[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // outputSpectra.cc: Print the spectra 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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[424] | 29 | #include <fstream> |
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[3] | 30 | #include <iomanip> |
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| 31 | #include <sstream> |
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| 32 | #include <string> |
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| 33 | #include <cpgplot.h> |
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| 34 | #include <math.h> |
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[394] | 35 | #include <wcslib/wcs.h> |
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[393] | 36 | #include <duchamp/param.hh> |
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| 37 | #include <duchamp/duchamp.hh> |
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| 38 | #include <duchamp/fitsHeader.hh> |
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| 39 | #include <duchamp/PixelMap/Object3D.hh> |
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| 40 | #include <duchamp/Cubes/cubes.hh> |
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[985] | 41 | #include <duchamp/Cubes/cubeUtils.hh> |
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[393] | 42 | #include <duchamp/Cubes/plots.hh> |
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| 43 | #include <duchamp/Utils/utils.hh> |
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| 44 | #include <duchamp/Utils/mycpgplot.hh> |
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[258] | 45 | |
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[146] | 46 | using namespace mycpgplot; |
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[258] | 47 | using namespace PixelInfo; |
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[3] | 48 | |
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[378] | 49 | namespace duchamp |
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[3] | 50 | { |
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| 51 | |
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[475] | 52 | std::string getIndivPlotName(std::string baseName, int objNum, int maxNumObj) |
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| 53 | { |
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| 54 | int width = int(floor(log10(float(maxNumObj))))+1; |
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| 55 | if(baseName.substr(baseName.size()-3,baseName.size())==".ps"){ |
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| 56 | std::stringstream ss; |
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| 57 | ss << baseName.substr(0,baseName.size()-3) |
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| 58 | << "-" << std::setw(width) << std::setfill('0') << objNum |
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| 59 | << ".ps"; |
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| 60 | return ss.str(); |
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| 61 | } |
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| 62 | else{ |
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| 63 | std::stringstream ss; |
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| 64 | ss << baseName |
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| 65 | << "-" << std::setw(width) << std::setfill('0') << objNum |
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| 66 | << ".ps"; |
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| 67 | return ss.str(); |
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| 68 | } |
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| 69 | } |
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| 70 | |
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[378] | 71 | void Cube::outputSpectra() |
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| 72 | { |
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[528] | 73 | /// @details |
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| 74 | /// The way to display individual detected objects. The standard way |
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| 75 | /// is plot the full spectrum, plus a zoomed-in spectrum showing just |
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| 76 | /// the object, plus the 0th-moment map. If there is no spectral |
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| 77 | /// axis, just the 0th moment map is plotted (using |
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| 78 | /// Cube::plotSource() rather than Cube::plotSpectrum()). |
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| 79 | /// |
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| 80 | /// It makes use of the SpectralPlot or CutoutPlot classes from |
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| 81 | /// plots.h, which size everything correctly. |
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| 82 | /// |
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| 83 | /// The main choice for SpectralPlot() is whether to use the peak |
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| 84 | /// pixel, in which case the spectrum is just that of the peak pixel, |
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| 85 | /// or the sum, where the spectrum is summed over all spatial pixels |
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| 86 | /// that are in the object. If a reconstruction has been done, that |
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| 87 | /// spectrum is plotted in red. The limits of the detection are |
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| 88 | /// marked in blue. A 0th moment map of the detection is also |
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| 89 | /// plotted, with a scale bar indicating the spatial scale. |
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[3] | 90 | |
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[378] | 91 | if(this->fullCols.size()==0) this->setupColumns(); |
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| 92 | // in case cols haven't been set -- need the precisions for printing values. |
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| 93 | |
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[475] | 94 | std::vector<bool> objectChoice = this->par.getObjectChoices(this->objectList->size()); |
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| 95 | |
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[378] | 96 | std::string spectrafile = this->par.getSpectraFile() + "/vcps"; |
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| 97 | if(this->getDimZ()<=1){ |
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| 98 | Plot::CutoutPlot newplot; |
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| 99 | if(newplot.setUpPlot(spectrafile.c_str())>0) { |
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| 100 | |
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[623] | 101 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[475] | 102 | // for each object in the cube, assuming it is wanted: |
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| 103 | if(objectChoice[nobj]) this->plotSource(this->objectList->at(nobj),newplot); |
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[378] | 104 | }// end of loop over objects. |
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[475] | 105 | cpgclos(); |
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[485] | 106 | |
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| 107 | if(this->par.getFlagUsePrevious()) std::cout << "\n"; |
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[623] | 108 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[475] | 109 | if(objectChoice[nobj] && this->par.getFlagUsePrevious()){ |
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[485] | 110 | std::cout << " Will output individual plot to " |
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[475] | 111 | << getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size()) << "\n"; |
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| 112 | Plot::CutoutPlot indivplot; |
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| 113 | indivplot.setUpPlot(getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size())+"/vcps"); |
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| 114 | this->plotSource(this->objectList->at(nobj),indivplot); |
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| 115 | cpgclos(); |
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| 116 | } |
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| 117 | } |
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[378] | 118 | } |
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[367] | 119 | } |
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[378] | 120 | else{ |
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| 121 | Plot::SpectralPlot newplot; |
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| 122 | if(newplot.setUpPlot(spectrafile.c_str())>0) { |
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[367] | 123 | |
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[623] | 124 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[475] | 125 | // for each object in the cube, assuming it is wanted: |
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| 126 | if(objectChoice[nobj]) this->plotSpectrum(nobj,newplot); |
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[378] | 127 | }// end of loop over objects. |
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[475] | 128 | cpgclos(); |
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[367] | 129 | |
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[485] | 130 | if(this->par.getFlagUsePrevious()) std::cout << "\n"; |
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[623] | 131 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[475] | 132 | if(objectChoice[nobj] && this->par.getFlagUsePrevious()){ |
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[485] | 133 | std::cout << " Will output individual plot to " |
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[475] | 134 | << getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size()) << "\n"; |
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| 135 | Plot::SpectralPlot indivplot; |
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| 136 | indivplot.setUpPlot(getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size())+"/vcps"); |
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| 137 | this->plotSpectrum(nobj,indivplot); |
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| 138 | cpgclos(); |
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| 139 | } |
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| 140 | } |
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| 141 | |
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[378] | 142 | } |
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[475] | 143 | |
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[367] | 144 | } |
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| 145 | } |
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[424] | 146 | //-------------------------------------------------------------------- |
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[103] | 147 | |
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[424] | 148 | void Cube::plotSpectrum(int objNum, Plot::SpectralPlot &plot) |
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| 149 | { |
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[528] | 150 | /// @details |
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| 151 | /// The way to print out the spectrum of a Detection. |
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| 152 | /// Makes use of the SpectralPlot class in plots.hh, which sizes |
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| 153 | /// everything correctly. |
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| 154 | /// |
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| 155 | /// The main choice for the user is whether to use the peak pixel, in |
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| 156 | /// which case the spectrum is just that of the peak pixel, or the |
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| 157 | /// sum, where the spectrum is summed over all spatial pixels that |
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| 158 | /// are in the object. |
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| 159 | /// |
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| 160 | /// If a reconstruction has been done, that spectrum is plotted in |
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| 161 | /// red, and if a baseline has been calculated that is also shown, in |
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| 162 | /// yellow. The spectral limits of the detection are marked in blue. |
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| 163 | /// A 0th moment map of the detection is also plotted, with a scale |
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| 164 | /// bar indicating the spatial size. |
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| 165 | /// |
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| 166 | /// \param objNum The number of the Detection to be plotted. |
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| 167 | /// \param plot The SpectralPlot object defining the PGPLOT device |
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| 168 | /// to plot the spectrum on. |
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[103] | 169 | |
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[378] | 170 | long zdim = this->axisDim[2]; |
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[3] | 171 | |
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[424] | 172 | this->objectList->at(objNum).calcFluxes(this->array, this->axisDim); |
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[103] | 173 | |
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[634] | 174 | double minMWvel=0,maxMWvel=0,xval,yval,zval; |
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[424] | 175 | xval = double(this->objectList->at(objNum).getXcentre()); |
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| 176 | yval = double(this->objectList->at(objNum).getYcentre()); |
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[378] | 177 | if(this->par.getFlagMW()){ |
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| 178 | zval = double(this->par.getMinMW()); |
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| 179 | minMWvel = this->head.pixToVel(xval,yval,zval); |
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| 180 | zval = double(this->par.getMaxMW()); |
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| 181 | maxMWvel = this->head.pixToVel(xval,yval,zval); |
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| 182 | } |
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[103] | 183 | |
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[378] | 184 | float *specx = new float[zdim]; |
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| 185 | float *specy = new float[zdim]; |
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| 186 | float *specy2 = new float[zdim]; |
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| 187 | float *base = new float[zdim]; |
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[463] | 188 | // float *specx, *specy, *specy2, *base; |
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[3] | 189 | |
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[424] | 190 | this->getSpectralArrays(objNum,specx,specy,specy2,base); |
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[3] | 191 | |
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[378] | 192 | std::string fluxLabel = "Flux"; |
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[436] | 193 | std::string fluxUnits = this->head.getFluxUnits(); |
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| 194 | std::string intFluxUnits;// = this->head.getIntFluxUnits(); |
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| 195 | // Rather than use the intFluxUnits from the header, which will be like Jy MHz, |
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| 196 | // we just use the pixel units, removing the /beam if necessary. |
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[498] | 197 | |
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[499] | 198 | if(fluxUnits.size()>5 && |
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[498] | 199 | makelower(fluxUnits.substr(fluxUnits.size()-5, |
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[436] | 200 | fluxUnits.size() )) == "/beam"){ |
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| 201 | intFluxUnits = fluxUnits.substr(0,fluxUnits.size()-5); |
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| 202 | } |
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| 203 | else intFluxUnits = fluxUnits; |
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| 204 | |
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| 205 | |
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[378] | 206 | if(this->par.getSpectralMethod()=="sum"){ |
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| 207 | fluxLabel = "Integrated " + fluxLabel; |
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[436] | 208 | if(this->head.isWCS()) { |
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| 209 | fluxLabel += " ["+intFluxUnits+"]"; |
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| 210 | } |
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[3] | 211 | } |
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[378] | 212 | else {// if(par.getSpectralMethod()=="peak"){ |
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| 213 | fluxLabel = "Peak " + fluxLabel; |
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[436] | 214 | if(this->head.isWCS()) fluxLabel += " ["+fluxUnits+"]"; |
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[45] | 215 | } |
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[3] | 216 | |
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[378] | 217 | float vmax,vmin,width; |
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| 218 | vmax = vmin = specx[0]; |
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| 219 | for(int i=1;i<zdim;i++){ |
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| 220 | if(specx[i]>vmax) vmax=specx[i]; |
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| 221 | if(specx[i]<vmin) vmin=specx[i]; |
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| 222 | } |
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[142] | 223 | |
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[378] | 224 | float max,min; |
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| 225 | int loc=0; |
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| 226 | if(this->par.getMinMW()>0) max = min = specy[0]; |
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[463] | 227 | else max = min = specy[this->par.getMaxMW()+1]; |
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[378] | 228 | for(int i=0;i<zdim;i++){ |
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| 229 | if(!this->par.isInMW(i)){ |
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| 230 | if(specy[i]>max) max=specy[i]; |
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| 231 | if(specy[i]<min){ |
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| 232 | min=specy[i]; |
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| 233 | loc = i; |
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| 234 | } |
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[3] | 235 | } |
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| 236 | } |
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[378] | 237 | // widen the ranges slightly so that the top & bottom & edges don't |
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| 238 | // lie on the axes. |
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| 239 | width = max - min; |
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| 240 | max += width * 0.05; |
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| 241 | min -= width * 0.05; |
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[463] | 242 | width = vmax - vmin; |
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[378] | 243 | vmax += width * 0.01; |
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| 244 | vmin -= width * 0.01; |
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[3] | 245 | |
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[378] | 246 | // now plot the resulting spectrum |
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| 247 | std::string label; |
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| 248 | if(this->head.isWCS()){ |
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| 249 | label = this->head.getSpectralDescription() + " [" + |
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| 250 | this->head.getSpectralUnits() + "]"; |
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| 251 | plot.gotoHeader(label); |
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| 252 | } |
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| 253 | else plot.gotoHeader("Spectral pixel value"); |
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[3] | 254 | |
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[378] | 255 | if(this->head.isWCS()){ |
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[424] | 256 | label = this->objectList->at(objNum).outputLabelWCS(); |
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[378] | 257 | plot.firstHeaderLine(label); |
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[424] | 258 | label = this->objectList->at(objNum).outputLabelFluxes(); |
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[378] | 259 | plot.secondHeaderLine(label); |
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| 260 | } |
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[424] | 261 | label = this->objectList->at(objNum).outputLabelWidths(); |
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[378] | 262 | plot.thirdHeaderLine(label); |
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[424] | 263 | label = this->objectList->at(objNum).outputLabelPix(); |
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[378] | 264 | plot.fourthHeaderLine(label); |
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[49] | 265 | |
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[378] | 266 | plot.gotoMainSpectrum(vmin,vmax,min,max,fluxLabel); |
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| 267 | cpgline(zdim,specx,specy); |
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| 268 | if(this->par.getFlagBaseline()){ |
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| 269 | cpgsci(DUCHAMP_BASELINE_SPECTRA_COLOUR); |
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| 270 | cpgline(zdim,specx,base); |
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| 271 | cpgsci(FOREGND); |
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| 272 | } |
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| 273 | if(this->reconExists){ |
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| 274 | cpgsci(DUCHAMP_RECON_SPECTRA_COLOUR); |
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| 275 | cpgline(zdim,specx,specy2); |
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| 276 | cpgsci(FOREGND); |
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| 277 | } |
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| 278 | if(this->par.getFlagMW()) plot.drawMWRange(minMWvel,maxMWvel); |
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[850] | 279 | drawSpectralRange(plot,this->objectList->at(objNum),this->head); |
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[3] | 280 | |
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[987] | 281 | if(this->par.getSpectralMethod()=="peak") |
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| 282 | plot.drawThresholds(this->par,this->Stats); |
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| 283 | |
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[378] | 284 | /**************************/ |
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| 285 | // ZOOM IN SPECTRALLY ON THE DETECTION. |
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[3] | 286 | |
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[957] | 287 | double minvel,maxvel; |
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[424] | 288 | if(this->head.isWCS()) getSmallVelRange(this->objectList->at(objNum),this->head,&minvel,&maxvel); |
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| 289 | else getSmallZRange(this->objectList->at(objNum),&minvel,&maxvel); |
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[3] | 290 | |
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[378] | 291 | // Find new max & min flux values |
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| 292 | std::swap(max,min); |
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| 293 | int ct = 0; |
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| 294 | for(int i=0;i<zdim;i++){ |
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| 295 | if((!this->par.isInMW(i))&&(specx[i]>=minvel)&&(specx[i]<=maxvel)){ |
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| 296 | ct++; |
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| 297 | if(specy[i]>max) max=specy[i]; |
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| 298 | if(specy[i]<min) min=specy[i]; |
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| 299 | } |
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[3] | 300 | } |
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[378] | 301 | // widen the flux range slightly so that the top & bottom don't lie |
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| 302 | // on the axes. |
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| 303 | width = max - min; |
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| 304 | max += width * 0.05; |
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| 305 | min -= width * 0.05; |
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[3] | 306 | |
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[378] | 307 | plot.gotoZoomSpectrum(minvel,maxvel,min,max); |
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| 308 | cpgline(zdim,specx,specy); |
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| 309 | if(this->par.getFlagBaseline()){ |
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| 310 | cpgsci(DUCHAMP_BASELINE_SPECTRA_COLOUR); |
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| 311 | cpgline(zdim,specx,base); |
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| 312 | cpgsci(FOREGND); |
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| 313 | } |
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| 314 | if(this->reconExists){ |
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| 315 | cpgsci(DUCHAMP_RECON_SPECTRA_COLOUR); |
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| 316 | cpgline(zdim,specx,specy2); |
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| 317 | cpgsci(FOREGND); |
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| 318 | } |
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| 319 | if(this->par.getFlagMW()) plot.drawMWRange(minMWvel,maxMWvel); |
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[850] | 320 | drawSpectralRange(plot,this->objectList->at(objNum),this->head); |
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[3] | 321 | |
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[987] | 322 | if(this->par.getSpectralMethod()=="peak") |
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| 323 | plot.drawThresholds(this->par,this->Stats); |
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| 324 | |
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[378] | 325 | /**************************/ |
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[3] | 326 | |
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[378] | 327 | // DRAW THE MOMENT MAP OF THE DETECTION -- SUMMED OVER ALL CHANNELS |
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[985] | 328 | if(this->numNondegDim>1){ |
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| 329 | plot.gotoMap(); |
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| 330 | this->drawMomentCutout(this->objectList->at(objNum)); |
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| 331 | } |
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[3] | 332 | |
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[378] | 333 | delete [] specx; |
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| 334 | delete [] specy; |
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| 335 | delete [] specy2; |
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| 336 | delete [] base; |
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[3] | 337 | |
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[378] | 338 | } |
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[424] | 339 | //-------------------------------------------------------------------- |
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[3] | 340 | |
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[850] | 341 | |
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[378] | 342 | void Cube::plotSource(Detection obj, Plot::CutoutPlot &plot) |
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| 343 | { |
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[528] | 344 | /// @details |
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| 345 | /// The way to print out the 2d image cutout of a Detection. |
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| 346 | /// Makes use of the CutoutPlot class in plots.hh, which sizes |
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| 347 | /// everything correctly. |
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| 348 | /// |
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| 349 | /// A 0th moment map of the detection is plotted, with a scale |
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| 350 | /// bar indicating the spatial size. |
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| 351 | /// |
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| 352 | /// Basic information on the source is printed next to it as well. |
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| 353 | /// |
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| 354 | /// \param obj The Detection to be plotted. |
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| 355 | /// \param plot The PGPLOT device to plot the spectrum on. |
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[367] | 356 | |
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[378] | 357 | obj.calcFluxes(this->array, this->axisDim); |
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[367] | 358 | |
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[378] | 359 | std::string label; |
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| 360 | plot.gotoHeader(); |
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[367] | 361 | |
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[378] | 362 | if(this->head.isWCS()){ |
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| 363 | label = obj.outputLabelWCS(); |
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| 364 | plot.firstHeaderLine(label); |
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| 365 | label = obj.outputLabelFluxes(); |
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| 366 | plot.secondHeaderLine(label); |
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| 367 | } |
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| 368 | label = obj.outputLabelWidths(); |
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| 369 | plot.thirdHeaderLine(label); |
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| 370 | label = obj.outputLabelPix(); |
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| 371 | plot.fourthHeaderLine(label); |
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| 372 | |
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| 373 | // DRAW THE MOMENT MAP OF THE DETECTION -- SUMMED OVER ALL CHANNELS |
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| 374 | plot.gotoMap(); |
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| 375 | this->drawMomentCutout(obj); |
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[367] | 376 | |
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| 377 | } |
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| 378 | |
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| 379 | } |
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