Mercurial > hg > orthanc-stone
annotate Framework/Volumes/VolumeReslicer.cpp @ 184:9523ce4f44cc wasm
removing PixelWriter
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 15 Mar 2018 15:44:41 +0100 |
parents | 98da3a8d4820 |
children | d61224de4883 |
rev | line source |
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1 #include "VolumeReslicer.h" |
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2 |
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3 #include "../Toolbox/GeometryToolbox.h" |
183 | 4 #include "../Toolbox/SubvoxelReader.h" |
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5 |
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6 #include <Core/Images/ImageTraits.h> |
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7 #include <Core/Logging.h> |
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8 #include <Core/OrthancException.h> |
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9 |
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10 #include <boost/math/special_functions/round.hpp> |
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11 |
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12 |
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13 namespace OrthancStone |
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14 { |
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15 // Anonymous namespace to avoid clashes between compilation modules |
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16 namespace |
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17 { |
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18 enum TransferFunction |
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19 { |
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20 TransferFunction_Copy, |
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21 TransferFunction_Float, |
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22 TransferFunction_Linear |
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23 }; |
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24 |
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25 |
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26 template <typename VoxelReader, |
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27 typename PixelWriter, |
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28 TransferFunction Function> |
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29 class PixelShader; |
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30 |
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31 |
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32 template <typename VoxelReader, |
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33 typename PixelWriter> |
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34 class PixelShader<VoxelReader, PixelWriter, TransferFunction_Copy> |
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35 { |
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36 private: |
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37 VoxelReader reader_; |
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38 |
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39 public: |
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40 PixelShader(const ImageBuffer3D& image, |
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41 float /* scaling */, |
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42 float /* offset */) : |
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43 reader_(image) |
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44 { |
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45 } |
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46 |
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47 ORTHANC_FORCE_INLINE |
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48 void Apply(typename PixelWriter::PixelType* pixel, |
177 | 49 float volumeX, |
50 float volumeY, | |
51 float volumeZ) | |
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52 { |
183 | 53 typename VoxelReader::PixelType value; |
54 | |
55 if (!reader_.GetValue(value, volumeX, volumeY, volumeZ)) | |
56 { | |
57 VoxelReader::Traits::SetMinValue(value); | |
58 } | |
59 | |
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60 PixelWriter::FloatToPixel(*pixel, VoxelReader::Traits::PixelToFloat(value)); |
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61 } |
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62 }; |
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63 |
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64 |
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65 template <typename VoxelReader, |
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66 typename PixelWriter> |
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67 class PixelShader<VoxelReader, PixelWriter, TransferFunction_Float> |
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68 { |
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69 private: |
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70 VoxelReader reader_; |
183 | 71 float outOfVolume_; |
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72 |
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73 public: |
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74 PixelShader(const ImageBuffer3D& image, |
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75 float /* scaling */, |
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76 float /* offset */) : |
183 | 77 reader_(image), |
78 outOfVolume_(static_cast<float>(std::numeric_limits<typename VoxelReader::PixelType>::min())) | |
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79 { |
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80 } |
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81 |
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82 ORTHANC_FORCE_INLINE |
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83 void Apply(typename PixelWriter::PixelType* pixel, |
177 | 84 float volumeX, |
85 float volumeY, | |
86 float volumeZ) | |
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87 { |
183 | 88 float value; |
89 | |
90 if (!reader_.GetFloatValue(value, volumeX, volumeY, volumeZ)) | |
91 { | |
92 value = outOfVolume_; | |
93 } | |
94 | |
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95 PixelWriter::FloatToPixel(*pixel, value); |
183 | 96 } |
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97 }; |
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98 |
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99 |
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100 template <typename VoxelReader, |
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101 typename PixelWriter> |
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102 class PixelShader<VoxelReader, PixelWriter, TransferFunction_Linear> |
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103 { |
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104 private: |
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105 VoxelReader reader_; |
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106 float scaling_; |
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107 float offset_; |
183 | 108 float outOfVolume_; |
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109 |
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110 public: |
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111 PixelShader(const ImageBuffer3D& image, |
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112 float scaling, |
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113 float offset) : |
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114 reader_(image), |
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115 scaling_(scaling), |
183 | 116 offset_(offset), |
117 outOfVolume_(static_cast<float>(std::numeric_limits<typename VoxelReader::PixelType>::min())) | |
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118 { |
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119 } |
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120 |
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121 ORTHANC_FORCE_INLINE |
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122 void Apply(typename PixelWriter::PixelType* pixel, |
177 | 123 float volumeX, |
124 float volumeY, | |
125 float volumeZ) | |
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126 { |
183 | 127 float value; |
128 | |
129 if (reader_.GetFloatValue(value, volumeX, volumeY, volumeZ)) | |
130 { | |
131 value = scaling_ * value + offset_; | |
132 } | |
133 else | |
134 { | |
135 value = outOfVolume_; | |
136 } | |
137 | |
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138 PixelWriter::FloatToPixel(*pixel, value); |
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139 } |
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140 }; |
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141 |
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142 |
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143 |
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144 class FastRowIterator : public boost::noncopyable |
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145 { |
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146 private: |
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147 float position_[3]; |
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148 float offset_[3]; |
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149 |
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150 public: |
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151 FastRowIterator(const Orthanc::ImageAccessor& slice, |
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152 const Extent2D& extent, |
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153 const CoordinateSystem3D& plane, |
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154 const OrientedBoundingBox& box, |
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155 unsigned int y) |
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156 { |
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157 const double width = static_cast<double>(slice.GetWidth()); |
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158 const double height = static_cast<double>(slice.GetHeight()); |
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159 assert(y < height); |
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160 |
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161 Vector q1 = plane.MapSliceToWorldCoordinates |
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162 (extent.GetX1() + extent.GetWidth() * static_cast<double>(0) / static_cast<double>(width + 1), |
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163 extent.GetY1() + extent.GetHeight() * static_cast<double>(y) / static_cast<double>(height + 1)); |
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164 |
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165 Vector q2 = plane.MapSliceToWorldCoordinates |
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166 (extent.GetX1() + extent.GetWidth() * static_cast<double>(width - 1) / static_cast<double>(width + 1), |
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167 extent.GetY1() + extent.GetHeight() * static_cast<double>(y) / static_cast<double>(height + 1)); |
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168 |
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169 Vector r1, r2; |
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170 box.ToInternalCoordinates(r1, q1); |
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171 box.ToInternalCoordinates(r2, q2); |
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172 |
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173 position_[0] = static_cast<float>(r1[0]); |
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174 position_[1] = static_cast<float>(r1[1]); |
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175 position_[2] = static_cast<float>(r1[2]); |
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176 |
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177 Vector tmp = (r2 - r1) / static_cast<double>(width - 1); |
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178 offset_[0] = static_cast<float>(tmp[0]); |
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179 offset_[1] = static_cast<float>(tmp[1]); |
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180 offset_[2] = static_cast<float>(tmp[2]); |
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181 } |
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182 |
180
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183 ORTHANC_FORCE_INLINE |
153
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184 void Next() |
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185 { |
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186 position_[0] += offset_[0]; |
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187 position_[1] += offset_[1]; |
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188 position_[2] += offset_[2]; |
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189 } |
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190 |
180
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191 ORTHANC_FORCE_INLINE |
177 | 192 void GetVolumeCoordinates(float& x, |
193 float& y, | |
194 float& z) const | |
153
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195 { |
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196 x = position_[0]; |
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197 y = position_[1]; |
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198 z = position_[2]; |
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199 } |
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200 }; |
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201 |
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202 |
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203 class SlowRowIterator : public boost::noncopyable |
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204 { |
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205 private: |
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206 const Orthanc::ImageAccessor& slice_; |
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207 const Extent2D& extent_; |
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208 const CoordinateSystem3D& plane_; |
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209 const OrientedBoundingBox& box_; |
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210 unsigned int x_; |
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211 unsigned int y_; |
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212 |
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213 public: |
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214 SlowRowIterator(const Orthanc::ImageAccessor& slice, |
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215 const Extent2D& extent, |
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216 const CoordinateSystem3D& plane, |
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217 const OrientedBoundingBox& box, |
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218 unsigned int y) : |
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219 slice_(slice), |
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220 extent_(extent), |
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221 plane_(plane), |
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222 box_(box), |
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223 x_(0), |
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224 y_(y) |
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225 { |
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226 assert(y_ < slice_.GetHeight()); |
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227 } |
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228 |
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229 void Next() |
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230 { |
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231 x_++; |
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232 } |
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233 |
177 | 234 void GetVolumeCoordinates(float& x, |
235 float& y, | |
236 float& z) const | |
153
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237 { |
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238 assert(x_ < slice_.GetWidth()); |
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239 |
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240 const double width = static_cast<double>(slice_.GetWidth()); |
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241 const double height = static_cast<double>(slice_.GetHeight()); |
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242 |
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243 Vector q = plane_.MapSliceToWorldCoordinates |
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244 (extent_.GetX1() + extent_.GetWidth() * static_cast<double>(x_) / (width + 1.0), |
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245 extent_.GetY1() + extent_.GetHeight() * static_cast<double>(y_) / (height + 1.0)); |
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246 |
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247 Vector r; |
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248 box_.ToInternalCoordinates(r, q); |
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249 |
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250 x = static_cast<float>(r[0]); |
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251 y = static_cast<float>(r[1]); |
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252 z = static_cast<float>(r[2]); |
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253 } |
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254 }; |
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255 |
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256 |
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257 template <typename RowIterator, |
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258 Orthanc::PixelFormat InputFormat, |
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259 Orthanc::PixelFormat OutputFormat, |
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260 ImageInterpolation Interpolation, |
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261 TransferFunction Function> |
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262 static void ProcessImage(Orthanc::ImageAccessor& slice, |
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263 const Extent2D& extent, |
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264 const ImageBuffer3D& source, |
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265 const CoordinateSystem3D& plane, |
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266 const OrientedBoundingBox& box, |
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267 float scaling, |
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268 float offset) |
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269 { |
183 | 270 typedef SubvoxelReader<InputFormat, Interpolation> Reader; |
184
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271 typedef Orthanc::PixelTraits<OutputFormat> Writer; |
183 | 272 typedef PixelShader<Reader, Writer, Function> Shader; |
153
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273 |
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274 const unsigned int outputWidth = slice.GetWidth(); |
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275 const unsigned int outputHeight = slice.GetHeight(); |
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276 |
183 | 277 const float sourceWidth = static_cast<float>(source.GetWidth()); |
278 const float sourceHeight = static_cast<float>(source.GetHeight()); | |
279 const float sourceDepth = static_cast<float>(source.GetDepth()); | |
280 | |
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281 Shader shader(source, scaling, offset); |
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282 |
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283 for (unsigned int y = 0; y < outputHeight; y++) |
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284 { |
184
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285 typename Writer::PixelType* p = |
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286 reinterpret_cast<typename Writer::PixelType*>(slice.GetRow(y)); |
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287 |
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288 RowIterator it(slice, extent, plane, box, y); |
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289 |
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290 for (unsigned int x = 0; x < outputWidth; x++, p++) |
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291 { |
177 | 292 float volumeX, volumeY, volumeZ; |
293 it.GetVolumeCoordinates(volumeX, volumeY, volumeZ); | |
183 | 294 |
295 shader.Apply(p, | |
296 volumeX * sourceWidth, | |
297 volumeY * sourceHeight, | |
298 volumeZ * sourceDepth); | |
153
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299 it.Next(); |
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300 } |
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301 } |
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302 } |
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303 |
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304 |
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305 template <typename RowIterator, |
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306 Orthanc::PixelFormat InputFormat, |
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307 Orthanc::PixelFormat OutputFormat> |
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308 static void ProcessImage(Orthanc::ImageAccessor& slice, |
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309 const Extent2D& extent, |
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310 const ImageBuffer3D& source, |
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311 const CoordinateSystem3D& plane, |
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312 const OrientedBoundingBox& box, |
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313 ImageInterpolation interpolation, |
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314 bool hasLinearFunction, |
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315 float scaling, |
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316 float offset) |
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317 { |
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318 if (hasLinearFunction) |
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319 { |
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320 switch (interpolation) |
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321 { |
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322 case ImageInterpolation_Nearest: |
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323 ProcessImage<RowIterator, InputFormat, OutputFormat, |
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324 ImageInterpolation_Nearest, TransferFunction_Linear> |
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325 (slice, extent, source, plane, box, scaling, offset); |
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326 break; |
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327 |
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328 case ImageInterpolation_Bilinear: |
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329 ProcessImage<RowIterator, InputFormat, OutputFormat, |
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330 ImageInterpolation_Bilinear, TransferFunction_Linear> |
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331 (slice, extent, source, plane, box, scaling, offset); |
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332 break; |
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333 |
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334 case ImageInterpolation_Trilinear: |
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335 ProcessImage<RowIterator, InputFormat, OutputFormat, |
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336 ImageInterpolation_Trilinear, TransferFunction_Linear> |
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337 (slice, extent, source, plane, box, scaling, offset); |
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338 break; |
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339 |
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340 default: |
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341 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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342 } |
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343 } |
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344 else |
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345 { |
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346 switch (interpolation) |
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347 { |
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348 case ImageInterpolation_Nearest: |
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349 ProcessImage<RowIterator, InputFormat, OutputFormat, |
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350 ImageInterpolation_Nearest, TransferFunction_Copy> |
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351 (slice, extent, source, plane, box, 0, 0); |
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352 break; |
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353 |
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354 case ImageInterpolation_Bilinear: |
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355 ProcessImage<RowIterator, InputFormat, OutputFormat, |
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356 ImageInterpolation_Bilinear, TransferFunction_Float> |
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357 (slice, extent, source, plane, box, 0, 0); |
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358 break; |
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359 |
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360 case ImageInterpolation_Trilinear: |
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361 ProcessImage<RowIterator, InputFormat, OutputFormat, |
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362 ImageInterpolation_Trilinear, TransferFunction_Float> |
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363 (slice, extent, source, plane, box, 0, 0); |
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364 break; |
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365 |
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366 default: |
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367 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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368 } |
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369 } |
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370 } |
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371 |
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372 |
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373 template <typename RowIterator> |
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374 static void ProcessImage(Orthanc::ImageAccessor& slice, |
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375 const Extent2D& extent, |
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376 const ImageBuffer3D& source, |
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377 const CoordinateSystem3D& plane, |
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378 const OrientedBoundingBox& box, |
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379 ImageInterpolation interpolation, |
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380 bool hasLinearFunction, |
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381 float scaling, |
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382 float offset) |
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383 { |
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384 if (source.GetFormat() == Orthanc::PixelFormat_Grayscale16 && |
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385 slice.GetFormat() == Orthanc::PixelFormat_Grayscale8) |
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386 { |
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387 ProcessImage<RowIterator, |
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388 Orthanc::PixelFormat_Grayscale16, |
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389 Orthanc::PixelFormat_Grayscale8> |
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390 (slice, extent, source, plane, box, interpolation, hasLinearFunction, scaling, offset); |
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391 } |
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392 else if (source.GetFormat() == Orthanc::PixelFormat_Grayscale16 && |
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393 slice.GetFormat() == Orthanc::PixelFormat_Grayscale16) |
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394 { |
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395 ProcessImage<RowIterator, |
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396 Orthanc::PixelFormat_Grayscale16, |
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397 Orthanc::PixelFormat_Grayscale16> |
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398 (slice, extent, source, plane, box, interpolation, hasLinearFunction, scaling, offset); |
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399 } |
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400 else if (source.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16 && |
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401 slice.GetFormat() == Orthanc::PixelFormat_BGRA32) |
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402 { |
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403 ProcessImage<RowIterator, |
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404 Orthanc::PixelFormat_SignedGrayscale16, |
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405 Orthanc::PixelFormat_BGRA32> |
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406 (slice, extent, source, plane, box, interpolation, hasLinearFunction, scaling, offset); |
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407 } |
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408 else if (source.GetFormat() == Orthanc::PixelFormat_Grayscale16 && |
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409 slice.GetFormat() == Orthanc::PixelFormat_BGRA32) |
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410 { |
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411 ProcessImage<RowIterator, |
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412 Orthanc::PixelFormat_Grayscale16, |
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413 Orthanc::PixelFormat_BGRA32> |
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414 (slice, extent, source, plane, box, interpolation, hasLinearFunction, scaling, offset); |
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415 } |
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416 else |
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417 { |
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418 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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419 } |
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420 } |
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421 } |
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422 |
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423 |
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424 |
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425 void VolumeReslicer::CheckIterators(const ImageBuffer3D& source, |
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426 const CoordinateSystem3D& plane, |
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427 const OrientedBoundingBox& box) const |
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428 { |
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429 for (unsigned int y = 0; y < slice_->GetHeight(); y++) |
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430 { |
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431 FastRowIterator fast(*slice_, extent_, plane, box, y); |
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432 SlowRowIterator slow(*slice_, extent_, plane, box, y); |
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433 |
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434 for (unsigned int x = 0; x < slice_->GetWidth(); x++) |
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435 { |
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436 float px, py, pz; |
177 | 437 fast.GetVolumeCoordinates(px, py, pz); |
153
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438 |
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439 float qx, qy, qz; |
177 | 440 slow.GetVolumeCoordinates(qx, qy, qz); |
153
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441 |
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442 Vector d; |
158
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LinearAlgebra toolbox
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154
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443 LinearAlgebra::AssignVector(d, px - qx, py - qy, pz - qz); |
153
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444 double norm = boost::numeric::ublas::norm_2(d); |
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445 if (norm > 0.0001) |
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446 { |
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447 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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448 } |
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449 |
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450 fast.Next(); |
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451 slow.Next(); |
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452 } |
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453 } |
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454 } |
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455 |
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456 |
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457 void VolumeReslicer::Reset() |
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458 { |
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459 success_ = false; |
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460 extent_.Reset(); |
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461 slice_.reset(NULL); |
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462 } |
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463 |
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464 |
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465 float VolumeReslicer::GetMinOutputValue() const |
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466 { |
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467 switch (outputFormat_) |
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468 { |
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469 case Orthanc::PixelFormat_Grayscale8: |
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470 case Orthanc::PixelFormat_Grayscale16: |
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471 case Orthanc::PixelFormat_BGRA32: |
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472 return 0.0f; |
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473 break; |
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474 |
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475 default: |
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476 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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477 } |
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|
478 } |
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|
479 |
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|
480 |
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481 float VolumeReslicer::GetMaxOutputValue() const |
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482 { |
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483 switch (outputFormat_) |
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484 { |
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485 case Orthanc::PixelFormat_Grayscale8: |
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486 case Orthanc::PixelFormat_BGRA32: |
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487 return static_cast<float>(std::numeric_limits<uint8_t>::max()); |
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488 break; |
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|
489 |
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490 case Orthanc::PixelFormat_Grayscale16: |
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491 return static_cast<float>(std::numeric_limits<uint16_t>::max()); |
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492 break; |
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|
493 |
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494 default: |
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495 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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|
496 } |
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|
497 } |
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diff
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|
498 |
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parents:
diff
changeset
|
499 |
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|
500 VolumeReslicer::VolumeReslicer() : |
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501 outputFormat_(Orthanc::PixelFormat_Grayscale8), |
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502 interpolation_(ImageInterpolation_Nearest), |
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503 fastMode_(true), |
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|
504 success_(false) |
ae531ab5dcd9
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diff
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|
505 { |
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|
506 ResetLinearFunction(); |
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parents:
diff
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|
507 } |
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parents:
diff
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|
508 |
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parents:
diff
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|
509 |
ae531ab5dcd9
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|
510 void VolumeReslicer::GetLinearFunction(float& scaling, |
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parents:
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511 float& offset) const |
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parents:
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|
512 { |
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513 if (hasLinearFunction_) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
514 { |
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parents:
diff
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|
515 scaling = scaling_; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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516 offset = offset_; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
517 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
518 else |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
519 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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520 scaling = 1.0f; |
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521 offset = 0.0f; |
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|
522 } |
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diff
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|
523 } |
ae531ab5dcd9
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
524 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
525 |
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diff
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|
526 void VolumeReslicer::ResetLinearFunction() |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
527 { |
ae531ab5dcd9
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parents:
diff
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|
528 Reset(); |
ae531ab5dcd9
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diff
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|
529 hasLinearFunction_ = false; |
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parents:
diff
changeset
|
530 scaling_ = 1.0f; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
531 offset_ = 0.0f; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
532 } |
ae531ab5dcd9
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parents:
diff
changeset
|
533 |
ae531ab5dcd9
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
534 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
535 void VolumeReslicer::SetLinearFunction(float scaling, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
536 float offset) |
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parents:
diff
changeset
|
537 { |
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new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
538 Reset(); |
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new class: VolumeReslicer
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diff
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|
539 hasLinearFunction_ = true; |
ae531ab5dcd9
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
540 scaling_ = scaling; |
ae531ab5dcd9
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parents:
diff
changeset
|
541 offset_ = offset; |
ae531ab5dcd9
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parents:
diff
changeset
|
542 } |
ae531ab5dcd9
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
543 |
ae531ab5dcd9
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
544 |
ae531ab5dcd9
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parents:
diff
changeset
|
545 void VolumeReslicer::SetWindow(float low, |
ae531ab5dcd9
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
546 float high) |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
547 { |
ae531ab5dcd9
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
548 //printf("Range in pixel values: %f->%f\n", low, high); |
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new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
549 float scaling = (GetMaxOutputValue() - GetMinOutputValue()) / (high - low); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
550 float offset = GetMinOutputValue() - scaling * low; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
551 |
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new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
552 SetLinearFunction(scaling, offset); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
553 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
554 /*float x = scaling_ * low + offset_; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
555 float y = scaling_ * high + offset_; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
556 printf("%f %f (should be %f->%f)\n", x, y, GetMinOutputValue(), GetMaxOutputValue());*/ |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
557 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
558 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
559 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
560 void VolumeReslicer::FitRange(const ImageBuffer3D& image) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
561 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
562 float minInputValue, maxInputValue; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
563 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
564 if (!image.GetRange(minInputValue, maxInputValue) || |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
565 maxInputValue < 1) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
566 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
567 ResetLinearFunction(); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
568 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
569 else |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
570 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
571 SetWindow(minInputValue, maxInputValue); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
572 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
573 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
574 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
575 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
576 void VolumeReslicer::SetWindowing(ImageWindowing windowing, |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
577 const ImageBuffer3D& image, |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
578 float rescaleSlope, |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
579 float rescaleIntercept) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
580 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
581 if (windowing == ImageWindowing_Custom || |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
582 windowing == ImageWindowing_Default) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
583 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
584 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
585 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
586 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
587 float center, width; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
588 ComputeWindowing(center, width, windowing, 0, 0); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
589 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
590 float a = (center - width / 2.0f - rescaleIntercept) / rescaleSlope; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
591 float b = (center + width / 2.0f - rescaleIntercept) / rescaleSlope; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
592 SetWindow(a, b); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
593 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
594 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
595 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
596 void VolumeReslicer::SetOutputFormat(Orthanc::PixelFormat format) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
597 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
598 if (format != Orthanc::PixelFormat_Grayscale8 && |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
599 format != Orthanc::PixelFormat_Grayscale16 && |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
600 format != Orthanc::PixelFormat_BGRA32) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
601 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
602 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
603 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
604 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
605 if (hasLinearFunction_) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
606 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
607 LOG(WARNING) << "Calls to VolumeReslicer::SetOutputFormat() should be done before VolumeReslicer::FitRange()"; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
608 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
609 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
610 outputFormat_ = format; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
611 Reset(); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
612 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
613 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
614 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
615 void VolumeReslicer::SetInterpolation(ImageInterpolation interpolation) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
616 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
617 if (interpolation != ImageInterpolation_Nearest && |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
618 interpolation != ImageInterpolation_Bilinear && |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
619 interpolation != ImageInterpolation_Trilinear) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
620 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
621 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
622 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
623 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
624 interpolation_ = interpolation; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
625 Reset(); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
626 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
627 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
628 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
629 const Extent2D& VolumeReslicer::GetOutputExtent() const |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
630 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
631 if (success_) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
632 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
633 return extent_; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
634 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
635 else |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
636 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
637 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
638 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
639 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
640 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
641 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
642 const Orthanc::ImageAccessor& VolumeReslicer::GetOutputSlice() const |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
643 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
644 if (success_) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
645 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
646 assert(slice_.get() != NULL); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
647 return *slice_; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
648 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
649 else |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
650 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
651 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
652 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
653 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
654 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
655 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
656 Orthanc::ImageAccessor* VolumeReslicer::ReleaseOutputSlice() |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
657 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
658 if (success_) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
659 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
660 assert(slice_.get() != NULL); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
661 success_ = false; |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
662 return slice_.release(); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
663 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
664 else |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
665 { |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
666 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
667 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
668 } |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
669 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
670 |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
671 void VolumeReslicer::Apply(const ImageBuffer3D& source, |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
672 const CoordinateSystem3D& plane) |
ae531ab5dcd9
new class: VolumeReslicer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
673 { |
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new class: VolumeReslicer
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674 // Choose the default voxel size as the finest voxel dimension |
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675 // of the source volumetric image |
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676 const OrthancStone::Vector dim = source.GetVoxelDimensions(OrthancStone::VolumeProjection_Axial); |
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677 double voxelSize = dim[0]; |
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678 |
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679 if (dim[1] < voxelSize) |
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680 { |
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681 voxelSize = dim[1]; |
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682 } |
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683 |
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684 if (dim[2] < voxelSize) |
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685 { |
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686 voxelSize = dim[2]; |
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687 } |
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688 |
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689 if (voxelSize <= 0) |
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690 { |
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691 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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692 } |
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693 |
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694 Apply(source, plane, voxelSize); |
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695 } |
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696 |
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697 |
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698 void VolumeReslicer::Apply(const ImageBuffer3D& source, |
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699 const CoordinateSystem3D& plane, |
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700 double voxelSize) |
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701 { |
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702 Reset(); |
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703 |
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704 // Firstly, compute the intersection of the source volumetric |
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705 // image with the reslicing plane. This leads to a polygon with 3 |
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706 // to 6 vertices. We compute the extent of the intersection |
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707 // polygon, with respect to the coordinate system of the reslicing |
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708 // plane. |
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709 OrientedBoundingBox box(source); |
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710 |
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711 if (!box.ComputeExtent(extent_, plane)) |
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712 { |
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713 // The plane does not intersect with the bounding box of the volume |
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714 slice_.reset(new Orthanc::Image(outputFormat_, 0, 0, false)); |
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715 success_ = true; |
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716 return; |
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717 } |
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718 |
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719 // Secondly, the extent together with the voxel size gives the |
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720 // size of the output image |
172 | 721 unsigned int width = boost::math::iround(extent_.GetWidth() / voxelSize); |
722 unsigned int height = boost::math::iround(extent_.GetHeight() / voxelSize); | |
153
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723 |
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724 slice_.reset(new Orthanc::Image(outputFormat_, width, height, false)); |
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725 |
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726 //CheckIterators(source, plane, box); |
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727 |
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728 if (fastMode_) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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729 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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730 ProcessImage<FastRowIterator>(*slice_, extent_, source, plane, box, |
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731 interpolation_, hasLinearFunction_, scaling_, offset_); |
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732 } |
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733 else |
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Sebastien Jodogne <s.jodogne@gmail.com>
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734 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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735 ProcessImage<SlowRowIterator>(*slice_, extent_, source, plane, box, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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736 interpolation_, hasLinearFunction_, scaling_, offset_); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
737 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
738 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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739 success_ = true; |
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740 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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741 } |