[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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| 269 | // Loop over rows in Table |
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| 270 | |
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| 271 | const uInt nRows = in[iTab]->nRow(); |
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| 272 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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| 273 | |
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| 274 | // Check conformance |
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| 275 | |
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| 276 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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| 277 | if (!shp.isEqual(shp2)) { |
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| 278 | throw (AipsError("Shapes for all rows must be the same")); |
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| 279 | } |
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| 280 | |
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| 281 | // If we are not doing scan averages, make checks for source and |
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| 282 | // frequency setup and warn if averaging across them |
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| 283 | |
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[410] | 284 | scanIDCol.getScalar(iRow, scanID); |
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[144] | 285 | |
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| 286 | // Get quantities from columns |
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| 287 | |
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| 288 | srcNameCol.getScalar(iRow, sourceName); |
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| 289 | mjdCol.get(iRow, time); |
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| 290 | tSysCol.get(iRow, tSys); |
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| 291 | intCol.get(iRow, interval); |
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| 292 | fqIDCol.get(iRow, freqID); |
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| 293 | |
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| 294 | // Initialize first source and freqID |
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| 295 | |
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| 296 | if (iRow==0 && iTab==0) { |
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| 297 | sourceNameStart = sourceName; |
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| 298 | freqIDStart = freqID; |
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| 299 | } |
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| 300 | |
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| 301 | // If we are doing scan averages, see if we are at the end of an |
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| 302 | // accumulation period (scan). We must check soutce names too, |
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| 303 | // since we might have two tables with one scan each but different |
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| 304 | // source names; we shouldn't average different sources together |
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| 305 | |
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| 306 | if (scanAv && ( (scanID != oldScanID) || |
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| 307 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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| 308 | |
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| 309 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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| 310 | |
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[518] | 311 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 312 | |
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[410] | 313 | // Get ScanContainer for the first row of this averaged Scan |
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| 314 | |
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| 315 | SDContainer scOut = in[iTab]->getSDContainer(rowStart); |
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| 316 | |
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[144] | 317 | // Fill scan container. The source and freqID come from the |
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| 318 | // first row of the first table that went into this average ( |
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| 319 | // should be the same for all rows in the scan average) |
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| 320 | |
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| 321 | Float nR(nAccum); |
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[410] | 322 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 323 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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| 324 | |
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| 325 | // Write container out to Table |
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| 326 | |
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[410] | 327 | pTabOut->putSDContainer(scOut); |
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[144] | 328 | |
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| 329 | // Reset accumulators |
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| 330 | |
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| 331 | sum = 0.0; |
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| 332 | sumSq = 0.0; |
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| 333 | nAccum = 0; |
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| 334 | // |
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| 335 | tSysSum =0.0; |
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[518] | 336 | tSysSqSum =0.0; |
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[144] | 337 | timeSum = 0.0; |
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| 338 | intSum = 0.0; |
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[221] | 339 | nPts = 0.0; |
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[144] | 340 | |
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| 341 | // Increment |
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| 342 | |
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| 343 | rowStart = iRow; // First row for next accumulation |
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| 344 | tableStart = iTab; // First table for next accumulation |
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| 345 | sourceNameStart = sourceName; // First source name for next accumulation |
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| 346 | freqIDStart = freqID; // First FreqID for next accumulation |
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| 347 | // |
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| 348 | oldScanID = scanID; |
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| 349 | outScanID += 1; // Scan ID for next accumulation period |
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[227] | 350 | } |
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[144] | 351 | |
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[146] | 352 | // Accumulate |
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[144] | 353 | |
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[518] | 354 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, tSysSqSum, |
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| 355 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis, |
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| 356 | nAxesSub, useMask, wtType); |
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[144] | 357 | // |
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| 358 | oldSourceName = sourceName; |
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| 359 | oldFreqID = freqID; |
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[184] | 360 | } |
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[144] | 361 | } |
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| 362 | |
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| 363 | // OK at this point we have accumulation data which is either |
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| 364 | // - accumulated from all tables into one row |
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| 365 | // or |
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| 366 | // - accumulated from the last scan average |
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| 367 | // |
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| 368 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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[410] | 369 | |
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[518] | 370 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 371 | |
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| 372 | // Create and fill container. The container we clone will be from |
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| 373 | // the last Table and the first row that went into the current |
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| 374 | // accumulation. It probably doesn't matter that much really... |
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| 375 | |
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| 376 | Float nR(nAccum); |
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[410] | 377 | SDContainer scOut = in[tableStart]->getSDContainer(rowStart); |
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| 378 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 379 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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[410] | 380 | pTabOut->putSDContainer(scOut); |
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[304] | 381 | pTabOut->resetCursor(); |
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[144] | 382 | // |
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| 383 | return CountedPtr<SDMemTable>(pTabOut); |
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[2] | 384 | } |
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[9] | 385 | |
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[144] | 386 | |
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| 387 | |
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[488] | 388 | CountedPtr<SDMemTable> SDMath::binaryOperate(const CountedPtr<SDMemTable>& |
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| 389 | left, |
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| 390 | const CountedPtr<SDMemTable>& |
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| 391 | right, |
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| 392 | const String& op, Bool preserve, |
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| 393 | Bool doTSys) const |
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[185] | 394 | { |
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[85] | 395 | |
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[248] | 396 | // Check operator |
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[130] | 397 | |
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[234] | 398 | String op2(op); |
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| 399 | op2.upcase(); |
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| 400 | uInt what = 0; |
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| 401 | if (op2=="ADD") { |
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| 402 | what = 0; |
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| 403 | } else if (op2=="SUB") { |
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| 404 | what = 1; |
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| 405 | } else if (op2=="MUL") { |
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| 406 | what = 2; |
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| 407 | } else if (op2=="DIV") { |
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| 408 | what = 3; |
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[248] | 409 | } else if (op2=="QUOTIENT") { |
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| 410 | what = 4; |
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[294] | 411 | doTSys = True; |
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[234] | 412 | } else { |
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[248] | 413 | throw( AipsError("Unrecognized operation")); |
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[234] | 414 | } |
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| 415 | |
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| 416 | // Check rows |
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| 417 | |
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[248] | 418 | const uInt nRowLeft = left->nRow(); |
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| 419 | const uInt nRowRight = right->nRow(); |
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| 420 | Bool ok = (nRowRight==1&&nRowLeft>0) || |
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| 421 | (nRowRight>=1&&nRowLeft==nRowRight); |
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| 422 | if (!ok) { |
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| 423 | throw (AipsError("The right Scan Table can have one row or the same number of rows as the left Scan Table")); |
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[234] | 424 | } |
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| 425 | |
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[248] | 426 | // Input Tables |
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[234] | 427 | |
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| 428 | const Table& tLeft = left->table(); |
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| 429 | const Table& tRight = right->table(); |
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[248] | 430 | |
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| 431 | // TSys columns |
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| 432 | |
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[294] | 433 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol; |
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| 434 | if (doTSys) { |
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| 435 | tSysLeftCol.attach(tLeft, "TSYS"); |
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| 436 | tSysRightCol.attach(tRight, "TSYS"); |
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| 437 | } |
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[234] | 438 | |
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[248] | 439 | // First row for right |
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[234] | 440 | |
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[248] | 441 | Array<Float> tSysLeftArr, tSysRightArr; |
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[294] | 442 | if (doTSys) tSysRightCol.get(0, tSysRightArr); |
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[248] | 443 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0)); |
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| 444 | IPosition shpRight = pMRight->shape(); |
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| 445 | |
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| 446 | // Output Table cloned from left |
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| 447 | |
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[234] | 448 | SDMemTable* pTabOut = new SDMemTable(*left, True); |
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[488] | 449 | pTabOut->appendToHistoryTable(right->getHistoryTable()); |
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[234] | 450 | // Loop over rows |
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| 451 | |
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[248] | 452 | for (uInt i=0; i<nRowLeft; i++) { |
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[234] | 453 | |
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| 454 | // Get data |
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[248] | 455 | |
---|
[234] | 456 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i)); |
---|
[248] | 457 | IPosition shpLeft = mLeft.shape(); |
---|
[294] | 458 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr); |
---|
[234] | 459 | // |
---|
[248] | 460 | if (nRowRight>1) { |
---|
| 461 | delete pMRight; |
---|
| 462 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i)); |
---|
| 463 | shpRight = pMRight->shape(); |
---|
[294] | 464 | if (doTSys) tSysRightCol.get(i, tSysRightArr); |
---|
[234] | 465 | } |
---|
[248] | 466 | // |
---|
| 467 | if (!shpRight.isEqual(shpLeft)) { |
---|
| 468 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 469 | } |
---|
[294] | 470 | if (doTSys) { |
---|
| 471 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) { |
---|
| 472 | throw(AipsError("left and right Tsys data are not conformant")); |
---|
| 473 | } |
---|
| 474 | if (!shpRight.isEqual(tSysRightArr.shape())) { |
---|
| 475 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 476 | } |
---|
[248] | 477 | } |
---|
[234] | 478 | |
---|
| 479 | // Make container |
---|
| 480 | |
---|
| 481 | SDContainer sc = left->getSDContainer(i); |
---|
| 482 | |
---|
| 483 | // Operate on data and TSys |
---|
| 484 | |
---|
| 485 | if (what==0) { |
---|
[248] | 486 | MaskedArray<Float> tmp = mLeft + *pMRight; |
---|
[234] | 487 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 488 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr); |
---|
[234] | 489 | } else if (what==1) { |
---|
[248] | 490 | MaskedArray<Float> tmp = mLeft - *pMRight; |
---|
[234] | 491 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 492 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr); |
---|
[234] | 493 | } else if (what==2) { |
---|
[248] | 494 | MaskedArray<Float> tmp = mLeft * *pMRight; |
---|
[234] | 495 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 496 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr); |
---|
[234] | 497 | } else if (what==3) { |
---|
[248] | 498 | MaskedArray<Float> tmp = mLeft / *pMRight; |
---|
[234] | 499 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 500 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr); |
---|
[248] | 501 | } else if (what==4) { |
---|
[488] | 502 | if (preserve) { |
---|
| 503 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
---|
| 504 | tSysRightArr; |
---|
| 505 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 506 | } else { |
---|
| 507 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
---|
| 508 | tSysLeftArr; |
---|
| 509 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 510 | } |
---|
| 511 | sc.putTsys(tSysRightArr); |
---|
[234] | 512 | } |
---|
| 513 | |
---|
| 514 | // Put new row in output Table |
---|
| 515 | |
---|
[171] | 516 | pTabOut->putSDContainer(sc); |
---|
[130] | 517 | } |
---|
[248] | 518 | if (pMRight) delete pMRight; |
---|
[304] | 519 | pTabOut->resetCursor(); |
---|
[488] | 520 | |
---|
[171] | 521 | return CountedPtr<SDMemTable>(pTabOut); |
---|
[9] | 522 | } |
---|
[48] | 523 | |
---|
[146] | 524 | |
---|
| 525 | |
---|
[185] | 526 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in, |
---|
[234] | 527 | const Vector<Bool>& mask, |
---|
| 528 | const String& which, Int row) const |
---|
[130] | 529 | // |
---|
| 530 | // Perhaps iteration over pol/beam/if should be in here |
---|
| 531 | // and inside the nrow iteration ? |
---|
| 532 | // |
---|
| 533 | { |
---|
| 534 | const uInt nRow = in->nRow(); |
---|
| 535 | |
---|
| 536 | // Specify cursor location |
---|
| 537 | |
---|
[152] | 538 | IPosition start, end; |
---|
[434] | 539 | Bool doAll = False; |
---|
| 540 | setCursorSlice (start, end, doAll, *in); |
---|
[130] | 541 | |
---|
| 542 | // Loop over rows |
---|
| 543 | |
---|
[234] | 544 | const uInt nEl = mask.nelements(); |
---|
| 545 | uInt iStart = 0; |
---|
| 546 | uInt iEnd = in->nRow()-1; |
---|
| 547 | // |
---|
| 548 | if (row>=0) { |
---|
| 549 | iStart = row; |
---|
| 550 | iEnd = row; |
---|
| 551 | } |
---|
| 552 | // |
---|
| 553 | std::vector<float> result(iEnd-iStart+1); |
---|
| 554 | for (uInt ii=iStart; ii <= iEnd; ++ii) { |
---|
[130] | 555 | |
---|
| 556 | // Get row and deconstruct |
---|
| 557 | |
---|
[434] | 558 | MaskedArray<Float> dataIn = (in->rowAsMaskedArray(ii))(start,end); |
---|
| 559 | Array<Float> v = dataIn.getArray().nonDegenerate(); |
---|
| 560 | Array<Bool> m = dataIn.getMask().nonDegenerate(); |
---|
[130] | 561 | |
---|
| 562 | // Access desired piece of data |
---|
| 563 | |
---|
[434] | 564 | // Array<Float> v((arr(start,end)).nonDegenerate()); |
---|
| 565 | // Array<Bool> m((barr(start,end)).nonDegenerate()); |
---|
[130] | 566 | |
---|
| 567 | // Apply OTF mask |
---|
| 568 | |
---|
| 569 | MaskedArray<Float> tmp; |
---|
| 570 | if (m.nelements()==nEl) { |
---|
[234] | 571 | tmp.setData(v,m&&mask); |
---|
[130] | 572 | } else { |
---|
| 573 | tmp.setData(v,m); |
---|
| 574 | } |
---|
| 575 | |
---|
| 576 | // Get statistic |
---|
| 577 | |
---|
[234] | 578 | result[ii-iStart] = mathutil::statistics(which, tmp); |
---|
[130] | 579 | } |
---|
| 580 | // |
---|
| 581 | return result; |
---|
| 582 | } |
---|
| 583 | |
---|
[146] | 584 | |
---|
[234] | 585 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const |
---|
[144] | 586 | { |
---|
[169] | 587 | SDHeader sh = in.getSDHeader(); |
---|
| 588 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[163] | 589 | |
---|
[169] | 590 | // Bin up SpectralCoordinates |
---|
[163] | 591 | |
---|
[169] | 592 | IPosition factors(1); |
---|
| 593 | factors(0) = width; |
---|
| 594 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 595 | CoordinateSystem cSys; |
---|
[288] | 596 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
[169] | 597 | CoordinateSystem cSysBin = |
---|
[185] | 598 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False); |
---|
[169] | 599 | // |
---|
| 600 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
---|
| 601 | pTabOut->setCoordinate(sCBin, j); |
---|
| 602 | } |
---|
[163] | 603 | |
---|
[169] | 604 | // Use RebinLattice to find shape |
---|
[130] | 605 | |
---|
[169] | 606 | IPosition shapeIn(1,sh.nchan); |
---|
[185] | 607 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors); |
---|
[169] | 608 | sh.nchan = shapeOut(0); |
---|
| 609 | pTabOut->putSDHeader(sh); |
---|
[144] | 610 | |
---|
[169] | 611 | // Loop over rows and bin along channel axis |
---|
| 612 | |
---|
| 613 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 614 | SDContainer sc = in.getSDContainer(i); |
---|
[144] | 615 | // |
---|
[169] | 616 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
---|
[144] | 617 | |
---|
[169] | 618 | // Bin up spectrum |
---|
[144] | 619 | |
---|
[169] | 620 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
---|
| 621 | MaskedArray<Float> marrout; |
---|
[221] | 622 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width); |
---|
[144] | 623 | |
---|
[169] | 624 | // Put back the binned data and flags |
---|
[144] | 625 | |
---|
[169] | 626 | IPosition ip2 = marrout.shape(); |
---|
| 627 | sc.resize(ip2); |
---|
[146] | 628 | // |
---|
[185] | 629 | putDataInSDC(sc, marrout.getArray(), marrout.getMask()); |
---|
[146] | 630 | |
---|
[169] | 631 | // Bin up Tsys. |
---|
[146] | 632 | |
---|
[169] | 633 | Array<Bool> allGood(tSys.shape(),True); |
---|
| 634 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
---|
[146] | 635 | // |
---|
[169] | 636 | MaskedArray<Float> tSysOut; |
---|
[221] | 637 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width); |
---|
[169] | 638 | sc.putTsys(tSysOut.getArray()); |
---|
[146] | 639 | // |
---|
[169] | 640 | pTabOut->putSDContainer(sc); |
---|
| 641 | } |
---|
| 642 | return pTabOut; |
---|
[146] | 643 | } |
---|
| 644 | |
---|
[488] | 645 | SDMemTable* SDMath::resample(const SDMemTable& in, const String& methodStr, |
---|
| 646 | Float width) const |
---|
[299] | 647 | // |
---|
| 648 | // Should add the possibility of width being specified in km/s. This means |
---|
| 649 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
| 650 | // average channel width (say at the reference pixel). Then we would need |
---|
| 651 | // to be careful to make sure each spectrum (of different freqID) |
---|
| 652 | // is the same length. |
---|
| 653 | // |
---|
| 654 | { |
---|
| 655 | Bool doVel = False; |
---|
[309] | 656 | if (doVel) { |
---|
| 657 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 658 | SpectralCoordinate sC = in.getSpectralCoordinate(j); |
---|
| 659 | } |
---|
| 660 | } |
---|
[299] | 661 | |
---|
| 662 | // Interpolation method |
---|
| 663 | |
---|
[317] | 664 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
| 665 | convertInterpString(interp, methodStr); |
---|
| 666 | Int interpMethod(interp); |
---|
[299] | 667 | |
---|
| 668 | // Make output table |
---|
| 669 | |
---|
| 670 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 671 | |
---|
| 672 | // Resample SpectralCoordinates (one per freqID) |
---|
| 673 | |
---|
| 674 | const uInt nCoord = in.nCoordinates(); |
---|
| 675 | Vector<Float> offset(1,0.0); |
---|
| 676 | Vector<Float> factors(1,1.0/width); |
---|
| 677 | Vector<Int> newShape; |
---|
| 678 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 679 | CoordinateSystem cSys; |
---|
| 680 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
| 681 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape); |
---|
| 682 | SpectralCoordinate sC = cSys2.spectralCoordinate(0); |
---|
| 683 | // |
---|
| 684 | pTabOut->setCoordinate(sC, j); |
---|
| 685 | } |
---|
| 686 | |
---|
| 687 | // Get header |
---|
| 688 | |
---|
| 689 | SDHeader sh = in.getSDHeader(); |
---|
| 690 | |
---|
| 691 | // Generate resampling vectors |
---|
| 692 | |
---|
| 693 | const uInt nChanIn = sh.nchan; |
---|
| 694 | Vector<Float> xIn(nChanIn); |
---|
| 695 | indgen(xIn); |
---|
| 696 | // |
---|
| 697 | Int fac = Int(nChanIn/width); |
---|
| 698 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
| 699 | uInt i = 0; |
---|
| 700 | Float x = 0.0; |
---|
| 701 | Bool more = True; |
---|
| 702 | while (more) { |
---|
| 703 | xOut(i) = x; |
---|
| 704 | // |
---|
| 705 | i++; |
---|
| 706 | x += width; |
---|
| 707 | if (x>nChanIn-1) more = False; |
---|
| 708 | } |
---|
| 709 | const uInt nChanOut = i; |
---|
| 710 | xOut.resize(nChanOut,True); |
---|
| 711 | // |
---|
| 712 | IPosition shapeIn(in.rowAsMaskedArray(0).shape()); |
---|
| 713 | sh.nchan = nChanOut; |
---|
| 714 | pTabOut->putSDHeader(sh); |
---|
| 715 | |
---|
| 716 | // Loop over rows and resample along channel axis |
---|
| 717 | |
---|
| 718 | Array<Float> valuesOut; |
---|
| 719 | Array<Bool> maskOut; |
---|
| 720 | Array<Float> tSysOut; |
---|
| 721 | Array<Bool> tSysMaskIn(shapeIn,True); |
---|
| 722 | Array<Bool> tSysMaskOut; |
---|
| 723 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 724 | |
---|
| 725 | // Get container |
---|
| 726 | |
---|
| 727 | SDContainer sc = in.getSDContainer(i); |
---|
| 728 | |
---|
| 729 | // Get data and Tsys |
---|
| 730 | |
---|
| 731 | const Array<Float>& tSysIn = sc.getTsys(); |
---|
| 732 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i)); |
---|
| 733 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 734 | Array<Bool> maskIn = dataIn.getMask(); |
---|
| 735 | |
---|
| 736 | // Interpolate data |
---|
| 737 | |
---|
| 738 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut, |
---|
| 739 | xIn, valuesIn, maskIn, |
---|
| 740 | interpMethod, True, True); |
---|
| 741 | sc.resize(valuesOut.shape()); |
---|
| 742 | putDataInSDC(sc, valuesOut, maskOut); |
---|
| 743 | |
---|
| 744 | // Interpolate TSys |
---|
| 745 | |
---|
| 746 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut, |
---|
| 747 | xIn, tSysIn, tSysMaskIn, |
---|
| 748 | interpMethod, True, True); |
---|
| 749 | sc.putTsys(tSysOut); |
---|
| 750 | |
---|
| 751 | // Put container in output |
---|
| 752 | |
---|
| 753 | pTabOut->putSDContainer(sc); |
---|
| 754 | } |
---|
| 755 | // |
---|
| 756 | return pTabOut; |
---|
| 757 | } |
---|
| 758 | |
---|
[248] | 759 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll, |
---|
[294] | 760 | uInt what, Bool doTSys) const |
---|
[152] | 761 | // |
---|
| 762 | // what = 0 Multiply |
---|
| 763 | // 1 Add |
---|
[146] | 764 | { |
---|
[152] | 765 | SDMemTable* pOut = new SDMemTable(in,False); |
---|
| 766 | const Table& tOut = pOut->table(); |
---|
[294] | 767 | ArrayColumn<Float> specCol(tOut,"SPECTRA"); |
---|
| 768 | ArrayColumn<Float> tSysCol(tOut,"TSYS"); |
---|
| 769 | Array<Float> tSysArr; |
---|
[434] | 770 | |
---|
| 771 | // Get data slice bounds |
---|
| 772 | |
---|
| 773 | IPosition start, end; |
---|
| 774 | setCursorSlice (start, end, doAll, in); |
---|
[146] | 775 | // |
---|
[434] | 776 | for (uInt i=0; i<tOut.nrow(); i++) { |
---|
[294] | 777 | |
---|
| 778 | // Modify data |
---|
| 779 | |
---|
[434] | 780 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
| 781 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference |
---|
| 782 | if (what==0) { |
---|
| 783 | dataIn2 *= val; |
---|
| 784 | } else if (what==1) { |
---|
| 785 | dataIn2 += val; |
---|
| 786 | } |
---|
| 787 | specCol.put(i, dataIn.getArray()); |
---|
[294] | 788 | |
---|
| 789 | // Modify Tsys |
---|
| 790 | |
---|
[434] | 791 | if (doTSys) { |
---|
| 792 | tSysCol.get(i, tSysArr); |
---|
| 793 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference |
---|
[152] | 794 | if (what==0) { |
---|
[434] | 795 | tSysArr2 *= val; |
---|
[152] | 796 | } else if (what==1) { |
---|
[434] | 797 | tSysArr2 += val; |
---|
[152] | 798 | } |
---|
[434] | 799 | tSysCol.put(i, tSysArr); |
---|
[152] | 800 | } |
---|
| 801 | } |
---|
| 802 | // |
---|
[146] | 803 | return pOut; |
---|
| 804 | } |
---|
| 805 | |
---|
[315] | 806 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask, |
---|
| 807 | const String& weightStr) const |
---|
[152] | 808 | // |
---|
[165] | 809 | // Average all polarizations together, weighted by variance |
---|
| 810 | // |
---|
| 811 | { |
---|
[315] | 812 | WeightType wtType = NONE; |
---|
[532] | 813 | convertWeightString(wtType, weightStr, True); |
---|
[165] | 814 | |
---|
| 815 | // Create output Table and reshape number of polarizations |
---|
| 816 | |
---|
| 817 | Bool clear=True; |
---|
| 818 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
| 819 | SDHeader header = pTabOut->getSDHeader(); |
---|
| 820 | header.npol = 1; |
---|
| 821 | pTabOut->putSDHeader(header); |
---|
[532] | 822 | // |
---|
| 823 | const Table& tabIn = in.table(); |
---|
[165] | 824 | |
---|
| 825 | // Shape of input and output data |
---|
| 826 | |
---|
[448] | 827 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape(); |
---|
[165] | 828 | IPosition shapeOut(shapeIn); |
---|
[262] | 829 | shapeOut(asap::PolAxis) = 1; // Average all polarizations |
---|
[315] | 830 | if (shapeIn(asap::PolAxis)==1) { |
---|
| 831 | throw(AipsError("The input has only one polarisation")); |
---|
| 832 | } |
---|
[165] | 833 | // |
---|
[532] | 834 | const uInt nRows = in.nRow(); |
---|
[262] | 835 | const uInt nChan = shapeIn(asap::ChanAxis); |
---|
[532] | 836 | AlwaysAssert(asap::nAxes==4,AipsError); |
---|
[165] | 837 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape |
---|
| 838 | IPosition start(4), end(4); |
---|
| 839 | |
---|
| 840 | // Output arrays |
---|
| 841 | |
---|
| 842 | Array<Float> outData(shapeOut, 0.0); |
---|
| 843 | Array<Bool> outMask(shapeOut, True); |
---|
[262] | 844 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane |
---|
[532] | 845 | |
---|
| 846 | // Attach Tsys column if needed |
---|
| 847 | |
---|
| 848 | ROArrayColumn<Float> tSysCol; |
---|
| 849 | Array<Float> tSys; |
---|
| 850 | if (wtType==TSYS) { |
---|
| 851 | tSysCol.attach(tabIn,"TSYS"); |
---|
| 852 | } |
---|
[165] | 853 | // |
---|
[262] | 854 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis)); |
---|
[165] | 855 | |
---|
| 856 | // Loop over rows |
---|
| 857 | |
---|
| 858 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 859 | |
---|
| 860 | // Get data for this row |
---|
| 861 | |
---|
| 862 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
| 863 | Array<Float>& arr = marr.getRWArray(); |
---|
| 864 | const Array<Bool>& barr = marr.getMask(); |
---|
[532] | 865 | |
---|
| 866 | // Get Tsys |
---|
[165] | 867 | |
---|
[532] | 868 | if (wtType==TSYS) { |
---|
| 869 | tSysCol.get(iRow,tSys); |
---|
| 870 | } |
---|
| 871 | |
---|
[165] | 872 | // Make iterators to iterate by pol-channel planes |
---|
[532] | 873 | // The tSys array is empty unless wtType=TSYS so only |
---|
| 874 | // access the iterator is that is the case |
---|
[165] | 875 | |
---|
| 876 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
---|
| 877 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes); |
---|
[532] | 878 | ReadOnlyArrayIterator<Float>* pItTsysPlane = 0; |
---|
| 879 | if (wtType==TSYS) pItTsysPlane = new ReadOnlyArrayIterator<Float>(tSys, axes); |
---|
[165] | 880 | |
---|
| 881 | // Accumulations |
---|
| 882 | |
---|
| 883 | Float fac = 1.0; |
---|
| 884 | Vector<Float> vecSum(nChan,0.0); |
---|
| 885 | |
---|
| 886 | // Iterate through data by pol-channel planes |
---|
| 887 | |
---|
| 888 | while (!itDataPlane.pastEnd()) { |
---|
| 889 | |
---|
| 890 | // Iterate through plane by polarization and accumulate Vectors |
---|
| 891 | |
---|
| 892 | Vector<Float> t1(nChan); t1 = 0.0; |
---|
| 893 | Vector<Bool> t2(nChan); t2 = True; |
---|
[532] | 894 | Float tSys = 0.0; |
---|
[165] | 895 | MaskedArray<Float> vecSum(t1,t2); |
---|
[315] | 896 | Float norm = 0.0; |
---|
[165] | 897 | { |
---|
| 898 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
---|
| 899 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
[532] | 900 | // |
---|
| 901 | ReadOnlyVectorIterator<Float>* pItTsysVec = 0; |
---|
| 902 | if (wtType==TSYS) { |
---|
| 903 | pItTsysVec = new ReadOnlyVectorIterator<Float>(pItTsysPlane->array(), 1); |
---|
| 904 | } |
---|
| 905 | // |
---|
[165] | 906 | while (!itDataVec.pastEnd()) { |
---|
| 907 | |
---|
[315] | 908 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum |
---|
[165] | 909 | |
---|
| 910 | if (useMask) { |
---|
| 911 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector()); |
---|
[532] | 912 | if (wtType==VAR) { |
---|
| 913 | fac = 1.0 / variance(spec); |
---|
| 914 | } else if (wtType==TSYS) { |
---|
| 915 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency |
---|
| 916 | fac = 1.0 / tSys / tSys; |
---|
| 917 | } |
---|
[165] | 918 | } else { |
---|
| 919 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector()); |
---|
[532] | 920 | if (wtType==VAR) { |
---|
| 921 | fac = 1.0 / variance(spec); |
---|
| 922 | } else if (wtType==TSYS) { |
---|
| 923 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency |
---|
| 924 | fac = 1.0 / tSys / tSys; |
---|
| 925 | } |
---|
[165] | 926 | } |
---|
| 927 | |
---|
| 928 | // Normalize spectrum (without OTF mask) and accumulate |
---|
| 929 | |
---|
| 930 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector()); |
---|
| 931 | vecSum += spec; |
---|
[315] | 932 | norm += fac; |
---|
[165] | 933 | |
---|
| 934 | // Next |
---|
| 935 | |
---|
| 936 | itDataVec.next(); |
---|
| 937 | itMaskVec.next(); |
---|
[532] | 938 | if (wtType==TSYS) pItTsysVec->next(); |
---|
[165] | 939 | } |
---|
[532] | 940 | |
---|
| 941 | // Clean up |
---|
| 942 | |
---|
| 943 | if (pItTsysVec) { |
---|
| 944 | delete pItTsysVec; |
---|
| 945 | pItTsysVec = 0; |
---|
| 946 | } |
---|
[165] | 947 | } |
---|
| 948 | |
---|
| 949 | // Normalize summed spectrum |
---|
| 950 | |
---|
[315] | 951 | vecSum /= norm; |
---|
[165] | 952 | |
---|
| 953 | // FInd position in input data array. We are iterating by pol-channel |
---|
| 954 | // plane so all that will change is beam and IF and that's what we want. |
---|
| 955 | |
---|
| 956 | IPosition pos = itDataPlane.pos(); |
---|
| 957 | |
---|
| 958 | // Write out data. This is a bit messy. We have to reform the Vector |
---|
| 959 | // accumulator into an Array of shape (1,1,1,nChan) |
---|
| 960 | |
---|
| 961 | start = pos; |
---|
| 962 | end = pos; |
---|
[262] | 963 | end(asap::ChanAxis) = nChan-1; |
---|
[165] | 964 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
---|
| 965 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
---|
| 966 | |
---|
| 967 | // Step to next beam/IF combination |
---|
| 968 | |
---|
| 969 | itDataPlane.next(); |
---|
| 970 | itMaskPlane.next(); |
---|
[532] | 971 | if (wtType==TSYS) pItTsysPlane->next(); |
---|
[165] | 972 | } |
---|
| 973 | |
---|
| 974 | // Generate output container and write it to output table |
---|
| 975 | |
---|
| 976 | SDContainer sc = in.getSDContainer(); |
---|
| 977 | sc.resize(shapeOut); |
---|
| 978 | // |
---|
[185] | 979 | putDataInSDC(sc, outData, outMask); |
---|
[165] | 980 | pTabOut->putSDContainer(sc); |
---|
[532] | 981 | // |
---|
| 982 | if (wtType==TSYS) { |
---|
| 983 | delete pItTsysPlane; |
---|
| 984 | pItTsysPlane = 0; |
---|
| 985 | } |
---|
[165] | 986 | } |
---|
[304] | 987 | |
---|
| 988 | // Set polarization cursor to 0 |
---|
| 989 | |
---|
| 990 | pTabOut->setPol(0); |
---|
[165] | 991 | // |
---|
| 992 | return pTabOut; |
---|
| 993 | } |
---|
[167] | 994 | |
---|
[169] | 995 | |
---|
[185] | 996 | SDMemTable* SDMath::smooth(const SDMemTable& in, |
---|
| 997 | const casa::String& kernelType, |
---|
[234] | 998 | casa::Float width, Bool doAll) const |
---|
[299] | 999 | // |
---|
| 1000 | // Should smooth TSys as well |
---|
| 1001 | // |
---|
[177] | 1002 | { |
---|
[169] | 1003 | |
---|
[177] | 1004 | // Number of channels |
---|
[169] | 1005 | |
---|
[434] | 1006 | const uInt nChan = in.nChan(); |
---|
[177] | 1007 | |
---|
| 1008 | // Generate Kernel |
---|
| 1009 | |
---|
[185] | 1010 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType); |
---|
[177] | 1011 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
| 1012 | |
---|
| 1013 | // Generate Convolver |
---|
| 1014 | |
---|
| 1015 | IPosition shape(1,nChan); |
---|
| 1016 | Convolver<Float> conv(kernel, shape); |
---|
| 1017 | |
---|
| 1018 | // New Table |
---|
| 1019 | |
---|
| 1020 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
| 1021 | |
---|
| 1022 | // Output Vectors |
---|
| 1023 | |
---|
[434] | 1024 | Vector<Float> valuesOut(nChan); |
---|
| 1025 | Vector<Bool> maskOut(nChan); |
---|
[177] | 1026 | |
---|
[434] | 1027 | // Get data slice bounds |
---|
| 1028 | |
---|
| 1029 | IPosition start, end; |
---|
| 1030 | setCursorSlice (start, end, doAll, in); |
---|
| 1031 | |
---|
[177] | 1032 | // Loop over rows in Table |
---|
| 1033 | |
---|
[434] | 1034 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
[177] | 1035 | |
---|
[434] | 1036 | // Get slice of data |
---|
[177] | 1037 | |
---|
[434] | 1038 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(ri); |
---|
[177] | 1039 | |
---|
[434] | 1040 | // Deconstruct and get slices which reference these arrays |
---|
[177] | 1041 | |
---|
[434] | 1042 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 1043 | Array<Bool> maskIn = dataIn.getMask(); |
---|
[177] | 1044 | // |
---|
[434] | 1045 | Array<Float> valuesIn2 = valuesIn(start,end); // ref to valuesIn |
---|
| 1046 | Array<Bool> maskIn2 = maskIn(start,end); |
---|
[177] | 1047 | |
---|
[434] | 1048 | // Iterate through by spectra |
---|
[177] | 1049 | |
---|
[434] | 1050 | VectorIterator<Float> itValues(valuesIn2, asap::ChanAxis); |
---|
| 1051 | VectorIterator<Bool> itMask(maskIn2, asap::ChanAxis); |
---|
| 1052 | while (!itValues.pastEnd()) { |
---|
| 1053 | |
---|
[177] | 1054 | // Smooth |
---|
| 1055 | |
---|
[434] | 1056 | if (kernelType==VectorKernel::HANNING) { |
---|
| 1057 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector()); |
---|
| 1058 | itMask.vector() = maskOut; |
---|
| 1059 | } else { |
---|
| 1060 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
| 1061 | conv.linearConv(valuesOut, itValues.vector()); |
---|
| 1062 | } |
---|
| 1063 | // |
---|
| 1064 | itValues.vector() = valuesOut; |
---|
| 1065 | // |
---|
| 1066 | itValues.next(); |
---|
| 1067 | itMask.next(); |
---|
| 1068 | } |
---|
[177] | 1069 | |
---|
| 1070 | // Create and put back |
---|
| 1071 | |
---|
[434] | 1072 | SDContainer sc = in.getSDContainer(ri); |
---|
| 1073 | putDataInSDC(sc, valuesIn, maskIn); |
---|
[177] | 1074 | // |
---|
[434] | 1075 | pTabOut->putSDContainer(sc); |
---|
| 1076 | } |
---|
[177] | 1077 | // |
---|
| 1078 | return pTabOut; |
---|
| 1079 | } |
---|
| 1080 | |
---|
| 1081 | |
---|
[262] | 1082 | |
---|
[488] | 1083 | SDMemTable* SDMath::convertFlux(const SDMemTable& in, Float D, Float etaAp, |
---|
| 1084 | Float JyPerK, Bool doAll) const |
---|
[221] | 1085 | // |
---|
[478] | 1086 | // etaAp = aperture efficiency (-1 means find) |
---|
| 1087 | // D = geometric diameter (m) (-1 means find) |
---|
[354] | 1088 | // JyPerK |
---|
[221] | 1089 | // |
---|
| 1090 | { |
---|
| 1091 | SDHeader sh = in.getSDHeader(); |
---|
| 1092 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[177] | 1093 | |
---|
[354] | 1094 | // Find out how to convert values into Jy and K (e.g. units might be mJy or mK) |
---|
[221] | 1095 | // Also automatically find out what we are converting to according to the |
---|
| 1096 | // flux unit |
---|
[177] | 1097 | |
---|
[221] | 1098 | Unit fluxUnit(sh.fluxunit); |
---|
| 1099 | Unit K(String("K")); |
---|
| 1100 | Unit JY(String("Jy")); |
---|
| 1101 | // |
---|
| 1102 | Bool toKelvin = True; |
---|
[354] | 1103 | Double cFac = 1.0; |
---|
[221] | 1104 | if (fluxUnit==JY) { |
---|
[414] | 1105 | cout << "Converting to K" << endl; |
---|
[221] | 1106 | // |
---|
| 1107 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1108 | Quantum<Double> t2 = t.get(JY); |
---|
[354] | 1109 | cFac = (t2 / t).getValue(); // value to Jy |
---|
[221] | 1110 | // |
---|
| 1111 | toKelvin = True; |
---|
| 1112 | sh.fluxunit = "K"; |
---|
| 1113 | } else if (fluxUnit==K) { |
---|
[414] | 1114 | cout << "Converting to Jy" << endl; |
---|
[221] | 1115 | // |
---|
| 1116 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1117 | Quantum<Double> t2 = t.get(K); |
---|
[354] | 1118 | cFac = (t2 / t).getValue(); // value to K |
---|
[221] | 1119 | // |
---|
| 1120 | toKelvin = False; |
---|
| 1121 | sh.fluxunit = "Jy"; |
---|
| 1122 | } else { |
---|
[248] | 1123 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 1124 | } |
---|
| 1125 | pTabOut->putSDHeader(sh); |
---|
[177] | 1126 | |
---|
[354] | 1127 | // Make sure input values are converted to either Jy or K first... |
---|
[221] | 1128 | |
---|
[354] | 1129 | Float factor = cFac; |
---|
[221] | 1130 | |
---|
[354] | 1131 | // Select method |
---|
[221] | 1132 | |
---|
[354] | 1133 | if (JyPerK>0.0) { |
---|
| 1134 | factor *= JyPerK; |
---|
| 1135 | if (toKelvin) factor = 1.0 / JyPerK; |
---|
| 1136 | // |
---|
[478] | 1137 | cout << "Jy/K = " << JyPerK << endl; |
---|
[354] | 1138 | Vector<Float> factors(in.nRow(), factor); |
---|
[480] | 1139 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
[354] | 1140 | } else if (etaAp>0.0) { |
---|
[478] | 1141 | Bool throwIt = True; |
---|
| 1142 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
| 1143 | SDAttr sda; |
---|
| 1144 | if (D < 0) D = sda.diameter(inst); |
---|
| 1145 | Float JyPerK = SDAttr::findJyPerK (etaAp,D); |
---|
| 1146 | cout << "Jy/K = " << JyPerK << endl; |
---|
| 1147 | factor *= JyPerK; |
---|
[354] | 1148 | if (toKelvin) { |
---|
| 1149 | factor = 1.0 / factor; |
---|
| 1150 | } |
---|
| 1151 | // |
---|
| 1152 | Vector<Float> factors(in.nRow(), factor); |
---|
[480] | 1153 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
[354] | 1154 | } else { |
---|
[221] | 1155 | |
---|
[354] | 1156 | // OK now we must deal with automatic look up of values. |
---|
| 1157 | // We must also deal with the fact that the factors need |
---|
| 1158 | // to be computed per IF and may be different and may |
---|
| 1159 | // change per integration. |
---|
[221] | 1160 | |
---|
[414] | 1161 | cout << "Looking up conversion factors" << endl; |
---|
[354] | 1162 | convertBrightnessUnits (pTabOut, in, toKelvin, cFac, doAll); |
---|
| 1163 | } |
---|
[221] | 1164 | // |
---|
| 1165 | return pTabOut; |
---|
| 1166 | } |
---|
| 1167 | |
---|
| 1168 | |
---|
[354] | 1169 | |
---|
| 1170 | |
---|
| 1171 | |
---|
[488] | 1172 | SDMemTable* SDMath::gainElevation(const SDMemTable& in, |
---|
| 1173 | const Vector<Float>& coeffs, |
---|
| 1174 | const String& fileName, |
---|
| 1175 | const String& methodStr, Bool doAll) const |
---|
[227] | 1176 | { |
---|
[234] | 1177 | |
---|
| 1178 | // Get header and clone output table |
---|
| 1179 | |
---|
[227] | 1180 | SDHeader sh = in.getSDHeader(); |
---|
| 1181 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1182 | |
---|
[234] | 1183 | // Get elevation data from SDMemTable and convert to degrees |
---|
[227] | 1184 | |
---|
| 1185 | const Table& tab = in.table(); |
---|
| 1186 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[234] | 1187 | Vector<Float> x = elev.getColumn(); |
---|
[363] | 1188 | x *= Float(180 / C::pi); // Degrees |
---|
[227] | 1189 | // |
---|
[234] | 1190 | const uInt nC = coeffs.nelements(); |
---|
| 1191 | if (fileName.length()>0 && nC>0) { |
---|
[248] | 1192 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
[234] | 1193 | } |
---|
| 1194 | |
---|
| 1195 | // Correct |
---|
| 1196 | |
---|
| 1197 | if (nC>0 || fileName.length()==0) { |
---|
| 1198 | |
---|
| 1199 | // Find instrument |
---|
| 1200 | |
---|
| 1201 | Bool throwIt = True; |
---|
[478] | 1202 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
[234] | 1203 | |
---|
| 1204 | // Set polynomial |
---|
| 1205 | |
---|
| 1206 | Polynomial<Float>* pPoly = 0; |
---|
| 1207 | Vector<Float> coeff; |
---|
| 1208 | String msg; |
---|
| 1209 | if (nC>0) { |
---|
| 1210 | pPoly = new Polynomial<Float>(nC); |
---|
| 1211 | coeff = coeffs; |
---|
| 1212 | msg = String("user"); |
---|
| 1213 | } else { |
---|
[363] | 1214 | SDAttr sdAttr; |
---|
| 1215 | coeff = sdAttr.gainElevationPoly(inst); |
---|
| 1216 | pPoly = new Polynomial<Float>(3); |
---|
[234] | 1217 | msg = String("built in"); |
---|
| 1218 | } |
---|
[227] | 1219 | // |
---|
[234] | 1220 | if (coeff.nelements()>0) { |
---|
| 1221 | pPoly->setCoefficients(coeff); |
---|
| 1222 | } else { |
---|
[363] | 1223 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
[234] | 1224 | } |
---|
| 1225 | // |
---|
[414] | 1226 | cout << "Making polynomial correction with " << msg << " coefficients" << endl; |
---|
[234] | 1227 | const uInt nRow = in.nRow(); |
---|
| 1228 | Vector<Float> factor(nRow); |
---|
| 1229 | for (uInt i=0; i<nRow; i++) { |
---|
[480] | 1230 | factor[i] = 1.0 / (*pPoly)(x[i]); |
---|
[234] | 1231 | } |
---|
| 1232 | delete pPoly; |
---|
| 1233 | // |
---|
[480] | 1234 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
[234] | 1235 | } else { |
---|
| 1236 | |
---|
| 1237 | // Indicate which columns to read from ascii file |
---|
| 1238 | |
---|
| 1239 | String col0("ELEVATION"); |
---|
| 1240 | String col1("FACTOR"); |
---|
| 1241 | |
---|
| 1242 | // Read and correct |
---|
| 1243 | |
---|
[414] | 1244 | cout << "Making correction from ascii Table" << endl; |
---|
[480] | 1245 | scaleFromAsciiTable (pTabOut, in, fileName, col0, col1, |
---|
| 1246 | methodStr, doAll, x, True); |
---|
[234] | 1247 | } |
---|
| 1248 | // |
---|
| 1249 | return pTabOut; |
---|
[230] | 1250 | } |
---|
[227] | 1251 | |
---|
[230] | 1252 | |
---|
[227] | 1253 | |
---|
[488] | 1254 | SDMemTable* SDMath::opacity(const SDMemTable& in, Float tau, Bool doAll) const |
---|
[234] | 1255 | { |
---|
[227] | 1256 | |
---|
[234] | 1257 | // Get header and clone output table |
---|
[227] | 1258 | |
---|
[234] | 1259 | SDHeader sh = in.getSDHeader(); |
---|
| 1260 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1261 | |
---|
| 1262 | // Get elevation data from SDMemTable and convert to degrees |
---|
| 1263 | |
---|
| 1264 | const Table& tab = in.table(); |
---|
| 1265 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 1266 | Vector<Float> zDist = elev.getColumn(); |
---|
| 1267 | zDist = Float(C::pi_2) - zDist; |
---|
| 1268 | |
---|
| 1269 | // Generate correction factor |
---|
| 1270 | |
---|
| 1271 | const uInt nRow = in.nRow(); |
---|
| 1272 | Vector<Float> factor(nRow); |
---|
| 1273 | Vector<Float> factor2(nRow); |
---|
| 1274 | for (uInt i=0; i<nRow; i++) { |
---|
| 1275 | factor[i] = exp(tau)/cos(zDist[i]); |
---|
| 1276 | } |
---|
| 1277 | |
---|
| 1278 | // Correct |
---|
| 1279 | |
---|
[480] | 1280 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
[234] | 1281 | // |
---|
| 1282 | return pTabOut; |
---|
| 1283 | } |
---|
| 1284 | |
---|
| 1285 | |
---|
[488] | 1286 | void SDMath::rotateXYPhase(SDMemTable& in, Float value, Bool doAll) |
---|
[457] | 1287 | // |
---|
| 1288 | // phase in degrees |
---|
[518] | 1289 | // assumes linear correlations |
---|
[457] | 1290 | // |
---|
| 1291 | { |
---|
| 1292 | if (in.nPol() != 4) { |
---|
| 1293 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
| 1294 | } |
---|
[518] | 1295 | // |
---|
| 1296 | SDHeader sh = in.getSDHeader(); |
---|
| 1297 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False); |
---|
| 1298 | SDAttr sdAtt; |
---|
| 1299 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
| 1300 | throw(AipsError("Only linear polarizations are supported")); |
---|
| 1301 | } |
---|
[457] | 1302 | // |
---|
| 1303 | const Table& tabIn = in.table(); |
---|
| 1304 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
| 1305 | IPosition start(asap::nAxes,0); |
---|
| 1306 | IPosition end(asap::nAxes); |
---|
[234] | 1307 | |
---|
[457] | 1308 | // Set cursor slice. Assumes shape the same for all rows |
---|
| 1309 | |
---|
| 1310 | setCursorSlice (start, end, doAll, in); |
---|
| 1311 | IPosition start3(start); |
---|
| 1312 | start3(asap::PolAxis) = 2; // Real(XY) |
---|
| 1313 | IPosition end3(end); |
---|
| 1314 | end3(asap::PolAxis) = 2; |
---|
| 1315 | // |
---|
| 1316 | IPosition start4(start); |
---|
| 1317 | start4(asap::PolAxis) = 3; // Imag (XY) |
---|
| 1318 | IPosition end4(end); |
---|
| 1319 | end4(asap::PolAxis) = 3; |
---|
| 1320 | // |
---|
| 1321 | uInt nRow = in.nRow(); |
---|
| 1322 | Array<Float> data; |
---|
| 1323 | for (uInt i=0; i<nRow;++i) { |
---|
| 1324 | specCol.get(i,data); |
---|
| 1325 | IPosition shape = data.shape(); |
---|
| 1326 | |
---|
| 1327 | // Get polarization slice references |
---|
| 1328 | |
---|
| 1329 | Array<Float> C3 = data(start3,end3); |
---|
| 1330 | Array<Float> C4 = data(start4,end4); |
---|
| 1331 | |
---|
| 1332 | // Rotate |
---|
| 1333 | |
---|
[502] | 1334 | SDPolUtil::rotatePhase(C3, C4, value); |
---|
[457] | 1335 | |
---|
| 1336 | // Put |
---|
| 1337 | |
---|
| 1338 | specCol.put(i,data); |
---|
| 1339 | } |
---|
| 1340 | } |
---|
[234] | 1341 | |
---|
[502] | 1342 | |
---|
| 1343 | |
---|
| 1344 | void SDMath::rotateLinPolPhase(SDMemTable& in, Float value, Bool doAll) |
---|
| 1345 | // |
---|
| 1346 | // phase in degrees |
---|
[518] | 1347 | // assumes linear correlations |
---|
[502] | 1348 | // |
---|
| 1349 | { |
---|
| 1350 | if (in.nPol() != 4) { |
---|
| 1351 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
| 1352 | } |
---|
[518] | 1353 | // |
---|
| 1354 | SDHeader sh = in.getSDHeader(); |
---|
| 1355 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False); |
---|
| 1356 | SDAttr sdAtt; |
---|
| 1357 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
| 1358 | throw(AipsError("Only linear polarizations are supported")); |
---|
| 1359 | } |
---|
[502] | 1360 | // |
---|
| 1361 | const Table& tabIn = in.table(); |
---|
| 1362 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
| 1363 | ROArrayColumn<Float> stokesCol(tabIn,"STOKES"); |
---|
| 1364 | IPosition start(asap::nAxes,0); |
---|
| 1365 | IPosition end(asap::nAxes); |
---|
| 1366 | |
---|
| 1367 | // Set cursor slice. Assumes shape the same for all rows |
---|
| 1368 | |
---|
| 1369 | setCursorSlice (start, end, doAll, in); |
---|
| 1370 | // |
---|
| 1371 | IPosition start1(start); |
---|
| 1372 | start1(asap::PolAxis) = 0; // C1 (XX) |
---|
| 1373 | IPosition end1(end); |
---|
| 1374 | end1(asap::PolAxis) = 0; |
---|
| 1375 | // |
---|
| 1376 | IPosition start2(start); |
---|
| 1377 | start2(asap::PolAxis) = 1; // C2 (YY) |
---|
| 1378 | IPosition end2(end); |
---|
| 1379 | end2(asap::PolAxis) = 1; |
---|
| 1380 | // |
---|
| 1381 | IPosition start3(start); |
---|
| 1382 | start3(asap::PolAxis) = 2; // C3 ( Real(XY) ) |
---|
| 1383 | IPosition end3(end); |
---|
| 1384 | end3(asap::PolAxis) = 2; |
---|
| 1385 | // |
---|
| 1386 | IPosition startI(start); |
---|
| 1387 | startI(asap::PolAxis) = 0; // I |
---|
| 1388 | IPosition endI(end); |
---|
| 1389 | endI(asap::PolAxis) = 0; |
---|
| 1390 | // |
---|
| 1391 | IPosition startQ(start); |
---|
| 1392 | startQ(asap::PolAxis) = 1; // Q |
---|
| 1393 | IPosition endQ(end); |
---|
| 1394 | endQ(asap::PolAxis) = 1; |
---|
| 1395 | // |
---|
| 1396 | IPosition startU(start); |
---|
| 1397 | startU(asap::PolAxis) = 2; // U |
---|
| 1398 | IPosition endU(end); |
---|
| 1399 | endU(asap::PolAxis) = 2; |
---|
| 1400 | |
---|
| 1401 | // |
---|
| 1402 | uInt nRow = in.nRow(); |
---|
| 1403 | Array<Float> data, stokes; |
---|
| 1404 | for (uInt i=0; i<nRow;++i) { |
---|
| 1405 | specCol.get(i,data); |
---|
| 1406 | stokesCol.get(i,stokes); |
---|
| 1407 | IPosition shape = data.shape(); |
---|
| 1408 | |
---|
| 1409 | // Get linear polarization slice references |
---|
| 1410 | |
---|
| 1411 | Array<Float> C1 = data(start1,end1); |
---|
| 1412 | Array<Float> C2 = data(start2,end2); |
---|
| 1413 | Array<Float> C3 = data(start3,end3); |
---|
| 1414 | |
---|
| 1415 | // Get STokes slice references |
---|
| 1416 | |
---|
| 1417 | Array<Float> I = stokes(startI,endI); |
---|
| 1418 | Array<Float> Q = stokes(startQ,endQ); |
---|
| 1419 | Array<Float> U = stokes(startU,endU); |
---|
| 1420 | |
---|
| 1421 | // Rotate |
---|
| 1422 | |
---|
| 1423 | SDPolUtil::rotateLinPolPhase(C1, C2, C3, I, Q, U, value); |
---|
| 1424 | |
---|
| 1425 | // Put |
---|
| 1426 | |
---|
| 1427 | specCol.put(i,data); |
---|
| 1428 | } |
---|
| 1429 | } |
---|
| 1430 | |
---|
[169] | 1431 | // 'private' functions |
---|
| 1432 | |
---|
[354] | 1433 | void SDMath::convertBrightnessUnits (SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 1434 | Bool toKelvin, Float cFac, Bool doAll) const |
---|
| 1435 | { |
---|
[309] | 1436 | |
---|
[354] | 1437 | // Get header |
---|
| 1438 | |
---|
| 1439 | SDHeader sh = in.getSDHeader(); |
---|
| 1440 | const uInt nChan = sh.nchan; |
---|
| 1441 | |
---|
| 1442 | // Get instrument |
---|
| 1443 | |
---|
| 1444 | Bool throwIt = True; |
---|
[478] | 1445 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
[354] | 1446 | |
---|
| 1447 | // Get Diameter (m) |
---|
| 1448 | |
---|
| 1449 | SDAttr sdAtt; |
---|
| 1450 | |
---|
| 1451 | // Get epoch of first row |
---|
| 1452 | |
---|
| 1453 | MEpoch dateObs = in.getEpoch(0); |
---|
| 1454 | |
---|
| 1455 | // Generate a Vector of correction factors. One per FreqID |
---|
| 1456 | |
---|
| 1457 | SDFrequencyTable sdft = in.getSDFreqTable(); |
---|
| 1458 | Vector<uInt> freqIDs; |
---|
| 1459 | // |
---|
| 1460 | Vector<Float> freqs(sdft.length()); |
---|
| 1461 | for (uInt i=0; i<sdft.length(); i++) { |
---|
| 1462 | freqs(i) = (nChan/2 - sdft.referencePixel(i))*sdft.increment(i) + sdft.referenceValue(i); |
---|
| 1463 | } |
---|
| 1464 | // |
---|
| 1465 | Vector<Float> JyPerK = sdAtt.JyPerK(inst, dateObs, freqs); |
---|
[414] | 1466 | cout << "Jy/K = " << JyPerK << endl; |
---|
[354] | 1467 | Vector<Float> factors = cFac * JyPerK; |
---|
| 1468 | if (toKelvin) factors = Float(1.0) / factors; |
---|
| 1469 | |
---|
[434] | 1470 | // Get data slice bounds |
---|
[354] | 1471 | |
---|
| 1472 | IPosition start, end; |
---|
[434] | 1473 | setCursorSlice (start, end, doAll, in); |
---|
[354] | 1474 | const uInt ifAxis = in.getIF(); |
---|
| 1475 | |
---|
| 1476 | // Iteration axes |
---|
| 1477 | |
---|
| 1478 | IPosition axes(asap::nAxes-1,0); |
---|
| 1479 | for (uInt i=0,j=0; i<asap::nAxes; i++) { |
---|
| 1480 | if (i!=asap::IFAxis) { |
---|
| 1481 | axes(j++) = i; |
---|
| 1482 | } |
---|
| 1483 | } |
---|
| 1484 | |
---|
| 1485 | // Loop over rows and apply correction factor |
---|
| 1486 | |
---|
| 1487 | Float factor = 1.0; |
---|
| 1488 | const uInt axis = asap::ChanAxis; |
---|
| 1489 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 1490 | |
---|
| 1491 | // Get data |
---|
| 1492 | |
---|
[434] | 1493 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(i); |
---|
| 1494 | Array<Float>& values = dataIn.getRWArray(); // Ref to dataIn |
---|
| 1495 | Array<Float> values2 = values(start,end); // Ref to values to dataIn |
---|
[354] | 1496 | |
---|
| 1497 | // Get SDCOntainer |
---|
| 1498 | |
---|
| 1499 | SDContainer sc = in.getSDContainer(i); |
---|
| 1500 | |
---|
| 1501 | // Get FreqIDs |
---|
| 1502 | |
---|
| 1503 | freqIDs = sc.getFreqMap(); |
---|
| 1504 | |
---|
| 1505 | // Now the conversion factor depends only upon frequency |
---|
| 1506 | // So we need to iterate through by IF only giving |
---|
| 1507 | // us BEAM/POL/CHAN cubes |
---|
| 1508 | |
---|
[434] | 1509 | ArrayIterator<Float> itIn(values2, axes); |
---|
| 1510 | uInt ax = 0; |
---|
| 1511 | while (!itIn.pastEnd()) { |
---|
| 1512 | itIn.array() *= factors(freqIDs(ax)); // Writes back to dataIn |
---|
| 1513 | itIn.next(); |
---|
[354] | 1514 | } |
---|
| 1515 | |
---|
| 1516 | // Write out |
---|
| 1517 | |
---|
| 1518 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
| 1519 | // |
---|
| 1520 | pTabOut->putSDContainer(sc); |
---|
| 1521 | } |
---|
| 1522 | } |
---|
| 1523 | |
---|
| 1524 | |
---|
| 1525 | |
---|
[309] | 1526 | SDMemTable* SDMath::frequencyAlign (const SDMemTable& in, |
---|
| 1527 | MFrequency::Types freqSystem, |
---|
[397] | 1528 | const String& refTime, |
---|
| 1529 | const String& methodStr, |
---|
| 1530 | Bool perFreqID) const |
---|
[267] | 1531 | { |
---|
| 1532 | // Get Header |
---|
| 1533 | |
---|
| 1534 | SDHeader sh = in.getSDHeader(); |
---|
| 1535 | const uInt nChan = sh.nchan; |
---|
| 1536 | const uInt nRows = in.nRow(); |
---|
[330] | 1537 | const uInt nIF = sh.nif; |
---|
[267] | 1538 | |
---|
| 1539 | // Get Table reference |
---|
| 1540 | |
---|
| 1541 | const Table& tabIn = in.table(); |
---|
| 1542 | |
---|
| 1543 | // Get Columns from Table |
---|
| 1544 | |
---|
[294] | 1545 | ROScalarColumn<Double> mjdCol(tabIn, "TIME"); |
---|
| 1546 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME"); |
---|
| 1547 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID"); |
---|
| 1548 | Vector<Double> times = mjdCol.getColumn(); |
---|
[267] | 1549 | |
---|
[397] | 1550 | // Generate DataDesc table |
---|
[330] | 1551 | |
---|
| 1552 | Matrix<uInt> ddIdx; |
---|
| 1553 | SDDataDesc dDesc; |
---|
[397] | 1554 | generateDataDescTable (ddIdx, dDesc, nIF, in, tabIn, srcCol, fqIDCol, perFreqID); |
---|
[267] | 1555 | |
---|
[294] | 1556 | // Get reference Epoch to time of first row or given String |
---|
[267] | 1557 | |
---|
| 1558 | Unit DAY(String("d")); |
---|
[272] | 1559 | MEpoch::Ref epochRef(in.getTimeReference()); |
---|
| 1560 | MEpoch refEpoch; |
---|
| 1561 | if (refTime.length()>0) { |
---|
| 1562 | refEpoch = epochFromString(refTime, in.getTimeReference()); |
---|
| 1563 | } else { |
---|
[288] | 1564 | refEpoch = in.getEpoch(0); |
---|
[272] | 1565 | } |
---|
[414] | 1566 | cout << "Aligning at reference Epoch " << formatEpoch(refEpoch) |
---|
| 1567 | << " in frame " << MFrequency::showType(freqSystem) << endl; |
---|
| 1568 | |
---|
[294] | 1569 | // Get Reference Position |
---|
[267] | 1570 | |
---|
[288] | 1571 | MPosition refPos = in.getAntennaPosition(); |
---|
[267] | 1572 | |
---|
[397] | 1573 | // Create FrequencyAligner Block. One FA for each possible |
---|
| 1574 | // source/freqID (perFreqID=True) or source/IF (perFreqID=False) combination |
---|
[267] | 1575 | |
---|
[330] | 1576 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length()); |
---|
[397] | 1577 | generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos, |
---|
| 1578 | refEpoch, perFreqID); |
---|
[267] | 1579 | |
---|
[397] | 1580 | // Generate and fill output Frequency Table. WHen perFreqID=True, there is one output FreqID |
---|
| 1581 | // for each entry in the SDDataDesc table. However, in perFreqID=False mode, there may be |
---|
| 1582 | // some degeneracy, so we need a little translation map |
---|
[330] | 1583 | |
---|
| 1584 | SDFrequencyTable freqTabOut = in.getSDFreqTable(); |
---|
| 1585 | freqTabOut.setLength(0); |
---|
| 1586 | Vector<String> units(1); |
---|
| 1587 | units = String("Hz"); |
---|
| 1588 | Bool linear=True; |
---|
| 1589 | // |
---|
[397] | 1590 | Vector<uInt> ddFQTrans(dDesc.length(),0); |
---|
[330] | 1591 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
| 1592 | |
---|
| 1593 | // Get Aligned SC in Hz |
---|
| 1594 | |
---|
| 1595 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear); |
---|
| 1596 | sC.setWorldAxisUnits(units); |
---|
| 1597 | |
---|
| 1598 | // Add FreqID |
---|
| 1599 | |
---|
[397] | 1600 | uInt idx = freqTabOut.addFrequency(sC.referencePixel()[0], |
---|
| 1601 | sC.referenceValue()[0], |
---|
| 1602 | sC.increment()[0]); |
---|
| 1603 | ddFQTrans(i) = idx; // output FreqID = ddFQTrans(ddIdx) |
---|
[330] | 1604 | } |
---|
| 1605 | |
---|
[317] | 1606 | // Interpolation method |
---|
| 1607 | |
---|
| 1608 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
| 1609 | convertInterpString(interp, methodStr); |
---|
| 1610 | |
---|
[267] | 1611 | // New output Table |
---|
| 1612 | |
---|
[414] | 1613 | cout << "Create output table" << endl; |
---|
[267] | 1614 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
[330] | 1615 | pTabOut->putSDFreqTable(freqTabOut); |
---|
[267] | 1616 | |
---|
| 1617 | // Loop over rows in Table |
---|
| 1618 | |
---|
[330] | 1619 | Bool extrapolate=False; |
---|
[294] | 1620 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis); |
---|
| 1621 | Bool useCachedAbcissa = False; |
---|
| 1622 | Bool first = True; |
---|
| 1623 | Bool ok; |
---|
| 1624 | Vector<Float> yOut; |
---|
| 1625 | Vector<Bool> maskOut; |
---|
[330] | 1626 | Vector<uInt> freqID(nIF); |
---|
[309] | 1627 | uInt ifIdx, faIdx; |
---|
[397] | 1628 | Vector<Double> xIn; |
---|
[267] | 1629 | // |
---|
[294] | 1630 | for (uInt iRow=0; iRow<nRows; ++iRow) { |
---|
| 1631 | if (iRow%10==0) { |
---|
[414] | 1632 | cout << "Processing row " << iRow << endl; |
---|
[294] | 1633 | } |
---|
[267] | 1634 | |
---|
| 1635 | // Get EPoch |
---|
| 1636 | |
---|
[294] | 1637 | Quantum<Double> tQ2(times[iRow],DAY); |
---|
| 1638 | MVEpoch mv2(tQ2); |
---|
| 1639 | MEpoch epoch(mv2, epochRef); |
---|
[267] | 1640 | |
---|
| 1641 | // Get copy of data |
---|
| 1642 | |
---|
[294] | 1643 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow)); |
---|
| 1644 | Array<Float> values = mArrIn.getArray(); |
---|
| 1645 | Array<Bool> mask = mArrIn.getMask(); |
---|
[267] | 1646 | |
---|
[309] | 1647 | // For each row, the Frequency abcissa will be the same regardless |
---|
[267] | 1648 | // of polarization. For all other axes (IF and BEAM) the abcissa |
---|
| 1649 | // will change. So we iterate through the data by pol-chan planes |
---|
[330] | 1650 | // to mimimize the work. Probably won't work for multiple beams |
---|
| 1651 | // at this point. |
---|
[267] | 1652 | |
---|
[294] | 1653 | ArrayIterator<Float> itValuesPlane(values, polChanAxes); |
---|
| 1654 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes); |
---|
| 1655 | while (!itValuesPlane.pastEnd()) { |
---|
[267] | 1656 | |
---|
[309] | 1657 | // Find the IF index and then the FA PtrBlock index |
---|
[267] | 1658 | |
---|
[294] | 1659 | const IPosition& pos = itValuesPlane.pos(); |
---|
| 1660 | ifIdx = pos(asap::IFAxis); |
---|
[330] | 1661 | faIdx = ddIdx(iRow,ifIdx); |
---|
[397] | 1662 | |
---|
| 1663 | // Generate abcissa for perIF. Could cache this in a Matrix |
---|
| 1664 | // on a per scan basis. Pretty expensive doing it for every row. |
---|
| 1665 | |
---|
| 1666 | if (!perFreqID) { |
---|
| 1667 | xIn.resize(nChan); |
---|
| 1668 | uInt fqID = dDesc.secID(ddIdx(iRow,ifIdx)); |
---|
| 1669 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID); |
---|
| 1670 | Double w; |
---|
| 1671 | for (uInt i=0; i<nChan; i++) { |
---|
| 1672 | sC.toWorld(w,Double(i)); |
---|
| 1673 | xIn[i] = w; |
---|
| 1674 | } |
---|
| 1675 | } |
---|
[267] | 1676 | // |
---|
[294] | 1677 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1); |
---|
| 1678 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
[330] | 1679 | |
---|
| 1680 | // Iterate through the plane by vector and align |
---|
| 1681 | |
---|
[294] | 1682 | first = True; |
---|
| 1683 | useCachedAbcissa=False; |
---|
| 1684 | while (!itValuesVec.pastEnd()) { |
---|
[397] | 1685 | if (perFreqID) { |
---|
| 1686 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(), |
---|
| 1687 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
| 1688 | interp, extrapolate); |
---|
| 1689 | } else { |
---|
| 1690 | ok = a[faIdx]->align (yOut, maskOut, xIn, itValuesVec.vector(), |
---|
| 1691 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
| 1692 | interp, extrapolate); |
---|
| 1693 | } |
---|
[330] | 1694 | // |
---|
[294] | 1695 | itValuesVec.vector() = yOut; |
---|
| 1696 | itMaskVec.vector() = maskOut; |
---|
[267] | 1697 | // |
---|
[294] | 1698 | itValuesVec.next(); |
---|
| 1699 | itMaskVec.next(); |
---|
[267] | 1700 | // |
---|
[294] | 1701 | if (first) { |
---|
| 1702 | useCachedAbcissa = True; |
---|
| 1703 | first = False; |
---|
| 1704 | } |
---|
| 1705 | } |
---|
[267] | 1706 | // |
---|
| 1707 | itValuesPlane.next(); |
---|
| 1708 | itMaskPlane.next(); |
---|
[294] | 1709 | } |
---|
[267] | 1710 | |
---|
[330] | 1711 | // Create SDContainer and put back |
---|
[267] | 1712 | |
---|
| 1713 | SDContainer sc = in.getSDContainer(iRow); |
---|
| 1714 | putDataInSDC(sc, values, mask); |
---|
[397] | 1715 | |
---|
| 1716 | // Set output FreqIDs |
---|
| 1717 | |
---|
[330] | 1718 | for (uInt i=0; i<nIF; i++) { |
---|
[397] | 1719 | uInt idx = ddIdx(iRow,i); // Index into SDDataDesc table |
---|
| 1720 | freqID(i) = ddFQTrans(idx); // FreqID in output FQ table |
---|
[330] | 1721 | } |
---|
| 1722 | sc.putFreqMap(freqID); |
---|
[267] | 1723 | // |
---|
| 1724 | pTabOut->putSDContainer(sc); |
---|
[294] | 1725 | } |
---|
[267] | 1726 | |
---|
[309] | 1727 | // Now we must set the base and extra frames to the |
---|
| 1728 | // input frame |
---|
| 1729 | |
---|
| 1730 | std::vector<string> info = pTabOut->getCoordInfo(); |
---|
| 1731 | info[1] = MFrequency::showType(freqSystem); // Conversion frame |
---|
| 1732 | info[3] = info[1]; // Base frame |
---|
| 1733 | pTabOut->setCoordInfo(info); |
---|
| 1734 | |
---|
[267] | 1735 | // Clean up PointerBlock |
---|
| 1736 | |
---|
[309] | 1737 | for (uInt i=0; i<a.nelements(); i++) delete a[i]; |
---|
[267] | 1738 | // |
---|
[309] | 1739 | return pTabOut; |
---|
[267] | 1740 | } |
---|
| 1741 | |
---|
| 1742 | |
---|
[185] | 1743 | void SDMath::fillSDC(SDContainer& sc, |
---|
| 1744 | const Array<Bool>& mask, |
---|
| 1745 | const Array<Float>& data, |
---|
| 1746 | const Array<Float>& tSys, |
---|
| 1747 | Int scanID, Double timeStamp, |
---|
| 1748 | Double interval, const String& sourceName, |
---|
[227] | 1749 | const Vector<uInt>& freqID) const |
---|
[167] | 1750 | { |
---|
[169] | 1751 | // Data and mask |
---|
[167] | 1752 | |
---|
[185] | 1753 | putDataInSDC(sc, data, mask); |
---|
[167] | 1754 | |
---|
[169] | 1755 | // TSys |
---|
| 1756 | |
---|
| 1757 | sc.putTsys(tSys); |
---|
| 1758 | |
---|
| 1759 | // Time things |
---|
| 1760 | |
---|
| 1761 | sc.timestamp = timeStamp; |
---|
| 1762 | sc.interval = interval; |
---|
| 1763 | sc.scanid = scanID; |
---|
[167] | 1764 | // |
---|
[169] | 1765 | sc.sourcename = sourceName; |
---|
| 1766 | sc.putFreqMap(freqID); |
---|
| 1767 | } |
---|
[167] | 1768 | |
---|
[185] | 1769 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum, |
---|
| 1770 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
| 1771 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
[518] | 1772 | Array<Float>& tSysSqSum, |
---|
[185] | 1773 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
| 1774 | const Vector<Bool>& mask, Double time, Double interval, |
---|
| 1775 | const Block<CountedPtr<SDMemTable> >& in, |
---|
| 1776 | uInt iTab, uInt iRow, uInt axis, |
---|
| 1777 | uInt nAxesSub, Bool useMask, |
---|
[227] | 1778 | WeightType wtType) const |
---|
[169] | 1779 | { |
---|
| 1780 | |
---|
| 1781 | // Get data |
---|
| 1782 | |
---|
| 1783 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
| 1784 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
| 1785 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
[167] | 1786 | // |
---|
[169] | 1787 | if (wtType==NONE) { |
---|
| 1788 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
| 1789 | nPts += n; // Only accumulates where mask==T |
---|
[518] | 1790 | } else if (wtType==TINT) { |
---|
| 1791 | |
---|
| 1792 | // We are weighting the data by integration time. |
---|
| 1793 | |
---|
| 1794 | valuesIn *= Float(interval); |
---|
| 1795 | |
---|
[169] | 1796 | } else if (wtType==VAR) { |
---|
[167] | 1797 | |
---|
[169] | 1798 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
| 1799 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
[167] | 1800 | |
---|
[169] | 1801 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1802 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
| 1803 | Float fac = 1.0; |
---|
| 1804 | IPosition pos(nAxesSub,0); |
---|
| 1805 | // |
---|
| 1806 | while (!itData.pastEnd()) { |
---|
[167] | 1807 | |
---|
[169] | 1808 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
[167] | 1809 | |
---|
[518] | 1810 | if (useMask) { |
---|
| 1811 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
| 1812 | fac = 1.0/variance(tmp); |
---|
| 1813 | } else { |
---|
| 1814 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
| 1815 | fac = 1.0/variance(tmp); |
---|
| 1816 | } |
---|
[169] | 1817 | |
---|
| 1818 | // Scale data |
---|
| 1819 | |
---|
[518] | 1820 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
[167] | 1821 | // |
---|
[169] | 1822 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
| 1823 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1824 | // because the spectral axis is the last one (so we can just |
---|
| 1825 | // copy the first nAXesSub positions out) |
---|
[167] | 1826 | |
---|
[518] | 1827 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1828 | sumSq(pos) += fac; |
---|
[169] | 1829 | // |
---|
[518] | 1830 | itData.next(); |
---|
| 1831 | itMask.next(); |
---|
[169] | 1832 | } |
---|
[536] | 1833 | } else if (wtType==TSYS || wtType==TINTSYS) { |
---|
[518] | 1834 | |
---|
| 1835 | // We are going to average the data, weighted by 1/Tsys**2 for each pol, beam and IF. |
---|
| 1836 | // So therefore we need to iterate through by spectrum (axis 3). Although |
---|
| 1837 | // Tsys is stored as a vector of length nChan, the values are replicated. |
---|
| 1838 | // We will take a short cut and just use the value from the first channel |
---|
| 1839 | // for now. |
---|
| 1840 | // |
---|
| 1841 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1842 | ReadOnlyVectorIterator<Float> itTSys(tSys, axis); |
---|
| 1843 | IPosition pos(nAxesSub,0); |
---|
| 1844 | // |
---|
[536] | 1845 | Float fac = 1.0; |
---|
| 1846 | if (wtType==TINTSYS) fac *= interval; |
---|
[518] | 1847 | while (!itData.pastEnd()) { |
---|
| 1848 | Float t = itTSys.vector()[0]; |
---|
[536] | 1849 | fac *= 1.0/t/t; |
---|
[518] | 1850 | |
---|
| 1851 | // Scale data |
---|
| 1852 | |
---|
| 1853 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
| 1854 | // |
---|
| 1855 | // Accumulate Tsys per if/pol/beam averaged over spectrum |
---|
| 1856 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1857 | // because the spectral axis is the last one (so we can just |
---|
| 1858 | // copy the first nAXesSub positions out) |
---|
| 1859 | |
---|
| 1860 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1861 | tSysSqSum(pos) += fac; |
---|
| 1862 | // |
---|
| 1863 | itData.next(); |
---|
| 1864 | itTSys.next(); |
---|
| 1865 | } |
---|
[169] | 1866 | } |
---|
[167] | 1867 | |
---|
[169] | 1868 | // Accumulate sum of (possibly scaled) data |
---|
| 1869 | |
---|
| 1870 | sum += dataIn; |
---|
| 1871 | |
---|
| 1872 | // Accumulate Tsys, time, and interval |
---|
| 1873 | |
---|
| 1874 | tSysSum += tSys; |
---|
| 1875 | timeSum += time; |
---|
| 1876 | intSum += interval; |
---|
| 1877 | nAccum += 1; |
---|
| 1878 | } |
---|
| 1879 | |
---|
| 1880 | |
---|
[518] | 1881 | void SDMath::normalize(MaskedArray<Float>& sum, |
---|
| 1882 | const Array<Float>& sumSq, |
---|
| 1883 | const Array<Float>& tSysSqSum, |
---|
| 1884 | const Array<Float>& nPts, |
---|
| 1885 | Double intSum, |
---|
| 1886 | WeightType wtType, Int axis, |
---|
| 1887 | Int nAxesSub) const |
---|
| 1888 | { |
---|
| 1889 | IPosition pos2(nAxesSub,0); |
---|
| 1890 | // |
---|
| 1891 | if (wtType==NONE) { |
---|
| 1892 | |
---|
| 1893 | // We just average by the number of points accumulated. |
---|
| 1894 | // We need to make a MA out of nPts so that no divide by |
---|
| 1895 | // zeros occur |
---|
| 1896 | |
---|
| 1897 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
| 1898 | sum /= t; |
---|
| 1899 | } else if (wtType==TINT) { |
---|
| 1900 | |
---|
| 1901 | // Average by sum of Tint |
---|
| 1902 | |
---|
| 1903 | sum /= Float(intSum); |
---|
| 1904 | } else if (wtType==VAR) { |
---|
| 1905 | |
---|
| 1906 | // Normalize each spectrum by sum(1/var) where the variance |
---|
| 1907 | // is worked out for each spectrum |
---|
| 1908 | |
---|
| 1909 | Array<Float>& data = sum.getRWArray(); |
---|
| 1910 | VectorIterator<Float> itData(data, axis); |
---|
| 1911 | while (!itData.pastEnd()) { |
---|
| 1912 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 1913 | itData.vector() /= sumSq(pos2); |
---|
| 1914 | itData.next(); |
---|
| 1915 | } |
---|
[536] | 1916 | } else if (wtType==TSYS || wtType==TINTSYS) { |
---|
[518] | 1917 | |
---|
[536] | 1918 | // Normalize each spectrum by sum(1/Tsys**2) (TSYS) or |
---|
| 1919 | // sum(Tint/Tsys**2) (TINTSYS) where the pseudo |
---|
[518] | 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"); |
---|
[536] | 1976 | } else if (tStr.contains(String("TINTSYS"))) { |
---|
| 1977 | wtType = TINTSYS; |
---|
| 1978 | msg = String("Weighting type selected : Tint&Tsys"); |
---|
[518] | 1979 | } else if (tStr.contains(String("TINT"))) { |
---|
| 1980 | wtType = TINT; |
---|
[519] | 1981 | msg = String("Weighting type selected : Tint"); |
---|
[169] | 1982 | } else if (tStr.contains(String("TSYS"))) { |
---|
| 1983 | wtType = TSYS; |
---|
[518] | 1984 | msg = String("Weighting type selected : Tsys"); |
---|
[169] | 1985 | } else { |
---|
[518] | 1986 | msg = String("Weighting type selected : None"); |
---|
| 1987 | throw(AipsError("Unrecognized weighting type")); |
---|
[167] | 1988 | } |
---|
[518] | 1989 | // |
---|
| 1990 | if (listType) cout << msg << endl; |
---|
[167] | 1991 | } |
---|
| 1992 | |
---|
[317] | 1993 | |
---|
| 1994 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type, |
---|
| 1995 | const casa::String& interp) const |
---|
[227] | 1996 | { |
---|
| 1997 | String tStr(interp); |
---|
| 1998 | tStr.upcase(); |
---|
| 1999 | if (tStr.contains(String("NEAR"))) { |
---|
[317] | 2000 | type = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
[227] | 2001 | } else if (tStr.contains(String("LIN"))) { |
---|
[317] | 2002 | type = InterpolateArray1D<Double,Float>::linear; |
---|
[227] | 2003 | } else if (tStr.contains(String("CUB"))) { |
---|
[317] | 2004 | type = InterpolateArray1D<Double,Float>::cubic; |
---|
[227] | 2005 | } else if (tStr.contains(String("SPL"))) { |
---|
[317] | 2006 | type = InterpolateArray1D<Double,Float>::spline; |
---|
[227] | 2007 | } else { |
---|
| 2008 | throw(AipsError("Unrecognized interpolation type")); |
---|
| 2009 | } |
---|
| 2010 | } |
---|
| 2011 | |
---|
[185] | 2012 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data, |
---|
[227] | 2013 | const Array<Bool>& mask) const |
---|
[169] | 2014 | { |
---|
| 2015 | sc.putSpectrum(data); |
---|
| 2016 | // |
---|
| 2017 | Array<uChar> outflags(data.shape()); |
---|
| 2018 | convertArray(outflags,!mask); |
---|
| 2019 | sc.putFlags(outflags); |
---|
| 2020 | } |
---|
[227] | 2021 | |
---|
| 2022 | Table SDMath::readAsciiFile (const String& fileName) const |
---|
| 2023 | { |
---|
[230] | 2024 | String formatString; |
---|
| 2025 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False); |
---|
[227] | 2026 | return tbl; |
---|
| 2027 | } |
---|
[230] | 2028 | |
---|
| 2029 | |
---|
[234] | 2030 | |
---|
[480] | 2031 | void SDMath::scaleFromAsciiTable(SDMemTable* pTabOut, |
---|
| 2032 | const SDMemTable& in, const String& fileName, |
---|
| 2033 | const String& col0, const String& col1, |
---|
| 2034 | const String& methodStr, Bool doAll, |
---|
| 2035 | const Vector<Float>& xOut, Bool doTSys) const |
---|
[230] | 2036 | { |
---|
| 2037 | |
---|
| 2038 | // Read gain-elevation ascii file data into a Table. |
---|
| 2039 | |
---|
[234] | 2040 | Table geTable = readAsciiFile (fileName); |
---|
[230] | 2041 | // |
---|
[480] | 2042 | scaleFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut, doTSys); |
---|
[230] | 2043 | } |
---|
| 2044 | |
---|
[480] | 2045 | void SDMath::scaleFromTable(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 2046 | const Table& tTable, const String& col0, |
---|
| 2047 | const String& col1, |
---|
| 2048 | const String& methodStr, Bool doAll, |
---|
| 2049 | const Vector<Float>& xOut, Bool doTsys) const |
---|
[230] | 2050 | { |
---|
| 2051 | |
---|
| 2052 | // Get data from Table |
---|
| 2053 | |
---|
| 2054 | ROScalarColumn<Float> geElCol(tTable, col0); |
---|
| 2055 | ROScalarColumn<Float> geFacCol(tTable, col1); |
---|
| 2056 | Vector<Float> xIn = geElCol.getColumn(); |
---|
| 2057 | Vector<Float> yIn = geFacCol.getColumn(); |
---|
| 2058 | Vector<Bool> maskIn(xIn.nelements(),True); |
---|
| 2059 | |
---|
| 2060 | // Interpolate (and extrapolate) with desired method |
---|
| 2061 | |
---|
[317] | 2062 | InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
[230] | 2063 | convertInterpString(method, methodStr); |
---|
[317] | 2064 | Int intMethod(method); |
---|
[230] | 2065 | // |
---|
| 2066 | Vector<Float> yOut; |
---|
| 2067 | Vector<Bool> maskOut; |
---|
| 2068 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut, |
---|
[317] | 2069 | xIn, yIn, maskIn, intMethod, |
---|
[230] | 2070 | True, True); |
---|
[234] | 2071 | // Apply |
---|
[230] | 2072 | |
---|
[480] | 2073 | scaleByVector(pTabOut, in, doAll, Float(1.0)/yOut, doTsys); |
---|
[234] | 2074 | } |
---|
| 2075 | |
---|
| 2076 | |
---|
[480] | 2077 | void SDMath::scaleByVector(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 2078 | Bool doAll, const Vector<Float>& factor, |
---|
| 2079 | Bool doTSys) const |
---|
[234] | 2080 | { |
---|
[270] | 2081 | |
---|
[434] | 2082 | // Set up data slice |
---|
[230] | 2083 | |
---|
| 2084 | IPosition start, end; |
---|
[434] | 2085 | setCursorSlice (start, end, doAll, in); |
---|
[230] | 2086 | |
---|
[480] | 2087 | // Get Tsys column |
---|
| 2088 | |
---|
| 2089 | const Table& tIn = in.table(); |
---|
| 2090 | ArrayColumn<Float> tSysCol(tIn, "TSYS"); |
---|
| 2091 | Array<Float> tSys; |
---|
| 2092 | |
---|
[270] | 2093 | // Loop over rows and apply correction factor |
---|
[230] | 2094 | |
---|
| 2095 | const uInt axis = asap::ChanAxis; |
---|
| 2096 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 2097 | |
---|
| 2098 | // Get data |
---|
| 2099 | |
---|
[434] | 2100 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
| 2101 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference to dataIn |
---|
[480] | 2102 | // |
---|
| 2103 | if (doTSys) { |
---|
| 2104 | tSysCol.get(i, tSys); |
---|
| 2105 | Array<Float> tSys2 = tSys(start,end) * factor[i]; |
---|
| 2106 | tSysCol.put(i, tSys); |
---|
| 2107 | } |
---|
[230] | 2108 | |
---|
| 2109 | // Apply factor |
---|
| 2110 | |
---|
[434] | 2111 | dataIn2 *= factor[i]; |
---|
[230] | 2112 | |
---|
| 2113 | // Write out |
---|
| 2114 | |
---|
[434] | 2115 | SDContainer sc = in.getSDContainer(i); |
---|
| 2116 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
[230] | 2117 | // |
---|
[434] | 2118 | pTabOut->putSDContainer(sc); |
---|
[230] | 2119 | } |
---|
| 2120 | } |
---|
| 2121 | |
---|
[234] | 2122 | |
---|
[262] | 2123 | |
---|
| 2124 | |
---|
[330] | 2125 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx, |
---|
| 2126 | SDDataDesc& dDesc, |
---|
| 2127 | uInt nIF, |
---|
| 2128 | const SDMemTable& in, |
---|
| 2129 | const Table& tabIn, |
---|
| 2130 | const ROScalarColumn<String>& srcCol, |
---|
[397] | 2131 | const ROArrayColumn<uInt>& fqIDCol, |
---|
| 2132 | Bool perFreqID) const |
---|
[330] | 2133 | { |
---|
| 2134 | const uInt nRows = tabIn.nrow(); |
---|
| 2135 | ddIdx.resize(nRows,nIF); |
---|
[262] | 2136 | // |
---|
[330] | 2137 | String srcName; |
---|
| 2138 | Vector<uInt> freqIDs; |
---|
| 2139 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 2140 | srcCol.get(iRow, srcName); |
---|
| 2141 | fqIDCol.get(iRow, freqIDs); |
---|
| 2142 | const MDirection& dir = in.getDirection(iRow); |
---|
| 2143 | // |
---|
[397] | 2144 | if (perFreqID) { |
---|
| 2145 | |
---|
| 2146 | // One entry per source/freqID pair |
---|
| 2147 | |
---|
| 2148 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
| 2149 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, freqIDs[iIF], dir, 0); |
---|
| 2150 | } |
---|
| 2151 | } else { |
---|
| 2152 | |
---|
| 2153 | // One entry per source/IF pair. Hang onto the FreqID as well |
---|
| 2154 | |
---|
| 2155 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
| 2156 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, iIF, dir, freqIDs[iIF]); |
---|
| 2157 | } |
---|
[262] | 2158 | } |
---|
| 2159 | } |
---|
| 2160 | } |
---|
[272] | 2161 | |
---|
[397] | 2162 | |
---|
| 2163 | |
---|
| 2164 | |
---|
| 2165 | |
---|
[272] | 2166 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const |
---|
| 2167 | { |
---|
| 2168 | Quantum<Double> qt; |
---|
| 2169 | if (MVTime::read(qt,str)) { |
---|
| 2170 | MVEpoch mv(qt); |
---|
| 2171 | MEpoch me(mv, timeRef); |
---|
| 2172 | return me; |
---|
| 2173 | } else { |
---|
| 2174 | throw(AipsError("Invalid format for Epoch string")); |
---|
| 2175 | } |
---|
| 2176 | } |
---|
| 2177 | |
---|
| 2178 | |
---|
| 2179 | String SDMath::formatEpoch(const MEpoch& epoch) const |
---|
| 2180 | { |
---|
| 2181 | MVTime mvt(epoch.getValue()); |
---|
| 2182 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")"); |
---|
| 2183 | } |
---|
| 2184 | |
---|
[294] | 2185 | |
---|
[309] | 2186 | |
---|
| 2187 | void SDMath::generateFrequencyAligners (PtrBlock<FrequencyAligner<Float>* >& a, |
---|
[330] | 2188 | const SDDataDesc& dDesc, |
---|
| 2189 | const SDMemTable& in, uInt nChan, |
---|
| 2190 | MFrequency::Types system, |
---|
| 2191 | const MPosition& refPos, |
---|
[397] | 2192 | const MEpoch& refEpoch, |
---|
| 2193 | Bool perFreqID) const |
---|
[294] | 2194 | { |
---|
[330] | 2195 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
[397] | 2196 | uInt ID = dDesc.ID(i); |
---|
| 2197 | uInt secID = dDesc.secID(i); |
---|
| 2198 | const MDirection& refDir = dDesc.secDir(i); |
---|
[330] | 2199 | // |
---|
[397] | 2200 | if (perFreqID) { |
---|
| 2201 | |
---|
| 2202 | // One aligner per source/FreqID pair. |
---|
| 2203 | |
---|
| 2204 | SpectralCoordinate sC = in.getSpectralCoordinate(ID); |
---|
| 2205 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
| 2206 | } else { |
---|
| 2207 | |
---|
| 2208 | // One aligner per source/IF pair. But we still need the FreqID to |
---|
| 2209 | // get the right SC. Hence the messing about with the secondary ID |
---|
| 2210 | |
---|
| 2211 | SpectralCoordinate sC = in.getSpectralCoordinate(secID); |
---|
| 2212 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
| 2213 | } |
---|
[294] | 2214 | } |
---|
| 2215 | } |
---|
[480] | 2216 | |
---|
| 2217 | Vector<uInt> SDMath::getRowRange (const SDMemTable& in) const |
---|
| 2218 | { |
---|
| 2219 | Vector<uInt> range(2); |
---|
| 2220 | range[0] = 0; |
---|
| 2221 | range[1] = in.nRow()-1; |
---|
| 2222 | return range; |
---|
| 2223 | } |
---|
| 2224 | |
---|
| 2225 | |
---|
| 2226 | Bool SDMath::rowInRange (uInt i, const Vector<uInt>& range) const |
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| 2227 | { |
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| 2228 | return (i>=range[0] && i<=range[1]); |
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| 2229 | } |
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