Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Volumes/ImageBuffer3D.h @ 2044:c9dadbe7c7b0 deep-learning

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Sun, 05 Mar 2023 15:05:58 +0100
parents 7053b8a0aaec
children 07964689cb0b
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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
1871
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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28956ed68280 agpl license
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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22
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23
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24 #pragma once
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25
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26 #include "../StoneEnumerations.h"
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27 #include "../Toolbox/LinearAlgebra.h"
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29 #include <Compatibility.h>
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30 #include <Images/Image.h>
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32 namespace OrthancStone
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33 {
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34 /*
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35
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36 IMPORTANT: The "ImageBuffer3D" class is *not* meant to be accessed
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37 directly by the end users using the "GetVoxelXXX()" methods,
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38 because of the swapping of the Z-axis (see below). The public
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39 interactions with this class should be limited to:
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40
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41 1- Using "SliceReader" and "SliceWriter" to access the raw slices,
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42 but only on the axial projection, *and* using the "z"
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43 coordinates returned by some "SlicesSorter" object
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44
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45 2- Extracting slices using a cutting plane through class deriving
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46 from the "IVolumeSlicer" interface
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47
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48
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49 IMPLEMENTATION NOTE: This classes stores volume images sliced across
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50 the Z axis, vertically, in the DECREASING Z-order along the normal
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51 (this is the REVERSE of the intuitive order):
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53 +---------------+
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54 | |
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55 | SLICE N-1 |
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56 | |
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57 +---------------+
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58 | |
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59 | SLICE N-2 |
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60 | |
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61 +---------------+
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62 | |
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63 | SLICE N-3 |
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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 | |
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69 | SLICE 2 |
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70 | |
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71 +---------------+
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72 | |
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73 | SLICE 1 |
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74 | |
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75 +---------------+
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76 | |
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77 | SLICE 0 |
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78 | |
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79 +---------------+
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80
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81 As you can see, if the 3d image has size width, height, depth, the 2d image has :
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82 - 2d width = 3d width
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83 - 2d height = 3d height * 3d depth
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84
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85 This explains the "depth_ - 1 - z" that are used throughout this class.
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86
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87 EXPLANATION: This allows to have the "SliceReader" and "SliceWriter"
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88 accessors for axial and coronal projections to directly access the
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89 same memory buffer (no memcpy is required), while being consistent
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90 with the Z-axis in coronal projection. The sagittal projection
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91 nevertheless needs a memcpy.
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93 */
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94
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95 class ImageBuffer3D : public boost::noncopyable
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96 {
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97 private:
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98 Orthanc::Image image_;
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99 Orthanc::PixelFormat format_;
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100 unsigned int width_;
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101 unsigned int height_;
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102 unsigned int depth_;
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103 bool computeRange_;
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104 bool hasRange_;
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105 float minValue_;
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106 float maxValue_;
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107 Matrix transform_;
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108 Matrix transformInverse_;
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109
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110 void ExtendImageRange(const Orthanc::ImageAccessor& slice);
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111
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112 void GetAxialSliceAccessor(Orthanc::ImageAccessor& target,
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113 unsigned int slice,
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114 bool readOnly);
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115
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116 void GetCoronalSliceAccessor(Orthanc::ImageAccessor& target,
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117 unsigned int slice,
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118 bool readOnly);
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120 Orthanc::Image* ExtractSagittalSlice(unsigned int slice) const;
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121
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122 void CommitSagittalSlice(unsigned int slice,
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123 const Orthanc::ImageAccessor& source);
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124
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125 template <typename T>
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126 T GetPixelUnchecked(unsigned int x,
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127 unsigned int y,
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128 unsigned int z) const
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129 {
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130 const uint8_t* buffer = reinterpret_cast<const uint8_t*>(image_.GetConstBuffer());
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131 const uint8_t* row = buffer + (y + height_ * (depth_ - 1 - z)) * image_.GetPitch();
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132 return reinterpret_cast<const T*>(row) [x];
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133 }
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134
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135 public:
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136 ImageBuffer3D(Orthanc::PixelFormat format,
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137 unsigned int width,
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138 unsigned int height,
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139 unsigned int depth,
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140 bool computeRange);
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141
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142 void Clear();
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143
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144 const Orthanc::ImageAccessor& GetInternalImage() const
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145 {
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146 return image_;
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147 }
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148
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149 unsigned int GetWidth() const
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150 {
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151 return width_;
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152 }
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153
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154 unsigned int GetHeight() const
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155 {
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156 return height_;
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157 }
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158
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159 unsigned int GetDepth() const
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160 {
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161 return depth_;
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162 }
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163
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164 Orthanc::PixelFormat GetFormat() const
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165 {
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166 return format_;
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167 }
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168
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169 unsigned int GetBytesPerPixel() const
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170 {
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171 return Orthanc::GetBytesPerPixel(format_);
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172 }
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173
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174 uint64_t GetEstimatedMemorySize() const;
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175
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176 bool GetRange(float& minValue,
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177 float& maxValue) const;
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178
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179 uint8_t GetVoxelGrayscale8Unchecked(unsigned int x,
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180 unsigned int y,
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181 unsigned int z) const
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182 {
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183 return GetPixelUnchecked<uint8_t>(x, y, z);
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184 }
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185
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186 uint16_t GetVoxelGrayscale16Unchecked(unsigned int x,
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187 unsigned int y,
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188 unsigned int z) const
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189 {
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190 return GetPixelUnchecked<uint16_t>(x, y, z);
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191 }
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192
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193 int16_t GetVoxelSignedGrayscale16Unchecked(unsigned int x,
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194 unsigned int y,
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195 unsigned int z) const
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196 {
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197 return GetPixelUnchecked<int16_t>(x, y, z);
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198 }
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199
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200 uint8_t GetVoxelGrayscale8(unsigned int x,
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201 unsigned int y,
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202 unsigned int z) const;
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203
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204 uint16_t GetVoxelGrayscale16(unsigned int x,
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205 unsigned int y,
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206 unsigned int z) const;
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207
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208
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209 class SliceReader : public boost::noncopyable
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210 {
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211 private:
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212 Orthanc::ImageAccessor accessor_;
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213 std::unique_ptr<Orthanc::Image> sagittal_; // Unused for axial and coronal
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214
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215 public:
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216 SliceReader(const ImageBuffer3D& that,
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217 VolumeProjection projection,
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218 unsigned int slice);
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219
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220 const Orthanc::ImageAccessor& GetAccessor() const
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221 {
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222 return accessor_;
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223 }
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224 };
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225
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226
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227 class SliceWriter : public boost::noncopyable
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228 {
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229 private:
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230 ImageBuffer3D& that_;
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231 bool modified_;
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232 Orthanc::ImageAccessor accessor_;
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233 std::unique_ptr<Orthanc::Image> sagittal_; // Unused for axial and coronal
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234 unsigned int slice_;
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235
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236 void Flush();
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237
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238 public:
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239 SliceWriter(ImageBuffer3D& that,
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240 VolumeProjection projection,
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241 unsigned int slice);
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242
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243 ~SliceWriter()
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244 {
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245 Flush();
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246 }
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247
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248 const Orthanc::ImageAccessor& GetAccessor() const
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249 {
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250 return accessor_;
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251 }
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252
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253 Orthanc::ImageAccessor& GetAccessor()
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254 {
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255 modified_ = true;
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256 return accessor_;
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257 }
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258 };
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259 };
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260 }