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annotate OrthancStone/Sources/Volumes/ImageBuffer3D.h @ 1785:58bebc904191

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notes in ImageBuffer3D
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 14 May 2021 19:07:51 +0200
parents 75d3e2ab1fe1
children 3889ae96d2e9
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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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28956ed68280 agpl 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 #pragma once
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24
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25 #include "../StoneEnumerations.h"
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26 #include "../Toolbox/LinearAlgebra.h"
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27
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28 #include <Compatibility.h>
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29 #include <Images/Image.h>
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31 namespace OrthancStone
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32 {
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33 /*
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34
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35 IMPORTANT: The "ImageBuffer3D" class is *not* meant to be accessed
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36 directly by the end users using the "GetVoxelXXX()" methods,
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37 because of the swapping of the Z-axis (see below). The public
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38 interactions with this class should be limited to:
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39
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40 1- Using "SliceReader" and "SliceWriter" to access the raw slices,
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41 but only on the axial projection, *and* using the "z"
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42 coordinates returned by some "SlicesSorter" object
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43
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44 2- Extracting slices using a cutting plane through class deriving
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45 from the "IVolumeSlicer" interface
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48 IMPLEMENTATION NOTE: This classes stores volume images sliced across
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49 the Z axis, vertically, in the DECREASING Z-order along the normal
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50 (this is the REVERSE of the intuitive order):
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52 +---------------+
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53 | |
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54 | SLICE N-1 |
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55 | |
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56 +---------------+
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57 | |
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58 | SLICE N-2 |
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59 | |
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60 +---------------+
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61 | |
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62 | SLICE N-3 |
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63 | |
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64 . .
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65 ...... ......
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66 . .
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67 | |
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68 | SLICE 2 |
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69 | |
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70 +---------------+
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71 | |
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72 | SLICE 1 |
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73 | |
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74 +---------------+
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75 | |
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76 | SLICE 0 |
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77 | |
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78 +---------------+
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79
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80 As you can see, if the 3d image has size width, height, depth, the 2d image has :
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81 - 2d width = 3d width
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82 - 2d height = 3d height * 3d depth
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83
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84 This explains the "depth_ - 1 - z" that are used throughout this class.
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85
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86 EXPLANATION: This allows to have the "SliceReader" and "SliceWriter"
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87 accessors for axial and coronal projections to directly access the
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88 same memory buffer (no memcpy is required), while being consistent
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89 with the Z-axis in coronal projection. The sagittal projection
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90 nevertheless needs a memcpy.
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91
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92 */
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93
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94 class ImageBuffer3D : public boost::noncopyable
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95 {
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96 private:
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97 Orthanc::Image image_;
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98 Orthanc::PixelFormat format_;
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99 unsigned int width_;
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100 unsigned int height_;
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101 unsigned int depth_;
119
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102 bool computeRange_;
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103 bool hasRange_;
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104 float minValue_;
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105 float maxValue_;
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106 Matrix transform_;
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107 Matrix transformInverse_;
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108
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109 void ExtendImageRange(const Orthanc::ImageAccessor& slice);
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110
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111 void GetAxialSliceAccessor(Orthanc::ImageAccessor& target,
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112 unsigned int slice,
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113 bool readOnly);
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114
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115 void GetCoronalSliceAccessor(Orthanc::ImageAccessor& target,
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116 unsigned int slice,
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117 bool readOnly);
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118
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119 Orthanc::Image* ExtractSagittalSlice(unsigned int slice) const;
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120
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121 void CommitSagittalSlice(unsigned int slice,
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122 const Orthanc::ImageAccessor& source);
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123
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124 template <typename T>
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125 T GetPixelUnchecked(unsigned int x,
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126 unsigned int y,
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127 unsigned int z) const
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128 {
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129 const uint8_t* buffer = reinterpret_cast<const uint8_t*>(image_.GetConstBuffer());
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130 const uint8_t* row = buffer + (y + height_ * (depth_ - 1 - z)) * image_.GetPitch();
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131 return reinterpret_cast<const T*>(row) [x];
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132 }
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133
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134 public:
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135 ImageBuffer3D(Orthanc::PixelFormat format,
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136 unsigned int width,
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137 unsigned int height,
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138 unsigned int depth,
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139 bool computeRange);
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140
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141 void Clear();
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142
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143 const Orthanc::ImageAccessor& GetInternalImage() const
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144 {
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145 return image_;
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146 }
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147
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148 unsigned int GetWidth() const
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149 {
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150 return width_;
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151 }
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152
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153 unsigned int GetHeight() const
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154 {
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155 return height_;
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156 }
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157
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158 unsigned int GetDepth() const
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159 {
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160 return depth_;
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161 }
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162
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163 Orthanc::PixelFormat GetFormat() const
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164 {
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165 return format_;
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166 }
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167
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168 unsigned int GetBytesPerPixel() const
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169 {
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170 return Orthanc::GetBytesPerPixel(format_);
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171 }
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172
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173 uint64_t GetEstimatedMemorySize() const;
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174
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175 bool GetRange(float& minValue,
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176 float& maxValue) const;
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177
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178 uint8_t GetVoxelGrayscale8Unchecked(unsigned int x,
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179 unsigned int y,
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180 unsigned int z) const
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181 {
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182 return GetPixelUnchecked<uint8_t>(x, y, z);
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183 }
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184
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185 uint16_t GetVoxelGrayscale16Unchecked(unsigned int x,
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186 unsigned int y,
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187 unsigned int z) const
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188 {
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189 return GetPixelUnchecked<uint16_t>(x, y, z);
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190 }
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191
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192 int16_t GetVoxelSignedGrayscale16Unchecked(unsigned int x,
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193 unsigned int y,
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194 unsigned int z) const
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195 {
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196 return GetPixelUnchecked<int16_t>(x, y, z);
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197 }
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198
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199 uint8_t GetVoxelGrayscale8(unsigned int x,
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200 unsigned int y,
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201 unsigned int z) const;
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202
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203 uint16_t GetVoxelGrayscale16(unsigned int x,
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204 unsigned int y,
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205 unsigned int z) const;
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206
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207
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208 class SliceReader : public boost::noncopyable
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209 {
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210 private:
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211 Orthanc::ImageAccessor accessor_;
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212 std::unique_ptr<Orthanc::Image> sagittal_; // Unused for axial and coronal
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213
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214 public:
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215 SliceReader(const ImageBuffer3D& that,
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216 VolumeProjection projection,
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217 unsigned int slice);
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218
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219 const Orthanc::ImageAccessor& GetAccessor() const
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220 {
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221 return accessor_;
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222 }
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223 };
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224
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225
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226 class SliceWriter : public boost::noncopyable
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227 {
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228 private:
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229 ImageBuffer3D& that_;
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230 bool modified_;
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231 Orthanc::ImageAccessor accessor_;
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232 std::unique_ptr<Orthanc::Image> sagittal_; // Unused for axial and coronal
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233 unsigned int slice_;
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234
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235 void Flush();
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236
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237 public:
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238 SliceWriter(ImageBuffer3D& that,
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239 VolumeProjection projection,
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240 unsigned int slice);
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241
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242 ~SliceWriter()
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243 {
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244 Flush();
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245 }
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246
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247 const Orthanc::ImageAccessor& GetAccessor() const
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248 {
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249 return accessor_;
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250 }
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251
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252 Orthanc::ImageAccessor& GetAccessor()
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253 {
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254 modified_ = true;
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255 return accessor_;
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256 }
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257 };
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258 };
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259 }