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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28 | #include <iostream> |
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29 | #include <fstream> |
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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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35 | #include <wcslib/wcs.h> |
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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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41 | #include <duchamp/Cubes/cubeUtils.hh> |
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42 | #include <duchamp/Plotting/CutoutPlot.hh> |
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43 | #include <duchamp/Plotting/SpectralPlot.hh> |
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44 | #include <duchamp/Utils/utils.hh> |
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45 | #include <duchamp/Utils/mycpgplot.hh> |
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46 | |
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47 | using namespace mycpgplot; |
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48 | using namespace PixelInfo; |
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49 | |
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50 | namespace duchamp |
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51 | { |
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52 | |
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53 | 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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72 | void Cube::outputSpectra() |
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73 | { |
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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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91 | |
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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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95 | std::vector<bool> objectChoice = this->par.getObjectChoices(this->objectList->size()); |
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96 | |
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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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102 | // This loop plots all spectra of selected objects in a single file |
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103 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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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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106 | }// end of loop over objects. |
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107 | cpgclos(); |
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108 | |
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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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111 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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112 | if(objectChoice[nobj] && this->par.getFlagPlotIndividualSpectra()){ |
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113 | std::cout << " Will output individual plot to " |
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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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121 | } |
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122 | } |
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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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126 | |
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127 | // This loop plots all spectra of selected objects in a single file |
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128 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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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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131 | }// end of loop over objects. |
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132 | cpgclos(); |
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133 | |
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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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136 | for(size_t nobj=0;nobj<this->objectList->size();nobj++){ |
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137 | if(objectChoice[nobj] && this->par.getFlagPlotIndividualSpectra()){ |
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138 | std::cout << " Will output individual plot to " |
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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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147 | } |
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148 | |
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149 | } |
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150 | } |
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151 | //-------------------------------------------------------------------- |
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152 | |
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153 | void Cube::plotSpectrum(int objNum, Plot::SpectralPlot &plot) |
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154 | { |
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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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174 | |
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175 | long zdim = this->axisDim[2]; |
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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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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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183 | // float *specx, *specy, *specy2, *base; |
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184 | |
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185 | this->getSpectralArrays(objNum,specx,specy,specy2,base); |
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186 | |
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187 | std::string fluxLabel = "Flux"; |
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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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192 | |
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193 | if(fluxUnits.size()>5 && |
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194 | makelower(fluxUnits.substr(fluxUnits.size()-5, |
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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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201 | if(this->par.getSpectralMethod()=="sum"){ |
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202 | fluxLabel = "Integrated " + fluxLabel; |
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203 | if(this->head.isWCS()) { |
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204 | fluxLabel += " ["+intFluxUnits+"]"; |
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205 | } |
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206 | } |
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207 | else {// if(par.getSpectralMethod()=="peak"){ |
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208 | fluxLabel = "Peak " + fluxLabel; |
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209 | if(this->head.isWCS()) fluxLabel += " ["+fluxUnits+"]"; |
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210 | } |
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211 | |
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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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218 | |
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219 | // Find the maximum & minimum values of the spectrum, ignoring flagged channels. |
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220 | float max=0.,min=0.; |
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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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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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226 | if(this->par.getFlagBaseline()){ |
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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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229 | } |
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230 | if(this->reconExists){ |
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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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233 | } |
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234 | haveStarted=true; |
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235 | } |
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236 | } |
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237 | |
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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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243 | width = vmax - vmin; |
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244 | vmax += width * 0.01; |
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245 | vmin -= width * 0.01; |
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246 | |
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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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255 | |
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256 | if(this->head.isWCS()){ |
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257 | label = this->objectList->at(objNum).outputLabelWCS(); |
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258 | plot.firstHeaderLine(label); |
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259 | label = this->objectList->at(objNum).outputLabelFluxes(); |
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260 | plot.secondHeaderLine(label); |
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261 | } |
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262 | label = this->objectList->at(objNum).outputLabelWidths(this->head); |
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263 | plot.thirdHeaderLine(label); |
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264 | label = this->objectList->at(objNum).outputLabelPix(); |
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265 | plot.fourthHeaderLine(label); |
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266 | |
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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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279 | this->drawFlaggedChannels(plot,xval,yval); |
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280 | drawSpectralRange(plot,this->objectList->at(objNum),this->head); |
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281 | |
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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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288 | |
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289 | /**************************/ |
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290 | // ZOOM IN SPECTRALLY ON THE DETECTION. |
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291 | |
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292 | double minvel,maxvel; |
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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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295 | |
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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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300 | if((!this->par.isFlaggedChannel(i))&&(specx[i]>=minvel)&&(specx[i]<=maxvel)){ |
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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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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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312 | } |
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313 | } |
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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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319 | |
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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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332 | this->drawFlaggedChannels(plot,xval,yval); |
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333 | drawSpectralRange(plot,this->objectList->at(objNum),this->head); |
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334 | |
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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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341 | /**************************/ |
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342 | |
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343 | // DRAW THE MOMENT MAP OF THE DETECTION -- SUMMED OVER ALL CHANNELS |
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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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348 | |
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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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353 | |
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354 | } |
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355 | //-------------------------------------------------------------------- |
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356 | |
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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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372 | maxvel = this->head.pixToVel(xval,yval,zval); |
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373 | plot.drawFlaggedChannelRange(minvel,maxvel); |
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374 | } |
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375 | } |
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376 | } |
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377 | |
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378 | |
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379 | void Cube::plotSource(Detection obj, Plot::CutoutPlot &plot) |
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380 | { |
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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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393 | |
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394 | std::string label; |
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395 | plot.gotoHeader(); |
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396 | |
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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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403 | label = obj.outputLabelWidths(this->head); |
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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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411 | |
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412 | } |
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413 | |
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414 | } |
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