[2] | 1 | //#--------------------------------------------------------------------------- |
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| 2 | //# SDMath.cc: A collection of single dish mathematical operations |
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| 3 | //#--------------------------------------------------------------------------- |
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| 4 | //# Copyright (C) 2004 |
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[125] | 5 | //# ATNF |
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[2] | 6 | //# |
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| 7 | //# This program is free software; you can redistribute it and/or modify it |
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| 8 | //# under the terms of the GNU General Public License as published by the Free |
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| 9 | //# Software Foundation; either version 2 of the License, or (at your option) |
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| 10 | //# any later version. |
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| 11 | //# |
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| 12 | //# This program is distributed in the hope that it will be useful, but |
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| 13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
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| 15 | //# Public License for more details. |
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| 16 | //# |
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| 17 | //# You should have received a copy of the GNU General Public License along |
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| 18 | //# with this program; if not, write to the Free Software Foundation, Inc., |
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| 19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA. |
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| 20 | //# |
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| 21 | //# Correspondence concerning this software should be addressed as follows: |
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| 22 | //# Internet email: Malte.Marquarding@csiro.au |
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| 23 | //# Postal address: Malte Marquarding, |
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| 24 | //# Australia Telescope National Facility, |
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| 25 | //# P.O. Box 76, |
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| 26 | //# Epping, NSW, 2121, |
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| 27 | //# AUSTRALIA |
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| 28 | //# |
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| 29 | //# $Id: |
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| 30 | //#--------------------------------------------------------------------------- |
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[38] | 31 | #include <vector> |
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| 32 | |
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[81] | 33 | #include <casa/aips.h> |
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[330] | 34 | #include <casa/iostream.h> |
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| 35 | #include <casa/iomanip.h> |
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[81] | 36 | #include <casa/BasicSL/String.h> |
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| 37 | #include <casa/Arrays/IPosition.h> |
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| 38 | #include <casa/Arrays/Array.h> |
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[130] | 39 | #include <casa/Arrays/ArrayIter.h> |
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| 40 | #include <casa/Arrays/VectorIter.h> |
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[81] | 41 | #include <casa/Arrays/ArrayMath.h> |
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| 42 | #include <casa/Arrays/ArrayLogical.h> |
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| 43 | #include <casa/Arrays/MaskedArray.h> |
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| 44 | #include <casa/Arrays/MaskArrMath.h> |
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| 45 | #include <casa/Arrays/MaskArrLogi.h> |
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[330] | 46 | #include <casa/Arrays/Matrix.h> |
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[234] | 47 | #include <casa/BasicMath/Math.h> |
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[221] | 48 | #include <casa/Containers/Block.h> |
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[262] | 49 | #include <casa/Exceptions.h> |
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| 50 | #include <casa/Quanta/Quantum.h> |
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| 51 | #include <casa/Quanta/Unit.h> |
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| 52 | #include <casa/Quanta/MVEpoch.h> |
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[272] | 53 | #include <casa/Quanta/MVTime.h> |
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[177] | 54 | #include <casa/Utilities/Assert.h> |
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[2] | 55 | |
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[262] | 56 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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| 57 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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| 58 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[309] | 59 | #include <coordinates/Coordinates/FrequencyAligner.h> |
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[262] | 60 | |
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| 61 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 62 | #include <lattices/Lattices/RebinLattice.h> |
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| 63 | |
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| 64 | #include <measures/Measures/MEpoch.h> |
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| 65 | #include <measures/Measures/MDirection.h> |
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| 66 | #include <measures/Measures/MPosition.h> |
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| 67 | |
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[177] | 68 | #include <scimath/Mathematics/VectorKernel.h> |
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| 69 | #include <scimath/Mathematics/Convolver.h> |
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[227] | 70 | #include <scimath/Mathematics/InterpolateArray1D.h> |
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[234] | 71 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 72 | |
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[81] | 73 | #include <tables/Tables/Table.h> |
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| 74 | #include <tables/Tables/ScalarColumn.h> |
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| 75 | #include <tables/Tables/ArrayColumn.h> |
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[227] | 76 | #include <tables/Tables/ReadAsciiTable.h> |
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[2] | 77 | |
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[38] | 78 | #include "MathUtils.h" |
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[232] | 79 | #include "SDDefs.h" |
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[354] | 80 | #include "SDAttr.h" |
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[2] | 81 | #include "SDContainer.h" |
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| 82 | #include "SDMemTable.h" |
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| 83 | |
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| 84 | #include "SDMath.h" |
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[457] | 85 | #include "SDPol.h" |
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[2] | 86 | |
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[125] | 87 | using namespace casa; |
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[83] | 88 | using namespace asap; |
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[2] | 89 | |
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[170] | 90 | |
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| 91 | SDMath::SDMath() |
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| 92 | {;} |
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| 93 | |
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[185] | 94 | SDMath::SDMath(const SDMath& other) |
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[170] | 95 | { |
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| 96 | |
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| 97 | // No state |
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| 98 | |
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| 99 | } |
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| 100 | |
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| 101 | SDMath& SDMath::operator=(const SDMath& other) |
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| 102 | { |
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| 103 | if (this != &other) { |
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| 104 | // No state |
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| 105 | } |
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| 106 | return *this; |
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| 107 | } |
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| 108 | |
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[183] | 109 | SDMath::~SDMath() |
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| 110 | {;} |
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[170] | 111 | |
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[183] | 112 | |
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[262] | 113 | |
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[488] | 114 | SDMemTable* SDMath::frequencyAlignment(const SDMemTable& in, |
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| 115 | const String& refTime, |
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| 116 | const String& method, |
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| 117 | Bool perFreqID) const |
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[262] | 118 | { |
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[309] | 119 | // Get frame info from Table |
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[262] | 120 | |
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| 121 | std::vector<std::string> info = in.getCoordInfo(); |
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[294] | 122 | |
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[309] | 123 | // Parse frequency system |
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[294] | 124 | |
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[309] | 125 | String systemStr(info[1]); |
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| 126 | String baseSystemStr(info[3]); |
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| 127 | if (baseSystemStr==systemStr) { |
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| 128 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe")); |
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[262] | 129 | } |
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[309] | 130 | // |
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| 131 | MFrequency::Types freqSystem; |
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| 132 | MFrequency::getType(freqSystem, systemStr); |
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[294] | 133 | |
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[267] | 134 | // Do it |
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[262] | 135 | |
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[488] | 136 | return frequencyAlign(in, freqSystem, refTime, method, perFreqID); |
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[267] | 137 | } |
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[262] | 138 | |
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| 139 | |
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| 140 | |
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[185] | 141 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in, |
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| 142 | const Vector<Bool>& mask, Bool scanAv, |
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[309] | 143 | const String& weightStr, Bool alignFreq) const |
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[130] | 144 | // |
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[144] | 145 | // Weighted averaging of spectra from one or more Tables. |
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[130] | 146 | // |
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| 147 | { |
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[2] | 148 | |
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[163] | 149 | // Convert weight type |
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| 150 | |
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| 151 | WeightType wtType = NONE; |
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[518] | 152 | convertWeightString(wtType, weightStr, True); |
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[163] | 153 | |
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[144] | 154 | // Create output Table by cloning from the first table |
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[2] | 155 | |
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[144] | 156 | SDMemTable* pTabOut = new SDMemTable(*in[0],True); |
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[488] | 157 | if (in.nelements() > 1) { |
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| 158 | for (uInt i=1; i < in.nelements(); ++i) { |
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| 159 | pTabOut->appendToHistoryTable(in[i]->getHistoryTable()); |
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| 160 | } |
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| 161 | } |
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[144] | 162 | // Setup |
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[130] | 163 | |
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[144] | 164 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change |
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| 165 | Array<Float> arr(shp); |
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| 166 | Array<Bool> barr(shp); |
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[221] | 167 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis)); |
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[130] | 168 | |
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[144] | 169 | // Columns from Tables |
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[130] | 170 | |
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[144] | 171 | ROArrayColumn<Float> tSysCol; |
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| 172 | ROScalarColumn<Double> mjdCol; |
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| 173 | ROScalarColumn<String> srcNameCol; |
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| 174 | ROScalarColumn<Double> intCol; |
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| 175 | ROArrayColumn<uInt> fqIDCol; |
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[410] | 176 | ROScalarColumn<Int> scanIDCol; |
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[130] | 177 | |
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[144] | 178 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam |
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| 179 | // Note that the mask of the accumulation array will ALWAYS remain ALL True. |
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| 180 | // The MA is only used so that when data which is masked Bad is added to it, |
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| 181 | // that data does not contribute. |
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| 182 | |
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| 183 | Array<Float> zero(shp); |
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| 184 | zero=0.0; |
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| 185 | Array<Bool> good(shp); |
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| 186 | good = True; |
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| 187 | MaskedArray<Float> sum(zero,good); |
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| 188 | |
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| 189 | // Counter arrays |
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| 190 | |
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| 191 | Array<Float> nPts(shp); // Number of points |
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| 192 | nPts = 0.0; |
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| 193 | Array<Float> nInc(shp); // Increment |
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| 194 | nInc = 1.0; |
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| 195 | |
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| 196 | // Create accumulation Array for variance. We accumulate for |
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| 197 | // each if,pol,beam, but average over channel. So we need |
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| 198 | // a shape with one less axis dropping channels. |
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| 199 | |
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| 200 | const uInt nAxesSub = shp.nelements() - 1; |
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| 201 | IPosition shp2(nAxesSub); |
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| 202 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) { |
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[221] | 203 | if (i!=asap::ChanAxis) { |
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[144] | 204 | shp2(j) = shp(i); |
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| 205 | j++; |
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| 206 | } |
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[2] | 207 | } |
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[144] | 208 | Array<Float> sumSq(shp2); |
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| 209 | sumSq = 0.0; |
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| 210 | IPosition pos2(nAxesSub,0); // For indexing |
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[130] | 211 | |
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[144] | 212 | // Time-related accumulators |
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[130] | 213 | |
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[144] | 214 | Double time; |
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| 215 | Double timeSum = 0.0; |
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| 216 | Double intSum = 0.0; |
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| 217 | Double interval = 0.0; |
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[130] | 218 | |
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[144] | 219 | // To get the right shape for the Tsys accumulator we need to |
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| 220 | // access a column from the first table. The shape of this |
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[518] | 221 | // array must not change. Note however that since the TSysSqSum |
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| 222 | // array is used in a normalization process, and that I ignore the |
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| 223 | // channel axis replication of values for now, it loses a dimension |
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[130] | 224 | |
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[518] | 225 | Array<Float> tSysSum, tSysSqSum; |
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[144] | 226 | { |
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| 227 | const Table& tabIn = in[0]->table(); |
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| 228 | tSysCol.attach(tabIn,"TSYS"); |
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| 229 | tSysSum.resize(tSysCol.shape(0)); |
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[518] | 230 | // |
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| 231 | tSysSqSum.resize(shp2); |
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[144] | 232 | } |
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| 233 | tSysSum =0.0; |
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[518] | 234 | tSysSqSum = 0.0; |
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[144] | 235 | Array<Float> tSys; |
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| 236 | |
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| 237 | // Scan and row tracking |
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| 238 | |
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| 239 | Int oldScanID = 0; |
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| 240 | Int outScanID = 0; |
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| 241 | Int scanID = 0; |
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| 242 | Int rowStart = 0; |
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| 243 | Int nAccum = 0; |
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| 244 | Int tableStart = 0; |
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| 245 | |
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| 246 | // Source and FreqID |
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| 247 | |
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| 248 | String sourceName, oldSourceName, sourceNameStart; |
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| 249 | Vector<uInt> freqID, freqIDStart, oldFreqID; |
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| 250 | |
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| 251 | // Loop over tables |
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| 252 | |
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| 253 | Float fac = 1.0; |
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| 254 | const uInt nTables = in.nelements(); |
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| 255 | for (uInt iTab=0; iTab<nTables; iTab++) { |
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| 256 | |
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[309] | 257 | // Should check that the frequency tables don't change if doing FreqAlignment |
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[221] | 258 | |
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[144] | 259 | // Attach columns to Table |
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| 260 | |
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| 261 | const Table& tabIn = in[iTab]->table(); |
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| 262 | tSysCol.attach(tabIn, "TSYS"); |
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| 263 | mjdCol.attach(tabIn, "TIME"); |
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| 264 | srcNameCol.attach(tabIn, "SRCNAME"); |
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| 265 | intCol.attach(tabIn, "INTERVAL"); |
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| 266 | fqIDCol.attach(tabIn, "FREQID"); |
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[410] | 267 | scanIDCol.attach(tabIn, "SCANID"); |
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[144] | 268 | |
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[410] | 269 | // Find list of start/end rows for each scan |
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| 270 | |
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[144] | 271 | // Loop over rows in Table |
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| 272 | |
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| 273 | const uInt nRows = in[iTab]->nRow(); |
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| 274 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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| 275 | |
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| 276 | // Check conformance |
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| 277 | |
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| 278 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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| 279 | if (!shp.isEqual(shp2)) { |
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| 280 | throw (AipsError("Shapes for all rows must be the same")); |
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| 281 | } |
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| 282 | |
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| 283 | // If we are not doing scan averages, make checks for source and |
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| 284 | // frequency setup and warn if averaging across them |
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| 285 | |
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[410] | 286 | scanIDCol.getScalar(iRow, scanID); |
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[144] | 287 | |
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| 288 | // Get quantities from columns |
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| 289 | |
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| 290 | srcNameCol.getScalar(iRow, sourceName); |
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| 291 | mjdCol.get(iRow, time); |
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| 292 | tSysCol.get(iRow, tSys); |
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| 293 | intCol.get(iRow, interval); |
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| 294 | fqIDCol.get(iRow, freqID); |
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| 295 | |
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| 296 | // Initialize first source and freqID |
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| 297 | |
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| 298 | if (iRow==0 && iTab==0) { |
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| 299 | sourceNameStart = sourceName; |
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| 300 | freqIDStart = freqID; |
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| 301 | } |
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| 302 | |
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| 303 | // If we are doing scan averages, see if we are at the end of an |
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| 304 | // accumulation period (scan). We must check soutce names too, |
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| 305 | // since we might have two tables with one scan each but different |
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| 306 | // source names; we shouldn't average different sources together |
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| 307 | |
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| 308 | if (scanAv && ( (scanID != oldScanID) || |
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| 309 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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| 310 | |
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| 311 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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| 312 | |
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[518] | 313 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 314 | |
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[410] | 315 | // Get ScanContainer for the first row of this averaged Scan |
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| 316 | |
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| 317 | SDContainer scOut = in[iTab]->getSDContainer(rowStart); |
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| 318 | |
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[144] | 319 | // Fill scan container. The source and freqID come from the |
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| 320 | // first row of the first table that went into this average ( |
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| 321 | // should be the same for all rows in the scan average) |
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| 322 | |
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| 323 | Float nR(nAccum); |
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[410] | 324 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 325 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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| 326 | |
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| 327 | // Write container out to Table |
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| 328 | |
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[410] | 329 | pTabOut->putSDContainer(scOut); |
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[144] | 330 | |
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| 331 | // Reset accumulators |
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| 332 | |
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| 333 | sum = 0.0; |
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| 334 | sumSq = 0.0; |
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| 335 | nAccum = 0; |
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| 336 | // |
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| 337 | tSysSum =0.0; |
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[518] | 338 | tSysSqSum =0.0; |
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[144] | 339 | timeSum = 0.0; |
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| 340 | intSum = 0.0; |
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[221] | 341 | nPts = 0.0; |
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[144] | 342 | |
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| 343 | // Increment |
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| 344 | |
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| 345 | rowStart = iRow; // First row for next accumulation |
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| 346 | tableStart = iTab; // First table for next accumulation |
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| 347 | sourceNameStart = sourceName; // First source name for next accumulation |
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| 348 | freqIDStart = freqID; // First FreqID for next accumulation |
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| 349 | // |
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| 350 | oldScanID = scanID; |
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| 351 | outScanID += 1; // Scan ID for next accumulation period |
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[227] | 352 | } |
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[144] | 353 | |
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[146] | 354 | // Accumulate |
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[144] | 355 | |
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[518] | 356 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, tSysSqSum, |
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| 357 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis, |
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| 358 | nAxesSub, useMask, wtType); |
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[144] | 359 | // |
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| 360 | oldSourceName = sourceName; |
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| 361 | oldFreqID = freqID; |
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[184] | 362 | } |
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[144] | 363 | } |
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| 364 | |
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| 365 | // OK at this point we have accumulation data which is either |
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| 366 | // - accumulated from all tables into one row |
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| 367 | // or |
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| 368 | // - accumulated from the last scan average |
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| 369 | // |
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| 370 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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[410] | 371 | |
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[518] | 372 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 373 | |
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| 374 | // Create and fill container. The container we clone will be from |
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| 375 | // the last Table and the first row that went into the current |
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| 376 | // accumulation. It probably doesn't matter that much really... |
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| 377 | |
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| 378 | Float nR(nAccum); |
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[410] | 379 | SDContainer scOut = in[tableStart]->getSDContainer(rowStart); |
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| 380 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 381 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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[410] | 382 | pTabOut->putSDContainer(scOut); |
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[304] | 383 | pTabOut->resetCursor(); |
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[144] | 384 | // |
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| 385 | return CountedPtr<SDMemTable>(pTabOut); |
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[2] | 386 | } |
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[9] | 387 | |
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[144] | 388 | |
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| 389 | |
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[488] | 390 | CountedPtr<SDMemTable> SDMath::binaryOperate(const CountedPtr<SDMemTable>& |
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| 391 | left, |
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| 392 | const CountedPtr<SDMemTable>& |
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| 393 | right, |
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| 394 | const String& op, Bool preserve, |
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| 395 | Bool doTSys) const |
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[185] | 396 | { |
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[85] | 397 | |
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[248] | 398 | // Check operator |
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[130] | 399 | |
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[234] | 400 | String op2(op); |
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| 401 | op2.upcase(); |
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| 402 | uInt what = 0; |
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| 403 | if (op2=="ADD") { |
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| 404 | what = 0; |
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| 405 | } else if (op2=="SUB") { |
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| 406 | what = 1; |
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| 407 | } else if (op2=="MUL") { |
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| 408 | what = 2; |
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| 409 | } else if (op2=="DIV") { |
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| 410 | what = 3; |
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[248] | 411 | } else if (op2=="QUOTIENT") { |
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| 412 | what = 4; |
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[294] | 413 | doTSys = True; |
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[234] | 414 | } else { |
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[248] | 415 | throw( AipsError("Unrecognized operation")); |
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[234] | 416 | } |
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| 417 | |
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| 418 | // Check rows |
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| 419 | |
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[248] | 420 | const uInt nRowLeft = left->nRow(); |
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| 421 | const uInt nRowRight = right->nRow(); |
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| 422 | Bool ok = (nRowRight==1&&nRowLeft>0) || |
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| 423 | (nRowRight>=1&&nRowLeft==nRowRight); |
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| 424 | if (!ok) { |
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| 425 | 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] | 426 | } |
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| 427 | |
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[248] | 428 | // Input Tables |
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[234] | 429 | |
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| 430 | const Table& tLeft = left->table(); |
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| 431 | const Table& tRight = right->table(); |
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[248] | 432 | |
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| 433 | // TSys columns |
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| 434 | |
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[294] | 435 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol; |
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| 436 | if (doTSys) { |
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| 437 | tSysLeftCol.attach(tLeft, "TSYS"); |
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| 438 | tSysRightCol.attach(tRight, "TSYS"); |
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| 439 | } |
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[234] | 440 | |
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[248] | 441 | // First row for right |
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[234] | 442 | |
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[248] | 443 | Array<Float> tSysLeftArr, tSysRightArr; |
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[294] | 444 | if (doTSys) tSysRightCol.get(0, tSysRightArr); |
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[248] | 445 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0)); |
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| 446 | IPosition shpRight = pMRight->shape(); |
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| 447 | |
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| 448 | // Output Table cloned from left |
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| 449 | |
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[234] | 450 | SDMemTable* pTabOut = new SDMemTable(*left, True); |
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[488] | 451 | pTabOut->appendToHistoryTable(right->getHistoryTable()); |
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[234] | 452 | // Loop over rows |
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| 453 | |
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[248] | 454 | for (uInt i=0; i<nRowLeft; i++) { |
---|
[234] | 455 | |
---|
| 456 | // Get data |
---|
[248] | 457 | |
---|
[234] | 458 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i)); |
---|
[248] | 459 | IPosition shpLeft = mLeft.shape(); |
---|
[294] | 460 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr); |
---|
[234] | 461 | // |
---|
[248] | 462 | if (nRowRight>1) { |
---|
| 463 | delete pMRight; |
---|
| 464 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i)); |
---|
| 465 | shpRight = pMRight->shape(); |
---|
[294] | 466 | if (doTSys) tSysRightCol.get(i, tSysRightArr); |
---|
[234] | 467 | } |
---|
[248] | 468 | // |
---|
| 469 | if (!shpRight.isEqual(shpLeft)) { |
---|
| 470 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 471 | } |
---|
[294] | 472 | if (doTSys) { |
---|
| 473 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) { |
---|
| 474 | throw(AipsError("left and right Tsys data are not conformant")); |
---|
| 475 | } |
---|
| 476 | if (!shpRight.isEqual(tSysRightArr.shape())) { |
---|
| 477 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 478 | } |
---|
[248] | 479 | } |
---|
[234] | 480 | |
---|
| 481 | // Make container |
---|
| 482 | |
---|
| 483 | SDContainer sc = left->getSDContainer(i); |
---|
| 484 | |
---|
| 485 | // Operate on data and TSys |
---|
| 486 | |
---|
| 487 | if (what==0) { |
---|
[248] | 488 | MaskedArray<Float> tmp = mLeft + *pMRight; |
---|
[234] | 489 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 490 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr); |
---|
[234] | 491 | } else if (what==1) { |
---|
[248] | 492 | MaskedArray<Float> tmp = mLeft - *pMRight; |
---|
[234] | 493 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 494 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr); |
---|
[234] | 495 | } else if (what==2) { |
---|
[248] | 496 | MaskedArray<Float> tmp = mLeft * *pMRight; |
---|
[234] | 497 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 498 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr); |
---|
[234] | 499 | } else if (what==3) { |
---|
[248] | 500 | MaskedArray<Float> tmp = mLeft / *pMRight; |
---|
[234] | 501 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 502 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr); |
---|
[248] | 503 | } else if (what==4) { |
---|
[488] | 504 | if (preserve) { |
---|
| 505 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
---|
| 506 | tSysRightArr; |
---|
| 507 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 508 | } else { |
---|
| 509 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
---|
| 510 | tSysLeftArr; |
---|
| 511 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 512 | } |
---|
| 513 | sc.putTsys(tSysRightArr); |
---|
[234] | 514 | } |
---|
| 515 | |
---|
| 516 | // Put new row in output Table |
---|
| 517 | |
---|
[171] | 518 | pTabOut->putSDContainer(sc); |
---|
[130] | 519 | } |
---|
[248] | 520 | if (pMRight) delete pMRight; |
---|
[304] | 521 | pTabOut->resetCursor(); |
---|
[488] | 522 | |
---|
[171] | 523 | return CountedPtr<SDMemTable>(pTabOut); |
---|
[9] | 524 | } |
---|
[48] | 525 | |
---|
[146] | 526 | |
---|
| 527 | |
---|
[185] | 528 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in, |
---|
[234] | 529 | const Vector<Bool>& mask, |
---|
| 530 | const String& which, Int row) const |
---|
[130] | 531 | // |
---|
| 532 | // Perhaps iteration over pol/beam/if should be in here |
---|
| 533 | // and inside the nrow iteration ? |
---|
| 534 | // |
---|
| 535 | { |
---|
| 536 | const uInt nRow = in->nRow(); |
---|
| 537 | |
---|
| 538 | // Specify cursor location |
---|
| 539 | |
---|
[152] | 540 | IPosition start, end; |
---|
[434] | 541 | Bool doAll = False; |
---|
| 542 | setCursorSlice (start, end, doAll, *in); |
---|
[130] | 543 | |
---|
| 544 | // Loop over rows |
---|
| 545 | |
---|
[234] | 546 | const uInt nEl = mask.nelements(); |
---|
| 547 | uInt iStart = 0; |
---|
| 548 | uInt iEnd = in->nRow()-1; |
---|
| 549 | // |
---|
| 550 | if (row>=0) { |
---|
| 551 | iStart = row; |
---|
| 552 | iEnd = row; |
---|
| 553 | } |
---|
| 554 | // |
---|
| 555 | std::vector<float> result(iEnd-iStart+1); |
---|
| 556 | for (uInt ii=iStart; ii <= iEnd; ++ii) { |
---|
[130] | 557 | |
---|
| 558 | // Get row and deconstruct |
---|
| 559 | |
---|
[434] | 560 | MaskedArray<Float> dataIn = (in->rowAsMaskedArray(ii))(start,end); |
---|
| 561 | Array<Float> v = dataIn.getArray().nonDegenerate(); |
---|
| 562 | Array<Bool> m = dataIn.getMask().nonDegenerate(); |
---|
[130] | 563 | |
---|
| 564 | // Access desired piece of data |
---|
| 565 | |
---|
[434] | 566 | // Array<Float> v((arr(start,end)).nonDegenerate()); |
---|
| 567 | // Array<Bool> m((barr(start,end)).nonDegenerate()); |
---|
[130] | 568 | |
---|
| 569 | // Apply OTF mask |
---|
| 570 | |
---|
| 571 | MaskedArray<Float> tmp; |
---|
| 572 | if (m.nelements()==nEl) { |
---|
[234] | 573 | tmp.setData(v,m&&mask); |
---|
[130] | 574 | } else { |
---|
| 575 | tmp.setData(v,m); |
---|
| 576 | } |
---|
| 577 | |
---|
| 578 | // Get statistic |
---|
| 579 | |
---|
[234] | 580 | result[ii-iStart] = mathutil::statistics(which, tmp); |
---|
[130] | 581 | } |
---|
| 582 | // |
---|
| 583 | return result; |
---|
| 584 | } |
---|
| 585 | |
---|
[146] | 586 | |
---|
[234] | 587 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const |
---|
[144] | 588 | { |
---|
[169] | 589 | SDHeader sh = in.getSDHeader(); |
---|
| 590 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[163] | 591 | |
---|
[169] | 592 | // Bin up SpectralCoordinates |
---|
[163] | 593 | |
---|
[169] | 594 | IPosition factors(1); |
---|
| 595 | factors(0) = width; |
---|
| 596 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 597 | CoordinateSystem cSys; |
---|
[288] | 598 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
[169] | 599 | CoordinateSystem cSysBin = |
---|
[185] | 600 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False); |
---|
[169] | 601 | // |
---|
| 602 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
---|
| 603 | pTabOut->setCoordinate(sCBin, j); |
---|
| 604 | } |
---|
[163] | 605 | |
---|
[169] | 606 | // Use RebinLattice to find shape |
---|
[130] | 607 | |
---|
[169] | 608 | IPosition shapeIn(1,sh.nchan); |
---|
[185] | 609 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors); |
---|
[169] | 610 | sh.nchan = shapeOut(0); |
---|
| 611 | pTabOut->putSDHeader(sh); |
---|
[144] | 612 | |
---|
[169] | 613 | // Loop over rows and bin along channel axis |
---|
| 614 | |
---|
| 615 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 616 | SDContainer sc = in.getSDContainer(i); |
---|
[144] | 617 | // |
---|
[169] | 618 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
---|
[144] | 619 | |
---|
[169] | 620 | // Bin up spectrum |
---|
[144] | 621 | |
---|
[169] | 622 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
---|
| 623 | MaskedArray<Float> marrout; |
---|
[221] | 624 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width); |
---|
[144] | 625 | |
---|
[169] | 626 | // Put back the binned data and flags |
---|
[144] | 627 | |
---|
[169] | 628 | IPosition ip2 = marrout.shape(); |
---|
| 629 | sc.resize(ip2); |
---|
[146] | 630 | // |
---|
[185] | 631 | putDataInSDC(sc, marrout.getArray(), marrout.getMask()); |
---|
[146] | 632 | |
---|
[169] | 633 | // Bin up Tsys. |
---|
[146] | 634 | |
---|
[169] | 635 | Array<Bool> allGood(tSys.shape(),True); |
---|
| 636 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
---|
[146] | 637 | // |
---|
[169] | 638 | MaskedArray<Float> tSysOut; |
---|
[221] | 639 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width); |
---|
[169] | 640 | sc.putTsys(tSysOut.getArray()); |
---|
[146] | 641 | // |
---|
[169] | 642 | pTabOut->putSDContainer(sc); |
---|
| 643 | } |
---|
| 644 | return pTabOut; |
---|
[146] | 645 | } |
---|
| 646 | |
---|
[488] | 647 | SDMemTable* SDMath::resample(const SDMemTable& in, const String& methodStr, |
---|
| 648 | Float width) const |
---|
[299] | 649 | // |
---|
| 650 | // Should add the possibility of width being specified in km/s. This means |
---|
| 651 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
| 652 | // average channel width (say at the reference pixel). Then we would need |
---|
| 653 | // to be careful to make sure each spectrum (of different freqID) |
---|
| 654 | // is the same length. |
---|
| 655 | // |
---|
| 656 | { |
---|
| 657 | Bool doVel = False; |
---|
[309] | 658 | if (doVel) { |
---|
| 659 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 660 | SpectralCoordinate sC = in.getSpectralCoordinate(j); |
---|
| 661 | } |
---|
| 662 | } |
---|
[299] | 663 | |
---|
| 664 | // Interpolation method |
---|
| 665 | |
---|
[317] | 666 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
| 667 | convertInterpString(interp, methodStr); |
---|
| 668 | Int interpMethod(interp); |
---|
[299] | 669 | |
---|
| 670 | // Make output table |
---|
| 671 | |
---|
| 672 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 673 | |
---|
| 674 | // Resample SpectralCoordinates (one per freqID) |
---|
| 675 | |
---|
| 676 | const uInt nCoord = in.nCoordinates(); |
---|
| 677 | Vector<Float> offset(1,0.0); |
---|
| 678 | Vector<Float> factors(1,1.0/width); |
---|
| 679 | Vector<Int> newShape; |
---|
| 680 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 681 | CoordinateSystem cSys; |
---|
| 682 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
| 683 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape); |
---|
| 684 | SpectralCoordinate sC = cSys2.spectralCoordinate(0); |
---|
| 685 | // |
---|
| 686 | pTabOut->setCoordinate(sC, j); |
---|
| 687 | } |
---|
| 688 | |
---|
| 689 | // Get header |
---|
| 690 | |
---|
| 691 | SDHeader sh = in.getSDHeader(); |
---|
| 692 | |
---|
| 693 | // Generate resampling vectors |
---|
| 694 | |
---|
| 695 | const uInt nChanIn = sh.nchan; |
---|
| 696 | Vector<Float> xIn(nChanIn); |
---|
| 697 | indgen(xIn); |
---|
| 698 | // |
---|
| 699 | Int fac = Int(nChanIn/width); |
---|
| 700 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
| 701 | uInt i = 0; |
---|
| 702 | Float x = 0.0; |
---|
| 703 | Bool more = True; |
---|
| 704 | while (more) { |
---|
| 705 | xOut(i) = x; |
---|
| 706 | // |
---|
| 707 | i++; |
---|
| 708 | x += width; |
---|
| 709 | if (x>nChanIn-1) more = False; |
---|
| 710 | } |
---|
| 711 | const uInt nChanOut = i; |
---|
| 712 | xOut.resize(nChanOut,True); |
---|
| 713 | // |
---|
| 714 | IPosition shapeIn(in.rowAsMaskedArray(0).shape()); |
---|
| 715 | sh.nchan = nChanOut; |
---|
| 716 | pTabOut->putSDHeader(sh); |
---|
| 717 | |
---|
| 718 | // Loop over rows and resample along channel axis |
---|
| 719 | |
---|
| 720 | Array<Float> valuesOut; |
---|
| 721 | Array<Bool> maskOut; |
---|
| 722 | Array<Float> tSysOut; |
---|
| 723 | Array<Bool> tSysMaskIn(shapeIn,True); |
---|
| 724 | Array<Bool> tSysMaskOut; |
---|
| 725 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 726 | |
---|
| 727 | // Get container |
---|
| 728 | |
---|
| 729 | SDContainer sc = in.getSDContainer(i); |
---|
| 730 | |
---|
| 731 | // Get data and Tsys |
---|
| 732 | |
---|
| 733 | const Array<Float>& tSysIn = sc.getTsys(); |
---|
| 734 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i)); |
---|
| 735 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 736 | Array<Bool> maskIn = dataIn.getMask(); |
---|
| 737 | |
---|
| 738 | // Interpolate data |
---|
| 739 | |
---|
| 740 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut, |
---|
| 741 | xIn, valuesIn, maskIn, |
---|
| 742 | interpMethod, True, True); |
---|
| 743 | sc.resize(valuesOut.shape()); |
---|
| 744 | putDataInSDC(sc, valuesOut, maskOut); |
---|
| 745 | |
---|
| 746 | // Interpolate TSys |
---|
| 747 | |
---|
| 748 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut, |
---|
| 749 | xIn, tSysIn, tSysMaskIn, |
---|
| 750 | interpMethod, True, True); |
---|
| 751 | sc.putTsys(tSysOut); |
---|
| 752 | |
---|
| 753 | // Put container in output |
---|
| 754 | |
---|
| 755 | pTabOut->putSDContainer(sc); |
---|
| 756 | } |
---|
| 757 | // |
---|
| 758 | return pTabOut; |
---|
| 759 | } |
---|
| 760 | |
---|
[248] | 761 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll, |
---|
[294] | 762 | uInt what, Bool doTSys) const |
---|
[152] | 763 | // |
---|
| 764 | // what = 0 Multiply |
---|
| 765 | // 1 Add |
---|
[146] | 766 | { |
---|
[152] | 767 | SDMemTable* pOut = new SDMemTable(in,False); |
---|
| 768 | const Table& tOut = pOut->table(); |
---|
[294] | 769 | ArrayColumn<Float> specCol(tOut,"SPECTRA"); |
---|
| 770 | ArrayColumn<Float> tSysCol(tOut,"TSYS"); |
---|
| 771 | Array<Float> tSysArr; |
---|
[434] | 772 | |
---|
| 773 | // Get data slice bounds |
---|
| 774 | |
---|
| 775 | IPosition start, end; |
---|
| 776 | setCursorSlice (start, end, doAll, in); |
---|
[146] | 777 | // |
---|
[434] | 778 | for (uInt i=0; i<tOut.nrow(); i++) { |
---|
[294] | 779 | |
---|
| 780 | // Modify data |
---|
| 781 | |
---|
[434] | 782 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
| 783 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference |
---|
| 784 | if (what==0) { |
---|
| 785 | dataIn2 *= val; |
---|
| 786 | } else if (what==1) { |
---|
| 787 | dataIn2 += val; |
---|
| 788 | } |
---|
| 789 | specCol.put(i, dataIn.getArray()); |
---|
[294] | 790 | |
---|
| 791 | // Modify Tsys |
---|
| 792 | |
---|
[434] | 793 | if (doTSys) { |
---|
| 794 | tSysCol.get(i, tSysArr); |
---|
| 795 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference |
---|
[152] | 796 | if (what==0) { |
---|
[434] | 797 | tSysArr2 *= val; |
---|
[152] | 798 | } else if (what==1) { |
---|
[434] | 799 | tSysArr2 += val; |
---|
[152] | 800 | } |
---|
[434] | 801 | tSysCol.put(i, tSysArr); |
---|
[152] | 802 | } |
---|
| 803 | } |
---|
| 804 | // |
---|
[146] | 805 | return pOut; |
---|
| 806 | } |
---|
| 807 | |
---|
[315] | 808 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask, |
---|
| 809 | const String& weightStr) const |
---|
[152] | 810 | // |
---|
[165] | 811 | // Average all polarizations together, weighted by variance |
---|
| 812 | // |
---|
| 813 | { |
---|
[315] | 814 | WeightType wtType = NONE; |
---|
[518] | 815 | convertWeightString(wtType, weightStr, False); |
---|
[165] | 816 | |
---|
| 817 | const uInt nRows = in.nRow(); |
---|
| 818 | |
---|
| 819 | // Create output Table and reshape number of polarizations |
---|
| 820 | |
---|
| 821 | Bool clear=True; |
---|
| 822 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
| 823 | SDHeader header = pTabOut->getSDHeader(); |
---|
| 824 | header.npol = 1; |
---|
| 825 | pTabOut->putSDHeader(header); |
---|
| 826 | |
---|
| 827 | // Shape of input and output data |
---|
| 828 | |
---|
[448] | 829 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape(); |
---|
[165] | 830 | IPosition shapeOut(shapeIn); |
---|
[262] | 831 | shapeOut(asap::PolAxis) = 1; // Average all polarizations |
---|
[315] | 832 | if (shapeIn(asap::PolAxis)==1) { |
---|
| 833 | throw(AipsError("The input has only one polarisation")); |
---|
| 834 | } |
---|
[165] | 835 | // |
---|
[262] | 836 | const uInt nChan = shapeIn(asap::ChanAxis); |
---|
[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 |
---|
[165] | 845 | // |
---|
[262] | 846 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis)); |
---|
[165] | 847 | |
---|
| 848 | // Loop over rows |
---|
| 849 | |
---|
| 850 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 851 | |
---|
| 852 | // Get data for this row |
---|
| 853 | |
---|
| 854 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
| 855 | Array<Float>& arr = marr.getRWArray(); |
---|
| 856 | const Array<Bool>& barr = marr.getMask(); |
---|
| 857 | |
---|
| 858 | // Make iterators to iterate by pol-channel planes |
---|
| 859 | |
---|
| 860 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
---|
| 861 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes); |
---|
| 862 | |
---|
| 863 | // Accumulations |
---|
| 864 | |
---|
| 865 | Float fac = 1.0; |
---|
| 866 | Vector<Float> vecSum(nChan,0.0); |
---|
| 867 | |
---|
| 868 | // Iterate through data by pol-channel planes |
---|
| 869 | |
---|
| 870 | while (!itDataPlane.pastEnd()) { |
---|
| 871 | |
---|
| 872 | // Iterate through plane by polarization and accumulate Vectors |
---|
| 873 | |
---|
| 874 | Vector<Float> t1(nChan); t1 = 0.0; |
---|
| 875 | Vector<Bool> t2(nChan); t2 = True; |
---|
| 876 | MaskedArray<Float> vecSum(t1,t2); |
---|
[315] | 877 | Float norm = 0.0; |
---|
[165] | 878 | { |
---|
| 879 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
---|
| 880 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
| 881 | while (!itDataVec.pastEnd()) { |
---|
| 882 | |
---|
[315] | 883 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum |
---|
[165] | 884 | |
---|
| 885 | if (useMask) { |
---|
| 886 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector()); |
---|
[315] | 887 | if (wtType==VAR) fac = 1.0 / variance(spec); |
---|
[165] | 888 | } else { |
---|
| 889 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector()); |
---|
[315] | 890 | if (wtType==VAR) fac = 1.0 / variance(spec); |
---|
[165] | 891 | } |
---|
| 892 | |
---|
| 893 | // Normalize spectrum (without OTF mask) and accumulate |
---|
| 894 | |
---|
| 895 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector()); |
---|
| 896 | vecSum += spec; |
---|
[315] | 897 | norm += fac; |
---|
[165] | 898 | |
---|
| 899 | // Next |
---|
| 900 | |
---|
| 901 | itDataVec.next(); |
---|
| 902 | itMaskVec.next(); |
---|
| 903 | } |
---|
| 904 | } |
---|
| 905 | |
---|
| 906 | // Normalize summed spectrum |
---|
| 907 | |
---|
[315] | 908 | vecSum /= norm; |
---|
[165] | 909 | |
---|
| 910 | // FInd position in input data array. We are iterating by pol-channel |
---|
| 911 | // plane so all that will change is beam and IF and that's what we want. |
---|
| 912 | |
---|
| 913 | IPosition pos = itDataPlane.pos(); |
---|
| 914 | |
---|
| 915 | // Write out data. This is a bit messy. We have to reform the Vector |
---|
| 916 | // accumulator into an Array of shape (1,1,1,nChan) |
---|
| 917 | |
---|
| 918 | start = pos; |
---|
| 919 | end = pos; |
---|
[262] | 920 | end(asap::ChanAxis) = nChan-1; |
---|
[165] | 921 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
---|
| 922 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
---|
| 923 | |
---|
| 924 | // Step to next beam/IF combination |
---|
| 925 | |
---|
| 926 | itDataPlane.next(); |
---|
| 927 | itMaskPlane.next(); |
---|
| 928 | } |
---|
| 929 | |
---|
| 930 | // Generate output container and write it to output table |
---|
| 931 | |
---|
| 932 | SDContainer sc = in.getSDContainer(); |
---|
| 933 | sc.resize(shapeOut); |
---|
| 934 | // |
---|
[185] | 935 | putDataInSDC(sc, outData, outMask); |
---|
[165] | 936 | pTabOut->putSDContainer(sc); |
---|
| 937 | } |
---|
[304] | 938 | |
---|
| 939 | // Set polarization cursor to 0 |
---|
| 940 | |
---|
| 941 | pTabOut->setPol(0); |
---|
[165] | 942 | // |
---|
| 943 | return pTabOut; |
---|
| 944 | } |
---|
[167] | 945 | |
---|
[169] | 946 | |
---|
[185] | 947 | SDMemTable* SDMath::smooth(const SDMemTable& in, |
---|
| 948 | const casa::String& kernelType, |
---|
[234] | 949 | casa::Float width, Bool doAll) const |
---|
[299] | 950 | // |
---|
| 951 | // Should smooth TSys as well |
---|
| 952 | // |
---|
[177] | 953 | { |
---|
[169] | 954 | |
---|
[177] | 955 | // Number of channels |
---|
[169] | 956 | |
---|
[434] | 957 | const uInt nChan = in.nChan(); |
---|
[177] | 958 | |
---|
| 959 | // Generate Kernel |
---|
| 960 | |
---|
[185] | 961 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType); |
---|
[177] | 962 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
| 963 | |
---|
| 964 | // Generate Convolver |
---|
| 965 | |
---|
| 966 | IPosition shape(1,nChan); |
---|
| 967 | Convolver<Float> conv(kernel, shape); |
---|
| 968 | |
---|
| 969 | // New Table |
---|
| 970 | |
---|
| 971 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
| 972 | |
---|
| 973 | // Output Vectors |
---|
| 974 | |
---|
[434] | 975 | Vector<Float> valuesOut(nChan); |
---|
| 976 | Vector<Bool> maskOut(nChan); |
---|
[177] | 977 | |
---|
[434] | 978 | // Get data slice bounds |
---|
| 979 | |
---|
| 980 | IPosition start, end; |
---|
| 981 | setCursorSlice (start, end, doAll, in); |
---|
| 982 | |
---|
[177] | 983 | // Loop over rows in Table |
---|
| 984 | |
---|
[434] | 985 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
[177] | 986 | |
---|
[434] | 987 | // Get slice of data |
---|
[177] | 988 | |
---|
[434] | 989 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(ri); |
---|
[177] | 990 | |
---|
[434] | 991 | // Deconstruct and get slices which reference these arrays |
---|
[177] | 992 | |
---|
[434] | 993 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 994 | Array<Bool> maskIn = dataIn.getMask(); |
---|
[177] | 995 | // |
---|
[434] | 996 | Array<Float> valuesIn2 = valuesIn(start,end); // ref to valuesIn |
---|
| 997 | Array<Bool> maskIn2 = maskIn(start,end); |
---|
[177] | 998 | |
---|
[434] | 999 | // Iterate through by spectra |
---|
[177] | 1000 | |
---|
[434] | 1001 | VectorIterator<Float> itValues(valuesIn2, asap::ChanAxis); |
---|
| 1002 | VectorIterator<Bool> itMask(maskIn2, asap::ChanAxis); |
---|
| 1003 | while (!itValues.pastEnd()) { |
---|
| 1004 | |
---|
[177] | 1005 | // Smooth |
---|
| 1006 | |
---|
[434] | 1007 | if (kernelType==VectorKernel::HANNING) { |
---|
| 1008 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector()); |
---|
| 1009 | itMask.vector() = maskOut; |
---|
| 1010 | } else { |
---|
| 1011 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
| 1012 | conv.linearConv(valuesOut, itValues.vector()); |
---|
| 1013 | } |
---|
| 1014 | // |
---|
| 1015 | itValues.vector() = valuesOut; |
---|
| 1016 | // |
---|
| 1017 | itValues.next(); |
---|
| 1018 | itMask.next(); |
---|
| 1019 | } |
---|
[177] | 1020 | |
---|
| 1021 | // Create and put back |
---|
| 1022 | |
---|
[434] | 1023 | SDContainer sc = in.getSDContainer(ri); |
---|
| 1024 | putDataInSDC(sc, valuesIn, maskIn); |
---|
[177] | 1025 | // |
---|
[434] | 1026 | pTabOut->putSDContainer(sc); |
---|
| 1027 | } |
---|
[177] | 1028 | // |
---|
| 1029 | return pTabOut; |
---|
| 1030 | } |
---|
| 1031 | |
---|
| 1032 | |
---|
[262] | 1033 | |
---|
[488] | 1034 | SDMemTable* SDMath::convertFlux(const SDMemTable& in, Float D, Float etaAp, |
---|
| 1035 | Float JyPerK, Bool doAll) const |
---|
[221] | 1036 | // |
---|
[478] | 1037 | // etaAp = aperture efficiency (-1 means find) |
---|
| 1038 | // D = geometric diameter (m) (-1 means find) |
---|
[354] | 1039 | // JyPerK |
---|
[221] | 1040 | // |
---|
| 1041 | { |
---|
| 1042 | SDHeader sh = in.getSDHeader(); |
---|
| 1043 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[177] | 1044 | |
---|
[354] | 1045 | // Find out how to convert values into Jy and K (e.g. units might be mJy or mK) |
---|
[221] | 1046 | // Also automatically find out what we are converting to according to the |
---|
| 1047 | // flux unit |
---|
[177] | 1048 | |
---|
[221] | 1049 | Unit fluxUnit(sh.fluxunit); |
---|
| 1050 | Unit K(String("K")); |
---|
| 1051 | Unit JY(String("Jy")); |
---|
| 1052 | // |
---|
| 1053 | Bool toKelvin = True; |
---|
[354] | 1054 | Double cFac = 1.0; |
---|
[221] | 1055 | if (fluxUnit==JY) { |
---|
[414] | 1056 | cout << "Converting to K" << endl; |
---|
[221] | 1057 | // |
---|
| 1058 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1059 | Quantum<Double> t2 = t.get(JY); |
---|
[354] | 1060 | cFac = (t2 / t).getValue(); // value to Jy |
---|
[221] | 1061 | // |
---|
| 1062 | toKelvin = True; |
---|
| 1063 | sh.fluxunit = "K"; |
---|
| 1064 | } else if (fluxUnit==K) { |
---|
[414] | 1065 | cout << "Converting to Jy" << endl; |
---|
[221] | 1066 | // |
---|
| 1067 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1068 | Quantum<Double> t2 = t.get(K); |
---|
[354] | 1069 | cFac = (t2 / t).getValue(); // value to K |
---|
[221] | 1070 | // |
---|
| 1071 | toKelvin = False; |
---|
| 1072 | sh.fluxunit = "Jy"; |
---|
| 1073 | } else { |
---|
[248] | 1074 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 1075 | } |
---|
| 1076 | pTabOut->putSDHeader(sh); |
---|
[177] | 1077 | |
---|
[354] | 1078 | // Make sure input values are converted to either Jy or K first... |
---|
[221] | 1079 | |
---|
[354] | 1080 | Float factor = cFac; |
---|
[221] | 1081 | |
---|
[354] | 1082 | // Select method |
---|
[221] | 1083 | |
---|
[354] | 1084 | if (JyPerK>0.0) { |
---|
| 1085 | factor *= JyPerK; |
---|
| 1086 | if (toKelvin) factor = 1.0 / JyPerK; |
---|
| 1087 | // |
---|
[478] | 1088 | cout << "Jy/K = " << JyPerK << endl; |
---|
[354] | 1089 | Vector<Float> factors(in.nRow(), factor); |
---|
[480] | 1090 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
[354] | 1091 | } else if (etaAp>0.0) { |
---|
[478] | 1092 | Bool throwIt = True; |
---|
| 1093 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
| 1094 | SDAttr sda; |
---|
| 1095 | if (D < 0) D = sda.diameter(inst); |
---|
| 1096 | Float JyPerK = SDAttr::findJyPerK (etaAp,D); |
---|
| 1097 | cout << "Jy/K = " << JyPerK << endl; |
---|
| 1098 | factor *= JyPerK; |
---|
[354] | 1099 | if (toKelvin) { |
---|
| 1100 | factor = 1.0 / factor; |
---|
| 1101 | } |
---|
| 1102 | // |
---|
| 1103 | Vector<Float> factors(in.nRow(), factor); |
---|
[480] | 1104 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
[354] | 1105 | } else { |
---|
[221] | 1106 | |
---|
[354] | 1107 | // OK now we must deal with automatic look up of values. |
---|
| 1108 | // We must also deal with the fact that the factors need |
---|
| 1109 | // to be computed per IF and may be different and may |
---|
| 1110 | // change per integration. |
---|
[221] | 1111 | |
---|
[414] | 1112 | cout << "Looking up conversion factors" << endl; |
---|
[354] | 1113 | convertBrightnessUnits (pTabOut, in, toKelvin, cFac, doAll); |
---|
| 1114 | } |
---|
[221] | 1115 | // |
---|
| 1116 | return pTabOut; |
---|
| 1117 | } |
---|
| 1118 | |
---|
| 1119 | |
---|
[354] | 1120 | |
---|
| 1121 | |
---|
| 1122 | |
---|
[488] | 1123 | SDMemTable* SDMath::gainElevation(const SDMemTable& in, |
---|
| 1124 | const Vector<Float>& coeffs, |
---|
| 1125 | const String& fileName, |
---|
| 1126 | const String& methodStr, Bool doAll) const |
---|
[227] | 1127 | { |
---|
[234] | 1128 | |
---|
| 1129 | // Get header and clone output table |
---|
| 1130 | |
---|
[227] | 1131 | SDHeader sh = in.getSDHeader(); |
---|
| 1132 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1133 | |
---|
[234] | 1134 | // Get elevation data from SDMemTable and convert to degrees |
---|
[227] | 1135 | |
---|
| 1136 | const Table& tab = in.table(); |
---|
| 1137 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[234] | 1138 | Vector<Float> x = elev.getColumn(); |
---|
[363] | 1139 | x *= Float(180 / C::pi); // Degrees |
---|
[227] | 1140 | // |
---|
[234] | 1141 | const uInt nC = coeffs.nelements(); |
---|
| 1142 | if (fileName.length()>0 && nC>0) { |
---|
[248] | 1143 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
[234] | 1144 | } |
---|
| 1145 | |
---|
| 1146 | // Correct |
---|
| 1147 | |
---|
| 1148 | if (nC>0 || fileName.length()==0) { |
---|
| 1149 | |
---|
| 1150 | // Find instrument |
---|
| 1151 | |
---|
| 1152 | Bool throwIt = True; |
---|
[478] | 1153 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
[234] | 1154 | |
---|
| 1155 | // Set polynomial |
---|
| 1156 | |
---|
| 1157 | Polynomial<Float>* pPoly = 0; |
---|
| 1158 | Vector<Float> coeff; |
---|
| 1159 | String msg; |
---|
| 1160 | if (nC>0) { |
---|
| 1161 | pPoly = new Polynomial<Float>(nC); |
---|
| 1162 | coeff = coeffs; |
---|
| 1163 | msg = String("user"); |
---|
| 1164 | } else { |
---|
[363] | 1165 | SDAttr sdAttr; |
---|
| 1166 | coeff = sdAttr.gainElevationPoly(inst); |
---|
| 1167 | pPoly = new Polynomial<Float>(3); |
---|
[234] | 1168 | msg = String("built in"); |
---|
| 1169 | } |
---|
[227] | 1170 | // |
---|
[234] | 1171 | if (coeff.nelements()>0) { |
---|
| 1172 | pPoly->setCoefficients(coeff); |
---|
| 1173 | } else { |
---|
[363] | 1174 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
[234] | 1175 | } |
---|
| 1176 | // |
---|
[414] | 1177 | cout << "Making polynomial correction with " << msg << " coefficients" << endl; |
---|
[234] | 1178 | const uInt nRow = in.nRow(); |
---|
| 1179 | Vector<Float> factor(nRow); |
---|
| 1180 | for (uInt i=0; i<nRow; i++) { |
---|
[480] | 1181 | factor[i] = 1.0 / (*pPoly)(x[i]); |
---|
[234] | 1182 | } |
---|
| 1183 | delete pPoly; |
---|
| 1184 | // |
---|
[480] | 1185 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
[234] | 1186 | } else { |
---|
| 1187 | |
---|
| 1188 | // Indicate which columns to read from ascii file |
---|
| 1189 | |
---|
| 1190 | String col0("ELEVATION"); |
---|
| 1191 | String col1("FACTOR"); |
---|
| 1192 | |
---|
| 1193 | // Read and correct |
---|
| 1194 | |
---|
[414] | 1195 | cout << "Making correction from ascii Table" << endl; |
---|
[480] | 1196 | scaleFromAsciiTable (pTabOut, in, fileName, col0, col1, |
---|
| 1197 | methodStr, doAll, x, True); |
---|
[234] | 1198 | } |
---|
| 1199 | // |
---|
| 1200 | return pTabOut; |
---|
[230] | 1201 | } |
---|
[227] | 1202 | |
---|
[230] | 1203 | |
---|
[227] | 1204 | |
---|
[488] | 1205 | SDMemTable* SDMath::opacity(const SDMemTable& in, Float tau, Bool doAll) const |
---|
[234] | 1206 | { |
---|
[227] | 1207 | |
---|
[234] | 1208 | // Get header and clone output table |
---|
[227] | 1209 | |
---|
[234] | 1210 | SDHeader sh = in.getSDHeader(); |
---|
| 1211 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1212 | |
---|
| 1213 | // Get elevation data from SDMemTable and convert to degrees |
---|
| 1214 | |
---|
| 1215 | const Table& tab = in.table(); |
---|
| 1216 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 1217 | Vector<Float> zDist = elev.getColumn(); |
---|
| 1218 | zDist = Float(C::pi_2) - zDist; |
---|
| 1219 | |
---|
| 1220 | // Generate correction factor |
---|
| 1221 | |
---|
| 1222 | const uInt nRow = in.nRow(); |
---|
| 1223 | Vector<Float> factor(nRow); |
---|
| 1224 | Vector<Float> factor2(nRow); |
---|
| 1225 | for (uInt i=0; i<nRow; i++) { |
---|
| 1226 | factor[i] = exp(tau)/cos(zDist[i]); |
---|
| 1227 | } |
---|
| 1228 | |
---|
| 1229 | // Correct |
---|
| 1230 | |
---|
[480] | 1231 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
[234] | 1232 | // |
---|
| 1233 | return pTabOut; |
---|
| 1234 | } |
---|
| 1235 | |
---|
| 1236 | |
---|
[488] | 1237 | void SDMath::rotateXYPhase(SDMemTable& in, Float value, Bool doAll) |
---|
[457] | 1238 | // |
---|
| 1239 | // phase in degrees |
---|
[518] | 1240 | // assumes linear correlations |
---|
[457] | 1241 | // |
---|
| 1242 | { |
---|
| 1243 | if (in.nPol() != 4) { |
---|
| 1244 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
| 1245 | } |
---|
[518] | 1246 | // |
---|
| 1247 | SDHeader sh = in.getSDHeader(); |
---|
| 1248 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False); |
---|
| 1249 | SDAttr sdAtt; |
---|
| 1250 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
| 1251 | throw(AipsError("Only linear polarizations are supported")); |
---|
| 1252 | } |
---|
[457] | 1253 | // |
---|
| 1254 | const Table& tabIn = in.table(); |
---|
| 1255 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
| 1256 | IPosition start(asap::nAxes,0); |
---|
| 1257 | IPosition end(asap::nAxes); |
---|
[234] | 1258 | |
---|
[457] | 1259 | // Set cursor slice. Assumes shape the same for all rows |
---|
| 1260 | |
---|
| 1261 | setCursorSlice (start, end, doAll, in); |
---|
| 1262 | IPosition start3(start); |
---|
| 1263 | start3(asap::PolAxis) = 2; // Real(XY) |
---|
| 1264 | IPosition end3(end); |
---|
| 1265 | end3(asap::PolAxis) = 2; |
---|
| 1266 | // |
---|
| 1267 | IPosition start4(start); |
---|
| 1268 | start4(asap::PolAxis) = 3; // Imag (XY) |
---|
| 1269 | IPosition end4(end); |
---|
| 1270 | end4(asap::PolAxis) = 3; |
---|
| 1271 | // |
---|
| 1272 | uInt nRow = in.nRow(); |
---|
| 1273 | Array<Float> data; |
---|
| 1274 | for (uInt i=0; i<nRow;++i) { |
---|
| 1275 | specCol.get(i,data); |
---|
| 1276 | IPosition shape = data.shape(); |
---|
| 1277 | |
---|
| 1278 | // Get polarization slice references |
---|
| 1279 | |
---|
| 1280 | Array<Float> C3 = data(start3,end3); |
---|
| 1281 | Array<Float> C4 = data(start4,end4); |
---|
| 1282 | |
---|
| 1283 | // Rotate |
---|
| 1284 | |
---|
[502] | 1285 | SDPolUtil::rotatePhase(C3, C4, value); |
---|
[457] | 1286 | |
---|
| 1287 | // Put |
---|
| 1288 | |
---|
| 1289 | specCol.put(i,data); |
---|
| 1290 | } |
---|
| 1291 | } |
---|
[234] | 1292 | |
---|
[502] | 1293 | |
---|
| 1294 | |
---|
| 1295 | void SDMath::rotateLinPolPhase(SDMemTable& in, Float value, Bool doAll) |
---|
| 1296 | // |
---|
| 1297 | // phase in degrees |
---|
[518] | 1298 | // assumes linear correlations |
---|
[502] | 1299 | // |
---|
| 1300 | { |
---|
| 1301 | if (in.nPol() != 4) { |
---|
| 1302 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
| 1303 | } |
---|
[518] | 1304 | // |
---|
| 1305 | SDHeader sh = in.getSDHeader(); |
---|
| 1306 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False); |
---|
| 1307 | SDAttr sdAtt; |
---|
| 1308 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
| 1309 | throw(AipsError("Only linear polarizations are supported")); |
---|
| 1310 | } |
---|
[502] | 1311 | // |
---|
| 1312 | const Table& tabIn = in.table(); |
---|
| 1313 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
| 1314 | ROArrayColumn<Float> stokesCol(tabIn,"STOKES"); |
---|
| 1315 | IPosition start(asap::nAxes,0); |
---|
| 1316 | IPosition end(asap::nAxes); |
---|
| 1317 | |
---|
| 1318 | // Set cursor slice. Assumes shape the same for all rows |
---|
| 1319 | |
---|
| 1320 | setCursorSlice (start, end, doAll, in); |
---|
| 1321 | // |
---|
| 1322 | IPosition start1(start); |
---|
| 1323 | start1(asap::PolAxis) = 0; // C1 (XX) |
---|
| 1324 | IPosition end1(end); |
---|
| 1325 | end1(asap::PolAxis) = 0; |
---|
| 1326 | // |
---|
| 1327 | IPosition start2(start); |
---|
| 1328 | start2(asap::PolAxis) = 1; // C2 (YY) |
---|
| 1329 | IPosition end2(end); |
---|
| 1330 | end2(asap::PolAxis) = 1; |
---|
| 1331 | // |
---|
| 1332 | IPosition start3(start); |
---|
| 1333 | start3(asap::PolAxis) = 2; // C3 ( Real(XY) ) |
---|
| 1334 | IPosition end3(end); |
---|
| 1335 | end3(asap::PolAxis) = 2; |
---|
| 1336 | // |
---|
| 1337 | IPosition startI(start); |
---|
| 1338 | startI(asap::PolAxis) = 0; // I |
---|
| 1339 | IPosition endI(end); |
---|
| 1340 | endI(asap::PolAxis) = 0; |
---|
| 1341 | // |
---|
| 1342 | IPosition startQ(start); |
---|
| 1343 | startQ(asap::PolAxis) = 1; // Q |
---|
| 1344 | IPosition endQ(end); |
---|
| 1345 | endQ(asap::PolAxis) = 1; |
---|
| 1346 | // |
---|
| 1347 | IPosition startU(start); |
---|
| 1348 | startU(asap::PolAxis) = 2; // U |
---|
| 1349 | IPosition endU(end); |
---|
| 1350 | endU(asap::PolAxis) = 2; |
---|
| 1351 | |
---|
| 1352 | // |
---|
| 1353 | uInt nRow = in.nRow(); |
---|
| 1354 | Array<Float> data, stokes; |
---|
| 1355 | for (uInt i=0; i<nRow;++i) { |
---|
| 1356 | specCol.get(i,data); |
---|
| 1357 | stokesCol.get(i,stokes); |
---|
| 1358 | IPosition shape = data.shape(); |
---|
| 1359 | |
---|
| 1360 | // Get linear polarization slice references |
---|
| 1361 | |
---|
| 1362 | Array<Float> C1 = data(start1,end1); |
---|
| 1363 | Array<Float> C2 = data(start2,end2); |
---|
| 1364 | Array<Float> C3 = data(start3,end3); |
---|
| 1365 | |
---|
| 1366 | // Get STokes slice references |
---|
| 1367 | |
---|
| 1368 | Array<Float> I = stokes(startI,endI); |
---|
| 1369 | Array<Float> Q = stokes(startQ,endQ); |
---|
| 1370 | Array<Float> U = stokes(startU,endU); |
---|
| 1371 | |
---|
| 1372 | // Rotate |
---|
| 1373 | |
---|
| 1374 | SDPolUtil::rotateLinPolPhase(C1, C2, C3, I, Q, U, value); |
---|
| 1375 | |
---|
| 1376 | // Put |
---|
| 1377 | |
---|
| 1378 | specCol.put(i,data); |
---|
| 1379 | } |
---|
| 1380 | } |
---|
| 1381 | |
---|
[169] | 1382 | // 'private' functions |
---|
| 1383 | |
---|
[354] | 1384 | void SDMath::convertBrightnessUnits (SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 1385 | Bool toKelvin, Float cFac, Bool doAll) const |
---|
| 1386 | { |
---|
[309] | 1387 | |
---|
[354] | 1388 | // Get header |
---|
| 1389 | |
---|
| 1390 | SDHeader sh = in.getSDHeader(); |
---|
| 1391 | const uInt nChan = sh.nchan; |
---|
| 1392 | |
---|
| 1393 | // Get instrument |
---|
| 1394 | |
---|
| 1395 | Bool throwIt = True; |
---|
[478] | 1396 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
[354] | 1397 | |
---|
| 1398 | // Get Diameter (m) |
---|
| 1399 | |
---|
| 1400 | SDAttr sdAtt; |
---|
| 1401 | |
---|
| 1402 | // Get epoch of first row |
---|
| 1403 | |
---|
| 1404 | MEpoch dateObs = in.getEpoch(0); |
---|
| 1405 | |
---|
| 1406 | // Generate a Vector of correction factors. One per FreqID |
---|
| 1407 | |
---|
| 1408 | SDFrequencyTable sdft = in.getSDFreqTable(); |
---|
| 1409 | Vector<uInt> freqIDs; |
---|
| 1410 | // |
---|
| 1411 | Vector<Float> freqs(sdft.length()); |
---|
| 1412 | for (uInt i=0; i<sdft.length(); i++) { |
---|
| 1413 | freqs(i) = (nChan/2 - sdft.referencePixel(i))*sdft.increment(i) + sdft.referenceValue(i); |
---|
| 1414 | } |
---|
| 1415 | // |
---|
| 1416 | Vector<Float> JyPerK = sdAtt.JyPerK(inst, dateObs, freqs); |
---|
[414] | 1417 | cout << "Jy/K = " << JyPerK << endl; |
---|
[354] | 1418 | Vector<Float> factors = cFac * JyPerK; |
---|
| 1419 | if (toKelvin) factors = Float(1.0) / factors; |
---|
| 1420 | |
---|
[434] | 1421 | // Get data slice bounds |
---|
[354] | 1422 | |
---|
| 1423 | IPosition start, end; |
---|
[434] | 1424 | setCursorSlice (start, end, doAll, in); |
---|
[354] | 1425 | const uInt ifAxis = in.getIF(); |
---|
| 1426 | |
---|
| 1427 | // Iteration axes |
---|
| 1428 | |
---|
| 1429 | IPosition axes(asap::nAxes-1,0); |
---|
| 1430 | for (uInt i=0,j=0; i<asap::nAxes; i++) { |
---|
| 1431 | if (i!=asap::IFAxis) { |
---|
| 1432 | axes(j++) = i; |
---|
| 1433 | } |
---|
| 1434 | } |
---|
| 1435 | |
---|
| 1436 | // Loop over rows and apply correction factor |
---|
| 1437 | |
---|
| 1438 | Float factor = 1.0; |
---|
| 1439 | const uInt axis = asap::ChanAxis; |
---|
| 1440 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 1441 | |
---|
| 1442 | // Get data |
---|
| 1443 | |
---|
[434] | 1444 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(i); |
---|
| 1445 | Array<Float>& values = dataIn.getRWArray(); // Ref to dataIn |
---|
| 1446 | Array<Float> values2 = values(start,end); // Ref to values to dataIn |
---|
[354] | 1447 | |
---|
| 1448 | // Get SDCOntainer |
---|
| 1449 | |
---|
| 1450 | SDContainer sc = in.getSDContainer(i); |
---|
| 1451 | |
---|
| 1452 | // Get FreqIDs |
---|
| 1453 | |
---|
| 1454 | freqIDs = sc.getFreqMap(); |
---|
| 1455 | |
---|
| 1456 | // Now the conversion factor depends only upon frequency |
---|
| 1457 | // So we need to iterate through by IF only giving |
---|
| 1458 | // us BEAM/POL/CHAN cubes |
---|
| 1459 | |
---|
[434] | 1460 | ArrayIterator<Float> itIn(values2, axes); |
---|
| 1461 | uInt ax = 0; |
---|
| 1462 | while (!itIn.pastEnd()) { |
---|
| 1463 | itIn.array() *= factors(freqIDs(ax)); // Writes back to dataIn |
---|
| 1464 | itIn.next(); |
---|
[354] | 1465 | } |
---|
| 1466 | |
---|
| 1467 | // Write out |
---|
| 1468 | |
---|
| 1469 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
| 1470 | // |
---|
| 1471 | pTabOut->putSDContainer(sc); |
---|
| 1472 | } |
---|
| 1473 | } |
---|
| 1474 | |
---|
| 1475 | |
---|
| 1476 | |
---|
[309] | 1477 | SDMemTable* SDMath::frequencyAlign (const SDMemTable& in, |
---|
| 1478 | MFrequency::Types freqSystem, |
---|
[397] | 1479 | const String& refTime, |
---|
| 1480 | const String& methodStr, |
---|
| 1481 | Bool perFreqID) const |
---|
[267] | 1482 | { |
---|
| 1483 | // Get Header |
---|
| 1484 | |
---|
| 1485 | SDHeader sh = in.getSDHeader(); |
---|
| 1486 | const uInt nChan = sh.nchan; |
---|
| 1487 | const uInt nRows = in.nRow(); |
---|
[330] | 1488 | const uInt nIF = sh.nif; |
---|
[267] | 1489 | |
---|
| 1490 | // Get Table reference |
---|
| 1491 | |
---|
| 1492 | const Table& tabIn = in.table(); |
---|
| 1493 | |
---|
| 1494 | // Get Columns from Table |
---|
| 1495 | |
---|
[294] | 1496 | ROScalarColumn<Double> mjdCol(tabIn, "TIME"); |
---|
| 1497 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME"); |
---|
| 1498 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID"); |
---|
| 1499 | Vector<Double> times = mjdCol.getColumn(); |
---|
[267] | 1500 | |
---|
[397] | 1501 | // Generate DataDesc table |
---|
[330] | 1502 | |
---|
| 1503 | Matrix<uInt> ddIdx; |
---|
| 1504 | SDDataDesc dDesc; |
---|
[397] | 1505 | generateDataDescTable (ddIdx, dDesc, nIF, in, tabIn, srcCol, fqIDCol, perFreqID); |
---|
[267] | 1506 | |
---|
[294] | 1507 | // Get reference Epoch to time of first row or given String |
---|
[267] | 1508 | |
---|
| 1509 | Unit DAY(String("d")); |
---|
[272] | 1510 | MEpoch::Ref epochRef(in.getTimeReference()); |
---|
| 1511 | MEpoch refEpoch; |
---|
| 1512 | if (refTime.length()>0) { |
---|
| 1513 | refEpoch = epochFromString(refTime, in.getTimeReference()); |
---|
| 1514 | } else { |
---|
[288] | 1515 | refEpoch = in.getEpoch(0); |
---|
[272] | 1516 | } |
---|
[414] | 1517 | cout << "Aligning at reference Epoch " << formatEpoch(refEpoch) |
---|
| 1518 | << " in frame " << MFrequency::showType(freqSystem) << endl; |
---|
| 1519 | |
---|
[294] | 1520 | // Get Reference Position |
---|
[267] | 1521 | |
---|
[288] | 1522 | MPosition refPos = in.getAntennaPosition(); |
---|
[267] | 1523 | |
---|
[397] | 1524 | // Create FrequencyAligner Block. One FA for each possible |
---|
| 1525 | // source/freqID (perFreqID=True) or source/IF (perFreqID=False) combination |
---|
[267] | 1526 | |
---|
[330] | 1527 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length()); |
---|
[397] | 1528 | generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos, |
---|
| 1529 | refEpoch, perFreqID); |
---|
[267] | 1530 | |
---|
[397] | 1531 | // Generate and fill output Frequency Table. WHen perFreqID=True, there is one output FreqID |
---|
| 1532 | // for each entry in the SDDataDesc table. However, in perFreqID=False mode, there may be |
---|
| 1533 | // some degeneracy, so we need a little translation map |
---|
[330] | 1534 | |
---|
| 1535 | SDFrequencyTable freqTabOut = in.getSDFreqTable(); |
---|
| 1536 | freqTabOut.setLength(0); |
---|
| 1537 | Vector<String> units(1); |
---|
| 1538 | units = String("Hz"); |
---|
| 1539 | Bool linear=True; |
---|
| 1540 | // |
---|
[397] | 1541 | Vector<uInt> ddFQTrans(dDesc.length(),0); |
---|
[330] | 1542 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
| 1543 | |
---|
| 1544 | // Get Aligned SC in Hz |
---|
| 1545 | |
---|
| 1546 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear); |
---|
| 1547 | sC.setWorldAxisUnits(units); |
---|
| 1548 | |
---|
| 1549 | // Add FreqID |
---|
| 1550 | |
---|
[397] | 1551 | uInt idx = freqTabOut.addFrequency(sC.referencePixel()[0], |
---|
| 1552 | sC.referenceValue()[0], |
---|
| 1553 | sC.increment()[0]); |
---|
| 1554 | ddFQTrans(i) = idx; // output FreqID = ddFQTrans(ddIdx) |
---|
[330] | 1555 | } |
---|
| 1556 | |
---|
[317] | 1557 | // Interpolation method |
---|
| 1558 | |
---|
| 1559 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
| 1560 | convertInterpString(interp, methodStr); |
---|
| 1561 | |
---|
[267] | 1562 | // New output Table |
---|
| 1563 | |
---|
[414] | 1564 | cout << "Create output table" << endl; |
---|
[267] | 1565 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
[330] | 1566 | pTabOut->putSDFreqTable(freqTabOut); |
---|
[267] | 1567 | |
---|
| 1568 | // Loop over rows in Table |
---|
| 1569 | |
---|
[330] | 1570 | Bool extrapolate=False; |
---|
[294] | 1571 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis); |
---|
| 1572 | Bool useCachedAbcissa = False; |
---|
| 1573 | Bool first = True; |
---|
| 1574 | Bool ok; |
---|
| 1575 | Vector<Float> yOut; |
---|
| 1576 | Vector<Bool> maskOut; |
---|
[330] | 1577 | Vector<uInt> freqID(nIF); |
---|
[309] | 1578 | uInt ifIdx, faIdx; |
---|
[397] | 1579 | Vector<Double> xIn; |
---|
[267] | 1580 | // |
---|
[294] | 1581 | for (uInt iRow=0; iRow<nRows; ++iRow) { |
---|
| 1582 | if (iRow%10==0) { |
---|
[414] | 1583 | cout << "Processing row " << iRow << endl; |
---|
[294] | 1584 | } |
---|
[267] | 1585 | |
---|
| 1586 | // Get EPoch |
---|
| 1587 | |
---|
[294] | 1588 | Quantum<Double> tQ2(times[iRow],DAY); |
---|
| 1589 | MVEpoch mv2(tQ2); |
---|
| 1590 | MEpoch epoch(mv2, epochRef); |
---|
[267] | 1591 | |
---|
| 1592 | // Get copy of data |
---|
| 1593 | |
---|
[294] | 1594 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow)); |
---|
| 1595 | Array<Float> values = mArrIn.getArray(); |
---|
| 1596 | Array<Bool> mask = mArrIn.getMask(); |
---|
[267] | 1597 | |
---|
[309] | 1598 | // For each row, the Frequency abcissa will be the same regardless |
---|
[267] | 1599 | // of polarization. For all other axes (IF and BEAM) the abcissa |
---|
| 1600 | // will change. So we iterate through the data by pol-chan planes |
---|
[330] | 1601 | // to mimimize the work. Probably won't work for multiple beams |
---|
| 1602 | // at this point. |
---|
[267] | 1603 | |
---|
[294] | 1604 | ArrayIterator<Float> itValuesPlane(values, polChanAxes); |
---|
| 1605 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes); |
---|
| 1606 | while (!itValuesPlane.pastEnd()) { |
---|
[267] | 1607 | |
---|
[309] | 1608 | // Find the IF index and then the FA PtrBlock index |
---|
[267] | 1609 | |
---|
[294] | 1610 | const IPosition& pos = itValuesPlane.pos(); |
---|
| 1611 | ifIdx = pos(asap::IFAxis); |
---|
[330] | 1612 | faIdx = ddIdx(iRow,ifIdx); |
---|
[397] | 1613 | |
---|
| 1614 | // Generate abcissa for perIF. Could cache this in a Matrix |
---|
| 1615 | // on a per scan basis. Pretty expensive doing it for every row. |
---|
| 1616 | |
---|
| 1617 | if (!perFreqID) { |
---|
| 1618 | xIn.resize(nChan); |
---|
| 1619 | uInt fqID = dDesc.secID(ddIdx(iRow,ifIdx)); |
---|
| 1620 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID); |
---|
| 1621 | Double w; |
---|
| 1622 | for (uInt i=0; i<nChan; i++) { |
---|
| 1623 | sC.toWorld(w,Double(i)); |
---|
| 1624 | xIn[i] = w; |
---|
| 1625 | } |
---|
| 1626 | } |
---|
[267] | 1627 | // |
---|
[294] | 1628 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1); |
---|
| 1629 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
[330] | 1630 | |
---|
| 1631 | // Iterate through the plane by vector and align |
---|
| 1632 | |
---|
[294] | 1633 | first = True; |
---|
| 1634 | useCachedAbcissa=False; |
---|
| 1635 | while (!itValuesVec.pastEnd()) { |
---|
[397] | 1636 | if (perFreqID) { |
---|
| 1637 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(), |
---|
| 1638 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
| 1639 | interp, extrapolate); |
---|
| 1640 | } else { |
---|
| 1641 | ok = a[faIdx]->align (yOut, maskOut, xIn, itValuesVec.vector(), |
---|
| 1642 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
| 1643 | interp, extrapolate); |
---|
| 1644 | } |
---|
[330] | 1645 | // |
---|
[294] | 1646 | itValuesVec.vector() = yOut; |
---|
| 1647 | itMaskVec.vector() = maskOut; |
---|
[267] | 1648 | // |
---|
[294] | 1649 | itValuesVec.next(); |
---|
| 1650 | itMaskVec.next(); |
---|
[267] | 1651 | // |
---|
[294] | 1652 | if (first) { |
---|
| 1653 | useCachedAbcissa = True; |
---|
| 1654 | first = False; |
---|
| 1655 | } |
---|
| 1656 | } |
---|
[267] | 1657 | // |
---|
| 1658 | itValuesPlane.next(); |
---|
| 1659 | itMaskPlane.next(); |
---|
[294] | 1660 | } |
---|
[267] | 1661 | |
---|
[330] | 1662 | // Create SDContainer and put back |
---|
[267] | 1663 | |
---|
| 1664 | SDContainer sc = in.getSDContainer(iRow); |
---|
| 1665 | putDataInSDC(sc, values, mask); |
---|
[397] | 1666 | |
---|
| 1667 | // Set output FreqIDs |
---|
| 1668 | |
---|
[330] | 1669 | for (uInt i=0; i<nIF; i++) { |
---|
[397] | 1670 | uInt idx = ddIdx(iRow,i); // Index into SDDataDesc table |
---|
| 1671 | freqID(i) = ddFQTrans(idx); // FreqID in output FQ table |
---|
[330] | 1672 | } |
---|
| 1673 | sc.putFreqMap(freqID); |
---|
[267] | 1674 | // |
---|
| 1675 | pTabOut->putSDContainer(sc); |
---|
[294] | 1676 | } |
---|
[267] | 1677 | |
---|
[309] | 1678 | // Now we must set the base and extra frames to the |
---|
| 1679 | // input frame |
---|
| 1680 | |
---|
| 1681 | std::vector<string> info = pTabOut->getCoordInfo(); |
---|
| 1682 | info[1] = MFrequency::showType(freqSystem); // Conversion frame |
---|
| 1683 | info[3] = info[1]; // Base frame |
---|
| 1684 | pTabOut->setCoordInfo(info); |
---|
| 1685 | |
---|
[267] | 1686 | // Clean up PointerBlock |
---|
| 1687 | |
---|
[309] | 1688 | for (uInt i=0; i<a.nelements(); i++) delete a[i]; |
---|
[267] | 1689 | // |
---|
[309] | 1690 | return pTabOut; |
---|
[267] | 1691 | } |
---|
| 1692 | |
---|
| 1693 | |
---|
[185] | 1694 | void SDMath::fillSDC(SDContainer& sc, |
---|
| 1695 | const Array<Bool>& mask, |
---|
| 1696 | const Array<Float>& data, |
---|
| 1697 | const Array<Float>& tSys, |
---|
| 1698 | Int scanID, Double timeStamp, |
---|
| 1699 | Double interval, const String& sourceName, |
---|
[227] | 1700 | const Vector<uInt>& freqID) const |
---|
[167] | 1701 | { |
---|
[169] | 1702 | // Data and mask |
---|
[167] | 1703 | |
---|
[185] | 1704 | putDataInSDC(sc, data, mask); |
---|
[167] | 1705 | |
---|
[169] | 1706 | // TSys |
---|
| 1707 | |
---|
| 1708 | sc.putTsys(tSys); |
---|
| 1709 | |
---|
| 1710 | // Time things |
---|
| 1711 | |
---|
| 1712 | sc.timestamp = timeStamp; |
---|
| 1713 | sc.interval = interval; |
---|
| 1714 | sc.scanid = scanID; |
---|
[167] | 1715 | // |
---|
[169] | 1716 | sc.sourcename = sourceName; |
---|
| 1717 | sc.putFreqMap(freqID); |
---|
| 1718 | } |
---|
[167] | 1719 | |
---|
[185] | 1720 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum, |
---|
| 1721 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
| 1722 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
[518] | 1723 | Array<Float>& tSysSqSum, |
---|
[185] | 1724 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
| 1725 | const Vector<Bool>& mask, Double time, Double interval, |
---|
| 1726 | const Block<CountedPtr<SDMemTable> >& in, |
---|
| 1727 | uInt iTab, uInt iRow, uInt axis, |
---|
| 1728 | uInt nAxesSub, Bool useMask, |
---|
[227] | 1729 | WeightType wtType) const |
---|
[169] | 1730 | { |
---|
| 1731 | |
---|
| 1732 | // Get data |
---|
| 1733 | |
---|
| 1734 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
| 1735 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
| 1736 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
[167] | 1737 | // |
---|
[169] | 1738 | if (wtType==NONE) { |
---|
| 1739 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
| 1740 | nPts += n; // Only accumulates where mask==T |
---|
[518] | 1741 | } else if (wtType==TINT) { |
---|
| 1742 | |
---|
| 1743 | // We are weighting the data by integration time. |
---|
| 1744 | |
---|
| 1745 | valuesIn *= Float(interval); |
---|
| 1746 | |
---|
[169] | 1747 | } else if (wtType==VAR) { |
---|
[167] | 1748 | |
---|
[169] | 1749 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
| 1750 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
[167] | 1751 | |
---|
[169] | 1752 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1753 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
| 1754 | Float fac = 1.0; |
---|
| 1755 | IPosition pos(nAxesSub,0); |
---|
| 1756 | // |
---|
| 1757 | while (!itData.pastEnd()) { |
---|
[167] | 1758 | |
---|
[169] | 1759 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
[167] | 1760 | |
---|
[518] | 1761 | if (useMask) { |
---|
| 1762 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
| 1763 | fac = 1.0/variance(tmp); |
---|
| 1764 | } else { |
---|
| 1765 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
| 1766 | fac = 1.0/variance(tmp); |
---|
| 1767 | } |
---|
[169] | 1768 | |
---|
| 1769 | // Scale data |
---|
| 1770 | |
---|
[518] | 1771 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
[167] | 1772 | // |
---|
[169] | 1773 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
| 1774 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1775 | // because the spectral axis is the last one (so we can just |
---|
| 1776 | // copy the first nAXesSub positions out) |
---|
[167] | 1777 | |
---|
[518] | 1778 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1779 | sumSq(pos) += fac; |
---|
[169] | 1780 | // |
---|
[518] | 1781 | itData.next(); |
---|
| 1782 | itMask.next(); |
---|
[169] | 1783 | } |
---|
| 1784 | } else if (wtType==TSYS) { |
---|
[518] | 1785 | |
---|
| 1786 | // We are going to average the data, weighted by 1/Tsys**2 for each pol, beam and IF. |
---|
| 1787 | // So therefore we need to iterate through by spectrum (axis 3). Although |
---|
| 1788 | // Tsys is stored as a vector of length nChan, the values are replicated. |
---|
| 1789 | // We will take a short cut and just use the value from the first channel |
---|
| 1790 | // for now. |
---|
| 1791 | // |
---|
| 1792 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1793 | ReadOnlyVectorIterator<Float> itTSys(tSys, axis); |
---|
| 1794 | Float fac = 1.0; |
---|
| 1795 | IPosition pos(nAxesSub,0); |
---|
| 1796 | // |
---|
| 1797 | while (!itData.pastEnd()) { |
---|
| 1798 | Float t = itTSys.vector()[0]; |
---|
| 1799 | fac = 1.0/t/t; |
---|
| 1800 | |
---|
| 1801 | // Scale data |
---|
| 1802 | |
---|
| 1803 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
| 1804 | // |
---|
| 1805 | // Accumulate Tsys per if/pol/beam averaged over spectrum |
---|
| 1806 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1807 | // because the spectral axis is the last one (so we can just |
---|
| 1808 | // copy the first nAXesSub positions out) |
---|
| 1809 | |
---|
| 1810 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1811 | tSysSqSum(pos) += fac; |
---|
| 1812 | // |
---|
| 1813 | itData.next(); |
---|
| 1814 | itTSys.next(); |
---|
| 1815 | } |
---|
[169] | 1816 | } |
---|
[167] | 1817 | |
---|
[169] | 1818 | // Accumulate sum of (possibly scaled) data |
---|
| 1819 | |
---|
| 1820 | sum += dataIn; |
---|
| 1821 | |
---|
| 1822 | // Accumulate Tsys, time, and interval |
---|
| 1823 | |
---|
| 1824 | tSysSum += tSys; |
---|
| 1825 | timeSum += time; |
---|
| 1826 | intSum += interval; |
---|
| 1827 | nAccum += 1; |
---|
| 1828 | } |
---|
| 1829 | |
---|
| 1830 | |
---|
[518] | 1831 | void SDMath::normalize(MaskedArray<Float>& sum, |
---|
| 1832 | const Array<Float>& sumSq, |
---|
| 1833 | const Array<Float>& tSysSqSum, |
---|
| 1834 | const Array<Float>& nPts, |
---|
| 1835 | Double intSum, |
---|
| 1836 | WeightType wtType, Int axis, |
---|
| 1837 | Int nAxesSub) const |
---|
| 1838 | { |
---|
| 1839 | IPosition pos2(nAxesSub,0); |
---|
| 1840 | // |
---|
| 1841 | if (wtType==NONE) { |
---|
| 1842 | |
---|
| 1843 | // We just average by the number of points accumulated. |
---|
| 1844 | // We need to make a MA out of nPts so that no divide by |
---|
| 1845 | // zeros occur |
---|
| 1846 | |
---|
| 1847 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
| 1848 | sum /= t; |
---|
| 1849 | } else if (wtType==TINT) { |
---|
| 1850 | |
---|
| 1851 | // Average by sum of Tint |
---|
| 1852 | |
---|
| 1853 | sum /= Float(intSum); |
---|
| 1854 | } else if (wtType==VAR) { |
---|
| 1855 | |
---|
| 1856 | // Normalize each spectrum by sum(1/var) where the variance |
---|
| 1857 | // is worked out for each spectrum |
---|
| 1858 | |
---|
| 1859 | Array<Float>& data = sum.getRWArray(); |
---|
| 1860 | VectorIterator<Float> itData(data, axis); |
---|
| 1861 | while (!itData.pastEnd()) { |
---|
| 1862 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 1863 | itData.vector() /= sumSq(pos2); |
---|
| 1864 | itData.next(); |
---|
| 1865 | } |
---|
| 1866 | } else if (wtType==TSYS) { |
---|
| 1867 | |
---|
| 1868 | // Normalize each spectrum by sum(1/Tsys**2) where the pseudo |
---|
| 1869 | // replication over channel for Tsys has been dropped. |
---|
| 1870 | |
---|
| 1871 | Array<Float>& data = sum.getRWArray(); |
---|
| 1872 | VectorIterator<Float> itData(data, axis); |
---|
| 1873 | while (!itData.pastEnd()) { |
---|
| 1874 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 1875 | itData.vector() /= tSysSqSum(pos2); |
---|
| 1876 | itData.next(); |
---|
| 1877 | } |
---|
| 1878 | } |
---|
| 1879 | } |
---|
| 1880 | |
---|
| 1881 | |
---|
| 1882 | |
---|
| 1883 | |
---|
[434] | 1884 | void SDMath::setCursorSlice (IPosition& start, IPosition& end, Bool doAll, const SDMemTable& in) const |
---|
[169] | 1885 | { |
---|
[434] | 1886 | const uInt nDim = asap::nAxes; |
---|
| 1887 | DebugAssert(nDim==4,AipsError); |
---|
[167] | 1888 | // |
---|
[169] | 1889 | start.resize(nDim); |
---|
[434] | 1890 | end.resize(nDim); |
---|
| 1891 | if (doAll) { |
---|
| 1892 | start = 0; |
---|
| 1893 | end(0) = in.nBeam()-1; |
---|
| 1894 | end(1) = in.nIF()-1; |
---|
| 1895 | end(2) = in.nPol()-1; |
---|
| 1896 | end(3) = in.nChan()-1; |
---|
| 1897 | } else { |
---|
| 1898 | start(0) = in.getBeam(); |
---|
| 1899 | end(0) = start(0); |
---|
[167] | 1900 | // |
---|
[434] | 1901 | start(1) = in.getIF(); |
---|
| 1902 | end(1) = start(1); |
---|
| 1903 | // |
---|
| 1904 | start(2) = in.getPol(); |
---|
| 1905 | end(2) = start(2); |
---|
| 1906 | // |
---|
| 1907 | start(3) = 0; |
---|
| 1908 | end(3) = in.nChan()-1; |
---|
| 1909 | } |
---|
[169] | 1910 | } |
---|
| 1911 | |
---|
| 1912 | |
---|
[518] | 1913 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr, |
---|
| 1914 | Bool listType) const |
---|
[169] | 1915 | { |
---|
| 1916 | String tStr(weightStr); |
---|
| 1917 | tStr.upcase(); |
---|
[518] | 1918 | String msg; |
---|
[169] | 1919 | if (tStr.contains(String("NONE"))) { |
---|
| 1920 | wtType = NONE; |
---|
[518] | 1921 | msg = String("Weighting type selected : None"); |
---|
[169] | 1922 | } else if (tStr.contains(String("VAR"))) { |
---|
| 1923 | wtType = VAR; |
---|
[518] | 1924 | msg = String("Weighting type selected : Variance"); |
---|
| 1925 | } else if (tStr.contains(String("TINT"))) { |
---|
| 1926 | wtType = TINT; |
---|
[519] | 1927 | msg = String("Weighting type selected : Tint"); |
---|
[169] | 1928 | } else if (tStr.contains(String("TSYS"))) { |
---|
| 1929 | wtType = TSYS; |
---|
[518] | 1930 | msg = String("Weighting type selected : Tsys"); |
---|
[169] | 1931 | } else { |
---|
[518] | 1932 | msg = String("Weighting type selected : None"); |
---|
| 1933 | throw(AipsError("Unrecognized weighting type")); |
---|
[167] | 1934 | } |
---|
[518] | 1935 | // |
---|
| 1936 | if (listType) cout << msg << endl; |
---|
[167] | 1937 | } |
---|
| 1938 | |
---|
[317] | 1939 | |
---|
| 1940 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type, |
---|
| 1941 | const casa::String& interp) const |
---|
[227] | 1942 | { |
---|
| 1943 | String tStr(interp); |
---|
| 1944 | tStr.upcase(); |
---|
| 1945 | if (tStr.contains(String("NEAR"))) { |
---|
[317] | 1946 | type = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
[227] | 1947 | } else if (tStr.contains(String("LIN"))) { |
---|
[317] | 1948 | type = InterpolateArray1D<Double,Float>::linear; |
---|
[227] | 1949 | } else if (tStr.contains(String("CUB"))) { |
---|
[317] | 1950 | type = InterpolateArray1D<Double,Float>::cubic; |
---|
[227] | 1951 | } else if (tStr.contains(String("SPL"))) { |
---|
[317] | 1952 | type = InterpolateArray1D<Double,Float>::spline; |
---|
[227] | 1953 | } else { |
---|
| 1954 | throw(AipsError("Unrecognized interpolation type")); |
---|
| 1955 | } |
---|
| 1956 | } |
---|
| 1957 | |
---|
[185] | 1958 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data, |
---|
[227] | 1959 | const Array<Bool>& mask) const |
---|
[169] | 1960 | { |
---|
| 1961 | sc.putSpectrum(data); |
---|
| 1962 | // |
---|
| 1963 | Array<uChar> outflags(data.shape()); |
---|
| 1964 | convertArray(outflags,!mask); |
---|
| 1965 | sc.putFlags(outflags); |
---|
| 1966 | } |
---|
[227] | 1967 | |
---|
| 1968 | Table SDMath::readAsciiFile (const String& fileName) const |
---|
| 1969 | { |
---|
[230] | 1970 | String formatString; |
---|
| 1971 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False); |
---|
[227] | 1972 | return tbl; |
---|
| 1973 | } |
---|
[230] | 1974 | |
---|
| 1975 | |
---|
[234] | 1976 | |
---|
[480] | 1977 | void SDMath::scaleFromAsciiTable(SDMemTable* pTabOut, |
---|
| 1978 | const SDMemTable& in, const String& fileName, |
---|
| 1979 | const String& col0, const String& col1, |
---|
| 1980 | const String& methodStr, Bool doAll, |
---|
| 1981 | const Vector<Float>& xOut, Bool doTSys) const |
---|
[230] | 1982 | { |
---|
| 1983 | |
---|
| 1984 | // Read gain-elevation ascii file data into a Table. |
---|
| 1985 | |
---|
[234] | 1986 | Table geTable = readAsciiFile (fileName); |
---|
[230] | 1987 | // |
---|
[480] | 1988 | scaleFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut, doTSys); |
---|
[230] | 1989 | } |
---|
| 1990 | |
---|
[480] | 1991 | void SDMath::scaleFromTable(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 1992 | const Table& tTable, const String& col0, |
---|
| 1993 | const String& col1, |
---|
| 1994 | const String& methodStr, Bool doAll, |
---|
| 1995 | const Vector<Float>& xOut, Bool doTsys) const |
---|
[230] | 1996 | { |
---|
| 1997 | |
---|
| 1998 | // Get data from Table |
---|
| 1999 | |
---|
| 2000 | ROScalarColumn<Float> geElCol(tTable, col0); |
---|
| 2001 | ROScalarColumn<Float> geFacCol(tTable, col1); |
---|
| 2002 | Vector<Float> xIn = geElCol.getColumn(); |
---|
| 2003 | Vector<Float> yIn = geFacCol.getColumn(); |
---|
| 2004 | Vector<Bool> maskIn(xIn.nelements(),True); |
---|
| 2005 | |
---|
| 2006 | // Interpolate (and extrapolate) with desired method |
---|
| 2007 | |
---|
[317] | 2008 | InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
[230] | 2009 | convertInterpString(method, methodStr); |
---|
[317] | 2010 | Int intMethod(method); |
---|
[230] | 2011 | // |
---|
| 2012 | Vector<Float> yOut; |
---|
| 2013 | Vector<Bool> maskOut; |
---|
| 2014 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut, |
---|
[317] | 2015 | xIn, yIn, maskIn, intMethod, |
---|
[230] | 2016 | True, True); |
---|
[234] | 2017 | // Apply |
---|
[230] | 2018 | |
---|
[480] | 2019 | scaleByVector(pTabOut, in, doAll, Float(1.0)/yOut, doTsys); |
---|
[234] | 2020 | } |
---|
| 2021 | |
---|
| 2022 | |
---|
[480] | 2023 | void SDMath::scaleByVector(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 2024 | Bool doAll, const Vector<Float>& factor, |
---|
| 2025 | Bool doTSys) const |
---|
[234] | 2026 | { |
---|
[270] | 2027 | |
---|
[434] | 2028 | // Set up data slice |
---|
[230] | 2029 | |
---|
| 2030 | IPosition start, end; |
---|
[434] | 2031 | setCursorSlice (start, end, doAll, in); |
---|
[230] | 2032 | |
---|
[480] | 2033 | // Get Tsys column |
---|
| 2034 | |
---|
| 2035 | const Table& tIn = in.table(); |
---|
| 2036 | ArrayColumn<Float> tSysCol(tIn, "TSYS"); |
---|
| 2037 | Array<Float> tSys; |
---|
| 2038 | |
---|
[270] | 2039 | // Loop over rows and apply correction factor |
---|
[230] | 2040 | |
---|
| 2041 | const uInt axis = asap::ChanAxis; |
---|
| 2042 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 2043 | |
---|
| 2044 | // Get data |
---|
| 2045 | |
---|
[434] | 2046 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
| 2047 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference to dataIn |
---|
[480] | 2048 | // |
---|
| 2049 | if (doTSys) { |
---|
| 2050 | tSysCol.get(i, tSys); |
---|
| 2051 | Array<Float> tSys2 = tSys(start,end) * factor[i]; |
---|
| 2052 | tSysCol.put(i, tSys); |
---|
| 2053 | } |
---|
[230] | 2054 | |
---|
| 2055 | // Apply factor |
---|
| 2056 | |
---|
[434] | 2057 | dataIn2 *= factor[i]; |
---|
[230] | 2058 | |
---|
| 2059 | // Write out |
---|
| 2060 | |
---|
[434] | 2061 | SDContainer sc = in.getSDContainer(i); |
---|
| 2062 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
[230] | 2063 | // |
---|
[434] | 2064 | pTabOut->putSDContainer(sc); |
---|
[230] | 2065 | } |
---|
| 2066 | } |
---|
| 2067 | |
---|
[234] | 2068 | |
---|
[262] | 2069 | |
---|
| 2070 | |
---|
[330] | 2071 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx, |
---|
| 2072 | SDDataDesc& dDesc, |
---|
| 2073 | uInt nIF, |
---|
| 2074 | const SDMemTable& in, |
---|
| 2075 | const Table& tabIn, |
---|
| 2076 | const ROScalarColumn<String>& srcCol, |
---|
[397] | 2077 | const ROArrayColumn<uInt>& fqIDCol, |
---|
| 2078 | Bool perFreqID) const |
---|
[330] | 2079 | { |
---|
| 2080 | const uInt nRows = tabIn.nrow(); |
---|
| 2081 | ddIdx.resize(nRows,nIF); |
---|
[262] | 2082 | // |
---|
[330] | 2083 | String srcName; |
---|
| 2084 | Vector<uInt> freqIDs; |
---|
| 2085 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 2086 | srcCol.get(iRow, srcName); |
---|
| 2087 | fqIDCol.get(iRow, freqIDs); |
---|
| 2088 | const MDirection& dir = in.getDirection(iRow); |
---|
| 2089 | // |
---|
[397] | 2090 | if (perFreqID) { |
---|
| 2091 | |
---|
| 2092 | // One entry per source/freqID pair |
---|
| 2093 | |
---|
| 2094 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
| 2095 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, freqIDs[iIF], dir, 0); |
---|
| 2096 | } |
---|
| 2097 | } else { |
---|
| 2098 | |
---|
| 2099 | // One entry per source/IF pair. Hang onto the FreqID as well |
---|
| 2100 | |
---|
| 2101 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
| 2102 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, iIF, dir, freqIDs[iIF]); |
---|
| 2103 | } |
---|
[262] | 2104 | } |
---|
| 2105 | } |
---|
| 2106 | } |
---|
[272] | 2107 | |
---|
[397] | 2108 | |
---|
| 2109 | |
---|
| 2110 | |
---|
| 2111 | |
---|
[272] | 2112 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const |
---|
| 2113 | { |
---|
| 2114 | Quantum<Double> qt; |
---|
| 2115 | if (MVTime::read(qt,str)) { |
---|
| 2116 | MVEpoch mv(qt); |
---|
| 2117 | MEpoch me(mv, timeRef); |
---|
| 2118 | return me; |
---|
| 2119 | } else { |
---|
| 2120 | throw(AipsError("Invalid format for Epoch string")); |
---|
| 2121 | } |
---|
| 2122 | } |
---|
| 2123 | |
---|
| 2124 | |
---|
| 2125 | String SDMath::formatEpoch(const MEpoch& epoch) const |
---|
| 2126 | { |
---|
| 2127 | MVTime mvt(epoch.getValue()); |
---|
| 2128 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")"); |
---|
| 2129 | } |
---|
| 2130 | |
---|
[294] | 2131 | |
---|
[309] | 2132 | |
---|
| 2133 | void SDMath::generateFrequencyAligners (PtrBlock<FrequencyAligner<Float>* >& a, |
---|
[330] | 2134 | const SDDataDesc& dDesc, |
---|
| 2135 | const SDMemTable& in, uInt nChan, |
---|
| 2136 | MFrequency::Types system, |
---|
| 2137 | const MPosition& refPos, |
---|
[397] | 2138 | const MEpoch& refEpoch, |
---|
| 2139 | Bool perFreqID) const |
---|
[294] | 2140 | { |
---|
[330] | 2141 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
[397] | 2142 | uInt ID = dDesc.ID(i); |
---|
| 2143 | uInt secID = dDesc.secID(i); |
---|
| 2144 | const MDirection& refDir = dDesc.secDir(i); |
---|
[330] | 2145 | // |
---|
[397] | 2146 | if (perFreqID) { |
---|
| 2147 | |
---|
| 2148 | // One aligner per source/FreqID pair. |
---|
| 2149 | |
---|
| 2150 | SpectralCoordinate sC = in.getSpectralCoordinate(ID); |
---|
| 2151 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
| 2152 | } else { |
---|
| 2153 | |
---|
| 2154 | // One aligner per source/IF pair. But we still need the FreqID to |
---|
| 2155 | // get the right SC. Hence the messing about with the secondary ID |
---|
| 2156 | |
---|
| 2157 | SpectralCoordinate sC = in.getSpectralCoordinate(secID); |
---|
| 2158 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
| 2159 | } |
---|
[294] | 2160 | } |
---|
| 2161 | } |
---|
[480] | 2162 | |
---|
| 2163 | Vector<uInt> SDMath::getRowRange (const SDMemTable& in) const |
---|
| 2164 | { |
---|
| 2165 | Vector<uInt> range(2); |
---|
| 2166 | range[0] = 0; |
---|
| 2167 | range[1] = in.nRow()-1; |
---|
| 2168 | return range; |
---|
| 2169 | } |
---|
| 2170 | |
---|
| 2171 | |
---|
| 2172 | Bool SDMath::rowInRange (uInt i, const Vector<uInt>& range) const |
---|
| 2173 | { |
---|
| 2174 | return (i>=range[0] && i<=range[1]); |
---|
| 2175 | } |
---|