Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1807:634ff8993f6a
Stone Web viewer: Patient birth date is now displayed in the overlays
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 20 May 2021 17:17:56 +0200 |
parents | 6c246f862b00 |
children | 385c268e8b56 |
rev | line source |
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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) 2017-2021 Osimis S.A., Belgium |
746 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
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8 * modify it under the terms of the GNU Lesser General Public License |
746 | 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 | |
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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15 * Lesser General Public License for more details. |
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16 * |
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17 * You should have received a copy of the GNU Lesser General Public |
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18 * License along with this program. If not, see |
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19 * <http://www.gnu.org/licenses/>. |
746 | 20 **/ |
21 | |
22 | |
23 #include "DicomInstanceParameters.h" | |
24 | |
25 #include "../Scene2D/ColorTextureSceneLayer.h" | |
26 #include "../Scene2D/FloatTextureSceneLayer.h" | |
1750 | 27 #include "GeometryToolbox.h" |
28 #include "ImageToolbox.h" | |
746 | 29 |
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30 #include <Images/Image.h> |
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31 #include <Images/ImageProcessing.h> |
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32 #include <Logging.h> |
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33 #include <OrthancException.h> |
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34 #include <Toolbox.h> |
746 | 35 |
36 | |
37 namespace OrthancStone | |
38 { | |
1636 | 39 static void ExtractFrameOffsets(Vector& target, |
40 const Orthanc::DicomMap& dicom, | |
41 unsigned int numberOfFrames) | |
746 | 42 { |
43 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html | |
44 | |
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45 std::string increment; |
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46 |
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47 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) |
746 | 48 { |
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49 Orthanc::Toolbox::ToUpperCase(increment); |
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50 |
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51 // We only support volumes where the FrameIncrementPointer (0028,0009) (required) contains |
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52 // the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) |
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53 if (increment != "3004,000C") |
746 | 54 { |
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55 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image"; |
1636 | 56 target.resize(0); |
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57 return; |
746 | 58 } |
59 } | |
60 | |
1636 | 61 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) || |
62 target.size() != numberOfFrames) | |
746 | 63 { |
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64 LOG(ERROR) << "The frame offset information (GridFrameOffsetVector (3004,000C)) is missing in a multiframe image"; |
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65 |
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66 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector! |
1636 | 67 target.resize(0); |
746 | 68 } |
69 } | |
70 | |
71 | |
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72 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) |
746 | 73 { |
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74 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || |
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75 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || |
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76 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
746 | 77 { |
78 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
79 } | |
80 | |
81 std::string s; | |
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82 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) |
746 | 83 { |
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84 sopClassUid_ = StringToSopClassUid(s); |
746 | 85 } |
86 else | |
87 { | |
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88 sopClassUid_ = SopClassUid_Other; |
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89 } |
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90 |
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91 uint32_t n; |
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92 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
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93 { |
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94 numberOfFrames_ = n; |
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95 } |
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96 else |
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97 { |
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98 numberOfFrames_ = 1; |
746 | 99 } |
100 | |
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101 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) || |
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102 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_)) |
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103 { |
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104 width_ = 0; |
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105 } |
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106 |
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107 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) || |
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108 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_)) |
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109 { |
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110 height_ = 0; |
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111 } |
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112 |
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113 |
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114 bool sliceThicknessPresent = true; |
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115 if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) |
746 | 116 { |
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117 if (numberOfFrames_ > 1) |
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118 { |
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119 LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image"; |
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120 } |
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121 |
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122 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
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123 sliceThicknessPresent = false; |
746 | 124 } |
125 | |
126 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); | |
127 | |
128 std::string position, orientation; | |
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129 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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130 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
746 | 131 { |
132 geometry_ = CoordinateSystem3D(position, orientation); | |
133 } | |
134 | |
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135 // Must be AFTER setting "numberOfFrames_" |
1639 | 136 if (numberOfFrames_ > 1) |
137 { | |
138 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_); | |
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139 |
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140 // if the slice thickness is unknown, we try to infer it from the sequence of grid frame offsets |
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141 // this only works if: |
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142 // - 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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143 // - the offsets are all equal, to some small tolerance |
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144 // - the offsets is positive (increasing throughout the frames) |
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145 if (!sliceThicknessPresent) |
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146 { |
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147 if (frameOffsets_.size() >= 2) |
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148 { |
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149 double sliceThickness = frameOffsets_[1] - frameOffsets_[0]; |
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150 bool sameSized = true; |
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151 if (sliceThickness > 0) |
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152 { |
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153 for (size_t i = 2; i < frameOffsets_.size(); ++i) |
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154 { |
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155 double currentThickness = frameOffsets_[i] - frameOffsets_[i-1]; |
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156 if (!LinearAlgebra::IsNear(sliceThickness, currentThickness)) |
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157 { |
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158 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)"; |
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159 sameSized = false; |
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160 break; |
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161 } |
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162 } |
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163 if (sameSized) |
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164 { |
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165 sliceThickness_ = sliceThickness; |
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166 LOG(INFO) << "SliceThickness was not specified in the Dicom but was inferred from GridFrameOffsetVector (3004,000C)."; |
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167 } |
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168 } |
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169 } |
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170 else |
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171 { |
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172 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: GridFrameOffsetVector not present or too small)"; |
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173 } |
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174 } |
1639 | 175 } |
176 else | |
177 { | |
178 frameOffsets_.resize(0); | |
179 } | |
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180 |
746 | 181 if (sopClassUid_ == SopClassUid_RTDose) |
182 { | |
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183 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); |
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184 |
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185 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) |
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186 { |
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187 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
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188 doseUnits_.clear(); |
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189 } |
746 | 190 } |
191 | |
192 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
193 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
194 { | |
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195 if (sopClassUid_ == SopClassUid_RTDose) |
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196 { |
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197 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; |
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198 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES |
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199 hasRescale_ = false; |
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200 } |
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201 else |
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202 { |
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203 hasRescale_ = true; |
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204 } |
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205 |
746 | 206 } |
207 else | |
208 { | |
209 hasRescale_ = false; | |
210 } | |
211 | |
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212 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) |
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213 { |
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214 if (sopClassUid_ == SopClassUid_RTDose) |
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215 { |
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216 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; |
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217 } |
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218 } |
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219 else |
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220 { |
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221 doseGridScaling_ = 1.0; |
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222 if (sopClassUid_ == SopClassUid_RTDose) |
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223 { |
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224 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; |
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225 } |
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226 } |
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227 |
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228 bool ok = false; |
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229 |
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230 if (LinearAlgebra::ParseVector(windowingPresetCenters_, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && |
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231 LinearAlgebra::ParseVector(windowingPresetWidths_, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH)) |
746 | 232 { |
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233 if (windowingPresetCenters_.size() == windowingPresetWidths_.size()) |
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234 { |
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235 ok = true; |
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236 } |
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237 else |
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238 { |
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239 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this"; |
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240 ok = false; |
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241 } |
746 | 242 } |
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243 |
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244 if (!ok) |
746 | 245 { |
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246 // Don't use "Vector::clear()", as it has not the same meaning as "std::vector::clear()" |
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247 windowingPresetCenters_.resize(0); |
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248 windowingPresetWidths_.resize(0); |
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249 } |
746 | 250 |
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251 // This computes the "IndexInSeries" metadata from Orthanc (check |
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252 // out "Orthanc::ServerIndex::Store()") |
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253 hasIndexInSeries_ = ( |
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254 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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255 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
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256 |
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257 if (!dicom.LookupStringValue( |
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258 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false)) |
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259 { |
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260 frameOfReferenceUid_.clear(); |
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261 } |
746 | 262 } |
263 | |
264 | |
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265 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const |
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266 { |
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267 assert(tags_.get() != NULL); |
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268 |
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269 if (imageInformation_.get() == NULL) |
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270 { |
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271 const_cast<DicomInstanceParameters&>(*this).imageInformation_. |
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272 reset(new Orthanc::DicomImageInformation(GetTags())); |
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273 |
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274 assert(imageInformation_->GetWidth() == GetWidth()); |
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275 assert(imageInformation_->GetHeight() == GetHeight()); |
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276 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames()); |
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277 } |
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278 |
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279 assert(imageInformation_.get() != NULL); |
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280 return *imageInformation_; |
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281 } |
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282 |
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283 |
1636 | 284 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const |
746 | 285 { |
1636 | 286 if (frame >= data_.numberOfFrames_) |
746 | 287 { |
288 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
289 } | |
1636 | 290 else if (data_.frameOffsets_.empty()) |
746 | 291 { |
1636 | 292 return data_.geometry_; |
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293 } |
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294 else |
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295 { |
1636 | 296 assert(data_.frameOffsets_.size() == data_.numberOfFrames_); |
746 | 297 |
298 return CoordinateSystem3D( | |
1636 | 299 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(), |
300 data_.geometry_.GetAxisX(), | |
301 data_.geometry_.GetAxisY()); | |
746 | 302 } |
303 } | |
304 | |
305 | |
1636 | 306 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame, |
307 const CoordinateSystem3D& plane) const | |
746 | 308 { |
1636 | 309 if (frame >= data_.numberOfFrames_) |
746 | 310 { |
311 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
312 } | |
313 | |
1636 | 314 CoordinateSystem3D tmp = data_.geometry_; |
746 | 315 |
316 if (frame != 0) | |
317 { | |
318 tmp = GetFrameGeometry(frame); | |
319 } | |
320 | |
321 double distance; | |
322 | |
757 | 323 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
1636 | 324 distance <= data_.sliceThickness_ / 2.0); |
746 | 325 } |
326 | |
1637 | 327 |
328 bool DicomInstanceParameters::IsColor() const | |
329 { | |
330 Orthanc::PhotometricInterpretation photometric = | |
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331 GetImageInformation().GetPhotometricInterpretation(); |
1637 | 332 |
333 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 && | |
334 photometric != Orthanc::PhotometricInterpretation_Monochrome2); | |
335 } | |
336 | |
337 | |
1636 | 338 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, |
339 bool useDouble) const | |
746 | 340 { |
341 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
342 { | |
343 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
344 } | |
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345 |
1636 | 346 double factor = data_.doseGridScaling_; |
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347 double offset = 0.0; |
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348 |
1636 | 349 if (data_.hasRescale_) |
746 | 350 { |
1636 | 351 factor *= data_.rescaleSlope_; |
352 offset = data_.rescaleIntercept_; | |
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353 } |
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354 |
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355 if (!LinearAlgebra::IsNear(factor, 1) || |
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356 !LinearAlgebra::IsNear(offset, 0)) |
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357 { |
746 | 358 const unsigned int width = image.GetWidth(); |
359 const unsigned int height = image.GetHeight(); | |
360 | |
361 for (unsigned int y = 0; y < height; y++) | |
362 { | |
363 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
364 | |
365 if (useDouble) | |
366 { | |
367 // Slower, accurate implementation using double | |
368 for (unsigned int x = 0; x < width; x++, p++) | |
369 { | |
370 double value = static_cast<double>(*p); | |
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371 *p = static_cast<float>(value * factor + offset); |
746 | 372 } |
373 } | |
374 else | |
375 { | |
376 // Fast, approximate implementation using float | |
377 for (unsigned int x = 0; x < width; x++, p++) | |
378 { | |
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379 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset); |
746 | 380 } |
381 } | |
382 } | |
383 } | |
384 } | |
385 | |
386 double DicomInstanceParameters::GetRescaleIntercept() const | |
387 { | |
388 if (data_.hasRescale_) | |
389 { | |
390 return data_.rescaleIntercept_; | |
391 } | |
392 else | |
393 { | |
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394 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
746 | 395 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
396 } | |
397 } | |
398 | |
399 | |
400 double DicomInstanceParameters::GetRescaleSlope() const | |
401 { | |
402 if (data_.hasRescale_) | |
403 { | |
404 return data_.rescaleSlope_; | |
405 } | |
406 else | |
407 { | |
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408 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
746 | 409 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
410 } | |
411 } | |
412 | |
413 | |
1637 | 414 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const |
415 { | |
416 if (GetSopClassUid() == SopClassUid_RTDose) | |
417 { | |
418 switch (GetImageInformation().GetBitsStored()) | |
419 { | |
420 case 16: | |
421 return Orthanc::PixelFormat_Grayscale16; | |
422 | |
423 case 32: | |
424 return Orthanc::PixelFormat_Grayscale32; | |
425 | |
426 default: | |
427 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
428 } | |
429 } | |
430 else if (IsColor()) | |
431 { | |
432 return Orthanc::PixelFormat_RGB24; | |
433 } | |
434 else if (GetImageInformation().IsSigned()) | |
435 { | |
436 return Orthanc::PixelFormat_SignedGrayscale16; | |
437 } | |
438 else | |
439 { | |
440 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
441 } | |
442 } | |
443 | |
444 | |
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445 size_t DicomInstanceParameters::GetWindowingPresetsCount() const |
746 | 446 { |
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447 assert(data_.windowingPresetCenters_.size() == data_.windowingPresetWidths_.size()); |
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448 return data_.windowingPresetCenters_.size(); |
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449 } |
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450 |
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451 |
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452 float DicomInstanceParameters::GetWindowingPresetCenter(size_t i) const |
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453 { |
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454 if (i < GetWindowingPresetsCount()) |
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455 { |
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456 return static_cast<float>(data_.windowingPresetCenters_[i]); |
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457 } |
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458 else |
746 | 459 { |
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460 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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461 } |
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462 } |
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463 |
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464 |
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465 float DicomInstanceParameters::GetWindowingPresetWidth(size_t i) const |
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466 { |
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467 if (i < GetWindowingPresetsCount()) |
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468 { |
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469 return static_cast<float>(data_.windowingPresetWidths_[i]); |
746 | 470 } |
471 else | |
472 { | |
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473 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
746 | 474 } |
475 } | |
476 | |
477 | |
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478 static void GetWindowingBounds(float& low, |
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479 float& high, |
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480 double center, // in |
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481 double width) // in |
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482 { |
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483 low = static_cast<float>(center - width / 2.0); |
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484 high = static_cast<float>(center + width / 2.0); |
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485 } |
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486 |
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487 |
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488 void DicomInstanceParameters::GetWindowingPresetsUnion(float& center, |
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489 float& width) const |
746 | 490 { |
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491 assert(tags_.get() != NULL); |
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492 size_t s = GetWindowingPresetsCount(); |
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493 |
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494 if (s > 0) |
746 | 495 { |
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496 // Use the largest windowing given all the preset windowings |
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497 // that are available in the DICOM tags |
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498 float low, high; |
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499 GetWindowingBounds(low, high, GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
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500 |
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501 for (size_t i = 1; i < s; i++) |
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502 { |
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503 float a, b; |
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504 GetWindowingBounds(a, b, GetWindowingPresetCenter(i), GetWindowingPresetWidth(i)); |
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505 low = std::min(low, a); |
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506 high = std::max(high, b); |
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507 } |
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508 |
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509 assert(low <= high); |
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510 |
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511 if (LinearAlgebra::IsNear(low, high)) |
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512 { |
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513 // Cannot infer a suitable windowing from the available tags |
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514 center = 128.0f; |
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515 width = 256.0f; |
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516 } |
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517 else |
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518 { |
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519 center = (low + high) / 2.0f; |
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520 width = (high - low); |
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521 } |
746 | 522 } |
523 else | |
524 { | |
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525 float a, b; |
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526 if (tags_->ParseFloat(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) && |
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527 tags_->ParseFloat(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE) && |
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528 a < b) |
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529 { |
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530 center = (a + b) / 2.0f; |
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531 width = (b - a); |
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532 } |
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533 else |
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534 { |
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535 // Cannot infer a suitable windowing from the available tags |
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536 center = 128.0f; |
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537 width = 256.0f; |
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538 } |
746 | 539 } |
540 } | |
541 | |
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542 |
768
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543 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
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diff
changeset
|
544 { |
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replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
545 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
546 pixelData.GetWidth(), |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
547 pixelData.GetHeight(), |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
548 false)); |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
549 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
550 |
1287
8e82fdc6200e
Heavy (temporary) logging in the path that leads
Benjamin Golinvaux <bgo@osimis.io>
parents:
1270
diff
changeset
|
551 |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
552 // Correct rescale slope/intercept if need be |
1636 | 553 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
554 ApplyRescaleAndDoseScaling(*converted, false); | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
555 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
556 return converted.release(); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
557 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
558 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
559 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
560 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
561 (const Orthanc::ImageAccessor& pixelData) const |
746 | 562 { |
1353
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
563 // { |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
564 // const Orthanc::ImageAccessor& source = pixelData; |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
565 // const void* sourceBuffer = source.GetConstBuffer(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
566 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
567 // int sourceWidth = source.GetWidth(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
568 // int sourceHeight = source.GetHeight(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
569 // int sourcePitch = source.GetPitch(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
570 |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
571 // // TODO: turn error into trace below |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
572 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
573 // << " W = " << sourceWidth << " H = " << sourceHeight |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
574 // << " P = " << sourcePitch << " B = " << sourceBufferInt |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
575 // << " B % 4 == " << sourceBufferInt % 4; |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
576 // } |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
577 |
746 | 578 assert(sizeof(float) == 4); |
579 | |
580 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
581 | |
582 if (sourceFormat != GetExpectedPixelFormat()) | |
583 { | |
584 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
585 } | |
586 | |
587 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
588 { | |
589 // This is the case of a color image. No conversion has to be done. | |
590 return new ColorTextureSceneLayer(pixelData); | |
591 } | |
592 else | |
593 { | |
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
594 // This is the case of a grayscale frame. Convert it to Float32. |
1298
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replacing std::auto_ptr by std::unique_ptr
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parents:
1291
diff
changeset
|
595 std::unique_ptr<FloatTextureSceneLayer> texture; |
746 | 596 |
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
597 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
746 | 598 { |
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
599 texture.reset(new FloatTextureSceneLayer(pixelData)); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
600 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
601 else |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
602 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
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parents:
1291
diff
changeset
|
603 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
746 | 604 texture.reset(new FloatTextureSceneLayer(*converted)); |
605 } | |
606 | |
1679
5b8b88e5bfd6
successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1677
diff
changeset
|
607 if (GetWindowingPresetsCount() > 0) |
746 | 608 { |
1679
5b8b88e5bfd6
successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1677
diff
changeset
|
609 texture->SetCustomWindowing(GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
746 | 610 } |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
611 |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
612 switch (GetImageInformation().GetPhotometricInterpretation()) |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
613 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
614 case Orthanc::PhotometricInterpretation_Monochrome1: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
615 texture->SetInverted(true); |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
616 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
1598
diff
changeset
|
617 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
618 case Orthanc::PhotometricInterpretation_Monochrome2: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
619 texture->SetInverted(false); |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
620 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
621 |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
1598
diff
changeset
|
622 default: |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
623 break; |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
624 } |
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
625 |
746 | 626 return texture.release(); |
627 } | |
628 } | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
629 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
630 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
631 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
632 (const Orthanc::ImageAccessor& pixelData) const |
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>
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1291
diff
changeset
|
634 std::unique_ptr<FloatTextureSceneLayer> texture; |
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
635 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
636 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
637 { |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
638 return new LookupTableTextureSceneLayer(pixelData); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
639 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
640 else |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
641 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
642 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
643 return new LookupTableTextureSceneLayer(*converted); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
644 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
645 } |
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
646 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
647 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
648 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
649 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
650 if (data_.hasIndexInSeries_) |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
651 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
652 return data_.indexInSeries_; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
653 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
654 else |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
655 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
656 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
657 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
658 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
659 } |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
660 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
661 |
1636 | 662 double DicomInstanceParameters::ApplyRescale(double value) const |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
663 { |
1636 | 664 double factor = data_.doseGridScaling_; |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
665 double offset = 0.0; |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
666 |
1636 | 667 if (data_.hasRescale_) |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
668 { |
1636 | 669 factor *= data_.rescaleSlope_; |
670 offset = data_.rescaleIntercept_; | |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
671 } |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
672 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
673 return (value * factor + offset); |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
674 } |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
675 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
676 |
1636 | 677 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
678 { |
1636 | 679 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
680 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
681 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
682 } |
1636 | 683 else if (data_.frameOffsets_.size() == 1) |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
684 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
685 spacing = 1; // Edge case: RT-DOSE with one single frame |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
686 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
687 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
688 else |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
689 { |
1636 | 690 assert(data_.frameOffsets_.size() == GetNumberOfFrames()); |
691 | |
692 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]); | |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
693 |
1636 | 694 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
|
695 { |
1636 | 696 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]; |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
697 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
698 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
699 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
700 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
701 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
702 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
703 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
704 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
705 } |
746 | 706 } |