1 | // ----------------------------------------------------------------------- |
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2 | // baseline.cc: Removing and replacing the spectral baseline of a Cube. |
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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 <iomanip> |
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30 | #include <duchamp/param.hh> |
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31 | #include <duchamp/ATrous/atrous.hh> |
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32 | #include <duchamp/Cubes/cubes.hh> |
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33 | #include <duchamp/Utils/feedback.hh> |
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34 | |
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35 | namespace duchamp |
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36 | { |
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37 | |
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38 | void Cube::removeBaseline() |
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39 | { |
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40 | /// @details |
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41 | /// A front-end to the findAtrousBaseline routine, specialised for the |
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42 | /// Cube data structure. Calls findAtrousBaseline on each spectrum individually. |
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43 | /// Upon exit, the original array minus its spectral baseline is stored |
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44 | /// in this->array and the baseline is in this->baseline. |
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45 | /// If the reconstructed array exists, the baseline is subtracted from |
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46 | /// it as well. |
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47 | |
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48 | float *spec = new float[this->axisDim[2]]; |
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49 | float *thisBaseline = new float[this->axisDim[2]]; |
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50 | size_t numSpec = this->axisDim[0]*this->axisDim[1]; |
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51 | |
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52 | ProgressBar bar; |
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53 | if(this->par.isVerbose()) bar.init(numSpec); |
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54 | for(size_t pix=0; pix<numSpec; pix++){ // for each spatial pixel... |
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55 | |
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56 | if(this->par.isVerbose() ) bar.update(pix+1); |
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57 | |
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58 | for(size_t z=0; z<this->axisDim[2]; z++) |
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59 | spec[z] = this->array[z*numSpec + pix]; |
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60 | |
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61 | if(this->par.getBaselineType()=="atrous") |
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62 | findAtrousBaseline(this->axisDim[2], spec, thisBaseline, this->par); |
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63 | else |
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64 | findMedianBaseline(this->axisDim[2], spec, this->par.getBaselineBoxWidth(), thisBaseline); |
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65 | |
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66 | for(size_t z=0; z<this->axisDim[2]; z++) { |
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67 | this->baseline[z*numSpec+pix] = thisBaseline[z]; |
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68 | if(!par.isBlank(this->array[z*numSpec+pix])){ |
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69 | this->array[z*numSpec+pix] -= thisBaseline[z]; |
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70 | if(this->reconExists) this->recon[z*numSpec+pix] -= thisBaseline[z]; |
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71 | } |
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72 | } |
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73 | |
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74 | } |
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75 | |
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76 | delete [] spec; |
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77 | delete [] thisBaseline; |
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78 | |
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79 | if(this->par.isVerbose()) bar.remove(); |
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80 | } |
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81 | |
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82 | |
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83 | |
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84 | void Cube::replaceBaseline(bool fixObjects) |
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85 | { |
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86 | /// @details |
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87 | /// A routine to replace the baseline flux on the reconstructed array |
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88 | /// (if it exists) and the fluxes of each of the detected objects (if any). |
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89 | |
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90 | if(this->par.getFlagBaseline()){ |
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91 | |
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92 | for(size_t i=0;i<this->numPixels;i++){ |
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93 | if(!(this->par.isBlank(this->array[i]))) |
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94 | this->array[i] += this->baseline[i]; |
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95 | } |
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96 | |
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97 | if(this->reconExists){ |
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98 | // if we made a reconstruction, we need to add the baseline back in |
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99 | // for plotting purposes |
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100 | for(size_t i=0;i<this->numPixels;i++){ |
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101 | if(!(this->par.isBlank(this->array[i]))) |
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102 | this->recon[i] += this->baseline[i]; |
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103 | } |
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104 | } |
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105 | |
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106 | if (fixObjects) { |
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107 | std::vector<Detection>::iterator obj; |
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108 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
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109 | // for each detection, correct the flux calculations. |
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110 | obj->calcFluxes(this->array, this->axisDim); |
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111 | } |
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112 | } |
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113 | |
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114 | } |
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115 | |
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116 | } |
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117 | |
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118 | } |
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