1 | // ----------------------------------------------------------------------- |
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2 | // ReadAndSearch.cc: Combining both the FITS reading and the searching. |
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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 <string> |
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31 | #include <wcslib/wcs.h> |
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32 | #include <wcslib/wcshdr.h> |
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33 | #include <wcslib/fitshdr.h> |
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34 | #include <wcslib/wcsfix.h> |
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35 | #include <wcslib/wcsunits.h> |
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36 | #define WCSLIB_GETWCSTAB // define this so that we don't try and |
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37 | // redefine wtbarr (this is a problem when |
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38 | // using gcc v.4+ |
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39 | #include <fitsio.h> |
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40 | #include <math.h> |
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41 | #include <duchamp/duchamp.hh> |
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42 | #include <duchamp/param.hh> |
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43 | #include <duchamp/Cubes/cubes.hh> |
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44 | #include <duchamp/Detection/detection.hh> |
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45 | #include <duchamp/ATrous/atrous.hh> |
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46 | #include <duchamp/Utils/utils.hh> |
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47 | |
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48 | std::string imageType[4] = {"point", "spectrum", "image", "cube"}; |
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49 | |
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50 | vector<Detection> readAndSearch(Param &par) |
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51 | { |
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52 | vector<Detection> outputList; |
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53 | |
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54 | short int maxdim=3; |
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55 | long *dimAxes = new long[maxdim]; |
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56 | for(int i=0;i<maxdim;i++) dimAxes[i]=1; |
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57 | long nelements; |
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58 | int bitpix,numAxes; |
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59 | int status = 0, nkeys; /* MUST initialize status */ |
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60 | fitsfile *fptr; |
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61 | |
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62 | std::string fname = par.getImageFile(); |
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63 | if(par.getFlagSubsection()){ |
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64 | par.parseSubsection(); |
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65 | fname+=par.getSubsection(); |
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66 | } |
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67 | |
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68 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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69 | fits_report_error(stderr, status); |
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70 | } |
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71 | |
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72 | status = 0; |
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73 | fits_get_img_param(fptr, maxdim, &bitpix, &numAxes, dimAxes, &status); |
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74 | if(status){ |
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75 | fits_report_error(stderr, status); |
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76 | } |
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77 | status = 0; |
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78 | fits_close_file(fptr, &status); |
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79 | if (status){ |
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80 | duchampWarning("readAndSearch","Error closing file: "); |
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81 | fits_report_error(stderr, status); |
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82 | } |
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83 | |
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84 | if(numAxes<=3) |
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85 | std::cout << "Dimensions of " << imageType[numAxes] << ": " << dimAxes[0]; |
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86 | else std::cout << "Dimensions of " << imageType[3] << ": " << dimAxes[0]; |
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87 | if(numAxes>1) std::cout << "x" << dimAxes[1]; |
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88 | if(numAxes>2) std::cout << "x" << dimAxes[2]; |
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89 | std::cout << std::endl; |
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90 | |
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91 | int anynul; |
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92 | long *fpixel = new long[numAxes]; |
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93 | long *lpixel = new long[numAxes]; |
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94 | long *inc = new long[numAxes]; // the data-sampling increment |
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95 | for(int i=0;i<numAxes;i++) inc[i]=1; |
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96 | |
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97 | //--------------------------------------------------------- |
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98 | // Read in spectra one at a time, reconstruct if necessary |
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99 | // and then search, adding found objects to cube's object list. |
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100 | |
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101 | fpixel[0] = 1; |
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102 | for(int i=2;i<numAxes;i++) fpixel[i] = 1; |
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103 | |
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104 | lpixel[0] = dimAxes[0]; |
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105 | lpixel[2] = dimAxes[2]; |
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106 | for(int i=3;i<numAxes;i++) lpixel[i] = 1; |
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107 | |
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108 | int numDetected = 0; |
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109 | |
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110 | std::cout << " 0: |"; |
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111 | printSpace(50); |
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112 | std::cout << "| " << std::setw(5) << numDetected << std::flush; |
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113 | printBackSpace(64); |
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114 | std::cout << std::flush; |
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115 | |
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116 | float *bigarray = new float[dimAxes[0] * dimAxes[2]]; |
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117 | float *array = new float[dimAxes[2]]; |
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118 | long *specdim = new long[2]; |
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119 | specdim[0] = dimAxes[2]; specdim[1]=1; |
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120 | |
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121 | float median,sigma; |
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122 | int pos,frac; |
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123 | |
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124 | Image *spectrum = new Image(specdim); |
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125 | spectrum->saveParam(par); |
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126 | spectrum->pars().setBeamSize(2.); // only neighbouring channels correlated |
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127 | |
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128 | for(int y=0;y<dimAxes[1];y++){ |
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129 | |
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130 | std::cout << std::setw(4) << y << ": " << std::flush; |
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131 | |
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132 | fpixel[1] = lpixel[1] = y+1; |
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133 | |
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134 | status = 0; |
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135 | if( fits_open_file(&fptr,fname.c_str(),READONLY,&status) ){ |
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136 | duchampWarning("readAndSearch","Error opening file: "); |
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137 | fits_report_error(stderr, status); |
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138 | } |
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139 | status = 0; |
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140 | fits_read_subset(fptr, TFLOAT, fpixel, lpixel, inc, NULL, bigarray, &anynul, &status); |
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141 | if(status){ |
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142 | duchampError("readAndSearch","There was an error reading in the data array:"); |
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143 | fits_report_error(stderr, status); |
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144 | } |
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145 | status = 0; |
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146 | fits_close_file(fptr, &status); |
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147 | if (status){ |
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148 | duchampWarning("readAndSearch","Error closing file: "); |
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149 | fits_report_error(stderr, status); |
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150 | } |
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151 | |
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152 | for(int x=0;x<dimAxes[0];x++){ |
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153 | |
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154 | pos = y*dimAxes[0]+x; |
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155 | frac = 100*(pos+1)/(dimAxes[1]*dimAxes[0]); |
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156 | if(frac%2 == 0){ |
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157 | std::cout << "|"; |
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158 | printHash(frac/2); |
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159 | printSpace(50-frac/2); |
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160 | std::cout << "| " << std::setw(5) << numDetected; |
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161 | printBackSpace(58); |
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162 | std::cout << std::flush; |
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163 | } |
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164 | |
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165 | for(int z=0;z<dimAxes[2];z++) array[z] = bigarray[z*dimAxes[0] + x]; |
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166 | |
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167 | median = findMedian(array,dimAxes[2]); |
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168 | spectrum->clearDetectionList(); |
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169 | if(par.getFlagATrous()){ |
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170 | float *recon = new float[dimAxes[2]]; |
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171 | atrous1DReconstruct(dimAxes[2],array,recon,par); |
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172 | float *resid = new float[dimAxes[2]]; |
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173 | for(int i=0;i<dimAxes[2];i++) resid[i] = array[i] - recon[i]; |
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174 | sigma = findMADFM(recon,dimAxes[2])/correctionFactor; |
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175 | spectrum->saveArray(recon,dimAxes[2]); |
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176 | delete [] recon; |
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177 | delete [] resid; |
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178 | spectrum->removeMW(); // only works if flagMW is true |
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179 | spectrum->setStats(median,sigma,par.getCut()); |
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180 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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181 | spectrum->setMinSize(par.getMinChannels()); |
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182 | spectrum->spectrumDetect(); |
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183 | } |
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184 | else{ |
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185 | sigma = findMADFM(array,dimAxes[2])/correctionFactor; |
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186 | spectrum->saveArray(array,dimAxes[2]); |
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187 | spectrum->removeMW(); // only works if flagMW is true |
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188 | spectrum->setStats(median,sigma,par.getCut()); |
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189 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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190 | spectrum->setMinSize(par.getMinChannels()); |
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191 | spectrum->spectrumDetect(); |
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192 | } |
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193 | |
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194 | numDetected += spectrum->getNumObj(); |
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195 | for(int obj=0;obj<spectrum->getNumObj();obj++){ |
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196 | Detection *object = new Detection; |
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197 | *object = spectrum->getObject(obj); |
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198 | for(int pix=0;pix<object->getSize();pix++) { |
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199 | // Fix up coordinates of each pixel to match original array |
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200 | object->setZ(pix, object->getX(pix)); |
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201 | object->setX(pix, x); |
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202 | object->setY(pix, y); |
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203 | object->setF(pix, array[object->getZ(pix)]); |
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204 | // NB: set F to the original value, not the recon value. |
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205 | } |
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206 | object->setOffsets(par); |
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207 | object->calcParams(); |
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208 | mergeIntoList(*object,outputList,par); |
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209 | delete object; |
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210 | } |
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211 | |
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212 | |
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213 | } // end of loop over y |
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214 | |
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215 | printBackSpace(6); |
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216 | std::cout << std::flush; |
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217 | } // end of loop over x |
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218 | |
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219 | delete spectrum; |
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220 | delete [] bigarray; |
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221 | delete [] array; |
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222 | delete [] fpixel; |
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223 | delete [] lpixel; |
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224 | delete [] inc; |
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225 | delete [] dimAxes; |
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226 | delete [] specdim; |
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227 | |
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228 | return outputList; |
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229 | |
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230 | } |
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