[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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[1314] | 169 | /*
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[805] | 170 | if ( allEQ(bflag, True) ) {
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[1314] | 171 | continue;//don't accumulate
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[144] | 172 | }
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[1314] | 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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[1308] | 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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[1308] | 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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[1308] | 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,
|
---|
| 380 | const std::string & mode,
|
---|
| 381 | bool preserve )
|
---|
[805] | 382 | {
|
---|
| 383 | /// @todo make other modes available
|
---|
| 384 | /// modes should be "nearest", "pair"
|
---|
| 385 | // make this operation non insitu
|
---|
| 386 | const Table& tin = in->table();
|
---|
| 387 | Table ons = tin(tin.col("SRCTYPE") == Int(0));
|
---|
| 388 | Table offs = tin(tin.col("SRCTYPE") == Int(1));
|
---|
| 389 | if ( offs.nrow() == 0 )
|
---|
| 390 | throw(AipsError("No 'off' scans present."));
|
---|
| 391 | // put all "on" scans into output table
|
---|
[701] | 392 |
|
---|
[805] | 393 | bool insitu = insitu_;
|
---|
| 394 | setInsitu(false);
|
---|
| 395 | CountedPtr< Scantable > out = getScantable(in, true);
|
---|
| 396 | setInsitu(insitu);
|
---|
| 397 | Table& tout = out->table();
|
---|
[248] | 398 |
|
---|
[805] | 399 | TableCopy::copyRows(tout, ons);
|
---|
| 400 | TableRow row(tout);
|
---|
| 401 | ROScalarColumn<Double> offtimeCol(offs, "TIME");
|
---|
| 402 | ArrayColumn<Float> outspecCol(tout, "SPECTRA");
|
---|
| 403 | ROArrayColumn<Float> outtsysCol(tout, "TSYS");
|
---|
| 404 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
|
---|
| 405 | for (uInt i=0; i < tout.nrow(); ++i) {
|
---|
| 406 | const TableRecord& rec = row.get(i);
|
---|
| 407 | Double ontime = rec.asDouble("TIME");
|
---|
| 408 | ROScalarColumn<Double> offtimeCol(offs, "TIME");
|
---|
| 409 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
|
---|
[1259] | 410 | // Timestamp may vary within a cycle ???!!!
|
---|
| 411 | // increase this by 0.5 sec in case of rounding errors...
|
---|
| 412 | // There might be a better way to do this.
|
---|
| 413 | mindeltat += 0.5;
|
---|
| 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) {
|
---|
| 908 | Instrument inst =
|
---|
[878] | 909 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True);
|
---|
| 910 | STAttr sda;
|
---|
[805] | 911 | if (d < 0) d = sda.diameter(inst);
|
---|
[996] | 912 | jyperk = STAttr::findJyPerK(etaap, d);
|
---|
[716] | 913 | ostringstream oss;
|
---|
[805] | 914 | oss << "Jy/K = " << jyperk;
|
---|
[716] | 915 | pushLog(String(oss));
|
---|
[805] | 916 | factor *= jyperk;
|
---|
| 917 | if ( tokelvin ) {
|
---|
[701] | 918 | factor = 1.0 / factor;
|
---|
| 919 | }
|
---|
[805] | 920 | Vector<Float> factors(tab.nrow(), factor);
|
---|
| 921 | scaleByVector(tab, factors, False);
|
---|
[354] | 922 | } else {
|
---|
[780] | 923 |
|
---|
[701] | 924 | // OK now we must deal with automatic look up of values.
|
---|
| 925 | // We must also deal with the fact that the factors need
|
---|
| 926 | // to be computed per IF and may be different and may
|
---|
| 927 | // change per integration.
|
---|
[780] | 928 |
|
---|
[716] | 929 | pushLog("Looking up conversion factors");
|
---|
[805] | 930 | convertBrightnessUnits(out, tokelvin, cfac);
|
---|
[701] | 931 | }
|
---|
[805] | 932 |
|
---|
| 933 | return out;
|
---|
[221] | 934 | }
|
---|
| 935 |
|
---|
[805] | 936 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
|
---|
| 937 | bool tokelvin, float cfac )
|
---|
[227] | 938 | {
|
---|
[805] | 939 | Table& table = in->table();
|
---|
| 940 | Instrument inst =
|
---|
[878] | 941 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
|
---|
[805] | 942 | TableIterator iter(table, "FREQ_ID");
|
---|
| 943 | STFrequencies stfreqs = in->frequencies();
|
---|
[878] | 944 | STAttr sdAtt;
|
---|
[805] | 945 | while (!iter.pastEnd()) {
|
---|
| 946 | Table tab = iter.table();
|
---|
| 947 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 948 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 949 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
|
---|
| 950 | MEpoch::ROScalarColumn timeCol(tab, "TIME");
|
---|
[234] | 951 |
|
---|
[805] | 952 | uInt freqid; freqidCol.get(0, freqid);
|
---|
| 953 | Vector<Float> tmpspec; specCol.get(0, tmpspec);
|
---|
[878] | 954 | // STAttr.JyPerK has a Vector interface... change sometime.
|
---|
[805] | 955 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
|
---|
| 956 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 957 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
|
---|
| 958 | Float factor = cfac * jyperk;
|
---|
| 959 | if ( tokelvin ) factor = Float(1.0) / factor;
|
---|
| 960 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
---|
| 961 | ma *= factor;
|
---|
| 962 | specCol.put(i, ma.getArray());
|
---|
| 963 | flagCol.put(i, flagsFromMA(ma));
|
---|
| 964 | }
|
---|
[867] | 965 | ++iter;
|
---|
[234] | 966 | }
|
---|
[230] | 967 | }
|
---|
[227] | 968 |
|
---|
[805] | 969 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
|
---|
| 970 | float tau )
|
---|
[234] | 971 | {
|
---|
[805] | 972 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
[926] | 973 |
|
---|
| 974 | Table tab = out->table();
|
---|
[234] | 975 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
---|
[805] | 976 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 977 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 978 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 979 | Float zdist = Float(C::pi_2) - elev(i);
|
---|
| 980 | Float factor = exp(tau)/cos(zdist);
|
---|
[926] | 981 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
---|
[805] | 982 | ma *= factor;
|
---|
| 983 | specCol.put(i, ma.getArray());
|
---|
| 984 | flagCol.put(i, flagsFromMA(ma));
|
---|
[234] | 985 | }
|
---|
[805] | 986 | return out;
|
---|
[234] | 987 | }
|
---|
| 988 |
|
---|
[805] | 989 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
|
---|
| 990 | const std::string& kernel, float width )
|
---|
[457] | 991 | {
|
---|
[805] | 992 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
[1033] | 993 | Table& table = out->table();
|
---|
[805] | 994 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
|
---|
| 995 | // same IFNO should have same no of channels
|
---|
| 996 | // this saves overhead
|
---|
| 997 | TableIterator iter(table, "IFNO");
|
---|
| 998 | while (!iter.pastEnd()) {
|
---|
| 999 | Table tab = iter.table();
|
---|
| 1000 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 1001 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 1002 | Vector<Float> tmpspec; specCol.get(0, tmpspec);
|
---|
| 1003 | uInt nchan = tmpspec.nelements();
|
---|
| 1004 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
|
---|
| 1005 | Convolver<Float> conv(kvec, IPosition(1,nchan));
|
---|
| 1006 | Vector<Float> spec;
|
---|
| 1007 | Vector<uChar> flag;
|
---|
| 1008 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 1009 | specCol.get(i, spec);
|
---|
| 1010 | flagCol.get(i, flag);
|
---|
| 1011 | Vector<Bool> mask(flag.nelements());
|
---|
| 1012 | convertArray(mask, flag);
|
---|
| 1013 | Vector<Float> specout;
|
---|
| 1014 | if ( type == VectorKernel::HANNING ) {
|
---|
| 1015 | Vector<Bool> maskout;
|
---|
[1033] | 1016 | mathutil::hanning(specout, maskout, spec , !mask);
|
---|
| 1017 | convertArray(flag, !maskout);
|
---|
[805] | 1018 | flagCol.put(i, flag);
|
---|
[1033] | 1019 | specCol.put(i, specout);
|
---|
| 1020 | } else {
|
---|
[805] | 1021 | mathutil::replaceMaskByZero(specout, mask);
|
---|
| 1022 | conv.linearConv(specout, spec);
|
---|
[1033] | 1023 | specCol.put(i, specout);
|
---|
[354] | 1024 | }
|
---|
[805] | 1025 | }
|
---|
[867] | 1026 | ++iter;
|
---|
[701] | 1027 | }
|
---|
[805] | 1028 | return out;
|
---|
[701] | 1029 | }
|
---|
[841] | 1030 |
|
---|
| 1031 | CountedPtr< Scantable >
|
---|
| 1032 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
|
---|
| 1033 | {
|
---|
| 1034 | if ( in.size() < 2 ) {
|
---|
[862] | 1035 | throw(AipsError("Need at least two scantables to perform a merge."));
|
---|
[841] | 1036 | }
|
---|
| 1037 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
|
---|
| 1038 | bool insitu = insitu_;
|
---|
| 1039 | setInsitu(false);
|
---|
[862] | 1040 | CountedPtr< Scantable > out = getScantable(*it, false);
|
---|
[841] | 1041 | setInsitu(insitu);
|
---|
| 1042 | Table& tout = out->table();
|
---|
| 1043 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
|
---|
[917] | 1044 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
|
---|
| 1045 | // Renumber SCANNO to be 0-based
|
---|
[926] | 1046 | Vector<uInt> scannos = scannocol.getColumn();
|
---|
| 1047 | uInt offset = min(scannos);
|
---|
[917] | 1048 | scannos -= offset;
|
---|
[926] | 1049 | scannocol.putColumn(scannos);
|
---|
| 1050 | uInt newscanno = max(scannos)+1;
|
---|
[862] | 1051 | ++it;
|
---|
[841] | 1052 | while ( it != in.end() ){
|
---|
| 1053 | if ( ! (*it)->conformant(*out) ) {
|
---|
| 1054 | // log message: "ignoring scantable i, as it isn't
|
---|
| 1055 | // conformant with the other(s)"
|
---|
| 1056 | cerr << "oh oh" << endl;
|
---|
| 1057 | ++it;
|
---|
| 1058 | continue;
|
---|
| 1059 | }
|
---|
[862] | 1060 | out->appendToHistoryTable((*it)->history());
|
---|
[841] | 1061 | const Table& tab = (*it)->table();
|
---|
| 1062 | TableIterator scanit(tab, "SCANNO");
|
---|
| 1063 | while (!scanit.pastEnd()) {
|
---|
| 1064 | TableIterator freqit(scanit.table(), "FREQ_ID");
|
---|
| 1065 | while ( !freqit.pastEnd() ) {
|
---|
| 1066 | Table thetab = freqit.table();
|
---|
| 1067 | uInt nrow = tout.nrow();
|
---|
| 1068 | //tout.addRow(thetab.nrow());
|
---|
| 1069 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
|
---|
| 1070 | ROTableRow row(thetab);
|
---|
| 1071 | for ( uInt i=0; i<thetab.nrow(); ++i) {
|
---|
| 1072 | uInt k = nrow+i;
|
---|
| 1073 | scannocol.put(k, newscanno);
|
---|
| 1074 | const TableRecord& rec = row.get(i);
|
---|
| 1075 | Double rv,rp,inc;
|
---|
| 1076 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
|
---|
| 1077 | uInt id;
|
---|
| 1078 | id = out->frequencies().addEntry(rp, rv, inc);
|
---|
| 1079 | freqidcol.put(k,id);
|
---|
| 1080 | String name,fname;Double rf;
|
---|
| 1081 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
|
---|
| 1082 | id = out->molecules().addEntry(rf, name, fname);
|
---|
| 1083 | molidcol.put(k, id);
|
---|
[961] | 1084 | Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
|
---|
| 1085 | (*it)->focus().getEntry(fax, ftan, frot, fhand,
|
---|
| 1086 | fmount,fuser, fxy, fxyp,
|
---|
| 1087 | rec.asuInt("FOCUS_ID"));
|
---|
| 1088 | id = out->focus().addEntry(fax, ftan, frot, fhand,
|
---|
| 1089 | fmount,fuser, fxy, fxyp);
|
---|
[841] | 1090 | focusidcol.put(k, id);
|
---|
| 1091 | }
|
---|
| 1092 | ++freqit;
|
---|
| 1093 | }
|
---|
| 1094 | ++newscanno;
|
---|
| 1095 | ++scanit;
|
---|
| 1096 | }
|
---|
| 1097 | ++it;
|
---|
| 1098 | }
|
---|
| 1099 | return out;
|
---|
| 1100 | }
|
---|
[896] | 1101 |
|
---|
| 1102 | CountedPtr< Scantable >
|
---|
| 1103 | STMath::invertPhase( const CountedPtr < Scantable >& in )
|
---|
| 1104 | {
|
---|
[996] | 1105 | return applyToPol(in, &STPol::invertPhase, Float(0.0));
|
---|
[896] | 1106 | }
|
---|
| 1107 |
|
---|
| 1108 | CountedPtr< Scantable >
|
---|
| 1109 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
|
---|
| 1110 | {
|
---|
| 1111 | return applyToPol(in, &STPol::rotatePhase, Float(phase));
|
---|
| 1112 | }
|
---|
| 1113 |
|
---|
| 1114 | CountedPtr< Scantable >
|
---|
| 1115 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
|
---|
| 1116 | {
|
---|
| 1117 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
|
---|
| 1118 | }
|
---|
| 1119 |
|
---|
| 1120 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
|
---|
| 1121 | STPol::polOperation fptr,
|
---|
| 1122 | Float phase )
|
---|
| 1123 | {
|
---|
| 1124 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 1125 | Table& tout = out->table();
|
---|
| 1126 | Block<String> cols(4);
|
---|
| 1127 | cols[0] = String("SCANNO");
|
---|
| 1128 | cols[1] = String("BEAMNO");
|
---|
| 1129 | cols[2] = String("IFNO");
|
---|
| 1130 | cols[3] = String("CYCLENO");
|
---|
| 1131 | TableIterator iter(tout, cols);
|
---|
[1015] | 1132 | STPol* stpol = STPol::getPolClass(out->factories_, out->getPolType() );
|
---|
[896] | 1133 | while (!iter.pastEnd()) {
|
---|
| 1134 | Table t = iter.table();
|
---|
| 1135 | ArrayColumn<Float> speccol(t, "SPECTRA");
|
---|
[1015] | 1136 | ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
|
---|
| 1137 | ScalarColumn<Float> parancol(t, "PARANGLE");
|
---|
[896] | 1138 | Matrix<Float> pols = speccol.getColumn();
|
---|
| 1139 | try {
|
---|
| 1140 | stpol->setSpectra(pols);
|
---|
[1015] | 1141 | Float fang,fhand,parang;
|
---|
| 1142 | fang = in->focusTable_.getTotalFeedAngle(focidcol(0));
|
---|
| 1143 | fhand = in->focusTable_.getFeedHand(focidcol(0));
|
---|
| 1144 | parang = parancol(0);
|
---|
| 1145 | /// @todo re-enable this
|
---|
| 1146 | // disable total feed angle to support paralactifying Caswell style
|
---|
| 1147 | stpol->setPhaseCorrections(parang, -parang, fhand);
|
---|
[896] | 1148 | (stpol->*fptr)(phase);
|
---|
| 1149 | speccol.putColumn(stpol->getSpectra());
|
---|
[1015] | 1150 | Matrix<Float> tmp = stpol->getSpectra();
|
---|
[896] | 1151 | } catch (AipsError& e) {
|
---|
| 1152 | delete stpol;stpol=0;
|
---|
| 1153 | throw(e);
|
---|
| 1154 | }
|
---|
| 1155 | ++iter;
|
---|
| 1156 | }
|
---|
[934] | 1157 | delete stpol;stpol=0;
|
---|
[896] | 1158 | return out;
|
---|
| 1159 | }
|
---|
| 1160 |
|
---|
| 1161 | CountedPtr< Scantable >
|
---|
| 1162 | STMath::swapPolarisations( const CountedPtr< Scantable > & in )
|
---|
| 1163 | {
|
---|
| 1164 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 1165 | Table& tout = out->table();
|
---|
| 1166 | Table t0 = tout(tout.col("POLNO") == 0);
|
---|
| 1167 | Table t1 = tout(tout.col("POLNO") == 1);
|
---|
| 1168 | if ( t0.nrow() != t1.nrow() )
|
---|
| 1169 | throw(AipsError("Inconsistent number of polarisations"));
|
---|
| 1170 | ArrayColumn<Float> speccol0(t0, "SPECTRA");
|
---|
| 1171 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
|
---|
| 1172 | ArrayColumn<Float> speccol1(t1, "SPECTRA");
|
---|
| 1173 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
|
---|
| 1174 | Matrix<Float> s0 = speccol0.getColumn();
|
---|
| 1175 | Matrix<uChar> f0 = flagcol0.getColumn();
|
---|
| 1176 | speccol0.putColumn(speccol1.getColumn());
|
---|
| 1177 | flagcol0.putColumn(flagcol1.getColumn());
|
---|
| 1178 | speccol1.putColumn(s0);
|
---|
| 1179 | flagcol1.putColumn(f0);
|
---|
| 1180 | return out;
|
---|
| 1181 | }
|
---|
[917] | 1182 |
|
---|
| 1183 | CountedPtr< Scantable >
|
---|
[940] | 1184 | STMath::averagePolarisations( const CountedPtr< Scantable > & in,
|
---|
| 1185 | const std::vector<bool>& mask,
|
---|
| 1186 | const std::string& weight )
|
---|
| 1187 | {
|
---|
[1232] | 1188 | if (in->npol() < 2 )
|
---|
| 1189 | throw(AipsError("averagePolarisations can only be applied to two or more"
|
---|
| 1190 | "polarisations"));
|
---|
[1010] | 1191 | bool insitu = insitu_;
|
---|
| 1192 | setInsitu(false);
|
---|
[1232] | 1193 | CountedPtr< Scantable > pols = getScantable(in, true);
|
---|
[1010] | 1194 | setInsitu(insitu);
|
---|
| 1195 | Table& tout = pols->table();
|
---|
[1232] | 1196 | std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
|
---|
| 1197 | Table tab = tableCommand(taql, in->table());
|
---|
| 1198 | if (tab.nrow() == 0 )
|
---|
| 1199 | throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
|
---|
| 1200 | TableCopy::copyRows(tout, tab);
|
---|
[1145] | 1201 | TableVector<uInt> vec(tout, "POLNO");
|
---|
[940] | 1202 | vec = 0;
|
---|
[1145] | 1203 | pols->table_.rwKeywordSet().define("nPol", Int(1));
|
---|
[1232] | 1204 | pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
|
---|
[1010] | 1205 | std::vector<CountedPtr<Scantable> > vpols;
|
---|
| 1206 | vpols.push_back(pols);
|
---|
[1232] | 1207 | CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
|
---|
[940] | 1208 | return out;
|
---|
| 1209 | }
|
---|
| 1210 |
|
---|
[1145] | 1211 | CountedPtr< Scantable >
|
---|
| 1212 | STMath::averageBeams( const CountedPtr< Scantable > & in,
|
---|
| 1213 | const std::vector<bool>& mask,
|
---|
| 1214 | const std::string& weight )
|
---|
| 1215 | {
|
---|
| 1216 | bool insitu = insitu_;
|
---|
| 1217 | setInsitu(false);
|
---|
| 1218 | CountedPtr< Scantable > beams = getScantable(in, false);
|
---|
| 1219 | setInsitu(insitu);
|
---|
| 1220 | Table& tout = beams->table();
|
---|
| 1221 | // give all rows the same BEAMNO
|
---|
| 1222 | TableVector<uInt> vec(tout, "BEAMNO");
|
---|
| 1223 | vec = 0;
|
---|
| 1224 | beams->table_.rwKeywordSet().define("nBeam", Int(1));
|
---|
| 1225 | std::vector<CountedPtr<Scantable> > vbeams;
|
---|
| 1226 | vbeams.push_back(beams);
|
---|
[1232] | 1227 | CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
|
---|
[1145] | 1228 | return out;
|
---|
| 1229 | }
|
---|
[940] | 1230 |
|
---|
[1145] | 1231 |
|
---|
[940] | 1232 | CountedPtr< Scantable >
|
---|
[917] | 1233 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
|
---|
| 1234 | const std::string & refTime,
|
---|
[926] | 1235 | const std::string & method)
|
---|
[917] | 1236 | {
|
---|
[940] | 1237 | // clone as this is not working insitu
|
---|
| 1238 | bool insitu = insitu_;
|
---|
| 1239 | setInsitu(false);
|
---|
[917] | 1240 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
[940] | 1241 | setInsitu(insitu);
|
---|
[917] | 1242 | Table& tout = out->table();
|
---|
| 1243 | // Get reference Epoch to time of first row or given String
|
---|
| 1244 | Unit DAY(String("d"));
|
---|
| 1245 | MEpoch::Ref epochRef(in->getTimeReference());
|
---|
| 1246 | MEpoch refEpoch;
|
---|
| 1247 | if (refTime.length()>0) {
|
---|
| 1248 | Quantum<Double> qt;
|
---|
| 1249 | if (MVTime::read(qt,refTime)) {
|
---|
| 1250 | MVEpoch mv(qt);
|
---|
| 1251 | refEpoch = MEpoch(mv, epochRef);
|
---|
| 1252 | } else {
|
---|
| 1253 | throw(AipsError("Invalid format for Epoch string"));
|
---|
| 1254 | }
|
---|
| 1255 | } else {
|
---|
| 1256 | refEpoch = in->timeCol_(0);
|
---|
| 1257 | }
|
---|
| 1258 | MPosition refPos = in->getAntennaPosition();
|
---|
[940] | 1259 |
|
---|
[996] | 1260 | InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
|
---|
[917] | 1261 | // test if user frame is different to base frame
|
---|
| 1262 | if ( in->frequencies().getFrameString(true)
|
---|
| 1263 | == in->frequencies().getFrameString(false) ) {
|
---|
[985] | 1264 | throw(AipsError("Can't convert as no output frame has been set"
|
---|
| 1265 | " (use set_freqframe) or it is aligned already."));
|
---|
[917] | 1266 | }
|
---|
| 1267 | MFrequency::Types system = in->frequencies().getFrame();
|
---|
[940] | 1268 | MVTime mvt(refEpoch.getValue());
|
---|
| 1269 | String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
|
---|
| 1270 | ostringstream oss;
|
---|
| 1271 | oss << "Aligned at reference Epoch " << epochout
|
---|
| 1272 | << " in frame " << MFrequency::showType(system);
|
---|
| 1273 | pushLog(String(oss));
|
---|
[917] | 1274 | // set up the iterator
|
---|
[926] | 1275 | Block<String> cols(4);
|
---|
| 1276 | // select by constant direction
|
---|
[917] | 1277 | cols[0] = String("SRCNAME");
|
---|
| 1278 | cols[1] = String("BEAMNO");
|
---|
| 1279 | // select by IF ( no of channels varies over this )
|
---|
| 1280 | cols[2] = String("IFNO");
|
---|
[926] | 1281 | // select by restfrequency
|
---|
| 1282 | cols[3] = String("MOLECULE_ID");
|
---|
[917] | 1283 | TableIterator iter(tout, cols);
|
---|
[926] | 1284 | while ( !iter.pastEnd() ) {
|
---|
[917] | 1285 | Table t = iter.table();
|
---|
| 1286 | MDirection::ROScalarColumn dirCol(t, "DIRECTION");
|
---|
[926] | 1287 | TableIterator fiter(t, "FREQ_ID");
|
---|
[917] | 1288 | // determine nchan from the first row. This should work as
|
---|
[926] | 1289 | // we are iterating over BEAMNO and IFNO // we should have constant direction
|
---|
| 1290 |
|
---|
[917] | 1291 | ROArrayColumn<Float> sCol(t, "SPECTRA");
|
---|
[926] | 1292 | MDirection direction = dirCol(0);
|
---|
[917] | 1293 | uInt nchan = sCol(0).nelements();
|
---|
[926] | 1294 | while ( !fiter.pastEnd() ) {
|
---|
| 1295 | Table ftab = fiter.table();
|
---|
| 1296 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
|
---|
| 1297 | // get the SpectralCoordinate for the freqid, which we are iterating over
|
---|
| 1298 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
|
---|
| 1299 | FrequencyAligner<Float> fa( sC, nchan, refEpoch,
|
---|
| 1300 | direction, refPos, system );
|
---|
| 1301 | // realign the SpectralCoordinate and put into the output Scantable
|
---|
| 1302 | Vector<String> units(1);
|
---|
| 1303 | units = String("Hz");
|
---|
| 1304 | Bool linear=True;
|
---|
| 1305 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
|
---|
| 1306 | sc2.setWorldAxisUnits(units);
|
---|
[934] | 1307 | uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
|
---|
| 1308 | sc2.referenceValue()[0],
|
---|
| 1309 | sc2.increment()[0]);
|
---|
| 1310 | TableVector<uInt> tvec(ftab, "FREQ_ID");
|
---|
| 1311 | tvec = id;
|
---|
[926] | 1312 | // create the "global" abcissa for alignment with same FREQ_ID
|
---|
| 1313 | Vector<Double> abc(nchan);
|
---|
[917] | 1314 | Double w;
|
---|
| 1315 | for (uInt i=0; i<nchan; i++) {
|
---|
| 1316 | sC.toWorld(w,Double(i));
|
---|
| 1317 | abc[i] = w;
|
---|
| 1318 | }
|
---|
[926] | 1319 | // cache abcissa for same time stamps, so iterate over those
|
---|
| 1320 | TableIterator timeiter(ftab, "TIME");
|
---|
| 1321 | while ( !timeiter.pastEnd() ) {
|
---|
| 1322 | Table tab = timeiter.table();
|
---|
| 1323 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 1324 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 1325 | MEpoch::ROScalarColumn timeCol(tab, "TIME");
|
---|
| 1326 | // use align abcissa cache after the first row
|
---|
| 1327 | bool first = true;
|
---|
| 1328 | // these rows should be just be POLNO
|
---|
[996] | 1329 | for (int i=0; i<int(tab.nrow()); ++i) {
|
---|
[926] | 1330 | // input values
|
---|
| 1331 | Vector<uChar> flag = flagCol(i);
|
---|
| 1332 | Vector<Bool> mask(flag.shape());
|
---|
| 1333 | Vector<Float> specOut, spec;
|
---|
| 1334 | spec = specCol(i);
|
---|
| 1335 | Vector<Bool> maskOut;Vector<uChar> flagOut;
|
---|
| 1336 | convertArray(mask, flag);
|
---|
| 1337 | // alignment
|
---|
| 1338 | Bool ok = fa.align(specOut, maskOut, abc, spec,
|
---|
| 1339 | mask, timeCol(i), !first,
|
---|
| 1340 | interp, False);
|
---|
| 1341 | // back into scantable
|
---|
| 1342 | flagOut.resize(maskOut.nelements());
|
---|
| 1343 | convertArray(flagOut, maskOut);
|
---|
| 1344 | flagCol.put(i, flagOut);
|
---|
| 1345 | specCol.put(i, specOut);
|
---|
| 1346 | // start abcissa caching
|
---|
| 1347 | first = false;
|
---|
[917] | 1348 | }
|
---|
[926] | 1349 | // next timestamp
|
---|
| 1350 | ++timeiter;
|
---|
[917] | 1351 | }
|
---|
[940] | 1352 | // next FREQ_ID
|
---|
[926] | 1353 | ++fiter;
|
---|
[917] | 1354 | }
|
---|
| 1355 | // next aligner
|
---|
| 1356 | ++iter;
|
---|
| 1357 | }
|
---|
[940] | 1358 | // set this afterwards to ensure we are doing insitu correctly.
|
---|
| 1359 | out->frequencies().setFrame(system, true);
|
---|
[917] | 1360 | return out;
|
---|
| 1361 | }
|
---|
[992] | 1362 |
|
---|
| 1363 | CountedPtr<Scantable>
|
---|
| 1364 | asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
|
---|
| 1365 | const std::string & newtype )
|
---|
| 1366 | {
|
---|
| 1367 | if (in->npol() != 2 && in->npol() != 4)
|
---|
| 1368 | throw(AipsError("Can only convert two or four polarisations."));
|
---|
| 1369 | if ( in->getPolType() == newtype )
|
---|
| 1370 | throw(AipsError("No need to convert."));
|
---|
[1000] | 1371 | if ( ! in->selector_.empty() )
|
---|
| 1372 | throw(AipsError("Can only convert whole scantable. Unset the selection."));
|
---|
[992] | 1373 | bool insitu = insitu_;
|
---|
| 1374 | setInsitu(false);
|
---|
| 1375 | CountedPtr< Scantable > out = getScantable(in, true);
|
---|
| 1376 | setInsitu(insitu);
|
---|
| 1377 | Table& tout = out->table();
|
---|
| 1378 | tout.rwKeywordSet().define("POLTYPE", String(newtype));
|
---|
| 1379 |
|
---|
| 1380 | Block<String> cols(4);
|
---|
| 1381 | cols[0] = "SCANNO";
|
---|
| 1382 | cols[1] = "CYCLENO";
|
---|
| 1383 | cols[2] = "BEAMNO";
|
---|
| 1384 | cols[3] = "IFNO";
|
---|
| 1385 | TableIterator it(in->originalTable_, cols);
|
---|
| 1386 | String basetype = in->getPolType();
|
---|
| 1387 | STPol* stpol = STPol::getPolClass(in->factories_, basetype);
|
---|
| 1388 | try {
|
---|
| 1389 | while ( !it.pastEnd() ) {
|
---|
| 1390 | Table tab = it.table();
|
---|
| 1391 | uInt row = tab.rowNumbers()[0];
|
---|
| 1392 | stpol->setSpectra(in->getPolMatrix(row));
|
---|
| 1393 | Float fang,fhand,parang;
|
---|
| 1394 | fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row));
|
---|
| 1395 | fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
|
---|
| 1396 | parang = in->paraCol_(row);
|
---|
| 1397 | /// @todo re-enable this
|
---|
| 1398 | // disable total feed angle to support paralactifying Caswell style
|
---|
| 1399 | stpol->setPhaseCorrections(parang, -parang, fhand);
|
---|
| 1400 | Int npolout = 0;
|
---|
| 1401 | for (uInt i=0; i<tab.nrow(); ++i) {
|
---|
| 1402 | Vector<Float> outvec = stpol->getSpectrum(i, newtype);
|
---|
| 1403 | if ( outvec.nelements() > 0 ) {
|
---|
| 1404 | tout.addRow();
|
---|
| 1405 | TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
|
---|
| 1406 | ArrayColumn<Float> sCol(tout,"SPECTRA");
|
---|
| 1407 | ScalarColumn<uInt> pCol(tout,"POLNO");
|
---|
| 1408 | sCol.put(tout.nrow()-1 ,outvec);
|
---|
| 1409 | pCol.put(tout.nrow()-1 ,uInt(npolout));
|
---|
| 1410 | npolout++;
|
---|
| 1411 | }
|
---|
| 1412 | }
|
---|
| 1413 | tout.rwKeywordSet().define("nPol", npolout);
|
---|
| 1414 | ++it;
|
---|
| 1415 | }
|
---|
| 1416 | } catch (AipsError& e) {
|
---|
| 1417 | delete stpol;
|
---|
| 1418 | throw(e);
|
---|
| 1419 | }
|
---|
| 1420 | delete stpol;
|
---|
| 1421 | return out;
|
---|
| 1422 | }
|
---|
[1066] | 1423 |
|
---|
[1143] | 1424 | CountedPtr< Scantable >
|
---|
[1140] | 1425 | asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
|
---|
| 1426 | const std::string & scantype )
|
---|
| 1427 | {
|
---|
| 1428 | bool insitu = insitu_;
|
---|
| 1429 | setInsitu(false);
|
---|
| 1430 | CountedPtr< Scantable > out = getScantable(in, true);
|
---|
| 1431 | setInsitu(insitu);
|
---|
| 1432 | Table& tout = out->table();
|
---|
| 1433 | std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
|
---|
| 1434 | if (scantype == "on") {
|
---|
| 1435 | taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
|
---|
| 1436 | }
|
---|
| 1437 | Table tab = tableCommand(taql, in->table());
|
---|
| 1438 | TableCopy::copyRows(tout, tab);
|
---|
| 1439 | if (scantype == "on") {
|
---|
[1143] | 1440 | // re-index SCANNO to 0
|
---|
[1140] | 1441 | TableVector<uInt> vec(tout, "SCANNO");
|
---|
| 1442 | vec = 0;
|
---|
| 1443 | }
|
---|
| 1444 | return out;
|
---|
| 1445 | }
|
---|
[1192] | 1446 |
|
---|
| 1447 | CountedPtr< Scantable >
|
---|
| 1448 | asap::STMath::lagFlag( const CountedPtr< Scantable > & in,
|
---|
[1200] | 1449 | double frequency, double width )
|
---|
[1192] | 1450 | {
|
---|
| 1451 | CountedPtr< Scantable > out = getScantable(in, false);
|
---|
| 1452 | Table& tout = out->table();
|
---|
| 1453 | TableIterator iter(tout, "FREQ_ID");
|
---|
| 1454 | FFTServer<Float,Complex> ffts;
|
---|
| 1455 | while ( !iter.pastEnd() ) {
|
---|
| 1456 | Table tab = iter.table();
|
---|
| 1457 | Double rp,rv,inc;
|
---|
| 1458 | ROTableRow row(tab);
|
---|
| 1459 | const TableRecord& rec = row.get(0);
|
---|
| 1460 | uInt freqid = rec.asuInt("FREQ_ID");
|
---|
| 1461 | out->frequencies().getEntry(rp, rv, inc, freqid);
|
---|
| 1462 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
---|
| 1463 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
---|
| 1464 | for (int i=0; i<int(tab.nrow()); ++i) {
|
---|
| 1465 | Vector<Float> spec = specCol(i);
|
---|
| 1466 | Vector<uChar> flag = flagCol(i);
|
---|
[1200] | 1467 | Int lag0 = Int(spec.nelements()*abs(inc)/(frequency+width)+0.5);
|
---|
| 1468 | Int lag1 = Int(spec.nelements()*abs(inc)/(frequency-width)+0.5);
|
---|
[1192] | 1469 | for (int k=0; k < flag.nelements(); ++k ) {
|
---|
| 1470 | if (flag[k] > 0) {
|
---|
| 1471 | spec[k] = 0.0;
|
---|
| 1472 | }
|
---|
| 1473 | }
|
---|
| 1474 | Vector<Complex> lags;
|
---|
[1203] | 1475 | ffts.fft0(lags, spec);
|
---|
[1200] | 1476 | Int start = max(0, lag0);
|
---|
| 1477 | Int end = min(Int(lags.nelements()-1), lag1);
|
---|
[1192] | 1478 | if (start == end) {
|
---|
| 1479 | lags[start] = Complex(0.0);
|
---|
| 1480 | } else {
|
---|
| 1481 | for (int j=start; j <=end ;++j) {
|
---|
| 1482 | lags[j] = Complex(0.0);
|
---|
| 1483 | }
|
---|
| 1484 | }
|
---|
[1203] | 1485 | ffts.fft0(spec, lags);
|
---|
[1192] | 1486 | specCol.put(i, spec);
|
---|
| 1487 | }
|
---|
| 1488 | ++iter;
|
---|
| 1489 | }
|
---|
| 1490 | return out;
|
---|
| 1491 | }
|
---|