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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5 | //# ATNF
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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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31 | #include <vector>
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32 |
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33 | #include <casa/aips.h>
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34 | #include <casa/iostream.h>
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35 | #include <casa/iomanip.h>
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36 | #include <casa/BasicSL/String.h>
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37 | #include <casa/Arrays/IPosition.h>
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38 | #include <casa/Arrays/Array.h>
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39 | #include <casa/Arrays/ArrayIter.h>
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40 | #include <casa/Arrays/VectorIter.h>
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41 | #include <casa/Arrays/ArrayMath.h>
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42 | #include <casa/Arrays/ArrayLogical.h>
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43 | #include <casa/Arrays/MaskedArray.h>
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44 | #include <casa/Arrays/MaskArrMath.h>
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45 | #include <casa/Arrays/MaskArrLogi.h>
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46 | #include <casa/Arrays/Matrix.h>
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47 | #include <casa/BasicMath/Math.h>
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48 | #include <casa/Containers/Block.h>
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49 | #include <casa/Exceptions.h>
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50 | #include <casa/Quanta/Quantum.h>
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51 | #include <casa/Quanta/Unit.h>
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52 | #include <casa/Quanta/MVEpoch.h>
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53 | #include <casa/Quanta/MVTime.h>
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54 | #include <casa/Utilities/Assert.h>
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55 |
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56 | #include <coordinates/Coordinates/SpectralCoordinate.h>
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57 | #include <coordinates/Coordinates/CoordinateSystem.h>
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58 | #include <coordinates/Coordinates/CoordinateUtil.h>
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59 | #include <coordinates/Coordinates/FrequencyAligner.h>
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60 |
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61 | #include <lattices/Lattices/LatticeUtilities.h>
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62 | #include <lattices/Lattices/RebinLattice.h>
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63 |
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64 | #include <measures/Measures/MEpoch.h>
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65 | #include <measures/Measures/MDirection.h>
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66 | #include <measures/Measures/MPosition.h>
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67 |
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68 | #include <scimath/Mathematics/VectorKernel.h>
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69 | #include <scimath/Mathematics/Convolver.h>
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70 | #include <scimath/Mathematics/InterpolateArray1D.h>
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71 | #include <scimath/Functionals/Polynomial.h>
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72 |
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73 | #include <tables/Tables/Table.h>
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74 | #include <tables/Tables/ScalarColumn.h>
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75 | #include <tables/Tables/ArrayColumn.h>
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76 | #include <tables/Tables/ReadAsciiTable.h>
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77 |
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78 | #include "MathUtils.h"
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79 | #include "SDDefs.h"
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80 | #include "SDAttr.h"
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81 | #include "SDContainer.h"
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82 | #include "SDMemTable.h"
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83 |
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84 | #include "SDMath.h"
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85 | #include "SDPol.h"
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86 |
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87 | using namespace casa;
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88 | using namespace asap;
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89 |
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90 |
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91 | SDMath::SDMath()
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92 | {;}
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93 |
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94 | SDMath::SDMath(const SDMath& other)
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95 | {
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96 |
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97 | // No state
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98 |
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99 | }
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100 |
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101 | SDMath& SDMath::operator=(const SDMath& other)
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102 | {
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103 | if (this != &other) {
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104 | // No state
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105 | }
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106 | return *this;
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107 | }
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108 |
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109 | SDMath::~SDMath()
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110 | {;}
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111 |
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112 |
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113 |
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114 | SDMemTable* SDMath::frequencyAlignment(const SDMemTable& in,
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115 | const String& refTime,
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116 | const String& method,
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117 | Bool perFreqID) const
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118 | {
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119 | // Get frame info from Table
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120 |
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121 | std::vector<std::string> info = in.getCoordInfo();
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122 |
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123 | // Parse frequency system
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124 |
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125 | String systemStr(info[1]);
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126 | String baseSystemStr(info[3]);
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127 | if (baseSystemStr==systemStr) {
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128 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe"));
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129 | }
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130 | //
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131 | MFrequency::Types freqSystem;
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132 | MFrequency::getType(freqSystem, systemStr);
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133 |
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134 | // Do it
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135 |
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136 | return frequencyAlign(in, freqSystem, refTime, method, perFreqID);
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137 | }
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138 |
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139 |
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140 |
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141 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in,
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142 | const Vector<Bool>& mask, Bool scanAv,
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143 | const String& weightStr, Bool alignFreq) const
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144 | //
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145 | // Weighted averaging of spectra from one or more Tables.
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146 | //
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147 | {
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148 |
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149 | // Convert weight type
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150 |
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151 | WeightType wtType = NONE;
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152 | convertWeightString(wtType, weightStr, True);
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153 |
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154 | // Create output Table by cloning from the first table
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155 |
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156 | SDMemTable* pTabOut = new SDMemTable(*in[0],True);
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157 | if (in.nelements() > 1) {
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158 | for (uInt i=1; i < in.nelements(); ++i) {
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159 | pTabOut->appendToHistoryTable(in[i]->getHistoryTable());
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160 | }
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161 | }
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162 | // Setup
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163 |
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164 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change
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165 | Array<Float> arr(shp);
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166 | Array<Bool> barr(shp);
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167 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis));
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168 |
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169 | // Columns from Tables
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170 |
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171 | ROArrayColumn<Float> tSysCol;
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172 | ROScalarColumn<Double> mjdCol;
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173 | ROScalarColumn<String> srcNameCol;
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174 | ROScalarColumn<Double> intCol;
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175 | ROArrayColumn<uInt> fqIDCol;
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176 | ROScalarColumn<Int> scanIDCol;
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177 |
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178 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam
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179 | // Note that the mask of the accumulation array will ALWAYS remain ALL True.
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180 | // The MA is only used so that when data which is masked Bad is added to it,
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181 | // that data does not contribute.
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182 |
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183 | Array<Float> zero(shp);
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184 | zero=0.0;
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185 | Array<Bool> good(shp);
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186 | good = True;
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187 | MaskedArray<Float> sum(zero,good);
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188 |
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189 | // Counter arrays
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190 |
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191 | Array<Float> nPts(shp); // Number of points
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192 | nPts = 0.0;
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193 | Array<Float> nInc(shp); // Increment
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194 | nInc = 1.0;
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195 |
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196 | // Create accumulation Array for variance. We accumulate for
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197 | // each if,pol,beam, but average over channel. So we need
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198 | // a shape with one less axis dropping channels.
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199 |
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200 | const uInt nAxesSub = shp.nelements() - 1;
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201 | IPosition shp2(nAxesSub);
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202 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) {
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203 | if (i!=asap::ChanAxis) {
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204 | shp2(j) = shp(i);
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205 | j++;
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206 | }
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207 | }
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208 | Array<Float> sumSq(shp2);
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209 | sumSq = 0.0;
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210 | IPosition pos2(nAxesSub,0); // For indexing
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211 |
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212 | // Time-related accumulators
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213 |
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214 | Double time;
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215 | Double timeSum = 0.0;
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216 | Double intSum = 0.0;
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217 | Double interval = 0.0;
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218 |
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219 | // To get the right shape for the Tsys accumulator we need to
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220 | // access a column from the first table. The shape of this
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221 | // array must not change. Note however that since the TSysSqSum
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222 | // array is used in a normalization process, and that I ignore the
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223 | // channel axis replication of values for now, it loses a dimension
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224 |
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225 | Array<Float> tSysSum, tSysSqSum;
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226 | {
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227 | const Table& tabIn = in[0]->table();
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228 | tSysCol.attach(tabIn,"TSYS");
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229 | tSysSum.resize(tSysCol.shape(0));
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230 | //
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231 | tSysSqSum.resize(shp2);
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232 | }
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233 | tSysSum =0.0;
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234 | tSysSqSum = 0.0;
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235 | Array<Float> tSys;
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236 |
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237 | // Scan and row tracking
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238 |
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239 | Int oldScanID = 0;
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240 | Int outScanID = 0;
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241 | Int scanID = 0;
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242 | Int rowStart = 0;
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243 | Int nAccum = 0;
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244 | Int tableStart = 0;
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245 |
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246 | // Source and FreqID
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247 |
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248 | String sourceName, oldSourceName, sourceNameStart;
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249 | Vector<uInt> freqID, freqIDStart, oldFreqID;
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250 |
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251 | // Loop over tables
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252 |
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253 | Float fac = 1.0;
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254 | const uInt nTables = in.nelements();
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255 | for (uInt iTab=0; iTab<nTables; iTab++) {
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256 |
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257 | // Should check that the frequency tables don't change if doing FreqAlignment
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258 |
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259 | // Attach columns to Table
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260 |
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261 | const Table& tabIn = in[iTab]->table();
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262 | tSysCol.attach(tabIn, "TSYS");
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263 | mjdCol.attach(tabIn, "TIME");
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264 | srcNameCol.attach(tabIn, "SRCNAME");
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265 | intCol.attach(tabIn, "INTERVAL");
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266 | fqIDCol.attach(tabIn, "FREQID");
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267 | scanIDCol.attach(tabIn, "SCANID");
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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 | scanIDCol.getScalar(iRow, scanID);
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285 |
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286 | // Get quantities from columns
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287 |
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288 | srcNameCol.getScalar(iRow, sourceName);
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289 | mjdCol.get(iRow, time);
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290 | tSysCol.get(iRow, tSys);
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291 | intCol.get(iRow, interval);
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292 | fqIDCol.get(iRow, freqID);
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293 |
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294 | // Initialize first source and freqID
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295 |
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296 | if (iRow==0 && iTab==0) {
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297 | sourceNameStart = sourceName;
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298 | freqIDStart = freqID;
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299 | }
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300 |
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301 | // If we are doing scan averages, see if we are at the end of an
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302 | // accumulation period (scan). We must check soutce names too,
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303 | // since we might have two tables with one scan each but different
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304 | // source names; we shouldn't average different sources together
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305 |
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306 | if (scanAv && ( (scanID != oldScanID) ||
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307 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) {
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308 |
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309 | // Normalize data in 'sum' accumulation array according to weighting scheme
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310 |
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311 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub);
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312 |
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313 | // Get ScanContainer for the first row of this averaged Scan
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314 |
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315 | SDContainer scOut = in[iTab]->getSDContainer(rowStart);
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316 |
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317 | // Fill scan container. The source and freqID come from the
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318 | // first row of the first table that went into this average (
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319 | // should be the same for all rows in the scan average)
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320 |
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321 | Float nR(nAccum);
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322 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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323 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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324 |
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325 | // Write container out to Table
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326 |
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327 | pTabOut->putSDContainer(scOut);
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328 |
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329 | // Reset accumulators
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330 |
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331 | sum = 0.0;
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332 | sumSq = 0.0;
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333 | nAccum = 0;
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334 | //
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335 | tSysSum =0.0;
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336 | tSysSqSum =0.0;
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337 | timeSum = 0.0;
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338 | intSum = 0.0;
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339 | nPts = 0.0;
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340 |
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341 | // Increment
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342 |
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343 | rowStart = iRow; // First row for next accumulation
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344 | tableStart = iTab; // First table for next accumulation
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345 | sourceNameStart = sourceName; // First source name for next accumulation
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346 | freqIDStart = freqID; // First FreqID for next accumulation
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347 | //
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348 | oldScanID = scanID;
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349 | outScanID += 1; // Scan ID for next accumulation period
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350 | }
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351 |
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352 | // Accumulate
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353 |
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354 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, tSysSqSum,
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355 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis,
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356 | nAxesSub, useMask, wtType);
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357 | //
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358 | oldSourceName = sourceName;
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359 | oldFreqID = freqID;
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360 | }
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361 | }
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362 |
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363 | // OK at this point we have accumulation data which is either
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364 | // - accumulated from all tables into one row
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365 | // or
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366 | // - accumulated from the last scan average
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367 | //
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368 | // Normalize data in 'sum' accumulation array according to weighting scheme
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369 |
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370 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, asap::ChanAxis, nAxesSub);
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371 |
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372 | // Create and fill container. The container we clone will be from
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373 | // the last Table and the first row that went into the current
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374 | // accumulation. It probably doesn't matter that much really...
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375 |
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376 | Float nR(nAccum);
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377 | SDContainer scOut = in[tableStart]->getSDContainer(rowStart);
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378 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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379 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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380 | pTabOut->putSDContainer(scOut);
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381 | pTabOut->resetCursor();
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382 | //
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383 | return CountedPtr<SDMemTable>(pTabOut);
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384 | }
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385 |
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386 |
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387 |
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388 | CountedPtr<SDMemTable> SDMath::binaryOperate(const CountedPtr<SDMemTable>&
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389 | left,
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390 | const CountedPtr<SDMemTable>&
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391 | right,
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392 | const String& op, Bool preserve,
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393 | Bool doTSys) const
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394 | {
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395 |
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396 | // Check operator
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397 |
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398 | String op2(op);
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399 | op2.upcase();
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400 | uInt what = 0;
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401 | if (op2=="ADD") {
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402 | what = 0;
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403 | } else if (op2=="SUB") {
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404 | what = 1;
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405 | } else if (op2=="MUL") {
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406 | what = 2;
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407 | } else if (op2=="DIV") {
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408 | what = 3;
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409 | } else if (op2=="QUOTIENT") {
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410 | what = 4;
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411 | doTSys = True;
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412 | } else {
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413 | throw( AipsError("Unrecognized operation"));
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414 | }
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415 |
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416 | // Check rows
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417 |
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418 | const uInt nRowLeft = left->nRow();
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419 | const uInt nRowRight = right->nRow();
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420 | Bool ok = (nRowRight==1&&nRowLeft>0) ||
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421 | (nRowRight>=1&&nRowLeft==nRowRight);
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422 | if (!ok) {
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423 | throw (AipsError("The right Scan Table can have one row or the same number of rows as the left Scan Table"));
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424 | }
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425 |
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426 | // Input Tables
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427 |
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428 | const Table& tLeft = left->table();
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429 | const Table& tRight = right->table();
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430 |
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431 | // TSys columns
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432 |
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433 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol;
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434 | if (doTSys) {
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435 | tSysLeftCol.attach(tLeft, "TSYS");
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436 | tSysRightCol.attach(tRight, "TSYS");
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437 | }
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438 |
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439 | // First row for right
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440 |
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441 | Array<Float> tSysLeftArr, tSysRightArr;
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442 | if (doTSys) tSysRightCol.get(0, tSysRightArr);
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443 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0));
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444 | IPosition shpRight = pMRight->shape();
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445 |
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446 | // Output Table cloned from left
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447 |
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448 | SDMemTable* pTabOut = new SDMemTable(*left, True);
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449 | pTabOut->appendToHistoryTable(right->getHistoryTable());
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450 | // Loop over rows
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451 |
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452 | for (uInt i=0; i<nRowLeft; i++) {
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453 |
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454 | // Get data
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455 |
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456 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i));
|
---|
457 | IPosition shpLeft = mLeft.shape();
|
---|
458 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr);
|
---|
459 | //
|
---|
460 | if (nRowRight>1) {
|
---|
461 | delete pMRight;
|
---|
462 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i));
|
---|
463 | shpRight = pMRight->shape();
|
---|
464 | if (doTSys) tSysRightCol.get(i, tSysRightArr);
|
---|
465 | }
|
---|
466 | //
|
---|
467 | if (!shpRight.isEqual(shpLeft)) {
|
---|
468 | throw(AipsError("left and right scan tables are not conformant"));
|
---|
469 | }
|
---|
470 | if (doTSys) {
|
---|
471 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) {
|
---|
472 | throw(AipsError("left and right Tsys data are not conformant"));
|
---|
473 | }
|
---|
474 | if (!shpRight.isEqual(tSysRightArr.shape())) {
|
---|
475 | throw(AipsError("left and right scan tables are not conformant"));
|
---|
476 | }
|
---|
477 | }
|
---|
478 |
|
---|
479 | // Make container
|
---|
480 |
|
---|
481 | SDContainer sc = left->getSDContainer(i);
|
---|
482 |
|
---|
483 | // Operate on data and TSys
|
---|
484 |
|
---|
485 | if (what==0) {
|
---|
486 | MaskedArray<Float> tmp = mLeft + *pMRight;
|
---|
487 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
488 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr);
|
---|
489 | } else if (what==1) {
|
---|
490 | MaskedArray<Float> tmp = mLeft - *pMRight;
|
---|
491 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
492 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr);
|
---|
493 | } else if (what==2) {
|
---|
494 | MaskedArray<Float> tmp = mLeft * *pMRight;
|
---|
495 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
496 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr);
|
---|
497 | } else if (what==3) {
|
---|
498 | MaskedArray<Float> tmp = mLeft / *pMRight;
|
---|
499 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
500 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr);
|
---|
501 | } else if (what==4) {
|
---|
502 | if (preserve) {
|
---|
503 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) -
|
---|
504 | tSysRightArr;
|
---|
505 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
506 | } else {
|
---|
507 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) -
|
---|
508 | tSysLeftArr;
|
---|
509 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
510 | }
|
---|
511 | sc.putTsys(tSysRightArr);
|
---|
512 | }
|
---|
513 |
|
---|
514 | // Put new row in output Table
|
---|
515 |
|
---|
516 | pTabOut->putSDContainer(sc);
|
---|
517 | }
|
---|
518 | if (pMRight) delete pMRight;
|
---|
519 | pTabOut->resetCursor();
|
---|
520 |
|
---|
521 | return CountedPtr<SDMemTable>(pTabOut);
|
---|
522 | }
|
---|
523 |
|
---|
524 |
|
---|
525 |
|
---|
526 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in,
|
---|
527 | const Vector<Bool>& mask,
|
---|
528 | const String& which, Int row) const
|
---|
529 | //
|
---|
530 | // Perhaps iteration over pol/beam/if should be in here
|
---|
531 | // and inside the nrow iteration ?
|
---|
532 | //
|
---|
533 | {
|
---|
534 | const uInt nRow = in->nRow();
|
---|
535 |
|
---|
536 | // Specify cursor location
|
---|
537 |
|
---|
538 | IPosition start, end;
|
---|
539 | Bool doAll = False;
|
---|
540 | setCursorSlice (start, end, doAll, *in);
|
---|
541 |
|
---|
542 | // Loop over rows
|
---|
543 |
|
---|
544 | const uInt nEl = mask.nelements();
|
---|
545 | uInt iStart = 0;
|
---|
546 | uInt iEnd = in->nRow()-1;
|
---|
547 | //
|
---|
548 | if (row>=0) {
|
---|
549 | iStart = row;
|
---|
550 | iEnd = row;
|
---|
551 | }
|
---|
552 | //
|
---|
553 | std::vector<float> result(iEnd-iStart+1);
|
---|
554 | for (uInt ii=iStart; ii <= iEnd; ++ii) {
|
---|
555 |
|
---|
556 | // Get row and deconstruct
|
---|
557 |
|
---|
558 | MaskedArray<Float> dataIn = (in->rowAsMaskedArray(ii))(start,end);
|
---|
559 | Array<Float> v = dataIn.getArray().nonDegenerate();
|
---|
560 | Array<Bool> m = dataIn.getMask().nonDegenerate();
|
---|
561 |
|
---|
562 | // Access desired piece of data
|
---|
563 |
|
---|
564 | // Array<Float> v((arr(start,end)).nonDegenerate());
|
---|
565 | // Array<Bool> m((barr(start,end)).nonDegenerate());
|
---|
566 |
|
---|
567 | // Apply OTF mask
|
---|
568 |
|
---|
569 | MaskedArray<Float> tmp;
|
---|
570 | if (m.nelements()==nEl) {
|
---|
571 | tmp.setData(v,m&&mask);
|
---|
572 | } else {
|
---|
573 | tmp.setData(v,m);
|
---|
574 | }
|
---|
575 |
|
---|
576 | // Get statistic
|
---|
577 |
|
---|
578 | result[ii-iStart] = mathutil::statistics(which, tmp);
|
---|
579 | }
|
---|
580 | //
|
---|
581 | return result;
|
---|
582 | }
|
---|
583 |
|
---|
584 |
|
---|
585 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const
|
---|
586 | {
|
---|
587 | SDHeader sh = in.getSDHeader();
|
---|
588 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
589 |
|
---|
590 | // Bin up SpectralCoordinates
|
---|
591 |
|
---|
592 | IPosition factors(1);
|
---|
593 | factors(0) = width;
|
---|
594 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
595 | CoordinateSystem cSys;
|
---|
596 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
597 | CoordinateSystem cSysBin =
|
---|
598 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False);
|
---|
599 | //
|
---|
600 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0);
|
---|
601 | pTabOut->setCoordinate(sCBin, j);
|
---|
602 | }
|
---|
603 |
|
---|
604 | // Use RebinLattice to find shape
|
---|
605 |
|
---|
606 | IPosition shapeIn(1,sh.nchan);
|
---|
607 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors);
|
---|
608 | sh.nchan = shapeOut(0);
|
---|
609 | pTabOut->putSDHeader(sh);
|
---|
610 |
|
---|
611 | // Loop over rows and bin along channel axis
|
---|
612 |
|
---|
613 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
614 | SDContainer sc = in.getSDContainer(i);
|
---|
615 | //
|
---|
616 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape
|
---|
617 |
|
---|
618 | // Bin up spectrum
|
---|
619 |
|
---|
620 | MaskedArray<Float> marr(in.rowAsMaskedArray(i));
|
---|
621 | MaskedArray<Float> marrout;
|
---|
622 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width);
|
---|
623 |
|
---|
624 | // Put back the binned data and flags
|
---|
625 |
|
---|
626 | IPosition ip2 = marrout.shape();
|
---|
627 | sc.resize(ip2);
|
---|
628 | //
|
---|
629 | putDataInSDC(sc, marrout.getArray(), marrout.getMask());
|
---|
630 |
|
---|
631 | // Bin up Tsys.
|
---|
632 |
|
---|
633 | Array<Bool> allGood(tSys.shape(),True);
|
---|
634 | MaskedArray<Float> tSysIn(tSys, allGood, True);
|
---|
635 | //
|
---|
636 | MaskedArray<Float> tSysOut;
|
---|
637 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width);
|
---|
638 | sc.putTsys(tSysOut.getArray());
|
---|
639 | //
|
---|
640 | pTabOut->putSDContainer(sc);
|
---|
641 | }
|
---|
642 | return pTabOut;
|
---|
643 | }
|
---|
644 |
|
---|
645 | SDMemTable* SDMath::resample(const SDMemTable& in, const String& methodStr,
|
---|
646 | Float width) const
|
---|
647 | //
|
---|
648 | // Should add the possibility of width being specified in km/s. This means
|
---|
649 | // that for each freqID (SpectralCoordinate) we will need to convert to an
|
---|
650 | // average channel width (say at the reference pixel). Then we would need
|
---|
651 | // to be careful to make sure each spectrum (of different freqID)
|
---|
652 | // is the same length.
|
---|
653 | //
|
---|
654 | {
|
---|
655 | Bool doVel = False;
|
---|
656 | if (doVel) {
|
---|
657 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
658 | SpectralCoordinate sC = in.getSpectralCoordinate(j);
|
---|
659 | }
|
---|
660 | }
|
---|
661 |
|
---|
662 | // Interpolation method
|
---|
663 |
|
---|
664 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
---|
665 | convertInterpString(interp, methodStr);
|
---|
666 | Int interpMethod(interp);
|
---|
667 |
|
---|
668 | // Make output table
|
---|
669 |
|
---|
670 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
671 |
|
---|
672 | // Resample SpectralCoordinates (one per freqID)
|
---|
673 |
|
---|
674 | const uInt nCoord = in.nCoordinates();
|
---|
675 | Vector<Float> offset(1,0.0);
|
---|
676 | Vector<Float> factors(1,1.0/width);
|
---|
677 | Vector<Int> newShape;
|
---|
678 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
679 | CoordinateSystem cSys;
|
---|
680 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
681 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape);
|
---|
682 | SpectralCoordinate sC = cSys2.spectralCoordinate(0);
|
---|
683 | //
|
---|
684 | pTabOut->setCoordinate(sC, j);
|
---|
685 | }
|
---|
686 |
|
---|
687 | // Get header
|
---|
688 |
|
---|
689 | SDHeader sh = in.getSDHeader();
|
---|
690 |
|
---|
691 | // Generate resampling vectors
|
---|
692 |
|
---|
693 | const uInt nChanIn = sh.nchan;
|
---|
694 | Vector<Float> xIn(nChanIn);
|
---|
695 | indgen(xIn);
|
---|
696 | //
|
---|
697 | Int fac = Int(nChanIn/width);
|
---|
698 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later
|
---|
699 | uInt i = 0;
|
---|
700 | Float x = 0.0;
|
---|
701 | Bool more = True;
|
---|
702 | while (more) {
|
---|
703 | xOut(i) = x;
|
---|
704 | //
|
---|
705 | i++;
|
---|
706 | x += width;
|
---|
707 | if (x>nChanIn-1) more = False;
|
---|
708 | }
|
---|
709 | const uInt nChanOut = i;
|
---|
710 | xOut.resize(nChanOut,True);
|
---|
711 | //
|
---|
712 | IPosition shapeIn(in.rowAsMaskedArray(0).shape());
|
---|
713 | sh.nchan = nChanOut;
|
---|
714 | pTabOut->putSDHeader(sh);
|
---|
715 |
|
---|
716 | // Loop over rows and resample along channel axis
|
---|
717 |
|
---|
718 | Array<Float> valuesOut;
|
---|
719 | Array<Bool> maskOut;
|
---|
720 | Array<Float> tSysOut;
|
---|
721 | Array<Bool> tSysMaskIn(shapeIn,True);
|
---|
722 | Array<Bool> tSysMaskOut;
|
---|
723 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
724 |
|
---|
725 | // Get container
|
---|
726 |
|
---|
727 | SDContainer sc = in.getSDContainer(i);
|
---|
728 |
|
---|
729 | // Get data and Tsys
|
---|
730 |
|
---|
731 | const Array<Float>& tSysIn = sc.getTsys();
|
---|
732 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i));
|
---|
733 | Array<Float> valuesIn = dataIn.getArray();
|
---|
734 | Array<Bool> maskIn = dataIn.getMask();
|
---|
735 |
|
---|
736 | // Interpolate data
|
---|
737 |
|
---|
738 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut,
|
---|
739 | xIn, valuesIn, maskIn,
|
---|
740 | interpMethod, True, True);
|
---|
741 | sc.resize(valuesOut.shape());
|
---|
742 | putDataInSDC(sc, valuesOut, maskOut);
|
---|
743 |
|
---|
744 | // Interpolate TSys
|
---|
745 |
|
---|
746 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut,
|
---|
747 | xIn, tSysIn, tSysMaskIn,
|
---|
748 | interpMethod, True, True);
|
---|
749 | sc.putTsys(tSysOut);
|
---|
750 |
|
---|
751 | // Put container in output
|
---|
752 |
|
---|
753 | pTabOut->putSDContainer(sc);
|
---|
754 | }
|
---|
755 | //
|
---|
756 | return pTabOut;
|
---|
757 | }
|
---|
758 |
|
---|
759 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll,
|
---|
760 | uInt what, Bool doTSys) const
|
---|
761 | //
|
---|
762 | // what = 0 Multiply
|
---|
763 | // 1 Add
|
---|
764 | {
|
---|
765 | SDMemTable* pOut = new SDMemTable(in,False);
|
---|
766 | const Table& tOut = pOut->table();
|
---|
767 | ArrayColumn<Float> specCol(tOut,"SPECTRA");
|
---|
768 | ArrayColumn<Float> tSysCol(tOut,"TSYS");
|
---|
769 | Array<Float> tSysArr;
|
---|
770 |
|
---|
771 | // Get data slice bounds
|
---|
772 |
|
---|
773 | IPosition start, end;
|
---|
774 | setCursorSlice (start, end, doAll, in);
|
---|
775 | //
|
---|
776 | for (uInt i=0; i<tOut.nrow(); i++) {
|
---|
777 |
|
---|
778 | // Modify data
|
---|
779 |
|
---|
780 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
|
---|
781 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference
|
---|
782 | if (what==0) {
|
---|
783 | dataIn2 *= val;
|
---|
784 | } else if (what==1) {
|
---|
785 | dataIn2 += val;
|
---|
786 | }
|
---|
787 | specCol.put(i, dataIn.getArray());
|
---|
788 |
|
---|
789 | // Modify Tsys
|
---|
790 |
|
---|
791 | if (doTSys) {
|
---|
792 | tSysCol.get(i, tSysArr);
|
---|
793 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference
|
---|
794 | if (what==0) {
|
---|
795 | tSysArr2 *= val;
|
---|
796 | } else if (what==1) {
|
---|
797 | tSysArr2 += val;
|
---|
798 | }
|
---|
799 | tSysCol.put(i, tSysArr);
|
---|
800 | }
|
---|
801 | }
|
---|
802 | //
|
---|
803 | return pOut;
|
---|
804 | }
|
---|
805 |
|
---|
806 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask,
|
---|
807 | const String& weightStr) const
|
---|
808 | //
|
---|
809 | // Average all polarizations together, weighted by variance
|
---|
810 | //
|
---|
811 | {
|
---|
812 | WeightType wtType = NONE;
|
---|
813 | convertWeightString(wtType, weightStr, True);
|
---|
814 |
|
---|
815 | // Create output Table and reshape number of polarizations
|
---|
816 |
|
---|
817 | Bool clear=True;
|
---|
818 | SDMemTable* pTabOut = new SDMemTable(in, clear);
|
---|
819 | SDHeader header = pTabOut->getSDHeader();
|
---|
820 | header.npol = 1;
|
---|
821 | pTabOut->putSDHeader(header);
|
---|
822 | //
|
---|
823 | const Table& tabIn = in.table();
|
---|
824 |
|
---|
825 | // Shape of input and output data
|
---|
826 |
|
---|
827 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape();
|
---|
828 | IPosition shapeOut(shapeIn);
|
---|
829 | shapeOut(asap::PolAxis) = 1; // Average all polarizations
|
---|
830 | if (shapeIn(asap::PolAxis)==1) {
|
---|
831 | throw(AipsError("The input has only one polarisation"));
|
---|
832 | }
|
---|
833 | //
|
---|
834 | const uInt nRows = in.nRow();
|
---|
835 | const uInt nChan = shapeIn(asap::ChanAxis);
|
---|
836 | AlwaysAssert(asap::nAxes==4,AipsError);
|
---|
837 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape
|
---|
838 | IPosition start(4), end(4);
|
---|
839 |
|
---|
840 | // Output arrays
|
---|
841 |
|
---|
842 | Array<Float> outData(shapeOut, 0.0);
|
---|
843 | Array<Bool> outMask(shapeOut, True);
|
---|
844 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane
|
---|
845 |
|
---|
846 | // Attach Tsys column if needed
|
---|
847 |
|
---|
848 | ROArrayColumn<Float> tSysCol;
|
---|
849 | Array<Float> tSys;
|
---|
850 | if (wtType==TSYS) {
|
---|
851 | tSysCol.attach(tabIn,"TSYS");
|
---|
852 | }
|
---|
853 | //
|
---|
854 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis));
|
---|
855 |
|
---|
856 | // Loop over rows
|
---|
857 |
|
---|
858 | for (uInt iRow=0; iRow<nRows; iRow++) {
|
---|
859 |
|
---|
860 | // Get data for this row
|
---|
861 |
|
---|
862 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow));
|
---|
863 | Array<Float>& arr = marr.getRWArray();
|
---|
864 | const Array<Bool>& barr = marr.getMask();
|
---|
865 |
|
---|
866 | // Get Tsys
|
---|
867 |
|
---|
868 | if (wtType==TSYS) {
|
---|
869 | tSysCol.get(iRow,tSys);
|
---|
870 | }
|
---|
871 |
|
---|
872 | // Make iterators to iterate by pol-channel planes
|
---|
873 | // The tSys array is empty unless wtType=TSYS so only
|
---|
874 | // access the iterator is that is the case
|
---|
875 |
|
---|
876 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes);
|
---|
877 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes);
|
---|
878 | ReadOnlyArrayIterator<Float>* pItTsysPlane = 0;
|
---|
879 | if (wtType==TSYS) pItTsysPlane = new ReadOnlyArrayIterator<Float>(tSys, axes);
|
---|
880 |
|
---|
881 | // Accumulations
|
---|
882 |
|
---|
883 | Float fac = 1.0;
|
---|
884 | Vector<Float> vecSum(nChan,0.0);
|
---|
885 |
|
---|
886 | // Iterate through data by pol-channel planes
|
---|
887 |
|
---|
888 | while (!itDataPlane.pastEnd()) {
|
---|
889 |
|
---|
890 | // Iterate through plane by polarization and accumulate Vectors
|
---|
891 |
|
---|
892 | Vector<Float> t1(nChan); t1 = 0.0;
|
---|
893 | Vector<Bool> t2(nChan); t2 = True;
|
---|
894 | Float tSys = 0.0;
|
---|
895 | MaskedArray<Float> vecSum(t1,t2);
|
---|
896 | Float norm = 0.0;
|
---|
897 | {
|
---|
898 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1);
|
---|
899 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
900 | //
|
---|
901 | ReadOnlyVectorIterator<Float>* pItTsysVec = 0;
|
---|
902 | if (wtType==TSYS) {
|
---|
903 | pItTsysVec = new ReadOnlyVectorIterator<Float>(pItTsysPlane->array(), 1);
|
---|
904 | }
|
---|
905 | //
|
---|
906 | while (!itDataVec.pastEnd()) {
|
---|
907 |
|
---|
908 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum
|
---|
909 |
|
---|
910 | if (useMask) {
|
---|
911 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector());
|
---|
912 | if (wtType==VAR) {
|
---|
913 | fac = 1.0 / variance(spec);
|
---|
914 | } else if (wtType==TSYS) {
|
---|
915 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency
|
---|
916 | fac = 1.0 / tSys / tSys;
|
---|
917 | }
|
---|
918 | } else {
|
---|
919 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector());
|
---|
920 | if (wtType==VAR) {
|
---|
921 | fac = 1.0 / variance(spec);
|
---|
922 | } else if (wtType==TSYS) {
|
---|
923 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency
|
---|
924 | fac = 1.0 / tSys / tSys;
|
---|
925 | }
|
---|
926 | }
|
---|
927 |
|
---|
928 | // Normalize spectrum (without OTF mask) and accumulate
|
---|
929 |
|
---|
930 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector());
|
---|
931 | vecSum += spec;
|
---|
932 | norm += fac;
|
---|
933 |
|
---|
934 | // Next
|
---|
935 |
|
---|
936 | itDataVec.next();
|
---|
937 | itMaskVec.next();
|
---|
938 | if (wtType==TSYS) pItTsysVec->next();
|
---|
939 | }
|
---|
940 |
|
---|
941 | // Clean up
|
---|
942 |
|
---|
943 | if (pItTsysVec) {
|
---|
944 | delete pItTsysVec;
|
---|
945 | pItTsysVec = 0;
|
---|
946 | }
|
---|
947 | }
|
---|
948 |
|
---|
949 | // Normalize summed spectrum
|
---|
950 |
|
---|
951 | vecSum /= norm;
|
---|
952 |
|
---|
953 | // FInd position in input data array. We are iterating by pol-channel
|
---|
954 | // plane so all that will change is beam and IF and that's what we want.
|
---|
955 |
|
---|
956 | IPosition pos = itDataPlane.pos();
|
---|
957 |
|
---|
958 | // Write out data. This is a bit messy. We have to reform the Vector
|
---|
959 | // accumulator into an Array of shape (1,1,1,nChan)
|
---|
960 |
|
---|
961 | start = pos;
|
---|
962 | end = pos;
|
---|
963 | end(asap::ChanAxis) = nChan-1;
|
---|
964 | outData(start,end) = vecSum.getArray().reform(vecShapeOut);
|
---|
965 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut);
|
---|
966 |
|
---|
967 | // Step to next beam/IF combination
|
---|
968 |
|
---|
969 | itDataPlane.next();
|
---|
970 | itMaskPlane.next();
|
---|
971 | if (wtType==TSYS) pItTsysPlane->next();
|
---|
972 | }
|
---|
973 |
|
---|
974 | // Generate output container and write it to output table
|
---|
975 |
|
---|
976 | SDContainer sc = in.getSDContainer();
|
---|
977 | sc.resize(shapeOut);
|
---|
978 | //
|
---|
979 | putDataInSDC(sc, outData, outMask);
|
---|
980 | pTabOut->putSDContainer(sc);
|
---|
981 | //
|
---|
982 | if (wtType==TSYS) {
|
---|
983 | delete pItTsysPlane;
|
---|
984 | pItTsysPlane = 0;
|
---|
985 | }
|
---|
986 | }
|
---|
987 |
|
---|
988 | // Set polarization cursor to 0
|
---|
989 |
|
---|
990 | pTabOut->setPol(0);
|
---|
991 | //
|
---|
992 | return pTabOut;
|
---|
993 | }
|
---|
994 |
|
---|
995 |
|
---|
996 | SDMemTable* SDMath::smooth(const SDMemTable& in,
|
---|
997 | const casa::String& kernelType,
|
---|
998 | casa::Float width, Bool doAll) const
|
---|
999 | //
|
---|
1000 | // Should smooth TSys as well
|
---|
1001 | //
|
---|
1002 | {
|
---|
1003 |
|
---|
1004 | // Number of channels
|
---|
1005 |
|
---|
1006 | const uInt nChan = in.nChan();
|
---|
1007 |
|
---|
1008 | // Generate Kernel
|
---|
1009 |
|
---|
1010 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType);
|
---|
1011 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False);
|
---|
1012 |
|
---|
1013 | // Generate Convolver
|
---|
1014 |
|
---|
1015 | IPosition shape(1,nChan);
|
---|
1016 | Convolver<Float> conv(kernel, shape);
|
---|
1017 |
|
---|
1018 | // New Table
|
---|
1019 |
|
---|
1020 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
1021 |
|
---|
1022 | // Output Vectors
|
---|
1023 |
|
---|
1024 | Vector<Float> valuesOut(nChan);
|
---|
1025 | Vector<Bool> maskOut(nChan);
|
---|
1026 |
|
---|
1027 | // Get data slice bounds
|
---|
1028 |
|
---|
1029 | IPosition start, end;
|
---|
1030 | setCursorSlice (start, end, doAll, in);
|
---|
1031 |
|
---|
1032 | // Loop over rows in Table
|
---|
1033 |
|
---|
1034 | for (uInt ri=0; ri < in.nRow(); ++ri) {
|
---|
1035 |
|
---|
1036 | // Get slice of data
|
---|
1037 |
|
---|
1038 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(ri);
|
---|
1039 |
|
---|
1040 | // Deconstruct and get slices which reference these arrays
|
---|
1041 |
|
---|
1042 | Array<Float> valuesIn = dataIn.getArray();
|
---|
1043 | Array<Bool> maskIn = dataIn.getMask();
|
---|
1044 | //
|
---|
1045 | Array<Float> valuesIn2 = valuesIn(start,end); // ref to valuesIn
|
---|
1046 | Array<Bool> maskIn2 = maskIn(start,end);
|
---|
1047 |
|
---|
1048 | // Iterate through by spectra
|
---|
1049 |
|
---|
1050 | VectorIterator<Float> itValues(valuesIn2, asap::ChanAxis);
|
---|
1051 | VectorIterator<Bool> itMask(maskIn2, asap::ChanAxis);
|
---|
1052 | while (!itValues.pastEnd()) {
|
---|
1053 |
|
---|
1054 | // Smooth
|
---|
1055 |
|
---|
1056 | if (kernelType==VectorKernel::HANNING) {
|
---|
1057 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector());
|
---|
1058 | itMask.vector() = maskOut;
|
---|
1059 | } else {
|
---|
1060 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector());
|
---|
1061 | conv.linearConv(valuesOut, itValues.vector());
|
---|
1062 | }
|
---|
1063 | //
|
---|
1064 | itValues.vector() = valuesOut;
|
---|
1065 | //
|
---|
1066 | itValues.next();
|
---|
1067 | itMask.next();
|
---|
1068 | }
|
---|
1069 |
|
---|
1070 | // Create and put back
|
---|
1071 |
|
---|
1072 | SDContainer sc = in.getSDContainer(ri);
|
---|
1073 | putDataInSDC(sc, valuesIn, maskIn);
|
---|
1074 | //
|
---|
1075 | pTabOut->putSDContainer(sc);
|
---|
1076 | }
|
---|
1077 | //
|
---|
1078 | return pTabOut;
|
---|
1079 | }
|
---|
1080 |
|
---|
1081 |
|
---|
1082 |
|
---|
1083 | SDMemTable* SDMath::convertFlux(const SDMemTable& in, Float D, Float etaAp,
|
---|
1084 | Float JyPerK, Bool doAll) const
|
---|
1085 | //
|
---|
1086 | // etaAp = aperture efficiency (-1 means find)
|
---|
1087 | // D = geometric diameter (m) (-1 means find)
|
---|
1088 | // JyPerK
|
---|
1089 | //
|
---|
1090 | {
|
---|
1091 | SDHeader sh = in.getSDHeader();
|
---|
1092 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
1093 |
|
---|
1094 | // Find out how to convert values into Jy and K (e.g. units might be mJy or mK)
|
---|
1095 | // Also automatically find out what we are converting to according to the
|
---|
1096 | // flux unit
|
---|
1097 |
|
---|
1098 | Unit fluxUnit(sh.fluxunit);
|
---|
1099 | Unit K(String("K"));
|
---|
1100 | Unit JY(String("Jy"));
|
---|
1101 | //
|
---|
1102 | Bool toKelvin = True;
|
---|
1103 | Double cFac = 1.0;
|
---|
1104 | if (fluxUnit==JY) {
|
---|
1105 | cout << "Converting to K" << endl;
|
---|
1106 | //
|
---|
1107 | Quantum<Double> t(1.0,fluxUnit);
|
---|
1108 | Quantum<Double> t2 = t.get(JY);
|
---|
1109 | cFac = (t2 / t).getValue(); // value to Jy
|
---|
1110 | //
|
---|
1111 | toKelvin = True;
|
---|
1112 | sh.fluxunit = "K";
|
---|
1113 | } else if (fluxUnit==K) {
|
---|
1114 | cout << "Converting to Jy" << endl;
|
---|
1115 | //
|
---|
1116 | Quantum<Double> t(1.0,fluxUnit);
|
---|
1117 | Quantum<Double> t2 = t.get(K);
|
---|
1118 | cFac = (t2 / t).getValue(); // value to K
|
---|
1119 | //
|
---|
1120 | toKelvin = False;
|
---|
1121 | sh.fluxunit = "Jy";
|
---|
1122 | } else {
|
---|
1123 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
|
---|
1124 | }
|
---|
1125 | pTabOut->putSDHeader(sh);
|
---|
1126 |
|
---|
1127 | // Make sure input values are converted to either Jy or K first...
|
---|
1128 |
|
---|
1129 | Float factor = cFac;
|
---|
1130 |
|
---|
1131 | // Select method
|
---|
1132 |
|
---|
1133 | if (JyPerK>0.0) {
|
---|
1134 | factor *= JyPerK;
|
---|
1135 | if (toKelvin) factor = 1.0 / JyPerK;
|
---|
1136 | //
|
---|
1137 | cout << "Jy/K = " << JyPerK << endl;
|
---|
1138 | Vector<Float> factors(in.nRow(), factor);
|
---|
1139 | scaleByVector(pTabOut, in, doAll, factors, False);
|
---|
1140 | } else if (etaAp>0.0) {
|
---|
1141 | Bool throwIt = True;
|
---|
1142 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt);
|
---|
1143 | SDAttr sda;
|
---|
1144 | if (D < 0) D = sda.diameter(inst);
|
---|
1145 | Float JyPerK = SDAttr::findJyPerK (etaAp,D);
|
---|
1146 | cout << "Jy/K = " << JyPerK << endl;
|
---|
1147 | factor *= JyPerK;
|
---|
1148 | if (toKelvin) {
|
---|
1149 | factor = 1.0 / factor;
|
---|
1150 | }
|
---|
1151 | //
|
---|
1152 | Vector<Float> factors(in.nRow(), factor);
|
---|
1153 | scaleByVector(pTabOut, in, doAll, factors, False);
|
---|
1154 | } else {
|
---|
1155 |
|
---|
1156 | // OK now we must deal with automatic look up of values.
|
---|
1157 | // We must also deal with the fact that the factors need
|
---|
1158 | // to be computed per IF and may be different and may
|
---|
1159 | // change per integration.
|
---|
1160 |
|
---|
1161 | cout << "Looking up conversion factors" << endl;
|
---|
1162 | convertBrightnessUnits (pTabOut, in, toKelvin, cFac, doAll);
|
---|
1163 | }
|
---|
1164 | //
|
---|
1165 | return pTabOut;
|
---|
1166 | }
|
---|
1167 |
|
---|
1168 |
|
---|
1169 |
|
---|
1170 |
|
---|
1171 |
|
---|
1172 | SDMemTable* SDMath::gainElevation(const SDMemTable& in,
|
---|
1173 | const Vector<Float>& coeffs,
|
---|
1174 | const String& fileName,
|
---|
1175 | const String& methodStr, Bool doAll) const
|
---|
1176 | {
|
---|
1177 |
|
---|
1178 | // Get header and clone output table
|
---|
1179 |
|
---|
1180 | SDHeader sh = in.getSDHeader();
|
---|
1181 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
1182 |
|
---|
1183 | // Get elevation data from SDMemTable and convert to degrees
|
---|
1184 |
|
---|
1185 | const Table& tab = in.table();
|
---|
1186 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
1187 | Vector<Float> x = elev.getColumn();
|
---|
1188 | x *= Float(180 / C::pi); // Degrees
|
---|
1189 | //
|
---|
1190 | const uInt nC = coeffs.nelements();
|
---|
1191 | if (fileName.length()>0 && nC>0) {
|
---|
1192 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
|
---|
1193 | }
|
---|
1194 |
|
---|
1195 | // Correct
|
---|
1196 |
|
---|
1197 | if (nC>0 || fileName.length()==0) {
|
---|
1198 |
|
---|
1199 | // Find instrument
|
---|
1200 |
|
---|
1201 | Bool throwIt = True;
|
---|
1202 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt);
|
---|
1203 |
|
---|
1204 | // Set polynomial
|
---|
1205 |
|
---|
1206 | Polynomial<Float>* pPoly = 0;
|
---|
1207 | Vector<Float> coeff;
|
---|
1208 | String msg;
|
---|
1209 | if (nC>0) {
|
---|
1210 | pPoly = new Polynomial<Float>(nC);
|
---|
1211 | coeff = coeffs;
|
---|
1212 | msg = String("user");
|
---|
1213 | } else {
|
---|
1214 | SDAttr sdAttr;
|
---|
1215 | coeff = sdAttr.gainElevationPoly(inst);
|
---|
1216 | pPoly = new Polynomial<Float>(3);
|
---|
1217 | msg = String("built in");
|
---|
1218 | }
|
---|
1219 | //
|
---|
1220 | if (coeff.nelements()>0) {
|
---|
1221 | pPoly->setCoefficients(coeff);
|
---|
1222 | } else {
|
---|
1223 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
|
---|
1224 | }
|
---|
1225 | //
|
---|
1226 | cout << "Making polynomial correction with " << msg << " coefficients" << endl;
|
---|
1227 | const uInt nRow = in.nRow();
|
---|
1228 | Vector<Float> factor(nRow);
|
---|
1229 | for (uInt i=0; i<nRow; i++) {
|
---|
1230 | factor[i] = 1.0 / (*pPoly)(x[i]);
|
---|
1231 | }
|
---|
1232 | delete pPoly;
|
---|
1233 | //
|
---|
1234 | scaleByVector (pTabOut, in, doAll, factor, True);
|
---|
1235 | } else {
|
---|
1236 |
|
---|
1237 | // Indicate which columns to read from ascii file
|
---|
1238 |
|
---|
1239 | String col0("ELEVATION");
|
---|
1240 | String col1("FACTOR");
|
---|
1241 |
|
---|
1242 | // Read and correct
|
---|
1243 |
|
---|
1244 | cout << "Making correction from ascii Table" << endl;
|
---|
1245 | scaleFromAsciiTable (pTabOut, in, fileName, col0, col1,
|
---|
1246 | methodStr, doAll, x, True);
|
---|
1247 | }
|
---|
1248 | //
|
---|
1249 | return pTabOut;
|
---|
1250 | }
|
---|
1251 |
|
---|
1252 |
|
---|
1253 |
|
---|
1254 | SDMemTable* SDMath::opacity(const SDMemTable& in, Float tau, Bool doAll) const
|
---|
1255 | {
|
---|
1256 |
|
---|
1257 | // Get header and clone output table
|
---|
1258 |
|
---|
1259 | SDHeader sh = in.getSDHeader();
|
---|
1260 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
1261 |
|
---|
1262 | // Get elevation data from SDMemTable and convert to degrees
|
---|
1263 |
|
---|
1264 | const Table& tab = in.table();
|
---|
1265 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
1266 | Vector<Float> zDist = elev.getColumn();
|
---|
1267 | zDist = Float(C::pi_2) - zDist;
|
---|
1268 |
|
---|
1269 | // Generate correction factor
|
---|
1270 |
|
---|
1271 | const uInt nRow = in.nRow();
|
---|
1272 | Vector<Float> factor(nRow);
|
---|
1273 | Vector<Float> factor2(nRow);
|
---|
1274 | for (uInt i=0; i<nRow; i++) {
|
---|
1275 | factor[i] = exp(tau)/cos(zDist[i]);
|
---|
1276 | }
|
---|
1277 |
|
---|
1278 | // Correct
|
---|
1279 |
|
---|
1280 | scaleByVector (pTabOut, in, doAll, factor, True);
|
---|
1281 | //
|
---|
1282 | return pTabOut;
|
---|
1283 | }
|
---|
1284 |
|
---|
1285 |
|
---|
1286 | void SDMath::rotateXYPhase(SDMemTable& in, Float value, Bool doAll)
|
---|
1287 | //
|
---|
1288 | // phase in degrees
|
---|
1289 | // assumes linear correlations
|
---|
1290 | //
|
---|
1291 | {
|
---|
1292 | if (in.nPol() != 4) {
|
---|
1293 | throw(AipsError("You must have 4 polarizations to run this function"));
|
---|
1294 | }
|
---|
1295 | //
|
---|
1296 | SDHeader sh = in.getSDHeader();
|
---|
1297 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False);
|
---|
1298 | SDAttr sdAtt;
|
---|
1299 | if (sdAtt.feedPolType(inst) != LINEAR) {
|
---|
1300 | throw(AipsError("Only linear polarizations are supported"));
|
---|
1301 | }
|
---|
1302 | //
|
---|
1303 | const Table& tabIn = in.table();
|
---|
1304 | ArrayColumn<Float> specCol(tabIn,"SPECTRA");
|
---|
1305 | IPosition start(asap::nAxes,0);
|
---|
1306 | IPosition end(asap::nAxes);
|
---|
1307 |
|
---|
1308 | // Set cursor slice. Assumes shape the same for all rows
|
---|
1309 |
|
---|
1310 | setCursorSlice (start, end, doAll, in);
|
---|
1311 | IPosition start3(start);
|
---|
1312 | start3(asap::PolAxis) = 2; // Real(XY)
|
---|
1313 | IPosition end3(end);
|
---|
1314 | end3(asap::PolAxis) = 2;
|
---|
1315 | //
|
---|
1316 | IPosition start4(start);
|
---|
1317 | start4(asap::PolAxis) = 3; // Imag (XY)
|
---|
1318 | IPosition end4(end);
|
---|
1319 | end4(asap::PolAxis) = 3;
|
---|
1320 | //
|
---|
1321 | uInt nRow = in.nRow();
|
---|
1322 | Array<Float> data;
|
---|
1323 | for (uInt i=0; i<nRow;++i) {
|
---|
1324 | specCol.get(i,data);
|
---|
1325 | IPosition shape = data.shape();
|
---|
1326 |
|
---|
1327 | // Get polarization slice references
|
---|
1328 |
|
---|
1329 | Array<Float> C3 = data(start3,end3);
|
---|
1330 | Array<Float> C4 = data(start4,end4);
|
---|
1331 |
|
---|
1332 | // Rotate
|
---|
1333 |
|
---|
1334 | SDPolUtil::rotatePhase(C3, C4, value);
|
---|
1335 |
|
---|
1336 | // Put
|
---|
1337 |
|
---|
1338 | specCol.put(i,data);
|
---|
1339 | }
|
---|
1340 | }
|
---|
1341 |
|
---|
1342 |
|
---|
1343 |
|
---|
1344 | void SDMath::rotateLinPolPhase(SDMemTable& in, Float value, Bool doAll)
|
---|
1345 | //
|
---|
1346 | // phase in degrees
|
---|
1347 | // assumes linear correlations
|
---|
1348 | //
|
---|
1349 | {
|
---|
1350 | if (in.nPol() != 4) {
|
---|
1351 | throw(AipsError("You must have 4 polarizations to run this function"));
|
---|
1352 | }
|
---|
1353 | //
|
---|
1354 | SDHeader sh = in.getSDHeader();
|
---|
1355 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, False);
|
---|
1356 | SDAttr sdAtt;
|
---|
1357 | if (sdAtt.feedPolType(inst) != LINEAR) {
|
---|
1358 | throw(AipsError("Only linear polarizations are supported"));
|
---|
1359 | }
|
---|
1360 | //
|
---|
1361 | const Table& tabIn = in.table();
|
---|
1362 | ArrayColumn<Float> specCol(tabIn,"SPECTRA");
|
---|
1363 | ROArrayColumn<Float> stokesCol(tabIn,"STOKES");
|
---|
1364 | IPosition start(asap::nAxes,0);
|
---|
1365 | IPosition end(asap::nAxes);
|
---|
1366 |
|
---|
1367 | // Set cursor slice. Assumes shape the same for all rows
|
---|
1368 |
|
---|
1369 | setCursorSlice (start, end, doAll, in);
|
---|
1370 | //
|
---|
1371 | IPosition start1(start);
|
---|
1372 | start1(asap::PolAxis) = 0; // C1 (XX)
|
---|
1373 | IPosition end1(end);
|
---|
1374 | end1(asap::PolAxis) = 0;
|
---|
1375 | //
|
---|
1376 | IPosition start2(start);
|
---|
1377 | start2(asap::PolAxis) = 1; // C2 (YY)
|
---|
1378 | IPosition end2(end);
|
---|
1379 | end2(asap::PolAxis) = 1;
|
---|
1380 | //
|
---|
1381 | IPosition start3(start);
|
---|
1382 | start3(asap::PolAxis) = 2; // C3 ( Real(XY) )
|
---|
1383 | IPosition end3(end);
|
---|
1384 | end3(asap::PolAxis) = 2;
|
---|
1385 | //
|
---|
1386 | IPosition startI(start);
|
---|
1387 | startI(asap::PolAxis) = 0; // I
|
---|
1388 | IPosition endI(end);
|
---|
1389 | endI(asap::PolAxis) = 0;
|
---|
1390 | //
|
---|
1391 | IPosition startQ(start);
|
---|
1392 | startQ(asap::PolAxis) = 1; // Q
|
---|
1393 | IPosition endQ(end);
|
---|
1394 | endQ(asap::PolAxis) = 1;
|
---|
1395 | //
|
---|
1396 | IPosition startU(start);
|
---|
1397 | startU(asap::PolAxis) = 2; // U
|
---|
1398 | IPosition endU(end);
|
---|
1399 | endU(asap::PolAxis) = 2;
|
---|
1400 |
|
---|
1401 | //
|
---|
1402 | uInt nRow = in.nRow();
|
---|
1403 | Array<Float> data, stokes;
|
---|
1404 | for (uInt i=0; i<nRow;++i) {
|
---|
1405 | specCol.get(i,data);
|
---|
1406 | stokesCol.get(i,stokes);
|
---|
1407 | IPosition shape = data.shape();
|
---|
1408 |
|
---|
1409 | // Get linear polarization slice references
|
---|
1410 |
|
---|
1411 | Array<Float> C1 = data(start1,end1);
|
---|
1412 | Array<Float> C2 = data(start2,end2);
|
---|
1413 | Array<Float> C3 = data(start3,end3);
|
---|
1414 |
|
---|
1415 | // Get STokes slice references
|
---|
1416 |
|
---|
1417 | Array<Float> I = stokes(startI,endI);
|
---|
1418 | Array<Float> Q = stokes(startQ,endQ);
|
---|
1419 | Array<Float> U = stokes(startU,endU);
|
---|
1420 |
|
---|
1421 | // Rotate
|
---|
1422 |
|
---|
1423 | SDPolUtil::rotateLinPolPhase(C1, C2, C3, I, Q, U, value);
|
---|
1424 |
|
---|
1425 | // Put
|
---|
1426 |
|
---|
1427 | specCol.put(i,data);
|
---|
1428 | }
|
---|
1429 | }
|
---|
1430 |
|
---|
1431 | // 'private' functions
|
---|
1432 |
|
---|
1433 | void SDMath::convertBrightnessUnits (SDMemTable* pTabOut, const SDMemTable& in,
|
---|
1434 | Bool toKelvin, Float cFac, Bool doAll) const
|
---|
1435 | {
|
---|
1436 |
|
---|
1437 | // Get header
|
---|
1438 |
|
---|
1439 | SDHeader sh = in.getSDHeader();
|
---|
1440 | const uInt nChan = sh.nchan;
|
---|
1441 |
|
---|
1442 | // Get instrument
|
---|
1443 |
|
---|
1444 | Bool throwIt = True;
|
---|
1445 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt);
|
---|
1446 |
|
---|
1447 | // Get Diameter (m)
|
---|
1448 |
|
---|
1449 | SDAttr sdAtt;
|
---|
1450 |
|
---|
1451 | // Get epoch of first row
|
---|
1452 |
|
---|
1453 | MEpoch dateObs = in.getEpoch(0);
|
---|
1454 |
|
---|
1455 | // Generate a Vector of correction factors. One per FreqID
|
---|
1456 |
|
---|
1457 | SDFrequencyTable sdft = in.getSDFreqTable();
|
---|
1458 | Vector<uInt> freqIDs;
|
---|
1459 | //
|
---|
1460 | Vector<Float> freqs(sdft.length());
|
---|
1461 | for (uInt i=0; i<sdft.length(); i++) {
|
---|
1462 | freqs(i) = (nChan/2 - sdft.referencePixel(i))*sdft.increment(i) + sdft.referenceValue(i);
|
---|
1463 | }
|
---|
1464 | //
|
---|
1465 | Vector<Float> JyPerK = sdAtt.JyPerK(inst, dateObs, freqs);
|
---|
1466 | cout << "Jy/K = " << JyPerK << endl;
|
---|
1467 | Vector<Float> factors = cFac * JyPerK;
|
---|
1468 | if (toKelvin) factors = Float(1.0) / factors;
|
---|
1469 |
|
---|
1470 | // Get data slice bounds
|
---|
1471 |
|
---|
1472 | IPosition start, end;
|
---|
1473 | setCursorSlice (start, end, doAll, in);
|
---|
1474 | const uInt ifAxis = in.getIF();
|
---|
1475 |
|
---|
1476 | // Iteration axes
|
---|
1477 |
|
---|
1478 | IPosition axes(asap::nAxes-1,0);
|
---|
1479 | for (uInt i=0,j=0; i<asap::nAxes; i++) {
|
---|
1480 | if (i!=asap::IFAxis) {
|
---|
1481 | axes(j++) = i;
|
---|
1482 | }
|
---|
1483 | }
|
---|
1484 |
|
---|
1485 | // Loop over rows and apply correction factor
|
---|
1486 |
|
---|
1487 | Float factor = 1.0;
|
---|
1488 | const uInt axis = asap::ChanAxis;
|
---|
1489 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
1490 |
|
---|
1491 | // Get data
|
---|
1492 |
|
---|
1493 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(i);
|
---|
1494 | Array<Float>& values = dataIn.getRWArray(); // Ref to dataIn
|
---|
1495 | Array<Float> values2 = values(start,end); // Ref to values to dataIn
|
---|
1496 |
|
---|
1497 | // Get SDCOntainer
|
---|
1498 |
|
---|
1499 | SDContainer sc = in.getSDContainer(i);
|
---|
1500 |
|
---|
1501 | // Get FreqIDs
|
---|
1502 |
|
---|
1503 | freqIDs = sc.getFreqMap();
|
---|
1504 |
|
---|
1505 | // Now the conversion factor depends only upon frequency
|
---|
1506 | // So we need to iterate through by IF only giving
|
---|
1507 | // us BEAM/POL/CHAN cubes
|
---|
1508 |
|
---|
1509 | ArrayIterator<Float> itIn(values2, axes);
|
---|
1510 | uInt ax = 0;
|
---|
1511 | while (!itIn.pastEnd()) {
|
---|
1512 | itIn.array() *= factors(freqIDs(ax)); // Writes back to dataIn
|
---|
1513 | itIn.next();
|
---|
1514 | }
|
---|
1515 |
|
---|
1516 | // Write out
|
---|
1517 |
|
---|
1518 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask());
|
---|
1519 | //
|
---|
1520 | pTabOut->putSDContainer(sc);
|
---|
1521 | }
|
---|
1522 | }
|
---|
1523 |
|
---|
1524 |
|
---|
1525 |
|
---|
1526 | SDMemTable* SDMath::frequencyAlign (const SDMemTable& in,
|
---|
1527 | MFrequency::Types freqSystem,
|
---|
1528 | const String& refTime,
|
---|
1529 | const String& methodStr,
|
---|
1530 | Bool perFreqID) const
|
---|
1531 | {
|
---|
1532 | // Get Header
|
---|
1533 |
|
---|
1534 | SDHeader sh = in.getSDHeader();
|
---|
1535 | const uInt nChan = sh.nchan;
|
---|
1536 | const uInt nRows = in.nRow();
|
---|
1537 | const uInt nIF = sh.nif;
|
---|
1538 |
|
---|
1539 | // Get Table reference
|
---|
1540 |
|
---|
1541 | const Table& tabIn = in.table();
|
---|
1542 |
|
---|
1543 | // Get Columns from Table
|
---|
1544 |
|
---|
1545 | ROScalarColumn<Double> mjdCol(tabIn, "TIME");
|
---|
1546 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME");
|
---|
1547 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID");
|
---|
1548 | Vector<Double> times = mjdCol.getColumn();
|
---|
1549 |
|
---|
1550 | // Generate DataDesc table
|
---|
1551 |
|
---|
1552 | Matrix<uInt> ddIdx;
|
---|
1553 | SDDataDesc dDesc;
|
---|
1554 | generateDataDescTable (ddIdx, dDesc, nIF, in, tabIn, srcCol, fqIDCol, perFreqID);
|
---|
1555 |
|
---|
1556 | // Get reference Epoch to time of first row or given String
|
---|
1557 |
|
---|
1558 | Unit DAY(String("d"));
|
---|
1559 | MEpoch::Ref epochRef(in.getTimeReference());
|
---|
1560 | MEpoch refEpoch;
|
---|
1561 | if (refTime.length()>0) {
|
---|
1562 | refEpoch = epochFromString(refTime, in.getTimeReference());
|
---|
1563 | } else {
|
---|
1564 | refEpoch = in.getEpoch(0);
|
---|
1565 | }
|
---|
1566 | cout << "Aligning at reference Epoch " << formatEpoch(refEpoch)
|
---|
1567 | << " in frame " << MFrequency::showType(freqSystem) << endl;
|
---|
1568 |
|
---|
1569 | // Get Reference Position
|
---|
1570 |
|
---|
1571 | MPosition refPos = in.getAntennaPosition();
|
---|
1572 |
|
---|
1573 | // Create FrequencyAligner Block. One FA for each possible
|
---|
1574 | // source/freqID (perFreqID=True) or source/IF (perFreqID=False) combination
|
---|
1575 |
|
---|
1576 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length());
|
---|
1577 | generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos,
|
---|
1578 | refEpoch, perFreqID);
|
---|
1579 |
|
---|
1580 | // Generate and fill output Frequency Table. WHen perFreqID=True, there is one output FreqID
|
---|
1581 | // for each entry in the SDDataDesc table. However, in perFreqID=False mode, there may be
|
---|
1582 | // some degeneracy, so we need a little translation map
|
---|
1583 |
|
---|
1584 | SDFrequencyTable freqTabOut = in.getSDFreqTable();
|
---|
1585 | freqTabOut.setLength(0);
|
---|
1586 | Vector<String> units(1);
|
---|
1587 | units = String("Hz");
|
---|
1588 | Bool linear=True;
|
---|
1589 | //
|
---|
1590 | Vector<uInt> ddFQTrans(dDesc.length(),0);
|
---|
1591 | for (uInt i=0; i<dDesc.length(); i++) {
|
---|
1592 |
|
---|
1593 | // Get Aligned SC in Hz
|
---|
1594 |
|
---|
1595 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear);
|
---|
1596 | sC.setWorldAxisUnits(units);
|
---|
1597 |
|
---|
1598 | // Add FreqID
|
---|
1599 |
|
---|
1600 | uInt idx = freqTabOut.addFrequency(sC.referencePixel()[0],
|
---|
1601 | sC.referenceValue()[0],
|
---|
1602 | sC.increment()[0]);
|
---|
1603 | ddFQTrans(i) = idx; // output FreqID = ddFQTrans(ddIdx)
|
---|
1604 | }
|
---|
1605 |
|
---|
1606 | // Interpolation method
|
---|
1607 |
|
---|
1608 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
---|
1609 | convertInterpString(interp, methodStr);
|
---|
1610 |
|
---|
1611 | // New output Table
|
---|
1612 |
|
---|
1613 | cout << "Create output table" << endl;
|
---|
1614 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
1615 | pTabOut->putSDFreqTable(freqTabOut);
|
---|
1616 |
|
---|
1617 | // Loop over rows in Table
|
---|
1618 |
|
---|
1619 | Bool extrapolate=False;
|
---|
1620 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis);
|
---|
1621 | Bool useCachedAbcissa = False;
|
---|
1622 | Bool first = True;
|
---|
1623 | Bool ok;
|
---|
1624 | Vector<Float> yOut;
|
---|
1625 | Vector<Bool> maskOut;
|
---|
1626 | Vector<uInt> freqID(nIF);
|
---|
1627 | uInt ifIdx, faIdx;
|
---|
1628 | Vector<Double> xIn;
|
---|
1629 | //
|
---|
1630 | for (uInt iRow=0; iRow<nRows; ++iRow) {
|
---|
1631 | if (iRow%10==0) {
|
---|
1632 | cout << "Processing row " << iRow << endl;
|
---|
1633 | }
|
---|
1634 |
|
---|
1635 | // Get EPoch
|
---|
1636 |
|
---|
1637 | Quantum<Double> tQ2(times[iRow],DAY);
|
---|
1638 | MVEpoch mv2(tQ2);
|
---|
1639 | MEpoch epoch(mv2, epochRef);
|
---|
1640 |
|
---|
1641 | // Get copy of data
|
---|
1642 |
|
---|
1643 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow));
|
---|
1644 | Array<Float> values = mArrIn.getArray();
|
---|
1645 | Array<Bool> mask = mArrIn.getMask();
|
---|
1646 |
|
---|
1647 | // For each row, the Frequency abcissa will be the same regardless
|
---|
1648 | // of polarization. For all other axes (IF and BEAM) the abcissa
|
---|
1649 | // will change. So we iterate through the data by pol-chan planes
|
---|
1650 | // to mimimize the work. Probably won't work for multiple beams
|
---|
1651 | // at this point.
|
---|
1652 |
|
---|
1653 | ArrayIterator<Float> itValuesPlane(values, polChanAxes);
|
---|
1654 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes);
|
---|
1655 | while (!itValuesPlane.pastEnd()) {
|
---|
1656 |
|
---|
1657 | // Find the IF index and then the FA PtrBlock index
|
---|
1658 |
|
---|
1659 | const IPosition& pos = itValuesPlane.pos();
|
---|
1660 | ifIdx = pos(asap::IFAxis);
|
---|
1661 | faIdx = ddIdx(iRow,ifIdx);
|
---|
1662 |
|
---|
1663 | // Generate abcissa for perIF. Could cache this in a Matrix
|
---|
1664 | // on a per scan basis. Pretty expensive doing it for every row.
|
---|
1665 |
|
---|
1666 | if (!perFreqID) {
|
---|
1667 | xIn.resize(nChan);
|
---|
1668 | uInt fqID = dDesc.secID(ddIdx(iRow,ifIdx));
|
---|
1669 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID);
|
---|
1670 | Double w;
|
---|
1671 | for (uInt i=0; i<nChan; i++) {
|
---|
1672 | sC.toWorld(w,Double(i));
|
---|
1673 | xIn[i] = w;
|
---|
1674 | }
|
---|
1675 | }
|
---|
1676 | //
|
---|
1677 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1);
|
---|
1678 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
1679 |
|
---|
1680 | // Iterate through the plane by vector and align
|
---|
1681 |
|
---|
1682 | first = True;
|
---|
1683 | useCachedAbcissa=False;
|
---|
1684 | while (!itValuesVec.pastEnd()) {
|
---|
1685 | if (perFreqID) {
|
---|
1686 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(),
|
---|
1687 | itMaskVec.vector(), epoch, useCachedAbcissa,
|
---|
1688 | interp, extrapolate);
|
---|
1689 | } else {
|
---|
1690 | ok = a[faIdx]->align (yOut, maskOut, xIn, itValuesVec.vector(),
|
---|
1691 | itMaskVec.vector(), epoch, useCachedAbcissa,
|
---|
1692 | interp, extrapolate);
|
---|
1693 | }
|
---|
1694 | //
|
---|
1695 | itValuesVec.vector() = yOut;
|
---|
1696 | itMaskVec.vector() = maskOut;
|
---|
1697 | //
|
---|
1698 | itValuesVec.next();
|
---|
1699 | itMaskVec.next();
|
---|
1700 | //
|
---|
1701 | if (first) {
|
---|
1702 | useCachedAbcissa = True;
|
---|
1703 | first = False;
|
---|
1704 | }
|
---|
1705 | }
|
---|
1706 | //
|
---|
1707 | itValuesPlane.next();
|
---|
1708 | itMaskPlane.next();
|
---|
1709 | }
|
---|
1710 |
|
---|
1711 | // Create SDContainer and put back
|
---|
1712 |
|
---|
1713 | SDContainer sc = in.getSDContainer(iRow);
|
---|
1714 | putDataInSDC(sc, values, mask);
|
---|
1715 |
|
---|
1716 | // Set output FreqIDs
|
---|
1717 |
|
---|
1718 | for (uInt i=0; i<nIF; i++) {
|
---|
1719 | uInt idx = ddIdx(iRow,i); // Index into SDDataDesc table
|
---|
1720 | freqID(i) = ddFQTrans(idx); // FreqID in output FQ table
|
---|
1721 | }
|
---|
1722 | sc.putFreqMap(freqID);
|
---|
1723 | //
|
---|
1724 | pTabOut->putSDContainer(sc);
|
---|
1725 | }
|
---|
1726 |
|
---|
1727 | // Now we must set the base and extra frames to the
|
---|
1728 | // input frame
|
---|
1729 |
|
---|
1730 | std::vector<string> info = pTabOut->getCoordInfo();
|
---|
1731 | info[1] = MFrequency::showType(freqSystem); // Conversion frame
|
---|
1732 | info[3] = info[1]; // Base frame
|
---|
1733 | pTabOut->setCoordInfo(info);
|
---|
1734 |
|
---|
1735 | // Clean up PointerBlock
|
---|
1736 |
|
---|
1737 | for (uInt i=0; i<a.nelements(); i++) delete a[i];
|
---|
1738 | //
|
---|
1739 | return pTabOut;
|
---|
1740 | }
|
---|
1741 |
|
---|
1742 |
|
---|
1743 | void SDMath::fillSDC(SDContainer& sc,
|
---|
1744 | const Array<Bool>& mask,
|
---|
1745 | const Array<Float>& data,
|
---|
1746 | const Array<Float>& tSys,
|
---|
1747 | Int scanID, Double timeStamp,
|
---|
1748 | Double interval, const String& sourceName,
|
---|
1749 | const Vector<uInt>& freqID) const
|
---|
1750 | {
|
---|
1751 | // Data and mask
|
---|
1752 |
|
---|
1753 | putDataInSDC(sc, data, mask);
|
---|
1754 |
|
---|
1755 | // TSys
|
---|
1756 |
|
---|
1757 | sc.putTsys(tSys);
|
---|
1758 |
|
---|
1759 | // Time things
|
---|
1760 |
|
---|
1761 | sc.timestamp = timeStamp;
|
---|
1762 | sc.interval = interval;
|
---|
1763 | sc.scanid = scanID;
|
---|
1764 | //
|
---|
1765 | sc.sourcename = sourceName;
|
---|
1766 | sc.putFreqMap(freqID);
|
---|
1767 | }
|
---|
1768 |
|
---|
1769 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum,
|
---|
1770 | MaskedArray<Float>& sum, Array<Float>& sumSq,
|
---|
1771 | Array<Float>& nPts, Array<Float>& tSysSum,
|
---|
1772 | Array<Float>& tSysSqSum,
|
---|
1773 | const Array<Float>& tSys, const Array<Float>& nInc,
|
---|
1774 | const Vector<Bool>& mask, Double time, Double interval,
|
---|
1775 | const Block<CountedPtr<SDMemTable> >& in,
|
---|
1776 | uInt iTab, uInt iRow, uInt axis,
|
---|
1777 | uInt nAxesSub, Bool useMask,
|
---|
1778 | WeightType wtType) const
|
---|
1779 | {
|
---|
1780 |
|
---|
1781 | // Get data
|
---|
1782 |
|
---|
1783 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow));
|
---|
1784 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference
|
---|
1785 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference
|
---|
1786 | //
|
---|
1787 | if (wtType==NONE) {
|
---|
1788 | const MaskedArray<Float> n(nInc,dataIn.getMask());
|
---|
1789 | nPts += n; // Only accumulates where mask==T
|
---|
1790 | } else if (wtType==TINT) {
|
---|
1791 |
|
---|
1792 | // We are weighting the data by integration time.
|
---|
1793 |
|
---|
1794 | valuesIn *= Float(interval);
|
---|
1795 |
|
---|
1796 | } else if (wtType==VAR) {
|
---|
1797 |
|
---|
1798 | // We are going to average the data, weighted by the noise for each pol, beam and IF.
|
---|
1799 | // So therefore we need to iterate through by spectrum (axis 3)
|
---|
1800 |
|
---|
1801 | VectorIterator<Float> itData(valuesIn, axis);
|
---|
1802 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis);
|
---|
1803 | Float fac = 1.0;
|
---|
1804 | IPosition pos(nAxesSub,0);
|
---|
1805 | //
|
---|
1806 | while (!itData.pastEnd()) {
|
---|
1807 |
|
---|
1808 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor
|
---|
1809 |
|
---|
1810 | if (useMask) {
|
---|
1811 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector());
|
---|
1812 | fac = 1.0/variance(tmp);
|
---|
1813 | } else {
|
---|
1814 | MaskedArray<Float> tmp(itData.vector(),itMask.vector());
|
---|
1815 | fac = 1.0/variance(tmp);
|
---|
1816 | }
|
---|
1817 |
|
---|
1818 | // Scale data
|
---|
1819 |
|
---|
1820 | itData.vector() *= fac; // Writes back into 'dataIn'
|
---|
1821 | //
|
---|
1822 | // Accumulate variance per if/pol/beam averaged over spectrum
|
---|
1823 | // This method to get pos2 from itData.pos() is only valid
|
---|
1824 | // because the spectral axis is the last one (so we can just
|
---|
1825 | // copy the first nAXesSub positions out)
|
---|
1826 |
|
---|
1827 | pos = itData.pos().getFirst(nAxesSub);
|
---|
1828 | sumSq(pos) += fac;
|
---|
1829 | //
|
---|
1830 | itData.next();
|
---|
1831 | itMask.next();
|
---|
1832 | }
|
---|
1833 | } else if (wtType==TSYS || wtType==TINTSYS) {
|
---|
1834 |
|
---|
1835 | // We are going to average the data, weighted by 1/Tsys**2 for each pol, beam and IF.
|
---|
1836 | // So therefore we need to iterate through by spectrum (axis 3). Although
|
---|
1837 | // Tsys is stored as a vector of length nChan, the values are replicated.
|
---|
1838 | // We will take a short cut and just use the value from the first channel
|
---|
1839 | // for now.
|
---|
1840 | //
|
---|
1841 | VectorIterator<Float> itData(valuesIn, axis);
|
---|
1842 | ReadOnlyVectorIterator<Float> itTSys(tSys, axis);
|
---|
1843 | IPosition pos(nAxesSub,0);
|
---|
1844 | //
|
---|
1845 | Float fac = 1.0;
|
---|
1846 | if (wtType==TINTSYS) fac *= interval;
|
---|
1847 | while (!itData.pastEnd()) {
|
---|
1848 | Float t = itTSys.vector()[0];
|
---|
1849 | fac *= 1.0/t/t;
|
---|
1850 |
|
---|
1851 | // Scale data
|
---|
1852 |
|
---|
1853 | itData.vector() *= fac; // Writes back into 'dataIn'
|
---|
1854 | //
|
---|
1855 | // Accumulate Tsys per if/pol/beam averaged over spectrum
|
---|
1856 | // This method to get pos2 from itData.pos() is only valid
|
---|
1857 | // because the spectral axis is the last one (so we can just
|
---|
1858 | // copy the first nAXesSub positions out)
|
---|
1859 |
|
---|
1860 | pos = itData.pos().getFirst(nAxesSub);
|
---|
1861 | tSysSqSum(pos) += fac;
|
---|
1862 | //
|
---|
1863 | itData.next();
|
---|
1864 | itTSys.next();
|
---|
1865 | }
|
---|
1866 | }
|
---|
1867 |
|
---|
1868 | // Accumulate sum of (possibly scaled) data
|
---|
1869 |
|
---|
1870 | sum += dataIn;
|
---|
1871 |
|
---|
1872 | // Accumulate Tsys, time, and interval
|
---|
1873 |
|
---|
1874 | tSysSum += tSys;
|
---|
1875 | timeSum += time;
|
---|
1876 | intSum += interval;
|
---|
1877 | nAccum += 1;
|
---|
1878 | }
|
---|
1879 |
|
---|
1880 |
|
---|
1881 | void SDMath::normalize(MaskedArray<Float>& sum,
|
---|
1882 | const Array<Float>& sumSq,
|
---|
1883 | const Array<Float>& tSysSqSum,
|
---|
1884 | const Array<Float>& nPts,
|
---|
1885 | Double intSum,
|
---|
1886 | WeightType wtType, Int axis,
|
---|
1887 | Int nAxesSub) const
|
---|
1888 | {
|
---|
1889 | IPosition pos2(nAxesSub,0);
|
---|
1890 | //
|
---|
1891 | if (wtType==NONE) {
|
---|
1892 |
|
---|
1893 | // We just average by the number of points accumulated.
|
---|
1894 | // We need to make a MA out of nPts so that no divide by
|
---|
1895 | // zeros occur
|
---|
1896 |
|
---|
1897 | MaskedArray<Float> t(nPts, (nPts>Float(0.0)));
|
---|
1898 | sum /= t;
|
---|
1899 | } else if (wtType==TINT) {
|
---|
1900 |
|
---|
1901 | // Average by sum of Tint
|
---|
1902 |
|
---|
1903 | sum /= Float(intSum);
|
---|
1904 | } else if (wtType==VAR) {
|
---|
1905 |
|
---|
1906 | // Normalize each spectrum by sum(1/var) where the variance
|
---|
1907 | // is worked out for each spectrum
|
---|
1908 |
|
---|
1909 | Array<Float>& data = sum.getRWArray();
|
---|
1910 | VectorIterator<Float> itData(data, axis);
|
---|
1911 | while (!itData.pastEnd()) {
|
---|
1912 | pos2 = itData.pos().getFirst(nAxesSub);
|
---|
1913 | itData.vector() /= sumSq(pos2);
|
---|
1914 | itData.next();
|
---|
1915 | }
|
---|
1916 | } else if (wtType==TSYS || wtType==TINTSYS) {
|
---|
1917 |
|
---|
1918 | // Normalize each spectrum by sum(1/Tsys**2) (TSYS) or
|
---|
1919 | // sum(Tint/Tsys**2) (TINTSYS) where the pseudo
|
---|
1920 | // replication over channel for Tsys has been dropped.
|
---|
1921 |
|
---|
1922 | Array<Float>& data = sum.getRWArray();
|
---|
1923 | VectorIterator<Float> itData(data, axis);
|
---|
1924 | while (!itData.pastEnd()) {
|
---|
1925 | pos2 = itData.pos().getFirst(nAxesSub);
|
---|
1926 | itData.vector() /= tSysSqSum(pos2);
|
---|
1927 | itData.next();
|
---|
1928 | }
|
---|
1929 | }
|
---|
1930 | }
|
---|
1931 |
|
---|
1932 |
|
---|
1933 |
|
---|
1934 |
|
---|
1935 | void SDMath::setCursorSlice (IPosition& start, IPosition& end, Bool doAll, const SDMemTable& in) const
|
---|
1936 | {
|
---|
1937 | const uInt nDim = asap::nAxes;
|
---|
1938 | DebugAssert(nDim==4,AipsError);
|
---|
1939 | //
|
---|
1940 | start.resize(nDim);
|
---|
1941 | end.resize(nDim);
|
---|
1942 | if (doAll) {
|
---|
1943 | start = 0;
|
---|
1944 | end(0) = in.nBeam()-1;
|
---|
1945 | end(1) = in.nIF()-1;
|
---|
1946 | end(2) = in.nPol()-1;
|
---|
1947 | end(3) = in.nChan()-1;
|
---|
1948 | } else {
|
---|
1949 | start(0) = in.getBeam();
|
---|
1950 | end(0) = start(0);
|
---|
1951 | //
|
---|
1952 | start(1) = in.getIF();
|
---|
1953 | end(1) = start(1);
|
---|
1954 | //
|
---|
1955 | start(2) = in.getPol();
|
---|
1956 | end(2) = start(2);
|
---|
1957 | //
|
---|
1958 | start(3) = 0;
|
---|
1959 | end(3) = in.nChan()-1;
|
---|
1960 | }
|
---|
1961 | }
|
---|
1962 |
|
---|
1963 |
|
---|
1964 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr,
|
---|
1965 | Bool listType) const
|
---|
1966 | {
|
---|
1967 | String tStr(weightStr);
|
---|
1968 | tStr.upcase();
|
---|
1969 | String msg;
|
---|
1970 | if (tStr.contains(String("NONE"))) {
|
---|
1971 | wtType = NONE;
|
---|
1972 | msg = String("Weighting type selected : None");
|
---|
1973 | } else if (tStr.contains(String("VAR"))) {
|
---|
1974 | wtType = VAR;
|
---|
1975 | msg = String("Weighting type selected : Variance");
|
---|
1976 | } else if (tStr.contains(String("TINTSYS"))) {
|
---|
1977 | wtType = TINTSYS;
|
---|
1978 | msg = String("Weighting type selected : Tint&Tsys");
|
---|
1979 | } else if (tStr.contains(String("TINT"))) {
|
---|
1980 | wtType = TINT;
|
---|
1981 | msg = String("Weighting type selected : Tint");
|
---|
1982 | } else if (tStr.contains(String("TSYS"))) {
|
---|
1983 | wtType = TSYS;
|
---|
1984 | msg = String("Weighting type selected : Tsys");
|
---|
1985 | } else {
|
---|
1986 | msg = String("Weighting type selected : None");
|
---|
1987 | throw(AipsError("Unrecognized weighting type"));
|
---|
1988 | }
|
---|
1989 | //
|
---|
1990 | if (listType) cout << msg << endl;
|
---|
1991 | }
|
---|
1992 |
|
---|
1993 |
|
---|
1994 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type,
|
---|
1995 | const casa::String& interp) const
|
---|
1996 | {
|
---|
1997 | String tStr(interp);
|
---|
1998 | tStr.upcase();
|
---|
1999 | if (tStr.contains(String("NEAR"))) {
|
---|
2000 | type = InterpolateArray1D<Double,Float>::nearestNeighbour;
|
---|
2001 | } else if (tStr.contains(String("LIN"))) {
|
---|
2002 | type = InterpolateArray1D<Double,Float>::linear;
|
---|
2003 | } else if (tStr.contains(String("CUB"))) {
|
---|
2004 | type = InterpolateArray1D<Double,Float>::cubic;
|
---|
2005 | } else if (tStr.contains(String("SPL"))) {
|
---|
2006 | type = InterpolateArray1D<Double,Float>::spline;
|
---|
2007 | } else {
|
---|
2008 | throw(AipsError("Unrecognized interpolation type"));
|
---|
2009 | }
|
---|
2010 | }
|
---|
2011 |
|
---|
2012 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data,
|
---|
2013 | const Array<Bool>& mask) const
|
---|
2014 | {
|
---|
2015 | sc.putSpectrum(data);
|
---|
2016 | //
|
---|
2017 | Array<uChar> outflags(data.shape());
|
---|
2018 | convertArray(outflags,!mask);
|
---|
2019 | sc.putFlags(outflags);
|
---|
2020 | }
|
---|
2021 |
|
---|
2022 | Table SDMath::readAsciiFile (const String& fileName) const
|
---|
2023 | {
|
---|
2024 | String formatString;
|
---|
2025 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False);
|
---|
2026 | return tbl;
|
---|
2027 | }
|
---|
2028 |
|
---|
2029 |
|
---|
2030 |
|
---|
2031 | void SDMath::scaleFromAsciiTable(SDMemTable* pTabOut,
|
---|
2032 | const SDMemTable& in, const String& fileName,
|
---|
2033 | const String& col0, const String& col1,
|
---|
2034 | const String& methodStr, Bool doAll,
|
---|
2035 | const Vector<Float>& xOut, Bool doTSys) const
|
---|
2036 | {
|
---|
2037 |
|
---|
2038 | // Read gain-elevation ascii file data into a Table.
|
---|
2039 |
|
---|
2040 | Table geTable = readAsciiFile (fileName);
|
---|
2041 | //
|
---|
2042 | scaleFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut, doTSys);
|
---|
2043 | }
|
---|
2044 |
|
---|
2045 | void SDMath::scaleFromTable(SDMemTable* pTabOut, const SDMemTable& in,
|
---|
2046 | const Table& tTable, const String& col0,
|
---|
2047 | const String& col1,
|
---|
2048 | const String& methodStr, Bool doAll,
|
---|
2049 | const Vector<Float>& xOut, Bool doTsys) const
|
---|
2050 | {
|
---|
2051 |
|
---|
2052 | // Get data from Table
|
---|
2053 |
|
---|
2054 | ROScalarColumn<Float> geElCol(tTable, col0);
|
---|
2055 | ROScalarColumn<Float> geFacCol(tTable, col1);
|
---|
2056 | Vector<Float> xIn = geElCol.getColumn();
|
---|
2057 | Vector<Float> yIn = geFacCol.getColumn();
|
---|
2058 | Vector<Bool> maskIn(xIn.nelements(),True);
|
---|
2059 |
|
---|
2060 | // Interpolate (and extrapolate) with desired method
|
---|
2061 |
|
---|
2062 | InterpolateArray1D<Double,Float>::InterpolationMethod method;
|
---|
2063 | convertInterpString(method, methodStr);
|
---|
2064 | Int intMethod(method);
|
---|
2065 | //
|
---|
2066 | Vector<Float> yOut;
|
---|
2067 | Vector<Bool> maskOut;
|
---|
2068 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut,
|
---|
2069 | xIn, yIn, maskIn, intMethod,
|
---|
2070 | True, True);
|
---|
2071 | // Apply
|
---|
2072 |
|
---|
2073 | scaleByVector(pTabOut, in, doAll, Float(1.0)/yOut, doTsys);
|
---|
2074 | }
|
---|
2075 |
|
---|
2076 |
|
---|
2077 | void SDMath::scaleByVector(SDMemTable* pTabOut, const SDMemTable& in,
|
---|
2078 | Bool doAll, const Vector<Float>& factor,
|
---|
2079 | Bool doTSys) const
|
---|
2080 | {
|
---|
2081 |
|
---|
2082 | // Set up data slice
|
---|
2083 |
|
---|
2084 | IPosition start, end;
|
---|
2085 | setCursorSlice (start, end, doAll, in);
|
---|
2086 |
|
---|
2087 | // Get Tsys column
|
---|
2088 |
|
---|
2089 | const Table& tIn = in.table();
|
---|
2090 | ArrayColumn<Float> tSysCol(tIn, "TSYS");
|
---|
2091 | Array<Float> tSys;
|
---|
2092 |
|
---|
2093 | // Loop over rows and apply correction factor
|
---|
2094 |
|
---|
2095 | const uInt axis = asap::ChanAxis;
|
---|
2096 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
2097 |
|
---|
2098 | // Get data
|
---|
2099 |
|
---|
2100 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i));
|
---|
2101 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference to dataIn
|
---|
2102 | //
|
---|
2103 | if (doTSys) {
|
---|
2104 | tSysCol.get(i, tSys);
|
---|
2105 | Array<Float> tSys2 = tSys(start,end) * factor[i];
|
---|
2106 | tSysCol.put(i, tSys);
|
---|
2107 | }
|
---|
2108 |
|
---|
2109 | // Apply factor
|
---|
2110 |
|
---|
2111 | dataIn2 *= factor[i];
|
---|
2112 |
|
---|
2113 | // Write out
|
---|
2114 |
|
---|
2115 | SDContainer sc = in.getSDContainer(i);
|
---|
2116 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask());
|
---|
2117 | //
|
---|
2118 | pTabOut->putSDContainer(sc);
|
---|
2119 | }
|
---|
2120 | }
|
---|
2121 |
|
---|
2122 |
|
---|
2123 |
|
---|
2124 |
|
---|
2125 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx,
|
---|
2126 | SDDataDesc& dDesc,
|
---|
2127 | uInt nIF,
|
---|
2128 | const SDMemTable& in,
|
---|
2129 | const Table& tabIn,
|
---|
2130 | const ROScalarColumn<String>& srcCol,
|
---|
2131 | const ROArrayColumn<uInt>& fqIDCol,
|
---|
2132 | Bool perFreqID) const
|
---|
2133 | {
|
---|
2134 | const uInt nRows = tabIn.nrow();
|
---|
2135 | ddIdx.resize(nRows,nIF);
|
---|
2136 | //
|
---|
2137 | String srcName;
|
---|
2138 | Vector<uInt> freqIDs;
|
---|
2139 | for (uInt iRow=0; iRow<nRows; iRow++) {
|
---|
2140 | srcCol.get(iRow, srcName);
|
---|
2141 | fqIDCol.get(iRow, freqIDs);
|
---|
2142 | const MDirection& dir = in.getDirection(iRow);
|
---|
2143 | //
|
---|
2144 | if (perFreqID) {
|
---|
2145 |
|
---|
2146 | // One entry per source/freqID pair
|
---|
2147 |
|
---|
2148 | for (uInt iIF=0; iIF<nIF; iIF++) {
|
---|
2149 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, freqIDs[iIF], dir, 0);
|
---|
2150 | }
|
---|
2151 | } else {
|
---|
2152 |
|
---|
2153 | // One entry per source/IF pair. Hang onto the FreqID as well
|
---|
2154 |
|
---|
2155 | for (uInt iIF=0; iIF<nIF; iIF++) {
|
---|
2156 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, iIF, dir, freqIDs[iIF]);
|
---|
2157 | }
|
---|
2158 | }
|
---|
2159 | }
|
---|
2160 | }
|
---|
2161 |
|
---|
2162 |
|
---|
2163 |
|
---|
2164 |
|
---|
2165 |
|
---|
2166 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const
|
---|
2167 | {
|
---|
2168 | Quantum<Double> qt;
|
---|
2169 | if (MVTime::read(qt,str)) {
|
---|
2170 | MVEpoch mv(qt);
|
---|
2171 | MEpoch me(mv, timeRef);
|
---|
2172 | return me;
|
---|
2173 | } else {
|
---|
2174 | throw(AipsError("Invalid format for Epoch string"));
|
---|
2175 | }
|
---|
2176 | }
|
---|
2177 |
|
---|
2178 |
|
---|
2179 | String SDMath::formatEpoch(const MEpoch& epoch) const
|
---|
2180 | {
|
---|
2181 | MVTime mvt(epoch.getValue());
|
---|
2182 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")");
|
---|
2183 | }
|
---|
2184 |
|
---|
2185 |
|
---|
2186 |
|
---|
2187 | void SDMath::generateFrequencyAligners (PtrBlock<FrequencyAligner<Float>* >& a,
|
---|
2188 | const SDDataDesc& dDesc,
|
---|
2189 | const SDMemTable& in, uInt nChan,
|
---|
2190 | MFrequency::Types system,
|
---|
2191 | const MPosition& refPos,
|
---|
2192 | const MEpoch& refEpoch,
|
---|
2193 | Bool perFreqID) const
|
---|
2194 | {
|
---|
2195 | for (uInt i=0; i<dDesc.length(); i++) {
|
---|
2196 | uInt ID = dDesc.ID(i);
|
---|
2197 | uInt secID = dDesc.secID(i);
|
---|
2198 | const MDirection& refDir = dDesc.secDir(i);
|
---|
2199 | //
|
---|
2200 | if (perFreqID) {
|
---|
2201 |
|
---|
2202 | // One aligner per source/FreqID pair.
|
---|
2203 |
|
---|
2204 | SpectralCoordinate sC = in.getSpectralCoordinate(ID);
|
---|
2205 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system);
|
---|
2206 | } else {
|
---|
2207 |
|
---|
2208 | // One aligner per source/IF pair. But we still need the FreqID to
|
---|
2209 | // get the right SC. Hence the messing about with the secondary ID
|
---|
2210 |
|
---|
2211 | SpectralCoordinate sC = in.getSpectralCoordinate(secID);
|
---|
2212 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system);
|
---|
2213 | }
|
---|
2214 | }
|
---|
2215 | }
|
---|
2216 |
|
---|
2217 | Vector<uInt> SDMath::getRowRange (const SDMemTable& in) const
|
---|
2218 | {
|
---|
2219 | Vector<uInt> range(2);
|
---|
2220 | range[0] = 0;
|
---|
2221 | range[1] = in.nRow()-1;
|
---|
2222 | return range;
|
---|
2223 | }
|
---|
2224 |
|
---|
2225 |
|
---|
2226 | Bool SDMath::rowInRange (uInt i, const Vector<uInt>& range) const
|
---|
2227 | {
|
---|
2228 | return (i>=range[0] && i<=range[1]);
|
---|
2229 | }
|
---|