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