[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 | using namespace Column; |
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| 54 | |
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| 55 | void Cube::outputDetectionsKarma(std::ostream &stream) |
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| 56 | { |
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| 57 | /** |
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| 58 | * Prints to a stream (provided) the list of detected objects in the cube |
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| 59 | * in the format of an annotation file for the Karma suite of programs. |
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| 60 | * Annotation file draws a box enclosing the detection, and writes the |
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| 61 | * ID number of the detection to the right of the box. |
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| 62 | */ |
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| 63 | |
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| 64 | std::string fname = this->par.getImageFile(); |
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| 65 | if(this->par.getFlagSubsection()) fname+=this->par.getSubsection(); |
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| 66 | stream << "# Duchamp Source Finder results for FITS file: " << fname << endl; |
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| 67 | if(this->par.getFlagFDR()) |
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| 68 | stream<<"# FDR Significance = " << this->par.getAlpha() << endl; |
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| 69 | else |
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| 70 | stream<<"# Threshold = " << this->par.getCut() << endl; |
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| 71 | if(this->par.getFlagATrous()){ |
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| 72 | stream<<"# The a trous reconstruction method was used, with the following parameters." << endl; |
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| 73 | stream<<"# ATrous Dimension = " << this->par.getReconDim() << endl; |
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| 74 | stream<<"# ATrous Threshold = " << this->par.getAtrousCut() << endl; |
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| 75 | stream<<"# ATrous Minimum Scale =" << this->par.getMinScale() << endl; |
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| 76 | stream<<"# ATrous Filter = " << this->par.getFilterName() << endl; |
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[156] | 77 | } |
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[378] | 78 | else stream << "# No ATrous reconstruction done." << endl; |
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| 79 | stream << "#\n"; |
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| 80 | stream << "COLOR RED" << endl; |
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| 81 | stream << "COORD W" << endl; |
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| 82 | for(int i=0;i<this->objectList->size();i++){ |
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| 83 | if(this->head.isWCS()){ |
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| 84 | float radius = this->objectList->at(i).getRAWidth()/120.; |
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| 85 | if(this->objectList->at(i).getDecWidth()/120.>radius) |
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| 86 | radius = this->objectList->at(i).getDecWidth()/120.; |
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| 87 | stream << "CIRCLE " |
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| 88 | << this->objectList->at(i).getRA() << " " |
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| 89 | << this->objectList->at(i).getDec() << " " |
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| 90 | << radius << endl; |
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| 91 | stream << "TEXT " |
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| 92 | << this->objectList->at(i).getRA() << " " |
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| 93 | << this->objectList->at(i).getDec() << " " |
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| 94 | << this->objectList->at(i).getID() << endl; |
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| 95 | } |
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| 96 | else{ |
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| 97 | float radius = this->objectList->at(i).getXmax() - |
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| 98 | this->objectList->at(i).getXmin() + 1; |
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| 99 | if(this->objectList->at(i).getYmax()-this->objectList->at(i).getYmin() + 1 |
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| 100 | > radius) |
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| 101 | radius = this->objectList->at(i).getYmax() - |
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| 102 | this->objectList->at(i).getYmin() + 1; |
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| 103 | stream << "CIRCLE " |
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| 104 | << this->objectList->at(i).getXcentre() << " " |
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| 105 | << this->objectList->at(i).getYcentre() << " " |
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| 106 | << radius << endl; |
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| 107 | stream << "TEXT " |
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| 108 | << this->objectList->at(i).getXcentre() << " " |
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| 109 | << this->objectList->at(i).getYcentre() << " " |
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| 110 | << this->objectList->at(i).getID() << endl; |
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| 111 | } |
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| 112 | } |
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[20] | 113 | |
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[378] | 114 | } |
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[20] | 115 | |
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[378] | 116 | std::string fixUnitsVOT(std::string oldstring) |
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| 117 | { |
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| 118 | /** Fix a string containing units to make it acceptable for a VOTable. |
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| 119 | * |
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| 120 | * This function makes the provided units string acceptable |
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| 121 | * according to the standard found at |
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| 122 | * http://vizier.u-strasbg.fr/doc/catstd-3.2.htx |
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| 123 | * This should then be able to convert the units used in the text |
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| 124 | * table to units suitable for putting in a VOTable. |
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| 125 | * |
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| 126 | * Specifically, it removes any square brackets [] from the |
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| 127 | * start/end of the string, and replaces blank spaces (representing |
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| 128 | * multiplication) with a '.' (full stop). |
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| 129 | */ |
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[234] | 130 | |
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[378] | 131 | std::string newstring; |
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| 132 | for(int i=0;i<oldstring.size();i++){ |
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| 133 | if((oldstring[i]!='[')&&(oldstring[i]!=']')){ |
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| 134 | if(oldstring[i]==' ') newstring += '.'; |
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| 135 | else newstring += oldstring[i]; |
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| 136 | } |
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[234] | 137 | } |
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[378] | 138 | return newstring; |
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[234] | 139 | } |
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| 140 | |
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[378] | 141 | void Cube::outputDetectionsVOTable(std::ostream &stream) |
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| 142 | { |
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| 143 | /** |
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| 144 | * Prints to a stream (provided) the list of detected objects in the cube |
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| 145 | * in a VOTable format. |
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| 146 | * Uses WCS information and assumes WCS parameters have been calculated for each |
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| 147 | * detected object. |
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| 148 | * If they have not (given by the isWCS() function), then those objects are not written... |
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| 149 | */ |
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[3] | 150 | |
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[378] | 151 | // Set up Column definitions here |
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| 152 | std::vector<Col> localCol; |
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| 153 | std::string posUCD[4]; |
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| 154 | localCol.push_back(this->fullCols[NUM]); // 0 = objID |
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| 155 | localCol.push_back(this->fullCols[NAME]); // 1 = name |
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| 156 | localCol.push_back(this->fullCols[RA]); // 2 = ra |
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| 157 | if(makelower(localCol[2].getName())=="ra"){ |
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| 158 | posUCD[0] = "pos.eq.ra;meta.main"; |
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| 159 | posUCD[2] = "phys.angSize;pos.eq.ra"; |
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| 160 | } |
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| 161 | else{ |
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| 162 | posUCD[0] = "pos.galactic.lat;meta.main"; |
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| 163 | posUCD[2] = "phys.angSize;pos.galactic.lat"; |
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| 164 | } |
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| 165 | localCol.push_back(this->fullCols[DEC]); // 3 = dec |
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| 166 | if(makelower(localCol[2].getName())=="dec"){ |
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| 167 | posUCD[1] = "pos.eq.dec;meta.main"; |
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| 168 | posUCD[3] = "phys.angSize;pos.eq.dec"; |
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| 169 | } |
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| 170 | else{ |
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| 171 | posUCD[1] = "pos.galactic.lon;meta.main"; |
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| 172 | posUCD[3] = "phys.angSize;pos.galactic.lon"; |
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| 173 | } |
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| 174 | localCol.push_back(this->fullCols[WRA]); // 4 = w_ra |
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| 175 | localCol.push_back(this->fullCols[WDEC]); // 5 = w_dec |
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| 176 | localCol.push_back(this->fullCols[VEL]); // 6 = vel |
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| 177 | localCol.push_back(this->fullCols[WVEL]); // 7 = w_vel |
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| 178 | if(this->head.isSpecOK()) |
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| 179 | localCol.push_back(this->fullCols[FINT]); // 8 = f_int |
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| 180 | else |
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| 181 | localCol.push_back(this->fullCols[FTOT]); // 8 = f_tot |
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| 182 | localCol.push_back(this->fullCols[FPEAK]); // 9 = f_peak |
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| 183 | localCol.push_back(this->fullCols[FLAG]); // 10 = flag |
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| 184 | localCol.push_back(this->fullCols[XCENT]); // 11 = x_cent |
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| 185 | localCol.push_back(this->fullCols[YCENT]); // 12 = y_cent |
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| 186 | localCol.push_back(this->fullCols[ZCENT]); // 13 = z_cent |
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| 187 | localCol.push_back(this->fullCols[XAV]); // 14 = x_av |
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| 188 | localCol.push_back(this->fullCols[YAV]); // 15 = y_av |
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| 189 | localCol.push_back(this->fullCols[ZAV]); // 16 = z_av |
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| 190 | localCol.push_back(this->fullCols[XPEAK]); // 17 = x_peak |
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| 191 | localCol.push_back(this->fullCols[YPEAK]); // 18 = y_peak |
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| 192 | localCol.push_back(this->fullCols[ZPEAK]); // 19 = z_peak |
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[103] | 193 | |
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[378] | 194 | stream<<"<?xml version=\"1.0\"?>\n"; |
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| 195 | stream<<"<VOTABLE version=\"1.1\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n"; |
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| 196 | stream<<" xsi:noNamespaceSchemaLocation=\"http://www.ivoa.net/xml/VOTable/VOTable/v1.1\">\n"; |
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[3] | 197 | |
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[378] | 198 | stream<<" <COOSYS ID=\"J2000\" equinox=\"J2000.\" epoch=\"J2000.\" system=\"eq_FK5\"/>\n"; |
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| 199 | stream<<" <RESOURCE name=\"Duchamp Output\">\n"; |
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| 200 | stream<<" <TABLE name=\"Detections\">\n"; |
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| 201 | stream<<" <DESCRIPTION>Detected sources and parameters from running the Duchamp source finder.</DESCRIPTION>\n"; |
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[3] | 202 | |
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[378] | 203 | // PARAM section -- parts that are not entry-specific ie. apply to whole dataset |
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| 204 | std::string fname = this->par.getImageFile(); |
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| 205 | if(this->par.getFlagSubsection()) fname+=this->par.getSubsection(); |
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| 206 | stream<<" <PARAM name=\"FITS file\" datatype=\"char\" ucd=\"meta.file;meta.fits\" value=\"" |
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| 207 | << fname << "\" arraysize=\""<<fname.size()<<"\"/>\n"; |
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| 208 | if(this->par.getFlagFDR()) |
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| 209 | stream<<" <PARAM name=\"FDR Significance\" datatype=\"float\" ucd=\"stat.param\" value=\"" |
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| 210 | << this->par.getAlpha() << "\"/>\n"; |
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| 211 | else |
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| 212 | stream<<" <PARAM name=\"Threshold\" datatype=\"float\" ucd=\"stat.snr\" value=\"" |
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| 213 | << this->par.getCut() << "\"/>\n"; |
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| 214 | if(this->par.getFlagATrous()){ |
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| 215 | std::string note = "The a trous reconstruction method was used, with the following parameters."; |
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| 216 | stream<<" <PARAM name=\"ATrous note\" datatype=\"char\" ucd=\"meta.note\" value=\"" |
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[277] | 217 | <<note << "\" arraysize=\"" << note.size() << "\"/>\n"; |
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[378] | 218 | stream<<" <PARAM name=\"ATrous Dimension\" datatype=\"int\" ucd=\"meta.code;stat\" value=\"" |
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| 219 | << this->par.getReconDim() << "\"/>\n"; |
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| 220 | stream<<" <PARAM name=\"ATrous Threshold\" datatype=\"float\" ucd=\"stat.snr\" value=\"" |
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| 221 | << this->par.getAtrousCut() << "\"/>\n"; |
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| 222 | stream<<" <PARAM name=\"ATrous Minimum Scale\" datatype=\"int\" ucd=\"stat.param\" value=\"" |
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| 223 | << this->par.getMinScale() << "\"/>\n"; |
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| 224 | stream<<" <PARAM name=\"ATrous Filter\" datatype=\"char\" ucd=\"meta.code;stat\" value=\"" |
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| 225 | << this->par.getFilterName() << "\" arraysize=\"" << this->par.getFilterName().size() << "\"/>\n"; |
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[277] | 226 | } |
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[378] | 227 | if(this->par.getFlagSmooth()){ |
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| 228 | if(this->par.getSmoothType()=="spectral"){ |
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| 229 | std::string note = "The cube was smoothed spectrally with a Hanning filter, with the following parameters."; |
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| 230 | stream<<" <PARAM name=\"Smoothing note\" datatype=\"char\" ucd=\"meta.note\" value=\"" |
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| 231 | <<note << "\" arraysize=\"" << note.size() << "\"/>\n"; |
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| 232 | stream<<" <PARAM name=\"Hanning filter width\" datatype=\"int\" ucd=\"meta.code;stat\" value=\"" |
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| 233 | << this->par.getHanningWidth() << "\"/>\n"; |
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| 234 | } |
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| 235 | else if(this->par.getSmoothType()=="spatial"){ |
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| 236 | std::string note = "The cube was smoothed spatially with a Gaussian kernel, with the following parameters."; |
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| 237 | stream<<" <PARAM name=\"Smoothing note\" datatype=\"char\" ucd=\"meta.note\" value=\"" |
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| 238 | <<note << "\" arraysize=\"" << note.size() << "\"/>\n"; |
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| 239 | stream<<" <PARAM name=\"Gaussian kernel major-axis FWHM\" datatype=\"int\" ucd=\"meta.code;stat\" value=\"" |
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| 240 | << this->par.getKernMaj() << "\"/>\n"; |
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| 241 | stream<<" <PARAM name=\"Gaussian kernel minor-axis FWHM\" datatype=\"int\" ucd=\"meta.code;stat\" value=\"" |
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| 242 | << this->par.getKernMin() << "\"/>\n"; |
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| 243 | stream<<" <PARAM name=\"Gaussian kernel position angle\" datatype=\"int\" ucd=\"meta.code;stat\" value=\"" |
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| 244 | << this->par.getKernPA() << "\"/>\n"; |
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| 245 | } |
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| 246 | } |
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| 247 | // FIELD section -- names, titles and info for each column. |
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| 248 | stream<<" <FIELD name=\"ID\" ID=\"col01\" ucd=\"meta.id\" datatype=\"int\" width=\"" |
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| 249 | <<localCol[0].getWidth()<<"\" unit=\"--\"/>\n"; |
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| 250 | stream<<" <FIELD name=\"Name\" ID=\"col02\" ucd=\"meta.id;meta.main\" datatype=\"char\" arraysize=\"" |
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| 251 | <<localCol[1].getWidth()<<"\" unit=\"--\"/>\n"; |
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| 252 | stream<<" <FIELD name=\""<<localCol[2].getName()<<"\" ID=\"col03\" ucd=\"" |
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| 253 | <<posUCD[0]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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| 254 | <<localCol[2].getWidth()<<"\" precision=\""<<prec[prPOS]<<"\" unit=\"deg\"/>\n"; |
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| 255 | stream<<" <FIELD name=\""<<localCol[3].getName()<<"\" ID=\"col04\" ucd=\"" |
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| 256 | <<posUCD[1]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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| 257 | <<localCol[3].getWidth()<<"\" precision=\""<<prec[prPOS]<<"\" unit=\"deg\"/>\n"; |
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| 258 | stream<<" <FIELD name=\""<<localCol[4].getName()<<"\" ID=\"col05\" ucd=\"" |
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| 259 | <<posUCD[2]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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| 260 | <<localCol[4].getWidth()<<"\" precision=\""<<prec[prWPOS]<<"\" unit=\"" |
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| 261 | <<fixUnitsVOT(localCol[4].getUnits())<<"\"/>\n"; |
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| 262 | stream<<" <FIELD name=\""<<localCol[5].getName()<<"\" ID=\"col06\" ucd=\"" |
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| 263 | <<posUCD[2]<<"\" ref=\"J2000\" datatype=\"float\" width=\"" |
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| 264 | <<localCol[5].getWidth()<<"\" precision=\""<<prec[prWPOS]<<"\" unit=\"" |
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| 265 | <<fixUnitsVOT(localCol[5].getUnits())<<"\"/>\n"; |
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| 266 | stream<<" <FIELD name=\"Vel\" ID=\"col07\" ucd=\"phys.veloc;src.dopplerVeloc\" datatype=\"float\" width=\"" |
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| 267 | <<localCol[6].getWidth()<<"\" precision=\""<<prec[prVEL]<<"\" unit=\"" |
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| 268 | <<fixUnitsVOT(localCol[6].getUnits())<<"\"/>\n"; |
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| 269 | stream<<" <FIELD name=\"w_Vel\" ID=\"col08\" ucd=\"phys.veloc;src.dopplerVeloc;spect.line.width\"" |
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| 270 | <<" datatype=\"float\" width=\""<<localCol[7].getWidth()<<"\" precision=\"" |
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| 271 | <<prec[prVEL]<<"\" unit=\""<<fixUnitsVOT(localCol[7].getUnits())<<"\"/>\n"; |
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| 272 | if(this->head.isSpecOK()) |
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| 273 | stream<<" <FIELD name=\"Integrated_Flux\" ID=\"col09\" ucd=\"phot.flux;spect.line.intensity\"" |
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| 274 | <<" datatype=\"float\" width=\""<<localCol[8].getWidth()<<"\" precision=\"" |
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| 275 | <<prec[prFLUX]<<"\" unit=\""<<fixUnitsVOT(localCol[8].getUnits())<<"\"/>\n"; |
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| 276 | else |
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| 277 | stream<<" <FIELD name=\"Total_Flux\" ID=\"col09\" ucd=\"phot.flux;spect.line.intensity\"" |
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| 278 | <<" datatype=\"float\" width=\""<<localCol[8].getWidth()<<"\" precision=\"" |
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| 279 | <<prec[prFLUX]<<"\" unit=\""<<fixUnitsVOT(localCol[8].getUnits())<<"\"/>\n"; |
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| 280 | stream<<" <FIELD name=\"Peak_Flux\" ID=\"col10\" ucd=\"phot.flux;spect.line.intensity\"" |
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| 281 | <<" datatype=\"float\" width=\""<<localCol[9].getWidth()<<"\" precision=\"" |
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| 282 | <<prec[prFLUX]<<"\" unit=\""<<fixUnitsVOT(localCol[9].getUnits())<<"\"/>\n"; |
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| 283 | stream<<" <FIELD name=\"Flag\" ID=\"col11\" ucd=\"meta.code.qual\" datatype=\"char\" arraysize=\"3\" unit=\"--\"/>\n"; |
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| 284 | stream<<" <FIELD name=\"X_Centroid\" ID=\"col12\" ucd=\"pos.cartesian.x\"" |
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| 285 | <<" datatype=\"float\" width=\""<<localCol[11].getWidth()<<"\" precision=\""<<localCol[11].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 286 | stream<<" <FIELD name=\"Y_Centroid\" ID=\"col13\" ucd=\"pos.cartesian.y\"" |
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| 287 | <<" datatype=\"float\" width=\""<<localCol[12].getWidth()<<"\" precision=\""<<localCol[12].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 288 | stream<<" <FIELD name=\"Z_Centroid\" ID=\"col14\" ucd=\"pos.cartesian.z\"" |
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| 289 | <<" datatype=\"float\" width=\""<<localCol[13].getWidth()<<"\" precision=\""<<localCol[13].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 290 | stream<<" <FIELD name=\"X_Av\" ID=\"col15\" ucd=\"pos.cartesian.x\"" |
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| 291 | <<" datatype=\"float\" width=\""<<localCol[14].getWidth()<<"\" precision=\""<<localCol[14].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 292 | stream<<" <FIELD name=\"Y_Av\" ID=\"col16\" ucd=\"pos.cartesian.y\"" |
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| 293 | <<" datatype=\"float\" width=\""<<localCol[15].getWidth()<<"\" precision=\""<<localCol[15].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 294 | stream<<" <FIELD name=\"Z_Av\" ID=\"col17\" ucd=\"pos.cartesian.z\"" |
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| 295 | <<" datatype=\"float\" width=\""<<localCol[16].getWidth()<<"\" precision=\""<<localCol[16].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 296 | stream<<" <FIELD name=\"X_Peak\" ID=\"col18\" ucd=\"pos.cartesian.x\"" |
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| 297 | <<" datatype=\"int\" width=\""<<localCol[17].getWidth()<<"\" precision=\""<<localCol[17].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 298 | stream<<" <FIELD name=\"Y_Peak\" ID=\"col19\" ucd=\"pos.cartesian.y\"" |
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| 299 | <<" datatype=\"int\" width=\""<<localCol[18].getWidth()<<"\" precision=\""<<localCol[18].getPrecision()<<"\" unit=\"\"/>\n"; |
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| 300 | stream<<" <FIELD name=\"Z_Peak\" ID=\"col20\" ucd=\"pos.cartesian.z\"" |
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| 301 | <<" datatype=\"int\" width=\""<<localCol[19].getWidth()<<"\" precision=\""<<localCol[19].getPrecision()<<"\" unit=\"\"/>\n"; |
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[3] | 302 | |
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| 303 | |
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[378] | 304 | stream<<" <DATA>\n" |
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| 305 | <<" <TABLEDATA>\n"; |
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[3] | 306 | |
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[378] | 307 | stream.setf(std::ios::fixed); |
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| 308 | for(int i=0;i<this->objectList->size();i++){ |
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| 309 | if(this->objectList->at(i).isWCS()){ |
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| 310 | stream<<" <TR>\n"; |
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| 311 | stream<<" <TD>"<<setw(localCol[0].getWidth())<<i+1<<"</TD>"; |
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| 312 | stream<<"<TD>" << setw(localCol[1].getWidth()) << this->objectList->at(i).getName() <<"</TD>"; |
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| 313 | stream<<setprecision(prec[prPOS]); |
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| 314 | stream<<"<TD>" << setw(localCol[2].getWidth()) << this->objectList->at(i).getRA() <<"</TD>"; |
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| 315 | stream<<"<TD>" << setw(localCol[3].getWidth()) << this->objectList->at(i).getDec() <<"</TD>"; |
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| 316 | stream<<setprecision(prec[prWPOS]); |
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| 317 | stream<<"<TD>" << setw(localCol[4].getWidth()) << this->objectList->at(i).getRAWidth() <<"</TD>"; |
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| 318 | stream<<"<TD>" << setw(localCol[5].getWidth()) << this->objectList->at(i).getDecWidth() <<"</TD>"; |
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| 319 | stream<<setprecision(prec[prVEL]); |
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| 320 | stream<<"<TD>" << setw(localCol[6].getWidth()) << this->objectList->at(i).getVel() <<"</TD>"; |
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| 321 | stream<<"<TD>" << setw(localCol[7].getWidth()) << this->objectList->at(i).getVelWidth() <<"</TD>"; |
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| 322 | stream<<setprecision(prec[prFLUX]); |
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| 323 | if(this->head.isSpecOK()) |
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| 324 | stream<<"<TD>" << setw(localCol[8].getWidth()) << this->objectList->at(i).getIntegFlux() <<"</TD>"; |
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| 325 | else |
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| 326 | stream<<"<TD>" << setw(localCol[8].getWidth()) << this->objectList->at(i).getTotalFlux() <<"</TD>"; |
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| 327 | stream<<"<TD>" << setw(localCol[9].getWidth()) << this->objectList->at(i).getPeakFlux() <<"</TD>"; |
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| 328 | stream<<"<TD>" << setw(localCol[10].getWidth())<< this->objectList->at(i).getFlagText() <<"</TD>"; |
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| 329 | stream<<"<TD>" << setw(localCol[11].getWidth())<< this->objectList->at(i).getXCentroid() <<"</TD>"; |
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| 330 | stream<<"<TD>" << setw(localCol[12].getWidth())<< this->objectList->at(i).getYCentroid() <<"</TD>"; |
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| 331 | stream<<"<TD>" << setw(localCol[13].getWidth())<< this->objectList->at(i).getZCentroid() <<"</TD>"; |
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| 332 | stream<<"<TD>" << setw(localCol[14].getWidth())<< this->objectList->at(i).getXAverage() <<"</TD>"; |
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| 333 | stream<<"<TD>" << setw(localCol[15].getWidth())<< this->objectList->at(i).getYAverage() <<"</TD>"; |
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| 334 | stream<<"<TD>" << setw(localCol[16].getWidth())<< this->objectList->at(i).getZAverage() <<"</TD>"; |
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| 335 | stream<<"<TD>" << setw(localCol[17].getWidth())<< this->objectList->at(i).getXPeak() <<"</TD>"; |
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| 336 | stream<<"<TD>" << setw(localCol[18].getWidth())<< this->objectList->at(i).getYPeak() <<"</TD>"; |
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| 337 | stream<<"<TD>" << setw(localCol[19].getWidth())<< this->objectList->at(i).getZPeak() <<"</TD>"; |
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[3] | 338 | |
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[378] | 339 | stream<<endl; |
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| 340 | stream<<" </TR>\n"; |
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| 341 | } |
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[3] | 342 | } |
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[378] | 343 | stream<<" </TABLEDATA>\n"; |
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| 344 | stream<<" </DATA>\n"; |
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| 345 | stream<<" </TABLE>\n"; |
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| 346 | stream<<" </RESOURCE>\n"; |
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| 347 | stream<<"</VOTABLE>\n"; |
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| 348 | resetiosflags(std::ios::fixed); |
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| 349 | |
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[3] | 350 | } |
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| 351 | |
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[378] | 352 | void Cube::prepareOutputFile() |
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| 353 | { |
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| 354 | /** |
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| 355 | * A function to write the paramters, time of execution, and |
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| 356 | * statistical information to the output file. |
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| 357 | */ |
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[3] | 358 | |
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[378] | 359 | std::string outfile; |
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| 360 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
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| 361 | else outfile = this->par.getOutFile(); |
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| 362 | std::ofstream output(outfile.c_str()); |
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| 363 | output<<"Results of the Duchamp source finder: "; |
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| 364 | time_t now = time(NULL); |
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| 365 | output << asctime( localtime(&now) ); |
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| 366 | this->showParam(output); |
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| 367 | output<<"--------------------\n"; |
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| 368 | output.close(); |
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| 369 | this->outputStats(); |
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[275] | 370 | |
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[378] | 371 | } |
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[275] | 372 | |
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[378] | 373 | void Cube::outputStats() |
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| 374 | { |
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| 375 | /** |
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| 376 | * A function to write the statistical information to the output |
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| 377 | * file. This writes the threshold, its equivalent S/N ratio, and |
---|
| 378 | * the noise level and spread. |
---|
| 379 | * |
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| 380 | * If smoothing has been done, the noise level & spread for the |
---|
| 381 | * original array are calculated and printed as well. |
---|
| 382 | */ |
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[275] | 383 | |
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[378] | 384 | std::string outfile; |
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| 385 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
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| 386 | else outfile = this->par.getOutFile(); |
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| 387 | std::ofstream output(outfile.c_str(),std::ios::app); |
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| 388 | output<<"Summary of statistics:\n"; |
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[385] | 389 | output<<"Detection threshold = " << this->Stats.getThreshold() |
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[378] | 390 | <<" " << this->head.getFluxUnits(); |
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| 391 | if(this->par.getFlagFDR()) |
---|
| 392 | output<<" (or S/N=" << this->Stats.getThresholdSNR()<<")"; |
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| 393 | if(this->par.getFlagSmooth()){ |
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| 394 | output << " in smoothed cube."; |
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| 395 | if(!this->par.getFlagUserThreshold()) |
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[385] | 396 | output<<"\nNoise level = " << this->Stats.getMiddle() |
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[378] | 397 | <<", Noise spread = " << this->Stats.getSpread() |
---|
| 398 | <<" in smoothed cube."; |
---|
| 399 | |
---|
| 400 | // calculate the stats for the original array, so that we can |
---|
| 401 | // quote S/N values correctly. |
---|
| 402 | this->par.setFlagSmooth(false); |
---|
| 403 | bool verb=this->par.isVerbose(); |
---|
| 404 | bool fdrflag=this->par.getFlagFDR(); |
---|
| 405 | this->par.setVerbosity(false); |
---|
| 406 | this->par.setFlagFDR(false); |
---|
| 407 | this->setCubeStats(); |
---|
| 408 | this->par.setVerbosity(verb); |
---|
| 409 | this->par.setFlagFDR(fdrflag); |
---|
| 410 | this->par.setFlagSmooth(true); |
---|
| 411 | |
---|
[385] | 412 | output << "\nNoise properties for the original cube are:"; |
---|
[378] | 413 | } |
---|
| 414 | |
---|
[275] | 415 | if(!this->par.getFlagUserThreshold()) |
---|
[385] | 416 | output<<"\nNoise level = " << this->Stats.getMiddle() |
---|
[275] | 417 | <<", Noise spread = " << this->Stats.getSpread() |
---|
[378] | 418 | <<"\n"; |
---|
[275] | 419 | |
---|
[378] | 420 | if(this->par.getFlagGrowth()){ |
---|
| 421 | StatsContainer<float> growthStats = this->Stats; |
---|
| 422 | growthStats.setThresholdSNR(this->par.getGrowthCut()); |
---|
| 423 | growthStats.setUseFDR(false); |
---|
| 424 | output<<" Detections grown down to threshold of " |
---|
| 425 | << growthStats.getThreshold() << ".\n"; |
---|
| 426 | } |
---|
| 427 | |
---|
[385] | 428 | output << "\nFull stats:\n" << this->Stats; |
---|
| 429 | |
---|
[378] | 430 | output<<"--------------------\n"; |
---|
| 431 | output.close(); |
---|
[298] | 432 | } |
---|
| 433 | |
---|
[378] | 434 | void Cube::outputDetectionList() |
---|
| 435 | { |
---|
| 436 | /** |
---|
| 437 | * A front-end to writing the full list of detected objects to a results |
---|
| 438 | * file and to cout. |
---|
| 439 | * Uses outputDetectionTextWCS for each objects. |
---|
| 440 | * Leaves the testing of whether the WCS parameters for each object |
---|
| 441 | * have been calculated to outputDetectionTextWCS. |
---|
| 442 | */ |
---|
[275] | 443 | |
---|
[378] | 444 | std::string outfile; |
---|
| 445 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
---|
| 446 | else outfile = this->par.getOutFile(); |
---|
| 447 | std::ofstream output(outfile.c_str(),std::ios::app); |
---|
| 448 | output<<"Total number of detections = "<<this->objectList->size()<<endl; |
---|
| 449 | output<<"--------------------\n"; |
---|
| 450 | output.close(); |
---|
[275] | 451 | |
---|
[378] | 452 | if(this->par.getFlagSeparateHeader()) |
---|
| 453 | output.open(this->par.getOutFile().c_str()); |
---|
| 454 | else |
---|
| 455 | output.open(this->par.getOutFile().c_str(),std::ios::app); |
---|
[363] | 456 | |
---|
[378] | 457 | if(this->objectList->size()>0){ |
---|
| 458 | this->setupColumns(); |
---|
| 459 | this->objectList->at(0).outputDetectionTextHeaderFull(output,this->fullCols); |
---|
| 460 | this->objectList->at(0).outputDetectionTextHeader(std::cout,this->fullCols); |
---|
| 461 | for(int i=0;i<this->objectList->size();i++){ |
---|
| 462 | this->objectList->at(i).outputDetectionTextWCSFull(output,this->fullCols); |
---|
| 463 | this->objectList->at(i).outputDetectionTextWCS(std::cout,this->fullCols); |
---|
| 464 | } |
---|
| 465 | } |
---|
[363] | 466 | |
---|
[378] | 467 | output.close(); |
---|
[3] | 468 | } |
---|
[275] | 469 | |
---|
[378] | 470 | void Cube::logDetectionList() |
---|
| 471 | { |
---|
| 472 | /** |
---|
| 473 | * A front-end to writing a list of detected objects to the log file. |
---|
| 474 | * Does not assume WCS, so uses outputDetectionText. |
---|
| 475 | * Designed to be used by searching routines before returning their |
---|
| 476 | * final list. |
---|
| 477 | */ |
---|
[3] | 478 | |
---|
[378] | 479 | if(this->objectList->size()>0){ |
---|
[3] | 480 | |
---|
[378] | 481 | long left = this->par.getBorderLeft(); |
---|
| 482 | long bottom = this->par.getBorderBottom(); |
---|
[258] | 483 | |
---|
[378] | 484 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
---|
| 485 | this->setupColumns(); |
---|
| 486 | this->objectList->at(0).outputDetectionTextHeader(fout,this->logCols); |
---|
[258] | 487 | |
---|
[378] | 488 | if(this->par.getFlagBaseline()){ |
---|
| 489 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
---|
| 490 | this->array[i] += this->baseline[i]; |
---|
| 491 | } |
---|
[258] | 492 | |
---|
[378] | 493 | for(int objCtr=0;objCtr<this->objectList->size();objCtr++){ |
---|
| 494 | Detection *obj = new Detection; |
---|
| 495 | *obj = objectList->at(objCtr); |
---|
| 496 | obj->setOffsets(par); |
---|
| 497 | if(this->par.getFlagCubeTrimmed()){ |
---|
| 498 | obj->pixels().addOffsets(left,bottom,0); |
---|
| 499 | } |
---|
| 500 | obj->calcFluxes(this->array, this->axisDim); |
---|
| 501 | obj->outputDetectionText(fout,this->logCols,objCtr+1); |
---|
| 502 | delete obj; |
---|
| 503 | } |
---|
[348] | 504 | |
---|
[378] | 505 | if(this->par.getFlagBaseline()){ |
---|
| 506 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
---|
| 507 | this->array[i] -= this->baseline[i]; |
---|
[348] | 508 | } |
---|
[378] | 509 | fout.close(); |
---|
| 510 | |
---|
[348] | 511 | } |
---|
| 512 | |
---|
[3] | 513 | } |
---|
[258] | 514 | |
---|
[378] | 515 | void Cube::logDetection(Detection obj, int counter) |
---|
| 516 | { |
---|
| 517 | /** |
---|
| 518 | * A front-end to writing a detected object to the log file. |
---|
| 519 | * Does not assume WCS, so uses outputDetectionText. |
---|
| 520 | * Corrects for changes to positions of pixels and removal of baselines. |
---|
| 521 | * Designed to be used by searching routines before returning their final |
---|
| 522 | * list. |
---|
| 523 | * \param obj Detection object to be written : passed by value, as we want |
---|
| 524 | * to potentially change positions etc, but not for the object in the |
---|
| 525 | * calling function. |
---|
| 526 | * \param counter The number to assign to the object : ideally its number |
---|
| 527 | * in a list of some kind. |
---|
| 528 | */ |
---|
[3] | 529 | |
---|
[378] | 530 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
---|
| 531 | // Need to deal with possibility of trimmed array |
---|
| 532 | long left = this->par.getBorderLeft(); |
---|
| 533 | long right = this->par.getBorderRight(); |
---|
| 534 | long top = this->par.getBorderTop(); |
---|
| 535 | long bottom = this->par.getBorderBottom(); |
---|
| 536 | long *tempDim = new long[3]; |
---|
| 537 | tempDim[0] = (this->axisDim[0] + left + right); |
---|
| 538 | tempDim[1] = (this->axisDim[1] + bottom + top); |
---|
| 539 | tempDim[2] = this->axisDim[2]; |
---|
| 540 | long tempsize = tempDim[0] * tempDim[1] * tempDim[2]; |
---|
| 541 | float *temparray = new float[tempsize]; |
---|
| 542 | // for(int i=0;i<this->numPixels;i++){ // loop over this->array |
---|
| 543 | for(int z=0;z<tempDim[2];z++){ |
---|
| 544 | for(int y=0;y<tempDim[1];y++){ |
---|
| 545 | for(int x=0;x<tempDim[0];x++){ |
---|
[3] | 546 | |
---|
[378] | 547 | bool isDud = (x<left) || (x>=this->axisDim[0]+left) || |
---|
| 548 | (y<bottom) || (y>=this->axisDim[1]+bottom); |
---|
[258] | 549 | |
---|
[378] | 550 | int temppos = x + tempDim[0]*y + tempDim[1]*tempDim[0]*z; |
---|
[258] | 551 | |
---|
[378] | 552 | int pos = (x-left) + (y-bottom)*this->axisDim[0] + |
---|
| 553 | z*this->axisDim[0]*this->axisDim[1]; |
---|
[258] | 554 | |
---|
[378] | 555 | if(isDud) temparray[temppos] = this->par.getBlankPixVal(); |
---|
| 556 | else temparray[temppos] = this->array[pos]; |
---|
[258] | 557 | |
---|
[378] | 558 | if(this->par.getFlagBaseline() && !isDud) |
---|
| 559 | temparray[temppos] += this->baseline[pos]; |
---|
[258] | 560 | |
---|
[378] | 561 | } |
---|
[258] | 562 | } |
---|
[3] | 563 | } |
---|
[378] | 564 | |
---|
| 565 | if(this->par.getFlagCubeTrimmed()){ |
---|
| 566 | obj.pixels().addOffsets(left,bottom,0); |
---|
| 567 | } |
---|
| 568 | obj.calcFluxes(temparray, this->axisDim); |
---|
| 569 | obj.outputDetectionText(fout,this->logCols,counter); |
---|
| 570 | delete [] temparray; |
---|
| 571 | delete [] tempDim; |
---|
| 572 | fout.close(); |
---|
[3] | 573 | } |
---|
[258] | 574 | |
---|
[3] | 575 | } |
---|