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 <casa/aips.h> |
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34 | #include <casa/BasicSL/String.h> |
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35 | #include <casa/Arrays/IPosition.h> |
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36 | #include <casa/Arrays/Array.h> |
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37 | #include <casa/Arrays/ArrayAccessor.h> |
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38 | #include <casa/Arrays/Slice.h> |
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39 | #include <casa/Arrays/ArrayMath.h> |
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40 | #include <casa/Arrays/ArrayLogical.h> |
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41 | #include <casa/Arrays/MaskedArray.h> |
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42 | #include <casa/Arrays/MaskArrMath.h> |
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43 | #include <casa/Arrays/MaskArrLogi.h> |
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44 | |
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45 | #include <tables/Tables/Table.h> |
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46 | #include <tables/Tables/ScalarColumn.h> |
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47 | #include <tables/Tables/ArrayColumn.h> |
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48 | |
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49 | #include <scimath/Fitting.h> |
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50 | #include <scimath/Fitting/LinearFit.h> |
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51 | #include <scimath/Functionals/CompiledFunction.h> |
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52 | #include <images/Images/ImageUtilities.h> |
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53 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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54 | #include <scimath/Mathematics/AutoDiff.h> |
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55 | #include <scimath/Mathematics/AutoDiffMath.h> |
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56 | |
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57 | #include "MathUtils.h" |
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58 | #include "SDContainer.h" |
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59 | #include "SDMemTable.h" |
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60 | |
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61 | #include "SDMath.h" |
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62 | |
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63 | using namespace asap; |
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64 | //using namespace asap::SDMath; |
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65 | |
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66 | CountedPtr<SDMemTable> SDMath::average(const CountedPtr<SDMemTable>& in) { |
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67 | Table t = in->table(); |
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68 | ROArrayColumn<Float> tsys(t, "TSYS"); |
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69 | ROScalarColumn<Double> mjd(t, "TIME"); |
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70 | ROScalarColumn<String> srcn(t, "SRCNAME"); |
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71 | ROScalarColumn<Double> integr(t, "INTERVAL"); |
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72 | ROArrayColumn<uInt> freqidc(t, "FREQID"); |
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73 | IPosition ip = in->rowAsMaskedArray(0).shape(); |
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74 | Array<Float> outarr(ip); outarr =0.0; |
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75 | Array<Float> narr(ip);narr = 0.0; |
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76 | Array<Float> narrinc(ip);narrinc = 1.0; |
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77 | |
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78 | Array<Float> tsarr(tsys.shape(0)); |
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79 | Array<Float> outtsarr(tsys.shape(0)); |
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80 | outtsarr =0.0; |
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81 | tsys.get(0, tsarr);// this is probably unneccessary as tsys should |
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82 | Double tme = 0.0; |
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83 | Double inttime = 0.0; |
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84 | |
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85 | for (uInt i=0; i < t.nrow(); i++) { |
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86 | // data stuff |
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87 | MaskedArray<Float> marr(in->rowAsMaskedArray(i)); |
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88 | outarr += marr; |
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89 | MaskedArray<Float> n(narrinc,marr.getMask()); |
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90 | narr += n; |
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91 | // get |
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92 | tsys.get(i, tsarr);// this is probably unneccessary as tsys should |
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93 | outtsarr += tsarr; // be constant |
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94 | Double tmp; |
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95 | mjd.get(i,tmp); |
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96 | tme += tmp;// average time |
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97 | integr.get(i,tmp); |
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98 | inttime += tmp; |
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99 | } |
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100 | // averaging using mask |
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101 | MaskedArray<Float> nma(narr,(narr > Float(0))); |
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102 | outarr /= nma; |
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103 | Array<Bool> outflagsb = !(nma.getMask()); |
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104 | Array<uChar> outflags(outflagsb.shape()); |
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105 | convertArray(outflags,outflagsb); |
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106 | SDContainer sc = in->getSDContainer(); |
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107 | Int n = t.nrow(); |
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108 | outtsarr /= Float(n); |
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109 | sc.timestamp = tme/Double(n); |
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110 | sc.interval = inttime; |
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111 | String tstr; srcn.getScalar(0,tstr);// get sourcename of "mid" point |
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112 | sc.sourcename = tstr; |
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113 | Vector<uInt> tvec; |
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114 | freqidc.get(0,tvec); |
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115 | sc.putFreqMap(tvec); |
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116 | sc.putTsys(outtsarr); |
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117 | sc.scanid = 0; |
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118 | sc.putSpectrum(outarr); |
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119 | sc.putFlags(outflags); |
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120 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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121 | sdmt->putSDContainer(sc); |
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122 | return CountedPtr<SDMemTable>(sdmt); |
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123 | } |
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124 | |
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125 | CountedPtr<SDMemTable> |
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126 | SDMath::quotient(const CountedPtr<SDMemTable>& on, |
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127 | const CountedPtr<SDMemTable>& off) { |
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128 | |
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129 | Table ton = on->table(); |
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130 | Table toff = off->table(); |
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131 | ROArrayColumn<Float> tsys(toff, "TSYS"); |
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132 | ROScalarColumn<Double> mjd(ton, "TIME"); |
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133 | ROScalarColumn<Double> integr(ton, "INTERVAL"); |
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134 | ROScalarColumn<String> srcn(ton, "SRCNAME"); |
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135 | ROArrayColumn<uInt> freqidc(ton, "FREQID"); |
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136 | |
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137 | MaskedArray<Float> mon(on->rowAsMaskedArray(0)); |
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138 | MaskedArray<Float> moff(off->rowAsMaskedArray(0)); |
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139 | IPosition ipon = mon.shape(); |
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140 | IPosition ipoff = moff.shape(); |
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141 | Array<Float> tsarr;//(tsys.shape(0)); |
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142 | tsys.get(0, tsarr); |
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143 | if (ipon != ipoff && ipon != tsarr.shape()) |
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144 | cerr << "on/off not conformant" << endl; |
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145 | |
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146 | MaskedArray<Float> tmp = (mon-moff); |
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147 | Array<Float> out(tmp.getArray()); |
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148 | out /= moff; |
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149 | out *= tsarr; |
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150 | Array<Bool> outflagsb = !(mon.getMask() && moff.getMask()); |
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151 | Array<uChar> outflags(outflagsb.shape()); |
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152 | convertArray(outflags,outflagsb); |
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153 | SDContainer sc = on->getSDContainer(); |
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154 | sc.putTsys(tsarr); |
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155 | sc.scanid = 0; |
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156 | sc.putSpectrum(out); |
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157 | sc.putFlags(outflags); |
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158 | SDMemTable* sdmt = new SDMemTable(*on, True); |
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159 | sdmt->putSDContainer(sc); |
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160 | return CountedPtr<SDMemTable>(sdmt); |
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161 | } |
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162 | |
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163 | CountedPtr<SDMemTable> |
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164 | SDMath::multiply(const CountedPtr<SDMemTable>& in, Float factor) { |
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165 | SDMemTable* sdmt = new SDMemTable(*in); |
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166 | Table t = sdmt->table(); |
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167 | ArrayColumn<Float> spec(t,"SPECTRA"); |
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168 | |
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169 | for (uInt i=0; i < t.nrow(); i++) { |
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170 | // data stuff |
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171 | MaskedArray<Float> marr(sdmt->rowAsMaskedArray(i)); |
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172 | marr *= factor; |
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173 | spec.put(i, marr.getArray()); |
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174 | } |
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175 | return CountedPtr<SDMemTable>(sdmt); |
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176 | } |
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177 | |
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178 | bool SDMath::fit(Vector<Float>& thefit, const Vector<Float>& data, |
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179 | const Vector<Bool>& mask, |
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180 | const std::string& fitexpr) { |
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181 | |
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182 | LinearFit<Float> fitter; |
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183 | Vector<Float> x(data.nelements()); |
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184 | indgen(x); |
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185 | CompiledFunction<AutoDiff<Float> > fn; |
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186 | fn.setFunction(String(fitexpr)); |
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187 | fitter.setFunction(fn); |
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188 | Vector<Float> out,out1; |
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189 | out = fitter.fit(x,data,&mask); |
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190 | thefit = data; |
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191 | fitter.residual(thefit, x); |
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192 | cout << "Parameter solution = " << out << endl; |
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193 | return True; |
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194 | } |
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195 | |
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196 | CountedPtr<SDMemTable> |
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197 | SDMath::baseline(const CountedPtr<SDMemTable>& in, |
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198 | const std::string& fitexpr, |
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199 | const std::vector<bool>& mask) { |
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200 | |
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201 | IPosition ip = in->rowAsMaskedArray(0).shape(); |
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202 | SDContainer sc = in->getSDContainer(); |
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203 | String sname(in->getSourceName()); |
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204 | String stim(in->getTime()); |
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205 | cout << "Fitting: " << String(fitexpr) << " to " |
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206 | << sname << " [" << stim << "]" << ":" <<endl; |
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207 | MaskedArray<Float> marr(in->rowAsMaskedArray(0)); |
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208 | Vector<Bool> inmask(mask); |
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209 | Array<Float> arr = marr.getArray(); |
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210 | Array<Bool> barr = marr.getMask(); |
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211 | for (uInt i=0; i<in->nBeam();++i) { |
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212 | for (uInt j=0; j<in->nIF();++j) { |
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213 | for (uInt k=0; k<in->nPol();++k) { |
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214 | IPosition start(4,i,j,k,0); |
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215 | IPosition end(4,i,j,k,in->nChan()-1); |
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216 | Array<Float> subArr(arr(start,end)); |
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217 | Array<Bool> subMask(barr(start,end)); |
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218 | Vector<Float> outv; |
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219 | Vector<Float> v(subArr.nonDegenerate()); |
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220 | Vector<Bool> m(subMask.nonDegenerate()); |
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221 | cout << "\t Polarisation " << k << "\t"; |
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222 | SDMath::fit(outv, v, m&&inmask, fitexpr); |
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223 | ArrayAccessor<Float, Axis<0> > aa0(outv); |
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224 | for (ArrayAccessor<Float, Axis<3> > aa(subArr); aa != aa.end();++aa) { |
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225 | (*aa) = (*aa0); |
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226 | aa0++; |
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227 | } |
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228 | } |
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229 | } |
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230 | } |
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231 | Array<uChar> outflags(barr.shape()); |
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232 | convertArray(outflags,!barr); |
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233 | sc.putSpectrum(arr); |
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234 | sc.putFlags(outflags); |
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235 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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236 | sdmt->putSDContainer(sc); |
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237 | return CountedPtr<SDMemTable>(sdmt); |
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238 | } |
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239 | |
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240 | |
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241 | CountedPtr<SDMemTable> |
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242 | SDMath::hanning(const CountedPtr<SDMemTable>& in) { |
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243 | |
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244 | //IPosition ip = in->rowAsMaskedArray(0).shape(); |
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245 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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246 | for (uInt ri=0; ri < in->nRow(); ++ri) { |
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247 | |
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248 | MaskedArray<Float> marr(in->rowAsMaskedArray(ri)); |
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249 | |
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250 | Array<Float> arr = marr.getArray(); |
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251 | Array<Bool> barr = marr.getMask(); |
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252 | for (uInt i=0; i<in->nBeam();++i) { |
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253 | for (uInt j=0; j<in->nIF();++j) { |
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254 | for (uInt k=0; k<in->nPol();++k) { |
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255 | IPosition start(4,i,j,k,0); |
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256 | IPosition end(4,i,j,k,in->nChan()-1); |
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257 | Array<Float> subArr(arr(start,end)); |
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258 | Array<Bool> subMask(barr(start,end)); |
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259 | Vector<Float> outv; |
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260 | Vector<Bool> outm; |
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261 | Vector<Float> v(subArr.nonDegenerate()); |
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262 | Vector<Bool> m(subMask.nonDegenerate()); |
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263 | ::hanning(outv,outm,v,m); |
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264 | ArrayAccessor<Float, Axis<0> > aa0(outv); |
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265 | ArrayAccessor<Bool, Axis<0> > ba0(outm); |
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266 | ArrayAccessor<Bool, Axis<3> > ba(subMask); |
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267 | for (ArrayAccessor<Float, Axis<3> > aa(subArr); aa != aa.end();++aa) { |
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268 | (*aa) = (*aa0); |
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269 | (*ba) = (*ba0); |
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270 | aa0++; |
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271 | ba0++; |
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272 | ba++; |
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273 | } |
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274 | } |
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275 | } |
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276 | } |
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277 | Array<uChar> outflags(barr.shape()); |
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278 | convertArray(outflags,!barr); |
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279 | SDContainer sc = in->getSDContainer(ri); |
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280 | sc.putSpectrum(arr); |
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281 | sc.putFlags(outflags); |
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282 | sdmt->putSDContainer(sc); |
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283 | } |
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284 | return CountedPtr<SDMemTable>(sdmt); |
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285 | } |
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286 | |
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287 | CountedPtr<SDMemTable> |
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288 | SDMath::averages(const Block<CountedPtr<SDMemTable> >& in, |
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289 | const Vector<Bool>& mask) { |
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290 | IPosition ip = in[0]->rowAsMaskedArray(0).shape(); |
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291 | Array<Float> arr(ip); |
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292 | Array<Bool> barr(ip); |
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293 | Double inttime = 0.0; |
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294 | |
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295 | uInt n = in[0]->nChan(); |
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296 | for (uInt i=0; i<in[0]->nBeam();++i) { |
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297 | for (uInt j=0; j<in[0]->nIF();++j) { |
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298 | for (uInt k=0; k<in[0]->nPol();++k) { |
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299 | Float stdevsqsum = 0.0; |
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300 | Vector<Float> initvec(n);initvec = 0.0; |
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301 | Vector<Bool> initmask(n);initmask = True; |
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302 | MaskedArray<Float> outmarr(initvec,initmask); |
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303 | inttime = 0.0; |
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304 | for (uInt bi=0; bi< in.nelements(); ++bi) { |
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305 | MaskedArray<Float> marr(in[bi]->rowAsMaskedArray(0)); |
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306 | inttime += in[bi]->getInterval(); |
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307 | Array<Float> arr = marr.getArray(); |
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308 | Array<Bool> barr = marr.getMask(); |
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309 | IPosition start(4,i,j,k,0); |
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310 | IPosition end(4,i,j,k,n-1); |
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311 | Array<Float> subArr(arr(start,end)); |
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312 | Array<Bool> subMask(barr(start,end)); |
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313 | Vector<Float> outv; |
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314 | Vector<Bool> outm; |
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315 | Vector<Float> v(subArr.nonDegenerate()); |
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316 | Vector<Bool> m(subMask.nonDegenerate()); |
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317 | MaskedArray<Float> tmparr(v,m); |
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318 | MaskedArray<Float> tmparr2(tmparr(mask)); |
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319 | Float stdvsq = pow(stddev(tmparr2),2); |
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320 | stdevsqsum+=1.0/stdvsq; |
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321 | tmparr /= stdvsq; |
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322 | outmarr += tmparr; |
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323 | } |
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324 | outmarr /= stdevsqsum; |
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325 | Array<Float> tarr(outmarr.getArray()); |
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326 | Array<Bool> tbarr(outmarr.getMask()); |
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327 | IPosition start(4,i,j,k,0); |
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328 | IPosition end(4,i,j,k,n-1); |
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329 | Array<Float> subArr(arr(start,end)); |
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330 | Array<Bool> subMask(barr(start,end)); |
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331 | ArrayAccessor<Float, Axis<0> > aa0(tarr); |
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332 | ArrayAccessor<Bool, Axis<0> > ba0(tbarr); |
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333 | ArrayAccessor<Bool, Axis<3> > ba(subMask); |
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334 | for (ArrayAccessor<Float, Axis<3> > aa(subArr); aa != aa.end();++aa) { |
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335 | (*aa) = (*aa0); |
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336 | (*ba) = (*ba0); |
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337 | aa0++; |
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338 | ba0++; |
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339 | ba++; |
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340 | } |
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341 | } |
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342 | } |
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343 | } |
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344 | Array<uChar> outflags(barr.shape()); |
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345 | convertArray(outflags,!barr); |
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346 | SDContainer sc = in[0]->getSDContainer(); |
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347 | sc.putSpectrum(arr); |
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348 | sc.putFlags(outflags); |
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349 | sc.interval = inttime; |
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350 | SDMemTable* sdmt = new SDMemTable(*in[0],True); |
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351 | sdmt->putSDContainer(sc); |
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352 | return CountedPtr<SDMemTable>(sdmt); |
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353 | } |
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354 | |
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355 | CountedPtr<SDMemTable> |
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356 | SDMath::averagePol(const CountedPtr<SDMemTable>& in, |
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357 | const Vector<Bool>& mask) { |
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358 | MaskedArray<Float> marr(in->rowAsMaskedArray(0)); |
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359 | uInt n = in->nChan(); |
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360 | IPosition ip = marr.shape(); |
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361 | Array<Float> arr = marr.getArray(); |
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362 | Array<Bool> barr = marr.getMask(); |
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363 | for (uInt i=0; i<in->nBeam();++i) { |
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364 | for (uInt j=0; j<in->nIF();++j) { |
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365 | Float stdevsqsum = 0.0; |
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366 | Vector<Float> initvec(n);initvec = 0.0; |
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367 | Vector<Bool> initmask(n);initmask = True; |
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368 | MaskedArray<Float> outmarr(initvec,initmask); |
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369 | for (uInt k=0; k<in->nPol();++k) { |
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370 | IPosition start(4,i,j,k,0); |
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371 | IPosition end(4,i,j,k,in->nChan()-1); |
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372 | Array<Float> subArr(arr(start,end)); |
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373 | Array<Bool> subMask(barr(start,end)); |
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374 | Vector<Float> outv; |
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375 | Vector<Bool> outm; |
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376 | Vector<Float> v(subArr.nonDegenerate()); |
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377 | Vector<Bool> m(subMask.nonDegenerate()); |
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378 | MaskedArray<Float> tmparr(v,m); |
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379 | MaskedArray<Float> tmparr2(tmparr(mask)); |
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380 | Float stdvsq = pow(stddev(tmparr2),2); |
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381 | stdevsqsum+=1.0/stdvsq; |
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382 | tmparr /= stdvsq; |
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383 | outmarr += tmparr; |
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384 | } |
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385 | outmarr /= stdevsqsum; |
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386 | Array<Float> tarr(outmarr.getArray()); |
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387 | Array<Bool> tbarr(outmarr.getMask()); |
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388 | // write averaged pol into all pols - fix up to refrom array |
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389 | for (uInt k=0; k<in->nPol();++k) { |
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390 | IPosition start(4,i,j,k,0); |
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391 | IPosition end(4,i,j,k,n-1); |
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392 | Array<Float> subArr(arr(start,end)); |
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393 | Array<Bool> subMask(barr(start,end)); |
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394 | ArrayAccessor<Float, Axis<0> > aa0(tarr); |
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395 | ArrayAccessor<Bool, Axis<0> > ba0(tbarr); |
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396 | ArrayAccessor<Bool, Axis<3> > ba(subMask); |
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397 | for (ArrayAccessor<Float, Axis<3> > aa(subArr); aa != aa.end();++aa) { |
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398 | (*aa) = (*aa0); |
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399 | (*ba) = (*ba0); |
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400 | aa0++; |
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401 | ba0++; |
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402 | ba++; |
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403 | } |
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404 | } |
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405 | } |
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406 | } |
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407 | |
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408 | Array<uChar> outflags(barr.shape()); |
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409 | convertArray(outflags,!barr); |
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410 | SDContainer sc = in->getSDContainer(); |
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411 | sc.putSpectrum(arr); |
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412 | sc.putFlags(outflags); |
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413 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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414 | sdmt->putSDContainer(sc); |
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415 | return CountedPtr<SDMemTable>(sdmt); |
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416 | } |
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417 | |
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418 | |
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419 | Float SDMath::rms(const CountedPtr<SDMemTable>& in, |
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420 | const std::vector<bool>& mask) { |
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421 | Float rmsval; |
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422 | Vector<Bool> msk(mask); |
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423 | IPosition ip = in->rowAsMaskedArray(0).shape(); |
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424 | MaskedArray<Float> marr(in->rowAsMaskedArray(0)); |
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425 | |
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426 | Array<Float> arr = marr.getArray(); |
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427 | Array<Bool> barr = marr.getMask(); |
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428 | uInt i,j,k; |
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429 | i = in->getBeam(); |
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430 | j = in->getIF(); |
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431 | k = in->getPol(); |
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432 | IPosition start(4,i,j,k,0); |
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433 | IPosition end(4,i,j,k,in->nChan()-1); |
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434 | Array<Float> subArr(arr(start,end)); |
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435 | Array<Bool> subMask(barr(start,end)); |
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436 | Array<Float> v(subArr.nonDegenerate()); |
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437 | Array<Bool> m(subMask.nonDegenerate()); |
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438 | MaskedArray<Float> tmp; |
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439 | if (msk.nelements() == m.nelements() ) { |
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440 | tmp.setData(v,m&&msk); |
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441 | } else { |
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442 | tmp.setData(v,m); |
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443 | } |
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444 | rmsval = stddev(tmp); |
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445 | return rmsval; |
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446 | } |
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447 | |
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448 | CountedPtr<SDMemTable> SDMath::bin(const CountedPtr<SDMemTable>& in, |
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449 | Int width) { |
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450 | |
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451 | SDHeader sh = in->getSDHeader(); |
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452 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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453 | |
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454 | MaskedArray<Float> tmpmarr(in->rowAsMaskedArray(0)); |
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455 | MaskedArray<Float> tmpmarr2; |
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456 | SpectralCoordinate outcoord; |
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457 | IPosition ip; |
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458 | for (uInt j=0; j<in->nCoordinates(); ++j) { |
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459 | SpectralCoordinate coord(in->getCoordinate(j)); |
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460 | ImageUtilities::bin(tmpmarr2, outcoord, tmpmarr, coord, 3, width); |
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461 | ip = tmpmarr2.shape(); |
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462 | sdmt->setCoordinate(outcoord,j); |
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463 | } |
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464 | sh.nchan = ip(3); |
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465 | sdmt->putSDHeader(sh); |
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466 | |
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467 | SpectralCoordinate tmpcoord2,tmpcoord; |
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468 | for (uInt i=0; i < in->nRow(); ++i) { |
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469 | MaskedArray<Float> marr(in->rowAsMaskedArray(i)); |
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470 | SDContainer sc = in->getSDContainer(i); |
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471 | Array<Float> arr = marr.getArray(); |
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472 | Array<Bool> barr = marr.getMask(); |
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473 | MaskedArray<Float> marrout; |
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474 | ImageUtilities::bin(marrout, tmpcoord2, marr, tmpcoord, 3, width); |
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475 | IPosition ip2 = marrout.shape(); |
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476 | sc.resize(ip2); |
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477 | sc.putSpectrum(marrout.getArray()); |
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478 | Array<uChar> outflags(ip2); |
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479 | convertArray(outflags,!(marrout.getMask())); |
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480 | sc.putFlags(outflags); |
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481 | MaskedArray<Float> tsys,tsysout; |
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482 | Array<Bool> dummy(ip);dummy = True; |
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483 | tsys.setData(sc.getTsys(),dummy); |
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484 | ImageUtilities::bin(tsysout, tmpcoord2, marr, tmpcoord, 3, width); |
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485 | sc.putTsys(tsysout.getArray()); |
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486 | sdmt->putSDContainer(sc); |
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487 | } |
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488 | return CountedPtr<SDMemTable>(sdmt); |
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489 | } |
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