[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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[716] | 33 | |
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[81] | 34 | #include <casa/aips.h> |
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[330] | 35 | #include <casa/iostream.h> |
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[716] | 36 | #include <casa/sstream.h> |
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[330] | 37 | #include <casa/iomanip.h> |
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[81] | 38 | #include <casa/BasicSL/String.h> |
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| 39 | #include <casa/Arrays/IPosition.h> |
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| 40 | #include <casa/Arrays/Array.h> |
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[130] | 41 | #include <casa/Arrays/ArrayIter.h> |
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| 42 | #include <casa/Arrays/VectorIter.h> |
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[81] | 43 | #include <casa/Arrays/ArrayMath.h> |
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| 44 | #include <casa/Arrays/ArrayLogical.h> |
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| 45 | #include <casa/Arrays/MaskedArray.h> |
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| 46 | #include <casa/Arrays/MaskArrMath.h> |
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| 47 | #include <casa/Arrays/MaskArrLogi.h> |
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[330] | 48 | #include <casa/Arrays/Matrix.h> |
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[234] | 49 | #include <casa/BasicMath/Math.h> |
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[262] | 50 | #include <casa/Exceptions.h> |
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| 51 | #include <casa/Quanta/Quantum.h> |
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| 52 | #include <casa/Quanta/Unit.h> |
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| 53 | #include <casa/Quanta/MVEpoch.h> |
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[272] | 54 | #include <casa/Quanta/MVTime.h> |
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[177] | 55 | #include <casa/Utilities/Assert.h> |
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[2] | 56 | |
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[262] | 57 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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| 58 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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| 59 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[309] | 60 | #include <coordinates/Coordinates/FrequencyAligner.h> |
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[262] | 61 | |
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| 62 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 63 | #include <lattices/Lattices/RebinLattice.h> |
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| 64 | |
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| 65 | #include <measures/Measures/MEpoch.h> |
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| 66 | #include <measures/Measures/MDirection.h> |
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| 67 | #include <measures/Measures/MPosition.h> |
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| 68 | |
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[177] | 69 | #include <scimath/Mathematics/VectorKernel.h> |
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| 70 | #include <scimath/Mathematics/Convolver.h> |
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[227] | 71 | #include <scimath/Mathematics/InterpolateArray1D.h> |
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[234] | 72 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 73 | |
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[81] | 74 | #include <tables/Tables/Table.h> |
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| 75 | #include <tables/Tables/ScalarColumn.h> |
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| 76 | #include <tables/Tables/ArrayColumn.h> |
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[227] | 77 | #include <tables/Tables/ReadAsciiTable.h> |
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[2] | 78 | |
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[38] | 79 | #include "MathUtils.h" |
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[232] | 80 | #include "SDDefs.h" |
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[354] | 81 | #include "SDAttr.h" |
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[2] | 82 | #include "SDContainer.h" |
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| 83 | #include "SDMemTable.h" |
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| 84 | |
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| 85 | #include "SDMath.h" |
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[457] | 86 | #include "SDPol.h" |
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[2] | 87 | |
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[125] | 88 | using namespace casa; |
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[83] | 89 | using namespace asap; |
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[2] | 90 | |
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[170] | 91 | |
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| 92 | SDMath::SDMath() |
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[716] | 93 | { |
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| 94 | } |
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[170] | 95 | |
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[185] | 96 | SDMath::SDMath(const SDMath& other) |
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[170] | 97 | { |
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| 98 | |
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| 99 | // No state |
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| 100 | |
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| 101 | } |
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| 102 | |
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| 103 | SDMath& SDMath::operator=(const SDMath& other) |
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| 104 | { |
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| 105 | if (this != &other) { |
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| 106 | // No state |
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| 107 | } |
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| 108 | return *this; |
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| 109 | } |
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| 110 | |
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[183] | 111 | SDMath::~SDMath() |
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| 112 | {;} |
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[170] | 113 | |
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[183] | 114 | |
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[488] | 115 | SDMemTable* SDMath::frequencyAlignment(const SDMemTable& in, |
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| 116 | const String& refTime, |
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| 117 | const String& method, |
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[716] | 118 | Bool perFreqID) |
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[262] | 119 | { |
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[701] | 120 | // Get frame info from Table |
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[262] | 121 | std::vector<std::string> info = in.getCoordInfo(); |
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[294] | 122 | |
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[701] | 123 | // Parse frequency system |
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[309] | 124 | String systemStr(info[1]); |
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| 125 | String baseSystemStr(info[3]); |
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| 126 | if (baseSystemStr==systemStr) { |
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[701] | 127 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe")); |
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[262] | 128 | } |
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[701] | 129 | |
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[309] | 130 | MFrequency::Types freqSystem; |
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| 131 | MFrequency::getType(freqSystem, systemStr); |
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[294] | 132 | |
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[488] | 133 | return frequencyAlign(in, freqSystem, refTime, method, perFreqID); |
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[267] | 134 | } |
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[262] | 135 | |
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| 136 | |
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| 137 | |
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[701] | 138 | CountedPtr<SDMemTable> |
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| 139 | SDMath::average(const std::vector<CountedPtr<SDMemTable> >& in, |
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| 140 | const Vector<Bool>& mask, Bool scanAv, |
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[716] | 141 | const String& weightStr, Bool alignFreq) |
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[144] | 142 | // Weighted averaging of spectra from one or more Tables. |
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[130] | 143 | { |
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[701] | 144 | // Convert weight type |
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[163] | 145 | WeightType wtType = NONE; |
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[518] | 146 | convertWeightString(wtType, weightStr, True); |
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[163] | 147 | |
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[701] | 148 | // Create output Table by cloning from the first table |
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[144] | 149 | SDMemTable* pTabOut = new SDMemTable(*in[0],True); |
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[653] | 150 | if (in.size() > 1) { |
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| 151 | for (uInt i=1; i < in.size(); ++i) { |
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[488] | 152 | pTabOut->appendToHistoryTable(in[i]->getHistoryTable()); |
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| 153 | } |
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| 154 | } |
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[701] | 155 | // Setup |
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[144] | 156 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change |
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| 157 | Array<Float> arr(shp); |
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| 158 | Array<Bool> barr(shp); |
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[221] | 159 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis)); |
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[130] | 160 | |
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[701] | 161 | // Columns from Tables |
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[144] | 162 | ROArrayColumn<Float> tSysCol; |
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| 163 | ROScalarColumn<Double> mjdCol; |
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| 164 | ROScalarColumn<String> srcNameCol; |
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| 165 | ROScalarColumn<Double> intCol; |
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| 166 | ROArrayColumn<uInt> fqIDCol; |
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[410] | 167 | ROScalarColumn<Int> scanIDCol; |
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[130] | 168 | |
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[701] | 169 | // Create accumulation MaskedArray. We accumulate for each |
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| 170 | // channel,if,pol,beam Note that the mask of the accumulation array |
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| 171 | // will ALWAYS remain ALL True. The MA is only used so that when |
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| 172 | // data which is masked Bad is added to it, that data does not |
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| 173 | // contribute. |
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[144] | 174 | |
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| 175 | Array<Float> zero(shp); |
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| 176 | zero=0.0; |
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| 177 | Array<Bool> good(shp); |
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| 178 | good = True; |
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| 179 | MaskedArray<Float> sum(zero,good); |
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| 180 | |
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[701] | 181 | // Counter arrays |
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[144] | 182 | Array<Float> nPts(shp); // Number of points |
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| 183 | nPts = 0.0; |
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| 184 | Array<Float> nInc(shp); // Increment |
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| 185 | nInc = 1.0; |
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| 186 | |
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[701] | 187 | // Create accumulation Array for variance. We accumulate for each |
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| 188 | // if,pol,beam, but average over channel. So we need a shape with |
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| 189 | // one less axis dropping channels. |
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[144] | 190 | const uInt nAxesSub = shp.nelements() - 1; |
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| 191 | IPosition shp2(nAxesSub); |
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| 192 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) { |
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[221] | 193 | if (i!=asap::ChanAxis) { |
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[144] | 194 | shp2(j) = shp(i); |
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| 195 | j++; |
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| 196 | } |
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[2] | 197 | } |
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[144] | 198 | Array<Float> sumSq(shp2); |
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| 199 | sumSq = 0.0; |
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| 200 | IPosition pos2(nAxesSub,0); // For indexing |
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[130] | 201 | |
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[701] | 202 | // Time-related accumulators |
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[144] | 203 | Double time; |
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| 204 | Double timeSum = 0.0; |
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| 205 | Double intSum = 0.0; |
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| 206 | Double interval = 0.0; |
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[130] | 207 | |
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[701] | 208 | // To get the right shape for the Tsys accumulator we need to access |
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| 209 | // a column from the first table. The shape of this array must not |
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| 210 | // change. Note however that since the TSysSqSum array is used in a |
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| 211 | // normalization process, and that I ignore the channel axis |
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| 212 | // replication of values for now, it loses a dimension |
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[130] | 213 | |
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[518] | 214 | Array<Float> tSysSum, tSysSqSum; |
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[144] | 215 | { |
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| 216 | const Table& tabIn = in[0]->table(); |
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| 217 | tSysCol.attach(tabIn,"TSYS"); |
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| 218 | tSysSum.resize(tSysCol.shape(0)); |
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[518] | 219 | tSysSqSum.resize(shp2); |
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[144] | 220 | } |
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[701] | 221 | tSysSum = 0.0; |
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[518] | 222 | tSysSqSum = 0.0; |
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[144] | 223 | Array<Float> tSys; |
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| 224 | |
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[701] | 225 | // Scan and row tracking |
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[144] | 226 | Int oldScanID = 0; |
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| 227 | Int outScanID = 0; |
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| 228 | Int scanID = 0; |
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| 229 | Int rowStart = 0; |
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| 230 | Int nAccum = 0; |
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| 231 | Int tableStart = 0; |
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| 232 | |
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[701] | 233 | // Source and FreqID |
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[144] | 234 | String sourceName, oldSourceName, sourceNameStart; |
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| 235 | Vector<uInt> freqID, freqIDStart, oldFreqID; |
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| 236 | |
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[701] | 237 | // Loop over tables |
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[144] | 238 | Float fac = 1.0; |
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[653] | 239 | const uInt nTables = in.size(); |
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[144] | 240 | for (uInt iTab=0; iTab<nTables; iTab++) { |
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| 241 | |
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[701] | 242 | // Should check that the frequency tables don't change if doing |
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| 243 | // FreqAlignment |
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| 244 | |
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| 245 | // Attach columns to Table |
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[144] | 246 | const Table& tabIn = in[iTab]->table(); |
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| 247 | tSysCol.attach(tabIn, "TSYS"); |
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| 248 | mjdCol.attach(tabIn, "TIME"); |
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| 249 | srcNameCol.attach(tabIn, "SRCNAME"); |
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| 250 | intCol.attach(tabIn, "INTERVAL"); |
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| 251 | fqIDCol.attach(tabIn, "FREQID"); |
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[410] | 252 | scanIDCol.attach(tabIn, "SCANID"); |
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[144] | 253 | |
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[701] | 254 | // Loop over rows in Table |
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[144] | 255 | const uInt nRows = in[iTab]->nRow(); |
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| 256 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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[701] | 257 | // Check conformance |
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[144] | 258 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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| 259 | if (!shp.isEqual(shp2)) { |
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[701] | 260 | delete pTabOut; |
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[144] | 261 | throw (AipsError("Shapes for all rows must be the same")); |
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| 262 | } |
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| 263 | |
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[701] | 264 | // If we are not doing scan averages, make checks for source |
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| 265 | // and frequency setup and warn if averaging across them |
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[410] | 266 | scanIDCol.getScalar(iRow, scanID); |
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[144] | 267 | |
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[701] | 268 | // Get quantities from columns |
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[144] | 269 | srcNameCol.getScalar(iRow, sourceName); |
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| 270 | mjdCol.get(iRow, time); |
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| 271 | tSysCol.get(iRow, tSys); |
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| 272 | intCol.get(iRow, interval); |
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| 273 | fqIDCol.get(iRow, freqID); |
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| 274 | |
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[701] | 275 | // Initialize first source and freqID |
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[144] | 276 | if (iRow==0 && iTab==0) { |
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| 277 | sourceNameStart = sourceName; |
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| 278 | freqIDStart = freqID; |
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| 279 | } |
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| 280 | |
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[701] | 281 | // If we are doing scan averages, see if we are at the end of |
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| 282 | // an accumulation period (scan). We must check soutce names |
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| 283 | // too, since we might have two tables with one scan each but |
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| 284 | // different source names; we shouldn't average different |
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| 285 | // sources together |
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[144] | 286 | if (scanAv && ( (scanID != oldScanID) || |
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| 287 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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| 288 | |
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[701] | 289 | // Normalize data in 'sum' accumulation array according to |
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| 290 | // weighting scheme |
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| 291 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, |
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| 292 | asap::ChanAxis, nAxesSub); |
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[144] | 293 | |
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[701] | 294 | // Get ScanContainer for the first row of this averaged Scan |
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[410] | 295 | SDContainer scOut = in[iTab]->getSDContainer(rowStart); |
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| 296 | |
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[701] | 297 | // Fill scan container. The source and freqID come from the |
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| 298 | // first row of the first table that went into this average |
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| 299 | // ( should be the same for all rows in the scan average) |
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[144] | 300 | |
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| 301 | Float nR(nAccum); |
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[410] | 302 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[701] | 303 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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| 304 | |
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| 305 | // Write container out to Table |
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[410] | 306 | pTabOut->putSDContainer(scOut); |
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[701] | 307 | |
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| 308 | // Reset accumulators |
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[144] | 309 | sum = 0.0; |
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| 310 | sumSq = 0.0; |
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| 311 | nAccum = 0; |
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[701] | 312 | |
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[144] | 313 | tSysSum =0.0; |
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[518] | 314 | tSysSqSum =0.0; |
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[144] | 315 | timeSum = 0.0; |
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| 316 | intSum = 0.0; |
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[221] | 317 | nPts = 0.0; |
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[144] | 318 | |
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[701] | 319 | // Increment |
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[144] | 320 | rowStart = iRow; // First row for next accumulation |
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| 321 | tableStart = iTab; // First table for next accumulation |
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[701] | 322 | sourceNameStart = sourceName; // First source name for next |
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| 323 | // accumulation |
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[144] | 324 | freqIDStart = freqID; // First FreqID for next accumulation |
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[701] | 325 | |
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[144] | 326 | oldScanID = scanID; |
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[701] | 327 | outScanID += 1; // Scan ID for next |
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| 328 | // accumulation period |
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[227] | 329 | } |
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[144] | 330 | |
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[701] | 331 | // Accumulate |
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| 332 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, |
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| 333 | tSysSum, tSysSqSum, tSys, |
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| 334 | nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis, |
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[518] | 335 | nAxesSub, useMask, wtType); |
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[701] | 336 | oldSourceName = sourceName; |
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| 337 | oldFreqID = freqID; |
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[184] | 338 | } |
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[144] | 339 | } |
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| 340 | |
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[701] | 341 | // OK at this point we have accumulation data which is either |
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| 342 | // - accumulated from all tables into one row |
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| 343 | // or |
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| 344 | // - accumulated from the last scan average |
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| 345 | // |
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| 346 | // Normalize data in 'sum' accumulation array according to weighting |
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| 347 | // scheme |
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[410] | 348 | |
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[701] | 349 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, |
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| 350 | asap::ChanAxis, nAxesSub); |
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[144] | 351 | |
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[701] | 352 | // Create and fill container. The container we clone will be from |
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| 353 | // the last Table and the first row that went into the current |
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| 354 | // accumulation. It probably doesn't matter that much really... |
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[144] | 355 | Float nR(nAccum); |
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[410] | 356 | SDContainer scOut = in[tableStart]->getSDContainer(rowStart); |
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| 357 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[701] | 358 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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[410] | 359 | pTabOut->putSDContainer(scOut); |
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[304] | 360 | pTabOut->resetCursor(); |
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[701] | 361 | |
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[144] | 362 | return CountedPtr<SDMemTable>(pTabOut); |
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[2] | 363 | } |
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[9] | 364 | |
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[144] | 365 | |
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| 366 | |
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[701] | 367 | CountedPtr<SDMemTable> |
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| 368 | SDMath::binaryOperate(const CountedPtr<SDMemTable>& left, |
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| 369 | const CountedPtr<SDMemTable>& right, |
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[716] | 370 | const String& op, Bool preserve, Bool doTSys) |
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[185] | 371 | { |
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[85] | 372 | |
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[701] | 373 | // Check operator |
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[234] | 374 | String op2(op); |
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| 375 | op2.upcase(); |
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| 376 | uInt what = 0; |
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| 377 | if (op2=="ADD") { |
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| 378 | what = 0; |
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| 379 | } else if (op2=="SUB") { |
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| 380 | what = 1; |
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| 381 | } else if (op2=="MUL") { |
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| 382 | what = 2; |
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| 383 | } else if (op2=="DIV") { |
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| 384 | what = 3; |
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[248] | 385 | } else if (op2=="QUOTIENT") { |
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| 386 | what = 4; |
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[294] | 387 | doTSys = True; |
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[234] | 388 | } else { |
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[248] | 389 | throw( AipsError("Unrecognized operation")); |
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[234] | 390 | } |
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| 391 | |
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[701] | 392 | // Check rows |
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[248] | 393 | const uInt nRowLeft = left->nRow(); |
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| 394 | const uInt nRowRight = right->nRow(); |
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[701] | 395 | Bool ok = (nRowRight==1 && nRowLeft>0) || |
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| 396 | (nRowRight>=1 && nRowLeft==nRowRight); |
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[248] | 397 | if (!ok) { |
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| 398 | 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] | 399 | } |
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| 400 | |
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[701] | 401 | // Input Tables |
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[234] | 402 | const Table& tLeft = left->table(); |
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| 403 | const Table& tRight = right->table(); |
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[248] | 404 | |
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[701] | 405 | // TSys columns |
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[294] | 406 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol; |
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| 407 | if (doTSys) { |
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[701] | 408 | tSysLeftCol.attach(tLeft, "TSYS"); |
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| 409 | tSysRightCol.attach(tRight, "TSYS"); |
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[294] | 410 | } |
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[234] | 411 | |
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[701] | 412 | // First row for right |
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[248] | 413 | Array<Float> tSysLeftArr, tSysRightArr; |
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[294] | 414 | if (doTSys) tSysRightCol.get(0, tSysRightArr); |
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[701] | 415 | MaskedArray<Float>* pMRight = |
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| 416 | new MaskedArray<Float>(right->rowAsMaskedArray(0)); |
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| 417 | |
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[248] | 418 | IPosition shpRight = pMRight->shape(); |
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| 419 | |
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[701] | 420 | // Output Table cloned from left |
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[234] | 421 | SDMemTable* pTabOut = new SDMemTable(*left, True); |
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[488] | 422 | pTabOut->appendToHistoryTable(right->getHistoryTable()); |
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[234] | 423 | |
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[701] | 424 | // Loop over rows |
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[248] | 425 | for (uInt i=0; i<nRowLeft; i++) { |
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[701] | 426 | |
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| 427 | // Get data |
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| 428 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i)); |
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| 429 | IPosition shpLeft = mLeft.shape(); |
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| 430 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr); |
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| 431 | |
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| 432 | if (nRowRight>1) { |
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| 433 | delete pMRight; |
---|
| 434 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i)); |
---|
| 435 | shpRight = pMRight->shape(); |
---|
| 436 | if (doTSys) tSysRightCol.get(i, tSysRightArr); |
---|
| 437 | } |
---|
[234] | 438 | |
---|
[701] | 439 | if (!shpRight.isEqual(shpLeft)) { |
---|
| 440 | delete pTabOut; |
---|
| 441 | delete pMRight; |
---|
| 442 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 443 | } |
---|
| 444 | if (doTSys) { |
---|
| 445 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) { |
---|
| 446 | delete pTabOut; |
---|
| 447 | delete pMRight; |
---|
| 448 | throw(AipsError("left and right Tsys data are not conformant")); |
---|
| 449 | } |
---|
| 450 | if (!shpRight.isEqual(tSysRightArr.shape())) { |
---|
| 451 | delete pTabOut; |
---|
| 452 | delete pMRight; |
---|
| 453 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 454 | } |
---|
| 455 | } |
---|
[248] | 456 | |
---|
[701] | 457 | // Make container |
---|
[234] | 458 | SDContainer sc = left->getSDContainer(i); |
---|
| 459 | |
---|
[701] | 460 | // Operate on data and TSys |
---|
[234] | 461 | if (what==0) { |
---|
[248] | 462 | MaskedArray<Float> tmp = mLeft + *pMRight; |
---|
[234] | 463 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 464 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr); |
---|
[234] | 465 | } else if (what==1) { |
---|
[248] | 466 | MaskedArray<Float> tmp = mLeft - *pMRight; |
---|
[234] | 467 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 468 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr); |
---|
[234] | 469 | } else if (what==2) { |
---|
[248] | 470 | MaskedArray<Float> tmp = mLeft * *pMRight; |
---|
[234] | 471 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 472 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr); |
---|
[234] | 473 | } else if (what==3) { |
---|
[248] | 474 | MaskedArray<Float> tmp = mLeft / *pMRight; |
---|
[234] | 475 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 476 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr); |
---|
[248] | 477 | } else if (what==4) { |
---|
[488] | 478 | if (preserve) { |
---|
| 479 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
---|
| 480 | tSysRightArr; |
---|
| 481 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 482 | } else { |
---|
| 483 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
---|
| 484 | tSysLeftArr; |
---|
| 485 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 486 | } |
---|
| 487 | sc.putTsys(tSysRightArr); |
---|
[234] | 488 | } |
---|
| 489 | |
---|
[701] | 490 | // Put new row in output Table |
---|
[171] | 491 | pTabOut->putSDContainer(sc); |
---|
[130] | 492 | } |
---|
[248] | 493 | if (pMRight) delete pMRight; |
---|
[304] | 494 | pTabOut->resetCursor(); |
---|
[701] | 495 | |
---|
[171] | 496 | return CountedPtr<SDMemTable>(pTabOut); |
---|
[9] | 497 | } |
---|
[48] | 498 | |
---|
[146] | 499 | |
---|
[185] | 500 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in, |
---|
[234] | 501 | const Vector<Bool>& mask, |
---|
| 502 | const String& which, Int row) const |
---|
[130] | 503 | // |
---|
| 504 | // Perhaps iteration over pol/beam/if should be in here |
---|
| 505 | // and inside the nrow iteration ? |
---|
| 506 | // |
---|
| 507 | { |
---|
| 508 | const uInt nRow = in->nRow(); |
---|
| 509 | |
---|
| 510 | // Specify cursor location |
---|
| 511 | |
---|
[152] | 512 | IPosition start, end; |
---|
[434] | 513 | Bool doAll = False; |
---|
[716] | 514 | setCursorSlice(start, end, doAll, *in); |
---|
[130] | 515 | |
---|
| 516 | // Loop over rows |
---|
| 517 | |
---|
[234] | 518 | const uInt nEl = mask.nelements(); |
---|
| 519 | uInt iStart = 0; |
---|
| 520 | uInt iEnd = in->nRow()-1; |
---|
| 521 | // |
---|
| 522 | if (row>=0) { |
---|
| 523 | iStart = row; |
---|
| 524 | iEnd = row; |
---|
| 525 | } |
---|
| 526 | // |
---|
| 527 | std::vector<float> result(iEnd-iStart+1); |
---|
| 528 | for (uInt ii=iStart; ii <= iEnd; ++ii) { |
---|
[130] | 529 | |
---|
| 530 | // Get row and deconstruct |
---|
| 531 | |
---|
[434] | 532 | MaskedArray<Float> dataIn = (in->rowAsMaskedArray(ii))(start,end); |
---|
| 533 | Array<Float> v = dataIn.getArray().nonDegenerate(); |
---|
| 534 | Array<Bool> m = dataIn.getMask().nonDegenerate(); |
---|
[130] | 535 | |
---|
| 536 | // Access desired piece of data |
---|
| 537 | |
---|
[434] | 538 | // Array<Float> v((arr(start,end)).nonDegenerate()); |
---|
| 539 | // Array<Bool> m((barr(start,end)).nonDegenerate()); |
---|
[130] | 540 | |
---|
| 541 | // Apply OTF mask |
---|
| 542 | |
---|
| 543 | MaskedArray<Float> tmp; |
---|
| 544 | if (m.nelements()==nEl) { |
---|
[234] | 545 | tmp.setData(v,m&&mask); |
---|
[130] | 546 | } else { |
---|
| 547 | tmp.setData(v,m); |
---|
| 548 | } |
---|
| 549 | |
---|
| 550 | // Get statistic |
---|
| 551 | |
---|
[234] | 552 | result[ii-iStart] = mathutil::statistics(which, tmp); |
---|
[130] | 553 | } |
---|
| 554 | // |
---|
| 555 | return result; |
---|
| 556 | } |
---|
| 557 | |
---|
[146] | 558 | |
---|
[716] | 559 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) |
---|
[144] | 560 | { |
---|
[169] | 561 | SDHeader sh = in.getSDHeader(); |
---|
| 562 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[163] | 563 | |
---|
[169] | 564 | // Bin up SpectralCoordinates |
---|
[163] | 565 | |
---|
[169] | 566 | IPosition factors(1); |
---|
| 567 | factors(0) = width; |
---|
| 568 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 569 | CoordinateSystem cSys; |
---|
[288] | 570 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
[169] | 571 | CoordinateSystem cSysBin = |
---|
[185] | 572 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False); |
---|
[169] | 573 | // |
---|
| 574 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
---|
| 575 | pTabOut->setCoordinate(sCBin, j); |
---|
| 576 | } |
---|
[163] | 577 | |
---|
[169] | 578 | // Use RebinLattice to find shape |
---|
[130] | 579 | |
---|
[169] | 580 | IPosition shapeIn(1,sh.nchan); |
---|
[185] | 581 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors); |
---|
[169] | 582 | sh.nchan = shapeOut(0); |
---|
| 583 | pTabOut->putSDHeader(sh); |
---|
[144] | 584 | |
---|
[169] | 585 | // Loop over rows and bin along channel axis |
---|
| 586 | |
---|
| 587 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 588 | SDContainer sc = in.getSDContainer(i); |
---|
[144] | 589 | // |
---|
[169] | 590 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
---|
[144] | 591 | |
---|
[169] | 592 | // Bin up spectrum |
---|
[144] | 593 | |
---|
[169] | 594 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
---|
| 595 | MaskedArray<Float> marrout; |
---|
[221] | 596 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width); |
---|
[144] | 597 | |
---|
[169] | 598 | // Put back the binned data and flags |
---|
[144] | 599 | |
---|
[169] | 600 | IPosition ip2 = marrout.shape(); |
---|
| 601 | sc.resize(ip2); |
---|
[146] | 602 | // |
---|
[185] | 603 | putDataInSDC(sc, marrout.getArray(), marrout.getMask()); |
---|
[146] | 604 | |
---|
[169] | 605 | // Bin up Tsys. |
---|
[146] | 606 | |
---|
[169] | 607 | Array<Bool> allGood(tSys.shape(),True); |
---|
| 608 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
---|
[146] | 609 | // |
---|
[169] | 610 | MaskedArray<Float> tSysOut; |
---|
[221] | 611 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width); |
---|
[169] | 612 | sc.putTsys(tSysOut.getArray()); |
---|
[146] | 613 | // |
---|
[169] | 614 | pTabOut->putSDContainer(sc); |
---|
| 615 | } |
---|
| 616 | return pTabOut; |
---|
[146] | 617 | } |
---|
| 618 | |
---|
[488] | 619 | SDMemTable* SDMath::resample(const SDMemTable& in, const String& methodStr, |
---|
[716] | 620 | Float width) |
---|
[299] | 621 | // |
---|
| 622 | // Should add the possibility of width being specified in km/s. This means |
---|
| 623 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
| 624 | // average channel width (say at the reference pixel). Then we would need |
---|
| 625 | // to be careful to make sure each spectrum (of different freqID) |
---|
| 626 | // is the same length. |
---|
| 627 | // |
---|
| 628 | { |
---|
| 629 | Bool doVel = False; |
---|
[309] | 630 | if (doVel) { |
---|
| 631 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 632 | SpectralCoordinate sC = in.getSpectralCoordinate(j); |
---|
| 633 | } |
---|
| 634 | } |
---|
[299] | 635 | |
---|
| 636 | // Interpolation method |
---|
| 637 | |
---|
[317] | 638 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
| 639 | convertInterpString(interp, methodStr); |
---|
| 640 | Int interpMethod(interp); |
---|
[299] | 641 | |
---|
| 642 | // Make output table |
---|
| 643 | |
---|
| 644 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 645 | |
---|
| 646 | // Resample SpectralCoordinates (one per freqID) |
---|
| 647 | |
---|
| 648 | const uInt nCoord = in.nCoordinates(); |
---|
| 649 | Vector<Float> offset(1,0.0); |
---|
| 650 | Vector<Float> factors(1,1.0/width); |
---|
| 651 | Vector<Int> newShape; |
---|
| 652 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 653 | CoordinateSystem cSys; |
---|
| 654 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
| 655 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape); |
---|
| 656 | SpectralCoordinate sC = cSys2.spectralCoordinate(0); |
---|
| 657 | // |
---|
| 658 | pTabOut->setCoordinate(sC, j); |
---|
| 659 | } |
---|
| 660 | |
---|
| 661 | // Get header |
---|
| 662 | |
---|
| 663 | SDHeader sh = in.getSDHeader(); |
---|
| 664 | |
---|
| 665 | // Generate resampling vectors |
---|
| 666 | |
---|
| 667 | const uInt nChanIn = sh.nchan; |
---|
| 668 | Vector<Float> xIn(nChanIn); |
---|
| 669 | indgen(xIn); |
---|
| 670 | // |
---|
| 671 | Int fac = Int(nChanIn/width); |
---|
| 672 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
| 673 | uInt i = 0; |
---|
| 674 | Float x = 0.0; |
---|
| 675 | Bool more = True; |
---|
| 676 | while (more) { |
---|
| 677 | xOut(i) = x; |
---|
| 678 | // |
---|
| 679 | i++; |
---|
| 680 | x += width; |
---|
| 681 | if (x>nChanIn-1) more = False; |
---|
| 682 | } |
---|
| 683 | const uInt nChanOut = i; |
---|
| 684 | xOut.resize(nChanOut,True); |
---|
| 685 | // |
---|
| 686 | IPosition shapeIn(in.rowAsMaskedArray(0).shape()); |
---|
| 687 | sh.nchan = nChanOut; |
---|
| 688 | pTabOut->putSDHeader(sh); |
---|
| 689 | |
---|
| 690 | // Loop over rows and resample along channel axis |
---|
| 691 | |
---|
| 692 | Array<Float> valuesOut; |
---|
| 693 | Array<Bool> maskOut; |
---|
| 694 | Array<Float> tSysOut; |
---|
| 695 | Array<Bool> tSysMaskIn(shapeIn,True); |
---|
| 696 | Array<Bool> tSysMaskOut; |
---|
| 697 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 698 | |
---|
| 699 | // Get container |
---|
| 700 | |
---|
| 701 | SDContainer sc = in.getSDContainer(i); |
---|
| 702 | |
---|
| 703 | // Get data and Tsys |
---|
| 704 | |
---|
| 705 | const Array<Float>& tSysIn = sc.getTsys(); |
---|
| 706 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i)); |
---|
| 707 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 708 | Array<Bool> maskIn = dataIn.getMask(); |
---|
| 709 | |
---|
| 710 | // Interpolate data |
---|
| 711 | |
---|
| 712 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut, |
---|
| 713 | xIn, valuesIn, maskIn, |
---|
| 714 | interpMethod, True, True); |
---|
| 715 | sc.resize(valuesOut.shape()); |
---|
| 716 | putDataInSDC(sc, valuesOut, maskOut); |
---|
| 717 | |
---|
| 718 | // Interpolate TSys |
---|
| 719 | |
---|
| 720 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut, |
---|
| 721 | xIn, tSysIn, tSysMaskIn, |
---|
| 722 | interpMethod, True, True); |
---|
| 723 | sc.putTsys(tSysOut); |
---|
| 724 | |
---|
| 725 | // Put container in output |
---|
| 726 | |
---|
| 727 | pTabOut->putSDContainer(sc); |
---|
| 728 | } |
---|
| 729 | // |
---|
| 730 | return pTabOut; |
---|
| 731 | } |
---|
| 732 | |
---|
[248] | 733 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll, |
---|
[716] | 734 | uInt what, Bool doTSys) |
---|
[152] | 735 | // |
---|
| 736 | // what = 0 Multiply |
---|
| 737 | // 1 Add |
---|
[146] | 738 | { |
---|
[152] | 739 | SDMemTable* pOut = new SDMemTable(in,False); |
---|
| 740 | const Table& tOut = pOut->table(); |
---|
[294] | 741 | ArrayColumn<Float> specCol(tOut,"SPECTRA"); |
---|
| 742 | ArrayColumn<Float> tSysCol(tOut,"TSYS"); |
---|
| 743 | Array<Float> tSysArr; |
---|
[434] | 744 | |
---|
| 745 | // Get data slice bounds |
---|
| 746 | |
---|
| 747 | IPosition start, end; |
---|
| 748 | setCursorSlice (start, end, doAll, in); |
---|
[146] | 749 | // |
---|
[434] | 750 | for (uInt i=0; i<tOut.nrow(); i++) { |
---|
[294] | 751 | |
---|
| 752 | // Modify data |
---|
| 753 | |
---|
[434] | 754 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
| 755 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference |
---|
| 756 | if (what==0) { |
---|
| 757 | dataIn2 *= val; |
---|
| 758 | } else if (what==1) { |
---|
| 759 | dataIn2 += val; |
---|
| 760 | } |
---|
| 761 | specCol.put(i, dataIn.getArray()); |
---|
[294] | 762 | |
---|
| 763 | // Modify Tsys |
---|
| 764 | |
---|
[434] | 765 | if (doTSys) { |
---|
| 766 | tSysCol.get(i, tSysArr); |
---|
| 767 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference |
---|
[152] | 768 | if (what==0) { |
---|
[434] | 769 | tSysArr2 *= val; |
---|
[152] | 770 | } else if (what==1) { |
---|
[434] | 771 | tSysArr2 += val; |
---|
[152] | 772 | } |
---|
[434] | 773 | tSysCol.put(i, tSysArr); |
---|
[152] | 774 | } |
---|
| 775 | } |
---|
| 776 | // |
---|
[146] | 777 | return pOut; |
---|
| 778 | } |
---|
| 779 | |
---|
[315] | 780 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask, |
---|
[716] | 781 | const String& weightStr) |
---|
[152] | 782 | // |
---|
[165] | 783 | // Average all polarizations together, weighted by variance |
---|
| 784 | // |
---|
| 785 | { |
---|
[315] | 786 | WeightType wtType = NONE; |
---|
[532] | 787 | convertWeightString(wtType, weightStr, True); |
---|
[165] | 788 | |
---|
| 789 | // Create output Table and reshape number of polarizations |
---|
| 790 | |
---|
| 791 | Bool clear=True; |
---|
| 792 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
| 793 | SDHeader header = pTabOut->getSDHeader(); |
---|
| 794 | header.npol = 1; |
---|
| 795 | pTabOut->putSDHeader(header); |
---|
[532] | 796 | // |
---|
| 797 | const Table& tabIn = in.table(); |
---|
[165] | 798 | |
---|
| 799 | // Shape of input and output data |
---|
| 800 | |
---|
[448] | 801 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape(); |
---|
[165] | 802 | IPosition shapeOut(shapeIn); |
---|
[262] | 803 | shapeOut(asap::PolAxis) = 1; // Average all polarizations |
---|
[315] | 804 | if (shapeIn(asap::PolAxis)==1) { |
---|
[701] | 805 | delete pTabOut; |
---|
| 806 | throw(AipsError("The input has only one polarisation")); |
---|
[315] | 807 | } |
---|
[165] | 808 | // |
---|
[532] | 809 | const uInt nRows = in.nRow(); |
---|
[262] | 810 | const uInt nChan = shapeIn(asap::ChanAxis); |
---|
[532] | 811 | AlwaysAssert(asap::nAxes==4,AipsError); |
---|
[165] | 812 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape |
---|
| 813 | IPosition start(4), end(4); |
---|
| 814 | |
---|
| 815 | // Output arrays |
---|
| 816 | |
---|
| 817 | Array<Float> outData(shapeOut, 0.0); |
---|
| 818 | Array<Bool> outMask(shapeOut, True); |
---|
[262] | 819 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane |
---|
[532] | 820 | |
---|
| 821 | // Attach Tsys column if needed |
---|
| 822 | |
---|
| 823 | ROArrayColumn<Float> tSysCol; |
---|
| 824 | Array<Float> tSys; |
---|
| 825 | if (wtType==TSYS) { |
---|
| 826 | tSysCol.attach(tabIn,"TSYS"); |
---|
| 827 | } |
---|
[165] | 828 | // |
---|
[262] | 829 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis)); |
---|
[165] | 830 | |
---|
| 831 | // Loop over rows |
---|
| 832 | |
---|
| 833 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 834 | |
---|
| 835 | // Get data for this row |
---|
| 836 | |
---|
| 837 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
| 838 | Array<Float>& arr = marr.getRWArray(); |
---|
| 839 | const Array<Bool>& barr = marr.getMask(); |
---|
[532] | 840 | |
---|
| 841 | // Get Tsys |
---|
[165] | 842 | |
---|
[532] | 843 | if (wtType==TSYS) { |
---|
| 844 | tSysCol.get(iRow,tSys); |
---|
| 845 | } |
---|
| 846 | |
---|
[165] | 847 | // Make iterators to iterate by pol-channel planes |
---|
[532] | 848 | // The tSys array is empty unless wtType=TSYS so only |
---|
| 849 | // access the iterator is that is the case |
---|
[165] | 850 | |
---|
| 851 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
---|
| 852 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes); |
---|
[532] | 853 | ReadOnlyArrayIterator<Float>* pItTsysPlane = 0; |
---|
[701] | 854 | if (wtType==TSYS) |
---|
| 855 | pItTsysPlane = new ReadOnlyArrayIterator<Float>(tSys, axes); |
---|
[165] | 856 | |
---|
| 857 | // Accumulations |
---|
| 858 | |
---|
| 859 | Float fac = 1.0; |
---|
| 860 | Vector<Float> vecSum(nChan,0.0); |
---|
| 861 | |
---|
| 862 | // Iterate through data by pol-channel planes |
---|
| 863 | |
---|
| 864 | while (!itDataPlane.pastEnd()) { |
---|
| 865 | |
---|
| 866 | // Iterate through plane by polarization and accumulate Vectors |
---|
| 867 | |
---|
| 868 | Vector<Float> t1(nChan); t1 = 0.0; |
---|
| 869 | Vector<Bool> t2(nChan); t2 = True; |
---|
[532] | 870 | Float tSys = 0.0; |
---|
[165] | 871 | MaskedArray<Float> vecSum(t1,t2); |
---|
[315] | 872 | Float norm = 0.0; |
---|
[165] | 873 | { |
---|
| 874 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
---|
| 875 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
[532] | 876 | // |
---|
| 877 | ReadOnlyVectorIterator<Float>* pItTsysVec = 0; |
---|
| 878 | if (wtType==TSYS) { |
---|
[701] | 879 | pItTsysVec = |
---|
| 880 | new ReadOnlyVectorIterator<Float>(pItTsysPlane->array(), 1); |
---|
[532] | 881 | } |
---|
| 882 | // |
---|
[165] | 883 | while (!itDataVec.pastEnd()) { |
---|
| 884 | |
---|
[315] | 885 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum |
---|
[165] | 886 | |
---|
| 887 | if (useMask) { |
---|
[701] | 888 | const MaskedArray<Float> spec(itDataVec.vector(), |
---|
| 889 | mask&&itMaskVec.vector()); |
---|
[532] | 890 | if (wtType==VAR) { |
---|
| 891 | fac = 1.0 / variance(spec); |
---|
| 892 | } else if (wtType==TSYS) { |
---|
| 893 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency |
---|
| 894 | fac = 1.0 / tSys / tSys; |
---|
| 895 | } |
---|
[165] | 896 | } else { |
---|
[701] | 897 | const MaskedArray<Float> spec(itDataVec.vector(), |
---|
| 898 | itMaskVec.vector()); |
---|
[532] | 899 | if (wtType==VAR) { |
---|
| 900 | fac = 1.0 / variance(spec); |
---|
| 901 | } else if (wtType==TSYS) { |
---|
| 902 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency |
---|
| 903 | fac = 1.0 / tSys / tSys; |
---|
| 904 | } |
---|
[165] | 905 | } |
---|
| 906 | |
---|
| 907 | // Normalize spectrum (without OTF mask) and accumulate |
---|
| 908 | |
---|
[701] | 909 | const MaskedArray<Float> spec(fac*itDataVec.vector(), |
---|
| 910 | itMaskVec.vector()); |
---|
[165] | 911 | vecSum += spec; |
---|
[315] | 912 | norm += fac; |
---|
[165] | 913 | |
---|
| 914 | // Next |
---|
| 915 | |
---|
| 916 | itDataVec.next(); |
---|
| 917 | itMaskVec.next(); |
---|
[532] | 918 | if (wtType==TSYS) pItTsysVec->next(); |
---|
[165] | 919 | } |
---|
[532] | 920 | |
---|
| 921 | // Clean up |
---|
| 922 | |
---|
| 923 | if (pItTsysVec) { |
---|
| 924 | delete pItTsysVec; |
---|
| 925 | pItTsysVec = 0; |
---|
| 926 | } |
---|
[165] | 927 | } |
---|
| 928 | |
---|
| 929 | // Normalize summed spectrum |
---|
| 930 | |
---|
[315] | 931 | vecSum /= norm; |
---|
[165] | 932 | |
---|
| 933 | // FInd position in input data array. We are iterating by pol-channel |
---|
| 934 | // plane so all that will change is beam and IF and that's what we want. |
---|
| 935 | |
---|
| 936 | IPosition pos = itDataPlane.pos(); |
---|
| 937 | |
---|
| 938 | // Write out data. This is a bit messy. We have to reform the Vector |
---|
| 939 | // accumulator into an Array of shape (1,1,1,nChan) |
---|
| 940 | |
---|
| 941 | start = pos; |
---|
| 942 | end = pos; |
---|
[262] | 943 | end(asap::ChanAxis) = nChan-1; |
---|
[165] | 944 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
---|
| 945 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
---|
| 946 | |
---|
| 947 | // Step to next beam/IF combination |
---|
| 948 | |
---|
| 949 | itDataPlane.next(); |
---|
| 950 | itMaskPlane.next(); |
---|
[532] | 951 | if (wtType==TSYS) pItTsysPlane->next(); |
---|
[165] | 952 | } |
---|
| 953 | |
---|
| 954 | // Generate output container and write it to output table |
---|
| 955 | |
---|
| 956 | SDContainer sc = in.getSDContainer(); |
---|
| 957 | sc.resize(shapeOut); |
---|
| 958 | // |
---|
[185] | 959 | putDataInSDC(sc, outData, outMask); |
---|
[165] | 960 | pTabOut->putSDContainer(sc); |
---|
[532] | 961 | // |
---|
| 962 | if (wtType==TSYS) { |
---|
| 963 | delete pItTsysPlane; |
---|
| 964 | pItTsysPlane = 0; |
---|
| 965 | } |
---|
[165] | 966 | } |
---|
[304] | 967 | |
---|
| 968 | // Set polarization cursor to 0 |
---|
| 969 | |
---|
| 970 | pTabOut->setPol(0); |
---|
[165] | 971 | // |
---|
| 972 | return pTabOut; |
---|
| 973 | } |
---|
[167] | 974 | |
---|
[169] | 975 | |
---|
[185] | 976 | SDMemTable* SDMath::smooth(const SDMemTable& in, |
---|
| 977 | const casa::String& kernelType, |
---|
[716] | 978 | casa::Float width, Bool doAll) |
---|
[299] | 979 | // |
---|
| 980 | // Should smooth TSys as well |
---|
| 981 | // |
---|
[177] | 982 | { |
---|
[169] | 983 | |
---|
[701] | 984 | // Number of channels |
---|
[434] | 985 | const uInt nChan = in.nChan(); |
---|
[177] | 986 | |
---|
[701] | 987 | // Generate Kernel |
---|
[185] | 988 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType); |
---|
[177] | 989 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
| 990 | |
---|
[701] | 991 | // Generate Convolver |
---|
[177] | 992 | IPosition shape(1,nChan); |
---|
| 993 | Convolver<Float> conv(kernel, shape); |
---|
| 994 | |
---|
[701] | 995 | // New Table |
---|
[177] | 996 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
| 997 | |
---|
[701] | 998 | // Output Vectors |
---|
[434] | 999 | Vector<Float> valuesOut(nChan); |
---|
| 1000 | Vector<Bool> maskOut(nChan); |
---|
[177] | 1001 | |
---|
[701] | 1002 | // Get data slice bounds |
---|
[434] | 1003 | IPosition start, end; |
---|
| 1004 | setCursorSlice (start, end, doAll, in); |
---|
| 1005 | |
---|
[701] | 1006 | // Loop over rows in Table |
---|
[434] | 1007 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
[177] | 1008 | |
---|
[701] | 1009 | // Get slice of data |
---|
[434] | 1010 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(ri); |
---|
[177] | 1011 | |
---|
[701] | 1012 | // Deconstruct and get slices which reference these arrays |
---|
[434] | 1013 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 1014 | Array<Bool> maskIn = dataIn.getMask(); |
---|
[701] | 1015 | |
---|
[434] | 1016 | Array<Float> valuesIn2 = valuesIn(start,end); // ref to valuesIn |
---|
| 1017 | Array<Bool> maskIn2 = maskIn(start,end); |
---|
[177] | 1018 | |
---|
[701] | 1019 | // Iterate through by spectra |
---|
[434] | 1020 | VectorIterator<Float> itValues(valuesIn2, asap::ChanAxis); |
---|
| 1021 | VectorIterator<Bool> itMask(maskIn2, asap::ChanAxis); |
---|
| 1022 | while (!itValues.pastEnd()) { |
---|
[701] | 1023 | |
---|
| 1024 | // Smooth |
---|
| 1025 | if (kernelType==VectorKernel::HANNING) { |
---|
| 1026 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), |
---|
| 1027 | itMask.vector()); |
---|
| 1028 | itMask.vector() = maskOut; |
---|
| 1029 | } else { |
---|
| 1030 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
| 1031 | conv.linearConv(valuesOut, itValues.vector()); |
---|
| 1032 | } |
---|
[177] | 1033 | |
---|
[701] | 1034 | itValues.vector() = valuesOut; |
---|
| 1035 | itValues.next(); |
---|
| 1036 | itMask.next(); |
---|
[434] | 1037 | } |
---|
[701] | 1038 | |
---|
| 1039 | // Create and put back |
---|
[434] | 1040 | SDContainer sc = in.getSDContainer(ri); |
---|
| 1041 | putDataInSDC(sc, valuesIn, maskIn); |
---|
[701] | 1042 | |
---|
[434] | 1043 | pTabOut->putSDContainer(sc); |
---|
| 1044 | } |
---|
[701] | 1045 | |
---|
[177] | 1046 | return pTabOut; |
---|
| 1047 | } |
---|
| 1048 | |
---|
| 1049 | |
---|
[262] | 1050 | |
---|
[488] | 1051 | SDMemTable* SDMath::convertFlux(const SDMemTable& in, Float D, Float etaAp, |
---|
[716] | 1052 | Float JyPerK, Bool doAll) |
---|
[221] | 1053 | // |
---|
[478] | 1054 | // etaAp = aperture efficiency (-1 means find) |
---|
| 1055 | // D = geometric diameter (m) (-1 means find) |
---|
[354] | 1056 | // JyPerK |
---|
[221] | 1057 | // |
---|
| 1058 | { |
---|
| 1059 | SDHeader sh = in.getSDHeader(); |
---|
| 1060 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[177] | 1061 | |
---|
[701] | 1062 | // Find out how to convert values into Jy and K (e.g. units might be |
---|
| 1063 | // mJy or mK) Also automatically find out what we are converting to |
---|
| 1064 | // according to the flux unit |
---|
[221] | 1065 | Unit fluxUnit(sh.fluxunit); |
---|
| 1066 | Unit K(String("K")); |
---|
| 1067 | Unit JY(String("Jy")); |
---|
[701] | 1068 | |
---|
[221] | 1069 | Bool toKelvin = True; |
---|
[354] | 1070 | Double cFac = 1.0; |
---|
[716] | 1071 | |
---|
[221] | 1072 | if (fluxUnit==JY) { |
---|
[716] | 1073 | pushLog("Converting to K"); |
---|
[701] | 1074 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1075 | Quantum<Double> t2 = t.get(JY); |
---|
| 1076 | cFac = (t2 / t).getValue(); // value to Jy |
---|
| 1077 | |
---|
| 1078 | toKelvin = True; |
---|
| 1079 | sh.fluxunit = "K"; |
---|
[221] | 1080 | } else if (fluxUnit==K) { |
---|
[716] | 1081 | pushLog("Converting to Jy"); |
---|
[701] | 1082 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1083 | Quantum<Double> t2 = t.get(K); |
---|
| 1084 | cFac = (t2 / t).getValue(); // value to K |
---|
| 1085 | |
---|
| 1086 | toKelvin = False; |
---|
| 1087 | sh.fluxunit = "Jy"; |
---|
[221] | 1088 | } else { |
---|
[701] | 1089 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 1090 | } |
---|
[716] | 1091 | |
---|
[221] | 1092 | pTabOut->putSDHeader(sh); |
---|
[701] | 1093 | |
---|
| 1094 | // Make sure input values are converted to either Jy or K first... |
---|
[354] | 1095 | Float factor = cFac; |
---|
[221] | 1096 | |
---|
[701] | 1097 | // Select method |
---|
[354] | 1098 | if (JyPerK>0.0) { |
---|
[701] | 1099 | factor *= JyPerK; |
---|
| 1100 | if (toKelvin) factor = 1.0 / JyPerK; |
---|
[716] | 1101 | ostringstream oss; |
---|
| 1102 | oss << "Jy/K = " << JyPerK; |
---|
| 1103 | pushLog(String(oss)); |
---|
[701] | 1104 | Vector<Float> factors(in.nRow(), factor); |
---|
| 1105 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
[354] | 1106 | } else if (etaAp>0.0) { |
---|
[701] | 1107 | Bool throwIt = True; |
---|
[716] | 1108 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, throwIt); |
---|
[701] | 1109 | SDAttr sda; |
---|
| 1110 | if (D < 0) D = sda.diameter(inst); |
---|
[716] | 1111 | Float JyPerK = SDAttr::findJyPerK(etaAp,D); |
---|
| 1112 | ostringstream oss; |
---|
| 1113 | oss << "Jy/K = " << JyPerK; |
---|
| 1114 | pushLog(String(oss)); |
---|
[701] | 1115 | factor *= JyPerK; |
---|
| 1116 | if (toKelvin) { |
---|
| 1117 | factor = 1.0 / factor; |
---|
| 1118 | } |
---|
| 1119 | |
---|
| 1120 | Vector<Float> factors(in.nRow(), factor); |
---|
| 1121 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
[354] | 1122 | } else { |
---|
[701] | 1123 | |
---|
| 1124 | // OK now we must deal with automatic look up of values. |
---|
| 1125 | // We must also deal with the fact that the factors need |
---|
| 1126 | // to be computed per IF and may be different and may |
---|
| 1127 | // change per integration. |
---|
| 1128 | |
---|
[716] | 1129 | pushLog("Looking up conversion factors"); |
---|
[701] | 1130 | convertBrightnessUnits (pTabOut, in, toKelvin, cFac, doAll); |
---|
| 1131 | } |
---|
[221] | 1132 | return pTabOut; |
---|
| 1133 | } |
---|
| 1134 | |
---|
| 1135 | |
---|
[488] | 1136 | SDMemTable* SDMath::gainElevation(const SDMemTable& in, |
---|
| 1137 | const Vector<Float>& coeffs, |
---|
| 1138 | const String& fileName, |
---|
[716] | 1139 | const String& methodStr, Bool doAll) |
---|
[227] | 1140 | { |
---|
[234] | 1141 | |
---|
[701] | 1142 | // Get header and clone output table |
---|
[227] | 1143 | SDHeader sh = in.getSDHeader(); |
---|
| 1144 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1145 | |
---|
[701] | 1146 | // Get elevation data from SDMemTable and convert to degrees |
---|
[227] | 1147 | const Table& tab = in.table(); |
---|
| 1148 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[234] | 1149 | Vector<Float> x = elev.getColumn(); |
---|
[363] | 1150 | x *= Float(180 / C::pi); // Degrees |
---|
[701] | 1151 | |
---|
[234] | 1152 | const uInt nC = coeffs.nelements(); |
---|
| 1153 | if (fileName.length()>0 && nC>0) { |
---|
[701] | 1154 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
[234] | 1155 | } |
---|
[701] | 1156 | |
---|
| 1157 | // Correct |
---|
[234] | 1158 | if (nC>0 || fileName.length()==0) { |
---|
[701] | 1159 | // Find instrument |
---|
[234] | 1160 | Bool throwIt = True; |
---|
[478] | 1161 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
[234] | 1162 | |
---|
[701] | 1163 | // Set polynomial |
---|
[234] | 1164 | Polynomial<Float>* pPoly = 0; |
---|
| 1165 | Vector<Float> coeff; |
---|
| 1166 | String msg; |
---|
| 1167 | if (nC>0) { |
---|
[701] | 1168 | pPoly = new Polynomial<Float>(nC); |
---|
| 1169 | coeff = coeffs; |
---|
| 1170 | msg = String("user"); |
---|
[234] | 1171 | } else { |
---|
[701] | 1172 | SDAttr sdAttr; |
---|
| 1173 | coeff = sdAttr.gainElevationPoly(inst); |
---|
| 1174 | pPoly = new Polynomial<Float>(3); |
---|
| 1175 | msg = String("built in"); |
---|
[234] | 1176 | } |
---|
[701] | 1177 | |
---|
[234] | 1178 | if (coeff.nelements()>0) { |
---|
[701] | 1179 | pPoly->setCoefficients(coeff); |
---|
[234] | 1180 | } else { |
---|
[701] | 1181 | delete pPoly; |
---|
| 1182 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
[234] | 1183 | } |
---|
[716] | 1184 | pushLog("Making polynomial correction with "+msg+" coefficients"); |
---|
[234] | 1185 | const uInt nRow = in.nRow(); |
---|
| 1186 | Vector<Float> factor(nRow); |
---|
| 1187 | for (uInt i=0; i<nRow; i++) { |
---|
[701] | 1188 | factor[i] = 1.0 / (*pPoly)(x[i]); |
---|
[234] | 1189 | } |
---|
| 1190 | delete pPoly; |
---|
[480] | 1191 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
[701] | 1192 | |
---|
[234] | 1193 | } else { |
---|
[701] | 1194 | |
---|
| 1195 | // Indicate which columns to read from ascii file |
---|
| 1196 | String col0("ELEVATION"); |
---|
| 1197 | String col1("FACTOR"); |
---|
| 1198 | |
---|
| 1199 | // Read and correct |
---|
| 1200 | |
---|
[716] | 1201 | pushLog("Making correction from ascii Table"); |
---|
[701] | 1202 | scaleFromAsciiTable (pTabOut, in, fileName, col0, col1, |
---|
| 1203 | methodStr, doAll, x, True); |
---|
| 1204 | } |
---|
[234] | 1205 | |
---|
[701] | 1206 | return pTabOut; |
---|
[230] | 1207 | } |
---|
| 1208 | |
---|
[227] | 1209 | |
---|
[716] | 1210 | SDMemTable* SDMath::opacity(const SDMemTable& in, Float tau, Bool doAll) |
---|
[234] | 1211 | { |
---|
[227] | 1212 | |
---|
[701] | 1213 | // Get header and clone output table |
---|
[227] | 1214 | |
---|
[234] | 1215 | SDHeader sh = in.getSDHeader(); |
---|
| 1216 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1217 | |
---|
| 1218 | // Get elevation data from SDMemTable and convert to degrees |
---|
| 1219 | |
---|
| 1220 | const Table& tab = in.table(); |
---|
| 1221 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 1222 | Vector<Float> zDist = elev.getColumn(); |
---|
| 1223 | zDist = Float(C::pi_2) - zDist; |
---|
| 1224 | |
---|
| 1225 | // Generate correction factor |
---|
| 1226 | |
---|
| 1227 | const uInt nRow = in.nRow(); |
---|
| 1228 | Vector<Float> factor(nRow); |
---|
| 1229 | Vector<Float> factor2(nRow); |
---|
| 1230 | for (uInt i=0; i<nRow; i++) { |
---|
| 1231 | factor[i] = exp(tau)/cos(zDist[i]); |
---|
| 1232 | } |
---|
| 1233 | |
---|
| 1234 | // Correct |
---|
| 1235 | |
---|
[480] | 1236 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
[701] | 1237 | |
---|
[234] | 1238 | return pTabOut; |
---|
| 1239 | } |
---|
| 1240 | |
---|
| 1241 | |
---|
[488] | 1242 | void SDMath::rotateXYPhase(SDMemTable& in, Float value, Bool doAll) |
---|
[457] | 1243 | // |
---|
| 1244 | // phase in degrees |
---|
[518] | 1245 | // assumes linear correlations |
---|
[457] | 1246 | // |
---|
| 1247 | { |
---|
[701] | 1248 | if (in.nPol() != 4) { |
---|
| 1249 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
| 1250 | } |
---|
| 1251 | |
---|
[518] | 1252 | SDHeader sh = in.getSDHeader(); |
---|
[716] | 1253 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, False); |
---|
[518] | 1254 | SDAttr sdAtt; |
---|
| 1255 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
| 1256 | throw(AipsError("Only linear polarizations are supported")); |
---|
| 1257 | } |
---|
[457] | 1258 | // |
---|
| 1259 | const Table& tabIn = in.table(); |
---|
| 1260 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
| 1261 | IPosition start(asap::nAxes,0); |
---|
| 1262 | IPosition end(asap::nAxes); |
---|
[234] | 1263 | |
---|
[457] | 1264 | // Set cursor slice. Assumes shape the same for all rows |
---|
| 1265 | |
---|
| 1266 | setCursorSlice (start, end, doAll, in); |
---|
| 1267 | IPosition start3(start); |
---|
| 1268 | start3(asap::PolAxis) = 2; // Real(XY) |
---|
| 1269 | IPosition end3(end); |
---|
| 1270 | end3(asap::PolAxis) = 2; |
---|
| 1271 | // |
---|
| 1272 | IPosition start4(start); |
---|
| 1273 | start4(asap::PolAxis) = 3; // Imag (XY) |
---|
| 1274 | IPosition end4(end); |
---|
| 1275 | end4(asap::PolAxis) = 3; |
---|
| 1276 | // |
---|
| 1277 | uInt nRow = in.nRow(); |
---|
| 1278 | Array<Float> data; |
---|
| 1279 | for (uInt i=0; i<nRow;++i) { |
---|
| 1280 | specCol.get(i,data); |
---|
| 1281 | IPosition shape = data.shape(); |
---|
| 1282 | |
---|
[701] | 1283 | // Get polarization slice references |
---|
[457] | 1284 | Array<Float> C3 = data(start3,end3); |
---|
| 1285 | Array<Float> C4 = data(start4,end4); |
---|
| 1286 | |
---|
[701] | 1287 | // Rotate |
---|
[502] | 1288 | SDPolUtil::rotatePhase(C3, C4, value); |
---|
[457] | 1289 | |
---|
[701] | 1290 | // Put |
---|
[457] | 1291 | specCol.put(i,data); |
---|
| 1292 | } |
---|
| 1293 | } |
---|
[234] | 1294 | |
---|
[502] | 1295 | |
---|
| 1296 | void SDMath::rotateLinPolPhase(SDMemTable& in, Float value, Bool doAll) |
---|
| 1297 | // |
---|
| 1298 | // phase in degrees |
---|
[518] | 1299 | // assumes linear correlations |
---|
[502] | 1300 | // |
---|
| 1301 | { |
---|
| 1302 | if (in.nPol() != 4) { |
---|
| 1303 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
| 1304 | } |
---|
[518] | 1305 | // |
---|
| 1306 | SDHeader sh = in.getSDHeader(); |
---|
[716] | 1307 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, False); |
---|
[518] | 1308 | SDAttr sdAtt; |
---|
| 1309 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
| 1310 | throw(AipsError("Only linear polarizations are supported")); |
---|
| 1311 | } |
---|
[502] | 1312 | // |
---|
| 1313 | const Table& tabIn = in.table(); |
---|
| 1314 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
| 1315 | ROArrayColumn<Float> stokesCol(tabIn,"STOKES"); |
---|
| 1316 | IPosition start(asap::nAxes,0); |
---|
| 1317 | IPosition end(asap::nAxes); |
---|
| 1318 | |
---|
| 1319 | // Set cursor slice. Assumes shape the same for all rows |
---|
| 1320 | |
---|
| 1321 | setCursorSlice (start, end, doAll, in); |
---|
| 1322 | // |
---|
| 1323 | IPosition start1(start); |
---|
| 1324 | start1(asap::PolAxis) = 0; // C1 (XX) |
---|
| 1325 | IPosition end1(end); |
---|
| 1326 | end1(asap::PolAxis) = 0; |
---|
| 1327 | // |
---|
| 1328 | IPosition start2(start); |
---|
| 1329 | start2(asap::PolAxis) = 1; // C2 (YY) |
---|
| 1330 | IPosition end2(end); |
---|
| 1331 | end2(asap::PolAxis) = 1; |
---|
| 1332 | // |
---|
| 1333 | IPosition start3(start); |
---|
| 1334 | start3(asap::PolAxis) = 2; // C3 ( Real(XY) ) |
---|
| 1335 | IPosition end3(end); |
---|
| 1336 | end3(asap::PolAxis) = 2; |
---|
| 1337 | // |
---|
| 1338 | IPosition startI(start); |
---|
| 1339 | startI(asap::PolAxis) = 0; // I |
---|
| 1340 | IPosition endI(end); |
---|
| 1341 | endI(asap::PolAxis) = 0; |
---|
| 1342 | // |
---|
| 1343 | IPosition startQ(start); |
---|
| 1344 | startQ(asap::PolAxis) = 1; // Q |
---|
| 1345 | IPosition endQ(end); |
---|
| 1346 | endQ(asap::PolAxis) = 1; |
---|
| 1347 | // |
---|
| 1348 | IPosition startU(start); |
---|
| 1349 | startU(asap::PolAxis) = 2; // U |
---|
| 1350 | IPosition endU(end); |
---|
| 1351 | endU(asap::PolAxis) = 2; |
---|
| 1352 | |
---|
| 1353 | // |
---|
| 1354 | uInt nRow = in.nRow(); |
---|
| 1355 | Array<Float> data, stokes; |
---|
| 1356 | for (uInt i=0; i<nRow;++i) { |
---|
| 1357 | specCol.get(i,data); |
---|
| 1358 | stokesCol.get(i,stokes); |
---|
| 1359 | IPosition shape = data.shape(); |
---|
| 1360 | |
---|
| 1361 | // Get linear polarization slice references |
---|
| 1362 | |
---|
| 1363 | Array<Float> C1 = data(start1,end1); |
---|
| 1364 | Array<Float> C2 = data(start2,end2); |
---|
| 1365 | Array<Float> C3 = data(start3,end3); |
---|
| 1366 | |
---|
| 1367 | // Get STokes slice references |
---|
| 1368 | |
---|
| 1369 | Array<Float> I = stokes(startI,endI); |
---|
| 1370 | Array<Float> Q = stokes(startQ,endQ); |
---|
| 1371 | Array<Float> U = stokes(startU,endU); |
---|
| 1372 | |
---|
| 1373 | // Rotate |
---|
| 1374 | |
---|
| 1375 | SDPolUtil::rotateLinPolPhase(C1, C2, C3, I, Q, U, value); |
---|
| 1376 | |
---|
| 1377 | // Put |
---|
| 1378 | |
---|
| 1379 | specCol.put(i,data); |
---|
| 1380 | } |
---|
| 1381 | } |
---|
| 1382 | |
---|
[169] | 1383 | // 'private' functions |
---|
| 1384 | |
---|
[354] | 1385 | void SDMath::convertBrightnessUnits (SDMemTable* pTabOut, const SDMemTable& in, |
---|
[716] | 1386 | Bool toKelvin, Float cFac, Bool doAll) |
---|
[354] | 1387 | { |
---|
[309] | 1388 | |
---|
[354] | 1389 | // Get header |
---|
| 1390 | |
---|
| 1391 | SDHeader sh = in.getSDHeader(); |
---|
| 1392 | const uInt nChan = sh.nchan; |
---|
| 1393 | |
---|
| 1394 | // Get instrument |
---|
| 1395 | |
---|
| 1396 | Bool throwIt = True; |
---|
[716] | 1397 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, throwIt); |
---|
[354] | 1398 | |
---|
| 1399 | // Get Diameter (m) |
---|
| 1400 | |
---|
| 1401 | SDAttr sdAtt; |
---|
| 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); |
---|
[716] | 1417 | ostringstream oss; |
---|
| 1418 | oss << "Jy/K = " << JyPerK; |
---|
| 1419 | pushLog(String(oss)); |
---|
[354] | 1420 | Vector<Float> factors = cFac * JyPerK; |
---|
| 1421 | if (toKelvin) factors = Float(1.0) / factors; |
---|
| 1422 | |
---|
[434] | 1423 | // Get data slice bounds |
---|
[354] | 1424 | |
---|
| 1425 | IPosition start, end; |
---|
[434] | 1426 | setCursorSlice (start, end, doAll, in); |
---|
[354] | 1427 | const uInt ifAxis = in.getIF(); |
---|
| 1428 | |
---|
| 1429 | // Iteration axes |
---|
| 1430 | |
---|
| 1431 | IPosition axes(asap::nAxes-1,0); |
---|
| 1432 | for (uInt i=0,j=0; i<asap::nAxes; i++) { |
---|
| 1433 | if (i!=asap::IFAxis) { |
---|
| 1434 | axes(j++) = i; |
---|
| 1435 | } |
---|
| 1436 | } |
---|
| 1437 | |
---|
| 1438 | // Loop over rows and apply correction factor |
---|
| 1439 | |
---|
| 1440 | Float factor = 1.0; |
---|
| 1441 | const uInt axis = asap::ChanAxis; |
---|
| 1442 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 1443 | |
---|
| 1444 | // Get data |
---|
| 1445 | |
---|
[434] | 1446 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(i); |
---|
| 1447 | Array<Float>& values = dataIn.getRWArray(); // Ref to dataIn |
---|
| 1448 | Array<Float> values2 = values(start,end); // Ref to values to dataIn |
---|
[354] | 1449 | |
---|
| 1450 | // Get SDCOntainer |
---|
| 1451 | |
---|
| 1452 | SDContainer sc = in.getSDContainer(i); |
---|
| 1453 | |
---|
| 1454 | // Get FreqIDs |
---|
| 1455 | |
---|
| 1456 | freqIDs = sc.getFreqMap(); |
---|
| 1457 | |
---|
| 1458 | // Now the conversion factor depends only upon frequency |
---|
| 1459 | // So we need to iterate through by IF only giving |
---|
| 1460 | // us BEAM/POL/CHAN cubes |
---|
| 1461 | |
---|
[434] | 1462 | ArrayIterator<Float> itIn(values2, axes); |
---|
| 1463 | uInt ax = 0; |
---|
| 1464 | while (!itIn.pastEnd()) { |
---|
| 1465 | itIn.array() *= factors(freqIDs(ax)); // Writes back to dataIn |
---|
| 1466 | itIn.next(); |
---|
[354] | 1467 | } |
---|
| 1468 | |
---|
| 1469 | // Write out |
---|
| 1470 | |
---|
| 1471 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
| 1472 | // |
---|
| 1473 | pTabOut->putSDContainer(sc); |
---|
| 1474 | } |
---|
| 1475 | } |
---|
| 1476 | |
---|
| 1477 | |
---|
| 1478 | |
---|
[701] | 1479 | SDMemTable* SDMath::frequencyAlign(const SDMemTable& in, |
---|
[309] | 1480 | MFrequency::Types freqSystem, |
---|
[397] | 1481 | const String& refTime, |
---|
| 1482 | const String& methodStr, |
---|
[716] | 1483 | Bool perFreqID) |
---|
[267] | 1484 | { |
---|
| 1485 | // Get Header |
---|
| 1486 | |
---|
| 1487 | SDHeader sh = in.getSDHeader(); |
---|
| 1488 | const uInt nChan = sh.nchan; |
---|
| 1489 | const uInt nRows = in.nRow(); |
---|
[330] | 1490 | const uInt nIF = sh.nif; |
---|
[267] | 1491 | |
---|
| 1492 | // Get Table reference |
---|
| 1493 | |
---|
| 1494 | const Table& tabIn = in.table(); |
---|
| 1495 | |
---|
| 1496 | // Get Columns from Table |
---|
| 1497 | |
---|
[294] | 1498 | ROScalarColumn<Double> mjdCol(tabIn, "TIME"); |
---|
| 1499 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME"); |
---|
| 1500 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID"); |
---|
| 1501 | Vector<Double> times = mjdCol.getColumn(); |
---|
[267] | 1502 | |
---|
[397] | 1503 | // Generate DataDesc table |
---|
[330] | 1504 | |
---|
| 1505 | Matrix<uInt> ddIdx; |
---|
| 1506 | SDDataDesc dDesc; |
---|
[701] | 1507 | generateDataDescTable(ddIdx, dDesc, nIF, in, tabIn, srcCol, |
---|
| 1508 | fqIDCol, perFreqID); |
---|
[267] | 1509 | |
---|
[294] | 1510 | // Get reference Epoch to time of first row or given String |
---|
[701] | 1511 | |
---|
[267] | 1512 | Unit DAY(String("d")); |
---|
[272] | 1513 | MEpoch::Ref epochRef(in.getTimeReference()); |
---|
| 1514 | MEpoch refEpoch; |
---|
| 1515 | if (refTime.length()>0) { |
---|
[701] | 1516 | refEpoch = epochFromString(refTime, in.getTimeReference()); |
---|
[272] | 1517 | } else { |
---|
[701] | 1518 | refEpoch = in.getEpoch(0); |
---|
[272] | 1519 | } |
---|
[716] | 1520 | pushLog("Aligning at reference Epoch "+formatEpoch(refEpoch) |
---|
| 1521 | +" in frame "+MFrequency::showType(freqSystem)); |
---|
[414] | 1522 | |
---|
[701] | 1523 | // Get Reference Position |
---|
| 1524 | |
---|
[288] | 1525 | MPosition refPos = in.getAntennaPosition(); |
---|
[701] | 1526 | |
---|
| 1527 | // Create FrequencyAligner Block. One FA for each possible |
---|
| 1528 | // source/freqID (perFreqID=True) or source/IF (perFreqID=False) |
---|
| 1529 | // combination |
---|
| 1530 | |
---|
[330] | 1531 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length()); |
---|
[397] | 1532 | generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos, |
---|
| 1533 | refEpoch, perFreqID); |
---|
[701] | 1534 | |
---|
| 1535 | // Generate and fill output Frequency Table. WHen perFreqID=True, |
---|
| 1536 | // there is one output FreqID for each entry in the SDDataDesc |
---|
| 1537 | // table. However, in perFreqID=False mode, there may be some |
---|
| 1538 | // degeneracy, so we need a little translation map |
---|
| 1539 | |
---|
[330] | 1540 | SDFrequencyTable freqTabOut = in.getSDFreqTable(); |
---|
| 1541 | freqTabOut.setLength(0); |
---|
| 1542 | Vector<String> units(1); |
---|
| 1543 | units = String("Hz"); |
---|
| 1544 | Bool linear=True; |
---|
[701] | 1545 | // |
---|
[397] | 1546 | Vector<uInt> ddFQTrans(dDesc.length(),0); |
---|
[330] | 1547 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
| 1548 | |
---|
[701] | 1549 | // Get Aligned SC in Hz |
---|
| 1550 | |
---|
| 1551 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear); |
---|
| 1552 | sC.setWorldAxisUnits(units); |
---|
| 1553 | |
---|
| 1554 | // Add FreqID |
---|
| 1555 | |
---|
| 1556 | uInt idx = freqTabOut.addFrequency(sC.referencePixel()[0], |
---|
| 1557 | sC.referenceValue()[0], |
---|
| 1558 | sC.increment()[0]); |
---|
| 1559 | // output FreqID = ddFQTrans(ddIdx) |
---|
| 1560 | ddFQTrans(i) = idx; |
---|
[330] | 1561 | } |
---|
[701] | 1562 | |
---|
| 1563 | // Interpolation method |
---|
| 1564 | |
---|
[317] | 1565 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
| 1566 | convertInterpString(interp, methodStr); |
---|
[701] | 1567 | |
---|
| 1568 | // New output Table |
---|
| 1569 | |
---|
[716] | 1570 | pushLog("Create output table"); |
---|
[267] | 1571 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
[330] | 1572 | pTabOut->putSDFreqTable(freqTabOut); |
---|
[701] | 1573 | |
---|
| 1574 | // Loop over rows in Table |
---|
| 1575 | |
---|
[330] | 1576 | Bool extrapolate=False; |
---|
[294] | 1577 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis); |
---|
| 1578 | Bool useCachedAbcissa = False; |
---|
| 1579 | Bool first = True; |
---|
| 1580 | Bool ok; |
---|
| 1581 | Vector<Float> yOut; |
---|
| 1582 | Vector<Bool> maskOut; |
---|
[330] | 1583 | Vector<uInt> freqID(nIF); |
---|
[309] | 1584 | uInt ifIdx, faIdx; |
---|
[397] | 1585 | Vector<Double> xIn; |
---|
[701] | 1586 | // |
---|
[294] | 1587 | for (uInt iRow=0; iRow<nRows; ++iRow) { |
---|
[701] | 1588 | if (iRow%10==0) { |
---|
[716] | 1589 | pushLog("Processing row "+iRow); |
---|
[701] | 1590 | } |
---|
| 1591 | |
---|
| 1592 | // Get EPoch |
---|
| 1593 | |
---|
[294] | 1594 | Quantum<Double> tQ2(times[iRow],DAY); |
---|
| 1595 | MVEpoch mv2(tQ2); |
---|
| 1596 | MEpoch epoch(mv2, epochRef); |
---|
[701] | 1597 | |
---|
| 1598 | // Get copy of data |
---|
| 1599 | |
---|
[294] | 1600 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow)); |
---|
| 1601 | Array<Float> values = mArrIn.getArray(); |
---|
| 1602 | Array<Bool> mask = mArrIn.getMask(); |
---|
[701] | 1603 | |
---|
| 1604 | // For each row, the Frequency abcissa will be the same |
---|
| 1605 | // regardless of polarization. For all other axes (IF and BEAM) |
---|
| 1606 | // the abcissa will change. So we iterate through the data by |
---|
| 1607 | // pol-chan planes to mimimize the work. Probably won't work for |
---|
| 1608 | // multiple beams at this point. |
---|
| 1609 | |
---|
[294] | 1610 | ArrayIterator<Float> itValuesPlane(values, polChanAxes); |
---|
| 1611 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes); |
---|
| 1612 | while (!itValuesPlane.pastEnd()) { |
---|
[267] | 1613 | |
---|
[701] | 1614 | // Find the IF index and then the FA PtrBlock index |
---|
| 1615 | |
---|
| 1616 | const IPosition& pos = itValuesPlane.pos(); |
---|
| 1617 | ifIdx = pos(asap::IFAxis); |
---|
| 1618 | faIdx = ddIdx(iRow,ifIdx); |
---|
| 1619 | |
---|
| 1620 | // Generate abcissa for perIF. Could cache this in a Matrix on |
---|
| 1621 | // a per scan basis. Pretty expensive doing it for every row. |
---|
| 1622 | |
---|
| 1623 | if (!perFreqID) { |
---|
| 1624 | xIn.resize(nChan); |
---|
| 1625 | uInt fqID = dDesc.secID(ddIdx(iRow,ifIdx)); |
---|
| 1626 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID); |
---|
[397] | 1627 | Double w; |
---|
| 1628 | for (uInt i=0; i<nChan; i++) { |
---|
[701] | 1629 | sC.toWorld(w,Double(i)); |
---|
[397] | 1630 | xIn[i] = w; |
---|
| 1631 | } |
---|
[701] | 1632 | } |
---|
| 1633 | |
---|
| 1634 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1); |
---|
| 1635 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
[330] | 1636 | |
---|
[701] | 1637 | // Iterate through the plane by vector and align |
---|
| 1638 | |
---|
[294] | 1639 | first = True; |
---|
| 1640 | useCachedAbcissa=False; |
---|
| 1641 | while (!itValuesVec.pastEnd()) { |
---|
[701] | 1642 | if (perFreqID) { |
---|
| 1643 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(), |
---|
| 1644 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
| 1645 | interp, extrapolate); |
---|
| 1646 | } else { |
---|
| 1647 | ok = a[faIdx]->align (yOut, maskOut, xIn, itValuesVec.vector(), |
---|
| 1648 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
| 1649 | interp, extrapolate); |
---|
| 1650 | } |
---|
| 1651 | // |
---|
| 1652 | itValuesVec.vector() = yOut; |
---|
| 1653 | itMaskVec.vector() = maskOut; |
---|
| 1654 | // |
---|
| 1655 | itValuesVec.next(); |
---|
| 1656 | itMaskVec.next(); |
---|
| 1657 | // |
---|
| 1658 | if (first) { |
---|
| 1659 | useCachedAbcissa = True; |
---|
| 1660 | first = False; |
---|
| 1661 | } |
---|
[294] | 1662 | } |
---|
[701] | 1663 | // |
---|
| 1664 | itValuesPlane.next(); |
---|
| 1665 | itMaskPlane.next(); |
---|
[294] | 1666 | } |
---|
[701] | 1667 | |
---|
| 1668 | // Create SDContainer and put back |
---|
| 1669 | |
---|
| 1670 | SDContainer sc = in.getSDContainer(iRow); |
---|
| 1671 | putDataInSDC(sc, values, mask); |
---|
| 1672 | |
---|
| 1673 | // Set output FreqIDs |
---|
| 1674 | |
---|
| 1675 | for (uInt i=0; i<nIF; i++) { |
---|
[397] | 1676 | uInt idx = ddIdx(iRow,i); // Index into SDDataDesc table |
---|
| 1677 | freqID(i) = ddFQTrans(idx); // FreqID in output FQ table |
---|
[701] | 1678 | } |
---|
| 1679 | sc.putFreqMap(freqID); |
---|
| 1680 | // |
---|
| 1681 | pTabOut->putSDContainer(sc); |
---|
[294] | 1682 | } |
---|
[701] | 1683 | |
---|
| 1684 | // Now we must set the base and extra frames to the input frame |
---|
[309] | 1685 | std::vector<string> info = pTabOut->getCoordInfo(); |
---|
| 1686 | info[1] = MFrequency::showType(freqSystem); // Conversion frame |
---|
| 1687 | info[3] = info[1]; // Base frame |
---|
| 1688 | pTabOut->setCoordInfo(info); |
---|
| 1689 | |
---|
[701] | 1690 | // Clean up PointerBlock |
---|
| 1691 | for (uInt i=0; i<a.nelements(); i++) delete a[i]; |
---|
[267] | 1692 | |
---|
[309] | 1693 | return pTabOut; |
---|
[267] | 1694 | } |
---|
| 1695 | |
---|
| 1696 | |
---|
[716] | 1697 | SDMemTable* SDMath::frequencySwitch(const SDMemTable& in) |
---|
[701] | 1698 | { |
---|
| 1699 | if (in.nIF() != 2) { |
---|
| 1700 | throw(AipsError("nIF != 2 ")); |
---|
| 1701 | } |
---|
| 1702 | Bool clear = True; |
---|
| 1703 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
| 1704 | const Table& tabIn = in.table(); |
---|
| 1705 | |
---|
| 1706 | // Shape of input and output data |
---|
| 1707 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape(); |
---|
| 1708 | |
---|
| 1709 | const uInt nRows = in.nRow(); |
---|
| 1710 | AlwaysAssert(asap::nAxes==4,AipsError); |
---|
| 1711 | |
---|
| 1712 | ROArrayColumn<Float> tSysCol; |
---|
| 1713 | Array<Float> tsys; |
---|
| 1714 | tSysCol.attach(tabIn,"TSYS"); |
---|
| 1715 | |
---|
| 1716 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 1717 | // Get data for this row |
---|
| 1718 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
| 1719 | tSysCol.get(iRow, tsys); |
---|
| 1720 | |
---|
| 1721 | // whole Array for IF 0 |
---|
| 1722 | IPosition start(asap::nAxes,0); |
---|
| 1723 | IPosition end = shapeIn-1; |
---|
| 1724 | end(asap::IFAxis) = 0; |
---|
| 1725 | |
---|
| 1726 | MaskedArray<Float> on = marr(start,end); |
---|
| 1727 | Array<Float> ton = tsys(start,end); |
---|
| 1728 | // Make a copy as "src" is a refrence which is manipulated. |
---|
| 1729 | // oncopy is needed for the inverse quotient |
---|
| 1730 | MaskedArray<Float> oncopy = on.copy(); |
---|
| 1731 | |
---|
| 1732 | // whole Array for IF 1 |
---|
| 1733 | start(asap::IFAxis) = 1; |
---|
| 1734 | end(asap::IFAxis) = 1; |
---|
| 1735 | |
---|
| 1736 | MaskedArray<Float> off = marr(start,end); |
---|
| 1737 | Array<Float> toff = tsys(start,end); |
---|
| 1738 | |
---|
| 1739 | on /= off; on -= 1.0f; |
---|
| 1740 | on *= ton; |
---|
| 1741 | off /= oncopy; off -= 1.0f; |
---|
| 1742 | off *= toff; |
---|
| 1743 | |
---|
| 1744 | SDContainer sc = in.getSDContainer(iRow); |
---|
| 1745 | putDataInSDC(sc, marr.getArray(), marr.getMask()); |
---|
| 1746 | pTabOut->putSDContainer(sc); |
---|
| 1747 | } |
---|
| 1748 | return pTabOut; |
---|
| 1749 | } |
---|
| 1750 | |
---|
[185] | 1751 | void SDMath::fillSDC(SDContainer& sc, |
---|
| 1752 | const Array<Bool>& mask, |
---|
| 1753 | const Array<Float>& data, |
---|
| 1754 | const Array<Float>& tSys, |
---|
| 1755 | Int scanID, Double timeStamp, |
---|
| 1756 | Double interval, const String& sourceName, |
---|
[716] | 1757 | const Vector<uInt>& freqID) |
---|
[167] | 1758 | { |
---|
[169] | 1759 | // Data and mask |
---|
[167] | 1760 | |
---|
[185] | 1761 | putDataInSDC(sc, data, mask); |
---|
[167] | 1762 | |
---|
[169] | 1763 | // TSys |
---|
| 1764 | |
---|
| 1765 | sc.putTsys(tSys); |
---|
| 1766 | |
---|
| 1767 | // Time things |
---|
| 1768 | |
---|
| 1769 | sc.timestamp = timeStamp; |
---|
| 1770 | sc.interval = interval; |
---|
| 1771 | sc.scanid = scanID; |
---|
[167] | 1772 | // |
---|
[169] | 1773 | sc.sourcename = sourceName; |
---|
| 1774 | sc.putFreqMap(freqID); |
---|
| 1775 | } |
---|
[167] | 1776 | |
---|
[185] | 1777 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum, |
---|
| 1778 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
| 1779 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
[518] | 1780 | Array<Float>& tSysSqSum, |
---|
[185] | 1781 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
| 1782 | const Vector<Bool>& mask, Double time, Double interval, |
---|
[653] | 1783 | const std::vector<CountedPtr<SDMemTable> >& in, |
---|
[185] | 1784 | uInt iTab, uInt iRow, uInt axis, |
---|
| 1785 | uInt nAxesSub, Bool useMask, |
---|
[716] | 1786 | WeightType wtType) |
---|
[169] | 1787 | { |
---|
| 1788 | |
---|
| 1789 | // Get data |
---|
| 1790 | |
---|
| 1791 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
| 1792 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
| 1793 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
[167] | 1794 | // |
---|
[169] | 1795 | if (wtType==NONE) { |
---|
| 1796 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
| 1797 | nPts += n; // Only accumulates where mask==T |
---|
[518] | 1798 | } else if (wtType==TINT) { |
---|
| 1799 | |
---|
| 1800 | // We are weighting the data by integration time. |
---|
| 1801 | |
---|
| 1802 | valuesIn *= Float(interval); |
---|
| 1803 | |
---|
[169] | 1804 | } else if (wtType==VAR) { |
---|
[167] | 1805 | |
---|
[169] | 1806 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
| 1807 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
[167] | 1808 | |
---|
[169] | 1809 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1810 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
| 1811 | Float fac = 1.0; |
---|
| 1812 | IPosition pos(nAxesSub,0); |
---|
| 1813 | // |
---|
| 1814 | while (!itData.pastEnd()) { |
---|
[167] | 1815 | |
---|
[169] | 1816 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
[167] | 1817 | |
---|
[518] | 1818 | if (useMask) { |
---|
| 1819 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
| 1820 | fac = 1.0/variance(tmp); |
---|
| 1821 | } else { |
---|
| 1822 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
| 1823 | fac = 1.0/variance(tmp); |
---|
| 1824 | } |
---|
[169] | 1825 | |
---|
| 1826 | // Scale data |
---|
| 1827 | |
---|
[518] | 1828 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
[167] | 1829 | // |
---|
[169] | 1830 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
| 1831 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1832 | // because the spectral axis is the last one (so we can just |
---|
| 1833 | // copy the first nAXesSub positions out) |
---|
[167] | 1834 | |
---|
[518] | 1835 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1836 | sumSq(pos) += fac; |
---|
[169] | 1837 | // |
---|
[518] | 1838 | itData.next(); |
---|
| 1839 | itMask.next(); |
---|
[169] | 1840 | } |
---|
[536] | 1841 | } else if (wtType==TSYS || wtType==TINTSYS) { |
---|
[518] | 1842 | |
---|
| 1843 | // We are going to average the data, weighted by 1/Tsys**2 for each pol, beam and IF. |
---|
| 1844 | // So therefore we need to iterate through by spectrum (axis 3). Although |
---|
| 1845 | // Tsys is stored as a vector of length nChan, the values are replicated. |
---|
| 1846 | // We will take a short cut and just use the value from the first channel |
---|
| 1847 | // for now. |
---|
| 1848 | // |
---|
| 1849 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1850 | ReadOnlyVectorIterator<Float> itTSys(tSys, axis); |
---|
| 1851 | IPosition pos(nAxesSub,0); |
---|
| 1852 | // |
---|
[536] | 1853 | Float fac = 1.0; |
---|
| 1854 | if (wtType==TINTSYS) fac *= interval; |
---|
[518] | 1855 | while (!itData.pastEnd()) { |
---|
| 1856 | Float t = itTSys.vector()[0]; |
---|
[536] | 1857 | fac *= 1.0/t/t; |
---|
[518] | 1858 | |
---|
| 1859 | // Scale data |
---|
| 1860 | |
---|
| 1861 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
| 1862 | // |
---|
| 1863 | // Accumulate Tsys per if/pol/beam averaged over spectrum |
---|
| 1864 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1865 | // because the spectral axis is the last one (so we can just |
---|
| 1866 | // copy the first nAXesSub positions out) |
---|
| 1867 | |
---|
| 1868 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1869 | tSysSqSum(pos) += fac; |
---|
| 1870 | // |
---|
| 1871 | itData.next(); |
---|
| 1872 | itTSys.next(); |
---|
| 1873 | } |
---|
[169] | 1874 | } |
---|
[167] | 1875 | |
---|
[169] | 1876 | // Accumulate sum of (possibly scaled) data |
---|
| 1877 | |
---|
| 1878 | sum += dataIn; |
---|
| 1879 | |
---|
| 1880 | // Accumulate Tsys, time, and interval |
---|
| 1881 | |
---|
| 1882 | tSysSum += tSys; |
---|
| 1883 | timeSum += time; |
---|
| 1884 | intSum += interval; |
---|
| 1885 | nAccum += 1; |
---|
| 1886 | } |
---|
| 1887 | |
---|
| 1888 | |
---|
[518] | 1889 | void SDMath::normalize(MaskedArray<Float>& sum, |
---|
| 1890 | const Array<Float>& sumSq, |
---|
| 1891 | const Array<Float>& tSysSqSum, |
---|
| 1892 | const Array<Float>& nPts, |
---|
| 1893 | Double intSum, |
---|
| 1894 | WeightType wtType, Int axis, |
---|
[716] | 1895 | Int nAxesSub) |
---|
[518] | 1896 | { |
---|
| 1897 | IPosition pos2(nAxesSub,0); |
---|
| 1898 | // |
---|
| 1899 | if (wtType==NONE) { |
---|
| 1900 | |
---|
| 1901 | // We just average by the number of points accumulated. |
---|
| 1902 | // We need to make a MA out of nPts so that no divide by |
---|
| 1903 | // zeros occur |
---|
| 1904 | |
---|
| 1905 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
| 1906 | sum /= t; |
---|
| 1907 | } else if (wtType==TINT) { |
---|
| 1908 | |
---|
| 1909 | // Average by sum of Tint |
---|
| 1910 | |
---|
| 1911 | sum /= Float(intSum); |
---|
| 1912 | } else if (wtType==VAR) { |
---|
| 1913 | |
---|
| 1914 | // Normalize each spectrum by sum(1/var) where the variance |
---|
| 1915 | // is worked out for each spectrum |
---|
| 1916 | |
---|
| 1917 | Array<Float>& data = sum.getRWArray(); |
---|
| 1918 | VectorIterator<Float> itData(data, axis); |
---|
| 1919 | while (!itData.pastEnd()) { |
---|
| 1920 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 1921 | itData.vector() /= sumSq(pos2); |
---|
| 1922 | itData.next(); |
---|
| 1923 | } |
---|
[536] | 1924 | } else if (wtType==TSYS || wtType==TINTSYS) { |
---|
[518] | 1925 | |
---|
[536] | 1926 | // Normalize each spectrum by sum(1/Tsys**2) (TSYS) or |
---|
| 1927 | // sum(Tint/Tsys**2) (TINTSYS) where the pseudo |
---|
[518] | 1928 | // replication over channel for Tsys has been dropped. |
---|
| 1929 | |
---|
| 1930 | Array<Float>& data = sum.getRWArray(); |
---|
| 1931 | VectorIterator<Float> itData(data, axis); |
---|
| 1932 | while (!itData.pastEnd()) { |
---|
| 1933 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 1934 | itData.vector() /= tSysSqSum(pos2); |
---|
| 1935 | itData.next(); |
---|
| 1936 | } |
---|
| 1937 | } |
---|
| 1938 | } |
---|
| 1939 | |
---|
| 1940 | |
---|
| 1941 | |
---|
| 1942 | |
---|
[434] | 1943 | void SDMath::setCursorSlice (IPosition& start, IPosition& end, Bool doAll, const SDMemTable& in) const |
---|
[169] | 1944 | { |
---|
[434] | 1945 | const uInt nDim = asap::nAxes; |
---|
| 1946 | DebugAssert(nDim==4,AipsError); |
---|
[167] | 1947 | // |
---|
[169] | 1948 | start.resize(nDim); |
---|
[434] | 1949 | end.resize(nDim); |
---|
| 1950 | if (doAll) { |
---|
| 1951 | start = 0; |
---|
| 1952 | end(0) = in.nBeam()-1; |
---|
| 1953 | end(1) = in.nIF()-1; |
---|
| 1954 | end(2) = in.nPol()-1; |
---|
| 1955 | end(3) = in.nChan()-1; |
---|
| 1956 | } else { |
---|
| 1957 | start(0) = in.getBeam(); |
---|
| 1958 | end(0) = start(0); |
---|
[167] | 1959 | // |
---|
[434] | 1960 | start(1) = in.getIF(); |
---|
| 1961 | end(1) = start(1); |
---|
| 1962 | // |
---|
| 1963 | start(2) = in.getPol(); |
---|
| 1964 | end(2) = start(2); |
---|
| 1965 | // |
---|
| 1966 | start(3) = 0; |
---|
| 1967 | end(3) = in.nChan()-1; |
---|
| 1968 | } |
---|
[169] | 1969 | } |
---|
| 1970 | |
---|
| 1971 | |
---|
[518] | 1972 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr, |
---|
[716] | 1973 | Bool listType) |
---|
[169] | 1974 | { |
---|
| 1975 | String tStr(weightStr); |
---|
| 1976 | tStr.upcase(); |
---|
[518] | 1977 | String msg; |
---|
[169] | 1978 | if (tStr.contains(String("NONE"))) { |
---|
| 1979 | wtType = NONE; |
---|
[518] | 1980 | msg = String("Weighting type selected : None"); |
---|
[169] | 1981 | } else if (tStr.contains(String("VAR"))) { |
---|
| 1982 | wtType = VAR; |
---|
[518] | 1983 | msg = String("Weighting type selected : Variance"); |
---|
[536] | 1984 | } else if (tStr.contains(String("TINTSYS"))) { |
---|
| 1985 | wtType = TINTSYS; |
---|
| 1986 | msg = String("Weighting type selected : Tint&Tsys"); |
---|
[518] | 1987 | } else if (tStr.contains(String("TINT"))) { |
---|
| 1988 | wtType = TINT; |
---|
[519] | 1989 | msg = String("Weighting type selected : Tint"); |
---|
[169] | 1990 | } else if (tStr.contains(String("TSYS"))) { |
---|
| 1991 | wtType = TSYS; |
---|
[518] | 1992 | msg = String("Weighting type selected : Tsys"); |
---|
[169] | 1993 | } else { |
---|
[518] | 1994 | msg = String("Weighting type selected : None"); |
---|
| 1995 | throw(AipsError("Unrecognized weighting type")); |
---|
[167] | 1996 | } |
---|
[518] | 1997 | // |
---|
[716] | 1998 | if (listType) pushLog(msg); |
---|
[167] | 1999 | } |
---|
| 2000 | |
---|
[317] | 2001 | |
---|
| 2002 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type, |
---|
[716] | 2003 | const casa::String& interp) |
---|
[227] | 2004 | { |
---|
| 2005 | String tStr(interp); |
---|
| 2006 | tStr.upcase(); |
---|
| 2007 | if (tStr.contains(String("NEAR"))) { |
---|
[317] | 2008 | type = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
[227] | 2009 | } else if (tStr.contains(String("LIN"))) { |
---|
[317] | 2010 | type = InterpolateArray1D<Double,Float>::linear; |
---|
[227] | 2011 | } else if (tStr.contains(String("CUB"))) { |
---|
[317] | 2012 | type = InterpolateArray1D<Double,Float>::cubic; |
---|
[227] | 2013 | } else if (tStr.contains(String("SPL"))) { |
---|
[317] | 2014 | type = InterpolateArray1D<Double,Float>::spline; |
---|
[227] | 2015 | } else { |
---|
| 2016 | throw(AipsError("Unrecognized interpolation type")); |
---|
| 2017 | } |
---|
| 2018 | } |
---|
| 2019 | |
---|
[185] | 2020 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data, |
---|
[716] | 2021 | const Array<Bool>& mask) |
---|
[169] | 2022 | { |
---|
| 2023 | sc.putSpectrum(data); |
---|
| 2024 | // |
---|
| 2025 | Array<uChar> outflags(data.shape()); |
---|
| 2026 | convertArray(outflags,!mask); |
---|
| 2027 | sc.putFlags(outflags); |
---|
| 2028 | } |
---|
[227] | 2029 | |
---|
[716] | 2030 | Table SDMath::readAsciiFile(const String& fileName) const |
---|
[227] | 2031 | { |
---|
[230] | 2032 | String formatString; |
---|
| 2033 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False); |
---|
[227] | 2034 | return tbl; |
---|
| 2035 | } |
---|
[230] | 2036 | |
---|
| 2037 | |
---|
[234] | 2038 | |
---|
[480] | 2039 | void SDMath::scaleFromAsciiTable(SDMemTable* pTabOut, |
---|
| 2040 | const SDMemTable& in, const String& fileName, |
---|
| 2041 | const String& col0, const String& col1, |
---|
| 2042 | const String& methodStr, Bool doAll, |
---|
[716] | 2043 | const Vector<Float>& xOut, Bool doTSys) |
---|
[230] | 2044 | { |
---|
| 2045 | |
---|
| 2046 | // Read gain-elevation ascii file data into a Table. |
---|
| 2047 | |
---|
[234] | 2048 | Table geTable = readAsciiFile (fileName); |
---|
[230] | 2049 | // |
---|
[480] | 2050 | scaleFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut, doTSys); |
---|
[230] | 2051 | } |
---|
| 2052 | |
---|
[480] | 2053 | void SDMath::scaleFromTable(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 2054 | const Table& tTable, const String& col0, |
---|
| 2055 | const String& col1, |
---|
| 2056 | const String& methodStr, Bool doAll, |
---|
[716] | 2057 | const Vector<Float>& xOut, Bool doTsys) |
---|
[230] | 2058 | { |
---|
| 2059 | |
---|
| 2060 | // Get data from Table |
---|
| 2061 | |
---|
| 2062 | ROScalarColumn<Float> geElCol(tTable, col0); |
---|
| 2063 | ROScalarColumn<Float> geFacCol(tTable, col1); |
---|
| 2064 | Vector<Float> xIn = geElCol.getColumn(); |
---|
| 2065 | Vector<Float> yIn = geFacCol.getColumn(); |
---|
| 2066 | Vector<Bool> maskIn(xIn.nelements(),True); |
---|
| 2067 | |
---|
| 2068 | // Interpolate (and extrapolate) with desired method |
---|
| 2069 | |
---|
[317] | 2070 | InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
[230] | 2071 | convertInterpString(method, methodStr); |
---|
[317] | 2072 | Int intMethod(method); |
---|
[230] | 2073 | // |
---|
| 2074 | Vector<Float> yOut; |
---|
| 2075 | Vector<Bool> maskOut; |
---|
| 2076 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut, |
---|
[317] | 2077 | xIn, yIn, maskIn, intMethod, |
---|
[230] | 2078 | True, True); |
---|
[234] | 2079 | // Apply |
---|
[230] | 2080 | |
---|
[480] | 2081 | scaleByVector(pTabOut, in, doAll, Float(1.0)/yOut, doTsys); |
---|
[234] | 2082 | } |
---|
| 2083 | |
---|
| 2084 | |
---|
[480] | 2085 | void SDMath::scaleByVector(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 2086 | Bool doAll, const Vector<Float>& factor, |
---|
[716] | 2087 | Bool doTSys) |
---|
[234] | 2088 | { |
---|
[270] | 2089 | |
---|
[434] | 2090 | // Set up data slice |
---|
[230] | 2091 | |
---|
| 2092 | IPosition start, end; |
---|
[434] | 2093 | setCursorSlice (start, end, doAll, in); |
---|
[230] | 2094 | |
---|
[480] | 2095 | // Get Tsys column |
---|
| 2096 | |
---|
| 2097 | const Table& tIn = in.table(); |
---|
| 2098 | ArrayColumn<Float> tSysCol(tIn, "TSYS"); |
---|
| 2099 | Array<Float> tSys; |
---|
| 2100 | |
---|
[270] | 2101 | // Loop over rows and apply correction factor |
---|
[230] | 2102 | |
---|
| 2103 | const uInt axis = asap::ChanAxis; |
---|
| 2104 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 2105 | |
---|
| 2106 | // Get data |
---|
| 2107 | |
---|
[434] | 2108 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
| 2109 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference to dataIn |
---|
[480] | 2110 | // |
---|
| 2111 | if (doTSys) { |
---|
| 2112 | tSysCol.get(i, tSys); |
---|
| 2113 | Array<Float> tSys2 = tSys(start,end) * factor[i]; |
---|
| 2114 | tSysCol.put(i, tSys); |
---|
| 2115 | } |
---|
[230] | 2116 | |
---|
| 2117 | // Apply factor |
---|
| 2118 | |
---|
[434] | 2119 | dataIn2 *= factor[i]; |
---|
[230] | 2120 | |
---|
| 2121 | // Write out |
---|
| 2122 | |
---|
[434] | 2123 | SDContainer sc = in.getSDContainer(i); |
---|
| 2124 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
[230] | 2125 | // |
---|
[434] | 2126 | pTabOut->putSDContainer(sc); |
---|
[230] | 2127 | } |
---|
| 2128 | } |
---|
| 2129 | |
---|
[234] | 2130 | |
---|
[262] | 2131 | |
---|
| 2132 | |
---|
[330] | 2133 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx, |
---|
| 2134 | SDDataDesc& dDesc, |
---|
| 2135 | uInt nIF, |
---|
| 2136 | const SDMemTable& in, |
---|
| 2137 | const Table& tabIn, |
---|
| 2138 | const ROScalarColumn<String>& srcCol, |
---|
[397] | 2139 | const ROArrayColumn<uInt>& fqIDCol, |
---|
[716] | 2140 | Bool perFreqID) |
---|
[330] | 2141 | { |
---|
| 2142 | const uInt nRows = tabIn.nrow(); |
---|
| 2143 | ddIdx.resize(nRows,nIF); |
---|
[262] | 2144 | // |
---|
[330] | 2145 | String srcName; |
---|
| 2146 | Vector<uInt> freqIDs; |
---|
| 2147 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 2148 | srcCol.get(iRow, srcName); |
---|
| 2149 | fqIDCol.get(iRow, freqIDs); |
---|
| 2150 | const MDirection& dir = in.getDirection(iRow); |
---|
| 2151 | // |
---|
[397] | 2152 | if (perFreqID) { |
---|
| 2153 | |
---|
| 2154 | // One entry per source/freqID pair |
---|
| 2155 | |
---|
| 2156 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
| 2157 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, freqIDs[iIF], dir, 0); |
---|
| 2158 | } |
---|
| 2159 | } else { |
---|
| 2160 | |
---|
| 2161 | // One entry per source/IF pair. Hang onto the FreqID as well |
---|
| 2162 | |
---|
| 2163 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
| 2164 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, iIF, dir, freqIDs[iIF]); |
---|
| 2165 | } |
---|
[262] | 2166 | } |
---|
| 2167 | } |
---|
| 2168 | } |
---|
[272] | 2169 | |
---|
[397] | 2170 | |
---|
| 2171 | |
---|
| 2172 | |
---|
| 2173 | |
---|
[716] | 2174 | MEpoch SDMath::epochFromString(const String& str, MEpoch::Types timeRef) |
---|
[272] | 2175 | { |
---|
| 2176 | Quantum<Double> qt; |
---|
| 2177 | if (MVTime::read(qt,str)) { |
---|
| 2178 | MVEpoch mv(qt); |
---|
| 2179 | MEpoch me(mv, timeRef); |
---|
| 2180 | return me; |
---|
| 2181 | } else { |
---|
| 2182 | throw(AipsError("Invalid format for Epoch string")); |
---|
| 2183 | } |
---|
| 2184 | } |
---|
| 2185 | |
---|
| 2186 | |
---|
| 2187 | String SDMath::formatEpoch(const MEpoch& epoch) const |
---|
| 2188 | { |
---|
| 2189 | MVTime mvt(epoch.getValue()); |
---|
| 2190 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")"); |
---|
| 2191 | } |
---|
| 2192 | |
---|
[294] | 2193 | |
---|
[309] | 2194 | |
---|
[701] | 2195 | void SDMath::generateFrequencyAligners(PtrBlock<FrequencyAligner<Float>* >& a, |
---|
| 2196 | const SDDataDesc& dDesc, |
---|
| 2197 | const SDMemTable& in, uInt nChan, |
---|
| 2198 | MFrequency::Types system, |
---|
| 2199 | const MPosition& refPos, |
---|
| 2200 | const MEpoch& refEpoch, |
---|
[716] | 2201 | Bool perFreqID) |
---|
[294] | 2202 | { |
---|
[330] | 2203 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
[397] | 2204 | uInt ID = dDesc.ID(i); |
---|
| 2205 | uInt secID = dDesc.secID(i); |
---|
| 2206 | const MDirection& refDir = dDesc.secDir(i); |
---|
[330] | 2207 | // |
---|
[397] | 2208 | if (perFreqID) { |
---|
| 2209 | |
---|
| 2210 | // One aligner per source/FreqID pair. |
---|
| 2211 | |
---|
| 2212 | SpectralCoordinate sC = in.getSpectralCoordinate(ID); |
---|
| 2213 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
| 2214 | } else { |
---|
| 2215 | |
---|
| 2216 | // One aligner per source/IF pair. But we still need the FreqID to |
---|
| 2217 | // get the right SC. Hence the messing about with the secondary ID |
---|
| 2218 | |
---|
| 2219 | SpectralCoordinate sC = in.getSpectralCoordinate(secID); |
---|
| 2220 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
| 2221 | } |
---|
[294] | 2222 | } |
---|
| 2223 | } |
---|
[480] | 2224 | |
---|
[701] | 2225 | Vector<uInt> SDMath::getRowRange(const SDMemTable& in) const |
---|
[480] | 2226 | { |
---|
| 2227 | Vector<uInt> range(2); |
---|
| 2228 | range[0] = 0; |
---|
| 2229 | range[1] = in.nRow()-1; |
---|
| 2230 | return range; |
---|
| 2231 | } |
---|
| 2232 | |
---|
| 2233 | |
---|
[701] | 2234 | Bool SDMath::rowInRange(uInt i, const Vector<uInt>& range) const |
---|
[480] | 2235 | { |
---|
| 2236 | return (i>=range[0] && i<=range[1]); |
---|
| 2237 | } |
---|
[701] | 2238 | |
---|