1 | // ----------------------------------------------------------------------- |
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2 | // momentMap.cc : functions to calculate the momment-0 map of the cube |
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3 | // ----------------------------------------------------------------------- |
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4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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5 | // |
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6 | // This program is free software; you can redistribute it and/or modify it |
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7 | // under the terms of the GNU General Public License as published by the |
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8 | // Free Software Foundation; either version 2 of the License, or (at your |
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9 | // option) any later version. |
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10 | // |
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11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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14 | // for more details. |
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15 | // |
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16 | // You should have received a copy of the GNU General Public License |
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17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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19 | // |
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20 | // Correspondence concerning Duchamp may be directed to: |
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21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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22 | // Postal address: Dr. Matthew Whiting |
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23 | // Australia Telescope National Facility, CSIRO |
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24 | // PO Box 76 |
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25 | // Epping NSW 1710 |
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26 | // AUSTRALIA |
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27 | // ----------------------------------------------------------------------- |
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28 | #include <iostream> |
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29 | #include <iomanip> |
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30 | #include <sstream> |
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31 | #include <math.h> |
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32 | #include <string.h> |
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33 | #include <duchamp/duchamp.hh> |
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34 | #include <duchamp/param.hh> |
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35 | #include <duchamp/fitsHeader.hh> |
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36 | #include <duchamp/Detection/detection.hh> |
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37 | #include <duchamp/PixelMap/Object3D.hh> |
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38 | #include <duchamp/Cubes/cubes.hh> |
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39 | #include <duchamp/Utils/utils.hh> |
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40 | |
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41 | using namespace PixelInfo; |
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42 | |
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43 | namespace duchamp |
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44 | { |
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45 | |
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46 | void Cube::getMomentMapForPlot(float *momentMap, float &z1, float &z2) |
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47 | { |
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48 | |
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49 | /// @details This returns the moment-0 map in a form suitable for |
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50 | /// plotting via pgplot. The map is transformed to log space, and |
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51 | /// the minimum & maximum values are also returned. |
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52 | /// @param momentMap The values of log10(momentMap). This array needs to be declared beforehand. |
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53 | /// @param z1 The minimum value of momentMap |
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54 | /// @param z2 The maximum value of momentMap |
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55 | |
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56 | |
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57 | long xdim=this->axisDim[0]; |
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58 | long ydim=this->axisDim[1]; |
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59 | |
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60 | std::vector<bool> detectedPixels = this->getMomentMap(momentMap); |
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61 | |
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62 | int count=0; |
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63 | for(int i=0;i<xdim*ydim;i++) { |
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64 | if(momentMap[i]>0.){ |
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65 | float logmm = log10(momentMap[i]); |
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66 | bool addPixel = detectedPixels[i]; |
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67 | if(addPixel){ |
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68 | if(count==0) z1 = z2 = logmm; |
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69 | else{ |
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70 | if(logmm < z1) z1 = logmm; |
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71 | if(logmm > z2) z2 = logmm; |
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72 | } |
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73 | count++; |
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74 | } |
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75 | } |
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76 | } |
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77 | |
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78 | for(int i=0;i<xdim*ydim;i++) { |
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79 | bool addPixel = detectedPixels[i]; |
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80 | addPixel = addPixel && (momentMap[i]>0.); |
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81 | if(!addPixel) momentMap[i] = z1-1.; |
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82 | else momentMap[i] = log10(momentMap[i]); |
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83 | } |
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84 | |
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85 | } |
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86 | |
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87 | std::vector<bool> Cube::getMomentMap(float *momentMap) |
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88 | { |
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89 | |
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90 | /// @details This populates the moment-0 map (ie. the map of |
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91 | /// integrated flux) for the cube. The momentMap array needs to be |
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92 | /// allocated before calling this function - it should be of the |
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93 | /// same spatial dimensions as the cube. The function returns |
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94 | /// a map showing which spatial pixels are detected. This provides |
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95 | /// a way of telling whether a given pixel is affected, as |
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96 | /// although the momentMap is initialised to zero, it is |
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97 | /// conceivable that a pixel with detections in its spectrum could |
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98 | /// yield a value of zero. The detection map is stored as a |
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99 | /// vector<bool> for compactness. |
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100 | /// @param momentMap Pointer to the array holding the moment map values, which needs to be allocated beforehand. |
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101 | /// @return detectedPixel The map showing which spatial pixels contain an object. |
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102 | |
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103 | size_t xdim=this->axisDim[0]; |
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104 | size_t ydim=this->axisDim[1]; |
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105 | size_t zdim=this->axisDim[2]; |
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106 | |
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107 | // get the list of objects that should be plotted. |
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108 | std::vector<bool> objectChoice = this->par.getObjectChoices(this->objectList->size()); |
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109 | |
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110 | bool *isObj = new bool[xdim*ydim*zdim]; |
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111 | for(size_t i=0;i<xdim*ydim*zdim;i++) isObj[i] = false; |
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112 | for(size_t i=0;i<this->objectList->size();i++){ |
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113 | if(objectChoice[i]){ |
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114 | std::vector<Voxel> voxlist = this->objectList->at(i).getPixelSet(); |
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115 | std::vector<Voxel>::iterator vox; |
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116 | for(vox=voxlist.begin();vox<voxlist.end();vox++){ |
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117 | size_t pixelpos = vox->getX() + xdim*vox->getY() + xdim*ydim*vox->getZ(); |
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118 | isObj[pixelpos] = true; |
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119 | } |
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120 | } |
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121 | } |
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122 | |
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123 | // Array containing the moment map, initialised to zero |
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124 | for(size_t i=0;i<xdim*ydim;i++) momentMap[i] = 0.; |
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125 | |
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126 | // Bool vector containing yes/no on whether a given spatial pixel has a detected object. |
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127 | // Initialise this to false everywhere. |
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128 | std::vector<bool> detectedPixels = std::vector<bool>(xdim*ydim,false); |
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129 | |
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130 | // if we are looking for negative features, we need to invert the |
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131 | // detected pixels for the moment map |
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132 | float sign = 1.; |
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133 | if(this->pars().getFlagNegative()) sign = -1.; |
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134 | |
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135 | float deltaVel; |
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136 | double x,y; |
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137 | |
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138 | double *zArray = new double[zdim]; |
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139 | for(size_t z=0; z<zdim; z++) zArray[z] = double(z); |
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140 | |
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141 | for(size_t pix=0; pix<xdim*ydim; pix++){ |
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142 | |
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143 | x = double(pix%xdim); |
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144 | y = double(pix/xdim); |
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145 | |
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146 | if(!this->isBlank(pix) && // only do this for non-blank pixels. Judge this by the first pixel of the channel. |
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147 | this->detectMap[pix] > 0 ){ // and only where something was detected in the spectrum. |
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148 | |
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149 | double * world = this->head.pixToVel(x,y,zArray,zdim); |
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150 | |
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151 | for(size_t z=0; z<zdim; z++){ |
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152 | size_t pos = z*xdim*ydim + pix; // the voxel in the cube |
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153 | if(isObj[pos]){ // if it's an object pixel... |
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154 | // delta-vel is half the distance between adjacent channels. |
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155 | // if at end, then just use 0-1 or (zdim-1)-(zdim-2) distance |
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156 | if(z==0){ |
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157 | if(zdim==1) deltaVel=1.; // pathological case -- if 2D image. |
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158 | else deltaVel = world[z+1] - world[z]; |
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159 | } |
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160 | else if(z==(zdim-1)) deltaVel = world[z-1] - world[z]; |
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161 | else deltaVel = (world[z+1] - world[z-1]) / 2.; |
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162 | |
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163 | momentMap[pix] += sign * this->array[pos] * fabs(deltaVel); |
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164 | detectedPixels[pix] = true; |
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165 | |
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166 | } |
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167 | } |
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168 | delete [] world; |
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169 | } |
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170 | |
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171 | } |
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172 | |
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173 | delete [] zArray; |
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174 | delete [] isObj; |
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175 | |
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176 | return detectedPixels; |
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177 | |
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178 | } |
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179 | |
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180 | |
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181 | } |
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