[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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[125] | 5 | //# ATNF |
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[2] | 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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[81] | 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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[130] | 37 | #include <casa/Arrays/ArrayIter.h> |
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| 38 | #include <casa/Arrays/VectorIter.h> |
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[81] | 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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[234] | 44 | #include <casa/BasicMath/Math.h> |
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[221] | 45 | #include <casa/Containers/Block.h> |
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| 46 | #include <casa/Quanta/QC.h> |
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[177] | 47 | #include <casa/Utilities/Assert.h> |
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[130] | 48 | #include <casa/Exceptions.h> |
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[2] | 49 | |
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[177] | 50 | #include <scimath/Mathematics/VectorKernel.h> |
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| 51 | #include <scimath/Mathematics/Convolver.h> |
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[227] | 52 | #include <scimath/Mathematics/InterpolateArray1D.h> |
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[234] | 53 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 54 | |
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[81] | 55 | #include <tables/Tables/Table.h> |
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| 56 | #include <tables/Tables/ScalarColumn.h> |
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| 57 | #include <tables/Tables/ArrayColumn.h> |
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[227] | 58 | #include <tables/Tables/ReadAsciiTable.h> |
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[2] | 59 | |
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[130] | 60 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 61 | #include <lattices/Lattices/RebinLattice.h> |
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[81] | 62 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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[130] | 63 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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| 64 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[221] | 65 | #include <coordinates/Coordinates/VelocityAligner.h> |
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[38] | 66 | |
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| 67 | #include "MathUtils.h" |
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[232] | 68 | #include "SDDefs.h" |
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[2] | 69 | #include "SDContainer.h" |
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| 70 | #include "SDMemTable.h" |
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| 71 | |
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| 72 | #include "SDMath.h" |
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| 73 | |
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[125] | 74 | using namespace casa; |
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[83] | 75 | using namespace asap; |
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[2] | 76 | |
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[170] | 77 | |
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| 78 | SDMath::SDMath() |
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| 79 | {;} |
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| 80 | |
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[185] | 81 | SDMath::SDMath(const SDMath& other) |
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[170] | 82 | { |
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| 83 | |
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| 84 | // No state |
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| 85 | |
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| 86 | } |
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| 87 | |
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| 88 | SDMath& SDMath::operator=(const SDMath& other) |
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| 89 | { |
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| 90 | if (this != &other) { |
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| 91 | // No state |
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| 92 | } |
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| 93 | return *this; |
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| 94 | } |
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| 95 | |
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[183] | 96 | SDMath::~SDMath() |
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| 97 | {;} |
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[170] | 98 | |
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[183] | 99 | |
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[185] | 100 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in, |
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| 101 | const Vector<Bool>& mask, Bool scanAv, |
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[234] | 102 | const String& weightStr) const |
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[221] | 103 | //Bool alignVelocity) |
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[130] | 104 | // |
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[144] | 105 | // Weighted averaging of spectra from one or more Tables. |
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[130] | 106 | // |
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| 107 | { |
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[221] | 108 | Bool alignVelocity = False; |
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[2] | 109 | |
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[163] | 110 | // Convert weight type |
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| 111 | |
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| 112 | WeightType wtType = NONE; |
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[185] | 113 | convertWeightString(wtType, weightStr); |
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[163] | 114 | |
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[144] | 115 | // Create output Table by cloning from the first table |
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[2] | 116 | |
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[144] | 117 | SDMemTable* pTabOut = new SDMemTable(*in[0],True); |
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[130] | 118 | |
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[144] | 119 | // Setup |
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[130] | 120 | |
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[144] | 121 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change |
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| 122 | Array<Float> arr(shp); |
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| 123 | Array<Bool> barr(shp); |
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[221] | 124 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis)); |
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[130] | 125 | |
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[144] | 126 | // Columns from Tables |
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[130] | 127 | |
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[144] | 128 | ROArrayColumn<Float> tSysCol; |
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| 129 | ROScalarColumn<Double> mjdCol; |
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| 130 | ROScalarColumn<String> srcNameCol; |
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| 131 | ROScalarColumn<Double> intCol; |
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| 132 | ROArrayColumn<uInt> fqIDCol; |
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[130] | 133 | |
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[144] | 134 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam |
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| 135 | // Note that the mask of the accumulation array will ALWAYS remain ALL True. |
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| 136 | // The MA is only used so that when data which is masked Bad is added to it, |
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| 137 | // that data does not contribute. |
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| 138 | |
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| 139 | Array<Float> zero(shp); |
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| 140 | zero=0.0; |
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| 141 | Array<Bool> good(shp); |
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| 142 | good = True; |
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| 143 | MaskedArray<Float> sum(zero,good); |
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| 144 | |
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| 145 | // Counter arrays |
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| 146 | |
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| 147 | Array<Float> nPts(shp); // Number of points |
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| 148 | nPts = 0.0; |
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| 149 | Array<Float> nInc(shp); // Increment |
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| 150 | nInc = 1.0; |
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| 151 | |
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| 152 | // Create accumulation Array for variance. We accumulate for |
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| 153 | // each if,pol,beam, but average over channel. So we need |
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| 154 | // a shape with one less axis dropping channels. |
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| 155 | |
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| 156 | const uInt nAxesSub = shp.nelements() - 1; |
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| 157 | IPosition shp2(nAxesSub); |
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| 158 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) { |
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[221] | 159 | if (i!=asap::ChanAxis) { |
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[144] | 160 | shp2(j) = shp(i); |
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| 161 | j++; |
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| 162 | } |
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[2] | 163 | } |
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[144] | 164 | Array<Float> sumSq(shp2); |
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| 165 | sumSq = 0.0; |
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| 166 | IPosition pos2(nAxesSub,0); // For indexing |
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[130] | 167 | |
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[144] | 168 | // Time-related accumulators |
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[130] | 169 | |
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[144] | 170 | Double time; |
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| 171 | Double timeSum = 0.0; |
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| 172 | Double intSum = 0.0; |
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| 173 | Double interval = 0.0; |
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[130] | 174 | |
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[144] | 175 | // To get the right shape for the Tsys accumulator we need to |
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| 176 | // access a column from the first table. The shape of this |
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| 177 | // array must not change |
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[130] | 178 | |
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[144] | 179 | Array<Float> tSysSum; |
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| 180 | { |
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| 181 | const Table& tabIn = in[0]->table(); |
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| 182 | tSysCol.attach(tabIn,"TSYS"); |
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| 183 | tSysSum.resize(tSysCol.shape(0)); |
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| 184 | } |
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| 185 | tSysSum =0.0; |
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| 186 | Array<Float> tSys; |
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| 187 | |
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| 188 | // Scan and row tracking |
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| 189 | |
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| 190 | Int oldScanID = 0; |
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| 191 | Int outScanID = 0; |
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| 192 | Int scanID = 0; |
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| 193 | Int rowStart = 0; |
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| 194 | Int nAccum = 0; |
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| 195 | Int tableStart = 0; |
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| 196 | |
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| 197 | // Source and FreqID |
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| 198 | |
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| 199 | String sourceName, oldSourceName, sourceNameStart; |
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| 200 | Vector<uInt> freqID, freqIDStart, oldFreqID; |
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| 201 | |
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[221] | 202 | // Velocity Aligner. We need an aligner for each Direction and FreqID |
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| 203 | // combination. I don't think there is anyway to know how many |
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| 204 | // directions there are. |
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| 205 | // For now, assume all Tables have the same Frequency Table |
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| 206 | |
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| 207 | /* |
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| 208 | { |
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| 209 | MEpoch::Ref timeRef(MEpoch::UTC); // Should be in header |
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| 210 | MDirection::Types dirRef(MDirection::J2000); // Should be in header |
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| 211 | // |
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| 212 | SDHeader sh = in[0].getSDHeader(); |
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| 213 | const uInt nChan = sh.nchan; |
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| 214 | // |
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| 215 | const SDFrequencyTable freqTab = in[0]->getSDFreqTable(); |
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| 216 | const uInt nFreqID = freqTab.length(); |
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| 217 | PtrBlock<const VelocityAligner<Float>* > vA(nFreqID); |
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| 218 | |
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| 219 | // Get first time from first table |
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| 220 | |
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| 221 | const Table& tabIn0 = in[0]->table(); |
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| 222 | mjdCol.attach(tabIn0, "TIME"); |
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| 223 | Double dTmp; |
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| 224 | mjdCol.get(0, dTmp); |
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| 225 | MVEpoch tmp2(Quantum<Double>(dTmp, Unit(String("d")))); |
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| 226 | MEpoch epoch(tmp2, timeRef); |
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| 227 | // |
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| 228 | for (uInt freqID=0; freqID<nFreqID; freqID++) { |
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| 229 | SpectralCoordinate sC = in[0]->getCoordinate(freqID); |
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| 230 | vA[freqID] = new VelocityAligner<Float>(sC, nChan, epoch, const MDirection& dir, |
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| 231 | const MPosition& pos, const String& velUnit, |
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| 232 | MDoppler::Types velType, MFrequency::Types velFreqSystem) |
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| 233 | } |
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| 234 | } |
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| 235 | */ |
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| 236 | |
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[144] | 237 | // Loop over tables |
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| 238 | |
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| 239 | Float fac = 1.0; |
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| 240 | const uInt nTables = in.nelements(); |
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| 241 | for (uInt iTab=0; iTab<nTables; iTab++) { |
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| 242 | |
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[221] | 243 | // Should check that the frequency tables don't change if doing VelocityAlignment |
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| 244 | |
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[144] | 245 | // Attach columns to Table |
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| 246 | |
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| 247 | const Table& tabIn = in[iTab]->table(); |
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| 248 | tSysCol.attach(tabIn, "TSYS"); |
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| 249 | mjdCol.attach(tabIn, "TIME"); |
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| 250 | srcNameCol.attach(tabIn, "SRCNAME"); |
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| 251 | intCol.attach(tabIn, "INTERVAL"); |
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| 252 | fqIDCol.attach(tabIn, "FREQID"); |
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| 253 | |
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| 254 | // Loop over rows in Table |
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| 255 | |
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| 256 | const uInt nRows = in[iTab]->nRow(); |
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| 257 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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| 258 | |
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| 259 | // Check conformance |
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| 260 | |
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| 261 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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| 262 | if (!shp.isEqual(shp2)) { |
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| 263 | throw (AipsError("Shapes for all rows must be the same")); |
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| 264 | } |
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| 265 | |
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| 266 | // If we are not doing scan averages, make checks for source and |
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| 267 | // frequency setup and warn if averaging across them |
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| 268 | |
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| 269 | // Get copy of Scan Container for this row |
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| 270 | |
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| 271 | SDContainer sc = in[iTab]->getSDContainer(iRow); |
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| 272 | scanID = sc.scanid; |
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| 273 | |
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| 274 | // Get quantities from columns |
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| 275 | |
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| 276 | srcNameCol.getScalar(iRow, sourceName); |
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| 277 | mjdCol.get(iRow, time); |
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| 278 | tSysCol.get(iRow, tSys); |
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| 279 | intCol.get(iRow, interval); |
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| 280 | fqIDCol.get(iRow, freqID); |
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| 281 | |
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| 282 | // Initialize first source and freqID |
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| 283 | |
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| 284 | if (iRow==0 && iTab==0) { |
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| 285 | sourceNameStart = sourceName; |
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| 286 | freqIDStart = freqID; |
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| 287 | } |
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| 288 | |
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| 289 | // If we are doing scan averages, see if we are at the end of an |
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| 290 | // accumulation period (scan). We must check soutce names too, |
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| 291 | // since we might have two tables with one scan each but different |
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| 292 | // source names; we shouldn't average different sources together |
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| 293 | |
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| 294 | if (scanAv && ( (scanID != oldScanID) || |
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| 295 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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| 296 | |
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| 297 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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| 298 | |
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[221] | 299 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 300 | |
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| 301 | // Fill scan container. The source and freqID come from the |
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| 302 | // first row of the first table that went into this average ( |
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| 303 | // should be the same for all rows in the scan average) |
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| 304 | |
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| 305 | Float nR(nAccum); |
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[185] | 306 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 307 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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| 308 | |
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| 309 | // Write container out to Table |
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| 310 | |
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| 311 | pTabOut->putSDContainer(sc); |
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| 312 | |
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| 313 | // Reset accumulators |
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| 314 | |
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| 315 | sum = 0.0; |
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| 316 | sumSq = 0.0; |
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| 317 | nAccum = 0; |
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| 318 | // |
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| 319 | tSysSum =0.0; |
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| 320 | timeSum = 0.0; |
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| 321 | intSum = 0.0; |
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[221] | 322 | nPts = 0.0; |
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[144] | 323 | |
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| 324 | // Increment |
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| 325 | |
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| 326 | rowStart = iRow; // First row for next accumulation |
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| 327 | tableStart = iTab; // First table for next accumulation |
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| 328 | sourceNameStart = sourceName; // First source name for next accumulation |
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| 329 | freqIDStart = freqID; // First FreqID for next accumulation |
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| 330 | // |
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| 331 | oldScanID = scanID; |
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| 332 | outScanID += 1; // Scan ID for next accumulation period |
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[227] | 333 | } |
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[144] | 334 | |
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[146] | 335 | // Accumulate |
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[144] | 336 | |
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[185] | 337 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, |
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[221] | 338 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis, |
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[146] | 339 | nAxesSub, useMask, wtType); |
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[144] | 340 | // |
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| 341 | oldSourceName = sourceName; |
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| 342 | oldFreqID = freqID; |
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[184] | 343 | } |
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[144] | 344 | } |
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| 345 | |
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| 346 | // OK at this point we have accumulation data which is either |
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| 347 | // - accumulated from all tables into one row |
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| 348 | // or |
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| 349 | // - accumulated from the last scan average |
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| 350 | // |
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| 351 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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[221] | 352 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 353 | |
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| 354 | // Create and fill container. The container we clone will be from |
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| 355 | // the last Table and the first row that went into the current |
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| 356 | // accumulation. It probably doesn't matter that much really... |
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| 357 | |
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| 358 | Float nR(nAccum); |
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| 359 | SDContainer sc = in[tableStart]->getSDContainer(rowStart); |
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[185] | 360 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 361 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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[221] | 362 | pTabOut->putSDContainer(sc); |
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[144] | 363 | // |
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| 364 | return CountedPtr<SDMemTable>(pTabOut); |
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[2] | 365 | } |
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[9] | 366 | |
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[144] | 367 | |
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| 368 | |
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[234] | 369 | CountedPtr<SDMemTable> SDMath::quotient(const CountedPtr<SDMemTable>& on, |
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| 370 | const CountedPtr<SDMemTable>& off, |
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| 371 | Bool preserveContinuum) const |
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[185] | 372 | { |
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[234] | 373 | const uInt nRowOn = on->nRow(); |
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| 374 | const uInt nRowOff = off->nRow(); |
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| 375 | Bool ok = (nRowOff==1&&nRowOn>0) || |
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| 376 | (nRowOn>0&&nRowOn==nRowOff); |
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| 377 | if (!ok) { |
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| 378 | throw (AipsError("The reference Scan Table can have one row or the same number of rows as the source Scan Table")); |
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[130] | 379 | } |
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[85] | 380 | |
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[130] | 381 | // Input Tables and columns |
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| 382 | |
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[234] | 383 | Table tabOn = on->table(); |
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| 384 | Table tabOff = off->table(); |
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| 385 | ROArrayColumn<Float> tSysOn(tabOn, "TSYS"); |
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| 386 | ROArrayColumn<Float> tSysOff(tabOff, "TSYS"); |
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[38] | 387 | |
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[130] | 388 | // Output Table cloned from input |
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[85] | 389 | |
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[171] | 390 | SDMemTable* pTabOut = new SDMemTable(*on, True); |
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[130] | 391 | |
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| 392 | // Loop over rows |
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| 393 | |
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[234] | 394 | MaskedArray<Float>* pMOff = new MaskedArray<Float>(off->rowAsMaskedArray(0)); |
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| 395 | IPosition shpOff = pMOff->shape(); |
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[130] | 396 | // |
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[234] | 397 | Array<Float> tSysOnArr, tSysOffArr; |
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| 398 | tSysOn.get(0, tSysOnArr); |
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| 399 | tSysOff.get(0, tSysOffArr); |
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| 400 | // |
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| 401 | for (uInt i=0; i<nRowOn; i++) { |
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| 402 | MaskedArray<Float> mOn(on->rowAsMaskedArray(i)); |
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| 403 | IPosition shpOn = mOn.shape(); |
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| 404 | // |
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| 405 | if (nRowOff>1) { |
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| 406 | delete pMOff; |
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| 407 | pMOff = new MaskedArray<Float>(off->rowAsMaskedArray(i)); |
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| 408 | shpOff = pMOff->shape(); |
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| 409 | if (!shpOn.isEqual(shpOff)) { |
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| 410 | throw(AipsError("on/off data are not conformant")); |
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| 411 | } |
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| 412 | // |
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| 413 | tSysOff.get(i, tSysOffArr); |
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| 414 | tSysOn.get(i, tSysOnArr); |
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| 415 | if (!tSysOnArr.shape().isEqual(tSysOffArr.shape())) { |
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| 416 | throw(AipsError("on/off Tsys data are not conformant")); |
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| 417 | } |
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| 418 | // |
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| 419 | if (!shpOn.isEqual(tSysOnArr.shape())) { |
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| 420 | throw(AipsError("Correlation and Tsys data are not conformant")); |
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| 421 | } |
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[130] | 422 | } |
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| 423 | |
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| 424 | // Compute quotient |
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| 425 | |
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[234] | 426 | MaskedArray<Float> tmp = (mOn-*pMOff); |
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[130] | 427 | Array<Float> out(tmp.getArray()); |
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[234] | 428 | out /= *pMOff; |
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| 429 | out *= tSysOffArr; |
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[130] | 430 | |
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[234] | 431 | // MaskedArray<Float> tmp2 = (tSysOnArr * mOn / *pMOff) - tSysOffArr; |
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| 432 | |
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| 433 | |
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[130] | 434 | // Fill container for this row |
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| 435 | |
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[184] | 436 | SDContainer sc = on->getSDContainer(i); |
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[163] | 437 | // |
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[234] | 438 | putDataInSDC(sc, out, tmp.getMask()); |
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| 439 | sc.putTsys(tSysOffArr); |
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[184] | 440 | sc.scanid = i; |
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[130] | 441 | |
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| 442 | // Put new row in output Table |
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[234] | 443 | |
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| 444 | pTabOut->putSDContainer(sc); |
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| 445 | } |
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| 446 | if (pMOff) delete pMOff; |
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| 447 | // |
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| 448 | return CountedPtr<SDMemTable>(pTabOut); |
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| 449 | } |
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[130] | 450 | |
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[234] | 451 | |
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| 452 | CountedPtr<SDMemTable> SDMath::simpleBinaryOperate (const CountedPtr<SDMemTable>& left, |
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| 453 | const CountedPtr<SDMemTable>& right, |
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| 454 | const String& op) const |
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| 455 | // |
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| 456 | // Simple binary Table operators. add, subtract, multiply, divide (what=0,1,2,3) |
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| 457 | // |
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| 458 | { |
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| 459 | |
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| 460 | // CHeck operator |
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| 461 | |
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| 462 | String op2(op); |
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| 463 | op2.upcase(); |
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| 464 | uInt what = 0; |
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| 465 | if (op2=="ADD") { |
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| 466 | what = 0; |
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| 467 | } else if (op2=="SUB") { |
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| 468 | what = 1; |
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| 469 | } else if (op2=="MUL") { |
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| 470 | what = 2; |
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| 471 | } else if (op2=="DIV") { |
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| 472 | what = 3; |
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| 473 | } else { |
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| 474 | throw AipsError("Unrecognized operation"); |
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| 475 | } |
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| 476 | |
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| 477 | // Check rows |
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| 478 | |
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| 479 | const uInt nRows = left->nRow(); |
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| 480 | if (right->nRow() != nRows) { |
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| 481 | throw (AipsError("Input Scan Tables must have the same number of rows")); |
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| 482 | } |
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| 483 | |
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| 484 | // Input Tables and columns |
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| 485 | |
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| 486 | const Table& tLeft = left->table(); |
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| 487 | const Table& tRight = right->table(); |
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| 488 | // |
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| 489 | ROArrayColumn<Float> tSysLeft(tLeft, "TSYS"); |
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| 490 | ROArrayColumn<Float> tSysRight(tRight, "TSYS"); |
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| 491 | |
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| 492 | // Output Table cloned from input |
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| 493 | |
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| 494 | SDMemTable* pTabOut = new SDMemTable(*left, True); |
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| 495 | |
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| 496 | // Loop over rows |
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| 497 | |
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| 498 | for (uInt i=0; i<nRows; i++) { |
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| 499 | |
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| 500 | // Get data |
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| 501 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i)); |
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| 502 | MaskedArray<Float> mRight(right->rowAsMaskedArray(i)); |
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| 503 | // |
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| 504 | IPosition shpLeft = mLeft.shape(); |
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| 505 | IPosition shpRight = mRight.shape(); |
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| 506 | if (!shpLeft.isEqual(shpRight)) { |
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| 507 | throw(AipsError("left/right Scan Tables are not conformant")); |
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| 508 | } |
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| 509 | |
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| 510 | // Get TSys |
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| 511 | |
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| 512 | Array<Float> tSysLeftArr, tSysRightArr; |
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| 513 | tSysLeft.get(i, tSysLeftArr); |
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| 514 | tSysRight.get(i, tSysRightArr); |
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| 515 | |
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| 516 | // Make container |
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| 517 | |
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| 518 | SDContainer sc = left->getSDContainer(i); |
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| 519 | |
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| 520 | // Operate on data and TSys |
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| 521 | |
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| 522 | if (what==0) { |
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| 523 | MaskedArray<Float> tmp = mLeft + mRight; |
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| 524 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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| 525 | sc.putTsys(tSysLeftArr+tSysRightArr); |
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| 526 | } else if (what==1) { |
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| 527 | MaskedArray<Float> tmp = mLeft - mRight; |
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| 528 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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| 529 | sc.putTsys(tSysLeftArr-tSysRightArr); |
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| 530 | } else if (what==2) { |
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| 531 | MaskedArray<Float> tmp = mLeft * mRight; |
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| 532 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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| 533 | sc.putTsys(tSysLeftArr*tSysRightArr); |
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| 534 | } else if (what==3) { |
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| 535 | MaskedArray<Float> tmp = mLeft / mRight; |
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| 536 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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| 537 | sc.putTsys(tSysLeftArr/tSysRightArr); |
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| 538 | } |
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| 539 | |
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| 540 | // Put new row in output Table |
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| 541 | |
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[171] | 542 | pTabOut->putSDContainer(sc); |
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[130] | 543 | } |
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| 544 | // |
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[171] | 545 | return CountedPtr<SDMemTable>(pTabOut); |
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[9] | 546 | } |
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[48] | 547 | |
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[146] | 548 | |
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| 549 | |
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[185] | 550 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in, |
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[234] | 551 | const Vector<Bool>& mask, |
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| 552 | const String& which, Int row) const |
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[130] | 553 | // |
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| 554 | // Perhaps iteration over pol/beam/if should be in here |
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| 555 | // and inside the nrow iteration ? |
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| 556 | // |
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| 557 | { |
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| 558 | const uInt nRow = in->nRow(); |
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| 559 | |
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| 560 | // Specify cursor location |
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| 561 | |
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[152] | 562 | IPosition start, end; |
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[185] | 563 | getCursorLocation(start, end, *in); |
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[130] | 564 | |
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| 565 | // Loop over rows |
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| 566 | |
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[234] | 567 | const uInt nEl = mask.nelements(); |
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| 568 | uInt iStart = 0; |
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| 569 | uInt iEnd = in->nRow()-1; |
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| 570 | // |
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| 571 | if (row>=0) { |
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| 572 | iStart = row; |
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| 573 | iEnd = row; |
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| 574 | } |
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| 575 | // |
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| 576 | std::vector<float> result(iEnd-iStart+1); |
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| 577 | for (uInt ii=iStart; ii <= iEnd; ++ii) { |
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[130] | 578 | |
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| 579 | // Get row and deconstruct |
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| 580 | |
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| 581 | MaskedArray<Float> marr(in->rowAsMaskedArray(ii)); |
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| 582 | Array<Float> arr = marr.getArray(); |
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| 583 | Array<Bool> barr = marr.getMask(); |
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| 584 | |
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| 585 | // Access desired piece of data |
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| 586 | |
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| 587 | Array<Float> v((arr(start,end)).nonDegenerate()); |
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| 588 | Array<Bool> m((barr(start,end)).nonDegenerate()); |
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| 589 | |
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| 590 | // Apply OTF mask |
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| 591 | |
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| 592 | MaskedArray<Float> tmp; |
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| 593 | if (m.nelements()==nEl) { |
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[234] | 594 | tmp.setData(v,m&&mask); |
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[130] | 595 | } else { |
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| 596 | tmp.setData(v,m); |
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| 597 | } |
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| 598 | |
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| 599 | // Get statistic |
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| 600 | |
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[234] | 601 | result[ii-iStart] = mathutil::statistics(which, tmp); |
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[130] | 602 | } |
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| 603 | // |
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| 604 | return result; |
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| 605 | } |
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| 606 | |
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[146] | 607 | |
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[234] | 608 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const |
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[144] | 609 | { |
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[169] | 610 | SDHeader sh = in.getSDHeader(); |
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| 611 | SDMemTable* pTabOut = new SDMemTable(in, True); |
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[163] | 612 | |
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[169] | 613 | // Bin up SpectralCoordinates |
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[163] | 614 | |
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[169] | 615 | IPosition factors(1); |
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| 616 | factors(0) = width; |
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| 617 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
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| 618 | CoordinateSystem cSys; |
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| 619 | cSys.addCoordinate(in.getCoordinate(j)); |
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| 620 | CoordinateSystem cSysBin = |
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[185] | 621 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False); |
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[169] | 622 | // |
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| 623 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
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| 624 | pTabOut->setCoordinate(sCBin, j); |
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| 625 | } |
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[163] | 626 | |
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[169] | 627 | // Use RebinLattice to find shape |
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[130] | 628 | |
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[169] | 629 | IPosition shapeIn(1,sh.nchan); |
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[185] | 630 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors); |
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[169] | 631 | sh.nchan = shapeOut(0); |
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| 632 | pTabOut->putSDHeader(sh); |
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[144] | 633 | |
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| 634 | |
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[169] | 635 | // Loop over rows and bin along channel axis |
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| 636 | |
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| 637 | for (uInt i=0; i < in.nRow(); ++i) { |
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| 638 | SDContainer sc = in.getSDContainer(i); |
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[144] | 639 | // |
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[169] | 640 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
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[144] | 641 | |
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[169] | 642 | // Bin up spectrum |
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[144] | 643 | |
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[169] | 644 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
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| 645 | MaskedArray<Float> marrout; |
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[221] | 646 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width); |
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[144] | 647 | |
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[169] | 648 | // Put back the binned data and flags |
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[144] | 649 | |
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[169] | 650 | IPosition ip2 = marrout.shape(); |
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| 651 | sc.resize(ip2); |
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[146] | 652 | // |
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[185] | 653 | putDataInSDC(sc, marrout.getArray(), marrout.getMask()); |
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[146] | 654 | |
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[169] | 655 | // Bin up Tsys. |
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[146] | 656 | |
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[169] | 657 | Array<Bool> allGood(tSys.shape(),True); |
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| 658 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
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[146] | 659 | // |
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[169] | 660 | MaskedArray<Float> tSysOut; |
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[221] | 661 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width); |
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[169] | 662 | sc.putTsys(tSysOut.getArray()); |
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[146] | 663 | // |
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[169] | 664 | pTabOut->putSDContainer(sc); |
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| 665 | } |
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| 666 | return pTabOut; |
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[146] | 667 | } |
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| 668 | |
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[185] | 669 | SDMemTable* SDMath::simpleOperate(const SDMemTable& in, Float val, Bool doAll, |
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[234] | 670 | uInt what) const |
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[152] | 671 | // |
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| 672 | // what = 0 Multiply |
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| 673 | // 1 Add |
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[146] | 674 | { |
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[152] | 675 | SDMemTable* pOut = new SDMemTable(in,False); |
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| 676 | const Table& tOut = pOut->table(); |
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| 677 | ArrayColumn<Float> spec(tOut,"SPECTRA"); |
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[146] | 678 | // |
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[152] | 679 | if (doAll) { |
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| 680 | for (uInt i=0; i < tOut.nrow(); i++) { |
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| 681 | |
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| 682 | // Get |
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| 683 | |
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| 684 | MaskedArray<Float> marr(pOut->rowAsMaskedArray(i)); |
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| 685 | |
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| 686 | // Operate |
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| 687 | |
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| 688 | if (what==0) { |
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| 689 | marr *= val; |
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| 690 | } else if (what==1) { |
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| 691 | marr += val; |
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| 692 | } |
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| 693 | |
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| 694 | // Put |
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| 695 | |
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| 696 | spec.put(i, marr.getArray()); |
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| 697 | } |
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| 698 | } else { |
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| 699 | |
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| 700 | // Get cursor location |
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| 701 | |
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| 702 | IPosition start, end; |
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[185] | 703 | getCursorLocation(start, end, in); |
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[152] | 704 | // |
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| 705 | for (uInt i=0; i < tOut.nrow(); i++) { |
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| 706 | |
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| 707 | // Get |
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| 708 | |
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| 709 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
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| 710 | |
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| 711 | // Modify. More work than we would like to deal with the mask |
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| 712 | |
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| 713 | Array<Float>& values = dataIn.getRWArray(); |
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| 714 | Array<Bool> mask(dataIn.getMask()); |
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| 715 | // |
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| 716 | Array<Float> values2 = values(start,end); |
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| 717 | Array<Bool> mask2 = mask(start,end); |
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| 718 | MaskedArray<Float> t(values2,mask2); |
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| 719 | if (what==0) { |
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| 720 | t *= val; |
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| 721 | } else if (what==1) { |
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| 722 | t += val; |
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| 723 | } |
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| 724 | values(start, end) = t.getArray(); // Write back into 'dataIn' |
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| 725 | |
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| 726 | // Put |
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| 727 | spec.put(i, dataIn.getArray()); |
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| 728 | } |
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| 729 | } |
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| 730 | // |
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[146] | 731 | return pOut; |
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| 732 | } |
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| 733 | |
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| 734 | |
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[152] | 735 | |
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[234] | 736 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask) const |
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[152] | 737 | // |
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[165] | 738 | // Average all polarizations together, weighted by variance |
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| 739 | // |
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| 740 | { |
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| 741 | // WeightType wtType = NONE; |
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[185] | 742 | // convertWeightString(wtType, weight); |
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[165] | 743 | |
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| 744 | const uInt nRows = in.nRow(); |
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[209] | 745 | const uInt polAxis = asap::PolAxis; // Polarization axis |
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| 746 | const uInt chanAxis = asap::ChanAxis; // Spectrum axis |
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[165] | 747 | |
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| 748 | // Create output Table and reshape number of polarizations |
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| 749 | |
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| 750 | Bool clear=True; |
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| 751 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
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| 752 | SDHeader header = pTabOut->getSDHeader(); |
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| 753 | header.npol = 1; |
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| 754 | pTabOut->putSDHeader(header); |
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| 755 | |
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| 756 | // Shape of input and output data |
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| 757 | |
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| 758 | const IPosition& shapeIn = in.rowAsMaskedArray(0u, False).shape(); |
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| 759 | IPosition shapeOut(shapeIn); |
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| 760 | shapeOut(polAxis) = 1; // Average all polarizations |
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| 761 | // |
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| 762 | const uInt nChan = shapeIn(chanAxis); |
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| 763 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape |
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| 764 | IPosition start(4), end(4); |
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| 765 | |
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| 766 | // Output arrays |
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| 767 | |
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| 768 | Array<Float> outData(shapeOut, 0.0); |
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| 769 | Array<Bool> outMask(shapeOut, True); |
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| 770 | const IPosition axes(2, 2, 3); // pol-channel plane |
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| 771 | // |
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| 772 | const Bool useMask = (mask.nelements() == shapeIn(chanAxis)); |
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| 773 | |
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| 774 | // Loop over rows |
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| 775 | |
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| 776 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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| 777 | |
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| 778 | // Get data for this row |
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| 779 | |
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| 780 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
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| 781 | Array<Float>& arr = marr.getRWArray(); |
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| 782 | const Array<Bool>& barr = marr.getMask(); |
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| 783 | |
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| 784 | // Make iterators to iterate by pol-channel planes |
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| 785 | |
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| 786 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
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| 787 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes); |
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| 788 | |
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| 789 | // Accumulations |
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| 790 | |
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| 791 | Float fac = 1.0; |
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| 792 | Vector<Float> vecSum(nChan,0.0); |
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| 793 | |
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| 794 | // Iterate through data by pol-channel planes |
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| 795 | |
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| 796 | while (!itDataPlane.pastEnd()) { |
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| 797 | |
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| 798 | // Iterate through plane by polarization and accumulate Vectors |
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| 799 | |
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| 800 | Vector<Float> t1(nChan); t1 = 0.0; |
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| 801 | Vector<Bool> t2(nChan); t2 = True; |
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| 802 | MaskedArray<Float> vecSum(t1,t2); |
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| 803 | Float varSum = 0.0; |
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| 804 | { |
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| 805 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
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| 806 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
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| 807 | while (!itDataVec.pastEnd()) { |
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| 808 | |
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| 809 | // Create MA of data & mask (optionally including OTF mask) and get variance |
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| 810 | |
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| 811 | if (useMask) { |
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| 812 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector()); |
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| 813 | fac = 1.0 / variance(spec); |
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| 814 | } else { |
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| 815 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector()); |
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| 816 | fac = 1.0 / variance(spec); |
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| 817 | } |
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| 818 | |
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| 819 | // Normalize spectrum (without OTF mask) and accumulate |
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| 820 | |
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| 821 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector()); |
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| 822 | vecSum += spec; |
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| 823 | varSum += fac; |
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| 824 | |
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| 825 | // Next |
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| 826 | |
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| 827 | itDataVec.next(); |
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| 828 | itMaskVec.next(); |
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| 829 | } |
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| 830 | } |
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| 831 | |
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| 832 | // Normalize summed spectrum |
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| 833 | |
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| 834 | vecSum /= varSum; |
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| 835 | |
---|
| 836 | // FInd position in input data array. We are iterating by pol-channel |
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| 837 | // plane so all that will change is beam and IF and that's what we want. |
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| 838 | |
---|
| 839 | IPosition pos = itDataPlane.pos(); |
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| 840 | |
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| 841 | // Write out data. This is a bit messy. We have to reform the Vector |
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| 842 | // accumulator into an Array of shape (1,1,1,nChan) |
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| 843 | |
---|
| 844 | start = pos; |
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| 845 | end = pos; |
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| 846 | end(chanAxis) = nChan-1; |
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| 847 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
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| 848 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
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| 849 | |
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| 850 | // Step to next beam/IF combination |
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| 851 | |
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| 852 | itDataPlane.next(); |
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| 853 | itMaskPlane.next(); |
---|
| 854 | } |
---|
| 855 | |
---|
| 856 | // Generate output container and write it to output table |
---|
| 857 | |
---|
| 858 | SDContainer sc = in.getSDContainer(); |
---|
| 859 | sc.resize(shapeOut); |
---|
| 860 | // |
---|
[185] | 861 | putDataInSDC(sc, outData, outMask); |
---|
[165] | 862 | pTabOut->putSDContainer(sc); |
---|
| 863 | } |
---|
| 864 | // |
---|
| 865 | return pTabOut; |
---|
| 866 | } |
---|
[167] | 867 | |
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[169] | 868 | |
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[185] | 869 | SDMemTable* SDMath::smooth(const SDMemTable& in, |
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| 870 | const casa::String& kernelType, |
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[234] | 871 | casa::Float width, Bool doAll) const |
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[177] | 872 | { |
---|
[169] | 873 | |
---|
[177] | 874 | // Number of channels |
---|
[169] | 875 | |
---|
[209] | 876 | const uInt chanAxis = asap::ChanAxis; // Spectral axis |
---|
[177] | 877 | SDHeader sh = in.getSDHeader(); |
---|
| 878 | const uInt nChan = sh.nchan; |
---|
| 879 | |
---|
| 880 | // Generate Kernel |
---|
| 881 | |
---|
[185] | 882 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType); |
---|
[177] | 883 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
| 884 | |
---|
| 885 | // Generate Convolver |
---|
| 886 | |
---|
| 887 | IPosition shape(1,nChan); |
---|
| 888 | Convolver<Float> conv(kernel, shape); |
---|
| 889 | |
---|
| 890 | // New Table |
---|
| 891 | |
---|
| 892 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
| 893 | |
---|
| 894 | // Get cursor location |
---|
| 895 | |
---|
| 896 | IPosition start, end; |
---|
[185] | 897 | getCursorLocation(start, end, in); |
---|
[177] | 898 | // |
---|
| 899 | IPosition shapeOut(4,1); |
---|
| 900 | |
---|
| 901 | // Output Vectors |
---|
| 902 | |
---|
| 903 | Vector<Float> valuesOut(nChan); |
---|
| 904 | Vector<Bool> maskOut(nChan); |
---|
| 905 | |
---|
| 906 | // Loop over rows in Table |
---|
| 907 | |
---|
| 908 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
| 909 | |
---|
| 910 | // Get copy of data |
---|
| 911 | |
---|
| 912 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(ri)); |
---|
| 913 | AlwaysAssert(dataIn.shape()(chanAxis)==nChan, AipsError); |
---|
| 914 | // |
---|
| 915 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 916 | Array<Bool> maskIn = dataIn.getMask(); |
---|
| 917 | |
---|
| 918 | // Branch depending on whether we smooth all locations or just |
---|
| 919 | // those pointed at by the current selection cursor |
---|
| 920 | |
---|
| 921 | if (doAll) { |
---|
[221] | 922 | uInt axis = asap::ChanAxis; |
---|
[177] | 923 | VectorIterator<Float> itValues(valuesIn, axis); |
---|
| 924 | VectorIterator<Bool> itMask(maskIn, axis); |
---|
| 925 | while (!itValues.pastEnd()) { |
---|
| 926 | |
---|
| 927 | // Smooth |
---|
| 928 | if (kernelType==VectorKernel::HANNING) { |
---|
| 929 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector()); |
---|
| 930 | itMask.vector() = maskOut; |
---|
| 931 | } else { |
---|
| 932 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
| 933 | conv.linearConv(valuesOut, itValues.vector()); |
---|
| 934 | } |
---|
| 935 | // |
---|
| 936 | itValues.vector() = valuesOut; |
---|
| 937 | // |
---|
| 938 | itValues.next(); |
---|
| 939 | itMask.next(); |
---|
| 940 | } |
---|
| 941 | } else { |
---|
| 942 | |
---|
| 943 | // Set multi-dim Vector shape |
---|
| 944 | |
---|
| 945 | shapeOut(chanAxis) = valuesIn.shape()(chanAxis); |
---|
| 946 | |
---|
| 947 | // Stuff about with shapes so that we don't have conformance run-time errors |
---|
| 948 | |
---|
| 949 | Vector<Float> valuesIn2 = valuesIn(start,end).nonDegenerate(); |
---|
| 950 | Vector<Bool> maskIn2 = maskIn(start,end).nonDegenerate(); |
---|
| 951 | |
---|
| 952 | // Smooth |
---|
| 953 | |
---|
| 954 | if (kernelType==VectorKernel::HANNING) { |
---|
| 955 | mathutil::hanning(valuesOut, maskOut, valuesIn2, maskIn2); |
---|
| 956 | maskIn(start,end) = maskOut.reform(shapeOut); |
---|
| 957 | } else { |
---|
| 958 | mathutil::replaceMaskByZero(valuesIn2, maskIn2); |
---|
| 959 | conv.linearConv(valuesOut, valuesIn2); |
---|
| 960 | } |
---|
| 961 | // |
---|
| 962 | valuesIn(start,end) = valuesOut.reform(shapeOut); |
---|
| 963 | } |
---|
| 964 | |
---|
| 965 | // Create and put back |
---|
| 966 | |
---|
| 967 | SDContainer sc = in.getSDContainer(ri); |
---|
[185] | 968 | putDataInSDC(sc, valuesIn, maskIn); |
---|
[177] | 969 | // |
---|
| 970 | pTabOut->putSDContainer(sc); |
---|
| 971 | } |
---|
| 972 | // |
---|
| 973 | return pTabOut; |
---|
| 974 | } |
---|
| 975 | |
---|
| 976 | |
---|
[234] | 977 | SDMemTable* SDMath::convertFlux (const SDMemTable& in, Float a, Float eta, Bool doAll) const |
---|
[221] | 978 | // |
---|
| 979 | // As it is, this function could be implemented with 'simpleOperate' |
---|
| 980 | // However, I anticipate that eventually we will look the conversion |
---|
| 981 | // values up in a Table and apply them in a frequency dependent way, |
---|
| 982 | // so I have implemented it fully here |
---|
| 983 | // |
---|
| 984 | { |
---|
| 985 | SDHeader sh = in.getSDHeader(); |
---|
| 986 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[177] | 987 | |
---|
[221] | 988 | // FInd out how to convert values into Jy and K (e.g. units might be mJy or mK) |
---|
| 989 | // Also automatically find out what we are converting to according to the |
---|
| 990 | // flux unit |
---|
[177] | 991 | |
---|
[221] | 992 | Unit fluxUnit(sh.fluxunit); |
---|
| 993 | Unit K(String("K")); |
---|
| 994 | Unit JY(String("Jy")); |
---|
| 995 | // |
---|
| 996 | Bool toKelvin = True; |
---|
| 997 | Double inFac = 1.0; |
---|
| 998 | if (fluxUnit==JY) { |
---|
| 999 | cerr << "Converting to K" << endl; |
---|
| 1000 | // |
---|
| 1001 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1002 | Quantum<Double> t2 = t.get(JY); |
---|
| 1003 | inFac = (t2 / t).getValue(); |
---|
| 1004 | // |
---|
| 1005 | toKelvin = True; |
---|
| 1006 | sh.fluxunit = "K"; |
---|
| 1007 | } else if (fluxUnit==K) { |
---|
| 1008 | cerr << "Converting to Jy" << endl; |
---|
| 1009 | // |
---|
| 1010 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1011 | Quantum<Double> t2 = t.get(K); |
---|
| 1012 | inFac = (t2 / t).getValue(); |
---|
| 1013 | // |
---|
| 1014 | toKelvin = False; |
---|
| 1015 | sh.fluxunit = "Jy"; |
---|
| 1016 | } else { |
---|
| 1017 | throw AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"); |
---|
| 1018 | } |
---|
| 1019 | pTabOut->putSDHeader(sh); |
---|
[177] | 1020 | |
---|
[221] | 1021 | // Compute conversion factor. 'a' and 'eta' are really frequency, time and |
---|
| 1022 | // telescope dependent and should be looked// up in a table |
---|
| 1023 | |
---|
[234] | 1024 | Float factor = 2.0 * inFac * 1.0e-7 * 1.0e26 * |
---|
| 1025 | QC::k.getValue(Unit(String("erg/K"))) / a / eta; |
---|
[221] | 1026 | if (toKelvin) { |
---|
| 1027 | factor = 1.0 / factor; |
---|
| 1028 | } |
---|
| 1029 | cerr << "Applying conversion factor = " << factor << endl; |
---|
| 1030 | |
---|
| 1031 | // For operations only on specified cursor location |
---|
| 1032 | |
---|
| 1033 | IPosition start, end; |
---|
| 1034 | getCursorLocation(start, end, in); |
---|
| 1035 | |
---|
| 1036 | // Loop over rows and apply factor to spectra |
---|
| 1037 | |
---|
| 1038 | const uInt axis = asap::ChanAxis; |
---|
| 1039 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 1040 | |
---|
| 1041 | // Get data |
---|
| 1042 | |
---|
| 1043 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
| 1044 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
| 1045 | const Array<Bool>& maskIn = dataIn.getMask(); |
---|
| 1046 | |
---|
| 1047 | // Need to apply correct conversion factor (frequency and time dependent) |
---|
| 1048 | // which should be sourced from a Table. For now we just apply the given |
---|
| 1049 | // factor to everything |
---|
| 1050 | |
---|
| 1051 | if (doAll) { |
---|
| 1052 | VectorIterator<Float> itValues(valuesIn, asap::ChanAxis); |
---|
| 1053 | while (!itValues.pastEnd()) { |
---|
| 1054 | itValues.vector() *= factor; // Writes back into dataIn |
---|
| 1055 | // |
---|
| 1056 | itValues.next(); |
---|
| 1057 | } |
---|
| 1058 | } else { |
---|
| 1059 | Array<Float> valuesIn2 = valuesIn(start,end); |
---|
| 1060 | valuesIn2 *= factor; |
---|
| 1061 | valuesIn(start,end) = valuesIn2; |
---|
| 1062 | } |
---|
| 1063 | |
---|
| 1064 | // Write out |
---|
| 1065 | |
---|
| 1066 | SDContainer sc = in.getSDContainer(i); |
---|
| 1067 | putDataInSDC(sc, valuesIn, maskIn); |
---|
| 1068 | // |
---|
| 1069 | pTabOut->putSDContainer(sc); |
---|
| 1070 | } |
---|
| 1071 | return pTabOut; |
---|
| 1072 | } |
---|
| 1073 | |
---|
| 1074 | |
---|
| 1075 | |
---|
[234] | 1076 | SDMemTable* SDMath::gainElevation (const SDMemTable& in, const Vector<Float>& coeffs, |
---|
| 1077 | const String& fileName, |
---|
| 1078 | const String& methodStr, Bool doAll) const |
---|
[227] | 1079 | { |
---|
[234] | 1080 | |
---|
| 1081 | // Get header and clone output table |
---|
| 1082 | |
---|
[227] | 1083 | SDHeader sh = in.getSDHeader(); |
---|
| 1084 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1085 | |
---|
[234] | 1086 | // Get elevation data from SDMemTable and convert to degrees |
---|
[227] | 1087 | |
---|
| 1088 | const Table& tab = in.table(); |
---|
| 1089 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[234] | 1090 | Vector<Float> x = elev.getColumn(); |
---|
| 1091 | x *= Float(180 / C::pi); |
---|
[227] | 1092 | // |
---|
[234] | 1093 | const uInt nC = coeffs.nelements(); |
---|
| 1094 | if (fileName.length()>0 && nC>0) { |
---|
| 1095 | throw AipsError("You must choose either polynomial coefficients or an ascii file, not both"); |
---|
| 1096 | } |
---|
| 1097 | |
---|
| 1098 | // Correct |
---|
| 1099 | |
---|
| 1100 | if (nC>0 || fileName.length()==0) { |
---|
| 1101 | |
---|
| 1102 | // Find instrument |
---|
| 1103 | |
---|
| 1104 | Bool throwIt = True; |
---|
| 1105 | Instrument inst = SDMemTable::convertInstrument (sh.antennaname, throwIt); |
---|
| 1106 | |
---|
| 1107 | // Set polynomial |
---|
| 1108 | |
---|
| 1109 | Polynomial<Float>* pPoly = 0; |
---|
| 1110 | Vector<Float> coeff; |
---|
| 1111 | String msg; |
---|
| 1112 | if (nC>0) { |
---|
| 1113 | pPoly = new Polynomial<Float>(nC); |
---|
| 1114 | coeff = coeffs; |
---|
| 1115 | msg = String("user"); |
---|
| 1116 | } else { |
---|
| 1117 | if (inst==PKSMULTIBEAM) { |
---|
| 1118 | } else if (inst==PKSSINGLEBEAM) { |
---|
| 1119 | } else if (inst==TIDBINBILLA) { |
---|
| 1120 | pPoly = new Polynomial<Float>(3); |
---|
| 1121 | coeff.resize(3); |
---|
| 1122 | coeff(0) = 3.58788e-1; |
---|
| 1123 | coeff(1) = 2.87243e-2; |
---|
| 1124 | coeff(2) = -3.219093e-4; |
---|
| 1125 | } else if (inst==MOPRA) { |
---|
| 1126 | } |
---|
| 1127 | msg = String("built in"); |
---|
| 1128 | } |
---|
[227] | 1129 | // |
---|
[234] | 1130 | if (coeff.nelements()>0) { |
---|
| 1131 | pPoly->setCoefficients(coeff); |
---|
| 1132 | } else { |
---|
| 1133 | throw AipsError("There is no known gain-el polynomial known for this instrument"); |
---|
| 1134 | } |
---|
| 1135 | // |
---|
| 1136 | cerr << "Making polynomial correction with " << msg << " coefficients" << endl; |
---|
| 1137 | const uInt nRow = in.nRow(); |
---|
| 1138 | Vector<Float> factor(nRow); |
---|
| 1139 | for (uInt i=0; i<nRow; i++) { |
---|
| 1140 | factor[i] = (*pPoly)(x[i]); |
---|
| 1141 | } |
---|
| 1142 | delete pPoly; |
---|
| 1143 | // |
---|
| 1144 | correctFromVector (pTabOut, in, doAll, factor); |
---|
| 1145 | } else { |
---|
| 1146 | |
---|
| 1147 | // Indicate which columns to read from ascii file |
---|
| 1148 | |
---|
| 1149 | String col0("ELEVATION"); |
---|
| 1150 | String col1("FACTOR"); |
---|
| 1151 | |
---|
| 1152 | // Read and correct |
---|
| 1153 | |
---|
| 1154 | cerr << "Making correction from ascii Table" << endl; |
---|
| 1155 | correctFromAsciiTable (pTabOut, in, fileName, col0, col1, |
---|
| 1156 | methodStr, doAll, x); |
---|
| 1157 | } |
---|
| 1158 | // |
---|
| 1159 | return pTabOut; |
---|
[230] | 1160 | } |
---|
[227] | 1161 | |
---|
[230] | 1162 | |
---|
[227] | 1163 | |
---|
[234] | 1164 | SDMemTable* SDMath::opacity (const SDMemTable& in, Float tau, Bool doAll) const |
---|
| 1165 | { |
---|
[227] | 1166 | |
---|
[234] | 1167 | // Get header and clone output table |
---|
[227] | 1168 | |
---|
[234] | 1169 | SDHeader sh = in.getSDHeader(); |
---|
| 1170 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1171 | |
---|
| 1172 | // Get elevation data from SDMemTable and convert to degrees |
---|
| 1173 | |
---|
| 1174 | const Table& tab = in.table(); |
---|
| 1175 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 1176 | Vector<Float> zDist = elev.getColumn(); |
---|
| 1177 | zDist = Float(C::pi_2) - zDist; |
---|
| 1178 | |
---|
| 1179 | // Generate correction factor |
---|
| 1180 | |
---|
| 1181 | const uInt nRow = in.nRow(); |
---|
| 1182 | Vector<Float> factor(nRow); |
---|
| 1183 | Vector<Float> factor2(nRow); |
---|
| 1184 | for (uInt i=0; i<nRow; i++) { |
---|
| 1185 | factor[i] = exp(tau)/cos(zDist[i]); |
---|
| 1186 | } |
---|
| 1187 | |
---|
| 1188 | // Correct |
---|
| 1189 | |
---|
| 1190 | correctFromVector (pTabOut, in, doAll, factor); |
---|
| 1191 | // |
---|
| 1192 | return pTabOut; |
---|
| 1193 | } |
---|
| 1194 | |
---|
| 1195 | |
---|
| 1196 | |
---|
| 1197 | |
---|
[169] | 1198 | // 'private' functions |
---|
| 1199 | |
---|
[185] | 1200 | void SDMath::fillSDC(SDContainer& sc, |
---|
| 1201 | const Array<Bool>& mask, |
---|
| 1202 | const Array<Float>& data, |
---|
| 1203 | const Array<Float>& tSys, |
---|
| 1204 | Int scanID, Double timeStamp, |
---|
| 1205 | Double interval, const String& sourceName, |
---|
[227] | 1206 | const Vector<uInt>& freqID) const |
---|
[167] | 1207 | { |
---|
[169] | 1208 | // Data and mask |
---|
[167] | 1209 | |
---|
[185] | 1210 | putDataInSDC(sc, data, mask); |
---|
[167] | 1211 | |
---|
[169] | 1212 | // TSys |
---|
| 1213 | |
---|
| 1214 | sc.putTsys(tSys); |
---|
| 1215 | |
---|
| 1216 | // Time things |
---|
| 1217 | |
---|
| 1218 | sc.timestamp = timeStamp; |
---|
| 1219 | sc.interval = interval; |
---|
| 1220 | sc.scanid = scanID; |
---|
[167] | 1221 | // |
---|
[169] | 1222 | sc.sourcename = sourceName; |
---|
| 1223 | sc.putFreqMap(freqID); |
---|
| 1224 | } |
---|
[167] | 1225 | |
---|
[185] | 1226 | void SDMath::normalize(MaskedArray<Float>& sum, |
---|
[169] | 1227 | const Array<Float>& sumSq, |
---|
| 1228 | const Array<Float>& nPts, |
---|
| 1229 | WeightType wtType, Int axis, |
---|
[227] | 1230 | Int nAxesSub) const |
---|
[169] | 1231 | { |
---|
| 1232 | IPosition pos2(nAxesSub,0); |
---|
| 1233 | // |
---|
| 1234 | if (wtType==NONE) { |
---|
[167] | 1235 | |
---|
[169] | 1236 | // We just average by the number of points accumulated. |
---|
| 1237 | // We need to make a MA out of nPts so that no divide by |
---|
| 1238 | // zeros occur |
---|
[167] | 1239 | |
---|
[169] | 1240 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
| 1241 | sum /= t; |
---|
| 1242 | } else if (wtType==VAR) { |
---|
[167] | 1243 | |
---|
[169] | 1244 | // Normalize each spectrum by sum(1/var) where the variance |
---|
| 1245 | // is worked out for each spectrum |
---|
| 1246 | |
---|
| 1247 | Array<Float>& data = sum.getRWArray(); |
---|
| 1248 | VectorIterator<Float> itData(data, axis); |
---|
| 1249 | while (!itData.pastEnd()) { |
---|
| 1250 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 1251 | itData.vector() /= sumSq(pos2); |
---|
| 1252 | itData.next(); |
---|
| 1253 | } |
---|
| 1254 | } else if (wtType==TSYS) { |
---|
| 1255 | } |
---|
| 1256 | } |
---|
| 1257 | |
---|
| 1258 | |
---|
[185] | 1259 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum, |
---|
| 1260 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
| 1261 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
| 1262 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
| 1263 | const Vector<Bool>& mask, Double time, Double interval, |
---|
| 1264 | const Block<CountedPtr<SDMemTable> >& in, |
---|
| 1265 | uInt iTab, uInt iRow, uInt axis, |
---|
| 1266 | uInt nAxesSub, Bool useMask, |
---|
[227] | 1267 | WeightType wtType) const |
---|
[169] | 1268 | { |
---|
| 1269 | |
---|
| 1270 | // Get data |
---|
| 1271 | |
---|
| 1272 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
| 1273 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
| 1274 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
[167] | 1275 | // |
---|
[169] | 1276 | if (wtType==NONE) { |
---|
| 1277 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
| 1278 | nPts += n; // Only accumulates where mask==T |
---|
| 1279 | } else if (wtType==VAR) { |
---|
[167] | 1280 | |
---|
[169] | 1281 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
| 1282 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
[167] | 1283 | |
---|
[169] | 1284 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1285 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
| 1286 | Float fac = 1.0; |
---|
| 1287 | IPosition pos(nAxesSub,0); |
---|
| 1288 | // |
---|
| 1289 | while (!itData.pastEnd()) { |
---|
[167] | 1290 | |
---|
[169] | 1291 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
[167] | 1292 | |
---|
[169] | 1293 | if (useMask) { |
---|
| 1294 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
| 1295 | fac = 1.0/variance(tmp); |
---|
| 1296 | } else { |
---|
| 1297 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
| 1298 | fac = 1.0/variance(tmp); |
---|
| 1299 | } |
---|
| 1300 | |
---|
| 1301 | // Scale data |
---|
| 1302 | |
---|
| 1303 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
[167] | 1304 | // |
---|
[169] | 1305 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
| 1306 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1307 | // because the spectral axis is the last one (so we can just |
---|
| 1308 | // copy the first nAXesSub positions out) |
---|
[167] | 1309 | |
---|
[169] | 1310 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1311 | sumSq(pos) += fac; |
---|
| 1312 | // |
---|
| 1313 | itData.next(); |
---|
| 1314 | itMask.next(); |
---|
| 1315 | } |
---|
| 1316 | } else if (wtType==TSYS) { |
---|
| 1317 | } |
---|
[167] | 1318 | |
---|
[169] | 1319 | // Accumulate sum of (possibly scaled) data |
---|
| 1320 | |
---|
| 1321 | sum += dataIn; |
---|
| 1322 | |
---|
| 1323 | // Accumulate Tsys, time, and interval |
---|
| 1324 | |
---|
| 1325 | tSysSum += tSys; |
---|
| 1326 | timeSum += time; |
---|
| 1327 | intSum += interval; |
---|
| 1328 | nAccum += 1; |
---|
| 1329 | } |
---|
| 1330 | |
---|
| 1331 | |
---|
| 1332 | |
---|
| 1333 | |
---|
[185] | 1334 | void SDMath::getCursorLocation(IPosition& start, IPosition& end, |
---|
[227] | 1335 | const SDMemTable& in) const |
---|
[169] | 1336 | { |
---|
| 1337 | const uInt nDim = 4; |
---|
| 1338 | const uInt i = in.getBeam(); |
---|
| 1339 | const uInt j = in.getIF(); |
---|
| 1340 | const uInt k = in.getPol(); |
---|
| 1341 | const uInt n = in.nChan(); |
---|
[167] | 1342 | // |
---|
[169] | 1343 | start.resize(nDim); |
---|
| 1344 | start(0) = i; |
---|
| 1345 | start(1) = j; |
---|
| 1346 | start(2) = k; |
---|
| 1347 | start(3) = 0; |
---|
[167] | 1348 | // |
---|
[169] | 1349 | end.resize(nDim); |
---|
| 1350 | end(0) = i; |
---|
| 1351 | end(1) = j; |
---|
| 1352 | end(2) = k; |
---|
| 1353 | end(3) = n-1; |
---|
| 1354 | } |
---|
| 1355 | |
---|
| 1356 | |
---|
[227] | 1357 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr) const |
---|
[169] | 1358 | { |
---|
| 1359 | String tStr(weightStr); |
---|
| 1360 | tStr.upcase(); |
---|
| 1361 | if (tStr.contains(String("NONE"))) { |
---|
| 1362 | wtType = NONE; |
---|
| 1363 | } else if (tStr.contains(String("VAR"))) { |
---|
| 1364 | wtType = VAR; |
---|
| 1365 | } else if (tStr.contains(String("TSYS"))) { |
---|
| 1366 | wtType = TSYS; |
---|
[185] | 1367 | throw(AipsError("T_sys weighting not yet implemented")); |
---|
[169] | 1368 | } else { |
---|
[185] | 1369 | throw(AipsError("Unrecognized weighting type")); |
---|
[167] | 1370 | } |
---|
| 1371 | } |
---|
| 1372 | |
---|
[227] | 1373 | void SDMath::convertInterpString(Int& type, const String& interp) const |
---|
| 1374 | { |
---|
| 1375 | String tStr(interp); |
---|
| 1376 | tStr.upcase(); |
---|
| 1377 | if (tStr.contains(String("NEAR"))) { |
---|
| 1378 | type = InterpolateArray1D<Float,Float>::nearestNeighbour; |
---|
| 1379 | } else if (tStr.contains(String("LIN"))) { |
---|
| 1380 | type = InterpolateArray1D<Float,Float>::linear; |
---|
| 1381 | } else if (tStr.contains(String("CUB"))) { |
---|
| 1382 | type = InterpolateArray1D<Float,Float>::cubic; |
---|
| 1383 | } else if (tStr.contains(String("SPL"))) { |
---|
| 1384 | type = InterpolateArray1D<Float,Float>::spline; |
---|
| 1385 | } else { |
---|
| 1386 | throw(AipsError("Unrecognized interpolation type")); |
---|
| 1387 | } |
---|
| 1388 | } |
---|
| 1389 | |
---|
[185] | 1390 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data, |
---|
[227] | 1391 | const Array<Bool>& mask) const |
---|
[169] | 1392 | { |
---|
| 1393 | sc.putSpectrum(data); |
---|
| 1394 | // |
---|
| 1395 | Array<uChar> outflags(data.shape()); |
---|
| 1396 | convertArray(outflags,!mask); |
---|
| 1397 | sc.putFlags(outflags); |
---|
| 1398 | } |
---|
[227] | 1399 | |
---|
| 1400 | Table SDMath::readAsciiFile (const String& fileName) const |
---|
| 1401 | { |
---|
[230] | 1402 | String formatString; |
---|
| 1403 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False); |
---|
[227] | 1404 | return tbl; |
---|
| 1405 | } |
---|
[230] | 1406 | |
---|
| 1407 | |
---|
[234] | 1408 | |
---|
| 1409 | void SDMath::correctFromAsciiTable(SDMemTable* pTabOut, |
---|
| 1410 | const SDMemTable& in, const String& fileName, |
---|
| 1411 | const String& col0, const String& col1, |
---|
| 1412 | const String& methodStr, Bool doAll, |
---|
| 1413 | const Vector<Float>& xOut) const |
---|
[230] | 1414 | { |
---|
| 1415 | |
---|
| 1416 | // Read gain-elevation ascii file data into a Table. |
---|
| 1417 | |
---|
[234] | 1418 | Table geTable = readAsciiFile (fileName); |
---|
[230] | 1419 | // |
---|
[234] | 1420 | correctFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut); |
---|
[230] | 1421 | } |
---|
| 1422 | |
---|
[234] | 1423 | void SDMath::correctFromTable(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 1424 | const Table& tTable, const String& col0, |
---|
| 1425 | const String& col1, |
---|
| 1426 | const String& methodStr, Bool doAll, |
---|
| 1427 | const Vector<Float>& xOut) const |
---|
[230] | 1428 | { |
---|
| 1429 | |
---|
| 1430 | // Get data from Table |
---|
| 1431 | |
---|
| 1432 | ROScalarColumn<Float> geElCol(tTable, col0); |
---|
| 1433 | ROScalarColumn<Float> geFacCol(tTable, col1); |
---|
| 1434 | Vector<Float> xIn = geElCol.getColumn(); |
---|
| 1435 | Vector<Float> yIn = geFacCol.getColumn(); |
---|
| 1436 | Vector<Bool> maskIn(xIn.nelements(),True); |
---|
| 1437 | |
---|
| 1438 | // Interpolate (and extrapolate) with desired method |
---|
| 1439 | |
---|
| 1440 | Int method = 0; |
---|
| 1441 | convertInterpString(method, methodStr); |
---|
| 1442 | // |
---|
| 1443 | Vector<Float> yOut; |
---|
| 1444 | Vector<Bool> maskOut; |
---|
| 1445 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut, |
---|
| 1446 | xIn, yIn, maskIn, method, |
---|
| 1447 | True, True); |
---|
[234] | 1448 | // Apply |
---|
[230] | 1449 | |
---|
[234] | 1450 | correctFromVector (pTabOut, in, doAll, yOut); |
---|
| 1451 | } |
---|
| 1452 | |
---|
| 1453 | |
---|
| 1454 | void SDMath::correctFromVector (SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 1455 | Bool doAll, const Vector<Float>& factor) const |
---|
| 1456 | { |
---|
[230] | 1457 | // For operations only on specified cursor location |
---|
| 1458 | |
---|
| 1459 | IPosition start, end; |
---|
| 1460 | getCursorLocation(start, end, in); |
---|
| 1461 | |
---|
| 1462 | // Loop over rows and interpolate correction factor |
---|
| 1463 | |
---|
| 1464 | const uInt axis = asap::ChanAxis; |
---|
| 1465 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 1466 | |
---|
| 1467 | // Get data |
---|
| 1468 | |
---|
| 1469 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
[234] | 1470 | Array<Float>& valuesIn = dataIn.getRWArray(); |
---|
[230] | 1471 | const Array<Bool>& maskIn = dataIn.getMask(); |
---|
| 1472 | |
---|
| 1473 | // Apply factor |
---|
| 1474 | |
---|
| 1475 | if (doAll) { |
---|
| 1476 | VectorIterator<Float> itValues(valuesIn, asap::ChanAxis); |
---|
| 1477 | while (!itValues.pastEnd()) { |
---|
[234] | 1478 | itValues.vector() *= factor(i); |
---|
[230] | 1479 | itValues.next(); |
---|
| 1480 | } |
---|
| 1481 | } else { |
---|
| 1482 | Array<Float> valuesIn2 = valuesIn(start,end); |
---|
[234] | 1483 | valuesIn2 *= factor(i); |
---|
[230] | 1484 | valuesIn(start,end) = valuesIn2; |
---|
| 1485 | } |
---|
| 1486 | |
---|
| 1487 | // Write out |
---|
| 1488 | |
---|
| 1489 | SDContainer sc = in.getSDContainer(i); |
---|
| 1490 | putDataInSDC(sc, valuesIn, maskIn); |
---|
| 1491 | // |
---|
| 1492 | pTabOut->putSDContainer(sc); |
---|
| 1493 | } |
---|
| 1494 | } |
---|
| 1495 | |
---|
[234] | 1496 | |
---|