1 | // ----------------------------------------------------------------------- |
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2 | // detectionIO.cc: Screen and File output of the detected objects. |
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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 <sstream> |
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30 | #include <fstream> |
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31 | #include <iomanip> |
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32 | #include <string> |
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33 | #include <vector> |
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34 | #include <time.h> |
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35 | #include <duchamp/param.hh> |
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36 | #include <duchamp/fitsHeader.hh> |
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37 | #include <duchamp/Cubes/cubes.hh> |
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38 | #include <duchamp/PixelMap/Object3D.hh> |
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39 | #include <duchamp/Detection/detection.hh> |
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40 | #include <duchamp/Detection/columns.hh> |
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41 | #include <duchamp/Utils/utils.hh> |
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42 | #include <duchamp/Utils/Statistics.hh> |
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43 | |
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44 | using std::endl; |
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45 | using std::setw; |
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46 | using std::setprecision; |
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47 | using namespace PixelInfo; |
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48 | using namespace Statistics; |
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49 | |
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50 | namespace duchamp |
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51 | { |
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52 | |
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53 | void Cube::outputDetectionsKarma(std::ostream &stream) |
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54 | { |
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55 | /// @details |
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56 | /// Prints to a stream (provided) the list of detected objects in the cube |
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57 | /// in the format of an annotation file for the Karma suite of programs. |
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58 | /// Annotation file draws a box enclosing the detection, and writes the |
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59 | /// ID number of the detection to the right of the box. |
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60 | |
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61 | std::string fname = this->par.getImageFile(); |
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62 | if(this->par.getFlagSubsection()) fname+=this->par.getSubsection(); |
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63 | stream << "# Duchamp Source Finder results for FITS file: " << fname << endl; |
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64 | if(this->par.getFlagFDR()) |
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65 | stream<<"# FDR Significance = " << this->par.getAlpha() << endl; |
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66 | else |
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67 | stream<<"# Threshold = " << this->par.getCut() << endl; |
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68 | if(this->par.getFlagATrous()){ |
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69 | stream<<"# The a trous reconstruction method was used, with the following parameters." << endl; |
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70 | stream<<"# ATrous Dimension = " << this->par.getReconDim() << endl; |
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71 | stream<<"# ATrous Threshold = " << this->par.getAtrousCut() << endl; |
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72 | stream<<"# ATrous Minimum Scale =" << this->par.getMinScale() << endl; |
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73 | stream<<"# ATrous Filter = " << this->par.getFilterName() << endl; |
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74 | } |
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75 | else if(this->par.getFlagSmooth()){ |
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76 | stream<<"# The data was smoothed prior to searching, with the following parameters." << endl; |
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77 | stream<<"# Smoothing type = " << this->par.getSmoothType() << endl; |
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78 | if(this->par.getSmoothType()=="spectral"){ |
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79 | stream << "# Hanning width = " << this->par.getHanningWidth() << endl; |
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80 | } |
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81 | else{ |
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82 | stream << "# Kernel Major axis = " << this->par.getKernMaj() << endl; |
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83 | if(this->par.getKernMin()>0) |
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84 | stream << "# Kernel Minor axis = " << this->par.getKernMin() << endl; |
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85 | else |
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86 | stream << "# Kernel Minor axis = " << this->par.getKernMaj() << endl; |
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87 | stream << "# Kernel Major axis = " << this->par.getKernPA() << endl; |
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88 | } |
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89 | } |
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90 | else stream << "# No ATrous reconstruction done." << endl; |
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91 | stream << "#\n"; |
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92 | stream << "COLOR RED" << endl; |
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93 | stream << "COORD W" << endl; |
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94 | stream << "FONT lucidasans-12" << endl; |
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95 | stream << std::setprecision(6); |
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96 | stream.setf(std::ios::fixed); |
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97 | double *pix = new double[3]; |
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98 | double *wld = new double[3]; |
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99 | std::vector<Detection>::iterator obj; |
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100 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
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101 | |
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102 | if(this->par.getAnnotationType()=="borders"){ |
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103 | std::vector<int> vertexSet = obj->getVertexSet(); |
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104 | for(int i=0;i<vertexSet.size()/4;i++){ |
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105 | pix[0] = vertexSet[i*4]-0.5; |
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106 | pix[1] = vertexSet[i*4+1]-0.5; |
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107 | pix[2] = obj->getZcentre(); |
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108 | this->head.pixToWCS(pix,wld); |
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109 | stream << "LINE " << wld[0] << " " << wld[1]; |
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110 | pix[0] = vertexSet[i*4+2]-0.5; |
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111 | pix[1] = vertexSet[i*4+3]-0.5; |
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112 | this->head.pixToWCS(pix,wld); |
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113 | stream << " " << wld[0] << " " << wld[1] << "\n"; |
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114 | } |
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115 | } |
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116 | else if(this->par.getAnnotationType()=="circles"){ |
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117 | float radius = obj->getRAWidth()/120.; |
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118 | if(obj->getDecWidth()/120.>radius) |
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119 | radius = obj->getDecWidth()/120.; |
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120 | stream << "CIRCLE " |
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121 | << obj->getRA() << " " |
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122 | << obj->getDec() << " " |
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123 | << radius << "\n"; |
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124 | } |
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125 | |
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126 | stream << "TEXT " |
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127 | << obj->getRA() << " " |
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128 | << obj->getDec() << " " |
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129 | << obj->getID() << "\n\n"; |
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130 | } |
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131 | |
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132 | delete [] pix; |
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133 | delete [] wld; |
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134 | |
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135 | } |
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136 | |
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137 | void Cube::prepareOutputFile() |
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138 | { |
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139 | /// @details |
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140 | /// A function to write the paramters, time of execution, and |
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141 | /// statistical information to the output file. |
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142 | |
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143 | std::string outfile; |
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144 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
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145 | else outfile = this->par.getOutFile(); |
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146 | std::ofstream output(outfile.c_str()); |
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147 | output<<"Results of the Duchamp source finder: "; |
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148 | time_t now = time(NULL); |
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149 | output << asctime( localtime(&now) ); |
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150 | this->showParam(output); |
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151 | output<<"--------------------\n"; |
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152 | output.close(); |
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153 | this->outputStats(); |
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154 | |
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155 | } |
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156 | |
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157 | void Cube::outputStats() |
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158 | { |
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159 | /// @details |
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160 | /// A function to write the statistical information to the output |
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161 | /// file. This writes the threshold, its equivalent S/N ratio, and |
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162 | /// the noise level and spread. |
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163 | /// |
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164 | /// If smoothing has been done, the noise level & spread for the |
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165 | /// original array are calculated and printed as well. |
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166 | |
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167 | std::string outfile; |
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168 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
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169 | else outfile = this->par.getOutFile(); |
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170 | std::ofstream output(outfile.c_str(),std::ios::app); |
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171 | output<<"Summary of statistics:\n"; |
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172 | output<<"Detection threshold = " << this->Stats.getThreshold() |
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173 | <<" " << this->head.getFluxUnits(); |
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174 | if(this->par.getFlagFDR()) |
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175 | output<<" (or S/N=" << this->Stats.getThresholdSNR()<<")"; |
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176 | if(this->par.getFlagSmooth()){ |
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177 | output << " in smoothed cube."; |
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178 | if(!this->par.getFlagUserThreshold()) |
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179 | output<<"\nNoise level = " << this->Stats.getMiddle() |
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180 | <<", Noise spread = " << this->Stats.getSpread() |
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181 | <<" in smoothed cube."; |
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182 | |
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183 | // calculate the stats for the original array, so that we can |
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184 | // quote S/N values correctly. |
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185 | this->par.setFlagSmooth(false); |
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186 | bool verb=this->par.isVerbose(); |
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187 | bool fdrflag=this->par.getFlagFDR(); |
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188 | this->par.setVerbosity(false); |
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189 | this->par.setFlagFDR(false); |
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190 | this->setCubeStats(); |
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191 | this->par.setVerbosity(verb); |
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192 | this->par.setFlagFDR(fdrflag); |
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193 | this->par.setFlagSmooth(true); |
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194 | |
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195 | output << "\nNoise properties for the original cube are:"; |
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196 | } |
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197 | |
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198 | if(!this->par.getFlagUserThreshold()) |
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199 | output<<"\nNoise level = " << this->Stats.getMiddle() |
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200 | <<", Noise spread = " << this->Stats.getSpread(); |
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201 | |
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202 | if(this->par.getFlagGrowth()){ |
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203 | StatsContainer<float> growthStats = this->Stats; |
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204 | if(this->par.getFlagUserGrowthThreshold()) |
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205 | growthStats.setThreshold(this->par.getGrowthThreshold()); |
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206 | else |
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207 | growthStats.setThresholdSNR(this->par.getGrowthCut()); |
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208 | growthStats.setUseFDR(false); |
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209 | output<<"\nDetections grown down to threshold of " |
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210 | << growthStats.getThreshold() << " " |
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211 | << this->head.getFluxUnits(); |
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212 | } |
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213 | |
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214 | if(!this->par.getFlagUserThreshold()) |
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215 | output << "\nFull stats:\n" << this->Stats; |
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216 | else |
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217 | output << "\n\nNot calculating full stats since threshold was provided directly.\n"; |
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218 | |
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219 | output<<"--------------------\n"; |
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220 | output.close(); |
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221 | } |
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222 | |
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223 | void Cube::outputDetectionList() |
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224 | { |
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225 | /// @details |
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226 | /// A front-end to writing the full list of detected objects to a results |
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227 | /// file and to cout. |
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228 | /// Leaves the testing of whether the WCS parameters for each object |
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229 | /// have been calculated to the printing function. |
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230 | |
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231 | std::string outfile; |
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232 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
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233 | else outfile = this->par.getOutFile(); |
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234 | std::ofstream output(outfile.c_str(),std::ios::app); |
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235 | output<<"Total number of detections = "<<this->objectList->size()<<endl; |
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236 | output<<"--------------------\n"; |
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237 | output.close(); |
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238 | |
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239 | if(this->par.getFlagSeparateHeader()) |
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240 | output.open(this->par.getOutFile().c_str()); |
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241 | else |
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242 | output.open(this->par.getOutFile().c_str(),std::ios::app); |
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243 | |
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244 | if(this->objectList->size()>0){ |
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245 | this->setupColumns(); |
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246 | outputTableHeader(output,this->fullCols,"file",this->head.isWCS()); |
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247 | outputTableHeader(std::cout,this->fullCols,"screen",this->head.isWCS()); |
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248 | std::vector<Detection>::iterator obj; |
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249 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
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250 | obj->printTableRow(output,this->fullCols,"file"); |
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251 | obj->printTableRow(std::cout,this->fullCols,"screen"); |
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252 | } |
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253 | } |
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254 | |
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255 | output.close(); |
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256 | } |
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257 | |
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258 | void Cube::prepareLogFile(int argc, char *argv[]) |
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259 | { |
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260 | /// @details |
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261 | /// Opens the log file so that it can be written to, and writes |
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262 | /// the parameter summary as well as the time of execution to the |
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263 | /// file. |
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264 | /// |
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265 | /// It also writes the command-line statement, hence the need for |
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266 | /// argv and argc. |
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267 | |
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268 | // Open the logfile and write the time on the first line |
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269 | std::ofstream logfile(this->par.getLogFile().c_str()); |
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270 | logfile << "New run of the Duchamp sourcefinder: "; |
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271 | time_t now = time(NULL); |
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272 | logfile << asctime( localtime(&now) ); |
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273 | // Write out the command-line statement |
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274 | logfile << "Executing statement : "; |
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275 | for(int i=0;i<argc;i++) logfile << argv[i] << " "; |
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276 | logfile << std::endl; |
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277 | logfile << this->par; |
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278 | logfile.close(); |
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279 | |
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280 | } |
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281 | |
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282 | |
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283 | void Cube::logDetectionList() |
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284 | { |
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285 | /// @details |
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286 | /// A front-end to writing a list of detected objects to the log file. |
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287 | /// Does not assume WCS is present. |
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288 | /// Designed to be used by searching routines before returning their |
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289 | /// final list. |
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290 | |
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291 | if(this->objectList->size()>0){ |
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292 | |
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293 | long left = this->par.getBorderLeft(); |
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294 | long bottom = this->par.getBorderBottom(); |
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295 | |
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296 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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297 | this->calcObjectFluxes(); |
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298 | this->setupColumns(); |
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299 | outputTableHeader(fout,this->fullCols,"log",this->head.isWCS()); |
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300 | |
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301 | if(this->par.getFlagBaseline()){ |
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302 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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303 | this->array[i] += this->baseline[i]; |
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304 | } |
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305 | |
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306 | for(int objCtr=0;objCtr<this->objectList->size();objCtr++){ |
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307 | Detection *obj = new Detection; |
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308 | *obj = objectList->at(objCtr); |
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309 | obj->setOffsets(par); |
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310 | if(this->par.getFlagCubeTrimmed()){ |
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311 | obj->pixels().addOffsets(left,bottom,0); |
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312 | } |
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313 | obj->calcFluxes(this->array, this->axisDim); |
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314 | obj->setID(objCtr+1); |
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315 | obj->printTableRow(fout,this->fullCols,"log"); |
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316 | delete obj; |
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317 | } |
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318 | |
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319 | if(this->par.getFlagBaseline()){ |
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320 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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321 | this->array[i] -= this->baseline[i]; |
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322 | } |
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323 | fout.close(); |
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324 | |
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325 | } |
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326 | |
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327 | } |
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328 | |
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329 | void Cube::logDetection(Detection obj, int counter) |
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330 | { |
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331 | /// @details |
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332 | /// A front-end to writing a detected object to the log file. |
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333 | /// Does not assume WCS is present. |
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334 | /// Corrects for changes to positions of pixels and removal of baselines. |
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335 | /// Designed to be used by searching routines before returning their final |
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336 | /// list. |
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337 | /// \param obj Detection object to be written : passed by value, as we want |
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338 | /// to potentially change positions etc, but not for the object in the |
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339 | /// calling function. |
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340 | /// \param counter The number to assign to the object : ideally its number |
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341 | /// in a list of some kind. |
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342 | |
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343 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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344 | // Need to deal with possibility of trimmed array |
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345 | long left = this->par.getBorderLeft(); |
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346 | long right = this->par.getBorderRight(); |
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347 | long top = this->par.getBorderTop(); |
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348 | long bottom = this->par.getBorderBottom(); |
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349 | long *tempDim = new long[3]; |
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350 | tempDim[0] = (this->axisDim[0] + left + right); |
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351 | tempDim[1] = (this->axisDim[1] + bottom + top); |
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352 | tempDim[2] = this->axisDim[2]; |
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353 | long tempsize = tempDim[0] * tempDim[1] * tempDim[2]; |
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354 | float *temparray = new float[tempsize]; |
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355 | // for(int i=0;i<this->numPixels;i++){ // loop over this->array |
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356 | for(int z=0;z<tempDim[2];z++){ |
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357 | for(int y=0;y<tempDim[1];y++){ |
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358 | for(int x=0;x<tempDim[0];x++){ |
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359 | |
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360 | bool isDud = (x<left) || (x>=this->axisDim[0]+left) || |
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361 | (y<bottom) || (y>=this->axisDim[1]+bottom); |
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362 | |
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363 | int temppos = x + tempDim[0]*y + tempDim[1]*tempDim[0]*z; |
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364 | |
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365 | int pos = (x-left) + (y-bottom)*this->axisDim[0] + |
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366 | z*this->axisDim[0]*this->axisDim[1]; |
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367 | |
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368 | if(isDud) temparray[temppos] = this->par.getBlankPixVal(); |
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369 | else temparray[temppos] = this->array[pos]; |
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370 | |
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371 | if(this->par.getFlagBaseline() && !isDud) |
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372 | temparray[temppos] += this->baseline[pos]; |
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373 | |
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374 | } |
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375 | } |
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376 | } |
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377 | |
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378 | if(this->par.getFlagCubeTrimmed()){ |
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379 | obj.pixels().addOffsets(left,bottom,0); |
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380 | } |
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381 | obj.calcFluxes(temparray, this->axisDim); |
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382 | obj.printTableRow(fout,this->fullCols,"log"); |
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383 | delete [] temparray; |
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384 | delete [] tempDim; |
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385 | fout.close(); |
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386 | } |
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387 | |
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388 | } |
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