Mercurial > hg > orthanc-stone
comparison OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1512:244ad1e4e76a
reorganization of folders
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 07 Jul 2020 16:21:02 +0200 |
parents | Framework/Toolbox/DicomInstanceParameters.cpp@970ee51fe01f |
children | 85e117739eca |
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1511:9dfeee74c1e6 | 1512:244ad1e4e76a |
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1 /** | |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * Copyright (C) 2017-2020 Osimis S.A., Belgium | |
6 * | |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
22 #include "DicomInstanceParameters.h" | |
23 | |
24 #include "../Scene2D/ColorTextureSceneLayer.h" | |
25 #include "../Scene2D/FloatTextureSceneLayer.h" | |
26 #include "../Toolbox/GeometryToolbox.h" | |
27 #include "../Toolbox/ImageToolbox.h" | |
28 | |
29 #include <Images/Image.h> | |
30 #include <Images/ImageProcessing.h> | |
31 #include <Logging.h> | |
32 #include <OrthancException.h> | |
33 #include <Toolbox.h> | |
34 | |
35 | |
36 namespace OrthancStone | |
37 { | |
38 void DicomInstanceParameters::Data::ComputeDoseOffsets(const Orthanc::DicomMap& dicom) | |
39 { | |
40 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html | |
41 | |
42 { | |
43 std::string increment; | |
44 | |
45 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) | |
46 { | |
47 Orthanc::Toolbox::ToUpperCase(increment); | |
48 if (increment != "3004,000C") // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) | |
49 { | |
50 LOG(ERROR) << "RT-DOSE: Bad value for the \"FrameIncrementPointer\" tag"; | |
51 return; | |
52 } | |
53 } | |
54 } | |
55 | |
56 if (!LinearAlgebra::ParseVector(frameOffsets_, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) || | |
57 frameOffsets_.size() < imageInformation_.GetNumberOfFrames()) | |
58 { | |
59 LOG(ERROR) << "RT-DOSE: No information about the 3D location of some slice(s)"; | |
60 frameOffsets_.clear(); | |
61 } | |
62 else | |
63 { | |
64 if (frameOffsets_.size() >= 2) | |
65 { | |
66 thickness_ = std::abs(frameOffsets_[1] - frameOffsets_[0]); | |
67 } | |
68 } | |
69 } | |
70 | |
71 | |
72 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) : | |
73 imageInformation_(dicom) | |
74 { | |
75 if (imageInformation_.GetNumberOfFrames() <= 0) | |
76 { | |
77 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
78 } | |
79 | |
80 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || | |
81 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || | |
82 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) | |
83 { | |
84 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
85 } | |
86 | |
87 std::string s; | |
88 if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) | |
89 { | |
90 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
91 } | |
92 else | |
93 { | |
94 sopClassUid_ = StringToSopClassUid(s); | |
95 } | |
96 | |
97 if (!dicom.ParseDouble(thickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) | |
98 { | |
99 thickness_ = 100.0 * std::numeric_limits<double>::epsilon(); | |
100 } | |
101 | |
102 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); | |
103 | |
104 std::string position, orientation; | |
105 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && | |
106 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) | |
107 { | |
108 geometry_ = CoordinateSystem3D(position, orientation); | |
109 } | |
110 | |
111 if (sopClassUid_ == SopClassUid_RTDose) | |
112 { | |
113 ComputeDoseOffsets(dicom); | |
114 | |
115 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); | |
116 | |
117 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) | |
118 { | |
119 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; | |
120 doseUnits_ = ""; | |
121 } | |
122 } | |
123 | |
124 isColor_ = (imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome1 && | |
125 imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome2); | |
126 | |
127 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
128 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
129 { | |
130 if (sopClassUid_ == SopClassUid_RTDose) | |
131 { | |
132 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; | |
133 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES | |
134 hasRescale_ = false; | |
135 } | |
136 else | |
137 { | |
138 hasRescale_ = true; | |
139 } | |
140 | |
141 } | |
142 else | |
143 { | |
144 hasRescale_ = false; | |
145 } | |
146 | |
147 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) | |
148 { | |
149 if (sopClassUid_ == SopClassUid_RTDose) | |
150 { | |
151 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; | |
152 } | |
153 } | |
154 else | |
155 { | |
156 doseGridScaling_ = 1.0; | |
157 if (sopClassUid_ == SopClassUid_RTDose) | |
158 { | |
159 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; | |
160 } | |
161 } | |
162 | |
163 Vector c, w; | |
164 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && | |
165 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) && | |
166 c.size() > 0 && | |
167 w.size() > 0) | |
168 { | |
169 hasDefaultWindowing_ = true; | |
170 defaultWindowingCenter_ = static_cast<float>(c[0]); | |
171 defaultWindowingWidth_ = static_cast<float>(w[0]); | |
172 } | |
173 else | |
174 { | |
175 hasDefaultWindowing_ = false; | |
176 defaultWindowingCenter_ = 0; | |
177 defaultWindowingWidth_ = 0; | |
178 } | |
179 | |
180 if (sopClassUid_ == SopClassUid_RTDose) | |
181 { | |
182 switch (imageInformation_.GetBitsStored()) | |
183 { | |
184 case 16: | |
185 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
186 break; | |
187 | |
188 case 32: | |
189 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32; | |
190 break; | |
191 | |
192 default: | |
193 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
194 } | |
195 } | |
196 else if (isColor_) | |
197 { | |
198 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24; | |
199 } | |
200 else if (imageInformation_.IsSigned()) | |
201 { | |
202 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16; | |
203 } | |
204 else | |
205 { | |
206 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
207 } | |
208 | |
209 // This computes the "IndexInSeries" metadata from Orthanc (check | |
210 // out "Orthanc::ServerIndex::Store()") | |
211 hasIndexInSeries_ = ( | |
212 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || | |
213 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); | |
214 } | |
215 | |
216 | |
217 CoordinateSystem3D DicomInstanceParameters::Data::GetFrameGeometry(unsigned int frame) const | |
218 { | |
219 if (frame == 0) | |
220 { | |
221 return geometry_; | |
222 } | |
223 else if (frame >= imageInformation_.GetNumberOfFrames()) | |
224 { | |
225 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
226 } | |
227 else if (sopClassUid_ == SopClassUid_RTDose) | |
228 { | |
229 if (frame >= frameOffsets_.size()) | |
230 { | |
231 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
232 } | |
233 | |
234 return CoordinateSystem3D( | |
235 geometry_.GetOrigin() + frameOffsets_[frame] * geometry_.GetNormal(), | |
236 geometry_.GetAxisX(), | |
237 geometry_.GetAxisY()); | |
238 } | |
239 else | |
240 { | |
241 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
242 } | |
243 } | |
244 | |
245 | |
246 bool DicomInstanceParameters::Data::IsPlaneWithinSlice(unsigned int frame, | |
247 const CoordinateSystem3D& plane) const | |
248 { | |
249 if (frame >= imageInformation_.GetNumberOfFrames()) | |
250 { | |
251 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
252 } | |
253 | |
254 CoordinateSystem3D tmp = geometry_; | |
255 | |
256 if (frame != 0) | |
257 { | |
258 tmp = GetFrameGeometry(frame); | |
259 } | |
260 | |
261 double distance; | |
262 | |
263 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && | |
264 distance <= thickness_ / 2.0); | |
265 } | |
266 | |
267 void DicomInstanceParameters::Data::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, | |
268 bool useDouble) const | |
269 { | |
270 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
271 { | |
272 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
273 } | |
274 | |
275 double factor = doseGridScaling_; | |
276 double offset = 0.0; | |
277 | |
278 if (hasRescale_) | |
279 { | |
280 factor *= rescaleSlope_; | |
281 offset = rescaleIntercept_; | |
282 } | |
283 | |
284 if ( (factor != 1.0) || (offset != 0.0) ) | |
285 { | |
286 const unsigned int width = image.GetWidth(); | |
287 const unsigned int height = image.GetHeight(); | |
288 | |
289 for (unsigned int y = 0; y < height; y++) | |
290 { | |
291 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
292 | |
293 if (useDouble) | |
294 { | |
295 // Slower, accurate implementation using double | |
296 for (unsigned int x = 0; x < width; x++, p++) | |
297 { | |
298 double value = static_cast<double>(*p); | |
299 *p = static_cast<float>(value * factor + offset); | |
300 } | |
301 } | |
302 else | |
303 { | |
304 // Fast, approximate implementation using float | |
305 for (unsigned int x = 0; x < width; x++, p++) | |
306 { | |
307 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset); | |
308 } | |
309 } | |
310 } | |
311 } | |
312 } | |
313 | |
314 double DicomInstanceParameters::GetRescaleIntercept() const | |
315 { | |
316 if (data_.hasRescale_) | |
317 { | |
318 return data_.rescaleIntercept_; | |
319 } | |
320 else | |
321 { | |
322 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; | |
323 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
324 } | |
325 } | |
326 | |
327 | |
328 double DicomInstanceParameters::GetRescaleSlope() const | |
329 { | |
330 if (data_.hasRescale_) | |
331 { | |
332 return data_.rescaleSlope_; | |
333 } | |
334 else | |
335 { | |
336 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; | |
337 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
338 } | |
339 } | |
340 | |
341 | |
342 float DicomInstanceParameters::GetDefaultWindowingCenter() const | |
343 { | |
344 if (data_.hasDefaultWindowing_) | |
345 { | |
346 return data_.defaultWindowingCenter_; | |
347 } | |
348 else | |
349 { | |
350 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): no default windowing"; | |
351 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
352 } | |
353 } | |
354 | |
355 | |
356 float DicomInstanceParameters::GetDefaultWindowingWidth() const | |
357 { | |
358 if (data_.hasDefaultWindowing_) | |
359 { | |
360 return data_.defaultWindowingWidth_; | |
361 } | |
362 else | |
363 { | |
364 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): no default windowing"; | |
365 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
366 } | |
367 } | |
368 | |
369 | |
370 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const | |
371 { | |
372 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, | |
373 pixelData.GetWidth(), | |
374 pixelData.GetHeight(), | |
375 false)); | |
376 Orthanc::ImageProcessing::Convert(*converted, pixelData); | |
377 | |
378 | |
379 // Correct rescale slope/intercept if need be | |
380 //data_.ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); | |
381 data_.ApplyRescaleAndDoseScaling(*converted, false); | |
382 | |
383 return converted.release(); | |
384 } | |
385 | |
386 | |
387 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture | |
388 (const Orthanc::ImageAccessor& pixelData) const | |
389 { | |
390 // { | |
391 // const Orthanc::ImageAccessor& source = pixelData; | |
392 // const void* sourceBuffer = source.GetConstBuffer(); | |
393 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); | |
394 // int sourceWidth = source.GetWidth(); | |
395 // int sourceHeight = source.GetHeight(); | |
396 // int sourcePitch = source.GetPitch(); | |
397 | |
398 // // TODO: turn error into trace below | |
399 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" | |
400 // << " W = " << sourceWidth << " H = " << sourceHeight | |
401 // << " P = " << sourcePitch << " B = " << sourceBufferInt | |
402 // << " B % 4 == " << sourceBufferInt % 4; | |
403 // } | |
404 | |
405 assert(sizeof(float) == 4); | |
406 | |
407 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
408 | |
409 if (sourceFormat != GetExpectedPixelFormat()) | |
410 { | |
411 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
412 } | |
413 | |
414 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
415 { | |
416 // This is the case of a color image. No conversion has to be done. | |
417 return new ColorTextureSceneLayer(pixelData); | |
418 } | |
419 else | |
420 { | |
421 // This is the case of a grayscale frame. Convert it to Float32. | |
422 std::unique_ptr<FloatTextureSceneLayer> texture; | |
423 | |
424 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) | |
425 { | |
426 texture.reset(new FloatTextureSceneLayer(pixelData)); | |
427 } | |
428 else | |
429 { | |
430 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); | |
431 texture.reset(new FloatTextureSceneLayer(*converted)); | |
432 } | |
433 | |
434 if (data_.hasDefaultWindowing_) | |
435 { | |
436 texture->SetCustomWindowing(data_.defaultWindowingCenter_, | |
437 data_.defaultWindowingWidth_); | |
438 } | |
439 | |
440 | |
441 if (data_.imageInformation_.GetPhotometricInterpretation() | |
442 == Orthanc::PhotometricInterpretation_Monochrome1) | |
443 { | |
444 texture->SetInverted(true); | |
445 } | |
446 else if (data_.imageInformation_.GetPhotometricInterpretation() | |
447 == Orthanc::PhotometricInterpretation_Monochrome2) | |
448 { | |
449 texture->SetInverted(false); | |
450 } | |
451 | |
452 return texture.release(); | |
453 } | |
454 } | |
455 | |
456 | |
457 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture | |
458 (const Orthanc::ImageAccessor& pixelData) const | |
459 { | |
460 std::unique_ptr<FloatTextureSceneLayer> texture; | |
461 | |
462 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) | |
463 { | |
464 return new LookupTableTextureSceneLayer(pixelData); | |
465 } | |
466 else | |
467 { | |
468 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); | |
469 return new LookupTableTextureSceneLayer(*converted); | |
470 } | |
471 } | |
472 | |
473 | |
474 unsigned int DicomInstanceParameters::GetIndexInSeries() const | |
475 { | |
476 if (data_.hasIndexInSeries_) | |
477 { | |
478 return data_.indexInSeries_; | |
479 } | |
480 else | |
481 { | |
482 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; | |
483 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); | |
484 } | |
485 } | |
486 | |
487 | |
488 double DicomInstanceParameters::Data::ApplyRescale(double value) const | |
489 { | |
490 double factor = doseGridScaling_; | |
491 double offset = 0.0; | |
492 | |
493 if (hasRescale_) | |
494 { | |
495 factor *= rescaleSlope_; | |
496 offset = rescaleIntercept_; | |
497 } | |
498 | |
499 return (value * factor + offset); | |
500 } | |
501 | |
502 | |
503 bool DicomInstanceParameters::Data::ComputeRegularSpacing(double& spacing) const | |
504 { | |
505 if (frameOffsets_.size() == 0) // Not a RT-DOSE | |
506 { | |
507 return false; | |
508 } | |
509 else if (frameOffsets_.size() == 1) | |
510 { | |
511 spacing = 1; // Edge case: RT-DOSE with one single frame | |
512 return true; | |
513 } | |
514 else | |
515 { | |
516 spacing = std::abs(frameOffsets_[1] - frameOffsets_[0]); | |
517 | |
518 for (size_t i = 1; i + 1 < frameOffsets_.size(); i++) | |
519 { | |
520 double s = frameOffsets_[i + 1] - frameOffsets_[i]; | |
521 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) | |
522 { | |
523 return false; | |
524 } | |
525 } | |
526 | |
527 return true; | |
528 } | |
529 } | |
530 } |