[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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[177] | 44 | #include <casa/Utilities/Assert.h> |
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[130] | 45 | #include <casa/Exceptions.h> |
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[2] | 46 | |
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[177] | 47 | #include <scimath/Mathematics/VectorKernel.h> |
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| 48 | #include <scimath/Mathematics/Convolver.h> |
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| 49 | |
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[81] | 50 | #include <tables/Tables/Table.h> |
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| 51 | #include <tables/Tables/ScalarColumn.h> |
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| 52 | #include <tables/Tables/ArrayColumn.h> |
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[2] | 53 | |
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[130] | 54 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 55 | #include <lattices/Lattices/RebinLattice.h> |
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[81] | 56 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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[130] | 57 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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| 58 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[38] | 59 | |
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| 60 | #include "MathUtils.h" |
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[2] | 61 | #include "SDContainer.h" |
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| 62 | #include "SDMemTable.h" |
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| 63 | |
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| 64 | #include "SDMath.h" |
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| 65 | |
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[125] | 66 | using namespace casa; |
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[83] | 67 | using namespace asap; |
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[2] | 68 | |
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[170] | 69 | |
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| 70 | SDMath::SDMath() |
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| 71 | {;} |
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| 72 | |
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| 73 | SDMath::SDMath (const SDMath& other) |
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| 74 | { |
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| 75 | |
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| 76 | // No state |
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| 77 | |
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| 78 | } |
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| 79 | |
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| 80 | SDMath& SDMath::operator=(const SDMath& other) |
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| 81 | { |
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| 82 | if (this != &other) { |
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| 83 | // No state |
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| 84 | } |
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| 85 | return *this; |
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| 86 | } |
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| 87 | |
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| 88 | |
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[144] | 89 | CountedPtr<SDMemTable> SDMath::average (const Block<CountedPtr<SDMemTable> >& in, |
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[177] | 90 | const Vector<Bool>& mask, Bool scanAv, |
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[144] | 91 | const std::string& weightStr) |
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[130] | 92 | // |
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[144] | 93 | // Weighted averaging of spectra from one or more Tables. |
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[130] | 94 | // |
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| 95 | { |
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[2] | 96 | |
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[163] | 97 | // Convert weight type |
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| 98 | |
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| 99 | WeightType wtType = NONE; |
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| 100 | convertWeightString (wtType, weightStr); |
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| 101 | |
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[144] | 102 | // Create output Table by cloning from the first table |
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[2] | 103 | |
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[144] | 104 | SDMemTable* pTabOut = new SDMemTable(*in[0],True); |
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[130] | 105 | |
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[144] | 106 | // Setup |
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[130] | 107 | |
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[144] | 108 | const uInt axis = 3; // Spectral axis |
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| 109 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change |
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| 110 | Array<Float> arr(shp); |
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| 111 | Array<Bool> barr(shp); |
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| 112 | const Bool useMask = (mask.nelements() == shp(axis)); |
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[130] | 113 | |
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[144] | 114 | // Columns from Tables |
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[130] | 115 | |
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[144] | 116 | ROArrayColumn<Float> tSysCol; |
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| 117 | ROScalarColumn<Double> mjdCol; |
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| 118 | ROScalarColumn<String> srcNameCol; |
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| 119 | ROScalarColumn<Double> intCol; |
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| 120 | ROArrayColumn<uInt> fqIDCol; |
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[130] | 121 | |
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[144] | 122 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam |
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| 123 | // Note that the mask of the accumulation array will ALWAYS remain ALL True. |
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| 124 | // The MA is only used so that when data which is masked Bad is added to it, |
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| 125 | // that data does not contribute. |
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| 126 | |
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| 127 | Array<Float> zero(shp); |
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| 128 | zero=0.0; |
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| 129 | Array<Bool> good(shp); |
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| 130 | good = True; |
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| 131 | MaskedArray<Float> sum(zero,good); |
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| 132 | |
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| 133 | // Counter arrays |
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| 134 | |
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| 135 | Array<Float> nPts(shp); // Number of points |
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| 136 | nPts = 0.0; |
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| 137 | Array<Float> nInc(shp); // Increment |
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| 138 | nInc = 1.0; |
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| 139 | |
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| 140 | // Create accumulation Array for variance. We accumulate for |
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| 141 | // each if,pol,beam, but average over channel. So we need |
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| 142 | // a shape with one less axis dropping channels. |
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| 143 | |
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| 144 | const uInt nAxesSub = shp.nelements() - 1; |
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| 145 | IPosition shp2(nAxesSub); |
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| 146 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) { |
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| 147 | if (i!=axis) { |
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| 148 | shp2(j) = shp(i); |
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| 149 | j++; |
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| 150 | } |
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[2] | 151 | } |
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[144] | 152 | Array<Float> sumSq(shp2); |
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| 153 | sumSq = 0.0; |
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| 154 | IPosition pos2(nAxesSub,0); // For indexing |
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[130] | 155 | |
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[144] | 156 | // Time-related accumulators |
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[130] | 157 | |
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[144] | 158 | Double time; |
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| 159 | Double timeSum = 0.0; |
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| 160 | Double intSum = 0.0; |
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| 161 | Double interval = 0.0; |
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[130] | 162 | |
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[144] | 163 | // To get the right shape for the Tsys accumulator we need to |
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| 164 | // access a column from the first table. The shape of this |
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| 165 | // array must not change |
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[130] | 166 | |
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[144] | 167 | Array<Float> tSysSum; |
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| 168 | { |
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| 169 | const Table& tabIn = in[0]->table(); |
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| 170 | tSysCol.attach(tabIn,"TSYS"); |
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| 171 | tSysSum.resize(tSysCol.shape(0)); |
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| 172 | } |
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| 173 | tSysSum =0.0; |
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| 174 | Array<Float> tSys; |
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| 175 | |
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| 176 | // Scan and row tracking |
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| 177 | |
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| 178 | Int oldScanID = 0; |
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| 179 | Int outScanID = 0; |
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| 180 | Int scanID = 0; |
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| 181 | Int rowStart = 0; |
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| 182 | Int nAccum = 0; |
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| 183 | Int tableStart = 0; |
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| 184 | |
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| 185 | // Source and FreqID |
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| 186 | |
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| 187 | String sourceName, oldSourceName, sourceNameStart; |
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| 188 | Vector<uInt> freqID, freqIDStart, oldFreqID; |
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| 189 | |
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| 190 | // Loop over tables |
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| 191 | |
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| 192 | Float fac = 1.0; |
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| 193 | const uInt nTables = in.nelements(); |
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| 194 | for (uInt iTab=0; iTab<nTables; iTab++) { |
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| 195 | |
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| 196 | // Attach columns to Table |
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| 197 | |
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| 198 | const Table& tabIn = in[iTab]->table(); |
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| 199 | tSysCol.attach(tabIn, "TSYS"); |
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| 200 | mjdCol.attach(tabIn, "TIME"); |
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| 201 | srcNameCol.attach(tabIn, "SRCNAME"); |
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| 202 | intCol.attach(tabIn, "INTERVAL"); |
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| 203 | fqIDCol.attach(tabIn, "FREQID"); |
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| 204 | |
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| 205 | // Loop over rows in Table |
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| 206 | |
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| 207 | const uInt nRows = in[iTab]->nRow(); |
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| 208 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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| 209 | |
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| 210 | // Check conformance |
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| 211 | |
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| 212 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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| 213 | if (!shp.isEqual(shp2)) { |
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| 214 | throw (AipsError("Shapes for all rows must be the same")); |
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| 215 | } |
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| 216 | |
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| 217 | // If we are not doing scan averages, make checks for source and |
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| 218 | // frequency setup and warn if averaging across them |
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| 219 | |
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| 220 | // Get copy of Scan Container for this row |
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| 221 | |
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| 222 | SDContainer sc = in[iTab]->getSDContainer(iRow); |
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| 223 | scanID = sc.scanid; |
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| 224 | |
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| 225 | // Get quantities from columns |
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| 226 | |
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| 227 | srcNameCol.getScalar(iRow, sourceName); |
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| 228 | mjdCol.get(iRow, time); |
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| 229 | tSysCol.get(iRow, tSys); |
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| 230 | intCol.get(iRow, interval); |
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| 231 | fqIDCol.get(iRow, freqID); |
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| 232 | |
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| 233 | // Initialize first source and freqID |
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| 234 | |
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| 235 | if (iRow==0 && iTab==0) { |
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| 236 | sourceNameStart = sourceName; |
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| 237 | freqIDStart = freqID; |
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| 238 | } |
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| 239 | |
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| 240 | // If we are doing scan averages, see if we are at the end of an |
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| 241 | // accumulation period (scan). We must check soutce names too, |
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| 242 | // since we might have two tables with one scan each but different |
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| 243 | // source names; we shouldn't average different sources together |
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| 244 | |
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| 245 | if (scanAv && ( (scanID != oldScanID) || |
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| 246 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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| 247 | |
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| 248 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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| 249 | |
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| 250 | normalize (sum, sumSq, nPts, wtType, axis, nAxesSub); |
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| 251 | |
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| 252 | // Fill scan container. The source and freqID come from the |
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| 253 | // first row of the first table that went into this average ( |
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| 254 | // should be the same for all rows in the scan average) |
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| 255 | |
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| 256 | Float nR(nAccum); |
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| 257 | fillSDC (sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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| 258 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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| 259 | |
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| 260 | // Write container out to Table |
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| 261 | |
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| 262 | pTabOut->putSDContainer(sc); |
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| 263 | |
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| 264 | // Reset accumulators |
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| 265 | |
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| 266 | sum = 0.0; |
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| 267 | sumSq = 0.0; |
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| 268 | nAccum = 0; |
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| 269 | // |
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| 270 | tSysSum =0.0; |
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| 271 | timeSum = 0.0; |
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| 272 | intSum = 0.0; |
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| 273 | |
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| 274 | // Increment |
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| 275 | |
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| 276 | rowStart = iRow; // First row for next accumulation |
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| 277 | tableStart = iTab; // First table for next accumulation |
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| 278 | sourceNameStart = sourceName; // First source name for next accumulation |
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| 279 | freqIDStart = freqID; // First FreqID for next accumulation |
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| 280 | // |
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| 281 | oldScanID = scanID; |
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| 282 | outScanID += 1; // Scan ID for next accumulation period |
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| 283 | } |
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| 284 | |
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[146] | 285 | // Accumulate |
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[144] | 286 | |
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[146] | 287 | accumulate (timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, |
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| 288 | tSys, nInc, mask, time, interval, in, iTab, iRow, axis, |
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| 289 | nAxesSub, useMask, wtType); |
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[144] | 290 | // |
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| 291 | oldSourceName = sourceName; |
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| 292 | oldFreqID = freqID; |
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| 293 | } |
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| 294 | } |
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| 295 | |
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| 296 | // OK at this point we have accumulation data which is either |
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| 297 | // - accumulated from all tables into one row |
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| 298 | // or |
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| 299 | // - accumulated from the last scan average |
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| 300 | // |
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| 301 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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| 302 | |
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| 303 | normalize (sum, sumSq, nPts, wtType, axis, nAxesSub); |
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| 304 | |
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| 305 | // Create and fill container. The container we clone will be from |
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| 306 | // the last Table and the first row that went into the current |
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| 307 | // accumulation. It probably doesn't matter that much really... |
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| 308 | |
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| 309 | Float nR(nAccum); |
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| 310 | SDContainer sc = in[tableStart]->getSDContainer(rowStart); |
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| 311 | fillSDC (sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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| 312 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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| 313 | // |
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| 314 | pTabOut->putSDContainer(sc); |
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| 315 | /* |
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| 316 | cout << endl; |
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| 317 | cout << "Last accumulation for output scan ID " << outScanID << endl; |
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| 318 | cout << " The first row in this accumulation is " << rowStart << endl; |
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| 319 | cout << " The number of rows accumulated is " << nAccum << endl; |
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| 320 | cout << " The first table in this accumulation is " << tableStart << endl; |
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| 321 | cout << " The first source in this accumulation is " << sourceNameStart << endl; |
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| 322 | cout << " The first freqID in this accumulation is " << freqIDStart << endl; |
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| 323 | cout << " Average time stamp = " << timeSum/nR << endl; |
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| 324 | cout << " Integrated time = " << intSum << endl; |
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| 325 | */ |
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| 326 | return CountedPtr<SDMemTable>(pTabOut); |
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[2] | 327 | } |
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[9] | 328 | |
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[144] | 329 | |
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| 330 | |
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[85] | 331 | CountedPtr<SDMemTable> |
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| 332 | SDMath::quotient(const CountedPtr<SDMemTable>& on, |
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[130] | 333 | const CountedPtr<SDMemTable>& off) |
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| 334 | // |
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| 335 | // Compute quotient spectrum |
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| 336 | // |
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| 337 | { |
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| 338 | const uInt nRows = on->nRow(); |
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| 339 | if (off->nRow() != nRows) { |
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| 340 | throw (AipsError("Input Scan Tables must have the same number of rows")); |
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| 341 | } |
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[85] | 342 | |
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[130] | 343 | // Input Tables and columns |
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| 344 | |
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[9] | 345 | Table ton = on->table(); |
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| 346 | Table toff = off->table(); |
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[85] | 347 | ROArrayColumn<Float> tsys(toff, "TSYS"); |
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[9] | 348 | ROScalarColumn<Double> mjd(ton, "TIME"); |
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[15] | 349 | ROScalarColumn<Double> integr(ton, "INTERVAL"); |
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[9] | 350 | ROScalarColumn<String> srcn(ton, "SRCNAME"); |
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[38] | 351 | ROArrayColumn<uInt> freqidc(ton, "FREQID"); |
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| 352 | |
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[130] | 353 | // Output Table cloned from input |
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[85] | 354 | |
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[171] | 355 | SDMemTable* pTabOut = new SDMemTable(*on, True); |
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[130] | 356 | |
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| 357 | // Loop over rows |
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| 358 | |
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| 359 | for (uInt i=0; i<nRows; i++) { |
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| 360 | MaskedArray<Float> mon(on->rowAsMaskedArray(i)); |
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| 361 | MaskedArray<Float> moff(off->rowAsMaskedArray(i)); |
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| 362 | IPosition ipon = mon.shape(); |
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| 363 | IPosition ipoff = moff.shape(); |
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| 364 | // |
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| 365 | Array<Float> tsarr; |
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| 366 | tsys.get(i, tsarr); |
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| 367 | if (ipon != ipoff && ipon != tsarr.shape()) { |
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| 368 | throw(AipsError("on/off not conformant")); |
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| 369 | } |
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| 370 | |
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| 371 | // Compute quotient |
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| 372 | |
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| 373 | MaskedArray<Float> tmp = (mon-moff); |
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| 374 | Array<Float> out(tmp.getArray()); |
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| 375 | out /= moff; |
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| 376 | out *= tsarr; |
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[163] | 377 | Array<Bool> outflagsb = mon.getMask() && moff.getMask(); |
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[130] | 378 | |
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| 379 | // Fill container for this row |
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| 380 | |
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| 381 | SDContainer sc = on->getSDContainer(); |
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[163] | 382 | // |
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| 383 | putDataInSDC (sc, out, outflagsb); |
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[130] | 384 | sc.putTsys(tsarr); |
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| 385 | sc.scanid = 0; |
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| 386 | |
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| 387 | // Put new row in output Table |
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| 388 | |
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[171] | 389 | pTabOut->putSDContainer(sc); |
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[130] | 390 | } |
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| 391 | // |
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[171] | 392 | return CountedPtr<SDMemTable>(pTabOut); |
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[9] | 393 | } |
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[48] | 394 | |
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[146] | 395 | |
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| 396 | |
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[130] | 397 | std::vector<float> SDMath::statistic (const CountedPtr<SDMemTable>& in, |
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[177] | 398 | const std::vector<bool>& mask, |
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| 399 | const String& which) |
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[130] | 400 | // |
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| 401 | // Perhaps iteration over pol/beam/if should be in here |
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| 402 | // and inside the nrow iteration ? |
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| 403 | // |
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| 404 | { |
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| 405 | const uInt nRow = in->nRow(); |
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| 406 | std::vector<float> result(nRow); |
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| 407 | Vector<Bool> msk(mask); |
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| 408 | |
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| 409 | // Specify cursor location |
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| 410 | |
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[152] | 411 | IPosition start, end; |
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| 412 | getCursorLocation (start, end, *in); |
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[130] | 413 | |
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| 414 | // Loop over rows |
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| 415 | |
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| 416 | const uInt nEl = msk.nelements(); |
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| 417 | for (uInt ii=0; ii < in->nRow(); ++ii) { |
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| 418 | |
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| 419 | // Get row and deconstruct |
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| 420 | |
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| 421 | MaskedArray<Float> marr(in->rowAsMaskedArray(ii)); |
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| 422 | Array<Float> arr = marr.getArray(); |
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| 423 | Array<Bool> barr = marr.getMask(); |
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| 424 | |
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| 425 | // Access desired piece of data |
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| 426 | |
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| 427 | Array<Float> v((arr(start,end)).nonDegenerate()); |
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| 428 | Array<Bool> m((barr(start,end)).nonDegenerate()); |
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| 429 | |
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| 430 | // Apply OTF mask |
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| 431 | |
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| 432 | MaskedArray<Float> tmp; |
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| 433 | if (m.nelements()==nEl) { |
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| 434 | tmp.setData(v,m&&msk); |
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| 435 | } else { |
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| 436 | tmp.setData(v,m); |
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| 437 | } |
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| 438 | |
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| 439 | // Get statistic |
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| 440 | |
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[144] | 441 | result[ii] = mathutil::statistics(which, tmp); |
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[130] | 442 | } |
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| 443 | // |
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| 444 | return result; |
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| 445 | } |
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| 446 | |
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[146] | 447 | |
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[169] | 448 | SDMemTable* SDMath::bin (const SDMemTable& in, Int width) |
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[144] | 449 | { |
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[169] | 450 | SDHeader sh = in.getSDHeader(); |
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| 451 | SDMemTable* pTabOut = new SDMemTable(in, True); |
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[163] | 452 | |
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[169] | 453 | // Bin up SpectralCoordinates |
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[163] | 454 | |
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[169] | 455 | IPosition factors(1); |
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| 456 | factors(0) = width; |
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| 457 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
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| 458 | CoordinateSystem cSys; |
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| 459 | cSys.addCoordinate(in.getCoordinate(j)); |
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| 460 | CoordinateSystem cSysBin = |
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| 461 | CoordinateUtil::makeBinnedCoordinateSystem (factors, cSys, False); |
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| 462 | // |
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| 463 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
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| 464 | pTabOut->setCoordinate(sCBin, j); |
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| 465 | } |
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[163] | 466 | |
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[169] | 467 | // Use RebinLattice to find shape |
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[130] | 468 | |
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[169] | 469 | IPosition shapeIn(1,sh.nchan); |
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| 470 | IPosition shapeOut = RebinLattice<Float>::rebinShape (shapeIn, factors); |
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| 471 | sh.nchan = shapeOut(0); |
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| 472 | pTabOut->putSDHeader(sh); |
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[144] | 473 | |
---|
| 474 | |
---|
[169] | 475 | // Loop over rows and bin along channel axis |
---|
| 476 | |
---|
| 477 | const uInt axis = 3; |
---|
| 478 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 479 | SDContainer sc = in.getSDContainer(i); |
---|
[144] | 480 | // |
---|
[169] | 481 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
---|
[144] | 482 | |
---|
[169] | 483 | // Bin up spectrum |
---|
[144] | 484 | |
---|
[169] | 485 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
---|
| 486 | MaskedArray<Float> marrout; |
---|
| 487 | LatticeUtilities::bin(marrout, marr, axis, width); |
---|
[144] | 488 | |
---|
[169] | 489 | // Put back the binned data and flags |
---|
[144] | 490 | |
---|
[169] | 491 | IPosition ip2 = marrout.shape(); |
---|
| 492 | sc.resize(ip2); |
---|
[146] | 493 | // |
---|
[169] | 494 | putDataInSDC (sc, marrout.getArray(), marrout.getMask()); |
---|
[146] | 495 | |
---|
[169] | 496 | // Bin up Tsys. |
---|
[146] | 497 | |
---|
[169] | 498 | Array<Bool> allGood(tSys.shape(),True); |
---|
| 499 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
---|
[146] | 500 | // |
---|
[169] | 501 | MaskedArray<Float> tSysOut; |
---|
| 502 | LatticeUtilities::bin(tSysOut, tSysIn, axis, width); |
---|
| 503 | sc.putTsys(tSysOut.getArray()); |
---|
[146] | 504 | // |
---|
[169] | 505 | pTabOut->putSDContainer(sc); |
---|
| 506 | } |
---|
| 507 | return pTabOut; |
---|
[146] | 508 | } |
---|
| 509 | |
---|
[169] | 510 | SDMemTable* SDMath::simpleOperate (const SDMemTable& in, Float val, Bool doAll, |
---|
| 511 | uInt what) |
---|
[152] | 512 | // |
---|
| 513 | // what = 0 Multiply |
---|
| 514 | // 1 Add |
---|
[146] | 515 | { |
---|
[152] | 516 | SDMemTable* pOut = new SDMemTable(in,False); |
---|
| 517 | const Table& tOut = pOut->table(); |
---|
| 518 | ArrayColumn<Float> spec(tOut,"SPECTRA"); |
---|
[146] | 519 | // |
---|
[152] | 520 | if (doAll) { |
---|
| 521 | for (uInt i=0; i < tOut.nrow(); i++) { |
---|
| 522 | |
---|
| 523 | // Get |
---|
| 524 | |
---|
| 525 | MaskedArray<Float> marr(pOut->rowAsMaskedArray(i)); |
---|
| 526 | |
---|
| 527 | // Operate |
---|
| 528 | |
---|
| 529 | if (what==0) { |
---|
| 530 | marr *= val; |
---|
| 531 | } else if (what==1) { |
---|
| 532 | marr += val; |
---|
| 533 | } |
---|
| 534 | |
---|
| 535 | // Put |
---|
| 536 | |
---|
| 537 | spec.put(i, marr.getArray()); |
---|
| 538 | } |
---|
| 539 | } else { |
---|
| 540 | |
---|
| 541 | // Get cursor location |
---|
| 542 | |
---|
| 543 | IPosition start, end; |
---|
| 544 | getCursorLocation (start, end, in); |
---|
| 545 | // |
---|
| 546 | for (uInt i=0; i < tOut.nrow(); i++) { |
---|
| 547 | |
---|
| 548 | // Get |
---|
| 549 | |
---|
| 550 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
| 551 | |
---|
| 552 | // Modify. More work than we would like to deal with the mask |
---|
| 553 | |
---|
| 554 | Array<Float>& values = dataIn.getRWArray(); |
---|
| 555 | Array<Bool> mask(dataIn.getMask()); |
---|
| 556 | // |
---|
| 557 | Array<Float> values2 = values(start,end); |
---|
| 558 | Array<Bool> mask2 = mask(start,end); |
---|
| 559 | MaskedArray<Float> t(values2,mask2); |
---|
| 560 | if (what==0) { |
---|
| 561 | t *= val; |
---|
| 562 | } else if (what==1) { |
---|
| 563 | t += val; |
---|
| 564 | } |
---|
| 565 | values(start, end) = t.getArray(); // Write back into 'dataIn' |
---|
| 566 | |
---|
| 567 | // Put |
---|
| 568 | spec.put(i, dataIn.getArray()); |
---|
| 569 | } |
---|
| 570 | } |
---|
| 571 | // |
---|
[146] | 572 | return pOut; |
---|
| 573 | } |
---|
| 574 | |
---|
| 575 | |
---|
[152] | 576 | |
---|
[169] | 577 | SDMemTable* SDMath::averagePol (const SDMemTable& in, const Vector<Bool>& mask) |
---|
[152] | 578 | // |
---|
[165] | 579 | // Average all polarizations together, weighted by variance |
---|
| 580 | // |
---|
| 581 | { |
---|
| 582 | // WeightType wtType = NONE; |
---|
| 583 | // convertWeightString (wtType, weight); |
---|
| 584 | |
---|
| 585 | const uInt nRows = in.nRow(); |
---|
| 586 | const uInt polAxis = 2; // Polarization axis |
---|
| 587 | const uInt chanAxis = 3; // Spectrum axis |
---|
| 588 | |
---|
| 589 | // Create output Table and reshape number of polarizations |
---|
| 590 | |
---|
| 591 | Bool clear=True; |
---|
| 592 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
| 593 | SDHeader header = pTabOut->getSDHeader(); |
---|
| 594 | header.npol = 1; |
---|
| 595 | pTabOut->putSDHeader(header); |
---|
| 596 | |
---|
| 597 | // Shape of input and output data |
---|
| 598 | |
---|
| 599 | const IPosition& shapeIn = in.rowAsMaskedArray(0u, False).shape(); |
---|
| 600 | IPosition shapeOut(shapeIn); |
---|
| 601 | shapeOut(polAxis) = 1; // Average all polarizations |
---|
| 602 | // |
---|
| 603 | const uInt nChan = shapeIn(chanAxis); |
---|
| 604 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape |
---|
| 605 | IPosition start(4), end(4); |
---|
| 606 | |
---|
| 607 | // Output arrays |
---|
| 608 | |
---|
| 609 | Array<Float> outData(shapeOut, 0.0); |
---|
| 610 | Array<Bool> outMask(shapeOut, True); |
---|
| 611 | const IPosition axes(2, 2, 3); // pol-channel plane |
---|
| 612 | // |
---|
| 613 | const Bool useMask = (mask.nelements() == shapeIn(chanAxis)); |
---|
| 614 | |
---|
| 615 | // Loop over rows |
---|
| 616 | |
---|
| 617 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 618 | |
---|
| 619 | // Get data for this row |
---|
| 620 | |
---|
| 621 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
| 622 | Array<Float>& arr = marr.getRWArray(); |
---|
| 623 | const Array<Bool>& barr = marr.getMask(); |
---|
| 624 | |
---|
| 625 | // Make iterators to iterate by pol-channel planes |
---|
| 626 | |
---|
| 627 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
---|
| 628 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes); |
---|
| 629 | |
---|
| 630 | // Accumulations |
---|
| 631 | |
---|
| 632 | Float fac = 1.0; |
---|
| 633 | Vector<Float> vecSum(nChan,0.0); |
---|
| 634 | |
---|
| 635 | // Iterate through data by pol-channel planes |
---|
| 636 | |
---|
| 637 | while (!itDataPlane.pastEnd()) { |
---|
| 638 | |
---|
| 639 | // Iterate through plane by polarization and accumulate Vectors |
---|
| 640 | |
---|
| 641 | Vector<Float> t1(nChan); t1 = 0.0; |
---|
| 642 | Vector<Bool> t2(nChan); t2 = True; |
---|
| 643 | MaskedArray<Float> vecSum(t1,t2); |
---|
| 644 | Float varSum = 0.0; |
---|
| 645 | { |
---|
| 646 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
---|
| 647 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
| 648 | while (!itDataVec.pastEnd()) { |
---|
| 649 | |
---|
| 650 | // Create MA of data & mask (optionally including OTF mask) and get variance |
---|
| 651 | |
---|
| 652 | if (useMask) { |
---|
| 653 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector()); |
---|
| 654 | fac = 1.0 / variance(spec); |
---|
| 655 | } else { |
---|
| 656 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector()); |
---|
| 657 | fac = 1.0 / variance(spec); |
---|
| 658 | } |
---|
| 659 | |
---|
| 660 | // Normalize spectrum (without OTF mask) and accumulate |
---|
| 661 | |
---|
| 662 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector()); |
---|
| 663 | vecSum += spec; |
---|
| 664 | varSum += fac; |
---|
| 665 | |
---|
| 666 | // Next |
---|
| 667 | |
---|
| 668 | itDataVec.next(); |
---|
| 669 | itMaskVec.next(); |
---|
| 670 | } |
---|
| 671 | } |
---|
| 672 | |
---|
| 673 | // Normalize summed spectrum |
---|
| 674 | |
---|
| 675 | vecSum /= varSum; |
---|
| 676 | |
---|
| 677 | // FInd position in input data array. We are iterating by pol-channel |
---|
| 678 | // plane so all that will change is beam and IF and that's what we want. |
---|
| 679 | |
---|
| 680 | IPosition pos = itDataPlane.pos(); |
---|
| 681 | |
---|
| 682 | // Write out data. This is a bit messy. We have to reform the Vector |
---|
| 683 | // accumulator into an Array of shape (1,1,1,nChan) |
---|
| 684 | |
---|
| 685 | start = pos; |
---|
| 686 | end = pos; |
---|
| 687 | end(chanAxis) = nChan-1; |
---|
| 688 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
---|
| 689 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
---|
| 690 | |
---|
| 691 | // Step to next beam/IF combination |
---|
| 692 | |
---|
| 693 | itDataPlane.next(); |
---|
| 694 | itMaskPlane.next(); |
---|
| 695 | } |
---|
| 696 | |
---|
| 697 | // Generate output container and write it to output table |
---|
| 698 | |
---|
| 699 | SDContainer sc = in.getSDContainer(); |
---|
| 700 | sc.resize(shapeOut); |
---|
| 701 | // |
---|
| 702 | putDataInSDC (sc, outData, outMask); |
---|
| 703 | pTabOut->putSDContainer(sc); |
---|
| 704 | } |
---|
| 705 | // |
---|
| 706 | return pTabOut; |
---|
| 707 | } |
---|
[167] | 708 | |
---|
[169] | 709 | |
---|
[177] | 710 | SDMemTable* SDMath::smooth (const SDMemTable& in, const casa::String& kernelType, |
---|
| 711 | casa::Float width, Bool doAll) |
---|
| 712 | { |
---|
[169] | 713 | |
---|
[177] | 714 | // Number of channels |
---|
[169] | 715 | |
---|
[177] | 716 | const uInt chanAxis = 3; // Spectral axis |
---|
| 717 | SDHeader sh = in.getSDHeader(); |
---|
| 718 | const uInt nChan = sh.nchan; |
---|
| 719 | |
---|
| 720 | // Generate Kernel |
---|
| 721 | |
---|
| 722 | VectorKernel::KernelTypes type = VectorKernel::toKernelType (kernelType); |
---|
| 723 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
| 724 | |
---|
| 725 | // Generate Convolver |
---|
| 726 | |
---|
| 727 | IPosition shape(1,nChan); |
---|
| 728 | Convolver<Float> conv(kernel, shape); |
---|
| 729 | |
---|
| 730 | // New Table |
---|
| 731 | |
---|
| 732 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
| 733 | |
---|
| 734 | // Get cursor location |
---|
| 735 | |
---|
| 736 | IPosition start, end; |
---|
| 737 | getCursorLocation (start, end, in); |
---|
| 738 | // |
---|
| 739 | IPosition shapeOut(4,1); |
---|
| 740 | |
---|
| 741 | // Output Vectors |
---|
| 742 | |
---|
| 743 | Vector<Float> valuesOut(nChan); |
---|
| 744 | Vector<Bool> maskOut(nChan); |
---|
| 745 | |
---|
| 746 | // Loop over rows in Table |
---|
| 747 | |
---|
| 748 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
| 749 | |
---|
| 750 | // Get copy of data |
---|
| 751 | |
---|
| 752 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(ri)); |
---|
| 753 | AlwaysAssert(dataIn.shape()(chanAxis)==nChan, AipsError); |
---|
| 754 | // |
---|
| 755 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 756 | Array<Bool> maskIn = dataIn.getMask(); |
---|
| 757 | |
---|
| 758 | // Branch depending on whether we smooth all locations or just |
---|
| 759 | // those pointed at by the current selection cursor |
---|
| 760 | |
---|
| 761 | if (doAll) { |
---|
| 762 | uInt axis = 3; |
---|
| 763 | VectorIterator<Float> itValues(valuesIn, axis); |
---|
| 764 | VectorIterator<Bool> itMask(maskIn, axis); |
---|
| 765 | while (!itValues.pastEnd()) { |
---|
| 766 | |
---|
| 767 | // Smooth |
---|
| 768 | if (kernelType==VectorKernel::HANNING) { |
---|
| 769 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector()); |
---|
| 770 | itMask.vector() = maskOut; |
---|
| 771 | } else { |
---|
| 772 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
| 773 | conv.linearConv(valuesOut, itValues.vector()); |
---|
| 774 | } |
---|
| 775 | // |
---|
| 776 | itValues.vector() = valuesOut; |
---|
| 777 | // |
---|
| 778 | itValues.next(); |
---|
| 779 | itMask.next(); |
---|
| 780 | } |
---|
| 781 | } else { |
---|
| 782 | |
---|
| 783 | // Set multi-dim Vector shape |
---|
| 784 | |
---|
| 785 | shapeOut(chanAxis) = valuesIn.shape()(chanAxis); |
---|
| 786 | |
---|
| 787 | // Stuff about with shapes so that we don't have conformance run-time errors |
---|
| 788 | |
---|
| 789 | Vector<Float> valuesIn2 = valuesIn(start,end).nonDegenerate(); |
---|
| 790 | Vector<Bool> maskIn2 = maskIn(start,end).nonDegenerate(); |
---|
| 791 | |
---|
| 792 | // Smooth |
---|
| 793 | |
---|
| 794 | if (kernelType==VectorKernel::HANNING) { |
---|
| 795 | mathutil::hanning(valuesOut, maskOut, valuesIn2, maskIn2); |
---|
| 796 | maskIn(start,end) = maskOut.reform(shapeOut); |
---|
| 797 | } else { |
---|
| 798 | mathutil::replaceMaskByZero(valuesIn2, maskIn2); |
---|
| 799 | conv.linearConv(valuesOut, valuesIn2); |
---|
| 800 | } |
---|
| 801 | // |
---|
| 802 | valuesIn(start,end) = valuesOut.reform(shapeOut); |
---|
| 803 | } |
---|
| 804 | |
---|
| 805 | // Create and put back |
---|
| 806 | |
---|
| 807 | SDContainer sc = in.getSDContainer(ri); |
---|
| 808 | putDataInSDC (sc, valuesIn, maskIn); |
---|
| 809 | // |
---|
| 810 | pTabOut->putSDContainer(sc); |
---|
| 811 | } |
---|
| 812 | // |
---|
| 813 | return pTabOut; |
---|
| 814 | } |
---|
| 815 | |
---|
| 816 | |
---|
| 817 | |
---|
| 818 | |
---|
| 819 | |
---|
[169] | 820 | // 'private' functions |
---|
| 821 | |
---|
| 822 | void SDMath::fillSDC (SDContainer& sc, |
---|
| 823 | const Array<Bool>& mask, |
---|
| 824 | const Array<Float>& data, |
---|
| 825 | const Array<Float>& tSys, |
---|
| 826 | Int scanID, Double timeStamp, |
---|
| 827 | Double interval, const String& sourceName, |
---|
| 828 | const Vector<uInt>& freqID) |
---|
[167] | 829 | { |
---|
[169] | 830 | // Data and mask |
---|
[167] | 831 | |
---|
[169] | 832 | putDataInSDC (sc, data, mask); |
---|
[167] | 833 | |
---|
[169] | 834 | // TSys |
---|
| 835 | |
---|
| 836 | sc.putTsys(tSys); |
---|
| 837 | |
---|
| 838 | // Time things |
---|
| 839 | |
---|
| 840 | sc.timestamp = timeStamp; |
---|
| 841 | sc.interval = interval; |
---|
| 842 | sc.scanid = scanID; |
---|
[167] | 843 | // |
---|
[169] | 844 | sc.sourcename = sourceName; |
---|
| 845 | sc.putFreqMap(freqID); |
---|
| 846 | } |
---|
[167] | 847 | |
---|
[169] | 848 | void SDMath::normalize (MaskedArray<Float>& sum, |
---|
| 849 | const Array<Float>& sumSq, |
---|
| 850 | const Array<Float>& nPts, |
---|
| 851 | WeightType wtType, Int axis, |
---|
| 852 | Int nAxesSub) |
---|
| 853 | { |
---|
| 854 | IPosition pos2(nAxesSub,0); |
---|
| 855 | // |
---|
| 856 | if (wtType==NONE) { |
---|
[167] | 857 | |
---|
[169] | 858 | // We just average by the number of points accumulated. |
---|
| 859 | // We need to make a MA out of nPts so that no divide by |
---|
| 860 | // zeros occur |
---|
[167] | 861 | |
---|
[169] | 862 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
| 863 | sum /= t; |
---|
| 864 | } else if (wtType==VAR) { |
---|
[167] | 865 | |
---|
[169] | 866 | // Normalize each spectrum by sum(1/var) where the variance |
---|
| 867 | // is worked out for each spectrum |
---|
| 868 | |
---|
| 869 | Array<Float>& data = sum.getRWArray(); |
---|
| 870 | VectorIterator<Float> itData(data, axis); |
---|
| 871 | while (!itData.pastEnd()) { |
---|
| 872 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 873 | itData.vector() /= sumSq(pos2); |
---|
| 874 | itData.next(); |
---|
| 875 | } |
---|
| 876 | } else if (wtType==TSYS) { |
---|
| 877 | } |
---|
| 878 | } |
---|
| 879 | |
---|
| 880 | |
---|
| 881 | void SDMath::accumulate (Double& timeSum, Double& intSum, Int& nAccum, |
---|
| 882 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
| 883 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
| 884 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
| 885 | const Vector<Bool>& mask, Double time, Double interval, |
---|
| 886 | const Block<CountedPtr<SDMemTable> >& in, |
---|
| 887 | uInt iTab, uInt iRow, uInt axis, |
---|
| 888 | uInt nAxesSub, Bool useMask, |
---|
| 889 | WeightType wtType) |
---|
| 890 | { |
---|
| 891 | |
---|
| 892 | // Get data |
---|
| 893 | |
---|
| 894 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
| 895 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
| 896 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
[167] | 897 | // |
---|
[169] | 898 | if (wtType==NONE) { |
---|
| 899 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
| 900 | nPts += n; // Only accumulates where mask==T |
---|
| 901 | } else if (wtType==VAR) { |
---|
[167] | 902 | |
---|
[169] | 903 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
| 904 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
[167] | 905 | |
---|
[169] | 906 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 907 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
| 908 | Float fac = 1.0; |
---|
| 909 | IPosition pos(nAxesSub,0); |
---|
| 910 | // |
---|
| 911 | while (!itData.pastEnd()) { |
---|
[167] | 912 | |
---|
[169] | 913 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
[167] | 914 | |
---|
[169] | 915 | if (useMask) { |
---|
| 916 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
| 917 | fac = 1.0/variance(tmp); |
---|
| 918 | } else { |
---|
| 919 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
| 920 | fac = 1.0/variance(tmp); |
---|
| 921 | } |
---|
| 922 | |
---|
| 923 | // Scale data |
---|
| 924 | |
---|
| 925 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
[167] | 926 | // |
---|
[169] | 927 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
| 928 | // This method to get pos2 from itData.pos() is only valid |
---|
| 929 | // because the spectral axis is the last one (so we can just |
---|
| 930 | // copy the first nAXesSub positions out) |
---|
[167] | 931 | |
---|
[169] | 932 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 933 | sumSq(pos) += fac; |
---|
| 934 | // |
---|
| 935 | itData.next(); |
---|
| 936 | itMask.next(); |
---|
| 937 | } |
---|
| 938 | } else if (wtType==TSYS) { |
---|
| 939 | } |
---|
[167] | 940 | |
---|
[169] | 941 | // Accumulate sum of (possibly scaled) data |
---|
| 942 | |
---|
| 943 | sum += dataIn; |
---|
| 944 | |
---|
| 945 | // Accumulate Tsys, time, and interval |
---|
| 946 | |
---|
| 947 | tSysSum += tSys; |
---|
| 948 | timeSum += time; |
---|
| 949 | intSum += interval; |
---|
| 950 | nAccum += 1; |
---|
| 951 | } |
---|
| 952 | |
---|
| 953 | |
---|
| 954 | |
---|
| 955 | |
---|
| 956 | void SDMath::getCursorLocation (IPosition& start, IPosition& end, |
---|
| 957 | const SDMemTable& in) |
---|
| 958 | { |
---|
| 959 | const uInt nDim = 4; |
---|
| 960 | const uInt i = in.getBeam(); |
---|
| 961 | const uInt j = in.getIF(); |
---|
| 962 | const uInt k = in.getPol(); |
---|
| 963 | const uInt n = in.nChan(); |
---|
[167] | 964 | // |
---|
[169] | 965 | start.resize(nDim); |
---|
| 966 | start(0) = i; |
---|
| 967 | start(1) = j; |
---|
| 968 | start(2) = k; |
---|
| 969 | start(3) = 0; |
---|
[167] | 970 | // |
---|
[169] | 971 | end.resize(nDim); |
---|
| 972 | end(0) = i; |
---|
| 973 | end(1) = j; |
---|
| 974 | end(2) = k; |
---|
| 975 | end(3) = n-1; |
---|
| 976 | } |
---|
| 977 | |
---|
| 978 | |
---|
| 979 | void SDMath::convertWeightString (WeightType& wtType, const std::string& weightStr) |
---|
| 980 | { |
---|
| 981 | String tStr(weightStr); |
---|
| 982 | tStr.upcase(); |
---|
| 983 | if (tStr.contains(String("NONE"))) { |
---|
| 984 | wtType = NONE; |
---|
| 985 | } else if (tStr.contains(String("VAR"))) { |
---|
| 986 | wtType = VAR; |
---|
| 987 | } else if (tStr.contains(String("TSYS"))) { |
---|
| 988 | wtType = TSYS; |
---|
| 989 | throw (AipsError("T_sys weighting not yet implemented")); |
---|
| 990 | } else { |
---|
| 991 | throw (AipsError("Unrecognized weighting type")); |
---|
[167] | 992 | } |
---|
| 993 | } |
---|
| 994 | |
---|
[169] | 995 | void SDMath::putDataInSDC (SDContainer& sc, const Array<Float>& data, |
---|
| 996 | const Array<Bool>& mask) |
---|
| 997 | { |
---|
| 998 | sc.putSpectrum(data); |
---|
| 999 | // |
---|
| 1000 | Array<uChar> outflags(data.shape()); |
---|
| 1001 | convertArray(outflags,!mask); |
---|
| 1002 | sc.putFlags(outflags); |
---|
| 1003 | } |
---|