Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomInstanceParameters.cpp @ 1091:5a18e6a395bc toa2019102301
Added DoseUnit tag retrieval to DicomInstanceParameters
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Wed, 23 Oct 2019 15:34:39 +0200 |
| parents | dd8ff977aaf2 |
| children | 7681f3943748 |
| 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 | |
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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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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 | |
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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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188 |
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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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191 hasIndexInSeries_ = ( |
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DicomInstanceParameters::GetIndexInSeries()
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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 } | |
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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 } |
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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 } |