Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1650:af312e145980
more tests for CoordinateSystem3D
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 13 Nov 2020 10:44:11 +0100 |
parents | 4e14735e98f8 |
children | 51bab5188a13 |
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) 2017-2020 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 |
746 | 183 Vector c, w; |
184 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && | |
185 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) && | |
186 c.size() > 0 && | |
187 w.size() > 0) | |
188 { | |
189 hasDefaultWindowing_ = true; | |
190 defaultWindowingCenter_ = static_cast<float>(c[0]); | |
191 defaultWindowingWidth_ = static_cast<float>(w[0]); | |
192 } | |
193 else | |
194 { | |
195 hasDefaultWindowing_ = false; | |
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196 defaultWindowingCenter_ = 0; |
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197 defaultWindowingWidth_ = 0; |
746 | 198 } |
199 | |
980
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200 // This computes the "IndexInSeries" metadata from Orthanc (check |
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201 // out "Orthanc::ServerIndex::Store()") |
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202 hasIndexInSeries_ = ( |
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203 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
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204 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
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205 |
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206 if (!dicom.LookupStringValue( |
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207 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false)) |
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208 { |
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209 frameOfReferenceUid_.clear(); |
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210 } |
746 | 211 } |
212 | |
213 | |
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214 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const |
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215 { |
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216 assert(tags_.get() != NULL); |
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217 |
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218 if (imageInformation_.get() == NULL) |
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219 { |
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220 const_cast<DicomInstanceParameters&>(*this).imageInformation_. |
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221 reset(new Orthanc::DicomImageInformation(GetTags())); |
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222 |
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223 assert(imageInformation_->GetWidth() == GetWidth()); |
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224 assert(imageInformation_->GetHeight() == GetHeight()); |
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225 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames()); |
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226 } |
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227 |
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228 assert(imageInformation_.get() != NULL); |
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229 return *imageInformation_; |
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230 } |
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231 |
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232 |
1636 | 233 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const |
746 | 234 { |
1636 | 235 if (frame >= data_.numberOfFrames_) |
746 | 236 { |
237 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
238 } | |
1636 | 239 else if (data_.frameOffsets_.empty()) |
746 | 240 { |
1636 | 241 return data_.geometry_; |
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242 } |
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243 else |
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244 { |
1636 | 245 assert(data_.frameOffsets_.size() == data_.numberOfFrames_); |
746 | 246 |
247 return CoordinateSystem3D( | |
1636 | 248 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(), |
249 data_.geometry_.GetAxisX(), | |
250 data_.geometry_.GetAxisY()); | |
746 | 251 } |
252 } | |
253 | |
254 | |
1636 | 255 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame, |
256 const CoordinateSystem3D& plane) const | |
746 | 257 { |
1636 | 258 if (frame >= data_.numberOfFrames_) |
746 | 259 { |
260 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
261 } | |
262 | |
1636 | 263 CoordinateSystem3D tmp = data_.geometry_; |
746 | 264 |
265 if (frame != 0) | |
266 { | |
267 tmp = GetFrameGeometry(frame); | |
268 } | |
269 | |
270 double distance; | |
271 | |
757 | 272 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
1636 | 273 distance <= data_.sliceThickness_ / 2.0); |
746 | 274 } |
275 | |
1637 | 276 |
277 bool DicomInstanceParameters::IsColor() const | |
278 { | |
279 Orthanc::PhotometricInterpretation photometric = | |
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280 GetImageInformation().GetPhotometricInterpretation(); |
1637 | 281 |
282 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 && | |
283 photometric != Orthanc::PhotometricInterpretation_Monochrome2); | |
284 } | |
285 | |
286 | |
1636 | 287 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, |
288 bool useDouble) const | |
746 | 289 { |
290 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
291 { | |
292 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
293 } | |
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294 |
1636 | 295 double factor = data_.doseGridScaling_; |
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296 double offset = 0.0; |
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297 |
1636 | 298 if (data_.hasRescale_) |
746 | 299 { |
1636 | 300 factor *= data_.rescaleSlope_; |
301 offset = data_.rescaleIntercept_; | |
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302 } |
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303 |
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304 if (!LinearAlgebra::IsNear(factor, 1) || |
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305 !LinearAlgebra::IsNear(offset, 0)) |
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306 { |
746 | 307 const unsigned int width = image.GetWidth(); |
308 const unsigned int height = image.GetHeight(); | |
309 | |
310 for (unsigned int y = 0; y < height; y++) | |
311 { | |
312 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
313 | |
314 if (useDouble) | |
315 { | |
316 // Slower, accurate implementation using double | |
317 for (unsigned int x = 0; x < width; x++, p++) | |
318 { | |
319 double value = static_cast<double>(*p); | |
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320 *p = static_cast<float>(value * factor + offset); |
746 | 321 } |
322 } | |
323 else | |
324 { | |
325 // Fast, approximate implementation using float | |
326 for (unsigned int x = 0; x < width; x++, p++) | |
327 { | |
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328 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset); |
746 | 329 } |
330 } | |
331 } | |
332 } | |
333 } | |
334 | |
335 double DicomInstanceParameters::GetRescaleIntercept() const | |
336 { | |
337 if (data_.hasRescale_) | |
338 { | |
339 return data_.rescaleIntercept_; | |
340 } | |
341 else | |
342 { | |
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343 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
746 | 344 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
345 } | |
346 } | |
347 | |
348 | |
349 double DicomInstanceParameters::GetRescaleSlope() const | |
350 { | |
351 if (data_.hasRescale_) | |
352 { | |
353 return data_.rescaleSlope_; | |
354 } | |
355 else | |
356 { | |
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357 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
746 | 358 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
359 } | |
360 } | |
361 | |
362 | |
1637 | 363 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const |
364 { | |
365 if (GetSopClassUid() == SopClassUid_RTDose) | |
366 { | |
367 switch (GetImageInformation().GetBitsStored()) | |
368 { | |
369 case 16: | |
370 return Orthanc::PixelFormat_Grayscale16; | |
371 | |
372 case 32: | |
373 return Orthanc::PixelFormat_Grayscale32; | |
374 | |
375 default: | |
376 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
377 } | |
378 } | |
379 else if (IsColor()) | |
380 { | |
381 return Orthanc::PixelFormat_RGB24; | |
382 } | |
383 else if (GetImageInformation().IsSigned()) | |
384 { | |
385 return Orthanc::PixelFormat_SignedGrayscale16; | |
386 } | |
387 else | |
388 { | |
389 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
390 } | |
391 } | |
392 | |
393 | |
746 | 394 float DicomInstanceParameters::GetDefaultWindowingCenter() const |
395 { | |
396 if (data_.hasDefaultWindowing_) | |
397 { | |
398 return data_.defaultWindowingCenter_; | |
399 } | |
400 else | |
401 { | |
1481 | 402 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): no default windowing"; |
746 | 403 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
404 } | |
405 } | |
406 | |
407 | |
408 float DicomInstanceParameters::GetDefaultWindowingWidth() const | |
409 { | |
410 if (data_.hasDefaultWindowing_) | |
411 { | |
412 return data_.defaultWindowingWidth_; | |
413 } | |
414 else | |
415 { | |
1481 | 416 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): no default windowing"; |
746 | 417 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
418 } | |
419 } | |
420 | |
421 | |
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422 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
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423 { |
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424 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
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425 pixelData.GetWidth(), |
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426 pixelData.GetHeight(), |
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427 false)); |
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428 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
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429 |
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430 |
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431 // Correct rescale slope/intercept if need be |
1636 | 432 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
433 ApplyRescaleAndDoseScaling(*converted, false); | |
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434 |
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435 return converted.release(); |
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436 } |
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437 |
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438 |
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439 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
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440 (const Orthanc::ImageAccessor& pixelData) const |
746 | 441 { |
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442 // { |
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443 // const Orthanc::ImageAccessor& source = pixelData; |
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444 // const void* sourceBuffer = source.GetConstBuffer(); |
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445 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); |
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446 // int sourceWidth = source.GetWidth(); |
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447 // int sourceHeight = source.GetHeight(); |
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448 // int sourcePitch = source.GetPitch(); |
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parents:
1300
diff
changeset
|
449 |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
450 // // TODO: turn error into trace below |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
451 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
452 // << " W = " << sourceWidth << " H = " << sourceHeight |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
453 // << " P = " << sourcePitch << " B = " << sourceBufferInt |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
454 // << " B % 4 == " << sourceBufferInt % 4; |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
455 // } |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
456 |
746 | 457 assert(sizeof(float) == 4); |
458 | |
459 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
460 | |
461 if (sourceFormat != GetExpectedPixelFormat()) | |
462 { | |
463 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
464 } | |
465 | |
466 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
467 { | |
468 // This is the case of a color image. No conversion has to be done. | |
469 return new ColorTextureSceneLayer(pixelData); | |
470 } | |
471 else | |
472 { | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
473 // This is the case of a grayscale frame. Convert it to Float32. |
1298
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replacing std::auto_ptr by std::unique_ptr
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parents:
1291
diff
changeset
|
474 std::unique_ptr<FloatTextureSceneLayer> texture; |
746 | 475 |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
476 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
746 | 477 { |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
478 texture.reset(new FloatTextureSceneLayer(pixelData)); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
479 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
480 else |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
481 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
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parents:
1291
diff
changeset
|
482 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
746 | 483 texture.reset(new FloatTextureSceneLayer(*converted)); |
484 } | |
485 | |
486 if (data_.hasDefaultWindowing_) | |
487 { | |
488 texture->SetCustomWindowing(data_.defaultWindowingCenter_, | |
489 data_.defaultWindowingWidth_); | |
490 } | |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
491 |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
492 switch (GetImageInformation().GetPhotometricInterpretation()) |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
493 { |
1634
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improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
494 case Orthanc::PhotometricInterpretation_Monochrome1: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
495 texture->SetInverted(true); |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
496 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
497 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
498 case Orthanc::PhotometricInterpretation_Monochrome2: |
a4418a489e86
improving robustness of DicomInstanceParameters
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parents:
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diff
changeset
|
499 texture->SetInverted(false); |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
500 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
501 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
502 default: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
503 break; |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
504 } |
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
505 |
746 | 506 return texture.release(); |
507 } | |
508 } | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
509 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
510 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
511 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
512 (const Orthanc::ImageAccessor& pixelData) const |
55411e7da2f7
LookupTableTextureSceneLayer
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parents:
762
diff
changeset
|
513 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
514 std::unique_ptr<FloatTextureSceneLayer> texture; |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
515 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
516 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
517 { |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
518 return new LookupTableTextureSceneLayer(pixelData); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
519 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
520 else |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
521 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
522 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
523 return new LookupTableTextureSceneLayer(*converted); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
524 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
525 } |
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
526 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
527 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
528 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
529 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
530 if (data_.hasIndexInSeries_) |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
531 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
532 return data_.indexInSeries_; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
533 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
534 else |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
535 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
536 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
537 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
538 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
539 } |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
540 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
541 |
1636 | 542 double DicomInstanceParameters::ApplyRescale(double value) const |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
543 { |
1636 | 544 double factor = data_.doseGridScaling_; |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
545 double offset = 0.0; |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
546 |
1636 | 547 if (data_.hasRescale_) |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
548 { |
1636 | 549 factor *= data_.rescaleSlope_; |
550 offset = data_.rescaleIntercept_; | |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
551 } |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
552 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
553 return (value * factor + offset); |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
554 } |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
555 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
556 |
1636 | 557 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
558 { |
1636 | 559 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
560 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
561 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
562 } |
1636 | 563 else if (data_.frameOffsets_.size() == 1) |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
564 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
565 spacing = 1; // Edge case: RT-DOSE with one single frame |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
566 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
567 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
568 else |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
569 { |
1636 | 570 assert(data_.frameOffsets_.size() == GetNumberOfFrames()); |
571 | |
572 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]); | |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
573 |
1636 | 574 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
|
575 { |
1636 | 576 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]; |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
577 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
578 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
579 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
580 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
581 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
582 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
583 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
584 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
585 } |
746 | 586 } |