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