[805] | 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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[38] | 12 | |
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[330] | 13 | #include <casa/iomanip.h> |
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[805] | 14 | #include <casa/Exceptions/Error.h> |
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| 15 | #include <casa/Containers/Block.h> |
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[81] | 16 | #include <casa/BasicSL/String.h> |
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[805] | 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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[81] | 22 | #include <casa/Arrays/ArrayMath.h> |
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[805] | 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/ExprNode.h> |
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| 27 | #include <tables/Tables/TableRecord.h> |
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| 28 | #include <tables/Tables/ReadAsciiTable.h> |
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[2] | 29 | |
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[262] | 30 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 31 | |
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[177] | 32 | #include <scimath/Mathematics/VectorKernel.h> |
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| 33 | #include <scimath/Mathematics/Convolver.h> |
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[234] | 34 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 35 | |
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[38] | 36 | #include "MathUtils.h" |
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[805] | 37 | #include "RowAccumulator.h" |
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[354] | 38 | #include "SDAttr.h" |
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[805] | 39 | #include "STMath.h" |
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[2] | 40 | |
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[805] | 41 | using namespace casa; |
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[2] | 42 | |
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[83] | 43 | using namespace asap; |
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[2] | 44 | |
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[805] | 45 | STMath::STMath(bool insitu) : |
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| 46 | insitu_(insitu) |
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[716] | 47 | { |
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| 48 | } |
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[170] | 49 | |
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| 50 | |
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[805] | 51 | STMath::~STMath() |
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[170] | 52 | { |
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| 53 | } |
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| 54 | |
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[805] | 55 | CountedPtr<Scantable> |
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| 56 | STMath::average( const std::vector<CountedPtr<Scantable> >& in, |
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[858] | 57 | const std::vector<bool>& mask, |
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[805] | 58 | const std::string& weight, |
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| 59 | const std::string& avmode, |
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| 60 | bool alignfreq) |
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[262] | 61 | { |
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[805] | 62 | if ( avmode == "SCAN" && in.size() != 1 ) |
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| 63 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables")); |
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| 64 | WeightType wtype = stringToWeight(weight); |
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| 65 | // output |
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| 66 | // clone as this is non insitu |
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| 67 | bool insitu = insitu_; |
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| 68 | setInsitu(false); |
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| 69 | CountedPtr< Scantable > out = getScantable(in[0], true); |
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| 70 | setInsitu(insitu); |
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[862] | 71 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin(); |
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| 72 | ++stit; |
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| 73 | while ( stit != in.end() ) { |
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| 74 | out->appendToHistoryTable((*stit)->history()); |
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| 75 | ++stit; |
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| 76 | } |
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[294] | 77 | |
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[805] | 78 | Table& tout = out->table(); |
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[701] | 79 | |
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[805] | 80 | /// @todo check if all scantables are conformant |
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[294] | 81 | |
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[805] | 82 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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| 83 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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| 84 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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| 85 | ScalarColumn<Double> mjdColOut(tout,"TIME"); |
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| 86 | ScalarColumn<Double> intColOut(tout,"INTERVAL"); |
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[262] | 87 | |
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[805] | 88 | // set up the output table rows. These are based on the structure of the |
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[862] | 89 | // FIRST scantable in the vector |
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[805] | 90 | const Table& baset = in[0]->table(); |
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[262] | 91 | |
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[805] | 92 | Block<String> cols(3); |
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| 93 | cols[0] = String("BEAMNO"); |
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| 94 | cols[1] = String("IFNO"); |
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| 95 | cols[2] = String("POLNO"); |
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| 96 | if ( avmode == "SOURCE" ) { |
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| 97 | cols.resize(4); |
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| 98 | cols[3] = String("SRCNAME"); |
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[488] | 99 | } |
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[805] | 100 | if ( avmode == "SCAN" && in.size() == 1) { |
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| 101 | cols.resize(4); |
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| 102 | cols[3] = String("SCANNO"); |
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[2] | 103 | } |
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[805] | 104 | uInt outrowCount = 0; |
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| 105 | TableIterator iter(baset, cols); |
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| 106 | while (!iter.pastEnd()) { |
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| 107 | Table subt = iter.table(); |
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| 108 | // copy the first row of this selection into the new table |
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| 109 | tout.addRow(); |
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| 110 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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| 111 | ++outrowCount; |
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| 112 | ++iter; |
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[144] | 113 | } |
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[805] | 114 | RowAccumulator acc(wtype); |
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[858] | 115 | Vector<Bool> cmask(mask); |
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| 116 | acc.setUserMask(cmask); |
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[805] | 117 | ROTableRow row(tout); |
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| 118 | ROArrayColumn<Float> specCol, tsysCol; |
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| 119 | ROArrayColumn<uChar> flagCol; |
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| 120 | ROScalarColumn<Double> mjdCol, intCol; |
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| 121 | ROScalarColumn<Int> scanIDCol; |
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[144] | 122 | |
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[805] | 123 | for (uInt i=0; i < tout.nrow(); ++i) { |
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| 124 | for ( int j=0; j < in.size(); ++j ) { |
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| 125 | const Table& tin = in[j]->table(); |
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| 126 | const TableRecord& rec = row.get(i); |
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| 127 | ROScalarColumn<Double> tmp(tin, "TIME"); |
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| 128 | Double td;tmp.get(0,td); |
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| 129 | Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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| 130 | && tin.col("IFNO") == Int(rec.asuInt("IFNO")) |
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| 131 | && tin.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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| 132 | Table subt; |
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| 133 | if ( avmode == "SOURCE") { |
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| 134 | subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") ); |
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| 135 | } else if (avmode == "SCAN") { |
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| 136 | subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) ); |
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| 137 | } else { |
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| 138 | subt = basesubt; |
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| 139 | } |
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| 140 | specCol.attach(subt,"SPECTRA"); |
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| 141 | flagCol.attach(subt,"FLAGTRA"); |
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| 142 | tsysCol.attach(subt,"TSYS"); |
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| 143 | intCol.attach(subt,"INTERVAL"); |
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| 144 | mjdCol.attach(subt,"TIME"); |
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| 145 | Vector<Float> spec,tsys; |
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| 146 | Vector<uChar> flag; |
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| 147 | Double inter,time; |
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| 148 | for (uInt k = 0; k < subt.nrow(); ++k ) { |
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| 149 | flagCol.get(k, flag); |
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| 150 | Vector<Bool> bflag(flag.shape()); |
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| 151 | convertArray(bflag, flag); |
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| 152 | if ( allEQ(bflag, True) ) { |
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| 153 | continue;//don't accumulate |
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[144] | 154 | } |
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[805] | 155 | specCol.get(k, spec); |
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| 156 | tsysCol.get(k, tsys); |
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| 157 | intCol.get(k, inter); |
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| 158 | mjdCol.get(k, time); |
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| 159 | // spectrum has to be added last to enable weighting by the other values |
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| 160 | acc.add(spec, !bflag, tsys, inter, time); |
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| 161 | } |
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| 162 | } |
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| 163 | //write out |
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| 164 | specColOut.put(i, acc.getSpectrum()); |
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| 165 | const Vector<Bool>& msk = acc.getMask(); |
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| 166 | Vector<uChar> flg(msk.shape()); |
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| 167 | convertArray(flg, !msk); |
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| 168 | flagColOut.put(i, flg); |
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| 169 | tsysColOut.put(i, acc.getTsys()); |
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| 170 | intColOut.put(i, acc.getInterval()); |
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| 171 | mjdColOut.put(i, acc.getTime()); |
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| 172 | acc.reset(); |
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[144] | 173 | } |
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[805] | 174 | return out; |
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[2] | 175 | } |
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[9] | 176 | |
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[805] | 177 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in, |
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| 178 | bool droprows) |
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[185] | 179 | { |
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[805] | 180 | if (insitu_) return in; |
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| 181 | else { |
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| 182 | // clone |
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| 183 | Scantable* tabp = new Scantable(*in, Bool(droprows)); |
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| 184 | return CountedPtr<Scantable>(tabp); |
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[234] | 185 | } |
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[805] | 186 | } |
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[234] | 187 | |
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[805] | 188 | CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in, |
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| 189 | float val, |
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| 190 | const std::string& mode, |
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| 191 | bool tsys ) |
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| 192 | { |
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| 193 | // modes are "ADD" and "MUL" |
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| 194 | CountedPtr< Scantable > out = getScantable(in, false); |
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| 195 | Table& tab = out->table(); |
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| 196 | ArrayColumn<Float> specCol(tab,"SPECTRA"); |
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| 197 | ArrayColumn<Float> tsysCol(tab,"TSYS"); |
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| 198 | for (uInt i=0; i<tab.nrow(); ++i) { |
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| 199 | Vector<Float> spec; |
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| 200 | Vector<Float> ts; |
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| 201 | specCol.get(i, spec); |
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| 202 | tsysCol.get(i, ts); |
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| 203 | if (mode == "MUL") { |
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| 204 | spec *= val; |
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| 205 | specCol.put(i, spec); |
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| 206 | if ( tsys ) { |
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| 207 | ts *= val; |
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| 208 | tsysCol.put(i, ts); |
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| 209 | } |
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| 210 | } else if ( mode == "ADD" ) { |
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| 211 | spec += val; |
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| 212 | specCol.put(i, spec); |
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| 213 | if ( tsys ) { |
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| 214 | ts += val; |
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| 215 | tsysCol.put(i, ts); |
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| 216 | } |
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| 217 | } |
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[234] | 218 | } |
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[805] | 219 | return out; |
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| 220 | } |
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[234] | 221 | |
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[805] | 222 | MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s, |
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| 223 | const Vector<uChar>& f) |
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| 224 | { |
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| 225 | Vector<Bool> mask; |
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| 226 | mask.resize(f.shape()); |
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| 227 | convertArray(mask, f); |
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| 228 | return MaskedArray<Float>(s,!mask); |
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| 229 | } |
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[248] | 230 | |
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[805] | 231 | Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma) |
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| 232 | { |
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| 233 | const Vector<Bool>& m = ma.getMask(); |
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| 234 | Vector<uChar> flags(m.shape()); |
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| 235 | convertArray(flags, !m); |
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| 236 | return flags; |
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| 237 | } |
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[234] | 238 | |
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[805] | 239 | CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable >& in, |
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| 240 | const std::string & mode, |
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| 241 | bool preserve ) |
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| 242 | { |
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| 243 | /// @todo make other modes available |
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| 244 | /// modes should be "nearest", "pair" |
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| 245 | // make this operation non insitu |
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| 246 | const Table& tin = in->table(); |
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| 247 | Table ons = tin(tin.col("SRCTYPE") == Int(0)); |
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| 248 | Table offs = tin(tin.col("SRCTYPE") == Int(1)); |
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| 249 | if ( offs.nrow() == 0 ) |
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| 250 | throw(AipsError("No 'off' scans present.")); |
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| 251 | // put all "on" scans into output table |
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[701] | 252 | |
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[805] | 253 | bool insitu = insitu_; |
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| 254 | setInsitu(false); |
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| 255 | CountedPtr< Scantable > out = getScantable(in, true); |
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| 256 | setInsitu(insitu); |
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| 257 | Table& tout = out->table(); |
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[248] | 258 | |
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[805] | 259 | TableCopy::copyRows(tout, ons); |
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| 260 | TableRow row(tout); |
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| 261 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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[234] | 262 | |
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[805] | 263 | ArrayColumn<Float> outspecCol(tout, "SPECTRA"); |
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| 264 | ROArrayColumn<Float> outtsysCol(tout, "TSYS"); |
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| 265 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA"); |
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[780] | 266 | |
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[805] | 267 | for (uInt i=0; i < tout.nrow(); ++i) { |
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| 268 | const TableRecord& rec = row.get(i); |
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| 269 | Double ontime = rec.asDouble("TIME"); |
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| 270 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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| 271 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime)); |
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| 272 | Table sel = offs( abs(offs.col("TIME")-ontime) <= mindeltat |
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| 273 | && offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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| 274 | && offs.col("IFNO") == Int(rec.asuInt("IFNO")) |
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| 275 | && offs.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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[780] | 276 | |
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[805] | 277 | TableRow offrow(sel); |
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| 278 | const TableRecord& offrec = offrow.get(0);//should only be one row |
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| 279 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
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| 280 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
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| 281 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
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| 282 | /// @fixme this assumes tsys is a scalar not vector |
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| 283 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
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| 284 | Vector<Float> specon, tsyson; |
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| 285 | outtsysCol.get(i, tsyson); |
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| 286 | outspecCol.get(i, specon); |
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| 287 | Vector<uChar> flagon; |
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| 288 | outflagCol.get(i, flagon); |
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| 289 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
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| 290 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
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| 291 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
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| 292 | if (preserve) { |
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| 293 | quot -= tsysoffscalar; |
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| 294 | } else { |
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| 295 | quot -= tsyson[0]; |
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[701] | 296 | } |
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[805] | 297 | outspecCol.put(i, quot.getArray()); |
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| 298 | outflagCol.put(i, flagsFromMA(quot)); |
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| 299 | } |
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| 300 | return out; |
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| 301 | } |
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[234] | 302 | |
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[805] | 303 | CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in ) |
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| 304 | { |
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| 305 | // make copy or reference |
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| 306 | CountedPtr< Scantable > out = getScantable(in, false); |
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| 307 | Table& tout = out->table(); |
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| 308 | Block<String> cols(3); |
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| 309 | cols[0] = String("SCANNO"); |
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| 310 | cols[1] = String("BEAMNO"); |
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| 311 | cols[2] = String("POLNO"); |
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| 312 | TableIterator iter(tout, cols); |
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| 313 | while (!iter.pastEnd()) { |
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| 314 | Table subt = iter.table(); |
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| 315 | // this should leave us with two rows for the two IFs....if not ignore |
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| 316 | if (subt.nrow() != 2 ) { |
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| 317 | continue; |
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[701] | 318 | } |
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[805] | 319 | ArrayColumn<Float> specCol(tout, "SPECTRA"); |
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| 320 | ArrayColumn<Float> tsysCol(tout, "TSYS"); |
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| 321 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA"); |
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| 322 | Vector<Float> onspec,offspec, ontsys, offtsys; |
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| 323 | Vector<uChar> onflag, offflag; |
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| 324 | tsysCol.get(0, ontsys); tsysCol.get(1, offtsys); |
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| 325 | specCol.get(0, onspec); specCol.get(1, offspec); |
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| 326 | flagCol.get(0, onflag); flagCol.get(1, offflag); |
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| 327 | MaskedArray<Float> on = maskedArray(onspec, onflag); |
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| 328 | MaskedArray<Float> off = maskedArray(offspec, offflag); |
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| 329 | MaskedArray<Float> oncopy = on.copy(); |
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[248] | 330 | |
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[805] | 331 | on /= off; on -= 1.0f; |
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| 332 | on *= ontsys[0]; |
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| 333 | off /= oncopy; off -= 1.0f; |
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| 334 | off *= offtsys[0]; |
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| 335 | specCol.put(0, on.getArray()); |
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| 336 | const Vector<Bool>& m0 = on.getMask(); |
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| 337 | Vector<uChar> flags0(m0.shape()); |
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| 338 | convertArray(flags0, !m0); |
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| 339 | flagCol.put(0, flags0); |
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[234] | 340 | |
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[805] | 341 | specCol.put(1, off.getArray()); |
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| 342 | const Vector<Bool>& m1 = off.getMask(); |
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| 343 | Vector<uChar> flags1(m1.shape()); |
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| 344 | convertArray(flags1, !m1); |
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| 345 | flagCol.put(1, flags1); |
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[234] | 346 | |
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[130] | 347 | } |
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[780] | 348 | |
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[805] | 349 | return out; |
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[9] | 350 | } |
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[48] | 351 | |
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[805] | 352 | std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in, |
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| 353 | const std::vector< bool > & mask, |
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| 354 | const std::string& which ) |
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[130] | 355 | { |
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| 356 | |
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[805] | 357 | Vector<Bool> m(mask); |
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| 358 | const Table& tab = in->table(); |
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| 359 | ROArrayColumn<Float> specCol(tab, "SPECTRA"); |
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| 360 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
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| 361 | std::vector<float> out; |
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| 362 | for (uInt i=0; i < tab.nrow(); ++i ) { |
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| 363 | Vector<Float> spec; specCol.get(i, spec); |
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| 364 | MaskedArray<Float> ma = maskedArray(spec, flagCol(i)); |
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| 365 | float outstat; |
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| 366 | if ( spec.nelements() == m.nelements() ) { |
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| 367 | outstat = mathutil::statistics(which, ma(m)); |
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| 368 | } else { |
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| 369 | outstat = mathutil::statistics(which, ma); |
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| 370 | } |
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| 371 | out.push_back(outstat); |
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[234] | 372 | } |
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[805] | 373 | return out; |
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[130] | 374 | } |
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| 375 | |
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[805] | 376 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in, |
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| 377 | int width ) |
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[144] | 378 | { |
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[841] | 379 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data.")); |
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[805] | 380 | CountedPtr< Scantable > out = getScantable(in, false); |
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| 381 | Table& tout = out->table(); |
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| 382 | out->frequencies().rescale(width, "BIN"); |
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| 383 | ArrayColumn<Float> specCol(tout, "SPECTRA"); |
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| 384 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA"); |
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| 385 | for (uInt i=0; i < tout.nrow(); ++i ) { |
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| 386 | MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i)); |
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| 387 | MaskedArray<Float> maout; |
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| 388 | LatticeUtilities::bin(maout, main, 0, Int(width)); |
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| 389 | /// @todo implement channel based tsys binning |
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| 390 | specCol.put(i, maout.getArray()); |
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| 391 | flagCol.put(i, flagsFromMA(maout)); |
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| 392 | // take only the first binned spectrum's length for the deprecated |
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| 393 | // global header item nChan |
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| 394 | if (i==0) tout.rwKeywordSet().define(String("nChan"), |
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| 395 | Int(maout.getArray().nelements())); |
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[169] | 396 | } |
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[805] | 397 | return out; |
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[146] | 398 | } |
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| 399 | |
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[805] | 400 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in, |
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| 401 | const std::string& method, |
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| 402 | float width ) |
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[299] | 403 | // |
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| 404 | // Should add the possibility of width being specified in km/s. This means |
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[780] | 405 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
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| 406 | // average channel width (say at the reference pixel). Then we would need |
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| 407 | // to be careful to make sure each spectrum (of different freqID) |
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[299] | 408 | // is the same length. |
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| 409 | // |
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| 410 | { |
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[317] | 411 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
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[805] | 412 | Int interpMethod(stringToIMethod(method)); |
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[299] | 413 | |
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[805] | 414 | CountedPtr< Scantable > out = getScantable(in, false); |
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| 415 | Table& tout = out->table(); |
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[299] | 416 | |
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| 417 | // Resample SpectralCoordinates (one per freqID) |
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[805] | 418 | out->frequencies().rescale(width, "RESAMPLE"); |
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| 419 | TableIterator iter(tout, "IFNO"); |
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| 420 | TableRow row(tout); |
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| 421 | while ( !iter.pastEnd() ) { |
---|
| 422 | Table tab = iter.table(); |
---|
| 423 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 424 | //ArrayColumn<Float> tsysCol(tout, "TSYS"); |
---|
| 425 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 426 | Vector<Float> spec; |
---|
| 427 | Vector<uChar> flag; |
---|
| 428 | specCol.get(0,spec); // the number of channels should be constant per IF |
---|
| 429 | uInt nChanIn = spec.nelements(); |
---|
| 430 | Vector<Float> xIn(nChanIn); indgen(xIn); |
---|
| 431 | Int fac = Int(nChanIn/width); |
---|
| 432 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
| 433 | uInt k = 0; |
---|
| 434 | Float x = 0.0; |
---|
| 435 | while (x < Float(nChanIn) ) { |
---|
| 436 | xOut(k) = x; |
---|
| 437 | k++; |
---|
| 438 | x += width; |
---|
| 439 | } |
---|
| 440 | uInt nChanOut = k; |
---|
| 441 | xOut.resize(nChanOut, True); |
---|
| 442 | // process all rows for this IFNO |
---|
| 443 | Vector<Float> specOut; |
---|
| 444 | Vector<Bool> maskOut; |
---|
| 445 | Vector<uChar> flagOut; |
---|
| 446 | for (uInt i=0; i < tab.nrow(); ++i) { |
---|
| 447 | specCol.get(i, spec); |
---|
| 448 | flagCol.get(i, flag); |
---|
| 449 | Vector<Bool> mask(flag.nelements()); |
---|
| 450 | convertArray(mask, flag); |
---|
[299] | 451 | |
---|
[805] | 452 | IPosition shapeIn(spec.shape()); |
---|
| 453 | //sh.nchan = nChanOut; |
---|
| 454 | InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut, |
---|
| 455 | xIn, spec, mask, |
---|
| 456 | interpMethod, True, True); |
---|
| 457 | /// @todo do the same for channel based Tsys |
---|
| 458 | flagOut.resize(maskOut.nelements()); |
---|
| 459 | convertArray(flagOut, maskOut); |
---|
| 460 | specCol.put(i, specOut); |
---|
| 461 | flagCol.put(i, flagOut); |
---|
| 462 | } |
---|
| 463 | ++iter; |
---|
[299] | 464 | } |
---|
| 465 | |
---|
[805] | 466 | return out; |
---|
| 467 | } |
---|
[299] | 468 | |
---|
[805] | 469 | STMath::imethod STMath::stringToIMethod(const std::string& in) |
---|
| 470 | { |
---|
| 471 | static STMath::imap lookup; |
---|
[299] | 472 | |
---|
[805] | 473 | // initialize the lookup table if necessary |
---|
| 474 | if ( lookup.empty() ) { |
---|
| 475 | lookup["NEAR"] = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
| 476 | lookup["LIN"] = InterpolateArray1D<Double,Float>::linear; |
---|
| 477 | lookup["CUB"] = InterpolateArray1D<Double,Float>::cubic; |
---|
| 478 | lookup["SPL"] = InterpolateArray1D<Double,Float>::spline; |
---|
[299] | 479 | } |
---|
| 480 | |
---|
[805] | 481 | STMath::imap::const_iterator iter = lookup.find(in); |
---|
[299] | 482 | |
---|
[805] | 483 | if ( lookup.end() == iter ) { |
---|
| 484 | std::string message = in; |
---|
| 485 | message += " is not a valid interpolation mode"; |
---|
| 486 | throw(AipsError(message)); |
---|
[299] | 487 | } |
---|
[805] | 488 | return iter->second; |
---|
[299] | 489 | } |
---|
| 490 | |
---|
[805] | 491 | WeightType STMath::stringToWeight(const std::string& in) |
---|
[146] | 492 | { |
---|
[805] | 493 | static std::map<std::string, WeightType> lookup; |
---|
[434] | 494 | |
---|
[805] | 495 | // initialize the lookup table if necessary |
---|
| 496 | if ( lookup.empty() ) { |
---|
| 497 | lookup["NONE"] = asap::NONE; |
---|
| 498 | lookup["TINT"] = asap::TINT; |
---|
| 499 | lookup["TINTSYS"] = asap::TINTSYS; |
---|
| 500 | lookup["TSYS"] = asap::TSYS; |
---|
| 501 | lookup["VAR"] = asap::VAR; |
---|
| 502 | } |
---|
[434] | 503 | |
---|
[805] | 504 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in); |
---|
[294] | 505 | |
---|
[805] | 506 | if ( lookup.end() == iter ) { |
---|
| 507 | std::string message = in; |
---|
| 508 | message += " is not a valid weighting mode"; |
---|
| 509 | throw(AipsError(message)); |
---|
| 510 | } |
---|
| 511 | return iter->second; |
---|
[146] | 512 | } |
---|
| 513 | |
---|
[805] | 514 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in, |
---|
| 515 | const Vector< Float > & coeffs, |
---|
| 516 | const std::string & filename, |
---|
| 517 | const std::string& method) |
---|
[165] | 518 | { |
---|
[805] | 519 | // Get elevation data from Scantable and convert to degrees |
---|
| 520 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 521 | Table& tab = in->table(); |
---|
| 522 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 523 | Vector<Float> x = elev.getColumn(); |
---|
| 524 | x *= Float(180 / C::pi); // Degrees |
---|
[165] | 525 | |
---|
[805] | 526 | const uInt nc = coeffs.nelements(); |
---|
| 527 | if ( filename.length() > 0 && nc > 0 ) { |
---|
| 528 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
[315] | 529 | } |
---|
[165] | 530 | |
---|
[805] | 531 | // Correct |
---|
| 532 | if ( nc > 0 || filename.length() == 0 ) { |
---|
| 533 | // Find instrument |
---|
| 534 | Bool throwit = True; |
---|
| 535 | Instrument inst = |
---|
| 536 | SDAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
| 537 | throwit); |
---|
[165] | 538 | |
---|
[805] | 539 | // Set polynomial |
---|
| 540 | Polynomial<Float>* ppoly = 0; |
---|
| 541 | Vector<Float> coeff; |
---|
| 542 | String msg; |
---|
| 543 | if ( nc > 0 ) { |
---|
| 544 | ppoly = new Polynomial<Float>(nc); |
---|
| 545 | coeff = coeffs; |
---|
| 546 | msg = String("user"); |
---|
| 547 | } else { |
---|
| 548 | SDAttr sdAttr; |
---|
| 549 | coeff = sdAttr.gainElevationPoly(inst); |
---|
| 550 | ppoly = new Polynomial<Float>(3); |
---|
| 551 | msg = String("built in"); |
---|
| 552 | } |
---|
[532] | 553 | |
---|
[805] | 554 | if ( coeff.nelements() > 0 ) { |
---|
| 555 | ppoly->setCoefficients(coeff); |
---|
| 556 | } else { |
---|
| 557 | delete ppoly; |
---|
| 558 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
| 559 | } |
---|
| 560 | ostringstream oss; |
---|
| 561 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl; |
---|
| 562 | oss << " " << coeff; |
---|
| 563 | pushLog(String(oss)); |
---|
| 564 | const uInt nrow = tab.nrow(); |
---|
| 565 | Vector<Float> factor(nrow); |
---|
| 566 | for ( uInt i=0; i < nrow; ++i ) { |
---|
| 567 | factor[i] = 1.0 / (*ppoly)(x[i]); |
---|
| 568 | } |
---|
| 569 | delete ppoly; |
---|
| 570 | scaleByVector(tab, factor, true); |
---|
[532] | 571 | |
---|
[805] | 572 | } else { |
---|
| 573 | // Read and correct |
---|
| 574 | pushLog("Making correction from ascii Table"); |
---|
| 575 | scaleFromAsciiTable(tab, filename, method, x, true); |
---|
[532] | 576 | } |
---|
[805] | 577 | return out; |
---|
| 578 | } |
---|
[165] | 579 | |
---|
[805] | 580 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename, |
---|
| 581 | const std::string& method, |
---|
| 582 | const Vector<Float>& xout, bool dotsys) |
---|
| 583 | { |
---|
[165] | 584 | |
---|
[805] | 585 | // Read gain-elevation ascii file data into a Table. |
---|
[165] | 586 | |
---|
[805] | 587 | String formatString; |
---|
| 588 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False); |
---|
| 589 | scaleFromTable(in, tbl, method, xout, dotsys); |
---|
| 590 | } |
---|
[165] | 591 | |
---|
[805] | 592 | void STMath::scaleFromTable(Table& in, |
---|
| 593 | const Table& table, |
---|
| 594 | const std::string& method, |
---|
| 595 | const Vector<Float>& xout, bool dotsys) |
---|
| 596 | { |
---|
[780] | 597 | |
---|
[805] | 598 | ROScalarColumn<Float> geElCol(table, "ELEVATION"); |
---|
| 599 | ROScalarColumn<Float> geFacCol(table, "FACTOR"); |
---|
| 600 | Vector<Float> xin = geElCol.getColumn(); |
---|
| 601 | Vector<Float> yin = geFacCol.getColumn(); |
---|
| 602 | Vector<Bool> maskin(xin.nelements(),True); |
---|
[165] | 603 | |
---|
[805] | 604 | // Interpolate (and extrapolate) with desired method |
---|
[532] | 605 | |
---|
[805] | 606 | //InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
| 607 | Int intmethod(stringToIMethod(method)); |
---|
[165] | 608 | |
---|
[805] | 609 | Vector<Float> yout; |
---|
| 610 | Vector<Bool> maskout; |
---|
| 611 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout, |
---|
| 612 | xin, yin, maskin, intmethod, |
---|
| 613 | True, True); |
---|
[165] | 614 | |
---|
[805] | 615 | scaleByVector(in, Float(1.0)/yout, dotsys); |
---|
[165] | 616 | } |
---|
[167] | 617 | |
---|
[805] | 618 | void STMath::scaleByVector( Table& in, |
---|
| 619 | const Vector< Float >& factor, |
---|
| 620 | bool dotsys ) |
---|
[177] | 621 | { |
---|
[805] | 622 | uInt nrow = in.nrow(); |
---|
| 623 | if ( factor.nelements() != nrow ) { |
---|
| 624 | throw(AipsError("factors.nelements() != table.nelements()")); |
---|
| 625 | } |
---|
| 626 | ArrayColumn<Float> specCol(in, "SPECTRA"); |
---|
| 627 | ArrayColumn<uChar> flagCol(in, "FLAGTRA"); |
---|
| 628 | ArrayColumn<Float> tsysCol(in, "TSYS"); |
---|
| 629 | for (uInt i=0; i < nrow; ++i) { |
---|
| 630 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
| 631 | ma *= factor[i]; |
---|
| 632 | specCol.put(i, ma.getArray()); |
---|
| 633 | flagCol.put(i, flagsFromMA(ma)); |
---|
| 634 | if ( dotsys ) { |
---|
| 635 | Vector<Float> tsys; |
---|
| 636 | tsysCol.get(i, tsys); |
---|
| 637 | tsys *= factor[i]; |
---|
| 638 | specCol.put(i,tsys); |
---|
| 639 | } |
---|
| 640 | } |
---|
[177] | 641 | } |
---|
| 642 | |
---|
[805] | 643 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in, |
---|
| 644 | float d, float etaap, |
---|
| 645 | float jyperk ) |
---|
[221] | 646 | { |
---|
[805] | 647 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 648 | Table& tab = in->table(); |
---|
| 649 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit")); |
---|
[221] | 650 | Unit K(String("K")); |
---|
| 651 | Unit JY(String("Jy")); |
---|
[701] | 652 | |
---|
[805] | 653 | bool tokelvin = true; |
---|
| 654 | Double cfac = 1.0; |
---|
[716] | 655 | |
---|
[805] | 656 | if ( fluxUnit == JY ) { |
---|
[716] | 657 | pushLog("Converting to K"); |
---|
[701] | 658 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 659 | Quantum<Double> t2 = t.get(JY); |
---|
[805] | 660 | cfac = (t2 / t).getValue(); // value to Jy |
---|
[780] | 661 | |
---|
[805] | 662 | tokelvin = true; |
---|
| 663 | out->setFluxUnit("K"); |
---|
| 664 | } else if ( fluxUnit == K ) { |
---|
[716] | 665 | pushLog("Converting to Jy"); |
---|
[701] | 666 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 667 | Quantum<Double> t2 = t.get(K); |
---|
[805] | 668 | cfac = (t2 / t).getValue(); // value to K |
---|
[780] | 669 | |
---|
[805] | 670 | tokelvin = false; |
---|
| 671 | out->setFluxUnit("Jy"); |
---|
[221] | 672 | } else { |
---|
[701] | 673 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 674 | } |
---|
[701] | 675 | // Make sure input values are converted to either Jy or K first... |
---|
[805] | 676 | Float factor = cfac; |
---|
[221] | 677 | |
---|
[701] | 678 | // Select method |
---|
[805] | 679 | if (jyperk > 0.0) { |
---|
| 680 | factor *= jyperk; |
---|
| 681 | if ( tokelvin ) factor = 1.0 / jyperk; |
---|
[716] | 682 | ostringstream oss; |
---|
[805] | 683 | oss << "Jy/K = " << jyperk; |
---|
[716] | 684 | pushLog(String(oss)); |
---|
[805] | 685 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 686 | scaleByVector(tab,factors, false); |
---|
| 687 | } else if ( etaap > 0.0) { |
---|
| 688 | Instrument inst = |
---|
| 689 | SDAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True); |
---|
[701] | 690 | SDAttr sda; |
---|
[805] | 691 | if (d < 0) d = sda.diameter(inst); |
---|
| 692 | Float jyPerk = SDAttr::findJyPerK(etaap, d); |
---|
[716] | 693 | ostringstream oss; |
---|
[805] | 694 | oss << "Jy/K = " << jyperk; |
---|
[716] | 695 | pushLog(String(oss)); |
---|
[805] | 696 | factor *= jyperk; |
---|
| 697 | if ( tokelvin ) { |
---|
[701] | 698 | factor = 1.0 / factor; |
---|
| 699 | } |
---|
[805] | 700 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 701 | scaleByVector(tab, factors, False); |
---|
[354] | 702 | } else { |
---|
[780] | 703 | |
---|
[701] | 704 | // OK now we must deal with automatic look up of values. |
---|
| 705 | // We must also deal with the fact that the factors need |
---|
| 706 | // to be computed per IF and may be different and may |
---|
| 707 | // change per integration. |
---|
[780] | 708 | |
---|
[716] | 709 | pushLog("Looking up conversion factors"); |
---|
[805] | 710 | convertBrightnessUnits(out, tokelvin, cfac); |
---|
[701] | 711 | } |
---|
[805] | 712 | |
---|
| 713 | return out; |
---|
[221] | 714 | } |
---|
| 715 | |
---|
[805] | 716 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in, |
---|
| 717 | bool tokelvin, float cfac ) |
---|
[227] | 718 | { |
---|
[805] | 719 | Table& table = in->table(); |
---|
| 720 | Instrument inst = |
---|
| 721 | SDAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True); |
---|
| 722 | TableIterator iter(table, "FREQ_ID"); |
---|
| 723 | STFrequencies stfreqs = in->frequencies(); |
---|
| 724 | SDAttr sdAtt; |
---|
| 725 | while (!iter.pastEnd()) { |
---|
| 726 | Table tab = iter.table(); |
---|
| 727 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 728 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 729 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID"); |
---|
| 730 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
[234] | 731 | |
---|
[805] | 732 | uInt freqid; freqidCol.get(0, freqid); |
---|
| 733 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
| 734 | // SDAttr.JyPerK has a Vector interface... change sometime. |
---|
| 735 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements())); |
---|
| 736 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 737 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0]; |
---|
| 738 | Float factor = cfac * jyperk; |
---|
| 739 | if ( tokelvin ) factor = Float(1.0) / factor; |
---|
| 740 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
| 741 | ma *= factor; |
---|
| 742 | specCol.put(i, ma.getArray()); |
---|
| 743 | flagCol.put(i, flagsFromMA(ma)); |
---|
| 744 | } |
---|
[234] | 745 | } |
---|
[230] | 746 | } |
---|
[227] | 747 | |
---|
[805] | 748 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in, |
---|
| 749 | float tau ) |
---|
[234] | 750 | { |
---|
[805] | 751 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 752 | Table& tab = in->table(); |
---|
[234] | 753 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[805] | 754 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 755 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 756 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 757 | Float zdist = Float(C::pi_2) - elev(i); |
---|
| 758 | Float factor = exp(tau)/cos(zdist); |
---|
| 759 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
| 760 | ma *= factor; |
---|
| 761 | specCol.put(i, ma.getArray()); |
---|
| 762 | flagCol.put(i, flagsFromMA(ma)); |
---|
[234] | 763 | } |
---|
[805] | 764 | return out; |
---|
[234] | 765 | } |
---|
| 766 | |
---|
[805] | 767 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in, |
---|
| 768 | const std::string& kernel, float width ) |
---|
[457] | 769 | { |
---|
[805] | 770 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 771 | Table& table = in->table(); |
---|
| 772 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel); |
---|
| 773 | // same IFNO should have same no of channels |
---|
| 774 | // this saves overhead |
---|
| 775 | TableIterator iter(table, "IFNO"); |
---|
| 776 | while (!iter.pastEnd()) { |
---|
| 777 | Table tab = iter.table(); |
---|
| 778 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 779 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 780 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
| 781 | uInt nchan = tmpspec.nelements(); |
---|
| 782 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False); |
---|
| 783 | Convolver<Float> conv(kvec, IPosition(1,nchan)); |
---|
| 784 | Vector<Float> spec; |
---|
| 785 | Vector<uChar> flag; |
---|
| 786 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 787 | specCol.get(i, spec); |
---|
| 788 | flagCol.get(i, flag); |
---|
| 789 | Vector<Bool> mask(flag.nelements()); |
---|
| 790 | convertArray(mask, flag); |
---|
| 791 | Vector<Float> specout; |
---|
| 792 | if ( type == VectorKernel::HANNING ) { |
---|
| 793 | Vector<Bool> maskout; |
---|
| 794 | mathutil::hanning(specout, maskout, spec , mask); |
---|
| 795 | convertArray(flag, maskout); |
---|
| 796 | flagCol.put(i, flag); |
---|
| 797 | } else { |
---|
| 798 | mathutil::replaceMaskByZero(specout, mask); |
---|
| 799 | conv.linearConv(specout, spec); |
---|
[354] | 800 | } |
---|
[805] | 801 | specCol.put(i, specout); |
---|
| 802 | } |
---|
[701] | 803 | } |
---|
[805] | 804 | return out; |
---|
[701] | 805 | } |
---|
[841] | 806 | |
---|
| 807 | CountedPtr< Scantable > |
---|
| 808 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in ) |
---|
| 809 | { |
---|
| 810 | if ( in.size() < 2 ) { |
---|
[862] | 811 | throw(AipsError("Need at least two scantables to perform a merge.")); |
---|
[841] | 812 | } |
---|
| 813 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin(); |
---|
| 814 | bool insitu = insitu_; |
---|
| 815 | setInsitu(false); |
---|
[862] | 816 | CountedPtr< Scantable > out = getScantable(*it, false); |
---|
[841] | 817 | setInsitu(insitu); |
---|
| 818 | Table& tout = out->table(); |
---|
| 819 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID"); |
---|
| 820 | ScalarColumn<uInt> scannocol(tout,"SCANNO"),focusidcol(tout,"FOCUS_ID"); |
---|
| 821 | uInt newscanno = max(scannocol.getColumn())+1; |
---|
[862] | 822 | ++it; |
---|
[841] | 823 | while ( it != in.end() ){ |
---|
| 824 | if ( ! (*it)->conformant(*out) ) { |
---|
| 825 | // log message: "ignoring scantable i, as it isn't |
---|
| 826 | // conformant with the other(s)" |
---|
| 827 | cerr << "oh oh" << endl; |
---|
| 828 | ++it; |
---|
| 829 | continue; |
---|
| 830 | } |
---|
[862] | 831 | out->appendToHistoryTable((*it)->history()); |
---|
[841] | 832 | const Table& tab = (*it)->table(); |
---|
| 833 | TableIterator scanit(tab, "SCANNO"); |
---|
| 834 | while (!scanit.pastEnd()) { |
---|
| 835 | TableIterator freqit(scanit.table(), "FREQ_ID"); |
---|
| 836 | while ( !freqit.pastEnd() ) { |
---|
| 837 | Table thetab = freqit.table(); |
---|
| 838 | uInt nrow = tout.nrow(); |
---|
| 839 | //tout.addRow(thetab.nrow()); |
---|
| 840 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow()); |
---|
| 841 | ROTableRow row(thetab); |
---|
| 842 | for ( uInt i=0; i<thetab.nrow(); ++i) { |
---|
| 843 | uInt k = nrow+i; |
---|
| 844 | scannocol.put(k, newscanno); |
---|
| 845 | const TableRecord& rec = row.get(i); |
---|
| 846 | Double rv,rp,inc; |
---|
| 847 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID")); |
---|
| 848 | uInt id; |
---|
| 849 | id = out->frequencies().addEntry(rp, rv, inc); |
---|
| 850 | freqidcol.put(k,id); |
---|
| 851 | String name,fname;Double rf; |
---|
| 852 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID")); |
---|
| 853 | id = out->molecules().addEntry(rf, name, fname); |
---|
| 854 | molidcol.put(k, id); |
---|
| 855 | Float frot,fang,ftan; |
---|
| 856 | (*it)->focus().getEntry(frot, fang, ftan, rec.asuInt("FOCUS_ID")); |
---|
| 857 | id = out->focus().addEntry(frot, fang, ftan); |
---|
| 858 | focusidcol.put(k, id); |
---|
| 859 | } |
---|
| 860 | ++freqit; |
---|
| 861 | } |
---|
| 862 | ++newscanno; |
---|
| 863 | ++scanit; |
---|
| 864 | } |
---|
| 865 | ++it; |
---|
| 866 | } |
---|
| 867 | return out; |
---|
| 868 | } |
---|