[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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[1192] | 33 | #include <scimath/Mathematics/FFTServer.h> |
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[2] | 34 | |
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[262] | 35 | #include <lattices/Lattices/LatticeUtilities.h> |
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| 36 | |
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[917] | 37 | #include <coordinates/Coordinates/SpectralCoordinate.h> |
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| 38 | #include <coordinates/Coordinates/CoordinateSystem.h> |
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| 39 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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| 40 | #include <coordinates/Coordinates/FrequencyAligner.h> |
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| 41 | |
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[177] | 42 | #include <scimath/Mathematics/VectorKernel.h> |
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| 43 | #include <scimath/Mathematics/Convolver.h> |
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[234] | 44 | #include <scimath/Functionals/Polynomial.h> |
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[177] | 45 | |
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[38] | 46 | #include "MathUtils.h" |
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[805] | 47 | #include "RowAccumulator.h" |
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[878] | 48 | #include "STAttr.h" |
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[805] | 49 | #include "STMath.h" |
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[2] | 50 | |
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[805] | 51 | using namespace casa; |
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[2] | 52 | |
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[83] | 53 | using namespace asap; |
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[2] | 54 | |
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[805] | 55 | STMath::STMath(bool insitu) : |
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| 56 | insitu_(insitu) |
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[716] | 57 | { |
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| 58 | } |
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[170] | 59 | |
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| 60 | |
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[805] | 61 | STMath::~STMath() |
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[170] | 62 | { |
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| 63 | } |
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| 64 | |
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[805] | 65 | CountedPtr<Scantable> |
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[977] | 66 | STMath::average( const std::vector<CountedPtr<Scantable> >& in, |
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[858] | 67 | const std::vector<bool>& mask, |
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[805] | 68 | const std::string& weight, |
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[977] | 69 | const std::string& avmode) |
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[262] | 70 | { |
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[977] | 71 | if ( avmode == "SCAN" && in.size() != 1 ) |
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[1066] | 72 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n" |
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| 73 | "Use merge first.")); |
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[805] | 74 | WeightType wtype = stringToWeight(weight); |
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[926] | 75 | |
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[805] | 76 | // output |
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| 77 | // clone as this is non insitu |
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| 78 | bool insitu = insitu_; |
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| 79 | setInsitu(false); |
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[977] | 80 | CountedPtr< Scantable > out = getScantable(in[0], true); |
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[805] | 81 | setInsitu(insitu); |
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[977] | 82 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin(); |
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[862] | 83 | ++stit; |
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[977] | 84 | while ( stit != in.end() ) { |
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[862] | 85 | out->appendToHistoryTable((*stit)->history()); |
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| 86 | ++stit; |
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| 87 | } |
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[294] | 88 | |
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[805] | 89 | Table& tout = out->table(); |
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[701] | 90 | |
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[805] | 91 | /// @todo check if all scantables are conformant |
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[294] | 92 | |
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[805] | 93 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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| 94 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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| 95 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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| 96 | ScalarColumn<Double> mjdColOut(tout,"TIME"); |
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| 97 | ScalarColumn<Double> intColOut(tout,"INTERVAL"); |
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[1008] | 98 | ScalarColumn<uInt> cycColOut(tout,"CYCLENO"); |
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[1145] | 99 | ScalarColumn<uInt> scanColOut(tout,"SCANNO"); |
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[262] | 100 | |
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[805] | 101 | // set up the output table rows. These are based on the structure of the |
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[862] | 102 | // FIRST scantable in the vector |
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[977] | 103 | const Table& baset = in[0]->table(); |
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[262] | 104 | |
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[805] | 105 | Block<String> cols(3); |
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| 106 | cols[0] = String("BEAMNO"); |
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| 107 | cols[1] = String("IFNO"); |
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| 108 | cols[2] = String("POLNO"); |
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| 109 | if ( avmode == "SOURCE" ) { |
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| 110 | cols.resize(4); |
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| 111 | cols[3] = String("SRCNAME"); |
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[488] | 112 | } |
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[977] | 113 | if ( avmode == "SCAN" && in.size() == 1) { |
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[805] | 114 | cols.resize(4); |
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| 115 | cols[3] = String("SCANNO"); |
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[2] | 116 | } |
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[805] | 117 | uInt outrowCount = 0; |
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| 118 | TableIterator iter(baset, cols); |
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| 119 | while (!iter.pastEnd()) { |
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| 120 | Table subt = iter.table(); |
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| 121 | // copy the first row of this selection into the new table |
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| 122 | tout.addRow(); |
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| 123 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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[1145] | 124 | // re-index to 0 |
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| 125 | if ( avmode != "SCAN" && avmode != "SOURCE" ) { |
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| 126 | scanColOut.put(outrowCount, uInt(0)); |
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| 127 | } |
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[805] | 128 | ++outrowCount; |
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| 129 | ++iter; |
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[144] | 130 | } |
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[805] | 131 | RowAccumulator acc(wtype); |
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[858] | 132 | Vector<Bool> cmask(mask); |
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| 133 | acc.setUserMask(cmask); |
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[805] | 134 | ROTableRow row(tout); |
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| 135 | ROArrayColumn<Float> specCol, tsysCol; |
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| 136 | ROArrayColumn<uChar> flagCol; |
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| 137 | ROScalarColumn<Double> mjdCol, intCol; |
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| 138 | ROScalarColumn<Int> scanIDCol; |
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[144] | 139 | |
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[1333] | 140 | Vector<uInt> rowstodelete; |
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| 141 | |
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[805] | 142 | for (uInt i=0; i < tout.nrow(); ++i) { |
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[996] | 143 | for ( int j=0; j < int(in.size()); ++j ) { |
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[977] | 144 | const Table& tin = in[j]->table(); |
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[805] | 145 | const TableRecord& rec = row.get(i); |
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| 146 | ROScalarColumn<Double> tmp(tin, "TIME"); |
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| 147 | Double td;tmp.get(0,td); |
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| 148 | Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
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| 149 | && tin.col("IFNO") == Int(rec.asuInt("IFNO")) |
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| 150 | && tin.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
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| 151 | Table subt; |
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| 152 | if ( avmode == "SOURCE") { |
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| 153 | subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") ); |
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| 154 | } else if (avmode == "SCAN") { |
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| 155 | subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) ); |
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| 156 | } else { |
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| 157 | subt = basesubt; |
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| 158 | } |
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| 159 | specCol.attach(subt,"SPECTRA"); |
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| 160 | flagCol.attach(subt,"FLAGTRA"); |
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| 161 | tsysCol.attach(subt,"TSYS"); |
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| 162 | intCol.attach(subt,"INTERVAL"); |
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| 163 | mjdCol.attach(subt,"TIME"); |
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| 164 | Vector<Float> spec,tsys; |
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| 165 | Vector<uChar> flag; |
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| 166 | Double inter,time; |
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| 167 | for (uInt k = 0; k < subt.nrow(); ++k ) { |
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| 168 | flagCol.get(k, flag); |
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| 169 | Vector<Bool> bflag(flag.shape()); |
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| 170 | convertArray(bflag, flag); |
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[1314] | 171 | /* |
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[805] | 172 | if ( allEQ(bflag, True) ) { |
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[1314] | 173 | continue;//don't accumulate |
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[144] | 174 | } |
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[1314] | 175 | */ |
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[805] | 176 | specCol.get(k, spec); |
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| 177 | tsysCol.get(k, tsys); |
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| 178 | intCol.get(k, inter); |
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| 179 | mjdCol.get(k, time); |
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| 180 | // spectrum has to be added last to enable weighting by the other values |
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| 181 | acc.add(spec, !bflag, tsys, inter, time); |
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| 182 | } |
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| 183 | } |
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[1333] | 184 | const Vector<Bool>& msk = acc.getMask(); |
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| 185 | if ( allEQ(msk, False) ) { |
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| 186 | uint n = rowstodelete.nelements(); |
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| 187 | rowstodelete.resize(n+1, True); |
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| 188 | rowstodelete[n] = i; |
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| 189 | continue; |
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| 190 | } |
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[805] | 191 | //write out |
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| 192 | Vector<uChar> flg(msk.shape()); |
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| 193 | convertArray(flg, !msk); |
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| 194 | flagColOut.put(i, flg); |
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[1333] | 195 | specColOut.put(i, acc.getSpectrum()); |
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[805] | 196 | tsysColOut.put(i, acc.getTsys()); |
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| 197 | intColOut.put(i, acc.getInterval()); |
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| 198 | mjdColOut.put(i, acc.getTime()); |
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[1008] | 199 | // we should only have one cycle now -> reset it to be 0 |
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| 200 | // frequency switched data has different CYCLENO for different IFNO |
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| 201 | // which requires resetting this value |
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| 202 | cycColOut.put(i, uInt(0)); |
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[805] | 203 | acc.reset(); |
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[144] | 204 | } |
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[1333] | 205 | if (rowstodelete.nelements() > 0) { |
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| 206 | cout << rowstodelete << endl; |
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| 207 | tout.removeRow(rowstodelete); |
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| 208 | if (tout.nrow() == 0) { |
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| 209 | throw(AipsError("Can't average fully flagged data.")); |
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| 210 | } |
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| 211 | } |
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[805] | 212 | return out; |
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[2] | 213 | } |
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[9] | 214 | |
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[1069] | 215 | CountedPtr< Scantable > |
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| 216 | STMath::averageChannel( const CountedPtr < Scantable > & in, |
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[1078] | 217 | const std::string & mode, |
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| 218 | const std::string& avmode ) |
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[1069] | 219 | { |
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| 220 | // clone as this is non insitu |
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| 221 | bool insitu = insitu_; |
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| 222 | setInsitu(false); |
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| 223 | CountedPtr< Scantable > out = getScantable(in, true); |
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| 224 | setInsitu(insitu); |
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| 225 | Table& tout = out->table(); |
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| 226 | ArrayColumn<Float> specColOut(tout,"SPECTRA"); |
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| 227 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA"); |
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| 228 | ArrayColumn<Float> tsysColOut(tout,"TSYS"); |
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[1140] | 229 | ScalarColumn<uInt> scanColOut(tout,"SCANNO"); |
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[1232] | 230 | ScalarColumn<Double> intColOut(tout, "INTERVAL"); |
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[1140] | 231 | Table tmp = in->table().sort("BEAMNO"); |
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[1069] | 232 | Block<String> cols(3); |
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| 233 | cols[0] = String("BEAMNO"); |
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| 234 | cols[1] = String("IFNO"); |
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| 235 | cols[2] = String("POLNO"); |
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[1078] | 236 | if ( avmode == "SCAN") { |
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| 237 | cols.resize(4); |
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| 238 | cols[3] = String("SCANNO"); |
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| 239 | } |
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[1069] | 240 | uInt outrowCount = 0; |
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| 241 | uChar userflag = 1 << 7; |
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[1140] | 242 | TableIterator iter(tmp, cols); |
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[1069] | 243 | while (!iter.pastEnd()) { |
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| 244 | Table subt = iter.table(); |
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| 245 | ROArrayColumn<Float> specCol, tsysCol; |
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| 246 | ROArrayColumn<uChar> flagCol; |
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[1232] | 247 | ROScalarColumn<Double> intCol(subt, "INTERVAL"); |
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[1069] | 248 | specCol.attach(subt,"SPECTRA"); |
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| 249 | flagCol.attach(subt,"FLAGTRA"); |
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| 250 | tsysCol.attach(subt,"TSYS"); |
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| 251 | tout.addRow(); |
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| 252 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1); |
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[1140] | 253 | if ( avmode != "SCAN") { |
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| 254 | scanColOut.put(outrowCount, uInt(0)); |
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| 255 | } |
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[1069] | 256 | Vector<Float> tmp; |
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| 257 | specCol.get(0, tmp); |
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| 258 | uInt nchan = tmp.nelements(); |
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[1078] | 259 | // have to do channel by channel here as MaskedArrMath |
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| 260 | // doesn't have partialMedians |
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[1069] | 261 | Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0))); |
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| 262 | Vector<Float> outspec(nchan); |
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| 263 | Vector<uChar> outflag(nchan,0); |
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| 264 | Vector<Float> outtsys(1);/// @fixme when tsys is channel based |
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| 265 | for (uInt i=0; i<nchan; ++i) { |
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| 266 | Vector<Float> specs = specCol.getColumn(Slicer(Slice(i))); |
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| 267 | MaskedArray<Float> ma = maskedArray(specs,flags); |
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| 268 | outspec[i] = median(ma); |
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| 269 | if ( allEQ(ma.getMask(), False) ) |
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| 270 | outflag[i] = userflag;// flag data |
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| 271 | } |
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| 272 | outtsys[0] = median(tsysCol.getColumn()); |
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| 273 | specColOut.put(outrowCount, outspec); |
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| 274 | flagColOut.put(outrowCount, outflag); |
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| 275 | tsysColOut.put(outrowCount, outtsys); |
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[1232] | 276 | Double intsum = sum(intCol.getColumn()); |
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| 277 | intColOut.put(outrowCount, intsum); |
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[1069] | 278 | ++outrowCount; |
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| 279 | ++iter; |
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| 280 | } |
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| 281 | return out; |
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| 282 | } |
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| 283 | |
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[805] | 284 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in, |
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| 285 | bool droprows) |
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[185] | 286 | { |
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[805] | 287 | if (insitu_) return in; |
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| 288 | else { |
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| 289 | // clone |
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| 290 | Scantable* tabp = new Scantable(*in, Bool(droprows)); |
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| 291 | return CountedPtr<Scantable>(tabp); |
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[234] | 292 | } |
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[805] | 293 | } |
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[234] | 294 | |
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[805] | 295 | CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in, |
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| 296 | float val, |
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| 297 | const std::string& mode, |
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| 298 | bool tsys ) |
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| 299 | { |
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| 300 | CountedPtr< Scantable > out = getScantable(in, false); |
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| 301 | Table& tab = out->table(); |
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| 302 | ArrayColumn<Float> specCol(tab,"SPECTRA"); |
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| 303 | ArrayColumn<Float> tsysCol(tab,"TSYS"); |
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| 304 | for (uInt i=0; i<tab.nrow(); ++i) { |
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| 305 | Vector<Float> spec; |
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| 306 | Vector<Float> ts; |
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| 307 | specCol.get(i, spec); |
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| 308 | tsysCol.get(i, ts); |
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[1308] | 309 | if (mode == "MUL" || mode == "DIV") { |
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| 310 | if (mode == "DIV") val = 1.0/val; |
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[805] | 311 | spec *= val; |
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| 312 | specCol.put(i, spec); |
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| 313 | if ( tsys ) { |
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| 314 | ts *= val; |
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| 315 | tsysCol.put(i, ts); |
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| 316 | } |
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[1308] | 317 | } else if ( mode == "ADD" || mode == "SUB") { |
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| 318 | if (mode == "SUB") val *= -1.0; |
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[805] | 319 | spec += val; |
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| 320 | specCol.put(i, spec); |
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| 321 | if ( tsys ) { |
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| 322 | ts += val; |
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| 323 | tsysCol.put(i, ts); |
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| 324 | } |
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| 325 | } |
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[234] | 326 | } |
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[805] | 327 | return out; |
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| 328 | } |
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[234] | 329 | |
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[1308] | 330 | CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left, |
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| 331 | const CountedPtr<Scantable>& right, |
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| 332 | const std::string& mode) |
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| 333 | { |
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| 334 | bool insitu = insitu_; |
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| 335 | if ( ! left->conformant(*right) ) { |
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| 336 | throw(AipsError("'left' and 'right' scantables are not conformant.")); |
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| 337 | } |
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| 338 | setInsitu(false); |
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| 339 | CountedPtr< Scantable > out = getScantable(left, false); |
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| 340 | setInsitu(insitu); |
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| 341 | Table& tout = out->table(); |
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| 342 | Block<String> coln(5); |
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| 343 | coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO"; |
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| 344 | coln[3] = "IFNO"; coln[4] = "POLNO"; |
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| 345 | Table tmpl = tout.sort(coln); |
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| 346 | Table tmpr = right->table().sort(coln); |
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| 347 | ArrayColumn<Float> lspecCol(tmpl,"SPECTRA"); |
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| 348 | ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA"); |
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| 349 | ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA"); |
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| 350 | ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA"); |
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| 351 | |
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| 352 | for (uInt i=0; i<tout.nrow(); ++i) { |
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| 353 | Vector<Float> lspecvec, rspecvec; |
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| 354 | Vector<uChar> lflagvec, rflagvec; |
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| 355 | lspecvec = lspecCol(i); rspecvec = rspecCol(i); |
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| 356 | lflagvec = lflagCol(i); rflagvec = rflagCol(i); |
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| 357 | MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec); |
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| 358 | MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec); |
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| 359 | if (mode == "ADD") { |
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| 360 | mleft += mright; |
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| 361 | } else if ( mode == "SUB") { |
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| 362 | mleft -= mright; |
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| 363 | } else if ( mode == "MUL") { |
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| 364 | mleft *= mright; |
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| 365 | } else if ( mode == "DIV") { |
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| 366 | mleft /= mright; |
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| 367 | } else { |
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| 368 | throw(AipsError("Illegal binary operator")); |
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| 369 | } |
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| 370 | lspecCol.put(i, mleft.getArray()); |
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| 371 | } |
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| 372 | return out; |
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| 373 | } |
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| 374 | |
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| 375 | |
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| 376 | |
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[805] | 377 | MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s, |
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| 378 | const Vector<uChar>& f) |
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| 379 | { |
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| 380 | Vector<Bool> mask; |
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| 381 | mask.resize(f.shape()); |
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| 382 | convertArray(mask, f); |
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| 383 | return MaskedArray<Float>(s,!mask); |
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| 384 | } |
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[248] | 385 | |
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[805] | 386 | Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma) |
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| 387 | { |
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| 388 | const Vector<Bool>& m = ma.getMask(); |
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| 389 | Vector<uChar> flags(m.shape()); |
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| 390 | convertArray(flags, !m); |
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| 391 | return flags; |
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| 392 | } |
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[234] | 393 | |
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[1066] | 394 | CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in, |
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| 395 | const std::string & mode, |
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| 396 | bool preserve ) |
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[805] | 397 | { |
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| 398 | /// @todo make other modes available |
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| 399 | /// modes should be "nearest", "pair" |
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| 400 | // make this operation non insitu |
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| 401 | const Table& tin = in->table(); |
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| 402 | Table ons = tin(tin.col("SRCTYPE") == Int(0)); |
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| 403 | Table offs = tin(tin.col("SRCTYPE") == Int(1)); |
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| 404 | if ( offs.nrow() == 0 ) |
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| 405 | throw(AipsError("No 'off' scans present.")); |
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| 406 | // put all "on" scans into output table |
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[701] | 407 | |
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[805] | 408 | bool insitu = insitu_; |
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| 409 | setInsitu(false); |
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| 410 | CountedPtr< Scantable > out = getScantable(in, true); |
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| 411 | setInsitu(insitu); |
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| 412 | Table& tout = out->table(); |
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[248] | 413 | |
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[805] | 414 | TableCopy::copyRows(tout, ons); |
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| 415 | TableRow row(tout); |
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| 416 | ROScalarColumn<Double> offtimeCol(offs, "TIME"); |
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| 417 | ArrayColumn<Float> outspecCol(tout, "SPECTRA"); |
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| 418 | ROArrayColumn<Float> outtsysCol(tout, "TSYS"); |
---|
| 419 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA"); |
---|
| 420 | for (uInt i=0; i < tout.nrow(); ++i) { |
---|
| 421 | const TableRecord& rec = row.get(i); |
---|
| 422 | Double ontime = rec.asDouble("TIME"); |
---|
[1321] | 423 | Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 424 | && offs.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 425 | && offs.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
---|
| 426 | ROScalarColumn<Double> offtimeCol(presel, "TIME"); |
---|
| 427 | |
---|
[805] | 428 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime)); |
---|
[1259] | 429 | // Timestamp may vary within a cycle ???!!! |
---|
[1321] | 430 | // increase this by 0.01 sec in case of rounding errors... |
---|
[1259] | 431 | // There might be a better way to do this. |
---|
[1321] | 432 | // fix to this fix. TIME is MJD, so 1.0d not 1.0s |
---|
| 433 | mindeltat += 0.01/24./60./60.; |
---|
| 434 | Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat); |
---|
[780] | 435 | |
---|
[1259] | 436 | if ( sel.nrow() < 1 ) { |
---|
| 437 | throw(AipsError("No closest in time found... This could be a rounding " |
---|
| 438 | "issue. Try quotient instead.")); |
---|
| 439 | } |
---|
[805] | 440 | TableRow offrow(sel); |
---|
| 441 | const TableRecord& offrec = offrow.get(0);//should only be one row |
---|
| 442 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
---|
| 443 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
---|
| 444 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
---|
| 445 | /// @fixme this assumes tsys is a scalar not vector |
---|
| 446 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
---|
| 447 | Vector<Float> specon, tsyson; |
---|
| 448 | outtsysCol.get(i, tsyson); |
---|
| 449 | outspecCol.get(i, specon); |
---|
| 450 | Vector<uChar> flagon; |
---|
| 451 | outflagCol.get(i, flagon); |
---|
| 452 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
---|
| 453 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
---|
| 454 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
---|
| 455 | if (preserve) { |
---|
| 456 | quot -= tsysoffscalar; |
---|
| 457 | } else { |
---|
| 458 | quot -= tsyson[0]; |
---|
[701] | 459 | } |
---|
[805] | 460 | outspecCol.put(i, quot.getArray()); |
---|
| 461 | outflagCol.put(i, flagsFromMA(quot)); |
---|
| 462 | } |
---|
[926] | 463 | // renumber scanno |
---|
| 464 | TableIterator it(tout, "SCANNO"); |
---|
| 465 | uInt i = 0; |
---|
| 466 | while ( !it.pastEnd() ) { |
---|
| 467 | Table t = it.table(); |
---|
| 468 | TableVector<uInt> vec(t, "SCANNO"); |
---|
| 469 | vec = i; |
---|
| 470 | ++i; |
---|
| 471 | ++it; |
---|
| 472 | } |
---|
[805] | 473 | return out; |
---|
| 474 | } |
---|
[234] | 475 | |
---|
[1066] | 476 | |
---|
| 477 | CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on, |
---|
| 478 | const CountedPtr< Scantable > & off, |
---|
| 479 | bool preserve ) |
---|
| 480 | { |
---|
| 481 | bool insitu = insitu_; |
---|
[1069] | 482 | if ( ! on->conformant(*off) ) { |
---|
| 483 | throw(AipsError("'on' and 'off' scantables are not conformant.")); |
---|
| 484 | } |
---|
[1066] | 485 | setInsitu(false); |
---|
| 486 | CountedPtr< Scantable > out = getScantable(on, false); |
---|
| 487 | setInsitu(insitu); |
---|
| 488 | Table& tout = out->table(); |
---|
| 489 | const Table& toff = off->table(); |
---|
| 490 | TableIterator sit(tout, "SCANNO"); |
---|
| 491 | TableIterator s2it(toff, "SCANNO"); |
---|
| 492 | while ( !sit.pastEnd() ) { |
---|
| 493 | Table ton = sit.table(); |
---|
| 494 | TableRow row(ton); |
---|
| 495 | Table t = s2it.table(); |
---|
| 496 | ArrayColumn<Float> outspecCol(ton, "SPECTRA"); |
---|
| 497 | ROArrayColumn<Float> outtsysCol(ton, "TSYS"); |
---|
| 498 | ArrayColumn<uChar> outflagCol(ton, "FLAGTRA"); |
---|
| 499 | for (uInt i=0; i < ton.nrow(); ++i) { |
---|
| 500 | const TableRecord& rec = row.get(i); |
---|
| 501 | Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 502 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 503 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) ); |
---|
[1145] | 504 | if ( offsel.nrow() == 0 ) |
---|
| 505 | throw AipsError("STMath::quotient: no matching off"); |
---|
[1066] | 506 | TableRow offrow(offsel); |
---|
| 507 | const TableRecord& offrec = offrow.get(0);//should be ncycles - take first |
---|
| 508 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA"); |
---|
| 509 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS"); |
---|
| 510 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA"); |
---|
| 511 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0)); |
---|
| 512 | Vector<Float> specon, tsyson; |
---|
| 513 | outtsysCol.get(i, tsyson); |
---|
| 514 | outspecCol.get(i, specon); |
---|
| 515 | Vector<uChar> flagon; |
---|
| 516 | outflagCol.get(i, flagon); |
---|
| 517 | MaskedArray<Float> mon = maskedArray(specon, flagon); |
---|
| 518 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff); |
---|
| 519 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff); |
---|
| 520 | if (preserve) { |
---|
| 521 | quot -= tsysoffscalar; |
---|
| 522 | } else { |
---|
| 523 | quot -= tsyson[0]; |
---|
| 524 | } |
---|
| 525 | outspecCol.put(i, quot.getArray()); |
---|
| 526 | outflagCol.put(i, flagsFromMA(quot)); |
---|
| 527 | } |
---|
| 528 | ++sit; |
---|
| 529 | ++s2it; |
---|
| 530 | // take the first off for each on scan which doesn't have a |
---|
| 531 | // matching off scan |
---|
| 532 | // non <= noff: matching pairs, non > noff matching pairs then first off |
---|
| 533 | if ( s2it.pastEnd() ) s2it.reset(); |
---|
| 534 | } |
---|
| 535 | return out; |
---|
| 536 | } |
---|
| 537 | |
---|
| 538 | |
---|
[805] | 539 | CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in ) |
---|
| 540 | { |
---|
| 541 | // make copy or reference |
---|
| 542 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 543 | Table& tout = out->table(); |
---|
[1008] | 544 | Block<String> cols(4); |
---|
[805] | 545 | cols[0] = String("SCANNO"); |
---|
[1008] | 546 | cols[1] = String("CYCLENO"); |
---|
| 547 | cols[2] = String("BEAMNO"); |
---|
| 548 | cols[3] = String("POLNO"); |
---|
[805] | 549 | TableIterator iter(tout, cols); |
---|
| 550 | while (!iter.pastEnd()) { |
---|
| 551 | Table subt = iter.table(); |
---|
| 552 | // this should leave us with two rows for the two IFs....if not ignore |
---|
| 553 | if (subt.nrow() != 2 ) { |
---|
| 554 | continue; |
---|
[701] | 555 | } |
---|
[1008] | 556 | ArrayColumn<Float> specCol(subt, "SPECTRA"); |
---|
| 557 | ArrayColumn<Float> tsysCol(subt, "TSYS"); |
---|
| 558 | ArrayColumn<uChar> flagCol(subt, "FLAGTRA"); |
---|
[805] | 559 | Vector<Float> onspec,offspec, ontsys, offtsys; |
---|
| 560 | Vector<uChar> onflag, offflag; |
---|
| 561 | tsysCol.get(0, ontsys); tsysCol.get(1, offtsys); |
---|
| 562 | specCol.get(0, onspec); specCol.get(1, offspec); |
---|
| 563 | flagCol.get(0, onflag); flagCol.get(1, offflag); |
---|
| 564 | MaskedArray<Float> on = maskedArray(onspec, onflag); |
---|
| 565 | MaskedArray<Float> off = maskedArray(offspec, offflag); |
---|
| 566 | MaskedArray<Float> oncopy = on.copy(); |
---|
[248] | 567 | |
---|
[805] | 568 | on /= off; on -= 1.0f; |
---|
| 569 | on *= ontsys[0]; |
---|
| 570 | off /= oncopy; off -= 1.0f; |
---|
| 571 | off *= offtsys[0]; |
---|
| 572 | specCol.put(0, on.getArray()); |
---|
| 573 | const Vector<Bool>& m0 = on.getMask(); |
---|
| 574 | Vector<uChar> flags0(m0.shape()); |
---|
| 575 | convertArray(flags0, !m0); |
---|
| 576 | flagCol.put(0, flags0); |
---|
[234] | 577 | |
---|
[805] | 578 | specCol.put(1, off.getArray()); |
---|
| 579 | const Vector<Bool>& m1 = off.getMask(); |
---|
| 580 | Vector<uChar> flags1(m1.shape()); |
---|
| 581 | convertArray(flags1, !m1); |
---|
| 582 | flagCol.put(1, flags1); |
---|
[867] | 583 | ++iter; |
---|
[130] | 584 | } |
---|
[780] | 585 | |
---|
[805] | 586 | return out; |
---|
[9] | 587 | } |
---|
[48] | 588 | |
---|
[805] | 589 | std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in, |
---|
| 590 | const std::vector< bool > & mask, |
---|
| 591 | const std::string& which ) |
---|
[130] | 592 | { |
---|
| 593 | |
---|
[805] | 594 | Vector<Bool> m(mask); |
---|
| 595 | const Table& tab = in->table(); |
---|
| 596 | ROArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 597 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 598 | std::vector<float> out; |
---|
| 599 | for (uInt i=0; i < tab.nrow(); ++i ) { |
---|
| 600 | Vector<Float> spec; specCol.get(i, spec); |
---|
[867] | 601 | Vector<uChar> flag; flagCol.get(i, flag); |
---|
| 602 | MaskedArray<Float> ma = maskedArray(spec, flag); |
---|
| 603 | float outstat = 0.0; |
---|
[805] | 604 | if ( spec.nelements() == m.nelements() ) { |
---|
| 605 | outstat = mathutil::statistics(which, ma(m)); |
---|
| 606 | } else { |
---|
| 607 | outstat = mathutil::statistics(which, ma); |
---|
| 608 | } |
---|
| 609 | out.push_back(outstat); |
---|
[234] | 610 | } |
---|
[805] | 611 | return out; |
---|
[130] | 612 | } |
---|
| 613 | |
---|
[805] | 614 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in, |
---|
| 615 | int width ) |
---|
[144] | 616 | { |
---|
[841] | 617 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data.")); |
---|
[805] | 618 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 619 | Table& tout = out->table(); |
---|
| 620 | out->frequencies().rescale(width, "BIN"); |
---|
| 621 | ArrayColumn<Float> specCol(tout, "SPECTRA"); |
---|
| 622 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA"); |
---|
| 623 | for (uInt i=0; i < tout.nrow(); ++i ) { |
---|
| 624 | MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i)); |
---|
| 625 | MaskedArray<Float> maout; |
---|
| 626 | LatticeUtilities::bin(maout, main, 0, Int(width)); |
---|
| 627 | /// @todo implement channel based tsys binning |
---|
| 628 | specCol.put(i, maout.getArray()); |
---|
| 629 | flagCol.put(i, flagsFromMA(maout)); |
---|
| 630 | // take only the first binned spectrum's length for the deprecated |
---|
| 631 | // global header item nChan |
---|
| 632 | if (i==0) tout.rwKeywordSet().define(String("nChan"), |
---|
| 633 | Int(maout.getArray().nelements())); |
---|
[169] | 634 | } |
---|
[805] | 635 | return out; |
---|
[146] | 636 | } |
---|
| 637 | |
---|
[805] | 638 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in, |
---|
| 639 | const std::string& method, |
---|
| 640 | float width ) |
---|
[299] | 641 | // |
---|
| 642 | // Should add the possibility of width being specified in km/s. This means |
---|
[780] | 643 | // that for each freqID (SpectralCoordinate) we will need to convert to an |
---|
| 644 | // average channel width (say at the reference pixel). Then we would need |
---|
| 645 | // to be careful to make sure each spectrum (of different freqID) |
---|
[299] | 646 | // is the same length. |
---|
| 647 | // |
---|
| 648 | { |
---|
[996] | 649 | //InterpolateArray1D<Double,Float>::InterpolationMethod interp; |
---|
[805] | 650 | Int interpMethod(stringToIMethod(method)); |
---|
[299] | 651 | |
---|
[805] | 652 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 653 | Table& tout = out->table(); |
---|
[299] | 654 | |
---|
| 655 | // Resample SpectralCoordinates (one per freqID) |
---|
[805] | 656 | out->frequencies().rescale(width, "RESAMPLE"); |
---|
| 657 | TableIterator iter(tout, "IFNO"); |
---|
| 658 | TableRow row(tout); |
---|
| 659 | while ( !iter.pastEnd() ) { |
---|
| 660 | Table tab = iter.table(); |
---|
| 661 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 662 | //ArrayColumn<Float> tsysCol(tout, "TSYS"); |
---|
| 663 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 664 | Vector<Float> spec; |
---|
| 665 | Vector<uChar> flag; |
---|
| 666 | specCol.get(0,spec); // the number of channels should be constant per IF |
---|
| 667 | uInt nChanIn = spec.nelements(); |
---|
| 668 | Vector<Float> xIn(nChanIn); indgen(xIn); |
---|
| 669 | Int fac = Int(nChanIn/width); |
---|
| 670 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later |
---|
| 671 | uInt k = 0; |
---|
| 672 | Float x = 0.0; |
---|
| 673 | while (x < Float(nChanIn) ) { |
---|
| 674 | xOut(k) = x; |
---|
| 675 | k++; |
---|
| 676 | x += width; |
---|
| 677 | } |
---|
| 678 | uInt nChanOut = k; |
---|
| 679 | xOut.resize(nChanOut, True); |
---|
| 680 | // process all rows for this IFNO |
---|
| 681 | Vector<Float> specOut; |
---|
| 682 | Vector<Bool> maskOut; |
---|
| 683 | Vector<uChar> flagOut; |
---|
| 684 | for (uInt i=0; i < tab.nrow(); ++i) { |
---|
| 685 | specCol.get(i, spec); |
---|
| 686 | flagCol.get(i, flag); |
---|
| 687 | Vector<Bool> mask(flag.nelements()); |
---|
| 688 | convertArray(mask, flag); |
---|
[299] | 689 | |
---|
[805] | 690 | IPosition shapeIn(spec.shape()); |
---|
| 691 | //sh.nchan = nChanOut; |
---|
| 692 | InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut, |
---|
| 693 | xIn, spec, mask, |
---|
| 694 | interpMethod, True, True); |
---|
| 695 | /// @todo do the same for channel based Tsys |
---|
| 696 | flagOut.resize(maskOut.nelements()); |
---|
| 697 | convertArray(flagOut, maskOut); |
---|
| 698 | specCol.put(i, specOut); |
---|
| 699 | flagCol.put(i, flagOut); |
---|
| 700 | } |
---|
| 701 | ++iter; |
---|
[299] | 702 | } |
---|
| 703 | |
---|
[805] | 704 | return out; |
---|
| 705 | } |
---|
[299] | 706 | |
---|
[805] | 707 | STMath::imethod STMath::stringToIMethod(const std::string& in) |
---|
| 708 | { |
---|
| 709 | static STMath::imap lookup; |
---|
[299] | 710 | |
---|
[805] | 711 | // initialize the lookup table if necessary |
---|
| 712 | if ( lookup.empty() ) { |
---|
[926] | 713 | lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour; |
---|
| 714 | lookup["linear"] = InterpolateArray1D<Double,Float>::linear; |
---|
| 715 | lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic; |
---|
| 716 | lookup["spline"] = InterpolateArray1D<Double,Float>::spline; |
---|
[299] | 717 | } |
---|
| 718 | |
---|
[805] | 719 | STMath::imap::const_iterator iter = lookup.find(in); |
---|
[299] | 720 | |
---|
[805] | 721 | if ( lookup.end() == iter ) { |
---|
| 722 | std::string message = in; |
---|
| 723 | message += " is not a valid interpolation mode"; |
---|
| 724 | throw(AipsError(message)); |
---|
[299] | 725 | } |
---|
[805] | 726 | return iter->second; |
---|
[299] | 727 | } |
---|
| 728 | |
---|
[805] | 729 | WeightType STMath::stringToWeight(const std::string& in) |
---|
[146] | 730 | { |
---|
[805] | 731 | static std::map<std::string, WeightType> lookup; |
---|
[434] | 732 | |
---|
[805] | 733 | // initialize the lookup table if necessary |
---|
| 734 | if ( lookup.empty() ) { |
---|
| 735 | lookup["NONE"] = asap::NONE; |
---|
| 736 | lookup["TINT"] = asap::TINT; |
---|
| 737 | lookup["TINTSYS"] = asap::TINTSYS; |
---|
| 738 | lookup["TSYS"] = asap::TSYS; |
---|
| 739 | lookup["VAR"] = asap::VAR; |
---|
| 740 | } |
---|
[434] | 741 | |
---|
[805] | 742 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in); |
---|
[294] | 743 | |
---|
[805] | 744 | if ( lookup.end() == iter ) { |
---|
| 745 | std::string message = in; |
---|
| 746 | message += " is not a valid weighting mode"; |
---|
| 747 | throw(AipsError(message)); |
---|
| 748 | } |
---|
| 749 | return iter->second; |
---|
[146] | 750 | } |
---|
| 751 | |
---|
[805] | 752 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in, |
---|
[867] | 753 | const vector< float > & coeff, |
---|
[805] | 754 | const std::string & filename, |
---|
| 755 | const std::string& method) |
---|
[165] | 756 | { |
---|
[805] | 757 | // Get elevation data from Scantable and convert to degrees |
---|
| 758 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[926] | 759 | Table& tab = out->table(); |
---|
[805] | 760 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
| 761 | Vector<Float> x = elev.getColumn(); |
---|
| 762 | x *= Float(180 / C::pi); // Degrees |
---|
[165] | 763 | |
---|
[867] | 764 | Vector<Float> coeffs(coeff); |
---|
[805] | 765 | const uInt nc = coeffs.nelements(); |
---|
| 766 | if ( filename.length() > 0 && nc > 0 ) { |
---|
| 767 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both")); |
---|
[315] | 768 | } |
---|
[165] | 769 | |
---|
[805] | 770 | // Correct |
---|
| 771 | if ( nc > 0 || filename.length() == 0 ) { |
---|
| 772 | // Find instrument |
---|
| 773 | Bool throwit = True; |
---|
| 774 | Instrument inst = |
---|
[878] | 775 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
[805] | 776 | throwit); |
---|
[165] | 777 | |
---|
[805] | 778 | // Set polynomial |
---|
| 779 | Polynomial<Float>* ppoly = 0; |
---|
| 780 | Vector<Float> coeff; |
---|
| 781 | String msg; |
---|
| 782 | if ( nc > 0 ) { |
---|
| 783 | ppoly = new Polynomial<Float>(nc); |
---|
| 784 | coeff = coeffs; |
---|
| 785 | msg = String("user"); |
---|
| 786 | } else { |
---|
[878] | 787 | STAttr sdAttr; |
---|
[805] | 788 | coeff = sdAttr.gainElevationPoly(inst); |
---|
| 789 | ppoly = new Polynomial<Float>(3); |
---|
| 790 | msg = String("built in"); |
---|
| 791 | } |
---|
[532] | 792 | |
---|
[805] | 793 | if ( coeff.nelements() > 0 ) { |
---|
| 794 | ppoly->setCoefficients(coeff); |
---|
| 795 | } else { |
---|
| 796 | delete ppoly; |
---|
| 797 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument")); |
---|
| 798 | } |
---|
| 799 | ostringstream oss; |
---|
| 800 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl; |
---|
| 801 | oss << " " << coeff; |
---|
| 802 | pushLog(String(oss)); |
---|
| 803 | const uInt nrow = tab.nrow(); |
---|
| 804 | Vector<Float> factor(nrow); |
---|
| 805 | for ( uInt i=0; i < nrow; ++i ) { |
---|
| 806 | factor[i] = 1.0 / (*ppoly)(x[i]); |
---|
| 807 | } |
---|
| 808 | delete ppoly; |
---|
| 809 | scaleByVector(tab, factor, true); |
---|
[532] | 810 | |
---|
[805] | 811 | } else { |
---|
| 812 | // Read and correct |
---|
| 813 | pushLog("Making correction from ascii Table"); |
---|
| 814 | scaleFromAsciiTable(tab, filename, method, x, true); |
---|
[532] | 815 | } |
---|
[805] | 816 | return out; |
---|
| 817 | } |
---|
[165] | 818 | |
---|
[805] | 819 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename, |
---|
| 820 | const std::string& method, |
---|
| 821 | const Vector<Float>& xout, bool dotsys) |
---|
| 822 | { |
---|
[165] | 823 | |
---|
[805] | 824 | // Read gain-elevation ascii file data into a Table. |
---|
[165] | 825 | |
---|
[805] | 826 | String formatString; |
---|
| 827 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False); |
---|
| 828 | scaleFromTable(in, tbl, method, xout, dotsys); |
---|
| 829 | } |
---|
[165] | 830 | |
---|
[805] | 831 | void STMath::scaleFromTable(Table& in, |
---|
| 832 | const Table& table, |
---|
| 833 | const std::string& method, |
---|
| 834 | const Vector<Float>& xout, bool dotsys) |
---|
| 835 | { |
---|
[780] | 836 | |
---|
[805] | 837 | ROScalarColumn<Float> geElCol(table, "ELEVATION"); |
---|
| 838 | ROScalarColumn<Float> geFacCol(table, "FACTOR"); |
---|
| 839 | Vector<Float> xin = geElCol.getColumn(); |
---|
| 840 | Vector<Float> yin = geFacCol.getColumn(); |
---|
| 841 | Vector<Bool> maskin(xin.nelements(),True); |
---|
[165] | 842 | |
---|
[805] | 843 | // Interpolate (and extrapolate) with desired method |
---|
[532] | 844 | |
---|
[996] | 845 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method); |
---|
[165] | 846 | |
---|
[805] | 847 | Vector<Float> yout; |
---|
| 848 | Vector<Bool> maskout; |
---|
| 849 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout, |
---|
[996] | 850 | xin, yin, maskin, interp, |
---|
[805] | 851 | True, True); |
---|
[165] | 852 | |
---|
[805] | 853 | scaleByVector(in, Float(1.0)/yout, dotsys); |
---|
[165] | 854 | } |
---|
[167] | 855 | |
---|
[805] | 856 | void STMath::scaleByVector( Table& in, |
---|
| 857 | const Vector< Float >& factor, |
---|
| 858 | bool dotsys ) |
---|
[177] | 859 | { |
---|
[805] | 860 | uInt nrow = in.nrow(); |
---|
| 861 | if ( factor.nelements() != nrow ) { |
---|
| 862 | throw(AipsError("factors.nelements() != table.nelements()")); |
---|
| 863 | } |
---|
| 864 | ArrayColumn<Float> specCol(in, "SPECTRA"); |
---|
| 865 | ArrayColumn<uChar> flagCol(in, "FLAGTRA"); |
---|
| 866 | ArrayColumn<Float> tsysCol(in, "TSYS"); |
---|
| 867 | for (uInt i=0; i < nrow; ++i) { |
---|
| 868 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
| 869 | ma *= factor[i]; |
---|
| 870 | specCol.put(i, ma.getArray()); |
---|
| 871 | flagCol.put(i, flagsFromMA(ma)); |
---|
| 872 | if ( dotsys ) { |
---|
[926] | 873 | Vector<Float> tsys = tsysCol(i); |
---|
[805] | 874 | tsys *= factor[i]; |
---|
[926] | 875 | tsysCol.put(i,tsys); |
---|
[805] | 876 | } |
---|
| 877 | } |
---|
[177] | 878 | } |
---|
| 879 | |
---|
[805] | 880 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in, |
---|
| 881 | float d, float etaap, |
---|
| 882 | float jyperk ) |
---|
[221] | 883 | { |
---|
[805] | 884 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 885 | Table& tab = in->table(); |
---|
| 886 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit")); |
---|
[221] | 887 | Unit K(String("K")); |
---|
| 888 | Unit JY(String("Jy")); |
---|
[701] | 889 | |
---|
[805] | 890 | bool tokelvin = true; |
---|
| 891 | Double cfac = 1.0; |
---|
[716] | 892 | |
---|
[805] | 893 | if ( fluxUnit == JY ) { |
---|
[716] | 894 | pushLog("Converting to K"); |
---|
[701] | 895 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 896 | Quantum<Double> t2 = t.get(JY); |
---|
[805] | 897 | cfac = (t2 / t).getValue(); // value to Jy |
---|
[780] | 898 | |
---|
[805] | 899 | tokelvin = true; |
---|
| 900 | out->setFluxUnit("K"); |
---|
| 901 | } else if ( fluxUnit == K ) { |
---|
[716] | 902 | pushLog("Converting to Jy"); |
---|
[701] | 903 | Quantum<Double> t(1.0,fluxUnit); |
---|
| 904 | Quantum<Double> t2 = t.get(K); |
---|
[805] | 905 | cfac = (t2 / t).getValue(); // value to K |
---|
[780] | 906 | |
---|
[805] | 907 | tokelvin = false; |
---|
| 908 | out->setFluxUnit("Jy"); |
---|
[221] | 909 | } else { |
---|
[701] | 910 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K")); |
---|
[221] | 911 | } |
---|
[701] | 912 | // Make sure input values are converted to either Jy or K first... |
---|
[805] | 913 | Float factor = cfac; |
---|
[221] | 914 | |
---|
[701] | 915 | // Select method |
---|
[805] | 916 | if (jyperk > 0.0) { |
---|
| 917 | factor *= jyperk; |
---|
| 918 | if ( tokelvin ) factor = 1.0 / jyperk; |
---|
[716] | 919 | ostringstream oss; |
---|
[805] | 920 | oss << "Jy/K = " << jyperk; |
---|
[716] | 921 | pushLog(String(oss)); |
---|
[805] | 922 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 923 | scaleByVector(tab,factors, false); |
---|
| 924 | } else if ( etaap > 0.0) { |
---|
[1319] | 925 | if (d < 0) { |
---|
| 926 | Instrument inst = |
---|
| 927 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), |
---|
| 928 | True); |
---|
| 929 | STAttr sda; |
---|
| 930 | d = sda.diameter(inst); |
---|
| 931 | } |
---|
[996] | 932 | jyperk = STAttr::findJyPerK(etaap, d); |
---|
[716] | 933 | ostringstream oss; |
---|
[805] | 934 | oss << "Jy/K = " << jyperk; |
---|
[716] | 935 | pushLog(String(oss)); |
---|
[805] | 936 | factor *= jyperk; |
---|
| 937 | if ( tokelvin ) { |
---|
[701] | 938 | factor = 1.0 / factor; |
---|
| 939 | } |
---|
[805] | 940 | Vector<Float> factors(tab.nrow(), factor); |
---|
| 941 | scaleByVector(tab, factors, False); |
---|
[354] | 942 | } else { |
---|
[780] | 943 | |
---|
[701] | 944 | // OK now we must deal with automatic look up of values. |
---|
| 945 | // We must also deal with the fact that the factors need |
---|
| 946 | // to be computed per IF and may be different and may |
---|
| 947 | // change per integration. |
---|
[780] | 948 | |
---|
[716] | 949 | pushLog("Looking up conversion factors"); |
---|
[805] | 950 | convertBrightnessUnits(out, tokelvin, cfac); |
---|
[701] | 951 | } |
---|
[805] | 952 | |
---|
| 953 | return out; |
---|
[221] | 954 | } |
---|
| 955 | |
---|
[805] | 956 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in, |
---|
| 957 | bool tokelvin, float cfac ) |
---|
[227] | 958 | { |
---|
[805] | 959 | Table& table = in->table(); |
---|
| 960 | Instrument inst = |
---|
[878] | 961 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True); |
---|
[805] | 962 | TableIterator iter(table, "FREQ_ID"); |
---|
| 963 | STFrequencies stfreqs = in->frequencies(); |
---|
[878] | 964 | STAttr sdAtt; |
---|
[805] | 965 | while (!iter.pastEnd()) { |
---|
| 966 | Table tab = iter.table(); |
---|
| 967 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 968 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 969 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID"); |
---|
| 970 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
[234] | 971 | |
---|
[805] | 972 | uInt freqid; freqidCol.get(0, freqid); |
---|
| 973 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
[878] | 974 | // STAttr.JyPerK has a Vector interface... change sometime. |
---|
[805] | 975 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements())); |
---|
| 976 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 977 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0]; |
---|
| 978 | Float factor = cfac * jyperk; |
---|
| 979 | if ( tokelvin ) factor = Float(1.0) / factor; |
---|
| 980 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
| 981 | ma *= factor; |
---|
| 982 | specCol.put(i, ma.getArray()); |
---|
| 983 | flagCol.put(i, flagsFromMA(ma)); |
---|
| 984 | } |
---|
[867] | 985 | ++iter; |
---|
[234] | 986 | } |
---|
[230] | 987 | } |
---|
[227] | 988 | |
---|
[805] | 989 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in, |
---|
| 990 | float tau ) |
---|
[234] | 991 | { |
---|
[805] | 992 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[926] | 993 | |
---|
| 994 | Table tab = out->table(); |
---|
[234] | 995 | ROScalarColumn<Float> elev(tab, "ELEVATION"); |
---|
[805] | 996 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 997 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 998 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 999 | Float zdist = Float(C::pi_2) - elev(i); |
---|
[1318] | 1000 | Float factor = exp(tau/cos(zdist)); |
---|
[926] | 1001 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i)); |
---|
[805] | 1002 | ma *= factor; |
---|
| 1003 | specCol.put(i, ma.getArray()); |
---|
| 1004 | flagCol.put(i, flagsFromMA(ma)); |
---|
[234] | 1005 | } |
---|
[805] | 1006 | return out; |
---|
[234] | 1007 | } |
---|
| 1008 | |
---|
[1373] | 1009 | CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in, |
---|
| 1010 | const std::string& kernel, |
---|
| 1011 | float width ) |
---|
| 1012 | { |
---|
| 1013 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 1014 | Table& table = out->table(); |
---|
| 1015 | ArrayColumn<Float> specCol(table, "SPECTRA"); |
---|
| 1016 | ArrayColumn<uChar> flagCol(table, "FLAGTRA"); |
---|
| 1017 | Vector<Float> spec; |
---|
| 1018 | Vector<uChar> flag; |
---|
| 1019 | for ( uInt i=0; i<table.nrow(); ++i) { |
---|
| 1020 | specCol.get(i, spec); |
---|
| 1021 | flagCol.get(i, flag); |
---|
| 1022 | Vector<Bool> mask(flag.nelements()); |
---|
| 1023 | convertArray(mask, flag); |
---|
| 1024 | Vector<Float> specout; |
---|
| 1025 | Vector<Bool> maskout; |
---|
| 1026 | if ( kernel == "hanning" ) { |
---|
| 1027 | mathutil::hanning(specout, maskout, spec , !mask); |
---|
| 1028 | convertArray(flag, !maskout); |
---|
| 1029 | } else if ( kernel == "rmedian" ) { |
---|
| 1030 | mathutil::runningMedian(specout, maskout, spec , mask, width); |
---|
| 1031 | convertArray(flag, maskout); |
---|
| 1032 | } |
---|
| 1033 | flagCol.put(i, flag); |
---|
| 1034 | specCol.put(i, specout); |
---|
| 1035 | } |
---|
| 1036 | return out; |
---|
| 1037 | } |
---|
| 1038 | |
---|
[805] | 1039 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in, |
---|
| 1040 | const std::string& kernel, float width ) |
---|
[457] | 1041 | { |
---|
[1373] | 1042 | if (kernel == "rmedian" || kernel == "hanning") { |
---|
| 1043 | return smoothOther(in, kernel, width); |
---|
| 1044 | } |
---|
[805] | 1045 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[1033] | 1046 | Table& table = out->table(); |
---|
[805] | 1047 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel); |
---|
| 1048 | // same IFNO should have same no of channels |
---|
| 1049 | // this saves overhead |
---|
| 1050 | TableIterator iter(table, "IFNO"); |
---|
| 1051 | while (!iter.pastEnd()) { |
---|
| 1052 | Table tab = iter.table(); |
---|
| 1053 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 1054 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 1055 | Vector<Float> tmpspec; specCol.get(0, tmpspec); |
---|
| 1056 | uInt nchan = tmpspec.nelements(); |
---|
| 1057 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False); |
---|
| 1058 | Convolver<Float> conv(kvec, IPosition(1,nchan)); |
---|
| 1059 | Vector<Float> spec; |
---|
| 1060 | Vector<uChar> flag; |
---|
| 1061 | for ( uInt i=0; i<tab.nrow(); ++i) { |
---|
| 1062 | specCol.get(i, spec); |
---|
| 1063 | flagCol.get(i, flag); |
---|
| 1064 | Vector<Bool> mask(flag.nelements()); |
---|
| 1065 | convertArray(mask, flag); |
---|
| 1066 | Vector<Float> specout; |
---|
[1373] | 1067 | mathutil::replaceMaskByZero(specout, mask); |
---|
| 1068 | conv.linearConv(specout, spec); |
---|
| 1069 | specCol.put(i, specout); |
---|
[805] | 1070 | } |
---|
[867] | 1071 | ++iter; |
---|
[701] | 1072 | } |
---|
[805] | 1073 | return out; |
---|
[701] | 1074 | } |
---|
[841] | 1075 | |
---|
| 1076 | CountedPtr< Scantable > |
---|
| 1077 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in ) |
---|
| 1078 | { |
---|
| 1079 | if ( in.size() < 2 ) { |
---|
[862] | 1080 | throw(AipsError("Need at least two scantables to perform a merge.")); |
---|
[841] | 1081 | } |
---|
| 1082 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin(); |
---|
| 1083 | bool insitu = insitu_; |
---|
| 1084 | setInsitu(false); |
---|
[862] | 1085 | CountedPtr< Scantable > out = getScantable(*it, false); |
---|
[841] | 1086 | setInsitu(insitu); |
---|
| 1087 | Table& tout = out->table(); |
---|
| 1088 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID"); |
---|
[917] | 1089 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID"); |
---|
| 1090 | // Renumber SCANNO to be 0-based |
---|
[926] | 1091 | Vector<uInt> scannos = scannocol.getColumn(); |
---|
| 1092 | uInt offset = min(scannos); |
---|
[917] | 1093 | scannos -= offset; |
---|
[926] | 1094 | scannocol.putColumn(scannos); |
---|
| 1095 | uInt newscanno = max(scannos)+1; |
---|
[862] | 1096 | ++it; |
---|
[841] | 1097 | while ( it != in.end() ){ |
---|
| 1098 | if ( ! (*it)->conformant(*out) ) { |
---|
| 1099 | // log message: "ignoring scantable i, as it isn't |
---|
| 1100 | // conformant with the other(s)" |
---|
| 1101 | cerr << "oh oh" << endl; |
---|
| 1102 | ++it; |
---|
| 1103 | continue; |
---|
| 1104 | } |
---|
[862] | 1105 | out->appendToHistoryTable((*it)->history()); |
---|
[841] | 1106 | const Table& tab = (*it)->table(); |
---|
| 1107 | TableIterator scanit(tab, "SCANNO"); |
---|
| 1108 | while (!scanit.pastEnd()) { |
---|
| 1109 | TableIterator freqit(scanit.table(), "FREQ_ID"); |
---|
| 1110 | while ( !freqit.pastEnd() ) { |
---|
| 1111 | Table thetab = freqit.table(); |
---|
| 1112 | uInt nrow = tout.nrow(); |
---|
| 1113 | //tout.addRow(thetab.nrow()); |
---|
| 1114 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow()); |
---|
| 1115 | ROTableRow row(thetab); |
---|
| 1116 | for ( uInt i=0; i<thetab.nrow(); ++i) { |
---|
| 1117 | uInt k = nrow+i; |
---|
| 1118 | scannocol.put(k, newscanno); |
---|
| 1119 | const TableRecord& rec = row.get(i); |
---|
| 1120 | Double rv,rp,inc; |
---|
| 1121 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID")); |
---|
| 1122 | uInt id; |
---|
| 1123 | id = out->frequencies().addEntry(rp, rv, inc); |
---|
| 1124 | freqidcol.put(k,id); |
---|
| 1125 | String name,fname;Double rf; |
---|
| 1126 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID")); |
---|
| 1127 | id = out->molecules().addEntry(rf, name, fname); |
---|
| 1128 | molidcol.put(k, id); |
---|
[961] | 1129 | Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp; |
---|
| 1130 | (*it)->focus().getEntry(fax, ftan, frot, fhand, |
---|
| 1131 | fmount,fuser, fxy, fxyp, |
---|
| 1132 | rec.asuInt("FOCUS_ID")); |
---|
| 1133 | id = out->focus().addEntry(fax, ftan, frot, fhand, |
---|
| 1134 | fmount,fuser, fxy, fxyp); |
---|
[841] | 1135 | focusidcol.put(k, id); |
---|
| 1136 | } |
---|
| 1137 | ++freqit; |
---|
| 1138 | } |
---|
| 1139 | ++newscanno; |
---|
| 1140 | ++scanit; |
---|
| 1141 | } |
---|
| 1142 | ++it; |
---|
| 1143 | } |
---|
| 1144 | return out; |
---|
| 1145 | } |
---|
[896] | 1146 | |
---|
| 1147 | CountedPtr< Scantable > |
---|
| 1148 | STMath::invertPhase( const CountedPtr < Scantable >& in ) |
---|
| 1149 | { |
---|
[996] | 1150 | return applyToPol(in, &STPol::invertPhase, Float(0.0)); |
---|
[896] | 1151 | } |
---|
| 1152 | |
---|
| 1153 | CountedPtr< Scantable > |
---|
| 1154 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
| 1155 | { |
---|
| 1156 | return applyToPol(in, &STPol::rotatePhase, Float(phase)); |
---|
| 1157 | } |
---|
| 1158 | |
---|
| 1159 | CountedPtr< Scantable > |
---|
| 1160 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase ) |
---|
| 1161 | { |
---|
| 1162 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase)); |
---|
| 1163 | } |
---|
| 1164 | |
---|
| 1165 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in, |
---|
| 1166 | STPol::polOperation fptr, |
---|
| 1167 | Float phase ) |
---|
| 1168 | { |
---|
| 1169 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 1170 | Table& tout = out->table(); |
---|
| 1171 | Block<String> cols(4); |
---|
| 1172 | cols[0] = String("SCANNO"); |
---|
| 1173 | cols[1] = String("BEAMNO"); |
---|
| 1174 | cols[2] = String("IFNO"); |
---|
| 1175 | cols[3] = String("CYCLENO"); |
---|
| 1176 | TableIterator iter(tout, cols); |
---|
[1384] | 1177 | CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_, |
---|
| 1178 | out->getPolType() ); |
---|
[896] | 1179 | while (!iter.pastEnd()) { |
---|
| 1180 | Table t = iter.table(); |
---|
| 1181 | ArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
[1015] | 1182 | ScalarColumn<uInt> focidcol(t, "FOCUS_ID"); |
---|
| 1183 | ScalarColumn<Float> parancol(t, "PARANGLE"); |
---|
[1384] | 1184 | Matrix<Float> pols(speccol.getColumn()); |
---|
[896] | 1185 | try { |
---|
| 1186 | stpol->setSpectra(pols); |
---|
[1015] | 1187 | Float fang,fhand,parang; |
---|
| 1188 | fang = in->focusTable_.getTotalFeedAngle(focidcol(0)); |
---|
| 1189 | fhand = in->focusTable_.getFeedHand(focidcol(0)); |
---|
| 1190 | parang = parancol(0); |
---|
| 1191 | /// @todo re-enable this |
---|
| 1192 | // disable total feed angle to support paralactifying Caswell style |
---|
| 1193 | stpol->setPhaseCorrections(parang, -parang, fhand); |
---|
[1384] | 1194 | // use a member function pointer in STPol. This only works on |
---|
| 1195 | // the STPol pointer itself, not the Counted Pointer so |
---|
| 1196 | // derefernce it. |
---|
| 1197 | (&(*(stpol))->*fptr)(phase); |
---|
[896] | 1198 | speccol.putColumn(stpol->getSpectra()); |
---|
| 1199 | } catch (AipsError& e) { |
---|
[1384] | 1200 | //delete stpol;stpol=0; |
---|
[896] | 1201 | throw(e); |
---|
| 1202 | } |
---|
| 1203 | ++iter; |
---|
| 1204 | } |
---|
[1384] | 1205 | //delete stpol;stpol=0; |
---|
[896] | 1206 | return out; |
---|
| 1207 | } |
---|
| 1208 | |
---|
| 1209 | CountedPtr< Scantable > |
---|
| 1210 | STMath::swapPolarisations( const CountedPtr< Scantable > & in ) |
---|
| 1211 | { |
---|
| 1212 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 1213 | Table& tout = out->table(); |
---|
| 1214 | Table t0 = tout(tout.col("POLNO") == 0); |
---|
| 1215 | Table t1 = tout(tout.col("POLNO") == 1); |
---|
| 1216 | if ( t0.nrow() != t1.nrow() ) |
---|
| 1217 | throw(AipsError("Inconsistent number of polarisations")); |
---|
| 1218 | ArrayColumn<Float> speccol0(t0, "SPECTRA"); |
---|
| 1219 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA"); |
---|
| 1220 | ArrayColumn<Float> speccol1(t1, "SPECTRA"); |
---|
| 1221 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA"); |
---|
| 1222 | Matrix<Float> s0 = speccol0.getColumn(); |
---|
| 1223 | Matrix<uChar> f0 = flagcol0.getColumn(); |
---|
| 1224 | speccol0.putColumn(speccol1.getColumn()); |
---|
| 1225 | flagcol0.putColumn(flagcol1.getColumn()); |
---|
| 1226 | speccol1.putColumn(s0); |
---|
| 1227 | flagcol1.putColumn(f0); |
---|
| 1228 | return out; |
---|
| 1229 | } |
---|
[917] | 1230 | |
---|
| 1231 | CountedPtr< Scantable > |
---|
[940] | 1232 | STMath::averagePolarisations( const CountedPtr< Scantable > & in, |
---|
| 1233 | const std::vector<bool>& mask, |
---|
| 1234 | const std::string& weight ) |
---|
| 1235 | { |
---|
[1232] | 1236 | if (in->npol() < 2 ) |
---|
| 1237 | throw(AipsError("averagePolarisations can only be applied to two or more" |
---|
| 1238 | "polarisations")); |
---|
[1010] | 1239 | bool insitu = insitu_; |
---|
| 1240 | setInsitu(false); |
---|
[1232] | 1241 | CountedPtr< Scantable > pols = getScantable(in, true); |
---|
[1010] | 1242 | setInsitu(insitu); |
---|
| 1243 | Table& tout = pols->table(); |
---|
[1232] | 1244 | std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]"; |
---|
| 1245 | Table tab = tableCommand(taql, in->table()); |
---|
| 1246 | if (tab.nrow() == 0 ) |
---|
| 1247 | throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1")); |
---|
| 1248 | TableCopy::copyRows(tout, tab); |
---|
[1145] | 1249 | TableVector<uInt> vec(tout, "POLNO"); |
---|
[940] | 1250 | vec = 0; |
---|
[1145] | 1251 | pols->table_.rwKeywordSet().define("nPol", Int(1)); |
---|
[1232] | 1252 | pols->table_.rwKeywordSet().define("POLTYPE", String("stokes")); |
---|
[1010] | 1253 | std::vector<CountedPtr<Scantable> > vpols; |
---|
| 1254 | vpols.push_back(pols); |
---|
[1232] | 1255 | CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN"); |
---|
[940] | 1256 | return out; |
---|
| 1257 | } |
---|
| 1258 | |
---|
[1145] | 1259 | CountedPtr< Scantable > |
---|
| 1260 | STMath::averageBeams( const CountedPtr< Scantable > & in, |
---|
| 1261 | const std::vector<bool>& mask, |
---|
| 1262 | const std::string& weight ) |
---|
| 1263 | { |
---|
| 1264 | bool insitu = insitu_; |
---|
| 1265 | setInsitu(false); |
---|
| 1266 | CountedPtr< Scantable > beams = getScantable(in, false); |
---|
| 1267 | setInsitu(insitu); |
---|
| 1268 | Table& tout = beams->table(); |
---|
| 1269 | // give all rows the same BEAMNO |
---|
| 1270 | TableVector<uInt> vec(tout, "BEAMNO"); |
---|
| 1271 | vec = 0; |
---|
| 1272 | beams->table_.rwKeywordSet().define("nBeam", Int(1)); |
---|
| 1273 | std::vector<CountedPtr<Scantable> > vbeams; |
---|
| 1274 | vbeams.push_back(beams); |
---|
[1232] | 1275 | CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN"); |
---|
[1145] | 1276 | return out; |
---|
| 1277 | } |
---|
[940] | 1278 | |
---|
[1145] | 1279 | |
---|
[940] | 1280 | CountedPtr< Scantable > |
---|
[917] | 1281 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in, |
---|
| 1282 | const std::string & refTime, |
---|
[926] | 1283 | const std::string & method) |
---|
[917] | 1284 | { |
---|
[940] | 1285 | // clone as this is not working insitu |
---|
| 1286 | bool insitu = insitu_; |
---|
| 1287 | setInsitu(false); |
---|
[917] | 1288 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
[940] | 1289 | setInsitu(insitu); |
---|
[917] | 1290 | Table& tout = out->table(); |
---|
| 1291 | // Get reference Epoch to time of first row or given String |
---|
| 1292 | Unit DAY(String("d")); |
---|
| 1293 | MEpoch::Ref epochRef(in->getTimeReference()); |
---|
| 1294 | MEpoch refEpoch; |
---|
| 1295 | if (refTime.length()>0) { |
---|
| 1296 | Quantum<Double> qt; |
---|
| 1297 | if (MVTime::read(qt,refTime)) { |
---|
| 1298 | MVEpoch mv(qt); |
---|
| 1299 | refEpoch = MEpoch(mv, epochRef); |
---|
| 1300 | } else { |
---|
| 1301 | throw(AipsError("Invalid format for Epoch string")); |
---|
| 1302 | } |
---|
| 1303 | } else { |
---|
| 1304 | refEpoch = in->timeCol_(0); |
---|
| 1305 | } |
---|
| 1306 | MPosition refPos = in->getAntennaPosition(); |
---|
[940] | 1307 | |
---|
[996] | 1308 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method); |
---|
[917] | 1309 | // test if user frame is different to base frame |
---|
| 1310 | if ( in->frequencies().getFrameString(true) |
---|
| 1311 | == in->frequencies().getFrameString(false) ) { |
---|
[985] | 1312 | throw(AipsError("Can't convert as no output frame has been set" |
---|
| 1313 | " (use set_freqframe) or it is aligned already.")); |
---|
[917] | 1314 | } |
---|
| 1315 | MFrequency::Types system = in->frequencies().getFrame(); |
---|
[940] | 1316 | MVTime mvt(refEpoch.getValue()); |
---|
| 1317 | String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")"); |
---|
| 1318 | ostringstream oss; |
---|
| 1319 | oss << "Aligned at reference Epoch " << epochout |
---|
| 1320 | << " in frame " << MFrequency::showType(system); |
---|
| 1321 | pushLog(String(oss)); |
---|
[917] | 1322 | // set up the iterator |
---|
[926] | 1323 | Block<String> cols(4); |
---|
| 1324 | // select by constant direction |
---|
[917] | 1325 | cols[0] = String("SRCNAME"); |
---|
| 1326 | cols[1] = String("BEAMNO"); |
---|
| 1327 | // select by IF ( no of channels varies over this ) |
---|
| 1328 | cols[2] = String("IFNO"); |
---|
[926] | 1329 | // select by restfrequency |
---|
| 1330 | cols[3] = String("MOLECULE_ID"); |
---|
[917] | 1331 | TableIterator iter(tout, cols); |
---|
[926] | 1332 | while ( !iter.pastEnd() ) { |
---|
[917] | 1333 | Table t = iter.table(); |
---|
| 1334 | MDirection::ROScalarColumn dirCol(t, "DIRECTION"); |
---|
[926] | 1335 | TableIterator fiter(t, "FREQ_ID"); |
---|
[917] | 1336 | // determine nchan from the first row. This should work as |
---|
[926] | 1337 | // we are iterating over BEAMNO and IFNO // we should have constant direction |
---|
| 1338 | |
---|
[917] | 1339 | ROArrayColumn<Float> sCol(t, "SPECTRA"); |
---|
[926] | 1340 | MDirection direction = dirCol(0); |
---|
[917] | 1341 | uInt nchan = sCol(0).nelements(); |
---|
[926] | 1342 | while ( !fiter.pastEnd() ) { |
---|
| 1343 | Table ftab = fiter.table(); |
---|
| 1344 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID"); |
---|
| 1345 | // get the SpectralCoordinate for the freqid, which we are iterating over |
---|
| 1346 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0)); |
---|
| 1347 | FrequencyAligner<Float> fa( sC, nchan, refEpoch, |
---|
| 1348 | direction, refPos, system ); |
---|
| 1349 | // realign the SpectralCoordinate and put into the output Scantable |
---|
| 1350 | Vector<String> units(1); |
---|
| 1351 | units = String("Hz"); |
---|
| 1352 | Bool linear=True; |
---|
| 1353 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear); |
---|
| 1354 | sc2.setWorldAxisUnits(units); |
---|
[934] | 1355 | uInt id = out->frequencies().addEntry(sc2.referencePixel()[0], |
---|
| 1356 | sc2.referenceValue()[0], |
---|
| 1357 | sc2.increment()[0]); |
---|
| 1358 | TableVector<uInt> tvec(ftab, "FREQ_ID"); |
---|
| 1359 | tvec = id; |
---|
[926] | 1360 | // create the "global" abcissa for alignment with same FREQ_ID |
---|
| 1361 | Vector<Double> abc(nchan); |
---|
[917] | 1362 | Double w; |
---|
| 1363 | for (uInt i=0; i<nchan; i++) { |
---|
| 1364 | sC.toWorld(w,Double(i)); |
---|
| 1365 | abc[i] = w; |
---|
| 1366 | } |
---|
[926] | 1367 | // cache abcissa for same time stamps, so iterate over those |
---|
| 1368 | TableIterator timeiter(ftab, "TIME"); |
---|
| 1369 | while ( !timeiter.pastEnd() ) { |
---|
| 1370 | Table tab = timeiter.table(); |
---|
| 1371 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 1372 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 1373 | MEpoch::ROScalarColumn timeCol(tab, "TIME"); |
---|
| 1374 | // use align abcissa cache after the first row |
---|
| 1375 | bool first = true; |
---|
| 1376 | // these rows should be just be POLNO |
---|
[996] | 1377 | for (int i=0; i<int(tab.nrow()); ++i) { |
---|
[926] | 1378 | // input values |
---|
| 1379 | Vector<uChar> flag = flagCol(i); |
---|
| 1380 | Vector<Bool> mask(flag.shape()); |
---|
| 1381 | Vector<Float> specOut, spec; |
---|
| 1382 | spec = specCol(i); |
---|
| 1383 | Vector<Bool> maskOut;Vector<uChar> flagOut; |
---|
| 1384 | convertArray(mask, flag); |
---|
| 1385 | // alignment |
---|
| 1386 | Bool ok = fa.align(specOut, maskOut, abc, spec, |
---|
| 1387 | mask, timeCol(i), !first, |
---|
| 1388 | interp, False); |
---|
| 1389 | // back into scantable |
---|
| 1390 | flagOut.resize(maskOut.nelements()); |
---|
| 1391 | convertArray(flagOut, maskOut); |
---|
| 1392 | flagCol.put(i, flagOut); |
---|
| 1393 | specCol.put(i, specOut); |
---|
| 1394 | // start abcissa caching |
---|
| 1395 | first = false; |
---|
[917] | 1396 | } |
---|
[926] | 1397 | // next timestamp |
---|
| 1398 | ++timeiter; |
---|
[917] | 1399 | } |
---|
[940] | 1400 | // next FREQ_ID |
---|
[926] | 1401 | ++fiter; |
---|
[917] | 1402 | } |
---|
| 1403 | // next aligner |
---|
| 1404 | ++iter; |
---|
| 1405 | } |
---|
[940] | 1406 | // set this afterwards to ensure we are doing insitu correctly. |
---|
| 1407 | out->frequencies().setFrame(system, true); |
---|
[917] | 1408 | return out; |
---|
| 1409 | } |
---|
[992] | 1410 | |
---|
| 1411 | CountedPtr<Scantable> |
---|
| 1412 | asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in, |
---|
| 1413 | const std::string & newtype ) |
---|
| 1414 | { |
---|
| 1415 | if (in->npol() != 2 && in->npol() != 4) |
---|
| 1416 | throw(AipsError("Can only convert two or four polarisations.")); |
---|
| 1417 | if ( in->getPolType() == newtype ) |
---|
| 1418 | throw(AipsError("No need to convert.")); |
---|
[1000] | 1419 | if ( ! in->selector_.empty() ) |
---|
| 1420 | throw(AipsError("Can only convert whole scantable. Unset the selection.")); |
---|
[992] | 1421 | bool insitu = insitu_; |
---|
| 1422 | setInsitu(false); |
---|
| 1423 | CountedPtr< Scantable > out = getScantable(in, true); |
---|
| 1424 | setInsitu(insitu); |
---|
| 1425 | Table& tout = out->table(); |
---|
| 1426 | tout.rwKeywordSet().define("POLTYPE", String(newtype)); |
---|
| 1427 | |
---|
| 1428 | Block<String> cols(4); |
---|
| 1429 | cols[0] = "SCANNO"; |
---|
| 1430 | cols[1] = "CYCLENO"; |
---|
| 1431 | cols[2] = "BEAMNO"; |
---|
| 1432 | cols[3] = "IFNO"; |
---|
| 1433 | TableIterator it(in->originalTable_, cols); |
---|
| 1434 | String basetype = in->getPolType(); |
---|
| 1435 | STPol* stpol = STPol::getPolClass(in->factories_, basetype); |
---|
| 1436 | try { |
---|
| 1437 | while ( !it.pastEnd() ) { |
---|
| 1438 | Table tab = it.table(); |
---|
| 1439 | uInt row = tab.rowNumbers()[0]; |
---|
| 1440 | stpol->setSpectra(in->getPolMatrix(row)); |
---|
| 1441 | Float fang,fhand,parang; |
---|
| 1442 | fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row)); |
---|
| 1443 | fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row)); |
---|
| 1444 | parang = in->paraCol_(row); |
---|
| 1445 | /// @todo re-enable this |
---|
| 1446 | // disable total feed angle to support paralactifying Caswell style |
---|
| 1447 | stpol->setPhaseCorrections(parang, -parang, fhand); |
---|
| 1448 | Int npolout = 0; |
---|
| 1449 | for (uInt i=0; i<tab.nrow(); ++i) { |
---|
| 1450 | Vector<Float> outvec = stpol->getSpectrum(i, newtype); |
---|
| 1451 | if ( outvec.nelements() > 0 ) { |
---|
| 1452 | tout.addRow(); |
---|
| 1453 | TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1); |
---|
| 1454 | ArrayColumn<Float> sCol(tout,"SPECTRA"); |
---|
| 1455 | ScalarColumn<uInt> pCol(tout,"POLNO"); |
---|
| 1456 | sCol.put(tout.nrow()-1 ,outvec); |
---|
| 1457 | pCol.put(tout.nrow()-1 ,uInt(npolout)); |
---|
| 1458 | npolout++; |
---|
| 1459 | } |
---|
| 1460 | } |
---|
| 1461 | tout.rwKeywordSet().define("nPol", npolout); |
---|
| 1462 | ++it; |
---|
| 1463 | } |
---|
| 1464 | } catch (AipsError& e) { |
---|
| 1465 | delete stpol; |
---|
| 1466 | throw(e); |
---|
| 1467 | } |
---|
| 1468 | delete stpol; |
---|
| 1469 | return out; |
---|
| 1470 | } |
---|
[1066] | 1471 | |
---|
[1143] | 1472 | CountedPtr< Scantable > |
---|
[1140] | 1473 | asap::STMath::mxExtract( const CountedPtr< Scantable > & in, |
---|
| 1474 | const std::string & scantype ) |
---|
| 1475 | { |
---|
| 1476 | bool insitu = insitu_; |
---|
| 1477 | setInsitu(false); |
---|
| 1478 | CountedPtr< Scantable > out = getScantable(in, true); |
---|
| 1479 | setInsitu(insitu); |
---|
| 1480 | Table& tout = out->table(); |
---|
| 1481 | std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO"; |
---|
| 1482 | if (scantype == "on") { |
---|
| 1483 | taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO"; |
---|
| 1484 | } |
---|
| 1485 | Table tab = tableCommand(taql, in->table()); |
---|
| 1486 | TableCopy::copyRows(tout, tab); |
---|
| 1487 | if (scantype == "on") { |
---|
[1143] | 1488 | // re-index SCANNO to 0 |
---|
[1140] | 1489 | TableVector<uInt> vec(tout, "SCANNO"); |
---|
| 1490 | vec = 0; |
---|
| 1491 | } |
---|
| 1492 | return out; |
---|
| 1493 | } |
---|
[1192] | 1494 | |
---|
| 1495 | CountedPtr< Scantable > |
---|
| 1496 | asap::STMath::lagFlag( const CountedPtr< Scantable > & in, |
---|
[1200] | 1497 | double frequency, double width ) |
---|
[1192] | 1498 | { |
---|
| 1499 | CountedPtr< Scantable > out = getScantable(in, false); |
---|
| 1500 | Table& tout = out->table(); |
---|
| 1501 | TableIterator iter(tout, "FREQ_ID"); |
---|
| 1502 | FFTServer<Float,Complex> ffts; |
---|
| 1503 | while ( !iter.pastEnd() ) { |
---|
| 1504 | Table tab = iter.table(); |
---|
| 1505 | Double rp,rv,inc; |
---|
| 1506 | ROTableRow row(tab); |
---|
| 1507 | const TableRecord& rec = row.get(0); |
---|
| 1508 | uInt freqid = rec.asuInt("FREQ_ID"); |
---|
| 1509 | out->frequencies().getEntry(rp, rv, inc, freqid); |
---|
| 1510 | ArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
| 1511 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
| 1512 | for (int i=0; i<int(tab.nrow()); ++i) { |
---|
| 1513 | Vector<Float> spec = specCol(i); |
---|
| 1514 | Vector<uChar> flag = flagCol(i); |
---|
[1200] | 1515 | Int lag0 = Int(spec.nelements()*abs(inc)/(frequency+width)+0.5); |
---|
| 1516 | Int lag1 = Int(spec.nelements()*abs(inc)/(frequency-width)+0.5); |
---|
[1192] | 1517 | for (int k=0; k < flag.nelements(); ++k ) { |
---|
| 1518 | if (flag[k] > 0) { |
---|
| 1519 | spec[k] = 0.0; |
---|
| 1520 | } |
---|
| 1521 | } |
---|
| 1522 | Vector<Complex> lags; |
---|
[1203] | 1523 | ffts.fft0(lags, spec); |
---|
[1200] | 1524 | Int start = max(0, lag0); |
---|
| 1525 | Int end = min(Int(lags.nelements()-1), lag1); |
---|
[1192] | 1526 | if (start == end) { |
---|
| 1527 | lags[start] = Complex(0.0); |
---|
| 1528 | } else { |
---|
| 1529 | for (int j=start; j <=end ;++j) { |
---|
| 1530 | lags[j] = Complex(0.0); |
---|
| 1531 | } |
---|
| 1532 | } |
---|
[1203] | 1533 | ffts.fft0(spec, lags); |
---|
[1192] | 1534 | specCol.put(i, spec); |
---|
| 1535 | } |
---|
| 1536 | ++iter; |
---|
| 1537 | } |
---|
| 1538 | return out; |
---|
| 1539 | } |
---|