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annotate Framework/Volumes/ImageBuffer3D.h @ 683:dbc1d8bfc68a

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reorganizing ImageBuffer3D
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 16 May 2019 16:01:36 +0200
parents b70e9be013e4
children 7719eb852dd5
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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) 2017-2019 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 Affero 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 * Affero 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 Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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21
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22 #pragma once
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23
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24 #include "../StoneEnumerations.h"
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25 #include "../Layers/RenderStyle.h"
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26 #include "../Toolbox/CoordinateSystem3D.h"
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27 #include "../Toolbox/DicomFrameConverter.h"
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28 #include "../Toolbox/ParallelSlices.h"
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29
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30 #include <Core/Images/Image.h>
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32 namespace OrthancStone
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33 {
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34 class ImageBuffer3D : public boost::noncopyable
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35 {
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36 private:
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37 CoordinateSystem3D axialGeometry_;
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38 CoordinateSystem3D coronalGeometry_;
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39 CoordinateSystem3D sagittalGeometry_;
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40 Vector voxelDimensions_;
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41 Orthanc::Image image_;
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42 Orthanc::PixelFormat format_;
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43 unsigned int width_;
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44 unsigned int height_;
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45 unsigned int depth_;
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46 bool computeRange_;
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47 bool hasRange_;
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48 float minValue_;
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49 float maxValue_;
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50 Matrix transform_;
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51 Matrix transformInverse_;
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52
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53 void UpdateGeometry();
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54
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55 void ExtendImageRange(const Orthanc::ImageAccessor& slice);
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57 void GetAxialSliceAccessor(Orthanc::ImageAccessor& target,
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58 unsigned int slice,
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59 bool readOnly) const;
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60
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61 void GetCoronalSliceAccessor(Orthanc::ImageAccessor& target,
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62 unsigned int slice,
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63 bool readOnly) const;
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65 Orthanc::Image* ExtractSagittalSlice(unsigned int slice) const;
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66
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67 template <typename T>
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68 T GetPixelUnchecked(unsigned int x,
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69 unsigned int y,
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70 unsigned int z) const
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71 {
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72 const uint8_t* buffer = reinterpret_cast<const uint8_t*>(image_.GetConstBuffer());
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73 const uint8_t* row = buffer + (y + height_ * (depth_ - 1 - z)) * image_.GetPitch();
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74 return reinterpret_cast<const T*>(row) [x];
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75 }
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76
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77 public:
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78 ImageBuffer3D(Orthanc::PixelFormat format,
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79 unsigned int width,
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80 unsigned int height,
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81 unsigned int depth,
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82 bool computeRange);
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83
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84 void Clear();
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85
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86 // Set the geometry of the first axial slice (i.e. the one whose
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87 // depth == 0)
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88 void SetAxialGeometry(const CoordinateSystem3D& geometry);
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89
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90 const CoordinateSystem3D& GetAxialGeometry() const
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91 {
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92 return axialGeometry_;
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93 }
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94
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95 const CoordinateSystem3D& GetCoronalGeometry() const
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96 {
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97 return coronalGeometry_;
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98 }
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99
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100 const CoordinateSystem3D& GetSagittalGeometry() const
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101 {
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102 return sagittalGeometry_;
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103 }
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104
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105 void SetVoxelDimensions(double x,
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106 double y,
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107 double z);
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108
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109 Vector GetVoxelDimensions(VolumeProjection projection) const;
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110
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111 void GetSliceSize(unsigned int& width,
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112 unsigned int& height,
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113 VolumeProjection projection);
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114
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115 const Orthanc::ImageAccessor& GetInternalImage() const
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116 {
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117 return image_;
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118 }
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119
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120 unsigned int GetWidth() const
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121 {
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122 return width_;
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123 }
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124
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125 unsigned int GetHeight() const
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126 {
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127 return height_;
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128 }
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129
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130 unsigned int GetDepth() const
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131 {
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132 return depth_;
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133 }
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134
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135 Orthanc::PixelFormat GetFormat() const
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136 {
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137 return format_;
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138 }
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139
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140 // TODO - Remove
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141 ParallelSlices* GetGeometry(VolumeProjection projection) const;
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142
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143 uint64_t GetEstimatedMemorySize() const;
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144
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145 bool GetRange(float& minValue,
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146 float& maxValue) const;
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147
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148 bool FitWindowingToRange(RenderStyle& style,
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149 const DicomFrameConverter& converter) const;
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150
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151 uint8_t GetVoxelGrayscale8Unchecked(unsigned int x,
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152 unsigned int y,
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153 unsigned int z) const
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154 {
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155 return GetPixelUnchecked<uint8_t>(x, y, z);
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156 }
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157
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158 uint16_t GetVoxelGrayscale16Unchecked(unsigned int x,
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159 unsigned int y,
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160 unsigned int z) const
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161 {
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162 return GetPixelUnchecked<uint16_t>(x, y, z);
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163 }
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164
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165 int16_t GetVoxelSignedGrayscale16Unchecked(unsigned int x,
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166 unsigned int y,
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167 unsigned int z) const
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168 {
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169 return GetPixelUnchecked<int16_t>(x, y, z);
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170 }
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171
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172 uint8_t GetVoxelGrayscale8(unsigned int x,
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173 unsigned int y,
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174 unsigned int z) const;
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175
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176 uint16_t GetVoxelGrayscale16(unsigned int x,
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177 unsigned int y,
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178 unsigned int z) const;
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179
187
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180 // Get the 3D position of a point in the volume, where x, y and z
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181 // lie in the [0;1] range
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182 Vector GetCoordinates(float x,
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183 float y,
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184 float z) const;
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185
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186 bool DetectProjection(VolumeProjection& projection,
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187 const CoordinateSystem3D& plane) const;
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188
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189
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190 class SliceReader : public boost::noncopyable
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191 {
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192 private:
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193 Orthanc::ImageAccessor accessor_;
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194 std::auto_ptr<Orthanc::Image> sagittal_; // Unused for axial and coronal
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195
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196 public:
192
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197 SliceReader(const ImageBuffer3D& that,
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198 VolumeProjection projection,
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199 unsigned int slice);
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200
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201 const Orthanc::ImageAccessor& GetAccessor() const
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202 {
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203 return accessor_;
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204 }
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205 };
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206
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207
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208 class SliceWriter : public boost::noncopyable
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209 {
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210 private:
119
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211 ImageBuffer3D& that_;
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212 bool modified_;
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213 Orthanc::ImageAccessor accessor_;
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214 std::auto_ptr<Orthanc::Image> sagittal_; // Unused for axial and coronal
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215
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216 void Flush();
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217
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218 public:
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219 SliceWriter(ImageBuffer3D& that,
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220 VolumeProjection projection,
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221 unsigned int slice);
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222
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223 ~SliceWriter()
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224 {
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225 Flush();
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226 }
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227
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228 const Orthanc::ImageAccessor& GetAccessor() const
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229 {
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230 return accessor_;
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231 }
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232
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233 Orthanc::ImageAccessor& GetAccessor()
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234 {
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235 modified_ = true;
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236 return accessor_;
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237 }
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238 };
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239 };
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240 }