Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1592:0d4b11ba86df
fix
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 23 Oct 2020 15:15:32 +0200 |
| parents | 85e117739eca |
| children | 4fb8fdf03314 |
| 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 | |
|
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
| 746 | 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" | |
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27 #include "../Toolbox/ImageToolbox.h" |
| 746 | 28 |
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29 #include <Images/Image.h> |
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30 #include <Images/ImageProcessing.h> |
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31 #include <Logging.h> |
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32 #include <OrthancException.h> |
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33 #include <Toolbox.h> |
| 746 | 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 | |
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45 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) |
| 746 | 46 { |
| 47 Orthanc::Toolbox::ToUpperCase(increment); | |
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48 if (increment != "3004,000C") // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) |
| 746 | 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 { | |
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66 thickness_ = std::abs(frameOffsets_[1] - frameOffsets_[0]); |
| 746 | 67 } |
| 68 } | |
| 69 } | |
| 70 | |
| 71 | |
| 72 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) : | |
| 73 imageInformation_(dicom) | |
| 74 { | |
| 1571 | 75 if (imageInformation_.GetNumberOfFrames() == 0) |
| 746 | 76 { |
| 77 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 78 } | |
| 79 | |
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80 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || |
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81 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || |
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82 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
| 746 | 83 { |
| 84 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 85 } | |
| 86 | |
| 87 std::string s; | |
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88 if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) |
| 746 | 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; | |
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105 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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106 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
| 746 | 107 { |
| 108 geometry_ = CoordinateSystem3D(position, orientation); | |
| 109 } | |
| 110 | |
| 111 if (sopClassUid_ == SopClassUid_RTDose) | |
| 112 { | |
| 113 ComputeDoseOffsets(dicom); | |
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114 |
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115 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); |
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116 |
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117 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) |
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118 { |
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119 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
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120 doseUnits_ = ""; |
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121 } |
| 746 | 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 { | |
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130 if (sopClassUid_ == SopClassUid_RTDose) |
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131 { |
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132 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; |
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133 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES |
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134 hasRescale_ = false; |
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135 } |
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136 else |
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137 { |
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138 hasRescale_ = true; |
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139 } |
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140 |
| 746 | 141 } |
| 142 else | |
| 143 { | |
| 144 hasRescale_ = false; | |
| 145 } | |
| 146 | |
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147 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) |
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148 { |
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149 if (sopClassUid_ == SopClassUid_RTDose) |
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150 { |
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151 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; |
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152 } |
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153 } |
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154 else |
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155 { |
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156 doseGridScaling_ = 1.0; |
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157 if (sopClassUid_ == SopClassUid_RTDose) |
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158 { |
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159 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; |
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160 } |
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161 } |
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162 |
| 746 | 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; | |
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176 defaultWindowingCenter_ = 0; |
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177 defaultWindowingWidth_ = 0; |
| 746 | 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 } | |
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208 |
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209 // This computes the "IndexInSeries" metadata from Orthanc (check |
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210 // out "Orthanc::ServerIndex::Store()") |
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211 hasIndexInSeries_ = ( |
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212 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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213 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
| 746 | 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 | |
| 757 | 263 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
| 746 | 264 distance <= thickness_ / 2.0); |
| 265 } | |
| 266 | |
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267 void DicomInstanceParameters::Data::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, |
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268 bool useDouble) const |
| 746 | 269 { |
| 270 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
| 271 { | |
| 272 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
| 273 } | |
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274 |
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275 double factor = doseGridScaling_; |
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276 double offset = 0.0; |
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277 |
| 746 | 278 if (hasRescale_) |
| 279 { | |
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280 factor *= rescaleSlope_; |
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281 offset = rescaleIntercept_; |
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282 } |
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283 |
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284 if ( (factor != 1.0) || (offset != 0.0) ) |
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285 { |
| 746 | 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); | |
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299 *p = static_cast<float>(value * factor + offset); |
| 746 | 300 } |
| 301 } | |
| 302 else | |
| 303 { | |
| 304 // Fast, approximate implementation using float | |
| 305 for (unsigned int x = 0; x < width; x++, p++) | |
| 306 { | |
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307 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset); |
| 746 | 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 { | |
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322 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
| 746 | 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 { | |
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336 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
| 746 | 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 { | |
| 1481 | 350 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): no default windowing"; |
| 746 | 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 { | |
| 1481 | 364 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): no default windowing"; |
| 746 | 365 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 366 } | |
| 367 } | |
| 368 | |
| 369 | |
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370 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
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371 { |
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372 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
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373 pixelData.GetWidth(), |
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374 pixelData.GetHeight(), |
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375 false)); |
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376 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
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377 |
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378 |
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379 // Correct rescale slope/intercept if need be |
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380 //data_.ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
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381 data_.ApplyRescaleAndDoseScaling(*converted, false); |
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382 |
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383 return converted.release(); |
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384 } |
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385 |
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386 |
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387 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
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388 (const Orthanc::ImageAccessor& pixelData) const |
| 746 | 389 { |
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390 // { |
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391 // const Orthanc::ImageAccessor& source = pixelData; |
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392 // const void* sourceBuffer = source.GetConstBuffer(); |
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393 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); |
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394 // int sourceWidth = source.GetWidth(); |
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395 // int sourceHeight = source.GetHeight(); |
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396 // int sourcePitch = source.GetPitch(); |
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397 |
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398 // // TODO: turn error into trace below |
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399 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" |
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400 // << " W = " << sourceWidth << " H = " << sourceHeight |
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401 // << " P = " << sourcePitch << " B = " << sourceBufferInt |
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402 // << " B % 4 == " << sourceBufferInt % 4; |
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403 // } |
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404 |
| 746 | 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 { | |
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421 // This is the case of a grayscale frame. Convert it to Float32. |
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422 std::unique_ptr<FloatTextureSceneLayer> texture; |
| 746 | 423 |
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424 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
| 746 | 425 { |
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426 texture.reset(new FloatTextureSceneLayer(pixelData)); |
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427 } |
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428 else |
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429 { |
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430 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
| 746 | 431 texture.reset(new FloatTextureSceneLayer(*converted)); |
| 432 } | |
| 433 | |
| 434 if (data_.hasDefaultWindowing_) | |
| 435 { | |
| 436 texture->SetCustomWindowing(data_.defaultWindowingCenter_, | |
| 437 data_.defaultWindowingWidth_); | |
| 438 } | |
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439 |
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440 |
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441 if (data_.imageInformation_.GetPhotometricInterpretation() |
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442 == Orthanc::PhotometricInterpretation_Monochrome1) |
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443 { |
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444 texture->SetInverted(true); |
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445 } |
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446 else if (data_.imageInformation_.GetPhotometricInterpretation() |
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447 == Orthanc::PhotometricInterpretation_Monochrome2) |
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448 { |
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449 texture->SetInverted(false); |
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450 } |
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451 |
| 746 | 452 return texture.release(); |
| 453 } | |
| 454 } | |
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455 |
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456 |
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457 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
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458 (const Orthanc::ImageAccessor& pixelData) const |
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459 { |
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460 std::unique_ptr<FloatTextureSceneLayer> texture; |
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461 |
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462 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
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463 { |
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464 return new LookupTableTextureSceneLayer(pixelData); |
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465 } |
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466 else |
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467 { |
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468 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
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469 return new LookupTableTextureSceneLayer(*converted); |
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470 } |
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471 } |
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472 |
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473 |
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474 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
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475 { |
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476 if (data_.hasIndexInSeries_) |
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477 { |
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478 return data_.indexInSeries_; |
|
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479 } |
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480 else |
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481 { |
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482 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
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483 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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484 } |
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485 } |
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1159
acb399643945
DicomInstanceParameters::ApplyRescale()
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486 |
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487 |
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488 double DicomInstanceParameters::Data::ApplyRescale(double value) const |
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489 { |
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490 double factor = doseGridScaling_; |
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491 double offset = 0.0; |
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492 |
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493 if (hasRescale_) |
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494 { |
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495 factor *= rescaleSlope_; |
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496 offset = rescaleIntercept_; |
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497 } |
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498 |
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499 return (value * factor + offset); |
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500 } |
|
1161
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501 |
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502 |
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503 bool DicomInstanceParameters::Data::ComputeRegularSpacing(double& spacing) const |
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504 { |
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505 if (frameOffsets_.size() == 0) // Not a RT-DOSE |
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506 { |
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507 return false; |
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508 } |
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509 else if (frameOffsets_.size() == 1) |
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510 { |
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511 spacing = 1; // Edge case: RT-DOSE with one single frame |
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512 return true; |
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513 } |
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514 else |
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515 { |
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516 spacing = std::abs(frameOffsets_[1] - frameOffsets_[0]); |
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517 |
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518 for (size_t i = 1; i + 1 < frameOffsets_.size(); i++) |
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519 { |
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520 double s = frameOffsets_[i + 1] - frameOffsets_[i]; |
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521 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
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522 { |
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523 return false; |
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524 } |
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|
525 } |
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|
526 |
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527 return true; |
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528 } |
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529 } |
| 746 | 530 } |