1 | #include <iostream> |
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2 | #include <iomanip> |
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3 | #include <fstream> |
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4 | #include <vector> |
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5 | #include <duchamp.hh> |
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6 | #include <Cubes/cubes.hh> |
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7 | #include <Utils/utils.hh> |
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8 | |
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9 | void Cube::CubicSearch() |
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10 | { |
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11 | /** |
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12 | * Cube::SimpleSearch3D() |
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13 | * A front end to the cubic searching routine that does not |
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14 | * involve any wavelet reconstruction. |
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15 | * If baseline-removal is required that is done prior to searching. |
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16 | * Once searching is complete, the detection map is updated and |
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17 | * the intermediate detections are logged in the log file. |
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18 | */ |
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19 | |
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20 | this->objectList = search3DArray(this->axisDim,this->array,this->par); |
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21 | |
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22 | this->updateDetectMap(); |
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23 | if(this->par.getFlagLog()) this->logDetectionList(); |
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24 | |
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25 | } |
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26 | |
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27 | |
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28 | vector <Detection> search3DArray(long *dim, float *Array, Param &par) |
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29 | { |
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30 | /** |
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31 | * cubicSearch |
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32 | * Takes a dimension array and data array as input (and Parameter set) |
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33 | * and searches for detections in a combination of 1D and 2D searches. |
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34 | * Returns a vector list of Detections. |
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35 | * No reconstruction is assumed to have taken place, so statistics are |
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36 | * calculated (using robust methods) from the data array itself. |
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37 | */ |
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38 | |
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39 | vector <Detection> outputList; |
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40 | long zdim = dim[2]; |
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41 | long xySize = dim[0] * dim[1]; |
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42 | long fullSize = zdim * xySize; |
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43 | int num = 0; |
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44 | |
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45 | float blankPixValue = par.getBlankPixVal(); |
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46 | bool *isGood = new bool[fullSize]; |
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47 | for(int pos=0;pos<fullSize;pos++){ |
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48 | isGood[pos] = !par.isBlank(Array[pos]) && !par.isInMW(pos/xySize); |
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49 | } |
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50 | bool *doChannel = new bool[xySize]; |
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51 | int goodSize=0; |
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52 | for(int npix=0; npix<xySize; npix++){ |
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53 | for(int z=0;z<zdim;z++) if(isGood[z*xySize+npix]) goodSize++; |
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54 | if(goodSize==0) doChannel[npix] = false; |
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55 | else doChannel[npix] = true; |
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56 | } |
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57 | |
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58 | // FIRST SEARCH -- IN EACH SPECTRUM. |
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59 | if(zdim>1){ |
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60 | if(par.isVerbose()) { |
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61 | std::cout << " 1D: "; |
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62 | initialiseMeter(); |
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63 | } |
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64 | |
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65 | for(int npix=0; npix<xySize; npix++){ |
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66 | |
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67 | if( par.isVerbose() && ((100*(npix+1)/xySize)%5 == 0) ) |
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68 | updateMeter((100*(npix+1)/xySize)/5); |
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69 | |
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70 | if(doChannel[npix]){ |
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71 | |
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72 | float *spec = new float[zdim]; |
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73 | float specMedian,specSigma; |
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74 | goodSize=0; |
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75 | for(int z=0;z<zdim;z++) |
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76 | if(isGood[z*xySize+npix]) spec[goodSize++] = Array[z*xySize+npix]; |
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77 | findMedianStats(spec,goodSize,specMedian,specSigma); |
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78 | specSigma /= correctionFactor; |
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79 | |
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80 | |
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81 | long *specdim = new long[2]; |
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82 | specdim[0] = zdim; specdim[1]=1; |
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83 | Image *spectrum = new Image(specdim); |
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84 | delete specdim; |
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85 | spectrum->saveParam(par); |
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86 | spectrum->pars().setBeamSize(2.); |
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87 | // beam size: for spectrum, only neighbouring channels correlated |
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88 | spectrum->extractSpectrum(Array,dim,npix); |
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89 | spectrum->removeMW(); // only works if flagMW is true |
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90 | spectrum->setStats(specMedian,specSigma,par.getCut()); |
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91 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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92 | spectrum->setMinSize(par.getMinChannels()); |
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93 | spectrum->spectrumDetect(); |
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94 | num += spectrum->getNumObj(); |
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95 | for(int obj=0;obj<spectrum->getNumObj();obj++){ |
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96 | Detection *object = new Detection; |
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97 | *object = spectrum->getObject(obj); |
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98 | for(int pix=0;pix<object->getSize();pix++) { |
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99 | // Fix up coordinates of each pixel to match original array |
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100 | object->setZ(pix, object->getX(pix)); |
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101 | object->setX(pix, npix%dim[0]); |
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102 | object->setY(pix, npix/dim[0]); |
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103 | } |
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104 | object->addOffsets(par); |
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105 | object->calcParams(); |
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106 | mergeIntoList(*object,outputList,par); |
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107 | delete object; |
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108 | } |
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109 | delete spectrum; |
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110 | } |
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111 | } |
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112 | |
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113 | // num = outputList.size(); |
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114 | if(par.isVerbose()) { |
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115 | printBackSpace(22); |
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116 | std::cout <<"Found " << num <<";" << std::flush; |
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117 | } |
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118 | |
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119 | } |
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120 | |
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121 | // SECOND SEARCH -- IN EACH CHANNEL |
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122 | if(par.isVerbose()){ |
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123 | std::cout << " 2D: "; |
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124 | initialiseMeter(); |
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125 | } |
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126 | |
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127 | num = 0; |
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128 | |
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129 | for(int z=0; z<zdim; z++){ |
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130 | |
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131 | if( par.isVerbose() && ((100*(z+1)/zdim)%5 == 0) ) |
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132 | updateMeter((100*(z+1)/zdim)/5); |
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133 | |
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134 | if(!par.isInMW(z)){ |
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135 | |
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136 | float *image = new float[xySize]; |
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137 | float imageMedian, imageSigma; |
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138 | goodSize=0; |
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139 | for(int npix=0; npix<xySize; npix++) { |
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140 | if(isGood[z*xySize + npix]) |
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141 | image[goodSize++] = Array[z*xySize + npix]; |
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142 | } |
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143 | findMedianStats(image,goodSize,imageMedian,imageSigma); |
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144 | imageSigma /= correctionFactor; |
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145 | |
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146 | long *imdim = new long[2]; |
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147 | imdim[0] = dim[0]; imdim[1] = dim[1]; |
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148 | Image *channelImage = new Image(imdim); |
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149 | delete imdim; |
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150 | channelImage->saveParam(par); |
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151 | channelImage->extractImage(Array,dim,z); |
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152 | channelImage->setStats(imageMedian,imageSigma,par.getCut()); |
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153 | if(par.getFlagFDR()) channelImage->setupFDR(); |
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154 | channelImage->setMinSize(par.getMinPix()); |
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155 | channelImage->lutz_detect(); |
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156 | num += channelImage->getNumObj(); |
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157 | for(int obj=0;obj<channelImage->getNumObj();obj++){ |
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158 | Detection *object = new Detection; |
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159 | *object = channelImage->getObject(obj); |
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160 | // Fix up coordinates of each pixel to match original array |
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161 | for(int pix=0;pix<object->getSize();pix++) object->setZ(pix, z); |
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162 | object->addOffsets(par); |
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163 | object->calcParams(); |
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164 | mergeIntoList(*object,outputList,par); |
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165 | delete object; |
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166 | } |
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167 | delete channelImage; |
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168 | } |
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169 | |
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170 | } |
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171 | |
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172 | if(par.isVerbose()){ |
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173 | printBackSpace(22); |
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174 | std::cout << "Found " << num << "."; |
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175 | printSpace(44); |
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176 | std::cout << std::endl << std::flush; |
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177 | } |
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178 | |
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179 | delete [] isGood; |
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180 | delete [] doChannel; |
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181 | |
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182 | return outputList; |
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183 | } |
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