1 | #include <iostream> |
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2 | #include <iomanip> |
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3 | #include <string> |
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4 | #include <wcs.h> |
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5 | #include <wcshdr.h> |
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6 | #include <fitshdr.h> |
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7 | #include <wcsfix.h> |
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8 | #include <wcsunits.h> |
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9 | #define WCSLIB_GETWCSTAB // define this so that we don't try and redefine wtbarr |
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10 | // (this is a problem when using gcc v.4+ |
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11 | #include <fitsio.h> |
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12 | #include <math.h> |
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13 | #include <duchamp.hh> |
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14 | #include <param.hh> |
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15 | #include <Cubes/cubes.hh> |
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16 | #include <Detection/detection.hh> |
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17 | #include <ATrous/atrous.hh> |
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18 | #include <Utils/utils.hh> |
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19 | |
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20 | string imageType[4] = {"point", "spectrum", "image", "cube"}; |
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21 | |
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22 | vector<Detection> readAndSearch(Param &par) |
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23 | { |
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24 | vector<Detection> outputList; |
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25 | |
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26 | short int maxdim=3; |
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27 | long *dimAxes = new long[maxdim]; |
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28 | for(int i=0;i<maxdim;i++) dimAxes[i]=1; |
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29 | long nelements; |
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30 | int bitpix,numAxes; |
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31 | int status = 0, nkeys; /* MUST initialize status */ |
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32 | fitsfile *fptr; |
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33 | |
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34 | string fname = par.getImageFile(); |
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35 | if(par.getFlagSubsection()){ |
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36 | par.parseSubsection(); |
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37 | fname+=par.getSubsection(); |
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38 | } |
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39 | |
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40 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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41 | fits_report_error(stderr, status); |
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42 | } |
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43 | |
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44 | status = 0; |
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45 | fits_get_img_param(fptr, maxdim, &bitpix, &numAxes, dimAxes, &status); |
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46 | if(status){ |
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47 | fits_report_error(stderr, status); |
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48 | } |
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49 | status = 0; |
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50 | fits_close_file(fptr, &status); |
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51 | if (status){ |
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52 | duchampWarning("readAndSearch","Error closing file: "); |
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53 | fits_report_error(stderr, status); |
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54 | } |
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55 | |
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56 | if(numAxes<=3) |
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57 | std::cout << "Dimensions of " << imageType[numAxes] << ": " << dimAxes[0]; |
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58 | else std::cout << "Dimensions of " << imageType[3] << ": " << dimAxes[0]; |
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59 | if(numAxes>1) std::cout << "x" << dimAxes[1]; |
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60 | if(numAxes>2) std::cout << "x" << dimAxes[2]; |
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61 | std::cout << std::endl; |
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62 | |
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63 | int anynul; |
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64 | long *fpixel = new long[numAxes]; |
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65 | long *lpixel = new long[numAxes]; |
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66 | long *inc = new long[numAxes]; // the data-sampling increment |
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67 | for(int i=0;i<numAxes;i++) inc[i]=1; |
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68 | |
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69 | //--------------------------------------------------------- |
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70 | // Read in spectra one at a time, reconstruct if necessary |
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71 | // and then search, adding found objects to cube's object list. |
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72 | |
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73 | fpixel[0] = 1; |
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74 | for(int i=2;i<numAxes;i++) fpixel[i] = 1; |
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75 | |
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76 | lpixel[0] = dimAxes[0]; |
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77 | lpixel[2] = dimAxes[2]; |
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78 | for(int i=3;i<numAxes;i++) lpixel[i] = 1; |
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79 | |
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80 | int numDetected = 0; |
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81 | |
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82 | std::cout << " 0: |"; |
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83 | printSpace(50); |
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84 | std::cout << "| " << std::setw(5) << numDetected << std::flush; |
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85 | printBackSpace(64); |
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86 | std::cout << std::flush; |
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87 | |
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88 | float *bigarray = new float[dimAxes[0] * dimAxes[2]]; |
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89 | float *array = new float[dimAxes[2]]; |
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90 | long *specdim = new long[2]; |
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91 | specdim[0] = dimAxes[2]; specdim[1]=1; |
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92 | |
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93 | float median,sigma; |
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94 | int pos,frac; |
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95 | |
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96 | Image *spectrum = new Image(specdim); |
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97 | spectrum->saveParam(par); |
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98 | spectrum->pars().setBeamSize(2.); // only neighbouring channels correlated |
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99 | |
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100 | for(int y=0;y<dimAxes[1];y++){ |
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101 | |
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102 | std::cout << std::setw(4) << y << ": " << std::flush; |
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103 | |
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104 | fpixel[1] = lpixel[1] = y+1; |
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105 | |
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106 | status = 0; |
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107 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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108 | duchampWarning("readAndSearch","Error opening file: "); |
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109 | fits_report_error(stderr, status); |
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110 | } |
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111 | status = 0; |
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112 | fits_read_subset(fptr, TFLOAT, fpixel, lpixel, inc, NULL, bigarray, &anynul, &status); |
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113 | if(status){ |
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114 | duchampError("readAndSearch","There was an error reading in the data array:"); |
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115 | fits_report_error(stderr, status); |
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116 | } |
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117 | status = 0; |
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118 | fits_close_file(fptr, &status); |
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119 | if (status){ |
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120 | duchampWarning("readAndSearch","Error closing file: "); |
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121 | fits_report_error(stderr, status); |
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122 | } |
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123 | |
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124 | for(int x=0;x<dimAxes[0];x++){ |
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125 | |
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126 | pos = y*dimAxes[0]+x; |
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127 | frac = 100*(pos+1)/(dimAxes[1]*dimAxes[0]); |
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128 | if(frac%2 == 0){ |
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129 | std::cout << "|"; |
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130 | printHash(frac/2); |
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131 | printSpace(50-frac/2); |
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132 | std::cout << "| " << std::setw(5) << numDetected; |
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133 | printBackSpace(58); |
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134 | std::cout << std::flush; |
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135 | } |
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136 | |
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137 | for(int z=0;z<dimAxes[2];z++) array[z] = bigarray[z*dimAxes[0] + x]; |
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138 | |
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139 | median = findMedian(array,dimAxes[2]); |
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140 | spectrum->clearDetectionList(); |
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141 | if(par.getFlagATrous()){ |
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142 | float *recon = new float[dimAxes[2]]; |
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143 | atrous1DReconstruct(dimAxes[2],array,recon,par); |
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144 | float *resid = new float[dimAxes[2]]; |
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145 | for(int i=0;i<dimAxes[2];i++) resid[i] = array[i] - recon[i]; |
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146 | sigma = findMADFM(recon,dimAxes[2])/correctionFactor; |
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147 | spectrum->saveArray(recon,dimAxes[2]); |
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148 | delete [] recon; |
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149 | delete [] resid; |
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150 | spectrum->removeMW(); // only works if flagMW is true |
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151 | spectrum->setStats(median,sigma,par.getCut()); |
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152 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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153 | spectrum->setMinSize(par.getMinChannels()); |
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154 | spectrum->spectrumDetect(); |
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155 | } |
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156 | else{ |
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157 | sigma = findMADFM(array,dimAxes[2])/correctionFactor; |
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158 | spectrum->saveArray(array,dimAxes[2]); |
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159 | spectrum->removeMW(); // only works if flagMW is true |
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160 | spectrum->setStats(median,sigma,par.getCut()); |
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161 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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162 | spectrum->setMinSize(par.getMinChannels()); |
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163 | spectrum->spectrumDetect(); |
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164 | } |
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165 | |
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166 | numDetected += spectrum->getNumObj(); |
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167 | for(int obj=0;obj<spectrum->getNumObj();obj++){ |
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168 | Detection *object = new Detection; |
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169 | *object = spectrum->getObject(obj); |
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170 | for(int pix=0;pix<object->getSize();pix++) { |
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171 | // Fix up coordinates of each pixel to match original array |
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172 | object->setZ(pix, object->getX(pix)); |
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173 | object->setX(pix, x); |
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174 | object->setY(pix, y); |
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175 | object->setF(pix, array[object->getZ(pix)]); |
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176 | // NB: set F to the original value, not the recon value. |
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177 | } |
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178 | object->addOffsets(par); |
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179 | object->calcParams(); |
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180 | mergeIntoList(*object,outputList,par); |
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181 | delete object; |
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182 | } |
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183 | |
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184 | |
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185 | } // end of loop over y |
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186 | |
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187 | printBackSpace(6); |
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188 | std::cout << std::flush; |
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189 | } // end of loop over x |
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190 | |
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191 | delete spectrum; |
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192 | delete [] bigarray; |
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193 | delete [] array; |
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194 | delete [] fpixel; |
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195 | delete [] lpixel; |
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196 | delete [] inc; |
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197 | delete [] dimAxes; |
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198 | delete [] specdim; |
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199 | |
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200 | return outputList; |
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201 | |
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202 | } |
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