[299] | 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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[3] | 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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[258] | 33 | #include <vector> |
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[80] | 34 | #include <time.h> |
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[393] | 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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[103] | 43 | |
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[3] | 44 | using std::endl; |
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| 45 | using std::setw; |
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| 46 | using std::setprecision; |
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[258] | 47 | using namespace PixelInfo; |
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[298] | 48 | using namespace Statistics; |
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[3] | 49 | |
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[378] | 50 | namespace duchamp |
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[20] | 51 | { |
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| 52 | |
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[378] | 53 | void Cube::outputDetectionsKarma(std::ostream &stream) |
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| 54 | { |
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[528] | 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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[378] | 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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[749] | 63 | stream << "# Duchamp Source Finder v."<< VERSION << endl; |
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| 64 | stream << "# Results for FITS file: " << fname << endl; |
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[378] | 65 | if(this->par.getFlagFDR()) |
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| 66 | stream<<"# FDR Significance = " << this->par.getAlpha() << endl; |
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| 67 | else |
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| 68 | stream<<"# Threshold = " << this->par.getCut() << endl; |
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| 69 | if(this->par.getFlagATrous()){ |
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| 70 | stream<<"# The a trous reconstruction method was used, with the following parameters." << endl; |
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[674] | 71 | stream<<"# Dimension = " << this->par.getReconDim() << endl; |
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| 72 | stream<<"# Threshold = " << this->par.getAtrousCut() << endl; |
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| 73 | stream<<"# Minimum Scale =" << this->par.getMinScale() << endl; |
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| 74 | stream<<"# Filter = " << this->par.getFilterName() << endl; |
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[156] | 75 | } |
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[431] | 76 | else if(this->par.getFlagSmooth()){ |
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| 77 | stream<<"# The data was smoothed prior to searching, with the following parameters." << endl; |
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| 78 | stream<<"# Smoothing type = " << this->par.getSmoothType() << endl; |
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| 79 | if(this->par.getSmoothType()=="spectral"){ |
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| 80 | stream << "# Hanning width = " << this->par.getHanningWidth() << endl; |
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| 81 | } |
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| 82 | else{ |
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| 83 | stream << "# Kernel Major axis = " << this->par.getKernMaj() << endl; |
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| 84 | if(this->par.getKernMin()>0) |
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| 85 | stream << "# Kernel Minor axis = " << this->par.getKernMin() << endl; |
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| 86 | else |
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| 87 | stream << "# Kernel Minor axis = " << this->par.getKernMaj() << endl; |
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| 88 | stream << "# Kernel Major axis = " << this->par.getKernPA() << endl; |
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| 89 | } |
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| 90 | } |
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[378] | 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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[509] | 94 | stream << "FONT lucidasans-12" << endl; |
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[431] | 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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[446] | 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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[623] | 104 | for(size_t i=0;i<vertexSet.size()/4;i++){ |
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[446] | 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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[378] | 115 | } |
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[446] | 116 | else if(this->par.getAnnotationType()=="circles"){ |
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[450] | 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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[446] | 120 | stream << "CIRCLE " |
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[450] | 121 | << obj->getRA() << " " |
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| 122 | << obj->getDec() << " " |
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[446] | 123 | << radius << "\n"; |
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| 124 | } |
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| 125 | |
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[431] | 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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[468] | 131 | |
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| 132 | delete [] pix; |
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| 133 | delete [] wld; |
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| 134 | |
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[378] | 135 | } |
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[20] | 136 | |
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[378] | 137 | void Cube::prepareOutputFile() |
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| 138 | { |
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[528] | 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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[3] | 142 | |
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[378] | 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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[749] | 147 | output<<"Results of the Duchamp source finder v."<<VERSION<<": "; |
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[378] | 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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[275] | 154 | |
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[378] | 155 | } |
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[275] | 156 | |
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[378] | 157 | void Cube::outputStats() |
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| 158 | { |
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[528] | 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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[275] | 166 | |
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[378] | 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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[385] | 172 | output<<"Detection threshold = " << this->Stats.getThreshold() |
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[378] | 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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[385] | 179 | output<<"\nNoise level = " << this->Stats.getMiddle() |
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[378] | 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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[385] | 195 | output << "\nNoise properties for the original cube are:"; |
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[378] | 196 | } |
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| 197 | |
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[275] | 198 | if(!this->par.getFlagUserThreshold()) |
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[385] | 199 | output<<"\nNoise level = " << this->Stats.getMiddle() |
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[461] | 200 | <<", Noise spread = " << this->Stats.getSpread(); |
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[275] | 201 | |
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[378] | 202 | if(this->par.getFlagGrowth()){ |
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| 203 | StatsContainer<float> growthStats = this->Stats; |
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[461] | 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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[378] | 208 | growthStats.setUseFDR(false); |
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[461] | 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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[378] | 212 | } |
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| 213 | |
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[422] | 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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[461] | 217 | output << "\n\nNot calculating full stats since threshold was provided directly.\n"; |
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[385] | 218 | |
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[378] | 219 | output<<"--------------------\n"; |
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| 220 | output.close(); |
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[298] | 221 | } |
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| 222 | |
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[378] | 223 | void Cube::outputDetectionList() |
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| 224 | { |
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[528] | 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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[275] | 230 | |
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[378] | 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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[275] | 238 | |
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[378] | 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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[363] | 243 | |
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[378] | 244 | if(this->objectList->size()>0){ |
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| 245 | this->setupColumns(); |
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[439] | 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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[440] | 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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[378] | 252 | } |
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| 253 | } |
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[363] | 254 | |
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[378] | 255 | output.close(); |
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[3] | 256 | } |
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[275] | 257 | |
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[418] | 258 | void Cube::prepareLogFile(int argc, char *argv[]) |
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| 259 | { |
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[528] | 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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[418] | 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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[749] | 270 | logfile << "New run of the Duchamp source finder v."<<VERSION<<": "; |
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[418] | 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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[659] | 283 | void Cube::logDetectionList(bool calcFluxes) |
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[378] | 284 | { |
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[528] | 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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[659] | 290 | /// @param[in] calcFluxes If true (the default), calculate the various flux parameters for each object. |
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[3] | 291 | |
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[378] | 292 | if(this->objectList->size()>0){ |
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[3] | 293 | |
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[378] | 294 | long left = this->par.getBorderLeft(); |
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| 295 | long bottom = this->par.getBorderBottom(); |
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[258] | 296 | |
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[378] | 297 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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[659] | 298 | if(calcFluxes) this->calcObjectFluxes(); |
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[378] | 299 | this->setupColumns(); |
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[440] | 300 | outputTableHeader(fout,this->fullCols,"log",this->head.isWCS()); |
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[258] | 301 | |
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[378] | 302 | if(this->par.getFlagBaseline()){ |
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| 303 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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| 304 | this->array[i] += this->baseline[i]; |
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| 305 | } |
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[258] | 306 | |
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[623] | 307 | for(size_t objCtr=0;objCtr<this->objectList->size();objCtr++){ |
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[577] | 308 | Detection obj = this->objectList->at(objCtr); |
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[570] | 309 | obj.setOffsets(par); |
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[378] | 310 | if(this->par.getFlagCubeTrimmed()){ |
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[570] | 311 | obj.addOffsets(left,bottom,0); |
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[378] | 312 | } |
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[659] | 313 | if(calcFluxes) obj.calcFluxes(this->array, this->axisDim); |
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[570] | 314 | obj.setID(objCtr+1); |
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| 315 | obj.printTableRow(fout,this->fullCols,"log"); |
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[378] | 316 | } |
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[348] | 317 | |
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[378] | 318 | if(this->par.getFlagBaseline()){ |
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| 319 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
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| 320 | this->array[i] -= this->baseline[i]; |
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[348] | 321 | } |
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[378] | 322 | fout.close(); |
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| 323 | |
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[348] | 324 | } |
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| 325 | |
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[3] | 326 | } |
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[258] | 327 | |
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[378] | 328 | void Cube::logDetection(Detection obj, int counter) |
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| 329 | { |
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[528] | 330 | /// @details |
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| 331 | /// A front-end to writing a detected object to the log file. |
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| 332 | /// Does not assume WCS is present. |
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| 333 | /// Corrects for changes to positions of pixels and removal of baselines. |
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| 334 | /// Designed to be used by searching routines before returning their final |
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| 335 | /// list. |
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| 336 | /// \param obj Detection object to be written : passed by value, as we want |
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| 337 | /// to potentially change positions etc, but not for the object in the |
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| 338 | /// calling function. |
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| 339 | /// \param counter The number to assign to the object : ideally its number |
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| 340 | /// in a list of some kind. |
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[3] | 341 | |
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[378] | 342 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
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| 343 | // Need to deal with possibility of trimmed array |
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| 344 | long left = this->par.getBorderLeft(); |
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| 345 | long right = this->par.getBorderRight(); |
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| 346 | long top = this->par.getBorderTop(); |
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| 347 | long bottom = this->par.getBorderBottom(); |
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| 348 | long *tempDim = new long[3]; |
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| 349 | tempDim[0] = (this->axisDim[0] + left + right); |
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| 350 | tempDim[1] = (this->axisDim[1] + bottom + top); |
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| 351 | tempDim[2] = this->axisDim[2]; |
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| 352 | long tempsize = tempDim[0] * tempDim[1] * tempDim[2]; |
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| 353 | float *temparray = new float[tempsize]; |
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| 354 | // for(int i=0;i<this->numPixels;i++){ // loop over this->array |
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| 355 | for(int z=0;z<tempDim[2];z++){ |
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| 356 | for(int y=0;y<tempDim[1];y++){ |
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| 357 | for(int x=0;x<tempDim[0];x++){ |
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[3] | 358 | |
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[378] | 359 | bool isDud = (x<left) || (x>=this->axisDim[0]+left) || |
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| 360 | (y<bottom) || (y>=this->axisDim[1]+bottom); |
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[258] | 361 | |
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[378] | 362 | int temppos = x + tempDim[0]*y + tempDim[1]*tempDim[0]*z; |
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[258] | 363 | |
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[378] | 364 | int pos = (x-left) + (y-bottom)*this->axisDim[0] + |
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| 365 | z*this->axisDim[0]*this->axisDim[1]; |
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[258] | 366 | |
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[378] | 367 | if(isDud) temparray[temppos] = this->par.getBlankPixVal(); |
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| 368 | else temparray[temppos] = this->array[pos]; |
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[258] | 369 | |
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[378] | 370 | if(this->par.getFlagBaseline() && !isDud) |
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| 371 | temparray[temppos] += this->baseline[pos]; |
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[258] | 372 | |
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[378] | 373 | } |
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[258] | 374 | } |
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[3] | 375 | } |
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[378] | 376 | |
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| 377 | if(this->par.getFlagCubeTrimmed()){ |
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[570] | 378 | obj.addOffsets(left,bottom,0); |
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[378] | 379 | } |
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| 380 | obj.calcFluxes(temparray, this->axisDim); |
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[441] | 381 | obj.printTableRow(fout,this->fullCols,"log"); |
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[378] | 382 | delete [] temparray; |
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| 383 | delete [] tempDim; |
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| 384 | fout.close(); |
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[3] | 385 | } |
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[258] | 386 | |
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[783] | 387 | |
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| 388 | void Cube::writeSpectralData() |
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| 389 | { |
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| 390 | /// @details |
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| 391 | /// A function to write, in ascii form, the spectra of each |
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| 392 | /// detected object to a file. The file consists of a column for |
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| 393 | /// the spectral coordinates, and one column for each object |
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| 394 | /// showing the flux at that spectral position. The units are the |
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| 395 | /// same as those shown in the graphical output. The filename is |
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| 396 | /// given by the Param::spectraTextFile parameter in the Cube::par |
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| 397 | /// parameter set. |
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| 398 | |
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| 399 | const int zdim = this->axisDim[2]; |
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| 400 | const int numObj = this->objectList->size(); |
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| 401 | float *specxOut = new float[zdim]; |
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| 402 | float *spectra = new float[numObj*zdim]; |
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| 403 | |
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| 404 | for(int obj=0; obj<numObj; obj++){ |
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| 405 | float *temp = new float[zdim]; |
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| 406 | float *specx = new float[zdim]; |
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| 407 | float *recon = new float[zdim]; |
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| 408 | float *base = new float[zdim]; |
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| 409 | this->getSpectralArrays(obj, specx, temp, recon, base); |
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| 410 | for(int z=0;z<zdim;z++) spectra[obj*zdim+z] = temp[z]; |
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| 411 | if(obj==0) for(int z=0;z<zdim;z++) specxOut[z] = specx[z]; |
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| 412 | delete [] specx; |
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| 413 | delete [] recon; |
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| 414 | delete [] base; |
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| 415 | delete [] temp; |
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| 416 | } |
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| 417 | |
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| 418 | std::ofstream fspec(this->par.getSpectraTextFile().c_str()); |
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| 419 | fspec.setf(std::ios::fixed); |
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| 420 | |
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| 421 | for(int z=0;z<zdim;z++){ |
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| 422 | |
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| 423 | fspec << std::setprecision(8); |
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| 424 | fspec << specxOut[z] << " "; |
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| 425 | for(int obj=0;obj<numObj; obj++) { |
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| 426 | fspec << spectra[obj*zdim+z] << " "; |
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| 427 | } |
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| 428 | fspec << "\n"; |
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| 429 | |
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| 430 | } |
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| 431 | fspec.close(); |
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| 432 | |
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| 433 | delete [] spectra; |
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| 434 | delete [] specxOut; |
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| 435 | |
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| 436 | } |
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| 437 | //-------------------------------------------------------------------- |
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| 438 | |
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| 439 | |
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[3] | 440 | } |
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