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