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/QC.h>
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54 | #include <casa/Quanta/MVTime.h>
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55 | #include <casa/Utilities/Assert.h>
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56 |
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57 | #include <coordinates/Coordinates/SpectralCoordinate.h>
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58 | #include <coordinates/Coordinates/CoordinateSystem.h>
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59 | #include <coordinates/Coordinates/CoordinateUtil.h>
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60 | #include <coordinates/Coordinates/FrequencyAligner.h>
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61 |
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62 | #include <lattices/Lattices/LatticeUtilities.h>
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63 | #include <lattices/Lattices/RebinLattice.h>
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64 |
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65 | #include <measures/Measures/MEpoch.h>
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66 | #include <measures/Measures/MDirection.h>
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67 | #include <measures/Measures/MPosition.h>
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68 |
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69 | #include <scimath/Mathematics/VectorKernel.h>
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70 | #include <scimath/Mathematics/Convolver.h>
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71 | #include <scimath/Mathematics/InterpolateArray1D.h>
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72 | #include <scimath/Functionals/Polynomial.h>
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73 |
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74 | #include <tables/Tables/Table.h>
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75 | #include <tables/Tables/ScalarColumn.h>
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76 | #include <tables/Tables/ArrayColumn.h>
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77 | #include <tables/Tables/ReadAsciiTable.h>
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78 |
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79 | #include "MathUtils.h"
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80 | #include "SDDefs.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 |
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86 | using namespace casa;
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87 | using namespace asap;
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88 |
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89 |
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90 | SDMath::SDMath()
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91 | {;}
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92 |
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93 | SDMath::SDMath(const SDMath& other)
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94 | {
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95 |
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96 | // No state
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97 |
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98 | }
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99 |
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100 | SDMath& SDMath::operator=(const SDMath& other)
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101 | {
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102 | if (this != &other) {
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103 | // No state
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104 | }
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105 | return *this;
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106 | }
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107 |
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108 | SDMath::~SDMath()
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109 | {;}
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110 |
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111 |
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112 |
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113 | SDMemTable* SDMath::frequencyAlignment (const SDMemTable& in, const String& refTime, const String& method) const
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114 | {
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115 |
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116 | // Get frame info from Table
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117 |
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118 | std::vector<std::string> info = in.getCoordInfo();
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119 |
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120 | // Parse frequency system
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121 |
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122 | String systemStr(info[1]);
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123 | String baseSystemStr(info[3]);
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124 | if (baseSystemStr==systemStr) {
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125 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe"));
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126 | }
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127 | //
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128 | MFrequency::Types freqSystem;
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129 | MFrequency::getType(freqSystem, systemStr);
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130 |
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131 | // Do it
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132 |
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133 | return frequencyAlign (in, freqSystem, refTime, method);
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134 | }
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135 |
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136 |
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137 |
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138 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in,
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139 | const Vector<Bool>& mask, Bool scanAv,
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140 | const String& weightStr, Bool alignFreq) const
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141 | //
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142 | // Weighted averaging of spectra from one or more Tables.
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143 | //
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144 | {
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145 |
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146 | // Convert weight type
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147 |
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148 | WeightType wtType = NONE;
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149 | convertWeightString(wtType, weightStr);
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150 |
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151 | // Create output Table by cloning from the first table
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152 |
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153 | SDMemTable* pTabOut = new SDMemTable(*in[0],True);
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154 |
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155 | // Setup
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156 |
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157 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change
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158 | Array<Float> arr(shp);
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159 | Array<Bool> barr(shp);
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160 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis));
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161 |
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162 | // Columns from Tables
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163 |
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164 | ROArrayColumn<Float> tSysCol;
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165 | ROScalarColumn<Double> mjdCol;
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166 | ROScalarColumn<String> srcNameCol;
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167 | ROScalarColumn<Double> intCol;
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168 | ROArrayColumn<uInt> fqIDCol;
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169 |
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170 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam
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171 | // Note that the mask of the accumulation array will ALWAYS remain ALL True.
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172 | // The MA is only used so that when data which is masked Bad is added to it,
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173 | // that data does not contribute.
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174 |
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175 | Array<Float> zero(shp);
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176 | zero=0.0;
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177 | Array<Bool> good(shp);
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178 | good = True;
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179 | MaskedArray<Float> sum(zero,good);
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180 |
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181 | // Counter arrays
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182 |
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183 | Array<Float> nPts(shp); // Number of points
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184 | nPts = 0.0;
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185 | Array<Float> nInc(shp); // Increment
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186 | nInc = 1.0;
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187 |
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188 | // Create accumulation Array for variance. We accumulate for
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189 | // each if,pol,beam, but average over channel. So we need
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190 | // a shape with one less axis dropping channels.
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191 |
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192 | const uInt nAxesSub = shp.nelements() - 1;
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193 | IPosition shp2(nAxesSub);
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194 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) {
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195 | if (i!=asap::ChanAxis) {
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196 | shp2(j) = shp(i);
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197 | j++;
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198 | }
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199 | }
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200 | Array<Float> sumSq(shp2);
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201 | sumSq = 0.0;
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202 | IPosition pos2(nAxesSub,0); // For indexing
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203 |
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204 | // Time-related accumulators
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205 |
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206 | Double time;
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207 | Double timeSum = 0.0;
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208 | Double intSum = 0.0;
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209 | Double interval = 0.0;
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210 |
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211 | // To get the right shape for the Tsys accumulator we need to
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212 | // access a column from the first table. The shape of this
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213 | // array must not change
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214 |
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215 | Array<Float> tSysSum;
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216 | {
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217 | const Table& tabIn = in[0]->table();
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218 | tSysCol.attach(tabIn,"TSYS");
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219 | tSysSum.resize(tSysCol.shape(0));
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220 | }
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221 | tSysSum =0.0;
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222 | Array<Float> tSys;
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223 |
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224 | // Scan and row tracking
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225 |
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226 | Int oldScanID = 0;
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227 | Int outScanID = 0;
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228 | Int scanID = 0;
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229 | Int rowStart = 0;
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230 | Int nAccum = 0;
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231 | Int tableStart = 0;
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232 |
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233 | // Source and FreqID
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234 |
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235 | String sourceName, oldSourceName, sourceNameStart;
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236 | Vector<uInt> freqID, freqIDStart, oldFreqID;
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237 |
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238 | // Loop over tables
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239 |
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240 | Float fac = 1.0;
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241 | const uInt nTables = in.nelements();
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242 | for (uInt iTab=0; iTab<nTables; iTab++) {
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243 |
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244 | // Should check that the frequency tables don't change if doing FreqAlignment
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245 |
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246 | // Attach columns to Table
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247 |
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248 | const Table& tabIn = in[iTab]->table();
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249 | tSysCol.attach(tabIn, "TSYS");
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250 | mjdCol.attach(tabIn, "TIME");
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251 | srcNameCol.attach(tabIn, "SRCNAME");
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252 | intCol.attach(tabIn, "INTERVAL");
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253 | fqIDCol.attach(tabIn, "FREQID");
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254 |
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255 | // Loop over rows in Table
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256 |
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257 | const uInt nRows = in[iTab]->nRow();
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258 | for (uInt iRow=0; iRow<nRows; iRow++) {
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259 |
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260 | // Check conformance
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261 |
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262 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape();
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263 | if (!shp.isEqual(shp2)) {
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264 | throw (AipsError("Shapes for all rows must be the same"));
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265 | }
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266 |
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267 | // If we are not doing scan averages, make checks for source and
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268 | // frequency setup and warn if averaging across them
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269 |
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270 | // Get copy of Scan Container for this row
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271 |
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272 | SDContainer sc = in[iTab]->getSDContainer(iRow);
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273 | scanID = sc.scanid;
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274 |
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275 | // Get quantities from columns
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276 |
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277 | srcNameCol.getScalar(iRow, sourceName);
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278 | mjdCol.get(iRow, time);
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279 | tSysCol.get(iRow, tSys);
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280 | intCol.get(iRow, interval);
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281 | fqIDCol.get(iRow, freqID);
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282 |
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283 | // Initialize first source and freqID
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284 |
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285 | if (iRow==0 && iTab==0) {
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286 | sourceNameStart = sourceName;
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287 | freqIDStart = freqID;
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288 | }
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289 |
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290 | // If we are doing scan averages, see if we are at the end of an
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291 | // accumulation period (scan). We must check soutce names too,
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292 | // since we might have two tables with one scan each but different
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293 | // source names; we shouldn't average different sources together
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294 |
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295 | if (scanAv && ( (scanID != oldScanID) ||
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296 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) {
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297 |
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298 | // Normalize data in 'sum' accumulation array according to weighting scheme
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299 |
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300 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub);
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301 |
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302 | // Fill scan container. The source and freqID come from the
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303 | // first row of the first table that went into this average (
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304 | // should be the same for all rows in the scan average)
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305 |
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306 | Float nR(nAccum);
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307 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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308 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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309 |
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310 | // Write container out to Table
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311 |
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312 | pTabOut->putSDContainer(sc);
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313 |
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314 | // Reset accumulators
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315 |
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316 | sum = 0.0;
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317 | sumSq = 0.0;
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318 | nAccum = 0;
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319 | //
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320 | tSysSum =0.0;
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321 | timeSum = 0.0;
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322 | intSum = 0.0;
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323 | nPts = 0.0;
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324 |
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325 | // Increment
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326 |
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327 | rowStart = iRow; // First row for next accumulation
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328 | tableStart = iTab; // First table for next accumulation
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329 | sourceNameStart = sourceName; // First source name for next accumulation
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330 | freqIDStart = freqID; // First FreqID for next accumulation
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331 | //
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332 | oldScanID = scanID;
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333 | outScanID += 1; // Scan ID for next accumulation period
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334 | }
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335 |
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336 | // Accumulate
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337 |
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338 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum,
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339 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis,
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340 | nAxesSub, useMask, wtType);
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341 | //
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342 | oldSourceName = sourceName;
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343 | oldFreqID = freqID;
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344 | }
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345 | }
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346 |
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347 | // OK at this point we have accumulation data which is either
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348 | // - accumulated from all tables into one row
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349 | // or
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350 | // - accumulated from the last scan average
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351 | //
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352 | // Normalize data in 'sum' accumulation array according to weighting scheme
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353 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub);
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354 |
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355 | // Create and fill container. The container we clone will be from
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356 | // the last Table and the first row that went into the current
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357 | // accumulation. It probably doesn't matter that much really...
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358 |
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359 | Float nR(nAccum);
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360 | SDContainer sc = in[tableStart]->getSDContainer(rowStart);
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361 | fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
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362 | timeSum/nR, intSum, sourceNameStart, freqIDStart);
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363 | pTabOut->putSDContainer(sc);
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364 | pTabOut->resetCursor();
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365 | //
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366 | return CountedPtr<SDMemTable>(pTabOut);
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367 | }
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368 |
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369 |
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370 |
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371 | CountedPtr<SDMemTable> SDMath::binaryOperate (const CountedPtr<SDMemTable>& left,
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372 | const CountedPtr<SDMemTable>& right,
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373 | const String& op, Bool preserve,
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374 | Bool doTSys) const
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375 | {
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376 |
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377 | // Check operator
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378 |
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379 | String op2(op);
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380 | op2.upcase();
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381 | uInt what = 0;
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382 | if (op2=="ADD") {
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383 | what = 0;
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384 | } else if (op2=="SUB") {
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385 | what = 1;
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386 | } else if (op2=="MUL") {
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387 | what = 2;
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388 | } else if (op2=="DIV") {
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389 | what = 3;
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390 | } else if (op2=="QUOTIENT") {
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391 | what = 4;
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392 | doTSys = True;
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393 | } else {
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394 | throw( AipsError("Unrecognized operation"));
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395 | }
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396 |
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397 | // Check rows
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398 |
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399 | const uInt nRowLeft = left->nRow();
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400 | const uInt nRowRight = right->nRow();
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401 | Bool ok = (nRowRight==1&&nRowLeft>0) ||
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402 | (nRowRight>=1&&nRowLeft==nRowRight);
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403 | if (!ok) {
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404 | 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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405 | }
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406 |
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407 | // Input Tables
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408 |
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409 | const Table& tLeft = left->table();
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410 | const Table& tRight = right->table();
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411 |
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412 | // TSys columns
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413 |
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414 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol;
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415 | if (doTSys) {
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416 | tSysLeftCol.attach(tLeft, "TSYS");
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417 | tSysRightCol.attach(tRight, "TSYS");
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418 | }
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419 |
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420 | // First row for right
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421 |
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422 | Array<Float> tSysLeftArr, tSysRightArr;
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423 | if (doTSys) tSysRightCol.get(0, tSysRightArr);
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424 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0));
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425 | IPosition shpRight = pMRight->shape();
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426 |
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427 | // Output Table cloned from left
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428 |
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429 | SDMemTable* pTabOut = new SDMemTable(*left, True);
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430 |
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431 | // Loop over rows
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432 |
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433 | for (uInt i=0; i<nRowLeft; i++) {
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434 |
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435 | // Get data
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436 |
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437 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i));
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438 | IPosition shpLeft = mLeft.shape();
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439 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr);
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440 | //
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441 | if (nRowRight>1) {
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442 | delete pMRight;
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443 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i));
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444 | shpRight = pMRight->shape();
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445 | if (doTSys) tSysRightCol.get(i, tSysRightArr);
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446 | }
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447 | //
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448 | if (!shpRight.isEqual(shpLeft)) {
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449 | throw(AipsError("left and right scan tables are not conformant"));
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450 | }
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451 | if (doTSys) {
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452 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) {
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453 | throw(AipsError("left and right Tsys data are not conformant"));
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454 | }
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455 | if (!shpRight.isEqual(tSysRightArr.shape())) {
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456 | throw(AipsError("left and right scan tables are not conformant"));
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457 | }
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458 | }
|
---|
459 |
|
---|
460 | // Make container
|
---|
461 |
|
---|
462 | SDContainer sc = left->getSDContainer(i);
|
---|
463 |
|
---|
464 | // Operate on data and TSys
|
---|
465 |
|
---|
466 | if (what==0) {
|
---|
467 | MaskedArray<Float> tmp = mLeft + *pMRight;
|
---|
468 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
469 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr);
|
---|
470 | } else if (what==1) {
|
---|
471 | MaskedArray<Float> tmp = mLeft - *pMRight;
|
---|
472 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
473 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr);
|
---|
474 | } else if (what==2) {
|
---|
475 | MaskedArray<Float> tmp = mLeft * *pMRight;
|
---|
476 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
477 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr);
|
---|
478 | } else if (what==3) {
|
---|
479 | MaskedArray<Float> tmp = mLeft / *pMRight;
|
---|
480 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
481 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr);
|
---|
482 | } else if (what==4) {
|
---|
483 | if (preserve) {
|
---|
484 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysRightArr;
|
---|
485 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
486 | } else {
|
---|
487 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysLeftArr;
|
---|
488 | putDataInSDC(sc, tmp.getArray(), tmp.getMask());
|
---|
489 | }
|
---|
490 | sc.putTsys(tSysRightArr);
|
---|
491 | }
|
---|
492 |
|
---|
493 | // Put new row in output Table
|
---|
494 |
|
---|
495 | pTabOut->putSDContainer(sc);
|
---|
496 | }
|
---|
497 | if (pMRight) delete pMRight;
|
---|
498 | pTabOut->resetCursor();
|
---|
499 | //
|
---|
500 | return CountedPtr<SDMemTable>(pTabOut);
|
---|
501 | }
|
---|
502 |
|
---|
503 |
|
---|
504 |
|
---|
505 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in,
|
---|
506 | const Vector<Bool>& mask,
|
---|
507 | const String& which, Int row) const
|
---|
508 | //
|
---|
509 | // Perhaps iteration over pol/beam/if should be in here
|
---|
510 | // and inside the nrow iteration ?
|
---|
511 | //
|
---|
512 | {
|
---|
513 | const uInt nRow = in->nRow();
|
---|
514 |
|
---|
515 | // Specify cursor location
|
---|
516 |
|
---|
517 | IPosition start, end;
|
---|
518 | getCursorLocation(start, end, *in);
|
---|
519 |
|
---|
520 | // Loop over rows
|
---|
521 |
|
---|
522 | const uInt nEl = mask.nelements();
|
---|
523 | uInt iStart = 0;
|
---|
524 | uInt iEnd = in->nRow()-1;
|
---|
525 | //
|
---|
526 | if (row>=0) {
|
---|
527 | iStart = row;
|
---|
528 | iEnd = row;
|
---|
529 | }
|
---|
530 | //
|
---|
531 | std::vector<float> result(iEnd-iStart+1);
|
---|
532 | for (uInt ii=iStart; ii <= iEnd; ++ii) {
|
---|
533 |
|
---|
534 | // Get row and deconstruct
|
---|
535 |
|
---|
536 | MaskedArray<Float> marr(in->rowAsMaskedArray(ii));
|
---|
537 | Array<Float> arr = marr.getArray();
|
---|
538 | Array<Bool> barr = marr.getMask();
|
---|
539 |
|
---|
540 | // Access desired piece of data
|
---|
541 |
|
---|
542 | Array<Float> v((arr(start,end)).nonDegenerate());
|
---|
543 | Array<Bool> m((barr(start,end)).nonDegenerate());
|
---|
544 |
|
---|
545 | // Apply OTF mask
|
---|
546 |
|
---|
547 | MaskedArray<Float> tmp;
|
---|
548 | if (m.nelements()==nEl) {
|
---|
549 | tmp.setData(v,m&&mask);
|
---|
550 | } else {
|
---|
551 | tmp.setData(v,m);
|
---|
552 | }
|
---|
553 |
|
---|
554 | // Get statistic
|
---|
555 |
|
---|
556 | result[ii-iStart] = mathutil::statistics(which, tmp);
|
---|
557 | }
|
---|
558 | //
|
---|
559 | return result;
|
---|
560 | }
|
---|
561 |
|
---|
562 |
|
---|
563 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const
|
---|
564 | {
|
---|
565 | SDHeader sh = in.getSDHeader();
|
---|
566 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
567 |
|
---|
568 | // Bin up SpectralCoordinates
|
---|
569 |
|
---|
570 | IPosition factors(1);
|
---|
571 | factors(0) = width;
|
---|
572 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
573 | CoordinateSystem cSys;
|
---|
574 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
575 | CoordinateSystem cSysBin =
|
---|
576 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False);
|
---|
577 | //
|
---|
578 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0);
|
---|
579 | pTabOut->setCoordinate(sCBin, j);
|
---|
580 | }
|
---|
581 |
|
---|
582 | // Use RebinLattice to find shape
|
---|
583 |
|
---|
584 | IPosition shapeIn(1,sh.nchan);
|
---|
585 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors);
|
---|
586 | sh.nchan = shapeOut(0);
|
---|
587 | pTabOut->putSDHeader(sh);
|
---|
588 |
|
---|
589 | // Loop over rows and bin along channel axis
|
---|
590 |
|
---|
591 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
592 | SDContainer sc = in.getSDContainer(i);
|
---|
593 | //
|
---|
594 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape
|
---|
595 |
|
---|
596 | // Bin up spectrum
|
---|
597 |
|
---|
598 | MaskedArray<Float> marr(in.rowAsMaskedArray(i));
|
---|
599 | MaskedArray<Float> marrout;
|
---|
600 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width);
|
---|
601 |
|
---|
602 | // Put back the binned data and flags
|
---|
603 |
|
---|
604 | IPosition ip2 = marrout.shape();
|
---|
605 | sc.resize(ip2);
|
---|
606 | //
|
---|
607 | putDataInSDC(sc, marrout.getArray(), marrout.getMask());
|
---|
608 |
|
---|
609 | // Bin up Tsys.
|
---|
610 |
|
---|
611 | Array<Bool> allGood(tSys.shape(),True);
|
---|
612 | MaskedArray<Float> tSysIn(tSys, allGood, True);
|
---|
613 | //
|
---|
614 | MaskedArray<Float> tSysOut;
|
---|
615 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width);
|
---|
616 | sc.putTsys(tSysOut.getArray());
|
---|
617 | //
|
---|
618 | pTabOut->putSDContainer(sc);
|
---|
619 | }
|
---|
620 | return pTabOut;
|
---|
621 | }
|
---|
622 |
|
---|
623 | SDMemTable* SDMath::resample (const SDMemTable& in, const String& methodStr,
|
---|
624 | Float width) const
|
---|
625 | //
|
---|
626 | // Should add the possibility of width being specified in km/s. This means
|
---|
627 | // that for each freqID (SpectralCoordinate) we will need to convert to an
|
---|
628 | // average channel width (say at the reference pixel). Then we would need
|
---|
629 | // to be careful to make sure each spectrum (of different freqID)
|
---|
630 | // is the same length.
|
---|
631 | //
|
---|
632 | {
|
---|
633 | Bool doVel = False;
|
---|
634 | if (doVel) {
|
---|
635 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
636 | SpectralCoordinate sC = in.getSpectralCoordinate(j);
|
---|
637 | }
|
---|
638 | }
|
---|
639 |
|
---|
640 | // Interpolation method
|
---|
641 |
|
---|
642 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
---|
643 | convertInterpString(interp, methodStr);
|
---|
644 | Int interpMethod(interp);
|
---|
645 |
|
---|
646 | // Make output table
|
---|
647 |
|
---|
648 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
649 |
|
---|
650 | // Resample SpectralCoordinates (one per freqID)
|
---|
651 |
|
---|
652 | const uInt nCoord = in.nCoordinates();
|
---|
653 | Vector<Float> offset(1,0.0);
|
---|
654 | Vector<Float> factors(1,1.0/width);
|
---|
655 | Vector<Int> newShape;
|
---|
656 | for (uInt j=0; j<in.nCoordinates(); ++j) {
|
---|
657 | CoordinateSystem cSys;
|
---|
658 | cSys.addCoordinate(in.getSpectralCoordinate(j));
|
---|
659 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape);
|
---|
660 | SpectralCoordinate sC = cSys2.spectralCoordinate(0);
|
---|
661 | //
|
---|
662 | pTabOut->setCoordinate(sC, j);
|
---|
663 | }
|
---|
664 |
|
---|
665 | // Get header
|
---|
666 |
|
---|
667 | SDHeader sh = in.getSDHeader();
|
---|
668 |
|
---|
669 | // Generate resampling vectors
|
---|
670 |
|
---|
671 | const uInt nChanIn = sh.nchan;
|
---|
672 | Vector<Float> xIn(nChanIn);
|
---|
673 | indgen(xIn);
|
---|
674 | //
|
---|
675 | Int fac = Int(nChanIn/width);
|
---|
676 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later
|
---|
677 | uInt i = 0;
|
---|
678 | Float x = 0.0;
|
---|
679 | Bool more = True;
|
---|
680 | while (more) {
|
---|
681 | xOut(i) = x;
|
---|
682 | //
|
---|
683 | i++;
|
---|
684 | x += width;
|
---|
685 | if (x>nChanIn-1) more = False;
|
---|
686 | }
|
---|
687 | const uInt nChanOut = i;
|
---|
688 | xOut.resize(nChanOut,True);
|
---|
689 | //
|
---|
690 | IPosition shapeIn(in.rowAsMaskedArray(0).shape());
|
---|
691 | sh.nchan = nChanOut;
|
---|
692 | pTabOut->putSDHeader(sh);
|
---|
693 |
|
---|
694 | // Loop over rows and resample along channel axis
|
---|
695 |
|
---|
696 | Array<Float> valuesOut;
|
---|
697 | Array<Bool> maskOut;
|
---|
698 | Array<Float> tSysOut;
|
---|
699 | Array<Bool> tSysMaskIn(shapeIn,True);
|
---|
700 | Array<Bool> tSysMaskOut;
|
---|
701 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
702 |
|
---|
703 | // Get container
|
---|
704 |
|
---|
705 | SDContainer sc = in.getSDContainer(i);
|
---|
706 |
|
---|
707 | // Get data and Tsys
|
---|
708 |
|
---|
709 | const Array<Float>& tSysIn = sc.getTsys();
|
---|
710 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i));
|
---|
711 | Array<Float> valuesIn = dataIn.getArray();
|
---|
712 | Array<Bool> maskIn = dataIn.getMask();
|
---|
713 |
|
---|
714 | // Interpolate data
|
---|
715 |
|
---|
716 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut,
|
---|
717 | xIn, valuesIn, maskIn,
|
---|
718 | interpMethod, True, True);
|
---|
719 | sc.resize(valuesOut.shape());
|
---|
720 | putDataInSDC(sc, valuesOut, maskOut);
|
---|
721 |
|
---|
722 | // Interpolate TSys
|
---|
723 |
|
---|
724 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut,
|
---|
725 | xIn, tSysIn, tSysMaskIn,
|
---|
726 | interpMethod, True, True);
|
---|
727 | sc.putTsys(tSysOut);
|
---|
728 |
|
---|
729 | // Put container in output
|
---|
730 |
|
---|
731 | pTabOut->putSDContainer(sc);
|
---|
732 | }
|
---|
733 | //
|
---|
734 | return pTabOut;
|
---|
735 | }
|
---|
736 |
|
---|
737 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll,
|
---|
738 | uInt what, Bool doTSys) const
|
---|
739 | //
|
---|
740 | // what = 0 Multiply
|
---|
741 | // 1 Add
|
---|
742 | {
|
---|
743 | SDMemTable* pOut = new SDMemTable(in,False);
|
---|
744 | const Table& tOut = pOut->table();
|
---|
745 | ArrayColumn<Float> specCol(tOut,"SPECTRA");
|
---|
746 | ArrayColumn<Float> tSysCol(tOut,"TSYS");
|
---|
747 | Array<Float> tSysArr;
|
---|
748 | //
|
---|
749 | if (doAll) {
|
---|
750 | for (uInt i=0; i < tOut.nrow(); i++) {
|
---|
751 |
|
---|
752 | // Modify data
|
---|
753 |
|
---|
754 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
|
---|
755 | if (what==0) {
|
---|
756 | dataIn *= val;
|
---|
757 | } else if (what==1) {
|
---|
758 | dataIn += val;
|
---|
759 | }
|
---|
760 | specCol.put(i, dataIn.getArray());
|
---|
761 |
|
---|
762 | // Modify Tsys
|
---|
763 |
|
---|
764 | if (doTSys) {
|
---|
765 | tSysCol.get(i, tSysArr);
|
---|
766 | if (what==0) {
|
---|
767 | tSysArr *= val;
|
---|
768 | } else if (what==1) {
|
---|
769 | tSysArr += val;
|
---|
770 | }
|
---|
771 | tSysCol.put(i, tSysArr);
|
---|
772 | }
|
---|
773 | }
|
---|
774 | } else {
|
---|
775 |
|
---|
776 | // Get cursor location
|
---|
777 |
|
---|
778 | IPosition start, end;
|
---|
779 | getCursorLocation(start, end, in);
|
---|
780 | //
|
---|
781 | for (uInt i=0; i < tOut.nrow(); i++) {
|
---|
782 |
|
---|
783 | // Modify data
|
---|
784 |
|
---|
785 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
|
---|
786 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference
|
---|
787 | if (what==0) {
|
---|
788 | dataIn2 *= val;
|
---|
789 | } else if (what==1) {
|
---|
790 | dataIn2 += val;
|
---|
791 | }
|
---|
792 | specCol.put(i, dataIn.getArray());
|
---|
793 |
|
---|
794 | // Modify Tsys
|
---|
795 |
|
---|
796 | if (doTSys) {
|
---|
797 | tSysCol.get(i, tSysArr);
|
---|
798 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference
|
---|
799 | if (what==0) {
|
---|
800 | tSysArr2 *= val;
|
---|
801 | } else if (what==1) {
|
---|
802 | tSysArr2 += val;
|
---|
803 | }
|
---|
804 | tSysCol.put(i, tSysArr);
|
---|
805 | }
|
---|
806 | }
|
---|
807 | }
|
---|
808 | //
|
---|
809 | return pOut;
|
---|
810 | }
|
---|
811 |
|
---|
812 |
|
---|
813 |
|
---|
814 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask,
|
---|
815 | const String& weightStr) const
|
---|
816 | //
|
---|
817 | // Average all polarizations together, weighted by variance
|
---|
818 | //
|
---|
819 | {
|
---|
820 | WeightType wtType = NONE;
|
---|
821 | convertWeightString(wtType, weightStr);
|
---|
822 |
|
---|
823 | const uInt nRows = in.nRow();
|
---|
824 |
|
---|
825 | // Create output Table and reshape number of polarizations
|
---|
826 |
|
---|
827 | Bool clear=True;
|
---|
828 | SDMemTable* pTabOut = new SDMemTable(in, clear);
|
---|
829 | SDHeader header = pTabOut->getSDHeader();
|
---|
830 | header.npol = 1;
|
---|
831 | pTabOut->putSDHeader(header);
|
---|
832 |
|
---|
833 | // Shape of input and output data
|
---|
834 |
|
---|
835 | const IPosition& shapeIn = in.rowAsMaskedArray(0u, False).shape();
|
---|
836 | IPosition shapeOut(shapeIn);
|
---|
837 | shapeOut(asap::PolAxis) = 1; // Average all polarizations
|
---|
838 | if (shapeIn(asap::PolAxis)==1) {
|
---|
839 | throw(AipsError("The input has only one polarisation"));
|
---|
840 | }
|
---|
841 | //
|
---|
842 | const uInt nChan = shapeIn(asap::ChanAxis);
|
---|
843 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape
|
---|
844 | IPosition start(4), end(4);
|
---|
845 |
|
---|
846 | // Output arrays
|
---|
847 |
|
---|
848 | Array<Float> outData(shapeOut, 0.0);
|
---|
849 | Array<Bool> outMask(shapeOut, True);
|
---|
850 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane
|
---|
851 | //
|
---|
852 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis));
|
---|
853 |
|
---|
854 | // Loop over rows
|
---|
855 |
|
---|
856 | for (uInt iRow=0; iRow<nRows; iRow++) {
|
---|
857 |
|
---|
858 | // Get data for this row
|
---|
859 |
|
---|
860 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow));
|
---|
861 | Array<Float>& arr = marr.getRWArray();
|
---|
862 | const Array<Bool>& barr = marr.getMask();
|
---|
863 |
|
---|
864 | // Make iterators to iterate by pol-channel planes
|
---|
865 |
|
---|
866 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes);
|
---|
867 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes);
|
---|
868 |
|
---|
869 | // Accumulations
|
---|
870 |
|
---|
871 | Float fac = 1.0;
|
---|
872 | Vector<Float> vecSum(nChan,0.0);
|
---|
873 |
|
---|
874 | // Iterate through data by pol-channel planes
|
---|
875 |
|
---|
876 | while (!itDataPlane.pastEnd()) {
|
---|
877 |
|
---|
878 | // Iterate through plane by polarization and accumulate Vectors
|
---|
879 |
|
---|
880 | Vector<Float> t1(nChan); t1 = 0.0;
|
---|
881 | Vector<Bool> t2(nChan); t2 = True;
|
---|
882 | MaskedArray<Float> vecSum(t1,t2);
|
---|
883 | Float norm = 0.0;
|
---|
884 | {
|
---|
885 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1);
|
---|
886 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
887 | while (!itDataVec.pastEnd()) {
|
---|
888 |
|
---|
889 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum
|
---|
890 |
|
---|
891 | if (useMask) {
|
---|
892 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector());
|
---|
893 | if (wtType==VAR) fac = 1.0 / variance(spec);
|
---|
894 | } else {
|
---|
895 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector());
|
---|
896 | if (wtType==VAR) fac = 1.0 / variance(spec);
|
---|
897 | }
|
---|
898 |
|
---|
899 | // Normalize spectrum (without OTF mask) and accumulate
|
---|
900 |
|
---|
901 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector());
|
---|
902 | vecSum += spec;
|
---|
903 | norm += fac;
|
---|
904 |
|
---|
905 | // Next
|
---|
906 |
|
---|
907 | itDataVec.next();
|
---|
908 | itMaskVec.next();
|
---|
909 | }
|
---|
910 | }
|
---|
911 |
|
---|
912 | // Normalize summed spectrum
|
---|
913 |
|
---|
914 | vecSum /= norm;
|
---|
915 |
|
---|
916 | // FInd position in input data array. We are iterating by pol-channel
|
---|
917 | // plane so all that will change is beam and IF and that's what we want.
|
---|
918 |
|
---|
919 | IPosition pos = itDataPlane.pos();
|
---|
920 |
|
---|
921 | // Write out data. This is a bit messy. We have to reform the Vector
|
---|
922 | // accumulator into an Array of shape (1,1,1,nChan)
|
---|
923 |
|
---|
924 | start = pos;
|
---|
925 | end = pos;
|
---|
926 | end(asap::ChanAxis) = nChan-1;
|
---|
927 | outData(start,end) = vecSum.getArray().reform(vecShapeOut);
|
---|
928 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut);
|
---|
929 |
|
---|
930 | // Step to next beam/IF combination
|
---|
931 |
|
---|
932 | itDataPlane.next();
|
---|
933 | itMaskPlane.next();
|
---|
934 | }
|
---|
935 |
|
---|
936 | // Generate output container and write it to output table
|
---|
937 |
|
---|
938 | SDContainer sc = in.getSDContainer();
|
---|
939 | sc.resize(shapeOut);
|
---|
940 | //
|
---|
941 | putDataInSDC(sc, outData, outMask);
|
---|
942 | pTabOut->putSDContainer(sc);
|
---|
943 | }
|
---|
944 |
|
---|
945 | // Set polarization cursor to 0
|
---|
946 |
|
---|
947 | pTabOut->setPol(0);
|
---|
948 | //
|
---|
949 | return pTabOut;
|
---|
950 | }
|
---|
951 |
|
---|
952 |
|
---|
953 | SDMemTable* SDMath::smooth(const SDMemTable& in,
|
---|
954 | const casa::String& kernelType,
|
---|
955 | casa::Float width, Bool doAll) const
|
---|
956 | //
|
---|
957 | // Should smooth TSys as well
|
---|
958 | //
|
---|
959 | {
|
---|
960 |
|
---|
961 | // Number of channels
|
---|
962 |
|
---|
963 | SDHeader sh = in.getSDHeader();
|
---|
964 | const uInt nChan = sh.nchan;
|
---|
965 |
|
---|
966 | // Generate Kernel
|
---|
967 |
|
---|
968 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType);
|
---|
969 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False);
|
---|
970 |
|
---|
971 | // Generate Convolver
|
---|
972 |
|
---|
973 | IPosition shape(1,nChan);
|
---|
974 | Convolver<Float> conv(kernel, shape);
|
---|
975 |
|
---|
976 | // New Table
|
---|
977 |
|
---|
978 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
979 |
|
---|
980 | // Get cursor location
|
---|
981 |
|
---|
982 | IPosition start, end;
|
---|
983 | getCursorLocation(start, end, in);
|
---|
984 | //
|
---|
985 | IPosition shapeOut(4,1);
|
---|
986 |
|
---|
987 | // Output Vectors
|
---|
988 |
|
---|
989 | Vector<Float> valuesOut(nChan);
|
---|
990 | Vector<Bool> maskOut(nChan);
|
---|
991 |
|
---|
992 | // Loop over rows in Table
|
---|
993 |
|
---|
994 | for (uInt ri=0; ri < in.nRow(); ++ri) {
|
---|
995 |
|
---|
996 | // Get copy of data
|
---|
997 |
|
---|
998 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(ri));
|
---|
999 | AlwaysAssert(dataIn.shape()(asap::ChanAxis)==nChan, AipsError);
|
---|
1000 | //
|
---|
1001 | Array<Float> valuesIn = dataIn.getArray();
|
---|
1002 | Array<Bool> maskIn = dataIn.getMask();
|
---|
1003 |
|
---|
1004 | // Branch depending on whether we smooth all locations or just
|
---|
1005 | // those pointed at by the current selection cursor
|
---|
1006 |
|
---|
1007 | if (doAll) {
|
---|
1008 | VectorIterator<Float> itValues(valuesIn, asap::ChanAxis);
|
---|
1009 | VectorIterator<Bool> itMask(maskIn, asap::ChanAxis);
|
---|
1010 | while (!itValues.pastEnd()) {
|
---|
1011 |
|
---|
1012 | // Smooth
|
---|
1013 | if (kernelType==VectorKernel::HANNING) {
|
---|
1014 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector());
|
---|
1015 | itMask.vector() = maskOut;
|
---|
1016 | } else {
|
---|
1017 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector());
|
---|
1018 | conv.linearConv(valuesOut, itValues.vector());
|
---|
1019 | }
|
---|
1020 | //
|
---|
1021 | itValues.vector() = valuesOut;
|
---|
1022 | //
|
---|
1023 | itValues.next();
|
---|
1024 | itMask.next();
|
---|
1025 | }
|
---|
1026 | } else {
|
---|
1027 |
|
---|
1028 | // Set multi-dim Vector shape
|
---|
1029 |
|
---|
1030 | shapeOut(asap::ChanAxis) = valuesIn.shape()(asap::ChanAxis);
|
---|
1031 |
|
---|
1032 | // Stuff about with shapes so that we don't have conformance run-time errors
|
---|
1033 |
|
---|
1034 | Vector<Float> valuesIn2 = valuesIn(start,end).nonDegenerate();
|
---|
1035 | Vector<Bool> maskIn2 = maskIn(start,end).nonDegenerate();
|
---|
1036 |
|
---|
1037 | // Smooth
|
---|
1038 |
|
---|
1039 | if (kernelType==VectorKernel::HANNING) {
|
---|
1040 | mathutil::hanning(valuesOut, maskOut, valuesIn2, maskIn2);
|
---|
1041 | maskIn(start,end) = maskOut.reform(shapeOut);
|
---|
1042 | } else {
|
---|
1043 | mathutil::replaceMaskByZero(valuesIn2, maskIn2);
|
---|
1044 | conv.linearConv(valuesOut, valuesIn2);
|
---|
1045 | }
|
---|
1046 | //
|
---|
1047 | valuesIn(start,end) = valuesOut.reform(shapeOut);
|
---|
1048 | }
|
---|
1049 |
|
---|
1050 | // Create and put back
|
---|
1051 |
|
---|
1052 | SDContainer sc = in.getSDContainer(ri);
|
---|
1053 | putDataInSDC(sc, valuesIn, maskIn);
|
---|
1054 | //
|
---|
1055 | pTabOut->putSDContainer(sc);
|
---|
1056 | }
|
---|
1057 | //
|
---|
1058 | return pTabOut;
|
---|
1059 | }
|
---|
1060 |
|
---|
1061 |
|
---|
1062 |
|
---|
1063 | SDMemTable* SDMath::convertFlux (const SDMemTable& in, Float a, Float eta, Bool doAll) const
|
---|
1064 | //
|
---|
1065 | // As it is, this function could be implemented with 'simpleOperate'
|
---|
1066 | // However, I anticipate that eventually we will look the conversion
|
---|
1067 | // values up in a Table and apply them in a frequency dependent way,
|
---|
1068 | // so I have implemented it fully here
|
---|
1069 | //
|
---|
1070 | {
|
---|
1071 | SDHeader sh = in.getSDHeader();
|
---|
1072 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
1073 |
|
---|
1074 | // FInd out how to convert values into Jy and K (e.g. units might be mJy or mK)
|
---|
1075 | // Also automatically find out what we are converting to according to the
|
---|
1076 | // flux unit
|
---|
1077 |
|
---|
1078 | Unit fluxUnit(sh.fluxunit);
|
---|
1079 | Unit K(String("K"));
|
---|
1080 | Unit JY(String("Jy"));
|
---|
1081 | //
|
---|
1082 | Bool toKelvin = True;
|
---|
1083 | Double inFac = 1.0;
|
---|
1084 | if (fluxUnit==JY) {
|
---|
1085 | cerr << "Converting to K" << endl;
|
---|
1086 | //
|
---|
1087 | Quantum<Double> t(1.0,fluxUnit);
|
---|
1088 | Quantum<Double> t2 = t.get(JY);
|
---|
1089 | inFac = (t2 / t).getValue();
|
---|
1090 | //
|
---|
1091 | toKelvin = True;
|
---|
1092 | sh.fluxunit = "K";
|
---|
1093 | } else if (fluxUnit==K) {
|
---|
1094 | cerr << "Converting to Jy" << endl;
|
---|
1095 | //
|
---|
1096 | Quantum<Double> t(1.0,fluxUnit);
|
---|
1097 | Quantum<Double> t2 = t.get(K);
|
---|
1098 | inFac = (t2 / t).getValue();
|
---|
1099 | //
|
---|
1100 | toKelvin = False;
|
---|
1101 | sh.fluxunit = "Jy";
|
---|
1102 | } else {
|
---|
1103 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
|
---|
1104 | }
|
---|
1105 | pTabOut->putSDHeader(sh);
|
---|
1106 |
|
---|
1107 | // Compute conversion factor. 'a' and 'eta' are really frequency, time and
|
---|
1108 | // telescope dependent and should be looked// up in a table
|
---|
1109 |
|
---|
1110 | Float factor = 2.0 * inFac * 1.0e-7 * 1.0e26 *
|
---|
1111 | QC::k.getValue(Unit(String("erg/K"))) / a / eta;
|
---|
1112 | if (toKelvin) {
|
---|
1113 | factor = 1.0 / factor;
|
---|
1114 | }
|
---|
1115 | cerr << "Applying conversion factor = " << factor << endl;
|
---|
1116 |
|
---|
1117 | // Generate correction vector. Apply same factor regardless
|
---|
1118 | // of beam/pol/IF. This will need to change somewhen.
|
---|
1119 |
|
---|
1120 | Vector<Float> factors(in.nRow(), factor);
|
---|
1121 |
|
---|
1122 | // Correct
|
---|
1123 |
|
---|
1124 | correctFromVector (pTabOut, in, doAll, factors);
|
---|
1125 | //
|
---|
1126 | return pTabOut;
|
---|
1127 | }
|
---|
1128 |
|
---|
1129 |
|
---|
1130 | SDMemTable* SDMath::gainElevation (const SDMemTable& in, const Vector<Float>& coeffs,
|
---|
1131 | const String& fileName,
|
---|
1132 | const String& methodStr, Bool doAll) const
|
---|
1133 | {
|
---|
1134 |
|
---|
1135 | // Get header and clone output table
|
---|
1136 |
|
---|
1137 | SDHeader sh = in.getSDHeader();
|
---|
1138 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
1139 |
|
---|
1140 | // Get elevation data from SDMemTable and convert to degrees
|
---|
1141 |
|
---|
1142 | const Table& tab = in.table();
|
---|
1143 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
1144 | Vector<Float> x = elev.getColumn();
|
---|
1145 | x *= Float(180 / C::pi);
|
---|
1146 | //
|
---|
1147 | const uInt nC = coeffs.nelements();
|
---|
1148 | if (fileName.length()>0 && nC>0) {
|
---|
1149 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
|
---|
1150 | }
|
---|
1151 |
|
---|
1152 | // Correct
|
---|
1153 |
|
---|
1154 | if (nC>0 || fileName.length()==0) {
|
---|
1155 |
|
---|
1156 | // Find instrument
|
---|
1157 |
|
---|
1158 | Bool throwIt = True;
|
---|
1159 | Instrument inst = SDMemTable::convertInstrument (sh.antennaname, throwIt);
|
---|
1160 |
|
---|
1161 | // Set polynomial
|
---|
1162 |
|
---|
1163 | Polynomial<Float>* pPoly = 0;
|
---|
1164 | Vector<Float> coeff;
|
---|
1165 | String msg;
|
---|
1166 | if (nC>0) {
|
---|
1167 | pPoly = new Polynomial<Float>(nC);
|
---|
1168 | coeff = coeffs;
|
---|
1169 | msg = String("user");
|
---|
1170 | } else {
|
---|
1171 | if (inst==ATPKSMB) {
|
---|
1172 | } else if (inst==ATPKSHOH) {
|
---|
1173 | } else if (inst==TIDBINBILLA) {
|
---|
1174 | pPoly = new Polynomial<Float>(3);
|
---|
1175 | coeff.resize(3);
|
---|
1176 | coeff(0) = 3.58788e-1;
|
---|
1177 | coeff(1) = 2.87243e-2;
|
---|
1178 | coeff(2) = -3.219093e-4;
|
---|
1179 | } else if (inst==ATMOPRA) {
|
---|
1180 | } else {
|
---|
1181 | }
|
---|
1182 | msg = String("built in");
|
---|
1183 | }
|
---|
1184 | //
|
---|
1185 | if (coeff.nelements()>0) {
|
---|
1186 | pPoly->setCoefficients(coeff);
|
---|
1187 | } else {
|
---|
1188 | throw(AipsError("There is no known gain-el polynomial known for this instrument"));
|
---|
1189 | }
|
---|
1190 | //
|
---|
1191 | cerr << "Making polynomial correction with " << msg << " coefficients" << endl;
|
---|
1192 | const uInt nRow = in.nRow();
|
---|
1193 | Vector<Float> factor(nRow);
|
---|
1194 | for (uInt i=0; i<nRow; i++) {
|
---|
1195 | factor[i] = (*pPoly)(x[i]);
|
---|
1196 | }
|
---|
1197 | delete pPoly;
|
---|
1198 | //
|
---|
1199 | correctFromVector (pTabOut, in, doAll, factor);
|
---|
1200 | } else {
|
---|
1201 |
|
---|
1202 | // Indicate which columns to read from ascii file
|
---|
1203 |
|
---|
1204 | String col0("ELEVATION");
|
---|
1205 | String col1("FACTOR");
|
---|
1206 |
|
---|
1207 | // Read and correct
|
---|
1208 |
|
---|
1209 | cerr << "Making correction from ascii Table" << endl;
|
---|
1210 | correctFromAsciiTable (pTabOut, in, fileName, col0, col1,
|
---|
1211 | methodStr, doAll, x);
|
---|
1212 | }
|
---|
1213 | //
|
---|
1214 | return pTabOut;
|
---|
1215 | }
|
---|
1216 |
|
---|
1217 |
|
---|
1218 |
|
---|
1219 | SDMemTable* SDMath::opacity (const SDMemTable& in, Float tau, Bool doAll) const
|
---|
1220 | {
|
---|
1221 |
|
---|
1222 | // Get header and clone output table
|
---|
1223 |
|
---|
1224 | SDHeader sh = in.getSDHeader();
|
---|
1225 | SDMemTable* pTabOut = new SDMemTable(in, True);
|
---|
1226 |
|
---|
1227 | // Get elevation data from SDMemTable and convert to degrees
|
---|
1228 |
|
---|
1229 | const Table& tab = in.table();
|
---|
1230 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
1231 | Vector<Float> zDist = elev.getColumn();
|
---|
1232 | zDist = Float(C::pi_2) - zDist;
|
---|
1233 |
|
---|
1234 | // Generate correction factor
|
---|
1235 |
|
---|
1236 | const uInt nRow = in.nRow();
|
---|
1237 | Vector<Float> factor(nRow);
|
---|
1238 | Vector<Float> factor2(nRow);
|
---|
1239 | for (uInt i=0; i<nRow; i++) {
|
---|
1240 | factor[i] = exp(tau)/cos(zDist[i]);
|
---|
1241 | }
|
---|
1242 |
|
---|
1243 | // Correct
|
---|
1244 |
|
---|
1245 | correctFromVector (pTabOut, in, doAll, factor);
|
---|
1246 | //
|
---|
1247 | return pTabOut;
|
---|
1248 | }
|
---|
1249 |
|
---|
1250 |
|
---|
1251 |
|
---|
1252 |
|
---|
1253 | // 'private' functions
|
---|
1254 |
|
---|
1255 |
|
---|
1256 | SDMemTable* SDMath::frequencyAlign (const SDMemTable& in,
|
---|
1257 | MFrequency::Types freqSystem,
|
---|
1258 | const String& refTime, const String& methodStr) const
|
---|
1259 | {
|
---|
1260 | // Get Header
|
---|
1261 |
|
---|
1262 | SDHeader sh = in.getSDHeader();
|
---|
1263 | const uInt nChan = sh.nchan;
|
---|
1264 | const uInt nRows = in.nRow();
|
---|
1265 | const uInt nIF = sh.nif;
|
---|
1266 |
|
---|
1267 | // Get Table reference
|
---|
1268 |
|
---|
1269 | const Table& tabIn = in.table();
|
---|
1270 |
|
---|
1271 | // Get Columns from Table
|
---|
1272 |
|
---|
1273 | ROScalarColumn<Double> mjdCol(tabIn, "TIME");
|
---|
1274 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME");
|
---|
1275 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID");
|
---|
1276 | Vector<Double> times = mjdCol.getColumn();
|
---|
1277 |
|
---|
1278 | // Generate DataDesc table
|
---|
1279 |
|
---|
1280 | Matrix<uInt> ddIdx;
|
---|
1281 | SDDataDesc dDesc;
|
---|
1282 | generateDataDescTable (ddIdx, dDesc, nIF, in, tabIn, srcCol, fqIDCol);
|
---|
1283 |
|
---|
1284 | // Get reference Epoch to time of first row or given String
|
---|
1285 |
|
---|
1286 | Unit DAY(String("d"));
|
---|
1287 | MEpoch::Ref epochRef(in.getTimeReference());
|
---|
1288 | MEpoch refEpoch;
|
---|
1289 | if (refTime.length()>0) {
|
---|
1290 | refEpoch = epochFromString(refTime, in.getTimeReference());
|
---|
1291 | } else {
|
---|
1292 | refEpoch = in.getEpoch(0);
|
---|
1293 | }
|
---|
1294 | cerr << "Aligning at reference Epoch " << formatEpoch(refEpoch) <<
|
---|
1295 | " in frame " << MFrequency::showType(freqSystem) << endl;
|
---|
1296 |
|
---|
1297 | // Get Reference Position
|
---|
1298 |
|
---|
1299 | MPosition refPos = in.getAntennaPosition();
|
---|
1300 |
|
---|
1301 | // Create FrequencyAligner Block. One VA for each possible
|
---|
1302 | // source/freqID combination
|
---|
1303 |
|
---|
1304 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length());
|
---|
1305 | generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos, refEpoch);
|
---|
1306 |
|
---|
1307 | // Generate and fill output Frequency Tabke
|
---|
1308 |
|
---|
1309 | SDFrequencyTable freqTabOut = in.getSDFreqTable();
|
---|
1310 | freqTabOut.setLength(0);
|
---|
1311 | Vector<String> units(1);
|
---|
1312 | units = String("Hz");
|
---|
1313 | Bool linear=True;
|
---|
1314 | //
|
---|
1315 | for (uInt i=0; i<dDesc.length(); i++) {
|
---|
1316 |
|
---|
1317 | // Get Aligned SC in Hz
|
---|
1318 |
|
---|
1319 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear);
|
---|
1320 | sC.setWorldAxisUnits(units);
|
---|
1321 |
|
---|
1322 | // Add FreqID
|
---|
1323 |
|
---|
1324 | freqTabOut.addFrequency(sC.referencePixel()[0],
|
---|
1325 | sC.referenceValue()[0],
|
---|
1326 | sC.increment()[0]);
|
---|
1327 | }
|
---|
1328 |
|
---|
1329 | // Interpolation method
|
---|
1330 |
|
---|
1331 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
---|
1332 | convertInterpString(interp, methodStr);
|
---|
1333 |
|
---|
1334 | // New output Table
|
---|
1335 |
|
---|
1336 | SDMemTable* pTabOut = new SDMemTable(in,True);
|
---|
1337 | pTabOut->putSDFreqTable(freqTabOut);
|
---|
1338 |
|
---|
1339 | // Loop over rows in Table
|
---|
1340 |
|
---|
1341 | Bool extrapolate=False;
|
---|
1342 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis);
|
---|
1343 | Bool useCachedAbcissa = False;
|
---|
1344 | Bool first = True;
|
---|
1345 | Bool ok;
|
---|
1346 | Vector<Float> yOut;
|
---|
1347 | Vector<Bool> maskOut;
|
---|
1348 | Vector<uInt> freqID(nIF);
|
---|
1349 | uInt ifIdx, faIdx;
|
---|
1350 | //
|
---|
1351 | for (uInt iRow=0; iRow<nRows; ++iRow) {
|
---|
1352 | if (iRow%10==0) {
|
---|
1353 | cerr << "Processing row " << iRow << endl;
|
---|
1354 | }
|
---|
1355 |
|
---|
1356 | // Get EPoch
|
---|
1357 |
|
---|
1358 | Quantum<Double> tQ2(times[iRow],DAY);
|
---|
1359 | MVEpoch mv2(tQ2);
|
---|
1360 | MEpoch epoch(mv2, epochRef);
|
---|
1361 |
|
---|
1362 | // Get copy of data
|
---|
1363 |
|
---|
1364 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow));
|
---|
1365 | Array<Float> values = mArrIn.getArray();
|
---|
1366 | Array<Bool> mask = mArrIn.getMask();
|
---|
1367 |
|
---|
1368 | // cerr << "values in = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl;
|
---|
1369 |
|
---|
1370 | // For each row, the Frequency abcissa will be the same regardless
|
---|
1371 | // of polarization. For all other axes (IF and BEAM) the abcissa
|
---|
1372 | // will change. So we iterate through the data by pol-chan planes
|
---|
1373 | // to mimimize the work. Probably won't work for multiple beams
|
---|
1374 | // at this point.
|
---|
1375 |
|
---|
1376 | ArrayIterator<Float> itValuesPlane(values, polChanAxes);
|
---|
1377 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes);
|
---|
1378 | while (!itValuesPlane.pastEnd()) {
|
---|
1379 |
|
---|
1380 | // Find the IF index and then the FA PtrBlock index
|
---|
1381 |
|
---|
1382 | const IPosition& pos = itValuesPlane.pos();
|
---|
1383 | ifIdx = pos(asap::IFAxis);
|
---|
1384 | faIdx = ddIdx(iRow,ifIdx);
|
---|
1385 | //
|
---|
1386 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1);
|
---|
1387 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
|
---|
1388 |
|
---|
1389 | // Iterate through the plane by vector and align
|
---|
1390 |
|
---|
1391 | first = True;
|
---|
1392 | useCachedAbcissa=False;
|
---|
1393 | while (!itValuesVec.pastEnd()) {
|
---|
1394 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(),
|
---|
1395 | itMaskVec.vector(), epoch, useCachedAbcissa,
|
---|
1396 | interp, extrapolate);
|
---|
1397 | //
|
---|
1398 | itValuesVec.vector() = yOut;
|
---|
1399 | itMaskVec.vector() = maskOut;
|
---|
1400 | //
|
---|
1401 | itValuesVec.next();
|
---|
1402 | itMaskVec.next();
|
---|
1403 | //
|
---|
1404 | if (first) {
|
---|
1405 | useCachedAbcissa = True;
|
---|
1406 | first = False;
|
---|
1407 | }
|
---|
1408 | }
|
---|
1409 | //
|
---|
1410 | itValuesPlane.next();
|
---|
1411 | itMaskPlane.next();
|
---|
1412 | }
|
---|
1413 |
|
---|
1414 | // cerr << "values out = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl;
|
---|
1415 |
|
---|
1416 | // Create SDContainer and put back
|
---|
1417 |
|
---|
1418 | SDContainer sc = in.getSDContainer(iRow);
|
---|
1419 | putDataInSDC(sc, values, mask);
|
---|
1420 | for (uInt i=0; i<nIF; i++) {
|
---|
1421 | uInt idx = ddIdx(iRow,i);
|
---|
1422 | freqID(i) = dDesc.freqID(idx);
|
---|
1423 | }
|
---|
1424 | sc.putFreqMap(freqID);
|
---|
1425 | //
|
---|
1426 | pTabOut->putSDContainer(sc);
|
---|
1427 | }
|
---|
1428 |
|
---|
1429 | // Now we must set the base and extra frames to the
|
---|
1430 | // input frame
|
---|
1431 |
|
---|
1432 | std::vector<string> info = pTabOut->getCoordInfo();
|
---|
1433 | info[1] = MFrequency::showType(freqSystem); // Conversion frame
|
---|
1434 | info[3] = info[1]; // Base frame
|
---|
1435 | pTabOut->setCoordInfo(info);
|
---|
1436 |
|
---|
1437 | // Clean up PointerBlock
|
---|
1438 |
|
---|
1439 | for (uInt i=0; i<a.nelements(); i++) delete a[i];
|
---|
1440 | //
|
---|
1441 | return pTabOut;
|
---|
1442 | }
|
---|
1443 |
|
---|
1444 |
|
---|
1445 | void SDMath::fillSDC(SDContainer& sc,
|
---|
1446 | const Array<Bool>& mask,
|
---|
1447 | const Array<Float>& data,
|
---|
1448 | const Array<Float>& tSys,
|
---|
1449 | Int scanID, Double timeStamp,
|
---|
1450 | Double interval, const String& sourceName,
|
---|
1451 | const Vector<uInt>& freqID) const
|
---|
1452 | {
|
---|
1453 | // Data and mask
|
---|
1454 |
|
---|
1455 | putDataInSDC(sc, data, mask);
|
---|
1456 |
|
---|
1457 | // TSys
|
---|
1458 |
|
---|
1459 | sc.putTsys(tSys);
|
---|
1460 |
|
---|
1461 | // Time things
|
---|
1462 |
|
---|
1463 | sc.timestamp = timeStamp;
|
---|
1464 | sc.interval = interval;
|
---|
1465 | sc.scanid = scanID;
|
---|
1466 | //
|
---|
1467 | sc.sourcename = sourceName;
|
---|
1468 | sc.putFreqMap(freqID);
|
---|
1469 | }
|
---|
1470 |
|
---|
1471 | void SDMath::normalize(MaskedArray<Float>& sum,
|
---|
1472 | const Array<Float>& sumSq,
|
---|
1473 | const Array<Float>& nPts,
|
---|
1474 | WeightType wtType, Int axis,
|
---|
1475 | Int nAxesSub) const
|
---|
1476 | {
|
---|
1477 | IPosition pos2(nAxesSub,0);
|
---|
1478 | //
|
---|
1479 | if (wtType==NONE) {
|
---|
1480 |
|
---|
1481 | // We just average by the number of points accumulated.
|
---|
1482 | // We need to make a MA out of nPts so that no divide by
|
---|
1483 | // zeros occur
|
---|
1484 |
|
---|
1485 | MaskedArray<Float> t(nPts, (nPts>Float(0.0)));
|
---|
1486 | sum /= t;
|
---|
1487 | } else if (wtType==VAR) {
|
---|
1488 |
|
---|
1489 | // Normalize each spectrum by sum(1/var) where the variance
|
---|
1490 | // is worked out for each spectrum
|
---|
1491 |
|
---|
1492 | Array<Float>& data = sum.getRWArray();
|
---|
1493 | VectorIterator<Float> itData(data, axis);
|
---|
1494 | while (!itData.pastEnd()) {
|
---|
1495 | pos2 = itData.pos().getFirst(nAxesSub);
|
---|
1496 | itData.vector() /= sumSq(pos2);
|
---|
1497 | itData.next();
|
---|
1498 | }
|
---|
1499 | } else if (wtType==TSYS) {
|
---|
1500 | }
|
---|
1501 | }
|
---|
1502 |
|
---|
1503 |
|
---|
1504 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum,
|
---|
1505 | MaskedArray<Float>& sum, Array<Float>& sumSq,
|
---|
1506 | Array<Float>& nPts, Array<Float>& tSysSum,
|
---|
1507 | const Array<Float>& tSys, const Array<Float>& nInc,
|
---|
1508 | const Vector<Bool>& mask, Double time, Double interval,
|
---|
1509 | const Block<CountedPtr<SDMemTable> >& in,
|
---|
1510 | uInt iTab, uInt iRow, uInt axis,
|
---|
1511 | uInt nAxesSub, Bool useMask,
|
---|
1512 | WeightType wtType) const
|
---|
1513 | {
|
---|
1514 |
|
---|
1515 | // Get data
|
---|
1516 |
|
---|
1517 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow));
|
---|
1518 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference
|
---|
1519 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference
|
---|
1520 | //
|
---|
1521 | if (wtType==NONE) {
|
---|
1522 | const MaskedArray<Float> n(nInc,dataIn.getMask());
|
---|
1523 | nPts += n; // Only accumulates where mask==T
|
---|
1524 | } else if (wtType==VAR) {
|
---|
1525 |
|
---|
1526 | // We are going to average the data, weighted by the noise for each pol, beam and IF.
|
---|
1527 | // So therefore we need to iterate through by spectrum (axis 3)
|
---|
1528 |
|
---|
1529 | VectorIterator<Float> itData(valuesIn, axis);
|
---|
1530 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis);
|
---|
1531 | Float fac = 1.0;
|
---|
1532 | IPosition pos(nAxesSub,0);
|
---|
1533 | //
|
---|
1534 | while (!itData.pastEnd()) {
|
---|
1535 |
|
---|
1536 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor
|
---|
1537 |
|
---|
1538 | if (useMask) {
|
---|
1539 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector());
|
---|
1540 | fac = 1.0/variance(tmp);
|
---|
1541 | } else {
|
---|
1542 | MaskedArray<Float> tmp(itData.vector(),itMask.vector());
|
---|
1543 | fac = 1.0/variance(tmp);
|
---|
1544 | }
|
---|
1545 |
|
---|
1546 | // Scale data
|
---|
1547 |
|
---|
1548 | itData.vector() *= fac; // Writes back into 'dataIn'
|
---|
1549 | //
|
---|
1550 | // Accumulate variance per if/pol/beam averaged over spectrum
|
---|
1551 | // This method to get pos2 from itData.pos() is only valid
|
---|
1552 | // because the spectral axis is the last one (so we can just
|
---|
1553 | // copy the first nAXesSub positions out)
|
---|
1554 |
|
---|
1555 | pos = itData.pos().getFirst(nAxesSub);
|
---|
1556 | sumSq(pos) += fac;
|
---|
1557 | //
|
---|
1558 | itData.next();
|
---|
1559 | itMask.next();
|
---|
1560 | }
|
---|
1561 | } else if (wtType==TSYS) {
|
---|
1562 | }
|
---|
1563 |
|
---|
1564 | // Accumulate sum of (possibly scaled) data
|
---|
1565 |
|
---|
1566 | sum += dataIn;
|
---|
1567 |
|
---|
1568 | // Accumulate Tsys, time, and interval
|
---|
1569 |
|
---|
1570 | tSysSum += tSys;
|
---|
1571 | timeSum += time;
|
---|
1572 | intSum += interval;
|
---|
1573 | nAccum += 1;
|
---|
1574 | }
|
---|
1575 |
|
---|
1576 |
|
---|
1577 |
|
---|
1578 |
|
---|
1579 | void SDMath::getCursorLocation(IPosition& start, IPosition& end,
|
---|
1580 | const SDMemTable& in) const
|
---|
1581 | {
|
---|
1582 | const uInt nDim = 4;
|
---|
1583 | const uInt i = in.getBeam();
|
---|
1584 | const uInt j = in.getIF();
|
---|
1585 | const uInt k = in.getPol();
|
---|
1586 | const uInt n = in.nChan();
|
---|
1587 | //
|
---|
1588 | start.resize(nDim);
|
---|
1589 | start(0) = i;
|
---|
1590 | start(1) = j;
|
---|
1591 | start(2) = k;
|
---|
1592 | start(3) = 0;
|
---|
1593 | //
|
---|
1594 | end.resize(nDim);
|
---|
1595 | end(0) = i;
|
---|
1596 | end(1) = j;
|
---|
1597 | end(2) = k;
|
---|
1598 | end(3) = n-1;
|
---|
1599 | }
|
---|
1600 |
|
---|
1601 |
|
---|
1602 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr) const
|
---|
1603 | {
|
---|
1604 | String tStr(weightStr);
|
---|
1605 | tStr.upcase();
|
---|
1606 | if (tStr.contains(String("NONE"))) {
|
---|
1607 | wtType = NONE;
|
---|
1608 | } else if (tStr.contains(String("VAR"))) {
|
---|
1609 | wtType = VAR;
|
---|
1610 | } else if (tStr.contains(String("TSYS"))) {
|
---|
1611 | wtType = TSYS;
|
---|
1612 | throw(AipsError("T_sys weighting not yet implemented"));
|
---|
1613 | } else {
|
---|
1614 | throw(AipsError("Unrecognized weighting type"));
|
---|
1615 | }
|
---|
1616 | }
|
---|
1617 |
|
---|
1618 |
|
---|
1619 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type,
|
---|
1620 | const casa::String& interp) const
|
---|
1621 | {
|
---|
1622 | String tStr(interp);
|
---|
1623 | tStr.upcase();
|
---|
1624 | if (tStr.contains(String("NEAR"))) {
|
---|
1625 | type = InterpolateArray1D<Double,Float>::nearestNeighbour;
|
---|
1626 | } else if (tStr.contains(String("LIN"))) {
|
---|
1627 | type = InterpolateArray1D<Double,Float>::linear;
|
---|
1628 | } else if (tStr.contains(String("CUB"))) {
|
---|
1629 | type = InterpolateArray1D<Double,Float>::cubic;
|
---|
1630 | } else if (tStr.contains(String("SPL"))) {
|
---|
1631 | type = InterpolateArray1D<Double,Float>::spline;
|
---|
1632 | } else {
|
---|
1633 | throw(AipsError("Unrecognized interpolation type"));
|
---|
1634 | }
|
---|
1635 | }
|
---|
1636 |
|
---|
1637 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data,
|
---|
1638 | const Array<Bool>& mask) const
|
---|
1639 | {
|
---|
1640 | sc.putSpectrum(data);
|
---|
1641 | //
|
---|
1642 | Array<uChar> outflags(data.shape());
|
---|
1643 | convertArray(outflags,!mask);
|
---|
1644 | sc.putFlags(outflags);
|
---|
1645 | }
|
---|
1646 |
|
---|
1647 | Table SDMath::readAsciiFile (const String& fileName) const
|
---|
1648 | {
|
---|
1649 | String formatString;
|
---|
1650 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False);
|
---|
1651 | return tbl;
|
---|
1652 | }
|
---|
1653 |
|
---|
1654 |
|
---|
1655 |
|
---|
1656 | void SDMath::correctFromAsciiTable(SDMemTable* pTabOut,
|
---|
1657 | const SDMemTable& in, const String& fileName,
|
---|
1658 | const String& col0, const String& col1,
|
---|
1659 | const String& methodStr, Bool doAll,
|
---|
1660 | const Vector<Float>& xOut) const
|
---|
1661 | {
|
---|
1662 |
|
---|
1663 | // Read gain-elevation ascii file data into a Table.
|
---|
1664 |
|
---|
1665 | Table geTable = readAsciiFile (fileName);
|
---|
1666 | //
|
---|
1667 | correctFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut);
|
---|
1668 | }
|
---|
1669 |
|
---|
1670 | void SDMath::correctFromTable(SDMemTable* pTabOut, const SDMemTable& in,
|
---|
1671 | const Table& tTable, const String& col0,
|
---|
1672 | const String& col1,
|
---|
1673 | const String& methodStr, Bool doAll,
|
---|
1674 | const Vector<Float>& xOut) const
|
---|
1675 | {
|
---|
1676 |
|
---|
1677 | // Get data from Table
|
---|
1678 |
|
---|
1679 | ROScalarColumn<Float> geElCol(tTable, col0);
|
---|
1680 | ROScalarColumn<Float> geFacCol(tTable, col1);
|
---|
1681 | Vector<Float> xIn = geElCol.getColumn();
|
---|
1682 | Vector<Float> yIn = geFacCol.getColumn();
|
---|
1683 | Vector<Bool> maskIn(xIn.nelements(),True);
|
---|
1684 |
|
---|
1685 | // Interpolate (and extrapolate) with desired method
|
---|
1686 |
|
---|
1687 | InterpolateArray1D<Double,Float>::InterpolationMethod method;
|
---|
1688 | convertInterpString(method, methodStr);
|
---|
1689 | Int intMethod(method);
|
---|
1690 | //
|
---|
1691 | Vector<Float> yOut;
|
---|
1692 | Vector<Bool> maskOut;
|
---|
1693 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut,
|
---|
1694 | xIn, yIn, maskIn, intMethod,
|
---|
1695 | True, True);
|
---|
1696 | // Apply
|
---|
1697 |
|
---|
1698 | correctFromVector (pTabOut, in, doAll, yOut);
|
---|
1699 | }
|
---|
1700 |
|
---|
1701 |
|
---|
1702 | void SDMath::correctFromVector (SDMemTable* pTabOut, const SDMemTable& in,
|
---|
1703 | Bool doAll, const Vector<Float>& factor) const
|
---|
1704 | {
|
---|
1705 |
|
---|
1706 | // For operations only on specified cursor location
|
---|
1707 |
|
---|
1708 | IPosition start, end;
|
---|
1709 | getCursorLocation(start, end, in);
|
---|
1710 |
|
---|
1711 | // Loop over rows and apply correction factor
|
---|
1712 |
|
---|
1713 | const uInt axis = asap::ChanAxis;
|
---|
1714 | for (uInt i=0; i < in.nRow(); ++i) {
|
---|
1715 |
|
---|
1716 | // Get data
|
---|
1717 |
|
---|
1718 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i));
|
---|
1719 |
|
---|
1720 | // Apply factor
|
---|
1721 |
|
---|
1722 | if (doAll) {
|
---|
1723 | dataIn *= factor[i];
|
---|
1724 | } else {
|
---|
1725 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference
|
---|
1726 | dataIn2 *= factor[i];
|
---|
1727 | }
|
---|
1728 |
|
---|
1729 | // Write out
|
---|
1730 |
|
---|
1731 | SDContainer sc = in.getSDContainer(i);
|
---|
1732 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask());
|
---|
1733 | //
|
---|
1734 | pTabOut->putSDContainer(sc);
|
---|
1735 | }
|
---|
1736 | }
|
---|
1737 |
|
---|
1738 |
|
---|
1739 |
|
---|
1740 |
|
---|
1741 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx,
|
---|
1742 | SDDataDesc& dDesc,
|
---|
1743 | uInt nIF,
|
---|
1744 | const SDMemTable& in,
|
---|
1745 | const Table& tabIn,
|
---|
1746 | const ROScalarColumn<String>& srcCol,
|
---|
1747 | const ROArrayColumn<uInt>& fqIDCol) const
|
---|
1748 | {
|
---|
1749 | const uInt nRows = tabIn.nrow();
|
---|
1750 | ddIdx.resize(nRows,nIF);
|
---|
1751 | //
|
---|
1752 | String srcName;
|
---|
1753 | Vector<uInt> freqIDs;
|
---|
1754 | for (uInt iRow=0; iRow<nRows; iRow++) {
|
---|
1755 | srcCol.get(iRow, srcName);
|
---|
1756 | fqIDCol.get(iRow, freqIDs);
|
---|
1757 | const MDirection& dir = in.getDirection(iRow);
|
---|
1758 | //
|
---|
1759 | for (uInt iIF=0; iIF<nIF; iIF++) {
|
---|
1760 | uInt idx = dDesc.addEntry(srcName, freqIDs[iIF], dir);
|
---|
1761 | ddIdx(iRow,iIF) = idx;
|
---|
1762 | }
|
---|
1763 | }
|
---|
1764 | }
|
---|
1765 |
|
---|
1766 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const
|
---|
1767 | {
|
---|
1768 | Quantum<Double> qt;
|
---|
1769 | if (MVTime::read(qt,str)) {
|
---|
1770 | MVEpoch mv(qt);
|
---|
1771 | MEpoch me(mv, timeRef);
|
---|
1772 | return me;
|
---|
1773 | } else {
|
---|
1774 | throw(AipsError("Invalid format for Epoch string"));
|
---|
1775 | }
|
---|
1776 | }
|
---|
1777 |
|
---|
1778 |
|
---|
1779 | String SDMath::formatEpoch(const MEpoch& epoch) const
|
---|
1780 | {
|
---|
1781 | MVTime mvt(epoch.getValue());
|
---|
1782 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")");
|
---|
1783 | }
|
---|
1784 |
|
---|
1785 |
|
---|
1786 |
|
---|
1787 | void SDMath::generateFrequencyAligners (PtrBlock<FrequencyAligner<Float>* >& a,
|
---|
1788 | const SDDataDesc& dDesc,
|
---|
1789 | const SDMemTable& in, uInt nChan,
|
---|
1790 | MFrequency::Types system,
|
---|
1791 | const MPosition& refPos,
|
---|
1792 | const MEpoch& refEpoch) const
|
---|
1793 | {
|
---|
1794 | for (uInt i=0; i<dDesc.length(); i++) {
|
---|
1795 | uInt freqID = dDesc.freqID(i);
|
---|
1796 | const MDirection& refDir = dDesc.direction(i);
|
---|
1797 | //
|
---|
1798 | SpectralCoordinate sC = in.getSpectralCoordinate(freqID);
|
---|
1799 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system);
|
---|
1800 | }
|
---|
1801 | }
|
---|
1802 |
|
---|
1803 |
|
---|