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