[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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[917] | 26 | #include <tables/Tables/TabVecMath.h> |
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[805] | 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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[2] | 30 | |
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[262] | 31 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 32 | |
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[917] | 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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[177] | 38 | #include <scimath/Mathematics/VectorKernel.h> |
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| 39 | #include <scimath/Mathematics/Convolver.h> |
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[234] | 40 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 41 | |
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[38] | 42 | #include "MathUtils.h" |
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[805] | 43 | #include "RowAccumulator.h" |
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[878] | 44 | #include "STAttr.h" |
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[805] | 45 | #include "STMath.h" |
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[2] | 46 | |
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[805] | 47 | using namespace casa; |
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[2] | 48 | |
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[83] | 49 | using namespace asap; |
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[2] | 50 | |
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[805] | 51 | STMath::STMath(bool insitu) : |
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| 52 | insitu_(insitu) |
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[716] | 53 | { |
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| 54 | } |
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[170] | 55 | |
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| 56 | |
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[805] | 57 | STMath::~STMath() |
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[170] | 58 | { |
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| 59 | } |
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| 60 | |
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[805] | 61 | CountedPtr<Scantable> |
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[926] | 62 | STMath::average( const std::vector<CountedPtr<Scantable> >& scantbls, |
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[858] | 63 | const std::vector<bool>& mask, |
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[805] | 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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[262] | 67 | { |
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[926] | 68 | if ( avmode == "SCAN" && scantbls.size() != 1 ) |
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[805] | 69 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables")); |
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| 70 | WeightType wtype = stringToWeight(weight); |
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[926] | 71 | |
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[934] | 72 | std::vector<CountedPtr<Scantable> >* in = |
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| 73 | const_cast<std::vector<CountedPtr<Scantable> >*>(&scantbls); |
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[926] | 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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[940] | 79 | |
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[926] | 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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[805] | 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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[926] | 89 | CountedPtr< Scantable > out = getScantable((*in)[0], true); |
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[805] | 90 | setInsitu(insitu); |
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[926] | 91 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in->begin(); |
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[862] | 92 | ++stit; |
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[926] | 93 | while ( stit != in->end() ) { |
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[862] | 94 | out->appendToHistoryTable((*stit)->history()); |
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| 95 | ++stit; |
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| 96 | } |
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[294] | 97 | |
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[805] | 98 | Table& tout = out->table(); |
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[701] | 99 | |
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[805] | 100 | /// @todo check if all scantables are conformant |
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[294] | 101 | |
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[805] | 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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[262] | 107 | |
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[805] | 108 | // set up the output table rows. These are based on the structure of the |
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[862] | 109 | // FIRST scantable in the vector |
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[926] | 110 | const Table& baset = (*in)[0]->table(); |
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[262] | 111 | |
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[805] | 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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[488] | 119 | } |
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[926] | 120 | if ( avmode == "SCAN" && in->size() == 1) { |
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[805] | 121 | cols.resize(4); |
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| 122 | cols[3] = String("SCANNO"); |
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[2] | 123 | } |
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[805] | 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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[144] | 133 | } |
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[805] | 134 | RowAccumulator acc(wtype); |
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[858] | 135 | Vector<Bool> cmask(mask); |
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| 136 | acc.setUserMask(cmask); |
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[805] | 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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[144] | 142 | |
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[805] | 143 | for (uInt i=0; i < tout.nrow(); ++i) { |
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[926] | 144 | for ( int j=0; j < in->size(); ++j ) { |
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| 145 | const Table& tin = (*in)[j]->table(); |
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[805] | 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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[144] | 174 | } |
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[805] | 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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[144] | 193 | } |
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[805] | 194 | return out; |
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[2] | 195 | } |
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[9] | 196 | |
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[805] | 197 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in, |
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| 198 | bool droprows) |
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[185] | 199 | { |
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[805] | 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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[234] | 205 | } |
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[805] | 206 | } |
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[234] | 207 | |
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[805] | 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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[234] | 238 | } |
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[805] | 239 | return out; |
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| 240 | } |
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[234] | 241 | |
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[805] | 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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[248] | 250 | |
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[805] | 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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[234] | 258 | |
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[805] | 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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[701] | 272 | |
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[805] | 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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[248] | 278 | |
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[805] | 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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[234] | 282 | |
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[805] | 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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[780] | 295 | |
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[805] | 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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[701] | 315 | } |
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[805] | 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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[926] | 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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[805] | 329 | return out; |
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| 330 | } |
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[234] | 331 | |
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[805] | 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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[701] | 347 | } |
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[805] | 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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[248] | 359 | |
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[805] | 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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[234] | 369 | |
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[805] | 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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[867] | 375 | ++iter; |
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[130] | 376 | } |
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[780] | 377 | |
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[805] | 378 | return out; |
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[9] | 379 | } |
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[48] | 380 | |
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[805] | 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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[130] | 384 | { |
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| 385 | |
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[805] | 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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[867] | 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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[805] | 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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[234] | 402 | } |
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[805] | 403 | return out; |
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[130] | 404 | } |
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| 405 | |
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[805] | 406 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in, |
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| 407 | int width ) |
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[144] | 408 | { |
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[841] | 409 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data.")); |
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[805] | 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)); |
---|
| 419 | /// @todo implement channel based tsys binning |
---|
| 420 | specCol.put(i, maout.getArray()); |
---|
| 421 | flagCol.put(i, flagsFromMA(maout)); |
---|
| 422 | // take only the first binned spectrum's length for the deprecated |
---|
| 423 | // global header item nChan |
---|
| 424 | if (i==0) tout.rwKeywordSet().define(String("nChan"), |
---|
| 425 | Int(maout.getArray().nelements())); |
---|
[169] | 426 | } |
---|
[805] | 427 | return out; |
---|
[146] | 428 | } |
---|
| 429 | |
---|
[805] | 430 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in, |
---|
| 431 | const std::string& method, |
---|
| 432 | float width ) |
---|
[299] | 433 | // |
---|
| 434 | // Should add the possibility of width being specified in km/s. This means |
---|
[780] | 435 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
| 436 | // average channel width (say at the reference pixel). Then we would need |
---|
| 437 | // to be careful to make sure each spectrum (of different freqID) |
---|
[299] | 438 | // is the same length. |
---|
| 439 | // |
---|
| 440 | { |
---|
[317] | 441 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
[805] | 442 | Int interpMethod(stringToIMethod(method)); |
---|
[299] | 443 | |
---|
[805] | 444 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 445 | Table& tout = out->table(); |
---|
[299] | 446 | |
---|
| 447 | // Resample SpectralCoordinates (one per freqID) |
---|
[805] | 448 | out->frequencies().rescale(width, "RESAMPLE"); |
---|
| 449 | TableIterator iter(tout, "IFNO"); |
---|
| 450 | TableRow row(tout); |
---|
| 451 | while ( !iter.pastEnd() ) { |
---|
| 452 | Table tab = iter.table(); |
---|
| 453 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 454 | //ArrayColumn<Float> tsysCol(tout, "TSYS"); |
---|
| 455 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 456 | Vector<Float> spec; |
---|
| 457 | Vector<uChar> flag; |
---|
| 458 | specCol.get(0,spec); // the number of channels should be constant per IF |
---|
| 459 | uInt nChanIn = spec.nelements(); |
---|
| 460 | Vector<Float> xIn(nChanIn); indgen(xIn); |
---|
| 461 | Int fac = Int(nChanIn/width); |
---|
| 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); |
---|
[299] | 481 | |
---|
[805] | 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; |
---|
[299] | 494 | } |
---|
| 495 | |
---|
[805] | 496 | return out; |
---|
| 497 | } |
---|
[299] | 498 | |
---|
[805] | 499 | STMath::imethod STMath::stringToIMethod(const std::string& in) |
---|
| 500 | { |
---|
| 501 | static STMath::imap lookup; |
---|
[299] | 502 | |
---|
[805] | 503 | // initialize the lookup table if necessary |
---|
| 504 | if ( lookup.empty() ) { |
---|
[926] | 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; |
---|
[299] | 509 | } |
---|
| 510 | |
---|
[805] | 511 | STMath::imap::const_iterator iter = lookup.find(in); |
---|
[299] | 512 | |
---|
[805] | 513 | if ( lookup.end() == iter ) { |
---|
| 514 | std::string message = in; |
---|
| 515 | message += " is not a valid interpolation mode"; |
---|
| 516 | throw(AipsError(message)); |
---|
[299] | 517 | } |
---|
[805] | 518 | return iter->second; |
---|
[299] | 519 | } |
---|
| 520 | |
---|
[805] | 521 | WeightType STMath::stringToWeight(const std::string& in) |
---|
[146] | 522 | { |
---|
[805] | 523 | static std::map<std::string, WeightType> lookup; |
---|
[434] | 524 | |
---|
[805] | 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 | } |
---|
[434] | 533 | |
---|
[805] | 534 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in); |
---|
[294] | 535 | |
---|
[805] | 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; |
---|
[146] | 542 | } |
---|
| 543 | |
---|
[805] | 544 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in, |
---|
[867] | 545 | const vector< float > & coeff, |
---|
[805] | 546 | const std::string & filename, |
---|
| 547 | const std::string& method) |
---|
[165] | 548 | { |
---|
[805] | 549 | // Get elevation data from Scantable and convert to degrees |
---|
| 550 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[926] | 551 | Table& tab = out->table(); |
---|
[805] | 552 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 553 | Vector<Float> x = elev.getColumn(); |
---|
| 554 | x *= Float(180 / C::pi); // Degrees |
---|
[165] | 555 | |
---|
[867] | 556 | Vector<Float> coeffs(coeff); |
---|
[805] | 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")); |
---|
[315] | 560 | } |
---|
[165] | 561 | |
---|
[805] | 562 | // Correct |
---|
| 563 | if ( nc > 0 || filename.length() == 0 ) { |
---|
| 564 | // Find instrument |
---|
| 565 | Bool throwit = True; |
---|
| 566 | Instrument inst = |
---|
[878] | 567 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
[805] | 568 | throwit); |
---|
[165] | 569 | |
---|
[805] | 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 { |
---|
[878] | 579 | STAttr sdAttr; |
---|
[805] | 580 | coeff = sdAttr.gainElevationPoly(inst); |
---|
| 581 | ppoly = new Polynomial<Float>(3); |
---|
| 582 | msg = String("built in"); |
---|
| 583 | } |
---|
[532] | 584 | |
---|
[805] | 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); |
---|
[532] | 602 | |
---|
[805] | 603 | } else { |
---|
| 604 | // Read and correct |
---|
| 605 | pushLog("Making correction from ascii Table"); |
---|
| 606 | scaleFromAsciiTable(tab, filename, method, x, true); |
---|
[532] | 607 | } |
---|
[805] | 608 | return out; |
---|
| 609 | } |
---|
[165] | 610 | |
---|
[805] | 611 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename, |
---|
| 612 | const std::string& method, |
---|
| 613 | const Vector<Float>& xout, bool dotsys) |
---|
| 614 | { |
---|
[165] | 615 | |
---|
[805] | 616 | // Read gain-elevation ascii file data into a Table. |
---|
[165] | 617 | |
---|
[805] | 618 | String formatString; |
---|
| 619 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False); |
---|
| 620 | scaleFromTable(in, tbl, method, xout, dotsys); |
---|
| 621 | } |
---|
[165] | 622 | |
---|
[805] | 623 | void STMath::scaleFromTable(Table& in, |
---|
| 624 | const Table& table, |
---|
| 625 | const std::string& method, |
---|
| 626 | const Vector<Float>& xout, bool dotsys) |
---|
| 627 | { |
---|
[780] | 628 | |
---|
[805] | 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); |
---|
[165] | 634 | |
---|
[805] | 635 | // Interpolate (and extrapolate) with desired method |
---|
[532] | 636 | |
---|
[805] | 637 | //InterpolateArray1D<Double,Float>::InterpolationMethod method; |
---|
| 638 | Int intmethod(stringToIMethod(method)); |
---|
[165] | 639 | |
---|
[805] | 640 | Vector<Float> yout; |
---|
| 641 | Vector<Bool> maskout; |
---|
| 642 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout, |
---|
| 643 | xin, yin, maskin, intmethod, |
---|
| 644 | True, True); |
---|
[165] | 645 | |
---|
[805] | 646 | scaleByVector(in, Float(1.0)/yout, dotsys); |
---|
[165] | 647 | } |
---|
[167] | 648 | |
---|
[805] | 649 | void STMath::scaleByVector( Table& in, |
---|
| 650 | const Vector< Float >& factor, |
---|
| 651 | bool dotsys ) |
---|
[177] | 652 | { |
---|
[805] | 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 ) { |
---|
[926] | 666 | Vector<Float> tsys = tsysCol(i); |
---|
[805] | 667 | tsys *= factor[i]; |
---|
[926] | 668 | tsysCol.put(i,tsys); |
---|
[805] | 669 | } |
---|
| 670 | } |
---|
[177] | 671 | } |
---|
| 672 | |
---|
[805] | 673 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in, |
---|
| 674 | float d, float etaap, |
---|
| 675 | float jyperk ) |
---|
[221] | 676 | { |
---|
[805] | 677 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 678 | Table& tab = in->table(); |
---|
| 679 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit")); |
---|
[221] | 680 | Unit K(String("K")); |
---|
| 681 | Unit JY(String("Jy")); |
---|
[701] | 682 | |
---|
[805] | 683 | bool tokelvin = true; |
---|
| 684 | Double cfac = 1.0; |
---|
[716] | 685 | |
---|
[805] | 686 | if ( fluxUnit == JY ) { |
---|
[716] | 687 | pushLog("Converting to K"); |
---|
[701] | 688 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 689 | Quantum<Double> t2 = t.get(JY); |
---|
[805] | 690 | cfac = (t2 / t).getValue(); // value to Jy |
---|
[780] | 691 | |
---|
[805] | 692 | tokelvin = true; |
---|
| 693 | out->setFluxUnit("K"); |
---|
| 694 | } else if ( fluxUnit == K ) { |
---|
[716] | 695 | pushLog("Converting to Jy"); |
---|
[701] | 696 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 697 | Quantum<Double> t2 = t.get(K); |
---|
[805] | 698 | cfac = (t2 / t).getValue(); // value to K |
---|
[780] | 699 | |
---|
[805] | 700 | tokelvin = false; |
---|
| 701 | out->setFluxUnit("Jy"); |
---|
[221] | 702 | } else { |
---|
[701] | 703 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 704 | } |
---|
[701] | 705 | // Make sure input values are converted to either Jy or K first... |
---|
[805] | 706 | Float factor = cfac; |
---|
[221] | 707 | |
---|
[701] | 708 | // Select method |
---|
[805] | 709 | if (jyperk > 0.0) { |
---|
| 710 | factor *= jyperk; |
---|
| 711 | if ( tokelvin ) factor = 1.0 / jyperk; |
---|
[716] | 712 | ostringstream oss; |
---|
[805] | 713 | oss << "Jy/K = " << jyperk; |
---|
[716] | 714 | pushLog(String(oss)); |
---|
[805] | 715 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 716 | scaleByVector(tab,factors, false); |
---|
| 717 | } else if ( etaap > 0.0) { |
---|
| 718 | Instrument inst = |
---|
[878] | 719 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True); |
---|
| 720 | STAttr sda; |
---|
[805] | 721 | if (d < 0) d = sda.diameter(inst); |
---|
[878] | 722 | Float jyPerk = STAttr::findJyPerK(etaap, d); |
---|
[716] | 723 | ostringstream oss; |
---|
[805] | 724 | oss << "Jy/K = " << jyperk; |
---|
[716] | 725 | pushLog(String(oss)); |
---|
[805] | 726 | factor *= jyperk; |
---|
| 727 | if ( tokelvin ) { |
---|
[701] | 728 | factor = 1.0 / factor; |
---|
| 729 | } |
---|
[805] | 730 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 731 | scaleByVector(tab, factors, False); |
---|
[354] | 732 | } else { |
---|
[780] | 733 | |
---|
[701] | 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. |
---|
[780] | 738 | |
---|
[716] | 739 | pushLog("Looking up conversion factors"); |
---|
[805] | 740 | convertBrightnessUnits(out, tokelvin, cfac); |
---|
[701] | 741 | } |
---|
[805] | 742 | |
---|
| 743 | return out; |
---|
[221] | 744 | } |
---|
| 745 | |
---|
[805] | 746 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in, |
---|
| 747 | bool tokelvin, float cfac ) |
---|
[227] | 748 | { |
---|
[805] | 749 | Table& table = in->table(); |
---|
| 750 | Instrument inst = |
---|
[878] | 751 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True); |
---|
[805] | 752 | TableIterator iter(table, "FREQ_ID"); |
---|
| 753 | STFrequencies stfreqs = in->frequencies(); |
---|
[878] | 754 | STAttr sdAtt; |
---|
[805] | 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"); |
---|
[234] | 761 | |
---|
[805] | 762 | uInt freqid; freqidCol.get(0, freqid); |
---|
| 763 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
[878] | 764 | // STAttr.JyPerK has a Vector interface... change sometime. |
---|
[805] | 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 | } |
---|
[867] | 775 | ++iter; |
---|
[234] | 776 | } |
---|
[230] | 777 | } |
---|
[227] | 778 | |
---|
[805] | 779 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in, |
---|
| 780 | float tau ) |
---|
[234] | 781 | { |
---|
[805] | 782 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[926] | 783 | |
---|
| 784 | Table tab = out->table(); |
---|
[234] | 785 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[805] | 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); |
---|
[926] | 791 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
[805] | 792 | ma *= factor; |
---|
| 793 | specCol.put(i, ma.getArray()); |
---|
| 794 | flagCol.put(i, flagsFromMA(ma)); |
---|
[234] | 795 | } |
---|
[805] | 796 | return out; |
---|
[234] | 797 | } |
---|
| 798 | |
---|
[805] | 799 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in, |
---|
| 800 | const std::string& kernel, float width ) |
---|
[457] | 801 | { |
---|
[805] | 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); |
---|
[354] | 832 | } |
---|
[805] | 833 | specCol.put(i, specout); |
---|
| 834 | } |
---|
[867] | 835 | ++iter; |
---|
[701] | 836 | } |
---|
[805] | 837 | return out; |
---|
[701] | 838 | } |
---|
[841] | 839 | |
---|
| 840 | CountedPtr< Scantable > |
---|
| 841 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in ) |
---|
| 842 | { |
---|
| 843 | if ( in.size() < 2 ) { |
---|
[862] | 844 | throw(AipsError("Need at least two scantables to perform a merge.")); |
---|
[841] | 845 | } |
---|
| 846 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin(); |
---|
| 847 | bool insitu = insitu_; |
---|
| 848 | setInsitu(false); |
---|
[862] | 849 | CountedPtr< Scantable > out = getScantable(*it, false); |
---|
[841] | 850 | setInsitu(insitu); |
---|
| 851 | Table& tout = out->table(); |
---|
| 852 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID"); |
---|
[917] | 853 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID"); |
---|
| 854 | // Renumber SCANNO to be 0-based |
---|
[926] | 855 | Vector<uInt> scannos = scannocol.getColumn(); |
---|
| 856 | uInt offset = min(scannos); |
---|
[917] | 857 | scannos -= offset; |
---|
[926] | 858 | scannocol.putColumn(scannos); |
---|
| 859 | uInt newscanno = max(scannos)+1; |
---|
[862] | 860 | ++it; |
---|
[841] | 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 | } |
---|
[862] | 869 | out->appendToHistoryTable((*it)->history()); |
---|
[841] | 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); |
---|
[961] | 893 | Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp; |
---|
| 894 | (*it)->focus().getEntry(fax, ftan, frot, fhand, |
---|
| 895 | fmount,fuser, fxy, fxyp, |
---|
| 896 | rec.asuInt("FOCUS_ID")); |
---|
| 897 | id = out->focus().addEntry(fax, ftan, frot, fhand, |
---|
| 898 | fmount,fuser, fxy, fxyp); |
---|
[841] | 899 | focusidcol.put(k, id); |
---|
| 900 | } |
---|
| 901 | ++freqit; |
---|
| 902 | } |
---|
| 903 | ++newscanno; |
---|
| 904 | ++scanit; |
---|
| 905 | } |
---|
| 906 | ++it; |
---|
| 907 | } |
---|
| 908 | return out; |
---|
| 909 | } |
---|
[896] | 910 | |
---|
| 911 | CountedPtr< Scantable > |
---|
| 912 | STMath::invertPhase( const CountedPtr < Scantable >& in ) |
---|
| 913 | { |
---|
| 914 | applyToPol(in, &STPol::invertPhase, Float(0.0)); |
---|
| 915 | } |
---|
| 916 | |
---|
| 917 | CountedPtr< Scantable > |
---|
| 918 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
| 919 | { |
---|
| 920 | return applyToPol(in, &STPol::rotatePhase, Float(phase)); |
---|
| 921 | } |
---|
| 922 | |
---|
| 923 | CountedPtr< Scantable > |
---|
| 924 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
| 925 | { |
---|
| 926 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase)); |
---|
| 927 | } |
---|
| 928 | |
---|
| 929 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in, |
---|
| 930 | STPol::polOperation fptr, |
---|
| 931 | Float phase ) |
---|
| 932 | { |
---|
| 933 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 934 | Table& tout = out->table(); |
---|
| 935 | Block<String> cols(4); |
---|
| 936 | cols[0] = String("SCANNO"); |
---|
| 937 | cols[1] = String("BEAMNO"); |
---|
| 938 | cols[2] = String("IFNO"); |
---|
| 939 | cols[3] = String("CYCLENO"); |
---|
| 940 | TableIterator iter(tout, cols); |
---|
| 941 | STPol* stpol = NULL; |
---|
[902] | 942 | stpol =STPol::getPolClass(out->factories_, out->getPolType() ); |
---|
[896] | 943 | while (!iter.pastEnd()) { |
---|
| 944 | Table t = iter.table(); |
---|
| 945 | ArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
| 946 | Matrix<Float> pols = speccol.getColumn(); |
---|
| 947 | try { |
---|
| 948 | stpol->setSpectra(pols); |
---|
| 949 | (stpol->*fptr)(phase); |
---|
| 950 | speccol.putColumn(stpol->getSpectra()); |
---|
| 951 | } catch (AipsError& e) { |
---|
| 952 | delete stpol;stpol=0; |
---|
| 953 | throw(e); |
---|
| 954 | } |
---|
| 955 | ++iter; |
---|
| 956 | } |
---|
[934] | 957 | delete stpol;stpol=0; |
---|
[896] | 958 | return out; |
---|
| 959 | } |
---|
| 960 | |
---|
| 961 | CountedPtr< Scantable > |
---|
| 962 | STMath::swapPolarisations( const CountedPtr< Scantable > & in ) |
---|
| 963 | { |
---|
| 964 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 965 | Table& tout = out->table(); |
---|
| 966 | Table t0 = tout(tout.col("POLNO") == 0); |
---|
| 967 | Table t1 = tout(tout.col("POLNO") == 1); |
---|
| 968 | if ( t0.nrow() != t1.nrow() ) |
---|
| 969 | throw(AipsError("Inconsistent number of polarisations")); |
---|
| 970 | ArrayColumn<Float> speccol0(t0, "SPECTRA"); |
---|
| 971 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA"); |
---|
| 972 | ArrayColumn<Float> speccol1(t1, "SPECTRA"); |
---|
| 973 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA"); |
---|
| 974 | Matrix<Float> s0 = speccol0.getColumn(); |
---|
| 975 | Matrix<uChar> f0 = flagcol0.getColumn(); |
---|
| 976 | speccol0.putColumn(speccol1.getColumn()); |
---|
| 977 | flagcol0.putColumn(flagcol1.getColumn()); |
---|
| 978 | speccol1.putColumn(s0); |
---|
| 979 | flagcol1.putColumn(f0); |
---|
| 980 | return out; |
---|
| 981 | } |
---|
[917] | 982 | |
---|
| 983 | CountedPtr< Scantable > |
---|
[940] | 984 | STMath::averagePolarisations( const CountedPtr< Scantable > & in, |
---|
| 985 | const std::vector<bool>& mask, |
---|
| 986 | const std::string& weight ) |
---|
| 987 | { |
---|
| 988 | if (in->getPolType() != "linear" || in->npol() != 2 ) |
---|
| 989 | throw(AipsError("averagePolarisations can only be applied to two linear polarisations.")); |
---|
| 990 | CountedPtr<Scantable> pol0( new Scantable(*in), false); |
---|
| 991 | CountedPtr<Scantable> pol1( new Scantable(*in), false); |
---|
| 992 | Table& tpol0 = pol0->table(); |
---|
| 993 | Table& tpol1 = pol1->table(); |
---|
| 994 | Vector<uInt> pol0rows = tpol0(tpol0.col("POLNO") == 0).rowNumbers(); |
---|
| 995 | Vector<uInt> pol1rows = tpol1(tpol1.col("POLNO") == 1).rowNumbers(); |
---|
| 996 | tpol0.removeRow(pol1rows); |
---|
| 997 | tpol1.removeRow(pol0rows); |
---|
| 998 | // give both tables the same POLNO |
---|
| 999 | TableVector<uInt> vec(tpol1,"POLNO"); |
---|
| 1000 | vec = 0; |
---|
| 1001 | std::vector<CountedPtr<Scantable> > pols; |
---|
| 1002 | pols.push_back(pol0); |
---|
| 1003 | pols.push_back(pol1); |
---|
| 1004 | CountedPtr< Scantable > out = average(pols, mask, weight, "NONE", false); |
---|
| 1005 | out->table_.rwKeywordSet().define("nPol",Int(1)); |
---|
| 1006 | return out; |
---|
| 1007 | } |
---|
| 1008 | |
---|
| 1009 | |
---|
| 1010 | CountedPtr< Scantable > |
---|
[917] | 1011 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in, |
---|
| 1012 | const std::string & refTime, |
---|
[926] | 1013 | const std::string & method) |
---|
[917] | 1014 | { |
---|
[940] | 1015 | // clone as this is not working insitu |
---|
| 1016 | bool insitu = insitu_; |
---|
| 1017 | setInsitu(false); |
---|
[917] | 1018 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[940] | 1019 | setInsitu(insitu); |
---|
[917] | 1020 | Table& tout = out->table(); |
---|
| 1021 | // clear ouput frequency table |
---|
[940] | 1022 | //Table ftable = out->frequencies().table(); |
---|
| 1023 | //ftable.removeRow(ftable.rowNumbers()); |
---|
[917] | 1024 | // Get reference Epoch to time of first row or given String |
---|
| 1025 | Unit DAY(String("d")); |
---|
| 1026 | MEpoch::Ref epochRef(in->getTimeReference()); |
---|
| 1027 | MEpoch refEpoch; |
---|
| 1028 | if (refTime.length()>0) { |
---|
| 1029 | Quantum<Double> qt; |
---|
| 1030 | if (MVTime::read(qt,refTime)) { |
---|
| 1031 | MVEpoch mv(qt); |
---|
| 1032 | refEpoch = MEpoch(mv, epochRef); |
---|
| 1033 | } else { |
---|
| 1034 | throw(AipsError("Invalid format for Epoch string")); |
---|
| 1035 | } |
---|
| 1036 | } else { |
---|
| 1037 | refEpoch = in->timeCol_(0); |
---|
| 1038 | } |
---|
| 1039 | MPosition refPos = in->getAntennaPosition(); |
---|
[940] | 1040 | |
---|
[917] | 1041 | InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
| 1042 | Int interpMethod(stringToIMethod(method)); |
---|
| 1043 | // test if user frame is different to base frame |
---|
| 1044 | if ( in->frequencies().getFrameString(true) |
---|
| 1045 | == in->frequencies().getFrameString(false) ) { |
---|
| 1046 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe")); |
---|
| 1047 | } |
---|
| 1048 | MFrequency::Types system = in->frequencies().getFrame(); |
---|
[940] | 1049 | MVTime mvt(refEpoch.getValue()); |
---|
| 1050 | String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")"); |
---|
| 1051 | ostringstream oss; |
---|
| 1052 | oss << "Aligned at reference Epoch " << epochout |
---|
| 1053 | << " in frame " << MFrequency::showType(system); |
---|
| 1054 | pushLog(String(oss)); |
---|
[917] | 1055 | // set up the iterator |
---|
[926] | 1056 | Block<String> cols(4); |
---|
| 1057 | // select by constant direction |
---|
[917] | 1058 | cols[0] = String("SRCNAME"); |
---|
| 1059 | cols[1] = String("BEAMNO"); |
---|
| 1060 | // select by IF ( no of channels varies over this ) |
---|
| 1061 | cols[2] = String("IFNO"); |
---|
[926] | 1062 | // select by restfrequency |
---|
| 1063 | cols[3] = String("MOLECULE_ID"); |
---|
[917] | 1064 | TableIterator iter(tout, cols); |
---|
[926] | 1065 | while ( !iter.pastEnd() ) { |
---|
[917] | 1066 | Table t = iter.table(); |
---|
| 1067 | MDirection::ROScalarColumn dirCol(t, "DIRECTION"); |
---|
[926] | 1068 | TableIterator fiter(t, "FREQ_ID"); |
---|
[917] | 1069 | // determine nchan from the first row. This should work as |
---|
[926] | 1070 | // we are iterating over BEAMNO and IFNO // we should have constant direction |
---|
| 1071 | |
---|
[917] | 1072 | ROArrayColumn<Float> sCol(t, "SPECTRA"); |
---|
[926] | 1073 | MDirection direction = dirCol(0); |
---|
[917] | 1074 | uInt nchan = sCol(0).nelements(); |
---|
[926] | 1075 | while ( !fiter.pastEnd() ) { |
---|
| 1076 | Table ftab = fiter.table(); |
---|
| 1077 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID"); |
---|
| 1078 | // get the SpectralCoordinate for the freqid, which we are iterating over |
---|
| 1079 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0)); |
---|
| 1080 | FrequencyAligner<Float> fa( sC, nchan, refEpoch, |
---|
| 1081 | direction, refPos, system ); |
---|
| 1082 | // realign the SpectralCoordinate and put into the output Scantable |
---|
| 1083 | Vector<String> units(1); |
---|
| 1084 | units = String("Hz"); |
---|
| 1085 | Bool linear=True; |
---|
| 1086 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear); |
---|
| 1087 | sc2.setWorldAxisUnits(units); |
---|
[934] | 1088 | uInt id = out->frequencies().addEntry(sc2.referencePixel()[0], |
---|
| 1089 | sc2.referenceValue()[0], |
---|
| 1090 | sc2.increment()[0]); |
---|
| 1091 | TableVector<uInt> tvec(ftab, "FREQ_ID"); |
---|
| 1092 | tvec = id; |
---|
[926] | 1093 | // create the "global" abcissa for alignment with same FREQ_ID |
---|
| 1094 | Vector<Double> abc(nchan); |
---|
[917] | 1095 | Double w; |
---|
| 1096 | for (uInt i=0; i<nchan; i++) { |
---|
| 1097 | sC.toWorld(w,Double(i)); |
---|
| 1098 | abc[i] = w; |
---|
| 1099 | } |
---|
[926] | 1100 | // cache abcissa for same time stamps, so iterate over those |
---|
| 1101 | TableIterator timeiter(ftab, "TIME"); |
---|
| 1102 | while ( !timeiter.pastEnd() ) { |
---|
| 1103 | Table tab = timeiter.table(); |
---|
| 1104 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 1105 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 1106 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
| 1107 | // use align abcissa cache after the first row |
---|
| 1108 | bool first = true; |
---|
| 1109 | // these rows should be just be POLNO |
---|
| 1110 | for (int i=0; i<tab.nrow(); ++i) { |
---|
| 1111 | // input values |
---|
| 1112 | Vector<uChar> flag = flagCol(i); |
---|
| 1113 | Vector<Bool> mask(flag.shape()); |
---|
| 1114 | Vector<Float> specOut, spec; |
---|
| 1115 | spec = specCol(i); |
---|
| 1116 | Vector<Bool> maskOut;Vector<uChar> flagOut; |
---|
| 1117 | convertArray(mask, flag); |
---|
| 1118 | // alignment |
---|
| 1119 | Bool ok = fa.align(specOut, maskOut, abc, spec, |
---|
| 1120 | mask, timeCol(i), !first, |
---|
| 1121 | interp, False); |
---|
| 1122 | // back into scantable |
---|
| 1123 | flagOut.resize(maskOut.nelements()); |
---|
| 1124 | convertArray(flagOut, maskOut); |
---|
| 1125 | flagCol.put(i, flagOut); |
---|
| 1126 | specCol.put(i, specOut); |
---|
| 1127 | // start abcissa caching |
---|
| 1128 | first = false; |
---|
[917] | 1129 | } |
---|
[926] | 1130 | // next timestamp |
---|
| 1131 | ++timeiter; |
---|
[917] | 1132 | } |
---|
[940] | 1133 | // next FREQ_ID |
---|
[926] | 1134 | ++fiter; |
---|
[917] | 1135 | } |
---|
| 1136 | // next aligner |
---|
| 1137 | ++iter; |
---|
| 1138 | } |
---|
[940] | 1139 | // set this afterwards to ensure we are doing insitu correctly. |
---|
| 1140 | out->frequencies().setFrame(system, true); |
---|
[917] | 1141 | return out; |
---|
| 1142 | } |
---|