[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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[262] | 46 | #include <casa/Exceptions.h>
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| 47 | #include <casa/Quanta/Quantum.h>
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| 48 | #include <casa/Quanta/Unit.h>
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| 49 | #include <casa/Quanta/MVEpoch.h>
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[221] | 50 | #include <casa/Quanta/QC.h>
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[272] | 51 | #include <casa/Quanta/MVTime.h>
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[177] | 52 | #include <casa/Utilities/Assert.h>
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[2] | 53 |
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[262] | 54 | #include <coordinates/Coordinates/SpectralCoordinate.h>
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| 55 | #include <coordinates/Coordinates/CoordinateSystem.h>
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| 56 | #include <coordinates/Coordinates/CoordinateUtil.h>
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| 57 | #include <coordinates/Coordinates/VelocityAligner.h>
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| 58 |
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| 59 | #include <lattices/Lattices/LatticeUtilities.h>
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| 60 | #include <lattices/Lattices/RebinLattice.h>
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| 61 |
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| 62 | #include <measures/Measures/MEpoch.h>
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| 63 | #include <measures/Measures/MDirection.h>
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| 64 | #include <measures/Measures/MPosition.h>
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| 65 |
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[177] | 66 | #include <scimath/Mathematics/VectorKernel.h>
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| 67 | #include <scimath/Mathematics/Convolver.h>
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[227] | 68 | #include <scimath/Mathematics/InterpolateArray1D.h>
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[234] | 69 | #include <scimath/Functionals/Polynomial.h>
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[177] | 70 |
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[81] | 71 | #include <tables/Tables/Table.h>
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| 72 | #include <tables/Tables/ScalarColumn.h>
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| 73 | #include <tables/Tables/ArrayColumn.h>
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[227] | 74 | #include <tables/Tables/ReadAsciiTable.h>
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[2] | 75 |
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[38] | 76 | #include "MathUtils.h"
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[232] | 77 | #include "SDDefs.h"
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[2] | 78 | #include "SDContainer.h"
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| 79 | #include "SDMemTable.h"
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| 80 |
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| 81 | #include "SDMath.h"
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| 82 |
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[125] | 83 | using namespace casa;
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[83] | 84 | using namespace asap;
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[2] | 85 |
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[170] | 86 |
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| 87 | SDMath::SDMath()
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| 88 | {;}
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| 89 |
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[185] | 90 | SDMath::SDMath(const SDMath& other)
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[170] | 91 | {
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| 92 |
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| 93 | // No state
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| 94 |
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| 95 | }
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| 96 |
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| 97 | SDMath& SDMath::operator=(const SDMath& other)
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| 98 | {
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| 99 | if (this != &other) {
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| 100 | // No state
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| 101 | }
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| 102 | return *this;
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| 103 | }
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| 104 |
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[183] | 105 | SDMath::~SDMath()
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| 106 | {;}
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[170] | 107 |
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[183] | 108 |
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[262] | 109 |
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[272] | 110 | SDMemTable* SDMath::velocityAlignment (const SDMemTable& in, const String& refTime) const
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[262] | 111 | {
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| 112 |
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[267] | 113 | // Get velocity/frame info from Table
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[262] | 114 |
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| 115 | std::vector<std::string> info = in.getCoordInfo();
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[294] | 116 |
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| 117 | // Parse unit ("" means channels)
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| 118 |
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[262] | 119 | String velUnit(info[0]);
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| 120 | if (velUnit.length()==0) {
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| 121 | throw(AipsError("You have not set a velocity abcissa unit - use function set_unit"));
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| 122 | } else {
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| 123 | Unit velUnitU(velUnit);
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| 124 | if (velUnitU!=Unit(String("m/s"))) {
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| 125 | throw(AipsError("Specified abcissa unit is not consistent with km/s - use function set_unit"));
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| 126 | }
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| 127 | }
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[294] | 128 |
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| 129 | // Parse doppler
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| 130 |
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[262] | 131 | String dopplerStr(info[2]);
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| 132 | String velSystemStr(info[1]);
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| 133 | String velBaseSystemStr(info[3]);
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| 134 | if (velBaseSystemStr==velSystemStr) {
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[267] | 135 | throw(AipsError("You have not set a velocity frame different from the initial - use function set_freqframe"));
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[262] | 136 | }
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[294] | 137 |
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| 138 | // Parse frequency system
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| 139 |
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[262] | 140 | MFrequency::Types velSystem;
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| 141 | MFrequency::getType(velSystem, velSystemStr);
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| 142 | MDoppler::Types doppler;
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| 143 | MDoppler::getType(doppler, dopplerStr);
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| 144 |
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[267] | 145 | // Do it
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[262] | 146 |
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[272] | 147 | return velocityAlign (in, velSystem, velUnit, doppler, refTime);
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[267] | 148 | }
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[262] | 149 |
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| 150 |
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| 151 |
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[185] | 152 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in,
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| 153 | const Vector<Bool>& mask, Bool scanAv,
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[248] | 154 | const String& weightStr, Bool alignVelocity) const
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[130] | 155 | //
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[144] | 156 | // Weighted averaging of spectra from one or more Tables.
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[130] | 157 | //
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| 158 | {
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[2] | 159 |
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[163] | 160 | // Convert weight type
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| 161 |
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| 162 | WeightType wtType = NONE;
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[185] | 163 | convertWeightString(wtType, weightStr);
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[163] | 164 |
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[144] | 165 | // Create output Table by cloning from the first table
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[2] | 166 |
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[144] | 167 | SDMemTable* pTabOut = new SDMemTable(*in[0],True);
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[130] | 168 |
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[144] | 169 | // Setup
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[130] | 170 |
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[144] | 171 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change
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| 172 | Array<Float> arr(shp);
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| 173 | Array<Bool> barr(shp);
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[221] | 174 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis));
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[130] | 175 |
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[144] | 176 | // Columns from Tables
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[130] | 177 |
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[144] | 178 | ROArrayColumn<Float> tSysCol;
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| 179 | ROScalarColumn<Double> mjdCol;
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| 180 | ROScalarColumn<String> srcNameCol;
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| 181 | ROScalarColumn<Double> intCol;
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| 182 | ROArrayColumn<uInt> fqIDCol;
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[130] | 183 |
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[144] | 184 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam
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| 185 | // Note that the mask of the accumulation array will ALWAYS remain ALL True.
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| 186 | // The MA is only used so that when data which is masked Bad is added to it,
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| 187 | // that data does not contribute.
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| 188 |
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| 189 | Array<Float> zero(shp);
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| 190 | zero=0.0;
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| 191 | Array<Bool> good(shp);
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| 192 | good = True;
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| 193 | MaskedArray<Float> sum(zero,good);
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| 194 |
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| 195 | // Counter arrays
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| 196 |
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| 197 | Array<Float> nPts(shp); // Number of points
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| 198 | nPts = 0.0;
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| 199 | Array<Float> nInc(shp); // Increment
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| 200 | nInc = 1.0;
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| 201 |
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| 202 | // Create accumulation Array for variance. We accumulate for
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| 203 | // each if,pol,beam, but average over channel. So we need
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| 204 | // a shape with one less axis dropping channels.
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| 205 |
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| 206 | const uInt nAxesSub = shp.nelements() - 1;
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| 207 | IPosition shp2(nAxesSub);
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| 208 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) {
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[221] | 209 | if (i!=asap::ChanAxis) {
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[144] | 210 | shp2(j) = shp(i);
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| 211 | j++;
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| 212 | }
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[2] | 213 | }
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[144] | 214 | Array<Float> sumSq(shp2);
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| 215 | sumSq = 0.0;
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| 216 | IPosition pos2(nAxesSub,0); // For indexing
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[130] | 217 |
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[144] | 218 | // Time-related accumulators
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[130] | 219 |
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[144] | 220 | Double time;
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| 221 | Double timeSum = 0.0;
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| 222 | Double intSum = 0.0;
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| 223 | Double interval = 0.0;
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[130] | 224 |
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[144] | 225 | // To get the right shape for the Tsys accumulator we need to
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| 226 | // access a column from the first table. The shape of this
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| 227 | // array must not change
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[130] | 228 |
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[144] | 229 | Array<Float> tSysSum;
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| 230 | {
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| 231 | const Table& tabIn = in[0]->table();
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| 232 | tSysCol.attach(tabIn,"TSYS");
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| 233 | tSysSum.resize(tSysCol.shape(0));
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| 234 | }
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| 235 | tSysSum =0.0;
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| 236 | Array<Float> tSys;
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| 237 |
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| 238 | // Scan and row tracking
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| 239 |
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| 240 | Int oldScanID = 0;
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| 241 | Int outScanID = 0;
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| 242 | Int scanID = 0;
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| 243 | Int rowStart = 0;
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| 244 | Int nAccum = 0;
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| 245 | Int tableStart = 0;
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| 246 |
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| 247 | // Source and FreqID
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| 248 |
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| 249 | String sourceName, oldSourceName, sourceNameStart;
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| 250 | Vector<uInt> freqID, freqIDStart, oldFreqID;
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| 251 |
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| 252 | // Loop over tables
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| 253 |
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| 254 | Float fac = 1.0;
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| 255 | const uInt nTables = in.nelements();
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| 256 | for (uInt iTab=0; iTab<nTables; iTab++) {
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| 257 |
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[221] | 258 | // Should check that the frequency tables don't change if doing VelocityAlignment
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| 259 |
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[144] | 260 | // Attach columns to Table
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| 261 |
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| 262 | const Table& tabIn = in[iTab]->table();
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| 263 | tSysCol.attach(tabIn, "TSYS");
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| 264 | mjdCol.attach(tabIn, "TIME");
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| 265 | srcNameCol.attach(tabIn, "SRCNAME");
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| 266 | intCol.attach(tabIn, "INTERVAL");
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| 267 | fqIDCol.attach(tabIn, "FREQID");
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| 268 |
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| 269 | // Loop over rows in Table
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| 270 |
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| 271 | const uInt nRows = in[iTab]->nRow();
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| 272 | for (uInt iRow=0; iRow<nRows; iRow++) {
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| 273 |
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| 274 | // Check conformance
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| 275 |
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| 276 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape();
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| 277 | if (!shp.isEqual(shp2)) {
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| 278 | throw (AipsError("Shapes for all rows must be the same"));
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| 279 | }
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| 280 |
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| 281 | // If we are not doing scan averages, make checks for source and
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| 282 | // frequency setup and warn if averaging across them
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| 283 |
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| 284 | // Get copy of Scan Container for this row
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| 285 |
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| 286 | SDContainer sc = in[iTab]->getSDContainer(iRow);
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| 287 | scanID = sc.scanid;
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| 288 |
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| 289 | // Get quantities from columns
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| 290 |
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| 291 | srcNameCol.getScalar(iRow, sourceName);
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| 292 | mjdCol.get(iRow, time);
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| 293 | tSysCol.get(iRow, tSys);
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| 294 | intCol.get(iRow, interval);
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| 295 | fqIDCol.get(iRow, freqID);
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| 296 |
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| 297 | // Initialize first source and freqID
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| 298 |
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| 299 | if (iRow==0 && iTab==0) {
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| 300 | sourceNameStart = sourceName;
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| 301 | freqIDStart = freqID;
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| 302 | }
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| 303 |
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| 304 | // If we are doing scan averages, see if we are at the end of an
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| 305 | // accumulation period (scan). We must check soutce names too,
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| 306 | // since we might have two tables with one scan each but different
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| 307 | // source names; we shouldn't average different sources together
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| 308 |
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| 309 | if (scanAv && ( (scanID != oldScanID) ||
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| 310 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) {
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| 311 |
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| 312 | // Normalize data in 'sum' accumulation array according to weighting scheme
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| 313 |
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[221] | 314 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub);
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[144] | 315 |
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| 316 | // Fill scan container. The source and freqID come from the
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| 317 | // first row of the first table that went into this average (
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| 318 | // should be the same for all rows in the scan average)
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| 319 |
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| 320 | Float nR(nAccum);
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[185] | 321 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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[144] | 322 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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| 323 |
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| 324 | // Write container out to Table
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| 325 |
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| 326 | pTabOut->putSDContainer(sc);
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| 327 |
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| 328 | // Reset accumulators
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| 329 |
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| 330 | sum = 0.0;
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| 331 | sumSq = 0.0;
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| 332 | nAccum = 0;
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| 333 | //
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| 334 | tSysSum =0.0;
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| 335 | timeSum = 0.0;
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| 336 | intSum = 0.0;
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[221] | 337 | nPts = 0.0;
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[144] | 338 |
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| 339 | // Increment
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| 340 |
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| 341 | rowStart = iRow; // First row for next accumulation
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| 342 | tableStart = iTab; // First table for next accumulation
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| 343 | sourceNameStart = sourceName; // First source name for next accumulation
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| 344 | freqIDStart = freqID; // First FreqID for next accumulation
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| 345 | //
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| 346 | oldScanID = scanID;
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| 347 | outScanID += 1; // Scan ID for next accumulation period
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[227] | 348 | }
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[144] | 349 |
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[146] | 350 | // Accumulate
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[144] | 351 |
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[185] | 352 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum,
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[221] | 353 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis,
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[146] | 354 | nAxesSub, useMask, wtType);
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[144] | 355 | //
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| 356 | oldSourceName = sourceName;
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| 357 | oldFreqID = freqID;
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[184] | 358 | }
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[144] | 359 | }
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| 360 |
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| 361 | // OK at this point we have accumulation data which is either
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| 362 | // - accumulated from all tables into one row
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| 363 | // or
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| 364 | // - accumulated from the last scan average
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| 365 | //
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| 366 | // Normalize data in 'sum' accumulation array according to weighting scheme
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[221] | 367 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub);
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[144] | 368 |
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| 369 | // Create and fill container. The container we clone will be from
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| 370 | // the last Table and the first row that went into the current
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| 371 | // accumulation. It probably doesn't matter that much really...
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| 372 |
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| 373 | Float nR(nAccum);
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| 374 | SDContainer sc = in[tableStart]->getSDContainer(rowStart);
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[185] | 375 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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[144] | 376 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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[221] | 377 | pTabOut->putSDContainer(sc);
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[304] | 378 | pTabOut->resetCursor();
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[144] | 379 | //
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| 380 | return CountedPtr<SDMemTable>(pTabOut);
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[2] | 381 | }
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[9] | 382 |
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[144] | 383 |
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| 384 |
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[248] | 385 | CountedPtr<SDMemTable> SDMath::binaryOperate (const CountedPtr<SDMemTable>& left,
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| 386 | const CountedPtr<SDMemTable>& right,
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[294] | 387 | const String& op, Bool preserve,
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| 388 | Bool doTSys) const
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[185] | 389 | {
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[85] | 390 |
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[248] | 391 | // Check operator
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[130] | 392 |
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[234] | 393 | String op2(op);
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| 394 | op2.upcase();
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| 395 | uInt what = 0;
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| 396 | if (op2=="ADD") {
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| 397 | what = 0;
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| 398 | } else if (op2=="SUB") {
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| 399 | what = 1;
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| 400 | } else if (op2=="MUL") {
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| 401 | what = 2;
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| 402 | } else if (op2=="DIV") {
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| 403 | what = 3;
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[248] | 404 | } else if (op2=="QUOTIENT") {
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| 405 | what = 4;
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[294] | 406 | doTSys = True;
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[234] | 407 | } else {
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[248] | 408 | throw( AipsError("Unrecognized operation"));
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[234] | 409 | }
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| 410 |
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| 411 | // Check rows
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| 412 |
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[248] | 413 | const uInt nRowLeft = left->nRow();
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| 414 | const uInt nRowRight = right->nRow();
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| 415 | Bool ok = (nRowRight==1&&nRowLeft>0) ||
|
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| 416 | (nRowRight>=1&&nRowLeft==nRowRight);
|
---|
| 417 | if (!ok) {
|
---|
| 418 | throw (AipsError("The right Scan Table can have one row or the same number of rows as the left Scan Table"));
|
---|
[234] | 419 | }
|
---|
| 420 |
|
---|
[248] | 421 | // Input Tables
|
---|
[234] | 422 |
|
---|
| 423 | const Table& tLeft = left->table();
|
---|
| 424 | const Table& tRight = right->table();
|
---|
[248] | 425 |
|
---|
| 426 | // TSys columns
|
---|
| 427 |
|
---|
[294] | 428 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol;
|
---|
| 429 | if (doTSys) {
|
---|
| 430 | tSysLeftCol.attach(tLeft, "TSYS");
|
---|
| 431 | tSysRightCol.attach(tRight, "TSYS");
|
---|
| 432 | }
|
---|
[234] | 433 |
|
---|
[248] | 434 | // First row for right
|
---|
[234] | 435 |
|
---|
[248] | 436 | Array<Float> tSysLeftArr, tSysRightArr;
|
---|
[294] | 437 | if (doTSys) tSysRightCol.get(0, tSysRightArr);
|
---|
[248] | 438 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0));
|
---|
| 439 | IPosition shpRight = pMRight->shape();
|
---|
| 440 |
|
---|
| 441 | // Output Table cloned from left
|
---|
| 442 |
|
---|
[234] | 443 | SDMemTable* pTabOut = new SDMemTable(*left, True);
|
---|
| 444 |
|
---|
| 445 | // Loop over rows
|
---|
| 446 |
|
---|
[248] | 447 | for (uInt i=0; i<nRowLeft; i++) {
|
---|
[234] | 448 |
|
---|
| 449 | // Get data
|
---|
[248] | 450 |
|
---|
[234] | 451 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i));
|
---|
[248] | 452 | IPosition shpLeft = mLeft.shape();
|
---|
[294] | 453 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr);
|
---|
[234] | 454 | //
|
---|
[248] | 455 | if (nRowRight>1) {
|
---|
| 456 | delete pMRight;
|
---|
| 457 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i));
|
---|
| 458 | shpRight = pMRight->shape();
|
---|
[294] | 459 | if (doTSys) tSysRightCol.get(i, tSysRightArr);
|
---|
[234] | 460 | }
|
---|
[248] | 461 | //
|
---|
| 462 | if (!shpRight.isEqual(shpLeft)) {
|
---|
| 463 | throw(AipsError("left and right scan tables are not conformant"));
|
---|
| 464 | }
|
---|
[294] | 465 | if (doTSys) {
|
---|
| 466 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) {
|
---|
| 467 | throw(AipsError("left and right Tsys data are not conformant"));
|
---|
| 468 | }
|
---|
| 469 | if (!shpRight.isEqual(tSysRightArr.shape())) {
|
---|
| 470 | throw(AipsError("left and right scan tables are not conformant"));
|
---|
| 471 | }
|
---|
[248] | 472 | }
|
---|
[234] | 473 |
|
---|
| 474 | // Make container
|
---|
| 475 |
|
---|
| 476 | SDContainer sc = left->getSDContainer(i);
|
---|
| 477 |
|
---|
| 478 | // Operate on data and TSys
|
---|
| 479 |
|
---|
| 480 | if (what==0) {
|
---|
[248] | 481 | MaskedArray<Float> tmp = mLeft + *pMRight;
|
---|
[234] | 482 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 483 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr);
|
---|
[234] | 484 | } else if (what==1) {
|
---|
[248] | 485 | MaskedArray<Float> tmp = mLeft - *pMRight;
|
---|
[234] | 486 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 487 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr);
|
---|
[234] | 488 | } else if (what==2) {
|
---|
[248] | 489 | MaskedArray<Float> tmp = mLeft * *pMRight;
|
---|
[234] | 490 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 491 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr);
|
---|
[234] | 492 | } else if (what==3) {
|
---|
[248] | 493 | MaskedArray<Float> tmp = mLeft / *pMRight;
|
---|
[234] | 494 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 495 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr);
|
---|
[248] | 496 | } else if (what==4) {
|
---|
| 497 | if (preserve) {
|
---|
| 498 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysRightArr;
|
---|
| 499 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
| 500 | } else {
|
---|
| 501 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysLeftArr;
|
---|
| 502 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
| 503 | }
|
---|
| 504 | sc.putTsys(tSysRightArr);
|
---|
[234] | 505 | }
|
---|
| 506 |
|
---|
| 507 | // Put new row in output Table
|
---|
| 508 |
|
---|
[171] | 509 | pTabOut->putSDContainer(sc);
|
---|
[130] | 510 | }
|
---|
[248] | 511 | if (pMRight) delete pMRight;
|
---|
[304] | 512 | pTabOut->resetCursor();
|
---|
[130] | 513 | //
|
---|
[171] | 514 | return CountedPtr<SDMemTable>(pTabOut);
|
---|
[9] | 515 | }
|
---|
[48] | 516 |
|
---|
[146] | 517 |
|
---|
| 518 |
|
---|
[185] | 519 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in,
|
---|
[234] | 520 | const Vector<Bool>& mask,
|
---|
| 521 | const String& which, Int row) const
|
---|
[130] | 522 | //
|
---|
| 523 | // Perhaps iteration over pol/beam/if should be in here
|
---|
| 524 | // and inside the nrow iteration ?
|
---|
| 525 | //
|
---|
| 526 | {
|
---|
| 527 | const uInt nRow = in->nRow();
|
---|
| 528 |
|
---|
| 529 | // Specify cursor location
|
---|
| 530 |
|
---|
[152] | 531 | IPosition start, end;
|
---|
[185] | 532 | getCursorLocation(start, end, *in);
|
---|
[130] | 533 |
|
---|
| 534 | // Loop over rows
|
---|
| 535 |
|
---|
[234] | 536 | const uInt nEl = mask.nelements();
|
---|
| 537 | uInt iStart = 0;
|
---|
| 538 | uInt iEnd = in->nRow()-1;
|
---|
| 539 | //
|
---|
| 540 | if (row>=0) {
|
---|
| 541 | iStart = row;
|
---|
| 542 | iEnd = row;
|
---|
| 543 | }
|
---|
| 544 | //
|
---|
| 545 | std::vector<float> result(iEnd-iStart+1);
|
---|
| 546 | for (uInt ii=iStart; ii <= iEnd; ++ii) {
|
---|
[130] | 547 |
|
---|
| 548 | // Get row and deconstruct
|
---|
| 549 |
|
---|
| 550 | MaskedArray<Float> marr(in->rowAsMaskedArray(ii));
|
---|
| 551 | Array<Float> arr = marr.getArray();
|
---|
| 552 | Array<Bool> barr = marr.getMask();
|
---|
| 553 |
|
---|
| 554 | // Access desired piece of data
|
---|
| 555 |
|
---|
| 556 | Array<Float> v((arr(start,end)).nonDegenerate());
|
---|
| 557 | Array<Bool> m((barr(start,end)).nonDegenerate());
|
---|
| 558 |
|
---|
| 559 | // Apply OTF mask
|
---|
| 560 |
|
---|
| 561 | MaskedArray<Float> tmp;
|
---|
| 562 | if (m.nelements()==nEl) {
|
---|
[234] | 563 | tmp.setData(v,m&&mask);
|
---|
[130] | 564 | } else {
|
---|
| 565 | tmp.setData(v,m);
|
---|
| 566 | }
|
---|
| 567 |
|
---|
| 568 | // Get statistic
|
---|
| 569 |
|
---|
[234] | 570 | result[ii-iStart] = mathutil::statistics(which, tmp);
|
---|
[130] | 571 | }
|
---|
| 572 | //
|
---|
| 573 | return result;
|
---|
| 574 | }
|
---|
| 575 |
|
---|
[146] | 576 |
|
---|
[234] | 577 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const
|
---|
[144] | 578 | {
|
---|
[169] | 579 | SDHeader sh = in.getSDHeader();
|
---|
| 580 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
[163] | 581 |
|
---|
[169] | 582 | // Bin up SpectralCoordinates
|
---|
[163] | 583 |
|
---|
[169] | 584 | IPosition factors(1);
|
---|
| 585 | factors(0) = width;
|
---|
| 586 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
| 587 | CoordinateSystem cSys;
|
---|
[288] | 588 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
[169] | 589 | CoordinateSystem cSysBin =
|
---|
[185] | 590 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False);
|
---|
[169] | 591 | //
|
---|
| 592 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0);
|
---|
| 593 | pTabOut->setCoordinate(sCBin, j);
|
---|
| 594 | }
|
---|
[163] | 595 |
|
---|
[169] | 596 | // Use RebinLattice to find shape
|
---|
[130] | 597 |
|
---|
[169] | 598 | IPosition shapeIn(1,sh.nchan);
|
---|
[185] | 599 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors);
|
---|
[169] | 600 | sh.nchan = shapeOut(0);
|
---|
| 601 | pTabOut->putSDHeader(sh);
|
---|
[144] | 602 |
|
---|
[169] | 603 | // Loop over rows and bin along channel axis
|
---|
| 604 |
|
---|
| 605 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
| 606 | SDContainer sc = in.getSDContainer(i);
|
---|
[144] | 607 | //
|
---|
[169] | 608 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape
|
---|
[144] | 609 |
|
---|
[169] | 610 | // Bin up spectrum
|
---|
[144] | 611 |
|
---|
[169] | 612 | MaskedArray<Float> marr(in.rowAsMaskedArray(i));
|
---|
| 613 | MaskedArray<Float> marrout;
|
---|
[221] | 614 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width);
|
---|
[144] | 615 |
|
---|
[169] | 616 | // Put back the binned data and flags
|
---|
[144] | 617 |
|
---|
[169] | 618 | IPosition ip2 = marrout.shape();
|
---|
| 619 | sc.resize(ip2);
|
---|
[146] | 620 | //
|
---|
[185] | 621 | putDataInSDC(sc, marrout.getArray(), marrout.getMask());
|
---|
[146] | 622 |
|
---|
[169] | 623 | // Bin up Tsys.
|
---|
[146] | 624 |
|
---|
[169] | 625 | Array<Bool> allGood(tSys.shape(),True);
|
---|
| 626 | MaskedArray<Float> tSysIn(tSys, allGood, True);
|
---|
[146] | 627 | //
|
---|
[169] | 628 | MaskedArray<Float> tSysOut;
|
---|
[221] | 629 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width);
|
---|
[169] | 630 | sc.putTsys(tSysOut.getArray());
|
---|
[146] | 631 | //
|
---|
[169] | 632 | pTabOut->putSDContainer(sc);
|
---|
| 633 | }
|
---|
| 634 | return pTabOut;
|
---|
[146] | 635 | }
|
---|
| 636 |
|
---|
[299] | 637 | SDMemTable* SDMath::resample (const SDMemTable& in, const String& methodStr,
|
---|
| 638 | Float width) const
|
---|
| 639 | //
|
---|
| 640 | // Should add the possibility of width being specified in km/s. This means
|
---|
| 641 | // that for each freqID (SpectralCoordinate) we will need to convert to an
|
---|
| 642 | // average channel width (say at the reference pixel). Then we would need
|
---|
| 643 | // to be careful to make sure each spectrum (of different freqID)
|
---|
| 644 | // is the same length.
|
---|
| 645 | //
|
---|
| 646 | {
|
---|
| 647 | Bool doVel = False;
|
---|
| 648 |
|
---|
| 649 | // Interpolation method
|
---|
| 650 |
|
---|
| 651 | Int interpMethod = 0;
|
---|
| 652 | convertInterpString(interpMethod, methodStr);
|
---|
| 653 |
|
---|
| 654 | // Make output table
|
---|
| 655 |
|
---|
| 656 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
| 657 |
|
---|
| 658 | // Resample SpectralCoordinates (one per freqID)
|
---|
| 659 |
|
---|
| 660 | const uInt nCoord = in.nCoordinates();
|
---|
| 661 | Vector<Float> offset(1,0.0);
|
---|
| 662 | Vector<Float> factors(1,1.0/width);
|
---|
| 663 | Vector<Int> newShape;
|
---|
| 664 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
| 665 | CoordinateSystem cSys;
|
---|
| 666 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
| 667 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape);
|
---|
| 668 | SpectralCoordinate sC = cSys2.spectralCoordinate(0);
|
---|
| 669 | //
|
---|
| 670 | pTabOut->setCoordinate(sC, j);
|
---|
| 671 | }
|
---|
| 672 |
|
---|
| 673 | // Get header
|
---|
| 674 |
|
---|
| 675 | SDHeader sh = in.getSDHeader();
|
---|
| 676 |
|
---|
| 677 | // Generate resampling vectors
|
---|
| 678 |
|
---|
| 679 | const uInt nChanIn = sh.nchan;
|
---|
| 680 | Vector<Float> xIn(nChanIn);
|
---|
| 681 | indgen(xIn);
|
---|
| 682 | //
|
---|
| 683 | Int fac = Int(nChanIn/width);
|
---|
| 684 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later
|
---|
| 685 | uInt i = 0;
|
---|
| 686 | Float x = 0.0;
|
---|
| 687 | Bool more = True;
|
---|
| 688 | while (more) {
|
---|
| 689 | xOut(i) = x;
|
---|
| 690 | //
|
---|
| 691 | i++;
|
---|
| 692 | x += width;
|
---|
| 693 | if (x>nChanIn-1) more = False;
|
---|
| 694 | }
|
---|
| 695 | const uInt nChanOut = i;
|
---|
| 696 | xOut.resize(nChanOut,True);
|
---|
| 697 | //
|
---|
| 698 | IPosition shapeIn(in.rowAsMaskedArray(0).shape());
|
---|
| 699 | sh.nchan = nChanOut;
|
---|
| 700 | pTabOut->putSDHeader(sh);
|
---|
| 701 |
|
---|
| 702 | // Loop over rows and resample along channel axis
|
---|
| 703 |
|
---|
| 704 | Array<Float> valuesOut;
|
---|
| 705 | Array<Bool> maskOut;
|
---|
| 706 | Array<Float> tSysOut;
|
---|
| 707 | Array<Bool> tSysMaskIn(shapeIn,True);
|
---|
| 708 | Array<Bool> tSysMaskOut;
|
---|
| 709 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
| 710 |
|
---|
| 711 | // Get container
|
---|
| 712 |
|
---|
| 713 | SDContainer sc = in.getSDContainer(i);
|
---|
| 714 |
|
---|
| 715 | // Get data and Tsys
|
---|
| 716 |
|
---|
| 717 | const Array<Float>& tSysIn = sc.getTsys();
|
---|
| 718 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i));
|
---|
| 719 | Array<Float> valuesIn = dataIn.getArray();
|
---|
| 720 | Array<Bool> maskIn = dataIn.getMask();
|
---|
| 721 |
|
---|
| 722 | // Interpolate data
|
---|
| 723 |
|
---|
| 724 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut,
|
---|
| 725 | xIn, valuesIn, maskIn,
|
---|
| 726 | interpMethod, True, True);
|
---|
| 727 | sc.resize(valuesOut.shape());
|
---|
| 728 | putDataInSDC(sc, valuesOut, maskOut);
|
---|
| 729 |
|
---|
| 730 | // Interpolate TSys
|
---|
| 731 |
|
---|
| 732 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut,
|
---|
| 733 | xIn, tSysIn, tSysMaskIn,
|
---|
| 734 | interpMethod, True, True);
|
---|
| 735 | sc.putTsys(tSysOut);
|
---|
| 736 |
|
---|
| 737 | // Put container in output
|
---|
| 738 |
|
---|
| 739 | pTabOut->putSDContainer(sc);
|
---|
| 740 | }
|
---|
| 741 | //
|
---|
| 742 | return pTabOut;
|
---|
| 743 | }
|
---|
| 744 |
|
---|
[248] | 745 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll,
|
---|
[294] | 746 | uInt what, Bool doTSys) const
|
---|
[152] | 747 | //
|
---|
| 748 | // what = 0 Multiply
|
---|
| 749 | // 1 Add
|
---|
[146] | 750 | {
|
---|
[152] | 751 | SDMemTable* pOut = new SDMemTable(in,False);
|
---|
| 752 | const Table& tOut = pOut->table();
|
---|
[294] | 753 | ArrayColumn<Float> specCol(tOut,"SPECTRA");
|
---|
| 754 | ArrayColumn<Float> tSysCol(tOut,"TSYS");
|
---|
| 755 | Array<Float> tSysArr;
|
---|
[146] | 756 | //
|
---|
[152] | 757 | if (doAll) {
|
---|
| 758 | for (uInt i=0; i < tOut.nrow(); i++) {
|
---|
[294] | 759 |
|
---|
| 760 | // Modify data
|
---|
| 761 |
|
---|
[270] | 762 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
|
---|
[152] | 763 | if (what==0) {
|
---|
[270] | 764 | dataIn *= val;
|
---|
[152] | 765 | } else if (what==1) {
|
---|
[270] | 766 | dataIn += val;
|
---|
[152] | 767 | }
|
---|
[294] | 768 | specCol.put(i, dataIn.getArray());
|
---|
| 769 |
|
---|
| 770 | // Modify Tsys
|
---|
| 771 |
|
---|
| 772 | if (doTSys) {
|
---|
| 773 | tSysCol.get(i, tSysArr);
|
---|
| 774 | if (what==0) {
|
---|
| 775 | tSysArr *= val;
|
---|
| 776 | } else if (what==1) {
|
---|
| 777 | tSysArr += val;
|
---|
| 778 | }
|
---|
| 779 | tSysCol.put(i, tSysArr);
|
---|
| 780 | }
|
---|
[152] | 781 | }
|
---|
| 782 | } else {
|
---|
| 783 |
|
---|
| 784 | // Get cursor location
|
---|
| 785 |
|
---|
| 786 | IPosition start, end;
|
---|
[185] | 787 | getCursorLocation(start, end, in);
|
---|
[152] | 788 | //
|
---|
| 789 | for (uInt i=0; i < tOut.nrow(); i++) {
|
---|
[294] | 790 |
|
---|
| 791 | // Modify data
|
---|
| 792 |
|
---|
[152] | 793 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
|
---|
[270] | 794 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference
|
---|
[152] | 795 | if (what==0) {
|
---|
[270] | 796 | dataIn2 *= val;
|
---|
[152] | 797 | } else if (what==1) {
|
---|
[270] | 798 | dataIn2 += val;
|
---|
[152] | 799 | }
|
---|
[294] | 800 | specCol.put(i, dataIn.getArray());
|
---|
| 801 |
|
---|
| 802 | // Modify Tsys
|
---|
| 803 |
|
---|
| 804 | if (doTSys) {
|
---|
| 805 | tSysCol.get(i, tSysArr);
|
---|
| 806 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference
|
---|
| 807 | if (what==0) {
|
---|
| 808 | tSysArr2 *= val;
|
---|
| 809 | } else if (what==1) {
|
---|
| 810 | tSysArr2 += val;
|
---|
| 811 | }
|
---|
| 812 | tSysCol.put(i, tSysArr);
|
---|
| 813 | }
|
---|
[152] | 814 | }
|
---|
| 815 | }
|
---|
| 816 | //
|
---|
[146] | 817 | return pOut;
|
---|
| 818 | }
|
---|
| 819 |
|
---|
| 820 |
|
---|
[152] | 821 |
|
---|
[234] | 822 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask) const
|
---|
[152] | 823 | //
|
---|
[165] | 824 | // Average all polarizations together, weighted by variance
|
---|
| 825 | //
|
---|
| 826 | {
|
---|
| 827 | // WeightType wtType = NONE;
|
---|
[185] | 828 | // convertWeightString(wtType, weight);
|
---|
[165] | 829 |
|
---|
| 830 | const uInt nRows = in.nRow();
|
---|
| 831 |
|
---|
| 832 | // Create output Table and reshape number of polarizations
|
---|
| 833 |
|
---|
| 834 | Bool clear=True;
|
---|
| 835 | SDMemTable* pTabOut = new SDMemTable(in, clear);
|
---|
| 836 | SDHeader header = pTabOut->getSDHeader();
|
---|
| 837 | header.npol = 1;
|
---|
| 838 | pTabOut->putSDHeader(header);
|
---|
| 839 |
|
---|
| 840 | // Shape of input and output data
|
---|
| 841 |
|
---|
| 842 | const IPosition& shapeIn = in.rowAsMaskedArray(0u, False).shape();
|
---|
| 843 | IPosition shapeOut(shapeIn);
|
---|
[262] | 844 | shapeOut(asap::PolAxis) = 1; // Average all polarizations
|
---|
[165] | 845 | //
|
---|
[262] | 846 | const uInt nChan = shapeIn(asap::ChanAxis);
|
---|
[165] | 847 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape
|
---|
| 848 | IPosition start(4), end(4);
|
---|
| 849 |
|
---|
| 850 | // Output arrays
|
---|
| 851 |
|
---|
| 852 | Array<Float> outData(shapeOut, 0.0);
|
---|
| 853 | Array<Bool> outMask(shapeOut, True);
|
---|
[262] | 854 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane
|
---|
[165] | 855 | //
|
---|
[262] | 856 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis));
|
---|
[165] | 857 |
|
---|
| 858 | // Loop over rows
|
---|
| 859 |
|
---|
| 860 | for (uInt iRow=0; iRow<nRows; iRow++) {
|
---|
| 861 |
|
---|
| 862 | // Get data for this row
|
---|
| 863 |
|
---|
| 864 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow));
|
---|
| 865 | Array<Float>& arr = marr.getRWArray();
|
---|
| 866 | const Array<Bool>& barr = marr.getMask();
|
---|
| 867 |
|
---|
| 868 | // Make iterators to iterate by pol-channel planes
|
---|
| 869 |
|
---|
| 870 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes);
|
---|
| 871 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes);
|
---|
| 872 |
|
---|
| 873 | // Accumulations
|
---|
| 874 |
|
---|
| 875 | Float fac = 1.0;
|
---|
| 876 | Vector<Float> vecSum(nChan,0.0);
|
---|
| 877 |
|
---|
| 878 | // Iterate through data by pol-channel planes
|
---|
| 879 |
|
---|
| 880 | while (!itDataPlane.pastEnd()) {
|
---|
| 881 |
|
---|
| 882 | // Iterate through plane by polarization and accumulate Vectors
|
---|
| 883 |
|
---|
| 884 | Vector<Float> t1(nChan); t1 = 0.0;
|
---|
| 885 | Vector<Bool> t2(nChan); t2 = True;
|
---|
| 886 | MaskedArray<Float> vecSum(t1,t2);
|
---|
| 887 | Float varSum = 0.0;
|
---|
| 888 | {
|
---|
| 889 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1);
|
---|
| 890 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
| 891 | while (!itDataVec.pastEnd()) {
|
---|
| 892 |
|
---|
| 893 | // Create MA of data & mask (optionally including OTF mask) and get variance
|
---|
| 894 |
|
---|
| 895 | if (useMask) {
|
---|
| 896 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector());
|
---|
| 897 | fac = 1.0 / variance(spec);
|
---|
| 898 | } else {
|
---|
| 899 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector());
|
---|
| 900 | fac = 1.0 / variance(spec);
|
---|
| 901 | }
|
---|
| 902 |
|
---|
| 903 | // Normalize spectrum (without OTF mask) and accumulate
|
---|
| 904 |
|
---|
| 905 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector());
|
---|
| 906 | vecSum += spec;
|
---|
| 907 | varSum += fac;
|
---|
| 908 |
|
---|
| 909 | // Next
|
---|
| 910 |
|
---|
| 911 | itDataVec.next();
|
---|
| 912 | itMaskVec.next();
|
---|
| 913 | }
|
---|
| 914 | }
|
---|
| 915 |
|
---|
| 916 | // Normalize summed spectrum
|
---|
| 917 |
|
---|
| 918 | vecSum /= varSum;
|
---|
| 919 |
|
---|
| 920 | // FInd position in input data array. We are iterating by pol-channel
|
---|
| 921 | // plane so all that will change is beam and IF and that's what we want.
|
---|
| 922 |
|
---|
| 923 | IPosition pos = itDataPlane.pos();
|
---|
| 924 |
|
---|
| 925 | // Write out data. This is a bit messy. We have to reform the Vector
|
---|
| 926 | // accumulator into an Array of shape (1,1,1,nChan)
|
---|
| 927 |
|
---|
| 928 | start = pos;
|
---|
| 929 | end = pos;
|
---|
[262] | 930 | end(asap::ChanAxis) = nChan-1;
|
---|
[165] | 931 | outData(start,end) = vecSum.getArray().reform(vecShapeOut);
|
---|
| 932 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut);
|
---|
| 933 |
|
---|
| 934 | // Step to next beam/IF combination
|
---|
| 935 |
|
---|
| 936 | itDataPlane.next();
|
---|
| 937 | itMaskPlane.next();
|
---|
| 938 | }
|
---|
| 939 |
|
---|
| 940 | // Generate output container and write it to output table
|
---|
| 941 |
|
---|
| 942 | SDContainer sc = in.getSDContainer();
|
---|
| 943 | sc.resize(shapeOut);
|
---|
| 944 | //
|
---|
[185] | 945 | putDataInSDC(sc, outData, outMask);
|
---|
[165] | 946 | pTabOut->putSDContainer(sc);
|
---|
| 947 | }
|
---|
[304] | 948 |
|
---|
| 949 | // Set polarization cursor to 0
|
---|
| 950 |
|
---|
| 951 | pTabOut->setPol(0);
|
---|
[165] | 952 | //
|
---|
| 953 | return pTabOut;
|
---|
| 954 | }
|
---|
[167] | 955 |
|
---|
[169] | 956 |
|
---|
[185] | 957 | SDMemTable* SDMath::smooth(const SDMemTable& in,
|
---|
| 958 | const casa::String& kernelType,
|
---|
[234] | 959 | casa::Float width, Bool doAll) const
|
---|
[299] | 960 | //
|
---|
| 961 | // Should smooth TSys as well
|
---|
| 962 | //
|
---|
[177] | 963 | {
|
---|
[169] | 964 |
|
---|
[177] | 965 | // Number of channels
|
---|
[169] | 966 |
|
---|
[177] | 967 | SDHeader sh = in.getSDHeader();
|
---|
| 968 | const uInt nChan = sh.nchan;
|
---|
| 969 |
|
---|
| 970 | // Generate Kernel
|
---|
| 971 |
|
---|
[185] | 972 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType);
|
---|
[177] | 973 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False);
|
---|
| 974 |
|
---|
| 975 | // Generate Convolver
|
---|
| 976 |
|
---|
| 977 | IPosition shape(1,nChan);
|
---|
| 978 | Convolver<Float> conv(kernel, shape);
|
---|
| 979 |
|
---|
| 980 | // New Table
|
---|
| 981 |
|
---|
| 982 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
| 983 |
|
---|
| 984 | // Get cursor location
|
---|
| 985 |
|
---|
| 986 | IPosition start, end;
|
---|
[185] | 987 | getCursorLocation(start, end, in);
|
---|
[177] | 988 | //
|
---|
| 989 | IPosition shapeOut(4,1);
|
---|
| 990 |
|
---|
| 991 | // Output Vectors
|
---|
| 992 |
|
---|
| 993 | Vector<Float> valuesOut(nChan);
|
---|
| 994 | Vector<Bool> maskOut(nChan);
|
---|
| 995 |
|
---|
| 996 | // Loop over rows in Table
|
---|
| 997 |
|
---|
| 998 | for (uInt ri=0; ri < in.nRow(); ++ri) {
|
---|
| 999 |
|
---|
| 1000 | // Get copy of data
|
---|
| 1001 |
|
---|
| 1002 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(ri));
|
---|
[262] | 1003 | AlwaysAssert(dataIn.shape()(asap::ChanAxis)==nChan, AipsError);
|
---|
[177] | 1004 | //
|
---|
| 1005 | Array<Float> valuesIn = dataIn.getArray();
|
---|
| 1006 | Array<Bool> maskIn = dataIn.getMask();
|
---|
| 1007 |
|
---|
| 1008 | // Branch depending on whether we smooth all locations or just
|
---|
| 1009 | // those pointed at by the current selection cursor
|
---|
| 1010 |
|
---|
| 1011 | if (doAll) {
|
---|
[299] | 1012 | VectorIterator<Float> itValues(valuesIn, asap::ChanAxis);
|
---|
| 1013 | VectorIterator<Bool> itMask(maskIn, asap::ChanAxis);
|
---|
[177] | 1014 | while (!itValues.pastEnd()) {
|
---|
| 1015 |
|
---|
| 1016 | // Smooth
|
---|
| 1017 | if (kernelType==VectorKernel::HANNING) {
|
---|
| 1018 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector());
|
---|
| 1019 | itMask.vector() = maskOut;
|
---|
| 1020 | } else {
|
---|
| 1021 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector());
|
---|
| 1022 | conv.linearConv(valuesOut, itValues.vector());
|
---|
| 1023 | }
|
---|
| 1024 | //
|
---|
| 1025 | itValues.vector() = valuesOut;
|
---|
| 1026 | //
|
---|
| 1027 | itValues.next();
|
---|
| 1028 | itMask.next();
|
---|
| 1029 | }
|
---|
| 1030 | } else {
|
---|
| 1031 |
|
---|
| 1032 | // Set multi-dim Vector shape
|
---|
| 1033 |
|
---|
[299] | 1034 | shapeOut(asap::ChanAxis) = valuesIn.shape()(asap::ChanAxis);
|
---|
[177] | 1035 |
|
---|
| 1036 | // Stuff about with shapes so that we don't have conformance run-time errors
|
---|
| 1037 |
|
---|
| 1038 | Vector<Float> valuesIn2 = valuesIn(start,end).nonDegenerate();
|
---|
| 1039 | Vector<Bool> maskIn2 = maskIn(start,end).nonDegenerate();
|
---|
| 1040 |
|
---|
| 1041 | // Smooth
|
---|
| 1042 |
|
---|
| 1043 | if (kernelType==VectorKernel::HANNING) {
|
---|
| 1044 | mathutil::hanning(valuesOut, maskOut, valuesIn2, maskIn2);
|
---|
| 1045 | maskIn(start,end) = maskOut.reform(shapeOut);
|
---|
| 1046 | } else {
|
---|
| 1047 | mathutil::replaceMaskByZero(valuesIn2, maskIn2);
|
---|
| 1048 | conv.linearConv(valuesOut, valuesIn2);
|
---|
| 1049 | }
|
---|
| 1050 | //
|
---|
| 1051 | valuesIn(start,end) = valuesOut.reform(shapeOut);
|
---|
| 1052 | }
|
---|
| 1053 |
|
---|
| 1054 | // Create and put back
|
---|
| 1055 |
|
---|
| 1056 | SDContainer sc = in.getSDContainer(ri);
|
---|
[185] | 1057 | putDataInSDC(sc, valuesIn, maskIn);
|
---|
[177] | 1058 | //
|
---|
| 1059 | pTabOut->putSDContainer(sc);
|
---|
| 1060 | }
|
---|
| 1061 | //
|
---|
| 1062 | return pTabOut;
|
---|
| 1063 | }
|
---|
| 1064 |
|
---|
| 1065 |
|
---|
[262] | 1066 |
|
---|
[234] | 1067 | SDMemTable* SDMath::convertFlux (const SDMemTable& in, Float a, Float eta, Bool doAll) const
|
---|
[221] | 1068 | //
|
---|
| 1069 | // As it is, this function could be implemented with 'simpleOperate'
|
---|
| 1070 | // However, I anticipate that eventually we will look the conversion
|
---|
| 1071 | // values up in a Table and apply them in a frequency dependent way,
|
---|
| 1072 | // so I have implemented it fully here
|
---|
| 1073 | //
|
---|
| 1074 | {
|
---|
| 1075 | SDHeader sh = in.getSDHeader();
|
---|
| 1076 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
[177] | 1077 |
|
---|
[221] | 1078 | // FInd out how to convert values into Jy and K (e.g. units might be mJy or mK)
|
---|
| 1079 | // Also automatically find out what we are converting to according to the
|
---|
| 1080 | // flux unit
|
---|
[177] | 1081 |
|
---|
[221] | 1082 | Unit fluxUnit(sh.fluxunit);
|
---|
| 1083 | Unit K(String("K"));
|
---|
| 1084 | Unit JY(String("Jy"));
|
---|
| 1085 | //
|
---|
| 1086 | Bool toKelvin = True;
|
---|
| 1087 | Double inFac = 1.0;
|
---|
| 1088 | if (fluxUnit==JY) {
|
---|
| 1089 | cerr << "Converting to K" << endl;
|
---|
| 1090 | //
|
---|
| 1091 | Quantum<Double> t(1.0,fluxUnit);
|
---|
| 1092 | Quantum<Double> t2 = t.get(JY);
|
---|
| 1093 | inFac = (t2 / t).getValue();
|
---|
| 1094 | //
|
---|
| 1095 | toKelvin = True;
|
---|
| 1096 | sh.fluxunit = "K";
|
---|
| 1097 | } else if (fluxUnit==K) {
|
---|
| 1098 | cerr << "Converting to Jy" << endl;
|
---|
| 1099 | //
|
---|
| 1100 | Quantum<Double> t(1.0,fluxUnit);
|
---|
| 1101 | Quantum<Double> t2 = t.get(K);
|
---|
| 1102 | inFac = (t2 / t).getValue();
|
---|
| 1103 | //
|
---|
| 1104 | toKelvin = False;
|
---|
| 1105 | sh.fluxunit = "Jy";
|
---|
| 1106 | } else {
|
---|
[248] | 1107 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
|
---|
[221] | 1108 | }
|
---|
| 1109 | pTabOut->putSDHeader(sh);
|
---|
[177] | 1110 |
|
---|
[221] | 1111 | // Compute conversion factor. 'a' and 'eta' are really frequency, time and
|
---|
| 1112 | // telescope dependent and should be looked// up in a table
|
---|
| 1113 |
|
---|
[234] | 1114 | Float factor = 2.0 * inFac * 1.0e-7 * 1.0e26 *
|
---|
| 1115 | QC::k.getValue(Unit(String("erg/K"))) / a / eta;
|
---|
[221] | 1116 | if (toKelvin) {
|
---|
| 1117 | factor = 1.0 / factor;
|
---|
| 1118 | }
|
---|
| 1119 | cerr << "Applying conversion factor = " << factor << endl;
|
---|
| 1120 |
|
---|
[270] | 1121 | // Generate correction vector. Apply same factor regardless
|
---|
| 1122 | // of beam/pol/IF. This will need to change somewhen.
|
---|
[221] | 1123 |
|
---|
[270] | 1124 | Vector<Float> factors(in.nRow(), factor);
|
---|
[221] | 1125 |
|
---|
[270] | 1126 | // Correct
|
---|
[221] | 1127 |
|
---|
[270] | 1128 | correctFromVector (pTabOut, in, doAll, factors);
|
---|
[221] | 1129 | //
|
---|
| 1130 | return pTabOut;
|
---|
| 1131 | }
|
---|
| 1132 |
|
---|
| 1133 |
|
---|
[234] | 1134 | SDMemTable* SDMath::gainElevation (const SDMemTable& in, const Vector<Float>& coeffs,
|
---|
| 1135 | const String& fileName,
|
---|
| 1136 | const String& methodStr, Bool doAll) const
|
---|
[227] | 1137 | {
|
---|
[234] | 1138 |
|
---|
| 1139 | // Get header and clone output table
|
---|
| 1140 |
|
---|
[227] | 1141 | SDHeader sh = in.getSDHeader();
|
---|
| 1142 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
| 1143 |
|
---|
[234] | 1144 | // Get elevation data from SDMemTable and convert to degrees
|
---|
[227] | 1145 |
|
---|
| 1146 | const Table& tab = in.table();
|
---|
| 1147 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
[234] | 1148 | Vector<Float> x = elev.getColumn();
|
---|
| 1149 | x *= Float(180 / C::pi);
|
---|
[227] | 1150 | //
|
---|
[234] | 1151 | const uInt nC = coeffs.nelements();
|
---|
| 1152 | if (fileName.length()>0 && nC>0) {
|
---|
[248] | 1153 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
|
---|
[234] | 1154 | }
|
---|
| 1155 |
|
---|
| 1156 | // Correct
|
---|
| 1157 |
|
---|
| 1158 | if (nC>0 || fileName.length()==0) {
|
---|
| 1159 |
|
---|
| 1160 | // Find instrument
|
---|
| 1161 |
|
---|
| 1162 | Bool throwIt = True;
|
---|
| 1163 | Instrument inst = SDMemTable::convertInstrument (sh.antennaname, throwIt);
|
---|
| 1164 |
|
---|
| 1165 | // Set polynomial
|
---|
| 1166 |
|
---|
| 1167 | Polynomial<Float>* pPoly = 0;
|
---|
| 1168 | Vector<Float> coeff;
|
---|
| 1169 | String msg;
|
---|
| 1170 | if (nC>0) {
|
---|
| 1171 | pPoly = new Polynomial<Float>(nC);
|
---|
| 1172 | coeff = coeffs;
|
---|
| 1173 | msg = String("user");
|
---|
| 1174 | } else {
|
---|
[292] | 1175 | if (inst==ATPKSMB) {
|
---|
| 1176 | } else if (inst==ATPKSHOH) {
|
---|
[234] | 1177 | } else if (inst==TIDBINBILLA) {
|
---|
| 1178 | pPoly = new Polynomial<Float>(3);
|
---|
| 1179 | coeff.resize(3);
|
---|
| 1180 | coeff(0) = 3.58788e-1;
|
---|
| 1181 | coeff(1) = 2.87243e-2;
|
---|
| 1182 | coeff(2) = -3.219093e-4;
|
---|
[292] | 1183 | } else if (inst==ATMOPRA) {
|
---|
| 1184 | } else {
|
---|
[234] | 1185 | }
|
---|
| 1186 | msg = String("built in");
|
---|
| 1187 | }
|
---|
[227] | 1188 | //
|
---|
[234] | 1189 | if (coeff.nelements()>0) {
|
---|
| 1190 | pPoly->setCoefficients(coeff);
|
---|
| 1191 | } else {
|
---|
[248] | 1192 | throw(AipsError("There is no known gain-el polynomial known for this instrument"));
|
---|
[234] | 1193 | }
|
---|
| 1194 | //
|
---|
| 1195 | cerr << "Making polynomial correction with " << msg << " coefficients" << endl;
|
---|
| 1196 | const uInt nRow = in.nRow();
|
---|
| 1197 | Vector<Float> factor(nRow);
|
---|
| 1198 | for (uInt i=0; i<nRow; i++) {
|
---|
| 1199 | factor[i] = (*pPoly)(x[i]);
|
---|
| 1200 | }
|
---|
| 1201 | delete pPoly;
|
---|
| 1202 | //
|
---|
| 1203 | correctFromVector (pTabOut, in, doAll, factor);
|
---|
| 1204 | } else {
|
---|
| 1205 |
|
---|
| 1206 | // Indicate which columns to read from ascii file
|
---|
| 1207 |
|
---|
| 1208 | String col0("ELEVATION");
|
---|
| 1209 | String col1("FACTOR");
|
---|
| 1210 |
|
---|
| 1211 | // Read and correct
|
---|
| 1212 |
|
---|
| 1213 | cerr << "Making correction from ascii Table" << endl;
|
---|
| 1214 | correctFromAsciiTable (pTabOut, in, fileName, col0, col1,
|
---|
| 1215 | methodStr, doAll, x);
|
---|
| 1216 | }
|
---|
| 1217 | //
|
---|
| 1218 | return pTabOut;
|
---|
[230] | 1219 | }
|
---|
[227] | 1220 |
|
---|
[230] | 1221 |
|
---|
[227] | 1222 |
|
---|
[234] | 1223 | SDMemTable* SDMath::opacity (const SDMemTable& in, Float tau, Bool doAll) const
|
---|
| 1224 | {
|
---|
[227] | 1225 |
|
---|
[234] | 1226 | // Get header and clone output table
|
---|
[227] | 1227 |
|
---|
[234] | 1228 | SDHeader sh = in.getSDHeader();
|
---|
| 1229 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
| 1230 |
|
---|
| 1231 | // Get elevation data from SDMemTable and convert to degrees
|
---|
| 1232 |
|
---|
| 1233 | const Table& tab = in.table();
|
---|
| 1234 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
| 1235 | Vector<Float> zDist = elev.getColumn();
|
---|
| 1236 | zDist = Float(C::pi_2) - zDist;
|
---|
| 1237 |
|
---|
| 1238 | // Generate correction factor
|
---|
| 1239 |
|
---|
| 1240 | const uInt nRow = in.nRow();
|
---|
| 1241 | Vector<Float> factor(nRow);
|
---|
| 1242 | Vector<Float> factor2(nRow);
|
---|
| 1243 | for (uInt i=0; i<nRow; i++) {
|
---|
| 1244 | factor[i] = exp(tau)/cos(zDist[i]);
|
---|
| 1245 | }
|
---|
| 1246 |
|
---|
| 1247 | // Correct
|
---|
| 1248 |
|
---|
| 1249 | correctFromVector (pTabOut, in, doAll, factor);
|
---|
| 1250 | //
|
---|
| 1251 | return pTabOut;
|
---|
| 1252 | }
|
---|
| 1253 |
|
---|
| 1254 |
|
---|
| 1255 |
|
---|
| 1256 |
|
---|
[169] | 1257 | // 'private' functions
|
---|
| 1258 |
|
---|
[267] | 1259 | SDMemTable* SDMath::velocityAlign (const SDMemTable& in,
|
---|
| 1260 | MFrequency::Types velSystem,
|
---|
| 1261 | const String& velUnit,
|
---|
[272] | 1262 | MDoppler::Types doppler,
|
---|
| 1263 | const String& refTime) const
|
---|
[267] | 1264 | {
|
---|
| 1265 | // Get Header
|
---|
| 1266 |
|
---|
| 1267 | SDHeader sh = in.getSDHeader();
|
---|
| 1268 | const uInt nChan = sh.nchan;
|
---|
| 1269 | const uInt nRows = in.nRow();
|
---|
| 1270 |
|
---|
| 1271 | // Get Table reference
|
---|
| 1272 |
|
---|
| 1273 | const Table& tabIn = in.table();
|
---|
| 1274 |
|
---|
| 1275 | // Get Columns from Table
|
---|
| 1276 |
|
---|
[294] | 1277 | ROScalarColumn<Double> mjdCol(tabIn, "TIME");
|
---|
| 1278 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME");
|
---|
| 1279 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID");
|
---|
[267] | 1280 | //
|
---|
[294] | 1281 | Vector<Double> times = mjdCol.getColumn();
|
---|
| 1282 | Vector<String> srcNames = srcCol.getColumn();
|
---|
| 1283 | Vector<uInt> freqID;
|
---|
[267] | 1284 |
|
---|
| 1285 | // Generate Source table
|
---|
| 1286 |
|
---|
| 1287 | Vector<String> srcTab;
|
---|
| 1288 | Vector<uInt> srcIdx, firstRow;
|
---|
| 1289 | generateSourceTable (srcTab, srcIdx, firstRow, srcNames);
|
---|
| 1290 | const uInt nSrcTab = srcTab.nelements();
|
---|
| 1291 | cerr << "Found " << srcTab.nelements() << " sources to align " << endl;
|
---|
| 1292 |
|
---|
[294] | 1293 | // Get reference Epoch to time of first row or given String
|
---|
[267] | 1294 |
|
---|
| 1295 | Unit DAY(String("d"));
|
---|
[272] | 1296 | MEpoch::Ref epochRef(in.getTimeReference());
|
---|
| 1297 | MEpoch refEpoch;
|
---|
| 1298 | if (refTime.length()>0) {
|
---|
| 1299 | refEpoch = epochFromString(refTime, in.getTimeReference());
|
---|
| 1300 | } else {
|
---|
[288] | 1301 | refEpoch = in.getEpoch(0);
|
---|
[272] | 1302 | }
|
---|
| 1303 | cerr << "Aligning at reference Epoch " << formatEpoch(refEpoch) << endl;
|
---|
[267] | 1304 |
|
---|
[294] | 1305 | // Get Reference Position
|
---|
[267] | 1306 |
|
---|
[288] | 1307 | MPosition refPos = in.getAntennaPosition();
|
---|
[267] | 1308 |
|
---|
| 1309 | // Get Frequency Table
|
---|
| 1310 |
|
---|
| 1311 | SDFrequencyTable fTab = in.getSDFreqTable();
|
---|
| 1312 | const uInt nFreqIDs = fTab.length();
|
---|
| 1313 |
|
---|
| 1314 | // Create VelocityAligner Block. One VA for each possible
|
---|
| 1315 | // source/freqID combination
|
---|
| 1316 |
|
---|
| 1317 | PtrBlock<VelocityAligner<Float>* > vA(nFreqIDs*nSrcTab);
|
---|
[294] | 1318 | generateVelocityAligners (vA, in, nChan, nFreqIDs, nSrcTab, firstRow,
|
---|
| 1319 | velSystem, velUnit, doppler, refPos, refEpoch);
|
---|
[267] | 1320 |
|
---|
| 1321 | // New output Table
|
---|
| 1322 |
|
---|
| 1323 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
| 1324 |
|
---|
| 1325 | // Loop over rows in Table
|
---|
| 1326 |
|
---|
[294] | 1327 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis);
|
---|
| 1328 | VelocityAligner<Float>::Method method = VelocityAligner<Float>::LINEAR;
|
---|
| 1329 | Bool extrapolate=False;
|
---|
| 1330 | Bool useCachedAbcissa = False;
|
---|
| 1331 | Bool first = True;
|
---|
| 1332 | Bool ok;
|
---|
| 1333 | Vector<Float> yOut;
|
---|
| 1334 | Vector<Bool> maskOut;
|
---|
| 1335 | uInt ifIdx, vaIdx;
|
---|
[267] | 1336 | //
|
---|
[294] | 1337 | for (uInt iRow=0; iRow<nRows; ++iRow) {
|
---|
| 1338 | if (iRow%10==0) {
|
---|
| 1339 | cerr << "Processing row " << iRow << endl;
|
---|
| 1340 | }
|
---|
[267] | 1341 |
|
---|
| 1342 | // Get EPoch
|
---|
| 1343 |
|
---|
[294] | 1344 | Quantum<Double> tQ2(times[iRow],DAY);
|
---|
| 1345 | MVEpoch mv2(tQ2);
|
---|
| 1346 | MEpoch epoch(mv2, epochRef);
|
---|
[267] | 1347 |
|
---|
| 1348 | // Get FreqID vector. One freqID per IF
|
---|
| 1349 |
|
---|
[294] | 1350 | fqIDCol.get(iRow, freqID);
|
---|
[267] | 1351 |
|
---|
| 1352 | // Get copy of data
|
---|
| 1353 |
|
---|
[294] | 1354 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow));
|
---|
| 1355 | Array<Float> values = mArrIn.getArray();
|
---|
| 1356 | Array<Bool> mask = mArrIn.getMask();
|
---|
[267] | 1357 |
|
---|
| 1358 | // cerr << "values in = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl;
|
---|
| 1359 |
|
---|
| 1360 | // For each row, the Velocity abcissa will be the same regardless
|
---|
| 1361 | // of polarization. For all other axes (IF and BEAM) the abcissa
|
---|
| 1362 | // will change. So we iterate through the data by pol-chan planes
|
---|
| 1363 | // to mimimize the work. At this point, I think the Direction
|
---|
| 1364 | // is stored as the same for each beam. DOn't know where the
|
---|
| 1365 | // offsets are or what to do about them right now. For now
|
---|
| 1366 | // all beams get same position and velocoity abcissa.
|
---|
| 1367 |
|
---|
[294] | 1368 | ArrayIterator<Float> itValuesPlane(values, polChanAxes);
|
---|
| 1369 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes);
|
---|
| 1370 | while (!itValuesPlane.pastEnd()) {
|
---|
[267] | 1371 |
|
---|
| 1372 | // Find the IF index and then the VA PtrBlock index
|
---|
| 1373 |
|
---|
[294] | 1374 | const IPosition& pos = itValuesPlane.pos();
|
---|
| 1375 | ifIdx = pos(asap::IFAxis);
|
---|
| 1376 | vaIdx = (srcIdx[iRow]*nFreqIDs) + freqID[ifIdx];
|
---|
[267] | 1377 | //
|
---|
[294] | 1378 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1);
|
---|
| 1379 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
[267] | 1380 | //
|
---|
[294] | 1381 | first = True;
|
---|
| 1382 | useCachedAbcissa=False;
|
---|
| 1383 | while (!itValuesVec.pastEnd()) {
|
---|
| 1384 | ok = vA[vaIdx]->align (yOut, maskOut, itValuesVec.vector(),
|
---|
| 1385 | itMaskVec.vector(), epoch, useCachedAbcissa,
|
---|
| 1386 | method, extrapolate);
|
---|
| 1387 | itValuesVec.vector() = yOut;
|
---|
| 1388 | itMaskVec.vector() = maskOut;
|
---|
[267] | 1389 | //
|
---|
[294] | 1390 | itValuesVec.next();
|
---|
| 1391 | itMaskVec.next();
|
---|
[267] | 1392 | //
|
---|
[294] | 1393 | if (first) {
|
---|
| 1394 | useCachedAbcissa = True;
|
---|
| 1395 | first = False;
|
---|
| 1396 | }
|
---|
| 1397 | }
|
---|
[267] | 1398 | //
|
---|
| 1399 | itValuesPlane.next();
|
---|
| 1400 | itMaskPlane.next();
|
---|
[294] | 1401 | }
|
---|
[267] | 1402 |
|
---|
| 1403 | // cerr << "values out = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl;
|
---|
| 1404 |
|
---|
| 1405 | // Create and put back
|
---|
| 1406 |
|
---|
| 1407 | SDContainer sc = in.getSDContainer(iRow);
|
---|
| 1408 | putDataInSDC(sc, values, mask);
|
---|
| 1409 | //
|
---|
| 1410 | pTabOut->putSDContainer(sc);
|
---|
[294] | 1411 | }
|
---|
[267] | 1412 |
|
---|
| 1413 | // Clean up PointerBlock
|
---|
| 1414 |
|
---|
| 1415 | for (uInt i=0; i<vA.nelements(); i++) delete vA[i];
|
---|
| 1416 | //
|
---|
[304] | 1417 | pTabOut->resetCursor();
|
---|
[267] | 1418 | return pTabOut;
|
---|
| 1419 | }
|
---|
| 1420 |
|
---|
| 1421 |
|
---|
[185] | 1422 | void SDMath::fillSDC(SDContainer& sc,
|
---|
| 1423 | const Array<Bool>& mask,
|
---|
| 1424 | const Array<Float>& data,
|
---|
| 1425 | const Array<Float>& tSys,
|
---|
| 1426 | Int scanID, Double timeStamp,
|
---|
| 1427 | Double interval, const String& sourceName,
|
---|
[227] | 1428 | const Vector<uInt>& freqID) const
|
---|
[167] | 1429 | {
|
---|
[169] | 1430 | // Data and mask
|
---|
[167] | 1431 |
|
---|
[185] | 1432 | putDataInSDC(sc, data, mask);
|
---|
[167] | 1433 |
|
---|
[169] | 1434 | // TSys
|
---|
| 1435 |
|
---|
| 1436 | sc.putTsys(tSys);
|
---|
| 1437 |
|
---|
| 1438 | // Time things
|
---|
| 1439 |
|
---|
| 1440 | sc.timestamp = timeStamp;
|
---|
| 1441 | sc.interval = interval;
|
---|
| 1442 | sc.scanid = scanID;
|
---|
[167] | 1443 | //
|
---|
[169] | 1444 | sc.sourcename = sourceName;
|
---|
| 1445 | sc.putFreqMap(freqID);
|
---|
| 1446 | }
|
---|
[167] | 1447 |
|
---|
[185] | 1448 | void SDMath::normalize(MaskedArray<Float>& sum,
|
---|
[169] | 1449 | const Array<Float>& sumSq,
|
---|
| 1450 | const Array<Float>& nPts,
|
---|
| 1451 | WeightType wtType, Int axis,
|
---|
[227] | 1452 | Int nAxesSub) const
|
---|
[169] | 1453 | {
|
---|
| 1454 | IPosition pos2(nAxesSub,0);
|
---|
| 1455 | //
|
---|
| 1456 | if (wtType==NONE) {
|
---|
[167] | 1457 |
|
---|
[169] | 1458 | // We just average by the number of points accumulated.
|
---|
| 1459 | // We need to make a MA out of nPts so that no divide by
|
---|
| 1460 | // zeros occur
|
---|
[167] | 1461 |
|
---|
[169] | 1462 | MaskedArray<Float> t(nPts, (nPts>Float(0.0)));
|
---|
| 1463 | sum /= t;
|
---|
| 1464 | } else if (wtType==VAR) {
|
---|
[167] | 1465 |
|
---|
[169] | 1466 | // Normalize each spectrum by sum(1/var) where the variance
|
---|
| 1467 | // is worked out for each spectrum
|
---|
| 1468 |
|
---|
| 1469 | Array<Float>& data = sum.getRWArray();
|
---|
| 1470 | VectorIterator<Float> itData(data, axis);
|
---|
| 1471 | while (!itData.pastEnd()) {
|
---|
| 1472 | pos2 = itData.pos().getFirst(nAxesSub);
|
---|
| 1473 | itData.vector() /= sumSq(pos2);
|
---|
| 1474 | itData.next();
|
---|
| 1475 | }
|
---|
| 1476 | } else if (wtType==TSYS) {
|
---|
| 1477 | }
|
---|
| 1478 | }
|
---|
| 1479 |
|
---|
| 1480 |
|
---|
[185] | 1481 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum,
|
---|
| 1482 | MaskedArray<Float>& sum, Array<Float>& sumSq,
|
---|
| 1483 | Array<Float>& nPts, Array<Float>& tSysSum,
|
---|
| 1484 | const Array<Float>& tSys, const Array<Float>& nInc,
|
---|
| 1485 | const Vector<Bool>& mask, Double time, Double interval,
|
---|
| 1486 | const Block<CountedPtr<SDMemTable> >& in,
|
---|
| 1487 | uInt iTab, uInt iRow, uInt axis,
|
---|
| 1488 | uInt nAxesSub, Bool useMask,
|
---|
[227] | 1489 | WeightType wtType) const
|
---|
[169] | 1490 | {
|
---|
| 1491 |
|
---|
| 1492 | // Get data
|
---|
| 1493 |
|
---|
| 1494 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow));
|
---|
| 1495 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference
|
---|
| 1496 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference
|
---|
[167] | 1497 | //
|
---|
[169] | 1498 | if (wtType==NONE) {
|
---|
| 1499 | const MaskedArray<Float> n(nInc,dataIn.getMask());
|
---|
| 1500 | nPts += n; // Only accumulates where mask==T
|
---|
| 1501 | } else if (wtType==VAR) {
|
---|
[167] | 1502 |
|
---|
[169] | 1503 | // We are going to average the data, weighted by the noise for each pol, beam and IF.
|
---|
| 1504 | // So therefore we need to iterate through by spectrum (axis 3)
|
---|
[167] | 1505 |
|
---|
[169] | 1506 | VectorIterator<Float> itData(valuesIn, axis);
|
---|
| 1507 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis);
|
---|
| 1508 | Float fac = 1.0;
|
---|
| 1509 | IPosition pos(nAxesSub,0);
|
---|
| 1510 | //
|
---|
| 1511 | while (!itData.pastEnd()) {
|
---|
[167] | 1512 |
|
---|
[169] | 1513 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor
|
---|
[167] | 1514 |
|
---|
[169] | 1515 | if (useMask) {
|
---|
| 1516 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector());
|
---|
| 1517 | fac = 1.0/variance(tmp);
|
---|
| 1518 | } else {
|
---|
| 1519 | MaskedArray<Float> tmp(itData.vector(),itMask.vector());
|
---|
| 1520 | fac = 1.0/variance(tmp);
|
---|
| 1521 | }
|
---|
| 1522 |
|
---|
| 1523 | // Scale data
|
---|
| 1524 |
|
---|
| 1525 | itData.vector() *= fac; // Writes back into 'dataIn'
|
---|
[167] | 1526 | //
|
---|
[169] | 1527 | // Accumulate variance per if/pol/beam averaged over spectrum
|
---|
| 1528 | // This method to get pos2 from itData.pos() is only valid
|
---|
| 1529 | // because the spectral axis is the last one (so we can just
|
---|
| 1530 | // copy the first nAXesSub positions out)
|
---|
[167] | 1531 |
|
---|
[169] | 1532 | pos = itData.pos().getFirst(nAxesSub);
|
---|
| 1533 | sumSq(pos) += fac;
|
---|
| 1534 | //
|
---|
| 1535 | itData.next();
|
---|
| 1536 | itMask.next();
|
---|
| 1537 | }
|
---|
| 1538 | } else if (wtType==TSYS) {
|
---|
| 1539 | }
|
---|
[167] | 1540 |
|
---|
[169] | 1541 | // Accumulate sum of (possibly scaled) data
|
---|
| 1542 |
|
---|
| 1543 | sum += dataIn;
|
---|
| 1544 |
|
---|
| 1545 | // Accumulate Tsys, time, and interval
|
---|
| 1546 |
|
---|
| 1547 | tSysSum += tSys;
|
---|
| 1548 | timeSum += time;
|
---|
| 1549 | intSum += interval;
|
---|
| 1550 | nAccum += 1;
|
---|
| 1551 | }
|
---|
| 1552 |
|
---|
| 1553 |
|
---|
| 1554 |
|
---|
| 1555 |
|
---|
[185] | 1556 | void SDMath::getCursorLocation(IPosition& start, IPosition& end,
|
---|
[227] | 1557 | const SDMemTable& in) const
|
---|
[169] | 1558 | {
|
---|
| 1559 | const uInt nDim = 4;
|
---|
| 1560 | const uInt i = in.getBeam();
|
---|
| 1561 | const uInt j = in.getIF();
|
---|
| 1562 | const uInt k = in.getPol();
|
---|
| 1563 | const uInt n = in.nChan();
|
---|
[167] | 1564 | //
|
---|
[169] | 1565 | start.resize(nDim);
|
---|
| 1566 | start(0) = i;
|
---|
| 1567 | start(1) = j;
|
---|
| 1568 | start(2) = k;
|
---|
| 1569 | start(3) = 0;
|
---|
[167] | 1570 | //
|
---|
[169] | 1571 | end.resize(nDim);
|
---|
| 1572 | end(0) = i;
|
---|
| 1573 | end(1) = j;
|
---|
| 1574 | end(2) = k;
|
---|
| 1575 | end(3) = n-1;
|
---|
| 1576 | }
|
---|
| 1577 |
|
---|
| 1578 |
|
---|
[227] | 1579 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr) const
|
---|
[169] | 1580 | {
|
---|
| 1581 | String tStr(weightStr);
|
---|
| 1582 | tStr.upcase();
|
---|
| 1583 | if (tStr.contains(String("NONE"))) {
|
---|
| 1584 | wtType = NONE;
|
---|
| 1585 | } else if (tStr.contains(String("VAR"))) {
|
---|
| 1586 | wtType = VAR;
|
---|
| 1587 | } else if (tStr.contains(String("TSYS"))) {
|
---|
| 1588 | wtType = TSYS;
|
---|
[185] | 1589 | throw(AipsError("T_sys weighting not yet implemented"));
|
---|
[169] | 1590 | } else {
|
---|
[185] | 1591 | throw(AipsError("Unrecognized weighting type"));
|
---|
[167] | 1592 | }
|
---|
| 1593 | }
|
---|
| 1594 |
|
---|
[227] | 1595 | void SDMath::convertInterpString(Int& type, const String& interp) const
|
---|
| 1596 | {
|
---|
| 1597 | String tStr(interp);
|
---|
| 1598 | tStr.upcase();
|
---|
| 1599 | if (tStr.contains(String("NEAR"))) {
|
---|
| 1600 | type = InterpolateArray1D<Float,Float>::nearestNeighbour;
|
---|
| 1601 | } else if (tStr.contains(String("LIN"))) {
|
---|
| 1602 | type = InterpolateArray1D<Float,Float>::linear;
|
---|
| 1603 | } else if (tStr.contains(String("CUB"))) {
|
---|
| 1604 | type = InterpolateArray1D<Float,Float>::cubic;
|
---|
| 1605 | } else if (tStr.contains(String("SPL"))) {
|
---|
| 1606 | type = InterpolateArray1D<Float,Float>::spline;
|
---|
| 1607 | } else {
|
---|
| 1608 | throw(AipsError("Unrecognized interpolation type"));
|
---|
| 1609 | }
|
---|
| 1610 | }
|
---|
| 1611 |
|
---|
[185] | 1612 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data,
|
---|
[227] | 1613 | const Array<Bool>& mask) const
|
---|
[169] | 1614 | {
|
---|
| 1615 | sc.putSpectrum(data);
|
---|
| 1616 | //
|
---|
| 1617 | Array<uChar> outflags(data.shape());
|
---|
| 1618 | convertArray(outflags,!mask);
|
---|
| 1619 | sc.putFlags(outflags);
|
---|
| 1620 | }
|
---|
[227] | 1621 |
|
---|
| 1622 | Table SDMath::readAsciiFile (const String& fileName) const
|
---|
| 1623 | {
|
---|
[230] | 1624 | String formatString;
|
---|
| 1625 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False);
|
---|
[227] | 1626 | return tbl;
|
---|
| 1627 | }
|
---|
[230] | 1628 |
|
---|
| 1629 |
|
---|
[234] | 1630 |
|
---|
| 1631 | void SDMath::correctFromAsciiTable(SDMemTable* pTabOut,
|
---|
| 1632 | const SDMemTable& in, const String& fileName,
|
---|
| 1633 | const String& col0, const String& col1,
|
---|
| 1634 | const String& methodStr, Bool doAll,
|
---|
| 1635 | const Vector<Float>& xOut) const
|
---|
[230] | 1636 | {
|
---|
| 1637 |
|
---|
| 1638 | // Read gain-elevation ascii file data into a Table.
|
---|
| 1639 |
|
---|
[234] | 1640 | Table geTable = readAsciiFile (fileName);
|
---|
[230] | 1641 | //
|
---|
[234] | 1642 | correctFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut);
|
---|
[230] | 1643 | }
|
---|
| 1644 |
|
---|
[234] | 1645 | void SDMath::correctFromTable(SDMemTable* pTabOut, const SDMemTable& in,
|
---|
| 1646 | const Table& tTable, const String& col0,
|
---|
| 1647 | const String& col1,
|
---|
| 1648 | const String& methodStr, Bool doAll,
|
---|
| 1649 | const Vector<Float>& xOut) const
|
---|
[230] | 1650 | {
|
---|
| 1651 |
|
---|
| 1652 | // Get data from Table
|
---|
| 1653 |
|
---|
| 1654 | ROScalarColumn<Float> geElCol(tTable, col0);
|
---|
| 1655 | ROScalarColumn<Float> geFacCol(tTable, col1);
|
---|
| 1656 | Vector<Float> xIn = geElCol.getColumn();
|
---|
| 1657 | Vector<Float> yIn = geFacCol.getColumn();
|
---|
| 1658 | Vector<Bool> maskIn(xIn.nelements(),True);
|
---|
| 1659 |
|
---|
| 1660 | // Interpolate (and extrapolate) with desired method
|
---|
| 1661 |
|
---|
| 1662 | Int method = 0;
|
---|
| 1663 | convertInterpString(method, methodStr);
|
---|
| 1664 | //
|
---|
| 1665 | Vector<Float> yOut;
|
---|
| 1666 | Vector<Bool> maskOut;
|
---|
| 1667 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut,
|
---|
| 1668 | xIn, yIn, maskIn, method,
|
---|
| 1669 | True, True);
|
---|
[234] | 1670 | // Apply
|
---|
[230] | 1671 |
|
---|
[234] | 1672 | correctFromVector (pTabOut, in, doAll, yOut);
|
---|
| 1673 | }
|
---|
| 1674 |
|
---|
| 1675 |
|
---|
| 1676 | void SDMath::correctFromVector (SDMemTable* pTabOut, const SDMemTable& in,
|
---|
| 1677 | Bool doAll, const Vector<Float>& factor) const
|
---|
| 1678 | {
|
---|
[270] | 1679 |
|
---|
[230] | 1680 | // For operations only on specified cursor location
|
---|
| 1681 |
|
---|
| 1682 | IPosition start, end;
|
---|
| 1683 | getCursorLocation(start, end, in);
|
---|
| 1684 |
|
---|
[270] | 1685 | // Loop over rows and apply correction factor
|
---|
[230] | 1686 |
|
---|
| 1687 | const uInt axis = asap::ChanAxis;
|
---|
| 1688 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
| 1689 |
|
---|
| 1690 | // Get data
|
---|
| 1691 |
|
---|
| 1692 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i));
|
---|
| 1693 |
|
---|
| 1694 | // Apply factor
|
---|
| 1695 |
|
---|
| 1696 | if (doAll) {
|
---|
[270] | 1697 | dataIn *= factor[i];
|
---|
[230] | 1698 | } else {
|
---|
[270] | 1699 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference
|
---|
| 1700 | dataIn2 *= factor[i];
|
---|
[230] | 1701 | }
|
---|
| 1702 |
|
---|
| 1703 | // Write out
|
---|
| 1704 |
|
---|
| 1705 | SDContainer sc = in.getSDContainer(i);
|
---|
[270] | 1706 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask());
|
---|
[230] | 1707 | //
|
---|
| 1708 | pTabOut->putSDContainer(sc);
|
---|
| 1709 | }
|
---|
| 1710 | }
|
---|
| 1711 |
|
---|
[234] | 1712 |
|
---|
[262] | 1713 | void SDMath::generateSourceTable (Vector<String>& srcTab,
|
---|
| 1714 | Vector<uInt>& srcIdx,
|
---|
| 1715 | Vector<uInt>& firstRow,
|
---|
| 1716 | const Vector<String>& srcNames) const
|
---|
| 1717 | //
|
---|
| 1718 | // This algorithm assumes that if there are multiple beams
|
---|
| 1719 | // that the source names are diffent. Oterwise we would need
|
---|
| 1720 | // to look atthe direction for each beam...
|
---|
| 1721 | //
|
---|
| 1722 | {
|
---|
| 1723 | const uInt nRow = srcNames.nelements();
|
---|
| 1724 | srcTab.resize(0);
|
---|
| 1725 | srcIdx.resize(nRow);
|
---|
| 1726 | firstRow.resize(0);
|
---|
| 1727 | //
|
---|
| 1728 | uInt nSrc = 0;
|
---|
| 1729 | for (uInt i=0; i<nRow; i++) {
|
---|
| 1730 | String srcName = srcNames[i];
|
---|
| 1731 |
|
---|
| 1732 | // Do we have this source already ?
|
---|
| 1733 |
|
---|
| 1734 | Int idx = -1;
|
---|
| 1735 | if (nSrc>0) {
|
---|
| 1736 | for (uInt j=0; j<nSrc; j++) {
|
---|
| 1737 | if (srcName==srcTab[j]) {
|
---|
| 1738 | idx = j;
|
---|
| 1739 | break;
|
---|
| 1740 | }
|
---|
| 1741 | }
|
---|
| 1742 | }
|
---|
| 1743 |
|
---|
| 1744 | // Add new entry if not found
|
---|
| 1745 |
|
---|
| 1746 | if (idx==-1) {
|
---|
| 1747 | nSrc++;
|
---|
| 1748 | srcTab.resize(nSrc,True);
|
---|
| 1749 | srcTab(nSrc-1) = srcName;
|
---|
| 1750 | idx = nSrc-1;
|
---|
| 1751 | //
|
---|
| 1752 | firstRow.resize(nSrc,True);
|
---|
| 1753 | firstRow(nSrc-1) = i; // First row for which this source occurs
|
---|
| 1754 | }
|
---|
| 1755 |
|
---|
| 1756 | // Set index for this row
|
---|
| 1757 |
|
---|
| 1758 | srcIdx[i] = idx;
|
---|
| 1759 | }
|
---|
| 1760 | }
|
---|
[272] | 1761 |
|
---|
| 1762 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const
|
---|
| 1763 | {
|
---|
| 1764 | Quantum<Double> qt;
|
---|
| 1765 | if (MVTime::read(qt,str)) {
|
---|
| 1766 | MVEpoch mv(qt);
|
---|
| 1767 | MEpoch me(mv, timeRef);
|
---|
| 1768 | return me;
|
---|
| 1769 | } else {
|
---|
| 1770 | throw(AipsError("Invalid format for Epoch string"));
|
---|
| 1771 | }
|
---|
| 1772 | }
|
---|
| 1773 |
|
---|
| 1774 |
|
---|
| 1775 | String SDMath::formatEpoch(const MEpoch& epoch) const
|
---|
| 1776 | {
|
---|
| 1777 | MVTime mvt(epoch.getValue());
|
---|
| 1778 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")");
|
---|
| 1779 | }
|
---|
| 1780 |
|
---|
[294] | 1781 |
|
---|
| 1782 | void SDMath::generateVelocityAligners (PtrBlock<VelocityAligner<Float>* >& vA,
|
---|
| 1783 | const SDMemTable& in, uInt nChan,
|
---|
| 1784 | uInt nFreqIDs, uInt nSrcTab,
|
---|
| 1785 | const Vector<uInt>& firstRow,
|
---|
| 1786 | MFrequency::Types velSystem,
|
---|
| 1787 | const String& velUnit,
|
---|
| 1788 | MDoppler::Types doppler,
|
---|
| 1789 | const MPosition& refPos,
|
---|
| 1790 | const MEpoch& refEpoch) const
|
---|
| 1791 | {
|
---|
| 1792 | for (uInt fqID=0; fqID<nFreqIDs; fqID++) {
|
---|
| 1793 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID);
|
---|
| 1794 | for (uInt iSrc=0; iSrc<nSrcTab; iSrc++) {
|
---|
| 1795 | MDirection refDir = in.getDirection(firstRow[iSrc]);
|
---|
| 1796 | uInt idx = (iSrc*nFreqIDs) + fqID;
|
---|
| 1797 | vA[idx] = new VelocityAligner<Float>(sC, nChan, refEpoch, refDir, refPos,
|
---|
| 1798 | velUnit, doppler, velSystem);
|
---|
| 1799 | }
|
---|
| 1800 | }
|
---|
| 1801 | }
|
---|
| 1802 |
|
---|