1 | // |
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2 | // C++ Implementation: STMath |
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3 | // |
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4 | // Description: |
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5 | // |
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6 | // |
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7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006 |
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8 | // |
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9 | // Copyright: See COPYING file that comes with this distribution |
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10 | // |
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11 | // |
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12 | |
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13 | #include <casa/iomanip.h> |
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14 | #include <casa/Exceptions/Error.h> |
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15 | #include <casa/Containers/Block.h> |
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16 | #include <casa/BasicSL/String.h> |
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17 | #include <casa/Arrays/MaskArrLogi.h> |
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18 | #include <casa/Arrays/MaskArrMath.h> |
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19 | #include <casa/Arrays/ArrayLogical.h> |
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20 | #include <casa/Arrays/ArrayMath.h> |
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21 | #include <casa/Arrays/Slice.h> |
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22 | #include <casa/Arrays/Slicer.h> |
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23 | #include <casa/Containers/RecordField.h> |
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24 | #include <tables/Tables/TableRow.h> |
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25 | #include <tables/Tables/TableVector.h> |
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26 | #include <tables/Tables/TabVecMath.h> |
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27 | #include <tables/Tables/ExprNode.h> |
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28 | #include <tables/Tables/TableRecord.h> |
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29 | #include <tables/Tables/TableParse.h> |
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30 | #include <tables/Tables/ReadAsciiTable.h> |
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31 | #include <tables/Tables/TableIter.h> |
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32 | #include <tables/Tables/TableCopy.h> |
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33 | #include <scimath/Mathematics/FFTServer.h> |
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34 | |
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35 | #include <lattices/Lattices/LatticeUtilities.h> |
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36 | |
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37 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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38 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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39 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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40 | #include <coordinates/Coordinates/FrequencyAligner.h> |
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41 | |
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42 | #include <scimath/Mathematics/VectorKernel.h> |
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43 | #include <scimath/Mathematics/Convolver.h> |
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44 | #include <scimath/Functionals/Polynomial.h> |
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45 | |
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46 | #include "MathUtils.h" |
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47 | #include "RowAccumulator.h" |
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48 | #include "STAttr.h" |
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49 | #include "STMath.h" |
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50 | #include "STSelector.h" |
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51 | |
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52 | using namespace casa; |
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53 | |
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54 | using namespace asap; |
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55 | |
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56 | STMath::STMath(bool insitu) : |
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57 | insitu_(insitu) |
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58 | { |
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59 | } |
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60 | |
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61 | |
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62 | STMath::~STMath() |
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63 | { |
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64 | } |
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65 | |
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66 | CountedPtr<Scantable> |
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67 | STMath::average( const std::vector<CountedPtr<Scantable> >& in, |
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68 | const std::vector<bool>& mask, |
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69 | const std::string& weight, |
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70 | const std::string& avmode) |
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71 | { |
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72 | if ( avmode == "SCAN" && in.size() != 1 ) |
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73 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n" |
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74 | "Use merge first.")); |
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75 | WeightType wtype = stringToWeight(weight); |
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76 | |
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77 | // output |
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78 | // clone as this is non insitu |
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79 | bool insitu = insitu_; |
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80 | setInsitu(false); |
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81 | CountedPtr< Scantable > out = getScantable(in[0], true); |
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82 | setInsitu(insitu); |
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83 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin(); |
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84 | ++stit; |
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85 | while ( stit != in.end() ) { |
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86 | out->appendToHistoryTable((*stit)->history()); |
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87 | ++stit; |
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88 | } |
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89 | |
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90 | Table& tout = out->table(); |
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91 | |
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92 | /// @todo check if all scantables are conformant |
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93 | |
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94 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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95 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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96 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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97 | ScalarColumn<Double> mjdColOut(tout,"TIME"); |
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98 | ScalarColumn<Double> intColOut(tout,"INTERVAL"); |
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99 | ScalarColumn<uInt> cycColOut(tout,"CYCLENO"); |
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100 | ScalarColumn<uInt> scanColOut(tout,"SCANNO"); |
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101 | |
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102 | // set up the output table rows. These are based on the structure of the |
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103 | // FIRST scantable in the vector |
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104 | const Table& baset = in[0]->table(); |
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105 | |
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106 | Block<String> cols(3); |
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107 | cols[0] = String("BEAMNO"); |
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108 | cols[1] = String("IFNO"); |
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109 | cols[2] = String("POLNO"); |
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110 | if ( avmode == "SOURCE" ) { |
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111 | cols.resize(4); |
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112 | cols[3] = String("SRCNAME"); |
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113 | } |
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114 | if ( avmode == "SCAN" && in.size() == 1) { |
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115 | cols.resize(4); |
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116 | cols[3] = String("SCANNO"); |
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117 | } |
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118 | uInt outrowCount = 0; |
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119 | TableIterator iter(baset, cols); |
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120 | while (!iter.pastEnd()) { |
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121 | Table subt = iter.table(); |
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122 | // copy the first row of this selection into the new table |
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123 | tout.addRow(); |
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124 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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125 | // re-index to 0 |
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126 | if ( avmode != "SCAN" && avmode != "SOURCE" ) { |
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127 | scanColOut.put(outrowCount, uInt(0)); |
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128 | } |
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129 | ++outrowCount; |
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130 | ++iter; |
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131 | } |
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132 | |
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133 | RowAccumulator acc(wtype); |
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134 | Vector<Bool> cmask(mask); |
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135 | acc.setUserMask(cmask); |
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136 | ROTableRow row(tout); |
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137 | ROArrayColumn<Float> specCol, tsysCol; |
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138 | ROArrayColumn<uChar> flagCol; |
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139 | ROScalarColumn<Double> mjdCol, intCol; |
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140 | ROScalarColumn<Int> scanIDCol; |
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141 | |
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142 | Vector<uInt> rowstodelete; |
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143 | |
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144 | for (uInt i=0; i < tout.nrow(); ++i) { |
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145 | for ( int j=0; j < int(in.size()); ++j ) { |
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146 | const Table& tin = in[j]->table(); |
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147 | const TableRecord& rec = row.get(i); |
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148 | ROScalarColumn<Double> tmp(tin, "TIME"); |
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149 | Double td;tmp.get(0,td); |
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150 | Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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151 | && tin.col("IFNO") == Int(rec.asuInt("IFNO")) |
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152 | && tin.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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153 | Table subt; |
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154 | if ( avmode == "SOURCE") { |
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155 | subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") ); |
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156 | } else if (avmode == "SCAN") { |
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157 | subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) ); |
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158 | } else { |
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159 | subt = basesubt; |
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160 | } |
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161 | specCol.attach(subt,"SPECTRA"); |
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162 | flagCol.attach(subt,"FLAGTRA"); |
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163 | tsysCol.attach(subt,"TSYS"); |
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164 | intCol.attach(subt,"INTERVAL"); |
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165 | mjdCol.attach(subt,"TIME"); |
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166 | Vector<Float> spec,tsys; |
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167 | Vector<uChar> flag; |
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168 | Double inter,time; |
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169 | for (uInt k = 0; k < subt.nrow(); ++k ) { |
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170 | flagCol.get(k, flag); |
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171 | Vector<Bool> bflag(flag.shape()); |
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172 | convertArray(bflag, flag); |
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173 | /* |
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174 | if ( allEQ(bflag, True) ) { |
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175 | continue;//don't accumulate |
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176 | } |
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177 | */ |
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178 | specCol.get(k, spec); |
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179 | tsysCol.get(k, tsys); |
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180 | intCol.get(k, inter); |
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181 | mjdCol.get(k, time); |
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182 | // spectrum has to be added last to enable weighting by the other values |
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183 | acc.add(spec, !bflag, tsys, inter, time); |
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184 | } |
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185 | } |
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186 | const Vector<Bool>& msk = acc.getMask(); |
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187 | if ( allEQ(msk, False) ) { |
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188 | uint n = rowstodelete.nelements(); |
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189 | rowstodelete.resize(n+1, True); |
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190 | rowstodelete[n] = i; |
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191 | continue; |
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192 | } |
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193 | //write out |
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194 | Vector<uChar> flg(msk.shape()); |
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195 | convertArray(flg, !msk); |
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196 | flagColOut.put(i, flg); |
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197 | specColOut.put(i, acc.getSpectrum()); |
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198 | tsysColOut.put(i, acc.getTsys()); |
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199 | intColOut.put(i, acc.getInterval()); |
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200 | mjdColOut.put(i, acc.getTime()); |
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201 | // we should only have one cycle now -> reset it to be 0 |
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202 | // frequency switched data has different CYCLENO for different IFNO |
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203 | // which requires resetting this value |
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204 | cycColOut.put(i, uInt(0)); |
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205 | acc.reset(); |
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206 | } |
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207 | if (rowstodelete.nelements() > 0) { |
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208 | tout.removeRow(rowstodelete); |
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209 | if (tout.nrow() == 0) { |
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210 | throw(AipsError("Can't average fully flagged data.")); |
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211 | } |
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212 | } |
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213 | return out; |
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214 | } |
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215 | |
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216 | CountedPtr< Scantable > |
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217 | STMath::averageChannel( const CountedPtr < Scantable > & in, |
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218 | const std::string & mode, |
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219 | const std::string& avmode ) |
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220 | { |
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221 | // clone as this is non insitu |
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222 | bool insitu = insitu_; |
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223 | setInsitu(false); |
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224 | CountedPtr< Scantable > out = getScantable(in, true); |
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225 | setInsitu(insitu); |
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226 | Table& tout = out->table(); |
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227 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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228 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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229 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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230 | ScalarColumn<uInt> scanColOut(tout,"SCANNO"); |
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231 | ScalarColumn<Double> intColOut(tout, "INTERVAL"); |
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232 | Table tmp = in->table().sort("BEAMNO"); |
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233 | Block<String> cols(3); |
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234 | cols[0] = String("BEAMNO"); |
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235 | cols[1] = String("IFNO"); |
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236 | cols[2] = String("POLNO"); |
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237 | if ( avmode == "SCAN") { |
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238 | cols.resize(4); |
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239 | cols[3] = String("SCANNO"); |
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240 | } |
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241 | uInt outrowCount = 0; |
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242 | uChar userflag = 1 << 7; |
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243 | TableIterator iter(tmp, cols); |
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244 | while (!iter.pastEnd()) { |
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245 | Table subt = iter.table(); |
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246 | ROArrayColumn<Float> specCol, tsysCol; |
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247 | ROArrayColumn<uChar> flagCol; |
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248 | ROScalarColumn<Double> intCol(subt, "INTERVAL"); |
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249 | specCol.attach(subt,"SPECTRA"); |
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250 | flagCol.attach(subt,"FLAGTRA"); |
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251 | tsysCol.attach(subt,"TSYS"); |
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252 | tout.addRow(); |
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253 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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254 | if ( avmode != "SCAN") { |
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255 | scanColOut.put(outrowCount, uInt(0)); |
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256 | } |
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257 | Vector<Float> tmp; |
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258 | specCol.get(0, tmp); |
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259 | uInt nchan = tmp.nelements(); |
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260 | // have to do channel by channel here as MaskedArrMath |
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261 | // doesn't have partialMedians |
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262 | Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0))); |
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263 | Vector<Float> outspec(nchan); |
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264 | Vector<uChar> outflag(nchan,0); |
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265 | Vector<Float> outtsys(1);/// @fixme when tsys is channel based |
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266 | for (uInt i=0; i<nchan; ++i) { |
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267 | Vector<Float> specs = specCol.getColumn(Slicer(Slice(i))); |
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268 | MaskedArray<Float> ma = maskedArray(specs,flags); |
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269 | outspec[i] = median(ma); |
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270 | if ( allEQ(ma.getMask(), False) ) |
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271 | outflag[i] = userflag;// flag data |
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272 | } |
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273 | outtsys[0] = median(tsysCol.getColumn()); |
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274 | specColOut.put(outrowCount, outspec); |
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275 | flagColOut.put(outrowCount, outflag); |
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276 | tsysColOut.put(outrowCount, outtsys); |
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277 | Double intsum = sum(intCol.getColumn()); |
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278 | intColOut.put(outrowCount, intsum); |
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279 | ++outrowCount; |
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280 | ++iter; |
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281 | } |
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282 | return out; |
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283 | } |
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284 | |
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285 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in, |
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286 | bool droprows) |
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287 | { |
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288 | if (insitu_) { |
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289 | return in; |
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290 | } |
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291 | else { |
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292 | // clone |
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293 | return CountedPtr<Scantable>(new Scantable(*in, Bool(droprows))); |
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294 | } |
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295 | } |
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296 | |
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297 | CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in, |
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298 | float val, |
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299 | const std::string& mode, |
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300 | bool tsys ) |
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301 | { |
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302 | CountedPtr< Scantable > out = getScantable(in, false); |
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303 | Table& tab = out->table(); |
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304 | ArrayColumn<Float> specCol(tab,"SPECTRA"); |
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305 | ArrayColumn<Float> tsysCol(tab,"TSYS"); |
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306 | for (uInt i=0; i<tab.nrow(); ++i) { |
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307 | Vector<Float> spec; |
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308 | Vector<Float> ts; |
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309 | specCol.get(i, spec); |
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310 | tsysCol.get(i, ts); |
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311 | if (mode == "MUL" || mode == "DIV") { |
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312 | if (mode == "DIV") val = 1.0/val; |
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313 | spec *= val; |
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314 | specCol.put(i, spec); |
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315 | if ( tsys ) { |
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316 | ts *= val; |
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317 | tsysCol.put(i, ts); |
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318 | } |
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319 | } else if ( mode == "ADD" || mode == "SUB") { |
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320 | if (mode == "SUB") val *= -1.0; |
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321 | spec += val; |
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322 | specCol.put(i, spec); |
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323 | if ( tsys ) { |
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324 | ts += val; |
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325 | tsysCol.put(i, ts); |
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326 | } |
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327 | } |
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328 | } |
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329 | return out; |
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330 | } |
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331 | |
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332 | CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left, |
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333 | const CountedPtr<Scantable>& right, |
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334 | const std::string& mode) |
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335 | { |
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336 | bool insitu = insitu_; |
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337 | if ( ! left->conformant(*right) ) { |
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338 | throw(AipsError("'left' and 'right' scantables are not conformant.")); |
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339 | } |
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340 | setInsitu(false); |
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341 | CountedPtr< Scantable > out = getScantable(left, false); |
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342 | setInsitu(insitu); |
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343 | Table& tout = out->table(); |
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344 | Block<String> coln(5); |
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345 | coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO"; |
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346 | coln[3] = "IFNO"; coln[4] = "POLNO"; |
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347 | Table tmpl = tout.sort(coln); |
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348 | Table tmpr = right->table().sort(coln); |
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349 | ArrayColumn<Float> lspecCol(tmpl,"SPECTRA"); |
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350 | ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA"); |
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351 | ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA"); |
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352 | ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA"); |
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353 | |
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354 | for (uInt i=0; i<tout.nrow(); ++i) { |
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355 | Vector<Float> lspecvec, rspecvec; |
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356 | Vector<uChar> lflagvec, rflagvec; |
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357 | lspecvec = lspecCol(i); rspecvec = rspecCol(i); |
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358 | lflagvec = lflagCol(i); rflagvec = rflagCol(i); |
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359 | MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec); |
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360 | MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec); |
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361 | if (mode == "ADD") { |
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362 | mleft += mright; |
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363 | } else if ( mode == "SUB") { |
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364 | mleft -= mright; |
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365 | } else if ( mode == "MUL") { |
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366 | mleft *= mright; |
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367 | } else if ( mode == "DIV") { |
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368 | mleft /= mright; |
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369 | } else { |
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370 | throw(AipsError("Illegal binary operator")); |
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371 | } |
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372 | lspecCol.put(i, mleft.getArray()); |
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373 | } |
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374 | return out; |
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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 | MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s, |
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380 | const Vector<uChar>& f) |
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381 | { |
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382 | Vector<Bool> mask; |
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383 | mask.resize(f.shape()); |
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384 | convertArray(mask, f); |
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385 | return MaskedArray<Float>(s,!mask); |
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386 | } |
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387 | |
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388 | Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma) |
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389 | { |
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390 | const Vector<Bool>& m = ma.getMask(); |
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391 | Vector<uChar> flags(m.shape()); |
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392 | convertArray(flags, !m); |
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393 | return flags; |
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394 | } |
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395 | |
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396 | CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in, |
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397 | const std::string & mode, |
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398 | bool preserve ) |
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399 | { |
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400 | /// @todo make other modes available |
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401 | /// modes should be "nearest", "pair" |
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402 | // make this operation non insitu |
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403 | const Table& tin = in->table(); |
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404 | Table ons = tin(tin.col("SRCTYPE") == Int(0)); |
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405 | Table offs = tin(tin.col("SRCTYPE") == Int(1)); |
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406 | if ( offs.nrow() == 0 ) |
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407 | throw(AipsError("No 'off' scans present.")); |
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408 | // put all "on" scans into output table |
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409 | |
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410 | bool insitu = insitu_; |
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411 | setInsitu(false); |
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412 | CountedPtr< Scantable > out = getScantable(in, true); |
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413 | setInsitu(insitu); |
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414 | Table& tout = out->table(); |
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415 | |
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416 | TableCopy::copyRows(tout, ons); |
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417 | TableRow row(tout); |
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418 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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419 | ArrayColumn<Float> outspecCol(tout, "SPECTRA"); |
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420 | ROArrayColumn<Float> outtsysCol(tout, "TSYS"); |
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421 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA"); |
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422 | for (uInt i=0; i < tout.nrow(); ++i) { |
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423 | const TableRecord& rec = row.get(i); |
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424 | Double ontime = rec.asDouble("TIME"); |
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425 | Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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426 | && offs.col("IFNO") == Int(rec.asuInt("IFNO")) |
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427 | && offs.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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428 | ROScalarColumn<Double> offtimeCol(presel, "TIME"); |
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429 | |
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430 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime)); |
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431 | // Timestamp may vary within a cycle ???!!! |
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432 | // increase this by 0.01 sec in case of rounding errors... |
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433 | // There might be a better way to do this. |
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434 | // fix to this fix. TIME is MJD, so 1.0d not 1.0s |
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435 | mindeltat += 0.01/24./60./60.; |
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436 | Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat); |
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437 | |
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438 | if ( sel.nrow() < 1 ) { |
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439 | throw(AipsError("No closest in time found... This could be a rounding " |
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440 | "issue. Try quotient instead.")); |
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441 | } |
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442 | TableRow offrow(sel); |
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443 | const TableRecord& offrec = offrow.get(0);//should only be one row |
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444 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
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445 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
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446 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
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447 | /// @fixme this assumes tsys is a scalar not vector |
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448 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
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449 | Vector<Float> specon, tsyson; |
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450 | outtsysCol.get(i, tsyson); |
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451 | outspecCol.get(i, specon); |
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452 | Vector<uChar> flagon; |
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453 | outflagCol.get(i, flagon); |
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454 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
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455 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
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456 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
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457 | if (preserve) { |
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458 | quot -= tsysoffscalar; |
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459 | } else { |
---|
460 | quot -= tsyson[0]; |
---|
461 | } |
---|
462 | outspecCol.put(i, quot.getArray()); |
---|
463 | outflagCol.put(i, flagsFromMA(quot)); |
---|
464 | } |
---|
465 | // renumber scanno |
---|
466 | TableIterator it(tout, "SCANNO"); |
---|
467 | uInt i = 0; |
---|
468 | while ( !it.pastEnd() ) { |
---|
469 | Table t = it.table(); |
---|
470 | TableVector<uInt> vec(t, "SCANNO"); |
---|
471 | vec = i; |
---|
472 | ++i; |
---|
473 | ++it; |
---|
474 | } |
---|
475 | return out; |
---|
476 | } |
---|
477 | |
---|
478 | |
---|
479 | CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on, |
---|
480 | const CountedPtr< Scantable > & off, |
---|
481 | bool preserve ) |
---|
482 | { |
---|
483 | bool insitu = insitu_; |
---|
484 | if ( ! on->conformant(*off) ) { |
---|
485 | throw(AipsError("'on' and 'off' scantables are not conformant.")); |
---|
486 | } |
---|
487 | setInsitu(false); |
---|
488 | CountedPtr< Scantable > out = getScantable(on, false); |
---|
489 | setInsitu(insitu); |
---|
490 | Table& tout = out->table(); |
---|
491 | const Table& toff = off->table(); |
---|
492 | TableIterator sit(tout, "SCANNO"); |
---|
493 | TableIterator s2it(toff, "SCANNO"); |
---|
494 | while ( !sit.pastEnd() ) { |
---|
495 | Table ton = sit.table(); |
---|
496 | TableRow row(ton); |
---|
497 | Table t = s2it.table(); |
---|
498 | ArrayColumn<Float> outspecCol(ton, "SPECTRA"); |
---|
499 | ROArrayColumn<Float> outtsysCol(ton, "TSYS"); |
---|
500 | ArrayColumn<uChar> outflagCol(ton, "FLAGTRA"); |
---|
501 | for (uInt i=0; i < ton.nrow(); ++i) { |
---|
502 | const TableRecord& rec = row.get(i); |
---|
503 | Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
504 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
505 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
---|
506 | if ( offsel.nrow() == 0 ) |
---|
507 | throw AipsError("STMath::quotient: no matching off"); |
---|
508 | TableRow offrow(offsel); |
---|
509 | const TableRecord& offrec = offrow.get(0);//should be ncycles - take first |
---|
510 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
---|
511 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
---|
512 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
---|
513 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
---|
514 | Vector<Float> specon, tsyson; |
---|
515 | outtsysCol.get(i, tsyson); |
---|
516 | outspecCol.get(i, specon); |
---|
517 | Vector<uChar> flagon; |
---|
518 | outflagCol.get(i, flagon); |
---|
519 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
---|
520 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
---|
521 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
---|
522 | if (preserve) { |
---|
523 | quot -= tsysoffscalar; |
---|
524 | } else { |
---|
525 | quot -= tsyson[0]; |
---|
526 | } |
---|
527 | outspecCol.put(i, quot.getArray()); |
---|
528 | outflagCol.put(i, flagsFromMA(quot)); |
---|
529 | } |
---|
530 | ++sit; |
---|
531 | ++s2it; |
---|
532 | // take the first off for each on scan which doesn't have a |
---|
533 | // matching off scan |
---|
534 | // non <= noff: matching pairs, non > noff matching pairs then first off |
---|
535 | if ( s2it.pastEnd() ) s2it.reset(); |
---|
536 | } |
---|
537 | return out; |
---|
538 | } |
---|
539 | |
---|
540 | // dototalpower (migration of GBTIDL procedure dototalpower.pro) |
---|
541 | // calibrate the CAL on-off pair. It calculate Tsys and average CAL on-off subintegrations |
---|
542 | // do it for each cycles in a specific scan. |
---|
543 | CountedPtr< Scantable > STMath::dototalpower( const CountedPtr< Scantable >& calon, |
---|
544 | const CountedPtr< Scantable >& caloff, Float tcal ) |
---|
545 | { |
---|
546 | if ( ! calon->conformant(*caloff) ) { |
---|
547 | throw(AipsError("'CAL on' and 'CAL off' scantables are not conformant.")); |
---|
548 | } |
---|
549 | setInsitu(false); |
---|
550 | CountedPtr< Scantable > out = getScantable(caloff, false); |
---|
551 | Table& tout = out->table(); |
---|
552 | const Table& tcon = calon->table(); |
---|
553 | Vector<Float> tcalout; |
---|
554 | Vector<Float> tcalout2; //debug |
---|
555 | |
---|
556 | if ( tout.nrow() != tcon.nrow() ) { |
---|
557 | throw(AipsError("Mismatch in number of rows to form cal on - off pair.")); |
---|
558 | } |
---|
559 | // iteration by scanno or cycle no. |
---|
560 | TableIterator sit(tout, "SCANNO"); |
---|
561 | TableIterator s2it(tcon, "SCANNO"); |
---|
562 | while ( !sit.pastEnd() ) { |
---|
563 | Table toff = sit.table(); |
---|
564 | TableRow row(toff); |
---|
565 | Table t = s2it.table(); |
---|
566 | ScalarColumn<Double> outintCol(toff, "INTERVAL"); |
---|
567 | ArrayColumn<Float> outspecCol(toff, "SPECTRA"); |
---|
568 | ArrayColumn<Float> outtsysCol(toff, "TSYS"); |
---|
569 | ArrayColumn<uChar> outflagCol(toff, "FLAGTRA"); |
---|
570 | ROScalarColumn<uInt> outtcalIdCol(toff, "TCAL_ID"); |
---|
571 | ROScalarColumn<uInt> outpolCol(toff, "POLNO"); |
---|
572 | ROScalarColumn<Double> onintCol(t, "INTERVAL"); |
---|
573 | ROArrayColumn<Float> onspecCol(t, "SPECTRA"); |
---|
574 | ROArrayColumn<Float> ontsysCol(t, "TSYS"); |
---|
575 | ROArrayColumn<uChar> onflagCol(t, "FLAGTRA"); |
---|
576 | //ROScalarColumn<uInt> ontcalIdCol(t, "TCAL_ID"); |
---|
577 | |
---|
578 | for (uInt i=0; i < toff.nrow(); ++i) { |
---|
579 | //skip these checks -> assumes the data order are the same between the cal on off pairs |
---|
580 | // |
---|
581 | Vector<Float> specCalon, specCaloff; |
---|
582 | // to store scalar (mean) tsys |
---|
583 | Vector<Float> tsysout(1); |
---|
584 | uInt tcalId, polno; |
---|
585 | Double offint, onint; |
---|
586 | outpolCol.get(i, polno); |
---|
587 | outspecCol.get(i, specCaloff); |
---|
588 | onspecCol.get(i, specCalon); |
---|
589 | Vector<uChar> flagCaloff, flagCalon; |
---|
590 | outflagCol.get(i, flagCaloff); |
---|
591 | onflagCol.get(i, flagCalon); |
---|
592 | outtcalIdCol.get(i, tcalId); |
---|
593 | outintCol.get(i, offint); |
---|
594 | onintCol.get(i, onint); |
---|
595 | // caluculate mean Tsys |
---|
596 | uInt nchan = specCaloff.nelements(); |
---|
597 | // percentage of edge cut off |
---|
598 | uInt pc = 10; |
---|
599 | uInt bchan = nchan/pc; |
---|
600 | uInt echan = nchan-bchan; |
---|
601 | |
---|
602 | Slicer chansl(IPosition(1,bchan-1), IPosition(1,echan-1), IPosition(1,1),Slicer::endIsLast); |
---|
603 | Vector<Float> testsubsp = specCaloff(chansl); |
---|
604 | MaskedArray<Float> spoff = maskedArray( specCaloff(chansl),flagCaloff(chansl) ); |
---|
605 | MaskedArray<Float> spon = maskedArray( specCalon(chansl),flagCalon(chansl) ); |
---|
606 | MaskedArray<Float> spdiff = spon-spoff; |
---|
607 | uInt noff = spoff.nelementsValid(); |
---|
608 | //uInt non = spon.nelementsValid(); |
---|
609 | uInt ndiff = spdiff.nelementsValid(); |
---|
610 | Float meantsys; |
---|
611 | |
---|
612 | /** |
---|
613 | Double subspec, subdiff; |
---|
614 | uInt usednchan; |
---|
615 | subspec = 0; |
---|
616 | subdiff = 0; |
---|
617 | usednchan = 0; |
---|
618 | for(uInt k=(bchan-1); k<echan; k++) { |
---|
619 | subspec += specCaloff[k]; |
---|
620 | subdiff += static_cast<Double>(specCalon[k]-specCaloff[k]); |
---|
621 | ++usednchan; |
---|
622 | } |
---|
623 | **/ |
---|
624 | // get tcal if input tcal <= 0 |
---|
625 | String tcalt; |
---|
626 | Float tcalUsed; |
---|
627 | tcalUsed = tcal; |
---|
628 | if ( tcal <= 0.0 ) { |
---|
629 | caloff->tcal().getEntry(tcalt, tcalout, tcalId); |
---|
630 | if (polno<=3) { |
---|
631 | tcalUsed = tcalout[polno]; |
---|
632 | } |
---|
633 | else { |
---|
634 | tcalUsed = tcalout[0]; |
---|
635 | } |
---|
636 | } |
---|
637 | |
---|
638 | Float meanoff; |
---|
639 | Float meandiff; |
---|
640 | if (noff && ndiff) { |
---|
641 | //Debug |
---|
642 | //if(noff!=ndiff) cerr<<"noff and ndiff is not equal"<<endl; |
---|
643 | meanoff = sum(spoff)/noff; |
---|
644 | meandiff = sum(spdiff)/ndiff; |
---|
645 | meantsys= (meanoff/meandiff )*tcalUsed + tcalUsed/2; |
---|
646 | } |
---|
647 | else { |
---|
648 | meantsys=1; |
---|
649 | } |
---|
650 | |
---|
651 | tsysout[0] = Float(meantsys); |
---|
652 | MaskedArray<Float> mcaloff = maskedArray(specCaloff, flagCaloff); |
---|
653 | MaskedArray<Float> mcalon = maskedArray(specCalon, flagCalon); |
---|
654 | MaskedArray<Float> sig = Float(0.5) * (mcaloff + mcalon); |
---|
655 | //uInt ncaloff = mcaloff.nelementsValid(); |
---|
656 | //uInt ncalon = mcalon.nelementsValid(); |
---|
657 | |
---|
658 | outintCol.put(i, offint+onint); |
---|
659 | outspecCol.put(i, sig.getArray()); |
---|
660 | outflagCol.put(i, flagsFromMA(sig)); |
---|
661 | outtsysCol.put(i, tsysout); |
---|
662 | } |
---|
663 | ++sit; |
---|
664 | ++s2it; |
---|
665 | } |
---|
666 | return out; |
---|
667 | } |
---|
668 | |
---|
669 | //dosigref - migrated from GBT IDL's dosigref.pro, do calibration of position switch |
---|
670 | // observatiions. |
---|
671 | // input: sig and ref scantables, and an optional boxcar smoothing width(default width=0, |
---|
672 | // no smoothing). |
---|
673 | // output: resultant scantable [= (sig-ref/ref)*tsys] |
---|
674 | CountedPtr< Scantable > STMath::dosigref( const CountedPtr < Scantable >& sig, |
---|
675 | const CountedPtr < Scantable >& ref, |
---|
676 | int smoothref, |
---|
677 | casa::Float tsysv, |
---|
678 | casa::Float tau ) |
---|
679 | { |
---|
680 | if ( ! ref->conformant(*sig) ) { |
---|
681 | throw(AipsError("'sig' and 'ref' scantables are not conformant.")); |
---|
682 | } |
---|
683 | setInsitu(false); |
---|
684 | CountedPtr< Scantable > out = getScantable(sig, false); |
---|
685 | CountedPtr< Scantable > smref; |
---|
686 | if ( smoothref > 1 ) { |
---|
687 | float fsmoothref = static_cast<float>(smoothref); |
---|
688 | std::string inkernel = "boxcar"; |
---|
689 | smref = smooth(ref, inkernel, fsmoothref ); |
---|
690 | ostringstream oss; |
---|
691 | oss<<"Applied smoothing of "<<fsmoothref<<" on the reference."<<endl; |
---|
692 | pushLog(String(oss)); |
---|
693 | } |
---|
694 | else { |
---|
695 | smref = ref; |
---|
696 | } |
---|
697 | Table& tout = out->table(); |
---|
698 | const Table& tref = smref->table(); |
---|
699 | if ( tout.nrow() != tref.nrow() ) { |
---|
700 | throw(AipsError("Mismatch in number of rows to form on-source and reference pair.")); |
---|
701 | } |
---|
702 | // iteration by scanno? or cycle no. |
---|
703 | TableIterator sit(tout, "SCANNO"); |
---|
704 | TableIterator s2it(tref, "SCANNO"); |
---|
705 | while ( !sit.pastEnd() ) { |
---|
706 | Table ton = sit.table(); |
---|
707 | Table t = s2it.table(); |
---|
708 | ScalarColumn<Double> outintCol(ton, "INTERVAL"); |
---|
709 | ArrayColumn<Float> outspecCol(ton, "SPECTRA"); |
---|
710 | ArrayColumn<Float> outtsysCol(ton, "TSYS"); |
---|
711 | ArrayColumn<uChar> outflagCol(ton, "FLAGTRA"); |
---|
712 | ArrayColumn<Float> refspecCol(t, "SPECTRA"); |
---|
713 | ROScalarColumn<Double> refintCol(t, "INTERVAL"); |
---|
714 | ROArrayColumn<Float> reftsysCol(t, "TSYS"); |
---|
715 | ArrayColumn<uChar> refflagCol(t, "FLAGTRA"); |
---|
716 | ROScalarColumn<Float> refelevCol(t, "ELEVATION"); |
---|
717 | for (uInt i=0; i < ton.nrow(); ++i) { |
---|
718 | |
---|
719 | Double onint, refint; |
---|
720 | Vector<Float> specon, specref; |
---|
721 | // to store scalar (mean) tsys |
---|
722 | Vector<Float> tsysref; |
---|
723 | outintCol.get(i, onint); |
---|
724 | refintCol.get(i, refint); |
---|
725 | outspecCol.get(i, specon); |
---|
726 | refspecCol.get(i, specref); |
---|
727 | Vector<uChar> flagref, flagon; |
---|
728 | outflagCol.get(i, flagon); |
---|
729 | refflagCol.get(i, flagref); |
---|
730 | reftsysCol.get(i, tsysref); |
---|
731 | |
---|
732 | Float tsysrefscalar; |
---|
733 | if ( tsysv > 0.0 ) { |
---|
734 | ostringstream oss; |
---|
735 | Float elev; |
---|
736 | refelevCol.get(i, elev); |
---|
737 | oss << "user specified Tsys = " << tsysv; |
---|
738 | // do recalc elevation if EL = 0 |
---|
739 | if ( elev == 0 ) { |
---|
740 | throw(AipsError("EL=0, elevation data is missing.")); |
---|
741 | } else { |
---|
742 | if ( tau <= 0.0 ) { |
---|
743 | throw(AipsError("Valid tau is not supplied.")); |
---|
744 | } else { |
---|
745 | tsysrefscalar = tsysv * exp(tau/elev); |
---|
746 | } |
---|
747 | } |
---|
748 | oss << ", corrected (for El) tsys= "<<tsysrefscalar; |
---|
749 | pushLog(String(oss)); |
---|
750 | } |
---|
751 | else { |
---|
752 | tsysrefscalar = tsysref[0]; |
---|
753 | } |
---|
754 | //get quotient spectrum |
---|
755 | MaskedArray<Float> mref = maskedArray(specref, flagref); |
---|
756 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
---|
757 | MaskedArray<Float> specres = tsysrefscalar*((mon - mref)/mref); |
---|
758 | Double resint = onint*refint*smoothref/(onint+refint*smoothref); |
---|
759 | |
---|
760 | //Debug |
---|
761 | //cerr<<"Tsys used="<<tsysrefscalar<<endl; |
---|
762 | // fill the result, replay signal tsys by reference tsys |
---|
763 | outintCol.put(i, resint); |
---|
764 | outspecCol.put(i, specres.getArray()); |
---|
765 | outflagCol.put(i, flagsFromMA(specres)); |
---|
766 | outtsysCol.put(i, tsysref); |
---|
767 | } |
---|
768 | ++sit; |
---|
769 | ++s2it; |
---|
770 | } |
---|
771 | return out; |
---|
772 | } |
---|
773 | |
---|
774 | CountedPtr< Scantable > STMath::donod(const casa::CountedPtr<Scantable>& s, |
---|
775 | const std::vector<int>& scans, |
---|
776 | int smoothref, |
---|
777 | casa::Float tsysv, |
---|
778 | casa::Float tau, |
---|
779 | casa::Float tcal ) |
---|
780 | |
---|
781 | { |
---|
782 | setInsitu(false); |
---|
783 | STSelector sel; |
---|
784 | std::vector<int> scan1, scan2, beams; |
---|
785 | std::vector< vector<int> > scanpair; |
---|
786 | std::vector<string> calstate; |
---|
787 | String msg; |
---|
788 | |
---|
789 | CountedPtr< Scantable > s1b1on, s1b1off, s1b2on, s1b2off; |
---|
790 | CountedPtr< Scantable > s2b1on, s2b1off, s2b2on, s2b2off; |
---|
791 | |
---|
792 | std::vector< CountedPtr< Scantable > > sctables; |
---|
793 | sctables.push_back(s1b1on); |
---|
794 | sctables.push_back(s1b1off); |
---|
795 | sctables.push_back(s1b2on); |
---|
796 | sctables.push_back(s1b2off); |
---|
797 | sctables.push_back(s2b1on); |
---|
798 | sctables.push_back(s2b1off); |
---|
799 | sctables.push_back(s2b2on); |
---|
800 | sctables.push_back(s2b2off); |
---|
801 | |
---|
802 | //check scanlist |
---|
803 | int n=s->checkScanInfo(scans); |
---|
804 | if (n==1) { |
---|
805 | throw(AipsError("Incorrect scan pairs. ")); |
---|
806 | } |
---|
807 | |
---|
808 | // Assume scans contain only a pair of consecutive scan numbers. |
---|
809 | // It is assumed that first beam, b1, is on target. |
---|
810 | // There is no check if the first beam is on or not. |
---|
811 | if ( scans.size()==1 ) { |
---|
812 | scan1.push_back(scans[0]); |
---|
813 | scan2.push_back(scans[0]+1); |
---|
814 | } else if ( scans.size()==2 ) { |
---|
815 | scan1.push_back(scans[0]); |
---|
816 | scan2.push_back(scans[1]); |
---|
817 | } else { |
---|
818 | if ( scans.size()%2 == 0 ) { |
---|
819 | for (uInt i=0; i<scans.size(); i++) { |
---|
820 | if (i%2 == 0) { |
---|
821 | scan1.push_back(scans[i]); |
---|
822 | } |
---|
823 | else { |
---|
824 | scan2.push_back(scans[i]); |
---|
825 | } |
---|
826 | } |
---|
827 | } else { |
---|
828 | throw(AipsError("Odd numbers of scans, cannot form pairs.")); |
---|
829 | } |
---|
830 | } |
---|
831 | scanpair.push_back(scan1); |
---|
832 | scanpair.push_back(scan2); |
---|
833 | calstate.push_back("*calon"); |
---|
834 | calstate.push_back("*[^calon]"); |
---|
835 | CountedPtr< Scantable > ws = getScantable(s, false); |
---|
836 | uInt l=0; |
---|
837 | while ( l < sctables.size() ) { |
---|
838 | for (uInt i=0; i < 2; i++) { |
---|
839 | for (uInt j=0; j < 2; j++) { |
---|
840 | for (uInt k=0; k < 2; k++) { |
---|
841 | sel.reset(); |
---|
842 | sel.setScans(scanpair[i]); |
---|
843 | sel.setName(calstate[k]); |
---|
844 | beams.clear(); |
---|
845 | beams.push_back(j); |
---|
846 | sel.setBeams(beams); |
---|
847 | ws->setSelection(sel); |
---|
848 | sctables[l]= getScantable(ws, false); |
---|
849 | l++; |
---|
850 | } |
---|
851 | } |
---|
852 | } |
---|
853 | } |
---|
854 | |
---|
855 | // replace here by splitData or getData functionality |
---|
856 | CountedPtr< Scantable > sig1; |
---|
857 | CountedPtr< Scantable > ref1; |
---|
858 | CountedPtr< Scantable > sig2; |
---|
859 | CountedPtr< Scantable > ref2; |
---|
860 | CountedPtr< Scantable > calb1; |
---|
861 | CountedPtr< Scantable > calb2; |
---|
862 | |
---|
863 | msg=String("Processing dototalpower for subset of the data"); |
---|
864 | ostringstream oss1; |
---|
865 | oss1 << msg << endl; |
---|
866 | pushLog(String(oss1)); |
---|
867 | // Debug for IRC CS data |
---|
868 | //float tcal1=7.0; |
---|
869 | //float tcal2=4.0; |
---|
870 | sig1 = dototalpower(sctables[0], sctables[1], tcal=tcal); |
---|
871 | ref1 = dototalpower(sctables[2], sctables[3], tcal=tcal); |
---|
872 | ref2 = dototalpower(sctables[4], sctables[5], tcal=tcal); |
---|
873 | sig2 = dototalpower(sctables[6], sctables[7], tcal=tcal); |
---|
874 | |
---|
875 | // correction of user-specified tsys for elevation here |
---|
876 | |
---|
877 | // dosigref calibration |
---|
878 | msg=String("Processing dosigref for subset of the data"); |
---|
879 | ostringstream oss2; |
---|
880 | oss2 << msg << endl; |
---|
881 | pushLog(String(oss2)); |
---|
882 | calb1=dosigref(sig1,ref2,smoothref,tsysv,tau); |
---|
883 | calb2=dosigref(sig2,ref1,smoothref,tsysv,tau); |
---|
884 | |
---|
885 | // iteration by scanno or cycle no. |
---|
886 | Table& tcalb1 = calb1->table(); |
---|
887 | Table& tcalb2 = calb2->table(); |
---|
888 | TableIterator sit(tcalb1, "SCANNO"); |
---|
889 | TableIterator s2it(tcalb2, "SCANNO"); |
---|
890 | while ( !sit.pastEnd() ) { |
---|
891 | Table t1 = sit.table(); |
---|
892 | Table t2= s2it.table(); |
---|
893 | ArrayColumn<Float> outspecCol(t1, "SPECTRA"); |
---|
894 | ArrayColumn<Float> outtsysCol(t1, "TSYS"); |
---|
895 | ArrayColumn<uChar> outflagCol(t1, "FLAGTRA"); |
---|
896 | ScalarColumn<Double> outintCol(t1, "INTERVAL"); |
---|
897 | ArrayColumn<Float> t2specCol(t2, "SPECTRA"); |
---|
898 | ROArrayColumn<Float> t2tsysCol(t2, "TSYS"); |
---|
899 | ArrayColumn<uChar> t2flagCol(t2, "FLAGTRA"); |
---|
900 | ROScalarColumn<Double> t2intCol(t2, "INTERVAL"); |
---|
901 | for (uInt i=0; i < t1.nrow(); ++i) { |
---|
902 | Vector<Float> spec1, spec2; |
---|
903 | // to store scalar (mean) tsys |
---|
904 | Vector<Float> tsys1, tsys2; |
---|
905 | Vector<uChar> flag1, flag2; |
---|
906 | Double tint1, tint2; |
---|
907 | outspecCol.get(i, spec1); |
---|
908 | t2specCol.get(i, spec2); |
---|
909 | outflagCol.get(i, flag1); |
---|
910 | t2flagCol.get(i, flag2); |
---|
911 | outtsysCol.get(i, tsys1); |
---|
912 | t2tsysCol.get(i, tsys2); |
---|
913 | outintCol.get(i, tint1); |
---|
914 | t2intCol.get(i, tint2); |
---|
915 | // average |
---|
916 | // assume scalar tsys for weights |
---|
917 | Float wt1, wt2, tsyssq1, tsyssq2; |
---|
918 | tsyssq1 = tsys1[0]*tsys1[0]; |
---|
919 | tsyssq2 = tsys2[0]*tsys2[0]; |
---|
920 | wt1 = Float(tint1)/tsyssq1; |
---|
921 | wt2 = Float(tint2)/tsyssq2; |
---|
922 | Float invsumwt=1/(wt1+wt2); |
---|
923 | MaskedArray<Float> mspec1 = maskedArray(spec1, flag1); |
---|
924 | MaskedArray<Float> mspec2 = maskedArray(spec2, flag2); |
---|
925 | MaskedArray<Float> avspec = invsumwt * (wt1*mspec1 + wt2*mspec2); |
---|
926 | //Array<Float> avtsys = Float(0.5) * (tsys1 + tsys2); |
---|
927 | // cerr<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<endl; |
---|
928 | tsys1[0] = sqrt(tsyssq1 + tsyssq2); |
---|
929 | Array<Float> avtsys = tsys1; |
---|
930 | |
---|
931 | outspecCol.put(i, avspec.getArray()); |
---|
932 | outflagCol.put(i, flagsFromMA(avspec)); |
---|
933 | outtsysCol.put(i, avtsys); |
---|
934 | } |
---|
935 | ++sit; |
---|
936 | ++s2it; |
---|
937 | } |
---|
938 | return calb1; |
---|
939 | } |
---|
940 | |
---|
941 | //GBTIDL version of frequency switched data calibration |
---|
942 | CountedPtr< Scantable > STMath::dofs( const CountedPtr< Scantable >& s, |
---|
943 | const std::vector<int>& scans, |
---|
944 | int smoothref, |
---|
945 | casa::Float tsysv, |
---|
946 | casa::Float tau, |
---|
947 | casa::Float tcal ) |
---|
948 | { |
---|
949 | |
---|
950 | |
---|
951 | STSelector sel; |
---|
952 | CountedPtr< Scantable > ws = getScantable(s, false); |
---|
953 | CountedPtr< Scantable > sig, sigwcal, ref, refwcal; |
---|
954 | CountedPtr< Scantable > calsig, calref, out; |
---|
955 | |
---|
956 | //split the data |
---|
957 | sel.setName("*_fs"); |
---|
958 | ws->setSelection(sel); |
---|
959 | sig = getScantable(ws,false); |
---|
960 | sel.reset(); |
---|
961 | sel.setName("*_fs_calon"); |
---|
962 | ws->setSelection(sel); |
---|
963 | sigwcal = getScantable(ws,false); |
---|
964 | sel.reset(); |
---|
965 | sel.setName("*_fsr"); |
---|
966 | ws->setSelection(sel); |
---|
967 | ref = getScantable(ws,false); |
---|
968 | sel.reset(); |
---|
969 | sel.setName("*_fsr_calon"); |
---|
970 | ws->setSelection(sel); |
---|
971 | refwcal = getScantable(ws,false); |
---|
972 | |
---|
973 | calsig = dototalpower(sigwcal, sig, tcal=tcal); |
---|
974 | calref = dototalpower(refwcal, ref, tcal=tcal); |
---|
975 | |
---|
976 | out=dosigref(calsig,calref,smoothref,tsysv,tau); |
---|
977 | |
---|
978 | return out; |
---|
979 | } |
---|
980 | |
---|
981 | |
---|
982 | CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in ) |
---|
983 | { |
---|
984 | // make copy or reference |
---|
985 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
986 | Table& tout = out->table(); |
---|
987 | Block<String> cols(4); |
---|
988 | cols[0] = String("SCANNO"); |
---|
989 | cols[1] = String("CYCLENO"); |
---|
990 | cols[2] = String("BEAMNO"); |
---|
991 | cols[3] = String("POLNO"); |
---|
992 | TableIterator iter(tout, cols); |
---|
993 | while (!iter.pastEnd()) { |
---|
994 | Table subt = iter.table(); |
---|
995 | // this should leave us with two rows for the two IFs....if not ignore |
---|
996 | if (subt.nrow() != 2 ) { |
---|
997 | continue; |
---|
998 | } |
---|
999 | ArrayColumn<Float> specCol(subt, "SPECTRA"); |
---|
1000 | ArrayColumn<Float> tsysCol(subt, "TSYS"); |
---|
1001 | ArrayColumn<uChar> flagCol(subt, "FLAGTRA"); |
---|
1002 | Vector<Float> onspec,offspec, ontsys, offtsys; |
---|
1003 | Vector<uChar> onflag, offflag; |
---|
1004 | tsysCol.get(0, ontsys); tsysCol.get(1, offtsys); |
---|
1005 | specCol.get(0, onspec); specCol.get(1, offspec); |
---|
1006 | flagCol.get(0, onflag); flagCol.get(1, offflag); |
---|
1007 | MaskedArray<Float> on = maskedArray(onspec, onflag); |
---|
1008 | MaskedArray<Float> off = maskedArray(offspec, offflag); |
---|
1009 | MaskedArray<Float> oncopy = on.copy(); |
---|
1010 | |
---|
1011 | on /= off; on -= 1.0f; |
---|
1012 | on *= ontsys[0]; |
---|
1013 | off /= oncopy; off -= 1.0f; |
---|
1014 | off *= offtsys[0]; |
---|
1015 | specCol.put(0, on.getArray()); |
---|
1016 | const Vector<Bool>& m0 = on.getMask(); |
---|
1017 | Vector<uChar> flags0(m0.shape()); |
---|
1018 | convertArray(flags0, !m0); |
---|
1019 | flagCol.put(0, flags0); |
---|
1020 | |
---|
1021 | specCol.put(1, off.getArray()); |
---|
1022 | const Vector<Bool>& m1 = off.getMask(); |
---|
1023 | Vector<uChar> flags1(m1.shape()); |
---|
1024 | convertArray(flags1, !m1); |
---|
1025 | flagCol.put(1, flags1); |
---|
1026 | ++iter; |
---|
1027 | } |
---|
1028 | |
---|
1029 | return out; |
---|
1030 | } |
---|
1031 | |
---|
1032 | std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in, |
---|
1033 | const std::vector< bool > & mask, |
---|
1034 | const std::string& which ) |
---|
1035 | { |
---|
1036 | |
---|
1037 | Vector<Bool> m(mask); |
---|
1038 | const Table& tab = in->table(); |
---|
1039 | ROArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1040 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1041 | std::vector<float> out; |
---|
1042 | for (uInt i=0; i < tab.nrow(); ++i ) { |
---|
1043 | Vector<Float> spec; specCol.get(i, spec); |
---|
1044 | Vector<uChar> flag; flagCol.get(i, flag); |
---|
1045 | MaskedArray<Float> ma = maskedArray(spec, flag); |
---|
1046 | float outstat = 0.0; |
---|
1047 | if ( spec.nelements() == m.nelements() ) { |
---|
1048 | outstat = mathutil::statistics(which, ma(m)); |
---|
1049 | } else { |
---|
1050 | outstat = mathutil::statistics(which, ma); |
---|
1051 | } |
---|
1052 | out.push_back(outstat); |
---|
1053 | } |
---|
1054 | return out; |
---|
1055 | } |
---|
1056 | |
---|
1057 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in, |
---|
1058 | int width ) |
---|
1059 | { |
---|
1060 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data.")); |
---|
1061 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1062 | Table& tout = out->table(); |
---|
1063 | out->frequencies().rescale(width, "BIN"); |
---|
1064 | ArrayColumn<Float> specCol(tout, "SPECTRA"); |
---|
1065 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA"); |
---|
1066 | for (uInt i=0; i < tout.nrow(); ++i ) { |
---|
1067 | MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i)); |
---|
1068 | MaskedArray<Float> maout; |
---|
1069 | LatticeUtilities::bin(maout, main, 0, Int(width)); |
---|
1070 | /// @todo implement channel based tsys binning |
---|
1071 | specCol.put(i, maout.getArray()); |
---|
1072 | flagCol.put(i, flagsFromMA(maout)); |
---|
1073 | // take only the first binned spectrum's length for the deprecated |
---|
1074 | // global header item nChan |
---|
1075 | if (i==0) tout.rwKeywordSet().define(String("nChan"), |
---|
1076 | Int(maout.getArray().nelements())); |
---|
1077 | } |
---|
1078 | return out; |
---|
1079 | } |
---|
1080 | |
---|
1081 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in, |
---|
1082 | const std::string& method, |
---|
1083 | float width ) |
---|
1084 | // |
---|
1085 | // Should add the possibility of width being specified in km/s. This means |
---|
1086 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
1087 | // average channel width (say at the reference pixel). Then we would need |
---|
1088 | // to be careful to make sure each spectrum (of different freqID) |
---|
1089 | // is the same length. |
---|
1090 | // |
---|
1091 | { |
---|
1092 | //InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
1093 | Int interpMethod(stringToIMethod(method)); |
---|
1094 | |
---|
1095 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1096 | Table& tout = out->table(); |
---|
1097 | |
---|
1098 | // Resample SpectralCoordinates (one per freqID) |
---|
1099 | out->frequencies().rescale(width, "RESAMPLE"); |
---|
1100 | TableIterator iter(tout, "IFNO"); |
---|
1101 | TableRow row(tout); |
---|
1102 | while ( !iter.pastEnd() ) { |
---|
1103 | Table tab = iter.table(); |
---|
1104 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1105 | //ArrayColumn<Float> tsysCol(tout, "TSYS"); |
---|
1106 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1107 | Vector<Float> spec; |
---|
1108 | Vector<uChar> flag; |
---|
1109 | specCol.get(0,spec); // the number of channels should be constant per IF |
---|
1110 | uInt nChanIn = spec.nelements(); |
---|
1111 | Vector<Float> xIn(nChanIn); indgen(xIn); |
---|
1112 | Int fac = Int(nChanIn/width); |
---|
1113 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
1114 | uInt k = 0; |
---|
1115 | Float x = 0.0; |
---|
1116 | while (x < Float(nChanIn) ) { |
---|
1117 | xOut(k) = x; |
---|
1118 | k++; |
---|
1119 | x += width; |
---|
1120 | } |
---|
1121 | uInt nChanOut = k; |
---|
1122 | xOut.resize(nChanOut, True); |
---|
1123 | // process all rows for this IFNO |
---|
1124 | Vector<Float> specOut; |
---|
1125 | Vector<Bool> maskOut; |
---|
1126 | Vector<uChar> flagOut; |
---|
1127 | for (uInt i=0; i < tab.nrow(); ++i) { |
---|
1128 | specCol.get(i, spec); |
---|
1129 | flagCol.get(i, flag); |
---|
1130 | Vector<Bool> mask(flag.nelements()); |
---|
1131 | convertArray(mask, flag); |
---|
1132 | |
---|
1133 | IPosition shapeIn(spec.shape()); |
---|
1134 | //sh.nchan = nChanOut; |
---|
1135 | InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut, |
---|
1136 | xIn, spec, mask, |
---|
1137 | interpMethod, True, True); |
---|
1138 | /// @todo do the same for channel based Tsys |
---|
1139 | flagOut.resize(maskOut.nelements()); |
---|
1140 | convertArray(flagOut, maskOut); |
---|
1141 | specCol.put(i, specOut); |
---|
1142 | flagCol.put(i, flagOut); |
---|
1143 | } |
---|
1144 | ++iter; |
---|
1145 | } |
---|
1146 | |
---|
1147 | return out; |
---|
1148 | } |
---|
1149 | |
---|
1150 | STMath::imethod STMath::stringToIMethod(const std::string& in) |
---|
1151 | { |
---|
1152 | static STMath::imap lookup; |
---|
1153 | |
---|
1154 | // initialize the lookup table if necessary |
---|
1155 | if ( lookup.empty() ) { |
---|
1156 | lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
1157 | lookup["linear"] = InterpolateArray1D<Double,Float>::linear; |
---|
1158 | lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic; |
---|
1159 | lookup["spline"] = InterpolateArray1D<Double,Float>::spline; |
---|
1160 | } |
---|
1161 | |
---|
1162 | STMath::imap::const_iterator iter = lookup.find(in); |
---|
1163 | |
---|
1164 | if ( lookup.end() == iter ) { |
---|
1165 | std::string message = in; |
---|
1166 | message += " is not a valid interpolation mode"; |
---|
1167 | throw(AipsError(message)); |
---|
1168 | } |
---|
1169 | return iter->second; |
---|
1170 | } |
---|
1171 | |
---|
1172 | WeightType STMath::stringToWeight(const std::string& in) |
---|
1173 | { |
---|
1174 | static std::map<std::string, WeightType> lookup; |
---|
1175 | |
---|
1176 | // initialize the lookup table if necessary |
---|
1177 | if ( lookup.empty() ) { |
---|
1178 | lookup["NONE"] = asap::NONE; |
---|
1179 | lookup["TINT"] = asap::TINT; |
---|
1180 | lookup["TINTSYS"] = asap::TINTSYS; |
---|
1181 | lookup["TSYS"] = asap::TSYS; |
---|
1182 | lookup["VAR"] = asap::VAR; |
---|
1183 | } |
---|
1184 | |
---|
1185 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in); |
---|
1186 | |
---|
1187 | if ( lookup.end() == iter ) { |
---|
1188 | std::string message = in; |
---|
1189 | message += " is not a valid weighting mode"; |
---|
1190 | throw(AipsError(message)); |
---|
1191 | } |
---|
1192 | return iter->second; |
---|
1193 | } |
---|
1194 | |
---|
1195 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in, |
---|
1196 | const vector< float > & coeff, |
---|
1197 | const std::string & filename, |
---|
1198 | const std::string& method) |
---|
1199 | { |
---|
1200 | // Get elevation data from Scantable and convert to degrees |
---|
1201 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1202 | Table& tab = out->table(); |
---|
1203 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
1204 | Vector<Float> x = elev.getColumn(); |
---|
1205 | x *= Float(180 / C::pi); // Degrees |
---|
1206 | |
---|
1207 | Vector<Float> coeffs(coeff); |
---|
1208 | const uInt nc = coeffs.nelements(); |
---|
1209 | if ( filename.length() > 0 && nc > 0 ) { |
---|
1210 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
1211 | } |
---|
1212 | |
---|
1213 | // Correct |
---|
1214 | if ( nc > 0 || filename.length() == 0 ) { |
---|
1215 | // Find instrument |
---|
1216 | Bool throwit = True; |
---|
1217 | Instrument inst = |
---|
1218 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
1219 | throwit); |
---|
1220 | |
---|
1221 | // Set polynomial |
---|
1222 | Polynomial<Float>* ppoly = 0; |
---|
1223 | Vector<Float> coeff; |
---|
1224 | String msg; |
---|
1225 | if ( nc > 0 ) { |
---|
1226 | ppoly = new Polynomial<Float>(nc); |
---|
1227 | coeff = coeffs; |
---|
1228 | msg = String("user"); |
---|
1229 | } else { |
---|
1230 | STAttr sdAttr; |
---|
1231 | coeff = sdAttr.gainElevationPoly(inst); |
---|
1232 | ppoly = new Polynomial<Float>(3); |
---|
1233 | msg = String("built in"); |
---|
1234 | } |
---|
1235 | |
---|
1236 | if ( coeff.nelements() > 0 ) { |
---|
1237 | ppoly->setCoefficients(coeff); |
---|
1238 | } else { |
---|
1239 | delete ppoly; |
---|
1240 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
1241 | } |
---|
1242 | ostringstream oss; |
---|
1243 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl; |
---|
1244 | oss << " " << coeff; |
---|
1245 | pushLog(String(oss)); |
---|
1246 | const uInt nrow = tab.nrow(); |
---|
1247 | Vector<Float> factor(nrow); |
---|
1248 | for ( uInt i=0; i < nrow; ++i ) { |
---|
1249 | factor[i] = 1.0 / (*ppoly)(x[i]); |
---|
1250 | } |
---|
1251 | delete ppoly; |
---|
1252 | scaleByVector(tab, factor, true); |
---|
1253 | |
---|
1254 | } else { |
---|
1255 | // Read and correct |
---|
1256 | pushLog("Making correction from ascii Table"); |
---|
1257 | scaleFromAsciiTable(tab, filename, method, x, true); |
---|
1258 | } |
---|
1259 | return out; |
---|
1260 | } |
---|
1261 | |
---|
1262 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename, |
---|
1263 | const std::string& method, |
---|
1264 | const Vector<Float>& xout, bool dotsys) |
---|
1265 | { |
---|
1266 | |
---|
1267 | // Read gain-elevation ascii file data into a Table. |
---|
1268 | |
---|
1269 | String formatString; |
---|
1270 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False); |
---|
1271 | scaleFromTable(in, tbl, method, xout, dotsys); |
---|
1272 | } |
---|
1273 | |
---|
1274 | void STMath::scaleFromTable(Table& in, |
---|
1275 | const Table& table, |
---|
1276 | const std::string& method, |
---|
1277 | const Vector<Float>& xout, bool dotsys) |
---|
1278 | { |
---|
1279 | |
---|
1280 | ROScalarColumn<Float> geElCol(table, "ELEVATION"); |
---|
1281 | ROScalarColumn<Float> geFacCol(table, "FACTOR"); |
---|
1282 | Vector<Float> xin = geElCol.getColumn(); |
---|
1283 | Vector<Float> yin = geFacCol.getColumn(); |
---|
1284 | Vector<Bool> maskin(xin.nelements(),True); |
---|
1285 | |
---|
1286 | // Interpolate (and extrapolate) with desired method |
---|
1287 | |
---|
1288 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method); |
---|
1289 | |
---|
1290 | Vector<Float> yout; |
---|
1291 | Vector<Bool> maskout; |
---|
1292 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout, |
---|
1293 | xin, yin, maskin, interp, |
---|
1294 | True, True); |
---|
1295 | |
---|
1296 | scaleByVector(in, Float(1.0)/yout, dotsys); |
---|
1297 | } |
---|
1298 | |
---|
1299 | void STMath::scaleByVector( Table& in, |
---|
1300 | const Vector< Float >& factor, |
---|
1301 | bool dotsys ) |
---|
1302 | { |
---|
1303 | uInt nrow = in.nrow(); |
---|
1304 | if ( factor.nelements() != nrow ) { |
---|
1305 | throw(AipsError("factors.nelements() != table.nelements()")); |
---|
1306 | } |
---|
1307 | ArrayColumn<Float> specCol(in, "SPECTRA"); |
---|
1308 | ArrayColumn<uChar> flagCol(in, "FLAGTRA"); |
---|
1309 | ArrayColumn<Float> tsysCol(in, "TSYS"); |
---|
1310 | for (uInt i=0; i < nrow; ++i) { |
---|
1311 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
1312 | ma *= factor[i]; |
---|
1313 | specCol.put(i, ma.getArray()); |
---|
1314 | flagCol.put(i, flagsFromMA(ma)); |
---|
1315 | if ( dotsys ) { |
---|
1316 | Vector<Float> tsys = tsysCol(i); |
---|
1317 | tsys *= factor[i]; |
---|
1318 | tsysCol.put(i,tsys); |
---|
1319 | } |
---|
1320 | } |
---|
1321 | } |
---|
1322 | |
---|
1323 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in, |
---|
1324 | float d, float etaap, |
---|
1325 | float jyperk ) |
---|
1326 | { |
---|
1327 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1328 | Table& tab = in->table(); |
---|
1329 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit")); |
---|
1330 | Unit K(String("K")); |
---|
1331 | Unit JY(String("Jy")); |
---|
1332 | |
---|
1333 | bool tokelvin = true; |
---|
1334 | Double cfac = 1.0; |
---|
1335 | |
---|
1336 | if ( fluxUnit == JY ) { |
---|
1337 | pushLog("Converting to K"); |
---|
1338 | Quantum<Double> t(1.0,fluxUnit); |
---|
1339 | Quantum<Double> t2 = t.get(JY); |
---|
1340 | cfac = (t2 / t).getValue(); // value to Jy |
---|
1341 | |
---|
1342 | tokelvin = true; |
---|
1343 | out->setFluxUnit("K"); |
---|
1344 | } else if ( fluxUnit == K ) { |
---|
1345 | pushLog("Converting to Jy"); |
---|
1346 | Quantum<Double> t(1.0,fluxUnit); |
---|
1347 | Quantum<Double> t2 = t.get(K); |
---|
1348 | cfac = (t2 / t).getValue(); // value to K |
---|
1349 | |
---|
1350 | tokelvin = false; |
---|
1351 | out->setFluxUnit("Jy"); |
---|
1352 | } else { |
---|
1353 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
1354 | } |
---|
1355 | // Make sure input values are converted to either Jy or K first... |
---|
1356 | Float factor = cfac; |
---|
1357 | |
---|
1358 | // Select method |
---|
1359 | if (jyperk > 0.0) { |
---|
1360 | factor *= jyperk; |
---|
1361 | if ( tokelvin ) factor = 1.0 / jyperk; |
---|
1362 | ostringstream oss; |
---|
1363 | oss << "Jy/K = " << jyperk; |
---|
1364 | pushLog(String(oss)); |
---|
1365 | Vector<Float> factors(tab.nrow(), factor); |
---|
1366 | scaleByVector(tab,factors, false); |
---|
1367 | } else if ( etaap > 0.0) { |
---|
1368 | if (d < 0) { |
---|
1369 | Instrument inst = |
---|
1370 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
1371 | True); |
---|
1372 | STAttr sda; |
---|
1373 | d = sda.diameter(inst); |
---|
1374 | } |
---|
1375 | jyperk = STAttr::findJyPerK(etaap, d); |
---|
1376 | ostringstream oss; |
---|
1377 | oss << "Jy/K = " << jyperk; |
---|
1378 | pushLog(String(oss)); |
---|
1379 | factor *= jyperk; |
---|
1380 | if ( tokelvin ) { |
---|
1381 | factor = 1.0 / factor; |
---|
1382 | } |
---|
1383 | Vector<Float> factors(tab.nrow(), factor); |
---|
1384 | scaleByVector(tab, factors, False); |
---|
1385 | } else { |
---|
1386 | |
---|
1387 | // OK now we must deal with automatic look up of values. |
---|
1388 | // We must also deal with the fact that the factors need |
---|
1389 | // to be computed per IF and may be different and may |
---|
1390 | // change per integration. |
---|
1391 | |
---|
1392 | pushLog("Looking up conversion factors"); |
---|
1393 | convertBrightnessUnits(out, tokelvin, cfac); |
---|
1394 | } |
---|
1395 | |
---|
1396 | return out; |
---|
1397 | } |
---|
1398 | |
---|
1399 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in, |
---|
1400 | bool tokelvin, float cfac ) |
---|
1401 | { |
---|
1402 | Table& table = in->table(); |
---|
1403 | Instrument inst = |
---|
1404 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True); |
---|
1405 | TableIterator iter(table, "FREQ_ID"); |
---|
1406 | STFrequencies stfreqs = in->frequencies(); |
---|
1407 | STAttr sdAtt; |
---|
1408 | while (!iter.pastEnd()) { |
---|
1409 | Table tab = iter.table(); |
---|
1410 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1411 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1412 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID"); |
---|
1413 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
1414 | |
---|
1415 | uInt freqid; freqidCol.get(0, freqid); |
---|
1416 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
1417 | // STAttr.JyPerK has a Vector interface... change sometime. |
---|
1418 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements())); |
---|
1419 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
1420 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0]; |
---|
1421 | Float factor = cfac * jyperk; |
---|
1422 | if ( tokelvin ) factor = Float(1.0) / factor; |
---|
1423 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
1424 | ma *= factor; |
---|
1425 | specCol.put(i, ma.getArray()); |
---|
1426 | flagCol.put(i, flagsFromMA(ma)); |
---|
1427 | } |
---|
1428 | ++iter; |
---|
1429 | } |
---|
1430 | } |
---|
1431 | |
---|
1432 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in, |
---|
1433 | float tau ) |
---|
1434 | { |
---|
1435 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1436 | |
---|
1437 | Table tab = out->table(); |
---|
1438 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
1439 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1440 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1441 | ArrayColumn<Float> tsysCol(tab, "TSYS"); |
---|
1442 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
1443 | Float zdist = Float(C::pi_2) - elev(i); |
---|
1444 | Float factor = exp(tau/cos(zdist)); |
---|
1445 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
1446 | ma *= factor; |
---|
1447 | specCol.put(i, ma.getArray()); |
---|
1448 | flagCol.put(i, flagsFromMA(ma)); |
---|
1449 | Vector<Float> tsys; |
---|
1450 | tsysCol.get(i, tsys); |
---|
1451 | tsys *= factor; |
---|
1452 | tsysCol.put(i, tsys); |
---|
1453 | } |
---|
1454 | return out; |
---|
1455 | } |
---|
1456 | |
---|
1457 | CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in, |
---|
1458 | const std::string& kernel, |
---|
1459 | float width ) |
---|
1460 | { |
---|
1461 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1462 | Table& table = out->table(); |
---|
1463 | ArrayColumn<Float> specCol(table, "SPECTRA"); |
---|
1464 | ArrayColumn<uChar> flagCol(table, "FLAGTRA"); |
---|
1465 | Vector<Float> spec; |
---|
1466 | Vector<uChar> flag; |
---|
1467 | for ( uInt i=0; i<table.nrow(); ++i) { |
---|
1468 | specCol.get(i, spec); |
---|
1469 | flagCol.get(i, flag); |
---|
1470 | Vector<Bool> mask(flag.nelements()); |
---|
1471 | convertArray(mask, flag); |
---|
1472 | Vector<Float> specout; |
---|
1473 | Vector<Bool> maskout; |
---|
1474 | if ( kernel == "hanning" ) { |
---|
1475 | mathutil::hanning(specout, maskout, spec , !mask); |
---|
1476 | convertArray(flag, !maskout); |
---|
1477 | } else if ( kernel == "rmedian" ) { |
---|
1478 | mathutil::runningMedian(specout, maskout, spec , mask, width); |
---|
1479 | convertArray(flag, maskout); |
---|
1480 | } |
---|
1481 | flagCol.put(i, flag); |
---|
1482 | specCol.put(i, specout); |
---|
1483 | } |
---|
1484 | return out; |
---|
1485 | } |
---|
1486 | |
---|
1487 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in, |
---|
1488 | const std::string& kernel, float width ) |
---|
1489 | { |
---|
1490 | if (kernel == "rmedian" || kernel == "hanning") { |
---|
1491 | return smoothOther(in, kernel, width); |
---|
1492 | } |
---|
1493 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1494 | Table& table = out->table(); |
---|
1495 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel); |
---|
1496 | // same IFNO should have same no of channels |
---|
1497 | // this saves overhead |
---|
1498 | TableIterator iter(table, "IFNO"); |
---|
1499 | while (!iter.pastEnd()) { |
---|
1500 | Table tab = iter.table(); |
---|
1501 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1502 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1503 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
1504 | uInt nchan = tmpspec.nelements(); |
---|
1505 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False); |
---|
1506 | Convolver<Float> conv(kvec, IPosition(1,nchan)); |
---|
1507 | Vector<Float> spec; |
---|
1508 | Vector<uChar> flag; |
---|
1509 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
1510 | specCol.get(i, spec); |
---|
1511 | flagCol.get(i, flag); |
---|
1512 | Vector<Bool> mask(flag.nelements()); |
---|
1513 | convertArray(mask, flag); |
---|
1514 | Vector<Float> specout; |
---|
1515 | mathutil::replaceMaskByZero(specout, mask); |
---|
1516 | conv.linearConv(specout, spec); |
---|
1517 | specCol.put(i, specout); |
---|
1518 | } |
---|
1519 | ++iter; |
---|
1520 | } |
---|
1521 | return out; |
---|
1522 | } |
---|
1523 | |
---|
1524 | CountedPtr< Scantable > |
---|
1525 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in ) |
---|
1526 | { |
---|
1527 | if ( in.size() < 2 ) { |
---|
1528 | throw(AipsError("Need at least two scantables to perform a merge.")); |
---|
1529 | } |
---|
1530 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin(); |
---|
1531 | bool insitu = insitu_; |
---|
1532 | setInsitu(false); |
---|
1533 | CountedPtr< Scantable > out = getScantable(*it, false); |
---|
1534 | setInsitu(insitu); |
---|
1535 | Table& tout = out->table(); |
---|
1536 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID"); |
---|
1537 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID"); |
---|
1538 | // Renumber SCANNO to be 0-based |
---|
1539 | Vector<uInt> scannos = scannocol.getColumn(); |
---|
1540 | uInt offset = min(scannos); |
---|
1541 | scannos -= offset; |
---|
1542 | scannocol.putColumn(scannos); |
---|
1543 | uInt newscanno = max(scannos)+1; |
---|
1544 | ++it; |
---|
1545 | while ( it != in.end() ){ |
---|
1546 | if ( ! (*it)->conformant(*out) ) { |
---|
1547 | // non conformant. |
---|
1548 | pushLog(String("Warning: Can't merge scantables as header info differs.")); |
---|
1549 | } |
---|
1550 | out->appendToHistoryTable((*it)->history()); |
---|
1551 | const Table& tab = (*it)->table(); |
---|
1552 | TableIterator scanit(tab, "SCANNO"); |
---|
1553 | while (!scanit.pastEnd()) { |
---|
1554 | TableIterator freqit(scanit.table(), "FREQ_ID"); |
---|
1555 | while ( !freqit.pastEnd() ) { |
---|
1556 | Table thetab = freqit.table(); |
---|
1557 | uInt nrow = tout.nrow(); |
---|
1558 | tout.addRow(thetab.nrow()); |
---|
1559 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow()); |
---|
1560 | ROTableRow row(thetab); |
---|
1561 | for ( uInt i=0; i<thetab.nrow(); ++i) { |
---|
1562 | uInt k = nrow+i; |
---|
1563 | scannocol.put(k, newscanno); |
---|
1564 | const TableRecord& rec = row.get(i); |
---|
1565 | Double rv,rp,inc; |
---|
1566 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID")); |
---|
1567 | uInt id; |
---|
1568 | id = out->frequencies().addEntry(rp, rv, inc); |
---|
1569 | freqidcol.put(k,id); |
---|
1570 | String name,fname;Double rf; |
---|
1571 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID")); |
---|
1572 | id = out->molecules().addEntry(rf, name, fname); |
---|
1573 | molidcol.put(k, id); |
---|
1574 | Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp; |
---|
1575 | (*it)->focus().getEntry(fax, ftan, frot, fhand, |
---|
1576 | fmount,fuser, fxy, fxyp, |
---|
1577 | rec.asuInt("FOCUS_ID")); |
---|
1578 | id = out->focus().addEntry(fax, ftan, frot, fhand, |
---|
1579 | fmount,fuser, fxy, fxyp); |
---|
1580 | focusidcol.put(k, id); |
---|
1581 | } |
---|
1582 | ++freqit; |
---|
1583 | } |
---|
1584 | ++newscanno; |
---|
1585 | ++scanit; |
---|
1586 | } |
---|
1587 | ++it; |
---|
1588 | } |
---|
1589 | return out; |
---|
1590 | } |
---|
1591 | |
---|
1592 | CountedPtr< Scantable > |
---|
1593 | STMath::invertPhase( const CountedPtr < Scantable >& in ) |
---|
1594 | { |
---|
1595 | return applyToPol(in, &STPol::invertPhase, Float(0.0)); |
---|
1596 | } |
---|
1597 | |
---|
1598 | CountedPtr< Scantable > |
---|
1599 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
1600 | { |
---|
1601 | return applyToPol(in, &STPol::rotatePhase, Float(phase)); |
---|
1602 | } |
---|
1603 | |
---|
1604 | CountedPtr< Scantable > |
---|
1605 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
1606 | { |
---|
1607 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase)); |
---|
1608 | } |
---|
1609 | |
---|
1610 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in, |
---|
1611 | STPol::polOperation fptr, |
---|
1612 | Float phase ) |
---|
1613 | { |
---|
1614 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1615 | Table& tout = out->table(); |
---|
1616 | Block<String> cols(4); |
---|
1617 | cols[0] = String("SCANNO"); |
---|
1618 | cols[1] = String("BEAMNO"); |
---|
1619 | cols[2] = String("IFNO"); |
---|
1620 | cols[3] = String("CYCLENO"); |
---|
1621 | TableIterator iter(tout, cols); |
---|
1622 | CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_, |
---|
1623 | out->getPolType() ); |
---|
1624 | while (!iter.pastEnd()) { |
---|
1625 | Table t = iter.table(); |
---|
1626 | ArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
1627 | ScalarColumn<uInt> focidcol(t, "FOCUS_ID"); |
---|
1628 | ScalarColumn<Float> parancol(t, "PARANGLE"); |
---|
1629 | Matrix<Float> pols(speccol.getColumn()); |
---|
1630 | try { |
---|
1631 | stpol->setSpectra(pols); |
---|
1632 | Float fang,fhand,parang; |
---|
1633 | fang = in->focusTable_.getTotalFeedAngle(focidcol(0)); |
---|
1634 | fhand = in->focusTable_.getFeedHand(focidcol(0)); |
---|
1635 | parang = parancol(0); |
---|
1636 | /// @todo re-enable this |
---|
1637 | // disable total feed angle to support paralactifying Caswell style |
---|
1638 | stpol->setPhaseCorrections(parang, -parang, fhand); |
---|
1639 | // use a member function pointer in STPol. This only works on |
---|
1640 | // the STPol pointer itself, not the Counted Pointer so |
---|
1641 | // derefernce it. |
---|
1642 | (&(*(stpol))->*fptr)(phase); |
---|
1643 | speccol.putColumn(stpol->getSpectra()); |
---|
1644 | } catch (AipsError& e) { |
---|
1645 | //delete stpol;stpol=0; |
---|
1646 | throw(e); |
---|
1647 | } |
---|
1648 | ++iter; |
---|
1649 | } |
---|
1650 | //delete stpol;stpol=0; |
---|
1651 | return out; |
---|
1652 | } |
---|
1653 | |
---|
1654 | CountedPtr< Scantable > |
---|
1655 | STMath::swapPolarisations( const CountedPtr< Scantable > & in ) |
---|
1656 | { |
---|
1657 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1658 | Table& tout = out->table(); |
---|
1659 | Table t0 = tout(tout.col("POLNO") == 0); |
---|
1660 | Table t1 = tout(tout.col("POLNO") == 1); |
---|
1661 | if ( t0.nrow() != t1.nrow() ) |
---|
1662 | throw(AipsError("Inconsistent number of polarisations")); |
---|
1663 | ArrayColumn<Float> speccol0(t0, "SPECTRA"); |
---|
1664 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA"); |
---|
1665 | ArrayColumn<Float> speccol1(t1, "SPECTRA"); |
---|
1666 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA"); |
---|
1667 | Matrix<Float> s0 = speccol0.getColumn(); |
---|
1668 | Matrix<uChar> f0 = flagcol0.getColumn(); |
---|
1669 | speccol0.putColumn(speccol1.getColumn()); |
---|
1670 | flagcol0.putColumn(flagcol1.getColumn()); |
---|
1671 | speccol1.putColumn(s0); |
---|
1672 | flagcol1.putColumn(f0); |
---|
1673 | return out; |
---|
1674 | } |
---|
1675 | |
---|
1676 | CountedPtr< Scantable > |
---|
1677 | STMath::averagePolarisations( const CountedPtr< Scantable > & in, |
---|
1678 | const std::vector<bool>& mask, |
---|
1679 | const std::string& weight ) |
---|
1680 | { |
---|
1681 | if (in->npol() < 2 ) |
---|
1682 | throw(AipsError("averagePolarisations can only be applied to two or more" |
---|
1683 | "polarisations")); |
---|
1684 | bool insitu = insitu_; |
---|
1685 | setInsitu(false); |
---|
1686 | CountedPtr< Scantable > pols = getScantable(in, true); |
---|
1687 | setInsitu(insitu); |
---|
1688 | Table& tout = pols->table(); |
---|
1689 | std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]"; |
---|
1690 | Table tab = tableCommand(taql, in->table()); |
---|
1691 | if (tab.nrow() == 0 ) |
---|
1692 | throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1")); |
---|
1693 | TableCopy::copyRows(tout, tab); |
---|
1694 | TableVector<uInt> vec(tout, "POLNO"); |
---|
1695 | vec = 0; |
---|
1696 | pols->table_.rwKeywordSet().define("nPol", Int(1)); |
---|
1697 | //pols->table_.rwKeywordSet().define("POLTYPE", String("stokes")); |
---|
1698 | pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType()); |
---|
1699 | std::vector<CountedPtr<Scantable> > vpols; |
---|
1700 | vpols.push_back(pols); |
---|
1701 | CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN"); |
---|
1702 | return out; |
---|
1703 | } |
---|
1704 | |
---|
1705 | CountedPtr< Scantable > |
---|
1706 | STMath::averageBeams( const CountedPtr< Scantable > & in, |
---|
1707 | const std::vector<bool>& mask, |
---|
1708 | const std::string& weight ) |
---|
1709 | { |
---|
1710 | bool insitu = insitu_; |
---|
1711 | setInsitu(false); |
---|
1712 | CountedPtr< Scantable > beams = getScantable(in, false); |
---|
1713 | setInsitu(insitu); |
---|
1714 | Table& tout = beams->table(); |
---|
1715 | // give all rows the same BEAMNO |
---|
1716 | TableVector<uInt> vec(tout, "BEAMNO"); |
---|
1717 | vec = 0; |
---|
1718 | beams->table_.rwKeywordSet().define("nBeam", Int(1)); |
---|
1719 | std::vector<CountedPtr<Scantable> > vbeams; |
---|
1720 | vbeams.push_back(beams); |
---|
1721 | CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN"); |
---|
1722 | return out; |
---|
1723 | } |
---|
1724 | |
---|
1725 | |
---|
1726 | CountedPtr< Scantable > |
---|
1727 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in, |
---|
1728 | const std::string & refTime, |
---|
1729 | const std::string & method) |
---|
1730 | { |
---|
1731 | // clone as this is not working insitu |
---|
1732 | bool insitu = insitu_; |
---|
1733 | setInsitu(false); |
---|
1734 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1735 | setInsitu(insitu); |
---|
1736 | Table& tout = out->table(); |
---|
1737 | // Get reference Epoch to time of first row or given String |
---|
1738 | Unit DAY(String("d")); |
---|
1739 | MEpoch::Ref epochRef(in->getTimeReference()); |
---|
1740 | MEpoch refEpoch; |
---|
1741 | if (refTime.length()>0) { |
---|
1742 | Quantum<Double> qt; |
---|
1743 | if (MVTime::read(qt,refTime)) { |
---|
1744 | MVEpoch mv(qt); |
---|
1745 | refEpoch = MEpoch(mv, epochRef); |
---|
1746 | } else { |
---|
1747 | throw(AipsError("Invalid format for Epoch string")); |
---|
1748 | } |
---|
1749 | } else { |
---|
1750 | refEpoch = in->timeCol_(0); |
---|
1751 | } |
---|
1752 | MPosition refPos = in->getAntennaPosition(); |
---|
1753 | |
---|
1754 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method); |
---|
1755 | /* |
---|
1756 | // Comment from MV. |
---|
1757 | // the following code has been commented out because different FREQ_IDs have to be aligned together even |
---|
1758 | // if the frame doesn't change. So far, lack of this check didn't cause any problems. |
---|
1759 | // test if user frame is different to base frame |
---|
1760 | if ( in->frequencies().getFrameString(true) |
---|
1761 | == in->frequencies().getFrameString(false) ) { |
---|
1762 | throw(AipsError("Can't convert as no output frame has been set" |
---|
1763 | " (use set_freqframe) or it is aligned already.")); |
---|
1764 | } |
---|
1765 | */ |
---|
1766 | MFrequency::Types system = in->frequencies().getFrame(); |
---|
1767 | MVTime mvt(refEpoch.getValue()); |
---|
1768 | String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")"); |
---|
1769 | ostringstream oss; |
---|
1770 | oss << "Aligned at reference Epoch " << epochout |
---|
1771 | << " in frame " << MFrequency::showType(system); |
---|
1772 | pushLog(String(oss)); |
---|
1773 | // set up the iterator |
---|
1774 | Block<String> cols(4); |
---|
1775 | // select by constant direction |
---|
1776 | cols[0] = String("SRCNAME"); |
---|
1777 | cols[1] = String("BEAMNO"); |
---|
1778 | // select by IF ( no of channels varies over this ) |
---|
1779 | cols[2] = String("IFNO"); |
---|
1780 | // select by restfrequency |
---|
1781 | cols[3] = String("MOLECULE_ID"); |
---|
1782 | TableIterator iter(tout, cols); |
---|
1783 | while ( !iter.pastEnd() ) { |
---|
1784 | Table t = iter.table(); |
---|
1785 | MDirection::ROScalarColumn dirCol(t, "DIRECTION"); |
---|
1786 | TableIterator fiter(t, "FREQ_ID"); |
---|
1787 | // determine nchan from the first row. This should work as |
---|
1788 | // we are iterating over BEAMNO and IFNO // we should have constant direction |
---|
1789 | |
---|
1790 | ROArrayColumn<Float> sCol(t, "SPECTRA"); |
---|
1791 | const MDirection direction = dirCol(0); |
---|
1792 | const uInt nchan = sCol(0).nelements(); |
---|
1793 | |
---|
1794 | // skip operations if there is nothing to align |
---|
1795 | if (fiter.pastEnd()) { |
---|
1796 | continue; |
---|
1797 | } |
---|
1798 | |
---|
1799 | Table ftab = fiter.table(); |
---|
1800 | // align all frequency ids with respect to the first encountered id |
---|
1801 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID"); |
---|
1802 | // get the SpectralCoordinate for the freqid, which we are iterating over |
---|
1803 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0)); |
---|
1804 | FrequencyAligner<Float> fa( sC, nchan, refEpoch, |
---|
1805 | direction, refPos, system ); |
---|
1806 | // realign the SpectralCoordinate and put into the output Scantable |
---|
1807 | Vector<String> units(1); |
---|
1808 | units = String("Hz"); |
---|
1809 | Bool linear=True; |
---|
1810 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear); |
---|
1811 | sc2.setWorldAxisUnits(units); |
---|
1812 | const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0], |
---|
1813 | sc2.referenceValue()[0], |
---|
1814 | sc2.increment()[0]); |
---|
1815 | while ( !fiter.pastEnd() ) { |
---|
1816 | ftab = fiter.table(); |
---|
1817 | // spectral coordinate for the current FREQ_ID |
---|
1818 | ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID"); |
---|
1819 | sC = in->frequencies().getSpectralCoordinate(freqidCol2(0)); |
---|
1820 | // create the "global" abcissa for alignment with same FREQ_ID |
---|
1821 | Vector<Double> abc(nchan); |
---|
1822 | for (uInt i=0; i<nchan; i++) { |
---|
1823 | Double w; |
---|
1824 | sC.toWorld(w,Double(i)); |
---|
1825 | abc[i] = w; |
---|
1826 | } |
---|
1827 | TableVector<uInt> tvec(ftab, "FREQ_ID"); |
---|
1828 | // assign new frequency id to all rows |
---|
1829 | tvec = id; |
---|
1830 | // cache abcissa for same time stamps, so iterate over those |
---|
1831 | TableIterator timeiter(ftab, "TIME"); |
---|
1832 | while ( !timeiter.pastEnd() ) { |
---|
1833 | Table tab = timeiter.table(); |
---|
1834 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1835 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1836 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
1837 | // use align abcissa cache after the first row |
---|
1838 | // these rows should be just be POLNO |
---|
1839 | bool first = true; |
---|
1840 | for (int i=0; i<int(tab.nrow()); ++i) { |
---|
1841 | // input values |
---|
1842 | Vector<uChar> flag = flagCol(i); |
---|
1843 | Vector<Bool> mask(flag.shape()); |
---|
1844 | Vector<Float> specOut, spec; |
---|
1845 | spec = specCol(i); |
---|
1846 | Vector<Bool> maskOut;Vector<uChar> flagOut; |
---|
1847 | convertArray(mask, flag); |
---|
1848 | // alignment |
---|
1849 | Bool ok = fa.align(specOut, maskOut, abc, spec, |
---|
1850 | mask, timeCol(i), !first, |
---|
1851 | interp, False); |
---|
1852 | // back into scantable |
---|
1853 | flagOut.resize(maskOut.nelements()); |
---|
1854 | convertArray(flagOut, maskOut); |
---|
1855 | flagCol.put(i, flagOut); |
---|
1856 | specCol.put(i, specOut); |
---|
1857 | // start abcissa caching |
---|
1858 | first = false; |
---|
1859 | } |
---|
1860 | // next timestamp |
---|
1861 | ++timeiter; |
---|
1862 | } |
---|
1863 | // next FREQ_ID |
---|
1864 | ++fiter; |
---|
1865 | } |
---|
1866 | // next aligner |
---|
1867 | ++iter; |
---|
1868 | } |
---|
1869 | // set this afterwards to ensure we are doing insitu correctly. |
---|
1870 | out->frequencies().setFrame(system, true); |
---|
1871 | return out; |
---|
1872 | } |
---|
1873 | |
---|
1874 | CountedPtr<Scantable> |
---|
1875 | asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in, |
---|
1876 | const std::string & newtype ) |
---|
1877 | { |
---|
1878 | if (in->npol() != 2 && in->npol() != 4) |
---|
1879 | throw(AipsError("Can only convert two or four polarisations.")); |
---|
1880 | if ( in->getPolType() == newtype ) |
---|
1881 | throw(AipsError("No need to convert.")); |
---|
1882 | if ( ! in->selector_.empty() ) |
---|
1883 | throw(AipsError("Can only convert whole scantable. Unset the selection.")); |
---|
1884 | bool insitu = insitu_; |
---|
1885 | setInsitu(false); |
---|
1886 | CountedPtr< Scantable > out = getScantable(in, true); |
---|
1887 | setInsitu(insitu); |
---|
1888 | Table& tout = out->table(); |
---|
1889 | tout.rwKeywordSet().define("POLTYPE", String(newtype)); |
---|
1890 | |
---|
1891 | Block<String> cols(4); |
---|
1892 | cols[0] = "SCANNO"; |
---|
1893 | cols[1] = "CYCLENO"; |
---|
1894 | cols[2] = "BEAMNO"; |
---|
1895 | cols[3] = "IFNO"; |
---|
1896 | TableIterator it(in->originalTable_, cols); |
---|
1897 | String basetype = in->getPolType(); |
---|
1898 | STPol* stpol = STPol::getPolClass(in->factories_, basetype); |
---|
1899 | try { |
---|
1900 | while ( !it.pastEnd() ) { |
---|
1901 | Table tab = it.table(); |
---|
1902 | uInt row = tab.rowNumbers()[0]; |
---|
1903 | stpol->setSpectra(in->getPolMatrix(row)); |
---|
1904 | Float fang,fhand,parang; |
---|
1905 | fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row)); |
---|
1906 | fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row)); |
---|
1907 | parang = in->paraCol_(row); |
---|
1908 | /// @todo re-enable this |
---|
1909 | // disable total feed angle to support paralactifying Caswell style |
---|
1910 | stpol->setPhaseCorrections(parang, -parang, fhand); |
---|
1911 | Int npolout = 0; |
---|
1912 | for (uInt i=0; i<tab.nrow(); ++i) { |
---|
1913 | Vector<Float> outvec = stpol->getSpectrum(i, newtype); |
---|
1914 | if ( outvec.nelements() > 0 ) { |
---|
1915 | tout.addRow(); |
---|
1916 | TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1); |
---|
1917 | ArrayColumn<Float> sCol(tout,"SPECTRA"); |
---|
1918 | ScalarColumn<uInt> pCol(tout,"POLNO"); |
---|
1919 | sCol.put(tout.nrow()-1 ,outvec); |
---|
1920 | pCol.put(tout.nrow()-1 ,uInt(npolout)); |
---|
1921 | npolout++; |
---|
1922 | } |
---|
1923 | } |
---|
1924 | tout.rwKeywordSet().define("nPol", npolout); |
---|
1925 | ++it; |
---|
1926 | } |
---|
1927 | } catch (AipsError& e) { |
---|
1928 | delete stpol; |
---|
1929 | throw(e); |
---|
1930 | } |
---|
1931 | delete stpol; |
---|
1932 | return out; |
---|
1933 | } |
---|
1934 | |
---|
1935 | CountedPtr< Scantable > |
---|
1936 | asap::STMath::mxExtract( const CountedPtr< Scantable > & in, |
---|
1937 | const std::string & scantype ) |
---|
1938 | { |
---|
1939 | bool insitu = insitu_; |
---|
1940 | setInsitu(false); |
---|
1941 | CountedPtr< Scantable > out = getScantable(in, true); |
---|
1942 | setInsitu(insitu); |
---|
1943 | Table& tout = out->table(); |
---|
1944 | std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO"; |
---|
1945 | if (scantype == "on") { |
---|
1946 | taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO"; |
---|
1947 | } |
---|
1948 | Table tab = tableCommand(taql, in->table()); |
---|
1949 | TableCopy::copyRows(tout, tab); |
---|
1950 | if (scantype == "on") { |
---|
1951 | // re-index SCANNO to 0 |
---|
1952 | TableVector<uInt> vec(tout, "SCANNO"); |
---|
1953 | vec = 0; |
---|
1954 | } |
---|
1955 | return out; |
---|
1956 | } |
---|
1957 | |
---|
1958 | CountedPtr< Scantable > |
---|
1959 | asap::STMath::lagFlag( const CountedPtr< Scantable > & in, |
---|
1960 | double frequency, double width ) |
---|
1961 | { |
---|
1962 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1963 | Table& tout = out->table(); |
---|
1964 | TableIterator iter(tout, "FREQ_ID"); |
---|
1965 | FFTServer<Float,Complex> ffts; |
---|
1966 | while ( !iter.pastEnd() ) { |
---|
1967 | Table tab = iter.table(); |
---|
1968 | Double rp,rv,inc; |
---|
1969 | ROTableRow row(tab); |
---|
1970 | const TableRecord& rec = row.get(0); |
---|
1971 | uInt freqid = rec.asuInt("FREQ_ID"); |
---|
1972 | out->frequencies().getEntry(rp, rv, inc, freqid); |
---|
1973 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1974 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1975 | for (int i=0; i<int(tab.nrow()); ++i) { |
---|
1976 | Vector<Float> spec = specCol(i); |
---|
1977 | Vector<uChar> flag = flagCol(i); |
---|
1978 | Int lag0 = Int(spec.nelements()*abs(inc)/(frequency+width)+0.5); |
---|
1979 | Int lag1 = Int(spec.nelements()*abs(inc)/(frequency-width)+0.5); |
---|
1980 | for (int k=0; k < flag.nelements(); ++k ) { |
---|
1981 | if (flag[k] > 0) { |
---|
1982 | spec[k] = 0.0; |
---|
1983 | } |
---|
1984 | } |
---|
1985 | Vector<Complex> lags; |
---|
1986 | ffts.fft0(lags, spec); |
---|
1987 | Int start = max(0, lag0); |
---|
1988 | Int end = min(Int(lags.nelements()-1), lag1); |
---|
1989 | if (start == end) { |
---|
1990 | lags[start] = Complex(0.0); |
---|
1991 | } else { |
---|
1992 | for (int j=start; j <=end ;++j) { |
---|
1993 | lags[j] = Complex(0.0); |
---|
1994 | } |
---|
1995 | } |
---|
1996 | ffts.fft0(spec, lags); |
---|
1997 | specCol.put(i, spec); |
---|
1998 | } |
---|
1999 | ++iter; |
---|
2000 | } |
---|
2001 | return out; |
---|
2002 | } |
---|