Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1746:4bedae500652
Automatically compute SliceThickness from
GridFrameOffsetVector when SliceThickness
is not present in the DICOM tags
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Fri, 12 Feb 2021 10:41:17 +0100 |
parents | 9ac2a65d4172 |
children | 5f74ebe2516b |
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" | |
27 #include "../Toolbox/GeometryToolbox.h" | |
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28 #include "../Toolbox/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 LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image"; |
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118 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
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119 sliceThicknessPresent = false; |
746 | 120 } |
121 | |
122 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); | |
123 | |
124 std::string position, orientation; | |
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125 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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126 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
746 | 127 { |
128 geometry_ = CoordinateSystem3D(position, orientation); | |
129 } | |
130 | |
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131 // Must be AFTER setting "numberOfFrames_" |
1639 | 132 if (numberOfFrames_ > 1) |
133 { | |
134 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_); | |
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135 |
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136 // if the slice thickness is unknown, we try to infer it from the sequence of grid frame offsets |
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137 // this only works if: |
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138 // - 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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139 // - the offsets are all equal, to some small tolerance |
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140 // - the offsets is positive (increasing throughout the frames) |
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141 if (!sliceThicknessPresent) |
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142 { |
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143 if (frameOffsets_.size() >= 2) |
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144 { |
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145 double sliceThickness = frameOffsets_[1] - frameOffsets_[0]; |
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146 bool sameSized = true; |
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147 if (sliceThickness > 0) |
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148 { |
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149 for (size_t i = 2; i < frameOffsets_.size(); ++i) |
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150 { |
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151 double currentThickness = frameOffsets_[i] - frameOffsets_[i-1]; |
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152 if (!LinearAlgebra::IsNear(sliceThickness, currentThickness)) |
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153 { |
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154 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)"; |
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155 sameSized = false; |
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156 break; |
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157 } |
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158 } |
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159 if (sameSized) |
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160 { |
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161 sliceThickness_ = sliceThickness; |
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162 LOG(INFO) << "SliceThickness was not specified in the Dicom but was inferred from GridFrameOffsetVector (3004,000C)."; |
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163 } |
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164 } |
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165 } |
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166 else |
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167 { |
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168 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: GridFrameOffsetVector not present or too small)"; |
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169 } |
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170 } |
1639 | 171 } |
172 else | |
173 { | |
174 frameOffsets_.resize(0); | |
175 } | |
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176 |
746 | 177 if (sopClassUid_ == SopClassUid_RTDose) |
178 { | |
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179 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); |
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180 |
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181 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) |
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182 { |
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183 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
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184 doseUnits_.clear(); |
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185 } |
746 | 186 } |
187 | |
188 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
189 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
190 { | |
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191 if (sopClassUid_ == SopClassUid_RTDose) |
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192 { |
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193 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; |
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194 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES |
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195 hasRescale_ = false; |
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196 } |
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197 else |
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198 { |
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199 hasRescale_ = true; |
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200 } |
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201 |
746 | 202 } |
203 else | |
204 { | |
205 hasRescale_ = false; | |
206 } | |
207 | |
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208 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) |
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209 { |
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210 if (sopClassUid_ == SopClassUid_RTDose) |
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211 { |
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212 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; |
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213 } |
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214 } |
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215 else |
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216 { |
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217 doseGridScaling_ = 1.0; |
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218 if (sopClassUid_ == SopClassUid_RTDose) |
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219 { |
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220 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; |
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221 } |
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222 } |
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223 |
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224 bool ok = false; |
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225 |
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226 if (LinearAlgebra::ParseVector(windowingPresetCenters_, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && |
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227 LinearAlgebra::ParseVector(windowingPresetWidths_, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH)) |
746 | 228 { |
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229 if (windowingPresetCenters_.size() == windowingPresetWidths_.size()) |
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230 { |
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231 ok = true; |
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232 } |
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233 else |
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234 { |
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235 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this"; |
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236 ok = false; |
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237 } |
746 | 238 } |
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239 |
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240 if (!ok) |
746 | 241 { |
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242 // Don't use "Vector::clear()", as it has not the same meaning as "std::vector::clear()" |
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243 windowingPresetCenters_.resize(0); |
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244 windowingPresetWidths_.resize(0); |
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245 } |
746 | 246 |
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247 // This computes the "IndexInSeries" metadata from Orthanc (check |
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248 // out "Orthanc::ServerIndex::Store()") |
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249 hasIndexInSeries_ = ( |
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250 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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251 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
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252 |
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253 if (!dicom.LookupStringValue( |
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254 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false)) |
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255 { |
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256 frameOfReferenceUid_.clear(); |
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257 } |
746 | 258 } |
259 | |
260 | |
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261 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const |
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262 { |
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263 assert(tags_.get() != NULL); |
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264 |
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265 if (imageInformation_.get() == NULL) |
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266 { |
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267 const_cast<DicomInstanceParameters&>(*this).imageInformation_. |
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268 reset(new Orthanc::DicomImageInformation(GetTags())); |
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269 |
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270 assert(imageInformation_->GetWidth() == GetWidth()); |
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271 assert(imageInformation_->GetHeight() == GetHeight()); |
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272 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames()); |
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273 } |
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274 |
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275 assert(imageInformation_.get() != NULL); |
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276 return *imageInformation_; |
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277 } |
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278 |
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279 |
1636 | 280 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const |
746 | 281 { |
1636 | 282 if (frame >= data_.numberOfFrames_) |
746 | 283 { |
284 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
285 } | |
1636 | 286 else if (data_.frameOffsets_.empty()) |
746 | 287 { |
1636 | 288 return data_.geometry_; |
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289 } |
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290 else |
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291 { |
1636 | 292 assert(data_.frameOffsets_.size() == data_.numberOfFrames_); |
746 | 293 |
294 return CoordinateSystem3D( | |
1636 | 295 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(), |
296 data_.geometry_.GetAxisX(), | |
297 data_.geometry_.GetAxisY()); | |
746 | 298 } |
299 } | |
300 | |
301 | |
1636 | 302 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame, |
303 const CoordinateSystem3D& plane) const | |
746 | 304 { |
1636 | 305 if (frame >= data_.numberOfFrames_) |
746 | 306 { |
307 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
308 } | |
309 | |
1636 | 310 CoordinateSystem3D tmp = data_.geometry_; |
746 | 311 |
312 if (frame != 0) | |
313 { | |
314 tmp = GetFrameGeometry(frame); | |
315 } | |
316 | |
317 double distance; | |
318 | |
757 | 319 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
1636 | 320 distance <= data_.sliceThickness_ / 2.0); |
746 | 321 } |
322 | |
1637 | 323 |
324 bool DicomInstanceParameters::IsColor() const | |
325 { | |
326 Orthanc::PhotometricInterpretation photometric = | |
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327 GetImageInformation().GetPhotometricInterpretation(); |
1637 | 328 |
329 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 && | |
330 photometric != Orthanc::PhotometricInterpretation_Monochrome2); | |
331 } | |
332 | |
333 | |
1636 | 334 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, |
335 bool useDouble) const | |
746 | 336 { |
337 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
338 { | |
339 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
340 } | |
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341 |
1636 | 342 double factor = data_.doseGridScaling_; |
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343 double offset = 0.0; |
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344 |
1636 | 345 if (data_.hasRescale_) |
746 | 346 { |
1636 | 347 factor *= data_.rescaleSlope_; |
348 offset = data_.rescaleIntercept_; | |
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349 } |
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350 |
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351 if (!LinearAlgebra::IsNear(factor, 1) || |
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352 !LinearAlgebra::IsNear(offset, 0)) |
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353 { |
746 | 354 const unsigned int width = image.GetWidth(); |
355 const unsigned int height = image.GetHeight(); | |
356 | |
357 for (unsigned int y = 0; y < height; y++) | |
358 { | |
359 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
360 | |
361 if (useDouble) | |
362 { | |
363 // Slower, accurate implementation using double | |
364 for (unsigned int x = 0; x < width; x++, p++) | |
365 { | |
366 double value = static_cast<double>(*p); | |
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367 *p = static_cast<float>(value * factor + offset); |
746 | 368 } |
369 } | |
370 else | |
371 { | |
372 // Fast, approximate implementation using float | |
373 for (unsigned int x = 0; x < width; x++, p++) | |
374 { | |
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375 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset); |
746 | 376 } |
377 } | |
378 } | |
379 } | |
380 } | |
381 | |
382 double DicomInstanceParameters::GetRescaleIntercept() const | |
383 { | |
384 if (data_.hasRescale_) | |
385 { | |
386 return data_.rescaleIntercept_; | |
387 } | |
388 else | |
389 { | |
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390 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
746 | 391 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
392 } | |
393 } | |
394 | |
395 | |
396 double DicomInstanceParameters::GetRescaleSlope() const | |
397 { | |
398 if (data_.hasRescale_) | |
399 { | |
400 return data_.rescaleSlope_; | |
401 } | |
402 else | |
403 { | |
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404 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
746 | 405 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
406 } | |
407 } | |
408 | |
409 | |
1637 | 410 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const |
411 { | |
412 if (GetSopClassUid() == SopClassUid_RTDose) | |
413 { | |
414 switch (GetImageInformation().GetBitsStored()) | |
415 { | |
416 case 16: | |
417 return Orthanc::PixelFormat_Grayscale16; | |
418 | |
419 case 32: | |
420 return Orthanc::PixelFormat_Grayscale32; | |
421 | |
422 default: | |
423 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
424 } | |
425 } | |
426 else if (IsColor()) | |
427 { | |
428 return Orthanc::PixelFormat_RGB24; | |
429 } | |
430 else if (GetImageInformation().IsSigned()) | |
431 { | |
432 return Orthanc::PixelFormat_SignedGrayscale16; | |
433 } | |
434 else | |
435 { | |
436 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
437 } | |
438 } | |
439 | |
440 | |
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441 size_t DicomInstanceParameters::GetWindowingPresetsCount() const |
746 | 442 { |
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443 assert(data_.windowingPresetCenters_.size() == data_.windowingPresetWidths_.size()); |
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444 return data_.windowingPresetCenters_.size(); |
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445 } |
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446 |
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447 |
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448 float DicomInstanceParameters::GetWindowingPresetCenter(size_t i) const |
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449 { |
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450 if (i < GetWindowingPresetsCount()) |
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451 { |
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452 return static_cast<float>(data_.windowingPresetCenters_[i]); |
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453 } |
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454 else |
746 | 455 { |
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456 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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457 } |
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458 } |
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459 |
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460 |
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461 float DicomInstanceParameters::GetWindowingPresetWidth(size_t i) const |
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462 { |
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463 if (i < GetWindowingPresetsCount()) |
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464 { |
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465 return static_cast<float>(data_.windowingPresetWidths_[i]); |
746 | 466 } |
467 else | |
468 { | |
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469 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
746 | 470 } |
471 } | |
472 | |
473 | |
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474 static void GetWindowingBounds(float& low, |
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475 float& high, |
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476 double center, // in |
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477 double width) // in |
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478 { |
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479 low = static_cast<float>(center - width / 2.0); |
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480 high = static_cast<float>(center + width / 2.0); |
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481 } |
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482 |
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483 |
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484 void DicomInstanceParameters::GetWindowingPresetsUnion(float& center, |
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485 float& width) const |
746 | 486 { |
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487 assert(tags_.get() != NULL); |
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488 size_t s = GetWindowingPresetsCount(); |
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489 |
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490 if (s > 0) |
746 | 491 { |
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492 // Use the largest windowing given all the preset windowings |
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493 // that are available in the DICOM tags |
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494 float low, high; |
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495 GetWindowingBounds(low, high, GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
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496 |
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497 for (size_t i = 1; i < s; i++) |
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498 { |
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499 float a, b; |
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500 GetWindowingBounds(a, b, GetWindowingPresetCenter(i), GetWindowingPresetWidth(i)); |
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501 low = std::min(low, a); |
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502 high = std::max(high, b); |
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503 } |
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504 |
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505 assert(low <= high); |
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506 |
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507 if (LinearAlgebra::IsNear(low, high)) |
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508 { |
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509 // Cannot infer a suitable windowing from the available tags |
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510 center = 128.0f; |
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511 width = 256.0f; |
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512 } |
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513 else |
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514 { |
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515 center = (low + high) / 2.0f; |
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516 width = (high - low); |
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517 } |
746 | 518 } |
519 else | |
520 { | |
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521 float a, b; |
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522 if (tags_->ParseFloat(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) && |
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523 tags_->ParseFloat(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE) && |
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524 a < b) |
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525 { |
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526 center = (a + b) / 2.0f; |
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527 width = (b - a); |
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528 } |
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529 else |
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530 { |
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531 // Cannot infer a suitable windowing from the available tags |
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532 center = 128.0f; |
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533 width = 256.0f; |
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534 } |
746 | 535 } |
536 } | |
537 | |
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538 |
768
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539 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
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540 { |
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541 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
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542 pixelData.GetWidth(), |
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543 pixelData.GetHeight(), |
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improving robustness of DicomInstanceParameters
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diff
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|
544 false)); |
768
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LookupTableTextureSceneLayer
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762
diff
changeset
|
545 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
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LookupTableTextureSceneLayer
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diff
changeset
|
546 |
1287
8e82fdc6200e
Heavy (temporary) logging in the path that leads
Benjamin Golinvaux <bgo@osimis.io>
parents:
1270
diff
changeset
|
547 |
768
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LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
548 // Correct rescale slope/intercept if need be |
1636 | 549 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
550 ApplyRescaleAndDoseScaling(*converted, false); | |
768
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LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
551 |
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LookupTableTextureSceneLayer
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diff
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552 return converted.release(); |
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LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
553 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
554 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
555 |
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LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
556 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
55411e7da2f7
LookupTableTextureSceneLayer
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diff
changeset
|
557 (const Orthanc::ImageAccessor& pixelData) const |
746 | 558 { |
1353
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diff
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|
559 // { |
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diff
changeset
|
560 // const Orthanc::ImageAccessor& source = pixelData; |
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Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
561 // const void* sourceBuffer = source.GetConstBuffer(); |
af65bce18951
Dummy commented debug block
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parents:
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diff
changeset
|
562 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); |
af65bce18951
Dummy commented debug block
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diff
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|
563 // int sourceWidth = source.GetWidth(); |
af65bce18951
Dummy commented debug block
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diff
changeset
|
564 // int sourceHeight = source.GetHeight(); |
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diff
changeset
|
565 // int sourcePitch = source.GetPitch(); |
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Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
566 |
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diff
changeset
|
567 // // TODO: turn error into trace below |
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diff
changeset
|
568 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" |
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Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
569 // << " W = " << sourceWidth << " H = " << sourceHeight |
af65bce18951
Dummy commented debug block
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diff
changeset
|
570 // << " P = " << sourcePitch << " B = " << sourceBufferInt |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
571 // << " B % 4 == " << sourceBufferInt % 4; |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
572 // } |
af65bce18951
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Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
573 |
746 | 574 assert(sizeof(float) == 4); |
575 | |
576 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
577 | |
578 if (sourceFormat != GetExpectedPixelFormat()) | |
579 { | |
580 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
581 } | |
582 | |
583 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
584 { | |
585 // This is the case of a color image. No conversion has to be done. | |
586 return new ColorTextureSceneLayer(pixelData); | |
587 } | |
588 else | |
589 { | |
768
55411e7da2f7
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parents:
762
diff
changeset
|
590 // This is the case of a grayscale frame. Convert it to Float32. |
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diff
changeset
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591 std::unique_ptr<FloatTextureSceneLayer> texture; |
746 | 592 |
768
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LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
593 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
746 | 594 { |
768
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LookupTableTextureSceneLayer
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parents:
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diff
changeset
|
595 texture.reset(new FloatTextureSceneLayer(pixelData)); |
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LookupTableTextureSceneLayer
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diff
changeset
|
596 } |
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LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
597 else |
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diff
changeset
|
598 { |
1298
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replacing std::auto_ptr by std::unique_ptr
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diff
changeset
|
599 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
746 | 600 texture.reset(new FloatTextureSceneLayer(*converted)); |
601 } | |
602 | |
1679
5b8b88e5bfd6
successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1677
diff
changeset
|
603 if (GetWindowingPresetsCount() > 0) |
746 | 604 { |
1679
5b8b88e5bfd6
successfully running unit tests in WebAssembly
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parents:
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diff
changeset
|
605 texture->SetCustomWindowing(GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
746 | 606 } |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
607 |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
608 switch (GetImageInformation().GetPhotometricInterpretation()) |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
609 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
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diff
changeset
|
610 case Orthanc::PhotometricInterpretation_Monochrome1: |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
611 texture->SetInverted(true); |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
612 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
1598
diff
changeset
|
613 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
614 case Orthanc::PhotometricInterpretation_Monochrome2: |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
615 texture->SetInverted(false); |
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improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
616 break; |
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improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
617 |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
618 default: |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
619 break; |
1206
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Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
620 } |
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
621 |
746 | 622 return texture.release(); |
623 } | |
624 } | |
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
625 |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
626 |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
627 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
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LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
628 (const Orthanc::ImageAccessor& pixelData) const |
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LookupTableTextureSceneLayer
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diff
changeset
|
629 { |
1298
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replacing std::auto_ptr by std::unique_ptr
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diff
changeset
|
630 std::unique_ptr<FloatTextureSceneLayer> texture; |
768
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LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
631 |
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LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
632 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
633 { |
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LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
634 return new LookupTableTextureSceneLayer(pixelData); |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
635 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
636 else |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
637 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
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parents:
1291
diff
changeset
|
638 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
639 return new LookupTableTextureSceneLayer(*converted); |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
640 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
641 } |
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
642 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
643 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
644 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
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 if (data_.hasIndexInSeries_) |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
647 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
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parents:
956
diff
changeset
|
648 return data_.indexInSeries_; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
649 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
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parents:
956
diff
changeset
|
650 else |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
651 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
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parents:
956
diff
changeset
|
652 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
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parents:
956
diff
changeset
|
653 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
654 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
655 } |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
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parents:
1141
diff
changeset
|
656 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
657 |
1636 | 658 double DicomInstanceParameters::ApplyRescale(double value) const |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
659 { |
1636 | 660 double factor = data_.doseGridScaling_; |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
661 double offset = 0.0; |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
662 |
1636 | 663 if (data_.hasRescale_) |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
664 { |
1636 | 665 factor *= data_.rescaleSlope_; |
666 offset = data_.rescaleIntercept_; | |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
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1141
diff
changeset
|
667 } |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
668 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
669 return (value * factor + offset); |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
670 } |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
671 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
672 |
1636 | 673 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const |
1161
19b1c8caade4
fix sagittal geometry
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parents:
1159
diff
changeset
|
674 { |
1636 | 675 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
676 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
677 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
678 } |
1636 | 679 else if (data_.frameOffsets_.size() == 1) |
1161
19b1c8caade4
fix sagittal geometry
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parents:
1159
diff
changeset
|
680 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
681 spacing = 1; // Edge case: RT-DOSE with one single frame |
19b1c8caade4
fix sagittal geometry
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parents:
1159
diff
changeset
|
682 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
683 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
684 else |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
685 { |
1636 | 686 assert(data_.frameOffsets_.size() == GetNumberOfFrames()); |
687 | |
688 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]); | |
1161
19b1c8caade4
fix sagittal geometry
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1159
diff
changeset
|
689 |
1636 | 690 for (size_t i = 1; i + 1 < data_.frameOffsets_.size(); i++) |
1161
19b1c8caade4
fix sagittal geometry
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parents:
1159
diff
changeset
|
691 { |
1636 | 692 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]; |
1161
19b1c8caade4
fix sagittal geometry
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parents:
1159
diff
changeset
|
693 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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1159
diff
changeset
|
694 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
695 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
696 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
697 } |
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 true; |
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 } |
746 | 702 } |