[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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[330] | 34 | #include <casa/iostream.h>
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| 35 | #include <casa/iomanip.h>
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[81] | 36 | #include <casa/BasicSL/String.h>
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| 37 | #include <casa/Arrays/IPosition.h>
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| 38 | #include <casa/Arrays/Array.h>
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[130] | 39 | #include <casa/Arrays/ArrayIter.h>
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| 40 | #include <casa/Arrays/VectorIter.h>
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[81] | 41 | #include <casa/Arrays/ArrayMath.h>
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| 42 | #include <casa/Arrays/ArrayLogical.h>
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| 43 | #include <casa/Arrays/MaskedArray.h>
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| 44 | #include <casa/Arrays/MaskArrMath.h>
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| 45 | #include <casa/Arrays/MaskArrLogi.h>
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[330] | 46 | #include <casa/Arrays/Matrix.h>
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[234] | 47 | #include <casa/BasicMath/Math.h>
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[221] | 48 | #include <casa/Containers/Block.h>
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[262] | 49 | #include <casa/Exceptions.h>
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| 50 | #include <casa/Quanta/Quantum.h>
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| 51 | #include <casa/Quanta/Unit.h>
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| 52 | #include <casa/Quanta/MVEpoch.h>
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[272] | 53 | #include <casa/Quanta/MVTime.h>
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[177] | 54 | #include <casa/Utilities/Assert.h>
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[2] | 55 |
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[262] | 56 | #include <coordinates/Coordinates/SpectralCoordinate.h>
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| 57 | #include <coordinates/Coordinates/CoordinateSystem.h>
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| 58 | #include <coordinates/Coordinates/CoordinateUtil.h>
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[309] | 59 | #include <coordinates/Coordinates/FrequencyAligner.h>
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[262] | 60 |
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| 61 | #include <lattices/Lattices/LatticeUtilities.h>
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| 62 | #include <lattices/Lattices/RebinLattice.h>
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| 63 |
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| 64 | #include <measures/Measures/MEpoch.h>
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| 65 | #include <measures/Measures/MDirection.h>
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| 66 | #include <measures/Measures/MPosition.h>
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| 67 |
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[177] | 68 | #include <scimath/Mathematics/VectorKernel.h>
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| 69 | #include <scimath/Mathematics/Convolver.h>
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[227] | 70 | #include <scimath/Mathematics/InterpolateArray1D.h>
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[234] | 71 | #include <scimath/Functionals/Polynomial.h>
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[177] | 72 |
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[81] | 73 | #include <tables/Tables/Table.h>
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| 74 | #include <tables/Tables/ScalarColumn.h>
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| 75 | #include <tables/Tables/ArrayColumn.h>
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[227] | 76 | #include <tables/Tables/ReadAsciiTable.h>
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[2] | 77 |
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[38] | 78 | #include "MathUtils.h"
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[232] | 79 | #include "SDDefs.h"
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[354] | 80 | #include "SDAttr.h"
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[2] | 81 | #include "SDContainer.h"
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| 82 | #include "SDMemTable.h"
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| 83 |
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| 84 | #include "SDMath.h"
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[457] | 85 | #include "SDPol.h"
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[2] | 86 |
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[125] | 87 | using namespace casa;
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[83] | 88 | using namespace asap;
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[2] | 89 |
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[170] | 90 |
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| 91 | SDMath::SDMath()
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| 92 | {;}
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| 93 |
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[185] | 94 | SDMath::SDMath(const SDMath& other)
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[170] | 95 | {
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| 96 |
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| 97 | // No state
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| 98 |
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| 99 | }
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| 100 |
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| 101 | SDMath& SDMath::operator=(const SDMath& other)
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| 102 | {
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| 103 | if (this != &other) {
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| 104 | // No state
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| 105 | }
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| 106 | return *this;
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| 107 | }
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| 108 |
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[183] | 109 | SDMath::~SDMath()
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| 110 | {;}
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[170] | 111 |
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[183] | 112 |
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[262] | 113 |
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[488] | 114 | SDMemTable* SDMath::frequencyAlignment(const SDMemTable& in,
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| 115 | const String& refTime,
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| 116 | const String& method,
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| 117 | Bool perFreqID) const
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[262] | 118 | {
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[309] | 119 | // Get frame info from Table
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[262] | 120 |
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| 121 | std::vector<std::string> info = in.getCoordInfo();
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[294] | 122 |
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[309] | 123 | // Parse frequency system
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[294] | 124 |
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[309] | 125 | String systemStr(info[1]);
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| 126 | String baseSystemStr(info[3]);
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| 127 | if (baseSystemStr==systemStr) {
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| 128 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe"));
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[262] | 129 | }
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[309] | 130 | //
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| 131 | MFrequency::Types freqSystem;
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| 132 | MFrequency::getType(freqSystem, systemStr);
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[294] | 133 |
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[267] | 134 | // Do it
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[262] | 135 |
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[488] | 136 | return frequencyAlign(in, freqSystem, refTime, method, perFreqID);
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[267] | 137 | }
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[262] | 138 |
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| 139 |
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| 140 |
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[185] | 141 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in,
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| 142 | const Vector<Bool>& mask, Bool scanAv,
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[309] | 143 | const String& weightStr, Bool alignFreq) const
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[130] | 144 | //
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[144] | 145 | // Weighted averaging of spectra from one or more Tables.
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[130] | 146 | //
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| 147 | {
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[2] | 148 |
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[163] | 149 | // Convert weight type
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| 150 |
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| 151 | WeightType wtType = NONE;
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[518] | 152 | convertWeightString(wtType, weightStr, True);
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[163] | 153 |
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[144] | 154 | // Create output Table by cloning from the first table
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[2] | 155 |
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[144] | 156 | SDMemTable* pTabOut = new SDMemTable(*in[0],True);
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[488] | 157 | if (in.nelements() > 1) {
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| 158 | for (uInt i=1; i < in.nelements(); ++i) {
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| 159 | pTabOut->appendToHistoryTable(in[i]->getHistoryTable());
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| 160 | }
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| 161 | }
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[144] | 162 | // Setup
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[130] | 163 |
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[144] | 164 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change
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| 165 | Array<Float> arr(shp);
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| 166 | Array<Bool> barr(shp);
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[221] | 167 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis));
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[130] | 168 |
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[144] | 169 | // Columns from Tables
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[130] | 170 |
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[144] | 171 | ROArrayColumn<Float> tSysCol;
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| 172 | ROScalarColumn<Double> mjdCol;
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| 173 | ROScalarColumn<String> srcNameCol;
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| 174 | ROScalarColumn<Double> intCol;
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| 175 | ROArrayColumn<uInt> fqIDCol;
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[410] | 176 | ROScalarColumn<Int> scanIDCol;
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[130] | 177 |
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[144] | 178 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam
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| 179 | // Note that the mask of the accumulation array will ALWAYS remain ALL True.
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| 180 | // The MA is only used so that when data which is masked Bad is added to it,
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| 181 | // that data does not contribute.
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| 182 |
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| 183 | Array<Float> zero(shp);
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| 184 | zero=0.0;
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| 185 | Array<Bool> good(shp);
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| 186 | good = True;
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| 187 | MaskedArray<Float> sum(zero,good);
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| 188 |
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| 189 | // Counter arrays
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| 190 |
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| 191 | Array<Float> nPts(shp); // Number of points
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| 192 | nPts = 0.0;
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| 193 | Array<Float> nInc(shp); // Increment
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| 194 | nInc = 1.0;
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| 195 |
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| 196 | // Create accumulation Array for variance. We accumulate for
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| 197 | // each if,pol,beam, but average over channel. So we need
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| 198 | // a shape with one less axis dropping channels.
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| 199 |
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| 200 | const uInt nAxesSub = shp.nelements() - 1;
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| 201 | IPosition shp2(nAxesSub);
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| 202 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) {
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[221] | 203 | if (i!=asap::ChanAxis) {
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[144] | 204 | shp2(j) = shp(i);
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| 205 | j++;
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| 206 | }
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[2] | 207 | }
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[144] | 208 | Array<Float> sumSq(shp2);
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| 209 | sumSq = 0.0;
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| 210 | IPosition pos2(nAxesSub,0); // For indexing
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[130] | 211 |
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[144] | 212 | // Time-related accumulators
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[130] | 213 |
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[144] | 214 | Double time;
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| 215 | Double timeSum = 0.0;
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| 216 | Double intSum = 0.0;
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| 217 | Double interval = 0.0;
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[130] | 218 |
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[144] | 219 | // To get the right shape for the Tsys accumulator we need to
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| 220 | // access a column from the first table. The shape of this
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[518] | 221 | // array must not change. Note however that since the TSysSqSum
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| 222 | // array is used in a normalization process, and that I ignore the
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| 223 | // channel axis replication of values for now, it loses a dimension
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[130] | 224 |
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[518] | 225 | Array<Float> tSysSum, tSysSqSum;
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[144] | 226 | {
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| 227 | const Table& tabIn = in[0]->table();
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| 228 | tSysCol.attach(tabIn,"TSYS");
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| 229 | tSysSum.resize(tSysCol.shape(0));
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[518] | 230 | //
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| 231 | tSysSqSum.resize(shp2);
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[144] | 232 | }
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| 233 | tSysSum =0.0;
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[518] | 234 | tSysSqSum = 0.0;
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[144] | 235 | Array<Float> tSys;
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| 236 |
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| 237 | // Scan and row tracking
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| 238 |
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| 239 | Int oldScanID = 0;
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| 240 | Int outScanID = 0;
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| 241 | Int scanID = 0;
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| 242 | Int rowStart = 0;
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| 243 | Int nAccum = 0;
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| 244 | Int tableStart = 0;
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| 245 |
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| 246 | // Source and FreqID
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| 247 |
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| 248 | String sourceName, oldSourceName, sourceNameStart;
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| 249 | Vector<uInt> freqID, freqIDStart, oldFreqID;
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| 250 |
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| 251 | // Loop over tables
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| 252 |
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| 253 | Float fac = 1.0;
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| 254 | const uInt nTables = in.nelements();
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| 255 | for (uInt iTab=0; iTab<nTables; iTab++) {
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| 256 |
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[309] | 257 | // Should check that the frequency tables don't change if doing FreqAlignment
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[221] | 258 |
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[144] | 259 | // Attach columns to Table
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| 260 |
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| 261 | const Table& tabIn = in[iTab]->table();
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| 262 | tSysCol.attach(tabIn, "TSYS");
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| 263 | mjdCol.attach(tabIn, "TIME");
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| 264 | srcNameCol.attach(tabIn, "SRCNAME");
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| 265 | intCol.attach(tabIn, "INTERVAL");
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| 266 | fqIDCol.attach(tabIn, "FREQID");
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[410] | 267 | scanIDCol.attach(tabIn, "SCANID");
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[144] | 268 |
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[410] | 269 | // Find list of start/end rows for each scan
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| 270 |
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[144] | 271 | // Loop over rows in Table
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| 272 |
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| 273 | const uInt nRows = in[iTab]->nRow();
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| 274 | for (uInt iRow=0; iRow<nRows; iRow++) {
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| 275 |
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| 276 | // Check conformance
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| 277 |
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| 278 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape();
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| 279 | if (!shp.isEqual(shp2)) {
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| 280 | throw (AipsError("Shapes for all rows must be the same"));
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| 281 | }
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| 282 |
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| 283 | // If we are not doing scan averages, make checks for source and
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| 284 | // frequency setup and warn if averaging across them
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| 285 |
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[410] | 286 | scanIDCol.getScalar(iRow, scanID);
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[144] | 287 |
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| 288 | // Get quantities from columns
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| 289 |
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| 290 | srcNameCol.getScalar(iRow, sourceName);
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| 291 | mjdCol.get(iRow, time);
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| 292 | tSysCol.get(iRow, tSys);
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| 293 | intCol.get(iRow, interval);
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| 294 | fqIDCol.get(iRow, freqID);
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| 295 |
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| 296 | // Initialize first source and freqID
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| 297 |
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| 298 | if (iRow==0 && iTab==0) {
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| 299 | sourceNameStart = sourceName;
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| 300 | freqIDStart = freqID;
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| 301 | }
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| 302 |
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| 303 | // If we are doing scan averages, see if we are at the end of an
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| 304 | // accumulation period (scan). We must check soutce names too,
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| 305 | // since we might have two tables with one scan each but different
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| 306 | // source names; we shouldn't average different sources together
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| 307 |
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| 308 | if (scanAv && ( (scanID != oldScanID) ||
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| 309 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) {
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| 310 |
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| 311 | // Normalize data in 'sum' accumulation array according to weighting scheme
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| 312 |
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[518] | 313 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub);
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[144] | 314 |
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[410] | 315 | // Get ScanContainer for the first row of this averaged Scan
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| 316 |
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| 317 | SDContainer scOut = in[iTab]->getSDContainer(rowStart);
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| 318 |
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[144] | 319 | // Fill scan container. The source and freqID come from the
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| 320 | // first row of the first table that went into this average (
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| 321 | // should be the same for all rows in the scan average)
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| 322 |
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| 323 | Float nR(nAccum);
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[410] | 324 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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[144] | 325 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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| 326 |
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| 327 | // Write container out to Table
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| 328 |
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[410] | 329 | pTabOut->putSDContainer(scOut);
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[144] | 330 |
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| 331 | // Reset accumulators
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| 332 |
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| 333 | sum = 0.0;
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| 334 | sumSq = 0.0;
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| 335 | nAccum = 0;
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| 336 | //
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| 337 | tSysSum =0.0;
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[518] | 338 | tSysSqSum =0.0;
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[144] | 339 | timeSum = 0.0;
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| 340 | intSum = 0.0;
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[221] | 341 | nPts = 0.0;
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[144] | 342 |
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| 343 | // Increment
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| 344 |
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| 345 | rowStart = iRow; // First row for next accumulation
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| 346 | tableStart = iTab; // First table for next accumulation
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| 347 | sourceNameStart = sourceName; // First source name for next accumulation
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| 348 | freqIDStart = freqID; // First FreqID for next accumulation
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| 349 | //
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| 350 | oldScanID = scanID;
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| 351 | outScanID += 1; // Scan ID for next accumulation period
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[227] | 352 | }
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[144] | 353 |
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[146] | 354 | // Accumulate
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[144] | 355 |
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[518] | 356 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, tSysSqSum,
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| 357 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis,
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| 358 | nAxesSub, useMask, wtType);
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[144] | 359 | //
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| 360 | oldSourceName = sourceName;
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| 361 | oldFreqID = freqID;
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[184] | 362 | }
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[144] | 363 | }
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| 364 |
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| 365 | // OK at this point we have accumulation data which is either
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| 366 | // - accumulated from all tables into one row
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| 367 | // or
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| 368 | // - accumulated from the last scan average
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| 369 | //
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| 370 | // Normalize data in 'sum' accumulation array according to weighting scheme
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[410] | 371 |
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[518] | 372 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub);
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[144] | 373 |
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| 374 | // Create and fill container. The container we clone will be from
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| 375 | // the last Table and the first row that went into the current
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| 376 | // accumulation. It probably doesn't matter that much really...
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| 377 |
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| 378 | Float nR(nAccum);
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[410] | 379 | SDContainer scOut = in[tableStart]->getSDContainer(rowStart);
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| 380 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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[144] | 381 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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[410] | 382 | pTabOut->putSDContainer(scOut);
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[304] | 383 | pTabOut->resetCursor();
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[144] | 384 | //
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| 385 | return CountedPtr<SDMemTable>(pTabOut);
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[2] | 386 | }
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[9] | 387 |
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[144] | 388 |
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| 389 |
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[488] | 390 | CountedPtr<SDMemTable> SDMath::binaryOperate(const CountedPtr<SDMemTable>&
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| 391 | left,
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| 392 | const CountedPtr<SDMemTable>&
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| 393 | right,
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| 394 | const String& op, Bool preserve,
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| 395 | Bool doTSys) const
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[185] | 396 | {
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[85] | 397 |
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[248] | 398 | // Check operator
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[130] | 399 |
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[234] | 400 | String op2(op);
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| 401 | op2.upcase();
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| 402 | uInt what = 0;
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| 403 | if (op2=="ADD") {
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| 404 | what = 0;
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| 405 | } else if (op2=="SUB") {
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| 406 | what = 1;
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| 407 | } else if (op2=="MUL") {
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| 408 | what = 2;
|
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| 409 | } else if (op2=="DIV") {
|
---|
| 410 | what = 3;
|
---|
[248] | 411 | } else if (op2=="QUOTIENT") {
|
---|
| 412 | what = 4;
|
---|
[294] | 413 | doTSys = True;
|
---|
[234] | 414 | } else {
|
---|
[248] | 415 | throw( AipsError("Unrecognized operation"));
|
---|
[234] | 416 | }
|
---|
| 417 |
|
---|
| 418 | // Check rows
|
---|
| 419 |
|
---|
[248] | 420 | const uInt nRowLeft = left->nRow();
|
---|
| 421 | const uInt nRowRight = right->nRow();
|
---|
| 422 | Bool ok = (nRowRight==1&&nRowLeft>0) ||
|
---|
| 423 | (nRowRight>=1&&nRowLeft==nRowRight);
|
---|
| 424 | if (!ok) {
|
---|
| 425 | throw (AipsError("The right Scan Table can have one row or the same number of rows as the left Scan Table"));
|
---|
[234] | 426 | }
|
---|
| 427 |
|
---|
[248] | 428 | // Input Tables
|
---|
[234] | 429 |
|
---|
| 430 | const Table& tLeft = left->table();
|
---|
| 431 | const Table& tRight = right->table();
|
---|
[248] | 432 |
|
---|
| 433 | // TSys columns
|
---|
| 434 |
|
---|
[294] | 435 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol;
|
---|
| 436 | if (doTSys) {
|
---|
| 437 | tSysLeftCol.attach(tLeft, "TSYS");
|
---|
| 438 | tSysRightCol.attach(tRight, "TSYS");
|
---|
| 439 | }
|
---|
[234] | 440 |
|
---|
[248] | 441 | // First row for right
|
---|
[234] | 442 |
|
---|
[248] | 443 | Array<Float> tSysLeftArr, tSysRightArr;
|
---|
[294] | 444 | if (doTSys) tSysRightCol.get(0, tSysRightArr);
|
---|
[248] | 445 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0));
|
---|
| 446 | IPosition shpRight = pMRight->shape();
|
---|
| 447 |
|
---|
| 448 | // Output Table cloned from left
|
---|
| 449 |
|
---|
[234] | 450 | SDMemTable* pTabOut = new SDMemTable(*left, True);
|
---|
[488] | 451 | pTabOut->appendToHistoryTable(right->getHistoryTable());
|
---|
[234] | 452 | // Loop over rows
|
---|
| 453 |
|
---|
[248] | 454 | for (uInt i=0; i<nRowLeft; i++) {
|
---|
[234] | 455 |
|
---|
| 456 | // Get data
|
---|
[248] | 457 |
|
---|
[234] | 458 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i));
|
---|
[248] | 459 | IPosition shpLeft = mLeft.shape();
|
---|
[294] | 460 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr);
|
---|
[234] | 461 | //
|
---|
[248] | 462 | if (nRowRight>1) {
|
---|
| 463 | delete pMRight;
|
---|
| 464 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i));
|
---|
| 465 | shpRight = pMRight->shape();
|
---|
[294] | 466 | if (doTSys) tSysRightCol.get(i, tSysRightArr);
|
---|
[234] | 467 | }
|
---|
[248] | 468 | //
|
---|
| 469 | if (!shpRight.isEqual(shpLeft)) {
|
---|
| 470 | throw(AipsError("left and right scan tables are not conformant"));
|
---|
| 471 | }
|
---|
[294] | 472 | if (doTSys) {
|
---|
| 473 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) {
|
---|
| 474 | throw(AipsError("left and right Tsys data are not conformant"));
|
---|
| 475 | }
|
---|
| 476 | if (!shpRight.isEqual(tSysRightArr.shape())) {
|
---|
| 477 | throw(AipsError("left and right scan tables are not conformant"));
|
---|
| 478 | }
|
---|
[248] | 479 | }
|
---|
[234] | 480 |
|
---|
| 481 | // Make container
|
---|
| 482 |
|
---|
| 483 | SDContainer sc = left->getSDContainer(i);
|
---|
| 484 |
|
---|
| 485 | // Operate on data and TSys
|
---|
| 486 |
|
---|
| 487 | if (what==0) {
|
---|
[248] | 488 | MaskedArray<Float> tmp = mLeft + *pMRight;
|
---|
[234] | 489 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 490 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr);
|
---|
[234] | 491 | } else if (what==1) {
|
---|
[248] | 492 | MaskedArray<Float> tmp = mLeft - *pMRight;
|
---|
[234] | 493 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 494 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr);
|
---|
[234] | 495 | } else if (what==2) {
|
---|
[248] | 496 | MaskedArray<Float> tmp = mLeft * *pMRight;
|
---|
[234] | 497 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 498 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr);
|
---|
[234] | 499 | } else if (what==3) {
|
---|
[248] | 500 | MaskedArray<Float> tmp = mLeft / *pMRight;
|
---|
[234] | 501 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
[294] | 502 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr);
|
---|
[248] | 503 | } else if (what==4) {
|
---|
[488] | 504 | if (preserve) {
|
---|
| 505 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) -
|
---|
| 506 | tSysRightArr;
|
---|
| 507 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
| 508 | } else {
|
---|
| 509 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) -
|
---|
| 510 | tSysLeftArr;
|
---|
| 511 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
| 512 | }
|
---|
| 513 | sc.putTsys(tSysRightArr);
|
---|
[234] | 514 | }
|
---|
| 515 |
|
---|
| 516 | // Put new row in output Table
|
---|
| 517 |
|
---|
[171] | 518 | pTabOut->putSDContainer(sc);
|
---|
[130] | 519 | }
|
---|
[248] | 520 | if (pMRight) delete pMRight;
|
---|
[304] | 521 | pTabOut->resetCursor();
|
---|
[488] | 522 |
|
---|
[171] | 523 | return CountedPtr<SDMemTable>(pTabOut);
|
---|
[9] | 524 | }
|
---|
[48] | 525 |
|
---|
[146] | 526 |
|
---|
| 527 |
|
---|
[185] | 528 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in,
|
---|
[234] | 529 | const Vector<Bool>& mask,
|
---|
| 530 | const String& which, Int row) const
|
---|
[130] | 531 | //
|
---|
| 532 | // Perhaps iteration over pol/beam/if should be in here
|
---|
| 533 | // and inside the nrow iteration ?
|
---|
| 534 | //
|
---|
| 535 | {
|
---|
| 536 | const uInt nRow = in->nRow();
|
---|
| 537 |
|
---|
| 538 | // Specify cursor location
|
---|
| 539 |
|
---|
[152] | 540 | IPosition start, end;
|
---|
[434] | 541 | Bool doAll = False;
|
---|
| 542 | setCursorSlice (start, end, doAll, *in);
|
---|
[130] | 543 |
|
---|
| 544 | // Loop over rows
|
---|
| 545 |
|
---|
[234] | 546 | const uInt nEl = mask.nelements();
|
---|
| 547 | uInt iStart = 0;
|
---|
| 548 | uInt iEnd = in->nRow()-1;
|
---|
| 549 | //
|
---|
| 550 | if (row>=0) {
|
---|
| 551 | iStart = row;
|
---|
| 552 | iEnd = row;
|
---|
| 553 | }
|
---|
| 554 | //
|
---|
| 555 | std::vector<float> result(iEnd-iStart+1);
|
---|
| 556 | for (uInt ii=iStart; ii <= iEnd; ++ii) {
|
---|
[130] | 557 |
|
---|
| 558 | // Get row and deconstruct
|
---|
| 559 |
|
---|
[434] | 560 | MaskedArray<Float> dataIn = (in->rowAsMaskedArray(ii))(start,end);
|
---|
| 561 | Array<Float> v = dataIn.getArray().nonDegenerate();
|
---|
| 562 | Array<Bool> m = dataIn.getMask().nonDegenerate();
|
---|
[130] | 563 |
|
---|
| 564 | // Access desired piece of data
|
---|
| 565 |
|
---|
[434] | 566 | // Array<Float> v((arr(start,end)).nonDegenerate());
|
---|
| 567 | // Array<Bool> m((barr(start,end)).nonDegenerate());
|
---|
[130] | 568 |
|
---|
| 569 | // Apply OTF mask
|
---|
| 570 |
|
---|
| 571 | MaskedArray<Float> tmp;
|
---|
| 572 | if (m.nelements()==nEl) {
|
---|
[234] | 573 | tmp.setData(v,m&&mask);
|
---|
[130] | 574 | } else {
|
---|
| 575 | tmp.setData(v,m);
|
---|
| 576 | }
|
---|
| 577 |
|
---|
| 578 | // Get statistic
|
---|
| 579 |
|
---|
[234] | 580 | result[ii-iStart] = mathutil::statistics(which, tmp);
|
---|
[130] | 581 | }
|
---|
| 582 | //
|
---|
| 583 | return result;
|
---|
| 584 | }
|
---|
| 585 |
|
---|
[146] | 586 |
|
---|
[234] | 587 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const
|
---|
[144] | 588 | {
|
---|
[169] | 589 | SDHeader sh = in.getSDHeader();
|
---|
| 590 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
[163] | 591 |
|
---|
[169] | 592 | // Bin up SpectralCoordinates
|
---|
[163] | 593 |
|
---|
[169] | 594 | IPosition factors(1);
|
---|
| 595 | factors(0) = width;
|
---|
| 596 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
| 597 | CoordinateSystem cSys;
|
---|
[288] | 598 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
[169] | 599 | CoordinateSystem cSysBin =
|
---|
[185] | 600 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False);
|
---|
[169] | 601 | //
|
---|
| 602 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0);
|
---|
| 603 | pTabOut->setCoordinate(sCBin, j);
|
---|
| 604 | }
|
---|
[163] | 605 |
|
---|
[169] | 606 | // Use RebinLattice to find shape
|
---|
[130] | 607 |
|
---|
[169] | 608 | IPosition shapeIn(1,sh.nchan);
|
---|
[185] | 609 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors);
|
---|
[169] | 610 | sh.nchan = shapeOut(0);
|
---|
| 611 | pTabOut->putSDHeader(sh);
|
---|
[144] | 612 |
|
---|
[169] | 613 | // Loop over rows and bin along channel axis
|
---|
| 614 |
|
---|
| 615 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
| 616 | SDContainer sc = in.getSDContainer(i);
|
---|
[144] | 617 | //
|
---|
[169] | 618 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape
|
---|
[144] | 619 |
|
---|
[169] | 620 | // Bin up spectrum
|
---|
[144] | 621 |
|
---|
[169] | 622 | MaskedArray<Float> marr(in.rowAsMaskedArray(i));
|
---|
| 623 | MaskedArray<Float> marrout;
|
---|
[221] | 624 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width);
|
---|
[144] | 625 |
|
---|
[169] | 626 | // Put back the binned data and flags
|
---|
[144] | 627 |
|
---|
[169] | 628 | IPosition ip2 = marrout.shape();
|
---|
| 629 | sc.resize(ip2);
|
---|
[146] | 630 | //
|
---|
[185] | 631 | putDataInSDC(sc, marrout.getArray(), marrout.getMask());
|
---|
[146] | 632 |
|
---|
[169] | 633 | // Bin up Tsys.
|
---|
[146] | 634 |
|
---|
[169] | 635 | Array<Bool> allGood(tSys.shape(),True);
|
---|
| 636 | MaskedArray<Float> tSysIn(tSys, allGood, True);
|
---|
[146] | 637 | //
|
---|
[169] | 638 | MaskedArray<Float> tSysOut;
|
---|
[221] | 639 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width);
|
---|
[169] | 640 | sc.putTsys(tSysOut.getArray());
|
---|
[146] | 641 | //
|
---|
[169] | 642 | pTabOut->putSDContainer(sc);
|
---|
| 643 | }
|
---|
| 644 | return pTabOut;
|
---|
[146] | 645 | }
|
---|
| 646 |
|
---|
[488] | 647 | SDMemTable* SDMath::resample(const SDMemTable& in, const String& methodStr,
|
---|
| 648 | Float width) const
|
---|
[299] | 649 | //
|
---|
| 650 | // Should add the possibility of width being specified in km/s. This means
|
---|
| 651 | // that for each freqID (SpectralCoordinate) we will need to convert to an
|
---|
| 652 | // average channel width (say at the reference pixel). Then we would need
|
---|
| 653 | // to be careful to make sure each spectrum (of different freqID)
|
---|
| 654 | // is the same length.
|
---|
| 655 | //
|
---|
| 656 | {
|
---|
| 657 | Bool doVel = False;
|
---|
[309] | 658 | if (doVel) {
|
---|
| 659 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
| 660 | SpectralCoordinate sC = in.getSpectralCoordinate(j);
|
---|
| 661 | }
|
---|
| 662 | }
|
---|
[299] | 663 |
|
---|
| 664 | // Interpolation method
|
---|
| 665 |
|
---|
[317] | 666 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
---|
| 667 | convertInterpString(interp, methodStr);
|
---|
| 668 | Int interpMethod(interp);
|
---|
[299] | 669 |
|
---|
| 670 | // Make output table
|
---|
| 671 |
|
---|
| 672 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
| 673 |
|
---|
| 674 | // Resample SpectralCoordinates (one per freqID)
|
---|
| 675 |
|
---|
| 676 | const uInt nCoord = in.nCoordinates();
|
---|
| 677 | Vector<Float> offset(1,0.0);
|
---|
| 678 | Vector<Float> factors(1,1.0/width);
|
---|
| 679 | Vector<Int> newShape;
|
---|
| 680 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
| 681 | CoordinateSystem cSys;
|
---|
| 682 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
| 683 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape);
|
---|
| 684 | SpectralCoordinate sC = cSys2.spectralCoordinate(0);
|
---|
| 685 | //
|
---|
| 686 | pTabOut->setCoordinate(sC, j);
|
---|
| 687 | }
|
---|
| 688 |
|
---|
| 689 | // Get header
|
---|
| 690 |
|
---|
| 691 | SDHeader sh = in.getSDHeader();
|
---|
| 692 |
|
---|
| 693 | // Generate resampling vectors
|
---|
| 694 |
|
---|
| 695 | const uInt nChanIn = sh.nchan;
|
---|
| 696 | Vector<Float> xIn(nChanIn);
|
---|
| 697 | indgen(xIn);
|
---|
| 698 | //
|
---|
| 699 | Int fac = Int(nChanIn/width);
|
---|
| 700 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later
|
---|
| 701 | uInt i = 0;
|
---|
| 702 | Float x = 0.0;
|
---|
| 703 | Bool more = True;
|
---|
| 704 | while (more) {
|
---|
| 705 | xOut(i) = x;
|
---|
| 706 | //
|
---|
| 707 | i++;
|
---|
| 708 | x += width;
|
---|
| 709 | if (x>nChanIn-1) more = False;
|
---|
| 710 | }
|
---|
| 711 | const uInt nChanOut = i;
|
---|
| 712 | xOut.resize(nChanOut,True);
|
---|
| 713 | //
|
---|
| 714 | IPosition shapeIn(in.rowAsMaskedArray(0).shape());
|
---|
| 715 | sh.nchan = nChanOut;
|
---|
| 716 | pTabOut->putSDHeader(sh);
|
---|
| 717 |
|
---|
| 718 | // Loop over rows and resample along channel axis
|
---|
| 719 |
|
---|
| 720 | Array<Float> valuesOut;
|
---|
| 721 | Array<Bool> maskOut;
|
---|
| 722 | Array<Float> tSysOut;
|
---|
| 723 | Array<Bool> tSysMaskIn(shapeIn,True);
|
---|
| 724 | Array<Bool> tSysMaskOut;
|
---|
| 725 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
| 726 |
|
---|
| 727 | // Get container
|
---|
| 728 |
|
---|
| 729 | SDContainer sc = in.getSDContainer(i);
|
---|
| 730 |
|
---|
| 731 | // Get data and Tsys
|
---|
| 732 |
|
---|
| 733 | const Array<Float>& tSysIn = sc.getTsys();
|
---|
| 734 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i));
|
---|
| 735 | Array<Float> valuesIn = dataIn.getArray();
|
---|
| 736 | Array<Bool> maskIn = dataIn.getMask();
|
---|
| 737 |
|
---|
| 738 | // Interpolate data
|
---|
| 739 |
|
---|
| 740 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut,
|
---|
| 741 | xIn, valuesIn, maskIn,
|
---|
| 742 | interpMethod, True, True);
|
---|
| 743 | sc.resize(valuesOut.shape());
|
---|
| 744 | putDataInSDC(sc, valuesOut, maskOut);
|
---|
| 745 |
|
---|
| 746 | // Interpolate TSys
|
---|
| 747 |
|
---|
| 748 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut,
|
---|
| 749 | xIn, tSysIn, tSysMaskIn,
|
---|
| 750 | interpMethod, True, True);
|
---|
| 751 | sc.putTsys(tSysOut);
|
---|
| 752 |
|
---|
| 753 | // Put container in output
|
---|
| 754 |
|
---|
| 755 | pTabOut->putSDContainer(sc);
|
---|
| 756 | }
|
---|
| 757 | //
|
---|
| 758 | return pTabOut;
|
---|
| 759 | }
|
---|
| 760 |
|
---|
[248] | 761 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll,
|
---|
[294] | 762 | uInt what, Bool doTSys) const
|
---|
[152] | 763 | //
|
---|
| 764 | // what = 0 Multiply
|
---|
| 765 | // 1 Add
|
---|
[146] | 766 | {
|
---|
[152] | 767 | SDMemTable* pOut = new SDMemTable(in,False);
|
---|
| 768 | const Table& tOut = pOut->table();
|
---|
[294] | 769 | ArrayColumn<Float> specCol(tOut,"SPECTRA");
|
---|
| 770 | ArrayColumn<Float> tSysCol(tOut,"TSYS");
|
---|
| 771 | Array<Float> tSysArr;
|
---|
[434] | 772 |
|
---|
| 773 | // Get data slice bounds
|
---|
| 774 |
|
---|
| 775 | IPosition start, end;
|
---|
| 776 | setCursorSlice (start, end, doAll, in);
|
---|
[146] | 777 | //
|
---|
[434] | 778 | for (uInt i=0; i<tOut.nrow(); i++) {
|
---|
[294] | 779 |
|
---|
| 780 | // Modify data
|
---|
| 781 |
|
---|
[434] | 782 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
|
---|
| 783 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference
|
---|
| 784 | if (what==0) {
|
---|
| 785 | dataIn2 *= val;
|
---|
| 786 | } else if (what==1) {
|
---|
| 787 | dataIn2 += val;
|
---|
| 788 | }
|
---|
| 789 | specCol.put(i, dataIn.getArray());
|
---|
[294] | 790 |
|
---|
| 791 | // Modify Tsys
|
---|
| 792 |
|
---|
[434] | 793 | if (doTSys) {
|
---|
| 794 | tSysCol.get(i, tSysArr);
|
---|
| 795 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference
|
---|
[152] | 796 | if (what==0) {
|
---|
[434] | 797 | tSysArr2 *= val;
|
---|
[152] | 798 | } else if (what==1) {
|
---|
[434] | 799 | tSysArr2 += val;
|
---|
[152] | 800 | }
|
---|
[434] | 801 | tSysCol.put(i, tSysArr);
|
---|
[152] | 802 | }
|
---|
| 803 | }
|
---|
| 804 | //
|
---|
[146] | 805 | return pOut;
|
---|
| 806 | }
|
---|
| 807 |
|
---|
[315] | 808 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask,
|
---|
| 809 | const String& weightStr) const
|
---|
[152] | 810 | //
|
---|
[165] | 811 | // Average all polarizations together, weighted by variance
|
---|
| 812 | //
|
---|
| 813 | {
|
---|
[315] | 814 | WeightType wtType = NONE;
|
---|
[532] | 815 | convertWeightString(wtType, weightStr, True);
|
---|
[165] | 816 |
|
---|
| 817 | // Create output Table and reshape number of polarizations
|
---|
| 818 |
|
---|
| 819 | Bool clear=True;
|
---|
| 820 | SDMemTable* pTabOut = new SDMemTable(in, clear);
|
---|
| 821 | SDHeader header = pTabOut->getSDHeader();
|
---|
| 822 | header.npol = 1;
|
---|
| 823 | pTabOut->putSDHeader(header);
|
---|
[532] | 824 | //
|
---|
| 825 | const Table& tabIn = in.table();
|
---|
[165] | 826 |
|
---|
| 827 | // Shape of input and output data
|
---|
| 828 |
|
---|
[448] | 829 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape();
|
---|
[165] | 830 | IPosition shapeOut(shapeIn);
|
---|
[262] | 831 | shapeOut(asap::PolAxis) = 1; // Average all polarizations
|
---|
[315] | 832 | if (shapeIn(asap::PolAxis)==1) {
|
---|
| 833 | throw(AipsError("The input has only one polarisation"));
|
---|
| 834 | }
|
---|
[165] | 835 | //
|
---|
[532] | 836 | const uInt nRows = in.nRow();
|
---|
[262] | 837 | const uInt nChan = shapeIn(asap::ChanAxis);
|
---|
[532] | 838 | AlwaysAssert(asap::nAxes==4,AipsError);
|
---|
[165] | 839 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape
|
---|
| 840 | IPosition start(4), end(4);
|
---|
| 841 |
|
---|
| 842 | // Output arrays
|
---|
| 843 |
|
---|
| 844 | Array<Float> outData(shapeOut, 0.0);
|
---|
| 845 | Array<Bool> outMask(shapeOut, True);
|
---|
[262] | 846 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane
|
---|
[532] | 847 |
|
---|
| 848 | // Attach Tsys column if needed
|
---|
| 849 |
|
---|
| 850 | ROArrayColumn<Float> tSysCol;
|
---|
| 851 | Array<Float> tSys;
|
---|
| 852 | if (wtType==TSYS) {
|
---|
| 853 | tSysCol.attach(tabIn,"TSYS");
|
---|
| 854 | }
|
---|
[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();
|
---|
[532] | 867 |
|
---|
| 868 | // Get Tsys
|
---|
[165] | 869 |
|
---|
[532] | 870 | if (wtType==TSYS) {
|
---|
| 871 | tSysCol.get(iRow,tSys);
|
---|
| 872 | }
|
---|
| 873 |
|
---|
[165] | 874 | // Make iterators to iterate by pol-channel planes
|
---|
[532] | 875 | // The tSys array is empty unless wtType=TSYS so only
|
---|
| 876 | // access the iterator is that is the case
|
---|
[165] | 877 |
|
---|
| 878 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes);
|
---|
| 879 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes);
|
---|
[532] | 880 | ReadOnlyArrayIterator<Float>* pItTsysPlane = 0;
|
---|
| 881 | if (wtType==TSYS) pItTsysPlane = new ReadOnlyArrayIterator<Float>(tSys, axes);
|
---|
[165] | 882 |
|
---|
| 883 | // Accumulations
|
---|
| 884 |
|
---|
| 885 | Float fac = 1.0;
|
---|
| 886 | Vector<Float> vecSum(nChan,0.0);
|
---|
| 887 |
|
---|
| 888 | // Iterate through data by pol-channel planes
|
---|
| 889 |
|
---|
| 890 | while (!itDataPlane.pastEnd()) {
|
---|
| 891 |
|
---|
| 892 | // Iterate through plane by polarization and accumulate Vectors
|
---|
| 893 |
|
---|
| 894 | Vector<Float> t1(nChan); t1 = 0.0;
|
---|
| 895 | Vector<Bool> t2(nChan); t2 = True;
|
---|
[532] | 896 | Float tSys = 0.0;
|
---|
[165] | 897 | MaskedArray<Float> vecSum(t1,t2);
|
---|
[315] | 898 | Float norm = 0.0;
|
---|
[165] | 899 | {
|
---|
| 900 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1);
|
---|
| 901 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
[532] | 902 | //
|
---|
| 903 | ReadOnlyVectorIterator<Float>* pItTsysVec = 0;
|
---|
| 904 | if (wtType==TSYS) {
|
---|
| 905 | pItTsysVec = new ReadOnlyVectorIterator<Float>(pItTsysPlane->array(), 1);
|
---|
| 906 | }
|
---|
| 907 | //
|
---|
[165] | 908 | while (!itDataVec.pastEnd()) {
|
---|
| 909 |
|
---|
[315] | 910 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum
|
---|
[165] | 911 |
|
---|
| 912 | if (useMask) {
|
---|
| 913 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector());
|
---|
[532] | 914 | if (wtType==VAR) {
|
---|
| 915 | fac = 1.0 / variance(spec);
|
---|
| 916 | } else if (wtType==TSYS) {
|
---|
| 917 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency
|
---|
| 918 | fac = 1.0 / tSys / tSys;
|
---|
| 919 | }
|
---|
[165] | 920 | } else {
|
---|
| 921 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector());
|
---|
[532] | 922 | if (wtType==VAR) {
|
---|
| 923 | fac = 1.0 / variance(spec);
|
---|
| 924 | } else if (wtType==TSYS) {
|
---|
| 925 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency
|
---|
| 926 | fac = 1.0 / tSys / tSys;
|
---|
| 927 | }
|
---|
[165] | 928 | }
|
---|
| 929 |
|
---|
| 930 | // Normalize spectrum (without OTF mask) and accumulate
|
---|
| 931 |
|
---|
| 932 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector());
|
---|
| 933 | vecSum += spec;
|
---|
[315] | 934 | norm += fac;
|
---|
[165] | 935 |
|
---|
| 936 | // Next
|
---|
| 937 |
|
---|
| 938 | itDataVec.next();
|
---|
| 939 | itMaskVec.next();
|
---|
[532] | 940 | if (wtType==TSYS) pItTsysVec->next();
|
---|
[165] | 941 | }
|
---|
[532] | 942 |
|
---|
| 943 | // Clean up
|
---|
| 944 |
|
---|
| 945 | if (pItTsysVec) {
|
---|
| 946 | delete pItTsysVec;
|
---|
| 947 | pItTsysVec = 0;
|
---|
| 948 | }
|
---|
[165] | 949 | }
|
---|
| 950 |
|
---|
| 951 | // Normalize summed spectrum
|
---|
| 952 |
|
---|
[315] | 953 | vecSum /= norm;
|
---|
[165] | 954 |
|
---|
| 955 | // FInd position in input data array. We are iterating by pol-channel
|
---|
| 956 | // plane so all that will change is beam and IF and that's what we want.
|
---|
| 957 |
|
---|
| 958 | IPosition pos = itDataPlane.pos();
|
---|
| 959 |
|
---|
| 960 | // Write out data. This is a bit messy. We have to reform the Vector
|
---|
| 961 | // accumulator into an Array of shape (1,1,1,nChan)
|
---|
| 962 |
|
---|
| 963 | start = pos;
|
---|
| 964 | end = pos;
|
---|
[262] | 965 | end(asap::ChanAxis) = nChan-1;
|
---|
[165] | 966 | outData(start,end) = vecSum.getArray().reform(vecShapeOut);
|
---|
| 967 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut);
|
---|
| 968 |
|
---|
| 969 | // Step to next beam/IF combination
|
---|
| 970 |
|
---|
| 971 | itDataPlane.next();
|
---|
| 972 | itMaskPlane.next();
|
---|
[532] | 973 | if (wtType==TSYS) pItTsysPlane->next();
|
---|
[165] | 974 | }
|
---|
| 975 |
|
---|
| 976 | // Generate output container and write it to output table
|
---|
| 977 |
|
---|
| 978 | SDContainer sc = in.getSDContainer();
|
---|
| 979 | sc.resize(shapeOut);
|
---|
| 980 | //
|
---|
[185] | 981 | putDataInSDC(sc, outData, outMask);
|
---|
[165] | 982 | pTabOut->putSDContainer(sc);
|
---|
[532] | 983 | //
|
---|
| 984 | if (wtType==TSYS) {
|
---|
| 985 | delete pItTsysPlane;
|
---|
| 986 | pItTsysPlane = 0;
|
---|
| 987 | }
|
---|
[165] | 988 | }
|
---|
[304] | 989 |
|
---|
| 990 | // Set polarization cursor to 0
|
---|
| 991 |
|
---|
| 992 | pTabOut->setPol(0);
|
---|
[165] | 993 | //
|
---|
| 994 | return pTabOut;
|
---|
| 995 | }
|
---|
[167] | 996 |
|
---|
[169] | 997 |
|
---|
[185] | 998 | SDMemTable* SDMath::smooth(const SDMemTable& in,
|
---|
| 999 | const casa::String& kernelType,
|
---|
[234] | 1000 | casa::Float width, Bool doAll) const
|
---|
[299] | 1001 | //
|
---|
| 1002 | // Should smooth TSys as well
|
---|
| 1003 | //
|
---|
[177] | 1004 | {
|
---|
[169] | 1005 |
|
---|
[177] | 1006 | // Number of channels
|
---|
[169] | 1007 |
|
---|
[434] | 1008 | const uInt nChan = in.nChan();
|
---|
[177] | 1009 |
|
---|
| 1010 | // Generate Kernel
|
---|
| 1011 |
|
---|
[185] | 1012 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType);
|
---|
[177] | 1013 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False);
|
---|
| 1014 |
|
---|
| 1015 | // Generate Convolver
|
---|
| 1016 |
|
---|
| 1017 | IPosition shape(1,nChan);
|
---|
| 1018 | Convolver<Float> conv(kernel, shape);
|
---|
| 1019 |
|
---|
| 1020 | // New Table
|
---|
| 1021 |
|
---|
| 1022 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
| 1023 |
|
---|
| 1024 | // Output Vectors
|
---|
| 1025 |
|
---|
[434] | 1026 | Vector<Float> valuesOut(nChan);
|
---|
| 1027 | Vector<Bool> maskOut(nChan);
|
---|
[177] | 1028 |
|
---|
[434] | 1029 | // Get data slice bounds
|
---|
| 1030 |
|
---|
| 1031 | IPosition start, end;
|
---|
| 1032 | setCursorSlice (start, end, doAll, in);
|
---|
| 1033 |
|
---|
[177] | 1034 | // Loop over rows in Table
|
---|
| 1035 |
|
---|
[434] | 1036 | for (uInt ri=0; ri < in.nRow(); ++ri) {
|
---|
[177] | 1037 |
|
---|
[434] | 1038 | // Get slice of data
|
---|
[177] | 1039 |
|
---|
[434] | 1040 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(ri);
|
---|
[177] | 1041 |
|
---|
[434] | 1042 | // Deconstruct and get slices which reference these arrays
|
---|
[177] | 1043 |
|
---|
[434] | 1044 | Array<Float> valuesIn = dataIn.getArray();
|
---|
| 1045 | Array<Bool> maskIn = dataIn.getMask();
|
---|
[177] | 1046 | //
|
---|
[434] | 1047 | Array<Float> valuesIn2 = valuesIn(start,end); // ref to valuesIn
|
---|
| 1048 | Array<Bool> maskIn2 = maskIn(start,end);
|
---|
[177] | 1049 |
|
---|
[434] | 1050 | // Iterate through by spectra
|
---|
[177] | 1051 |
|
---|
[434] | 1052 | VectorIterator<Float> itValues(valuesIn2, asap::ChanAxis);
|
---|
| 1053 | VectorIterator<Bool> itMask(maskIn2, asap::ChanAxis);
|
---|
| 1054 | while (!itValues.pastEnd()) {
|
---|
| 1055 |
|
---|
[177] | 1056 | // Smooth
|
---|
| 1057 |
|
---|
[434] | 1058 | if (kernelType==VectorKernel::HANNING) {
|
---|
| 1059 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector());
|
---|
| 1060 | itMask.vector() = maskOut;
|
---|
| 1061 | } else {
|
---|
| 1062 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector());
|
---|
| 1063 | conv.linearConv(valuesOut, itValues.vector());
|
---|
| 1064 | }
|
---|
| 1065 | //
|
---|
| 1066 | itValues.vector() = valuesOut;
|
---|
| 1067 | //
|
---|
| 1068 | itValues.next();
|
---|
| 1069 | itMask.next();
|
---|
| 1070 | }
|
---|
[177] | 1071 |
|
---|
| 1072 | // Create and put back
|
---|
| 1073 |
|
---|
[434] | 1074 | SDContainer sc = in.getSDContainer(ri);
|
---|
| 1075 | putDataInSDC(sc, valuesIn, maskIn);
|
---|
[177] | 1076 | //
|
---|
[434] | 1077 | pTabOut->putSDContainer(sc);
|
---|
| 1078 | }
|
---|
[177] | 1079 | //
|
---|
| 1080 | return pTabOut;
|
---|
| 1081 | }
|
---|
| 1082 |
|
---|
| 1083 |
|
---|
[262] | 1084 |
|
---|
[488] | 1085 | SDMemTable* SDMath::convertFlux(const SDMemTable& in, Float D, Float etaAp,
|
---|
| 1086 | Float JyPerK, Bool doAll) const
|
---|
[221] | 1087 | //
|
---|
[478] | 1088 | // etaAp = aperture efficiency (-1 means find)
|
---|
| 1089 | // D = geometric diameter (m) (-1 means find)
|
---|
[354] | 1090 | // JyPerK
|
---|
[221] | 1091 | //
|
---|
| 1092 | {
|
---|
| 1093 | SDHeader sh = in.getSDHeader();
|
---|
| 1094 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
[177] | 1095 |
|
---|
[354] | 1096 | // Find out how to convert values into Jy and K (e.g. units might be mJy or mK)
|
---|
[221] | 1097 | // Also automatically find out what we are converting to according to the
|
---|
| 1098 | // flux unit
|
---|
[177] | 1099 |
|
---|
[221] | 1100 | Unit fluxUnit(sh.fluxunit);
|
---|
| 1101 | Unit K(String("K"));
|
---|
| 1102 | Unit JY(String("Jy"));
|
---|
| 1103 | //
|
---|
| 1104 | Bool toKelvin = True;
|
---|
[354] | 1105 | Double cFac = 1.0;
|
---|
[221] | 1106 | if (fluxUnit==JY) {
|
---|
[414] | 1107 | cout << "Converting to K" << endl;
|
---|
[221] | 1108 | //
|
---|
| 1109 | Quantum<Double> t(1.0,fluxUnit);
|
---|
| 1110 | Quantum<Double> t2 = t.get(JY);
|
---|
[354] | 1111 | cFac = (t2 / t).getValue(); // value to Jy
|
---|
[221] | 1112 | //
|
---|
| 1113 | toKelvin = True;
|
---|
| 1114 | sh.fluxunit = "K";
|
---|
| 1115 | } else if (fluxUnit==K) {
|
---|
[414] | 1116 | cout << "Converting to Jy" << endl;
|
---|
[221] | 1117 | //
|
---|
| 1118 | Quantum<Double> t(1.0,fluxUnit);
|
---|
| 1119 | Quantum<Double> t2 = t.get(K);
|
---|
[354] | 1120 | cFac = (t2 / t).getValue(); // value to K
|
---|
[221] | 1121 | //
|
---|
| 1122 | toKelvin = False;
|
---|
| 1123 | sh.fluxunit = "Jy";
|
---|
| 1124 | } else {
|
---|
[248] | 1125 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
|
---|
[221] | 1126 | }
|
---|
| 1127 | pTabOut->putSDHeader(sh);
|
---|
[177] | 1128 |
|
---|
[354] | 1129 | // Make sure input values are converted to either Jy or K first...
|
---|
[221] | 1130 |
|
---|
[354] | 1131 | Float factor = cFac;
|
---|
[221] | 1132 |
|
---|
[354] | 1133 | // Select method
|
---|
[221] | 1134 |
|
---|
[354] | 1135 | if (JyPerK>0.0) {
|
---|
| 1136 | factor *= JyPerK;
|
---|
| 1137 | if (toKelvin) factor = 1.0 / JyPerK;
|
---|
| 1138 | //
|
---|
[478] | 1139 | cout << "Jy/K = " << JyPerK << endl;
|
---|
[354] | 1140 | Vector<Float> factors(in.nRow(), factor);
|
---|
[480] | 1141 | scaleByVector(pTabOut, in, doAll, factors, False);
|
---|
[354] | 1142 | } else if (etaAp>0.0) {
|
---|
[478] | 1143 | Bool throwIt = True;
|
---|
| 1144 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt);
|
---|
| 1145 | SDAttr sda;
|
---|
| 1146 | if (D < 0) D = sda.diameter(inst);
|
---|
| 1147 | Float JyPerK = SDAttr::findJyPerK (etaAp,D);
|
---|
| 1148 | cout << "Jy/K = " << JyPerK << endl;
|
---|
| 1149 | factor *= JyPerK;
|
---|
[354] | 1150 | if (toKelvin) {
|
---|
| 1151 | factor = 1.0 / factor;
|
---|
| 1152 | }
|
---|
| 1153 | //
|
---|
| 1154 | Vector<Float> factors(in.nRow(), factor);
|
---|
[480] | 1155 | scaleByVector(pTabOut, in, doAll, factors, False);
|
---|
[354] | 1156 | } else {
|
---|
[221] | 1157 |
|
---|
[354] | 1158 | // OK now we must deal with automatic look up of values.
|
---|
| 1159 | // We must also deal with the fact that the factors need
|
---|
| 1160 | // to be computed per IF and may be different and may
|
---|
| 1161 | // change per integration.
|
---|
[221] | 1162 |
|
---|
[414] | 1163 | cout << "Looking up conversion factors" << endl;
|
---|
[354] | 1164 | convertBrightnessUnits (pTabOut, in, toKelvin, cFac, doAll);
|
---|
| 1165 | }
|
---|
[221] | 1166 | //
|
---|
| 1167 | return pTabOut;
|
---|
| 1168 | }
|
---|
| 1169 |
|
---|
| 1170 |
|
---|
[354] | 1171 |
|
---|
| 1172 |
|
---|
| 1173 |
|
---|
[488] | 1174 | SDMemTable* SDMath::gainElevation(const SDMemTable& in,
|
---|
| 1175 | const Vector<Float>& coeffs,
|
---|
| 1176 | const String& fileName,
|
---|
| 1177 | const String& methodStr, Bool doAll) const
|
---|
[227] | 1178 | {
|
---|
[234] | 1179 |
|
---|
| 1180 | // Get header and clone output table
|
---|
| 1181 |
|
---|
[227] | 1182 | SDHeader sh = in.getSDHeader();
|
---|
| 1183 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
| 1184 |
|
---|
[234] | 1185 | // Get elevation data from SDMemTable and convert to degrees
|
---|
[227] | 1186 |
|
---|
| 1187 | const Table& tab = in.table();
|
---|
| 1188 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
[234] | 1189 | Vector<Float> x = elev.getColumn();
|
---|
[363] | 1190 | x *= Float(180 / C::pi); // Degrees
|
---|
[227] | 1191 | //
|
---|
[234] | 1192 | const uInt nC = coeffs.nelements();
|
---|
| 1193 | if (fileName.length()>0 && nC>0) {
|
---|
[248] | 1194 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
|
---|
[234] | 1195 | }
|
---|
| 1196 |
|
---|
| 1197 | // Correct
|
---|
| 1198 |
|
---|
| 1199 | if (nC>0 || fileName.length()==0) {
|
---|
| 1200 |
|
---|
| 1201 | // Find instrument
|
---|
| 1202 |
|
---|
| 1203 | Bool throwIt = True;
|
---|
[478] | 1204 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt);
|
---|
[234] | 1205 |
|
---|
| 1206 | // Set polynomial
|
---|
| 1207 |
|
---|
| 1208 | Polynomial<Float>* pPoly = 0;
|
---|
| 1209 | Vector<Float> coeff;
|
---|
| 1210 | String msg;
|
---|
| 1211 | if (nC>0) {
|
---|
| 1212 | pPoly = new Polynomial<Float>(nC);
|
---|
| 1213 | coeff = coeffs;
|
---|
| 1214 | msg = String("user");
|
---|
| 1215 | } else {
|
---|
[363] | 1216 | SDAttr sdAttr;
|
---|
| 1217 | coeff = sdAttr.gainElevationPoly(inst);
|
---|
| 1218 | pPoly = new Polynomial<Float>(3);
|
---|
[234] | 1219 | msg = String("built in");
|
---|
| 1220 | }
|
---|
[227] | 1221 | //
|
---|
[234] | 1222 | if (coeff.nelements()>0) {
|
---|
| 1223 | pPoly->setCoefficients(coeff);
|
---|
| 1224 | } else {
|
---|
[363] | 1225 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
|
---|
[234] | 1226 | }
|
---|
| 1227 | //
|
---|
[414] | 1228 | cout << "Making polynomial correction with " << msg << " coefficients" << endl;
|
---|
[234] | 1229 | const uInt nRow = in.nRow();
|
---|
| 1230 | Vector<Float> factor(nRow);
|
---|
| 1231 | for (uInt i=0; i<nRow; i++) {
|
---|
[480] | 1232 | factor[i] = 1.0 / (*pPoly)(x[i]);
|
---|
[234] | 1233 | }
|
---|
| 1234 | delete pPoly;
|
---|
| 1235 | //
|
---|
[480] | 1236 | scaleByVector (pTabOut, in, doAll, factor, True);
|
---|
[234] | 1237 | } else {
|
---|
| 1238 |
|
---|
| 1239 | // Indicate which columns to read from ascii file
|
---|
| 1240 |
|
---|
| 1241 | String col0("ELEVATION");
|
---|
| 1242 | String col1("FACTOR");
|
---|
| 1243 |
|
---|
| 1244 | // Read and correct
|
---|
| 1245 |
|
---|
[414] | 1246 | cout << "Making correction from ascii Table" << endl;
|
---|
[480] | 1247 | scaleFromAsciiTable (pTabOut, in, fileName, col0, col1,
|
---|
| 1248 | methodStr, doAll, x, True);
|
---|
[234] | 1249 | }
|
---|
| 1250 | //
|
---|
| 1251 | return pTabOut;
|
---|
[230] | 1252 | }
|
---|
[227] | 1253 |
|
---|
[230] | 1254 |
|
---|
[227] | 1255 |
|
---|
[488] | 1256 | SDMemTable* SDMath::opacity(const SDMemTable& in, Float tau, Bool doAll) const
|
---|
[234] | 1257 | {
|
---|
[227] | 1258 |
|
---|
[234] | 1259 | // Get header and clone output table
|
---|
[227] | 1260 |
|
---|
[234] | 1261 | SDHeader sh = in.getSDHeader();
|
---|
| 1262 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
| 1263 |
|
---|
| 1264 | // Get elevation data from SDMemTable and convert to degrees
|
---|
| 1265 |
|
---|
| 1266 | const Table& tab = in.table();
|
---|
| 1267 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
| 1268 | Vector<Float> zDist = elev.getColumn();
|
---|
| 1269 | zDist = Float(C::pi_2) - zDist;
|
---|
| 1270 |
|
---|
| 1271 | // Generate correction factor
|
---|
| 1272 |
|
---|
| 1273 | const uInt nRow = in.nRow();
|
---|
| 1274 | Vector<Float> factor(nRow);
|
---|
| 1275 | Vector<Float> factor2(nRow);
|
---|
| 1276 | for (uInt i=0; i<nRow; i++) {
|
---|
| 1277 | factor[i] = exp(tau)/cos(zDist[i]);
|
---|
| 1278 | }
|
---|
| 1279 |
|
---|
| 1280 | // Correct
|
---|
| 1281 |
|
---|
[480] | 1282 | scaleByVector (pTabOut, in, doAll, factor, True);
|
---|
[234] | 1283 | //
|
---|
| 1284 | return pTabOut;
|
---|
| 1285 | }
|
---|
| 1286 |
|
---|
| 1287 |
|
---|
[488] | 1288 | void SDMath::rotateXYPhase(SDMemTable& in, Float value, Bool doAll)
|
---|
[457] | 1289 | //
|
---|
| 1290 | // phase in degrees
|
---|
[518] | 1291 | // assumes linear correlations
|
---|
[457] | 1292 | //
|
---|
| 1293 | {
|
---|
| 1294 | if (in.nPol() != 4) {
|
---|
| 1295 | throw(AipsError("You must have 4 polarizations to run this function"));
|
---|
| 1296 | }
|
---|
[518] | 1297 | //
|
---|
| 1298 | SDHeader sh = in.getSDHeader();
|
---|
| 1299 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False);
|
---|
| 1300 | SDAttr sdAtt;
|
---|
| 1301 | if (sdAtt.feedPolType(inst) != LINEAR) {
|
---|
| 1302 | throw(AipsError("Only linear polarizations are supported"));
|
---|
| 1303 | }
|
---|
[457] | 1304 | //
|
---|
| 1305 | const Table& tabIn = in.table();
|
---|
| 1306 | ArrayColumn<Float> specCol(tabIn,"SPECTRA");
|
---|
| 1307 | IPosition start(asap::nAxes,0);
|
---|
| 1308 | IPosition end(asap::nAxes);
|
---|
[234] | 1309 |
|
---|
[457] | 1310 | // Set cursor slice. Assumes shape the same for all rows
|
---|
| 1311 |
|
---|
| 1312 | setCursorSlice (start, end, doAll, in);
|
---|
| 1313 | IPosition start3(start);
|
---|
| 1314 | start3(asap::PolAxis) = 2; // Real(XY)
|
---|
| 1315 | IPosition end3(end);
|
---|
| 1316 | end3(asap::PolAxis) = 2;
|
---|
| 1317 | //
|
---|
| 1318 | IPosition start4(start);
|
---|
| 1319 | start4(asap::PolAxis) = 3; // Imag (XY)
|
---|
| 1320 | IPosition end4(end);
|
---|
| 1321 | end4(asap::PolAxis) = 3;
|
---|
| 1322 | //
|
---|
| 1323 | uInt nRow = in.nRow();
|
---|
| 1324 | Array<Float> data;
|
---|
| 1325 | for (uInt i=0; i<nRow;++i) {
|
---|
| 1326 | specCol.get(i,data);
|
---|
| 1327 | IPosition shape = data.shape();
|
---|
| 1328 |
|
---|
| 1329 | // Get polarization slice references
|
---|
| 1330 |
|
---|
| 1331 | Array<Float> C3 = data(start3,end3);
|
---|
| 1332 | Array<Float> C4 = data(start4,end4);
|
---|
| 1333 |
|
---|
| 1334 | // Rotate
|
---|
| 1335 |
|
---|
[502] | 1336 | SDPolUtil::rotatePhase(C3, C4, value);
|
---|
[457] | 1337 |
|
---|
| 1338 | // Put
|
---|
| 1339 |
|
---|
| 1340 | specCol.put(i,data);
|
---|
| 1341 | }
|
---|
| 1342 | }
|
---|
[234] | 1343 |
|
---|
[502] | 1344 |
|
---|
| 1345 |
|
---|
| 1346 | void SDMath::rotateLinPolPhase(SDMemTable& in, Float value, Bool doAll)
|
---|
| 1347 | //
|
---|
| 1348 | // phase in degrees
|
---|
[518] | 1349 | // assumes linear correlations
|
---|
[502] | 1350 | //
|
---|
| 1351 | {
|
---|
| 1352 | if (in.nPol() != 4) {
|
---|
| 1353 | throw(AipsError("You must have 4 polarizations to run this function"));
|
---|
| 1354 | }
|
---|
[518] | 1355 | //
|
---|
| 1356 | SDHeader sh = in.getSDHeader();
|
---|
| 1357 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False);
|
---|
| 1358 | SDAttr sdAtt;
|
---|
| 1359 | if (sdAtt.feedPolType(inst) != LINEAR) {
|
---|
| 1360 | throw(AipsError("Only linear polarizations are supported"));
|
---|
| 1361 | }
|
---|
[502] | 1362 | //
|
---|
| 1363 | const Table& tabIn = in.table();
|
---|
| 1364 | ArrayColumn<Float> specCol(tabIn,"SPECTRA");
|
---|
| 1365 | ROArrayColumn<Float> stokesCol(tabIn,"STOKES");
|
---|
| 1366 | IPosition start(asap::nAxes,0);
|
---|
| 1367 | IPosition end(asap::nAxes);
|
---|
| 1368 |
|
---|
| 1369 | // Set cursor slice. Assumes shape the same for all rows
|
---|
| 1370 |
|
---|
| 1371 | setCursorSlice (start, end, doAll, in);
|
---|
| 1372 | //
|
---|
| 1373 | IPosition start1(start);
|
---|
| 1374 | start1(asap::PolAxis) = 0; // C1 (XX)
|
---|
| 1375 | IPosition end1(end);
|
---|
| 1376 | end1(asap::PolAxis) = 0;
|
---|
| 1377 | //
|
---|
| 1378 | IPosition start2(start);
|
---|
| 1379 | start2(asap::PolAxis) = 1; // C2 (YY)
|
---|
| 1380 | IPosition end2(end);
|
---|
| 1381 | end2(asap::PolAxis) = 1;
|
---|
| 1382 | //
|
---|
| 1383 | IPosition start3(start);
|
---|
| 1384 | start3(asap::PolAxis) = 2; // C3 ( Real(XY) )
|
---|
| 1385 | IPosition end3(end);
|
---|
| 1386 | end3(asap::PolAxis) = 2;
|
---|
| 1387 | //
|
---|
| 1388 | IPosition startI(start);
|
---|
| 1389 | startI(asap::PolAxis) = 0; // I
|
---|
| 1390 | IPosition endI(end);
|
---|
| 1391 | endI(asap::PolAxis) = 0;
|
---|
| 1392 | //
|
---|
| 1393 | IPosition startQ(start);
|
---|
| 1394 | startQ(asap::PolAxis) = 1; // Q
|
---|
| 1395 | IPosition endQ(end);
|
---|
| 1396 | endQ(asap::PolAxis) = 1;
|
---|
| 1397 | //
|
---|
| 1398 | IPosition startU(start);
|
---|
| 1399 | startU(asap::PolAxis) = 2; // U
|
---|
| 1400 | IPosition endU(end);
|
---|
| 1401 | endU(asap::PolAxis) = 2;
|
---|
| 1402 |
|
---|
| 1403 | //
|
---|
| 1404 | uInt nRow = in.nRow();
|
---|
| 1405 | Array<Float> data, stokes;
|
---|
| 1406 | for (uInt i=0; i<nRow;++i) {
|
---|
| 1407 | specCol.get(i,data);
|
---|
| 1408 | stokesCol.get(i,stokes);
|
---|
| 1409 | IPosition shape = data.shape();
|
---|
| 1410 |
|
---|
| 1411 | // Get linear polarization slice references
|
---|
| 1412 |
|
---|
| 1413 | Array<Float> C1 = data(start1,end1);
|
---|
| 1414 | Array<Float> C2 = data(start2,end2);
|
---|
| 1415 | Array<Float> C3 = data(start3,end3);
|
---|
| 1416 |
|
---|
| 1417 | // Get STokes slice references
|
---|
| 1418 |
|
---|
| 1419 | Array<Float> I = stokes(startI,endI);
|
---|
| 1420 | Array<Float> Q = stokes(startQ,endQ);
|
---|
| 1421 | Array<Float> U = stokes(startU,endU);
|
---|
| 1422 |
|
---|
| 1423 | // Rotate
|
---|
| 1424 |
|
---|
| 1425 | SDPolUtil::rotateLinPolPhase(C1, C2, C3, I, Q, U, value);
|
---|
| 1426 |
|
---|
| 1427 | // Put
|
---|
| 1428 |
|
---|
| 1429 | specCol.put(i,data);
|
---|
| 1430 | }
|
---|
| 1431 | }
|
---|
| 1432 |
|
---|
[169] | 1433 | // 'private' functions
|
---|
| 1434 |
|
---|
[354] | 1435 | void SDMath::convertBrightnessUnits (SDMemTable* pTabOut, const SDMemTable& in,
|
---|
| 1436 | Bool toKelvin, Float cFac, Bool doAll) const
|
---|
| 1437 | {
|
---|
[309] | 1438 |
|
---|
[354] | 1439 | // Get header
|
---|
| 1440 |
|
---|
| 1441 | SDHeader sh = in.getSDHeader();
|
---|
| 1442 | const uInt nChan = sh.nchan;
|
---|
| 1443 |
|
---|
| 1444 | // Get instrument
|
---|
| 1445 |
|
---|
| 1446 | Bool throwIt = True;
|
---|
[478] | 1447 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt);
|
---|
[354] | 1448 |
|
---|
| 1449 | // Get Diameter (m)
|
---|
| 1450 |
|
---|
| 1451 | SDAttr sdAtt;
|
---|
| 1452 |
|
---|
| 1453 | // Get epoch of first row
|
---|
| 1454 |
|
---|
| 1455 | MEpoch dateObs = in.getEpoch(0);
|
---|
| 1456 |
|
---|
| 1457 | // Generate a Vector of correction factors. One per FreqID
|
---|
| 1458 |
|
---|
| 1459 | SDFrequencyTable sdft = in.getSDFreqTable();
|
---|
| 1460 | Vector<uInt> freqIDs;
|
---|
| 1461 | //
|
---|
| 1462 | Vector<Float> freqs(sdft.length());
|
---|
| 1463 | for (uInt i=0; i<sdft.length(); i++) {
|
---|
| 1464 | freqs(i) = (nChan/2 - sdft.referencePixel(i))*sdft.increment(i) + sdft.referenceValue(i);
|
---|
| 1465 | }
|
---|
| 1466 | //
|
---|
| 1467 | Vector<Float> JyPerK = sdAtt.JyPerK(inst, dateObs, freqs);
|
---|
[414] | 1468 | cout << "Jy/K = " << JyPerK << endl;
|
---|
[354] | 1469 | Vector<Float> factors = cFac * JyPerK;
|
---|
| 1470 | if (toKelvin) factors = Float(1.0) / factors;
|
---|
| 1471 |
|
---|
[434] | 1472 | // Get data slice bounds
|
---|
[354] | 1473 |
|
---|
| 1474 | IPosition start, end;
|
---|
[434] | 1475 | setCursorSlice (start, end, doAll, in);
|
---|
[354] | 1476 | const uInt ifAxis = in.getIF();
|
---|
| 1477 |
|
---|
| 1478 | // Iteration axes
|
---|
| 1479 |
|
---|
| 1480 | IPosition axes(asap::nAxes-1,0);
|
---|
| 1481 | for (uInt i=0,j=0; i<asap::nAxes; i++) {
|
---|
| 1482 | if (i!=asap::IFAxis) {
|
---|
| 1483 | axes(j++) = i;
|
---|
| 1484 | }
|
---|
| 1485 | }
|
---|
| 1486 |
|
---|
| 1487 | // Loop over rows and apply correction factor
|
---|
| 1488 |
|
---|
| 1489 | Float factor = 1.0;
|
---|
| 1490 | const uInt axis = asap::ChanAxis;
|
---|
| 1491 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
| 1492 |
|
---|
| 1493 | // Get data
|
---|
| 1494 |
|
---|
[434] | 1495 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(i);
|
---|
| 1496 | Array<Float>& values = dataIn.getRWArray(); // Ref to dataIn
|
---|
| 1497 | Array<Float> values2 = values(start,end); // Ref to values to dataIn
|
---|
[354] | 1498 |
|
---|
| 1499 | // Get SDCOntainer
|
---|
| 1500 |
|
---|
| 1501 | SDContainer sc = in.getSDContainer(i);
|
---|
| 1502 |
|
---|
| 1503 | // Get FreqIDs
|
---|
| 1504 |
|
---|
| 1505 | freqIDs = sc.getFreqMap();
|
---|
| 1506 |
|
---|
| 1507 | // Now the conversion factor depends only upon frequency
|
---|
| 1508 | // So we need to iterate through by IF only giving
|
---|
| 1509 | // us BEAM/POL/CHAN cubes
|
---|
| 1510 |
|
---|
[434] | 1511 | ArrayIterator<Float> itIn(values2, axes);
|
---|
| 1512 | uInt ax = 0;
|
---|
| 1513 | while (!itIn.pastEnd()) {
|
---|
| 1514 | itIn.array() *= factors(freqIDs(ax)); // Writes back to dataIn
|
---|
| 1515 | itIn.next();
|
---|
[354] | 1516 | }
|
---|
| 1517 |
|
---|
| 1518 | // Write out
|
---|
| 1519 |
|
---|
| 1520 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask());
|
---|
| 1521 | //
|
---|
| 1522 | pTabOut->putSDContainer(sc);
|
---|
| 1523 | }
|
---|
| 1524 | }
|
---|
| 1525 |
|
---|
| 1526 |
|
---|
| 1527 |
|
---|
[309] | 1528 | SDMemTable* SDMath::frequencyAlign (const SDMemTable& in,
|
---|
| 1529 | MFrequency::Types freqSystem,
|
---|
[397] | 1530 | const String& refTime,
|
---|
| 1531 | const String& methodStr,
|
---|
| 1532 | Bool perFreqID) const
|
---|
[267] | 1533 | {
|
---|
| 1534 | // Get Header
|
---|
| 1535 |
|
---|
| 1536 | SDHeader sh = in.getSDHeader();
|
---|
| 1537 | const uInt nChan = sh.nchan;
|
---|
| 1538 | const uInt nRows = in.nRow();
|
---|
[330] | 1539 | const uInt nIF = sh.nif;
|
---|
[267] | 1540 |
|
---|
| 1541 | // Get Table reference
|
---|
| 1542 |
|
---|
| 1543 | const Table& tabIn = in.table();
|
---|
| 1544 |
|
---|
| 1545 | // Get Columns from Table
|
---|
| 1546 |
|
---|
[294] | 1547 | ROScalarColumn<Double> mjdCol(tabIn, "TIME");
|
---|
| 1548 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME");
|
---|
| 1549 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID");
|
---|
| 1550 | Vector<Double> times = mjdCol.getColumn();
|
---|
[267] | 1551 |
|
---|
[397] | 1552 | // Generate DataDesc table
|
---|
[330] | 1553 |
|
---|
| 1554 | Matrix<uInt> ddIdx;
|
---|
| 1555 | SDDataDesc dDesc;
|
---|
[397] | 1556 | generateDataDescTable (ddIdx, dDesc, nIF, in, tabIn, srcCol, fqIDCol, perFreqID);
|
---|
[267] | 1557 |
|
---|
[294] | 1558 | // Get reference Epoch to time of first row or given String
|
---|
[267] | 1559 |
|
---|
| 1560 | Unit DAY(String("d"));
|
---|
[272] | 1561 | MEpoch::Ref epochRef(in.getTimeReference());
|
---|
| 1562 | MEpoch refEpoch;
|
---|
| 1563 | if (refTime.length()>0) {
|
---|
| 1564 | refEpoch = epochFromString(refTime, in.getTimeReference());
|
---|
| 1565 | } else {
|
---|
[288] | 1566 | refEpoch = in.getEpoch(0);
|
---|
[272] | 1567 | }
|
---|
[414] | 1568 | cout << "Aligning at reference Epoch " << formatEpoch(refEpoch)
|
---|
| 1569 | << " in frame " << MFrequency::showType(freqSystem) << endl;
|
---|
| 1570 |
|
---|
[294] | 1571 | // Get Reference Position
|
---|
[267] | 1572 |
|
---|
[288] | 1573 | MPosition refPos = in.getAntennaPosition();
|
---|
[267] | 1574 |
|
---|
[397] | 1575 | // Create FrequencyAligner Block. One FA for each possible
|
---|
| 1576 | // source/freqID (perFreqID=True) or source/IF (perFreqID=False) combination
|
---|
[267] | 1577 |
|
---|
[330] | 1578 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length());
|
---|
[397] | 1579 | generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos,
|
---|
| 1580 | refEpoch, perFreqID);
|
---|
[267] | 1581 |
|
---|
[397] | 1582 | // Generate and fill output Frequency Table. WHen perFreqID=True, there is one output FreqID
|
---|
| 1583 | // for each entry in the SDDataDesc table. However, in perFreqID=False mode, there may be
|
---|
| 1584 | // some degeneracy, so we need a little translation map
|
---|
[330] | 1585 |
|
---|
| 1586 | SDFrequencyTable freqTabOut = in.getSDFreqTable();
|
---|
| 1587 | freqTabOut.setLength(0);
|
---|
| 1588 | Vector<String> units(1);
|
---|
| 1589 | units = String("Hz");
|
---|
| 1590 | Bool linear=True;
|
---|
| 1591 | //
|
---|
[397] | 1592 | Vector<uInt> ddFQTrans(dDesc.length(),0);
|
---|
[330] | 1593 | for (uInt i=0; i<dDesc.length(); i++) {
|
---|
| 1594 |
|
---|
| 1595 | // Get Aligned SC in Hz
|
---|
| 1596 |
|
---|
| 1597 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear);
|
---|
| 1598 | sC.setWorldAxisUnits(units);
|
---|
| 1599 |
|
---|
| 1600 | // Add FreqID
|
---|
| 1601 |
|
---|
[397] | 1602 | uInt idx = freqTabOut.addFrequency(sC.referencePixel()[0],
|
---|
| 1603 | sC.referenceValue()[0],
|
---|
| 1604 | sC.increment()[0]);
|
---|
| 1605 | ddFQTrans(i) = idx; // output FreqID = ddFQTrans(ddIdx)
|
---|
[330] | 1606 | }
|
---|
| 1607 |
|
---|
[317] | 1608 | // Interpolation method
|
---|
| 1609 |
|
---|
| 1610 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
---|
| 1611 | convertInterpString(interp, methodStr);
|
---|
| 1612 |
|
---|
[267] | 1613 | // New output Table
|
---|
| 1614 |
|
---|
[414] | 1615 | cout << "Create output table" << endl;
|
---|
[267] | 1616 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
[330] | 1617 | pTabOut->putSDFreqTable(freqTabOut);
|
---|
[267] | 1618 |
|
---|
| 1619 | // Loop over rows in Table
|
---|
| 1620 |
|
---|
[330] | 1621 | Bool extrapolate=False;
|
---|
[294] | 1622 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis);
|
---|
| 1623 | Bool useCachedAbcissa = False;
|
---|
| 1624 | Bool first = True;
|
---|
| 1625 | Bool ok;
|
---|
| 1626 | Vector<Float> yOut;
|
---|
| 1627 | Vector<Bool> maskOut;
|
---|
[330] | 1628 | Vector<uInt> freqID(nIF);
|
---|
[309] | 1629 | uInt ifIdx, faIdx;
|
---|
[397] | 1630 | Vector<Double> xIn;
|
---|
[267] | 1631 | //
|
---|
[294] | 1632 | for (uInt iRow=0; iRow<nRows; ++iRow) {
|
---|
| 1633 | if (iRow%10==0) {
|
---|
[414] | 1634 | cout << "Processing row " << iRow << endl;
|
---|
[294] | 1635 | }
|
---|
[267] | 1636 |
|
---|
| 1637 | // Get EPoch
|
---|
| 1638 |
|
---|
[294] | 1639 | Quantum<Double> tQ2(times[iRow],DAY);
|
---|
| 1640 | MVEpoch mv2(tQ2);
|
---|
| 1641 | MEpoch epoch(mv2, epochRef);
|
---|
[267] | 1642 |
|
---|
| 1643 | // Get copy of data
|
---|
| 1644 |
|
---|
[294] | 1645 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow));
|
---|
| 1646 | Array<Float> values = mArrIn.getArray();
|
---|
| 1647 | Array<Bool> mask = mArrIn.getMask();
|
---|
[267] | 1648 |
|
---|
[309] | 1649 | // For each row, the Frequency abcissa will be the same regardless
|
---|
[267] | 1650 | // of polarization. For all other axes (IF and BEAM) the abcissa
|
---|
| 1651 | // will change. So we iterate through the data by pol-chan planes
|
---|
[330] | 1652 | // to mimimize the work. Probably won't work for multiple beams
|
---|
| 1653 | // at this point.
|
---|
[267] | 1654 |
|
---|
[294] | 1655 | ArrayIterator<Float> itValuesPlane(values, polChanAxes);
|
---|
| 1656 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes);
|
---|
| 1657 | while (!itValuesPlane.pastEnd()) {
|
---|
[267] | 1658 |
|
---|
[309] | 1659 | // Find the IF index and then the FA PtrBlock index
|
---|
[267] | 1660 |
|
---|
[294] | 1661 | const IPosition& pos = itValuesPlane.pos();
|
---|
| 1662 | ifIdx = pos(asap::IFAxis);
|
---|
[330] | 1663 | faIdx = ddIdx(iRow,ifIdx);
|
---|
[397] | 1664 |
|
---|
| 1665 | // Generate abcissa for perIF. Could cache this in a Matrix
|
---|
| 1666 | // on a per scan basis. Pretty expensive doing it for every row.
|
---|
| 1667 |
|
---|
| 1668 | if (!perFreqID) {
|
---|
| 1669 | xIn.resize(nChan);
|
---|
| 1670 | uInt fqID = dDesc.secID(ddIdx(iRow,ifIdx));
|
---|
| 1671 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID);
|
---|
| 1672 | Double w;
|
---|
| 1673 | for (uInt i=0; i<nChan; i++) {
|
---|
| 1674 | sC.toWorld(w,Double(i));
|
---|
| 1675 | xIn[i] = w;
|
---|
| 1676 | }
|
---|
| 1677 | }
|
---|
[267] | 1678 | //
|
---|
[294] | 1679 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1);
|
---|
| 1680 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
[330] | 1681 |
|
---|
| 1682 | // Iterate through the plane by vector and align
|
---|
| 1683 |
|
---|
[294] | 1684 | first = True;
|
---|
| 1685 | useCachedAbcissa=False;
|
---|
| 1686 | while (!itValuesVec.pastEnd()) {
|
---|
[397] | 1687 | if (perFreqID) {
|
---|
| 1688 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(),
|
---|
| 1689 | itMaskVec.vector(), epoch, useCachedAbcissa,
|
---|
| 1690 | interp, extrapolate);
|
---|
| 1691 | } else {
|
---|
| 1692 | ok = a[faIdx]->align (yOut, maskOut, xIn, itValuesVec.vector(),
|
---|
| 1693 | itMaskVec.vector(), epoch, useCachedAbcissa,
|
---|
| 1694 | interp, extrapolate);
|
---|
| 1695 | }
|
---|
[330] | 1696 | //
|
---|
[294] | 1697 | itValuesVec.vector() = yOut;
|
---|
| 1698 | itMaskVec.vector() = maskOut;
|
---|
[267] | 1699 | //
|
---|
[294] | 1700 | itValuesVec.next();
|
---|
| 1701 | itMaskVec.next();
|
---|
[267] | 1702 | //
|
---|
[294] | 1703 | if (first) {
|
---|
| 1704 | useCachedAbcissa = True;
|
---|
| 1705 | first = False;
|
---|
| 1706 | }
|
---|
| 1707 | }
|
---|
[267] | 1708 | //
|
---|
| 1709 | itValuesPlane.next();
|
---|
| 1710 | itMaskPlane.next();
|
---|
[294] | 1711 | }
|
---|
[267] | 1712 |
|
---|
[330] | 1713 | // Create SDContainer and put back
|
---|
[267] | 1714 |
|
---|
| 1715 | SDContainer sc = in.getSDContainer(iRow);
|
---|
| 1716 | putDataInSDC(sc, values, mask);
|
---|
[397] | 1717 |
|
---|
| 1718 | // Set output FreqIDs
|
---|
| 1719 |
|
---|
[330] | 1720 | for (uInt i=0; i<nIF; i++) {
|
---|
[397] | 1721 | uInt idx = ddIdx(iRow,i); // Index into SDDataDesc table
|
---|
| 1722 | freqID(i) = ddFQTrans(idx); // FreqID in output FQ table
|
---|
[330] | 1723 | }
|
---|
| 1724 | sc.putFreqMap(freqID);
|
---|
[267] | 1725 | //
|
---|
| 1726 | pTabOut->putSDContainer(sc);
|
---|
[294] | 1727 | }
|
---|
[267] | 1728 |
|
---|
[309] | 1729 | // Now we must set the base and extra frames to the
|
---|
| 1730 | // input frame
|
---|
| 1731 |
|
---|
| 1732 | std::vector<string> info = pTabOut->getCoordInfo();
|
---|
| 1733 | info[1] = MFrequency::showType(freqSystem); // Conversion frame
|
---|
| 1734 | info[3] = info[1]; // Base frame
|
---|
| 1735 | pTabOut->setCoordInfo(info);
|
---|
| 1736 |
|
---|
[267] | 1737 | // Clean up PointerBlock
|
---|
| 1738 |
|
---|
[309] | 1739 | for (uInt i=0; i<a.nelements(); i++) delete a[i];
|
---|
[267] | 1740 | //
|
---|
[309] | 1741 | return pTabOut;
|
---|
[267] | 1742 | }
|
---|
| 1743 |
|
---|
| 1744 |
|
---|
[185] | 1745 | void SDMath::fillSDC(SDContainer& sc,
|
---|
| 1746 | const Array<Bool>& mask,
|
---|
| 1747 | const Array<Float>& data,
|
---|
| 1748 | const Array<Float>& tSys,
|
---|
| 1749 | Int scanID, Double timeStamp,
|
---|
| 1750 | Double interval, const String& sourceName,
|
---|
[227] | 1751 | const Vector<uInt>& freqID) const
|
---|
[167] | 1752 | {
|
---|
[169] | 1753 | // Data and mask
|
---|
[167] | 1754 |
|
---|
[185] | 1755 | putDataInSDC(sc, data, mask);
|
---|
[167] | 1756 |
|
---|
[169] | 1757 | // TSys
|
---|
| 1758 |
|
---|
| 1759 | sc.putTsys(tSys);
|
---|
| 1760 |
|
---|
| 1761 | // Time things
|
---|
| 1762 |
|
---|
| 1763 | sc.timestamp = timeStamp;
|
---|
| 1764 | sc.interval = interval;
|
---|
| 1765 | sc.scanid = scanID;
|
---|
[167] | 1766 | //
|
---|
[169] | 1767 | sc.sourcename = sourceName;
|
---|
| 1768 | sc.putFreqMap(freqID);
|
---|
| 1769 | }
|
---|
[167] | 1770 |
|
---|
[185] | 1771 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum,
|
---|
| 1772 | MaskedArray<Float>& sum, Array<Float>& sumSq,
|
---|
| 1773 | Array<Float>& nPts, Array<Float>& tSysSum,
|
---|
[518] | 1774 | Array<Float>& tSysSqSum,
|
---|
[185] | 1775 | const Array<Float>& tSys, const Array<Float>& nInc,
|
---|
| 1776 | const Vector<Bool>& mask, Double time, Double interval,
|
---|
| 1777 | const Block<CountedPtr<SDMemTable> >& in,
|
---|
| 1778 | uInt iTab, uInt iRow, uInt axis,
|
---|
| 1779 | uInt nAxesSub, Bool useMask,
|
---|
[227] | 1780 | WeightType wtType) const
|
---|
[169] | 1781 | {
|
---|
| 1782 |
|
---|
| 1783 | // Get data
|
---|
| 1784 |
|
---|
| 1785 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow));
|
---|
| 1786 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference
|
---|
| 1787 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference
|
---|
[167] | 1788 | //
|
---|
[169] | 1789 | if (wtType==NONE) {
|
---|
| 1790 | const MaskedArray<Float> n(nInc,dataIn.getMask());
|
---|
| 1791 | nPts += n; // Only accumulates where mask==T
|
---|
[518] | 1792 | } else if (wtType==TINT) {
|
---|
| 1793 |
|
---|
| 1794 | // We are weighting the data by integration time.
|
---|
| 1795 |
|
---|
| 1796 | valuesIn *= Float(interval);
|
---|
| 1797 |
|
---|
[169] | 1798 | } else if (wtType==VAR) {
|
---|
[167] | 1799 |
|
---|
[169] | 1800 | // We are going to average the data, weighted by the noise for each pol, beam and IF.
|
---|
| 1801 | // So therefore we need to iterate through by spectrum (axis 3)
|
---|
[167] | 1802 |
|
---|
[169] | 1803 | VectorIterator<Float> itData(valuesIn, axis);
|
---|
| 1804 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis);
|
---|
| 1805 | Float fac = 1.0;
|
---|
| 1806 | IPosition pos(nAxesSub,0);
|
---|
| 1807 | //
|
---|
| 1808 | while (!itData.pastEnd()) {
|
---|
[167] | 1809 |
|
---|
[169] | 1810 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor
|
---|
[167] | 1811 |
|
---|
[518] | 1812 | if (useMask) {
|
---|
| 1813 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector());
|
---|
| 1814 | fac = 1.0/variance(tmp);
|
---|
| 1815 | } else {
|
---|
| 1816 | MaskedArray<Float> tmp(itData.vector(),itMask.vector());
|
---|
| 1817 | fac = 1.0/variance(tmp);
|
---|
| 1818 | }
|
---|
[169] | 1819 |
|
---|
| 1820 | // Scale data
|
---|
| 1821 |
|
---|
[518] | 1822 | itData.vector() *= fac; // Writes back into 'dataIn'
|
---|
[167] | 1823 | //
|
---|
[169] | 1824 | // Accumulate variance per if/pol/beam averaged over spectrum
|
---|
| 1825 | // This method to get pos2 from itData.pos() is only valid
|
---|
| 1826 | // because the spectral axis is the last one (so we can just
|
---|
| 1827 | // copy the first nAXesSub positions out)
|
---|
[167] | 1828 |
|
---|
[518] | 1829 | pos = itData.pos().getFirst(nAxesSub);
|
---|
| 1830 | sumSq(pos) += fac;
|
---|
[169] | 1831 | //
|
---|
[518] | 1832 | itData.next();
|
---|
| 1833 | itMask.next();
|
---|
[169] | 1834 | }
|
---|
| 1835 | } else if (wtType==TSYS) {
|
---|
[518] | 1836 |
|
---|
| 1837 | // We are going to average the data, weighted by 1/Tsys**2 for each pol, beam and IF.
|
---|
| 1838 | // So therefore we need to iterate through by spectrum (axis 3). Although
|
---|
| 1839 | // Tsys is stored as a vector of length nChan, the values are replicated.
|
---|
| 1840 | // We will take a short cut and just use the value from the first channel
|
---|
| 1841 | // for now.
|
---|
| 1842 | //
|
---|
| 1843 | VectorIterator<Float> itData(valuesIn, axis);
|
---|
| 1844 | ReadOnlyVectorIterator<Float> itTSys(tSys, axis);
|
---|
| 1845 | Float fac = 1.0;
|
---|
| 1846 | IPosition pos(nAxesSub,0);
|
---|
| 1847 | //
|
---|
| 1848 | while (!itData.pastEnd()) {
|
---|
| 1849 | Float t = itTSys.vector()[0];
|
---|
| 1850 | fac = 1.0/t/t;
|
---|
| 1851 |
|
---|
| 1852 | // Scale data
|
---|
| 1853 |
|
---|
| 1854 | itData.vector() *= fac; // Writes back into 'dataIn'
|
---|
| 1855 | //
|
---|
| 1856 | // Accumulate Tsys per if/pol/beam averaged over spectrum
|
---|
| 1857 | // This method to get pos2 from itData.pos() is only valid
|
---|
| 1858 | // because the spectral axis is the last one (so we can just
|
---|
| 1859 | // copy the first nAXesSub positions out)
|
---|
| 1860 |
|
---|
| 1861 | pos = itData.pos().getFirst(nAxesSub);
|
---|
| 1862 | tSysSqSum(pos) += fac;
|
---|
| 1863 | //
|
---|
| 1864 | itData.next();
|
---|
| 1865 | itTSys.next();
|
---|
| 1866 | }
|
---|
[169] | 1867 | }
|
---|
[167] | 1868 |
|
---|
[169] | 1869 | // Accumulate sum of (possibly scaled) data
|
---|
| 1870 |
|
---|
| 1871 | sum += dataIn;
|
---|
| 1872 |
|
---|
| 1873 | // Accumulate Tsys, time, and interval
|
---|
| 1874 |
|
---|
| 1875 | tSysSum += tSys;
|
---|
| 1876 | timeSum += time;
|
---|
| 1877 | intSum += interval;
|
---|
| 1878 | nAccum += 1;
|
---|
| 1879 | }
|
---|
| 1880 |
|
---|
| 1881 |
|
---|
[518] | 1882 | void SDMath::normalize(MaskedArray<Float>& sum,
|
---|
| 1883 | const Array<Float>& sumSq,
|
---|
| 1884 | const Array<Float>& tSysSqSum,
|
---|
| 1885 | const Array<Float>& nPts,
|
---|
| 1886 | Double intSum,
|
---|
| 1887 | WeightType wtType, Int axis,
|
---|
| 1888 | Int nAxesSub) const
|
---|
| 1889 | {
|
---|
| 1890 | IPosition pos2(nAxesSub,0);
|
---|
| 1891 | //
|
---|
| 1892 | if (wtType==NONE) {
|
---|
| 1893 |
|
---|
| 1894 | // We just average by the number of points accumulated.
|
---|
| 1895 | // We need to make a MA out of nPts so that no divide by
|
---|
| 1896 | // zeros occur
|
---|
| 1897 |
|
---|
| 1898 | MaskedArray<Float> t(nPts, (nPts>Float(0.0)));
|
---|
| 1899 | sum /= t;
|
---|
| 1900 | } else if (wtType==TINT) {
|
---|
| 1901 |
|
---|
| 1902 | // Average by sum of Tint
|
---|
| 1903 |
|
---|
| 1904 | sum /= Float(intSum);
|
---|
| 1905 | } else if (wtType==VAR) {
|
---|
| 1906 |
|
---|
| 1907 | // Normalize each spectrum by sum(1/var) where the variance
|
---|
| 1908 | // is worked out for each spectrum
|
---|
| 1909 |
|
---|
| 1910 | Array<Float>& data = sum.getRWArray();
|
---|
| 1911 | VectorIterator<Float> itData(data, axis);
|
---|
| 1912 | while (!itData.pastEnd()) {
|
---|
| 1913 | pos2 = itData.pos().getFirst(nAxesSub);
|
---|
| 1914 | itData.vector() /= sumSq(pos2);
|
---|
| 1915 | itData.next();
|
---|
| 1916 | }
|
---|
| 1917 | } else if (wtType==TSYS) {
|
---|
| 1918 |
|
---|
| 1919 | // Normalize each spectrum by sum(1/Tsys**2) where the pseudo
|
---|
| 1920 | // replication over channel for Tsys has been dropped.
|
---|
| 1921 |
|
---|
| 1922 | Array<Float>& data = sum.getRWArray();
|
---|
| 1923 | VectorIterator<Float> itData(data, axis);
|
---|
| 1924 | while (!itData.pastEnd()) {
|
---|
| 1925 | pos2 = itData.pos().getFirst(nAxesSub);
|
---|
| 1926 | itData.vector() /= tSysSqSum(pos2);
|
---|
| 1927 | itData.next();
|
---|
| 1928 | }
|
---|
| 1929 | }
|
---|
| 1930 | }
|
---|
| 1931 |
|
---|
| 1932 |
|
---|
| 1933 |
|
---|
| 1934 |
|
---|
[434] | 1935 | void SDMath::setCursorSlice (IPosition& start, IPosition& end, Bool doAll, const SDMemTable& in) const
|
---|
[169] | 1936 | {
|
---|
[434] | 1937 | const uInt nDim = asap::nAxes;
|
---|
| 1938 | DebugAssert(nDim==4,AipsError);
|
---|
[167] | 1939 | //
|
---|
[169] | 1940 | start.resize(nDim);
|
---|
[434] | 1941 | end.resize(nDim);
|
---|
| 1942 | if (doAll) {
|
---|
| 1943 | start = 0;
|
---|
| 1944 | end(0) = in.nBeam()-1;
|
---|
| 1945 | end(1) = in.nIF()-1;
|
---|
| 1946 | end(2) = in.nPol()-1;
|
---|
| 1947 | end(3) = in.nChan()-1;
|
---|
| 1948 | } else {
|
---|
| 1949 | start(0) = in.getBeam();
|
---|
| 1950 | end(0) = start(0);
|
---|
[167] | 1951 | //
|
---|
[434] | 1952 | start(1) = in.getIF();
|
---|
| 1953 | end(1) = start(1);
|
---|
| 1954 | //
|
---|
| 1955 | start(2) = in.getPol();
|
---|
| 1956 | end(2) = start(2);
|
---|
| 1957 | //
|
---|
| 1958 | start(3) = 0;
|
---|
| 1959 | end(3) = in.nChan()-1;
|
---|
| 1960 | }
|
---|
[169] | 1961 | }
|
---|
| 1962 |
|
---|
| 1963 |
|
---|
[518] | 1964 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr,
|
---|
| 1965 | Bool listType) const
|
---|
[169] | 1966 | {
|
---|
| 1967 | String tStr(weightStr);
|
---|
| 1968 | tStr.upcase();
|
---|
[518] | 1969 | String msg;
|
---|
[169] | 1970 | if (tStr.contains(String("NONE"))) {
|
---|
| 1971 | wtType = NONE;
|
---|
[518] | 1972 | msg = String("Weighting type selected : None");
|
---|
[169] | 1973 | } else if (tStr.contains(String("VAR"))) {
|
---|
| 1974 | wtType = VAR;
|
---|
[518] | 1975 | msg = String("Weighting type selected : Variance");
|
---|
| 1976 | } else if (tStr.contains(String("TINT"))) {
|
---|
| 1977 | wtType = TINT;
|
---|
[519] | 1978 | msg = String("Weighting type selected : Tint");
|
---|
[169] | 1979 | } else if (tStr.contains(String("TSYS"))) {
|
---|
| 1980 | wtType = TSYS;
|
---|
[518] | 1981 | msg = String("Weighting type selected : Tsys");
|
---|
[169] | 1982 | } else {
|
---|
[518] | 1983 | msg = String("Weighting type selected : None");
|
---|
| 1984 | throw(AipsError("Unrecognized weighting type"));
|
---|
[167] | 1985 | }
|
---|
[518] | 1986 | //
|
---|
| 1987 | if (listType) cout << msg << endl;
|
---|
[167] | 1988 | }
|
---|
| 1989 |
|
---|
[317] | 1990 |
|
---|
| 1991 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type,
|
---|
| 1992 | const casa::String& interp) const
|
---|
[227] | 1993 | {
|
---|
| 1994 | String tStr(interp);
|
---|
| 1995 | tStr.upcase();
|
---|
| 1996 | if (tStr.contains(String("NEAR"))) {
|
---|
[317] | 1997 | type = InterpolateArray1D<Double,Float>::nearestNeighbour;
|
---|
[227] | 1998 | } else if (tStr.contains(String("LIN"))) {
|
---|
[317] | 1999 | type = InterpolateArray1D<Double,Float>::linear;
|
---|
[227] | 2000 | } else if (tStr.contains(String("CUB"))) {
|
---|
[317] | 2001 | type = InterpolateArray1D<Double,Float>::cubic;
|
---|
[227] | 2002 | } else if (tStr.contains(String("SPL"))) {
|
---|
[317] | 2003 | type = InterpolateArray1D<Double,Float>::spline;
|
---|
[227] | 2004 | } else {
|
---|
| 2005 | throw(AipsError("Unrecognized interpolation type"));
|
---|
| 2006 | }
|
---|
| 2007 | }
|
---|
| 2008 |
|
---|
[185] | 2009 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data,
|
---|
[227] | 2010 | const Array<Bool>& mask) const
|
---|
[169] | 2011 | {
|
---|
| 2012 | sc.putSpectrum(data);
|
---|
| 2013 | //
|
---|
| 2014 | Array<uChar> outflags(data.shape());
|
---|
| 2015 | convertArray(outflags,!mask);
|
---|
| 2016 | sc.putFlags(outflags);
|
---|
| 2017 | }
|
---|
[227] | 2018 |
|
---|
| 2019 | Table SDMath::readAsciiFile (const String& fileName) const
|
---|
| 2020 | {
|
---|
[230] | 2021 | String formatString;
|
---|
| 2022 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False);
|
---|
[227] | 2023 | return tbl;
|
---|
| 2024 | }
|
---|
[230] | 2025 |
|
---|
| 2026 |
|
---|
[234] | 2027 |
|
---|
[480] | 2028 | void SDMath::scaleFromAsciiTable(SDMemTable* pTabOut,
|
---|
| 2029 | const SDMemTable& in, const String& fileName,
|
---|
| 2030 | const String& col0, const String& col1,
|
---|
| 2031 | const String& methodStr, Bool doAll,
|
---|
| 2032 | const Vector<Float>& xOut, Bool doTSys) const
|
---|
[230] | 2033 | {
|
---|
| 2034 |
|
---|
| 2035 | // Read gain-elevation ascii file data into a Table.
|
---|
| 2036 |
|
---|
[234] | 2037 | Table geTable = readAsciiFile (fileName);
|
---|
[230] | 2038 | //
|
---|
[480] | 2039 | scaleFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut, doTSys);
|
---|
[230] | 2040 | }
|
---|
| 2041 |
|
---|
[480] | 2042 | void SDMath::scaleFromTable(SDMemTable* pTabOut, const SDMemTable& in,
|
---|
| 2043 | const Table& tTable, const String& col0,
|
---|
| 2044 | const String& col1,
|
---|
| 2045 | const String& methodStr, Bool doAll,
|
---|
| 2046 | const Vector<Float>& xOut, Bool doTsys) const
|
---|
[230] | 2047 | {
|
---|
| 2048 |
|
---|
| 2049 | // Get data from Table
|
---|
| 2050 |
|
---|
| 2051 | ROScalarColumn<Float> geElCol(tTable, col0);
|
---|
| 2052 | ROScalarColumn<Float> geFacCol(tTable, col1);
|
---|
| 2053 | Vector<Float> xIn = geElCol.getColumn();
|
---|
| 2054 | Vector<Float> yIn = geFacCol.getColumn();
|
---|
| 2055 | Vector<Bool> maskIn(xIn.nelements(),True);
|
---|
| 2056 |
|
---|
| 2057 | // Interpolate (and extrapolate) with desired method
|
---|
| 2058 |
|
---|
[317] | 2059 | InterpolateArray1D<Double,Float>::InterpolationMethod method;
|
---|
[230] | 2060 | convertInterpString(method, methodStr);
|
---|
[317] | 2061 | Int intMethod(method);
|
---|
[230] | 2062 | //
|
---|
| 2063 | Vector<Float> yOut;
|
---|
| 2064 | Vector<Bool> maskOut;
|
---|
| 2065 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut,
|
---|
[317] | 2066 | xIn, yIn, maskIn, intMethod,
|
---|
[230] | 2067 | True, True);
|
---|
[234] | 2068 | // Apply
|
---|
[230] | 2069 |
|
---|
[480] | 2070 | scaleByVector(pTabOut, in, doAll, Float(1.0)/yOut, doTsys);
|
---|
[234] | 2071 | }
|
---|
| 2072 |
|
---|
| 2073 |
|
---|
[480] | 2074 | void SDMath::scaleByVector(SDMemTable* pTabOut, const SDMemTable& in,
|
---|
| 2075 | Bool doAll, const Vector<Float>& factor,
|
---|
| 2076 | Bool doTSys) const
|
---|
[234] | 2077 | {
|
---|
[270] | 2078 |
|
---|
[434] | 2079 | // Set up data slice
|
---|
[230] | 2080 |
|
---|
| 2081 | IPosition start, end;
|
---|
[434] | 2082 | setCursorSlice (start, end, doAll, in);
|
---|
[230] | 2083 |
|
---|
[480] | 2084 | // Get Tsys column
|
---|
| 2085 |
|
---|
| 2086 | const Table& tIn = in.table();
|
---|
| 2087 | ArrayColumn<Float> tSysCol(tIn, "TSYS");
|
---|
| 2088 | Array<Float> tSys;
|
---|
| 2089 |
|
---|
[270] | 2090 | // Loop over rows and apply correction factor
|
---|
[230] | 2091 |
|
---|
| 2092 | const uInt axis = asap::ChanAxis;
|
---|
| 2093 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
| 2094 |
|
---|
| 2095 | // Get data
|
---|
| 2096 |
|
---|
[434] | 2097 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i));
|
---|
| 2098 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference to dataIn
|
---|
[480] | 2099 | //
|
---|
| 2100 | if (doTSys) {
|
---|
| 2101 | tSysCol.get(i, tSys);
|
---|
| 2102 | Array<Float> tSys2 = tSys(start,end) * factor[i];
|
---|
| 2103 | tSysCol.put(i, tSys);
|
---|
| 2104 | }
|
---|
[230] | 2105 |
|
---|
| 2106 | // Apply factor
|
---|
| 2107 |
|
---|
[434] | 2108 | dataIn2 *= factor[i];
|
---|
[230] | 2109 |
|
---|
| 2110 | // Write out
|
---|
| 2111 |
|
---|
[434] | 2112 | SDContainer sc = in.getSDContainer(i);
|
---|
| 2113 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask());
|
---|
[230] | 2114 | //
|
---|
[434] | 2115 | pTabOut->putSDContainer(sc);
|
---|
[230] | 2116 | }
|
---|
| 2117 | }
|
---|
| 2118 |
|
---|
[234] | 2119 |
|
---|
[262] | 2120 |
|
---|
| 2121 |
|
---|
[330] | 2122 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx,
|
---|
| 2123 | SDDataDesc& dDesc,
|
---|
| 2124 | uInt nIF,
|
---|
| 2125 | const SDMemTable& in,
|
---|
| 2126 | const Table& tabIn,
|
---|
| 2127 | const ROScalarColumn<String>& srcCol,
|
---|
[397] | 2128 | const ROArrayColumn<uInt>& fqIDCol,
|
---|
| 2129 | Bool perFreqID) const
|
---|
[330] | 2130 | {
|
---|
| 2131 | const uInt nRows = tabIn.nrow();
|
---|
| 2132 | ddIdx.resize(nRows,nIF);
|
---|
[262] | 2133 | //
|
---|
[330] | 2134 | String srcName;
|
---|
| 2135 | Vector<uInt> freqIDs;
|
---|
| 2136 | for (uInt iRow=0; iRow<nRows; iRow++) {
|
---|
| 2137 | srcCol.get(iRow, srcName);
|
---|
| 2138 | fqIDCol.get(iRow, freqIDs);
|
---|
| 2139 | const MDirection& dir = in.getDirection(iRow);
|
---|
| 2140 | //
|
---|
[397] | 2141 | if (perFreqID) {
|
---|
| 2142 |
|
---|
| 2143 | // One entry per source/freqID pair
|
---|
| 2144 |
|
---|
| 2145 | for (uInt iIF=0; iIF<nIF; iIF++) {
|
---|
| 2146 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, freqIDs[iIF], dir, 0);
|
---|
| 2147 | }
|
---|
| 2148 | } else {
|
---|
| 2149 |
|
---|
| 2150 | // One entry per source/IF pair. Hang onto the FreqID as well
|
---|
| 2151 |
|
---|
| 2152 | for (uInt iIF=0; iIF<nIF; iIF++) {
|
---|
| 2153 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, iIF, dir, freqIDs[iIF]);
|
---|
| 2154 | }
|
---|
[262] | 2155 | }
|
---|
| 2156 | }
|
---|
| 2157 | }
|
---|
[272] | 2158 |
|
---|
[397] | 2159 |
|
---|
| 2160 |
|
---|
| 2161 |
|
---|
| 2162 |
|
---|
[272] | 2163 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const
|
---|
| 2164 | {
|
---|
| 2165 | Quantum<Double> qt;
|
---|
| 2166 | if (MVTime::read(qt,str)) {
|
---|
| 2167 | MVEpoch mv(qt);
|
---|
| 2168 | MEpoch me(mv, timeRef);
|
---|
| 2169 | return me;
|
---|
| 2170 | } else {
|
---|
| 2171 | throw(AipsError("Invalid format for Epoch string"));
|
---|
| 2172 | }
|
---|
| 2173 | }
|
---|
| 2174 |
|
---|
| 2175 |
|
---|
| 2176 | String SDMath::formatEpoch(const MEpoch& epoch) const
|
---|
| 2177 | {
|
---|
| 2178 | MVTime mvt(epoch.getValue());
|
---|
| 2179 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")");
|
---|
| 2180 | }
|
---|
| 2181 |
|
---|
[294] | 2182 |
|
---|
[309] | 2183 |
|
---|
| 2184 | void SDMath::generateFrequencyAligners (PtrBlock<FrequencyAligner<Float>* >& a,
|
---|
[330] | 2185 | const SDDataDesc& dDesc,
|
---|
| 2186 | const SDMemTable& in, uInt nChan,
|
---|
| 2187 | MFrequency::Types system,
|
---|
| 2188 | const MPosition& refPos,
|
---|
[397] | 2189 | const MEpoch& refEpoch,
|
---|
| 2190 | Bool perFreqID) const
|
---|
[294] | 2191 | {
|
---|
[330] | 2192 | for (uInt i=0; i<dDesc.length(); i++) {
|
---|
[397] | 2193 | uInt ID = dDesc.ID(i);
|
---|
| 2194 | uInt secID = dDesc.secID(i);
|
---|
| 2195 | const MDirection& refDir = dDesc.secDir(i);
|
---|
[330] | 2196 | //
|
---|
[397] | 2197 | if (perFreqID) {
|
---|
| 2198 |
|
---|
| 2199 | // One aligner per source/FreqID pair.
|
---|
| 2200 |
|
---|
| 2201 | SpectralCoordinate sC = in.getSpectralCoordinate(ID);
|
---|
| 2202 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system);
|
---|
| 2203 | } else {
|
---|
| 2204 |
|
---|
| 2205 | // One aligner per source/IF pair. But we still need the FreqID to
|
---|
| 2206 | // get the right SC. Hence the messing about with the secondary ID
|
---|
| 2207 |
|
---|
| 2208 | SpectralCoordinate sC = in.getSpectralCoordinate(secID);
|
---|
| 2209 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system);
|
---|
| 2210 | }
|
---|
[294] | 2211 | }
|
---|
| 2212 | }
|
---|
[480] | 2213 |
|
---|
| 2214 | Vector<uInt> SDMath::getRowRange (const SDMemTable& in) const
|
---|
| 2215 | {
|
---|
| 2216 | Vector<uInt> range(2);
|
---|
| 2217 | range[0] = 0;
|
---|
| 2218 | range[1] = in.nRow()-1;
|
---|
| 2219 | return range;
|
---|
| 2220 | }
|
---|
| 2221 |
|
---|
| 2222 |
|
---|
| 2223 | Bool SDMath::rowInRange (uInt i, const Vector<uInt>& range) const
|
---|
| 2224 | {
|
---|
| 2225 | return (i>=range[0] && i<=range[1]);
|
---|
| 2226 | }
|
---|