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 <tables/Tables/TableIter.h> |
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18 | #include <tables/Tables/TableCopy.h> |
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19 | #include <casa/Arrays/MaskArrLogi.h> |
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20 | #include <casa/Arrays/MaskArrMath.h> |
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21 | #include <casa/Arrays/ArrayLogical.h> |
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22 | #include <casa/Arrays/ArrayMath.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/ReadAsciiTable.h> |
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30 | |
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31 | #include <lattices/Lattices/LatticeUtilities.h> |
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32 | |
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33 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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34 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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35 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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36 | #include <coordinates/Coordinates/FrequencyAligner.h> |
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37 | |
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38 | #include <scimath/Mathematics/VectorKernel.h> |
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39 | #include <scimath/Mathematics/Convolver.h> |
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40 | #include <scimath/Functionals/Polynomial.h> |
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41 | |
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42 | #include "MathUtils.h" |
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43 | #include "RowAccumulator.h" |
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44 | #include "STAttr.h" |
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45 | #include "STMath.h" |
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46 | |
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47 | using namespace casa; |
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48 | |
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49 | using namespace asap; |
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50 | |
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51 | STMath::STMath(bool insitu) : |
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52 | insitu_(insitu) |
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53 | { |
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54 | } |
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55 | |
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56 | |
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57 | STMath::~STMath() |
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58 | { |
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59 | } |
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60 | |
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61 | CountedPtr<Scantable> |
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62 | STMath::average( const std::vector<CountedPtr<Scantable> >& scantbls, |
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63 | const std::vector<bool>& mask, |
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64 | const std::string& weight, |
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65 | const std::string& avmode, |
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66 | bool alignfreq) |
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67 | { |
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68 | if ( avmode == "SCAN" && scantbls.size() != 1 ) |
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69 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables")); |
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70 | WeightType wtype = stringToWeight(weight); |
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71 | |
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72 | std::vector<CountedPtr<Scantable> >* in = |
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73 | const_cast<std::vector<CountedPtr<Scantable> >*>(&scantbls); |
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74 | std::vector<CountedPtr<Scantable> > inaligned; |
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75 | if ( alignfreq ) { |
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76 | // take first row of first scantable as reference epoch |
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77 | String epoch = scantbls[0]->getTime(0); |
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78 | for (int i=0; i< scantbls.size(); ++i ) { |
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79 | |
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80 | inaligned.push_back(frequencyAlign(scantbls[i], epoch)); |
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81 | } |
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82 | in = &inaligned; |
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83 | } |
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84 | |
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85 | // output |
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86 | // clone as this is non insitu |
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87 | bool insitu = insitu_; |
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88 | setInsitu(false); |
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89 | CountedPtr< Scantable > out = getScantable((*in)[0], true); |
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90 | setInsitu(insitu); |
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91 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in->begin(); |
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92 | ++stit; |
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93 | while ( stit != in->end() ) { |
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94 | out->appendToHistoryTable((*stit)->history()); |
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95 | ++stit; |
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96 | } |
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97 | |
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98 | Table& tout = out->table(); |
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99 | |
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100 | /// @todo check if all scantables are conformant |
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101 | |
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102 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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103 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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104 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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105 | ScalarColumn<Double> mjdColOut(tout,"TIME"); |
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106 | ScalarColumn<Double> intColOut(tout,"INTERVAL"); |
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107 | |
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108 | // set up the output table rows. These are based on the structure of the |
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109 | // FIRST scantable in the vector |
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110 | const Table& baset = (*in)[0]->table(); |
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111 | |
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112 | Block<String> cols(3); |
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113 | cols[0] = String("BEAMNO"); |
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114 | cols[1] = String("IFNO"); |
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115 | cols[2] = String("POLNO"); |
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116 | if ( avmode == "SOURCE" ) { |
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117 | cols.resize(4); |
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118 | cols[3] = String("SRCNAME"); |
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119 | } |
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120 | if ( avmode == "SCAN" && in->size() == 1) { |
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121 | cols.resize(4); |
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122 | cols[3] = String("SCANNO"); |
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123 | } |
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124 | uInt outrowCount = 0; |
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125 | TableIterator iter(baset, cols); |
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126 | while (!iter.pastEnd()) { |
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127 | Table subt = iter.table(); |
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128 | // copy the first row of this selection into the new table |
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129 | tout.addRow(); |
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130 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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131 | ++outrowCount; |
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132 | ++iter; |
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133 | } |
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134 | RowAccumulator acc(wtype); |
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135 | Vector<Bool> cmask(mask); |
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136 | acc.setUserMask(cmask); |
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137 | ROTableRow row(tout); |
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138 | ROArrayColumn<Float> specCol, tsysCol; |
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139 | ROArrayColumn<uChar> flagCol; |
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140 | ROScalarColumn<Double> mjdCol, intCol; |
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141 | ROScalarColumn<Int> scanIDCol; |
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142 | |
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143 | for (uInt i=0; i < tout.nrow(); ++i) { |
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144 | for ( int j=0; j < in->size(); ++j ) { |
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145 | const Table& tin = (*in)[j]->table(); |
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146 | const TableRecord& rec = row.get(i); |
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147 | ROScalarColumn<Double> tmp(tin, "TIME"); |
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148 | Double td;tmp.get(0,td); |
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149 | Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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150 | && tin.col("IFNO") == Int(rec.asuInt("IFNO")) |
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151 | && tin.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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152 | Table subt; |
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153 | if ( avmode == "SOURCE") { |
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154 | subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") ); |
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155 | } else if (avmode == "SCAN") { |
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156 | subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) ); |
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157 | } else { |
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158 | subt = basesubt; |
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159 | } |
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160 | specCol.attach(subt,"SPECTRA"); |
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161 | flagCol.attach(subt,"FLAGTRA"); |
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162 | tsysCol.attach(subt,"TSYS"); |
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163 | intCol.attach(subt,"INTERVAL"); |
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164 | mjdCol.attach(subt,"TIME"); |
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165 | Vector<Float> spec,tsys; |
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166 | Vector<uChar> flag; |
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167 | Double inter,time; |
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168 | for (uInt k = 0; k < subt.nrow(); ++k ) { |
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169 | flagCol.get(k, flag); |
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170 | Vector<Bool> bflag(flag.shape()); |
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171 | convertArray(bflag, flag); |
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172 | if ( allEQ(bflag, True) ) { |
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173 | continue;//don't accumulate |
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174 | } |
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175 | specCol.get(k, spec); |
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176 | tsysCol.get(k, tsys); |
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177 | intCol.get(k, inter); |
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178 | mjdCol.get(k, time); |
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179 | // spectrum has to be added last to enable weighting by the other values |
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180 | acc.add(spec, !bflag, tsys, inter, time); |
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181 | } |
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182 | } |
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183 | //write out |
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184 | specColOut.put(i, acc.getSpectrum()); |
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185 | const Vector<Bool>& msk = acc.getMask(); |
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186 | Vector<uChar> flg(msk.shape()); |
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187 | convertArray(flg, !msk); |
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188 | flagColOut.put(i, flg); |
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189 | tsysColOut.put(i, acc.getTsys()); |
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190 | intColOut.put(i, acc.getInterval()); |
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191 | mjdColOut.put(i, acc.getTime()); |
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192 | acc.reset(); |
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193 | } |
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194 | return out; |
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195 | } |
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196 | |
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197 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in, |
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198 | bool droprows) |
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199 | { |
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200 | if (insitu_) return in; |
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201 | else { |
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202 | // clone |
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203 | Scantable* tabp = new Scantable(*in, Bool(droprows)); |
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204 | return CountedPtr<Scantable>(tabp); |
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205 | } |
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206 | } |
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207 | |
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208 | CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in, |
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209 | float val, |
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210 | const std::string& mode, |
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211 | bool tsys ) |
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212 | { |
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213 | // modes are "ADD" and "MUL" |
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214 | CountedPtr< Scantable > out = getScantable(in, false); |
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215 | Table& tab = out->table(); |
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216 | ArrayColumn<Float> specCol(tab,"SPECTRA"); |
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217 | ArrayColumn<Float> tsysCol(tab,"TSYS"); |
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218 | for (uInt i=0; i<tab.nrow(); ++i) { |
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219 | Vector<Float> spec; |
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220 | Vector<Float> ts; |
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221 | specCol.get(i, spec); |
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222 | tsysCol.get(i, ts); |
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223 | if (mode == "MUL") { |
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224 | spec *= val; |
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225 | specCol.put(i, spec); |
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226 | if ( tsys ) { |
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227 | ts *= val; |
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228 | tsysCol.put(i, ts); |
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229 | } |
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230 | } else if ( mode == "ADD" ) { |
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231 | spec += val; |
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232 | specCol.put(i, spec); |
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233 | if ( tsys ) { |
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234 | ts += val; |
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235 | tsysCol.put(i, ts); |
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236 | } |
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237 | } |
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238 | } |
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239 | return out; |
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240 | } |
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241 | |
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242 | MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s, |
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243 | const Vector<uChar>& f) |
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244 | { |
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245 | Vector<Bool> mask; |
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246 | mask.resize(f.shape()); |
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247 | convertArray(mask, f); |
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248 | return MaskedArray<Float>(s,!mask); |
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249 | } |
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250 | |
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251 | Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma) |
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252 | { |
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253 | const Vector<Bool>& m = ma.getMask(); |
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254 | Vector<uChar> flags(m.shape()); |
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255 | convertArray(flags, !m); |
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256 | return flags; |
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257 | } |
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258 | |
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259 | CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable >& in, |
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260 | const std::string & mode, |
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261 | bool preserve ) |
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262 | { |
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263 | /// @todo make other modes available |
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264 | /// modes should be "nearest", "pair" |
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265 | // make this operation non insitu |
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266 | const Table& tin = in->table(); |
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267 | Table ons = tin(tin.col("SRCTYPE") == Int(0)); |
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268 | Table offs = tin(tin.col("SRCTYPE") == Int(1)); |
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269 | if ( offs.nrow() == 0 ) |
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270 | throw(AipsError("No 'off' scans present.")); |
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271 | // put all "on" scans into output table |
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272 | |
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273 | bool insitu = insitu_; |
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274 | setInsitu(false); |
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275 | CountedPtr< Scantable > out = getScantable(in, true); |
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276 | setInsitu(insitu); |
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277 | Table& tout = out->table(); |
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278 | |
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279 | TableCopy::copyRows(tout, ons); |
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280 | TableRow row(tout); |
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281 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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282 | |
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283 | ArrayColumn<Float> outspecCol(tout, "SPECTRA"); |
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284 | ROArrayColumn<Float> outtsysCol(tout, "TSYS"); |
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285 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA"); |
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286 | for (uInt i=0; i < tout.nrow(); ++i) { |
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287 | const TableRecord& rec = row.get(i); |
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288 | Double ontime = rec.asDouble("TIME"); |
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289 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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290 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime)); |
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291 | Table sel = offs( abs(offs.col("TIME")-ontime) <= mindeltat |
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292 | && offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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293 | && offs.col("IFNO") == Int(rec.asuInt("IFNO")) |
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294 | && offs.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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295 | |
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296 | TableRow offrow(sel); |
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297 | const TableRecord& offrec = offrow.get(0);//should only be one row |
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298 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
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299 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
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300 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
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301 | /// @fixme this assumes tsys is a scalar not vector |
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302 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
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303 | Vector<Float> specon, tsyson; |
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304 | outtsysCol.get(i, tsyson); |
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305 | outspecCol.get(i, specon); |
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306 | Vector<uChar> flagon; |
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307 | outflagCol.get(i, flagon); |
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308 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
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309 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
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310 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
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311 | if (preserve) { |
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312 | quot -= tsysoffscalar; |
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313 | } else { |
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314 | quot -= tsyson[0]; |
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315 | } |
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316 | outspecCol.put(i, quot.getArray()); |
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317 | outflagCol.put(i, flagsFromMA(quot)); |
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318 | } |
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319 | // renumber scanno |
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320 | TableIterator it(tout, "SCANNO"); |
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321 | uInt i = 0; |
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322 | while ( !it.pastEnd() ) { |
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323 | Table t = it.table(); |
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324 | TableVector<uInt> vec(t, "SCANNO"); |
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325 | vec = i; |
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326 | ++i; |
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327 | ++it; |
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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::freqSwitch( const CountedPtr< Scantable >& in ) |
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333 | { |
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334 | // make copy or reference |
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335 | CountedPtr< Scantable > out = getScantable(in, false); |
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336 | Table& tout = out->table(); |
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337 | Block<String> cols(3); |
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338 | cols[0] = String("SCANNO"); |
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339 | cols[1] = String("BEAMNO"); |
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340 | cols[2] = String("POLNO"); |
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341 | TableIterator iter(tout, cols); |
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342 | while (!iter.pastEnd()) { |
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343 | Table subt = iter.table(); |
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344 | // this should leave us with two rows for the two IFs....if not ignore |
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345 | if (subt.nrow() != 2 ) { |
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346 | continue; |
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347 | } |
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348 | ArrayColumn<Float> specCol(tout, "SPECTRA"); |
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349 | ArrayColumn<Float> tsysCol(tout, "TSYS"); |
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350 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA"); |
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351 | Vector<Float> onspec,offspec, ontsys, offtsys; |
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352 | Vector<uChar> onflag, offflag; |
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353 | tsysCol.get(0, ontsys); tsysCol.get(1, offtsys); |
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354 | specCol.get(0, onspec); specCol.get(1, offspec); |
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355 | flagCol.get(0, onflag); flagCol.get(1, offflag); |
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356 | MaskedArray<Float> on = maskedArray(onspec, onflag); |
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357 | MaskedArray<Float> off = maskedArray(offspec, offflag); |
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358 | MaskedArray<Float> oncopy = on.copy(); |
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359 | |
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360 | on /= off; on -= 1.0f; |
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361 | on *= ontsys[0]; |
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362 | off /= oncopy; off -= 1.0f; |
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363 | off *= offtsys[0]; |
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364 | specCol.put(0, on.getArray()); |
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365 | const Vector<Bool>& m0 = on.getMask(); |
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366 | Vector<uChar> flags0(m0.shape()); |
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367 | convertArray(flags0, !m0); |
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368 | flagCol.put(0, flags0); |
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369 | |
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370 | specCol.put(1, off.getArray()); |
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371 | const Vector<Bool>& m1 = off.getMask(); |
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372 | Vector<uChar> flags1(m1.shape()); |
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373 | convertArray(flags1, !m1); |
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374 | flagCol.put(1, flags1); |
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375 | ++iter; |
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376 | } |
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377 | |
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378 | return out; |
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379 | } |
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380 | |
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381 | std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in, |
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382 | const std::vector< bool > & mask, |
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383 | const std::string& which ) |
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384 | { |
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385 | |
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386 | Vector<Bool> m(mask); |
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387 | const Table& tab = in->table(); |
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388 | ROArrayColumn<Float> specCol(tab, "SPECTRA"); |
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389 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
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390 | std::vector<float> out; |
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391 | for (uInt i=0; i < tab.nrow(); ++i ) { |
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392 | Vector<Float> spec; specCol.get(i, spec); |
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393 | Vector<uChar> flag; flagCol.get(i, flag); |
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394 | MaskedArray<Float> ma = maskedArray(spec, flag); |
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395 | float outstat = 0.0; |
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396 | if ( spec.nelements() == m.nelements() ) { |
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397 | outstat = mathutil::statistics(which, ma(m)); |
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398 | } else { |
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399 | outstat = mathutil::statistics(which, ma); |
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400 | } |
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401 | out.push_back(outstat); |
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402 | } |
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403 | return out; |
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404 | } |
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405 | |
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406 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in, |
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407 | int width ) |
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408 | { |
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409 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data.")); |
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410 | CountedPtr< Scantable > out = getScantable(in, false); |
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411 | Table& tout = out->table(); |
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412 | out->frequencies().rescale(width, "BIN"); |
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413 | ArrayColumn<Float> specCol(tout, "SPECTRA"); |
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414 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA"); |
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415 | for (uInt i=0; i < tout.nrow(); ++i ) { |
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416 | MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i)); |
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417 | MaskedArray<Float> maout; |
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418 | LatticeUtilities::bin(maout, main, 0, Int(width)); |
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419 | /// @todo implement channel based tsys binning |
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420 | specCol.put(i, maout.getArray()); |
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421 | flagCol.put(i, flagsFromMA(maout)); |
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422 | // take only the first binned spectrum's length for the deprecated |
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423 | // global header item nChan |
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424 | if (i==0) tout.rwKeywordSet().define(String("nChan"), |
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425 | Int(maout.getArray().nelements())); |
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426 | } |
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427 | return out; |
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428 | } |
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429 | |
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430 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in, |
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431 | const std::string& method, |
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432 | float width ) |
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433 | // |
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434 | // Should add the possibility of width being specified in km/s. This means |
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435 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
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436 | // average channel width (say at the reference pixel). Then we would need |
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437 | // to be careful to make sure each spectrum (of different freqID) |
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438 | // is the same length. |
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439 | // |
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440 | { |
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441 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
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442 | Int interpMethod(stringToIMethod(method)); |
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443 | |
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444 | CountedPtr< Scantable > out = getScantable(in, false); |
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445 | Table& tout = out->table(); |
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446 | |
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447 | // Resample SpectralCoordinates (one per freqID) |
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448 | out->frequencies().rescale(width, "RESAMPLE"); |
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449 | TableIterator iter(tout, "IFNO"); |
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450 | TableRow row(tout); |
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451 | while ( !iter.pastEnd() ) { |
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452 | Table tab = iter.table(); |
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453 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
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454 | //ArrayColumn<Float> tsysCol(tout, "TSYS"); |
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455 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
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456 | Vector<Float> spec; |
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457 | Vector<uChar> flag; |
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458 | specCol.get(0,spec); // the number of channels should be constant per IF |
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459 | uInt nChanIn = spec.nelements(); |
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460 | Vector<Float> xIn(nChanIn); indgen(xIn); |
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461 | Int fac = Int(nChanIn/width); |
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462 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
463 | uInt k = 0; |
---|
464 | Float x = 0.0; |
---|
465 | while (x < Float(nChanIn) ) { |
---|
466 | xOut(k) = x; |
---|
467 | k++; |
---|
468 | x += width; |
---|
469 | } |
---|
470 | uInt nChanOut = k; |
---|
471 | xOut.resize(nChanOut, True); |
---|
472 | // process all rows for this IFNO |
---|
473 | Vector<Float> specOut; |
---|
474 | Vector<Bool> maskOut; |
---|
475 | Vector<uChar> flagOut; |
---|
476 | for (uInt i=0; i < tab.nrow(); ++i) { |
---|
477 | specCol.get(i, spec); |
---|
478 | flagCol.get(i, flag); |
---|
479 | Vector<Bool> mask(flag.nelements()); |
---|
480 | convertArray(mask, flag); |
---|
481 | |
---|
482 | IPosition shapeIn(spec.shape()); |
---|
483 | //sh.nchan = nChanOut; |
---|
484 | InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut, |
---|
485 | xIn, spec, mask, |
---|
486 | interpMethod, True, True); |
---|
487 | /// @todo do the same for channel based Tsys |
---|
488 | flagOut.resize(maskOut.nelements()); |
---|
489 | convertArray(flagOut, maskOut); |
---|
490 | specCol.put(i, specOut); |
---|
491 | flagCol.put(i, flagOut); |
---|
492 | } |
---|
493 | ++iter; |
---|
494 | } |
---|
495 | |
---|
496 | return out; |
---|
497 | } |
---|
498 | |
---|
499 | STMath::imethod STMath::stringToIMethod(const std::string& in) |
---|
500 | { |
---|
501 | static STMath::imap lookup; |
---|
502 | |
---|
503 | // initialize the lookup table if necessary |
---|
504 | if ( lookup.empty() ) { |
---|
505 | lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
506 | lookup["linear"] = InterpolateArray1D<Double,Float>::linear; |
---|
507 | lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic; |
---|
508 | lookup["spline"] = InterpolateArray1D<Double,Float>::spline; |
---|
509 | } |
---|
510 | |
---|
511 | STMath::imap::const_iterator iter = lookup.find(in); |
---|
512 | |
---|
513 | if ( lookup.end() == iter ) { |
---|
514 | std::string message = in; |
---|
515 | message += " is not a valid interpolation mode"; |
---|
516 | throw(AipsError(message)); |
---|
517 | } |
---|
518 | return iter->second; |
---|
519 | } |
---|
520 | |
---|
521 | WeightType STMath::stringToWeight(const std::string& in) |
---|
522 | { |
---|
523 | static std::map<std::string, WeightType> lookup; |
---|
524 | |
---|
525 | // initialize the lookup table if necessary |
---|
526 | if ( lookup.empty() ) { |
---|
527 | lookup["NONE"] = asap::NONE; |
---|
528 | lookup["TINT"] = asap::TINT; |
---|
529 | lookup["TINTSYS"] = asap::TINTSYS; |
---|
530 | lookup["TSYS"] = asap::TSYS; |
---|
531 | lookup["VAR"] = asap::VAR; |
---|
532 | } |
---|
533 | |
---|
534 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in); |
---|
535 | |
---|
536 | if ( lookup.end() == iter ) { |
---|
537 | std::string message = in; |
---|
538 | message += " is not a valid weighting mode"; |
---|
539 | throw(AipsError(message)); |
---|
540 | } |
---|
541 | return iter->second; |
---|
542 | } |
---|
543 | |
---|
544 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in, |
---|
545 | const vector< float > & coeff, |
---|
546 | const std::string & filename, |
---|
547 | const std::string& method) |
---|
548 | { |
---|
549 | // Get elevation data from Scantable and convert to degrees |
---|
550 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
551 | Table& tab = out->table(); |
---|
552 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
553 | Vector<Float> x = elev.getColumn(); |
---|
554 | x *= Float(180 / C::pi); // Degrees |
---|
555 | |
---|
556 | Vector<Float> coeffs(coeff); |
---|
557 | const uInt nc = coeffs.nelements(); |
---|
558 | if ( filename.length() > 0 && nc > 0 ) { |
---|
559 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
560 | } |
---|
561 | |
---|
562 | // Correct |
---|
563 | if ( nc > 0 || filename.length() == 0 ) { |
---|
564 | // Find instrument |
---|
565 | Bool throwit = True; |
---|
566 | Instrument inst = |
---|
567 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
568 | throwit); |
---|
569 | |
---|
570 | // Set polynomial |
---|
571 | Polynomial<Float>* ppoly = 0; |
---|
572 | Vector<Float> coeff; |
---|
573 | String msg; |
---|
574 | if ( nc > 0 ) { |
---|
575 | ppoly = new Polynomial<Float>(nc); |
---|
576 | coeff = coeffs; |
---|
577 | msg = String("user"); |
---|
578 | } else { |
---|
579 | STAttr sdAttr; |
---|
580 | coeff = sdAttr.gainElevationPoly(inst); |
---|
581 | ppoly = new Polynomial<Float>(3); |
---|
582 | msg = String("built in"); |
---|
583 | } |
---|
584 | |
---|
585 | if ( coeff.nelements() > 0 ) { |
---|
586 | ppoly->setCoefficients(coeff); |
---|
587 | } else { |
---|
588 | delete ppoly; |
---|
589 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
590 | } |
---|
591 | ostringstream oss; |
---|
592 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl; |
---|
593 | oss << " " << coeff; |
---|
594 | pushLog(String(oss)); |
---|
595 | const uInt nrow = tab.nrow(); |
---|
596 | Vector<Float> factor(nrow); |
---|
597 | for ( uInt i=0; i < nrow; ++i ) { |
---|
598 | factor[i] = 1.0 / (*ppoly)(x[i]); |
---|
599 | } |
---|
600 | delete ppoly; |
---|
601 | scaleByVector(tab, factor, true); |
---|
602 | |
---|
603 | } else { |
---|
604 | // Read and correct |
---|
605 | pushLog("Making correction from ascii Table"); |
---|
606 | scaleFromAsciiTable(tab, filename, method, x, true); |
---|
607 | } |
---|
608 | return out; |
---|
609 | } |
---|
610 | |
---|
611 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename, |
---|
612 | const std::string& method, |
---|
613 | const Vector<Float>& xout, bool dotsys) |
---|
614 | { |
---|
615 | |
---|
616 | // Read gain-elevation ascii file data into a Table. |
---|
617 | |
---|
618 | String formatString; |
---|
619 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False); |
---|
620 | scaleFromTable(in, tbl, method, xout, dotsys); |
---|
621 | } |
---|
622 | |
---|
623 | void STMath::scaleFromTable(Table& in, |
---|
624 | const Table& table, |
---|
625 | const std::string& method, |
---|
626 | const Vector<Float>& xout, bool dotsys) |
---|
627 | { |
---|
628 | |
---|
629 | ROScalarColumn<Float> geElCol(table, "ELEVATION"); |
---|
630 | ROScalarColumn<Float> geFacCol(table, "FACTOR"); |
---|
631 | Vector<Float> xin = geElCol.getColumn(); |
---|
632 | Vector<Float> yin = geFacCol.getColumn(); |
---|
633 | Vector<Bool> maskin(xin.nelements(),True); |
---|
634 | |
---|
635 | // Interpolate (and extrapolate) with desired method |
---|
636 | |
---|
637 | //InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
638 | Int intmethod(stringToIMethod(method)); |
---|
639 | |
---|
640 | Vector<Float> yout; |
---|
641 | Vector<Bool> maskout; |
---|
642 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout, |
---|
643 | xin, yin, maskin, intmethod, |
---|
644 | True, True); |
---|
645 | |
---|
646 | scaleByVector(in, Float(1.0)/yout, dotsys); |
---|
647 | } |
---|
648 | |
---|
649 | void STMath::scaleByVector( Table& in, |
---|
650 | const Vector< Float >& factor, |
---|
651 | bool dotsys ) |
---|
652 | { |
---|
653 | uInt nrow = in.nrow(); |
---|
654 | if ( factor.nelements() != nrow ) { |
---|
655 | throw(AipsError("factors.nelements() != table.nelements()")); |
---|
656 | } |
---|
657 | ArrayColumn<Float> specCol(in, "SPECTRA"); |
---|
658 | ArrayColumn<uChar> flagCol(in, "FLAGTRA"); |
---|
659 | ArrayColumn<Float> tsysCol(in, "TSYS"); |
---|
660 | for (uInt i=0; i < nrow; ++i) { |
---|
661 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
662 | ma *= factor[i]; |
---|
663 | specCol.put(i, ma.getArray()); |
---|
664 | flagCol.put(i, flagsFromMA(ma)); |
---|
665 | if ( dotsys ) { |
---|
666 | Vector<Float> tsys = tsysCol(i); |
---|
667 | tsys *= factor[i]; |
---|
668 | tsysCol.put(i,tsys); |
---|
669 | } |
---|
670 | } |
---|
671 | } |
---|
672 | |
---|
673 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in, |
---|
674 | float d, float etaap, |
---|
675 | float jyperk ) |
---|
676 | { |
---|
677 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
678 | Table& tab = in->table(); |
---|
679 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit")); |
---|
680 | Unit K(String("K")); |
---|
681 | Unit JY(String("Jy")); |
---|
682 | |
---|
683 | bool tokelvin = true; |
---|
684 | Double cfac = 1.0; |
---|
685 | |
---|
686 | if ( fluxUnit == JY ) { |
---|
687 | pushLog("Converting to K"); |
---|
688 | Quantum<Double> t(1.0,fluxUnit); |
---|
689 | Quantum<Double> t2 = t.get(JY); |
---|
690 | cfac = (t2 / t).getValue(); // value to Jy |
---|
691 | |
---|
692 | tokelvin = true; |
---|
693 | out->setFluxUnit("K"); |
---|
694 | } else if ( fluxUnit == K ) { |
---|
695 | pushLog("Converting to Jy"); |
---|
696 | Quantum<Double> t(1.0,fluxUnit); |
---|
697 | Quantum<Double> t2 = t.get(K); |
---|
698 | cfac = (t2 / t).getValue(); // value to K |
---|
699 | |
---|
700 | tokelvin = false; |
---|
701 | out->setFluxUnit("Jy"); |
---|
702 | } else { |
---|
703 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
704 | } |
---|
705 | // Make sure input values are converted to either Jy or K first... |
---|
706 | Float factor = cfac; |
---|
707 | |
---|
708 | // Select method |
---|
709 | if (jyperk > 0.0) { |
---|
710 | factor *= jyperk; |
---|
711 | if ( tokelvin ) factor = 1.0 / jyperk; |
---|
712 | ostringstream oss; |
---|
713 | oss << "Jy/K = " << jyperk; |
---|
714 | pushLog(String(oss)); |
---|
715 | Vector<Float> factors(tab.nrow(), factor); |
---|
716 | scaleByVector(tab,factors, false); |
---|
717 | } else if ( etaap > 0.0) { |
---|
718 | Instrument inst = |
---|
719 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True); |
---|
720 | STAttr sda; |
---|
721 | if (d < 0) d = sda.diameter(inst); |
---|
722 | Float jyPerk = STAttr::findJyPerK(etaap, d); |
---|
723 | ostringstream oss; |
---|
724 | oss << "Jy/K = " << jyperk; |
---|
725 | pushLog(String(oss)); |
---|
726 | factor *= jyperk; |
---|
727 | if ( tokelvin ) { |
---|
728 | factor = 1.0 / factor; |
---|
729 | } |
---|
730 | Vector<Float> factors(tab.nrow(), factor); |
---|
731 | scaleByVector(tab, factors, False); |
---|
732 | } else { |
---|
733 | |
---|
734 | // OK now we must deal with automatic look up of values. |
---|
735 | // We must also deal with the fact that the factors need |
---|
736 | // to be computed per IF and may be different and may |
---|
737 | // change per integration. |
---|
738 | |
---|
739 | pushLog("Looking up conversion factors"); |
---|
740 | convertBrightnessUnits(out, tokelvin, cfac); |
---|
741 | } |
---|
742 | |
---|
743 | return out; |
---|
744 | } |
---|
745 | |
---|
746 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in, |
---|
747 | bool tokelvin, float cfac ) |
---|
748 | { |
---|
749 | Table& table = in->table(); |
---|
750 | Instrument inst = |
---|
751 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True); |
---|
752 | TableIterator iter(table, "FREQ_ID"); |
---|
753 | STFrequencies stfreqs = in->frequencies(); |
---|
754 | STAttr sdAtt; |
---|
755 | while (!iter.pastEnd()) { |
---|
756 | Table tab = iter.table(); |
---|
757 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
758 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
759 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID"); |
---|
760 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
761 | |
---|
762 | uInt freqid; freqidCol.get(0, freqid); |
---|
763 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
764 | // STAttr.JyPerK has a Vector interface... change sometime. |
---|
765 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements())); |
---|
766 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
767 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0]; |
---|
768 | Float factor = cfac * jyperk; |
---|
769 | if ( tokelvin ) factor = Float(1.0) / factor; |
---|
770 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
771 | ma *= factor; |
---|
772 | specCol.put(i, ma.getArray()); |
---|
773 | flagCol.put(i, flagsFromMA(ma)); |
---|
774 | } |
---|
775 | ++iter; |
---|
776 | } |
---|
777 | } |
---|
778 | |
---|
779 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in, |
---|
780 | float tau ) |
---|
781 | { |
---|
782 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
783 | |
---|
784 | Table tab = out->table(); |
---|
785 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
786 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
787 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
788 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
789 | Float zdist = Float(C::pi_2) - elev(i); |
---|
790 | Float factor = exp(tau)/cos(zdist); |
---|
791 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
792 | ma *= factor; |
---|
793 | specCol.put(i, ma.getArray()); |
---|
794 | flagCol.put(i, flagsFromMA(ma)); |
---|
795 | } |
---|
796 | return out; |
---|
797 | } |
---|
798 | |
---|
799 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in, |
---|
800 | const std::string& kernel, float width ) |
---|
801 | { |
---|
802 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
803 | Table& table = in->table(); |
---|
804 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel); |
---|
805 | // same IFNO should have same no of channels |
---|
806 | // this saves overhead |
---|
807 | TableIterator iter(table, "IFNO"); |
---|
808 | while (!iter.pastEnd()) { |
---|
809 | Table tab = iter.table(); |
---|
810 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
811 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
812 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
813 | uInt nchan = tmpspec.nelements(); |
---|
814 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False); |
---|
815 | Convolver<Float> conv(kvec, IPosition(1,nchan)); |
---|
816 | Vector<Float> spec; |
---|
817 | Vector<uChar> flag; |
---|
818 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
819 | specCol.get(i, spec); |
---|
820 | flagCol.get(i, flag); |
---|
821 | Vector<Bool> mask(flag.nelements()); |
---|
822 | convertArray(mask, flag); |
---|
823 | Vector<Float> specout; |
---|
824 | if ( type == VectorKernel::HANNING ) { |
---|
825 | Vector<Bool> maskout; |
---|
826 | mathutil::hanning(specout, maskout, spec , mask); |
---|
827 | convertArray(flag, maskout); |
---|
828 | flagCol.put(i, flag); |
---|
829 | } else { |
---|
830 | mathutil::replaceMaskByZero(specout, mask); |
---|
831 | conv.linearConv(specout, spec); |
---|
832 | } |
---|
833 | specCol.put(i, specout); |
---|
834 | } |
---|
835 | ++iter; |
---|
836 | } |
---|
837 | return out; |
---|
838 | } |
---|
839 | |
---|
840 | CountedPtr< Scantable > |
---|
841 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in ) |
---|
842 | { |
---|
843 | if ( in.size() < 2 ) { |
---|
844 | throw(AipsError("Need at least two scantables to perform a merge.")); |
---|
845 | } |
---|
846 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin(); |
---|
847 | bool insitu = insitu_; |
---|
848 | setInsitu(false); |
---|
849 | CountedPtr< Scantable > out = getScantable(*it, false); |
---|
850 | setInsitu(insitu); |
---|
851 | Table& tout = out->table(); |
---|
852 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID"); |
---|
853 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID"); |
---|
854 | // Renumber SCANNO to be 0-based |
---|
855 | Vector<uInt> scannos = scannocol.getColumn(); |
---|
856 | uInt offset = min(scannos); |
---|
857 | scannos -= offset; |
---|
858 | scannocol.putColumn(scannos); |
---|
859 | uInt newscanno = max(scannos)+1; |
---|
860 | ++it; |
---|
861 | while ( it != in.end() ){ |
---|
862 | if ( ! (*it)->conformant(*out) ) { |
---|
863 | // log message: "ignoring scantable i, as it isn't |
---|
864 | // conformant with the other(s)" |
---|
865 | cerr << "oh oh" << endl; |
---|
866 | ++it; |
---|
867 | continue; |
---|
868 | } |
---|
869 | out->appendToHistoryTable((*it)->history()); |
---|
870 | const Table& tab = (*it)->table(); |
---|
871 | TableIterator scanit(tab, "SCANNO"); |
---|
872 | while (!scanit.pastEnd()) { |
---|
873 | TableIterator freqit(scanit.table(), "FREQ_ID"); |
---|
874 | while ( !freqit.pastEnd() ) { |
---|
875 | Table thetab = freqit.table(); |
---|
876 | uInt nrow = tout.nrow(); |
---|
877 | //tout.addRow(thetab.nrow()); |
---|
878 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow()); |
---|
879 | ROTableRow row(thetab); |
---|
880 | for ( uInt i=0; i<thetab.nrow(); ++i) { |
---|
881 | uInt k = nrow+i; |
---|
882 | scannocol.put(k, newscanno); |
---|
883 | const TableRecord& rec = row.get(i); |
---|
884 | Double rv,rp,inc; |
---|
885 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID")); |
---|
886 | uInt id; |
---|
887 | id = out->frequencies().addEntry(rp, rv, inc); |
---|
888 | freqidcol.put(k,id); |
---|
889 | String name,fname;Double rf; |
---|
890 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID")); |
---|
891 | id = out->molecules().addEntry(rf, name, fname); |
---|
892 | molidcol.put(k, id); |
---|
893 | Float frot,fang,ftan; |
---|
894 | (*it)->focus().getEntry(frot, fang, ftan, rec.asuInt("FOCUS_ID")); |
---|
895 | id = out->focus().addEntry(frot, fang, ftan); |
---|
896 | focusidcol.put(k, id); |
---|
897 | } |
---|
898 | ++freqit; |
---|
899 | } |
---|
900 | ++newscanno; |
---|
901 | ++scanit; |
---|
902 | } |
---|
903 | ++it; |
---|
904 | } |
---|
905 | return out; |
---|
906 | } |
---|
907 | |
---|
908 | CountedPtr< Scantable > |
---|
909 | STMath::invertPhase( const CountedPtr < Scantable >& in ) |
---|
910 | { |
---|
911 | applyToPol(in, &STPol::invertPhase, Float(0.0)); |
---|
912 | } |
---|
913 | |
---|
914 | CountedPtr< Scantable > |
---|
915 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
916 | { |
---|
917 | return applyToPol(in, &STPol::rotatePhase, Float(phase)); |
---|
918 | } |
---|
919 | |
---|
920 | CountedPtr< Scantable > |
---|
921 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
922 | { |
---|
923 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase)); |
---|
924 | } |
---|
925 | |
---|
926 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in, |
---|
927 | STPol::polOperation fptr, |
---|
928 | Float phase ) |
---|
929 | { |
---|
930 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
931 | Table& tout = out->table(); |
---|
932 | Block<String> cols(4); |
---|
933 | cols[0] = String("SCANNO"); |
---|
934 | cols[1] = String("BEAMNO"); |
---|
935 | cols[2] = String("IFNO"); |
---|
936 | cols[3] = String("CYCLENO"); |
---|
937 | TableIterator iter(tout, cols); |
---|
938 | STPol* stpol = NULL; |
---|
939 | stpol =STPol::getPolClass(out->factories_, out->getPolType() ); |
---|
940 | while (!iter.pastEnd()) { |
---|
941 | Table t = iter.table(); |
---|
942 | ArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
943 | Matrix<Float> pols = speccol.getColumn(); |
---|
944 | try { |
---|
945 | stpol->setSpectra(pols); |
---|
946 | (stpol->*fptr)(phase); |
---|
947 | speccol.putColumn(stpol->getSpectra()); |
---|
948 | } catch (AipsError& e) { |
---|
949 | delete stpol;stpol=0; |
---|
950 | throw(e); |
---|
951 | } |
---|
952 | ++iter; |
---|
953 | } |
---|
954 | delete stpol;stpol=0; |
---|
955 | return out; |
---|
956 | } |
---|
957 | |
---|
958 | CountedPtr< Scantable > |
---|
959 | STMath::swapPolarisations( const CountedPtr< Scantable > & in ) |
---|
960 | { |
---|
961 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
962 | Table& tout = out->table(); |
---|
963 | Table t0 = tout(tout.col("POLNO") == 0); |
---|
964 | Table t1 = tout(tout.col("POLNO") == 1); |
---|
965 | if ( t0.nrow() != t1.nrow() ) |
---|
966 | throw(AipsError("Inconsistent number of polarisations")); |
---|
967 | ArrayColumn<Float> speccol0(t0, "SPECTRA"); |
---|
968 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA"); |
---|
969 | ArrayColumn<Float> speccol1(t1, "SPECTRA"); |
---|
970 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA"); |
---|
971 | Matrix<Float> s0 = speccol0.getColumn(); |
---|
972 | Matrix<uChar> f0 = flagcol0.getColumn(); |
---|
973 | speccol0.putColumn(speccol1.getColumn()); |
---|
974 | flagcol0.putColumn(flagcol1.getColumn()); |
---|
975 | speccol1.putColumn(s0); |
---|
976 | flagcol1.putColumn(f0); |
---|
977 | return out; |
---|
978 | } |
---|
979 | |
---|
980 | CountedPtr< Scantable > |
---|
981 | STMath::averagePolarisations( const CountedPtr< Scantable > & in, |
---|
982 | const std::vector<bool>& mask, |
---|
983 | const std::string& weight ) |
---|
984 | { |
---|
985 | if (in->getPolType() != "linear" || in->npol() != 2 ) |
---|
986 | throw(AipsError("averagePolarisations can only be applied to two linear polarisations.")); |
---|
987 | CountedPtr<Scantable> pol0( new Scantable(*in), false); |
---|
988 | CountedPtr<Scantable> pol1( new Scantable(*in), false); |
---|
989 | Table& tpol0 = pol0->table(); |
---|
990 | Table& tpol1 = pol1->table(); |
---|
991 | Vector<uInt> pol0rows = tpol0(tpol0.col("POLNO") == 0).rowNumbers(); |
---|
992 | Vector<uInt> pol1rows = tpol1(tpol1.col("POLNO") == 1).rowNumbers(); |
---|
993 | tpol0.removeRow(pol1rows); |
---|
994 | tpol1.removeRow(pol0rows); |
---|
995 | // give both tables the same POLNO |
---|
996 | TableVector<uInt> vec(tpol1,"POLNO"); |
---|
997 | vec = 0; |
---|
998 | std::vector<CountedPtr<Scantable> > pols; |
---|
999 | pols.push_back(pol0); |
---|
1000 | pols.push_back(pol1); |
---|
1001 | CountedPtr< Scantable > out = average(pols, mask, weight, "NONE", false); |
---|
1002 | out->table_.rwKeywordSet().define("nPol",Int(1)); |
---|
1003 | return out; |
---|
1004 | } |
---|
1005 | |
---|
1006 | |
---|
1007 | CountedPtr< Scantable > |
---|
1008 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in, |
---|
1009 | const std::string & refTime, |
---|
1010 | const std::string & method) |
---|
1011 | { |
---|
1012 | // clone as this is not working insitu |
---|
1013 | bool insitu = insitu_; |
---|
1014 | setInsitu(false); |
---|
1015 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
1016 | setInsitu(insitu); |
---|
1017 | Table& tout = out->table(); |
---|
1018 | // clear ouput frequency table |
---|
1019 | //Table ftable = out->frequencies().table(); |
---|
1020 | //ftable.removeRow(ftable.rowNumbers()); |
---|
1021 | // Get reference Epoch to time of first row or given String |
---|
1022 | Unit DAY(String("d")); |
---|
1023 | MEpoch::Ref epochRef(in->getTimeReference()); |
---|
1024 | MEpoch refEpoch; |
---|
1025 | if (refTime.length()>0) { |
---|
1026 | Quantum<Double> qt; |
---|
1027 | if (MVTime::read(qt,refTime)) { |
---|
1028 | MVEpoch mv(qt); |
---|
1029 | refEpoch = MEpoch(mv, epochRef); |
---|
1030 | } else { |
---|
1031 | throw(AipsError("Invalid format for Epoch string")); |
---|
1032 | } |
---|
1033 | } else { |
---|
1034 | refEpoch = in->timeCol_(0); |
---|
1035 | } |
---|
1036 | MPosition refPos = in->getAntennaPosition(); |
---|
1037 | |
---|
1038 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
1039 | Int interpMethod(stringToIMethod(method)); |
---|
1040 | // test if user frame is different to base frame |
---|
1041 | if ( in->frequencies().getFrameString(true) |
---|
1042 | == in->frequencies().getFrameString(false) ) { |
---|
1043 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe")); |
---|
1044 | } |
---|
1045 | MFrequency::Types system = in->frequencies().getFrame(); |
---|
1046 | MVTime mvt(refEpoch.getValue()); |
---|
1047 | String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")"); |
---|
1048 | ostringstream oss; |
---|
1049 | oss << "Aligned at reference Epoch " << epochout |
---|
1050 | << " in frame " << MFrequency::showType(system); |
---|
1051 | pushLog(String(oss)); |
---|
1052 | // set up the iterator |
---|
1053 | Block<String> cols(4); |
---|
1054 | // select by constant direction |
---|
1055 | cols[0] = String("SRCNAME"); |
---|
1056 | cols[1] = String("BEAMNO"); |
---|
1057 | // select by IF ( no of channels varies over this ) |
---|
1058 | cols[2] = String("IFNO"); |
---|
1059 | // select by restfrequency |
---|
1060 | cols[3] = String("MOLECULE_ID"); |
---|
1061 | TableIterator iter(tout, cols); |
---|
1062 | while ( !iter.pastEnd() ) { |
---|
1063 | Table t = iter.table(); |
---|
1064 | MDirection::ROScalarColumn dirCol(t, "DIRECTION"); |
---|
1065 | TableIterator fiter(t, "FREQ_ID"); |
---|
1066 | // determine nchan from the first row. This should work as |
---|
1067 | // we are iterating over BEAMNO and IFNO // we should have constant direction |
---|
1068 | |
---|
1069 | ROArrayColumn<Float> sCol(t, "SPECTRA"); |
---|
1070 | MDirection direction = dirCol(0); |
---|
1071 | uInt nchan = sCol(0).nelements(); |
---|
1072 | while ( !fiter.pastEnd() ) { |
---|
1073 | Table ftab = fiter.table(); |
---|
1074 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID"); |
---|
1075 | // get the SpectralCoordinate for the freqid, which we are iterating over |
---|
1076 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0)); |
---|
1077 | FrequencyAligner<Float> fa( sC, nchan, refEpoch, |
---|
1078 | direction, refPos, system ); |
---|
1079 | // realign the SpectralCoordinate and put into the output Scantable |
---|
1080 | Vector<String> units(1); |
---|
1081 | units = String("Hz"); |
---|
1082 | Bool linear=True; |
---|
1083 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear); |
---|
1084 | sc2.setWorldAxisUnits(units); |
---|
1085 | uInt id = out->frequencies().addEntry(sc2.referencePixel()[0], |
---|
1086 | sc2.referenceValue()[0], |
---|
1087 | sc2.increment()[0]); |
---|
1088 | TableVector<uInt> tvec(ftab, "FREQ_ID"); |
---|
1089 | tvec = id; |
---|
1090 | // create the "global" abcissa for alignment with same FREQ_ID |
---|
1091 | Vector<Double> abc(nchan); |
---|
1092 | Double w; |
---|
1093 | for (uInt i=0; i<nchan; i++) { |
---|
1094 | sC.toWorld(w,Double(i)); |
---|
1095 | abc[i] = w; |
---|
1096 | } |
---|
1097 | // cache abcissa for same time stamps, so iterate over those |
---|
1098 | TableIterator timeiter(ftab, "TIME"); |
---|
1099 | while ( !timeiter.pastEnd() ) { |
---|
1100 | Table tab = timeiter.table(); |
---|
1101 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
1102 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
1103 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
1104 | // use align abcissa cache after the first row |
---|
1105 | bool first = true; |
---|
1106 | // these rows should be just be POLNO |
---|
1107 | for (int i=0; i<tab.nrow(); ++i) { |
---|
1108 | // input values |
---|
1109 | Vector<uChar> flag = flagCol(i); |
---|
1110 | Vector<Bool> mask(flag.shape()); |
---|
1111 | Vector<Float> specOut, spec; |
---|
1112 | spec = specCol(i); |
---|
1113 | Vector<Bool> maskOut;Vector<uChar> flagOut; |
---|
1114 | convertArray(mask, flag); |
---|
1115 | // alignment |
---|
1116 | Bool ok = fa.align(specOut, maskOut, abc, spec, |
---|
1117 | mask, timeCol(i), !first, |
---|
1118 | interp, False); |
---|
1119 | // back into scantable |
---|
1120 | flagOut.resize(maskOut.nelements()); |
---|
1121 | convertArray(flagOut, maskOut); |
---|
1122 | flagCol.put(i, flagOut); |
---|
1123 | specCol.put(i, specOut); |
---|
1124 | // start abcissa caching |
---|
1125 | first = false; |
---|
1126 | } |
---|
1127 | // next timestamp |
---|
1128 | ++timeiter; |
---|
1129 | } |
---|
1130 | // next FREQ_ID |
---|
1131 | ++fiter; |
---|
1132 | } |
---|
1133 | // next aligner |
---|
1134 | ++iter; |
---|
1135 | } |
---|
1136 | // set this afterwards to ensure we are doing insitu correctly. |
---|
1137 | out->frequencies().setFrame(system, true); |
---|
1138 | return out; |
---|
1139 | } |
---|