[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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[1242] | 42 | #include <duchamp/Plotting/CutoutPlot.hh> |
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| 43 | #include <duchamp/Plotting/SpectralPlot.hh> |
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[393] | 44 | #include <duchamp/Utils/utils.hh> |
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| 45 | #include <duchamp/Utils/mycpgplot.hh> |
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[258] | 46 | |
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[146] | 47 | using namespace mycpgplot; |
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[258] | 48 | using namespace PixelInfo; |
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[3] | 49 | |
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[378] | 50 | namespace duchamp |
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[3] | 51 | { |
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| 52 | |
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[475] | 53 | std::string getIndivPlotName(std::string baseName, int objNum, int maxNumObj) |
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| 54 | { |
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| 55 | int width = int(floor(log10(float(maxNumObj))))+1; |
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| 56 | if(baseName.substr(baseName.size()-3,baseName.size())==".ps"){ |
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| 57 | std::stringstream ss; |
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| 58 | ss << baseName.substr(0,baseName.size()-3) |
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| 59 | << "-" << std::setw(width) << std::setfill('0') << objNum |
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| 60 | << ".ps"; |
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| 61 | return ss.str(); |
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| 62 | } |
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| 63 | else{ |
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| 64 | std::stringstream ss; |
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| 65 | ss << baseName |
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| 66 | << "-" << std::setw(width) << std::setfill('0') << objNum |
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| 67 | << ".ps"; |
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| 68 | return ss.str(); |
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| 69 | } |
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| 70 | } |
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| 71 | |
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[378] | 72 | void Cube::outputSpectra() |
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| 73 | { |
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[528] | 74 | /// @details |
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| 75 | /// The way to display individual detected objects. The standard way |
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| 76 | /// is plot the full spectrum, plus a zoomed-in spectrum showing just |
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| 77 | /// the object, plus the 0th-moment map. If there is no spectral |
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| 78 | /// axis, just the 0th moment map is plotted (using |
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| 79 | /// Cube::plotSource() rather than Cube::plotSpectrum()). |
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| 80 | /// |
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| 81 | /// It makes use of the SpectralPlot or CutoutPlot classes from |
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| 82 | /// plots.h, which size everything correctly. |
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| 83 | /// |
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| 84 | /// The main choice for SpectralPlot() is whether to use the peak |
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| 85 | /// pixel, in which case the spectrum is just that of the peak pixel, |
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| 86 | /// or the sum, where the spectrum is summed over all spatial pixels |
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| 87 | /// that are in the object. If a reconstruction has been done, that |
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| 88 | /// spectrum is plotted in red. The limits of the detection are |
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| 89 | /// marked in blue. A 0th moment map of the detection is also |
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| 90 | /// plotted, with a scale bar indicating the spatial scale. |
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[1430] | 91 | |
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[378] | 92 | if(this->fullCols.size()==0) this->setupColumns(); |
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| 93 | // in case cols haven't been set -- need the precisions for printing values. |
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| 94 | |
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[475] | 95 | std::vector<bool> objectChoice = this->par.getObjectChoices(this->objectList->size()); |
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| 96 | |
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[378] | 97 | std::string spectrafile = this->par.getSpectraFile() + "/vcps"; |
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| 98 | if(this->getDimZ()<=1){ |
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| 99 | Plot::CutoutPlot newplot; |
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| 100 | if(newplot.setUpPlot(spectrafile.c_str())>0) { |
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| 101 | |
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[1148] | 102 | // This loop plots all spectra of selected objects in a single file |
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[623] | 103 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[475] | 104 | // for each object in the cube, assuming it is wanted: |
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| 105 | if(objectChoice[nobj]) this->plotSource(this->objectList->at(nobj),newplot); |
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[378] | 106 | }// end of loop over objects. |
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[475] | 107 | cpgclos(); |
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[485] | 108 | |
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[1148] | 109 | // This loop plots spectra of selected objects in their own file |
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| 110 | if(this->par.getFlagPlotIndividualSpectra()) std::cout << "\n"; |
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[623] | 111 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[1148] | 112 | if(objectChoice[nobj] && this->par.getFlagPlotIndividualSpectra()){ |
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[485] | 113 | std::cout << " Will output individual plot to " |
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[475] | 114 | << getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size()) << "\n"; |
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| 115 | Plot::CutoutPlot indivplot; |
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| 116 | indivplot.setUpPlot(getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size())+"/vcps"); |
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| 117 | this->plotSource(this->objectList->at(nobj),indivplot); |
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| 118 | cpgclos(); |
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| 119 | } |
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| 120 | } |
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[378] | 121 | } |
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[367] | 122 | } |
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[378] | 123 | else{ |
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| 124 | Plot::SpectralPlot newplot; |
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| 125 | if(newplot.setUpPlot(spectrafile.c_str())>0) { |
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[367] | 126 | |
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[1148] | 127 | // This loop plots all spectra of selected objects in a single file |
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[623] | 128 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[475] | 129 | // for each object in the cube, assuming it is wanted: |
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| 130 | if(objectChoice[nobj]) this->plotSpectrum(nobj,newplot); |
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[378] | 131 | }// end of loop over objects. |
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[475] | 132 | cpgclos(); |
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[367] | 133 | |
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[1148] | 134 | // This loop plots spectra of selected objects in their own file |
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| 135 | if(this->par.getFlagPlotIndividualSpectra()) std::cout << "\n"; |
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[623] | 136 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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[1148] | 137 | if(objectChoice[nobj] && this->par.getFlagPlotIndividualSpectra()){ |
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[485] | 138 | std::cout << " Will output individual plot to " |
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[475] | 139 | << getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size()) << "\n"; |
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| 140 | Plot::SpectralPlot indivplot; |
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| 141 | indivplot.setUpPlot(getIndivPlotName(this->par.getSpectraFile(),nobj+1,this->objectList->size())+"/vcps"); |
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| 142 | this->plotSpectrum(nobj,indivplot); |
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| 143 | cpgclos(); |
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| 144 | } |
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| 145 | } |
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| 146 | |
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[378] | 147 | } |
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[475] | 148 | |
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[367] | 149 | } |
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| 150 | } |
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[424] | 151 | //-------------------------------------------------------------------- |
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[103] | 152 | |
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[424] | 153 | void Cube::plotSpectrum(int objNum, Plot::SpectralPlot &plot) |
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| 154 | { |
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[528] | 155 | /// @details |
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| 156 | /// The way to print out the spectrum of a Detection. |
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| 157 | /// Makes use of the SpectralPlot class in plots.hh, which sizes |
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| 158 | /// everything correctly. |
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| 159 | /// |
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| 160 | /// The main choice for the user is whether to use the peak pixel, in |
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| 161 | /// which case the spectrum is just that of the peak pixel, or the |
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| 162 | /// sum, where the spectrum is summed over all spatial pixels that |
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| 163 | /// are in the object. |
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| 164 | /// |
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| 165 | /// If a reconstruction has been done, that spectrum is plotted in |
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| 166 | /// red, and if a baseline has been calculated that is also shown, in |
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| 167 | /// yellow. The spectral limits of the detection are marked in blue. |
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| 168 | /// A 0th moment map of the detection is also plotted, with a scale |
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| 169 | /// bar indicating the spatial size. |
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| 170 | /// |
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| 171 | /// \param objNum The number of the Detection to be plotted. |
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| 172 | /// \param plot The SpectralPlot object defining the PGPLOT device |
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| 173 | /// to plot the spectrum on. |
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[103] | 174 | |
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[378] | 175 | long zdim = this->axisDim[2]; |
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[1242] | 176 | double xval = double(this->objectList->at(objNum).getXcentre()); |
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| 177 | double yval = double(this->objectList->at(objNum).getYcentre()); |
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| 178 | |
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[378] | 179 | float *specx = new float[zdim]; |
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| 180 | float *specy = new float[zdim]; |
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| 181 | float *specy2 = new float[zdim]; |
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| 182 | float *base = new float[zdim]; |
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[463] | 183 | // float *specx, *specy, *specy2, *base; |
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[3] | 184 | |
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[424] | 185 | this->getSpectralArrays(objNum,specx,specy,specy2,base); |
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[3] | 186 | |
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[378] | 187 | std::string fluxLabel = "Flux"; |
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[436] | 188 | std::string fluxUnits = this->head.getFluxUnits(); |
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| 189 | std::string intFluxUnits;// = this->head.getIntFluxUnits(); |
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| 190 | // Rather than use the intFluxUnits from the header, which will be like Jy MHz, |
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| 191 | // we just use the pixel units, removing the /beam if necessary. |
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[498] | 192 | |
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[499] | 193 | if(fluxUnits.size()>5 && |
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[498] | 194 | makelower(fluxUnits.substr(fluxUnits.size()-5, |
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[436] | 195 | fluxUnits.size() )) == "/beam"){ |
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| 196 | intFluxUnits = fluxUnits.substr(0,fluxUnits.size()-5); |
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| 197 | } |
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| 198 | else intFluxUnits = fluxUnits; |
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| 199 | |
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| 200 | |
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[378] | 201 | if(this->par.getSpectralMethod()=="sum"){ |
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| 202 | fluxLabel = "Integrated " + fluxLabel; |
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[436] | 203 | if(this->head.isWCS()) { |
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| 204 | fluxLabel += " ["+intFluxUnits+"]"; |
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| 205 | } |
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[3] | 206 | } |
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[378] | 207 | else {// if(par.getSpectralMethod()=="peak"){ |
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| 208 | fluxLabel = "Peak " + fluxLabel; |
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[436] | 209 | if(this->head.isWCS()) fluxLabel += " ["+fluxUnits+"]"; |
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[45] | 210 | } |
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[3] | 211 | |
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[378] | 212 | float vmax,vmin,width; |
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| 213 | vmax = vmin = specx[0]; |
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| 214 | for(int i=1;i<zdim;i++){ |
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| 215 | if(specx[i]>vmax) vmax=specx[i]; |
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| 216 | if(specx[i]<vmin) vmin=specx[i]; |
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| 217 | } |
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[142] | 218 | |
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[1242] | 219 | // Find the maximum & minimum values of the spectrum, ignoring flagged channels. |
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[1370] | 220 | float max=0.,min=0.; |
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[1242] | 221 | bool haveStarted=false; |
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| 222 | for(int z=0;z<zdim;z++){ |
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| 223 | if(!this->par.isFlaggedChannel(z)){ |
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[1244] | 224 | if(specy[z]>max || !haveStarted) max=specy[z]; |
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| 225 | if(specy[z]<min || !haveStarted) min=specy[z]; |
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[1242] | 226 | if(this->par.getFlagBaseline()){ |
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[1244] | 227 | if(base[z]>max || !haveStarted) max=base[z]; |
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| 228 | if(base[z]<min || !haveStarted) min=base[z]; |
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[1242] | 229 | } |
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| 230 | if(this->reconExists){ |
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[1244] | 231 | if(specy2[z]>max || !haveStarted) max=specy2[z]; |
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| 232 | if(specy2[z]<min || !haveStarted) min=specy2[z]; |
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[1242] | 233 | } |
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| 234 | haveStarted=true; |
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[378] | 235 | } |
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[3] | 236 | } |
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[1186] | 237 | |
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[378] | 238 | // widen the ranges slightly so that the top & bottom & edges don't |
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| 239 | // lie on the axes. |
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| 240 | width = max - min; |
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| 241 | max += width * 0.05; |
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| 242 | min -= width * 0.05; |
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[463] | 243 | width = vmax - vmin; |
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[378] | 244 | vmax += width * 0.01; |
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| 245 | vmin -= width * 0.01; |
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[3] | 246 | |
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[378] | 247 | // now plot the resulting spectrum |
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| 248 | std::string label; |
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| 249 | if(this->head.isWCS()){ |
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| 250 | label = this->head.getSpectralDescription() + " [" + |
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| 251 | this->head.getSpectralUnits() + "]"; |
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| 252 | plot.gotoHeader(label); |
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| 253 | } |
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| 254 | else plot.gotoHeader("Spectral pixel value"); |
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[3] | 255 | |
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[378] | 256 | if(this->head.isWCS()){ |
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[424] | 257 | label = this->objectList->at(objNum).outputLabelWCS(); |
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[378] | 258 | plot.firstHeaderLine(label); |
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[424] | 259 | label = this->objectList->at(objNum).outputLabelFluxes(); |
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[378] | 260 | plot.secondHeaderLine(label); |
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| 261 | } |
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[1133] | 262 | label = this->objectList->at(objNum).outputLabelWidths(this->head); |
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[378] | 263 | plot.thirdHeaderLine(label); |
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[424] | 264 | label = this->objectList->at(objNum).outputLabelPix(); |
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[378] | 265 | plot.fourthHeaderLine(label); |
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[49] | 266 | |
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[378] | 267 | plot.gotoMainSpectrum(vmin,vmax,min,max,fluxLabel); |
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| 268 | cpgline(zdim,specx,specy); |
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| 269 | if(this->par.getFlagBaseline()){ |
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| 270 | cpgsci(DUCHAMP_BASELINE_SPECTRA_COLOUR); |
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| 271 | cpgline(zdim,specx,base); |
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| 272 | cpgsci(FOREGND); |
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| 273 | } |
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| 274 | if(this->reconExists){ |
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| 275 | cpgsci(DUCHAMP_RECON_SPECTRA_COLOUR); |
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| 276 | cpgline(zdim,specx,specy2); |
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| 277 | cpgsci(FOREGND); |
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| 278 | } |
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[1242] | 279 | this->drawFlaggedChannels(plot,xval,yval); |
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[850] | 280 | drawSpectralRange(plot,this->objectList->at(objNum),this->head); |
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[3] | 281 | |
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[1258] | 282 | if(this->par.getSpectralMethod()=="peak"){ |
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| 283 | if(this->par.getFlagBaseline()) |
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| 284 | plot.drawThresholds(this->par,this->Stats,specx,base,zdim); |
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| 285 | else |
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| 286 | plot.drawThresholds(this->par,this->Stats); |
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| 287 | } |
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[987] | 288 | |
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[378] | 289 | /**************************/ |
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| 290 | // ZOOM IN SPECTRALLY ON THE DETECTION. |
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[3] | 291 | |
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[957] | 292 | double minvel,maxvel; |
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[424] | 293 | if(this->head.isWCS()) getSmallVelRange(this->objectList->at(objNum),this->head,&minvel,&maxvel); |
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| 294 | else getSmallZRange(this->objectList->at(objNum),&minvel,&maxvel); |
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[3] | 295 | |
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[378] | 296 | // Find new max & min flux values |
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| 297 | std::swap(max,min); |
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| 298 | int ct = 0; |
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| 299 | for(int i=0;i<zdim;i++){ |
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[1242] | 300 | if((!this->par.isFlaggedChannel(i))&&(specx[i]>=minvel)&&(specx[i]<=maxvel)){ |
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[378] | 301 | ct++; |
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| 302 | if(specy[i]>max) max=specy[i]; |
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| 303 | if(specy[i]<min) min=specy[i]; |
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[1118] | 304 | if(this->par.getFlagBaseline()){ |
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| 305 | if(base[i]>max) max=base[i]; |
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| 306 | if(base[i]<min) min=base[i]; |
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| 307 | } |
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| 308 | if(this->reconExists){ |
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| 309 | if(specy2[i]>max) max=specy2[i]; |
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| 310 | if(specy2[i]<min) min=specy2[i]; |
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| 311 | } |
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[378] | 312 | } |
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[3] | 313 | } |
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[378] | 314 | // widen the flux range slightly so that the top & bottom don't lie |
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| 315 | // on the axes. |
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| 316 | width = max - min; |
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| 317 | max += width * 0.05; |
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| 318 | min -= width * 0.05; |
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[3] | 319 | |
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[378] | 320 | plot.gotoZoomSpectrum(minvel,maxvel,min,max); |
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| 321 | cpgline(zdim,specx,specy); |
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| 322 | if(this->par.getFlagBaseline()){ |
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| 323 | cpgsci(DUCHAMP_BASELINE_SPECTRA_COLOUR); |
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| 324 | cpgline(zdim,specx,base); |
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| 325 | cpgsci(FOREGND); |
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| 326 | } |
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| 327 | if(this->reconExists){ |
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| 328 | cpgsci(DUCHAMP_RECON_SPECTRA_COLOUR); |
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| 329 | cpgline(zdim,specx,specy2); |
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| 330 | cpgsci(FOREGND); |
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| 331 | } |
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[1242] | 332 | this->drawFlaggedChannels(plot,xval,yval); |
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[850] | 333 | drawSpectralRange(plot,this->objectList->at(objNum),this->head); |
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[3] | 334 | |
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[1258] | 335 | if(this->par.getSpectralMethod()=="peak"){ |
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| 336 | if(this->par.getFlagBaseline()) |
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| 337 | plot.drawThresholds(this->par,this->Stats,specx,base,zdim); |
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| 338 | else |
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| 339 | plot.drawThresholds(this->par,this->Stats); |
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| 340 | } |
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[378] | 341 | /**************************/ |
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[3] | 342 | |
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[378] | 343 | // DRAW THE MOMENT MAP OF THE DETECTION -- SUMMED OVER ALL CHANNELS |
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[985] | 344 | if(this->numNondegDim>1){ |
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| 345 | plot.gotoMap(); |
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| 346 | this->drawMomentCutout(this->objectList->at(objNum)); |
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| 347 | } |
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[3] | 348 | |
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[378] | 349 | delete [] specx; |
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| 350 | delete [] specy; |
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| 351 | delete [] specy2; |
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| 352 | delete [] base; |
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[3] | 353 | |
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[378] | 354 | } |
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[424] | 355 | //-------------------------------------------------------------------- |
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[3] | 356 | |
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[1242] | 357 | void Cube::drawFlaggedChannels(Plot::SpectralPlot &plot, double xval, double yval) |
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| 358 | { |
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| 359 | std::vector<int> flaggedChannels = this->par.getFlaggedChannels(); |
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| 360 | if(flaggedChannels.size()>0){ |
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| 361 | Object2D contiguousFlaggedChans; |
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| 362 | for(size_t i=0;i<flaggedChannels.size();i++){ |
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| 363 | contiguousFlaggedChans.addPixel(flaggedChannels[i],0); |
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| 364 | } |
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| 365 | // each scan in the object2D is a contiguous range of flagged channels |
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| 366 | std::vector<Scan> rangeList=contiguousFlaggedChans.getScanlist(); |
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| 367 | double minvel=0,maxvel=0,zval; |
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| 368 | for(size_t i=0;i<rangeList.size();i++){ |
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| 369 | zval = double(rangeList[i].getX()-0.5); |
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| 370 | minvel = this->head.pixToVel(xval,yval,zval); |
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| 371 | zval = double(rangeList[i].getXmax()+0.5); |
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[1245] | 372 | maxvel = this->head.pixToVel(xval,yval,zval); |
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[1242] | 373 | plot.drawFlaggedChannelRange(minvel,maxvel); |
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| 374 | } |
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| 375 | } |
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| 376 | } |
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[850] | 377 | |
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[1242] | 378 | |
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[378] | 379 | void Cube::plotSource(Detection obj, Plot::CutoutPlot &plot) |
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| 380 | { |
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[528] | 381 | /// @details |
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| 382 | /// The way to print out the 2d image cutout of a Detection. |
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| 383 | /// Makes use of the CutoutPlot class in plots.hh, which sizes |
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| 384 | /// everything correctly. |
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| 385 | /// |
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| 386 | /// A 0th moment map of the detection is plotted, with a scale |
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| 387 | /// bar indicating the spatial size. |
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| 388 | /// |
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| 389 | /// Basic information on the source is printed next to it as well. |
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| 390 | /// |
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| 391 | /// \param obj The Detection to be plotted. |
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| 392 | /// \param plot The PGPLOT device to plot the spectrum on. |
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[367] | 393 | |
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[378] | 394 | std::string label; |
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| 395 | plot.gotoHeader(); |
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[367] | 396 | |
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[378] | 397 | if(this->head.isWCS()){ |
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| 398 | label = obj.outputLabelWCS(); |
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| 399 | plot.firstHeaderLine(label); |
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| 400 | label = obj.outputLabelFluxes(); |
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| 401 | plot.secondHeaderLine(label); |
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| 402 | } |
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[1133] | 403 | label = obj.outputLabelWidths(this->head); |
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[378] | 404 | plot.thirdHeaderLine(label); |
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| 405 | label = obj.outputLabelPix(); |
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| 406 | plot.fourthHeaderLine(label); |
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| 407 | |
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| 408 | // DRAW THE MOMENT MAP OF THE DETECTION -- SUMMED OVER ALL CHANNELS |
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| 409 | plot.gotoMap(); |
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| 410 | this->drawMomentCutout(obj); |
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[367] | 411 | |
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| 412 | } |
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| 413 | |
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| 414 | } |
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