Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomInstanceParameters.cpp @ 981:c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Fri, 06 Sep 2019 09:38:18 +0200 |
| parents | a7351ad54960 |
| children | 8e497a4e3d96 |
| rev | line source |
|---|---|
| 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 | |
| 44 if (dicom.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) | |
| 45 { | |
| 46 Orthanc::Toolbox::ToUpperCase(increment); | |
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OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
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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 | |
| 79 if (!dicom.CopyToString(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || | |
| 80 !dicom.CopyToString(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || | |
| 81 !dicom.CopyToString(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) | |
| 82 { | |
| 83 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 84 } | |
| 85 | |
| 86 std::string s; | |
| 87 if (!dicom.CopyToString(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) | |
| 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; | |
| 104 if (dicom.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && | |
| 105 dicom.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) | |
| 106 { | |
| 107 geometry_ = CoordinateSystem3D(position, orientation); | |
| 108 } | |
| 109 | |
| 110 if (sopClassUid_ == SopClassUid_RTDose) | |
| 111 { | |
| 112 ComputeDoseOffsets(dicom); | |
| 113 } | |
| 114 | |
| 115 isColor_ = (imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome1 && | |
| 116 imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome2); | |
| 117 | |
| 118 double doseGridScaling; | |
| 119 | |
| 120 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
| 121 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
| 122 { | |
| 123 hasRescale_ = true; | |
| 124 } | |
| 125 else if (dicom.ParseDouble(doseGridScaling, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) | |
| 126 { | |
| 127 hasRescale_ = true; | |
| 128 rescaleIntercept_ = 0; | |
| 129 rescaleSlope_ = doseGridScaling; | |
| 130 } | |
| 131 else | |
| 132 { | |
| 133 hasRescale_ = false; | |
| 134 } | |
| 135 | |
| 136 Vector c, w; | |
| 137 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && | |
| 138 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) && | |
| 139 c.size() > 0 && | |
| 140 w.size() > 0) | |
| 141 { | |
| 142 hasDefaultWindowing_ = true; | |
| 143 defaultWindowingCenter_ = static_cast<float>(c[0]); | |
| 144 defaultWindowingWidth_ = static_cast<float>(w[0]); | |
| 145 } | |
| 146 else | |
| 147 { | |
| 148 hasDefaultWindowing_ = false; | |
| 149 } | |
| 150 | |
| 151 if (sopClassUid_ == SopClassUid_RTDose) | |
| 152 { | |
| 153 switch (imageInformation_.GetBitsStored()) | |
| 154 { | |
| 155 case 16: | |
| 156 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
| 157 break; | |
| 158 | |
| 159 case 32: | |
| 160 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32; | |
| 161 break; | |
| 162 | |
| 163 default: | |
| 164 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 165 } | |
| 166 } | |
| 167 else if (isColor_) | |
| 168 { | |
| 169 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24; | |
| 170 } | |
| 171 else if (imageInformation_.IsSigned()) | |
| 172 { | |
| 173 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16; | |
| 174 } | |
| 175 else | |
| 176 { | |
| 177 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
| 178 } | |
| 179 } | |
| 180 | |
| 181 | |
| 182 CoordinateSystem3D DicomInstanceParameters::Data::GetFrameGeometry(unsigned int frame) const | |
| 183 { | |
| 184 if (frame == 0) | |
| 185 { | |
| 186 return geometry_; | |
| 187 } | |
| 188 else if (frame >= imageInformation_.GetNumberOfFrames()) | |
| 189 { | |
| 190 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 191 } | |
| 192 else if (sopClassUid_ == SopClassUid_RTDose) | |
| 193 { | |
| 194 if (frame >= frameOffsets_.size()) | |
| 195 { | |
| 196 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 197 } | |
| 198 | |
| 199 return CoordinateSystem3D( | |
| 200 geometry_.GetOrigin() + frameOffsets_[frame] * geometry_.GetNormal(), | |
| 201 geometry_.GetAxisX(), | |
| 202 geometry_.GetAxisY()); | |
| 203 } | |
| 204 else | |
| 205 { | |
| 206 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 207 } | |
| 208 } | |
| 209 | |
| 210 | |
| 211 bool DicomInstanceParameters::Data::IsPlaneWithinSlice(unsigned int frame, | |
| 212 const CoordinateSystem3D& plane) const | |
| 213 { | |
| 214 if (frame >= imageInformation_.GetNumberOfFrames()) | |
| 215 { | |
| 216 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 217 } | |
| 218 | |
| 219 CoordinateSystem3D tmp = geometry_; | |
| 220 | |
| 221 if (frame != 0) | |
| 222 { | |
| 223 tmp = GetFrameGeometry(frame); | |
| 224 } | |
| 225 | |
| 226 double distance; | |
| 227 | |
| 757 | 228 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
| 746 | 229 distance <= thickness_ / 2.0); |
| 230 } | |
| 231 | |
| 232 | |
| 233 void DicomInstanceParameters::Data::ApplyRescale(Orthanc::ImageAccessor& image, | |
| 234 bool useDouble) const | |
| 235 { | |
| 236 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
| 237 { | |
| 238 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
| 239 } | |
| 240 | |
| 241 if (hasRescale_) | |
| 242 { | |
| 243 const unsigned int width = image.GetWidth(); | |
| 244 const unsigned int height = image.GetHeight(); | |
| 245 | |
| 246 for (unsigned int y = 0; y < height; y++) | |
| 247 { | |
| 248 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
| 249 | |
| 250 if (useDouble) | |
| 251 { | |
| 252 // Slower, accurate implementation using double | |
| 253 for (unsigned int x = 0; x < width; x++, p++) | |
| 254 { | |
| 255 double value = static_cast<double>(*p); | |
| 256 *p = static_cast<float>(value * rescaleSlope_ + rescaleIntercept_); | |
| 257 } | |
| 258 } | |
| 259 else | |
| 260 { | |
| 261 // Fast, approximate implementation using float | |
| 262 for (unsigned int x = 0; x < width; x++, p++) | |
| 263 { | |
| 264 *p = (*p) * static_cast<float>(rescaleSlope_) + static_cast<float>(rescaleIntercept_); | |
| 265 } | |
| 266 } | |
| 267 } | |
| 268 } | |
| 269 } | |
| 270 | |
| 271 double DicomInstanceParameters::GetRescaleIntercept() const | |
| 272 { | |
| 273 if (data_.hasRescale_) | |
| 274 { | |
| 275 return data_.rescaleIntercept_; | |
| 276 } | |
| 277 else | |
| 278 { | |
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279 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
| 746 | 280 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 281 } | |
| 282 } | |
| 283 | |
| 284 | |
| 285 double DicomInstanceParameters::GetRescaleSlope() const | |
| 286 { | |
| 287 if (data_.hasRescale_) | |
| 288 { | |
| 289 return data_.rescaleSlope_; | |
| 290 } | |
| 291 else | |
| 292 { | |
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293 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
| 746 | 294 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 295 } | |
| 296 } | |
| 297 | |
| 298 | |
| 299 float DicomInstanceParameters::GetDefaultWindowingCenter() const | |
| 300 { | |
| 301 if (data_.hasDefaultWindowing_) | |
| 302 { | |
| 303 return data_.defaultWindowingCenter_; | |
| 304 } | |
| 305 else | |
| 306 { | |
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307 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): !data_.hasRescale_"; |
| 746 | 308 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 309 } | |
| 310 } | |
| 311 | |
| 312 | |
| 313 float DicomInstanceParameters::GetDefaultWindowingWidth() const | |
| 314 { | |
| 315 if (data_.hasDefaultWindowing_) | |
| 316 { | |
| 317 return data_.defaultWindowingWidth_; | |
| 318 } | |
| 319 else | |
| 320 { | |
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321 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): !data_.hasRescale_"; |
| 746 | 322 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 323 } | |
| 324 } | |
| 325 | |
| 326 | |
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327 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
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328 { |
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329 std::auto_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
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330 pixelData.GetWidth(), |
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331 pixelData.GetHeight(), |
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332 false)); |
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333 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
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334 |
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335 // Correct rescale slope/intercept if need be |
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336 data_.ApplyRescale(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
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337 |
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338 return converted.release(); |
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339 } |
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340 |
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341 |
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342 |
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343 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
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344 (const Orthanc::ImageAccessor& pixelData) const |
| 746 | 345 { |
| 346 assert(sizeof(float) == 4); | |
| 347 | |
| 348 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
| 349 | |
| 350 if (sourceFormat != GetExpectedPixelFormat()) | |
| 351 { | |
| 352 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
| 353 } | |
| 354 | |
| 355 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
| 356 { | |
| 357 // This is the case of a color image. No conversion has to be done. | |
| 358 return new ColorTextureSceneLayer(pixelData); | |
| 359 } | |
| 360 else | |
| 361 { | |
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362 // This is the case of a grayscale frame. Convert it to Float32. |
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363 std::auto_ptr<FloatTextureSceneLayer> texture; |
| 746 | 364 |
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365 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
| 746 | 366 { |
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367 texture.reset(new FloatTextureSceneLayer(pixelData)); |
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368 } |
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369 else |
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370 { |
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371 std::auto_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
| 746 | 372 texture.reset(new FloatTextureSceneLayer(*converted)); |
| 373 } | |
| 374 | |
| 375 if (data_.hasDefaultWindowing_) | |
| 376 { | |
| 377 texture->SetCustomWindowing(data_.defaultWindowingCenter_, | |
| 378 data_.defaultWindowingWidth_); | |
| 379 } | |
| 380 | |
| 381 return texture.release(); | |
| 382 } | |
| 383 } | |
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384 |
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385 |
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386 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
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387 (const Orthanc::ImageAccessor& pixelData) const |
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388 { |
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389 std::auto_ptr<FloatTextureSceneLayer> texture; |
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390 |
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391 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
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392 { |
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393 return new LookupTableTextureSceneLayer(pixelData); |
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394 } |
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LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
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395 else |
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55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
396 { |
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55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
397 std::auto_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
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55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
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398 return new LookupTableTextureSceneLayer(*converted); |
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55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
399 } |
|
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
400 } |
| 746 | 401 } |