[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 <casa/Arrays/MaskArrLogi.h> |
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| 18 | #include <casa/Arrays/MaskArrMath.h> |
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| 19 | #include <casa/Arrays/ArrayLogical.h> |
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[81] | 20 | #include <casa/Arrays/ArrayMath.h> |
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[1066] | 21 | #include <casa/Arrays/Slice.h> |
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| 22 | #include <casa/Arrays/Slicer.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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[1140] | 29 | #include <tables/Tables/TableParse.h> |
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[805] | 30 | #include <tables/Tables/ReadAsciiTable.h> |
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[1140] | 31 | #include <tables/Tables/TableIter.h> |
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| 32 | #include <tables/Tables/TableCopy.h> |
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[2] | 33 | |
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[262] | 34 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 35 | |
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[917] | 36 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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| 37 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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| 38 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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| 39 | #include <coordinates/Coordinates/FrequencyAligner.h> |
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| 40 | |
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[177] | 41 | #include <scimath/Mathematics/VectorKernel.h> |
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| 42 | #include <scimath/Mathematics/Convolver.h> |
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[234] | 43 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 44 | |
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[38] | 45 | #include "MathUtils.h" |
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[805] | 46 | #include "RowAccumulator.h" |
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[878] | 47 | #include "STAttr.h" |
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[805] | 48 | #include "STMath.h" |
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[2] | 49 | |
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[805] | 50 | using namespace casa; |
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[2] | 51 | |
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[83] | 52 | using namespace asap; |
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[2] | 53 | |
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[805] | 54 | STMath::STMath(bool insitu) : |
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| 55 | insitu_(insitu) |
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[716] | 56 | { |
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| 57 | } |
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[170] | 58 | |
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| 59 | |
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[805] | 60 | STMath::~STMath() |
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[170] | 61 | { |
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| 62 | } |
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| 63 | |
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[805] | 64 | CountedPtr<Scantable> |
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[977] | 65 | STMath::average( const std::vector<CountedPtr<Scantable> >& in, |
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[858] | 66 | const std::vector<bool>& mask, |
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[805] | 67 | const std::string& weight, |
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[977] | 68 | const std::string& avmode) |
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[262] | 69 | { |
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[977] | 70 | if ( avmode == "SCAN" && in.size() != 1 ) |
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[1066] | 71 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n" |
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| 72 | "Use merge first.")); |
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[805] | 73 | WeightType wtype = stringToWeight(weight); |
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[926] | 74 | |
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[805] | 75 | // output |
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| 76 | // clone as this is non insitu |
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| 77 | bool insitu = insitu_; |
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| 78 | setInsitu(false); |
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[977] | 79 | CountedPtr< Scantable > out = getScantable(in[0], true); |
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[805] | 80 | setInsitu(insitu); |
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[977] | 81 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin(); |
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[862] | 82 | ++stit; |
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[977] | 83 | while ( stit != in.end() ) { |
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[862] | 84 | out->appendToHistoryTable((*stit)->history()); |
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| 85 | ++stit; |
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| 86 | } |
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[294] | 87 | |
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[805] | 88 | Table& tout = out->table(); |
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[701] | 89 | |
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[805] | 90 | /// @todo check if all scantables are conformant |
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[294] | 91 | |
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[805] | 92 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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| 93 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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| 94 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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| 95 | ScalarColumn<Double> mjdColOut(tout,"TIME"); |
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| 96 | ScalarColumn<Double> intColOut(tout,"INTERVAL"); |
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[1008] | 97 | ScalarColumn<uInt> cycColOut(tout,"CYCLENO"); |
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[1145] | 98 | ScalarColumn<uInt> scanColOut(tout,"SCANNO"); |
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[262] | 99 | |
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[805] | 100 | // set up the output table rows. These are based on the structure of the |
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[862] | 101 | // FIRST scantable in the vector |
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[977] | 102 | const Table& baset = in[0]->table(); |
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[262] | 103 | |
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[805] | 104 | Block<String> cols(3); |
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| 105 | cols[0] = String("BEAMNO"); |
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| 106 | cols[1] = String("IFNO"); |
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| 107 | cols[2] = String("POLNO"); |
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| 108 | if ( avmode == "SOURCE" ) { |
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| 109 | cols.resize(4); |
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| 110 | cols[3] = String("SRCNAME"); |
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[488] | 111 | } |
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[977] | 112 | if ( avmode == "SCAN" && in.size() == 1) { |
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[805] | 113 | cols.resize(4); |
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| 114 | cols[3] = String("SCANNO"); |
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[2] | 115 | } |
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[805] | 116 | uInt outrowCount = 0; |
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| 117 | TableIterator iter(baset, cols); |
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| 118 | while (!iter.pastEnd()) { |
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| 119 | Table subt = iter.table(); |
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| 120 | // copy the first row of this selection into the new table |
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| 121 | tout.addRow(); |
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| 122 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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[1145] | 123 | // re-index to 0 |
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| 124 | if ( avmode != "SCAN" && avmode != "SOURCE" ) { |
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| 125 | scanColOut.put(outrowCount, uInt(0)); |
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| 126 | } |
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[805] | 127 | ++outrowCount; |
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| 128 | ++iter; |
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[144] | 129 | } |
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[805] | 130 | RowAccumulator acc(wtype); |
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[858] | 131 | Vector<Bool> cmask(mask); |
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| 132 | acc.setUserMask(cmask); |
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[805] | 133 | ROTableRow row(tout); |
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| 134 | ROArrayColumn<Float> specCol, tsysCol; |
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| 135 | ROArrayColumn<uChar> flagCol; |
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| 136 | ROScalarColumn<Double> mjdCol, intCol; |
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| 137 | ROScalarColumn<Int> scanIDCol; |
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[144] | 138 | |
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[805] | 139 | for (uInt i=0; i < tout.nrow(); ++i) { |
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[996] | 140 | for ( int j=0; j < int(in.size()); ++j ) { |
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[977] | 141 | const Table& tin = in[j]->table(); |
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[805] | 142 | const TableRecord& rec = row.get(i); |
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| 143 | ROScalarColumn<Double> tmp(tin, "TIME"); |
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| 144 | Double td;tmp.get(0,td); |
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| 145 | Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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| 146 | && tin.col("IFNO") == Int(rec.asuInt("IFNO")) |
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| 147 | && tin.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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| 148 | Table subt; |
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| 149 | if ( avmode == "SOURCE") { |
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| 150 | subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") ); |
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| 151 | } else if (avmode == "SCAN") { |
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| 152 | subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) ); |
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| 153 | } else { |
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| 154 | subt = basesubt; |
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| 155 | } |
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| 156 | specCol.attach(subt,"SPECTRA"); |
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| 157 | flagCol.attach(subt,"FLAGTRA"); |
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| 158 | tsysCol.attach(subt,"TSYS"); |
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| 159 | intCol.attach(subt,"INTERVAL"); |
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| 160 | mjdCol.attach(subt,"TIME"); |
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| 161 | Vector<Float> spec,tsys; |
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| 162 | Vector<uChar> flag; |
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| 163 | Double inter,time; |
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| 164 | for (uInt k = 0; k < subt.nrow(); ++k ) { |
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| 165 | flagCol.get(k, flag); |
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| 166 | Vector<Bool> bflag(flag.shape()); |
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| 167 | convertArray(bflag, flag); |
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| 168 | if ( allEQ(bflag, True) ) { |
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| 169 | continue;//don't accumulate |
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[144] | 170 | } |
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[805] | 171 | specCol.get(k, spec); |
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| 172 | tsysCol.get(k, tsys); |
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| 173 | intCol.get(k, inter); |
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| 174 | mjdCol.get(k, time); |
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| 175 | // spectrum has to be added last to enable weighting by the other values |
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| 176 | acc.add(spec, !bflag, tsys, inter, time); |
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| 177 | } |
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| 178 | } |
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| 179 | //write out |
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| 180 | specColOut.put(i, acc.getSpectrum()); |
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| 181 | const Vector<Bool>& msk = acc.getMask(); |
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| 182 | Vector<uChar> flg(msk.shape()); |
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| 183 | convertArray(flg, !msk); |
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| 184 | flagColOut.put(i, flg); |
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| 185 | tsysColOut.put(i, acc.getTsys()); |
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| 186 | intColOut.put(i, acc.getInterval()); |
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| 187 | mjdColOut.put(i, acc.getTime()); |
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[1008] | 188 | // we should only have one cycle now -> reset it to be 0 |
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| 189 | // frequency switched data has different CYCLENO for different IFNO |
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| 190 | // which requires resetting this value |
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| 191 | cycColOut.put(i, uInt(0)); |
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[805] | 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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[1069] | 197 | CountedPtr< Scantable > |
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| 198 | STMath::averageChannel( const CountedPtr < Scantable > & in, |
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[1078] | 199 | const std::string & mode, |
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| 200 | const std::string& avmode ) |
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[1069] | 201 | { |
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| 202 | // clone as this is non insitu |
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| 203 | bool insitu = insitu_; |
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| 204 | setInsitu(false); |
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| 205 | CountedPtr< Scantable > out = getScantable(in, true); |
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| 206 | setInsitu(insitu); |
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| 207 | Table& tout = out->table(); |
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| 208 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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| 209 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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| 210 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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[1140] | 211 | ScalarColumn<uInt> scanColOut(tout,"SCANNO"); |
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| 212 | Table tmp = in->table().sort("BEAMNO"); |
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[1069] | 213 | Block<String> cols(3); |
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| 214 | cols[0] = String("BEAMNO"); |
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| 215 | cols[1] = String("IFNO"); |
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| 216 | cols[2] = String("POLNO"); |
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[1078] | 217 | if ( avmode == "SCAN") { |
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| 218 | cols.resize(4); |
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| 219 | cols[3] = String("SCANNO"); |
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| 220 | } |
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[1069] | 221 | uInt outrowCount = 0; |
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| 222 | uChar userflag = 1 << 7; |
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[1140] | 223 | TableIterator iter(tmp, cols); |
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[1069] | 224 | while (!iter.pastEnd()) { |
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| 225 | Table subt = iter.table(); |
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| 226 | ROArrayColumn<Float> specCol, tsysCol; |
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| 227 | ROArrayColumn<uChar> flagCol; |
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| 228 | specCol.attach(subt,"SPECTRA"); |
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| 229 | flagCol.attach(subt,"FLAGTRA"); |
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| 230 | tsysCol.attach(subt,"TSYS"); |
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| 231 | tout.addRow(); |
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| 232 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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[1140] | 233 | if ( avmode != "SCAN") { |
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| 234 | scanColOut.put(outrowCount, uInt(0)); |
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| 235 | } |
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[1069] | 236 | Vector<Float> tmp; |
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| 237 | specCol.get(0, tmp); |
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| 238 | uInt nchan = tmp.nelements(); |
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[1078] | 239 | // have to do channel by channel here as MaskedArrMath |
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| 240 | // doesn't have partialMedians |
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[1069] | 241 | Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0))); |
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| 242 | Vector<Float> outspec(nchan); |
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| 243 | Vector<uChar> outflag(nchan,0); |
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| 244 | Vector<Float> outtsys(1);/// @fixme when tsys is channel based |
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| 245 | for (uInt i=0; i<nchan; ++i) { |
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| 246 | Vector<Float> specs = specCol.getColumn(Slicer(Slice(i))); |
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| 247 | MaskedArray<Float> ma = maskedArray(specs,flags); |
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| 248 | outspec[i] = median(ma); |
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| 249 | if ( allEQ(ma.getMask(), False) ) |
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| 250 | outflag[i] = userflag;// flag data |
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| 251 | } |
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| 252 | outtsys[0] = median(tsysCol.getColumn()); |
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| 253 | specColOut.put(outrowCount, outspec); |
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| 254 | flagColOut.put(outrowCount, outflag); |
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| 255 | tsysColOut.put(outrowCount, outtsys); |
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| 256 | |
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| 257 | ++outrowCount; |
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| 258 | ++iter; |
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| 259 | } |
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| 260 | return out; |
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| 261 | } |
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| 262 | |
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[805] | 263 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in, |
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| 264 | bool droprows) |
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[185] | 265 | { |
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[805] | 266 | if (insitu_) return in; |
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| 267 | else { |
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| 268 | // clone |
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| 269 | Scantable* tabp = new Scantable(*in, Bool(droprows)); |
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| 270 | return CountedPtr<Scantable>(tabp); |
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[234] | 271 | } |
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[805] | 272 | } |
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[234] | 273 | |
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[805] | 274 | CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in, |
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| 275 | float val, |
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| 276 | const std::string& mode, |
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| 277 | bool tsys ) |
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| 278 | { |
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| 279 | // modes are "ADD" and "MUL" |
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| 280 | CountedPtr< Scantable > out = getScantable(in, false); |
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| 281 | Table& tab = out->table(); |
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| 282 | ArrayColumn<Float> specCol(tab,"SPECTRA"); |
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| 283 | ArrayColumn<Float> tsysCol(tab,"TSYS"); |
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| 284 | for (uInt i=0; i<tab.nrow(); ++i) { |
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| 285 | Vector<Float> spec; |
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| 286 | Vector<Float> ts; |
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| 287 | specCol.get(i, spec); |
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| 288 | tsysCol.get(i, ts); |
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| 289 | if (mode == "MUL") { |
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| 290 | spec *= val; |
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| 291 | specCol.put(i, spec); |
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| 292 | if ( tsys ) { |
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| 293 | ts *= val; |
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| 294 | tsysCol.put(i, ts); |
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| 295 | } |
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| 296 | } else if ( mode == "ADD" ) { |
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| 297 | spec += val; |
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| 298 | specCol.put(i, spec); |
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| 299 | if ( tsys ) { |
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| 300 | ts += val; |
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| 301 | tsysCol.put(i, ts); |
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| 302 | } |
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| 303 | } |
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[234] | 304 | } |
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[805] | 305 | return out; |
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| 306 | } |
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[234] | 307 | |
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[805] | 308 | MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s, |
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| 309 | const Vector<uChar>& f) |
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| 310 | { |
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| 311 | Vector<Bool> mask; |
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| 312 | mask.resize(f.shape()); |
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| 313 | convertArray(mask, f); |
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| 314 | return MaskedArray<Float>(s,!mask); |
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| 315 | } |
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[248] | 316 | |
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[805] | 317 | Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma) |
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| 318 | { |
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| 319 | const Vector<Bool>& m = ma.getMask(); |
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| 320 | Vector<uChar> flags(m.shape()); |
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| 321 | convertArray(flags, !m); |
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| 322 | return flags; |
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| 323 | } |
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[234] | 324 | |
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[1066] | 325 | CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in, |
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| 326 | const std::string & mode, |
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| 327 | bool preserve ) |
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[805] | 328 | { |
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| 329 | /// @todo make other modes available |
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| 330 | /// modes should be "nearest", "pair" |
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| 331 | // make this operation non insitu |
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| 332 | const Table& tin = in->table(); |
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| 333 | Table ons = tin(tin.col("SRCTYPE") == Int(0)); |
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| 334 | Table offs = tin(tin.col("SRCTYPE") == Int(1)); |
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| 335 | if ( offs.nrow() == 0 ) |
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| 336 | throw(AipsError("No 'off' scans present.")); |
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| 337 | // put all "on" scans into output table |
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[701] | 338 | |
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[805] | 339 | bool insitu = insitu_; |
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| 340 | setInsitu(false); |
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| 341 | CountedPtr< Scantable > out = getScantable(in, true); |
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| 342 | setInsitu(insitu); |
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| 343 | Table& tout = out->table(); |
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[248] | 344 | |
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[805] | 345 | TableCopy::copyRows(tout, ons); |
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| 346 | TableRow row(tout); |
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| 347 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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[234] | 348 | |
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[805] | 349 | ArrayColumn<Float> outspecCol(tout, "SPECTRA"); |
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| 350 | ROArrayColumn<Float> outtsysCol(tout, "TSYS"); |
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| 351 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA"); |
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| 352 | for (uInt i=0; i < tout.nrow(); ++i) { |
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| 353 | const TableRecord& rec = row.get(i); |
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| 354 | Double ontime = rec.asDouble("TIME"); |
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| 355 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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| 356 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime)); |
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| 357 | Table sel = offs( abs(offs.col("TIME")-ontime) <= mindeltat |
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| 358 | && offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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| 359 | && offs.col("IFNO") == Int(rec.asuInt("IFNO")) |
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| 360 | && offs.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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[780] | 361 | |
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[805] | 362 | TableRow offrow(sel); |
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| 363 | const TableRecord& offrec = offrow.get(0);//should only be one row |
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| 364 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
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| 365 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
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| 366 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
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| 367 | /// @fixme this assumes tsys is a scalar not vector |
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| 368 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
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| 369 | Vector<Float> specon, tsyson; |
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| 370 | outtsysCol.get(i, tsyson); |
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| 371 | outspecCol.get(i, specon); |
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| 372 | Vector<uChar> flagon; |
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| 373 | outflagCol.get(i, flagon); |
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| 374 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
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| 375 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
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| 376 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
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| 377 | if (preserve) { |
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| 378 | quot -= tsysoffscalar; |
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| 379 | } else { |
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| 380 | quot -= tsyson[0]; |
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[701] | 381 | } |
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[805] | 382 | outspecCol.put(i, quot.getArray()); |
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| 383 | outflagCol.put(i, flagsFromMA(quot)); |
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| 384 | } |
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[926] | 385 | // renumber scanno |
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| 386 | TableIterator it(tout, "SCANNO"); |
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| 387 | uInt i = 0; |
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| 388 | while ( !it.pastEnd() ) { |
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| 389 | Table t = it.table(); |
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| 390 | TableVector<uInt> vec(t, "SCANNO"); |
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| 391 | vec = i; |
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| 392 | ++i; |
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| 393 | ++it; |
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| 394 | } |
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[805] | 395 | return out; |
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| 396 | } |
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[234] | 397 | |
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[1066] | 398 | |
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| 399 | CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on, |
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| 400 | const CountedPtr< Scantable > & off, |
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| 401 | bool preserve ) |
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| 402 | { |
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| 403 | bool insitu = insitu_; |
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[1069] | 404 | if ( ! on->conformant(*off) ) { |
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| 405 | throw(AipsError("'on' and 'off' scantables are not conformant.")); |
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| 406 | } |
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[1066] | 407 | setInsitu(false); |
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| 408 | CountedPtr< Scantable > out = getScantable(on, false); |
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| 409 | setInsitu(insitu); |
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| 410 | Table& tout = out->table(); |
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| 411 | const Table& toff = off->table(); |
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| 412 | TableIterator sit(tout, "SCANNO"); |
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| 413 | TableIterator s2it(toff, "SCANNO"); |
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| 414 | while ( !sit.pastEnd() ) { |
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| 415 | Table ton = sit.table(); |
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| 416 | TableRow row(ton); |
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| 417 | Table t = s2it.table(); |
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| 418 | ArrayColumn<Float> outspecCol(ton, "SPECTRA"); |
---|
| 419 | ROArrayColumn<Float> outtsysCol(ton, "TSYS"); |
---|
| 420 | ArrayColumn<uChar> outflagCol(ton, "FLAGTRA"); |
---|
| 421 | for (uInt i=0; i < ton.nrow(); ++i) { |
---|
| 422 | const TableRecord& rec = row.get(i); |
---|
| 423 | Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 424 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 425 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
---|
[1145] | 426 | if ( offsel.nrow() == 0 ) |
---|
| 427 | throw AipsError("STMath::quotient: no matching off"); |
---|
[1066] | 428 | TableRow offrow(offsel); |
---|
| 429 | const TableRecord& offrec = offrow.get(0);//should be ncycles - take first |
---|
| 430 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
---|
| 431 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
---|
| 432 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
---|
| 433 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
---|
| 434 | Vector<Float> specon, tsyson; |
---|
| 435 | outtsysCol.get(i, tsyson); |
---|
| 436 | outspecCol.get(i, specon); |
---|
| 437 | Vector<uChar> flagon; |
---|
| 438 | outflagCol.get(i, flagon); |
---|
| 439 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
---|
| 440 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
---|
| 441 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
---|
| 442 | if (preserve) { |
---|
| 443 | quot -= tsysoffscalar; |
---|
| 444 | } else { |
---|
| 445 | quot -= tsyson[0]; |
---|
| 446 | } |
---|
| 447 | outspecCol.put(i, quot.getArray()); |
---|
| 448 | outflagCol.put(i, flagsFromMA(quot)); |
---|
| 449 | } |
---|
| 450 | ++sit; |
---|
| 451 | ++s2it; |
---|
| 452 | // take the first off for each on scan which doesn't have a |
---|
| 453 | // matching off scan |
---|
| 454 | // non <= noff: matching pairs, non > noff matching pairs then first off |
---|
| 455 | if ( s2it.pastEnd() ) s2it.reset(); |
---|
| 456 | } |
---|
| 457 | return out; |
---|
| 458 | } |
---|
| 459 | |
---|
| 460 | |
---|
[805] | 461 | CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in ) |
---|
| 462 | { |
---|
| 463 | // make copy or reference |
---|
| 464 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 465 | Table& tout = out->table(); |
---|
[1008] | 466 | Block<String> cols(4); |
---|
[805] | 467 | cols[0] = String("SCANNO"); |
---|
[1008] | 468 | cols[1] = String("CYCLENO"); |
---|
| 469 | cols[2] = String("BEAMNO"); |
---|
| 470 | cols[3] = String("POLNO"); |
---|
[805] | 471 | TableIterator iter(tout, cols); |
---|
| 472 | while (!iter.pastEnd()) { |
---|
| 473 | Table subt = iter.table(); |
---|
| 474 | // this should leave us with two rows for the two IFs....if not ignore |
---|
| 475 | if (subt.nrow() != 2 ) { |
---|
| 476 | continue; |
---|
[701] | 477 | } |
---|
[1008] | 478 | ArrayColumn<Float> specCol(subt, "SPECTRA"); |
---|
| 479 | ArrayColumn<Float> tsysCol(subt, "TSYS"); |
---|
| 480 | ArrayColumn<uChar> flagCol(subt, "FLAGTRA"); |
---|
[805] | 481 | Vector<Float> onspec,offspec, ontsys, offtsys; |
---|
| 482 | Vector<uChar> onflag, offflag; |
---|
| 483 | tsysCol.get(0, ontsys); tsysCol.get(1, offtsys); |
---|
| 484 | specCol.get(0, onspec); specCol.get(1, offspec); |
---|
| 485 | flagCol.get(0, onflag); flagCol.get(1, offflag); |
---|
| 486 | MaskedArray<Float> on = maskedArray(onspec, onflag); |
---|
| 487 | MaskedArray<Float> off = maskedArray(offspec, offflag); |
---|
| 488 | MaskedArray<Float> oncopy = on.copy(); |
---|
[248] | 489 | |
---|
[805] | 490 | on /= off; on -= 1.0f; |
---|
| 491 | on *= ontsys[0]; |
---|
| 492 | off /= oncopy; off -= 1.0f; |
---|
| 493 | off *= offtsys[0]; |
---|
| 494 | specCol.put(0, on.getArray()); |
---|
| 495 | const Vector<Bool>& m0 = on.getMask(); |
---|
| 496 | Vector<uChar> flags0(m0.shape()); |
---|
| 497 | convertArray(flags0, !m0); |
---|
| 498 | flagCol.put(0, flags0); |
---|
[234] | 499 | |
---|
[805] | 500 | specCol.put(1, off.getArray()); |
---|
| 501 | const Vector<Bool>& m1 = off.getMask(); |
---|
| 502 | Vector<uChar> flags1(m1.shape()); |
---|
| 503 | convertArray(flags1, !m1); |
---|
| 504 | flagCol.put(1, flags1); |
---|
[867] | 505 | ++iter; |
---|
[130] | 506 | } |
---|
[780] | 507 | |
---|
[805] | 508 | return out; |
---|
[9] | 509 | } |
---|
[48] | 510 | |
---|
[805] | 511 | std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in, |
---|
| 512 | const std::vector< bool > & mask, |
---|
| 513 | const std::string& which ) |
---|
[130] | 514 | { |
---|
| 515 | |
---|
[805] | 516 | Vector<Bool> m(mask); |
---|
| 517 | const Table& tab = in->table(); |
---|
| 518 | ROArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 519 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 520 | std::vector<float> out; |
---|
| 521 | for (uInt i=0; i < tab.nrow(); ++i ) { |
---|
| 522 | Vector<Float> spec; specCol.get(i, spec); |
---|
[867] | 523 | Vector<uChar> flag; flagCol.get(i, flag); |
---|
| 524 | MaskedArray<Float> ma = maskedArray(spec, flag); |
---|
| 525 | float outstat = 0.0; |
---|
[805] | 526 | if ( spec.nelements() == m.nelements() ) { |
---|
| 527 | outstat = mathutil::statistics(which, ma(m)); |
---|
| 528 | } else { |
---|
| 529 | outstat = mathutil::statistics(which, ma); |
---|
| 530 | } |
---|
| 531 | out.push_back(outstat); |
---|
[234] | 532 | } |
---|
[805] | 533 | return out; |
---|
[130] | 534 | } |
---|
| 535 | |
---|
[805] | 536 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in, |
---|
| 537 | int width ) |
---|
[144] | 538 | { |
---|
[841] | 539 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data.")); |
---|
[805] | 540 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 541 | Table& tout = out->table(); |
---|
| 542 | out->frequencies().rescale(width, "BIN"); |
---|
| 543 | ArrayColumn<Float> specCol(tout, "SPECTRA"); |
---|
| 544 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA"); |
---|
| 545 | for (uInt i=0; i < tout.nrow(); ++i ) { |
---|
| 546 | MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i)); |
---|
| 547 | MaskedArray<Float> maout; |
---|
| 548 | LatticeUtilities::bin(maout, main, 0, Int(width)); |
---|
| 549 | /// @todo implement channel based tsys binning |
---|
| 550 | specCol.put(i, maout.getArray()); |
---|
| 551 | flagCol.put(i, flagsFromMA(maout)); |
---|
| 552 | // take only the first binned spectrum's length for the deprecated |
---|
| 553 | // global header item nChan |
---|
| 554 | if (i==0) tout.rwKeywordSet().define(String("nChan"), |
---|
| 555 | Int(maout.getArray().nelements())); |
---|
[169] | 556 | } |
---|
[805] | 557 | return out; |
---|
[146] | 558 | } |
---|
| 559 | |
---|
[805] | 560 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in, |
---|
| 561 | const std::string& method, |
---|
| 562 | float width ) |
---|
[299] | 563 | // |
---|
| 564 | // Should add the possibility of width being specified in km/s. This means |
---|
[780] | 565 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
| 566 | // average channel width (say at the reference pixel). Then we would need |
---|
| 567 | // to be careful to make sure each spectrum (of different freqID) |
---|
[299] | 568 | // is the same length. |
---|
| 569 | // |
---|
| 570 | { |
---|
[996] | 571 | //InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
[805] | 572 | Int interpMethod(stringToIMethod(method)); |
---|
[299] | 573 | |
---|
[805] | 574 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 575 | Table& tout = out->table(); |
---|
[299] | 576 | |
---|
| 577 | // Resample SpectralCoordinates (one per freqID) |
---|
[805] | 578 | out->frequencies().rescale(width, "RESAMPLE"); |
---|
| 579 | TableIterator iter(tout, "IFNO"); |
---|
| 580 | TableRow row(tout); |
---|
| 581 | while ( !iter.pastEnd() ) { |
---|
| 582 | Table tab = iter.table(); |
---|
| 583 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 584 | //ArrayColumn<Float> tsysCol(tout, "TSYS"); |
---|
| 585 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 586 | Vector<Float> spec; |
---|
| 587 | Vector<uChar> flag; |
---|
| 588 | specCol.get(0,spec); // the number of channels should be constant per IF |
---|
| 589 | uInt nChanIn = spec.nelements(); |
---|
| 590 | Vector<Float> xIn(nChanIn); indgen(xIn); |
---|
| 591 | Int fac = Int(nChanIn/width); |
---|
| 592 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
| 593 | uInt k = 0; |
---|
| 594 | Float x = 0.0; |
---|
| 595 | while (x < Float(nChanIn) ) { |
---|
| 596 | xOut(k) = x; |
---|
| 597 | k++; |
---|
| 598 | x += width; |
---|
| 599 | } |
---|
| 600 | uInt nChanOut = k; |
---|
| 601 | xOut.resize(nChanOut, True); |
---|
| 602 | // process all rows for this IFNO |
---|
| 603 | Vector<Float> specOut; |
---|
| 604 | Vector<Bool> maskOut; |
---|
| 605 | Vector<uChar> flagOut; |
---|
| 606 | for (uInt i=0; i < tab.nrow(); ++i) { |
---|
| 607 | specCol.get(i, spec); |
---|
| 608 | flagCol.get(i, flag); |
---|
| 609 | Vector<Bool> mask(flag.nelements()); |
---|
| 610 | convertArray(mask, flag); |
---|
[299] | 611 | |
---|
[805] | 612 | IPosition shapeIn(spec.shape()); |
---|
| 613 | //sh.nchan = nChanOut; |
---|
| 614 | InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut, |
---|
| 615 | xIn, spec, mask, |
---|
| 616 | interpMethod, True, True); |
---|
| 617 | /// @todo do the same for channel based Tsys |
---|
| 618 | flagOut.resize(maskOut.nelements()); |
---|
| 619 | convertArray(flagOut, maskOut); |
---|
| 620 | specCol.put(i, specOut); |
---|
| 621 | flagCol.put(i, flagOut); |
---|
| 622 | } |
---|
| 623 | ++iter; |
---|
[299] | 624 | } |
---|
| 625 | |
---|
[805] | 626 | return out; |
---|
| 627 | } |
---|
[299] | 628 | |
---|
[805] | 629 | STMath::imethod STMath::stringToIMethod(const std::string& in) |
---|
| 630 | { |
---|
| 631 | static STMath::imap lookup; |
---|
[299] | 632 | |
---|
[805] | 633 | // initialize the lookup table if necessary |
---|
| 634 | if ( lookup.empty() ) { |
---|
[926] | 635 | lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
| 636 | lookup["linear"] = InterpolateArray1D<Double,Float>::linear; |
---|
| 637 | lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic; |
---|
| 638 | lookup["spline"] = InterpolateArray1D<Double,Float>::spline; |
---|
[299] | 639 | } |
---|
| 640 | |
---|
[805] | 641 | STMath::imap::const_iterator iter = lookup.find(in); |
---|
[299] | 642 | |
---|
[805] | 643 | if ( lookup.end() == iter ) { |
---|
| 644 | std::string message = in; |
---|
| 645 | message += " is not a valid interpolation mode"; |
---|
| 646 | throw(AipsError(message)); |
---|
[299] | 647 | } |
---|
[805] | 648 | return iter->second; |
---|
[299] | 649 | } |
---|
| 650 | |
---|
[805] | 651 | WeightType STMath::stringToWeight(const std::string& in) |
---|
[146] | 652 | { |
---|
[805] | 653 | static std::map<std::string, WeightType> lookup; |
---|
[434] | 654 | |
---|
[805] | 655 | // initialize the lookup table if necessary |
---|
| 656 | if ( lookup.empty() ) { |
---|
| 657 | lookup["NONE"] = asap::NONE; |
---|
| 658 | lookup["TINT"] = asap::TINT; |
---|
| 659 | lookup["TINTSYS"] = asap::TINTSYS; |
---|
| 660 | lookup["TSYS"] = asap::TSYS; |
---|
| 661 | lookup["VAR"] = asap::VAR; |
---|
| 662 | } |
---|
[434] | 663 | |
---|
[805] | 664 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in); |
---|
[294] | 665 | |
---|
[805] | 666 | if ( lookup.end() == iter ) { |
---|
| 667 | std::string message = in; |
---|
| 668 | message += " is not a valid weighting mode"; |
---|
| 669 | throw(AipsError(message)); |
---|
| 670 | } |
---|
| 671 | return iter->second; |
---|
[146] | 672 | } |
---|
| 673 | |
---|
[805] | 674 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in, |
---|
[867] | 675 | const vector< float > & coeff, |
---|
[805] | 676 | const std::string & filename, |
---|
| 677 | const std::string& method) |
---|
[165] | 678 | { |
---|
[805] | 679 | // Get elevation data from Scantable and convert to degrees |
---|
| 680 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[926] | 681 | Table& tab = out->table(); |
---|
[805] | 682 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 683 | Vector<Float> x = elev.getColumn(); |
---|
| 684 | x *= Float(180 / C::pi); // Degrees |
---|
[165] | 685 | |
---|
[867] | 686 | Vector<Float> coeffs(coeff); |
---|
[805] | 687 | const uInt nc = coeffs.nelements(); |
---|
| 688 | if ( filename.length() > 0 && nc > 0 ) { |
---|
| 689 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
[315] | 690 | } |
---|
[165] | 691 | |
---|
[805] | 692 | // Correct |
---|
| 693 | if ( nc > 0 || filename.length() == 0 ) { |
---|
| 694 | // Find instrument |
---|
| 695 | Bool throwit = True; |
---|
| 696 | Instrument inst = |
---|
[878] | 697 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
[805] | 698 | throwit); |
---|
[165] | 699 | |
---|
[805] | 700 | // Set polynomial |
---|
| 701 | Polynomial<Float>* ppoly = 0; |
---|
| 702 | Vector<Float> coeff; |
---|
| 703 | String msg; |
---|
| 704 | if ( nc > 0 ) { |
---|
| 705 | ppoly = new Polynomial<Float>(nc); |
---|
| 706 | coeff = coeffs; |
---|
| 707 | msg = String("user"); |
---|
| 708 | } else { |
---|
[878] | 709 | STAttr sdAttr; |
---|
[805] | 710 | coeff = sdAttr.gainElevationPoly(inst); |
---|
| 711 | ppoly = new Polynomial<Float>(3); |
---|
| 712 | msg = String("built in"); |
---|
| 713 | } |
---|
[532] | 714 | |
---|
[805] | 715 | if ( coeff.nelements() > 0 ) { |
---|
| 716 | ppoly->setCoefficients(coeff); |
---|
| 717 | } else { |
---|
| 718 | delete ppoly; |
---|
| 719 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
| 720 | } |
---|
| 721 | ostringstream oss; |
---|
| 722 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl; |
---|
| 723 | oss << " " << coeff; |
---|
| 724 | pushLog(String(oss)); |
---|
| 725 | const uInt nrow = tab.nrow(); |
---|
| 726 | Vector<Float> factor(nrow); |
---|
| 727 | for ( uInt i=0; i < nrow; ++i ) { |
---|
| 728 | factor[i] = 1.0 / (*ppoly)(x[i]); |
---|
| 729 | } |
---|
| 730 | delete ppoly; |
---|
| 731 | scaleByVector(tab, factor, true); |
---|
[532] | 732 | |
---|
[805] | 733 | } else { |
---|
| 734 | // Read and correct |
---|
| 735 | pushLog("Making correction from ascii Table"); |
---|
| 736 | scaleFromAsciiTable(tab, filename, method, x, true); |
---|
[532] | 737 | } |
---|
[805] | 738 | return out; |
---|
| 739 | } |
---|
[165] | 740 | |
---|
[805] | 741 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename, |
---|
| 742 | const std::string& method, |
---|
| 743 | const Vector<Float>& xout, bool dotsys) |
---|
| 744 | { |
---|
[165] | 745 | |
---|
[805] | 746 | // Read gain-elevation ascii file data into a Table. |
---|
[165] | 747 | |
---|
[805] | 748 | String formatString; |
---|
| 749 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False); |
---|
| 750 | scaleFromTable(in, tbl, method, xout, dotsys); |
---|
| 751 | } |
---|
[165] | 752 | |
---|
[805] | 753 | void STMath::scaleFromTable(Table& in, |
---|
| 754 | const Table& table, |
---|
| 755 | const std::string& method, |
---|
| 756 | const Vector<Float>& xout, bool dotsys) |
---|
| 757 | { |
---|
[780] | 758 | |
---|
[805] | 759 | ROScalarColumn<Float> geElCol(table, "ELEVATION"); |
---|
| 760 | ROScalarColumn<Float> geFacCol(table, "FACTOR"); |
---|
| 761 | Vector<Float> xin = geElCol.getColumn(); |
---|
| 762 | Vector<Float> yin = geFacCol.getColumn(); |
---|
| 763 | Vector<Bool> maskin(xin.nelements(),True); |
---|
[165] | 764 | |
---|
[805] | 765 | // Interpolate (and extrapolate) with desired method |
---|
[532] | 766 | |
---|
[996] | 767 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method); |
---|
[165] | 768 | |
---|
[805] | 769 | Vector<Float> yout; |
---|
| 770 | Vector<Bool> maskout; |
---|
| 771 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout, |
---|
[996] | 772 | xin, yin, maskin, interp, |
---|
[805] | 773 | True, True); |
---|
[165] | 774 | |
---|
[805] | 775 | scaleByVector(in, Float(1.0)/yout, dotsys); |
---|
[165] | 776 | } |
---|
[167] | 777 | |
---|
[805] | 778 | void STMath::scaleByVector( Table& in, |
---|
| 779 | const Vector< Float >& factor, |
---|
| 780 | bool dotsys ) |
---|
[177] | 781 | { |
---|
[805] | 782 | uInt nrow = in.nrow(); |
---|
| 783 | if ( factor.nelements() != nrow ) { |
---|
| 784 | throw(AipsError("factors.nelements() != table.nelements()")); |
---|
| 785 | } |
---|
| 786 | ArrayColumn<Float> specCol(in, "SPECTRA"); |
---|
| 787 | ArrayColumn<uChar> flagCol(in, "FLAGTRA"); |
---|
| 788 | ArrayColumn<Float> tsysCol(in, "TSYS"); |
---|
| 789 | for (uInt i=0; i < nrow; ++i) { |
---|
| 790 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
| 791 | ma *= factor[i]; |
---|
| 792 | specCol.put(i, ma.getArray()); |
---|
| 793 | flagCol.put(i, flagsFromMA(ma)); |
---|
| 794 | if ( dotsys ) { |
---|
[926] | 795 | Vector<Float> tsys = tsysCol(i); |
---|
[805] | 796 | tsys *= factor[i]; |
---|
[926] | 797 | tsysCol.put(i,tsys); |
---|
[805] | 798 | } |
---|
| 799 | } |
---|
[177] | 800 | } |
---|
| 801 | |
---|
[805] | 802 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in, |
---|
| 803 | float d, float etaap, |
---|
| 804 | float jyperk ) |
---|
[221] | 805 | { |
---|
[805] | 806 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 807 | Table& tab = in->table(); |
---|
| 808 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit")); |
---|
[221] | 809 | Unit K(String("K")); |
---|
| 810 | Unit JY(String("Jy")); |
---|
[701] | 811 | |
---|
[805] | 812 | bool tokelvin = true; |
---|
| 813 | Double cfac = 1.0; |
---|
[716] | 814 | |
---|
[805] | 815 | if ( fluxUnit == JY ) { |
---|
[716] | 816 | pushLog("Converting to K"); |
---|
[701] | 817 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 818 | Quantum<Double> t2 = t.get(JY); |
---|
[805] | 819 | cfac = (t2 / t).getValue(); // value to Jy |
---|
[780] | 820 | |
---|
[805] | 821 | tokelvin = true; |
---|
| 822 | out->setFluxUnit("K"); |
---|
| 823 | } else if ( fluxUnit == K ) { |
---|
[716] | 824 | pushLog("Converting to Jy"); |
---|
[701] | 825 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 826 | Quantum<Double> t2 = t.get(K); |
---|
[805] | 827 | cfac = (t2 / t).getValue(); // value to K |
---|
[780] | 828 | |
---|
[805] | 829 | tokelvin = false; |
---|
| 830 | out->setFluxUnit("Jy"); |
---|
[221] | 831 | } else { |
---|
[701] | 832 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 833 | } |
---|
[701] | 834 | // Make sure input values are converted to either Jy or K first... |
---|
[805] | 835 | Float factor = cfac; |
---|
[221] | 836 | |
---|
[701] | 837 | // Select method |
---|
[805] | 838 | if (jyperk > 0.0) { |
---|
| 839 | factor *= jyperk; |
---|
| 840 | if ( tokelvin ) factor = 1.0 / jyperk; |
---|
[716] | 841 | ostringstream oss; |
---|
[805] | 842 | oss << "Jy/K = " << jyperk; |
---|
[716] | 843 | pushLog(String(oss)); |
---|
[805] | 844 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 845 | scaleByVector(tab,factors, false); |
---|
| 846 | } else if ( etaap > 0.0) { |
---|
| 847 | Instrument inst = |
---|
[878] | 848 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True); |
---|
| 849 | STAttr sda; |
---|
[805] | 850 | if (d < 0) d = sda.diameter(inst); |
---|
[996] | 851 | jyperk = STAttr::findJyPerK(etaap, d); |
---|
[716] | 852 | ostringstream oss; |
---|
[805] | 853 | oss << "Jy/K = " << jyperk; |
---|
[716] | 854 | pushLog(String(oss)); |
---|
[805] | 855 | factor *= jyperk; |
---|
| 856 | if ( tokelvin ) { |
---|
[701] | 857 | factor = 1.0 / factor; |
---|
| 858 | } |
---|
[805] | 859 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 860 | scaleByVector(tab, factors, False); |
---|
[354] | 861 | } else { |
---|
[780] | 862 | |
---|
[701] | 863 | // OK now we must deal with automatic look up of values. |
---|
| 864 | // We must also deal with the fact that the factors need |
---|
| 865 | // to be computed per IF and may be different and may |
---|
| 866 | // change per integration. |
---|
[780] | 867 | |
---|
[716] | 868 | pushLog("Looking up conversion factors"); |
---|
[805] | 869 | convertBrightnessUnits(out, tokelvin, cfac); |
---|
[701] | 870 | } |
---|
[805] | 871 | |
---|
| 872 | return out; |
---|
[221] | 873 | } |
---|
| 874 | |
---|
[805] | 875 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in, |
---|
| 876 | bool tokelvin, float cfac ) |
---|
[227] | 877 | { |
---|
[805] | 878 | Table& table = in->table(); |
---|
| 879 | Instrument inst = |
---|
[878] | 880 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True); |
---|
[805] | 881 | TableIterator iter(table, "FREQ_ID"); |
---|
| 882 | STFrequencies stfreqs = in->frequencies(); |
---|
[878] | 883 | STAttr sdAtt; |
---|
[805] | 884 | while (!iter.pastEnd()) { |
---|
| 885 | Table tab = iter.table(); |
---|
| 886 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 887 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 888 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID"); |
---|
| 889 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
[234] | 890 | |
---|
[805] | 891 | uInt freqid; freqidCol.get(0, freqid); |
---|
| 892 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
[878] | 893 | // STAttr.JyPerK has a Vector interface... change sometime. |
---|
[805] | 894 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements())); |
---|
| 895 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 896 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0]; |
---|
| 897 | Float factor = cfac * jyperk; |
---|
| 898 | if ( tokelvin ) factor = Float(1.0) / factor; |
---|
| 899 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
| 900 | ma *= factor; |
---|
| 901 | specCol.put(i, ma.getArray()); |
---|
| 902 | flagCol.put(i, flagsFromMA(ma)); |
---|
| 903 | } |
---|
[867] | 904 | ++iter; |
---|
[234] | 905 | } |
---|
[230] | 906 | } |
---|
[227] | 907 | |
---|
[805] | 908 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in, |
---|
| 909 | float tau ) |
---|
[234] | 910 | { |
---|
[805] | 911 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[926] | 912 | |
---|
| 913 | Table tab = out->table(); |
---|
[234] | 914 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[805] | 915 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 916 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 917 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 918 | Float zdist = Float(C::pi_2) - elev(i); |
---|
| 919 | Float factor = exp(tau)/cos(zdist); |
---|
[926] | 920 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
[805] | 921 | ma *= factor; |
---|
| 922 | specCol.put(i, ma.getArray()); |
---|
| 923 | flagCol.put(i, flagsFromMA(ma)); |
---|
[234] | 924 | } |
---|
[805] | 925 | return out; |
---|
[234] | 926 | } |
---|
| 927 | |
---|
[805] | 928 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in, |
---|
| 929 | const std::string& kernel, float width ) |
---|
[457] | 930 | { |
---|
[805] | 931 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[1033] | 932 | Table& table = out->table(); |
---|
[805] | 933 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel); |
---|
| 934 | // same IFNO should have same no of channels |
---|
| 935 | // this saves overhead |
---|
| 936 | TableIterator iter(table, "IFNO"); |
---|
| 937 | while (!iter.pastEnd()) { |
---|
| 938 | Table tab = iter.table(); |
---|
| 939 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 940 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 941 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
| 942 | uInt nchan = tmpspec.nelements(); |
---|
| 943 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False); |
---|
| 944 | Convolver<Float> conv(kvec, IPosition(1,nchan)); |
---|
| 945 | Vector<Float> spec; |
---|
| 946 | Vector<uChar> flag; |
---|
| 947 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 948 | specCol.get(i, spec); |
---|
| 949 | flagCol.get(i, flag); |
---|
| 950 | Vector<Bool> mask(flag.nelements()); |
---|
| 951 | convertArray(mask, flag); |
---|
| 952 | Vector<Float> specout; |
---|
| 953 | if ( type == VectorKernel::HANNING ) { |
---|
| 954 | Vector<Bool> maskout; |
---|
[1033] | 955 | mathutil::hanning(specout, maskout, spec , !mask); |
---|
| 956 | convertArray(flag, !maskout); |
---|
[805] | 957 | flagCol.put(i, flag); |
---|
[1033] | 958 | specCol.put(i, specout); |
---|
| 959 | } else { |
---|
[805] | 960 | mathutil::replaceMaskByZero(specout, mask); |
---|
| 961 | conv.linearConv(specout, spec); |
---|
[1033] | 962 | specCol.put(i, specout); |
---|
[354] | 963 | } |
---|
[805] | 964 | } |
---|
[867] | 965 | ++iter; |
---|
[701] | 966 | } |
---|
[805] | 967 | return out; |
---|
[701] | 968 | } |
---|
[841] | 969 | |
---|
| 970 | CountedPtr< Scantable > |
---|
| 971 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in ) |
---|
| 972 | { |
---|
| 973 | if ( in.size() < 2 ) { |
---|
[862] | 974 | throw(AipsError("Need at least two scantables to perform a merge.")); |
---|
[841] | 975 | } |
---|
| 976 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin(); |
---|
| 977 | bool insitu = insitu_; |
---|
| 978 | setInsitu(false); |
---|
[862] | 979 | CountedPtr< Scantable > out = getScantable(*it, false); |
---|
[841] | 980 | setInsitu(insitu); |
---|
| 981 | Table& tout = out->table(); |
---|
| 982 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID"); |
---|
[917] | 983 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID"); |
---|
| 984 | // Renumber SCANNO to be 0-based |
---|
[926] | 985 | Vector<uInt> scannos = scannocol.getColumn(); |
---|
| 986 | uInt offset = min(scannos); |
---|
[917] | 987 | scannos -= offset; |
---|
[926] | 988 | scannocol.putColumn(scannos); |
---|
| 989 | uInt newscanno = max(scannos)+1; |
---|
[862] | 990 | ++it; |
---|
[841] | 991 | while ( it != in.end() ){ |
---|
| 992 | if ( ! (*it)->conformant(*out) ) { |
---|
| 993 | // log message: "ignoring scantable i, as it isn't |
---|
| 994 | // conformant with the other(s)" |
---|
| 995 | cerr << "oh oh" << endl; |
---|
| 996 | ++it; |
---|
| 997 | continue; |
---|
| 998 | } |
---|
[862] | 999 | out->appendToHistoryTable((*it)->history()); |
---|
[841] | 1000 | const Table& tab = (*it)->table(); |
---|
| 1001 | TableIterator scanit(tab, "SCANNO"); |
---|
| 1002 | while (!scanit.pastEnd()) { |
---|
| 1003 | TableIterator freqit(scanit.table(), "FREQ_ID"); |
---|
| 1004 | while ( !freqit.pastEnd() ) { |
---|
| 1005 | Table thetab = freqit.table(); |
---|
| 1006 | uInt nrow = tout.nrow(); |
---|
| 1007 | //tout.addRow(thetab.nrow()); |
---|
| 1008 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow()); |
---|
| 1009 | ROTableRow row(thetab); |
---|
| 1010 | for ( uInt i=0; i<thetab.nrow(); ++i) { |
---|
| 1011 | uInt k = nrow+i; |
---|
| 1012 | scannocol.put(k, newscanno); |
---|
| 1013 | const TableRecord& rec = row.get(i); |
---|
| 1014 | Double rv,rp,inc; |
---|
| 1015 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID")); |
---|
| 1016 | uInt id; |
---|
| 1017 | id = out->frequencies().addEntry(rp, rv, inc); |
---|
| 1018 | freqidcol.put(k,id); |
---|
| 1019 | String name,fname;Double rf; |
---|
| 1020 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID")); |
---|
| 1021 | id = out->molecules().addEntry(rf, name, fname); |
---|
| 1022 | molidcol.put(k, id); |
---|
[961] | 1023 | Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp; |
---|
| 1024 | (*it)->focus().getEntry(fax, ftan, frot, fhand, |
---|
| 1025 | fmount,fuser, fxy, fxyp, |
---|
| 1026 | rec.asuInt("FOCUS_ID")); |
---|
| 1027 | id = out->focus().addEntry(fax, ftan, frot, fhand, |
---|
| 1028 | fmount,fuser, fxy, fxyp); |
---|
[841] | 1029 | focusidcol.put(k, id); |
---|
| 1030 | } |
---|
| 1031 | ++freqit; |
---|
| 1032 | } |
---|
| 1033 | ++newscanno; |
---|
| 1034 | ++scanit; |
---|
| 1035 | } |
---|
| 1036 | ++it; |
---|
| 1037 | } |
---|
| 1038 | return out; |
---|
| 1039 | } |
---|
[896] | 1040 | |
---|
| 1041 | CountedPtr< Scantable > |
---|
| 1042 | STMath::invertPhase( const CountedPtr < Scantable >& in ) |
---|
| 1043 | { |
---|
[996] | 1044 | return applyToPol(in, &STPol::invertPhase, Float(0.0)); |
---|
[896] | 1045 | } |
---|
| 1046 | |
---|
| 1047 | CountedPtr< Scantable > |
---|
| 1048 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
| 1049 | { |
---|
| 1050 | return applyToPol(in, &STPol::rotatePhase, Float(phase)); |
---|
| 1051 | } |
---|
| 1052 | |
---|
| 1053 | CountedPtr< Scantable > |
---|
| 1054 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
| 1055 | { |
---|
| 1056 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase)); |
---|
| 1057 | } |
---|
| 1058 | |
---|
| 1059 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in, |
---|
| 1060 | STPol::polOperation fptr, |
---|
| 1061 | Float phase ) |
---|
| 1062 | { |
---|
| 1063 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 1064 | Table& tout = out->table(); |
---|
| 1065 | Block<String> cols(4); |
---|
| 1066 | cols[0] = String("SCANNO"); |
---|
| 1067 | cols[1] = String("BEAMNO"); |
---|
| 1068 | cols[2] = String("IFNO"); |
---|
| 1069 | cols[3] = String("CYCLENO"); |
---|
| 1070 | TableIterator iter(tout, cols); |
---|
[1015] | 1071 | STPol* stpol = STPol::getPolClass(out->factories_, out->getPolType() ); |
---|
[896] | 1072 | while (!iter.pastEnd()) { |
---|
| 1073 | Table t = iter.table(); |
---|
| 1074 | ArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
[1015] | 1075 | ScalarColumn<uInt> focidcol(t, "FOCUS_ID"); |
---|
| 1076 | ScalarColumn<Float> parancol(t, "PARANGLE"); |
---|
[896] | 1077 | Matrix<Float> pols = speccol.getColumn(); |
---|
| 1078 | try { |
---|
| 1079 | stpol->setSpectra(pols); |
---|
[1015] | 1080 | Float fang,fhand,parang; |
---|
| 1081 | fang = in->focusTable_.getTotalFeedAngle(focidcol(0)); |
---|
| 1082 | fhand = in->focusTable_.getFeedHand(focidcol(0)); |
---|
| 1083 | parang = parancol(0); |
---|
| 1084 | /// @todo re-enable this |
---|
| 1085 | // disable total feed angle to support paralactifying Caswell style |
---|
| 1086 | stpol->setPhaseCorrections(parang, -parang, fhand); |
---|
[896] | 1087 | (stpol->*fptr)(phase); |
---|
| 1088 | speccol.putColumn(stpol->getSpectra()); |
---|
[1015] | 1089 | Matrix<Float> tmp = stpol->getSpectra(); |
---|
[896] | 1090 | } catch (AipsError& e) { |
---|
| 1091 | delete stpol;stpol=0; |
---|
| 1092 | throw(e); |
---|
| 1093 | } |
---|
| 1094 | ++iter; |
---|
| 1095 | } |
---|
[934] | 1096 | delete stpol;stpol=0; |
---|
[896] | 1097 | return out; |
---|
| 1098 | } |
---|
| 1099 | |
---|
| 1100 | CountedPtr< Scantable > |
---|
| 1101 | STMath::swapPolarisations( const CountedPtr< Scantable > & in ) |
---|
| 1102 | { |
---|
| 1103 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 1104 | Table& tout = out->table(); |
---|
| 1105 | Table t0 = tout(tout.col("POLNO") == 0); |
---|
| 1106 | Table t1 = tout(tout.col("POLNO") == 1); |
---|
| 1107 | if ( t0.nrow() != t1.nrow() ) |
---|
| 1108 | throw(AipsError("Inconsistent number of polarisations")); |
---|
| 1109 | ArrayColumn<Float> speccol0(t0, "SPECTRA"); |
---|
| 1110 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA"); |
---|
| 1111 | ArrayColumn<Float> speccol1(t1, "SPECTRA"); |
---|
| 1112 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA"); |
---|
| 1113 | Matrix<Float> s0 = speccol0.getColumn(); |
---|
| 1114 | Matrix<uChar> f0 = flagcol0.getColumn(); |
---|
| 1115 | speccol0.putColumn(speccol1.getColumn()); |
---|
| 1116 | flagcol0.putColumn(flagcol1.getColumn()); |
---|
| 1117 | speccol1.putColumn(s0); |
---|
| 1118 | flagcol1.putColumn(f0); |
---|
| 1119 | return out; |
---|
| 1120 | } |
---|
[917] | 1121 | |
---|
| 1122 | CountedPtr< Scantable > |
---|
[940] | 1123 | STMath::averagePolarisations( const CountedPtr< Scantable > & in, |
---|
| 1124 | const std::vector<bool>& mask, |
---|
| 1125 | const std::string& weight ) |
---|
| 1126 | { |
---|
| 1127 | if (in->getPolType() != "linear" || in->npol() != 2 ) |
---|
| 1128 | throw(AipsError("averagePolarisations can only be applied to two linear polarisations.")); |
---|
[1010] | 1129 | bool insitu = insitu_; |
---|
| 1130 | setInsitu(false); |
---|
| 1131 | CountedPtr< Scantable > pols = getScantable(in, false); |
---|
| 1132 | setInsitu(insitu); |
---|
| 1133 | Table& tout = pols->table(); |
---|
| 1134 | // give all rows the same POLNO |
---|
[1145] | 1135 | TableVector<uInt> vec(tout, "POLNO"); |
---|
[940] | 1136 | vec = 0; |
---|
[1145] | 1137 | pols->table_.rwKeywordSet().define("nPol", Int(1)); |
---|
[1010] | 1138 | std::vector<CountedPtr<Scantable> > vpols; |
---|
| 1139 | vpols.push_back(pols); |
---|
| 1140 | CountedPtr< Scantable > out = average(vpols, mask, weight, "NONE"); |
---|
[940] | 1141 | return out; |
---|
| 1142 | } |
---|
| 1143 | |
---|
[1145] | 1144 | CountedPtr< Scantable > |
---|
| 1145 | STMath::averageBeams( const CountedPtr< Scantable > & in, |
---|
| 1146 | const std::vector<bool>& mask, |
---|
| 1147 | const std::string& weight ) |
---|
| 1148 | { |
---|
| 1149 | bool insitu = insitu_; |
---|
| 1150 | setInsitu(false); |
---|
| 1151 | CountedPtr< Scantable > beams = getScantable(in, false); |
---|
| 1152 | setInsitu(insitu); |
---|
| 1153 | Table& tout = beams->table(); |
---|
| 1154 | // give all rows the same BEAMNO |
---|
| 1155 | TableVector<uInt> vec(tout, "BEAMNO"); |
---|
| 1156 | vec = 0; |
---|
| 1157 | beams->table_.rwKeywordSet().define("nBeam", Int(1)); |
---|
| 1158 | std::vector<CountedPtr<Scantable> > vbeams; |
---|
| 1159 | vbeams.push_back(beams); |
---|
| 1160 | CountedPtr< Scantable > out = average(vbeams, mask, weight, "NONE"); |
---|
| 1161 | return out; |
---|
| 1162 | } |
---|
[940] | 1163 | |
---|
[1145] | 1164 | |
---|
[940] | 1165 | CountedPtr< Scantable > |
---|
[917] | 1166 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in, |
---|
| 1167 | const std::string & refTime, |
---|
[926] | 1168 | const std::string & method) |
---|
[917] | 1169 | { |
---|
[940] | 1170 | // clone as this is not working insitu |
---|
| 1171 | bool insitu = insitu_; |
---|
| 1172 | setInsitu(false); |
---|
[917] | 1173 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[940] | 1174 | setInsitu(insitu); |
---|
[917] | 1175 | Table& tout = out->table(); |
---|
| 1176 | // Get reference Epoch to time of first row or given String |
---|
| 1177 | Unit DAY(String("d")); |
---|
| 1178 | MEpoch::Ref epochRef(in->getTimeReference()); |
---|
| 1179 | MEpoch refEpoch; |
---|
| 1180 | if (refTime.length()>0) { |
---|
| 1181 | Quantum<Double> qt; |
---|
| 1182 | if (MVTime::read(qt,refTime)) { |
---|
| 1183 | MVEpoch mv(qt); |
---|
| 1184 | refEpoch = MEpoch(mv, epochRef); |
---|
| 1185 | } else { |
---|
| 1186 | throw(AipsError("Invalid format for Epoch string")); |
---|
| 1187 | } |
---|
| 1188 | } else { |
---|
| 1189 | refEpoch = in->timeCol_(0); |
---|
| 1190 | } |
---|
| 1191 | MPosition refPos = in->getAntennaPosition(); |
---|
[940] | 1192 | |
---|
[996] | 1193 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method); |
---|
[917] | 1194 | // test if user frame is different to base frame |
---|
| 1195 | if ( in->frequencies().getFrameString(true) |
---|
| 1196 | == in->frequencies().getFrameString(false) ) { |
---|
[985] | 1197 | throw(AipsError("Can't convert as no output frame has been set" |
---|
| 1198 | " (use set_freqframe) or it is aligned already.")); |
---|
[917] | 1199 | } |
---|
| 1200 | MFrequency::Types system = in->frequencies().getFrame(); |
---|
[940] | 1201 | MVTime mvt(refEpoch.getValue()); |
---|
| 1202 | String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")"); |
---|
| 1203 | ostringstream oss; |
---|
| 1204 | oss << "Aligned at reference Epoch " << epochout |
---|
| 1205 | << " in frame " << MFrequency::showType(system); |
---|
| 1206 | pushLog(String(oss)); |
---|
[917] | 1207 | // set up the iterator |
---|
[926] | 1208 | Block<String> cols(4); |
---|
| 1209 | // select by constant direction |
---|
[917] | 1210 | cols[0] = String("SRCNAME"); |
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| 1211 | cols[1] = String("BEAMNO"); |
---|
| 1212 | // select by IF ( no of channels varies over this ) |
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| 1213 | cols[2] = String("IFNO"); |
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[926] | 1214 | // select by restfrequency |
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| 1215 | cols[3] = String("MOLECULE_ID"); |
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[917] | 1216 | TableIterator iter(tout, cols); |
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[926] | 1217 | while ( !iter.pastEnd() ) { |
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[917] | 1218 | Table t = iter.table(); |
---|
| 1219 | MDirection::ROScalarColumn dirCol(t, "DIRECTION"); |
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[926] | 1220 | TableIterator fiter(t, "FREQ_ID"); |
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[917] | 1221 | // determine nchan from the first row. This should work as |
---|
[926] | 1222 | // we are iterating over BEAMNO and IFNO // we should have constant direction |
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| 1223 | |
---|
[917] | 1224 | ROArrayColumn<Float> sCol(t, "SPECTRA"); |
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[926] | 1225 | MDirection direction = dirCol(0); |
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[917] | 1226 | uInt nchan = sCol(0).nelements(); |
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[926] | 1227 | while ( !fiter.pastEnd() ) { |
---|
| 1228 | Table ftab = fiter.table(); |
---|
| 1229 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID"); |
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| 1230 | // get the SpectralCoordinate for the freqid, which we are iterating over |
---|
| 1231 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0)); |
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| 1232 | FrequencyAligner<Float> fa( sC, nchan, refEpoch, |
---|
| 1233 | direction, refPos, system ); |
---|
| 1234 | // realign the SpectralCoordinate and put into the output Scantable |
---|
| 1235 | Vector<String> units(1); |
---|
| 1236 | units = String("Hz"); |
---|
| 1237 | Bool linear=True; |
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| 1238 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear); |
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| 1239 | sc2.setWorldAxisUnits(units); |
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[934] | 1240 | uInt id = out->frequencies().addEntry(sc2.referencePixel()[0], |
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| 1241 | sc2.referenceValue()[0], |
---|
| 1242 | sc2.increment()[0]); |
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| 1243 | TableVector<uInt> tvec(ftab, "FREQ_ID"); |
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| 1244 | tvec = id; |
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[926] | 1245 | // create the "global" abcissa for alignment with same FREQ_ID |
---|
| 1246 | Vector<Double> abc(nchan); |
---|
[917] | 1247 | Double w; |
---|
| 1248 | for (uInt i=0; i<nchan; i++) { |
---|
| 1249 | sC.toWorld(w,Double(i)); |
---|
| 1250 | abc[i] = w; |
---|
| 1251 | } |
---|
[926] | 1252 | // cache abcissa for same time stamps, so iterate over those |
---|
| 1253 | TableIterator timeiter(ftab, "TIME"); |
---|
| 1254 | while ( !timeiter.pastEnd() ) { |
---|
| 1255 | Table tab = timeiter.table(); |
---|
| 1256 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
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| 1257 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 1258 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
| 1259 | // use align abcissa cache after the first row |
---|
| 1260 | bool first = true; |
---|
| 1261 | // these rows should be just be POLNO |
---|
[996] | 1262 | for (int i=0; i<int(tab.nrow()); ++i) { |
---|
[926] | 1263 | // input values |
---|
| 1264 | Vector<uChar> flag = flagCol(i); |
---|
| 1265 | Vector<Bool> mask(flag.shape()); |
---|
| 1266 | Vector<Float> specOut, spec; |
---|
| 1267 | spec = specCol(i); |
---|
| 1268 | Vector<Bool> maskOut;Vector<uChar> flagOut; |
---|
| 1269 | convertArray(mask, flag); |
---|
| 1270 | // alignment |
---|
| 1271 | Bool ok = fa.align(specOut, maskOut, abc, spec, |
---|
| 1272 | mask, timeCol(i), !first, |
---|
| 1273 | interp, False); |
---|
| 1274 | // back into scantable |
---|
| 1275 | flagOut.resize(maskOut.nelements()); |
---|
| 1276 | convertArray(flagOut, maskOut); |
---|
| 1277 | flagCol.put(i, flagOut); |
---|
| 1278 | specCol.put(i, specOut); |
---|
| 1279 | // start abcissa caching |
---|
| 1280 | first = false; |
---|
[917] | 1281 | } |
---|
[926] | 1282 | // next timestamp |
---|
| 1283 | ++timeiter; |
---|
[917] | 1284 | } |
---|
[940] | 1285 | // next FREQ_ID |
---|
[926] | 1286 | ++fiter; |
---|
[917] | 1287 | } |
---|
| 1288 | // next aligner |
---|
| 1289 | ++iter; |
---|
| 1290 | } |
---|
[940] | 1291 | // set this afterwards to ensure we are doing insitu correctly. |
---|
| 1292 | out->frequencies().setFrame(system, true); |
---|
[917] | 1293 | return out; |
---|
| 1294 | } |
---|
[992] | 1295 | |
---|
| 1296 | CountedPtr<Scantable> |
---|
| 1297 | asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in, |
---|
| 1298 | const std::string & newtype ) |
---|
| 1299 | { |
---|
| 1300 | if (in->npol() != 2 && in->npol() != 4) |
---|
| 1301 | throw(AipsError("Can only convert two or four polarisations.")); |
---|
| 1302 | if ( in->getPolType() == newtype ) |
---|
| 1303 | throw(AipsError("No need to convert.")); |
---|
[1000] | 1304 | if ( ! in->selector_.empty() ) |
---|
| 1305 | throw(AipsError("Can only convert whole scantable. Unset the selection.")); |
---|
[992] | 1306 | bool insitu = insitu_; |
---|
| 1307 | setInsitu(false); |
---|
| 1308 | CountedPtr< Scantable > out = getScantable(in, true); |
---|
| 1309 | setInsitu(insitu); |
---|
| 1310 | Table& tout = out->table(); |
---|
| 1311 | tout.rwKeywordSet().define("POLTYPE", String(newtype)); |
---|
| 1312 | |
---|
| 1313 | Block<String> cols(4); |
---|
| 1314 | cols[0] = "SCANNO"; |
---|
| 1315 | cols[1] = "CYCLENO"; |
---|
| 1316 | cols[2] = "BEAMNO"; |
---|
| 1317 | cols[3] = "IFNO"; |
---|
| 1318 | TableIterator it(in->originalTable_, cols); |
---|
| 1319 | String basetype = in->getPolType(); |
---|
| 1320 | STPol* stpol = STPol::getPolClass(in->factories_, basetype); |
---|
| 1321 | try { |
---|
| 1322 | while ( !it.pastEnd() ) { |
---|
| 1323 | Table tab = it.table(); |
---|
| 1324 | uInt row = tab.rowNumbers()[0]; |
---|
| 1325 | stpol->setSpectra(in->getPolMatrix(row)); |
---|
| 1326 | Float fang,fhand,parang; |
---|
| 1327 | fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row)); |
---|
| 1328 | fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row)); |
---|
| 1329 | parang = in->paraCol_(row); |
---|
| 1330 | /// @todo re-enable this |
---|
| 1331 | // disable total feed angle to support paralactifying Caswell style |
---|
| 1332 | stpol->setPhaseCorrections(parang, -parang, fhand); |
---|
| 1333 | Int npolout = 0; |
---|
| 1334 | for (uInt i=0; i<tab.nrow(); ++i) { |
---|
| 1335 | Vector<Float> outvec = stpol->getSpectrum(i, newtype); |
---|
| 1336 | if ( outvec.nelements() > 0 ) { |
---|
| 1337 | tout.addRow(); |
---|
| 1338 | TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1); |
---|
| 1339 | ArrayColumn<Float> sCol(tout,"SPECTRA"); |
---|
| 1340 | ScalarColumn<uInt> pCol(tout,"POLNO"); |
---|
| 1341 | sCol.put(tout.nrow()-1 ,outvec); |
---|
| 1342 | pCol.put(tout.nrow()-1 ,uInt(npolout)); |
---|
| 1343 | npolout++; |
---|
| 1344 | } |
---|
| 1345 | } |
---|
| 1346 | tout.rwKeywordSet().define("nPol", npolout); |
---|
| 1347 | ++it; |
---|
| 1348 | } |
---|
| 1349 | } catch (AipsError& e) { |
---|
| 1350 | delete stpol; |
---|
| 1351 | throw(e); |
---|
| 1352 | } |
---|
| 1353 | delete stpol; |
---|
| 1354 | return out; |
---|
| 1355 | } |
---|
[1066] | 1356 | |
---|
[1143] | 1357 | CountedPtr< Scantable > |
---|
[1140] | 1358 | asap::STMath::mxExtract( const CountedPtr< Scantable > & in, |
---|
| 1359 | const std::string & scantype ) |
---|
| 1360 | { |
---|
| 1361 | bool insitu = insitu_; |
---|
| 1362 | setInsitu(false); |
---|
| 1363 | CountedPtr< Scantable > out = getScantable(in, true); |
---|
| 1364 | setInsitu(insitu); |
---|
| 1365 | Table& tout = out->table(); |
---|
| 1366 | std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO"; |
---|
| 1367 | if (scantype == "on") { |
---|
| 1368 | taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO"; |
---|
| 1369 | } |
---|
| 1370 | Table tab = tableCommand(taql, in->table()); |
---|
| 1371 | TableCopy::copyRows(tout, tab); |
---|
| 1372 | if (scantype == "on") { |
---|
[1143] | 1373 | // re-index SCANNO to 0 |
---|
[1140] | 1374 | TableVector<uInt> vec(tout, "SCANNO"); |
---|
| 1375 | vec = 0; |
---|
| 1376 | } |
---|
| 1377 | return out; |
---|
| 1378 | } |
---|