1 | //#--------------------------------------------------------------------------- |
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2 | //# SDMath.cc: A collection of single dish mathematical operations |
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3 | //#--------------------------------------------------------------------------- |
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4 | //# Copyright (C) 2004 |
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5 | //# Malte Marquarding, ATNF |
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6 | //# |
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7 | //# This program is free software; you can redistribute it and/or modify it |
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8 | //# under the terms of the GNU General Public License as published by the Free |
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9 | //# Software Foundation; either version 2 of the License, or (at your option) |
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10 | //# any later version. |
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11 | //# |
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12 | //# This program is distributed in the hope that it will be useful, but |
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13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of |
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14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
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15 | //# Public License for more details. |
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16 | //# |
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17 | //# You should have received a copy of the GNU General Public License along |
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18 | //# with this program; if not, write to the Free Software Foundation, Inc., |
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19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA. |
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20 | //# |
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21 | //# Correspondence concerning this software should be addressed as follows: |
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22 | //# Internet email: Malte.Marquarding@csiro.au |
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23 | //# Postal address: Malte Marquarding, |
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24 | //# Australia Telescope National Facility, |
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25 | //# P.O. Box 76, |
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26 | //# Epping, NSW, 2121, |
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27 | //# AUSTRALIA |
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28 | //# |
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29 | //# $Id: |
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30 | //#--------------------------------------------------------------------------- |
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31 | #include <vector> |
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32 | |
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33 | #include <aips/aips.h> |
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34 | #include <aips/Utilities/String.h> |
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35 | #include <aips/Arrays/IPosition.h> |
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36 | #include <aips/Arrays/Array.h> |
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37 | #include <aips/Arrays/ArrayAccessor.h> |
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38 | #include <aips/Arrays/Slice.h> |
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39 | #include <aips/Arrays/ArrayMath.h> |
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40 | #include <aips/Arrays/ArrayLogical.h> |
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41 | #include <aips/Arrays/MaskedArray.h> |
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42 | #include <aips/Arrays/MaskArrMath.h> |
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43 | #include <aips/Arrays/MaskArrLogi.h> |
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44 | |
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45 | #include <aips/Tables/Table.h> |
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46 | #include <aips/Tables/ScalarColumn.h> |
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47 | #include <aips/Tables/ArrayColumn.h> |
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48 | |
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49 | #include <aips/Fitting.h> |
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50 | #include <trial/Fitting/LinearFit.h> |
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51 | #include <trial/Functionals/CompiledFunction.h> |
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52 | #include <aips/Mathematics/AutoDiff.h> |
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53 | #include <aips/Mathematics/AutoDiffMath.h> |
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54 | |
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55 | #include "MathUtils.h" |
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56 | #include "SDContainer.h" |
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57 | #include "SDMemTable.h" |
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58 | |
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59 | #include "SDMath.h" |
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60 | |
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61 | using namespace atnf_sd; |
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62 | |
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63 | static CountedPtr<SDMemTable> SDMath::average(const CountedPtr<SDMemTable>& in) { |
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64 | Table t = in->table(); |
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65 | ROArrayColumn<Float> tsys(t, "TSYS"); |
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66 | ROScalarColumn<Double> mjd(t, "TIME"); |
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67 | ROScalarColumn<String> srcn(t, "SRCNAME"); |
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68 | ROScalarColumn<Double> integr(t, "INTERVAL"); |
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69 | ROArrayColumn<uInt> freqidc(t, "FREQID"); |
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70 | IPosition ip = in->rowAsMaskedArray(0).shape(); |
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71 | Array<Float> outarr(ip); outarr =0.0; |
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72 | Array<Float> narr(ip);narr = 0.0; |
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73 | Array<Float> narrinc(ip);narrinc = 1.0; |
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74 | |
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75 | Array<Float> tsarr(tsys.shape(0)); |
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76 | Array<Float> outtsarr(tsys.shape(0)); |
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77 | Double tme = 0.0; |
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78 | Double inttime = 0.0; |
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79 | |
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80 | for (uInt i=0; i < t.nrow(); i++) { |
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81 | // data stuff |
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82 | MaskedArray<Float> marr(in->rowAsMaskedArray(i)); |
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83 | outarr += marr; |
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84 | MaskedArray<Float> n(narrinc,marr.getMask()); |
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85 | narr += n; |
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86 | // get |
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87 | tsys.get(i, tsarr);// this is probably unneccessary as tsys should |
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88 | outtsarr += tsarr; // be constant |
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89 | Double tmp; |
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90 | mjd.get(i,tmp); |
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91 | tme += tmp;// average time |
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92 | integr.get(i,tmp); |
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93 | inttime += tmp; |
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94 | } |
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95 | // averaging using mask |
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96 | MaskedArray<Float> nma(narr,(narr > Float(0))); |
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97 | outarr /= nma; |
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98 | Array<Bool> outflagsb = !(nma.getMask()); |
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99 | Array<uChar> outflags(outflagsb.shape()); |
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100 | convertArray(outflags,outflagsb); |
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101 | SDContainer sc(ip(0),ip(1),ip(2),ip(3)); |
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102 | |
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103 | Int n = t.nrow(); |
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104 | outtsarr /= Float(n/2); |
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105 | sc.timestamp = tme/Double(n/2); |
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106 | sc.interval =inttime; |
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107 | String tstr; srcn.getScalar(0,tstr);// get sourcename of "mid" point |
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108 | sc.sourcename = tstr; |
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109 | Vector<uInt> tvec; |
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110 | freqidc.get(0,tvec); |
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111 | sc.putFreqMap(tvec); |
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112 | sc.scanid = 0; |
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113 | sc.putSpectrum(outarr); |
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114 | sc.putFlags(outflags); |
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115 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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116 | sdmt->putSDContainer(sc); |
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117 | return CountedPtr<SDMemTable>(sdmt); |
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118 | } |
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119 | |
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120 | static CountedPtr<SDMemTable> |
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121 | SDMath::quotient(const CountedPtr<SDMemTable>& on, |
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122 | const CountedPtr<SDMemTable>& off) { |
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123 | |
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124 | Table ton = on->table(); |
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125 | Table toff = off->table(); |
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126 | ROArrayColumn<Float> tsys(toff, "TSYS"); |
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127 | ROScalarColumn<Double> mjd(ton, "TIME"); |
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128 | ROScalarColumn<Double> integr(ton, "INTERVAL"); |
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129 | ROScalarColumn<String> srcn(ton, "SRCNAME"); |
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130 | ROArrayColumn<uInt> freqidc(ton, "FREQID"); |
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131 | |
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132 | MaskedArray<Float> mon(on->rowAsMaskedArray(0)); |
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133 | MaskedArray<Float> moff(off->rowAsMaskedArray(0)); |
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134 | IPosition ipon = mon.shape(); |
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135 | IPosition ipoff = moff.shape(); |
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136 | Array<Float> tsarr(tsys.shape(0)); |
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137 | |
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138 | if (ipon != ipoff && ipon != tsarr.shape()) |
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139 | cerr << "on/off not conformant" << endl; |
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140 | |
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141 | //IPosition test = mon.shape()/2; |
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142 | MaskedArray<Float> tmp = (mon-moff); |
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143 | Array<Float> out(tmp.getArray()); |
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144 | out /= moff; |
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145 | out *= tsarr; |
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146 | Array<Bool> outflagsb = !(mon.getMask() && moff.getMask()); |
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147 | Array<uChar> outflags(outflagsb.shape()); |
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148 | convertArray(outflags,outflagsb); |
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149 | |
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150 | SDContainer sc(ipon(0),ipon(1),ipon(2),ipon(3)); |
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151 | String tstr; srcn.getScalar(0,tstr);// get sourcename of "on" scan |
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152 | sc.sourcename = tstr; |
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153 | Double tme; mjd.getScalar(0,tme);// get time of "on" scan |
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154 | sc.timestamp = tme; |
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155 | integr.getScalar(0,tme); |
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156 | sc.interval = tme; |
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157 | Vector<uInt> tvec; |
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158 | freqidc.get(0,tvec); |
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159 | sc.putFreqMap(tvec); |
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160 | sc.scanid = 0; |
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161 | sc.putSpectrum(out); |
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162 | sc.putFlags(outflags); |
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163 | SDMemTable* sdmt = new SDMemTable(*on, True); |
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164 | sdmt->putSDContainer(sc); |
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165 | return CountedPtr<SDMemTable>(sdmt); |
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166 | |
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167 | } |
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168 | static CountedPtr<SDMemTable> |
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169 | SDMath::multiply(const CountedPtr<SDMemTable>& in, Float factor) { |
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170 | SDMemTable* sdmt = new SDMemTable(*in); |
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171 | Table t = sdmt->table(); |
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172 | ArrayColumn<Float> spec(t,"SPECTRA"); |
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173 | |
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174 | for (uInt i=0; i < t.nrow(); i++) { |
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175 | // data stuff |
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176 | MaskedArray<Float> marr(sdmt->rowAsMaskedArray(i)); |
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177 | marr *= factor; |
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178 | spec.put(i, marr.getArray()); |
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179 | } |
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180 | return CountedPtr<SDMemTable>(sdmt); |
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181 | } |
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182 | static std::vector<float> SDMath::baseline(const CountedPtr<SDMemTable>& in, |
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183 | const std::string& fitexpr) { |
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184 | cout << "Fitting: " << fitexpr << endl; |
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185 | Table t = in->table(); |
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186 | LinearFit<Float> fitter; |
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187 | Vector<Float> y; |
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188 | in->getSpectrum(y, 0); |
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189 | Vector<Bool> m; |
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190 | in->getMask(m, 0); |
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191 | Vector<Float> x(y.nelements()); |
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192 | indgen(x); |
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193 | CompiledFunction<AutoDiff<Float> > fn; |
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194 | fn.setFunction(String(fitexpr)); |
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195 | fitter.setFunction(fn); |
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196 | Vector<Float> out,out1; |
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197 | out = fitter.fit(x,y,&m); |
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198 | out1 = y; |
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199 | fitter.residual(out1,x); |
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200 | cout << "solution =" << out << endl; |
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201 | std::vector<float> fitted; |
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202 | out1.tovector(fitted); |
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203 | return fitted; |
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204 | } |
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205 | |
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206 | |
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207 | static CountedPtr<SDMemTable> |
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208 | SDMath::hanning(const CountedPtr<SDMemTable>& in) { |
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209 | IPosition ip = in->rowAsMaskedArray(0).shape(); |
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210 | MaskedArray<Float> marr(in->rowAsMaskedArray(0)); |
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211 | |
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212 | Array<Float> arr = marr.getArray(); |
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213 | Array<Bool> barr = marr.getMask(); |
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214 | for (uInt i=0; i<in->nBeam();++i) { |
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215 | for (uInt j=0; j<in->nIF();++j) { |
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216 | for (uInt k=0; k<in->nPol();++k) { |
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217 | IPosition start(4,i,j,k,0); |
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218 | IPosition end(4,i,j,k,in->nChan()-1); |
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219 | Array<Float> subArr(arr(start,end)); |
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220 | Array<Bool> subMask(barr(start,end)); |
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221 | Vector<Float> outv; |
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222 | Vector<Bool> outm; |
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223 | Vector<Float> v(subArr.nonDegenerate()); |
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224 | Vector<Bool> m(subMask.nonDegenerate()); |
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225 | ::hanning(outv,outm,v,m); |
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226 | ArrayAccessor<Float, Axis<0> > aa0(outv); |
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227 | ArrayAccessor<Bool, Axis<0> > ba0(outm); |
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228 | ArrayAccessor<Bool, Axis<3> > ba(subMask); |
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229 | for (ArrayAccessor<Float, Axis<3> > aa(subArr); aa != aa.end();++aa) { |
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230 | (*aa) = (*aa0); |
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231 | (*ba) = (*ba0); |
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232 | aa0++; |
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233 | ba0++; |
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234 | ba++; |
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235 | } |
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236 | } |
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237 | } |
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238 | } |
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239 | Array<uChar> outflags(barr.shape()); |
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240 | convertArray(outflags,!barr); |
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241 | SDContainer sc = in->getSDContainer(); |
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242 | sc.putSpectrum(arr); |
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243 | sc.putFlags(outflags); |
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244 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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245 | sdmt->putSDContainer(sc); |
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246 | return CountedPtr<SDMemTable>(sdmt); |
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247 | } |
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248 | |
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249 | /* |
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250 | static Float SDMath::rms(const SDMemTable& in, uInt whichRow) { |
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251 | Table t = in.table(); |
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252 | MaskedArray<Float> marr(in.rowAsMaskedArray(whichRow,True)); |
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253 | |
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254 | } |
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255 | */ |
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