Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomInstanceParameters.cpp @ 1303:83af7e562b45 broker
IGeometryProvider interface for deprecated loaders (required for AB testing in older app)
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Wed, 04 Mar 2020 09:44:09 +0100 |
| parents | 7ec8fea061b9 |
| children | 6ab03e429f06 |
| 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" | |
| 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(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
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119 doseUnits_ = ""; |
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120 } |
| 746 | 121 } |
| 122 | |
| 123 isColor_ = (imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome1 && | |
| 124 imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome2); | |
| 125 | |
| 126 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
| 127 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
| 128 { | |
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129 if (sopClassUid_ == SopClassUid_RTDose) |
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130 { |
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131 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; |
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132 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES |
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133 hasRescale_ = false; |
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134 } |
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135 else |
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136 { |
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137 hasRescale_ = true; |
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138 } |
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139 |
| 746 | 140 } |
| 141 else | |
| 142 { | |
| 143 hasRescale_ = false; | |
| 144 } | |
| 145 | |
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146 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) |
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147 { |
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148 if (sopClassUid_ == SopClassUid_RTDose) |
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149 { |
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150 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; |
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151 } |
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152 } |
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153 else |
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154 { |
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155 doseGridScaling_ = 1.0; |
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156 if (sopClassUid_ == SopClassUid_RTDose) |
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157 { |
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158 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; |
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159 } |
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160 } |
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161 |
| 746 | 162 Vector c, w; |
| 163 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && | |
| 164 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) && | |
| 165 c.size() > 0 && | |
| 166 w.size() > 0) | |
| 167 { | |
| 168 hasDefaultWindowing_ = true; | |
| 169 defaultWindowingCenter_ = static_cast<float>(c[0]); | |
| 170 defaultWindowingWidth_ = static_cast<float>(w[0]); | |
| 171 } | |
| 172 else | |
| 173 { | |
| 174 hasDefaultWindowing_ = false; | |
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175 defaultWindowingCenter_ = 0; |
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176 defaultWindowingWidth_ = 0; |
| 746 | 177 } |
| 178 | |
| 179 if (sopClassUid_ == SopClassUid_RTDose) | |
| 180 { | |
| 181 switch (imageInformation_.GetBitsStored()) | |
| 182 { | |
| 183 case 16: | |
| 184 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
| 185 break; | |
| 186 | |
| 187 case 32: | |
| 188 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32; | |
| 189 break; | |
| 190 | |
| 191 default: | |
| 192 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 193 } | |
| 194 } | |
| 195 else if (isColor_) | |
| 196 { | |
| 197 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24; | |
| 198 } | |
| 199 else if (imageInformation_.IsSigned()) | |
| 200 { | |
| 201 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16; | |
| 202 } | |
| 203 else | |
| 204 { | |
| 205 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; | |
| 206 } | |
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207 |
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208 // This computes the "IndexInSeries" metadata from Orthanc (check |
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209 // out "Orthanc::ServerIndex::Store()") |
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210 hasIndexInSeries_ = ( |
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211 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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212 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
| 746 | 213 } |
| 214 | |
| 215 | |
| 216 CoordinateSystem3D DicomInstanceParameters::Data::GetFrameGeometry(unsigned int frame) const | |
| 217 { | |
| 218 if (frame == 0) | |
| 219 { | |
| 220 return geometry_; | |
| 221 } | |
| 222 else if (frame >= imageInformation_.GetNumberOfFrames()) | |
| 223 { | |
| 224 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 225 } | |
| 226 else if (sopClassUid_ == SopClassUid_RTDose) | |
| 227 { | |
| 228 if (frame >= frameOffsets_.size()) | |
| 229 { | |
| 230 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 231 } | |
| 232 | |
| 233 return CoordinateSystem3D( | |
| 234 geometry_.GetOrigin() + frameOffsets_[frame] * geometry_.GetNormal(), | |
| 235 geometry_.GetAxisX(), | |
| 236 geometry_.GetAxisY()); | |
| 237 } | |
| 238 else | |
| 239 { | |
| 240 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 241 } | |
| 242 } | |
| 243 | |
| 244 | |
| 245 bool DicomInstanceParameters::Data::IsPlaneWithinSlice(unsigned int frame, | |
| 246 const CoordinateSystem3D& plane) const | |
| 247 { | |
| 248 if (frame >= imageInformation_.GetNumberOfFrames()) | |
| 249 { | |
| 250 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 251 } | |
| 252 | |
| 253 CoordinateSystem3D tmp = geometry_; | |
| 254 | |
| 255 if (frame != 0) | |
| 256 { | |
| 257 tmp = GetFrameGeometry(frame); | |
| 258 } | |
| 259 | |
| 260 double distance; | |
| 261 | |
| 757 | 262 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
| 746 | 263 distance <= thickness_ / 2.0); |
| 264 } | |
| 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 { | |
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350 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): !data_.hasRescale_"; |
| 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 { | |
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364 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): !data_.hasRescale_"; |
| 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::auto_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 // Correct rescale slope/intercept if need be |
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379 //data_.ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
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380 data_.ApplyRescaleAndDoseScaling(*converted, false); |
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381 |
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382 return converted.release(); |
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383 } |
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384 |
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385 |
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386 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
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387 (const Orthanc::ImageAccessor& pixelData) const |
| 746 | 388 { |
| 389 assert(sizeof(float) == 4); | |
| 390 | |
| 391 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
| 392 | |
| 393 if (sourceFormat != GetExpectedPixelFormat()) | |
| 394 { | |
| 395 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
| 396 } | |
| 397 | |
| 398 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
| 399 { | |
| 400 // This is the case of a color image. No conversion has to be done. | |
| 401 return new ColorTextureSceneLayer(pixelData); | |
| 402 } | |
| 403 else | |
| 404 { | |
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405 // This is the case of a grayscale frame. Convert it to Float32. |
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406 std::auto_ptr<FloatTextureSceneLayer> texture; |
| 746 | 407 |
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408 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
| 746 | 409 { |
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410 texture.reset(new FloatTextureSceneLayer(pixelData)); |
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411 } |
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412 else |
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413 { |
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414 std::auto_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
| 746 | 415 texture.reset(new FloatTextureSceneLayer(*converted)); |
| 416 } | |
| 417 | |
| 418 if (data_.hasDefaultWindowing_) | |
| 419 { | |
| 420 texture->SetCustomWindowing(data_.defaultWindowingCenter_, | |
| 421 data_.defaultWindowingWidth_); | |
| 422 } | |
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423 |
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424 |
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425 if (data_.imageInformation_.GetPhotometricInterpretation() |
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426 == Orthanc::PhotometricInterpretation_Monochrome1) |
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427 { |
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428 texture->SetInverted(true); |
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429 } |
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430 else if (data_.imageInformation_.GetPhotometricInterpretation() |
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431 == Orthanc::PhotometricInterpretation_Monochrome2) |
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432 { |
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433 texture->SetInverted(false); |
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434 } |
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435 |
| 746 | 436 return texture.release(); |
| 437 } | |
| 438 } | |
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439 |
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440 |
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441 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
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442 (const Orthanc::ImageAccessor& pixelData) const |
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443 { |
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444 std::auto_ptr<FloatTextureSceneLayer> texture; |
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445 |
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446 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
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447 { |
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448 return new LookupTableTextureSceneLayer(pixelData); |
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449 } |
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450 else |
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451 { |
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452 std::auto_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
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453 return new LookupTableTextureSceneLayer(*converted); |
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454 } |
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455 } |
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456 |
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457 |
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458 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
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459 { |
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460 if (data_.hasIndexInSeries_) |
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461 { |
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462 return data_.indexInSeries_; |
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463 } |
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464 else |
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465 { |
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466 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
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467 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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468 } |
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469 } |
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470 |
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471 |
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472 double DicomInstanceParameters::Data::ApplyRescale(double value) const |
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473 { |
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474 double factor = doseGridScaling_; |
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475 double offset = 0.0; |
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476 |
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477 if (hasRescale_) |
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478 { |
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479 factor *= rescaleSlope_; |
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480 offset = rescaleIntercept_; |
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481 } |
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482 |
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483 return (value * factor + offset); |
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484 } |
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1161
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485 |
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486 |
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487 bool DicomInstanceParameters::Data::ComputeRegularSpacing(double& spacing) const |
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488 { |
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489 if (frameOffsets_.size() == 0) // Not a RT-DOSE |
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490 { |
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491 return false; |
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492 } |
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493 else if (frameOffsets_.size() == 1) |
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494 { |
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495 spacing = 1; // Edge case: RT-DOSE with one single frame |
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496 return true; |
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497 } |
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498 else |
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499 { |
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500 spacing = std::abs(frameOffsets_[1] - frameOffsets_[0]); |
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501 |
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502 for (size_t i = 1; i + 1 < frameOffsets_.size(); i++) |
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503 { |
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504 double s = frameOffsets_[i + 1] - frameOffsets_[i]; |
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505 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
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506 { |
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507 return false; |
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508 } |
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509 } |
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510 |
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511 return true; |
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512 } |
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513 } |
| 746 | 514 } |