[2] | 1 | //#--------------------------------------------------------------------------- |
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| 2 | //# SDMath.cc: A collection of single dish mathematical operations |
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| 3 | //#--------------------------------------------------------------------------- |
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| 4 | //# Copyright (C) 2004 |
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[125] | 5 | //# ATNF |
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[2] | 6 | //# |
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| 7 | //# This program is free software; you can redistribute it and/or modify it |
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| 8 | //# under the terms of the GNU General Public License as published by the Free |
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| 9 | //# Software Foundation; either version 2 of the License, or (at your option) |
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| 10 | //# any later version. |
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| 11 | //# |
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| 12 | //# This program is distributed in the hope that it will be useful, but |
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| 13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
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| 15 | //# Public License for more details. |
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| 16 | //# |
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| 17 | //# You should have received a copy of the GNU General Public License along |
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| 18 | //# with this program; if not, write to the Free Software Foundation, Inc., |
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| 19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA. |
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| 20 | //# |
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| 21 | //# Correspondence concerning this software should be addressed as follows: |
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| 22 | //# Internet email: Malte.Marquarding@csiro.au |
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| 23 | //# Postal address: Malte Marquarding, |
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| 24 | //# Australia Telescope National Facility, |
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| 25 | //# P.O. Box 76, |
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| 26 | //# Epping, NSW, 2121, |
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| 27 | //# AUSTRALIA |
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| 28 | //# |
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| 29 | //# $Id: |
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| 30 | //#--------------------------------------------------------------------------- |
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[38] | 31 | #include <vector> |
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| 32 | |
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[81] | 33 | #include <casa/aips.h> |
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| 34 | #include <casa/BasicSL/String.h> |
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| 35 | #include <casa/Arrays/IPosition.h> |
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| 36 | #include <casa/Arrays/Array.h> |
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[130] | 37 | #include <casa/Arrays/ArrayIter.h> |
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| 38 | #include <casa/Arrays/VectorIter.h> |
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[81] | 39 | #include <casa/Arrays/ArrayMath.h> |
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| 40 | #include <casa/Arrays/ArrayLogical.h> |
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| 41 | #include <casa/Arrays/MaskedArray.h> |
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| 42 | #include <casa/Arrays/MaskArrMath.h> |
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| 43 | #include <casa/Arrays/MaskArrLogi.h> |
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[234] | 44 | #include <casa/BasicMath/Math.h> |
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[221] | 45 | #include <casa/Containers/Block.h> |
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[262] | 46 | #include <casa/Exceptions.h> |
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| 47 | #include <casa/Quanta/Quantum.h> |
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| 48 | #include <casa/Quanta/Unit.h> |
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| 49 | #include <casa/Quanta/MVEpoch.h> |
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[221] | 50 | #include <casa/Quanta/QC.h> |
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[272] | 51 | #include <casa/Quanta/MVTime.h> |
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[177] | 52 | #include <casa/Utilities/Assert.h> |
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[2] | 53 | |
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[262] | 54 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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| 55 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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| 56 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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| 57 | #include <coordinates/Coordinates/VelocityAligner.h> |
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| 58 | |
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| 59 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 60 | #include <lattices/Lattices/RebinLattice.h> |
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| 61 | |
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| 62 | #include <measures/Measures/MEpoch.h> |
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| 63 | #include <measures/Measures/MDirection.h> |
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| 64 | #include <measures/Measures/MPosition.h> |
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| 65 | |
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[177] | 66 | #include <scimath/Mathematics/VectorKernel.h> |
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| 67 | #include <scimath/Mathematics/Convolver.h> |
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[227] | 68 | #include <scimath/Mathematics/InterpolateArray1D.h> |
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[234] | 69 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 70 | |
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[81] | 71 | #include <tables/Tables/Table.h> |
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| 72 | #include <tables/Tables/ScalarColumn.h> |
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| 73 | #include <tables/Tables/ArrayColumn.h> |
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[227] | 74 | #include <tables/Tables/ReadAsciiTable.h> |
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[2] | 75 | |
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[38] | 76 | #include "MathUtils.h" |
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[232] | 77 | #include "SDDefs.h" |
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[2] | 78 | #include "SDContainer.h" |
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| 79 | #include "SDMemTable.h" |
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| 80 | |
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| 81 | #include "SDMath.h" |
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| 82 | |
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[125] | 83 | using namespace casa; |
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[83] | 84 | using namespace asap; |
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[2] | 85 | |
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[170] | 86 | |
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| 87 | SDMath::SDMath() |
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| 88 | {;} |
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| 89 | |
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[185] | 90 | SDMath::SDMath(const SDMath& other) |
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[170] | 91 | { |
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| 92 | |
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| 93 | // No state |
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| 94 | |
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| 95 | } |
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| 96 | |
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| 97 | SDMath& SDMath::operator=(const SDMath& other) |
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| 98 | { |
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| 99 | if (this != &other) { |
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| 100 | // No state |
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| 101 | } |
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| 102 | return *this; |
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| 103 | } |
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| 104 | |
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[183] | 105 | SDMath::~SDMath() |
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| 106 | {;} |
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[170] | 107 | |
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[183] | 108 | |
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[262] | 109 | |
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[272] | 110 | SDMemTable* SDMath::velocityAlignment (const SDMemTable& in, const String& refTime) const |
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[262] | 111 | { |
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| 112 | |
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[267] | 113 | // Get velocity/frame info from Table |
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[262] | 114 | |
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| 115 | std::vector<std::string> info = in.getCoordInfo(); |
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[294] | 116 | |
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| 117 | // Parse unit ("" means channels) |
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| 118 | |
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[262] | 119 | String velUnit(info[0]); |
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| 120 | if (velUnit.length()==0) { |
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| 121 | throw(AipsError("You have not set a velocity abcissa unit - use function set_unit")); |
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| 122 | } else { |
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| 123 | Unit velUnitU(velUnit); |
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| 124 | if (velUnitU!=Unit(String("m/s"))) { |
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| 125 | throw(AipsError("Specified abcissa unit is not consistent with km/s - use function set_unit")); |
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| 126 | } |
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| 127 | } |
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[294] | 128 | |
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| 129 | // Parse doppler |
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| 130 | |
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[262] | 131 | String dopplerStr(info[2]); |
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| 132 | String velSystemStr(info[1]); |
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| 133 | String velBaseSystemStr(info[3]); |
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| 134 | if (velBaseSystemStr==velSystemStr) { |
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[267] | 135 | throw(AipsError("You have not set a velocity frame different from the initial - use function set_freqframe")); |
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[262] | 136 | } |
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[294] | 137 | |
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| 138 | // Parse frequency system |
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| 139 | |
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[262] | 140 | MFrequency::Types velSystem; |
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| 141 | MFrequency::getType(velSystem, velSystemStr); |
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| 142 | MDoppler::Types doppler; |
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| 143 | MDoppler::getType(doppler, dopplerStr); |
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| 144 | |
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[267] | 145 | // Do it |
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[262] | 146 | |
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[272] | 147 | return velocityAlign (in, velSystem, velUnit, doppler, refTime); |
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[267] | 148 | } |
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[262] | 149 | |
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| 150 | |
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| 151 | |
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[185] | 152 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in, |
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| 153 | const Vector<Bool>& mask, Bool scanAv, |
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[248] | 154 | const String& weightStr, Bool alignVelocity) const |
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[130] | 155 | // |
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[144] | 156 | // Weighted averaging of spectra from one or more Tables. |
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[130] | 157 | // |
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| 158 | { |
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[2] | 159 | |
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[163] | 160 | // Convert weight type |
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| 161 | |
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| 162 | WeightType wtType = NONE; |
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[185] | 163 | convertWeightString(wtType, weightStr); |
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[163] | 164 | |
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[144] | 165 | // Create output Table by cloning from the first table |
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[2] | 166 | |
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[144] | 167 | SDMemTable* pTabOut = new SDMemTable(*in[0],True); |
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[130] | 168 | |
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[144] | 169 | // Setup |
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[130] | 170 | |
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[144] | 171 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change |
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| 172 | Array<Float> arr(shp); |
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| 173 | Array<Bool> barr(shp); |
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[221] | 174 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis)); |
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[130] | 175 | |
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[144] | 176 | // Columns from Tables |
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[130] | 177 | |
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[144] | 178 | ROArrayColumn<Float> tSysCol; |
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| 179 | ROScalarColumn<Double> mjdCol; |
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| 180 | ROScalarColumn<String> srcNameCol; |
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| 181 | ROScalarColumn<Double> intCol; |
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| 182 | ROArrayColumn<uInt> fqIDCol; |
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[130] | 183 | |
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[144] | 184 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam |
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| 185 | // Note that the mask of the accumulation array will ALWAYS remain ALL True. |
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| 186 | // The MA is only used so that when data which is masked Bad is added to it, |
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| 187 | // that data does not contribute. |
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| 188 | |
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| 189 | Array<Float> zero(shp); |
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| 190 | zero=0.0; |
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| 191 | Array<Bool> good(shp); |
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| 192 | good = True; |
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| 193 | MaskedArray<Float> sum(zero,good); |
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| 194 | |
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| 195 | // Counter arrays |
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| 196 | |
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| 197 | Array<Float> nPts(shp); // Number of points |
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| 198 | nPts = 0.0; |
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| 199 | Array<Float> nInc(shp); // Increment |
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| 200 | nInc = 1.0; |
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| 201 | |
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| 202 | // Create accumulation Array for variance. We accumulate for |
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| 203 | // each if,pol,beam, but average over channel. So we need |
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| 204 | // a shape with one less axis dropping channels. |
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| 205 | |
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| 206 | const uInt nAxesSub = shp.nelements() - 1; |
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| 207 | IPosition shp2(nAxesSub); |
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| 208 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) { |
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[221] | 209 | if (i!=asap::ChanAxis) { |
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[144] | 210 | shp2(j) = shp(i); |
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| 211 | j++; |
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| 212 | } |
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[2] | 213 | } |
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[144] | 214 | Array<Float> sumSq(shp2); |
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| 215 | sumSq = 0.0; |
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| 216 | IPosition pos2(nAxesSub,0); // For indexing |
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[130] | 217 | |
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[144] | 218 | // Time-related accumulators |
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[130] | 219 | |
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[144] | 220 | Double time; |
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| 221 | Double timeSum = 0.0; |
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| 222 | Double intSum = 0.0; |
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| 223 | Double interval = 0.0; |
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[130] | 224 | |
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[144] | 225 | // To get the right shape for the Tsys accumulator we need to |
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| 226 | // access a column from the first table. The shape of this |
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| 227 | // array must not change |
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[130] | 228 | |
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[144] | 229 | Array<Float> tSysSum; |
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| 230 | { |
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| 231 | const Table& tabIn = in[0]->table(); |
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| 232 | tSysCol.attach(tabIn,"TSYS"); |
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| 233 | tSysSum.resize(tSysCol.shape(0)); |
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| 234 | } |
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| 235 | tSysSum =0.0; |
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| 236 | Array<Float> tSys; |
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| 237 | |
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| 238 | // Scan and row tracking |
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| 239 | |
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| 240 | Int oldScanID = 0; |
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| 241 | Int outScanID = 0; |
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| 242 | Int scanID = 0; |
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| 243 | Int rowStart = 0; |
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| 244 | Int nAccum = 0; |
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| 245 | Int tableStart = 0; |
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| 246 | |
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| 247 | // Source and FreqID |
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| 248 | |
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| 249 | String sourceName, oldSourceName, sourceNameStart; |
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| 250 | Vector<uInt> freqID, freqIDStart, oldFreqID; |
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| 251 | |
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| 252 | // Loop over tables |
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| 253 | |
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| 254 | Float fac = 1.0; |
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| 255 | const uInt nTables = in.nelements(); |
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| 256 | for (uInt iTab=0; iTab<nTables; iTab++) { |
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| 257 | |
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[221] | 258 | // Should check that the frequency tables don't change if doing VelocityAlignment |
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| 259 | |
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[144] | 260 | // Attach columns to Table |
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| 261 | |
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| 262 | const Table& tabIn = in[iTab]->table(); |
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| 263 | tSysCol.attach(tabIn, "TSYS"); |
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| 264 | mjdCol.attach(tabIn, "TIME"); |
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| 265 | srcNameCol.attach(tabIn, "SRCNAME"); |
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| 266 | intCol.attach(tabIn, "INTERVAL"); |
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| 267 | fqIDCol.attach(tabIn, "FREQID"); |
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| 268 | |
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| 269 | // Loop over rows in Table |
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| 270 | |
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| 271 | const uInt nRows = in[iTab]->nRow(); |
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| 272 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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| 273 | |
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| 274 | // Check conformance |
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| 275 | |
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| 276 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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| 277 | if (!shp.isEqual(shp2)) { |
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| 278 | throw (AipsError("Shapes for all rows must be the same")); |
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| 279 | } |
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| 280 | |
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| 281 | // If we are not doing scan averages, make checks for source and |
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| 282 | // frequency setup and warn if averaging across them |
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| 283 | |
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| 284 | // Get copy of Scan Container for this row |
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| 285 | |
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| 286 | SDContainer sc = in[iTab]->getSDContainer(iRow); |
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| 287 | scanID = sc.scanid; |
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| 288 | |
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| 289 | // Get quantities from columns |
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| 290 | |
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| 291 | srcNameCol.getScalar(iRow, sourceName); |
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| 292 | mjdCol.get(iRow, time); |
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| 293 | tSysCol.get(iRow, tSys); |
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| 294 | intCol.get(iRow, interval); |
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| 295 | fqIDCol.get(iRow, freqID); |
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| 296 | |
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| 297 | // Initialize first source and freqID |
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| 298 | |
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| 299 | if (iRow==0 && iTab==0) { |
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| 300 | sourceNameStart = sourceName; |
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| 301 | freqIDStart = freqID; |
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| 302 | } |
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| 303 | |
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| 304 | // If we are doing scan averages, see if we are at the end of an |
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| 305 | // accumulation period (scan). We must check soutce names too, |
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| 306 | // since we might have two tables with one scan each but different |
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| 307 | // source names; we shouldn't average different sources together |
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| 308 | |
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| 309 | if (scanAv && ( (scanID != oldScanID) || |
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| 310 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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| 311 | |
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| 312 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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| 313 | |
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[221] | 314 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 315 | |
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| 316 | // Fill scan container. The source and freqID come from the |
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| 317 | // first row of the first table that went into this average ( |
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| 318 | // should be the same for all rows in the scan average) |
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| 319 | |
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| 320 | Float nR(nAccum); |
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[185] | 321 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 322 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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| 323 | |
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| 324 | // Write container out to Table |
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| 325 | |
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| 326 | pTabOut->putSDContainer(sc); |
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| 327 | |
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| 328 | // Reset accumulators |
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| 329 | |
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| 330 | sum = 0.0; |
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| 331 | sumSq = 0.0; |
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| 332 | nAccum = 0; |
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| 333 | // |
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| 334 | tSysSum =0.0; |
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| 335 | timeSum = 0.0; |
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| 336 | intSum = 0.0; |
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[221] | 337 | nPts = 0.0; |
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[144] | 338 | |
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| 339 | // Increment |
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| 340 | |
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| 341 | rowStart = iRow; // First row for next accumulation |
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| 342 | tableStart = iTab; // First table for next accumulation |
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| 343 | sourceNameStart = sourceName; // First source name for next accumulation |
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| 344 | freqIDStart = freqID; // First FreqID for next accumulation |
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| 345 | // |
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| 346 | oldScanID = scanID; |
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| 347 | outScanID += 1; // Scan ID for next accumulation period |
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[227] | 348 | } |
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[144] | 349 | |
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[146] | 350 | // Accumulate |
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[144] | 351 | |
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[185] | 352 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, |
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[221] | 353 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis, |
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[146] | 354 | nAxesSub, useMask, wtType); |
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[144] | 355 | // |
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| 356 | oldSourceName = sourceName; |
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| 357 | oldFreqID = freqID; |
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[184] | 358 | } |
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[144] | 359 | } |
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| 360 | |
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| 361 | // OK at this point we have accumulation data which is either |
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| 362 | // - accumulated from all tables into one row |
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| 363 | // or |
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| 364 | // - accumulated from the last scan average |
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| 365 | // |
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| 366 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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[221] | 367 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub); |
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[144] | 368 | |
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| 369 | // Create and fill container. The container we clone will be from |
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| 370 | // the last Table and the first row that went into the current |
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| 371 | // accumulation. It probably doesn't matter that much really... |
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| 372 | |
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| 373 | Float nR(nAccum); |
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| 374 | SDContainer sc = in[tableStart]->getSDContainer(rowStart); |
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[185] | 375 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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[144] | 376 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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[221] | 377 | pTabOut->putSDContainer(sc); |
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[304] | 378 | pTabOut->resetCursor(); |
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[144] | 379 | // |
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| 380 | return CountedPtr<SDMemTable>(pTabOut); |
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[2] | 381 | } |
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[9] | 382 | |
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[144] | 383 | |
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| 384 | |
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[248] | 385 | CountedPtr<SDMemTable> SDMath::binaryOperate (const CountedPtr<SDMemTable>& left, |
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| 386 | const CountedPtr<SDMemTable>& right, |
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[294] | 387 | const String& op, Bool preserve, |
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| 388 | Bool doTSys) const |
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[185] | 389 | { |
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[85] | 390 | |
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[248] | 391 | // Check operator |
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[130] | 392 | |
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[234] | 393 | String op2(op); |
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| 394 | op2.upcase(); |
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| 395 | uInt what = 0; |
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| 396 | if (op2=="ADD") { |
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| 397 | what = 0; |
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| 398 | } else if (op2=="SUB") { |
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| 399 | what = 1; |
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| 400 | } else if (op2=="MUL") { |
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| 401 | what = 2; |
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| 402 | } else if (op2=="DIV") { |
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| 403 | what = 3; |
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[248] | 404 | } else if (op2=="QUOTIENT") { |
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| 405 | what = 4; |
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[294] | 406 | doTSys = True; |
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[234] | 407 | } else { |
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[248] | 408 | throw( AipsError("Unrecognized operation")); |
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[234] | 409 | } |
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| 410 | |
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| 411 | // Check rows |
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| 412 | |
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[248] | 413 | const uInt nRowLeft = left->nRow(); |
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| 414 | const uInt nRowRight = right->nRow(); |
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| 415 | Bool ok = (nRowRight==1&&nRowLeft>0) || |
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| 416 | (nRowRight>=1&&nRowLeft==nRowRight); |
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| 417 | if (!ok) { |
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| 418 | 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] | 419 | } |
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| 420 | |
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[248] | 421 | // Input Tables |
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[234] | 422 | |
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| 423 | const Table& tLeft = left->table(); |
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| 424 | const Table& tRight = right->table(); |
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[248] | 425 | |
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| 426 | // TSys columns |
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| 427 | |
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[294] | 428 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol; |
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| 429 | if (doTSys) { |
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| 430 | tSysLeftCol.attach(tLeft, "TSYS"); |
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| 431 | tSysRightCol.attach(tRight, "TSYS"); |
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| 432 | } |
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[234] | 433 | |
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[248] | 434 | // First row for right |
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[234] | 435 | |
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[248] | 436 | Array<Float> tSysLeftArr, tSysRightArr; |
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[294] | 437 | if (doTSys) tSysRightCol.get(0, tSysRightArr); |
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[248] | 438 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0)); |
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| 439 | IPosition shpRight = pMRight->shape(); |
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| 440 | |
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| 441 | // Output Table cloned from left |
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| 442 | |
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[234] | 443 | SDMemTable* pTabOut = new SDMemTable(*left, True); |
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| 444 | |
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| 445 | // Loop over rows |
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| 446 | |
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[248] | 447 | for (uInt i=0; i<nRowLeft; i++) { |
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[234] | 448 | |
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| 449 | // Get data |
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[248] | 450 | |
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[234] | 451 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i)); |
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[248] | 452 | IPosition shpLeft = mLeft.shape(); |
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[294] | 453 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr); |
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[234] | 454 | // |
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[248] | 455 | if (nRowRight>1) { |
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| 456 | delete pMRight; |
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| 457 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i)); |
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| 458 | shpRight = pMRight->shape(); |
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[294] | 459 | if (doTSys) tSysRightCol.get(i, tSysRightArr); |
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[234] | 460 | } |
---|
[248] | 461 | // |
---|
| 462 | if (!shpRight.isEqual(shpLeft)) { |
---|
| 463 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 464 | } |
---|
[294] | 465 | if (doTSys) { |
---|
| 466 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) { |
---|
| 467 | throw(AipsError("left and right Tsys data are not conformant")); |
---|
| 468 | } |
---|
| 469 | if (!shpRight.isEqual(tSysRightArr.shape())) { |
---|
| 470 | throw(AipsError("left and right scan tables are not conformant")); |
---|
| 471 | } |
---|
[248] | 472 | } |
---|
[234] | 473 | |
---|
| 474 | // Make container |
---|
| 475 | |
---|
| 476 | SDContainer sc = left->getSDContainer(i); |
---|
| 477 | |
---|
| 478 | // Operate on data and TSys |
---|
| 479 | |
---|
| 480 | if (what==0) { |
---|
[248] | 481 | MaskedArray<Float> tmp = mLeft + *pMRight; |
---|
[234] | 482 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 483 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr); |
---|
[234] | 484 | } else if (what==1) { |
---|
[248] | 485 | MaskedArray<Float> tmp = mLeft - *pMRight; |
---|
[234] | 486 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 487 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr); |
---|
[234] | 488 | } else if (what==2) { |
---|
[248] | 489 | MaskedArray<Float> tmp = mLeft * *pMRight; |
---|
[234] | 490 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 491 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr); |
---|
[234] | 492 | } else if (what==3) { |
---|
[248] | 493 | MaskedArray<Float> tmp = mLeft / *pMRight; |
---|
[234] | 494 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
[294] | 495 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr); |
---|
[248] | 496 | } else if (what==4) { |
---|
| 497 | if (preserve) { |
---|
| 498 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysRightArr; |
---|
| 499 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 500 | } else { |
---|
| 501 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysLeftArr; |
---|
| 502 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
---|
| 503 | } |
---|
| 504 | sc.putTsys(tSysRightArr); |
---|
[234] | 505 | } |
---|
| 506 | |
---|
| 507 | // Put new row in output Table |
---|
| 508 | |
---|
[171] | 509 | pTabOut->putSDContainer(sc); |
---|
[130] | 510 | } |
---|
[248] | 511 | if (pMRight) delete pMRight; |
---|
[304] | 512 | pTabOut->resetCursor(); |
---|
[130] | 513 | // |
---|
[171] | 514 | return CountedPtr<SDMemTable>(pTabOut); |
---|
[9] | 515 | } |
---|
[48] | 516 | |
---|
[146] | 517 | |
---|
| 518 | |
---|
[185] | 519 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in, |
---|
[234] | 520 | const Vector<Bool>& mask, |
---|
| 521 | const String& which, Int row) const |
---|
[130] | 522 | // |
---|
| 523 | // Perhaps iteration over pol/beam/if should be in here |
---|
| 524 | // and inside the nrow iteration ? |
---|
| 525 | // |
---|
| 526 | { |
---|
| 527 | const uInt nRow = in->nRow(); |
---|
| 528 | |
---|
| 529 | // Specify cursor location |
---|
| 530 | |
---|
[152] | 531 | IPosition start, end; |
---|
[185] | 532 | getCursorLocation(start, end, *in); |
---|
[130] | 533 | |
---|
| 534 | // Loop over rows |
---|
| 535 | |
---|
[234] | 536 | const uInt nEl = mask.nelements(); |
---|
| 537 | uInt iStart = 0; |
---|
| 538 | uInt iEnd = in->nRow()-1; |
---|
| 539 | // |
---|
| 540 | if (row>=0) { |
---|
| 541 | iStart = row; |
---|
| 542 | iEnd = row; |
---|
| 543 | } |
---|
| 544 | // |
---|
| 545 | std::vector<float> result(iEnd-iStart+1); |
---|
| 546 | for (uInt ii=iStart; ii <= iEnd; ++ii) { |
---|
[130] | 547 | |
---|
| 548 | // Get row and deconstruct |
---|
| 549 | |
---|
| 550 | MaskedArray<Float> marr(in->rowAsMaskedArray(ii)); |
---|
| 551 | Array<Float> arr = marr.getArray(); |
---|
| 552 | Array<Bool> barr = marr.getMask(); |
---|
| 553 | |
---|
| 554 | // Access desired piece of data |
---|
| 555 | |
---|
| 556 | Array<Float> v((arr(start,end)).nonDegenerate()); |
---|
| 557 | Array<Bool> m((barr(start,end)).nonDegenerate()); |
---|
| 558 | |
---|
| 559 | // Apply OTF mask |
---|
| 560 | |
---|
| 561 | MaskedArray<Float> tmp; |
---|
| 562 | if (m.nelements()==nEl) { |
---|
[234] | 563 | tmp.setData(v,m&&mask); |
---|
[130] | 564 | } else { |
---|
| 565 | tmp.setData(v,m); |
---|
| 566 | } |
---|
| 567 | |
---|
| 568 | // Get statistic |
---|
| 569 | |
---|
[234] | 570 | result[ii-iStart] = mathutil::statistics(which, tmp); |
---|
[130] | 571 | } |
---|
| 572 | // |
---|
| 573 | return result; |
---|
| 574 | } |
---|
| 575 | |
---|
[146] | 576 | |
---|
[234] | 577 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const |
---|
[144] | 578 | { |
---|
[169] | 579 | SDHeader sh = in.getSDHeader(); |
---|
| 580 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[163] | 581 | |
---|
[169] | 582 | // Bin up SpectralCoordinates |
---|
[163] | 583 | |
---|
[169] | 584 | IPosition factors(1); |
---|
| 585 | factors(0) = width; |
---|
| 586 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 587 | CoordinateSystem cSys; |
---|
[288] | 588 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
[169] | 589 | CoordinateSystem cSysBin = |
---|
[185] | 590 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False); |
---|
[169] | 591 | // |
---|
| 592 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
---|
| 593 | pTabOut->setCoordinate(sCBin, j); |
---|
| 594 | } |
---|
[163] | 595 | |
---|
[169] | 596 | // Use RebinLattice to find shape |
---|
[130] | 597 | |
---|
[169] | 598 | IPosition shapeIn(1,sh.nchan); |
---|
[185] | 599 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors); |
---|
[169] | 600 | sh.nchan = shapeOut(0); |
---|
| 601 | pTabOut->putSDHeader(sh); |
---|
[144] | 602 | |
---|
[169] | 603 | // Loop over rows and bin along channel axis |
---|
| 604 | |
---|
| 605 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 606 | SDContainer sc = in.getSDContainer(i); |
---|
[144] | 607 | // |
---|
[169] | 608 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
---|
[144] | 609 | |
---|
[169] | 610 | // Bin up spectrum |
---|
[144] | 611 | |
---|
[169] | 612 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
---|
| 613 | MaskedArray<Float> marrout; |
---|
[221] | 614 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width); |
---|
[144] | 615 | |
---|
[169] | 616 | // Put back the binned data and flags |
---|
[144] | 617 | |
---|
[169] | 618 | IPosition ip2 = marrout.shape(); |
---|
| 619 | sc.resize(ip2); |
---|
[146] | 620 | // |
---|
[185] | 621 | putDataInSDC(sc, marrout.getArray(), marrout.getMask()); |
---|
[146] | 622 | |
---|
[169] | 623 | // Bin up Tsys. |
---|
[146] | 624 | |
---|
[169] | 625 | Array<Bool> allGood(tSys.shape(),True); |
---|
| 626 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
---|
[146] | 627 | // |
---|
[169] | 628 | MaskedArray<Float> tSysOut; |
---|
[221] | 629 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width); |
---|
[169] | 630 | sc.putTsys(tSysOut.getArray()); |
---|
[146] | 631 | // |
---|
[169] | 632 | pTabOut->putSDContainer(sc); |
---|
| 633 | } |
---|
| 634 | return pTabOut; |
---|
[146] | 635 | } |
---|
| 636 | |
---|
[299] | 637 | SDMemTable* SDMath::resample (const SDMemTable& in, const String& methodStr, |
---|
| 638 | Float width) const |
---|
| 639 | // |
---|
| 640 | // Should add the possibility of width being specified in km/s. This means |
---|
| 641 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
| 642 | // average channel width (say at the reference pixel). Then we would need |
---|
| 643 | // to be careful to make sure each spectrum (of different freqID) |
---|
| 644 | // is the same length. |
---|
| 645 | // |
---|
| 646 | { |
---|
| 647 | Bool doVel = False; |
---|
| 648 | |
---|
| 649 | // Interpolation method |
---|
| 650 | |
---|
| 651 | Int interpMethod = 0; |
---|
| 652 | convertInterpString(interpMethod, methodStr); |
---|
| 653 | |
---|
| 654 | // Make output table |
---|
| 655 | |
---|
| 656 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 657 | |
---|
| 658 | // Resample SpectralCoordinates (one per freqID) |
---|
| 659 | |
---|
| 660 | const uInt nCoord = in.nCoordinates(); |
---|
| 661 | Vector<Float> offset(1,0.0); |
---|
| 662 | Vector<Float> factors(1,1.0/width); |
---|
| 663 | Vector<Int> newShape; |
---|
| 664 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
| 665 | CoordinateSystem cSys; |
---|
| 666 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
| 667 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape); |
---|
| 668 | SpectralCoordinate sC = cSys2.spectralCoordinate(0); |
---|
| 669 | // |
---|
| 670 | pTabOut->setCoordinate(sC, j); |
---|
| 671 | } |
---|
| 672 | |
---|
| 673 | // Get header |
---|
| 674 | |
---|
| 675 | SDHeader sh = in.getSDHeader(); |
---|
| 676 | |
---|
| 677 | // Generate resampling vectors |
---|
| 678 | |
---|
| 679 | const uInt nChanIn = sh.nchan; |
---|
| 680 | Vector<Float> xIn(nChanIn); |
---|
| 681 | indgen(xIn); |
---|
| 682 | // |
---|
| 683 | Int fac = Int(nChanIn/width); |
---|
| 684 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
| 685 | uInt i = 0; |
---|
| 686 | Float x = 0.0; |
---|
| 687 | Bool more = True; |
---|
| 688 | while (more) { |
---|
| 689 | xOut(i) = x; |
---|
| 690 | // |
---|
| 691 | i++; |
---|
| 692 | x += width; |
---|
| 693 | if (x>nChanIn-1) more = False; |
---|
| 694 | } |
---|
| 695 | const uInt nChanOut = i; |
---|
| 696 | xOut.resize(nChanOut,True); |
---|
| 697 | // |
---|
| 698 | IPosition shapeIn(in.rowAsMaskedArray(0).shape()); |
---|
| 699 | sh.nchan = nChanOut; |
---|
| 700 | pTabOut->putSDHeader(sh); |
---|
| 701 | |
---|
| 702 | // Loop over rows and resample along channel axis |
---|
| 703 | |
---|
| 704 | Array<Float> valuesOut; |
---|
| 705 | Array<Bool> maskOut; |
---|
| 706 | Array<Float> tSysOut; |
---|
| 707 | Array<Bool> tSysMaskIn(shapeIn,True); |
---|
| 708 | Array<Bool> tSysMaskOut; |
---|
| 709 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 710 | |
---|
| 711 | // Get container |
---|
| 712 | |
---|
| 713 | SDContainer sc = in.getSDContainer(i); |
---|
| 714 | |
---|
| 715 | // Get data and Tsys |
---|
| 716 | |
---|
| 717 | const Array<Float>& tSysIn = sc.getTsys(); |
---|
| 718 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i)); |
---|
| 719 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 720 | Array<Bool> maskIn = dataIn.getMask(); |
---|
| 721 | |
---|
| 722 | // Interpolate data |
---|
| 723 | |
---|
| 724 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut, |
---|
| 725 | xIn, valuesIn, maskIn, |
---|
| 726 | interpMethod, True, True); |
---|
| 727 | sc.resize(valuesOut.shape()); |
---|
| 728 | putDataInSDC(sc, valuesOut, maskOut); |
---|
| 729 | |
---|
| 730 | // Interpolate TSys |
---|
| 731 | |
---|
| 732 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut, |
---|
| 733 | xIn, tSysIn, tSysMaskIn, |
---|
| 734 | interpMethod, True, True); |
---|
| 735 | sc.putTsys(tSysOut); |
---|
| 736 | |
---|
| 737 | // Put container in output |
---|
| 738 | |
---|
| 739 | pTabOut->putSDContainer(sc); |
---|
| 740 | } |
---|
| 741 | // |
---|
| 742 | return pTabOut; |
---|
| 743 | } |
---|
| 744 | |
---|
[248] | 745 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll, |
---|
[294] | 746 | uInt what, Bool doTSys) const |
---|
[152] | 747 | // |
---|
| 748 | // what = 0 Multiply |
---|
| 749 | // 1 Add |
---|
[146] | 750 | { |
---|
[152] | 751 | SDMemTable* pOut = new SDMemTable(in,False); |
---|
| 752 | const Table& tOut = pOut->table(); |
---|
[294] | 753 | ArrayColumn<Float> specCol(tOut,"SPECTRA"); |
---|
| 754 | ArrayColumn<Float> tSysCol(tOut,"TSYS"); |
---|
| 755 | Array<Float> tSysArr; |
---|
[146] | 756 | // |
---|
[152] | 757 | if (doAll) { |
---|
| 758 | for (uInt i=0; i < tOut.nrow(); i++) { |
---|
[294] | 759 | |
---|
| 760 | // Modify data |
---|
| 761 | |
---|
[270] | 762 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
[152] | 763 | if (what==0) { |
---|
[270] | 764 | dataIn *= val; |
---|
[152] | 765 | } else if (what==1) { |
---|
[270] | 766 | dataIn += val; |
---|
[152] | 767 | } |
---|
[294] | 768 | specCol.put(i, dataIn.getArray()); |
---|
| 769 | |
---|
| 770 | // Modify Tsys |
---|
| 771 | |
---|
| 772 | if (doTSys) { |
---|
| 773 | tSysCol.get(i, tSysArr); |
---|
| 774 | if (what==0) { |
---|
| 775 | tSysArr *= val; |
---|
| 776 | } else if (what==1) { |
---|
| 777 | tSysArr += val; |
---|
| 778 | } |
---|
| 779 | tSysCol.put(i, tSysArr); |
---|
| 780 | } |
---|
[152] | 781 | } |
---|
| 782 | } else { |
---|
| 783 | |
---|
| 784 | // Get cursor location |
---|
| 785 | |
---|
| 786 | IPosition start, end; |
---|
[185] | 787 | getCursorLocation(start, end, in); |
---|
[152] | 788 | // |
---|
| 789 | for (uInt i=0; i < tOut.nrow(); i++) { |
---|
[294] | 790 | |
---|
| 791 | // Modify data |
---|
| 792 | |
---|
[152] | 793 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
[270] | 794 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference |
---|
[152] | 795 | if (what==0) { |
---|
[270] | 796 | dataIn2 *= val; |
---|
[152] | 797 | } else if (what==1) { |
---|
[270] | 798 | dataIn2 += val; |
---|
[152] | 799 | } |
---|
[294] | 800 | specCol.put(i, dataIn.getArray()); |
---|
| 801 | |
---|
| 802 | // Modify Tsys |
---|
| 803 | |
---|
| 804 | if (doTSys) { |
---|
| 805 | tSysCol.get(i, tSysArr); |
---|
| 806 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference |
---|
| 807 | if (what==0) { |
---|
| 808 | tSysArr2 *= val; |
---|
| 809 | } else if (what==1) { |
---|
| 810 | tSysArr2 += val; |
---|
| 811 | } |
---|
| 812 | tSysCol.put(i, tSysArr); |
---|
| 813 | } |
---|
[152] | 814 | } |
---|
| 815 | } |
---|
| 816 | // |
---|
[146] | 817 | return pOut; |
---|
| 818 | } |
---|
| 819 | |
---|
| 820 | |
---|
[152] | 821 | |
---|
[234] | 822 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask) const |
---|
[152] | 823 | // |
---|
[165] | 824 | // Average all polarizations together, weighted by variance |
---|
| 825 | // |
---|
| 826 | { |
---|
| 827 | // WeightType wtType = NONE; |
---|
[185] | 828 | // convertWeightString(wtType, weight); |
---|
[165] | 829 | |
---|
| 830 | const uInt nRows = in.nRow(); |
---|
| 831 | |
---|
| 832 | // Create output Table and reshape number of polarizations |
---|
| 833 | |
---|
| 834 | Bool clear=True; |
---|
| 835 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
| 836 | SDHeader header = pTabOut->getSDHeader(); |
---|
| 837 | header.npol = 1; |
---|
| 838 | pTabOut->putSDHeader(header); |
---|
| 839 | |
---|
| 840 | // Shape of input and output data |
---|
| 841 | |
---|
| 842 | const IPosition& shapeIn = in.rowAsMaskedArray(0u, False).shape(); |
---|
| 843 | IPosition shapeOut(shapeIn); |
---|
[262] | 844 | shapeOut(asap::PolAxis) = 1; // Average all polarizations |
---|
[165] | 845 | // |
---|
[262] | 846 | const uInt nChan = shapeIn(asap::ChanAxis); |
---|
[165] | 847 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape |
---|
| 848 | IPosition start(4), end(4); |
---|
| 849 | |
---|
| 850 | // Output arrays |
---|
| 851 | |
---|
| 852 | Array<Float> outData(shapeOut, 0.0); |
---|
| 853 | Array<Bool> outMask(shapeOut, True); |
---|
[262] | 854 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane |
---|
[165] | 855 | // |
---|
[262] | 856 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis)); |
---|
[165] | 857 | |
---|
| 858 | // Loop over rows |
---|
| 859 | |
---|
| 860 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
| 861 | |
---|
| 862 | // Get data for this row |
---|
| 863 | |
---|
| 864 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
| 865 | Array<Float>& arr = marr.getRWArray(); |
---|
| 866 | const Array<Bool>& barr = marr.getMask(); |
---|
| 867 | |
---|
| 868 | // Make iterators to iterate by pol-channel planes |
---|
| 869 | |
---|
| 870 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
---|
| 871 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes); |
---|
| 872 | |
---|
| 873 | // Accumulations |
---|
| 874 | |
---|
| 875 | Float fac = 1.0; |
---|
| 876 | Vector<Float> vecSum(nChan,0.0); |
---|
| 877 | |
---|
| 878 | // Iterate through data by pol-channel planes |
---|
| 879 | |
---|
| 880 | while (!itDataPlane.pastEnd()) { |
---|
| 881 | |
---|
| 882 | // Iterate through plane by polarization and accumulate Vectors |
---|
| 883 | |
---|
| 884 | Vector<Float> t1(nChan); t1 = 0.0; |
---|
| 885 | Vector<Bool> t2(nChan); t2 = True; |
---|
| 886 | MaskedArray<Float> vecSum(t1,t2); |
---|
| 887 | Float varSum = 0.0; |
---|
| 888 | { |
---|
| 889 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
---|
| 890 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
| 891 | while (!itDataVec.pastEnd()) { |
---|
| 892 | |
---|
| 893 | // Create MA of data & mask (optionally including OTF mask) and get variance |
---|
| 894 | |
---|
| 895 | if (useMask) { |
---|
| 896 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector()); |
---|
| 897 | fac = 1.0 / variance(spec); |
---|
| 898 | } else { |
---|
| 899 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector()); |
---|
| 900 | fac = 1.0 / variance(spec); |
---|
| 901 | } |
---|
| 902 | |
---|
| 903 | // Normalize spectrum (without OTF mask) and accumulate |
---|
| 904 | |
---|
| 905 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector()); |
---|
| 906 | vecSum += spec; |
---|
| 907 | varSum += fac; |
---|
| 908 | |
---|
| 909 | // Next |
---|
| 910 | |
---|
| 911 | itDataVec.next(); |
---|
| 912 | itMaskVec.next(); |
---|
| 913 | } |
---|
| 914 | } |
---|
| 915 | |
---|
| 916 | // Normalize summed spectrum |
---|
| 917 | |
---|
| 918 | vecSum /= varSum; |
---|
| 919 | |
---|
| 920 | // FInd position in input data array. We are iterating by pol-channel |
---|
| 921 | // plane so all that will change is beam and IF and that's what we want. |
---|
| 922 | |
---|
| 923 | IPosition pos = itDataPlane.pos(); |
---|
| 924 | |
---|
| 925 | // Write out data. This is a bit messy. We have to reform the Vector |
---|
| 926 | // accumulator into an Array of shape (1,1,1,nChan) |
---|
| 927 | |
---|
| 928 | start = pos; |
---|
| 929 | end = pos; |
---|
[262] | 930 | end(asap::ChanAxis) = nChan-1; |
---|
[165] | 931 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
---|
| 932 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
---|
| 933 | |
---|
| 934 | // Step to next beam/IF combination |
---|
| 935 | |
---|
| 936 | itDataPlane.next(); |
---|
| 937 | itMaskPlane.next(); |
---|
| 938 | } |
---|
| 939 | |
---|
| 940 | // Generate output container and write it to output table |
---|
| 941 | |
---|
| 942 | SDContainer sc = in.getSDContainer(); |
---|
| 943 | sc.resize(shapeOut); |
---|
| 944 | // |
---|
[185] | 945 | putDataInSDC(sc, outData, outMask); |
---|
[165] | 946 | pTabOut->putSDContainer(sc); |
---|
| 947 | } |
---|
[304] | 948 | |
---|
| 949 | // Set polarization cursor to 0 |
---|
| 950 | |
---|
| 951 | pTabOut->setPol(0); |
---|
[165] | 952 | // |
---|
| 953 | return pTabOut; |
---|
| 954 | } |
---|
[167] | 955 | |
---|
[169] | 956 | |
---|
[185] | 957 | SDMemTable* SDMath::smooth(const SDMemTable& in, |
---|
| 958 | const casa::String& kernelType, |
---|
[234] | 959 | casa::Float width, Bool doAll) const |
---|
[299] | 960 | // |
---|
| 961 | // Should smooth TSys as well |
---|
| 962 | // |
---|
[177] | 963 | { |
---|
[169] | 964 | |
---|
[177] | 965 | // Number of channels |
---|
[169] | 966 | |
---|
[177] | 967 | SDHeader sh = in.getSDHeader(); |
---|
| 968 | const uInt nChan = sh.nchan; |
---|
| 969 | |
---|
| 970 | // Generate Kernel |
---|
| 971 | |
---|
[185] | 972 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType); |
---|
[177] | 973 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
| 974 | |
---|
| 975 | // Generate Convolver |
---|
| 976 | |
---|
| 977 | IPosition shape(1,nChan); |
---|
| 978 | Convolver<Float> conv(kernel, shape); |
---|
| 979 | |
---|
| 980 | // New Table |
---|
| 981 | |
---|
| 982 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
| 983 | |
---|
| 984 | // Get cursor location |
---|
| 985 | |
---|
| 986 | IPosition start, end; |
---|
[185] | 987 | getCursorLocation(start, end, in); |
---|
[177] | 988 | // |
---|
| 989 | IPosition shapeOut(4,1); |
---|
| 990 | |
---|
| 991 | // Output Vectors |
---|
| 992 | |
---|
| 993 | Vector<Float> valuesOut(nChan); |
---|
| 994 | Vector<Bool> maskOut(nChan); |
---|
| 995 | |
---|
| 996 | // Loop over rows in Table |
---|
| 997 | |
---|
| 998 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
| 999 | |
---|
| 1000 | // Get copy of data |
---|
| 1001 | |
---|
| 1002 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(ri)); |
---|
[262] | 1003 | AlwaysAssert(dataIn.shape()(asap::ChanAxis)==nChan, AipsError); |
---|
[177] | 1004 | // |
---|
| 1005 | Array<Float> valuesIn = dataIn.getArray(); |
---|
| 1006 | Array<Bool> maskIn = dataIn.getMask(); |
---|
| 1007 | |
---|
| 1008 | // Branch depending on whether we smooth all locations or just |
---|
| 1009 | // those pointed at by the current selection cursor |
---|
| 1010 | |
---|
| 1011 | if (doAll) { |
---|
[299] | 1012 | VectorIterator<Float> itValues(valuesIn, asap::ChanAxis); |
---|
| 1013 | VectorIterator<Bool> itMask(maskIn, asap::ChanAxis); |
---|
[177] | 1014 | while (!itValues.pastEnd()) { |
---|
| 1015 | |
---|
| 1016 | // Smooth |
---|
| 1017 | if (kernelType==VectorKernel::HANNING) { |
---|
| 1018 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector()); |
---|
| 1019 | itMask.vector() = maskOut; |
---|
| 1020 | } else { |
---|
| 1021 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
| 1022 | conv.linearConv(valuesOut, itValues.vector()); |
---|
| 1023 | } |
---|
| 1024 | // |
---|
| 1025 | itValues.vector() = valuesOut; |
---|
| 1026 | // |
---|
| 1027 | itValues.next(); |
---|
| 1028 | itMask.next(); |
---|
| 1029 | } |
---|
| 1030 | } else { |
---|
| 1031 | |
---|
| 1032 | // Set multi-dim Vector shape |
---|
| 1033 | |
---|
[299] | 1034 | shapeOut(asap::ChanAxis) = valuesIn.shape()(asap::ChanAxis); |
---|
[177] | 1035 | |
---|
| 1036 | // Stuff about with shapes so that we don't have conformance run-time errors |
---|
| 1037 | |
---|
| 1038 | Vector<Float> valuesIn2 = valuesIn(start,end).nonDegenerate(); |
---|
| 1039 | Vector<Bool> maskIn2 = maskIn(start,end).nonDegenerate(); |
---|
| 1040 | |
---|
| 1041 | // Smooth |
---|
| 1042 | |
---|
| 1043 | if (kernelType==VectorKernel::HANNING) { |
---|
| 1044 | mathutil::hanning(valuesOut, maskOut, valuesIn2, maskIn2); |
---|
| 1045 | maskIn(start,end) = maskOut.reform(shapeOut); |
---|
| 1046 | } else { |
---|
| 1047 | mathutil::replaceMaskByZero(valuesIn2, maskIn2); |
---|
| 1048 | conv.linearConv(valuesOut, valuesIn2); |
---|
| 1049 | } |
---|
| 1050 | // |
---|
| 1051 | valuesIn(start,end) = valuesOut.reform(shapeOut); |
---|
| 1052 | } |
---|
| 1053 | |
---|
| 1054 | // Create and put back |
---|
| 1055 | |
---|
| 1056 | SDContainer sc = in.getSDContainer(ri); |
---|
[185] | 1057 | putDataInSDC(sc, valuesIn, maskIn); |
---|
[177] | 1058 | // |
---|
| 1059 | pTabOut->putSDContainer(sc); |
---|
| 1060 | } |
---|
| 1061 | // |
---|
| 1062 | return pTabOut; |
---|
| 1063 | } |
---|
| 1064 | |
---|
| 1065 | |
---|
[262] | 1066 | |
---|
[234] | 1067 | SDMemTable* SDMath::convertFlux (const SDMemTable& in, Float a, Float eta, Bool doAll) const |
---|
[221] | 1068 | // |
---|
| 1069 | // As it is, this function could be implemented with 'simpleOperate' |
---|
| 1070 | // However, I anticipate that eventually we will look the conversion |
---|
| 1071 | // values up in a Table and apply them in a frequency dependent way, |
---|
| 1072 | // so I have implemented it fully here |
---|
| 1073 | // |
---|
| 1074 | { |
---|
| 1075 | SDHeader sh = in.getSDHeader(); |
---|
| 1076 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
[177] | 1077 | |
---|
[221] | 1078 | // FInd out how to convert values into Jy and K (e.g. units might be mJy or mK) |
---|
| 1079 | // Also automatically find out what we are converting to according to the |
---|
| 1080 | // flux unit |
---|
[177] | 1081 | |
---|
[221] | 1082 | Unit fluxUnit(sh.fluxunit); |
---|
| 1083 | Unit K(String("K")); |
---|
| 1084 | Unit JY(String("Jy")); |
---|
| 1085 | // |
---|
| 1086 | Bool toKelvin = True; |
---|
| 1087 | Double inFac = 1.0; |
---|
| 1088 | if (fluxUnit==JY) { |
---|
| 1089 | cerr << "Converting to K" << endl; |
---|
| 1090 | // |
---|
| 1091 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1092 | Quantum<Double> t2 = t.get(JY); |
---|
| 1093 | inFac = (t2 / t).getValue(); |
---|
| 1094 | // |
---|
| 1095 | toKelvin = True; |
---|
| 1096 | sh.fluxunit = "K"; |
---|
| 1097 | } else if (fluxUnit==K) { |
---|
| 1098 | cerr << "Converting to Jy" << endl; |
---|
| 1099 | // |
---|
| 1100 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 1101 | Quantum<Double> t2 = t.get(K); |
---|
| 1102 | inFac = (t2 / t).getValue(); |
---|
| 1103 | // |
---|
| 1104 | toKelvin = False; |
---|
| 1105 | sh.fluxunit = "Jy"; |
---|
| 1106 | } else { |
---|
[248] | 1107 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 1108 | } |
---|
| 1109 | pTabOut->putSDHeader(sh); |
---|
[177] | 1110 | |
---|
[221] | 1111 | // Compute conversion factor. 'a' and 'eta' are really frequency, time and |
---|
| 1112 | // telescope dependent and should be looked// up in a table |
---|
| 1113 | |
---|
[234] | 1114 | Float factor = 2.0 * inFac * 1.0e-7 * 1.0e26 * |
---|
| 1115 | QC::k.getValue(Unit(String("erg/K"))) / a / eta; |
---|
[221] | 1116 | if (toKelvin) { |
---|
| 1117 | factor = 1.0 / factor; |
---|
| 1118 | } |
---|
| 1119 | cerr << "Applying conversion factor = " << factor << endl; |
---|
| 1120 | |
---|
[270] | 1121 | // Generate correction vector. Apply same factor regardless |
---|
| 1122 | // of beam/pol/IF. This will need to change somewhen. |
---|
[221] | 1123 | |
---|
[270] | 1124 | Vector<Float> factors(in.nRow(), factor); |
---|
[221] | 1125 | |
---|
[270] | 1126 | // Correct |
---|
[221] | 1127 | |
---|
[270] | 1128 | correctFromVector (pTabOut, in, doAll, factors); |
---|
[221] | 1129 | // |
---|
| 1130 | return pTabOut; |
---|
| 1131 | } |
---|
| 1132 | |
---|
| 1133 | |
---|
[234] | 1134 | SDMemTable* SDMath::gainElevation (const SDMemTable& in, const Vector<Float>& coeffs, |
---|
| 1135 | const String& fileName, |
---|
| 1136 | const String& methodStr, Bool doAll) const |
---|
[227] | 1137 | { |
---|
[234] | 1138 | |
---|
| 1139 | // Get header and clone output table |
---|
| 1140 | |
---|
[227] | 1141 | SDHeader sh = in.getSDHeader(); |
---|
| 1142 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1143 | |
---|
[234] | 1144 | // Get elevation data from SDMemTable and convert to degrees |
---|
[227] | 1145 | |
---|
| 1146 | const Table& tab = in.table(); |
---|
| 1147 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[234] | 1148 | Vector<Float> x = elev.getColumn(); |
---|
| 1149 | x *= Float(180 / C::pi); |
---|
[227] | 1150 | // |
---|
[234] | 1151 | const uInt nC = coeffs.nelements(); |
---|
| 1152 | if (fileName.length()>0 && nC>0) { |
---|
[248] | 1153 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
[234] | 1154 | } |
---|
| 1155 | |
---|
| 1156 | // Correct |
---|
| 1157 | |
---|
| 1158 | if (nC>0 || fileName.length()==0) { |
---|
| 1159 | |
---|
| 1160 | // Find instrument |
---|
| 1161 | |
---|
| 1162 | Bool throwIt = True; |
---|
| 1163 | Instrument inst = SDMemTable::convertInstrument (sh.antennaname, throwIt); |
---|
| 1164 | |
---|
| 1165 | // Set polynomial |
---|
| 1166 | |
---|
| 1167 | Polynomial<Float>* pPoly = 0; |
---|
| 1168 | Vector<Float> coeff; |
---|
| 1169 | String msg; |
---|
| 1170 | if (nC>0) { |
---|
| 1171 | pPoly = new Polynomial<Float>(nC); |
---|
| 1172 | coeff = coeffs; |
---|
| 1173 | msg = String("user"); |
---|
| 1174 | } else { |
---|
[292] | 1175 | if (inst==ATPKSMB) { |
---|
| 1176 | } else if (inst==ATPKSHOH) { |
---|
[234] | 1177 | } else if (inst==TIDBINBILLA) { |
---|
| 1178 | pPoly = new Polynomial<Float>(3); |
---|
| 1179 | coeff.resize(3); |
---|
| 1180 | coeff(0) = 3.58788e-1; |
---|
| 1181 | coeff(1) = 2.87243e-2; |
---|
| 1182 | coeff(2) = -3.219093e-4; |
---|
[292] | 1183 | } else if (inst==ATMOPRA) { |
---|
| 1184 | } else { |
---|
[234] | 1185 | } |
---|
| 1186 | msg = String("built in"); |
---|
| 1187 | } |
---|
[227] | 1188 | // |
---|
[234] | 1189 | if (coeff.nelements()>0) { |
---|
| 1190 | pPoly->setCoefficients(coeff); |
---|
| 1191 | } else { |
---|
[248] | 1192 | throw(AipsError("There is no known gain-el polynomial known for this instrument")); |
---|
[234] | 1193 | } |
---|
| 1194 | // |
---|
| 1195 | cerr << "Making polynomial correction with " << msg << " coefficients" << endl; |
---|
| 1196 | const uInt nRow = in.nRow(); |
---|
| 1197 | Vector<Float> factor(nRow); |
---|
| 1198 | for (uInt i=0; i<nRow; i++) { |
---|
| 1199 | factor[i] = (*pPoly)(x[i]); |
---|
| 1200 | } |
---|
| 1201 | delete pPoly; |
---|
| 1202 | // |
---|
| 1203 | correctFromVector (pTabOut, in, doAll, factor); |
---|
| 1204 | } else { |
---|
| 1205 | |
---|
| 1206 | // Indicate which columns to read from ascii file |
---|
| 1207 | |
---|
| 1208 | String col0("ELEVATION"); |
---|
| 1209 | String col1("FACTOR"); |
---|
| 1210 | |
---|
| 1211 | // Read and correct |
---|
| 1212 | |
---|
| 1213 | cerr << "Making correction from ascii Table" << endl; |
---|
| 1214 | correctFromAsciiTable (pTabOut, in, fileName, col0, col1, |
---|
| 1215 | methodStr, doAll, x); |
---|
| 1216 | } |
---|
| 1217 | // |
---|
| 1218 | return pTabOut; |
---|
[230] | 1219 | } |
---|
[227] | 1220 | |
---|
[230] | 1221 | |
---|
[227] | 1222 | |
---|
[234] | 1223 | SDMemTable* SDMath::opacity (const SDMemTable& in, Float tau, Bool doAll) const |
---|
| 1224 | { |
---|
[227] | 1225 | |
---|
[234] | 1226 | // Get header and clone output table |
---|
[227] | 1227 | |
---|
[234] | 1228 | SDHeader sh = in.getSDHeader(); |
---|
| 1229 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
| 1230 | |
---|
| 1231 | // Get elevation data from SDMemTable and convert to degrees |
---|
| 1232 | |
---|
| 1233 | const Table& tab = in.table(); |
---|
| 1234 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 1235 | Vector<Float> zDist = elev.getColumn(); |
---|
| 1236 | zDist = Float(C::pi_2) - zDist; |
---|
| 1237 | |
---|
| 1238 | // Generate correction factor |
---|
| 1239 | |
---|
| 1240 | const uInt nRow = in.nRow(); |
---|
| 1241 | Vector<Float> factor(nRow); |
---|
| 1242 | Vector<Float> factor2(nRow); |
---|
| 1243 | for (uInt i=0; i<nRow; i++) { |
---|
| 1244 | factor[i] = exp(tau)/cos(zDist[i]); |
---|
| 1245 | } |
---|
| 1246 | |
---|
| 1247 | // Correct |
---|
| 1248 | |
---|
| 1249 | correctFromVector (pTabOut, in, doAll, factor); |
---|
| 1250 | // |
---|
| 1251 | return pTabOut; |
---|
| 1252 | } |
---|
| 1253 | |
---|
| 1254 | |
---|
| 1255 | |
---|
| 1256 | |
---|
[169] | 1257 | // 'private' functions |
---|
| 1258 | |
---|
[267] | 1259 | SDMemTable* SDMath::velocityAlign (const SDMemTable& in, |
---|
| 1260 | MFrequency::Types velSystem, |
---|
| 1261 | const String& velUnit, |
---|
[272] | 1262 | MDoppler::Types doppler, |
---|
| 1263 | const String& refTime) const |
---|
[267] | 1264 | { |
---|
| 1265 | // Get Header |
---|
| 1266 | |
---|
| 1267 | SDHeader sh = in.getSDHeader(); |
---|
| 1268 | const uInt nChan = sh.nchan; |
---|
| 1269 | const uInt nRows = in.nRow(); |
---|
| 1270 | |
---|
| 1271 | // Get Table reference |
---|
| 1272 | |
---|
| 1273 | const Table& tabIn = in.table(); |
---|
| 1274 | |
---|
| 1275 | // Get Columns from Table |
---|
| 1276 | |
---|
[294] | 1277 | ROScalarColumn<Double> mjdCol(tabIn, "TIME"); |
---|
| 1278 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME"); |
---|
| 1279 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID"); |
---|
[267] | 1280 | // |
---|
[294] | 1281 | Vector<Double> times = mjdCol.getColumn(); |
---|
| 1282 | Vector<String> srcNames = srcCol.getColumn(); |
---|
| 1283 | Vector<uInt> freqID; |
---|
[267] | 1284 | |
---|
| 1285 | // Generate Source table |
---|
| 1286 | |
---|
| 1287 | Vector<String> srcTab; |
---|
| 1288 | Vector<uInt> srcIdx, firstRow; |
---|
| 1289 | generateSourceTable (srcTab, srcIdx, firstRow, srcNames); |
---|
| 1290 | const uInt nSrcTab = srcTab.nelements(); |
---|
| 1291 | cerr << "Found " << srcTab.nelements() << " sources to align " << endl; |
---|
| 1292 | |
---|
[294] | 1293 | // Get reference Epoch to time of first row or given String |
---|
[267] | 1294 | |
---|
| 1295 | Unit DAY(String("d")); |
---|
[272] | 1296 | MEpoch::Ref epochRef(in.getTimeReference()); |
---|
| 1297 | MEpoch refEpoch; |
---|
| 1298 | if (refTime.length()>0) { |
---|
| 1299 | refEpoch = epochFromString(refTime, in.getTimeReference()); |
---|
| 1300 | } else { |
---|
[288] | 1301 | refEpoch = in.getEpoch(0); |
---|
[272] | 1302 | } |
---|
| 1303 | cerr << "Aligning at reference Epoch " << formatEpoch(refEpoch) << endl; |
---|
[267] | 1304 | |
---|
[294] | 1305 | // Get Reference Position |
---|
[267] | 1306 | |
---|
[288] | 1307 | MPosition refPos = in.getAntennaPosition(); |
---|
[267] | 1308 | |
---|
| 1309 | // Get Frequency Table |
---|
| 1310 | |
---|
| 1311 | SDFrequencyTable fTab = in.getSDFreqTable(); |
---|
| 1312 | const uInt nFreqIDs = fTab.length(); |
---|
| 1313 | |
---|
| 1314 | // Create VelocityAligner Block. One VA for each possible |
---|
| 1315 | // source/freqID combination |
---|
| 1316 | |
---|
| 1317 | PtrBlock<VelocityAligner<Float>* > vA(nFreqIDs*nSrcTab); |
---|
[294] | 1318 | generateVelocityAligners (vA, in, nChan, nFreqIDs, nSrcTab, firstRow, |
---|
| 1319 | velSystem, velUnit, doppler, refPos, refEpoch); |
---|
[267] | 1320 | |
---|
| 1321 | // New output Table |
---|
| 1322 | |
---|
| 1323 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
| 1324 | |
---|
| 1325 | // Loop over rows in Table |
---|
| 1326 | |
---|
[294] | 1327 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis); |
---|
| 1328 | VelocityAligner<Float>::Method method = VelocityAligner<Float>::LINEAR; |
---|
| 1329 | Bool extrapolate=False; |
---|
| 1330 | Bool useCachedAbcissa = False; |
---|
| 1331 | Bool first = True; |
---|
| 1332 | Bool ok; |
---|
| 1333 | Vector<Float> yOut; |
---|
| 1334 | Vector<Bool> maskOut; |
---|
| 1335 | uInt ifIdx, vaIdx; |
---|
[267] | 1336 | // |
---|
[294] | 1337 | for (uInt iRow=0; iRow<nRows; ++iRow) { |
---|
| 1338 | if (iRow%10==0) { |
---|
| 1339 | cerr << "Processing row " << iRow << endl; |
---|
| 1340 | } |
---|
[267] | 1341 | |
---|
| 1342 | // Get EPoch |
---|
| 1343 | |
---|
[294] | 1344 | Quantum<Double> tQ2(times[iRow],DAY); |
---|
| 1345 | MVEpoch mv2(tQ2); |
---|
| 1346 | MEpoch epoch(mv2, epochRef); |
---|
[267] | 1347 | |
---|
| 1348 | // Get FreqID vector. One freqID per IF |
---|
| 1349 | |
---|
[294] | 1350 | fqIDCol.get(iRow, freqID); |
---|
[267] | 1351 | |
---|
| 1352 | // Get copy of data |
---|
| 1353 | |
---|
[294] | 1354 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow)); |
---|
| 1355 | Array<Float> values = mArrIn.getArray(); |
---|
| 1356 | Array<Bool> mask = mArrIn.getMask(); |
---|
[267] | 1357 | |
---|
| 1358 | // cerr << "values in = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl; |
---|
| 1359 | |
---|
| 1360 | // For each row, the Velocity abcissa will be the same regardless |
---|
| 1361 | // of polarization. For all other axes (IF and BEAM) the abcissa |
---|
| 1362 | // will change. So we iterate through the data by pol-chan planes |
---|
| 1363 | // to mimimize the work. At this point, I think the Direction |
---|
| 1364 | // is stored as the same for each beam. DOn't know where the |
---|
| 1365 | // offsets are or what to do about them right now. For now |
---|
| 1366 | // all beams get same position and velocoity abcissa. |
---|
| 1367 | |
---|
[294] | 1368 | ArrayIterator<Float> itValuesPlane(values, polChanAxes); |
---|
| 1369 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes); |
---|
| 1370 | while (!itValuesPlane.pastEnd()) { |
---|
[267] | 1371 | |
---|
| 1372 | // Find the IF index and then the VA PtrBlock index |
---|
| 1373 | |
---|
[294] | 1374 | const IPosition& pos = itValuesPlane.pos(); |
---|
| 1375 | ifIdx = pos(asap::IFAxis); |
---|
| 1376 | vaIdx = (srcIdx[iRow]*nFreqIDs) + freqID[ifIdx]; |
---|
[267] | 1377 | // |
---|
[294] | 1378 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1); |
---|
| 1379 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
[267] | 1380 | // |
---|
[294] | 1381 | first = True; |
---|
| 1382 | useCachedAbcissa=False; |
---|
| 1383 | while (!itValuesVec.pastEnd()) { |
---|
| 1384 | ok = vA[vaIdx]->align (yOut, maskOut, itValuesVec.vector(), |
---|
| 1385 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
| 1386 | method, extrapolate); |
---|
| 1387 | itValuesVec.vector() = yOut; |
---|
| 1388 | itMaskVec.vector() = maskOut; |
---|
[267] | 1389 | // |
---|
[294] | 1390 | itValuesVec.next(); |
---|
| 1391 | itMaskVec.next(); |
---|
[267] | 1392 | // |
---|
[294] | 1393 | if (first) { |
---|
| 1394 | useCachedAbcissa = True; |
---|
| 1395 | first = False; |
---|
| 1396 | } |
---|
| 1397 | } |
---|
[267] | 1398 | // |
---|
| 1399 | itValuesPlane.next(); |
---|
| 1400 | itMaskPlane.next(); |
---|
[294] | 1401 | } |
---|
[267] | 1402 | |
---|
| 1403 | // cerr << "values out = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl; |
---|
| 1404 | |
---|
| 1405 | // Create and put back |
---|
| 1406 | |
---|
| 1407 | SDContainer sc = in.getSDContainer(iRow); |
---|
| 1408 | putDataInSDC(sc, values, mask); |
---|
| 1409 | // |
---|
| 1410 | pTabOut->putSDContainer(sc); |
---|
[294] | 1411 | } |
---|
[267] | 1412 | |
---|
| 1413 | // Clean up PointerBlock |
---|
| 1414 | |
---|
| 1415 | for (uInt i=0; i<vA.nelements(); i++) delete vA[i]; |
---|
| 1416 | // |
---|
[304] | 1417 | pTabOut->resetCursor(); |
---|
[267] | 1418 | return pTabOut; |
---|
| 1419 | } |
---|
| 1420 | |
---|
| 1421 | |
---|
[185] | 1422 | void SDMath::fillSDC(SDContainer& sc, |
---|
| 1423 | const Array<Bool>& mask, |
---|
| 1424 | const Array<Float>& data, |
---|
| 1425 | const Array<Float>& tSys, |
---|
| 1426 | Int scanID, Double timeStamp, |
---|
| 1427 | Double interval, const String& sourceName, |
---|
[227] | 1428 | const Vector<uInt>& freqID) const |
---|
[167] | 1429 | { |
---|
[169] | 1430 | // Data and mask |
---|
[167] | 1431 | |
---|
[185] | 1432 | putDataInSDC(sc, data, mask); |
---|
[167] | 1433 | |
---|
[169] | 1434 | // TSys |
---|
| 1435 | |
---|
| 1436 | sc.putTsys(tSys); |
---|
| 1437 | |
---|
| 1438 | // Time things |
---|
| 1439 | |
---|
| 1440 | sc.timestamp = timeStamp; |
---|
| 1441 | sc.interval = interval; |
---|
| 1442 | sc.scanid = scanID; |
---|
[167] | 1443 | // |
---|
[169] | 1444 | sc.sourcename = sourceName; |
---|
| 1445 | sc.putFreqMap(freqID); |
---|
| 1446 | } |
---|
[167] | 1447 | |
---|
[185] | 1448 | void SDMath::normalize(MaskedArray<Float>& sum, |
---|
[169] | 1449 | const Array<Float>& sumSq, |
---|
| 1450 | const Array<Float>& nPts, |
---|
| 1451 | WeightType wtType, Int axis, |
---|
[227] | 1452 | Int nAxesSub) const |
---|
[169] | 1453 | { |
---|
| 1454 | IPosition pos2(nAxesSub,0); |
---|
| 1455 | // |
---|
| 1456 | if (wtType==NONE) { |
---|
[167] | 1457 | |
---|
[169] | 1458 | // We just average by the number of points accumulated. |
---|
| 1459 | // We need to make a MA out of nPts so that no divide by |
---|
| 1460 | // zeros occur |
---|
[167] | 1461 | |
---|
[169] | 1462 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
| 1463 | sum /= t; |
---|
| 1464 | } else if (wtType==VAR) { |
---|
[167] | 1465 | |
---|
[169] | 1466 | // Normalize each spectrum by sum(1/var) where the variance |
---|
| 1467 | // is worked out for each spectrum |
---|
| 1468 | |
---|
| 1469 | Array<Float>& data = sum.getRWArray(); |
---|
| 1470 | VectorIterator<Float> itData(data, axis); |
---|
| 1471 | while (!itData.pastEnd()) { |
---|
| 1472 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
| 1473 | itData.vector() /= sumSq(pos2); |
---|
| 1474 | itData.next(); |
---|
| 1475 | } |
---|
| 1476 | } else if (wtType==TSYS) { |
---|
| 1477 | } |
---|
| 1478 | } |
---|
| 1479 | |
---|
| 1480 | |
---|
[185] | 1481 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum, |
---|
| 1482 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
| 1483 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
| 1484 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
| 1485 | const Vector<Bool>& mask, Double time, Double interval, |
---|
| 1486 | const Block<CountedPtr<SDMemTable> >& in, |
---|
| 1487 | uInt iTab, uInt iRow, uInt axis, |
---|
| 1488 | uInt nAxesSub, Bool useMask, |
---|
[227] | 1489 | WeightType wtType) const |
---|
[169] | 1490 | { |
---|
| 1491 | |
---|
| 1492 | // Get data |
---|
| 1493 | |
---|
| 1494 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
| 1495 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
| 1496 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
[167] | 1497 | // |
---|
[169] | 1498 | if (wtType==NONE) { |
---|
| 1499 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
| 1500 | nPts += n; // Only accumulates where mask==T |
---|
| 1501 | } else if (wtType==VAR) { |
---|
[167] | 1502 | |
---|
[169] | 1503 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
| 1504 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
[167] | 1505 | |
---|
[169] | 1506 | VectorIterator<Float> itData(valuesIn, axis); |
---|
| 1507 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
| 1508 | Float fac = 1.0; |
---|
| 1509 | IPosition pos(nAxesSub,0); |
---|
| 1510 | // |
---|
| 1511 | while (!itData.pastEnd()) { |
---|
[167] | 1512 | |
---|
[169] | 1513 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
[167] | 1514 | |
---|
[169] | 1515 | if (useMask) { |
---|
| 1516 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
| 1517 | fac = 1.0/variance(tmp); |
---|
| 1518 | } else { |
---|
| 1519 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
| 1520 | fac = 1.0/variance(tmp); |
---|
| 1521 | } |
---|
| 1522 | |
---|
| 1523 | // Scale data |
---|
| 1524 | |
---|
| 1525 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
[167] | 1526 | // |
---|
[169] | 1527 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
| 1528 | // This method to get pos2 from itData.pos() is only valid |
---|
| 1529 | // because the spectral axis is the last one (so we can just |
---|
| 1530 | // copy the first nAXesSub positions out) |
---|
[167] | 1531 | |
---|
[169] | 1532 | pos = itData.pos().getFirst(nAxesSub); |
---|
| 1533 | sumSq(pos) += fac; |
---|
| 1534 | // |
---|
| 1535 | itData.next(); |
---|
| 1536 | itMask.next(); |
---|
| 1537 | } |
---|
| 1538 | } else if (wtType==TSYS) { |
---|
| 1539 | } |
---|
[167] | 1540 | |
---|
[169] | 1541 | // Accumulate sum of (possibly scaled) data |
---|
| 1542 | |
---|
| 1543 | sum += dataIn; |
---|
| 1544 | |
---|
| 1545 | // Accumulate Tsys, time, and interval |
---|
| 1546 | |
---|
| 1547 | tSysSum += tSys; |
---|
| 1548 | timeSum += time; |
---|
| 1549 | intSum += interval; |
---|
| 1550 | nAccum += 1; |
---|
| 1551 | } |
---|
| 1552 | |
---|
| 1553 | |
---|
| 1554 | |
---|
| 1555 | |
---|
[185] | 1556 | void SDMath::getCursorLocation(IPosition& start, IPosition& end, |
---|
[227] | 1557 | const SDMemTable& in) const |
---|
[169] | 1558 | { |
---|
| 1559 | const uInt nDim = 4; |
---|
| 1560 | const uInt i = in.getBeam(); |
---|
| 1561 | const uInt j = in.getIF(); |
---|
| 1562 | const uInt k = in.getPol(); |
---|
| 1563 | const uInt n = in.nChan(); |
---|
[167] | 1564 | // |
---|
[169] | 1565 | start.resize(nDim); |
---|
| 1566 | start(0) = i; |
---|
| 1567 | start(1) = j; |
---|
| 1568 | start(2) = k; |
---|
| 1569 | start(3) = 0; |
---|
[167] | 1570 | // |
---|
[169] | 1571 | end.resize(nDim); |
---|
| 1572 | end(0) = i; |
---|
| 1573 | end(1) = j; |
---|
| 1574 | end(2) = k; |
---|
| 1575 | end(3) = n-1; |
---|
| 1576 | } |
---|
| 1577 | |
---|
| 1578 | |
---|
[227] | 1579 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr) const |
---|
[169] | 1580 | { |
---|
| 1581 | String tStr(weightStr); |
---|
| 1582 | tStr.upcase(); |
---|
| 1583 | if (tStr.contains(String("NONE"))) { |
---|
| 1584 | wtType = NONE; |
---|
| 1585 | } else if (tStr.contains(String("VAR"))) { |
---|
| 1586 | wtType = VAR; |
---|
| 1587 | } else if (tStr.contains(String("TSYS"))) { |
---|
| 1588 | wtType = TSYS; |
---|
[185] | 1589 | throw(AipsError("T_sys weighting not yet implemented")); |
---|
[169] | 1590 | } else { |
---|
[185] | 1591 | throw(AipsError("Unrecognized weighting type")); |
---|
[167] | 1592 | } |
---|
| 1593 | } |
---|
| 1594 | |
---|
[227] | 1595 | void SDMath::convertInterpString(Int& type, const String& interp) const |
---|
| 1596 | { |
---|
| 1597 | String tStr(interp); |
---|
| 1598 | tStr.upcase(); |
---|
| 1599 | if (tStr.contains(String("NEAR"))) { |
---|
| 1600 | type = InterpolateArray1D<Float,Float>::nearestNeighbour; |
---|
| 1601 | } else if (tStr.contains(String("LIN"))) { |
---|
| 1602 | type = InterpolateArray1D<Float,Float>::linear; |
---|
| 1603 | } else if (tStr.contains(String("CUB"))) { |
---|
| 1604 | type = InterpolateArray1D<Float,Float>::cubic; |
---|
| 1605 | } else if (tStr.contains(String("SPL"))) { |
---|
| 1606 | type = InterpolateArray1D<Float,Float>::spline; |
---|
| 1607 | } else { |
---|
| 1608 | throw(AipsError("Unrecognized interpolation type")); |
---|
| 1609 | } |
---|
| 1610 | } |
---|
| 1611 | |
---|
[185] | 1612 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data, |
---|
[227] | 1613 | const Array<Bool>& mask) const |
---|
[169] | 1614 | { |
---|
| 1615 | sc.putSpectrum(data); |
---|
| 1616 | // |
---|
| 1617 | Array<uChar> outflags(data.shape()); |
---|
| 1618 | convertArray(outflags,!mask); |
---|
| 1619 | sc.putFlags(outflags); |
---|
| 1620 | } |
---|
[227] | 1621 | |
---|
| 1622 | Table SDMath::readAsciiFile (const String& fileName) const |
---|
| 1623 | { |
---|
[230] | 1624 | String formatString; |
---|
| 1625 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False); |
---|
[227] | 1626 | return tbl; |
---|
| 1627 | } |
---|
[230] | 1628 | |
---|
| 1629 | |
---|
[234] | 1630 | |
---|
| 1631 | void SDMath::correctFromAsciiTable(SDMemTable* pTabOut, |
---|
| 1632 | const SDMemTable& in, const String& fileName, |
---|
| 1633 | const String& col0, const String& col1, |
---|
| 1634 | const String& methodStr, Bool doAll, |
---|
| 1635 | const Vector<Float>& xOut) const |
---|
[230] | 1636 | { |
---|
| 1637 | |
---|
| 1638 | // Read gain-elevation ascii file data into a Table. |
---|
| 1639 | |
---|
[234] | 1640 | Table geTable = readAsciiFile (fileName); |
---|
[230] | 1641 | // |
---|
[234] | 1642 | correctFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut); |
---|
[230] | 1643 | } |
---|
| 1644 | |
---|
[234] | 1645 | void SDMath::correctFromTable(SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 1646 | const Table& tTable, const String& col0, |
---|
| 1647 | const String& col1, |
---|
| 1648 | const String& methodStr, Bool doAll, |
---|
| 1649 | const Vector<Float>& xOut) const |
---|
[230] | 1650 | { |
---|
| 1651 | |
---|
| 1652 | // Get data from Table |
---|
| 1653 | |
---|
| 1654 | ROScalarColumn<Float> geElCol(tTable, col0); |
---|
| 1655 | ROScalarColumn<Float> geFacCol(tTable, col1); |
---|
| 1656 | Vector<Float> xIn = geElCol.getColumn(); |
---|
| 1657 | Vector<Float> yIn = geFacCol.getColumn(); |
---|
| 1658 | Vector<Bool> maskIn(xIn.nelements(),True); |
---|
| 1659 | |
---|
| 1660 | // Interpolate (and extrapolate) with desired method |
---|
| 1661 | |
---|
| 1662 | Int method = 0; |
---|
| 1663 | convertInterpString(method, methodStr); |
---|
| 1664 | // |
---|
| 1665 | Vector<Float> yOut; |
---|
| 1666 | Vector<Bool> maskOut; |
---|
| 1667 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut, |
---|
| 1668 | xIn, yIn, maskIn, method, |
---|
| 1669 | True, True); |
---|
[234] | 1670 | // Apply |
---|
[230] | 1671 | |
---|
[234] | 1672 | correctFromVector (pTabOut, in, doAll, yOut); |
---|
| 1673 | } |
---|
| 1674 | |
---|
| 1675 | |
---|
| 1676 | void SDMath::correctFromVector (SDMemTable* pTabOut, const SDMemTable& in, |
---|
| 1677 | Bool doAll, const Vector<Float>& factor) const |
---|
| 1678 | { |
---|
[270] | 1679 | |
---|
[230] | 1680 | // For operations only on specified cursor location |
---|
| 1681 | |
---|
| 1682 | IPosition start, end; |
---|
| 1683 | getCursorLocation(start, end, in); |
---|
| 1684 | |
---|
[270] | 1685 | // Loop over rows and apply correction factor |
---|
[230] | 1686 | |
---|
| 1687 | const uInt axis = asap::ChanAxis; |
---|
| 1688 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
| 1689 | |
---|
| 1690 | // Get data |
---|
| 1691 | |
---|
| 1692 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
| 1693 | |
---|
| 1694 | // Apply factor |
---|
| 1695 | |
---|
| 1696 | if (doAll) { |
---|
[270] | 1697 | dataIn *= factor[i]; |
---|
[230] | 1698 | } else { |
---|
[270] | 1699 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference |
---|
| 1700 | dataIn2 *= factor[i]; |
---|
[230] | 1701 | } |
---|
| 1702 | |
---|
| 1703 | // Write out |
---|
| 1704 | |
---|
| 1705 | SDContainer sc = in.getSDContainer(i); |
---|
[270] | 1706 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
[230] | 1707 | // |
---|
| 1708 | pTabOut->putSDContainer(sc); |
---|
| 1709 | } |
---|
| 1710 | } |
---|
| 1711 | |
---|
[234] | 1712 | |
---|
[262] | 1713 | void SDMath::generateSourceTable (Vector<String>& srcTab, |
---|
| 1714 | Vector<uInt>& srcIdx, |
---|
| 1715 | Vector<uInt>& firstRow, |
---|
| 1716 | const Vector<String>& srcNames) const |
---|
| 1717 | // |
---|
| 1718 | // This algorithm assumes that if there are multiple beams |
---|
| 1719 | // that the source names are diffent. Oterwise we would need |
---|
| 1720 | // to look atthe direction for each beam... |
---|
| 1721 | // |
---|
| 1722 | { |
---|
| 1723 | const uInt nRow = srcNames.nelements(); |
---|
| 1724 | srcTab.resize(0); |
---|
| 1725 | srcIdx.resize(nRow); |
---|
| 1726 | firstRow.resize(0); |
---|
| 1727 | // |
---|
| 1728 | uInt nSrc = 0; |
---|
| 1729 | for (uInt i=0; i<nRow; i++) { |
---|
| 1730 | String srcName = srcNames[i]; |
---|
| 1731 | |
---|
| 1732 | // Do we have this source already ? |
---|
| 1733 | |
---|
| 1734 | Int idx = -1; |
---|
| 1735 | if (nSrc>0) { |
---|
| 1736 | for (uInt j=0; j<nSrc; j++) { |
---|
| 1737 | if (srcName==srcTab[j]) { |
---|
| 1738 | idx = j; |
---|
| 1739 | break; |
---|
| 1740 | } |
---|
| 1741 | } |
---|
| 1742 | } |
---|
| 1743 | |
---|
| 1744 | // Add new entry if not found |
---|
| 1745 | |
---|
| 1746 | if (idx==-1) { |
---|
| 1747 | nSrc++; |
---|
| 1748 | srcTab.resize(nSrc,True); |
---|
| 1749 | srcTab(nSrc-1) = srcName; |
---|
| 1750 | idx = nSrc-1; |
---|
| 1751 | // |
---|
| 1752 | firstRow.resize(nSrc,True); |
---|
| 1753 | firstRow(nSrc-1) = i; // First row for which this source occurs |
---|
| 1754 | } |
---|
| 1755 | |
---|
| 1756 | // Set index for this row |
---|
| 1757 | |
---|
| 1758 | srcIdx[i] = idx; |
---|
| 1759 | } |
---|
| 1760 | } |
---|
[272] | 1761 | |
---|
| 1762 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const |
---|
| 1763 | { |
---|
| 1764 | Quantum<Double> qt; |
---|
| 1765 | if (MVTime::read(qt,str)) { |
---|
| 1766 | MVEpoch mv(qt); |
---|
| 1767 | MEpoch me(mv, timeRef); |
---|
| 1768 | return me; |
---|
| 1769 | } else { |
---|
| 1770 | throw(AipsError("Invalid format for Epoch string")); |
---|
| 1771 | } |
---|
| 1772 | } |
---|
| 1773 | |
---|
| 1774 | |
---|
| 1775 | String SDMath::formatEpoch(const MEpoch& epoch) const |
---|
| 1776 | { |
---|
| 1777 | MVTime mvt(epoch.getValue()); |
---|
| 1778 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")"); |
---|
| 1779 | } |
---|
| 1780 | |
---|
[294] | 1781 | |
---|
| 1782 | void SDMath::generateVelocityAligners (PtrBlock<VelocityAligner<Float>* >& vA, |
---|
| 1783 | const SDMemTable& in, uInt nChan, |
---|
| 1784 | uInt nFreqIDs, uInt nSrcTab, |
---|
| 1785 | const Vector<uInt>& firstRow, |
---|
| 1786 | MFrequency::Types velSystem, |
---|
| 1787 | const String& velUnit, |
---|
| 1788 | MDoppler::Types doppler, |
---|
| 1789 | const MPosition& refPos, |
---|
| 1790 | const MEpoch& refEpoch) const |
---|
| 1791 | { |
---|
| 1792 | for (uInt fqID=0; fqID<nFreqIDs; fqID++) { |
---|
| 1793 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID); |
---|
| 1794 | for (uInt iSrc=0; iSrc<nSrcTab; iSrc++) { |
---|
| 1795 | MDirection refDir = in.getDirection(firstRow[iSrc]); |
---|
| 1796 | uInt idx = (iSrc*nFreqIDs) + fqID; |
---|
| 1797 | vA[idx] = new VelocityAligner<Float>(sC, nChan, refEpoch, refDir, refPos, |
---|
| 1798 | velUnit, doppler, velSystem); |
---|
| 1799 | } |
---|
| 1800 | } |
---|
| 1801 | } |
---|
| 1802 | |
---|