | |
428 case PixelFormat_Grayscale16: | |
429 case PixelFormat_SignedGrayscale16: | |
430 { | |
431 int64_t a, b; | |
432 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
433 json["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); | |
434 json["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
435 json["color"] = false; | |
436 | |
437 windowCenter = static_cast<float>(a + b) / 2.0f; | |
438 | |
439 if (a == b) | |
440 { | |
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441 windowWidth = 256.0f; // Arbitrary value |
0 | 442 } |
443 else | |
444 { | |
445 windowWidth = static_cast<float>(b - a) / 2.0f; | |
446 } | |
447 | |
448 break; | |
449 } | |
450 | |
451 case PixelFormat_RGB24: | |
452 json["minPixelValue"] = 0; | |
453 json["maxPixelValue"] = 255; | |
454 json["color"] = true; | |
455 windowCenter = 127.5f; | |
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456 windowWidth = 256.0f; |
0 | 457 break; |
458 | |
459 default: | |
460 return false; | |
461 } | |
462 | |
463 const gdcm::Image& image = pimpl_->GetImage(); | |
464 json["slope"] = image.GetSlope(); | |
465 json["intercept"] = image.GetIntercept(); | |
466 json["rows"] = image.GetRows(); | |
467 json["columns"] = image.GetColumns(); | |
468 json["height"] = image.GetRows(); | |
469 json["width"] = image.GetColumns(); | |
470 json["columnPixelSpacing"] = image.GetSpacing(1); | |
471 json["rowPixelSpacing"] = image.GetSpacing(0); | |
472 | |
473 json["windowCenter"] = windowCenter * image.GetSlope() + image.GetIntercept(); | |
474 json["windowWidth"] = windowWidth * image.GetSlope(); | |
475 | |
476 try | |
477 { | |
478 std::string width, center; | |
479 if (GetTag(center, 0x0028, 0x1050 /*DICOM_TAG_WINDOW_CENTER*/) && | |
480 GetTag(width, 0x0028, 0x1051 /*DICOM_TAG_WINDOW_WIDTH*/)) | |
481 { | |
482 float a = boost::lexical_cast<float>(width); | |
483 float b = boost::lexical_cast<float>(center); | |
484 json["windowWidth"] = a; | |
485 json["windowCenter"] = b; | |
486 } | |
487 } | |
488 catch (boost::bad_lexical_cast&) | |
489 { | |
490 } | |
491 | |
492 return true; | |
493 } | |
494 | |
495 | |
496 bool ParsedDicomImage::EncodeUsingDeflate(Json::Value& result, | |
497 uint8_t compressionLevel /* between 0 and 9 */) | |
498 { | |
499 using namespace Orthanc; | |
500 | |
501 ImageAccessor accessor; | |
31 | 502 if (!pimpl_->GetAccessor(accessor)) |
0 | 503 { |
504 return false; | |
505 } | |
506 | |
507 result = Json::objectValue; | |
508 result["Orthanc"] = Json::objectValue; | |
509 if (!GetCornerstoneMetadata(result)) | |
510 { | |
511 return false; | |
512 } | |
513 | |
514 ImageBuffer buffer; | |
515 buffer.SetMinimalPitchForced(true); | |
516 | |
517 ImageAccessor converted; | |
518 | |
519 | |
520 switch (accessor.GetFormat()) | |
521 { | |
522 case Orthanc::PixelFormat_RGB24: | |
523 converted = accessor; | |
524 break; | |
525 | |
526 case Orthanc::PixelFormat_Grayscale8: | |
527 case Orthanc::PixelFormat_Grayscale16: | |
528 buffer.SetFormat(Orthanc::PixelFormat_SignedGrayscale16); | |
529 buffer.SetWidth(accessor.GetWidth()); | |
530 buffer.SetHeight(accessor.GetHeight()); | |
531 converted = buffer.GetAccessor(); | |
532 ImageProcessing::Convert(converted, accessor); | |
533 break; | |
534 | |
535 case Orthanc::PixelFormat_SignedGrayscale16: | |
536 converted = accessor; | |
537 break; | |
538 | |
539 default: | |
540 // Unsupported pixel format | |
541 return false; | |
542 } | |
543 | |
544 // Sanity check: The pitch must be minimal | |
545 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
546 GetBytesPerPixel(converted.GetFormat())); | |
547 result["Orthanc"]["Compression"] = "Deflate"; | |
548 result["sizeInBytes"] = converted.GetSize(); | |
549 | |
550 std::string z; | |
79 | 551 CompressUsingDeflate(z, pimpl_->GetContext(), converted.GetConstBuffer(), converted.GetSize()); |
0 | 552 |
553 result["Orthanc"]["PixelData"] = base64_encode(z); | |
554 | |
555 return true; | |
556 } | |
557 | |
558 | |
559 | |
560 bool ParsedDicomImage::EncodeUsingJpeg(Json::Value& result, | |
561 uint8_t quality /* between 0 and 100 */) | |
562 { | |
563 using namespace Orthanc; | |
564 | |
565 ImageAccessor accessor; | |
31 | 566 if (!pimpl_->GetAccessor(accessor)) |
0 | 567 { |
568 return false; | |
569 } | |
570 | |
571 result = Json::objectValue; | |
572 result["Orthanc"] = Json::objectValue; | |
573 GetCornerstoneMetadata(result); | |
574 | |
575 ImageBuffer buffer; | |
576 buffer.SetMinimalPitchForced(true); | |
577 | |
578 ImageAccessor converted; | |
579 | |
580 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
581 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
582 { | |
583 result["Orthanc"]["Stretched"] = false; | |
584 converted = accessor; | |
585 } | |
586 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || | |
587 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
588 { | |
589 result["Orthanc"]["Stretched"] = true; | |
590 buffer.SetFormat(Orthanc::PixelFormat_Grayscale8); | |
591 buffer.SetWidth(accessor.GetWidth()); | |
592 buffer.SetHeight(accessor.GetHeight()); | |
593 converted = buffer.GetAccessor(); | |
594 | |
595 int64_t a, b; | |
596 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
597 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
598 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
599 | |
600 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
601 { | |
602 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
603 } | |
604 else | |
605 { | |
606 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
607 } | |
608 } | |
609 else | |
610 { | |
611 return false; | |
612 } | |
613 | |
614 result["Orthanc"]["Compression"] = "Jpeg"; | |
615 result["sizeInBytes"] = converted.GetSize(); | |
616 | |
617 std::string jpeg; | |
79 | 618 WriteJpegToMemory(jpeg, pimpl_->GetContext(), converted, quality); |
619 | |
0 | 620 result["Orthanc"]["PixelData"] = base64_encode(jpeg); |
621 return true; | |
622 } | |
26 | 623 } |