Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1924:f4050908c6bc
display of overlays
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 23 Mar 2022 12:24:35 +0100 |
| parents | ed4831e08961 |
| children | d84bdcbd8bf1 |
| 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) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 746 | 7 * |
| 8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
| 746 | 10 * as published by the Free Software Foundation, either version 3 of |
| 11 * the License, or (at your option) any later version. | |
| 12 * | |
| 13 * This program is distributed in the hope that it will be useful, but | |
| 14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
|
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
| 746 | 21 **/ |
| 22 | |
| 23 | |
| 24 #include "DicomInstanceParameters.h" | |
| 25 | |
| 26 #include "../Scene2D/ColorTextureSceneLayer.h" | |
| 27 #include "../Scene2D/FloatTextureSceneLayer.h" | |
| 1750 | 28 #include "GeometryToolbox.h" |
| 29 #include "ImageToolbox.h" | |
| 746 | 30 |
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31 #include <Images/Image.h> |
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32 #include <Images/ImageProcessing.h> |
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33 #include <Logging.h> |
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34 #include <OrthancException.h> |
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35 #include <Toolbox.h> |
| 746 | 36 |
| 37 | |
| 38 namespace OrthancStone | |
| 39 { | |
| 1636 | 40 static void ExtractFrameOffsets(Vector& target, |
| 41 const Orthanc::DicomMap& dicom, | |
| 42 unsigned int numberOfFrames) | |
| 746 | 43 { |
| 44 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html | |
| 45 | |
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46 std::string increment; |
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47 |
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48 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) |
| 746 | 49 { |
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50 Orthanc::Toolbox::ToUpperCase(increment); |
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51 |
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52 // We only support volumes where the FrameIncrementPointer (0028,0009) (required) contains |
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53 // the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) |
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54 if (increment != "3004,000C") |
| 746 | 55 { |
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56 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image"; |
| 1636 | 57 target.resize(0); |
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58 return; |
| 746 | 59 } |
| 60 } | |
| 61 | |
| 1636 | 62 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) || |
| 63 target.size() != numberOfFrames) | |
| 746 | 64 { |
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65 LOG(ERROR) << "The frame offset information (GridFrameOffsetVector (3004,000C)) is missing in a multiframe image"; |
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66 |
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67 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector! |
| 1636 | 68 target.resize(0); |
| 746 | 69 } |
| 70 } | |
| 71 | |
| 72 | |
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73 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) |
| 746 | 74 { |
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75 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || |
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76 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || |
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77 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
| 746 | 78 { |
| 79 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 80 } | |
| 81 | |
| 82 std::string s; | |
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83 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) |
| 746 | 84 { |
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85 sopClassUid_ = StringToSopClassUid(s); |
| 746 | 86 } |
| 87 else | |
| 88 { | |
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89 sopClassUid_ = SopClassUid_Other; |
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90 } |
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91 |
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92 uint32_t n; |
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93 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
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94 { |
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95 hasNumberOfFrames_ = true; |
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96 numberOfFrames_ = n; |
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97 } |
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98 else |
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99 { |
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100 hasNumberOfFrames_ = false; |
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101 numberOfFrames_ = 1; |
| 746 | 102 } |
| 103 | |
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104 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) || |
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105 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_)) |
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106 { |
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107 width_ = 0; |
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108 } |
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109 |
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110 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) || |
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111 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_)) |
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112 { |
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113 height_ = 0; |
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114 } |
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115 |
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116 |
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117 bool sliceThicknessPresent = true; |
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118 if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) |
| 746 | 119 { |
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120 if (numberOfFrames_ > 1) |
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121 { |
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122 LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image"; |
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123 } |
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124 |
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125 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
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126 sliceThicknessPresent = false; |
| 746 | 127 } |
| 128 | |
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129 hasPixelSpacing_ = GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); |
| 746 | 130 |
| 131 std::string position, orientation; | |
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132 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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133 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
| 746 | 134 { |
| 135 geometry_ = CoordinateSystem3D(position, orientation); | |
| 136 } | |
| 137 | |
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138 // Must be AFTER setting "numberOfFrames_" |
| 1639 | 139 if (numberOfFrames_ > 1) |
| 140 { | |
| 141 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_); | |
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142 |
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143 // if the slice thickness is unknown, we try to infer it from the sequence of grid frame offsets |
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144 // this only works if: |
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145 // - the first offset is 0.0 (case (a) of http://dicom.nema.org/medical/Dicom/2017c/output/chtml/part03/sect_C.8.8.3.2.html) |
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146 // - the offsets are all equal, to some small tolerance |
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147 // - the offsets is positive (increasing throughout the frames) |
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148 if (!sliceThicknessPresent) |
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149 { |
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150 if (frameOffsets_.size() >= 2) |
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151 { |
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152 double sliceThickness = frameOffsets_[1] - frameOffsets_[0]; |
| 1817 | 153 |
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154 if (sliceThickness > 0) |
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155 { |
| 1817 | 156 bool sameSized = true; |
| 157 | |
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158 for (size_t i = 2; i < frameOffsets_.size(); ++i) |
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159 { |
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160 double currentThickness = frameOffsets_[i] - frameOffsets_[i-1]; |
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161 if (!LinearAlgebra::IsNear(sliceThickness, currentThickness)) |
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162 { |
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163 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)"; |
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164 sameSized = false; |
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165 break; |
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166 } |
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167 } |
| 1817 | 168 |
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169 if (sameSized) |
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170 { |
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171 sliceThickness_ = sliceThickness; |
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172 LOG(INFO) << "SliceThickness was not specified in the Dicom but was inferred from GridFrameOffsetVector (3004,000C)."; |
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173 } |
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174 } |
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175 } |
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176 else |
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177 { |
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178 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: GridFrameOffsetVector not present or too small)"; |
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179 } |
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180 } |
| 1639 | 181 } |
| 182 else | |
| 183 { | |
| 184 frameOffsets_.resize(0); | |
| 185 } | |
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186 |
| 746 | 187 if (sopClassUid_ == SopClassUid_RTDose) |
| 188 { | |
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189 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); |
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190 |
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191 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) |
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192 { |
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193 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
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194 doseUnits_.clear(); |
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195 } |
| 746 | 196 } |
| 197 | |
| 198 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
| 199 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
| 200 { | |
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201 if (sopClassUid_ == SopClassUid_RTDose) |
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202 { |
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203 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; |
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204 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES |
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205 hasRescale_ = false; |
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206 } |
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207 else |
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208 { |
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209 hasRescale_ = true; |
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210 } |
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211 |
| 746 | 212 } |
| 213 else | |
| 214 { | |
| 215 hasRescale_ = false; | |
| 216 } | |
| 217 | |
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218 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) |
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219 { |
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220 if (sopClassUid_ == SopClassUid_RTDose) |
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221 { |
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222 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; |
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223 } |
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224 } |
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225 else |
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226 { |
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227 doseGridScaling_ = 1.0; |
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228 if (sopClassUid_ == SopClassUid_RTDose) |
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229 { |
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230 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; |
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231 } |
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232 } |
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233 |
|
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234 bool ok = false; |
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235 |
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236 if (LinearAlgebra::ParseVector(windowingPresetCenters_, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && |
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237 LinearAlgebra::ParseVector(windowingPresetWidths_, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH)) |
| 746 | 238 { |
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239 if (windowingPresetCenters_.size() == windowingPresetWidths_.size()) |
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240 { |
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241 ok = true; |
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242 } |
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243 else |
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244 { |
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245 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this"; |
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246 ok = false; |
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247 } |
| 746 | 248 } |
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249 |
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250 if (!ok) |
| 746 | 251 { |
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252 // Don't use "Vector::clear()", as it has not the same meaning as "std::vector::clear()" |
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253 windowingPresetCenters_.resize(0); |
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254 windowingPresetWidths_.resize(0); |
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255 } |
| 746 | 256 |
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257 // This computes the "IndexInSeries" metadata from Orthanc (check |
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258 // out "Orthanc::ServerIndex::Store()") |
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259 hasIndexInSeries_ = ( |
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260 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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261 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
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262 |
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263 if (!dicom.LookupStringValue( |
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264 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false)) |
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265 { |
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266 frameOfReferenceUid_.clear(); |
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267 } |
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268 |
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269 if (!dicom.HasTag(Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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270 !dicom.GetValue(Orthanc::DICOM_TAG_INSTANCE_NUMBER).ParseInteger32(instanceNumber_)) |
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271 { |
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272 instanceNumber_ = 0; |
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273 } |
| 746 | 274 } |
| 275 | |
| 276 | |
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277 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const |
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278 { |
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279 assert(tags_.get() != NULL); |
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280 |
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281 if (imageInformation_.get() == NULL) |
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282 { |
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283 const_cast<DicomInstanceParameters&>(*this).imageInformation_. |
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284 reset(new Orthanc::DicomImageInformation(GetTags())); |
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285 |
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286 assert(imageInformation_->GetWidth() == GetWidth()); |
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287 assert(imageInformation_->GetHeight() == GetHeight()); |
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288 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames()); |
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289 } |
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290 |
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291 assert(imageInformation_.get() != NULL); |
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292 return *imageInformation_; |
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293 } |
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294 |
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295 |
| 1636 | 296 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const |
| 746 | 297 { |
| 1636 | 298 if (frame >= data_.numberOfFrames_) |
| 746 | 299 { |
| 300 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 301 } | |
| 1636 | 302 else if (data_.frameOffsets_.empty()) |
| 746 | 303 { |
| 1636 | 304 return data_.geometry_; |
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305 } |
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306 else |
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307 { |
| 1636 | 308 assert(data_.frameOffsets_.size() == data_.numberOfFrames_); |
| 746 | 309 |
| 310 return CoordinateSystem3D( | |
| 1636 | 311 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(), |
| 312 data_.geometry_.GetAxisX(), | |
| 313 data_.geometry_.GetAxisY()); | |
| 746 | 314 } |
| 315 } | |
| 316 | |
| 317 | |
| 1636 | 318 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame, |
| 319 const CoordinateSystem3D& plane) const | |
| 746 | 320 { |
| 1636 | 321 if (frame >= data_.numberOfFrames_) |
| 746 | 322 { |
| 323 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 324 } | |
| 325 | |
| 1636 | 326 CoordinateSystem3D tmp = data_.geometry_; |
| 746 | 327 |
| 328 if (frame != 0) | |
| 329 { | |
| 330 tmp = GetFrameGeometry(frame); | |
| 331 } | |
| 332 | |
| 333 double distance; | |
| 334 | |
| 757 | 335 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
| 1636 | 336 distance <= data_.sliceThickness_ / 2.0); |
| 746 | 337 } |
| 338 | |
| 1637 | 339 |
| 340 bool DicomInstanceParameters::IsColor() const | |
| 341 { | |
| 342 Orthanc::PhotometricInterpretation photometric = | |
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343 GetImageInformation().GetPhotometricInterpretation(); |
| 1637 | 344 |
| 345 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 && | |
| 346 photometric != Orthanc::PhotometricInterpretation_Monochrome2); | |
| 347 } | |
| 348 | |
| 349 | |
| 1636 | 350 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, |
| 351 bool useDouble) const | |
| 746 | 352 { |
| 353 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
| 354 { | |
| 355 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
| 356 } | |
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357 |
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358 double scaling = data_.doseGridScaling_; |
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359 double offset = 0.0; |
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360 |
| 1636 | 361 if (data_.hasRescale_) |
| 746 | 362 { |
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363 scaling *= data_.rescaleSlope_; |
| 1636 | 364 offset = data_.rescaleIntercept_; |
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365 } |
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366 |
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367 Orthanc::ImageProcessing::ShiftScale2(image, offset, scaling, false); |
| 746 | 368 } |
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369 |
| 746 | 370 |
| 371 double DicomInstanceParameters::GetRescaleIntercept() const | |
| 372 { | |
| 373 if (data_.hasRescale_) | |
| 374 { | |
| 375 return data_.rescaleIntercept_; | |
| 376 } | |
| 377 else | |
| 378 { | |
|
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379 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
| 746 | 380 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 381 } | |
| 382 } | |
| 383 | |
| 384 | |
| 385 double DicomInstanceParameters::GetRescaleSlope() const | |
| 386 { | |
| 387 if (data_.hasRescale_) | |
| 388 { | |
| 389 return data_.rescaleSlope_; | |
| 390 } | |
| 391 else | |
| 392 { | |
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393 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
| 746 | 394 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 395 } | |
| 396 } | |
| 397 | |
| 398 | |
| 1637 | 399 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const |
| 400 { | |
| 401 if (GetSopClassUid() == SopClassUid_RTDose) | |
| 402 { | |
| 403 switch (GetImageInformation().GetBitsStored()) | |
| 404 { | |
| 405 case 16: | |
| 406 return Orthanc::PixelFormat_Grayscale16; | |
| 407 | |
| 408 case 32: | |
| 409 return Orthanc::PixelFormat_Grayscale32; | |
| 410 | |
| 411 default: | |
| 412 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
| 413 } | |
| 414 } | |
| 415 else if (IsColor()) | |
| 416 { | |
| 417 return Orthanc::PixelFormat_RGB24; | |
| 418 } | |
| 419 else if (GetImageInformation().IsSigned()) | |
| 420 { | |
| 421 return Orthanc::PixelFormat_SignedGrayscale16; | |
| 422 } | |
| 423 else | |
| 424 { | |
| 425 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
| 426 } | |
| 427 } | |
| 428 | |
| 429 | |
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430 size_t DicomInstanceParameters::GetWindowingPresetsCount() const |
| 746 | 431 { |
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432 assert(data_.windowingPresetCenters_.size() == data_.windowingPresetWidths_.size()); |
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433 return data_.windowingPresetCenters_.size(); |
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434 } |
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435 |
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436 |
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437 float DicomInstanceParameters::GetWindowingPresetCenter(size_t i) const |
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438 { |
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439 if (i < GetWindowingPresetsCount()) |
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440 { |
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441 return static_cast<float>(data_.windowingPresetCenters_[i]); |
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442 } |
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443 else |
| 746 | 444 { |
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445 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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446 } |
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447 } |
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448 |
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449 |
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450 float DicomInstanceParameters::GetWindowingPresetWidth(size_t i) const |
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451 { |
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452 if (i < GetWindowingPresetsCount()) |
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453 { |
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454 return static_cast<float>(data_.windowingPresetWidths_[i]); |
| 746 | 455 } |
| 456 else | |
| 457 { | |
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458 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 746 | 459 } |
| 460 } | |
| 461 | |
| 462 | |
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463 static void GetWindowingBounds(float& low, |
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464 float& high, |
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465 double center, // in |
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466 double width) // in |
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467 { |
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468 low = static_cast<float>(center - width / 2.0); |
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469 high = static_cast<float>(center + width / 2.0); |
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470 } |
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471 |
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472 |
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473 void DicomInstanceParameters::GetWindowingPresetsUnion(float& center, |
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474 float& width) const |
| 746 | 475 { |
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476 assert(tags_.get() != NULL); |
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477 size_t s = GetWindowingPresetsCount(); |
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478 |
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479 if (s > 0) |
| 746 | 480 { |
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481 // Use the largest windowing given all the preset windowings |
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482 // that are available in the DICOM tags |
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483 float low, high; |
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484 GetWindowingBounds(low, high, GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
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485 |
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486 for (size_t i = 1; i < s; i++) |
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487 { |
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488 float a, b; |
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489 GetWindowingBounds(a, b, GetWindowingPresetCenter(i), GetWindowingPresetWidth(i)); |
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490 low = std::min(low, a); |
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491 high = std::max(high, b); |
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492 } |
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493 |
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494 assert(low <= high); |
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495 |
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496 if (LinearAlgebra::IsNear(low, high)) |
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497 { |
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498 // Cannot infer a suitable windowing from the available tags |
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499 center = 128.0f; |
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500 width = 256.0f; |
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501 } |
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502 else |
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503 { |
|
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504 center = (low + high) / 2.0f; |
|
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505 width = (high - low); |
|
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|
506 } |
| 746 | 507 } |
| 508 else | |
| 509 { | |
|
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|
510 float a, b; |
|
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511 if (tags_->ParseFloat(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) && |
|
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|
512 tags_->ParseFloat(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE) && |
|
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|
513 a < b) |
|
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|
514 { |
|
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515 center = (a + b) / 2.0f; |
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516 width = (b - a); |
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517 } |
|
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518 else |
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519 { |
|
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520 // Cannot infer a suitable windowing from the available tags |
|
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521 center = 128.0f; |
|
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522 width = 256.0f; |
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523 } |
| 746 | 524 } |
| 525 } | |
| 526 | |
|
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|
527 |
|
768
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|
528 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
|
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529 { |
|
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|
530 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
|
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531 pixelData.GetWidth(), |
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532 pixelData.GetHeight(), |
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533 false)); |
|
768
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534 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
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535 |
|
1287
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|
536 |
|
768
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|
537 // Correct rescale slope/intercept if need be |
| 1636 | 538 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
| 539 ApplyRescaleAndDoseScaling(*converted, false); | |
|
768
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|
540 |
|
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|
541 return converted.release(); |
|
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changeset
|
542 } |
|
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changeset
|
543 |
|
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|
544 |
|
1919
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added DicomInstanceParameters::CreateOverlayTexture()
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diff
changeset
|
545 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture( |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
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diff
changeset
|
546 const Orthanc::ImageAccessor& pixelData) const |
| 746 | 547 { |
|
1353
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|
548 // { |
|
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549 // const Orthanc::ImageAccessor& source = pixelData; |
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550 // const void* sourceBuffer = source.GetConstBuffer(); |
|
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|
551 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); |
|
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|
552 // int sourceWidth = source.GetWidth(); |
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|
553 // int sourceHeight = source.GetHeight(); |
|
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|
554 // int sourcePitch = source.GetPitch(); |
|
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|
555 |
|
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|
556 // // TODO: turn error into trace below |
|
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|
557 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" |
|
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|
558 // << " W = " << sourceWidth << " H = " << sourceHeight |
|
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|
559 // << " P = " << sourcePitch << " B = " << sourceBufferInt |
|
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|
560 // << " B % 4 == " << sourceBufferInt % 4; |
|
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|
561 // } |
|
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|
562 |
| 746 | 563 assert(sizeof(float) == 4); |
| 564 | |
| 565 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
| 566 | |
| 567 if (sourceFormat != GetExpectedPixelFormat()) | |
| 568 { | |
| 569 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
| 570 } | |
| 571 | |
|
1911
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changeset
|
572 std::unique_ptr<TextureBaseSceneLayer> texture; |
|
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diff
changeset
|
573 |
| 746 | 574 if (sourceFormat == Orthanc::PixelFormat_RGB24) |
| 575 { | |
| 576 // This is the case of a color image. No conversion has to be done. | |
|
1911
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changeset
|
577 texture.reset(new ColorTextureSceneLayer(pixelData)); |
| 746 | 578 } |
| 579 else | |
| 580 { | |
|
768
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diff
changeset
|
581 // This is the case of a grayscale frame. Convert it to Float32. |
|
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changeset
|
582 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
| 746 | 583 { |
|
768
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diff
changeset
|
584 texture.reset(new FloatTextureSceneLayer(pixelData)); |
|
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|
585 } |
|
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diff
changeset
|
586 else |
|
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diff
changeset
|
587 { |
|
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changeset
|
588 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
| 746 | 589 texture.reset(new FloatTextureSceneLayer(*converted)); |
| 590 } | |
| 591 | |
|
1911
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
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diff
changeset
|
592 FloatTextureSceneLayer& floatTexture = dynamic_cast<FloatTextureSceneLayer&>(*texture); |
|
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changeset
|
593 |
|
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|
594 if (GetWindowingPresetsCount() > 0) |
| 746 | 595 { |
|
1911
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
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diff
changeset
|
596 floatTexture.SetCustomWindowing(GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
| 746 | 597 } |
|
1206
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Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
598 |
|
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
599 switch (GetImageInformation().GetPhotometricInterpretation()) |
|
1206
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Fixed photometric interpretation in texture creation
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diff
changeset
|
600 { |
|
1634
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diff
changeset
|
601 case Orthanc::PhotometricInterpretation_Monochrome1: |
|
1911
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DicomInstanceParameters::CreateTexture() now sets pixel spacing
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diff
changeset
|
602 floatTexture.SetInverted(true); |
|
1634
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diff
changeset
|
603 break; |
|
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diff
changeset
|
604 |
|
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improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
605 case Orthanc::PhotometricInterpretation_Monochrome2: |
|
1911
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
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diff
changeset
|
606 floatTexture.SetInverted(false); |
|
1634
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improving robustness of DicomInstanceParameters
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diff
changeset
|
607 break; |
|
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improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
608 |
|
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improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
609 default: |
|
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improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
610 break; |
|
1206
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Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
611 } |
|
1911
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
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parents:
1871
diff
changeset
|
612 } |
|
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
613 |
|
1911
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
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parents:
1871
diff
changeset
|
614 if (HasPixelSpacing()) |
|
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
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parents:
1871
diff
changeset
|
615 { |
|
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
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1871
diff
changeset
|
616 texture->SetPixelSpacing(GetPixelSpacingX(), GetPixelSpacingY()); |
| 746 | 617 } |
|
1911
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1871
diff
changeset
|
618 |
|
898774b4e02d
DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1871
diff
changeset
|
619 return texture.release(); |
| 746 | 620 } |
|
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
621 |
|
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
622 |
|
1919
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
623 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture( |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
624 const Orthanc::ImageAccessor& pixelData) const |
|
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
625 { |
|
1919
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
626 std::unique_ptr<LookupTableTextureSceneLayer> texture; |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
627 |
|
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
628 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
|
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
629 { |
|
1919
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
630 texture.reset(new LookupTableTextureSceneLayer(pixelData)); |
|
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
631 } |
|
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
632 else |
|
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
633 { |
|
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
634 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
|
1919
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
635 texture.reset(new LookupTableTextureSceneLayer(*converted)); |
|
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
636 } |
|
1919
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
637 |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
638 if (HasPixelSpacing()) |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
639 { |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
640 texture->SetPixelSpacing(GetPixelSpacingX(), GetPixelSpacingY()); |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
641 } |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
642 |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
643 return texture.release(); |
|
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
644 } |
|
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
645 |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
646 |
|
1919
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
647 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateOverlayTexture( |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
648 int originX, |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
649 int originY, |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
650 const Orthanc::ImageAccessor& overlay) const |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
651 { |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
652 if (overlay.GetFormat() != Orthanc::PixelFormat_Grayscale8) |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
653 { |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
654 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
655 } |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
656 |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
657 std::unique_ptr<LookupTableTextureSceneLayer> texture(CreateLookupTableTexture(overlay)); |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
658 |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
659 texture->SetOrigin(static_cast<double>(originX - 1) * texture->GetPixelSpacingX(), |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
660 static_cast<double>(originY - 1) * texture->GetPixelSpacingY()); |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
661 |
|
1924
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
662 std::vector<uint8_t> lut(4 * 256); |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
663 for (size_t i = 0; i < 256; i++) |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
664 { |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
665 if (i < 127) |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
666 { |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
667 // Black pixels are converted to transparent pixels |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
668 lut[4 * i] = 0; |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
669 lut[4 * i + 1] = 0; |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
670 lut[4 * i + 2] = 0; |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
671 lut[4 * i + 3] = 0; // alpha |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
672 } |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
673 else |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
674 { |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
675 // White pixels are converted to opaque white |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
676 lut[4 * i] = 255; |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
677 lut[4 * i + 1] = 255; |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
678 lut[4 * i + 2] = 255; |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
679 lut[4 * i + 3] = 255; // alpha |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
680 } |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
681 } |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
682 |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
683 texture->SetLookupTable(lut); |
|
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
684 |
|
1919
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
685 return texture.release(); |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
686 } |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
687 |
|
ed4831e08961
added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1911
diff
changeset
|
688 |
|
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
689 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
690 { |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
691 if (data_.hasIndexInSeries_) |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
692 { |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
693 return data_.indexInSeries_; |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
694 } |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
695 else |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
696 { |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
697 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
698 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
699 } |
|
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
700 } |
|
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
701 |
|
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
702 |
| 1636 | 703 double DicomInstanceParameters::ApplyRescale(double value) const |
|
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
704 { |
|
1924
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
705 double scaling = data_.doseGridScaling_; |
|
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
706 double offset = 0.0; |
|
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
707 |
| 1636 | 708 if (data_.hasRescale_) |
|
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
709 { |
|
1924
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
710 scaling *= data_.rescaleSlope_; |
| 1636 | 711 offset = data_.rescaleIntercept_; |
|
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
712 } |
|
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
713 |
|
1924
f4050908c6bc
display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1919
diff
changeset
|
714 return (value * scaling + offset); |
|
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
715 } |
|
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
716 |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
717 |
| 1636 | 718 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const |
|
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
719 { |
| 1636 | 720 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE |
|
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
721 { |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
722 return false; |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
723 } |
| 1636 | 724 else if (data_.frameOffsets_.size() == 1) |
|
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
725 { |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
726 spacing = 1; // Edge case: RT-DOSE with one single frame |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
727 return true; |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
728 } |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
729 else |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
730 { |
| 1636 | 731 assert(data_.frameOffsets_.size() == GetNumberOfFrames()); |
| 732 | |
| 733 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]); | |
|
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
734 |
| 1636 | 735 for (size_t i = 1; i + 1 < data_.frameOffsets_.size(); i++) |
|
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
736 { |
| 1636 | 737 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]; |
|
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
738 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
739 { |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
740 return false; |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
741 } |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
742 } |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
743 |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
744 return true; |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
745 } |
|
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
746 } |
|
1822
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
747 |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
748 |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
749 void DicomInstanceParameters::SetPixelSpacing(double pixelSpacingX, |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
750 double pixelSpacingY) |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
751 { |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
752 data_.hasPixelSpacing_ = true; |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
753 data_.pixelSpacingX_ = pixelSpacingX; |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
754 data_.pixelSpacingY_ = pixelSpacingY; |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
755 } |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
756 |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
757 |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1821
diff
changeset
|
758 static const Json::Value* LookupDicomWebSingleValue(const Json::Value& dicomweb, |
|
0489fe25ce48
support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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759 const std::string& tag, |
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760 const std::string& vr) |
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761 { |
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762 static const char* const VALUE = "Value"; |
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763 static const char* const VR = "vr"; |
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764 |
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765 if (dicomweb.type() == Json::objectValue && |
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766 dicomweb.isMember(tag) && |
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767 dicomweb[tag].type() == Json::objectValue && |
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768 dicomweb[tag].isMember(VALUE) && |
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769 dicomweb[tag].isMember(VR) && |
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770 dicomweb[tag][VR].type() == Json::stringValue && |
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771 dicomweb[tag][VR].asString() == vr && |
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772 dicomweb[tag][VALUE].type() == Json::arrayValue && |
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773 dicomweb[tag][VALUE].size() == 1u) |
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774 { |
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775 return &dicomweb[tag][VALUE][0]; |
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776 } |
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777 else |
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778 { |
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779 return NULL; |
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780 } |
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781 } |
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782 |
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783 |
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784 void DicomInstanceParameters::EnrichUsingDicomWeb(const Json::Value& dicomweb) |
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785 { |
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786 /** |
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787 * Use DICOM tag "SequenceOfUltrasoundRegions" (0018,6011) in |
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788 * order to derive the pixel spacing on ultrasound (US) images |
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789 **/ |
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790 |
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791 if (!data_.hasPixelSpacing_) |
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792 { |
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793 const Json::Value* region = LookupDicomWebSingleValue(dicomweb, "00186011", "SQ"); |
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794 if (region != NULL) |
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795 { |
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796 const Json::Value* physicalUnitsXDirection = LookupDicomWebSingleValue(*region, "00186024", "US"); |
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797 const Json::Value* physicalUnitsYDirection = LookupDicomWebSingleValue(*region, "00186026", "US"); |
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798 const Json::Value* physicalDeltaX = LookupDicomWebSingleValue(*region, "0018602C", "FD"); |
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799 const Json::Value* physicalDeltaY = LookupDicomWebSingleValue(*region, "0018602E", "FD"); |
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800 |
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801 if (physicalUnitsXDirection != NULL && |
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802 physicalUnitsYDirection != NULL && |
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803 physicalDeltaX != NULL && |
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804 physicalDeltaY != NULL && |
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805 physicalUnitsXDirection->type() == Json::intValue && |
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806 physicalUnitsYDirection->type() == Json::intValue && |
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807 physicalUnitsXDirection->asInt() == 0x0003 && // Centimeters |
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808 physicalUnitsYDirection->asInt() == 0x0003 && // Centimeters |
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809 physicalDeltaX->isNumeric() && |
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810 physicalDeltaY->isNumeric()) |
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811 { |
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812 // Scene coordinates are expressed in millimeters => multiplication by 10 |
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813 SetPixelSpacing(10.0 * physicalDeltaX->asDouble(), |
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814 10.0 * physicalDeltaY->asDouble()); |
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815 } |
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816 } |
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817 } |
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818 } |
| 746 | 819 } |