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 | |
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34 | #include <casa/aips.h> |
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35 | #include <casa/iostream.h> |
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36 | #include <casa/sstream.h> |
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37 | #include <casa/iomanip.h> |
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38 | #include <casa/BasicSL/String.h> |
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39 | #include <casa/Arrays/IPosition.h> |
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40 | #include <casa/Arrays/Array.h> |
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41 | #include <casa/Arrays/ArrayIter.h> |
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42 | #include <casa/Arrays/VectorIter.h> |
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43 | #include <casa/Arrays/ArrayMath.h> |
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44 | #include <casa/Arrays/ArrayLogical.h> |
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45 | #include <casa/Arrays/MaskedArray.h> |
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46 | #include <casa/Arrays/MaskArrMath.h> |
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47 | #include <casa/Arrays/MaskArrLogi.h> |
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48 | #include <casa/Arrays/Matrix.h> |
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49 | #include <casa/BasicMath/Math.h> |
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50 | #include <casa/Exceptions.h> |
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51 | #include <casa/Quanta/Quantum.h> |
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52 | #include <casa/Quanta/Unit.h> |
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53 | #include <casa/Quanta/MVEpoch.h> |
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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 "SDAttr.h" |
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82 | #include "SDContainer.h" |
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83 | #include "SDMemTable.h" |
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84 | |
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85 | #include "SDMath.h" |
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86 | #include "SDPol.h" |
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87 | |
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88 | using namespace casa; |
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89 | using namespace asap; |
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90 | |
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91 | |
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92 | SDMath::SDMath() |
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93 | { |
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94 | } |
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95 | |
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96 | SDMath::SDMath(const SDMath& other) |
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97 | { |
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98 | |
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99 | // No state |
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100 | |
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101 | } |
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102 | |
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103 | SDMath& SDMath::operator=(const SDMath& other) |
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104 | { |
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105 | if (this != &other) { |
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106 | // No state |
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107 | } |
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108 | return *this; |
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109 | } |
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110 | |
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111 | SDMath::~SDMath() |
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112 | {;} |
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113 | |
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114 | |
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115 | SDMemTable* SDMath::frequencyAlignment(const SDMemTable& in, |
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116 | const String& refTime, |
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117 | const String& method, |
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118 | Bool perFreqID) |
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119 | { |
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120 | // Get frame info from Table |
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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 | String systemStr(info[1]); |
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125 | String baseSystemStr(info[3]); |
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126 | if (baseSystemStr==systemStr) { |
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127 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe")); |
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128 | } |
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129 | |
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130 | MFrequency::Types freqSystem; |
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131 | MFrequency::getType(freqSystem, systemStr); |
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132 | |
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133 | return frequencyAlign(in, freqSystem, refTime, method, perFreqID); |
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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> |
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139 | SDMath::average(const std::vector<CountedPtr<SDMemTable> >& in, |
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140 | const Vector<Bool>& mask, Bool scanAv, |
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141 | const String& weightStr, Bool alignFreq) |
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142 | // Weighted averaging of spectra from one or more Tables. |
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143 | { |
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144 | // Convert weight type |
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145 | WeightType wtType = NONE; |
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146 | convertWeightString(wtType, weightStr, True); |
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147 | |
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148 | // Create output Table by cloning from the first table |
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149 | SDMemTable* pTabOut = new SDMemTable(*in[0],True); |
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150 | if (in.size() > 1) { |
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151 | for (uInt i=1; i < in.size(); ++i) { |
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152 | pTabOut->appendToHistoryTable(in[i]->getHistoryTable()); |
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153 | } |
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154 | } |
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155 | // Setup |
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156 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change |
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157 | Array<Float> arr(shp); |
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158 | Array<Bool> barr(shp); |
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159 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis)); |
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160 | |
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161 | // Columns from Tables |
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162 | ROArrayColumn<Float> tSysCol; |
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163 | ROScalarColumn<Double> mjdCol; |
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164 | ROScalarColumn<String> srcNameCol; |
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165 | ROScalarColumn<Double> intCol; |
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166 | ROArrayColumn<uInt> fqIDCol; |
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167 | ROScalarColumn<Int> scanIDCol; |
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168 | |
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169 | // Create accumulation MaskedArray. We accumulate for each |
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170 | // channel,if,pol,beam Note that the mask of the accumulation array |
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171 | // will ALWAYS remain ALL True. The MA is only used so that when |
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172 | // data which is masked Bad is added to it, that data does not |
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173 | // contribute. |
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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 | Array<Float> nPts(shp); // Number of points |
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183 | nPts = 0.0; |
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184 | Array<Float> nInc(shp); // Increment |
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185 | nInc = 1.0; |
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186 | |
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187 | // Create accumulation Array for variance. We accumulate for each |
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188 | // if,pol,beam, but average over channel. So we need a shape with |
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189 | // one less axis dropping channels. |
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190 | const uInt nAxesSub = shp.nelements() - 1; |
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191 | IPosition shp2(nAxesSub); |
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192 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) { |
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193 | if (i!=asap::ChanAxis) { |
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194 | shp2(j) = shp(i); |
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195 | j++; |
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196 | } |
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197 | } |
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198 | Array<Float> sumSq(shp2); |
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199 | sumSq = 0.0; |
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200 | IPosition pos2(nAxesSub,0); // For indexing |
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201 | |
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202 | // Time-related accumulators |
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203 | Double time; |
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204 | Double timeSum = 0.0; |
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205 | Double intSum = 0.0; |
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206 | Double interval = 0.0; |
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207 | |
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208 | // To get the right shape for the Tsys accumulator we need to access |
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209 | // a column from the first table. The shape of this array must not |
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210 | // change. Note however that since the TSysSqSum array is used in a |
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211 | // normalization process, and that I ignore the channel axis |
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212 | // replication of values for now, it loses a dimension |
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213 | |
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214 | Array<Float> tSysSum, tSysSqSum; |
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215 | { |
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216 | const Table& tabIn = in[0]->table(); |
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217 | tSysCol.attach(tabIn,"TSYS"); |
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218 | tSysSum.resize(tSysCol.shape(0)); |
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219 | tSysSqSum.resize(shp2); |
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220 | } |
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221 | tSysSum = 0.0; |
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222 | tSysSqSum = 0.0; |
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223 | Array<Float> tSys; |
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224 | |
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225 | // Scan and row tracking |
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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 | String sourceName, oldSourceName, sourceNameStart; |
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235 | Vector<uInt> freqID, freqIDStart, oldFreqID; |
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236 | |
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237 | // Loop over tables |
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238 | Float fac = 1.0; |
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239 | const uInt nTables = in.size(); |
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240 | for (uInt iTab=0; iTab<nTables; iTab++) { |
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241 | |
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242 | // Should check that the frequency tables don't change if doing |
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243 | // FreqAlignment |
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244 | |
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245 | // Attach columns to Table |
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246 | const Table& tabIn = in[iTab]->table(); |
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247 | tSysCol.attach(tabIn, "TSYS"); |
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248 | mjdCol.attach(tabIn, "TIME"); |
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249 | srcNameCol.attach(tabIn, "SRCNAME"); |
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250 | intCol.attach(tabIn, "INTERVAL"); |
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251 | fqIDCol.attach(tabIn, "FREQID"); |
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252 | scanIDCol.attach(tabIn, "SCANID"); |
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253 | |
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254 | // Loop over rows in Table |
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255 | const uInt nRows = in[iTab]->nRow(); |
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256 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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257 | // Check conformance |
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258 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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259 | if (!shp.isEqual(shp2)) { |
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260 | delete pTabOut; |
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261 | throw (AipsError("Shapes for all rows must be the same")); |
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262 | } |
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263 | |
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264 | // If we are not doing scan averages, make checks for source |
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265 | // and frequency setup and warn if averaging across them |
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266 | scanIDCol.getScalar(iRow, scanID); |
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267 | |
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268 | // Get quantities from columns |
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269 | srcNameCol.getScalar(iRow, sourceName); |
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270 | mjdCol.get(iRow, time); |
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271 | tSysCol.get(iRow, tSys); |
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272 | intCol.get(iRow, interval); |
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273 | fqIDCol.get(iRow, freqID); |
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274 | |
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275 | // Initialize first source and freqID |
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276 | if (iRow==0 && iTab==0) { |
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277 | sourceNameStart = sourceName; |
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278 | freqIDStart = freqID; |
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279 | } |
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280 | |
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281 | // If we are doing scan averages, see if we are at the end of |
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282 | // an accumulation period (scan). We must check soutce names |
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283 | // too, since we might have two tables with one scan each but |
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284 | // different source names; we shouldn't average different |
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285 | // sources together |
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286 | if (scanAv && ( (scanID != oldScanID) || |
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287 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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288 | |
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289 | // Normalize data in 'sum' accumulation array according to |
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290 | // weighting scheme |
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291 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, |
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292 | asap::ChanAxis, nAxesSub); |
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293 | |
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294 | // Get ScanContainer for the first row of this averaged Scan |
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295 | SDContainer scOut = in[iTab]->getSDContainer(rowStart); |
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296 | |
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297 | // Fill scan container. The source and freqID come from the |
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298 | // first row of the first table that went into this average |
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299 | // ( should be the same for all rows in the scan average) |
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300 | |
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301 | Float nR(nAccum); |
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302 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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303 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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304 | |
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305 | // Write container out to Table |
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306 | pTabOut->putSDContainer(scOut); |
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307 | |
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308 | // Reset accumulators |
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309 | sum = 0.0; |
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310 | sumSq = 0.0; |
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311 | nAccum = 0; |
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312 | |
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313 | tSysSum =0.0; |
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314 | tSysSqSum =0.0; |
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315 | timeSum = 0.0; |
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316 | intSum = 0.0; |
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317 | nPts = 0.0; |
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318 | |
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319 | // Increment |
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320 | rowStart = iRow; // First row for next accumulation |
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321 | tableStart = iTab; // First table for next accumulation |
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322 | sourceNameStart = sourceName; // First source name for next |
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323 | // accumulation |
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324 | freqIDStart = freqID; // First FreqID for next accumulation |
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325 | |
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326 | oldScanID = scanID; |
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327 | outScanID += 1; // Scan ID for next |
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328 | // accumulation period |
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329 | } |
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330 | |
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331 | // Accumulate |
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332 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, |
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333 | tSysSum, tSysSqSum, tSys, |
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334 | nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis, |
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335 | nAxesSub, useMask, wtType); |
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336 | oldSourceName = sourceName; |
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337 | oldFreqID = freqID; |
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338 | } |
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339 | } |
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340 | |
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341 | // OK at this point we have accumulation data which is either |
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342 | // - accumulated from all tables into one row |
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343 | // or |
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344 | // - accumulated from the last scan average |
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345 | // |
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346 | // Normalize data in 'sum' accumulation array according to weighting |
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347 | // scheme |
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348 | |
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349 | normalize(sum, sumSq, tSysSqSum, nPts, intSum, wtType, |
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350 | asap::ChanAxis, nAxesSub); |
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351 | |
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352 | // Create and fill container. The container we clone will be from |
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353 | // the last Table and the first row that went into the current |
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354 | // accumulation. It probably doesn't matter that much really... |
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355 | Float nR(nAccum); |
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356 | SDContainer scOut = in[tableStart]->getSDContainer(rowStart); |
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357 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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358 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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359 | pTabOut->putSDContainer(scOut); |
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360 | pTabOut->resetCursor(); |
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361 | |
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362 | return CountedPtr<SDMemTable>(pTabOut); |
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363 | } |
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364 | |
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365 | |
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366 | |
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367 | CountedPtr<SDMemTable> |
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368 | SDMath::binaryOperate(const CountedPtr<SDMemTable>& left, |
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369 | const CountedPtr<SDMemTable>& right, |
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370 | const String& op, Bool preserve, Bool doTSys) |
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371 | { |
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372 | |
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373 | // Check operator |
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374 | String op2(op); |
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375 | op2.upcase(); |
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376 | uInt what = 0; |
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377 | if (op2=="ADD") { |
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378 | what = 0; |
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379 | } else if (op2=="SUB") { |
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380 | what = 1; |
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381 | } else if (op2=="MUL") { |
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382 | what = 2; |
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383 | } else if (op2=="DIV") { |
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384 | what = 3; |
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385 | } else if (op2=="QUOTIENT") { |
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386 | what = 4; |
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387 | doTSys = True; |
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388 | } else { |
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389 | throw( AipsError("Unrecognized operation")); |
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390 | } |
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391 | |
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392 | // Check rows |
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393 | const uInt nRowLeft = left->nRow(); |
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394 | const uInt nRowRight = right->nRow(); |
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395 | Bool ok = (nRowRight==1 && nRowLeft>0) || |
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396 | (nRowRight>=1 && nRowLeft==nRowRight); |
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397 | if (!ok) { |
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398 | throw (AipsError("The right Scan Table can have one row or the same number of rows as the left Scan Table")); |
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399 | } |
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400 | |
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401 | // Input Tables |
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402 | const Table& tLeft = left->table(); |
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403 | const Table& tRight = right->table(); |
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404 | |
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405 | // TSys columns |
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406 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol; |
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407 | if (doTSys) { |
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408 | tSysLeftCol.attach(tLeft, "TSYS"); |
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409 | tSysRightCol.attach(tRight, "TSYS"); |
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410 | } |
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411 | |
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412 | // First row for right |
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413 | Array<Float> tSysLeftArr, tSysRightArr; |
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414 | if (doTSys) tSysRightCol.get(0, tSysRightArr); |
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415 | MaskedArray<Float>* pMRight = |
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416 | new MaskedArray<Float>(right->rowAsMaskedArray(0)); |
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417 | |
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418 | IPosition shpRight = pMRight->shape(); |
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419 | |
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420 | // Output Table cloned from left |
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421 | SDMemTable* pTabOut = new SDMemTable(*left, True); |
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422 | pTabOut->appendToHistoryTable(right->getHistoryTable()); |
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423 | |
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424 | // Loop over rows |
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425 | for (uInt i=0; i<nRowLeft; i++) { |
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426 | |
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427 | // Get data |
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428 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i)); |
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429 | IPosition shpLeft = mLeft.shape(); |
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430 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr); |
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431 | |
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432 | if (nRowRight>1) { |
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433 | delete pMRight; |
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434 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i)); |
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435 | shpRight = pMRight->shape(); |
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436 | if (doTSys) tSysRightCol.get(i, tSysRightArr); |
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437 | } |
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438 | |
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439 | if (!shpRight.isEqual(shpLeft)) { |
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440 | delete pTabOut; |
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441 | delete pMRight; |
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442 | throw(AipsError("left and right scan tables are not conformant")); |
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443 | } |
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444 | if (doTSys) { |
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445 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) { |
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446 | delete pTabOut; |
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447 | delete pMRight; |
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448 | throw(AipsError("left and right Tsys data are not conformant")); |
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449 | } |
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450 | if (!shpRight.isEqual(tSysRightArr.shape())) { |
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451 | delete pTabOut; |
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452 | delete pMRight; |
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453 | throw(AipsError("left and right scan tables are not conformant")); |
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454 | } |
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455 | } |
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456 | |
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457 | // Make container |
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458 | SDContainer sc = left->getSDContainer(i); |
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459 | |
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460 | // Operate on data and TSys |
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461 | if (what==0) { |
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462 | MaskedArray<Float> tmp = mLeft + *pMRight; |
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463 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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464 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr); |
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465 | } else if (what==1) { |
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466 | MaskedArray<Float> tmp = mLeft - *pMRight; |
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467 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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468 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr); |
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469 | } else if (what==2) { |
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470 | MaskedArray<Float> tmp = mLeft * *pMRight; |
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471 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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472 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr); |
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473 | } else if (what==3) { |
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474 | MaskedArray<Float> tmp = mLeft / *pMRight; |
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475 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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476 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr); |
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477 | } else if (what==4) { |
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478 | if (preserve) { |
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479 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
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480 | tSysRightArr; |
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481 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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482 | } else { |
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483 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
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484 | tSysLeftArr; |
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485 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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486 | } |
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487 | sc.putTsys(tSysRightArr); |
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488 | } |
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489 | |
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490 | // Put new row in output Table |
---|
491 | pTabOut->putSDContainer(sc); |
---|
492 | } |
---|
493 | if (pMRight) delete pMRight; |
---|
494 | pTabOut->resetCursor(); |
---|
495 | |
---|
496 | return CountedPtr<SDMemTable>(pTabOut); |
---|
497 | } |
---|
498 | |
---|
499 | |
---|
500 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in, |
---|
501 | const Vector<Bool>& mask, |
---|
502 | const String& which, Int row) const |
---|
503 | // |
---|
504 | // Perhaps iteration over pol/beam/if should be in here |
---|
505 | // and inside the nrow iteration ? |
---|
506 | // |
---|
507 | { |
---|
508 | const uInt nRow = in->nRow(); |
---|
509 | |
---|
510 | // Specify cursor location |
---|
511 | |
---|
512 | IPosition start, end; |
---|
513 | Bool doAll = False; |
---|
514 | setCursorSlice(start, end, doAll, *in); |
---|
515 | |
---|
516 | // Loop over rows |
---|
517 | |
---|
518 | const uInt nEl = mask.nelements(); |
---|
519 | uInt iStart = 0; |
---|
520 | uInt iEnd = in->nRow()-1; |
---|
521 | // |
---|
522 | if (row>=0) { |
---|
523 | iStart = row; |
---|
524 | iEnd = row; |
---|
525 | } |
---|
526 | // |
---|
527 | std::vector<float> result(iEnd-iStart+1); |
---|
528 | for (uInt ii=iStart; ii <= iEnd; ++ii) { |
---|
529 | |
---|
530 | // Get row and deconstruct |
---|
531 | |
---|
532 | MaskedArray<Float> dataIn = (in->rowAsMaskedArray(ii))(start,end); |
---|
533 | Array<Float> v = dataIn.getArray().nonDegenerate(); |
---|
534 | Array<Bool> m = dataIn.getMask().nonDegenerate(); |
---|
535 | |
---|
536 | // Access desired piece of data |
---|
537 | |
---|
538 | // Array<Float> v((arr(start,end)).nonDegenerate()); |
---|
539 | // Array<Bool> m((barr(start,end)).nonDegenerate()); |
---|
540 | |
---|
541 | // Apply OTF mask |
---|
542 | |
---|
543 | MaskedArray<Float> tmp; |
---|
544 | if (m.nelements()==nEl) { |
---|
545 | tmp.setData(v,m&&mask); |
---|
546 | } else { |
---|
547 | tmp.setData(v,m); |
---|
548 | } |
---|
549 | |
---|
550 | // Get statistic |
---|
551 | |
---|
552 | result[ii-iStart] = mathutil::statistics(which, tmp); |
---|
553 | } |
---|
554 | // |
---|
555 | return result; |
---|
556 | } |
---|
557 | |
---|
558 | |
---|
559 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) |
---|
560 | { |
---|
561 | SDHeader sh = in.getSDHeader(); |
---|
562 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
563 | |
---|
564 | // Bin up SpectralCoordinates |
---|
565 | |
---|
566 | IPosition factors(1); |
---|
567 | factors(0) = width; |
---|
568 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
569 | CoordinateSystem cSys; |
---|
570 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
571 | CoordinateSystem cSysBin = |
---|
572 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False); |
---|
573 | // |
---|
574 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
---|
575 | pTabOut->setCoordinate(sCBin, j); |
---|
576 | } |
---|
577 | |
---|
578 | // Use RebinLattice to find shape |
---|
579 | |
---|
580 | IPosition shapeIn(1,sh.nchan); |
---|
581 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors); |
---|
582 | sh.nchan = shapeOut(0); |
---|
583 | pTabOut->putSDHeader(sh); |
---|
584 | |
---|
585 | // Loop over rows and bin along channel axis |
---|
586 | |
---|
587 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
588 | SDContainer sc = in.getSDContainer(i); |
---|
589 | // |
---|
590 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
---|
591 | |
---|
592 | // Bin up spectrum |
---|
593 | |
---|
594 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
---|
595 | MaskedArray<Float> marrout; |
---|
596 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width); |
---|
597 | |
---|
598 | // Put back the binned data and flags |
---|
599 | |
---|
600 | IPosition ip2 = marrout.shape(); |
---|
601 | sc.resize(ip2); |
---|
602 | // |
---|
603 | putDataInSDC(sc, marrout.getArray(), marrout.getMask()); |
---|
604 | |
---|
605 | // Bin up Tsys. |
---|
606 | |
---|
607 | Array<Bool> allGood(tSys.shape(),True); |
---|
608 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
---|
609 | // |
---|
610 | MaskedArray<Float> tSysOut; |
---|
611 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width); |
---|
612 | sc.putTsys(tSysOut.getArray()); |
---|
613 | // |
---|
614 | pTabOut->putSDContainer(sc); |
---|
615 | } |
---|
616 | return pTabOut; |
---|
617 | } |
---|
618 | |
---|
619 | SDMemTable* SDMath::resample(const SDMemTable& in, const String& methodStr, |
---|
620 | Float width) |
---|
621 | // |
---|
622 | // Should add the possibility of width being specified in km/s. This means |
---|
623 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
624 | // average channel width (say at the reference pixel). Then we would need |
---|
625 | // to be careful to make sure each spectrum (of different freqID) |
---|
626 | // is the same length. |
---|
627 | // |
---|
628 | { |
---|
629 | Bool doVel = False; |
---|
630 | if (doVel) { |
---|
631 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
632 | SpectralCoordinate sC = in.getSpectralCoordinate(j); |
---|
633 | } |
---|
634 | } |
---|
635 | |
---|
636 | // Interpolation method |
---|
637 | |
---|
638 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
639 | convertInterpString(interp, methodStr); |
---|
640 | Int interpMethod(interp); |
---|
641 | |
---|
642 | // Make output table |
---|
643 | |
---|
644 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
645 | |
---|
646 | // Resample SpectralCoordinates (one per freqID) |
---|
647 | |
---|
648 | const uInt nCoord = in.nCoordinates(); |
---|
649 | Vector<Float> offset(1,0.0); |
---|
650 | Vector<Float> factors(1,1.0/width); |
---|
651 | Vector<Int> newShape; |
---|
652 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
653 | CoordinateSystem cSys; |
---|
654 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
655 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape); |
---|
656 | SpectralCoordinate sC = cSys2.spectralCoordinate(0); |
---|
657 | // |
---|
658 | pTabOut->setCoordinate(sC, j); |
---|
659 | } |
---|
660 | |
---|
661 | // Get header |
---|
662 | |
---|
663 | SDHeader sh = in.getSDHeader(); |
---|
664 | |
---|
665 | // Generate resampling vectors |
---|
666 | |
---|
667 | const uInt nChanIn = sh.nchan; |
---|
668 | Vector<Float> xIn(nChanIn); |
---|
669 | indgen(xIn); |
---|
670 | // |
---|
671 | Int fac = Int(nChanIn/width); |
---|
672 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
673 | uInt i = 0; |
---|
674 | Float x = 0.0; |
---|
675 | Bool more = True; |
---|
676 | while (more) { |
---|
677 | xOut(i) = x; |
---|
678 | // |
---|
679 | i++; |
---|
680 | x += width; |
---|
681 | if (x>nChanIn-1) more = False; |
---|
682 | } |
---|
683 | const uInt nChanOut = i; |
---|
684 | xOut.resize(nChanOut,True); |
---|
685 | // |
---|
686 | IPosition shapeIn(in.rowAsMaskedArray(0).shape()); |
---|
687 | sh.nchan = nChanOut; |
---|
688 | pTabOut->putSDHeader(sh); |
---|
689 | |
---|
690 | // Loop over rows and resample along channel axis |
---|
691 | |
---|
692 | Array<Float> valuesOut; |
---|
693 | Array<Bool> maskOut; |
---|
694 | Array<Float> tSysOut; |
---|
695 | Array<Bool> tSysMaskIn(shapeIn,True); |
---|
696 | Array<Bool> tSysMaskOut; |
---|
697 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
698 | |
---|
699 | // Get container |
---|
700 | |
---|
701 | SDContainer sc = in.getSDContainer(i); |
---|
702 | |
---|
703 | // Get data and Tsys |
---|
704 | |
---|
705 | const Array<Float>& tSysIn = sc.getTsys(); |
---|
706 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i)); |
---|
707 | Array<Float> valuesIn = dataIn.getArray(); |
---|
708 | Array<Bool> maskIn = dataIn.getMask(); |
---|
709 | |
---|
710 | // Interpolate data |
---|
711 | |
---|
712 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut, |
---|
713 | xIn, valuesIn, maskIn, |
---|
714 | interpMethod, True, True); |
---|
715 | sc.resize(valuesOut.shape()); |
---|
716 | putDataInSDC(sc, valuesOut, maskOut); |
---|
717 | |
---|
718 | // Interpolate TSys |
---|
719 | |
---|
720 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut, |
---|
721 | xIn, tSysIn, tSysMaskIn, |
---|
722 | interpMethod, True, True); |
---|
723 | sc.putTsys(tSysOut); |
---|
724 | |
---|
725 | // Put container in output |
---|
726 | |
---|
727 | pTabOut->putSDContainer(sc); |
---|
728 | } |
---|
729 | // |
---|
730 | return pTabOut; |
---|
731 | } |
---|
732 | |
---|
733 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll, |
---|
734 | uInt what, Bool doTSys) |
---|
735 | // |
---|
736 | // what = 0 Multiply |
---|
737 | // 1 Add |
---|
738 | { |
---|
739 | SDMemTable* pOut = new SDMemTable(in,False); |
---|
740 | const Table& tOut = pOut->table(); |
---|
741 | ArrayColumn<Float> specCol(tOut,"SPECTRA"); |
---|
742 | ArrayColumn<Float> tSysCol(tOut,"TSYS"); |
---|
743 | Array<Float> tSysArr; |
---|
744 | |
---|
745 | // Get data slice bounds |
---|
746 | |
---|
747 | IPosition start, end; |
---|
748 | setCursorSlice (start, end, doAll, in); |
---|
749 | // |
---|
750 | for (uInt i=0; i<tOut.nrow(); i++) { |
---|
751 | |
---|
752 | // Modify data |
---|
753 | |
---|
754 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
755 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference |
---|
756 | if (what==0) { |
---|
757 | dataIn2 *= val; |
---|
758 | } else if (what==1) { |
---|
759 | dataIn2 += val; |
---|
760 | } |
---|
761 | specCol.put(i, dataIn.getArray()); |
---|
762 | |
---|
763 | // Modify Tsys |
---|
764 | |
---|
765 | if (doTSys) { |
---|
766 | tSysCol.get(i, tSysArr); |
---|
767 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference |
---|
768 | if (what==0) { |
---|
769 | tSysArr2 *= val; |
---|
770 | } else if (what==1) { |
---|
771 | tSysArr2 += val; |
---|
772 | } |
---|
773 | tSysCol.put(i, tSysArr); |
---|
774 | } |
---|
775 | } |
---|
776 | // |
---|
777 | return pOut; |
---|
778 | } |
---|
779 | |
---|
780 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask, |
---|
781 | const String& weightStr) |
---|
782 | // |
---|
783 | // Average all polarizations together, weighted by variance |
---|
784 | // |
---|
785 | { |
---|
786 | WeightType wtType = NONE; |
---|
787 | convertWeightString(wtType, weightStr, True); |
---|
788 | |
---|
789 | // Create output Table and reshape number of polarizations |
---|
790 | |
---|
791 | Bool clear=True; |
---|
792 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
793 | SDHeader header = pTabOut->getSDHeader(); |
---|
794 | header.npol = 1; |
---|
795 | pTabOut->putSDHeader(header); |
---|
796 | // |
---|
797 | const Table& tabIn = in.table(); |
---|
798 | |
---|
799 | // Shape of input and output data |
---|
800 | |
---|
801 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape(); |
---|
802 | IPosition shapeOut(shapeIn); |
---|
803 | shapeOut(asap::PolAxis) = 1; // Average all polarizations |
---|
804 | if (shapeIn(asap::PolAxis)==1) { |
---|
805 | delete pTabOut; |
---|
806 | throw(AipsError("The input has only one polarisation")); |
---|
807 | } |
---|
808 | // |
---|
809 | const uInt nRows = in.nRow(); |
---|
810 | const uInt nChan = shapeIn(asap::ChanAxis); |
---|
811 | AlwaysAssert(asap::nAxes==4,AipsError); |
---|
812 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape |
---|
813 | IPosition start(4), end(4); |
---|
814 | |
---|
815 | // Output arrays |
---|
816 | |
---|
817 | Array<Float> outData(shapeOut, 0.0); |
---|
818 | Array<Bool> outMask(shapeOut, True); |
---|
819 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane |
---|
820 | |
---|
821 | // Attach Tsys column if needed |
---|
822 | |
---|
823 | ROArrayColumn<Float> tSysCol; |
---|
824 | Array<Float> tSys; |
---|
825 | if (wtType==TSYS) { |
---|
826 | tSysCol.attach(tabIn,"TSYS"); |
---|
827 | } |
---|
828 | // |
---|
829 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis)); |
---|
830 | |
---|
831 | // Loop over rows |
---|
832 | |
---|
833 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
834 | |
---|
835 | // Get data for this row |
---|
836 | |
---|
837 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
838 | Array<Float>& arr = marr.getRWArray(); |
---|
839 | const Array<Bool>& barr = marr.getMask(); |
---|
840 | |
---|
841 | // Get Tsys |
---|
842 | |
---|
843 | if (wtType==TSYS) { |
---|
844 | tSysCol.get(iRow,tSys); |
---|
845 | } |
---|
846 | |
---|
847 | // Make iterators to iterate by pol-channel planes |
---|
848 | // The tSys array is empty unless wtType=TSYS so only |
---|
849 | // access the iterator is that is the case |
---|
850 | |
---|
851 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
---|
852 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes); |
---|
853 | ReadOnlyArrayIterator<Float>* pItTsysPlane = 0; |
---|
854 | if (wtType==TSYS) |
---|
855 | pItTsysPlane = new ReadOnlyArrayIterator<Float>(tSys, axes); |
---|
856 | |
---|
857 | // Accumulations |
---|
858 | |
---|
859 | Float fac = 1.0; |
---|
860 | Vector<Float> vecSum(nChan,0.0); |
---|
861 | |
---|
862 | // Iterate through data by pol-channel planes |
---|
863 | |
---|
864 | while (!itDataPlane.pastEnd()) { |
---|
865 | |
---|
866 | // Iterate through plane by polarization and accumulate Vectors |
---|
867 | |
---|
868 | Vector<Float> t1(nChan); t1 = 0.0; |
---|
869 | Vector<Bool> t2(nChan); t2 = True; |
---|
870 | Float tSys = 0.0; |
---|
871 | MaskedArray<Float> vecSum(t1,t2); |
---|
872 | Float norm = 0.0; |
---|
873 | { |
---|
874 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
---|
875 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
876 | // |
---|
877 | ReadOnlyVectorIterator<Float>* pItTsysVec = 0; |
---|
878 | if (wtType==TSYS) { |
---|
879 | pItTsysVec = |
---|
880 | new ReadOnlyVectorIterator<Float>(pItTsysPlane->array(), 1); |
---|
881 | } |
---|
882 | // |
---|
883 | while (!itDataVec.pastEnd()) { |
---|
884 | |
---|
885 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum |
---|
886 | |
---|
887 | if (useMask) { |
---|
888 | const MaskedArray<Float> spec(itDataVec.vector(), |
---|
889 | mask&&itMaskVec.vector()); |
---|
890 | if (wtType==VAR) { |
---|
891 | fac = 1.0 / variance(spec); |
---|
892 | } else if (wtType==TSYS) { |
---|
893 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency |
---|
894 | fac = 1.0 / tSys / tSys; |
---|
895 | } |
---|
896 | } else { |
---|
897 | const MaskedArray<Float> spec(itDataVec.vector(), |
---|
898 | itMaskVec.vector()); |
---|
899 | if (wtType==VAR) { |
---|
900 | fac = 1.0 / variance(spec); |
---|
901 | } else if (wtType==TSYS) { |
---|
902 | tSys = pItTsysVec->vector()[0]; // Drop pseudo channel dependency |
---|
903 | fac = 1.0 / tSys / tSys; |
---|
904 | } |
---|
905 | } |
---|
906 | |
---|
907 | // Normalize spectrum (without OTF mask) and accumulate |
---|
908 | |
---|
909 | const MaskedArray<Float> spec(fac*itDataVec.vector(), |
---|
910 | itMaskVec.vector()); |
---|
911 | vecSum += spec; |
---|
912 | norm += fac; |
---|
913 | |
---|
914 | // Next |
---|
915 | |
---|
916 | itDataVec.next(); |
---|
917 | itMaskVec.next(); |
---|
918 | if (wtType==TSYS) pItTsysVec->next(); |
---|
919 | } |
---|
920 | |
---|
921 | // Clean up |
---|
922 | |
---|
923 | if (pItTsysVec) { |
---|
924 | delete pItTsysVec; |
---|
925 | pItTsysVec = 0; |
---|
926 | } |
---|
927 | } |
---|
928 | |
---|
929 | // Normalize summed spectrum |
---|
930 | |
---|
931 | vecSum /= norm; |
---|
932 | |
---|
933 | // FInd position in input data array. We are iterating by pol-channel |
---|
934 | // plane so all that will change is beam and IF and that's what we want. |
---|
935 | |
---|
936 | IPosition pos = itDataPlane.pos(); |
---|
937 | |
---|
938 | // Write out data. This is a bit messy. We have to reform the Vector |
---|
939 | // accumulator into an Array of shape (1,1,1,nChan) |
---|
940 | |
---|
941 | start = pos; |
---|
942 | end = pos; |
---|
943 | end(asap::ChanAxis) = nChan-1; |
---|
944 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
---|
945 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
---|
946 | |
---|
947 | // Step to next beam/IF combination |
---|
948 | |
---|
949 | itDataPlane.next(); |
---|
950 | itMaskPlane.next(); |
---|
951 | if (wtType==TSYS) pItTsysPlane->next(); |
---|
952 | } |
---|
953 | |
---|
954 | // Generate output container and write it to output table |
---|
955 | |
---|
956 | SDContainer sc = in.getSDContainer(); |
---|
957 | sc.resize(shapeOut); |
---|
958 | // |
---|
959 | putDataInSDC(sc, outData, outMask); |
---|
960 | pTabOut->putSDContainer(sc); |
---|
961 | // |
---|
962 | if (wtType==TSYS) { |
---|
963 | delete pItTsysPlane; |
---|
964 | pItTsysPlane = 0; |
---|
965 | } |
---|
966 | } |
---|
967 | |
---|
968 | // Set polarization cursor to 0 |
---|
969 | |
---|
970 | pTabOut->setPol(0); |
---|
971 | // |
---|
972 | return pTabOut; |
---|
973 | } |
---|
974 | |
---|
975 | |
---|
976 | SDMemTable* SDMath::smooth(const SDMemTable& in, |
---|
977 | const casa::String& kernelType, |
---|
978 | casa::Float width, Bool doAll) |
---|
979 | // |
---|
980 | // Should smooth TSys as well |
---|
981 | // |
---|
982 | { |
---|
983 | |
---|
984 | // Number of channels |
---|
985 | const uInt nChan = in.nChan(); |
---|
986 | |
---|
987 | // Generate Kernel |
---|
988 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType); |
---|
989 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
990 | |
---|
991 | // Generate Convolver |
---|
992 | IPosition shape(1,nChan); |
---|
993 | Convolver<Float> conv(kernel, shape); |
---|
994 | |
---|
995 | // New Table |
---|
996 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
997 | |
---|
998 | // Output Vectors |
---|
999 | Vector<Float> valuesOut(nChan); |
---|
1000 | Vector<Bool> maskOut(nChan); |
---|
1001 | |
---|
1002 | // Get data slice bounds |
---|
1003 | IPosition start, end; |
---|
1004 | setCursorSlice (start, end, doAll, in); |
---|
1005 | |
---|
1006 | // Loop over rows in Table |
---|
1007 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
1008 | |
---|
1009 | // Get slice of data |
---|
1010 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(ri); |
---|
1011 | |
---|
1012 | // Deconstruct and get slices which reference these arrays |
---|
1013 | Array<Float> valuesIn = dataIn.getArray(); |
---|
1014 | Array<Bool> maskIn = dataIn.getMask(); |
---|
1015 | |
---|
1016 | Array<Float> valuesIn2 = valuesIn(start,end); // ref to valuesIn |
---|
1017 | Array<Bool> maskIn2 = maskIn(start,end); |
---|
1018 | |
---|
1019 | // Iterate through by spectra |
---|
1020 | VectorIterator<Float> itValues(valuesIn2, asap::ChanAxis); |
---|
1021 | VectorIterator<Bool> itMask(maskIn2, asap::ChanAxis); |
---|
1022 | while (!itValues.pastEnd()) { |
---|
1023 | |
---|
1024 | // Smooth |
---|
1025 | if (kernelType==VectorKernel::HANNING) { |
---|
1026 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), |
---|
1027 | itMask.vector()); |
---|
1028 | itMask.vector() = maskOut; |
---|
1029 | } else { |
---|
1030 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
1031 | conv.linearConv(valuesOut, itValues.vector()); |
---|
1032 | } |
---|
1033 | |
---|
1034 | itValues.vector() = valuesOut; |
---|
1035 | itValues.next(); |
---|
1036 | itMask.next(); |
---|
1037 | } |
---|
1038 | |
---|
1039 | // Create and put back |
---|
1040 | SDContainer sc = in.getSDContainer(ri); |
---|
1041 | putDataInSDC(sc, valuesIn, maskIn); |
---|
1042 | |
---|
1043 | pTabOut->putSDContainer(sc); |
---|
1044 | } |
---|
1045 | |
---|
1046 | return pTabOut; |
---|
1047 | } |
---|
1048 | |
---|
1049 | |
---|
1050 | |
---|
1051 | SDMemTable* SDMath::convertFlux(const SDMemTable& in, Float D, Float etaAp, |
---|
1052 | Float JyPerK, Bool doAll) |
---|
1053 | // |
---|
1054 | // etaAp = aperture efficiency (-1 means find) |
---|
1055 | // D = geometric diameter (m) (-1 means find) |
---|
1056 | // JyPerK |
---|
1057 | // |
---|
1058 | { |
---|
1059 | SDHeader sh = in.getSDHeader(); |
---|
1060 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
1061 | |
---|
1062 | // Find out how to convert values into Jy and K (e.g. units might be |
---|
1063 | // mJy or mK) Also automatically find out what we are converting to |
---|
1064 | // according to the flux unit |
---|
1065 | Unit fluxUnit(sh.fluxunit); |
---|
1066 | Unit K(String("K")); |
---|
1067 | Unit JY(String("Jy")); |
---|
1068 | |
---|
1069 | Bool toKelvin = True; |
---|
1070 | Double cFac = 1.0; |
---|
1071 | |
---|
1072 | if (fluxUnit==JY) { |
---|
1073 | pushLog("Converting to K"); |
---|
1074 | Quantum<Double> t(1.0,fluxUnit); |
---|
1075 | Quantum<Double> t2 = t.get(JY); |
---|
1076 | cFac = (t2 / t).getValue(); // value to Jy |
---|
1077 | |
---|
1078 | toKelvin = True; |
---|
1079 | sh.fluxunit = "K"; |
---|
1080 | } else if (fluxUnit==K) { |
---|
1081 | pushLog("Converting to Jy"); |
---|
1082 | Quantum<Double> t(1.0,fluxUnit); |
---|
1083 | Quantum<Double> t2 = t.get(K); |
---|
1084 | cFac = (t2 / t).getValue(); // value to K |
---|
1085 | |
---|
1086 | toKelvin = False; |
---|
1087 | sh.fluxunit = "Jy"; |
---|
1088 | } else { |
---|
1089 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
1090 | } |
---|
1091 | |
---|
1092 | pTabOut->putSDHeader(sh); |
---|
1093 | |
---|
1094 | // Make sure input values are converted to either Jy or K first... |
---|
1095 | Float factor = cFac; |
---|
1096 | |
---|
1097 | // Select method |
---|
1098 | if (JyPerK>0.0) { |
---|
1099 | factor *= JyPerK; |
---|
1100 | if (toKelvin) factor = 1.0 / JyPerK; |
---|
1101 | ostringstream oss; |
---|
1102 | oss << "Jy/K = " << JyPerK; |
---|
1103 | pushLog(String(oss)); |
---|
1104 | Vector<Float> factors(in.nRow(), factor); |
---|
1105 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
1106 | } else if (etaAp>0.0) { |
---|
1107 | Bool throwIt = True; |
---|
1108 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, throwIt); |
---|
1109 | SDAttr sda; |
---|
1110 | if (D < 0) D = sda.diameter(inst); |
---|
1111 | Float JyPerK = SDAttr::findJyPerK(etaAp,D); |
---|
1112 | ostringstream oss; |
---|
1113 | oss << "Jy/K = " << JyPerK; |
---|
1114 | pushLog(String(oss)); |
---|
1115 | factor *= JyPerK; |
---|
1116 | if (toKelvin) { |
---|
1117 | factor = 1.0 / factor; |
---|
1118 | } |
---|
1119 | |
---|
1120 | Vector<Float> factors(in.nRow(), factor); |
---|
1121 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
1122 | } else { |
---|
1123 | |
---|
1124 | // OK now we must deal with automatic look up of values. |
---|
1125 | // We must also deal with the fact that the factors need |
---|
1126 | // to be computed per IF and may be different and may |
---|
1127 | // change per integration. |
---|
1128 | |
---|
1129 | pushLog("Looking up conversion factors"); |
---|
1130 | convertBrightnessUnits (pTabOut, in, toKelvin, cFac, doAll); |
---|
1131 | } |
---|
1132 | return pTabOut; |
---|
1133 | } |
---|
1134 | |
---|
1135 | |
---|
1136 | SDMemTable* SDMath::gainElevation(const SDMemTable& in, |
---|
1137 | const Vector<Float>& coeffs, |
---|
1138 | const String& fileName, |
---|
1139 | const String& methodStr, Bool doAll) |
---|
1140 | { |
---|
1141 | |
---|
1142 | // Get header and clone output table |
---|
1143 | SDHeader sh = in.getSDHeader(); |
---|
1144 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
1145 | |
---|
1146 | // Get elevation data from SDMemTable and convert to degrees |
---|
1147 | const Table& tab = in.table(); |
---|
1148 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
1149 | Vector<Float> x = elev.getColumn(); |
---|
1150 | x *= Float(180 / C::pi); // Degrees |
---|
1151 | |
---|
1152 | const uInt nC = coeffs.nelements(); |
---|
1153 | if (fileName.length()>0 && nC>0) { |
---|
1154 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
1155 | } |
---|
1156 | |
---|
1157 | // Correct |
---|
1158 | if (nC>0 || fileName.length()==0) { |
---|
1159 | // Find instrument |
---|
1160 | Bool throwIt = True; |
---|
1161 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
1162 | |
---|
1163 | // Set polynomial |
---|
1164 | Polynomial<Float>* pPoly = 0; |
---|
1165 | Vector<Float> coeff; |
---|
1166 | String msg; |
---|
1167 | if (nC>0) { |
---|
1168 | pPoly = new Polynomial<Float>(nC); |
---|
1169 | coeff = coeffs; |
---|
1170 | msg = String("user"); |
---|
1171 | } else { |
---|
1172 | SDAttr sdAttr; |
---|
1173 | coeff = sdAttr.gainElevationPoly(inst); |
---|
1174 | pPoly = new Polynomial<Float>(3); |
---|
1175 | msg = String("built in"); |
---|
1176 | } |
---|
1177 | |
---|
1178 | if (coeff.nelements()>0) { |
---|
1179 | pPoly->setCoefficients(coeff); |
---|
1180 | } else { |
---|
1181 | delete pPoly; |
---|
1182 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
1183 | } |
---|
1184 | ostringstream oss; |
---|
1185 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl; |
---|
1186 | oss << " " << coeff; |
---|
1187 | pushLog(String(oss)); |
---|
1188 | const uInt nRow = in.nRow(); |
---|
1189 | Vector<Float> factor(nRow); |
---|
1190 | for (uInt i=0; i<nRow; i++) { |
---|
1191 | factor[i] = 1.0 / (*pPoly)(x[i]); |
---|
1192 | } |
---|
1193 | delete pPoly; |
---|
1194 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
1195 | |
---|
1196 | } else { |
---|
1197 | |
---|
1198 | // Indicate which columns to read from ascii file |
---|
1199 | String col0("ELEVATION"); |
---|
1200 | String col1("FACTOR"); |
---|
1201 | |
---|
1202 | // Read and correct |
---|
1203 | |
---|
1204 | pushLog("Making correction from ascii Table"); |
---|
1205 | scaleFromAsciiTable (pTabOut, in, fileName, col0, col1, |
---|
1206 | methodStr, doAll, x, True); |
---|
1207 | } |
---|
1208 | |
---|
1209 | return pTabOut; |
---|
1210 | } |
---|
1211 | |
---|
1212 | |
---|
1213 | SDMemTable* SDMath::opacity(const SDMemTable& in, Float tau, Bool doAll) |
---|
1214 | { |
---|
1215 | |
---|
1216 | // Get header and clone output table |
---|
1217 | |
---|
1218 | SDHeader sh = in.getSDHeader(); |
---|
1219 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
1220 | |
---|
1221 | // Get elevation data from SDMemTable and convert to degrees |
---|
1222 | |
---|
1223 | const Table& tab = in.table(); |
---|
1224 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
1225 | Vector<Float> zDist = elev.getColumn(); |
---|
1226 | zDist = Float(C::pi_2) - zDist; |
---|
1227 | |
---|
1228 | // Generate correction factor |
---|
1229 | |
---|
1230 | const uInt nRow = in.nRow(); |
---|
1231 | Vector<Float> factor(nRow); |
---|
1232 | Vector<Float> factor2(nRow); |
---|
1233 | for (uInt i=0; i<nRow; i++) { |
---|
1234 | factor[i] = exp(tau)/cos(zDist[i]); |
---|
1235 | } |
---|
1236 | |
---|
1237 | // Correct |
---|
1238 | |
---|
1239 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
1240 | |
---|
1241 | return pTabOut; |
---|
1242 | } |
---|
1243 | |
---|
1244 | |
---|
1245 | void SDMath::rotateXYPhase(SDMemTable& in, Float value, Bool doAll) |
---|
1246 | // |
---|
1247 | // phase in degrees |
---|
1248 | // assumes linear correlations |
---|
1249 | // |
---|
1250 | { |
---|
1251 | if (in.nPol() != 4) { |
---|
1252 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
1253 | } |
---|
1254 | |
---|
1255 | SDHeader sh = in.getSDHeader(); |
---|
1256 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, False); |
---|
1257 | SDAttr sdAtt; |
---|
1258 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
1259 | throw(AipsError("Only linear polarizations are supported")); |
---|
1260 | } |
---|
1261 | // |
---|
1262 | const Table& tabIn = in.table(); |
---|
1263 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
1264 | IPosition start(asap::nAxes,0); |
---|
1265 | IPosition end(asap::nAxes); |
---|
1266 | |
---|
1267 | // Set cursor slice. Assumes shape the same for all rows |
---|
1268 | |
---|
1269 | setCursorSlice (start, end, doAll, in); |
---|
1270 | IPosition start3(start); |
---|
1271 | start3(asap::PolAxis) = 2; // Real(XY) |
---|
1272 | IPosition end3(end); |
---|
1273 | end3(asap::PolAxis) = 2; |
---|
1274 | // |
---|
1275 | IPosition start4(start); |
---|
1276 | start4(asap::PolAxis) = 3; // Imag (XY) |
---|
1277 | IPosition end4(end); |
---|
1278 | end4(asap::PolAxis) = 3; |
---|
1279 | // |
---|
1280 | uInt nRow = in.nRow(); |
---|
1281 | Array<Float> data; |
---|
1282 | for (uInt i=0; i<nRow;++i) { |
---|
1283 | specCol.get(i,data); |
---|
1284 | IPosition shape = data.shape(); |
---|
1285 | |
---|
1286 | // Get polarization slice references |
---|
1287 | Array<Float> C3 = data(start3,end3); |
---|
1288 | Array<Float> C4 = data(start4,end4); |
---|
1289 | |
---|
1290 | // Rotate |
---|
1291 | SDPolUtil::rotatePhase(C3, C4, value); |
---|
1292 | |
---|
1293 | // Put |
---|
1294 | specCol.put(i,data); |
---|
1295 | } |
---|
1296 | } |
---|
1297 | |
---|
1298 | |
---|
1299 | void SDMath::rotateLinPolPhase(SDMemTable& in, Float value, Bool doAll) |
---|
1300 | // |
---|
1301 | // phase in degrees |
---|
1302 | // assumes linear correlations |
---|
1303 | // |
---|
1304 | { |
---|
1305 | if (in.nPol() != 4) { |
---|
1306 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
1307 | } |
---|
1308 | // |
---|
1309 | SDHeader sh = in.getSDHeader(); |
---|
1310 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, False); |
---|
1311 | SDAttr sdAtt; |
---|
1312 | if (sdAtt.feedPolType(inst) != LINEAR) { |
---|
1313 | throw(AipsError("Only linear polarizations are supported")); |
---|
1314 | } |
---|
1315 | // |
---|
1316 | const Table& tabIn = in.table(); |
---|
1317 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
1318 | ROArrayColumn<Float> stokesCol(tabIn,"STOKES"); |
---|
1319 | IPosition start(asap::nAxes,0); |
---|
1320 | IPosition end(asap::nAxes); |
---|
1321 | |
---|
1322 | // Set cursor slice. Assumes shape the same for all rows |
---|
1323 | |
---|
1324 | setCursorSlice (start, end, doAll, in); |
---|
1325 | // |
---|
1326 | IPosition start1(start); |
---|
1327 | start1(asap::PolAxis) = 0; // C1 (XX) |
---|
1328 | IPosition end1(end); |
---|
1329 | end1(asap::PolAxis) = 0; |
---|
1330 | // |
---|
1331 | IPosition start2(start); |
---|
1332 | start2(asap::PolAxis) = 1; // C2 (YY) |
---|
1333 | IPosition end2(end); |
---|
1334 | end2(asap::PolAxis) = 1; |
---|
1335 | // |
---|
1336 | IPosition start3(start); |
---|
1337 | start3(asap::PolAxis) = 2; // C3 ( Real(XY) ) |
---|
1338 | IPosition end3(end); |
---|
1339 | end3(asap::PolAxis) = 2; |
---|
1340 | // |
---|
1341 | IPosition startI(start); |
---|
1342 | startI(asap::PolAxis) = 0; // I |
---|
1343 | IPosition endI(end); |
---|
1344 | endI(asap::PolAxis) = 0; |
---|
1345 | // |
---|
1346 | IPosition startQ(start); |
---|
1347 | startQ(asap::PolAxis) = 1; // Q |
---|
1348 | IPosition endQ(end); |
---|
1349 | endQ(asap::PolAxis) = 1; |
---|
1350 | // |
---|
1351 | IPosition startU(start); |
---|
1352 | startU(asap::PolAxis) = 2; // U |
---|
1353 | IPosition endU(end); |
---|
1354 | endU(asap::PolAxis) = 2; |
---|
1355 | |
---|
1356 | // |
---|
1357 | uInt nRow = in.nRow(); |
---|
1358 | Array<Float> data, stokes; |
---|
1359 | for (uInt i=0; i<nRow;++i) { |
---|
1360 | specCol.get(i,data); |
---|
1361 | stokesCol.get(i,stokes); |
---|
1362 | IPosition shape = data.shape(); |
---|
1363 | |
---|
1364 | // Get linear polarization slice references |
---|
1365 | |
---|
1366 | Array<Float> C1 = data(start1,end1); |
---|
1367 | Array<Float> C2 = data(start2,end2); |
---|
1368 | Array<Float> C3 = data(start3,end3); |
---|
1369 | |
---|
1370 | // Get STokes slice references |
---|
1371 | |
---|
1372 | Array<Float> I = stokes(startI,endI); |
---|
1373 | Array<Float> Q = stokes(startQ,endQ); |
---|
1374 | Array<Float> U = stokes(startU,endU); |
---|
1375 | |
---|
1376 | // Rotate |
---|
1377 | |
---|
1378 | SDPolUtil::rotateLinPolPhase(C1, C2, C3, I, Q, U, value); |
---|
1379 | |
---|
1380 | // Put |
---|
1381 | |
---|
1382 | specCol.put(i,data); |
---|
1383 | } |
---|
1384 | } |
---|
1385 | |
---|
1386 | // 'private' functions |
---|
1387 | |
---|
1388 | void SDMath::convertBrightnessUnits (SDMemTable* pTabOut, const SDMemTable& in, |
---|
1389 | Bool toKelvin, Float cFac, Bool doAll) |
---|
1390 | { |
---|
1391 | |
---|
1392 | // Get header |
---|
1393 | |
---|
1394 | SDHeader sh = in.getSDHeader(); |
---|
1395 | const uInt nChan = sh.nchan; |
---|
1396 | |
---|
1397 | // Get instrument |
---|
1398 | |
---|
1399 | Bool throwIt = True; |
---|
1400 | Instrument inst = SDAttr::convertInstrument(sh.antennaname, throwIt); |
---|
1401 | |
---|
1402 | // Get Diameter (m) |
---|
1403 | |
---|
1404 | SDAttr sdAtt; |
---|
1405 | // Get epoch of first row |
---|
1406 | |
---|
1407 | MEpoch dateObs = in.getEpoch(0); |
---|
1408 | |
---|
1409 | // Generate a Vector of correction factors. One per FreqID |
---|
1410 | |
---|
1411 | SDFrequencyTable sdft = in.getSDFreqTable(); |
---|
1412 | Vector<uInt> freqIDs; |
---|
1413 | // |
---|
1414 | Vector<Float> freqs(sdft.length()); |
---|
1415 | for (uInt i=0; i<sdft.length(); i++) { |
---|
1416 | freqs(i) = (nChan/2 - sdft.referencePixel(i))*sdft.increment(i) + sdft.referenceValue(i); |
---|
1417 | } |
---|
1418 | // |
---|
1419 | Vector<Float> JyPerK = sdAtt.JyPerK(inst, dateObs, freqs); |
---|
1420 | ostringstream oss; |
---|
1421 | oss << "Jy/K = " << JyPerK; |
---|
1422 | pushLog(String(oss)); |
---|
1423 | Vector<Float> factors = cFac * JyPerK; |
---|
1424 | if (toKelvin) factors = Float(1.0) / factors; |
---|
1425 | |
---|
1426 | // Get data slice bounds |
---|
1427 | |
---|
1428 | IPosition start, end; |
---|
1429 | setCursorSlice (start, end, doAll, in); |
---|
1430 | const uInt ifAxis = in.getIF(); |
---|
1431 | |
---|
1432 | // Iteration axes |
---|
1433 | |
---|
1434 | IPosition axes(asap::nAxes-1,0); |
---|
1435 | for (uInt i=0,j=0; i<asap::nAxes; i++) { |
---|
1436 | if (i!=asap::IFAxis) { |
---|
1437 | axes(j++) = i; |
---|
1438 | } |
---|
1439 | } |
---|
1440 | |
---|
1441 | // Loop over rows and apply correction factor |
---|
1442 | |
---|
1443 | Float factor = 1.0; |
---|
1444 | const uInt axis = asap::ChanAxis; |
---|
1445 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
1446 | |
---|
1447 | // Get data |
---|
1448 | |
---|
1449 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(i); |
---|
1450 | Array<Float>& values = dataIn.getRWArray(); // Ref to dataIn |
---|
1451 | Array<Float> values2 = values(start,end); // Ref to values to dataIn |
---|
1452 | |
---|
1453 | // Get SDCOntainer |
---|
1454 | |
---|
1455 | SDContainer sc = in.getSDContainer(i); |
---|
1456 | |
---|
1457 | // Get FreqIDs |
---|
1458 | |
---|
1459 | freqIDs = sc.getFreqMap(); |
---|
1460 | |
---|
1461 | // Now the conversion factor depends only upon frequency |
---|
1462 | // So we need to iterate through by IF only giving |
---|
1463 | // us BEAM/POL/CHAN cubes |
---|
1464 | |
---|
1465 | ArrayIterator<Float> itIn(values2, axes); |
---|
1466 | uInt ax = 0; |
---|
1467 | while (!itIn.pastEnd()) { |
---|
1468 | itIn.array() *= factors(freqIDs(ax)); // Writes back to dataIn |
---|
1469 | itIn.next(); |
---|
1470 | } |
---|
1471 | |
---|
1472 | // Write out |
---|
1473 | |
---|
1474 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
1475 | // |
---|
1476 | pTabOut->putSDContainer(sc); |
---|
1477 | } |
---|
1478 | } |
---|
1479 | |
---|
1480 | |
---|
1481 | |
---|
1482 | SDMemTable* SDMath::frequencyAlign(const SDMemTable& in, |
---|
1483 | MFrequency::Types freqSystem, |
---|
1484 | const String& refTime, |
---|
1485 | const String& methodStr, |
---|
1486 | Bool perFreqID) |
---|
1487 | { |
---|
1488 | // Get Header |
---|
1489 | |
---|
1490 | SDHeader sh = in.getSDHeader(); |
---|
1491 | const uInt nChan = sh.nchan; |
---|
1492 | const uInt nRows = in.nRow(); |
---|
1493 | const uInt nIF = sh.nif; |
---|
1494 | |
---|
1495 | // Get Table reference |
---|
1496 | |
---|
1497 | const Table& tabIn = in.table(); |
---|
1498 | |
---|
1499 | // Get Columns from Table |
---|
1500 | |
---|
1501 | ROScalarColumn<Double> mjdCol(tabIn, "TIME"); |
---|
1502 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME"); |
---|
1503 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID"); |
---|
1504 | Vector<Double> times = mjdCol.getColumn(); |
---|
1505 | |
---|
1506 | // Generate DataDesc table |
---|
1507 | |
---|
1508 | Matrix<uInt> ddIdx; |
---|
1509 | SDDataDesc dDesc; |
---|
1510 | generateDataDescTable(ddIdx, dDesc, nIF, in, tabIn, srcCol, |
---|
1511 | fqIDCol, perFreqID); |
---|
1512 | |
---|
1513 | // Get reference Epoch to time of first row or given String |
---|
1514 | |
---|
1515 | Unit DAY(String("d")); |
---|
1516 | MEpoch::Ref epochRef(in.getTimeReference()); |
---|
1517 | MEpoch refEpoch; |
---|
1518 | if (refTime.length()>0) { |
---|
1519 | refEpoch = epochFromString(refTime, in.getTimeReference()); |
---|
1520 | } else { |
---|
1521 | refEpoch = in.getEpoch(0); |
---|
1522 | } |
---|
1523 | ostringstream oss; |
---|
1524 | oss << "Aligned at reference Epoch " << formatEpoch(refEpoch) << " in frame " << MFrequency::showType(freqSystem); |
---|
1525 | pushLog(String(oss)); |
---|
1526 | |
---|
1527 | // Get Reference Position |
---|
1528 | |
---|
1529 | MPosition refPos = in.getAntennaPosition(); |
---|
1530 | |
---|
1531 | // Create FrequencyAligner Block. One FA for each possible |
---|
1532 | // source/freqID (perFreqID=True) or source/IF (perFreqID=False) |
---|
1533 | // combination |
---|
1534 | |
---|
1535 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length()); |
---|
1536 | generateFrequencyAligners(a, dDesc, in, nChan, freqSystem, refPos, |
---|
1537 | refEpoch, perFreqID); |
---|
1538 | |
---|
1539 | // Generate and fill output Frequency Table. WHen perFreqID=True, |
---|
1540 | // there is one output FreqID for each entry in the SDDataDesc |
---|
1541 | // table. However, in perFreqID=False mode, there may be some |
---|
1542 | // degeneracy, so we need a little translation map |
---|
1543 | |
---|
1544 | SDFrequencyTable freqTabOut = in.getSDFreqTable(); |
---|
1545 | freqTabOut.setLength(0); |
---|
1546 | Vector<String> units(1); |
---|
1547 | units = String("Hz"); |
---|
1548 | Bool linear=True; |
---|
1549 | // |
---|
1550 | Vector<uInt> ddFQTrans(dDesc.length(),0); |
---|
1551 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
1552 | |
---|
1553 | // Get Aligned SC in Hz |
---|
1554 | |
---|
1555 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear); |
---|
1556 | sC.setWorldAxisUnits(units); |
---|
1557 | |
---|
1558 | // Add FreqID |
---|
1559 | |
---|
1560 | uInt idx = freqTabOut.addFrequency(sC.referencePixel()[0], |
---|
1561 | sC.referenceValue()[0], |
---|
1562 | sC.increment()[0]); |
---|
1563 | // output FreqID = ddFQTrans(ddIdx) |
---|
1564 | ddFQTrans(i) = idx; |
---|
1565 | } |
---|
1566 | |
---|
1567 | // Interpolation method |
---|
1568 | |
---|
1569 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
1570 | convertInterpString(interp, methodStr); |
---|
1571 | |
---|
1572 | // New output Table |
---|
1573 | |
---|
1574 | //pushLog("Create output table"); |
---|
1575 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
1576 | pTabOut->putSDFreqTable(freqTabOut); |
---|
1577 | |
---|
1578 | // Loop over rows in Table |
---|
1579 | |
---|
1580 | Bool extrapolate=False; |
---|
1581 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis); |
---|
1582 | Bool useCachedAbcissa = False; |
---|
1583 | Bool first = True; |
---|
1584 | Bool ok; |
---|
1585 | Vector<Float> yOut; |
---|
1586 | Vector<Bool> maskOut; |
---|
1587 | Vector<uInt> freqID(nIF); |
---|
1588 | uInt ifIdx, faIdx; |
---|
1589 | Vector<Double> xIn; |
---|
1590 | // |
---|
1591 | for (uInt iRow=0; iRow<nRows; ++iRow) { |
---|
1592 | // if (iRow%10==0) { |
---|
1593 | // ostringstream oss; |
---|
1594 | // oss << "Processing row " << iRow; |
---|
1595 | // pushLog(String(oss)); |
---|
1596 | // } |
---|
1597 | |
---|
1598 | // Get EPoch |
---|
1599 | |
---|
1600 | Quantum<Double> tQ2(times[iRow],DAY); |
---|
1601 | MVEpoch mv2(tQ2); |
---|
1602 | MEpoch epoch(mv2, epochRef); |
---|
1603 | |
---|
1604 | // Get copy of data |
---|
1605 | |
---|
1606 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow)); |
---|
1607 | Array<Float> values = mArrIn.getArray(); |
---|
1608 | Array<Bool> mask = mArrIn.getMask(); |
---|
1609 | |
---|
1610 | // For each row, the Frequency abcissa will be the same |
---|
1611 | // regardless of polarization. For all other axes (IF and BEAM) |
---|
1612 | // the abcissa will change. So we iterate through the data by |
---|
1613 | // pol-chan planes to mimimize the work. Probably won't work for |
---|
1614 | // multiple beams at this point. |
---|
1615 | |
---|
1616 | ArrayIterator<Float> itValuesPlane(values, polChanAxes); |
---|
1617 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes); |
---|
1618 | while (!itValuesPlane.pastEnd()) { |
---|
1619 | |
---|
1620 | // Find the IF index and then the FA PtrBlock index |
---|
1621 | |
---|
1622 | const IPosition& pos = itValuesPlane.pos(); |
---|
1623 | ifIdx = pos(asap::IFAxis); |
---|
1624 | faIdx = ddIdx(iRow,ifIdx); |
---|
1625 | |
---|
1626 | // Generate abcissa for perIF. Could cache this in a Matrix on |
---|
1627 | // a per scan basis. Pretty expensive doing it for every row. |
---|
1628 | |
---|
1629 | if (!perFreqID) { |
---|
1630 | xIn.resize(nChan); |
---|
1631 | uInt fqID = dDesc.secID(ddIdx(iRow,ifIdx)); |
---|
1632 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID); |
---|
1633 | Double w; |
---|
1634 | for (uInt i=0; i<nChan; i++) { |
---|
1635 | sC.toWorld(w,Double(i)); |
---|
1636 | xIn[i] = w; |
---|
1637 | } |
---|
1638 | } |
---|
1639 | |
---|
1640 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1); |
---|
1641 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
1642 | |
---|
1643 | // Iterate through the plane by vector and align |
---|
1644 | |
---|
1645 | first = True; |
---|
1646 | useCachedAbcissa=False; |
---|
1647 | while (!itValuesVec.pastEnd()) { |
---|
1648 | if (perFreqID) { |
---|
1649 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(), |
---|
1650 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
1651 | interp, extrapolate); |
---|
1652 | } else { |
---|
1653 | ok = a[faIdx]->align (yOut, maskOut, xIn, itValuesVec.vector(), |
---|
1654 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
1655 | interp, extrapolate); |
---|
1656 | } |
---|
1657 | // |
---|
1658 | itValuesVec.vector() = yOut; |
---|
1659 | itMaskVec.vector() = maskOut; |
---|
1660 | // |
---|
1661 | itValuesVec.next(); |
---|
1662 | itMaskVec.next(); |
---|
1663 | // |
---|
1664 | if (first) { |
---|
1665 | useCachedAbcissa = True; |
---|
1666 | first = False; |
---|
1667 | } |
---|
1668 | } |
---|
1669 | // |
---|
1670 | itValuesPlane.next(); |
---|
1671 | itMaskPlane.next(); |
---|
1672 | } |
---|
1673 | |
---|
1674 | // Create SDContainer and put back |
---|
1675 | |
---|
1676 | SDContainer sc = in.getSDContainer(iRow); |
---|
1677 | putDataInSDC(sc, values, mask); |
---|
1678 | |
---|
1679 | // Set output FreqIDs |
---|
1680 | |
---|
1681 | for (uInt i=0; i<nIF; i++) { |
---|
1682 | uInt idx = ddIdx(iRow,i); // Index into SDDataDesc table |
---|
1683 | freqID(i) = ddFQTrans(idx); // FreqID in output FQ table |
---|
1684 | } |
---|
1685 | sc.putFreqMap(freqID); |
---|
1686 | // |
---|
1687 | pTabOut->putSDContainer(sc); |
---|
1688 | } |
---|
1689 | |
---|
1690 | // Now we must set the base and extra frames to the input frame |
---|
1691 | std::vector<string> info = pTabOut->getCoordInfo(); |
---|
1692 | info[1] = MFrequency::showType(freqSystem); // Conversion frame |
---|
1693 | info[3] = info[1]; // Base frame |
---|
1694 | pTabOut->setCoordInfo(info); |
---|
1695 | |
---|
1696 | // Clean up PointerBlock |
---|
1697 | for (uInt i=0; i<a.nelements(); i++) delete a[i]; |
---|
1698 | |
---|
1699 | return pTabOut; |
---|
1700 | } |
---|
1701 | |
---|
1702 | |
---|
1703 | SDMemTable* SDMath::frequencySwitch(const SDMemTable& in) |
---|
1704 | { |
---|
1705 | if (in.nIF() != 2) { |
---|
1706 | throw(AipsError("nIF != 2 ")); |
---|
1707 | } |
---|
1708 | Bool clear = True; |
---|
1709 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
1710 | const Table& tabIn = in.table(); |
---|
1711 | |
---|
1712 | // Shape of input and output data |
---|
1713 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape(); |
---|
1714 | |
---|
1715 | const uInt nRows = in.nRow(); |
---|
1716 | AlwaysAssert(asap::nAxes==4,AipsError); |
---|
1717 | |
---|
1718 | ROArrayColumn<Float> tSysCol; |
---|
1719 | Array<Float> tsys; |
---|
1720 | tSysCol.attach(tabIn,"TSYS"); |
---|
1721 | |
---|
1722 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
1723 | // Get data for this row |
---|
1724 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
1725 | tSysCol.get(iRow, tsys); |
---|
1726 | |
---|
1727 | // whole Array for IF 0 |
---|
1728 | IPosition start(asap::nAxes,0); |
---|
1729 | IPosition end = shapeIn-1; |
---|
1730 | end(asap::IFAxis) = 0; |
---|
1731 | |
---|
1732 | MaskedArray<Float> on = marr(start,end); |
---|
1733 | Array<Float> ton = tsys(start,end); |
---|
1734 | // Make a copy as "src" is a refrence which is manipulated. |
---|
1735 | // oncopy is needed for the inverse quotient |
---|
1736 | MaskedArray<Float> oncopy = on.copy(); |
---|
1737 | |
---|
1738 | // whole Array for IF 1 |
---|
1739 | start(asap::IFAxis) = 1; |
---|
1740 | end(asap::IFAxis) = 1; |
---|
1741 | |
---|
1742 | MaskedArray<Float> off = marr(start,end); |
---|
1743 | Array<Float> toff = tsys(start,end); |
---|
1744 | |
---|
1745 | on /= off; on -= 1.0f; |
---|
1746 | on *= ton; |
---|
1747 | off /= oncopy; off -= 1.0f; |
---|
1748 | off *= toff; |
---|
1749 | |
---|
1750 | SDContainer sc = in.getSDContainer(iRow); |
---|
1751 | putDataInSDC(sc, marr.getArray(), marr.getMask()); |
---|
1752 | pTabOut->putSDContainer(sc); |
---|
1753 | } |
---|
1754 | return pTabOut; |
---|
1755 | } |
---|
1756 | |
---|
1757 | void SDMath::fillSDC(SDContainer& sc, |
---|
1758 | const Array<Bool>& mask, |
---|
1759 | const Array<Float>& data, |
---|
1760 | const Array<Float>& tSys, |
---|
1761 | Int scanID, Double timeStamp, |
---|
1762 | Double interval, const String& sourceName, |
---|
1763 | const Vector<uInt>& freqID) |
---|
1764 | { |
---|
1765 | // Data and mask |
---|
1766 | |
---|
1767 | putDataInSDC(sc, data, mask); |
---|
1768 | |
---|
1769 | // TSys |
---|
1770 | |
---|
1771 | sc.putTsys(tSys); |
---|
1772 | |
---|
1773 | // Time things |
---|
1774 | |
---|
1775 | sc.timestamp = timeStamp; |
---|
1776 | sc.interval = interval; |
---|
1777 | sc.scanid = scanID; |
---|
1778 | // |
---|
1779 | sc.sourcename = sourceName; |
---|
1780 | sc.putFreqMap(freqID); |
---|
1781 | } |
---|
1782 | |
---|
1783 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum, |
---|
1784 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
1785 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
1786 | Array<Float>& tSysSqSum, |
---|
1787 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
1788 | const Vector<Bool>& mask, Double time, Double interval, |
---|
1789 | const std::vector<CountedPtr<SDMemTable> >& in, |
---|
1790 | uInt iTab, uInt iRow, uInt axis, |
---|
1791 | uInt nAxesSub, Bool useMask, |
---|
1792 | WeightType wtType) |
---|
1793 | { |
---|
1794 | |
---|
1795 | // Get data |
---|
1796 | |
---|
1797 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
1798 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
1799 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
1800 | // |
---|
1801 | if (wtType==NONE) { |
---|
1802 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
1803 | nPts += n; // Only accumulates where mask==T |
---|
1804 | } else if (wtType==TINT) { |
---|
1805 | |
---|
1806 | // We are weighting the data by integration time. |
---|
1807 | |
---|
1808 | valuesIn *= Float(interval); |
---|
1809 | |
---|
1810 | } else if (wtType==VAR) { |
---|
1811 | |
---|
1812 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
1813 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
1814 | |
---|
1815 | VectorIterator<Float> itData(valuesIn, axis); |
---|
1816 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
1817 | Float fac = 1.0; |
---|
1818 | IPosition pos(nAxesSub,0); |
---|
1819 | // |
---|
1820 | while (!itData.pastEnd()) { |
---|
1821 | |
---|
1822 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
1823 | |
---|
1824 | if (useMask) { |
---|
1825 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
1826 | fac = 1.0/variance(tmp); |
---|
1827 | } else { |
---|
1828 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
1829 | fac = 1.0/variance(tmp); |
---|
1830 | } |
---|
1831 | |
---|
1832 | // Scale data |
---|
1833 | |
---|
1834 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
1835 | // |
---|
1836 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
1837 | // This method to get pos2 from itData.pos() is only valid |
---|
1838 | // because the spectral axis is the last one (so we can just |
---|
1839 | // copy the first nAXesSub positions out) |
---|
1840 | |
---|
1841 | pos = itData.pos().getFirst(nAxesSub); |
---|
1842 | sumSq(pos) += fac; |
---|
1843 | // |
---|
1844 | itData.next(); |
---|
1845 | itMask.next(); |
---|
1846 | } |
---|
1847 | } else if (wtType==TSYS || wtType==TINTSYS) { |
---|
1848 | |
---|
1849 | // We are going to average the data, weighted by 1/Tsys**2 for each pol, beam and IF. |
---|
1850 | // So therefore we need to iterate through by spectrum (axis 3). Although |
---|
1851 | // Tsys is stored as a vector of length nChan, the values are replicated. |
---|
1852 | // We will take a short cut and just use the value from the first channel |
---|
1853 | // for now. |
---|
1854 | // |
---|
1855 | VectorIterator<Float> itData(valuesIn, axis); |
---|
1856 | ReadOnlyVectorIterator<Float> itTSys(tSys, axis); |
---|
1857 | IPosition pos(nAxesSub,0); |
---|
1858 | // |
---|
1859 | Float fac = 1.0; |
---|
1860 | if (wtType==TINTSYS) fac *= interval; |
---|
1861 | while (!itData.pastEnd()) { |
---|
1862 | Float t = itTSys.vector()[0]; |
---|
1863 | fac *= 1.0/t/t; |
---|
1864 | |
---|
1865 | // Scale data |
---|
1866 | |
---|
1867 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
1868 | // |
---|
1869 | // Accumulate Tsys per if/pol/beam averaged over spectrum |
---|
1870 | // This method to get pos2 from itData.pos() is only valid |
---|
1871 | // because the spectral axis is the last one (so we can just |
---|
1872 | // copy the first nAXesSub positions out) |
---|
1873 | |
---|
1874 | pos = itData.pos().getFirst(nAxesSub); |
---|
1875 | tSysSqSum(pos) += fac; |
---|
1876 | // |
---|
1877 | itData.next(); |
---|
1878 | itTSys.next(); |
---|
1879 | } |
---|
1880 | } |
---|
1881 | |
---|
1882 | // Accumulate sum of (possibly scaled) data |
---|
1883 | |
---|
1884 | sum += dataIn; |
---|
1885 | |
---|
1886 | // Accumulate Tsys, time, and interval |
---|
1887 | |
---|
1888 | tSysSum += tSys; |
---|
1889 | timeSum += time; |
---|
1890 | intSum += interval; |
---|
1891 | nAccum += 1; |
---|
1892 | } |
---|
1893 | |
---|
1894 | |
---|
1895 | void SDMath::normalize(MaskedArray<Float>& sum, |
---|
1896 | const Array<Float>& sumSq, |
---|
1897 | const Array<Float>& tSysSqSum, |
---|
1898 | const Array<Float>& nPts, |
---|
1899 | Double intSum, |
---|
1900 | WeightType wtType, Int axis, |
---|
1901 | Int nAxesSub) |
---|
1902 | { |
---|
1903 | IPosition pos2(nAxesSub,0); |
---|
1904 | // |
---|
1905 | if (wtType==NONE) { |
---|
1906 | |
---|
1907 | // We just average by the number of points accumulated. |
---|
1908 | // We need to make a MA out of nPts so that no divide by |
---|
1909 | // zeros occur |
---|
1910 | |
---|
1911 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
1912 | sum /= t; |
---|
1913 | } else if (wtType==TINT) { |
---|
1914 | |
---|
1915 | // Average by sum of Tint |
---|
1916 | |
---|
1917 | sum /= Float(intSum); |
---|
1918 | } else if (wtType==VAR) { |
---|
1919 | |
---|
1920 | // Normalize each spectrum by sum(1/var) where the variance |
---|
1921 | // is worked out for each spectrum |
---|
1922 | |
---|
1923 | Array<Float>& data = sum.getRWArray(); |
---|
1924 | VectorIterator<Float> itData(data, axis); |
---|
1925 | while (!itData.pastEnd()) { |
---|
1926 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
1927 | itData.vector() /= sumSq(pos2); |
---|
1928 | itData.next(); |
---|
1929 | } |
---|
1930 | } else if (wtType==TSYS || wtType==TINTSYS) { |
---|
1931 | |
---|
1932 | // Normalize each spectrum by sum(1/Tsys**2) (TSYS) or |
---|
1933 | // sum(Tint/Tsys**2) (TINTSYS) where the pseudo |
---|
1934 | // replication over channel for Tsys has been dropped. |
---|
1935 | |
---|
1936 | Array<Float>& data = sum.getRWArray(); |
---|
1937 | VectorIterator<Float> itData(data, axis); |
---|
1938 | while (!itData.pastEnd()) { |
---|
1939 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
1940 | itData.vector() /= tSysSqSum(pos2); |
---|
1941 | itData.next(); |
---|
1942 | } |
---|
1943 | } |
---|
1944 | } |
---|
1945 | |
---|
1946 | |
---|
1947 | |
---|
1948 | |
---|
1949 | void SDMath::setCursorSlice (IPosition& start, IPosition& end, Bool doAll, const SDMemTable& in) const |
---|
1950 | { |
---|
1951 | const uInt nDim = asap::nAxes; |
---|
1952 | DebugAssert(nDim==4,AipsError); |
---|
1953 | // |
---|
1954 | start.resize(nDim); |
---|
1955 | end.resize(nDim); |
---|
1956 | if (doAll) { |
---|
1957 | start = 0; |
---|
1958 | end(0) = in.nBeam()-1; |
---|
1959 | end(1) = in.nIF()-1; |
---|
1960 | end(2) = in.nPol()-1; |
---|
1961 | end(3) = in.nChan()-1; |
---|
1962 | } else { |
---|
1963 | start(0) = in.getBeam(); |
---|
1964 | end(0) = start(0); |
---|
1965 | // |
---|
1966 | start(1) = in.getIF(); |
---|
1967 | end(1) = start(1); |
---|
1968 | // |
---|
1969 | start(2) = in.getPol(); |
---|
1970 | end(2) = start(2); |
---|
1971 | // |
---|
1972 | start(3) = 0; |
---|
1973 | end(3) = in.nChan()-1; |
---|
1974 | } |
---|
1975 | } |
---|
1976 | |
---|
1977 | |
---|
1978 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr, |
---|
1979 | Bool listType) |
---|
1980 | { |
---|
1981 | String tStr(weightStr); |
---|
1982 | tStr.upcase(); |
---|
1983 | String msg; |
---|
1984 | if (tStr.contains(String("NONE"))) { |
---|
1985 | wtType = NONE; |
---|
1986 | msg = String("Weighting type selected : None"); |
---|
1987 | } else if (tStr.contains(String("VAR"))) { |
---|
1988 | wtType = VAR; |
---|
1989 | msg = String("Weighting type selected : Variance"); |
---|
1990 | } else if (tStr.contains(String("TINTSYS"))) { |
---|
1991 | wtType = TINTSYS; |
---|
1992 | msg = String("Weighting type selected : Tint&Tsys"); |
---|
1993 | } else if (tStr.contains(String("TINT"))) { |
---|
1994 | wtType = TINT; |
---|
1995 | msg = String("Weighting type selected : Tint"); |
---|
1996 | } else if (tStr.contains(String("TSYS"))) { |
---|
1997 | wtType = TSYS; |
---|
1998 | msg = String("Weighting type selected : Tsys"); |
---|
1999 | } else { |
---|
2000 | msg = String("Weighting type selected : None"); |
---|
2001 | throw(AipsError("Unrecognized weighting type")); |
---|
2002 | } |
---|
2003 | // |
---|
2004 | if (listType) pushLog(msg); |
---|
2005 | } |
---|
2006 | |
---|
2007 | |
---|
2008 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type, |
---|
2009 | const casa::String& interp) |
---|
2010 | { |
---|
2011 | String tStr(interp); |
---|
2012 | tStr.upcase(); |
---|
2013 | if (tStr.contains(String("NEAR"))) { |
---|
2014 | type = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
2015 | } else if (tStr.contains(String("LIN"))) { |
---|
2016 | type = InterpolateArray1D<Double,Float>::linear; |
---|
2017 | } else if (tStr.contains(String("CUB"))) { |
---|
2018 | type = InterpolateArray1D<Double,Float>::cubic; |
---|
2019 | } else if (tStr.contains(String("SPL"))) { |
---|
2020 | type = InterpolateArray1D<Double,Float>::spline; |
---|
2021 | } else { |
---|
2022 | throw(AipsError("Unrecognized interpolation type")); |
---|
2023 | } |
---|
2024 | } |
---|
2025 | |
---|
2026 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data, |
---|
2027 | const Array<Bool>& mask) |
---|
2028 | { |
---|
2029 | sc.putSpectrum(data); |
---|
2030 | // |
---|
2031 | Array<uChar> outflags(data.shape()); |
---|
2032 | convertArray(outflags,!mask); |
---|
2033 | sc.putFlags(outflags); |
---|
2034 | } |
---|
2035 | |
---|
2036 | Table SDMath::readAsciiFile(const String& fileName) const |
---|
2037 | { |
---|
2038 | String formatString; |
---|
2039 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False); |
---|
2040 | return tbl; |
---|
2041 | } |
---|
2042 | |
---|
2043 | |
---|
2044 | |
---|
2045 | void SDMath::scaleFromAsciiTable(SDMemTable* pTabOut, |
---|
2046 | const SDMemTable& in, const String& fileName, |
---|
2047 | const String& col0, const String& col1, |
---|
2048 | const String& methodStr, Bool doAll, |
---|
2049 | const Vector<Float>& xOut, Bool doTSys) |
---|
2050 | { |
---|
2051 | |
---|
2052 | // Read gain-elevation ascii file data into a Table. |
---|
2053 | |
---|
2054 | Table geTable = readAsciiFile (fileName); |
---|
2055 | // |
---|
2056 | scaleFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut, doTSys); |
---|
2057 | } |
---|
2058 | |
---|
2059 | void SDMath::scaleFromTable(SDMemTable* pTabOut, const SDMemTable& in, |
---|
2060 | const Table& tTable, const String& col0, |
---|
2061 | const String& col1, |
---|
2062 | const String& methodStr, Bool doAll, |
---|
2063 | const Vector<Float>& xOut, Bool doTsys) |
---|
2064 | { |
---|
2065 | |
---|
2066 | // Get data from Table |
---|
2067 | |
---|
2068 | ROScalarColumn<Float> geElCol(tTable, col0); |
---|
2069 | ROScalarColumn<Float> geFacCol(tTable, col1); |
---|
2070 | Vector<Float> xIn = geElCol.getColumn(); |
---|
2071 | Vector<Float> yIn = geFacCol.getColumn(); |
---|
2072 | Vector<Bool> maskIn(xIn.nelements(),True); |
---|
2073 | |
---|
2074 | // Interpolate (and extrapolate) with desired method |
---|
2075 | |
---|
2076 | InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
2077 | convertInterpString(method, methodStr); |
---|
2078 | Int intMethod(method); |
---|
2079 | // |
---|
2080 | Vector<Float> yOut; |
---|
2081 | Vector<Bool> maskOut; |
---|
2082 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut, |
---|
2083 | xIn, yIn, maskIn, intMethod, |
---|
2084 | True, True); |
---|
2085 | // Apply |
---|
2086 | |
---|
2087 | scaleByVector(pTabOut, in, doAll, Float(1.0)/yOut, doTsys); |
---|
2088 | } |
---|
2089 | |
---|
2090 | |
---|
2091 | void SDMath::scaleByVector(SDMemTable* pTabOut, const SDMemTable& in, |
---|
2092 | Bool doAll, const Vector<Float>& factor, |
---|
2093 | Bool doTSys) |
---|
2094 | { |
---|
2095 | |
---|
2096 | // Set up data slice |
---|
2097 | |
---|
2098 | IPosition start, end; |
---|
2099 | setCursorSlice (start, end, doAll, in); |
---|
2100 | |
---|
2101 | // Get Tsys column |
---|
2102 | |
---|
2103 | const Table& tIn = in.table(); |
---|
2104 | ArrayColumn<Float> tSysCol(tIn, "TSYS"); |
---|
2105 | Array<Float> tSys; |
---|
2106 | |
---|
2107 | // Loop over rows and apply correction factor |
---|
2108 | |
---|
2109 | const uInt axis = asap::ChanAxis; |
---|
2110 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
2111 | |
---|
2112 | // Get data |
---|
2113 | |
---|
2114 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
2115 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference to dataIn |
---|
2116 | // |
---|
2117 | if (doTSys) { |
---|
2118 | tSysCol.get(i, tSys); |
---|
2119 | Array<Float> tSys2 = tSys(start,end) * factor[i]; |
---|
2120 | tSysCol.put(i, tSys); |
---|
2121 | } |
---|
2122 | |
---|
2123 | // Apply factor |
---|
2124 | |
---|
2125 | dataIn2 *= factor[i]; |
---|
2126 | |
---|
2127 | // Write out |
---|
2128 | |
---|
2129 | SDContainer sc = in.getSDContainer(i); |
---|
2130 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
2131 | // |
---|
2132 | pTabOut->putSDContainer(sc); |
---|
2133 | } |
---|
2134 | } |
---|
2135 | |
---|
2136 | |
---|
2137 | |
---|
2138 | |
---|
2139 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx, |
---|
2140 | SDDataDesc& dDesc, |
---|
2141 | uInt nIF, |
---|
2142 | const SDMemTable& in, |
---|
2143 | const Table& tabIn, |
---|
2144 | const ROScalarColumn<String>& srcCol, |
---|
2145 | const ROArrayColumn<uInt>& fqIDCol, |
---|
2146 | Bool perFreqID) |
---|
2147 | { |
---|
2148 | const uInt nRows = tabIn.nrow(); |
---|
2149 | ddIdx.resize(nRows,nIF); |
---|
2150 | // |
---|
2151 | String srcName; |
---|
2152 | Vector<uInt> freqIDs; |
---|
2153 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
2154 | srcCol.get(iRow, srcName); |
---|
2155 | fqIDCol.get(iRow, freqIDs); |
---|
2156 | const MDirection& dir = in.getDirection(iRow); |
---|
2157 | // |
---|
2158 | if (perFreqID) { |
---|
2159 | |
---|
2160 | // One entry per source/freqID pair |
---|
2161 | |
---|
2162 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
2163 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, freqIDs[iIF], dir, 0); |
---|
2164 | } |
---|
2165 | } else { |
---|
2166 | |
---|
2167 | // One entry per source/IF pair. Hang onto the FreqID as well |
---|
2168 | |
---|
2169 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
2170 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, iIF, dir, freqIDs[iIF]); |
---|
2171 | } |
---|
2172 | } |
---|
2173 | } |
---|
2174 | } |
---|
2175 | |
---|
2176 | |
---|
2177 | |
---|
2178 | |
---|
2179 | |
---|
2180 | MEpoch SDMath::epochFromString(const String& str, MEpoch::Types timeRef) |
---|
2181 | { |
---|
2182 | Quantum<Double> qt; |
---|
2183 | if (MVTime::read(qt,str)) { |
---|
2184 | MVEpoch mv(qt); |
---|
2185 | MEpoch me(mv, timeRef); |
---|
2186 | return me; |
---|
2187 | } else { |
---|
2188 | throw(AipsError("Invalid format for Epoch string")); |
---|
2189 | } |
---|
2190 | } |
---|
2191 | |
---|
2192 | |
---|
2193 | String SDMath::formatEpoch(const MEpoch& epoch) const |
---|
2194 | { |
---|
2195 | MVTime mvt(epoch.getValue()); |
---|
2196 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")"); |
---|
2197 | } |
---|
2198 | |
---|
2199 | |
---|
2200 | |
---|
2201 | void SDMath::generateFrequencyAligners(PtrBlock<FrequencyAligner<Float>* >& a, |
---|
2202 | const SDDataDesc& dDesc, |
---|
2203 | const SDMemTable& in, uInt nChan, |
---|
2204 | MFrequency::Types system, |
---|
2205 | const MPosition& refPos, |
---|
2206 | const MEpoch& refEpoch, |
---|
2207 | Bool perFreqID) |
---|
2208 | { |
---|
2209 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
2210 | uInt ID = dDesc.ID(i); |
---|
2211 | uInt secID = dDesc.secID(i); |
---|
2212 | const MDirection& refDir = dDesc.secDir(i); |
---|
2213 | // |
---|
2214 | if (perFreqID) { |
---|
2215 | |
---|
2216 | // One aligner per source/FreqID pair. |
---|
2217 | |
---|
2218 | SpectralCoordinate sC = in.getSpectralCoordinate(ID); |
---|
2219 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
2220 | } else { |
---|
2221 | |
---|
2222 | // One aligner per source/IF pair. But we still need the FreqID to |
---|
2223 | // get the right SC. Hence the messing about with the secondary ID |
---|
2224 | |
---|
2225 | SpectralCoordinate sC = in.getSpectralCoordinate(secID); |
---|
2226 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
2227 | } |
---|
2228 | } |
---|
2229 | } |
---|
2230 | |
---|
2231 | Vector<uInt> SDMath::getRowRange(const SDMemTable& in) const |
---|
2232 | { |
---|
2233 | Vector<uInt> range(2); |
---|
2234 | range[0] = 0; |
---|
2235 | range[1] = in.nRow()-1; |
---|
2236 | return range; |
---|
2237 | } |
---|
2238 | |
---|
2239 | |
---|
2240 | Bool SDMath::rowInRange(uInt i, const Vector<uInt>& range) const |
---|
2241 | { |
---|
2242 | return (i>=range[0] && i<=range[1]); |
---|
2243 | } |
---|
2244 | |
---|