1 | //#--------------------------------------------------------------------------- |
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2 | //# SDMath.cc: A collection of single dish mathematical operations |
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3 | //#--------------------------------------------------------------------------- |
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4 | //# Copyright (C) 2004 |
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5 | //# ATNF |
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6 | //# |
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7 | //# This program is free software; you can redistribute it and/or modify it |
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8 | //# under the terms of the GNU General Public License as published by the Free |
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9 | //# Software Foundation; either version 2 of the License, or (at your option) |
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10 | //# any later version. |
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11 | //# |
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12 | //# This program is distributed in the hope that it will be useful, but |
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13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of |
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14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
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15 | //# Public License for more details. |
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16 | //# |
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17 | //# You should have received a copy of the GNU General Public License along |
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18 | //# with this program; if not, write to the Free Software Foundation, Inc., |
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19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA. |
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20 | //# |
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21 | //# Correspondence concerning this software should be addressed as follows: |
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22 | //# Internet email: Malte.Marquarding@csiro.au |
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23 | //# Postal address: Malte Marquarding, |
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24 | //# Australia Telescope National Facility, |
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25 | //# P.O. Box 76, |
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26 | //# Epping, NSW, 2121, |
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27 | //# AUSTRALIA |
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28 | //# |
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29 | //# $Id: |
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30 | //#--------------------------------------------------------------------------- |
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31 | #include <vector> |
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32 | |
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33 | #include <casa/aips.h> |
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34 | #include <casa/iostream.h> |
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35 | #include <casa/iomanip.h> |
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36 | #include <casa/BasicSL/String.h> |
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37 | #include <casa/Arrays/IPosition.h> |
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38 | #include <casa/Arrays/Array.h> |
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39 | #include <casa/Arrays/ArrayIter.h> |
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40 | #include <casa/Arrays/VectorIter.h> |
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41 | #include <casa/Arrays/ArrayMath.h> |
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42 | #include <casa/Arrays/ArrayLogical.h> |
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43 | #include <casa/Arrays/MaskedArray.h> |
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44 | #include <casa/Arrays/MaskArrMath.h> |
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45 | #include <casa/Arrays/MaskArrLogi.h> |
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46 | #include <casa/Arrays/Matrix.h> |
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47 | #include <casa/BasicMath/Math.h> |
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48 | #include <casa/Containers/Block.h> |
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49 | #include <casa/Exceptions.h> |
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50 | #include <casa/Quanta/Quantum.h> |
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51 | #include <casa/Quanta/Unit.h> |
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52 | #include <casa/Quanta/MVEpoch.h> |
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53 | #include <casa/Quanta/MVTime.h> |
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54 | #include <casa/Utilities/Assert.h> |
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55 | |
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56 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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57 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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58 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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59 | #include <coordinates/Coordinates/FrequencyAligner.h> |
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60 | |
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61 | #include <lattices/Lattices/LatticeUtilities.h> |
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62 | #include <lattices/Lattices/RebinLattice.h> |
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63 | |
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64 | #include <measures/Measures/MEpoch.h> |
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65 | #include <measures/Measures/MDirection.h> |
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66 | #include <measures/Measures/MPosition.h> |
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67 | |
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68 | #include <scimath/Mathematics/VectorKernel.h> |
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69 | #include <scimath/Mathematics/Convolver.h> |
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70 | #include <scimath/Mathematics/InterpolateArray1D.h> |
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71 | #include <scimath/Functionals/Polynomial.h> |
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72 | |
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73 | #include <tables/Tables/Table.h> |
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74 | #include <tables/Tables/ScalarColumn.h> |
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75 | #include <tables/Tables/ArrayColumn.h> |
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76 | #include <tables/Tables/ReadAsciiTable.h> |
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77 | |
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78 | #include "MathUtils.h" |
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79 | #include "SDDefs.h" |
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80 | #include "SDAttr.h" |
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81 | #include "SDContainer.h" |
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82 | #include "SDMemTable.h" |
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83 | |
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84 | #include "SDMath.h" |
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85 | #include "SDPol.h" |
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86 | |
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87 | using namespace casa; |
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88 | using namespace asap; |
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89 | |
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90 | |
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91 | SDMath::SDMath() |
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92 | {;} |
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93 | |
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94 | SDMath::SDMath(const SDMath& other) |
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95 | { |
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96 | |
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97 | // No state |
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98 | |
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99 | } |
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100 | |
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101 | SDMath& SDMath::operator=(const SDMath& other) |
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102 | { |
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103 | if (this != &other) { |
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104 | // No state |
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105 | } |
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106 | return *this; |
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107 | } |
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108 | |
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109 | SDMath::~SDMath() |
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110 | {;} |
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111 | |
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112 | |
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113 | |
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114 | SDMemTable* SDMath::frequencyAlignment(const SDMemTable& in, |
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115 | const String& refTime, |
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116 | const String& method, |
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117 | Bool perFreqID) const |
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118 | { |
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119 | // Get frame info from Table |
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120 | |
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121 | std::vector<std::string> info = in.getCoordInfo(); |
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122 | |
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123 | // Parse frequency system |
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124 | |
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125 | String systemStr(info[1]); |
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126 | String baseSystemStr(info[3]); |
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127 | if (baseSystemStr==systemStr) { |
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128 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe")); |
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129 | } |
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130 | // |
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131 | MFrequency::Types freqSystem; |
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132 | MFrequency::getType(freqSystem, systemStr); |
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133 | |
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134 | // Do it |
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135 | |
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136 | return frequencyAlign(in, freqSystem, refTime, method, perFreqID); |
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137 | } |
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138 | |
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139 | |
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140 | |
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141 | CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in, |
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142 | const Vector<Bool>& mask, Bool scanAv, |
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143 | const String& weightStr, Bool alignFreq) const |
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144 | // |
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145 | // Weighted averaging of spectra from one or more Tables. |
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146 | // |
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147 | { |
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148 | |
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149 | // Convert weight type |
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150 | |
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151 | WeightType wtType = NONE; |
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152 | convertWeightString(wtType, weightStr); |
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153 | |
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154 | // Create output Table by cloning from the first table |
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155 | |
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156 | SDMemTable* pTabOut = new SDMemTable(*in[0],True); |
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157 | if (in.nelements() > 1) { |
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158 | for (uInt i=1; i < in.nelements(); ++i) { |
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159 | pTabOut->appendToHistoryTable(in[i]->getHistoryTable()); |
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160 | } |
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161 | } |
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162 | // Setup |
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163 | |
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164 | IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change |
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165 | Array<Float> arr(shp); |
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166 | Array<Bool> barr(shp); |
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167 | const Bool useMask = (mask.nelements() == shp(asap::ChanAxis)); |
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168 | |
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169 | // Columns from Tables |
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170 | |
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171 | ROArrayColumn<Float> tSysCol; |
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172 | ROScalarColumn<Double> mjdCol; |
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173 | ROScalarColumn<String> srcNameCol; |
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174 | ROScalarColumn<Double> intCol; |
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175 | ROArrayColumn<uInt> fqIDCol; |
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176 | ROScalarColumn<Int> scanIDCol; |
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177 | |
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178 | // Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam |
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179 | // Note that the mask of the accumulation array will ALWAYS remain ALL True. |
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180 | // The MA is only used so that when data which is masked Bad is added to it, |
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181 | // that data does not contribute. |
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182 | |
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183 | Array<Float> zero(shp); |
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184 | zero=0.0; |
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185 | Array<Bool> good(shp); |
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186 | good = True; |
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187 | MaskedArray<Float> sum(zero,good); |
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188 | |
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189 | // Counter arrays |
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190 | |
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191 | Array<Float> nPts(shp); // Number of points |
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192 | nPts = 0.0; |
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193 | Array<Float> nInc(shp); // Increment |
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194 | nInc = 1.0; |
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195 | |
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196 | // Create accumulation Array for variance. We accumulate for |
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197 | // each if,pol,beam, but average over channel. So we need |
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198 | // a shape with one less axis dropping channels. |
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199 | |
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200 | const uInt nAxesSub = shp.nelements() - 1; |
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201 | IPosition shp2(nAxesSub); |
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202 | for (uInt i=0,j=0; i<(nAxesSub+1); i++) { |
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203 | if (i!=asap::ChanAxis) { |
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204 | shp2(j) = shp(i); |
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205 | j++; |
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206 | } |
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207 | } |
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208 | Array<Float> sumSq(shp2); |
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209 | sumSq = 0.0; |
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210 | IPosition pos2(nAxesSub,0); // For indexing |
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211 | |
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212 | // Time-related accumulators |
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213 | |
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214 | Double time; |
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215 | Double timeSum = 0.0; |
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216 | Double intSum = 0.0; |
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217 | Double interval = 0.0; |
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218 | |
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219 | // To get the right shape for the Tsys accumulator we need to |
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220 | // access a column from the first table. The shape of this |
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221 | // array must not change |
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222 | |
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223 | Array<Float> tSysSum; |
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224 | { |
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225 | const Table& tabIn = in[0]->table(); |
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226 | tSysCol.attach(tabIn,"TSYS"); |
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227 | tSysSum.resize(tSysCol.shape(0)); |
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228 | } |
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229 | tSysSum =0.0; |
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230 | Array<Float> tSys; |
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231 | |
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232 | // Scan and row tracking |
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233 | |
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234 | Int oldScanID = 0; |
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235 | Int outScanID = 0; |
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236 | Int scanID = 0; |
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237 | Int rowStart = 0; |
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238 | Int nAccum = 0; |
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239 | Int tableStart = 0; |
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240 | |
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241 | // Source and FreqID |
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242 | |
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243 | String sourceName, oldSourceName, sourceNameStart; |
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244 | Vector<uInt> freqID, freqIDStart, oldFreqID; |
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245 | |
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246 | // Loop over tables |
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247 | |
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248 | Float fac = 1.0; |
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249 | const uInt nTables = in.nelements(); |
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250 | for (uInt iTab=0; iTab<nTables; iTab++) { |
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251 | |
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252 | // Should check that the frequency tables don't change if doing FreqAlignment |
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253 | |
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254 | // Attach columns to Table |
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255 | |
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256 | const Table& tabIn = in[iTab]->table(); |
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257 | tSysCol.attach(tabIn, "TSYS"); |
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258 | mjdCol.attach(tabIn, "TIME"); |
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259 | srcNameCol.attach(tabIn, "SRCNAME"); |
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260 | intCol.attach(tabIn, "INTERVAL"); |
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261 | fqIDCol.attach(tabIn, "FREQID"); |
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262 | scanIDCol.attach(tabIn, "SCANID"); |
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263 | |
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264 | // Find list of start/end rows for each scan |
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265 | |
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266 | // Loop over rows in Table |
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267 | |
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268 | const uInt nRows = in[iTab]->nRow(); |
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269 | for (uInt iRow=0; iRow<nRows; iRow++) { |
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270 | |
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271 | // Check conformance |
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272 | |
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273 | IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape(); |
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274 | if (!shp.isEqual(shp2)) { |
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275 | throw (AipsError("Shapes for all rows must be the same")); |
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276 | } |
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277 | |
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278 | // If we are not doing scan averages, make checks for source and |
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279 | // frequency setup and warn if averaging across them |
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280 | |
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281 | scanIDCol.getScalar(iRow, scanID); |
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282 | |
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283 | // Get quantities from columns |
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284 | |
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285 | srcNameCol.getScalar(iRow, sourceName); |
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286 | mjdCol.get(iRow, time); |
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287 | tSysCol.get(iRow, tSys); |
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288 | intCol.get(iRow, interval); |
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289 | fqIDCol.get(iRow, freqID); |
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290 | |
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291 | // Initialize first source and freqID |
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292 | |
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293 | if (iRow==0 && iTab==0) { |
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294 | sourceNameStart = sourceName; |
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295 | freqIDStart = freqID; |
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296 | } |
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297 | |
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298 | // If we are doing scan averages, see if we are at the end of an |
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299 | // accumulation period (scan). We must check soutce names too, |
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300 | // since we might have two tables with one scan each but different |
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301 | // source names; we shouldn't average different sources together |
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302 | |
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303 | if (scanAv && ( (scanID != oldScanID) || |
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304 | (iRow==0 && iTab>0 && sourceName!=oldSourceName))) { |
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305 | |
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306 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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307 | |
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308 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub); |
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309 | |
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310 | // Get ScanContainer for the first row of this averaged Scan |
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311 | |
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312 | SDContainer scOut = in[iTab]->getSDContainer(rowStart); |
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313 | |
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314 | // Fill scan container. The source and freqID come from the |
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315 | // first row of the first table that went into this average ( |
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316 | // should be the same for all rows in the scan average) |
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317 | |
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318 | Float nR(nAccum); |
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319 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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320 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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321 | |
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322 | // Write container out to Table |
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323 | |
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324 | pTabOut->putSDContainer(scOut); |
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325 | |
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326 | // Reset accumulators |
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327 | |
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328 | sum = 0.0; |
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329 | sumSq = 0.0; |
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330 | nAccum = 0; |
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331 | // |
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332 | tSysSum =0.0; |
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333 | timeSum = 0.0; |
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334 | intSum = 0.0; |
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335 | nPts = 0.0; |
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336 | |
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337 | // Increment |
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338 | |
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339 | rowStart = iRow; // First row for next accumulation |
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340 | tableStart = iTab; // First table for next accumulation |
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341 | sourceNameStart = sourceName; // First source name for next accumulation |
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342 | freqIDStart = freqID; // First FreqID for next accumulation |
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343 | // |
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344 | oldScanID = scanID; |
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345 | outScanID += 1; // Scan ID for next accumulation period |
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346 | } |
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347 | |
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348 | // Accumulate |
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349 | |
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350 | accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum, |
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351 | tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis, |
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352 | nAxesSub, useMask, wtType); |
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353 | // |
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354 | oldSourceName = sourceName; |
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355 | oldFreqID = freqID; |
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356 | } |
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357 | } |
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358 | |
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359 | // OK at this point we have accumulation data which is either |
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360 | // - accumulated from all tables into one row |
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361 | // or |
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362 | // - accumulated from the last scan average |
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363 | // |
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364 | // Normalize data in 'sum' accumulation array according to weighting scheme |
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365 | |
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366 | normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub); |
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367 | |
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368 | // Create and fill container. The container we clone will be from |
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369 | // the last Table and the first row that went into the current |
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370 | // accumulation. It probably doesn't matter that much really... |
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371 | |
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372 | Float nR(nAccum); |
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373 | SDContainer scOut = in[tableStart]->getSDContainer(rowStart); |
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374 | fillSDC(scOut, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID, |
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375 | timeSum/nR, intSum, sourceNameStart, freqIDStart); |
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376 | pTabOut->putSDContainer(scOut); |
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377 | pTabOut->resetCursor(); |
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378 | // |
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379 | return CountedPtr<SDMemTable>(pTabOut); |
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380 | } |
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381 | |
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382 | |
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383 | |
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384 | CountedPtr<SDMemTable> SDMath::binaryOperate(const CountedPtr<SDMemTable>& |
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385 | left, |
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386 | const CountedPtr<SDMemTable>& |
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387 | right, |
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388 | const String& op, Bool preserve, |
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389 | Bool doTSys) const |
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390 | { |
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391 | |
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392 | // Check operator |
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393 | |
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394 | String op2(op); |
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395 | op2.upcase(); |
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396 | uInt what = 0; |
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397 | if (op2=="ADD") { |
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398 | what = 0; |
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399 | } else if (op2=="SUB") { |
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400 | what = 1; |
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401 | } else if (op2=="MUL") { |
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402 | what = 2; |
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403 | } else if (op2=="DIV") { |
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404 | what = 3; |
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405 | } else if (op2=="QUOTIENT") { |
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406 | what = 4; |
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407 | doTSys = True; |
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408 | } else { |
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409 | throw( AipsError("Unrecognized operation")); |
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410 | } |
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411 | |
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412 | // Check rows |
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413 | |
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414 | const uInt nRowLeft = left->nRow(); |
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415 | const uInt nRowRight = right->nRow(); |
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416 | Bool ok = (nRowRight==1&&nRowLeft>0) || |
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417 | (nRowRight>=1&&nRowLeft==nRowRight); |
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418 | if (!ok) { |
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419 | 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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420 | } |
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421 | |
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422 | // Input Tables |
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423 | |
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424 | const Table& tLeft = left->table(); |
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425 | const Table& tRight = right->table(); |
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426 | |
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427 | // TSys columns |
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428 | |
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429 | ROArrayColumn<Float> tSysLeftCol, tSysRightCol; |
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430 | if (doTSys) { |
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431 | tSysLeftCol.attach(tLeft, "TSYS"); |
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432 | tSysRightCol.attach(tRight, "TSYS"); |
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433 | } |
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434 | |
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435 | // First row for right |
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436 | |
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437 | Array<Float> tSysLeftArr, tSysRightArr; |
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438 | if (doTSys) tSysRightCol.get(0, tSysRightArr); |
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439 | MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0)); |
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440 | IPosition shpRight = pMRight->shape(); |
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441 | |
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442 | // Output Table cloned from left |
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443 | |
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444 | SDMemTable* pTabOut = new SDMemTable(*left, True); |
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445 | pTabOut->appendToHistoryTable(right->getHistoryTable()); |
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446 | // Loop over rows |
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447 | |
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448 | for (uInt i=0; i<nRowLeft; i++) { |
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449 | |
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450 | // Get data |
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451 | |
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452 | MaskedArray<Float> mLeft(left->rowAsMaskedArray(i)); |
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453 | IPosition shpLeft = mLeft.shape(); |
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454 | if (doTSys) tSysLeftCol.get(i, tSysLeftArr); |
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455 | // |
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456 | if (nRowRight>1) { |
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457 | delete pMRight; |
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458 | pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i)); |
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459 | shpRight = pMRight->shape(); |
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460 | if (doTSys) tSysRightCol.get(i, tSysRightArr); |
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461 | } |
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462 | // |
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463 | if (!shpRight.isEqual(shpLeft)) { |
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464 | throw(AipsError("left and right scan tables are not conformant")); |
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465 | } |
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466 | if (doTSys) { |
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467 | if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) { |
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468 | throw(AipsError("left and right Tsys data are not conformant")); |
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469 | } |
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470 | if (!shpRight.isEqual(tSysRightArr.shape())) { |
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471 | throw(AipsError("left and right scan tables are not conformant")); |
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472 | } |
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473 | } |
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474 | |
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475 | // Make container |
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476 | |
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477 | SDContainer sc = left->getSDContainer(i); |
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478 | |
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479 | // Operate on data and TSys |
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480 | |
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481 | if (what==0) { |
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482 | MaskedArray<Float> tmp = mLeft + *pMRight; |
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483 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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484 | if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr); |
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485 | } else if (what==1) { |
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486 | MaskedArray<Float> tmp = mLeft - *pMRight; |
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487 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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488 | if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr); |
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489 | } else if (what==2) { |
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490 | MaskedArray<Float> tmp = mLeft * *pMRight; |
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491 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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492 | if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr); |
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493 | } else if (what==3) { |
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494 | MaskedArray<Float> tmp = mLeft / *pMRight; |
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495 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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496 | if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr); |
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497 | } else if (what==4) { |
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498 | if (preserve) { |
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499 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
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500 | tSysRightArr; |
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501 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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502 | } else { |
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503 | MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - |
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504 | tSysLeftArr; |
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505 | putDataInSDC(sc, tmp.getArray(), tmp.getMask()); |
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506 | } |
---|
507 | sc.putTsys(tSysRightArr); |
---|
508 | } |
---|
509 | |
---|
510 | // Put new row in output Table |
---|
511 | |
---|
512 | pTabOut->putSDContainer(sc); |
---|
513 | } |
---|
514 | if (pMRight) delete pMRight; |
---|
515 | pTabOut->resetCursor(); |
---|
516 | |
---|
517 | return CountedPtr<SDMemTable>(pTabOut); |
---|
518 | } |
---|
519 | |
---|
520 | |
---|
521 | |
---|
522 | std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in, |
---|
523 | const Vector<Bool>& mask, |
---|
524 | const String& which, Int row) const |
---|
525 | // |
---|
526 | // Perhaps iteration over pol/beam/if should be in here |
---|
527 | // and inside the nrow iteration ? |
---|
528 | // |
---|
529 | { |
---|
530 | const uInt nRow = in->nRow(); |
---|
531 | |
---|
532 | // Specify cursor location |
---|
533 | |
---|
534 | IPosition start, end; |
---|
535 | Bool doAll = False; |
---|
536 | setCursorSlice (start, end, doAll, *in); |
---|
537 | |
---|
538 | // Loop over rows |
---|
539 | |
---|
540 | const uInt nEl = mask.nelements(); |
---|
541 | uInt iStart = 0; |
---|
542 | uInt iEnd = in->nRow()-1; |
---|
543 | // |
---|
544 | if (row>=0) { |
---|
545 | iStart = row; |
---|
546 | iEnd = row; |
---|
547 | } |
---|
548 | // |
---|
549 | std::vector<float> result(iEnd-iStart+1); |
---|
550 | for (uInt ii=iStart; ii <= iEnd; ++ii) { |
---|
551 | |
---|
552 | // Get row and deconstruct |
---|
553 | |
---|
554 | MaskedArray<Float> dataIn = (in->rowAsMaskedArray(ii))(start,end); |
---|
555 | Array<Float> v = dataIn.getArray().nonDegenerate(); |
---|
556 | Array<Bool> m = dataIn.getMask().nonDegenerate(); |
---|
557 | |
---|
558 | // Access desired piece of data |
---|
559 | |
---|
560 | // Array<Float> v((arr(start,end)).nonDegenerate()); |
---|
561 | // Array<Bool> m((barr(start,end)).nonDegenerate()); |
---|
562 | |
---|
563 | // Apply OTF mask |
---|
564 | |
---|
565 | MaskedArray<Float> tmp; |
---|
566 | if (m.nelements()==nEl) { |
---|
567 | tmp.setData(v,m&&mask); |
---|
568 | } else { |
---|
569 | tmp.setData(v,m); |
---|
570 | } |
---|
571 | |
---|
572 | // Get statistic |
---|
573 | |
---|
574 | result[ii-iStart] = mathutil::statistics(which, tmp); |
---|
575 | } |
---|
576 | // |
---|
577 | return result; |
---|
578 | } |
---|
579 | |
---|
580 | |
---|
581 | SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const |
---|
582 | { |
---|
583 | SDHeader sh = in.getSDHeader(); |
---|
584 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
585 | |
---|
586 | // Bin up SpectralCoordinates |
---|
587 | |
---|
588 | IPosition factors(1); |
---|
589 | factors(0) = width; |
---|
590 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
591 | CoordinateSystem cSys; |
---|
592 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
593 | CoordinateSystem cSysBin = |
---|
594 | CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False); |
---|
595 | // |
---|
596 | SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0); |
---|
597 | pTabOut->setCoordinate(sCBin, j); |
---|
598 | } |
---|
599 | |
---|
600 | // Use RebinLattice to find shape |
---|
601 | |
---|
602 | IPosition shapeIn(1,sh.nchan); |
---|
603 | IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors); |
---|
604 | sh.nchan = shapeOut(0); |
---|
605 | pTabOut->putSDHeader(sh); |
---|
606 | |
---|
607 | // Loop over rows and bin along channel axis |
---|
608 | |
---|
609 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
610 | SDContainer sc = in.getSDContainer(i); |
---|
611 | // |
---|
612 | Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape |
---|
613 | |
---|
614 | // Bin up spectrum |
---|
615 | |
---|
616 | MaskedArray<Float> marr(in.rowAsMaskedArray(i)); |
---|
617 | MaskedArray<Float> marrout; |
---|
618 | LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width); |
---|
619 | |
---|
620 | // Put back the binned data and flags |
---|
621 | |
---|
622 | IPosition ip2 = marrout.shape(); |
---|
623 | sc.resize(ip2); |
---|
624 | // |
---|
625 | putDataInSDC(sc, marrout.getArray(), marrout.getMask()); |
---|
626 | |
---|
627 | // Bin up Tsys. |
---|
628 | |
---|
629 | Array<Bool> allGood(tSys.shape(),True); |
---|
630 | MaskedArray<Float> tSysIn(tSys, allGood, True); |
---|
631 | // |
---|
632 | MaskedArray<Float> tSysOut; |
---|
633 | LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width); |
---|
634 | sc.putTsys(tSysOut.getArray()); |
---|
635 | // |
---|
636 | pTabOut->putSDContainer(sc); |
---|
637 | } |
---|
638 | return pTabOut; |
---|
639 | } |
---|
640 | |
---|
641 | SDMemTable* SDMath::resample(const SDMemTable& in, const String& methodStr, |
---|
642 | Float width) const |
---|
643 | // |
---|
644 | // Should add the possibility of width being specified in km/s. This means |
---|
645 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
646 | // average channel width (say at the reference pixel). Then we would need |
---|
647 | // to be careful to make sure each spectrum (of different freqID) |
---|
648 | // is the same length. |
---|
649 | // |
---|
650 | { |
---|
651 | Bool doVel = False; |
---|
652 | if (doVel) { |
---|
653 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
654 | SpectralCoordinate sC = in.getSpectralCoordinate(j); |
---|
655 | } |
---|
656 | } |
---|
657 | |
---|
658 | // Interpolation method |
---|
659 | |
---|
660 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
661 | convertInterpString(interp, methodStr); |
---|
662 | Int interpMethod(interp); |
---|
663 | |
---|
664 | // Make output table |
---|
665 | |
---|
666 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
667 | |
---|
668 | // Resample SpectralCoordinates (one per freqID) |
---|
669 | |
---|
670 | const uInt nCoord = in.nCoordinates(); |
---|
671 | Vector<Float> offset(1,0.0); |
---|
672 | Vector<Float> factors(1,1.0/width); |
---|
673 | Vector<Int> newShape; |
---|
674 | for (uInt j=0; j<in.nCoordinates(); ++j) { |
---|
675 | CoordinateSystem cSys; |
---|
676 | cSys.addCoordinate(in.getSpectralCoordinate(j)); |
---|
677 | CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape); |
---|
678 | SpectralCoordinate sC = cSys2.spectralCoordinate(0); |
---|
679 | // |
---|
680 | pTabOut->setCoordinate(sC, j); |
---|
681 | } |
---|
682 | |
---|
683 | // Get header |
---|
684 | |
---|
685 | SDHeader sh = in.getSDHeader(); |
---|
686 | |
---|
687 | // Generate resampling vectors |
---|
688 | |
---|
689 | const uInt nChanIn = sh.nchan; |
---|
690 | Vector<Float> xIn(nChanIn); |
---|
691 | indgen(xIn); |
---|
692 | // |
---|
693 | Int fac = Int(nChanIn/width); |
---|
694 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
695 | uInt i = 0; |
---|
696 | Float x = 0.0; |
---|
697 | Bool more = True; |
---|
698 | while (more) { |
---|
699 | xOut(i) = x; |
---|
700 | // |
---|
701 | i++; |
---|
702 | x += width; |
---|
703 | if (x>nChanIn-1) more = False; |
---|
704 | } |
---|
705 | const uInt nChanOut = i; |
---|
706 | xOut.resize(nChanOut,True); |
---|
707 | // |
---|
708 | IPosition shapeIn(in.rowAsMaskedArray(0).shape()); |
---|
709 | sh.nchan = nChanOut; |
---|
710 | pTabOut->putSDHeader(sh); |
---|
711 | |
---|
712 | // Loop over rows and resample along channel axis |
---|
713 | |
---|
714 | Array<Float> valuesOut; |
---|
715 | Array<Bool> maskOut; |
---|
716 | Array<Float> tSysOut; |
---|
717 | Array<Bool> tSysMaskIn(shapeIn,True); |
---|
718 | Array<Bool> tSysMaskOut; |
---|
719 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
720 | |
---|
721 | // Get container |
---|
722 | |
---|
723 | SDContainer sc = in.getSDContainer(i); |
---|
724 | |
---|
725 | // Get data and Tsys |
---|
726 | |
---|
727 | const Array<Float>& tSysIn = sc.getTsys(); |
---|
728 | const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i)); |
---|
729 | Array<Float> valuesIn = dataIn.getArray(); |
---|
730 | Array<Bool> maskIn = dataIn.getMask(); |
---|
731 | |
---|
732 | // Interpolate data |
---|
733 | |
---|
734 | InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut, |
---|
735 | xIn, valuesIn, maskIn, |
---|
736 | interpMethod, True, True); |
---|
737 | sc.resize(valuesOut.shape()); |
---|
738 | putDataInSDC(sc, valuesOut, maskOut); |
---|
739 | |
---|
740 | // Interpolate TSys |
---|
741 | |
---|
742 | InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut, |
---|
743 | xIn, tSysIn, tSysMaskIn, |
---|
744 | interpMethod, True, True); |
---|
745 | sc.putTsys(tSysOut); |
---|
746 | |
---|
747 | // Put container in output |
---|
748 | |
---|
749 | pTabOut->putSDContainer(sc); |
---|
750 | } |
---|
751 | // |
---|
752 | return pTabOut; |
---|
753 | } |
---|
754 | |
---|
755 | SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll, |
---|
756 | uInt what, Bool doTSys) const |
---|
757 | // |
---|
758 | // what = 0 Multiply |
---|
759 | // 1 Add |
---|
760 | { |
---|
761 | SDMemTable* pOut = new SDMemTable(in,False); |
---|
762 | const Table& tOut = pOut->table(); |
---|
763 | ArrayColumn<Float> specCol(tOut,"SPECTRA"); |
---|
764 | ArrayColumn<Float> tSysCol(tOut,"TSYS"); |
---|
765 | Array<Float> tSysArr; |
---|
766 | |
---|
767 | // Get data slice bounds |
---|
768 | |
---|
769 | IPosition start, end; |
---|
770 | setCursorSlice (start, end, doAll, in); |
---|
771 | // |
---|
772 | for (uInt i=0; i<tOut.nrow(); i++) { |
---|
773 | |
---|
774 | // Modify data |
---|
775 | |
---|
776 | MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i)); |
---|
777 | MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference |
---|
778 | if (what==0) { |
---|
779 | dataIn2 *= val; |
---|
780 | } else if (what==1) { |
---|
781 | dataIn2 += val; |
---|
782 | } |
---|
783 | specCol.put(i, dataIn.getArray()); |
---|
784 | |
---|
785 | // Modify Tsys |
---|
786 | |
---|
787 | if (doTSys) { |
---|
788 | tSysCol.get(i, tSysArr); |
---|
789 | Array<Float> tSysArr2 = tSysArr(start,end); // Reference |
---|
790 | if (what==0) { |
---|
791 | tSysArr2 *= val; |
---|
792 | } else if (what==1) { |
---|
793 | tSysArr2 += val; |
---|
794 | } |
---|
795 | tSysCol.put(i, tSysArr); |
---|
796 | } |
---|
797 | } |
---|
798 | // |
---|
799 | return pOut; |
---|
800 | } |
---|
801 | |
---|
802 | SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask, |
---|
803 | const String& weightStr) const |
---|
804 | // |
---|
805 | // Average all polarizations together, weighted by variance |
---|
806 | // |
---|
807 | { |
---|
808 | WeightType wtType = NONE; |
---|
809 | convertWeightString(wtType, weightStr); |
---|
810 | |
---|
811 | const uInt nRows = in.nRow(); |
---|
812 | |
---|
813 | // Create output Table and reshape number of polarizations |
---|
814 | |
---|
815 | Bool clear=True; |
---|
816 | SDMemTable* pTabOut = new SDMemTable(in, clear); |
---|
817 | SDHeader header = pTabOut->getSDHeader(); |
---|
818 | header.npol = 1; |
---|
819 | pTabOut->putSDHeader(header); |
---|
820 | |
---|
821 | // Shape of input and output data |
---|
822 | |
---|
823 | const IPosition& shapeIn = in.rowAsMaskedArray(0).shape(); |
---|
824 | IPosition shapeOut(shapeIn); |
---|
825 | shapeOut(asap::PolAxis) = 1; // Average all polarizations |
---|
826 | if (shapeIn(asap::PolAxis)==1) { |
---|
827 | throw(AipsError("The input has only one polarisation")); |
---|
828 | } |
---|
829 | // |
---|
830 | const uInt nChan = shapeIn(asap::ChanAxis); |
---|
831 | const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape |
---|
832 | IPosition start(4), end(4); |
---|
833 | |
---|
834 | // Output arrays |
---|
835 | |
---|
836 | Array<Float> outData(shapeOut, 0.0); |
---|
837 | Array<Bool> outMask(shapeOut, True); |
---|
838 | const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane |
---|
839 | // |
---|
840 | const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis)); |
---|
841 | |
---|
842 | // Loop over rows |
---|
843 | |
---|
844 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
845 | |
---|
846 | // Get data for this row |
---|
847 | |
---|
848 | MaskedArray<Float> marr(in.rowAsMaskedArray(iRow)); |
---|
849 | Array<Float>& arr = marr.getRWArray(); |
---|
850 | const Array<Bool>& barr = marr.getMask(); |
---|
851 | |
---|
852 | // Make iterators to iterate by pol-channel planes |
---|
853 | |
---|
854 | ReadOnlyArrayIterator<Float> itDataPlane(arr, axes); |
---|
855 | ReadOnlyArrayIterator<Bool> itMaskPlane(barr, 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 | MaskedArray<Float> vecSum(t1,t2); |
---|
871 | Float norm = 0.0; |
---|
872 | { |
---|
873 | ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1); |
---|
874 | ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
875 | while (!itDataVec.pastEnd()) { |
---|
876 | |
---|
877 | // Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum |
---|
878 | |
---|
879 | if (useMask) { |
---|
880 | const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector()); |
---|
881 | if (wtType==VAR) fac = 1.0 / variance(spec); |
---|
882 | } else { |
---|
883 | const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector()); |
---|
884 | if (wtType==VAR) fac = 1.0 / variance(spec); |
---|
885 | } |
---|
886 | |
---|
887 | // Normalize spectrum (without OTF mask) and accumulate |
---|
888 | |
---|
889 | const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector()); |
---|
890 | vecSum += spec; |
---|
891 | norm += fac; |
---|
892 | |
---|
893 | // Next |
---|
894 | |
---|
895 | itDataVec.next(); |
---|
896 | itMaskVec.next(); |
---|
897 | } |
---|
898 | } |
---|
899 | |
---|
900 | // Normalize summed spectrum |
---|
901 | |
---|
902 | vecSum /= norm; |
---|
903 | |
---|
904 | // FInd position in input data array. We are iterating by pol-channel |
---|
905 | // plane so all that will change is beam and IF and that's what we want. |
---|
906 | |
---|
907 | IPosition pos = itDataPlane.pos(); |
---|
908 | |
---|
909 | // Write out data. This is a bit messy. We have to reform the Vector |
---|
910 | // accumulator into an Array of shape (1,1,1,nChan) |
---|
911 | |
---|
912 | start = pos; |
---|
913 | end = pos; |
---|
914 | end(asap::ChanAxis) = nChan-1; |
---|
915 | outData(start,end) = vecSum.getArray().reform(vecShapeOut); |
---|
916 | outMask(start,end) = vecSum.getMask().reform(vecShapeOut); |
---|
917 | |
---|
918 | // Step to next beam/IF combination |
---|
919 | |
---|
920 | itDataPlane.next(); |
---|
921 | itMaskPlane.next(); |
---|
922 | } |
---|
923 | |
---|
924 | // Generate output container and write it to output table |
---|
925 | |
---|
926 | SDContainer sc = in.getSDContainer(); |
---|
927 | sc.resize(shapeOut); |
---|
928 | // |
---|
929 | putDataInSDC(sc, outData, outMask); |
---|
930 | pTabOut->putSDContainer(sc); |
---|
931 | } |
---|
932 | |
---|
933 | // Set polarization cursor to 0 |
---|
934 | |
---|
935 | pTabOut->setPol(0); |
---|
936 | // |
---|
937 | return pTabOut; |
---|
938 | } |
---|
939 | |
---|
940 | |
---|
941 | SDMemTable* SDMath::smooth(const SDMemTable& in, |
---|
942 | const casa::String& kernelType, |
---|
943 | casa::Float width, Bool doAll) const |
---|
944 | // |
---|
945 | // Should smooth TSys as well |
---|
946 | // |
---|
947 | { |
---|
948 | |
---|
949 | // Number of channels |
---|
950 | |
---|
951 | const uInt nChan = in.nChan(); |
---|
952 | |
---|
953 | // Generate Kernel |
---|
954 | |
---|
955 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType); |
---|
956 | Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False); |
---|
957 | |
---|
958 | // Generate Convolver |
---|
959 | |
---|
960 | IPosition shape(1,nChan); |
---|
961 | Convolver<Float> conv(kernel, shape); |
---|
962 | |
---|
963 | // New Table |
---|
964 | |
---|
965 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
966 | |
---|
967 | // Output Vectors |
---|
968 | |
---|
969 | Vector<Float> valuesOut(nChan); |
---|
970 | Vector<Bool> maskOut(nChan); |
---|
971 | |
---|
972 | // Get data slice bounds |
---|
973 | |
---|
974 | IPosition start, end; |
---|
975 | setCursorSlice (start, end, doAll, in); |
---|
976 | |
---|
977 | // Loop over rows in Table |
---|
978 | |
---|
979 | for (uInt ri=0; ri < in.nRow(); ++ri) { |
---|
980 | |
---|
981 | // Get slice of data |
---|
982 | |
---|
983 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(ri); |
---|
984 | |
---|
985 | // Deconstruct and get slices which reference these arrays |
---|
986 | |
---|
987 | Array<Float> valuesIn = dataIn.getArray(); |
---|
988 | Array<Bool> maskIn = dataIn.getMask(); |
---|
989 | // |
---|
990 | Array<Float> valuesIn2 = valuesIn(start,end); // ref to valuesIn |
---|
991 | Array<Bool> maskIn2 = maskIn(start,end); |
---|
992 | |
---|
993 | // Iterate through by spectra |
---|
994 | |
---|
995 | VectorIterator<Float> itValues(valuesIn2, asap::ChanAxis); |
---|
996 | VectorIterator<Bool> itMask(maskIn2, asap::ChanAxis); |
---|
997 | while (!itValues.pastEnd()) { |
---|
998 | |
---|
999 | // Smooth |
---|
1000 | |
---|
1001 | if (kernelType==VectorKernel::HANNING) { |
---|
1002 | mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector()); |
---|
1003 | itMask.vector() = maskOut; |
---|
1004 | } else { |
---|
1005 | mathutil::replaceMaskByZero(itValues.vector(), itMask.vector()); |
---|
1006 | conv.linearConv(valuesOut, itValues.vector()); |
---|
1007 | } |
---|
1008 | // |
---|
1009 | itValues.vector() = valuesOut; |
---|
1010 | // |
---|
1011 | itValues.next(); |
---|
1012 | itMask.next(); |
---|
1013 | } |
---|
1014 | |
---|
1015 | // Create and put back |
---|
1016 | |
---|
1017 | SDContainer sc = in.getSDContainer(ri); |
---|
1018 | putDataInSDC(sc, valuesIn, maskIn); |
---|
1019 | // |
---|
1020 | pTabOut->putSDContainer(sc); |
---|
1021 | } |
---|
1022 | // |
---|
1023 | return pTabOut; |
---|
1024 | } |
---|
1025 | |
---|
1026 | |
---|
1027 | |
---|
1028 | SDMemTable* SDMath::convertFlux(const SDMemTable& in, Float D, Float etaAp, |
---|
1029 | Float JyPerK, Bool doAll) const |
---|
1030 | // |
---|
1031 | // etaAp = aperture efficiency (-1 means find) |
---|
1032 | // D = geometric diameter (m) (-1 means find) |
---|
1033 | // JyPerK |
---|
1034 | // |
---|
1035 | { |
---|
1036 | SDHeader sh = in.getSDHeader(); |
---|
1037 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
1038 | |
---|
1039 | // Find out how to convert values into Jy and K (e.g. units might be mJy or mK) |
---|
1040 | // Also automatically find out what we are converting to according to the |
---|
1041 | // flux unit |
---|
1042 | |
---|
1043 | Unit fluxUnit(sh.fluxunit); |
---|
1044 | Unit K(String("K")); |
---|
1045 | Unit JY(String("Jy")); |
---|
1046 | // |
---|
1047 | Bool toKelvin = True; |
---|
1048 | Double cFac = 1.0; |
---|
1049 | if (fluxUnit==JY) { |
---|
1050 | cout << "Converting to K" << endl; |
---|
1051 | // |
---|
1052 | Quantum<Double> t(1.0,fluxUnit); |
---|
1053 | Quantum<Double> t2 = t.get(JY); |
---|
1054 | cFac = (t2 / t).getValue(); // value to Jy |
---|
1055 | // |
---|
1056 | toKelvin = True; |
---|
1057 | sh.fluxunit = "K"; |
---|
1058 | } else if (fluxUnit==K) { |
---|
1059 | cout << "Converting to Jy" << endl; |
---|
1060 | // |
---|
1061 | Quantum<Double> t(1.0,fluxUnit); |
---|
1062 | Quantum<Double> t2 = t.get(K); |
---|
1063 | cFac = (t2 / t).getValue(); // value to K |
---|
1064 | // |
---|
1065 | toKelvin = False; |
---|
1066 | sh.fluxunit = "Jy"; |
---|
1067 | } else { |
---|
1068 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
1069 | } |
---|
1070 | pTabOut->putSDHeader(sh); |
---|
1071 | |
---|
1072 | // Make sure input values are converted to either Jy or K first... |
---|
1073 | |
---|
1074 | Float factor = cFac; |
---|
1075 | |
---|
1076 | // Select method |
---|
1077 | |
---|
1078 | if (JyPerK>0.0) { |
---|
1079 | factor *= JyPerK; |
---|
1080 | if (toKelvin) factor = 1.0 / JyPerK; |
---|
1081 | // |
---|
1082 | cout << "Jy/K = " << JyPerK << endl; |
---|
1083 | Vector<Float> factors(in.nRow(), factor); |
---|
1084 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
1085 | } else if (etaAp>0.0) { |
---|
1086 | Bool throwIt = True; |
---|
1087 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
1088 | SDAttr sda; |
---|
1089 | if (D < 0) D = sda.diameter(inst); |
---|
1090 | Float JyPerK = SDAttr::findJyPerK (etaAp,D); |
---|
1091 | cout << "Jy/K = " << JyPerK << endl; |
---|
1092 | factor *= JyPerK; |
---|
1093 | if (toKelvin) { |
---|
1094 | factor = 1.0 / factor; |
---|
1095 | } |
---|
1096 | // |
---|
1097 | Vector<Float> factors(in.nRow(), factor); |
---|
1098 | scaleByVector(pTabOut, in, doAll, factors, False); |
---|
1099 | } else { |
---|
1100 | |
---|
1101 | // OK now we must deal with automatic look up of values. |
---|
1102 | // We must also deal with the fact that the factors need |
---|
1103 | // to be computed per IF and may be different and may |
---|
1104 | // change per integration. |
---|
1105 | |
---|
1106 | cout << "Looking up conversion factors" << endl; |
---|
1107 | convertBrightnessUnits (pTabOut, in, toKelvin, cFac, doAll); |
---|
1108 | } |
---|
1109 | // |
---|
1110 | return pTabOut; |
---|
1111 | } |
---|
1112 | |
---|
1113 | |
---|
1114 | |
---|
1115 | |
---|
1116 | |
---|
1117 | SDMemTable* SDMath::gainElevation(const SDMemTable& in, |
---|
1118 | const Vector<Float>& coeffs, |
---|
1119 | const String& fileName, |
---|
1120 | const String& methodStr, Bool doAll) const |
---|
1121 | { |
---|
1122 | |
---|
1123 | // Get header and clone output table |
---|
1124 | |
---|
1125 | SDHeader sh = in.getSDHeader(); |
---|
1126 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
1127 | |
---|
1128 | // Get elevation data from SDMemTable and convert to degrees |
---|
1129 | |
---|
1130 | const Table& tab = in.table(); |
---|
1131 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
1132 | Vector<Float> x = elev.getColumn(); |
---|
1133 | x *= Float(180 / C::pi); // Degrees |
---|
1134 | // |
---|
1135 | const uInt nC = coeffs.nelements(); |
---|
1136 | if (fileName.length()>0 && nC>0) { |
---|
1137 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
1138 | } |
---|
1139 | |
---|
1140 | // Correct |
---|
1141 | |
---|
1142 | if (nC>0 || fileName.length()==0) { |
---|
1143 | |
---|
1144 | // Find instrument |
---|
1145 | |
---|
1146 | Bool throwIt = True; |
---|
1147 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
1148 | |
---|
1149 | // Set polynomial |
---|
1150 | |
---|
1151 | Polynomial<Float>* pPoly = 0; |
---|
1152 | Vector<Float> coeff; |
---|
1153 | String msg; |
---|
1154 | if (nC>0) { |
---|
1155 | pPoly = new Polynomial<Float>(nC); |
---|
1156 | coeff = coeffs; |
---|
1157 | msg = String("user"); |
---|
1158 | } else { |
---|
1159 | SDAttr sdAttr; |
---|
1160 | coeff = sdAttr.gainElevationPoly(inst); |
---|
1161 | pPoly = new Polynomial<Float>(3); |
---|
1162 | msg = String("built in"); |
---|
1163 | } |
---|
1164 | // |
---|
1165 | if (coeff.nelements()>0) { |
---|
1166 | pPoly->setCoefficients(coeff); |
---|
1167 | } else { |
---|
1168 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
1169 | } |
---|
1170 | // |
---|
1171 | cout << "Making polynomial correction with " << msg << " coefficients" << endl; |
---|
1172 | const uInt nRow = in.nRow(); |
---|
1173 | Vector<Float> factor(nRow); |
---|
1174 | for (uInt i=0; i<nRow; i++) { |
---|
1175 | factor[i] = 1.0 / (*pPoly)(x[i]); |
---|
1176 | } |
---|
1177 | delete pPoly; |
---|
1178 | // |
---|
1179 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
1180 | } else { |
---|
1181 | |
---|
1182 | // Indicate which columns to read from ascii file |
---|
1183 | |
---|
1184 | String col0("ELEVATION"); |
---|
1185 | String col1("FACTOR"); |
---|
1186 | |
---|
1187 | // Read and correct |
---|
1188 | |
---|
1189 | cout << "Making correction from ascii Table" << endl; |
---|
1190 | scaleFromAsciiTable (pTabOut, in, fileName, col0, col1, |
---|
1191 | methodStr, doAll, x, True); |
---|
1192 | } |
---|
1193 | // |
---|
1194 | return pTabOut; |
---|
1195 | } |
---|
1196 | |
---|
1197 | |
---|
1198 | |
---|
1199 | SDMemTable* SDMath::opacity(const SDMemTable& in, Float tau, Bool doAll) const |
---|
1200 | { |
---|
1201 | |
---|
1202 | // Get header and clone output table |
---|
1203 | |
---|
1204 | SDHeader sh = in.getSDHeader(); |
---|
1205 | SDMemTable* pTabOut = new SDMemTable(in, True); |
---|
1206 | |
---|
1207 | // Get elevation data from SDMemTable and convert to degrees |
---|
1208 | |
---|
1209 | const Table& tab = in.table(); |
---|
1210 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
1211 | Vector<Float> zDist = elev.getColumn(); |
---|
1212 | zDist = Float(C::pi_2) - zDist; |
---|
1213 | |
---|
1214 | // Generate correction factor |
---|
1215 | |
---|
1216 | const uInt nRow = in.nRow(); |
---|
1217 | Vector<Float> factor(nRow); |
---|
1218 | Vector<Float> factor2(nRow); |
---|
1219 | for (uInt i=0; i<nRow; i++) { |
---|
1220 | factor[i] = exp(tau)/cos(zDist[i]); |
---|
1221 | } |
---|
1222 | |
---|
1223 | // Correct |
---|
1224 | |
---|
1225 | scaleByVector (pTabOut, in, doAll, factor, True); |
---|
1226 | // |
---|
1227 | return pTabOut; |
---|
1228 | } |
---|
1229 | |
---|
1230 | |
---|
1231 | void SDMath::rotateXYPhase(SDMemTable& in, Float value, Bool doAll) |
---|
1232 | // |
---|
1233 | // phase in degrees |
---|
1234 | // Applies to all Beams and IFs |
---|
1235 | // Might want to optionally select on Beam/IF |
---|
1236 | // |
---|
1237 | { |
---|
1238 | if (in.nPol() != 4) { |
---|
1239 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
1240 | } |
---|
1241 | // |
---|
1242 | const Table& tabIn = in.table(); |
---|
1243 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
1244 | IPosition start(asap::nAxes,0); |
---|
1245 | IPosition end(asap::nAxes); |
---|
1246 | |
---|
1247 | // Set cursor slice. Assumes shape the same for all rows |
---|
1248 | |
---|
1249 | setCursorSlice (start, end, doAll, in); |
---|
1250 | IPosition start3(start); |
---|
1251 | start3(asap::PolAxis) = 2; // Real(XY) |
---|
1252 | IPosition end3(end); |
---|
1253 | end3(asap::PolAxis) = 2; |
---|
1254 | // |
---|
1255 | IPosition start4(start); |
---|
1256 | start4(asap::PolAxis) = 3; // Imag (XY) |
---|
1257 | IPosition end4(end); |
---|
1258 | end4(asap::PolAxis) = 3; |
---|
1259 | // |
---|
1260 | uInt nRow = in.nRow(); |
---|
1261 | Array<Float> data; |
---|
1262 | for (uInt i=0; i<nRow;++i) { |
---|
1263 | specCol.get(i,data); |
---|
1264 | IPosition shape = data.shape(); |
---|
1265 | |
---|
1266 | // Get polarization slice references |
---|
1267 | |
---|
1268 | Array<Float> C3 = data(start3,end3); |
---|
1269 | Array<Float> C4 = data(start4,end4); |
---|
1270 | |
---|
1271 | // Rotate |
---|
1272 | |
---|
1273 | SDPolUtil::rotatePhase(C3, C4, value); |
---|
1274 | |
---|
1275 | // Put |
---|
1276 | |
---|
1277 | specCol.put(i,data); |
---|
1278 | } |
---|
1279 | } |
---|
1280 | |
---|
1281 | |
---|
1282 | |
---|
1283 | void SDMath::rotateLinPolPhase(SDMemTable& in, Float value, Bool doAll) |
---|
1284 | // |
---|
1285 | // phase in degrees |
---|
1286 | // Applies to all Beams and IFs |
---|
1287 | // Might want to optionally select on Beam/IF |
---|
1288 | // |
---|
1289 | { |
---|
1290 | if (in.nPol() != 4) { |
---|
1291 | throw(AipsError("You must have 4 polarizations to run this function")); |
---|
1292 | } |
---|
1293 | // |
---|
1294 | const Table& tabIn = in.table(); |
---|
1295 | ArrayColumn<Float> specCol(tabIn,"SPECTRA"); |
---|
1296 | ROArrayColumn<Float> stokesCol(tabIn,"STOKES"); |
---|
1297 | IPosition start(asap::nAxes,0); |
---|
1298 | IPosition end(asap::nAxes); |
---|
1299 | |
---|
1300 | // Set cursor slice. Assumes shape the same for all rows |
---|
1301 | |
---|
1302 | setCursorSlice (start, end, doAll, in); |
---|
1303 | // |
---|
1304 | IPosition start1(start); |
---|
1305 | start1(asap::PolAxis) = 0; // C1 (XX) |
---|
1306 | IPosition end1(end); |
---|
1307 | end1(asap::PolAxis) = 0; |
---|
1308 | // |
---|
1309 | IPosition start2(start); |
---|
1310 | start2(asap::PolAxis) = 1; // C2 (YY) |
---|
1311 | IPosition end2(end); |
---|
1312 | end2(asap::PolAxis) = 1; |
---|
1313 | // |
---|
1314 | IPosition start3(start); |
---|
1315 | start3(asap::PolAxis) = 2; // C3 ( Real(XY) ) |
---|
1316 | IPosition end3(end); |
---|
1317 | end3(asap::PolAxis) = 2; |
---|
1318 | // |
---|
1319 | IPosition startI(start); |
---|
1320 | startI(asap::PolAxis) = 0; // I |
---|
1321 | IPosition endI(end); |
---|
1322 | endI(asap::PolAxis) = 0; |
---|
1323 | // |
---|
1324 | IPosition startQ(start); |
---|
1325 | startQ(asap::PolAxis) = 1; // Q |
---|
1326 | IPosition endQ(end); |
---|
1327 | endQ(asap::PolAxis) = 1; |
---|
1328 | // |
---|
1329 | IPosition startU(start); |
---|
1330 | startU(asap::PolAxis) = 2; // U |
---|
1331 | IPosition endU(end); |
---|
1332 | endU(asap::PolAxis) = 2; |
---|
1333 | |
---|
1334 | // |
---|
1335 | uInt nRow = in.nRow(); |
---|
1336 | Array<Float> data, stokes; |
---|
1337 | for (uInt i=0; i<nRow;++i) { |
---|
1338 | specCol.get(i,data); |
---|
1339 | stokesCol.get(i,stokes); |
---|
1340 | IPosition shape = data.shape(); |
---|
1341 | |
---|
1342 | // Get linear polarization slice references |
---|
1343 | |
---|
1344 | Array<Float> C1 = data(start1,end1); |
---|
1345 | Array<Float> C2 = data(start2,end2); |
---|
1346 | Array<Float> C3 = data(start3,end3); |
---|
1347 | |
---|
1348 | // Get STokes slice references |
---|
1349 | |
---|
1350 | Array<Float> I = stokes(startI,endI); |
---|
1351 | Array<Float> Q = stokes(startQ,endQ); |
---|
1352 | Array<Float> U = stokes(startU,endU); |
---|
1353 | |
---|
1354 | // Rotate |
---|
1355 | |
---|
1356 | SDPolUtil::rotateLinPolPhase(C1, C2, C3, I, Q, U, value); |
---|
1357 | |
---|
1358 | // Put |
---|
1359 | |
---|
1360 | specCol.put(i,data); |
---|
1361 | } |
---|
1362 | } |
---|
1363 | |
---|
1364 | // 'private' functions |
---|
1365 | |
---|
1366 | void SDMath::convertBrightnessUnits (SDMemTable* pTabOut, const SDMemTable& in, |
---|
1367 | Bool toKelvin, Float cFac, Bool doAll) const |
---|
1368 | { |
---|
1369 | |
---|
1370 | // Get header |
---|
1371 | |
---|
1372 | SDHeader sh = in.getSDHeader(); |
---|
1373 | const uInt nChan = sh.nchan; |
---|
1374 | |
---|
1375 | // Get instrument |
---|
1376 | |
---|
1377 | Bool throwIt = True; |
---|
1378 | Instrument inst = SDAttr::convertInstrument (sh.antennaname, throwIt); |
---|
1379 | |
---|
1380 | // Get Diameter (m) |
---|
1381 | |
---|
1382 | SDAttr sdAtt; |
---|
1383 | |
---|
1384 | // Get epoch of first row |
---|
1385 | |
---|
1386 | MEpoch dateObs = in.getEpoch(0); |
---|
1387 | |
---|
1388 | // Generate a Vector of correction factors. One per FreqID |
---|
1389 | |
---|
1390 | SDFrequencyTable sdft = in.getSDFreqTable(); |
---|
1391 | Vector<uInt> freqIDs; |
---|
1392 | // |
---|
1393 | Vector<Float> freqs(sdft.length()); |
---|
1394 | for (uInt i=0; i<sdft.length(); i++) { |
---|
1395 | freqs(i) = (nChan/2 - sdft.referencePixel(i))*sdft.increment(i) + sdft.referenceValue(i); |
---|
1396 | } |
---|
1397 | // |
---|
1398 | Vector<Float> JyPerK = sdAtt.JyPerK(inst, dateObs, freqs); |
---|
1399 | cout << "Jy/K = " << JyPerK << endl; |
---|
1400 | Vector<Float> factors = cFac * JyPerK; |
---|
1401 | if (toKelvin) factors = Float(1.0) / factors; |
---|
1402 | |
---|
1403 | // Get data slice bounds |
---|
1404 | |
---|
1405 | IPosition start, end; |
---|
1406 | setCursorSlice (start, end, doAll, in); |
---|
1407 | const uInt ifAxis = in.getIF(); |
---|
1408 | |
---|
1409 | // Iteration axes |
---|
1410 | |
---|
1411 | IPosition axes(asap::nAxes-1,0); |
---|
1412 | for (uInt i=0,j=0; i<asap::nAxes; i++) { |
---|
1413 | if (i!=asap::IFAxis) { |
---|
1414 | axes(j++) = i; |
---|
1415 | } |
---|
1416 | } |
---|
1417 | |
---|
1418 | // Loop over rows and apply correction factor |
---|
1419 | |
---|
1420 | Float factor = 1.0; |
---|
1421 | const uInt axis = asap::ChanAxis; |
---|
1422 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
1423 | |
---|
1424 | // Get data |
---|
1425 | |
---|
1426 | MaskedArray<Float> dataIn = in.rowAsMaskedArray(i); |
---|
1427 | Array<Float>& values = dataIn.getRWArray(); // Ref to dataIn |
---|
1428 | Array<Float> values2 = values(start,end); // Ref to values to dataIn |
---|
1429 | |
---|
1430 | // Get SDCOntainer |
---|
1431 | |
---|
1432 | SDContainer sc = in.getSDContainer(i); |
---|
1433 | |
---|
1434 | // Get FreqIDs |
---|
1435 | |
---|
1436 | freqIDs = sc.getFreqMap(); |
---|
1437 | |
---|
1438 | // Now the conversion factor depends only upon frequency |
---|
1439 | // So we need to iterate through by IF only giving |
---|
1440 | // us BEAM/POL/CHAN cubes |
---|
1441 | |
---|
1442 | ArrayIterator<Float> itIn(values2, axes); |
---|
1443 | uInt ax = 0; |
---|
1444 | while (!itIn.pastEnd()) { |
---|
1445 | itIn.array() *= factors(freqIDs(ax)); // Writes back to dataIn |
---|
1446 | itIn.next(); |
---|
1447 | } |
---|
1448 | |
---|
1449 | // Write out |
---|
1450 | |
---|
1451 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
1452 | // |
---|
1453 | pTabOut->putSDContainer(sc); |
---|
1454 | } |
---|
1455 | } |
---|
1456 | |
---|
1457 | |
---|
1458 | |
---|
1459 | SDMemTable* SDMath::frequencyAlign (const SDMemTable& in, |
---|
1460 | MFrequency::Types freqSystem, |
---|
1461 | const String& refTime, |
---|
1462 | const String& methodStr, |
---|
1463 | Bool perFreqID) const |
---|
1464 | { |
---|
1465 | // Get Header |
---|
1466 | |
---|
1467 | SDHeader sh = in.getSDHeader(); |
---|
1468 | const uInt nChan = sh.nchan; |
---|
1469 | const uInt nRows = in.nRow(); |
---|
1470 | const uInt nIF = sh.nif; |
---|
1471 | |
---|
1472 | // Get Table reference |
---|
1473 | |
---|
1474 | const Table& tabIn = in.table(); |
---|
1475 | |
---|
1476 | // Get Columns from Table |
---|
1477 | |
---|
1478 | ROScalarColumn<Double> mjdCol(tabIn, "TIME"); |
---|
1479 | ROScalarColumn<String> srcCol(tabIn, "SRCNAME"); |
---|
1480 | ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID"); |
---|
1481 | Vector<Double> times = mjdCol.getColumn(); |
---|
1482 | |
---|
1483 | // Generate DataDesc table |
---|
1484 | |
---|
1485 | Matrix<uInt> ddIdx; |
---|
1486 | SDDataDesc dDesc; |
---|
1487 | generateDataDescTable (ddIdx, dDesc, nIF, in, tabIn, srcCol, fqIDCol, perFreqID); |
---|
1488 | |
---|
1489 | // Get reference Epoch to time of first row or given String |
---|
1490 | |
---|
1491 | Unit DAY(String("d")); |
---|
1492 | MEpoch::Ref epochRef(in.getTimeReference()); |
---|
1493 | MEpoch refEpoch; |
---|
1494 | if (refTime.length()>0) { |
---|
1495 | refEpoch = epochFromString(refTime, in.getTimeReference()); |
---|
1496 | } else { |
---|
1497 | refEpoch = in.getEpoch(0); |
---|
1498 | } |
---|
1499 | cout << "Aligning at reference Epoch " << formatEpoch(refEpoch) |
---|
1500 | << " in frame " << MFrequency::showType(freqSystem) << endl; |
---|
1501 | |
---|
1502 | // Get Reference Position |
---|
1503 | |
---|
1504 | MPosition refPos = in.getAntennaPosition(); |
---|
1505 | |
---|
1506 | // Create FrequencyAligner Block. One FA for each possible |
---|
1507 | // source/freqID (perFreqID=True) or source/IF (perFreqID=False) combination |
---|
1508 | |
---|
1509 | PtrBlock<FrequencyAligner<Float>* > a(dDesc.length()); |
---|
1510 | generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos, |
---|
1511 | refEpoch, perFreqID); |
---|
1512 | |
---|
1513 | // Generate and fill output Frequency Table. WHen perFreqID=True, there is one output FreqID |
---|
1514 | // for each entry in the SDDataDesc table. However, in perFreqID=False mode, there may be |
---|
1515 | // some degeneracy, so we need a little translation map |
---|
1516 | |
---|
1517 | SDFrequencyTable freqTabOut = in.getSDFreqTable(); |
---|
1518 | freqTabOut.setLength(0); |
---|
1519 | Vector<String> units(1); |
---|
1520 | units = String("Hz"); |
---|
1521 | Bool linear=True; |
---|
1522 | // |
---|
1523 | Vector<uInt> ddFQTrans(dDesc.length(),0); |
---|
1524 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
1525 | |
---|
1526 | // Get Aligned SC in Hz |
---|
1527 | |
---|
1528 | SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear); |
---|
1529 | sC.setWorldAxisUnits(units); |
---|
1530 | |
---|
1531 | // Add FreqID |
---|
1532 | |
---|
1533 | uInt idx = freqTabOut.addFrequency(sC.referencePixel()[0], |
---|
1534 | sC.referenceValue()[0], |
---|
1535 | sC.increment()[0]); |
---|
1536 | ddFQTrans(i) = idx; // output FreqID = ddFQTrans(ddIdx) |
---|
1537 | } |
---|
1538 | |
---|
1539 | // Interpolation method |
---|
1540 | |
---|
1541 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
1542 | convertInterpString(interp, methodStr); |
---|
1543 | |
---|
1544 | // New output Table |
---|
1545 | |
---|
1546 | cout << "Create output table" << endl; |
---|
1547 | SDMemTable* pTabOut = new SDMemTable(in,True); |
---|
1548 | pTabOut->putSDFreqTable(freqTabOut); |
---|
1549 | |
---|
1550 | // Loop over rows in Table |
---|
1551 | |
---|
1552 | Bool extrapolate=False; |
---|
1553 | const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis); |
---|
1554 | Bool useCachedAbcissa = False; |
---|
1555 | Bool first = True; |
---|
1556 | Bool ok; |
---|
1557 | Vector<Float> yOut; |
---|
1558 | Vector<Bool> maskOut; |
---|
1559 | Vector<uInt> freqID(nIF); |
---|
1560 | uInt ifIdx, faIdx; |
---|
1561 | Vector<Double> xIn; |
---|
1562 | // |
---|
1563 | for (uInt iRow=0; iRow<nRows; ++iRow) { |
---|
1564 | if (iRow%10==0) { |
---|
1565 | cout << "Processing row " << iRow << endl; |
---|
1566 | } |
---|
1567 | |
---|
1568 | // Get EPoch |
---|
1569 | |
---|
1570 | Quantum<Double> tQ2(times[iRow],DAY); |
---|
1571 | MVEpoch mv2(tQ2); |
---|
1572 | MEpoch epoch(mv2, epochRef); |
---|
1573 | |
---|
1574 | // Get copy of data |
---|
1575 | |
---|
1576 | const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow)); |
---|
1577 | Array<Float> values = mArrIn.getArray(); |
---|
1578 | Array<Bool> mask = mArrIn.getMask(); |
---|
1579 | |
---|
1580 | // For each row, the Frequency abcissa will be the same regardless |
---|
1581 | // of polarization. For all other axes (IF and BEAM) the abcissa |
---|
1582 | // will change. So we iterate through the data by pol-chan planes |
---|
1583 | // to mimimize the work. Probably won't work for multiple beams |
---|
1584 | // at this point. |
---|
1585 | |
---|
1586 | ArrayIterator<Float> itValuesPlane(values, polChanAxes); |
---|
1587 | ArrayIterator<Bool> itMaskPlane(mask, polChanAxes); |
---|
1588 | while (!itValuesPlane.pastEnd()) { |
---|
1589 | |
---|
1590 | // Find the IF index and then the FA PtrBlock index |
---|
1591 | |
---|
1592 | const IPosition& pos = itValuesPlane.pos(); |
---|
1593 | ifIdx = pos(asap::IFAxis); |
---|
1594 | faIdx = ddIdx(iRow,ifIdx); |
---|
1595 | |
---|
1596 | // Generate abcissa for perIF. Could cache this in a Matrix |
---|
1597 | // on a per scan basis. Pretty expensive doing it for every row. |
---|
1598 | |
---|
1599 | if (!perFreqID) { |
---|
1600 | xIn.resize(nChan); |
---|
1601 | uInt fqID = dDesc.secID(ddIdx(iRow,ifIdx)); |
---|
1602 | SpectralCoordinate sC = in.getSpectralCoordinate(fqID); |
---|
1603 | Double w; |
---|
1604 | for (uInt i=0; i<nChan; i++) { |
---|
1605 | sC.toWorld(w,Double(i)); |
---|
1606 | xIn[i] = w; |
---|
1607 | } |
---|
1608 | } |
---|
1609 | // |
---|
1610 | VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1); |
---|
1611 | VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1); |
---|
1612 | |
---|
1613 | // Iterate through the plane by vector and align |
---|
1614 | |
---|
1615 | first = True; |
---|
1616 | useCachedAbcissa=False; |
---|
1617 | while (!itValuesVec.pastEnd()) { |
---|
1618 | if (perFreqID) { |
---|
1619 | ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(), |
---|
1620 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
1621 | interp, extrapolate); |
---|
1622 | } else { |
---|
1623 | ok = a[faIdx]->align (yOut, maskOut, xIn, itValuesVec.vector(), |
---|
1624 | itMaskVec.vector(), epoch, useCachedAbcissa, |
---|
1625 | interp, extrapolate); |
---|
1626 | } |
---|
1627 | // |
---|
1628 | itValuesVec.vector() = yOut; |
---|
1629 | itMaskVec.vector() = maskOut; |
---|
1630 | // |
---|
1631 | itValuesVec.next(); |
---|
1632 | itMaskVec.next(); |
---|
1633 | // |
---|
1634 | if (first) { |
---|
1635 | useCachedAbcissa = True; |
---|
1636 | first = False; |
---|
1637 | } |
---|
1638 | } |
---|
1639 | // |
---|
1640 | itValuesPlane.next(); |
---|
1641 | itMaskPlane.next(); |
---|
1642 | } |
---|
1643 | |
---|
1644 | // Create SDContainer and put back |
---|
1645 | |
---|
1646 | SDContainer sc = in.getSDContainer(iRow); |
---|
1647 | putDataInSDC(sc, values, mask); |
---|
1648 | |
---|
1649 | // Set output FreqIDs |
---|
1650 | |
---|
1651 | for (uInt i=0; i<nIF; i++) { |
---|
1652 | uInt idx = ddIdx(iRow,i); // Index into SDDataDesc table |
---|
1653 | freqID(i) = ddFQTrans(idx); // FreqID in output FQ table |
---|
1654 | } |
---|
1655 | sc.putFreqMap(freqID); |
---|
1656 | // |
---|
1657 | pTabOut->putSDContainer(sc); |
---|
1658 | } |
---|
1659 | |
---|
1660 | // Now we must set the base and extra frames to the |
---|
1661 | // input frame |
---|
1662 | |
---|
1663 | std::vector<string> info = pTabOut->getCoordInfo(); |
---|
1664 | info[1] = MFrequency::showType(freqSystem); // Conversion frame |
---|
1665 | info[3] = info[1]; // Base frame |
---|
1666 | pTabOut->setCoordInfo(info); |
---|
1667 | |
---|
1668 | // Clean up PointerBlock |
---|
1669 | |
---|
1670 | for (uInt i=0; i<a.nelements(); i++) delete a[i]; |
---|
1671 | // |
---|
1672 | return pTabOut; |
---|
1673 | } |
---|
1674 | |
---|
1675 | |
---|
1676 | void SDMath::fillSDC(SDContainer& sc, |
---|
1677 | const Array<Bool>& mask, |
---|
1678 | const Array<Float>& data, |
---|
1679 | const Array<Float>& tSys, |
---|
1680 | Int scanID, Double timeStamp, |
---|
1681 | Double interval, const String& sourceName, |
---|
1682 | const Vector<uInt>& freqID) const |
---|
1683 | { |
---|
1684 | // Data and mask |
---|
1685 | |
---|
1686 | putDataInSDC(sc, data, mask); |
---|
1687 | |
---|
1688 | // TSys |
---|
1689 | |
---|
1690 | sc.putTsys(tSys); |
---|
1691 | |
---|
1692 | // Time things |
---|
1693 | |
---|
1694 | sc.timestamp = timeStamp; |
---|
1695 | sc.interval = interval; |
---|
1696 | sc.scanid = scanID; |
---|
1697 | // |
---|
1698 | sc.sourcename = sourceName; |
---|
1699 | sc.putFreqMap(freqID); |
---|
1700 | } |
---|
1701 | |
---|
1702 | void SDMath::normalize(MaskedArray<Float>& sum, |
---|
1703 | const Array<Float>& sumSq, |
---|
1704 | const Array<Float>& nPts, |
---|
1705 | WeightType wtType, Int axis, |
---|
1706 | Int nAxesSub) const |
---|
1707 | { |
---|
1708 | IPosition pos2(nAxesSub,0); |
---|
1709 | // |
---|
1710 | if (wtType==NONE) { |
---|
1711 | |
---|
1712 | // We just average by the number of points accumulated. |
---|
1713 | // We need to make a MA out of nPts so that no divide by |
---|
1714 | // zeros occur |
---|
1715 | |
---|
1716 | MaskedArray<Float> t(nPts, (nPts>Float(0.0))); |
---|
1717 | sum /= t; |
---|
1718 | } else if (wtType==VAR) { |
---|
1719 | |
---|
1720 | // Normalize each spectrum by sum(1/var) where the variance |
---|
1721 | // is worked out for each spectrum |
---|
1722 | |
---|
1723 | Array<Float>& data = sum.getRWArray(); |
---|
1724 | VectorIterator<Float> itData(data, axis); |
---|
1725 | while (!itData.pastEnd()) { |
---|
1726 | pos2 = itData.pos().getFirst(nAxesSub); |
---|
1727 | itData.vector() /= sumSq(pos2); |
---|
1728 | itData.next(); |
---|
1729 | } |
---|
1730 | } else if (wtType==TSYS) { |
---|
1731 | } |
---|
1732 | } |
---|
1733 | |
---|
1734 | |
---|
1735 | void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum, |
---|
1736 | MaskedArray<Float>& sum, Array<Float>& sumSq, |
---|
1737 | Array<Float>& nPts, Array<Float>& tSysSum, |
---|
1738 | const Array<Float>& tSys, const Array<Float>& nInc, |
---|
1739 | const Vector<Bool>& mask, Double time, Double interval, |
---|
1740 | const Block<CountedPtr<SDMemTable> >& in, |
---|
1741 | uInt iTab, uInt iRow, uInt axis, |
---|
1742 | uInt nAxesSub, Bool useMask, |
---|
1743 | WeightType wtType) const |
---|
1744 | { |
---|
1745 | |
---|
1746 | // Get data |
---|
1747 | |
---|
1748 | MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow)); |
---|
1749 | Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference |
---|
1750 | const Array<Bool>& maskIn = dataIn.getMask(); // RO reference |
---|
1751 | // |
---|
1752 | if (wtType==NONE) { |
---|
1753 | const MaskedArray<Float> n(nInc,dataIn.getMask()); |
---|
1754 | nPts += n; // Only accumulates where mask==T |
---|
1755 | } else if (wtType==VAR) { |
---|
1756 | |
---|
1757 | // We are going to average the data, weighted by the noise for each pol, beam and IF. |
---|
1758 | // So therefore we need to iterate through by spectrum (axis 3) |
---|
1759 | |
---|
1760 | VectorIterator<Float> itData(valuesIn, axis); |
---|
1761 | ReadOnlyVectorIterator<Bool> itMask(maskIn, axis); |
---|
1762 | Float fac = 1.0; |
---|
1763 | IPosition pos(nAxesSub,0); |
---|
1764 | // |
---|
1765 | while (!itData.pastEnd()) { |
---|
1766 | |
---|
1767 | // Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor |
---|
1768 | |
---|
1769 | if (useMask) { |
---|
1770 | MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector()); |
---|
1771 | fac = 1.0/variance(tmp); |
---|
1772 | } else { |
---|
1773 | MaskedArray<Float> tmp(itData.vector(),itMask.vector()); |
---|
1774 | fac = 1.0/variance(tmp); |
---|
1775 | } |
---|
1776 | |
---|
1777 | // Scale data |
---|
1778 | |
---|
1779 | itData.vector() *= fac; // Writes back into 'dataIn' |
---|
1780 | // |
---|
1781 | // Accumulate variance per if/pol/beam averaged over spectrum |
---|
1782 | // This method to get pos2 from itData.pos() is only valid |
---|
1783 | // because the spectral axis is the last one (so we can just |
---|
1784 | // copy the first nAXesSub positions out) |
---|
1785 | |
---|
1786 | pos = itData.pos().getFirst(nAxesSub); |
---|
1787 | sumSq(pos) += fac; |
---|
1788 | // |
---|
1789 | itData.next(); |
---|
1790 | itMask.next(); |
---|
1791 | } |
---|
1792 | } else if (wtType==TSYS) { |
---|
1793 | } |
---|
1794 | |
---|
1795 | // Accumulate sum of (possibly scaled) data |
---|
1796 | |
---|
1797 | sum += dataIn; |
---|
1798 | |
---|
1799 | // Accumulate Tsys, time, and interval |
---|
1800 | |
---|
1801 | tSysSum += tSys; |
---|
1802 | timeSum += time; |
---|
1803 | intSum += interval; |
---|
1804 | nAccum += 1; |
---|
1805 | } |
---|
1806 | |
---|
1807 | |
---|
1808 | void SDMath::setCursorSlice (IPosition& start, IPosition& end, Bool doAll, const SDMemTable& in) const |
---|
1809 | { |
---|
1810 | const uInt nDim = asap::nAxes; |
---|
1811 | DebugAssert(nDim==4,AipsError); |
---|
1812 | // |
---|
1813 | start.resize(nDim); |
---|
1814 | end.resize(nDim); |
---|
1815 | if (doAll) { |
---|
1816 | start = 0; |
---|
1817 | end(0) = in.nBeam()-1; |
---|
1818 | end(1) = in.nIF()-1; |
---|
1819 | end(2) = in.nPol()-1; |
---|
1820 | end(3) = in.nChan()-1; |
---|
1821 | } else { |
---|
1822 | start(0) = in.getBeam(); |
---|
1823 | end(0) = start(0); |
---|
1824 | // |
---|
1825 | start(1) = in.getIF(); |
---|
1826 | end(1) = start(1); |
---|
1827 | // |
---|
1828 | start(2) = in.getPol(); |
---|
1829 | end(2) = start(2); |
---|
1830 | // |
---|
1831 | start(3) = 0; |
---|
1832 | end(3) = in.nChan()-1; |
---|
1833 | } |
---|
1834 | } |
---|
1835 | |
---|
1836 | |
---|
1837 | void SDMath::convertWeightString(WeightType& wtType, const String& weightStr) const |
---|
1838 | { |
---|
1839 | String tStr(weightStr); |
---|
1840 | tStr.upcase(); |
---|
1841 | if (tStr.contains(String("NONE"))) { |
---|
1842 | wtType = NONE; |
---|
1843 | } else if (tStr.contains(String("VAR"))) { |
---|
1844 | wtType = VAR; |
---|
1845 | } else if (tStr.contains(String("TSYS"))) { |
---|
1846 | wtType = TSYS; |
---|
1847 | throw(AipsError("T_sys weighting not yet implemented")); |
---|
1848 | } else { |
---|
1849 | throw(AipsError("Unrecognized weighting type")); |
---|
1850 | } |
---|
1851 | } |
---|
1852 | |
---|
1853 | |
---|
1854 | void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type, |
---|
1855 | const casa::String& interp) const |
---|
1856 | { |
---|
1857 | String tStr(interp); |
---|
1858 | tStr.upcase(); |
---|
1859 | if (tStr.contains(String("NEAR"))) { |
---|
1860 | type = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
1861 | } else if (tStr.contains(String("LIN"))) { |
---|
1862 | type = InterpolateArray1D<Double,Float>::linear; |
---|
1863 | } else if (tStr.contains(String("CUB"))) { |
---|
1864 | type = InterpolateArray1D<Double,Float>::cubic; |
---|
1865 | } else if (tStr.contains(String("SPL"))) { |
---|
1866 | type = InterpolateArray1D<Double,Float>::spline; |
---|
1867 | } else { |
---|
1868 | throw(AipsError("Unrecognized interpolation type")); |
---|
1869 | } |
---|
1870 | } |
---|
1871 | |
---|
1872 | void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data, |
---|
1873 | const Array<Bool>& mask) const |
---|
1874 | { |
---|
1875 | sc.putSpectrum(data); |
---|
1876 | // |
---|
1877 | Array<uChar> outflags(data.shape()); |
---|
1878 | convertArray(outflags,!mask); |
---|
1879 | sc.putFlags(outflags); |
---|
1880 | } |
---|
1881 | |
---|
1882 | Table SDMath::readAsciiFile (const String& fileName) const |
---|
1883 | { |
---|
1884 | String formatString; |
---|
1885 | Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False); |
---|
1886 | return tbl; |
---|
1887 | } |
---|
1888 | |
---|
1889 | |
---|
1890 | |
---|
1891 | void SDMath::scaleFromAsciiTable(SDMemTable* pTabOut, |
---|
1892 | const SDMemTable& in, const String& fileName, |
---|
1893 | const String& col0, const String& col1, |
---|
1894 | const String& methodStr, Bool doAll, |
---|
1895 | const Vector<Float>& xOut, Bool doTSys) const |
---|
1896 | { |
---|
1897 | |
---|
1898 | // Read gain-elevation ascii file data into a Table. |
---|
1899 | |
---|
1900 | Table geTable = readAsciiFile (fileName); |
---|
1901 | // |
---|
1902 | scaleFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut, doTSys); |
---|
1903 | } |
---|
1904 | |
---|
1905 | void SDMath::scaleFromTable(SDMemTable* pTabOut, const SDMemTable& in, |
---|
1906 | const Table& tTable, const String& col0, |
---|
1907 | const String& col1, |
---|
1908 | const String& methodStr, Bool doAll, |
---|
1909 | const Vector<Float>& xOut, Bool doTsys) const |
---|
1910 | { |
---|
1911 | |
---|
1912 | // Get data from Table |
---|
1913 | |
---|
1914 | ROScalarColumn<Float> geElCol(tTable, col0); |
---|
1915 | ROScalarColumn<Float> geFacCol(tTable, col1); |
---|
1916 | Vector<Float> xIn = geElCol.getColumn(); |
---|
1917 | Vector<Float> yIn = geFacCol.getColumn(); |
---|
1918 | Vector<Bool> maskIn(xIn.nelements(),True); |
---|
1919 | |
---|
1920 | // Interpolate (and extrapolate) with desired method |
---|
1921 | |
---|
1922 | InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
1923 | convertInterpString(method, methodStr); |
---|
1924 | Int intMethod(method); |
---|
1925 | // |
---|
1926 | Vector<Float> yOut; |
---|
1927 | Vector<Bool> maskOut; |
---|
1928 | InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut, |
---|
1929 | xIn, yIn, maskIn, intMethod, |
---|
1930 | True, True); |
---|
1931 | // Apply |
---|
1932 | |
---|
1933 | scaleByVector(pTabOut, in, doAll, Float(1.0)/yOut, doTsys); |
---|
1934 | } |
---|
1935 | |
---|
1936 | |
---|
1937 | void SDMath::scaleByVector(SDMemTable* pTabOut, const SDMemTable& in, |
---|
1938 | Bool doAll, const Vector<Float>& factor, |
---|
1939 | Bool doTSys) const |
---|
1940 | { |
---|
1941 | |
---|
1942 | // Set up data slice |
---|
1943 | |
---|
1944 | IPosition start, end; |
---|
1945 | setCursorSlice (start, end, doAll, in); |
---|
1946 | |
---|
1947 | // Get Tsys column |
---|
1948 | |
---|
1949 | const Table& tIn = in.table(); |
---|
1950 | ArrayColumn<Float> tSysCol(tIn, "TSYS"); |
---|
1951 | Array<Float> tSys; |
---|
1952 | |
---|
1953 | // Loop over rows and apply correction factor |
---|
1954 | |
---|
1955 | const uInt axis = asap::ChanAxis; |
---|
1956 | for (uInt i=0; i < in.nRow(); ++i) { |
---|
1957 | |
---|
1958 | // Get data |
---|
1959 | |
---|
1960 | MaskedArray<Float> dataIn(in.rowAsMaskedArray(i)); |
---|
1961 | MaskedArray<Float> dataIn2 = dataIn(start,end); // reference to dataIn |
---|
1962 | // |
---|
1963 | if (doTSys) { |
---|
1964 | tSysCol.get(i, tSys); |
---|
1965 | Array<Float> tSys2 = tSys(start,end) * factor[i]; |
---|
1966 | tSysCol.put(i, tSys); |
---|
1967 | } |
---|
1968 | |
---|
1969 | // Apply factor |
---|
1970 | |
---|
1971 | dataIn2 *= factor[i]; |
---|
1972 | |
---|
1973 | // Write out |
---|
1974 | |
---|
1975 | SDContainer sc = in.getSDContainer(i); |
---|
1976 | putDataInSDC(sc, dataIn.getArray(), dataIn.getMask()); |
---|
1977 | // |
---|
1978 | pTabOut->putSDContainer(sc); |
---|
1979 | } |
---|
1980 | } |
---|
1981 | |
---|
1982 | |
---|
1983 | |
---|
1984 | |
---|
1985 | void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx, |
---|
1986 | SDDataDesc& dDesc, |
---|
1987 | uInt nIF, |
---|
1988 | const SDMemTable& in, |
---|
1989 | const Table& tabIn, |
---|
1990 | const ROScalarColumn<String>& srcCol, |
---|
1991 | const ROArrayColumn<uInt>& fqIDCol, |
---|
1992 | Bool perFreqID) const |
---|
1993 | { |
---|
1994 | const uInt nRows = tabIn.nrow(); |
---|
1995 | ddIdx.resize(nRows,nIF); |
---|
1996 | // |
---|
1997 | String srcName; |
---|
1998 | Vector<uInt> freqIDs; |
---|
1999 | for (uInt iRow=0; iRow<nRows; iRow++) { |
---|
2000 | srcCol.get(iRow, srcName); |
---|
2001 | fqIDCol.get(iRow, freqIDs); |
---|
2002 | const MDirection& dir = in.getDirection(iRow); |
---|
2003 | // |
---|
2004 | if (perFreqID) { |
---|
2005 | |
---|
2006 | // One entry per source/freqID pair |
---|
2007 | |
---|
2008 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
2009 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, freqIDs[iIF], dir, 0); |
---|
2010 | } |
---|
2011 | } else { |
---|
2012 | |
---|
2013 | // One entry per source/IF pair. Hang onto the FreqID as well |
---|
2014 | |
---|
2015 | for (uInt iIF=0; iIF<nIF; iIF++) { |
---|
2016 | ddIdx(iRow,iIF) = dDesc.addEntry(srcName, iIF, dir, freqIDs[iIF]); |
---|
2017 | } |
---|
2018 | } |
---|
2019 | } |
---|
2020 | } |
---|
2021 | |
---|
2022 | |
---|
2023 | |
---|
2024 | |
---|
2025 | |
---|
2026 | MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const |
---|
2027 | { |
---|
2028 | Quantum<Double> qt; |
---|
2029 | if (MVTime::read(qt,str)) { |
---|
2030 | MVEpoch mv(qt); |
---|
2031 | MEpoch me(mv, timeRef); |
---|
2032 | return me; |
---|
2033 | } else { |
---|
2034 | throw(AipsError("Invalid format for Epoch string")); |
---|
2035 | } |
---|
2036 | } |
---|
2037 | |
---|
2038 | |
---|
2039 | String SDMath::formatEpoch(const MEpoch& epoch) const |
---|
2040 | { |
---|
2041 | MVTime mvt(epoch.getValue()); |
---|
2042 | return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")"); |
---|
2043 | } |
---|
2044 | |
---|
2045 | |
---|
2046 | |
---|
2047 | void SDMath::generateFrequencyAligners (PtrBlock<FrequencyAligner<Float>* >& a, |
---|
2048 | const SDDataDesc& dDesc, |
---|
2049 | const SDMemTable& in, uInt nChan, |
---|
2050 | MFrequency::Types system, |
---|
2051 | const MPosition& refPos, |
---|
2052 | const MEpoch& refEpoch, |
---|
2053 | Bool perFreqID) const |
---|
2054 | { |
---|
2055 | for (uInt i=0; i<dDesc.length(); i++) { |
---|
2056 | uInt ID = dDesc.ID(i); |
---|
2057 | uInt secID = dDesc.secID(i); |
---|
2058 | const MDirection& refDir = dDesc.secDir(i); |
---|
2059 | // |
---|
2060 | if (perFreqID) { |
---|
2061 | |
---|
2062 | // One aligner per source/FreqID pair. |
---|
2063 | |
---|
2064 | SpectralCoordinate sC = in.getSpectralCoordinate(ID); |
---|
2065 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
2066 | } else { |
---|
2067 | |
---|
2068 | // One aligner per source/IF pair. But we still need the FreqID to |
---|
2069 | // get the right SC. Hence the messing about with the secondary ID |
---|
2070 | |
---|
2071 | SpectralCoordinate sC = in.getSpectralCoordinate(secID); |
---|
2072 | a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system); |
---|
2073 | } |
---|
2074 | } |
---|
2075 | } |
---|
2076 | |
---|
2077 | Vector<uInt> SDMath::getRowRange (const SDMemTable& in) const |
---|
2078 | { |
---|
2079 | Vector<uInt> range(2); |
---|
2080 | range[0] = 0; |
---|
2081 | range[1] = in.nRow()-1; |
---|
2082 | return range; |
---|
2083 | } |
---|
2084 | |
---|
2085 | |
---|
2086 | Bool SDMath::rowInRange (uInt i, const Vector<uInt>& range) const |
---|
2087 | { |
---|
2088 | return (i>=range[0] && i<=range[1]); |
---|
2089 | } |
---|