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annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1772:6c246f862b00

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unit test VolumeRendering.Basic
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 12 May 2021 17:24:24 +0200
parents 5f74ebe2516b
children 385c268e8b56
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
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6 *
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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
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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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/>.
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20 **/
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21
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22
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23 #include "DicomInstanceParameters.h"
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24
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25 #include "../Scene2D/ColorTextureSceneLayer.h"
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26 #include "../Scene2D/FloatTextureSceneLayer.h"
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27 #include "GeometryToolbox.h"
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28 #include "ImageToolbox.h"
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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>
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35
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36
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37 namespace OrthancStone
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38 {
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39 static void ExtractFrameOffsets(Vector& target,
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40 const Orthanc::DicomMap& dicom,
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41 unsigned int numberOfFrames)
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42 {
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43 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
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44
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45 std::string increment;
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47 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
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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")
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54 {
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55 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image";
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56 target.resize(0);
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57 return;
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58 }
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59 }
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60
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61 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) ||
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62 target.size() != numberOfFrames)
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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!
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67 target.resize(0);
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68 }
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69 }
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70
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71
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72 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom)
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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))
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77 {
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78 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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79 }
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80
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81 std::string s;
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82 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
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83 {
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84 sopClassUid_ = StringToSopClassUid(s);
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85 }
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86 else
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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;
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99 }
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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))
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116 {
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117 if (numberOfFrames_ > 1)
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118 {
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119 LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image";
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120 }
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121
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122 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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123 sliceThicknessPresent = false;
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124 }
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125
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126 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom);
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127
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128 std::string position, orientation;
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129 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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130 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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131 {
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132 geometry_ = CoordinateSystem3D(position, orientation);
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133 }
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134
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135 // Must be AFTER setting "numberOfFrames_"
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136 if (numberOfFrames_ > 1)
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137 {
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138 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_);
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139
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140 // if the slice thickness is unknown, we try to infer it from the sequence of grid frame offsets
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141 // this only works if:
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142 // - the first offset is 0.0 (case (a) of http://dicom.nema.org/medical/Dicom/2017c/output/chtml/part03/sect_C.8.8.3.2.html)
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143 // - the offsets are all equal, to some small tolerance
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144 // - the offsets is positive (increasing throughout the frames)
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145 if (!sliceThicknessPresent)
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diff changeset
146 {
4bedae500652 Automatically compute SliceThickness from
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147 if (frameOffsets_.size() >= 2)
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148 {
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149 double sliceThickness = frameOffsets_[1] - frameOffsets_[0];
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150 bool sameSized = true;
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151 if (sliceThickness > 0)
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152 {
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153 for (size_t i = 2; i < frameOffsets_.size(); ++i)
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154 {
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155 double currentThickness = frameOffsets_[i] - frameOffsets_[i-1];
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156 if (!LinearAlgebra::IsNear(sliceThickness, currentThickness))
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157 {
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158 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)";
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159 sameSized = false;
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160 break;
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161 }
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parents: 1739
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162 }
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parents: 1739
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163 if (sameSized)
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164 {
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165 sliceThickness_ = sliceThickness;
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166 LOG(INFO) << "SliceThickness was not specified in the Dicom but was inferred from GridFrameOffsetVector (3004,000C).";
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167 }
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parents: 1739
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168 }
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parents: 1739
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169 }
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parents: 1739
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170 else
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171 {
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172 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: GridFrameOffsetVector not present or too small)";
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173 }
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parents: 1739
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174 }
1639
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175 }
5cdc5b98f14d cppcheck
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176 else
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177 {
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178 frameOffsets_.resize(0);
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179 }
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180
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181 if (sopClassUid_ == SopClassUid_RTDose)
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182 {
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183 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002);
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184
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185 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false))
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parents: 1027
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186 {
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187 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_;
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188 doseUnits_.clear();
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189 }
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190 }
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191
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192 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
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193 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
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194 {
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195 if (sopClassUid_ == SopClassUid_RTDose)
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196 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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197 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_;
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198 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES
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199 hasRescale_ = false;
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200 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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diff changeset
201 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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diff changeset
202 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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diff changeset
203 hasRescale_ = true;
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diff changeset
204 }
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diff changeset
205
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206 }
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diff changeset
207 else
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208 {
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209 hasRescale_ = false;
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210 }
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211
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diff changeset
212 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING))
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diff changeset
213 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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diff changeset
214 if (sopClassUid_ == SopClassUid_RTDose)
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215 {
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diff changeset
216 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_;
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parents: 1091
diff changeset
217 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
218 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
219 else
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parents: 1091
diff changeset
220 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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221 doseGridScaling_ = 1.0;
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222 if (sopClassUid_ == SopClassUid_RTDose)
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parents: 1091
diff changeset
223 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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224 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0";
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225 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
226 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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diff changeset
227
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228 bool ok = false;
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229
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230 if (LinearAlgebra::ParseVector(windowingPresetCenters_, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
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231 LinearAlgebra::ParseVector(windowingPresetWidths_, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH))
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232 {
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233 if (windowingPresetCenters_.size() == windowingPresetWidths_.size())
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234 {
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235 ok = true;
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236 }
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parents: 1646
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237 else
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diff changeset
238 {
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239 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this";
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240 ok = false;
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241 }
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242 }
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243
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244 if (!ok)
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245 {
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246 // Don't use "Vector::clear()", as it has not the same meaning as "std::vector::clear()"
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247 windowingPresetCenters_.resize(0);
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248 windowingPresetWidths_.resize(0);
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249 }
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250
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251 // This computes the "IndexInSeries" metadata from Orthanc (check
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252 // out "Orthanc::ServerIndex::Store()")
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253 hasIndexInSeries_ = (
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254 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) ||
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255 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX));
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256
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257 if (!dicom.LookupStringValue(
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258 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false))
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259 {
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260 frameOfReferenceUid_.clear();
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261 }
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262 }
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parents:
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263
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264
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265 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const
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266 {
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267 assert(tags_.get() != NULL);
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268
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269 if (imageInformation_.get() == NULL)
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270 {
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271 const_cast<DicomInstanceParameters&>(*this).imageInformation_.
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272 reset(new Orthanc::DicomImageInformation(GetTags()));
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273
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274 assert(imageInformation_->GetWidth() == GetWidth());
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275 assert(imageInformation_->GetHeight() == GetHeight());
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276 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames());
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277 }
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diff changeset
278
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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diff changeset
279 assert(imageInformation_.get() != NULL);
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280 return *imageInformation_;
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diff changeset
281 }
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282
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283
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284 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const
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285 {
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286 if (frame >= data_.numberOfFrames_)
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287 {
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288 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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289 }
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290 else if (data_.frameOffsets_.empty())
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291 {
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292 return data_.geometry_;
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293 }
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diff changeset
294 else
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diff changeset
295 {
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296 assert(data_.frameOffsets_.size() == data_.numberOfFrames_);
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297
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298 return CoordinateSystem3D(
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299 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(),
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300 data_.geometry_.GetAxisX(),
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301 data_.geometry_.GetAxisY());
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302 }
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parents:
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303 }
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parents:
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304
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parents:
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305
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306 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame,
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307 const CoordinateSystem3D& plane) const
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308 {
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diff changeset
309 if (frame >= data_.numberOfFrames_)
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310 {
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311 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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312 }
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313
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314 CoordinateSystem3D tmp = data_.geometry_;
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315
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316 if (frame != 0)
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parents:
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317 {
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diff changeset
318 tmp = GetFrameGeometry(frame);
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parents:
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319 }
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320
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321 double distance;
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322
757
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323 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) &&
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diff changeset
324 distance <= data_.sliceThickness_ / 2.0);
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325 }
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parents:
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326
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327
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diff changeset
328 bool DicomInstanceParameters::IsColor() const
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diff changeset
329 {
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diff changeset
330 Orthanc::PhotometricInterpretation photometric =
1642
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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diff changeset
331 GetImageInformation().GetPhotometricInterpretation();
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332
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333 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 &&
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
334 photometric != Orthanc::PhotometricInterpretation_Monochrome2);
Sebastien Jodogne <s.jodogne@gmail.com>
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335 }
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diff changeset
336
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diff changeset
337
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diff changeset
338 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image,
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339 bool useDouble) const
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parents:
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340 {
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parents:
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341 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
342 {
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parents:
diff changeset
343 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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parents:
diff changeset
344 }
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parents: 1091
diff changeset
345
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346 double factor = data_.doseGridScaling_;
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parents: 1091
diff changeset
347 double offset = 0.0;
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parents: 1091
diff changeset
348
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diff changeset
349 if (data_.hasRescale_)
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parents:
diff changeset
350 {
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diff changeset
351 factor *= data_.rescaleSlope_;
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diff changeset
352 offset = data_.rescaleIntercept_;
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parents: 1091
diff changeset
353 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
354
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parents: 1598
diff changeset
355 if (!LinearAlgebra::IsNear(factor, 1) ||
a4418a489e86 improving robustness of DicomInstanceParameters
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parents: 1598
diff changeset
356 !LinearAlgebra::IsNear(offset, 0))
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parents: 1091
diff changeset
357 {
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parents:
diff changeset
358 const unsigned int width = image.GetWidth();
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parents:
diff changeset
359 const unsigned int height = image.GetHeight();
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parents:
diff changeset
360
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parents:
diff changeset
361 for (unsigned int y = 0; y < height; y++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 {
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parents:
diff changeset
363 float* p = reinterpret_cast<float*>(image.GetRow(y));
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parents:
diff changeset
364
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parents:
diff changeset
365 if (useDouble)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
366 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 // Slower, accurate implementation using double
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parents:
diff changeset
368 for (unsigned int x = 0; x < width; x++, p++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369 {
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parents:
diff changeset
370 double value = static_cast<double>(*p);
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parents: 1091
diff changeset
371 *p = static_cast<float>(value * factor + offset);
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parents:
diff changeset
372 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
373 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
374 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
375 {
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parents:
diff changeset
376 // Fast, approximate implementation using float
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parents:
diff changeset
377 for (unsigned int x = 0; x < width; x++, p++)
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parents:
diff changeset
378 {
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parents: 1091
diff changeset
379 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset);
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parents:
diff changeset
380 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
381 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
382 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
383 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
384 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
385
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parents:
diff changeset
386 double DicomInstanceParameters::GetRescaleIntercept() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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387 {
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parents:
diff changeset
388 if (data_.hasRescale_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 {
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parents:
diff changeset
390 return data_.rescaleIntercept_;
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parents:
diff changeset
391 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
392 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
393 {
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parents: 949
diff changeset
394 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_";
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parents:
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395 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
396 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
397 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
398
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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400 double DicomInstanceParameters::GetRescaleSlope() const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
401 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402 if (data_.hasRescale_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
403 {
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parents:
diff changeset
404 return data_.rescaleSlope_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
406 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407 {
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parents: 949
diff changeset
408 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_";
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409 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
410 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
411 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
412
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parents:
diff changeset
413
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diff changeset
414 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const
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diff changeset
415 {
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parents: 1636
diff changeset
416 if (GetSopClassUid() == SopClassUid_RTDose)
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parents: 1636
diff changeset
417 {
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parents: 1636
diff changeset
418 switch (GetImageInformation().GetBitsStored())
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parents: 1636
diff changeset
419 {
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parents: 1636
diff changeset
420 case 16:
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diff changeset
421 return Orthanc::PixelFormat_Grayscale16;
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diff changeset
422
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
423 case 32:
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
424 return Orthanc::PixelFormat_Grayscale32;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
425
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
426 default:
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
427 return Orthanc::PixelFormat_Grayscale16; // Rough guess
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
428 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
429 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
430 else if (IsColor())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
431 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
432 return Orthanc::PixelFormat_RGB24;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
433 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
434 else if (GetImageInformation().IsSigned())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
435 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
436 return Orthanc::PixelFormat_SignedGrayscale16;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
437 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
438 else
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
439 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
440 return Orthanc::PixelFormat_Grayscale16; // Rough guess
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
441 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
442 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
443
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
444
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
445 size_t DicomInstanceParameters::GetWindowingPresetsCount() const
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
446 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
447 assert(data_.windowingPresetCenters_.size() == data_.windowingPresetWidths_.size());
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
448 return data_.windowingPresetCenters_.size();
1677
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
449 }
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
450
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
451
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
452 float DicomInstanceParameters::GetWindowingPresetCenter(size_t i) const
1677
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
453 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
454 if (i < GetWindowingPresetsCount())
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
455 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
456 return static_cast<float>(data_.windowingPresetCenters_[i]);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
457 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
458 else
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
459 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
460 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
461 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
462 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
463
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
464
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
465 float DicomInstanceParameters::GetWindowingPresetWidth(size_t i) const
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
466 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
467 if (i < GetWindowingPresetsCount())
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
468 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
469 return static_cast<float>(data_.windowingPresetWidths_[i]);
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
470 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
471 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
472 {
1677
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
473 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
474 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
475 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
476
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
477
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
478 static void GetWindowingBounds(float& low,
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
479 float& high,
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
480 double center, // in
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
481 double width) // in
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
482 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
483 low = static_cast<float>(center - width / 2.0);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
484 high = static_cast<float>(center + width / 2.0);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
485 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
486
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
487
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
488 void DicomInstanceParameters::GetWindowingPresetsUnion(float& center,
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
489 float& width) const
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
490 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
491 assert(tags_.get() != NULL);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
492 size_t s = GetWindowingPresetsCount();
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
493
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
494 if (s > 0)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
495 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
496 // Use the largest windowing given all the preset windowings
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
497 // that are available in the DICOM tags
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
498 float low, high;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
499 GetWindowingBounds(low, high, GetWindowingPresetCenter(0), GetWindowingPresetWidth(0));
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
500
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
501 for (size_t i = 1; i < s; i++)
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
502 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
503 float a, b;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
504 GetWindowingBounds(a, b, GetWindowingPresetCenter(i), GetWindowingPresetWidth(i));
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
505 low = std::min(low, a);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
506 high = std::max(high, b);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
507 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
508
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
509 assert(low <= high);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
510
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
511 if (LinearAlgebra::IsNear(low, high))
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
512 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
513 // Cannot infer a suitable windowing from the available tags
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
514 center = 128.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
515 width = 256.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
516 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
517 else
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
518 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
519 center = (low + high) / 2.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
520 width = (high - low);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
521 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
522 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
523 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
524 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
525 float a, b;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
526 if (tags_->ParseFloat(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) &&
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
527 tags_->ParseFloat(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE) &&
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
528 a < b)
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
529 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
530 center = (a + b) / 2.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
531 width = (b - a);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
532 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
533 else
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
534 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
535 // Cannot infer a suitable windowing from the available tags
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
536 center = 128.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
537 width = 256.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
538 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
539 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
540 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
541
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
542
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
543 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
544 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
545 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32,
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
546 pixelData.GetWidth(),
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
547 pixelData.GetHeight(),
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
548 false));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
549 Orthanc::ImageProcessing::Convert(*converted, pixelData);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
550
1287
8e82fdc6200e Heavy (temporary) logging in the path that leads
Benjamin Golinvaux <bgo@osimis.io>
parents: 1270
diff changeset
551
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
552 // Correct rescale slope/intercept if need be
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
553 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32));
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
554 ApplyRescaleAndDoseScaling(*converted, false);
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
555
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
556 return converted.release();
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
557 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
558
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
559
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
560 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
561 (const Orthanc::ImageAccessor& pixelData) const
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
562 {
1353
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
563 // {
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
564 // const Orthanc::ImageAccessor& source = pixelData;
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
565 // const void* sourceBuffer = source.GetConstBuffer();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
566 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer);
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
567 // int sourceWidth = source.GetWidth();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
568 // int sourceHeight = source.GetHeight();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
569 // int sourcePitch = source.GetPitch();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
570
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
571 // // TODO: turn error into trace below
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
572 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:"
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
573 // << " W = " << sourceWidth << " H = " << sourceHeight
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
574 // << " P = " << sourcePitch << " B = " << sourceBufferInt
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
575 // << " B % 4 == " << sourceBufferInt % 4;
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
576 // }
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
577
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
578 assert(sizeof(float) == 4);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
579
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
580 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat();
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
581
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
582 if (sourceFormat != GetExpectedPixelFormat())
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
583 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
584 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
585 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
586
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
587 if (sourceFormat == Orthanc::PixelFormat_RGB24)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
588 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
589 // This is the case of a color image. No conversion has to be done.
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
590 return new ColorTextureSceneLayer(pixelData);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
591 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
592 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
593 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
594 // This is the case of a grayscale frame. Convert it to Float32.
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
595 std::unique_ptr<FloatTextureSceneLayer> texture;
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
596
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
597 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
598 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
599 texture.reset(new FloatTextureSceneLayer(pixelData));
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
600 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
601 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
602 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
603 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
604 texture.reset(new FloatTextureSceneLayer(*converted));
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
605 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
606
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
607 if (GetWindowingPresetsCount() > 0)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
608 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
609 texture->SetCustomWindowing(GetWindowingPresetCenter(0), GetWindowingPresetWidth(0));
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
610 }
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
611
1642
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
612 switch (GetImageInformation().GetPhotometricInterpretation())
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
613 {
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
614 case Orthanc::PhotometricInterpretation_Monochrome1:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
615 texture->SetInverted(true);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
616 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
617
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
618 case Orthanc::PhotometricInterpretation_Monochrome2:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
619 texture->SetInverted(false);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
620 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
621
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
622 default:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
623 break;
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
624 }
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
625
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
626 return texture.release();
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
627 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
628 }
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
629
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
630
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
631 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
632 (const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
633 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
634 std::unique_ptr<FloatTextureSceneLayer> texture;
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
635
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
636 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
637 {
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
638 return new LookupTableTextureSceneLayer(pixelData);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
639 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
640 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
641 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
642 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
643 return new LookupTableTextureSceneLayer(*converted);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
644 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
645 }
980
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
646
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
647
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
648 unsigned int DicomInstanceParameters::GetIndexInSeries() const
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
649 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
650 if (data_.hasIndexInSeries_)
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
651 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
652 return data_.indexInSeries_;
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
653 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
654 else
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
655 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
656 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_";
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
657 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
658 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
659 }
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
660
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
661
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
662 double DicomInstanceParameters::ApplyRescale(double value) const
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
663 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
664 double factor = data_.doseGridScaling_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
665 double offset = 0.0;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
666
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
667 if (data_.hasRescale_)
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
668 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
669 factor *= data_.rescaleSlope_;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
670 offset = data_.rescaleIntercept_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
671 }
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
672
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
673 return (value * factor + offset);
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
674 }
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
675
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
676
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
677 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
678 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
679 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
680 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
681 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
682 }
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
683 else if (data_.frameOffsets_.size() == 1)
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
684 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
685 spacing = 1; // Edge case: RT-DOSE with one single frame
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
686 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
687 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
688 else
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
689 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
690 assert(data_.frameOffsets_.size() == GetNumberOfFrames());
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
691
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
692 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]);
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
693
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
694 for (size_t i = 1; i + 1 < data_.frameOffsets_.size(); i++)
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
695 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
696 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i];
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
697 if (!LinearAlgebra::IsNear(spacing, s, 0.001))
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
698 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
699 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
700 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
701 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
702
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
703 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
704 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
705 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
706 }