Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1729:f62f5ee5a432
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 02 Dec 2020 07:08:29 +0100 |
parents | 5b8b88e5bfd6 |
children | 9ac2a65d4172 |
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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) 2017-2020 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 // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) |
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52 if (increment != "3004,000C") |
746 | 53 { |
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54 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image"; |
1636 | 55 target.resize(0); |
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56 return; |
746 | 57 } |
58 } | |
59 | |
1636 | 60 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) || |
61 target.size() != numberOfFrames) | |
746 | 62 { |
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63 LOG(INFO) << "The frame offset information is missing in a multiframe image"; |
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64 |
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65 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector! |
1636 | 66 target.resize(0); |
746 | 67 } |
68 } | |
69 | |
70 | |
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71 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) |
746 | 72 { |
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73 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || |
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74 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || |
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75 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
746 | 76 { |
77 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
78 } | |
79 | |
80 std::string s; | |
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81 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) |
746 | 82 { |
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83 sopClassUid_ = StringToSopClassUid(s); |
746 | 84 } |
85 else | |
86 { | |
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87 sopClassUid_ = SopClassUid_Other; |
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88 } |
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89 |
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90 uint32_t n; |
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91 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
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92 { |
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93 numberOfFrames_ = n; |
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94 } |
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95 else |
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96 { |
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97 numberOfFrames_ = 1; |
746 | 98 } |
99 | |
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100 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) || |
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101 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_)) |
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102 { |
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103 width_ = 0; |
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104 } |
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105 |
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106 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) || |
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107 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_)) |
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108 { |
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109 height_ = 0; |
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110 } |
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111 |
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112 if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) |
746 | 113 { |
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114 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
746 | 115 } |
116 | |
117 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); | |
118 | |
119 std::string position, orientation; | |
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120 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
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121 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
746 | 122 { |
123 geometry_ = CoordinateSystem3D(position, orientation); | |
124 } | |
125 | |
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126 // Must be AFTER setting "numberOfFrames_" |
1639 | 127 if (numberOfFrames_ > 1) |
128 { | |
129 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_); | |
130 } | |
131 else | |
132 { | |
133 frameOffsets_.resize(0); | |
134 } | |
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135 |
746 | 136 if (sopClassUid_ == SopClassUid_RTDose) |
137 { | |
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138 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); |
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139 |
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140 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) |
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141 { |
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142 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
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143 doseUnits_.clear(); |
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144 } |
746 | 145 } |
146 | |
147 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
148 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
149 { | |
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150 if (sopClassUid_ == SopClassUid_RTDose) |
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151 { |
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152 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; |
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153 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES |
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154 hasRescale_ = false; |
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155 } |
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156 else |
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157 { |
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158 hasRescale_ = true; |
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159 } |
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160 |
746 | 161 } |
162 else | |
163 { | |
164 hasRescale_ = false; | |
165 } | |
166 | |
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167 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) |
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168 { |
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169 if (sopClassUid_ == SopClassUid_RTDose) |
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170 { |
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171 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; |
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172 } |
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173 } |
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174 else |
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175 { |
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176 doseGridScaling_ = 1.0; |
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177 if (sopClassUid_ == SopClassUid_RTDose) |
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178 { |
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179 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; |
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180 } |
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181 } |
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182 |
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183 bool ok = false; |
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184 |
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185 if (LinearAlgebra::ParseVector(windowingPresetCenters_, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && |
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186 LinearAlgebra::ParseVector(windowingPresetWidths_, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH)) |
746 | 187 { |
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188 if (windowingPresetCenters_.size() == windowingPresetWidths_.size()) |
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189 { |
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190 ok = true; |
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191 } |
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192 else |
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193 { |
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194 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this"; |
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195 ok = false; |
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196 } |
746 | 197 } |
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198 |
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199 if (!ok) |
746 | 200 { |
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201 // Don't use "Vector::clear()", as it has not the same meaning as "std::vector::clear()" |
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202 windowingPresetCenters_.resize(0); |
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203 windowingPresetWidths_.resize(0); |
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204 } |
746 | 205 |
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206 // This computes the "IndexInSeries" metadata from Orthanc (check |
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207 // out "Orthanc::ServerIndex::Store()") |
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208 hasIndexInSeries_ = ( |
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209 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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210 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
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211 |
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212 if (!dicom.LookupStringValue( |
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213 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false)) |
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214 { |
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215 frameOfReferenceUid_.clear(); |
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216 } |
746 | 217 } |
218 | |
219 | |
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220 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const |
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221 { |
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222 assert(tags_.get() != NULL); |
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223 |
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224 if (imageInformation_.get() == NULL) |
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225 { |
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226 const_cast<DicomInstanceParameters&>(*this).imageInformation_. |
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227 reset(new Orthanc::DicomImageInformation(GetTags())); |
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228 |
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229 assert(imageInformation_->GetWidth() == GetWidth()); |
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230 assert(imageInformation_->GetHeight() == GetHeight()); |
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231 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames()); |
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232 } |
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233 |
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234 assert(imageInformation_.get() != NULL); |
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235 return *imageInformation_; |
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236 } |
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237 |
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238 |
1636 | 239 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const |
746 | 240 { |
1636 | 241 if (frame >= data_.numberOfFrames_) |
746 | 242 { |
243 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
244 } | |
1636 | 245 else if (data_.frameOffsets_.empty()) |
746 | 246 { |
1636 | 247 return data_.geometry_; |
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248 } |
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249 else |
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250 { |
1636 | 251 assert(data_.frameOffsets_.size() == data_.numberOfFrames_); |
746 | 252 |
253 return CoordinateSystem3D( | |
1636 | 254 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(), |
255 data_.geometry_.GetAxisX(), | |
256 data_.geometry_.GetAxisY()); | |
746 | 257 } |
258 } | |
259 | |
260 | |
1636 | 261 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame, |
262 const CoordinateSystem3D& plane) const | |
746 | 263 { |
1636 | 264 if (frame >= data_.numberOfFrames_) |
746 | 265 { |
266 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
267 } | |
268 | |
1636 | 269 CoordinateSystem3D tmp = data_.geometry_; |
746 | 270 |
271 if (frame != 0) | |
272 { | |
273 tmp = GetFrameGeometry(frame); | |
274 } | |
275 | |
276 double distance; | |
277 | |
757 | 278 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
1636 | 279 distance <= data_.sliceThickness_ / 2.0); |
746 | 280 } |
281 | |
1637 | 282 |
283 bool DicomInstanceParameters::IsColor() const | |
284 { | |
285 Orthanc::PhotometricInterpretation photometric = | |
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286 GetImageInformation().GetPhotometricInterpretation(); |
1637 | 287 |
288 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 && | |
289 photometric != Orthanc::PhotometricInterpretation_Monochrome2); | |
290 } | |
291 | |
292 | |
1636 | 293 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, |
294 bool useDouble) const | |
746 | 295 { |
296 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
297 { | |
298 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
299 } | |
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300 |
1636 | 301 double factor = data_.doseGridScaling_; |
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302 double offset = 0.0; |
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303 |
1636 | 304 if (data_.hasRescale_) |
746 | 305 { |
1636 | 306 factor *= data_.rescaleSlope_; |
307 offset = data_.rescaleIntercept_; | |
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308 } |
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309 |
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310 if (!LinearAlgebra::IsNear(factor, 1) || |
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311 !LinearAlgebra::IsNear(offset, 0)) |
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312 { |
746 | 313 const unsigned int width = image.GetWidth(); |
314 const unsigned int height = image.GetHeight(); | |
315 | |
316 for (unsigned int y = 0; y < height; y++) | |
317 { | |
318 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
319 | |
320 if (useDouble) | |
321 { | |
322 // Slower, accurate implementation using double | |
323 for (unsigned int x = 0; x < width; x++, p++) | |
324 { | |
325 double value = static_cast<double>(*p); | |
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326 *p = static_cast<float>(value * factor + offset); |
746 | 327 } |
328 } | |
329 else | |
330 { | |
331 // Fast, approximate implementation using float | |
332 for (unsigned int x = 0; x < width; x++, p++) | |
333 { | |
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334 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset); |
746 | 335 } |
336 } | |
337 } | |
338 } | |
339 } | |
340 | |
341 double DicomInstanceParameters::GetRescaleIntercept() const | |
342 { | |
343 if (data_.hasRescale_) | |
344 { | |
345 return data_.rescaleIntercept_; | |
346 } | |
347 else | |
348 { | |
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349 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
746 | 350 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
351 } | |
352 } | |
353 | |
354 | |
355 double DicomInstanceParameters::GetRescaleSlope() const | |
356 { | |
357 if (data_.hasRescale_) | |
358 { | |
359 return data_.rescaleSlope_; | |
360 } | |
361 else | |
362 { | |
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363 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
746 | 364 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
365 } | |
366 } | |
367 | |
368 | |
1637 | 369 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const |
370 { | |
371 if (GetSopClassUid() == SopClassUid_RTDose) | |
372 { | |
373 switch (GetImageInformation().GetBitsStored()) | |
374 { | |
375 case 16: | |
376 return Orthanc::PixelFormat_Grayscale16; | |
377 | |
378 case 32: | |
379 return Orthanc::PixelFormat_Grayscale32; | |
380 | |
381 default: | |
382 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
383 } | |
384 } | |
385 else if (IsColor()) | |
386 { | |
387 return Orthanc::PixelFormat_RGB24; | |
388 } | |
389 else if (GetImageInformation().IsSigned()) | |
390 { | |
391 return Orthanc::PixelFormat_SignedGrayscale16; | |
392 } | |
393 else | |
394 { | |
395 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
396 } | |
397 } | |
398 | |
399 | |
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400 size_t DicomInstanceParameters::GetWindowingPresetsCount() const |
746 | 401 { |
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402 assert(data_.windowingPresetCenters_.size() == data_.windowingPresetWidths_.size()); |
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403 return data_.windowingPresetCenters_.size(); |
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404 } |
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405 |
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406 |
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407 float DicomInstanceParameters::GetWindowingPresetCenter(size_t i) const |
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408 { |
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409 if (i < GetWindowingPresetsCount()) |
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410 { |
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411 return static_cast<float>(data_.windowingPresetCenters_[i]); |
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412 } |
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413 else |
746 | 414 { |
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415 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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416 } |
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417 } |
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418 |
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419 |
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420 float DicomInstanceParameters::GetWindowingPresetWidth(size_t i) const |
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421 { |
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422 if (i < GetWindowingPresetsCount()) |
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423 { |
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424 return static_cast<float>(data_.windowingPresetWidths_[i]); |
746 | 425 } |
426 else | |
427 { | |
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428 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
746 | 429 } |
430 } | |
431 | |
432 | |
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433 static void GetWindowingBounds(float& low, |
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434 float& high, |
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435 double center, // in |
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436 double width) // in |
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437 { |
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438 low = static_cast<float>(center - width / 2.0); |
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439 high = static_cast<float>(center + width / 2.0); |
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440 } |
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441 |
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442 |
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443 void DicomInstanceParameters::GetWindowingPresetsUnion(float& center, |
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444 float& width) const |
746 | 445 { |
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446 assert(tags_.get() != NULL); |
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447 size_t s = GetWindowingPresetsCount(); |
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448 |
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449 if (s > 0) |
746 | 450 { |
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451 // Use the largest windowing given all the preset windowings |
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452 // that are available in the DICOM tags |
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453 float low, high; |
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454 GetWindowingBounds(low, high, GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
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455 |
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456 for (size_t i = 1; i < s; i++) |
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457 { |
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458 float a, b; |
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459 GetWindowingBounds(a, b, GetWindowingPresetCenter(i), GetWindowingPresetWidth(i)); |
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460 low = std::min(low, a); |
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461 high = std::max(high, b); |
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462 } |
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463 |
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464 assert(low <= high); |
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465 |
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466 if (LinearAlgebra::IsNear(low, high)) |
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467 { |
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468 // Cannot infer a suitable windowing from the available tags |
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469 center = 128.0f; |
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470 width = 256.0f; |
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471 } |
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472 else |
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473 { |
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474 center = (low + high) / 2.0f; |
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475 width = (high - low); |
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476 } |
746 | 477 } |
478 else | |
479 { | |
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480 float a, b; |
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481 if (tags_->ParseFloat(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) && |
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482 tags_->ParseFloat(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE) && |
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483 a < b) |
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484 { |
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485 center = (a + b) / 2.0f; |
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486 width = (b - a); |
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487 } |
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488 else |
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489 { |
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490 // Cannot infer a suitable windowing from the available tags |
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491 center = 128.0f; |
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492 width = 256.0f; |
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493 } |
746 | 494 } |
495 } | |
496 | |
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497 |
768
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498 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
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499 { |
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500 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
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501 pixelData.GetWidth(), |
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502 pixelData.GetHeight(), |
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503 false)); |
768
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504 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
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505 |
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506 |
768
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507 // Correct rescale slope/intercept if need be |
1636 | 508 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
509 ApplyRescaleAndDoseScaling(*converted, false); | |
768
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510 |
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511 return converted.release(); |
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512 } |
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513 |
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514 |
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515 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
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516 (const Orthanc::ImageAccessor& pixelData) const |
746 | 517 { |
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518 // { |
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519 // const Orthanc::ImageAccessor& source = pixelData; |
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520 // const void* sourceBuffer = source.GetConstBuffer(); |
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521 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); |
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522 // int sourceWidth = source.GetWidth(); |
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523 // int sourceHeight = source.GetHeight(); |
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524 // int sourcePitch = source.GetPitch(); |
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525 |
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526 // // TODO: turn error into trace below |
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527 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" |
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528 // << " W = " << sourceWidth << " H = " << sourceHeight |
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529 // << " P = " << sourcePitch << " B = " << sourceBufferInt |
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530 // << " B % 4 == " << sourceBufferInt % 4; |
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531 // } |
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532 |
746 | 533 assert(sizeof(float) == 4); |
534 | |
535 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
536 | |
537 if (sourceFormat != GetExpectedPixelFormat()) | |
538 { | |
539 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
540 } | |
541 | |
542 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
543 { | |
544 // This is the case of a color image. No conversion has to be done. | |
545 return new ColorTextureSceneLayer(pixelData); | |
546 } | |
547 else | |
548 { | |
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549 // This is the case of a grayscale frame. Convert it to Float32. |
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550 std::unique_ptr<FloatTextureSceneLayer> texture; |
746 | 551 |
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552 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
746 | 553 { |
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554 texture.reset(new FloatTextureSceneLayer(pixelData)); |
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555 } |
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556 else |
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557 { |
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558 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
746 | 559 texture.reset(new FloatTextureSceneLayer(*converted)); |
560 } | |
561 | |
1679
5b8b88e5bfd6
successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1677
diff
changeset
|
562 if (GetWindowingPresetsCount() > 0) |
746 | 563 { |
1679
5b8b88e5bfd6
successfully running unit tests in WebAssembly
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parents:
1677
diff
changeset
|
564 texture->SetCustomWindowing(GetWindowingPresetCenter(0), GetWindowingPresetWidth(0)); |
746 | 565 } |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
566 |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
567 switch (GetImageInformation().GetPhotometricInterpretation()) |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
568 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
569 case Orthanc::PhotometricInterpretation_Monochrome1: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
570 texture->SetInverted(true); |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
571 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
572 |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
1598
diff
changeset
|
573 case Orthanc::PhotometricInterpretation_Monochrome2: |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
1598
diff
changeset
|
574 texture->SetInverted(false); |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
575 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
576 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
577 default: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
578 break; |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
579 } |
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
580 |
746 | 581 return texture.release(); |
582 } | |
583 } | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
584 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
585 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
586 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
587 (const Orthanc::ImageAccessor& pixelData) const |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
588 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
589 std::unique_ptr<FloatTextureSceneLayer> texture; |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
590 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
591 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
592 { |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
593 return new LookupTableTextureSceneLayer(pixelData); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
594 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
595 else |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
596 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
597 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
768
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
598 return new LookupTableTextureSceneLayer(*converted); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
599 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
600 } |
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
601 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
602 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
603 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
604 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
605 if (data_.hasIndexInSeries_) |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
606 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
607 return data_.indexInSeries_; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
608 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
609 else |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
610 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
611 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
612 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
613 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
614 } |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
615 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
616 |
1636 | 617 double DicomInstanceParameters::ApplyRescale(double value) const |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
618 { |
1636 | 619 double factor = data_.doseGridScaling_; |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
620 double offset = 0.0; |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
621 |
1636 | 622 if (data_.hasRescale_) |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
623 { |
1636 | 624 factor *= data_.rescaleSlope_; |
625 offset = data_.rescaleIntercept_; | |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
626 } |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
627 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
628 return (value * factor + offset); |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
629 } |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
630 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
631 |
1636 | 632 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
633 { |
1636 | 634 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
635 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
636 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
637 } |
1636 | 638 else if (data_.frameOffsets_.size() == 1) |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
639 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
640 spacing = 1; // Edge case: RT-DOSE with one single frame |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
641 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
642 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
643 else |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
644 { |
1636 | 645 assert(data_.frameOffsets_.size() == GetNumberOfFrames()); |
646 | |
647 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]); | |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
648 |
1636 | 649 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
|
650 { |
1636 | 651 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]; |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
652 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
653 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
654 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
655 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
656 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
657 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
658 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
659 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
660 } |
746 | 661 } |