[2] | 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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[38] | 31 | #include <vector> |
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| 32 | |
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[2] | 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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[38] | 37 | #include <aips/Arrays/ArrayAccessor.h> |
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| 38 | #include <aips/Arrays/Slice.h> |
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[2] | 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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[38] | 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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[2] | 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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[15] | 68 | ROScalarColumn<Double> integr(t, "INTERVAL"); |
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[38] | 69 | ROArrayColumn<uInt> freqidc(t, "FREQID"); |
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[2] | 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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[15] | 78 | Double inttime = 0.0; |
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[2] | 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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[15] | 92 | integr.get(i,tmp); |
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| 93 | inttime += tmp; |
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[2] | 94 | } |
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| 95 | // averaging using mask |
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[9] | 96 | MaskedArray<Float> nma(narr,(narr > Float(0))); |
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[2] | 97 | outarr /= nma; |
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[9] | 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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[2] | 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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[15] | 106 | sc.interval =inttime; |
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| 107 | String tstr; srcn.getScalar(0,tstr);// get sourcename of "mid" point |
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[2] | 108 | sc.sourcename = tstr; |
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[38] | 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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[2] | 113 | sc.putSpectrum(outarr); |
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[9] | 114 | sc.putFlags(outflags); |
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[15] | 115 | SDMemTable* sdmt = new SDMemTable(*in,True); |
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[2] | 116 | sdmt->putSDContainer(sc); |
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| 117 | return CountedPtr<SDMemTable>(sdmt); |
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| 118 | } |
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[9] | 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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[15] | 126 | ROArrayColumn<Float> tsys(toff, "TSYS"); |
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[9] | 127 | ROScalarColumn<Double> mjd(ton, "TIME"); |
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[15] | 128 | ROScalarColumn<Double> integr(ton, "INTERVAL"); |
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[9] | 129 | ROScalarColumn<String> srcn(ton, "SRCNAME"); |
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[38] | 130 | ROArrayColumn<uInt> freqidc(ton, "FREQID"); |
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| 131 | |
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[9] | 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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[15] | 155 | integr.getScalar(0,tme); |
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| 156 | sc.interval = tme; |
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[38] | 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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[9] | 161 | sc.putSpectrum(out); |
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| 162 | sc.putFlags(outflags); |
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[15] | 163 | SDMemTable* sdmt = new SDMemTable(*on, True); |
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[9] | 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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[15] | 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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[9] | 173 | |
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[15] | 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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[38] | 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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[15] | 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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