Mercurial > hg > orthanc-webviewer
comparison Plugin/ParsedDicomImage.cpp @ 0:02f7a0400a91
initial commit
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 25 Feb 2015 13:45:35 +0100 |
parents | |
children | 828c61fc8253 |
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-1:000000000000 | 0:02f7a0400a91 |
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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 | |
23 #include "../Orthanc/OrthancException.h" | |
24 #include "../Orthanc/Toolbox.h" | |
25 #include "../Orthanc/ImageFormats/ImageProcessing.h" | |
26 #include "../Orthanc/ImageFormats/ImageBuffer.h" | |
27 #include "JpegWriter.h" | |
28 #include "ViewerToolbox.h" | |
29 | |
30 #include <gdcmImageReader.h> | |
31 #include <gdcmImageChangePlanarConfiguration.h> | |
32 #include <gdcmImageChangePhotometricInterpretation.h> | |
33 #include <boost/lexical_cast.hpp> | |
34 #include <boost/math/special_functions/round.hpp> | |
35 | |
36 #include "../Resources/ThirdParty/base64/base64.h" | |
37 | |
38 | |
39 namespace OrthancPlugins | |
40 { | |
41 struct ParsedDicomImage::PImpl | |
42 { | |
43 gdcm::ImageReader reader_; | |
44 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_; | |
45 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_; | |
46 std::string decoded_; | |
47 | |
48 const gdcm::Image& GetImage() const | |
49 { | |
50 if (interleaved_.get() != NULL) | |
51 { | |
52 return interleaved_->GetOutput(); | |
53 } | |
54 | |
55 if (photometric_.get() != NULL) | |
56 { | |
57 return photometric_->GetOutput(); | |
58 } | |
59 | |
60 return reader_.GetImage(); | |
61 } | |
62 | |
63 | |
64 const gdcm::DataSet& GetDataSet() const | |
65 { | |
66 return reader_.GetFile().GetDataSet(); | |
67 } | |
68 }; | |
69 | |
70 | |
71 template <typename TargetType, typename SourceType> | |
72 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
73 const Orthanc::ImageAccessor& source, | |
74 SourceType source1, TargetType target1, | |
75 SourceType source2, TargetType target2) | |
76 { | |
77 if (source.GetWidth() != target.GetWidth() || | |
78 source.GetHeight() != target.GetHeight()) | |
79 { | |
80 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
81 } | |
82 | |
83 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
84 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
85 | |
86 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
87 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
88 | |
89 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
90 { | |
91 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
92 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
93 | |
94 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
95 { | |
96 float v = (scale * static_cast<float>(*p)) + offset; | |
97 | |
98 if (v > maxValue) | |
99 { | |
100 *q = std::numeric_limits<TargetType>::max(); | |
101 } | |
102 else if (v < minValue) | |
103 { | |
104 *q = std::numeric_limits<TargetType>::min(); | |
105 } | |
106 else | |
107 { | |
108 *q = static_cast<TargetType>(boost::math::iround(v)); | |
109 } | |
110 } | |
111 } | |
112 } | |
113 | |
114 | |
115 void ParsedDicomImage::Setup(const std::string& dicom) | |
116 { | |
117 // Prepare a memory stream over the DICOM instance | |
118 std::stringstream stream(dicom); | |
119 | |
120 // Parse the DICOM instance using GDCM | |
121 pimpl_->reader_.SetStream(stream); | |
122 if (!pimpl_->reader_.Read()) | |
123 { | |
124 throw Orthanc::OrthancException("GDCM cannot extract an image from this DICOM instance"); | |
125 } | |
126 | |
127 // Change photometric interpretation, if required | |
128 { | |
129 const gdcm::Image& image = pimpl_->GetImage(); | |
130 if (image.GetPixelFormat().GetSamplesPerPixel() == 1) | |
131 { | |
132 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 && | |
133 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2) | |
134 { | |
135 pimpl_->photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
136 pimpl_->photometric_->SetInput(image); | |
137 pimpl_->photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); | |
138 if (!pimpl_->photometric_->Change()) | |
139 { | |
140 throw Orthanc::OrthancException("GDCM cannot change the photometric interpretation"); | |
141 } | |
142 } | |
143 } | |
144 else | |
145 { | |
146 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
147 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB) | |
148 { | |
149 pimpl_->photometric_.reset(new gdcm::ImageChangePhotometricInterpretation()); | |
150 pimpl_->photometric_->SetInput(image); | |
151 pimpl_->photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); | |
152 if (!pimpl_->photometric_->Change()) | |
153 { | |
154 throw Orthanc::OrthancException("GDCM cannot change the photometric interpretation"); | |
155 } | |
156 } | |
157 } | |
158 } | |
159 | |
160 // Possibly convert planar configuration to interleaved | |
161 { | |
162 const gdcm::Image& image = pimpl_->GetImage(); | |
163 if (image.GetPlanarConfiguration() != 0 && | |
164 image.GetPixelFormat().GetSamplesPerPixel() != 1) | |
165 { | |
166 pimpl_->interleaved_.reset(new gdcm::ImageChangePlanarConfiguration()); | |
167 pimpl_->interleaved_->SetInput(image); | |
168 if (!pimpl_->interleaved_->Change()) | |
169 { | |
170 throw Orthanc::OrthancException("GDCM cannot change the planar configuration to interleaved"); | |
171 } | |
172 } | |
173 } | |
174 | |
175 // Decode the image to the memory buffer | |
176 { | |
177 const gdcm::Image& image = pimpl_->GetImage(); | |
178 pimpl_->decoded_.resize(image.GetBufferLength()); | |
179 | |
180 if (pimpl_->decoded_.size() > 0) | |
181 { | |
182 image.GetBuffer(&pimpl_->decoded_[0]); | |
183 } | |
184 } | |
185 } | |
186 | |
187 | |
188 ParsedDicomImage::ParsedDicomImage(const std::string& dicom) : pimpl_(new PImpl) | |
189 { | |
190 Setup(dicom); | |
191 } | |
192 | |
193 | |
194 bool ParsedDicomImage::GetTag(std::string& result, | |
195 uint16_t group, | |
196 uint16_t element, | |
197 bool stripSpaces) | |
198 { | |
199 const gdcm::Tag tag(group, element); | |
200 | |
201 if (pimpl_->GetDataSet().FindDataElement(tag)) | |
202 { | |
203 const gdcm::ByteValue* value = pimpl_->GetDataSet().GetDataElement(tag).GetByteValue(); | |
204 if (value) | |
205 { | |
206 result = std::string(value->GetPointer(), value->GetLength()); | |
207 | |
208 if (stripSpaces) | |
209 { | |
210 result = Orthanc::Toolbox::StripSpaces(result); | |
211 } | |
212 | |
213 return true; | |
214 } | |
215 } | |
216 | |
217 return false; | |
218 } | |
219 | |
220 | |
221 bool ParsedDicomImage::GetAccessor(Orthanc::ImageAccessor& accessor) | |
222 { | |
223 const gdcm::Image& image = pimpl_->GetImage(); | |
224 | |
225 size_t size = pimpl_->decoded_.size(); | |
226 void* buffer = (size ? &pimpl_->decoded_[0] : NULL); | |
227 unsigned int height = image.GetRows(); | |
228 unsigned int width = image.GetColumns(); | |
229 | |
230 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 && | |
231 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 || | |
232 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2)) | |
233 { | |
234 switch (image.GetPixelFormat()) | |
235 { | |
236 case gdcm::PixelFormat::UINT16: | |
237 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale16, width, height, 2 * width, buffer); | |
238 return true; | |
239 | |
240 case gdcm::PixelFormat::INT16: | |
241 accessor.AssignWritable(Orthanc::PixelFormat_SignedGrayscale16, width, height, 2 * width, buffer); | |
242 return true; | |
243 | |
244 case gdcm::PixelFormat::UINT8: | |
245 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale8, width, height, width, buffer); | |
246 return true; | |
247 } | |
248 } | |
249 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 && | |
250 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB) | |
251 { | |
252 switch (image.GetPixelFormat()) | |
253 { | |
254 case gdcm::PixelFormat::UINT8: | |
255 accessor.AssignWritable(Orthanc::PixelFormat_RGB24, width, height, 3 * width, buffer); | |
256 return true; | |
257 } | |
258 } | |
259 | |
260 return false; | |
261 } | |
262 | |
263 bool ParsedDicomImage::GetCornerstoneMetadata(Json::Value& json) | |
264 { | |
265 using namespace Orthanc; | |
266 | |
267 ImageAccessor accessor; | |
268 if (!GetAccessor(accessor)) | |
269 { | |
270 return false; | |
271 } | |
272 | |
273 float windowCenter, windowWidth; | |
274 | |
275 switch (accessor.GetFormat()) | |
276 { | |
277 case PixelFormat_Grayscale8: | |
278 case PixelFormat_Grayscale16: | |
279 case PixelFormat_SignedGrayscale16: | |
280 { | |
281 int64_t a, b; | |
282 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
283 json["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); | |
284 json["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
285 json["color"] = false; | |
286 | |
287 windowCenter = static_cast<float>(a + b) / 2.0f; | |
288 | |
289 if (a == b) | |
290 { | |
291 windowWidth = 127.5f; // Arbitrary value | |
292 } | |
293 else | |
294 { | |
295 windowWidth = static_cast<float>(b - a) / 2.0f; | |
296 } | |
297 | |
298 break; | |
299 } | |
300 | |
301 case PixelFormat_RGB24: | |
302 json["minPixelValue"] = 0; | |
303 json["maxPixelValue"] = 255; | |
304 json["color"] = true; | |
305 windowCenter = 127.5f; | |
306 windowWidth = 127.5f; | |
307 break; | |
308 | |
309 default: | |
310 return false; | |
311 } | |
312 | |
313 const gdcm::Image& image = pimpl_->GetImage(); | |
314 json["slope"] = image.GetSlope(); | |
315 json["intercept"] = image.GetIntercept(); | |
316 json["rows"] = image.GetRows(); | |
317 json["columns"] = image.GetColumns(); | |
318 json["height"] = image.GetRows(); | |
319 json["width"] = image.GetColumns(); | |
320 json["columnPixelSpacing"] = image.GetSpacing(1); | |
321 json["rowPixelSpacing"] = image.GetSpacing(0); | |
322 | |
323 json["windowCenter"] = windowCenter * image.GetSlope() + image.GetIntercept(); | |
324 json["windowWidth"] = windowWidth * image.GetSlope(); | |
325 | |
326 try | |
327 { | |
328 std::string width, center; | |
329 if (GetTag(center, 0x0028, 0x1050 /*DICOM_TAG_WINDOW_CENTER*/) && | |
330 GetTag(width, 0x0028, 0x1051 /*DICOM_TAG_WINDOW_WIDTH*/)) | |
331 { | |
332 float a = boost::lexical_cast<float>(width); | |
333 float b = boost::lexical_cast<float>(center); | |
334 json["windowWidth"] = a; | |
335 json["windowCenter"] = b; | |
336 } | |
337 } | |
338 catch (boost::bad_lexical_cast&) | |
339 { | |
340 } | |
341 | |
342 return true; | |
343 } | |
344 | |
345 | |
346 bool ParsedDicomImage::EncodeUsingDeflate(Json::Value& result, | |
347 uint8_t compressionLevel /* between 0 and 9 */) | |
348 { | |
349 using namespace Orthanc; | |
350 | |
351 ImageAccessor accessor; | |
352 if (!GetAccessor(accessor)) | |
353 { | |
354 return false; | |
355 } | |
356 | |
357 result = Json::objectValue; | |
358 result["Orthanc"] = Json::objectValue; | |
359 if (!GetCornerstoneMetadata(result)) | |
360 { | |
361 return false; | |
362 } | |
363 | |
364 ImageBuffer buffer; | |
365 buffer.SetMinimalPitchForced(true); | |
366 | |
367 ImageAccessor converted; | |
368 | |
369 | |
370 switch (accessor.GetFormat()) | |
371 { | |
372 case Orthanc::PixelFormat_RGB24: | |
373 converted = accessor; | |
374 break; | |
375 | |
376 case Orthanc::PixelFormat_Grayscale8: | |
377 case Orthanc::PixelFormat_Grayscale16: | |
378 buffer.SetFormat(Orthanc::PixelFormat_SignedGrayscale16); | |
379 buffer.SetWidth(accessor.GetWidth()); | |
380 buffer.SetHeight(accessor.GetHeight()); | |
381 converted = buffer.GetAccessor(); | |
382 ImageProcessing::Convert(converted, accessor); | |
383 break; | |
384 | |
385 case Orthanc::PixelFormat_SignedGrayscale16: | |
386 converted = accessor; | |
387 break; | |
388 | |
389 default: | |
390 // Unsupported pixel format | |
391 return false; | |
392 } | |
393 | |
394 // Sanity check: The pitch must be minimal | |
395 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
396 GetBytesPerPixel(converted.GetFormat())); | |
397 result["Orthanc"]["Compression"] = "Deflate"; | |
398 result["sizeInBytes"] = converted.GetSize(); | |
399 | |
400 std::string z; | |
401 if (!CompressUsingDeflate(z, converted.GetConstBuffer(), converted.GetSize(), compressionLevel)) | |
402 { | |
403 return false; | |
404 } | |
405 | |
406 result["Orthanc"]["PixelData"] = base64_encode(z); | |
407 | |
408 return true; | |
409 } | |
410 | |
411 | |
412 | |
413 bool ParsedDicomImage::EncodeUsingJpeg(Json::Value& result, | |
414 uint8_t quality /* between 0 and 100 */) | |
415 { | |
416 using namespace Orthanc; | |
417 | |
418 ImageAccessor accessor; | |
419 if (!GetAccessor(accessor)) | |
420 { | |
421 return false; | |
422 } | |
423 | |
424 result = Json::objectValue; | |
425 result["Orthanc"] = Json::objectValue; | |
426 GetCornerstoneMetadata(result); | |
427 | |
428 ImageBuffer buffer; | |
429 buffer.SetMinimalPitchForced(true); | |
430 | |
431 ImageAccessor converted; | |
432 | |
433 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
434 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
435 { | |
436 result["Orthanc"]["Stretched"] = false; | |
437 converted = accessor; | |
438 } | |
439 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || | |
440 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
441 { | |
442 result["Orthanc"]["Stretched"] = true; | |
443 buffer.SetFormat(Orthanc::PixelFormat_Grayscale8); | |
444 buffer.SetWidth(accessor.GetWidth()); | |
445 buffer.SetHeight(accessor.GetHeight()); | |
446 converted = buffer.GetAccessor(); | |
447 | |
448 int64_t a, b; | |
449 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
450 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
451 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
452 | |
453 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
454 { | |
455 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
456 } | |
457 else | |
458 { | |
459 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
460 } | |
461 } | |
462 else | |
463 { | |
464 return false; | |
465 } | |
466 | |
467 result["Orthanc"]["Compression"] = "Jpeg"; | |
468 result["sizeInBytes"] = converted.GetSize(); | |
469 | |
470 std::string jpeg; | |
471 OrthancPlugins::JpegWriter writer; | |
472 writer.SetQuality(quality); | |
473 writer.WriteToMemory(jpeg, converted); | |
474 result["Orthanc"]["PixelData"] = base64_encode(jpeg); | |
475 return true; | |
476 } | |
477 }; |