Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomInstanceParameters.cpp @ 1094:dead648f8ff1
Added tag toa2019102302 for changeset df76d3083031
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Wed, 23 Oct 2019 16:10:35 +0200 |
parents | 5a18e6a395bc |
children | 7681f3943748 |
rev | line source |
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746 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * Copyright (C) 2017-2019 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 | |
28 #include <Core/Images/Image.h> | |
29 #include <Core/Images/ImageProcessing.h> | |
30 #include <Core/Logging.h> | |
31 #include <Core/OrthancException.h> | |
32 #include <Core/Toolbox.h> | |
33 | |
34 | |
35 namespace OrthancStone | |
36 { | |
37 void DicomInstanceParameters::Data::ComputeDoseOffsets(const Orthanc::DicomMap& dicom) | |
38 { | |
39 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html | |
40 | |
41 { | |
42 std::string increment; | |
43 | |
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44 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) |
746 | 45 { |
46 Orthanc::Toolbox::ToUpperCase(increment); | |
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47 if (increment != "3004,000C") // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) |
746 | 48 { |
49 LOG(ERROR) << "RT-DOSE: Bad value for the \"FrameIncrementPointer\" tag"; | |
50 return; | |
51 } | |
52 } | |
53 } | |
54 | |
55 if (!LinearAlgebra::ParseVector(frameOffsets_, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) || | |
56 frameOffsets_.size() < imageInformation_.GetNumberOfFrames()) | |
57 { | |
58 LOG(ERROR) << "RT-DOSE: No information about the 3D location of some slice(s)"; | |
59 frameOffsets_.clear(); | |
60 } | |
61 else | |
62 { | |
63 if (frameOffsets_.size() >= 2) | |
64 { | |
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65 thickness_ = std::abs(frameOffsets_[1] - frameOffsets_[0]); |
746 | 66 } |
67 } | |
68 } | |
69 | |
70 | |
71 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) : | |
72 imageInformation_(dicom) | |
73 { | |
74 if (imageInformation_.GetNumberOfFrames() <= 0) | |
75 { | |
76 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
77 } | |
78 | |
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79 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || |
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80 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || |
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81 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
746 | 82 { |
83 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
84 } | |
85 | |
86 std::string s; | |
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87 if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) |
746 | 88 { |
89 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
90 } | |
91 else | |
92 { | |
93 sopClassUid_ = StringToSopClassUid(s); | |
94 } | |
95 | |
96 if (!dicom.ParseDouble(thickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) | |
97 { | |
98 thickness_ = 100.0 * std::numeric_limits<double>::epsilon(); | |
99 } | |
100 | |
101 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); | |
102 | |
103 std::string position, orientation; | |
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104 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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105 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
746 | 106 { |
107 geometry_ = CoordinateSystem3D(position, orientation); | |
108 } | |
109 | |
110 if (sopClassUid_ == SopClassUid_RTDose) | |
111 { | |
112 ComputeDoseOffsets(dicom); | |
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113 |
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114 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); |
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115 |
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116 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) |
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117 { |
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118 LOG(WARNING) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
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119 doseUnits_ = ""; |
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120 } |
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121 |
746 | 122 } |
123 | |
124 isColor_ = (imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome1 && | |
125 imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome2); | |
126 | |
127 double doseGridScaling; | |
128 | |
129 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
130 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
131 { | |
132 hasRescale_ = true; | |
133 } | |
134 else if (dicom.ParseDouble(doseGridScaling, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) | |
135 { | |
136 hasRescale_ = true; | |
137 rescaleIntercept_ = 0; | |
138 rescaleSlope_ = doseGridScaling; | |
139 } | |
140 else | |
141 { | |
142 hasRescale_ = false; | |
143 } | |
144 | |
145 Vector c, w; | |
146 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && | |
147 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) && | |
148 c.size() > 0 && | |
149 w.size() > 0) | |
150 { | |
151 hasDefaultWindowing_ = true; | |
152 defaultWindowingCenter_ = static_cast<float>(c[0]); | |
153 defaultWindowingWidth_ = static_cast<float>(w[0]); | |
154 } | |
155 else | |
156 { | |
157 hasDefaultWindowing_ = false; | |
158 } | |
159 | |
160 if (sopClassUid_ == SopClassUid_RTDose) | |
161 { | |
162 switch (imageInformation_.GetBitsStored()) | |
163 { | |
164 case 16: | |
165 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
166 break; | |
167 | |
168 case 32: | |
169 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32; | |
170 break; | |
171 | |
172 default: | |
173 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
174 } | |
175 } | |
176 else if (isColor_) | |
177 { | |
178 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24; | |
179 } | |
180 else if (imageInformation_.IsSigned()) | |
181 { | |
182 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16; | |
183 } | |
184 else | |
185 { | |
186 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
187 } | |
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DicomInstanceParameters::GetIndexInSeries()
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188 |
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DicomInstanceParameters::GetIndexInSeries()
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189 // This computes the "IndexInSeries" metadata from Orthanc (check |
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DicomInstanceParameters::GetIndexInSeries()
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190 // out "Orthanc::ServerIndex::Store()") |
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DicomInstanceParameters::GetIndexInSeries()
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191 hasIndexInSeries_ = ( |
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192 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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193 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
746 | 194 } |
195 | |
196 | |
197 CoordinateSystem3D DicomInstanceParameters::Data::GetFrameGeometry(unsigned int frame) const | |
198 { | |
199 if (frame == 0) | |
200 { | |
201 return geometry_; | |
202 } | |
203 else if (frame >= imageInformation_.GetNumberOfFrames()) | |
204 { | |
205 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
206 } | |
207 else if (sopClassUid_ == SopClassUid_RTDose) | |
208 { | |
209 if (frame >= frameOffsets_.size()) | |
210 { | |
211 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
212 } | |
213 | |
214 return CoordinateSystem3D( | |
215 geometry_.GetOrigin() + frameOffsets_[frame] * geometry_.GetNormal(), | |
216 geometry_.GetAxisX(), | |
217 geometry_.GetAxisY()); | |
218 } | |
219 else | |
220 { | |
221 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
222 } | |
223 } | |
224 | |
225 | |
226 bool DicomInstanceParameters::Data::IsPlaneWithinSlice(unsigned int frame, | |
227 const CoordinateSystem3D& plane) const | |
228 { | |
229 if (frame >= imageInformation_.GetNumberOfFrames()) | |
230 { | |
231 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
232 } | |
233 | |
234 CoordinateSystem3D tmp = geometry_; | |
235 | |
236 if (frame != 0) | |
237 { | |
238 tmp = GetFrameGeometry(frame); | |
239 } | |
240 | |
241 double distance; | |
242 | |
757 | 243 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
746 | 244 distance <= thickness_ / 2.0); |
245 } | |
246 | |
247 | |
248 void DicomInstanceParameters::Data::ApplyRescale(Orthanc::ImageAccessor& image, | |
249 bool useDouble) const | |
250 { | |
251 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
252 { | |
253 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
254 } | |
255 | |
256 if (hasRescale_) | |
257 { | |
258 const unsigned int width = image.GetWidth(); | |
259 const unsigned int height = image.GetHeight(); | |
260 | |
261 for (unsigned int y = 0; y < height; y++) | |
262 { | |
263 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
264 | |
265 if (useDouble) | |
266 { | |
267 // Slower, accurate implementation using double | |
268 for (unsigned int x = 0; x < width; x++, p++) | |
269 { | |
270 double value = static_cast<double>(*p); | |
271 *p = static_cast<float>(value * rescaleSlope_ + rescaleIntercept_); | |
272 } | |
273 } | |
274 else | |
275 { | |
276 // Fast, approximate implementation using float | |
277 for (unsigned int x = 0; x < width; x++, p++) | |
278 { | |
279 *p = (*p) * static_cast<float>(rescaleSlope_) + static_cast<float>(rescaleIntercept_); | |
280 } | |
281 } | |
282 } | |
283 } | |
284 } | |
285 | |
286 double DicomInstanceParameters::GetRescaleIntercept() const | |
287 { | |
288 if (data_.hasRescale_) | |
289 { | |
290 return data_.rescaleIntercept_; | |
291 } | |
292 else | |
293 { | |
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294 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
746 | 295 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
296 } | |
297 } | |
298 | |
299 | |
300 double DicomInstanceParameters::GetRescaleSlope() const | |
301 { | |
302 if (data_.hasRescale_) | |
303 { | |
304 return data_.rescaleSlope_; | |
305 } | |
306 else | |
307 { | |
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308 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
746 | 309 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
310 } | |
311 } | |
312 | |
313 | |
314 float DicomInstanceParameters::GetDefaultWindowingCenter() const | |
315 { | |
316 if (data_.hasDefaultWindowing_) | |
317 { | |
318 return data_.defaultWindowingCenter_; | |
319 } | |
320 else | |
321 { | |
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322 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): !data_.hasRescale_"; |
746 | 323 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
324 } | |
325 } | |
326 | |
327 | |
328 float DicomInstanceParameters::GetDefaultWindowingWidth() const | |
329 { | |
330 if (data_.hasDefaultWindowing_) | |
331 { | |
332 return data_.defaultWindowingWidth_; | |
333 } | |
334 else | |
335 { | |
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336 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): !data_.hasRescale_"; |
746 | 337 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
338 } | |
339 } | |
340 | |
341 | |
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342 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
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343 { |
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344 std::auto_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
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345 pixelData.GetWidth(), |
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346 pixelData.GetHeight(), |
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347 false)); |
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348 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
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349 |
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350 // Correct rescale slope/intercept if need be |
1026 | 351 //data_.ApplyRescale(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
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352 data_.ApplyRescale(*converted, false); |
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353 |
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354 return converted.release(); |
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355 } |
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356 |
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357 |
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358 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
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359 (const Orthanc::ImageAccessor& pixelData) const |
746 | 360 { |
361 assert(sizeof(float) == 4); | |
362 | |
363 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
364 | |
365 if (sourceFormat != GetExpectedPixelFormat()) | |
366 { | |
367 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
368 } | |
369 | |
370 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
371 { | |
372 // This is the case of a color image. No conversion has to be done. | |
373 return new ColorTextureSceneLayer(pixelData); | |
374 } | |
375 else | |
376 { | |
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377 // This is the case of a grayscale frame. Convert it to Float32. |
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378 std::auto_ptr<FloatTextureSceneLayer> texture; |
746 | 379 |
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380 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
746 | 381 { |
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382 texture.reset(new FloatTextureSceneLayer(pixelData)); |
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383 } |
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384 else |
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385 { |
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386 std::auto_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
746 | 387 texture.reset(new FloatTextureSceneLayer(*converted)); |
388 } | |
389 | |
390 if (data_.hasDefaultWindowing_) | |
391 { | |
392 texture->SetCustomWindowing(data_.defaultWindowingCenter_, | |
393 data_.defaultWindowingWidth_); | |
394 } | |
395 | |
396 return texture.release(); | |
397 } | |
398 } | |
768
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399 |
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400 |
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401 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
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402 (const Orthanc::ImageAccessor& pixelData) const |
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403 { |
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404 std::auto_ptr<FloatTextureSceneLayer> texture; |
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405 |
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406 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
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407 { |
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408 return new LookupTableTextureSceneLayer(pixelData); |
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409 } |
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410 else |
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411 { |
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412 std::auto_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
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413 return new LookupTableTextureSceneLayer(*converted); |
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414 } |
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415 } |
980
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416 |
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417 |
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418 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
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419 { |
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420 if (data_.hasIndexInSeries_) |
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421 { |
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422 return data_.indexInSeries_; |
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423 } |
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424 else |
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425 { |
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426 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
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427 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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428 } |
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429 } |
746 | 430 } |