| 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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| 12 |
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| 13 | #include <casa/iomanip.h>
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| 14 | #include <casa/Exceptions/Error.h>
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| 15 | #include <casa/Containers/Block.h>
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| 16 | #include <casa/BasicSL/String.h>
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| 17 | #include <tables/Tables/TableIter.h>
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| 18 | #include <tables/Tables/TableCopy.h>
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| 19 | #include <casa/Arrays/MaskArrLogi.h>
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| 20 | #include <casa/Arrays/MaskArrMath.h>
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| 21 | #include <casa/Arrays/ArrayLogical.h>
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| 22 | #include <casa/Arrays/ArrayMath.h>
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| 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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| 26 | #include <tables/Tables/TabVecMath.h>
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| 27 | #include <tables/Tables/ExprNode.h>
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| 28 | #include <tables/Tables/TableRecord.h>
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| 29 | #include <tables/Tables/ReadAsciiTable.h>
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| 30 |
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| 31 | #include <lattices/Lattices/LatticeUtilities.h>
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| 32 |
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| 33 | #include <coordinates/Coordinates/SpectralCoordinate.h>
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| 34 | #include <coordinates/Coordinates/CoordinateSystem.h>
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| 35 | #include <coordinates/Coordinates/CoordinateUtil.h>
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| 36 | #include <coordinates/Coordinates/FrequencyAligner.h>
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| 37 |
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| 38 | #include <scimath/Mathematics/VectorKernel.h>
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| 39 | #include <scimath/Mathematics/Convolver.h>
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| 40 | #include <scimath/Functionals/Polynomial.h>
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| 41 |
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| 42 | #include "MathUtils.h"
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| 43 | #include "RowAccumulator.h"
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| 44 | #include "STAttr.h"
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| 45 | #include "STMath.h"
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| 46 |
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| 47 | using namespace casa;
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| 48 |
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| 49 | using namespace asap;
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| 50 |
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| 51 | STMath::STMath(bool insitu) :
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| 52 | insitu_(insitu)
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| 53 | {
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| 54 | }
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| 55 |
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| 56 |
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| 57 | STMath::~STMath()
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| 58 | {
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| 59 | }
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| 60 |
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| 61 | CountedPtr<Scantable>
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| 62 | STMath::average( const std::vector<CountedPtr<Scantable> >& scantbls,
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| 63 | const std::vector<bool>& mask,
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| 64 | const std::string& weight,
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| 65 | const std::string& avmode,
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| 66 | bool alignfreq)
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| 67 | {
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| 68 | if ( avmode == "SCAN" && scantbls.size() != 1 )
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| 69 | throw(AipsError("Can't perform 'SCAN' averaging on multiple tables"));
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| 70 | WeightType wtype = stringToWeight(weight);
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| 71 |
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| 72 | std::vector<CountedPtr<Scantable> >* in = const_cast<std::vector<CountedPtr<Scantable> >*>(&scantbls);
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| 73 | std::vector<CountedPtr<Scantable> > inaligned;
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| 74 | if ( alignfreq ) {
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| 75 | // take first row of first scantable as reference epoch
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| 76 | String epoch = scantbls[0]->getTime(0);
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| 77 | for (int i=0; i< scantbls.size(); ++i ) {
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| 78 | inaligned.push_back(frequencyAlign(scantbls[i], epoch));
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| 79 | }
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| 80 | in = &inaligned;
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| 81 | }
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| 82 |
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| 83 | // output
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| 84 | // clone as this is non insitu
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| 85 | bool insitu = insitu_;
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| 86 | setInsitu(false);
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| 87 | CountedPtr< Scantable > out = getScantable((*in)[0], true);
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| 88 | setInsitu(insitu);
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| 89 | std::vector<CountedPtr<Scantable> >::const_iterator stit = in->begin();
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| 90 | ++stit;
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| 91 | while ( stit != in->end() ) {
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| 92 | out->appendToHistoryTable((*stit)->history());
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| 93 | ++stit;
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| 94 | }
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| 95 |
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| 96 | Table& tout = out->table();
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| 97 |
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| 98 | /// @todo check if all scantables are conformant
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| 99 |
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| 100 | ArrayColumn<Float> specColOut(tout,"SPECTRA");
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| 101 | ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
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| 102 | ArrayColumn<Float> tsysColOut(tout,"TSYS");
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| 103 | ScalarColumn<Double> mjdColOut(tout,"TIME");
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| 104 | ScalarColumn<Double> intColOut(tout,"INTERVAL");
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| 105 |
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| 106 | // set up the output table rows. These are based on the structure of the
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| 107 | // FIRST scantable in the vector
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| 108 | const Table& baset = (*in)[0]->table();
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| 109 |
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| 110 | Block<String> cols(3);
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| 111 | cols[0] = String("BEAMNO");
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| 112 | cols[1] = String("IFNO");
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| 113 | cols[2] = String("POLNO");
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| 114 | if ( avmode == "SOURCE" ) {
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| 115 | cols.resize(4);
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| 116 | cols[3] = String("SRCNAME");
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| 117 | }
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| 118 | if ( avmode == "SCAN" && in->size() == 1) {
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| 119 | cols.resize(4);
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| 120 | cols[3] = String("SCANNO");
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| 121 | }
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| 122 | uInt outrowCount = 0;
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| 123 | TableIterator iter(baset, cols);
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| 124 | while (!iter.pastEnd()) {
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| 125 | Table subt = iter.table();
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| 126 | // copy the first row of this selection into the new table
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| 127 | tout.addRow();
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| 128 | TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
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| 129 | ++outrowCount;
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| 130 | ++iter;
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| 131 | }
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| 132 | RowAccumulator acc(wtype);
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| 133 | Vector<Bool> cmask(mask);
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| 134 | acc.setUserMask(cmask);
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| 135 | ROTableRow row(tout);
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| 136 | ROArrayColumn<Float> specCol, tsysCol;
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| 137 | ROArrayColumn<uChar> flagCol;
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| 138 | ROScalarColumn<Double> mjdCol, intCol;
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| 139 | ROScalarColumn<Int> scanIDCol;
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| 140 |
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| 141 | for (uInt i=0; i < tout.nrow(); ++i) {
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| 142 | for ( int j=0; j < in->size(); ++j ) {
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| 143 | const Table& tin = (*in)[j]->table();
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| 144 | const TableRecord& rec = row.get(i);
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| 145 | ROScalarColumn<Double> tmp(tin, "TIME");
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| 146 | Double td;tmp.get(0,td);
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| 147 | Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
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| 148 | && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
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| 149 | && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
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| 150 | Table subt;
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| 151 | if ( avmode == "SOURCE") {
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| 152 | subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
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| 153 | } else if (avmode == "SCAN") {
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| 154 | subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
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| 155 | } else {
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| 156 | subt = basesubt;
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| 157 | }
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| 158 | specCol.attach(subt,"SPECTRA");
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| 159 | flagCol.attach(subt,"FLAGTRA");
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| 160 | tsysCol.attach(subt,"TSYS");
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| 161 | intCol.attach(subt,"INTERVAL");
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| 162 | mjdCol.attach(subt,"TIME");
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| 163 | Vector<Float> spec,tsys;
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| 164 | Vector<uChar> flag;
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| 165 | Double inter,time;
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| 166 | for (uInt k = 0; k < subt.nrow(); ++k ) {
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| 167 | flagCol.get(k, flag);
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| 168 | Vector<Bool> bflag(flag.shape());
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| 169 | convertArray(bflag, flag);
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| 170 | if ( allEQ(bflag, True) ) {
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| 171 | continue;//don't accumulate
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| 172 | }
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| 173 | specCol.get(k, spec);
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| 174 | tsysCol.get(k, tsys);
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| 175 | intCol.get(k, inter);
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| 176 | mjdCol.get(k, time);
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| 177 | // spectrum has to be added last to enable weighting by the other values
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| 178 | acc.add(spec, !bflag, tsys, inter, time);
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| 179 | }
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| 180 | }
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| 181 | //write out
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| 182 | specColOut.put(i, acc.getSpectrum());
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| 183 | const Vector<Bool>& msk = acc.getMask();
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| 184 | Vector<uChar> flg(msk.shape());
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| 185 | convertArray(flg, !msk);
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| 186 | flagColOut.put(i, flg);
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| 187 | tsysColOut.put(i, acc.getTsys());
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| 188 | intColOut.put(i, acc.getInterval());
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| 189 | mjdColOut.put(i, acc.getTime());
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| 190 | acc.reset();
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| 191 | }
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| 192 | return out;
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| 193 | }
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| 194 |
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| 195 | CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
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| 196 | bool droprows)
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| 197 | {
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| 198 | if (insitu_) return in;
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| 199 | else {
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| 200 | // clone
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| 201 | Scantable* tabp = new Scantable(*in, Bool(droprows));
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| 202 | return CountedPtr<Scantable>(tabp);
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| 203 | }
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| 204 | }
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| 205 |
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| 206 | CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
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| 207 | float val,
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| 208 | const std::string& mode,
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| 209 | bool tsys )
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| 210 | {
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| 211 | // modes are "ADD" and "MUL"
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| 212 | CountedPtr< Scantable > out = getScantable(in, false);
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| 213 | Table& tab = out->table();
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| 214 | ArrayColumn<Float> specCol(tab,"SPECTRA");
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| 215 | ArrayColumn<Float> tsysCol(tab,"TSYS");
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| 216 | for (uInt i=0; i<tab.nrow(); ++i) {
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| 217 | Vector<Float> spec;
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| 218 | Vector<Float> ts;
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| 219 | specCol.get(i, spec);
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| 220 | tsysCol.get(i, ts);
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| 221 | if (mode == "MUL") {
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| 222 | spec *= val;
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| 223 | specCol.put(i, spec);
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| 224 | if ( tsys ) {
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| 225 | ts *= val;
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| 226 | tsysCol.put(i, ts);
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| 227 | }
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| 228 | } else if ( mode == "ADD" ) {
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| 229 | spec += val;
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| 230 | specCol.put(i, spec);
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| 231 | if ( tsys ) {
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| 232 | ts += val;
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| 233 | tsysCol.put(i, ts);
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| 234 | }
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| 235 | }
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| 236 | }
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| 237 | return out;
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| 238 | }
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| 239 |
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| 240 | MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
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| 241 | const Vector<uChar>& f)
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| 242 | {
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| 243 | Vector<Bool> mask;
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| 244 | mask.resize(f.shape());
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| 245 | convertArray(mask, f);
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| 246 | return MaskedArray<Float>(s,!mask);
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| 247 | }
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| 248 |
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| 249 | Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
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| 250 | {
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| 251 | const Vector<Bool>& m = ma.getMask();
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| 252 | Vector<uChar> flags(m.shape());
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| 253 | convertArray(flags, !m);
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| 254 | return flags;
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| 255 | }
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| 256 |
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| 257 | CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable >& in,
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| 258 | const std::string & mode,
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| 259 | bool preserve )
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| 260 | {
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| 261 | /// @todo make other modes available
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| 262 | /// modes should be "nearest", "pair"
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| 263 | // make this operation non insitu
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| 264 | const Table& tin = in->table();
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| 265 | Table ons = tin(tin.col("SRCTYPE") == Int(0));
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| 266 | Table offs = tin(tin.col("SRCTYPE") == Int(1));
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| 267 | if ( offs.nrow() == 0 )
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| 268 | throw(AipsError("No 'off' scans present."));
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| 269 | // put all "on" scans into output table
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| 270 |
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| 271 | bool insitu = insitu_;
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| 272 | setInsitu(false);
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| 273 | CountedPtr< Scantable > out = getScantable(in, true);
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| 274 | setInsitu(insitu);
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| 275 | Table& tout = out->table();
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| 276 |
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| 277 | TableCopy::copyRows(tout, ons);
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| 278 | TableRow row(tout);
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| 279 | ROScalarColumn<Double> offtimeCol(offs, "TIME");
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| 280 |
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| 281 | ArrayColumn<Float> outspecCol(tout, "SPECTRA");
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| 282 | ROArrayColumn<Float> outtsysCol(tout, "TSYS");
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| 283 | ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
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| 284 | for (uInt i=0; i < tout.nrow(); ++i) {
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| 285 | const TableRecord& rec = row.get(i);
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| 286 | Double ontime = rec.asDouble("TIME");
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| 287 | ROScalarColumn<Double> offtimeCol(offs, "TIME");
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| 288 | Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
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| 289 | Table sel = offs( abs(offs.col("TIME")-ontime) <= mindeltat
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| 290 | && offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
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| 291 | && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
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| 292 | && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
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| 293 |
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| 294 | TableRow offrow(sel);
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| 295 | const TableRecord& offrec = offrow.get(0);//should only be one row
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| 296 | RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
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| 297 | RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
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| 298 | RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
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| 299 | /// @fixme this assumes tsys is a scalar not vector
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| 300 | Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
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| 301 | Vector<Float> specon, tsyson;
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| 302 | outtsysCol.get(i, tsyson);
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| 303 | outspecCol.get(i, specon);
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| 304 | Vector<uChar> flagon;
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| 305 | outflagCol.get(i, flagon);
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| 306 | MaskedArray<Float> mon = maskedArray(specon, flagon);
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| 307 | MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
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| 308 | MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
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| 309 | if (preserve) {
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| 310 | quot -= tsysoffscalar;
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| 311 | } else {
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| 312 | quot -= tsyson[0];
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| 313 | }
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| 314 | outspecCol.put(i, quot.getArray());
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| 315 | outflagCol.put(i, flagsFromMA(quot));
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| 316 | }
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| 317 | // renumber scanno
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| 318 | TableIterator it(tout, "SCANNO");
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| 319 | uInt i = 0;
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| 320 | while ( !it.pastEnd() ) {
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| 321 | Table t = it.table();
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| 322 | TableVector<uInt> vec(t, "SCANNO");
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| 323 | vec = i;
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| 324 | ++i;
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| 325 | ++it;
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| 326 | }
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| 327 | return out;
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| 328 | }
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| 329 |
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| 330 | CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
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| 331 | {
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| 332 | // make copy or reference
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| 333 | CountedPtr< Scantable > out = getScantable(in, false);
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| 334 | Table& tout = out->table();
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| 335 | Block<String> cols(3);
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| 336 | cols[0] = String("SCANNO");
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| 337 | cols[1] = String("BEAMNO");
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| 338 | cols[2] = String("POLNO");
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| 339 | TableIterator iter(tout, cols);
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| 340 | while (!iter.pastEnd()) {
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| 341 | Table subt = iter.table();
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| 342 | // this should leave us with two rows for the two IFs....if not ignore
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| 343 | if (subt.nrow() != 2 ) {
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| 344 | continue;
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| 345 | }
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| 346 | ArrayColumn<Float> specCol(tout, "SPECTRA");
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| 347 | ArrayColumn<Float> tsysCol(tout, "TSYS");
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| 348 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
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| 349 | Vector<Float> onspec,offspec, ontsys, offtsys;
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| 350 | Vector<uChar> onflag, offflag;
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| 351 | tsysCol.get(0, ontsys); tsysCol.get(1, offtsys);
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| 352 | specCol.get(0, onspec); specCol.get(1, offspec);
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| 353 | flagCol.get(0, onflag); flagCol.get(1, offflag);
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| 354 | MaskedArray<Float> on = maskedArray(onspec, onflag);
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| 355 | MaskedArray<Float> off = maskedArray(offspec, offflag);
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| 356 | MaskedArray<Float> oncopy = on.copy();
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| 357 |
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| 358 | on /= off; on -= 1.0f;
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| 359 | on *= ontsys[0];
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| 360 | off /= oncopy; off -= 1.0f;
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| 361 | off *= offtsys[0];
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| 362 | specCol.put(0, on.getArray());
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| 363 | const Vector<Bool>& m0 = on.getMask();
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| 364 | Vector<uChar> flags0(m0.shape());
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| 365 | convertArray(flags0, !m0);
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| 366 | flagCol.put(0, flags0);
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| 367 |
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| 368 | specCol.put(1, off.getArray());
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| 369 | const Vector<Bool>& m1 = off.getMask();
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| 370 | Vector<uChar> flags1(m1.shape());
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| 371 | convertArray(flags1, !m1);
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| 372 | flagCol.put(1, flags1);
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| 373 | ++iter;
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| 374 | }
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| 375 |
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| 376 | return out;
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| 377 | }
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| 378 |
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| 379 | std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
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| 380 | const std::vector< bool > & mask,
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| 381 | const std::string& which )
|
|---|
| 382 | {
|
|---|
| 383 |
|
|---|
| 384 | Vector<Bool> m(mask);
|
|---|
| 385 | const Table& tab = in->table();
|
|---|
| 386 | ROArrayColumn<Float> specCol(tab, "SPECTRA");
|
|---|
| 387 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
|---|
| 388 | std::vector<float> out;
|
|---|
| 389 | for (uInt i=0; i < tab.nrow(); ++i ) {
|
|---|
| 390 | Vector<Float> spec; specCol.get(i, spec);
|
|---|
| 391 | Vector<uChar> flag; flagCol.get(i, flag);
|
|---|
| 392 | MaskedArray<Float> ma = maskedArray(spec, flag);
|
|---|
| 393 | float outstat = 0.0;
|
|---|
| 394 | if ( spec.nelements() == m.nelements() ) {
|
|---|
| 395 | outstat = mathutil::statistics(which, ma(m));
|
|---|
| 396 | } else {
|
|---|
| 397 | outstat = mathutil::statistics(which, ma);
|
|---|
| 398 | }
|
|---|
| 399 | out.push_back(outstat);
|
|---|
| 400 | }
|
|---|
| 401 | return out;
|
|---|
| 402 | }
|
|---|
| 403 |
|
|---|
| 404 | CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
|
|---|
| 405 | int width )
|
|---|
| 406 | {
|
|---|
| 407 | if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
|
|---|
| 408 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 409 | Table& tout = out->table();
|
|---|
| 410 | out->frequencies().rescale(width, "BIN");
|
|---|
| 411 | ArrayColumn<Float> specCol(tout, "SPECTRA");
|
|---|
| 412 | ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
|
|---|
| 413 | for (uInt i=0; i < tout.nrow(); ++i ) {
|
|---|
| 414 | MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
|
|---|
| 415 | MaskedArray<Float> maout;
|
|---|
| 416 | LatticeUtilities::bin(maout, main, 0, Int(width));
|
|---|
| 417 | /// @todo implement channel based tsys binning
|
|---|
| 418 | specCol.put(i, maout.getArray());
|
|---|
| 419 | flagCol.put(i, flagsFromMA(maout));
|
|---|
| 420 | // take only the first binned spectrum's length for the deprecated
|
|---|
| 421 | // global header item nChan
|
|---|
| 422 | if (i==0) tout.rwKeywordSet().define(String("nChan"),
|
|---|
| 423 | Int(maout.getArray().nelements()));
|
|---|
| 424 | }
|
|---|
| 425 | return out;
|
|---|
| 426 | }
|
|---|
| 427 |
|
|---|
| 428 | CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
|
|---|
| 429 | const std::string& method,
|
|---|
| 430 | float width )
|
|---|
| 431 | //
|
|---|
| 432 | // Should add the possibility of width being specified in km/s. This means
|
|---|
| 433 | // that for each freqID (SpectralCoordinate) we will need to convert to an
|
|---|
| 434 | // average channel width (say at the reference pixel). Then we would need
|
|---|
| 435 | // to be careful to make sure each spectrum (of different freqID)
|
|---|
| 436 | // is the same length.
|
|---|
| 437 | //
|
|---|
| 438 | {
|
|---|
| 439 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
|---|
| 440 | Int interpMethod(stringToIMethod(method));
|
|---|
| 441 |
|
|---|
| 442 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 443 | Table& tout = out->table();
|
|---|
| 444 |
|
|---|
| 445 | // Resample SpectralCoordinates (one per freqID)
|
|---|
| 446 | out->frequencies().rescale(width, "RESAMPLE");
|
|---|
| 447 | TableIterator iter(tout, "IFNO");
|
|---|
| 448 | TableRow row(tout);
|
|---|
| 449 | while ( !iter.pastEnd() ) {
|
|---|
| 450 | Table tab = iter.table();
|
|---|
| 451 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
|---|
| 452 | //ArrayColumn<Float> tsysCol(tout, "TSYS");
|
|---|
| 453 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
|---|
| 454 | Vector<Float> spec;
|
|---|
| 455 | Vector<uChar> flag;
|
|---|
| 456 | specCol.get(0,spec); // the number of channels should be constant per IF
|
|---|
| 457 | uInt nChanIn = spec.nelements();
|
|---|
| 458 | Vector<Float> xIn(nChanIn); indgen(xIn);
|
|---|
| 459 | Int fac = Int(nChanIn/width);
|
|---|
| 460 | Vector<Float> xOut(fac+10); // 10 to be safe - resize later
|
|---|
| 461 | uInt k = 0;
|
|---|
| 462 | Float x = 0.0;
|
|---|
| 463 | while (x < Float(nChanIn) ) {
|
|---|
| 464 | xOut(k) = x;
|
|---|
| 465 | k++;
|
|---|
| 466 | x += width;
|
|---|
| 467 | }
|
|---|
| 468 | uInt nChanOut = k;
|
|---|
| 469 | xOut.resize(nChanOut, True);
|
|---|
| 470 | // process all rows for this IFNO
|
|---|
| 471 | Vector<Float> specOut;
|
|---|
| 472 | Vector<Bool> maskOut;
|
|---|
| 473 | Vector<uChar> flagOut;
|
|---|
| 474 | for (uInt i=0; i < tab.nrow(); ++i) {
|
|---|
| 475 | specCol.get(i, spec);
|
|---|
| 476 | flagCol.get(i, flag);
|
|---|
| 477 | Vector<Bool> mask(flag.nelements());
|
|---|
| 478 | convertArray(mask, flag);
|
|---|
| 479 |
|
|---|
| 480 | IPosition shapeIn(spec.shape());
|
|---|
| 481 | //sh.nchan = nChanOut;
|
|---|
| 482 | InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
|
|---|
| 483 | xIn, spec, mask,
|
|---|
| 484 | interpMethod, True, True);
|
|---|
| 485 | /// @todo do the same for channel based Tsys
|
|---|
| 486 | flagOut.resize(maskOut.nelements());
|
|---|
| 487 | convertArray(flagOut, maskOut);
|
|---|
| 488 | specCol.put(i, specOut);
|
|---|
| 489 | flagCol.put(i, flagOut);
|
|---|
| 490 | }
|
|---|
| 491 | ++iter;
|
|---|
| 492 | }
|
|---|
| 493 |
|
|---|
| 494 | return out;
|
|---|
| 495 | }
|
|---|
| 496 |
|
|---|
| 497 | STMath::imethod STMath::stringToIMethod(const std::string& in)
|
|---|
| 498 | {
|
|---|
| 499 | static STMath::imap lookup;
|
|---|
| 500 |
|
|---|
| 501 | // initialize the lookup table if necessary
|
|---|
| 502 | if ( lookup.empty() ) {
|
|---|
| 503 | lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
|
|---|
| 504 | lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
|
|---|
| 505 | lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
|
|---|
| 506 | lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
|
|---|
| 507 | }
|
|---|
| 508 |
|
|---|
| 509 | STMath::imap::const_iterator iter = lookup.find(in);
|
|---|
| 510 |
|
|---|
| 511 | if ( lookup.end() == iter ) {
|
|---|
| 512 | std::string message = in;
|
|---|
| 513 | message += " is not a valid interpolation mode";
|
|---|
| 514 | throw(AipsError(message));
|
|---|
| 515 | }
|
|---|
| 516 | return iter->second;
|
|---|
| 517 | }
|
|---|
| 518 |
|
|---|
| 519 | WeightType STMath::stringToWeight(const std::string& in)
|
|---|
| 520 | {
|
|---|
| 521 | static std::map<std::string, WeightType> lookup;
|
|---|
| 522 |
|
|---|
| 523 | // initialize the lookup table if necessary
|
|---|
| 524 | if ( lookup.empty() ) {
|
|---|
| 525 | lookup["NONE"] = asap::NONE;
|
|---|
| 526 | lookup["TINT"] = asap::TINT;
|
|---|
| 527 | lookup["TINTSYS"] = asap::TINTSYS;
|
|---|
| 528 | lookup["TSYS"] = asap::TSYS;
|
|---|
| 529 | lookup["VAR"] = asap::VAR;
|
|---|
| 530 | }
|
|---|
| 531 |
|
|---|
| 532 | std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
|
|---|
| 533 |
|
|---|
| 534 | if ( lookup.end() == iter ) {
|
|---|
| 535 | std::string message = in;
|
|---|
| 536 | message += " is not a valid weighting mode";
|
|---|
| 537 | throw(AipsError(message));
|
|---|
| 538 | }
|
|---|
| 539 | return iter->second;
|
|---|
| 540 | }
|
|---|
| 541 |
|
|---|
| 542 | CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
|
|---|
| 543 | const vector< float > & coeff,
|
|---|
| 544 | const std::string & filename,
|
|---|
| 545 | const std::string& method)
|
|---|
| 546 | {
|
|---|
| 547 | // Get elevation data from Scantable and convert to degrees
|
|---|
| 548 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 549 | Table& tab = out->table();
|
|---|
| 550 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
|---|
| 551 | Vector<Float> x = elev.getColumn();
|
|---|
| 552 | x *= Float(180 / C::pi); // Degrees
|
|---|
| 553 |
|
|---|
| 554 | Vector<Float> coeffs(coeff);
|
|---|
| 555 | const uInt nc = coeffs.nelements();
|
|---|
| 556 | if ( filename.length() > 0 && nc > 0 ) {
|
|---|
| 557 | throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
|
|---|
| 558 | }
|
|---|
| 559 |
|
|---|
| 560 | // Correct
|
|---|
| 561 | if ( nc > 0 || filename.length() == 0 ) {
|
|---|
| 562 | // Find instrument
|
|---|
| 563 | Bool throwit = True;
|
|---|
| 564 | Instrument inst =
|
|---|
| 565 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
|
|---|
| 566 | throwit);
|
|---|
| 567 |
|
|---|
| 568 | // Set polynomial
|
|---|
| 569 | Polynomial<Float>* ppoly = 0;
|
|---|
| 570 | Vector<Float> coeff;
|
|---|
| 571 | String msg;
|
|---|
| 572 | if ( nc > 0 ) {
|
|---|
| 573 | ppoly = new Polynomial<Float>(nc);
|
|---|
| 574 | coeff = coeffs;
|
|---|
| 575 | msg = String("user");
|
|---|
| 576 | } else {
|
|---|
| 577 | STAttr sdAttr;
|
|---|
| 578 | coeff = sdAttr.gainElevationPoly(inst);
|
|---|
| 579 | ppoly = new Polynomial<Float>(3);
|
|---|
| 580 | msg = String("built in");
|
|---|
| 581 | }
|
|---|
| 582 |
|
|---|
| 583 | if ( coeff.nelements() > 0 ) {
|
|---|
| 584 | ppoly->setCoefficients(coeff);
|
|---|
| 585 | } else {
|
|---|
| 586 | delete ppoly;
|
|---|
| 587 | throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
|
|---|
| 588 | }
|
|---|
| 589 | ostringstream oss;
|
|---|
| 590 | oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
|
|---|
| 591 | oss << " " << coeff;
|
|---|
| 592 | pushLog(String(oss));
|
|---|
| 593 | const uInt nrow = tab.nrow();
|
|---|
| 594 | Vector<Float> factor(nrow);
|
|---|
| 595 | for ( uInt i=0; i < nrow; ++i ) {
|
|---|
| 596 | factor[i] = 1.0 / (*ppoly)(x[i]);
|
|---|
| 597 | }
|
|---|
| 598 | delete ppoly;
|
|---|
| 599 | scaleByVector(tab, factor, true);
|
|---|
| 600 |
|
|---|
| 601 | } else {
|
|---|
| 602 | // Read and correct
|
|---|
| 603 | pushLog("Making correction from ascii Table");
|
|---|
| 604 | scaleFromAsciiTable(tab, filename, method, x, true);
|
|---|
| 605 | }
|
|---|
| 606 | return out;
|
|---|
| 607 | }
|
|---|
| 608 |
|
|---|
| 609 | void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
|
|---|
| 610 | const std::string& method,
|
|---|
| 611 | const Vector<Float>& xout, bool dotsys)
|
|---|
| 612 | {
|
|---|
| 613 |
|
|---|
| 614 | // Read gain-elevation ascii file data into a Table.
|
|---|
| 615 |
|
|---|
| 616 | String formatString;
|
|---|
| 617 | Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
|
|---|
| 618 | scaleFromTable(in, tbl, method, xout, dotsys);
|
|---|
| 619 | }
|
|---|
| 620 |
|
|---|
| 621 | void STMath::scaleFromTable(Table& in,
|
|---|
| 622 | const Table& table,
|
|---|
| 623 | const std::string& method,
|
|---|
| 624 | const Vector<Float>& xout, bool dotsys)
|
|---|
| 625 | {
|
|---|
| 626 |
|
|---|
| 627 | ROScalarColumn<Float> geElCol(table, "ELEVATION");
|
|---|
| 628 | ROScalarColumn<Float> geFacCol(table, "FACTOR");
|
|---|
| 629 | Vector<Float> xin = geElCol.getColumn();
|
|---|
| 630 | Vector<Float> yin = geFacCol.getColumn();
|
|---|
| 631 | Vector<Bool> maskin(xin.nelements(),True);
|
|---|
| 632 |
|
|---|
| 633 | // Interpolate (and extrapolate) with desired method
|
|---|
| 634 |
|
|---|
| 635 | //InterpolateArray1D<Double,Float>::InterpolationMethod method;
|
|---|
| 636 | Int intmethod(stringToIMethod(method));
|
|---|
| 637 |
|
|---|
| 638 | Vector<Float> yout;
|
|---|
| 639 | Vector<Bool> maskout;
|
|---|
| 640 | InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
|
|---|
| 641 | xin, yin, maskin, intmethod,
|
|---|
| 642 | True, True);
|
|---|
| 643 |
|
|---|
| 644 | scaleByVector(in, Float(1.0)/yout, dotsys);
|
|---|
| 645 | }
|
|---|
| 646 |
|
|---|
| 647 | void STMath::scaleByVector( Table& in,
|
|---|
| 648 | const Vector< Float >& factor,
|
|---|
| 649 | bool dotsys )
|
|---|
| 650 | {
|
|---|
| 651 | uInt nrow = in.nrow();
|
|---|
| 652 | if ( factor.nelements() != nrow ) {
|
|---|
| 653 | throw(AipsError("factors.nelements() != table.nelements()"));
|
|---|
| 654 | }
|
|---|
| 655 | ArrayColumn<Float> specCol(in, "SPECTRA");
|
|---|
| 656 | ArrayColumn<uChar> flagCol(in, "FLAGTRA");
|
|---|
| 657 | ArrayColumn<Float> tsysCol(in, "TSYS");
|
|---|
| 658 | for (uInt i=0; i < nrow; ++i) {
|
|---|
| 659 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
|---|
| 660 | ma *= factor[i];
|
|---|
| 661 | specCol.put(i, ma.getArray());
|
|---|
| 662 | flagCol.put(i, flagsFromMA(ma));
|
|---|
| 663 | if ( dotsys ) {
|
|---|
| 664 | Vector<Float> tsys = tsysCol(i);
|
|---|
| 665 | tsys *= factor[i];
|
|---|
| 666 | tsysCol.put(i,tsys);
|
|---|
| 667 | }
|
|---|
| 668 | }
|
|---|
| 669 | }
|
|---|
| 670 |
|
|---|
| 671 | CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
|
|---|
| 672 | float d, float etaap,
|
|---|
| 673 | float jyperk )
|
|---|
| 674 | {
|
|---|
| 675 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 676 | Table& tab = in->table();
|
|---|
| 677 | Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
|
|---|
| 678 | Unit K(String("K"));
|
|---|
| 679 | Unit JY(String("Jy"));
|
|---|
| 680 |
|
|---|
| 681 | bool tokelvin = true;
|
|---|
| 682 | Double cfac = 1.0;
|
|---|
| 683 |
|
|---|
| 684 | if ( fluxUnit == JY ) {
|
|---|
| 685 | pushLog("Converting to K");
|
|---|
| 686 | Quantum<Double> t(1.0,fluxUnit);
|
|---|
| 687 | Quantum<Double> t2 = t.get(JY);
|
|---|
| 688 | cfac = (t2 / t).getValue(); // value to Jy
|
|---|
| 689 |
|
|---|
| 690 | tokelvin = true;
|
|---|
| 691 | out->setFluxUnit("K");
|
|---|
| 692 | } else if ( fluxUnit == K ) {
|
|---|
| 693 | pushLog("Converting to Jy");
|
|---|
| 694 | Quantum<Double> t(1.0,fluxUnit);
|
|---|
| 695 | Quantum<Double> t2 = t.get(K);
|
|---|
| 696 | cfac = (t2 / t).getValue(); // value to K
|
|---|
| 697 |
|
|---|
| 698 | tokelvin = false;
|
|---|
| 699 | out->setFluxUnit("Jy");
|
|---|
| 700 | } else {
|
|---|
| 701 | throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
|
|---|
| 702 | }
|
|---|
| 703 | // Make sure input values are converted to either Jy or K first...
|
|---|
| 704 | Float factor = cfac;
|
|---|
| 705 |
|
|---|
| 706 | // Select method
|
|---|
| 707 | if (jyperk > 0.0) {
|
|---|
| 708 | factor *= jyperk;
|
|---|
| 709 | if ( tokelvin ) factor = 1.0 / jyperk;
|
|---|
| 710 | ostringstream oss;
|
|---|
| 711 | oss << "Jy/K = " << jyperk;
|
|---|
| 712 | pushLog(String(oss));
|
|---|
| 713 | Vector<Float> factors(tab.nrow(), factor);
|
|---|
| 714 | scaleByVector(tab,factors, false);
|
|---|
| 715 | } else if ( etaap > 0.0) {
|
|---|
| 716 | Instrument inst =
|
|---|
| 717 | STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True);
|
|---|
| 718 | STAttr sda;
|
|---|
| 719 | if (d < 0) d = sda.diameter(inst);
|
|---|
| 720 | Float jyPerk = STAttr::findJyPerK(etaap, d);
|
|---|
| 721 | ostringstream oss;
|
|---|
| 722 | oss << "Jy/K = " << jyperk;
|
|---|
| 723 | pushLog(String(oss));
|
|---|
| 724 | factor *= jyperk;
|
|---|
| 725 | if ( tokelvin ) {
|
|---|
| 726 | factor = 1.0 / factor;
|
|---|
| 727 | }
|
|---|
| 728 | Vector<Float> factors(tab.nrow(), factor);
|
|---|
| 729 | scaleByVector(tab, factors, False);
|
|---|
| 730 | } else {
|
|---|
| 731 |
|
|---|
| 732 | // OK now we must deal with automatic look up of values.
|
|---|
| 733 | // We must also deal with the fact that the factors need
|
|---|
| 734 | // to be computed per IF and may be different and may
|
|---|
| 735 | // change per integration.
|
|---|
| 736 |
|
|---|
| 737 | pushLog("Looking up conversion factors");
|
|---|
| 738 | convertBrightnessUnits(out, tokelvin, cfac);
|
|---|
| 739 | }
|
|---|
| 740 |
|
|---|
| 741 | return out;
|
|---|
| 742 | }
|
|---|
| 743 |
|
|---|
| 744 | void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
|
|---|
| 745 | bool tokelvin, float cfac )
|
|---|
| 746 | {
|
|---|
| 747 | Table& table = in->table();
|
|---|
| 748 | Instrument inst =
|
|---|
| 749 | STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
|
|---|
| 750 | TableIterator iter(table, "FREQ_ID");
|
|---|
| 751 | STFrequencies stfreqs = in->frequencies();
|
|---|
| 752 | STAttr sdAtt;
|
|---|
| 753 | while (!iter.pastEnd()) {
|
|---|
| 754 | Table tab = iter.table();
|
|---|
| 755 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
|---|
| 756 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
|---|
| 757 | ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
|
|---|
| 758 | MEpoch::ROScalarColumn timeCol(tab, "TIME");
|
|---|
| 759 |
|
|---|
| 760 | uInt freqid; freqidCol.get(0, freqid);
|
|---|
| 761 | Vector<Float> tmpspec; specCol.get(0, tmpspec);
|
|---|
| 762 | // STAttr.JyPerK has a Vector interface... change sometime.
|
|---|
| 763 | Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
|
|---|
| 764 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
|---|
| 765 | Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
|
|---|
| 766 | Float factor = cfac * jyperk;
|
|---|
| 767 | if ( tokelvin ) factor = Float(1.0) / factor;
|
|---|
| 768 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
|---|
| 769 | ma *= factor;
|
|---|
| 770 | specCol.put(i, ma.getArray());
|
|---|
| 771 | flagCol.put(i, flagsFromMA(ma));
|
|---|
| 772 | }
|
|---|
| 773 | ++iter;
|
|---|
| 774 | }
|
|---|
| 775 | }
|
|---|
| 776 |
|
|---|
| 777 | CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
|
|---|
| 778 | float tau )
|
|---|
| 779 | {
|
|---|
| 780 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 781 |
|
|---|
| 782 | Table tab = out->table();
|
|---|
| 783 | ROScalarColumn<Float> elev(tab, "ELEVATION");
|
|---|
| 784 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
|---|
| 785 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
|---|
| 786 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
|---|
| 787 | Float zdist = Float(C::pi_2) - elev(i);
|
|---|
| 788 | Float factor = exp(tau)/cos(zdist);
|
|---|
| 789 | MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
|
|---|
| 790 | ma *= factor;
|
|---|
| 791 | specCol.put(i, ma.getArray());
|
|---|
| 792 | flagCol.put(i, flagsFromMA(ma));
|
|---|
| 793 | }
|
|---|
| 794 | return out;
|
|---|
| 795 | }
|
|---|
| 796 |
|
|---|
| 797 | CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
|
|---|
| 798 | const std::string& kernel, float width )
|
|---|
| 799 | {
|
|---|
| 800 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 801 | Table& table = in->table();
|
|---|
| 802 | VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
|
|---|
| 803 | // same IFNO should have same no of channels
|
|---|
| 804 | // this saves overhead
|
|---|
| 805 | TableIterator iter(table, "IFNO");
|
|---|
| 806 | while (!iter.pastEnd()) {
|
|---|
| 807 | Table tab = iter.table();
|
|---|
| 808 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
|---|
| 809 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
|---|
| 810 | Vector<Float> tmpspec; specCol.get(0, tmpspec);
|
|---|
| 811 | uInt nchan = tmpspec.nelements();
|
|---|
| 812 | Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
|
|---|
| 813 | Convolver<Float> conv(kvec, IPosition(1,nchan));
|
|---|
| 814 | Vector<Float> spec;
|
|---|
| 815 | Vector<uChar> flag;
|
|---|
| 816 | for ( uInt i=0; i<tab.nrow(); ++i) {
|
|---|
| 817 | specCol.get(i, spec);
|
|---|
| 818 | flagCol.get(i, flag);
|
|---|
| 819 | Vector<Bool> mask(flag.nelements());
|
|---|
| 820 | convertArray(mask, flag);
|
|---|
| 821 | Vector<Float> specout;
|
|---|
| 822 | if ( type == VectorKernel::HANNING ) {
|
|---|
| 823 | Vector<Bool> maskout;
|
|---|
| 824 | mathutil::hanning(specout, maskout, spec , mask);
|
|---|
| 825 | convertArray(flag, maskout);
|
|---|
| 826 | flagCol.put(i, flag);
|
|---|
| 827 | } else {
|
|---|
| 828 | mathutil::replaceMaskByZero(specout, mask);
|
|---|
| 829 | conv.linearConv(specout, spec);
|
|---|
| 830 | }
|
|---|
| 831 | specCol.put(i, specout);
|
|---|
| 832 | }
|
|---|
| 833 | ++iter;
|
|---|
| 834 | }
|
|---|
| 835 | return out;
|
|---|
| 836 | }
|
|---|
| 837 |
|
|---|
| 838 | CountedPtr< Scantable >
|
|---|
| 839 | STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
|
|---|
| 840 | {
|
|---|
| 841 | if ( in.size() < 2 ) {
|
|---|
| 842 | throw(AipsError("Need at least two scantables to perform a merge."));
|
|---|
| 843 | }
|
|---|
| 844 | std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
|
|---|
| 845 | bool insitu = insitu_;
|
|---|
| 846 | setInsitu(false);
|
|---|
| 847 | CountedPtr< Scantable > out = getScantable(*it, false);
|
|---|
| 848 | setInsitu(insitu);
|
|---|
| 849 | Table& tout = out->table();
|
|---|
| 850 | ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
|
|---|
| 851 | ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
|
|---|
| 852 | // Renumber SCANNO to be 0-based
|
|---|
| 853 | Vector<uInt> scannos = scannocol.getColumn();
|
|---|
| 854 | uInt offset = min(scannos);
|
|---|
| 855 | scannos -= offset;
|
|---|
| 856 | scannocol.putColumn(scannos);
|
|---|
| 857 | uInt newscanno = max(scannos)+1;
|
|---|
| 858 | ++it;
|
|---|
| 859 | while ( it != in.end() ){
|
|---|
| 860 | if ( ! (*it)->conformant(*out) ) {
|
|---|
| 861 | // log message: "ignoring scantable i, as it isn't
|
|---|
| 862 | // conformant with the other(s)"
|
|---|
| 863 | cerr << "oh oh" << endl;
|
|---|
| 864 | ++it;
|
|---|
| 865 | continue;
|
|---|
| 866 | }
|
|---|
| 867 | out->appendToHistoryTable((*it)->history());
|
|---|
| 868 | const Table& tab = (*it)->table();
|
|---|
| 869 | TableIterator scanit(tab, "SCANNO");
|
|---|
| 870 | while (!scanit.pastEnd()) {
|
|---|
| 871 | TableIterator freqit(scanit.table(), "FREQ_ID");
|
|---|
| 872 | while ( !freqit.pastEnd() ) {
|
|---|
| 873 | Table thetab = freqit.table();
|
|---|
| 874 | uInt nrow = tout.nrow();
|
|---|
| 875 | //tout.addRow(thetab.nrow());
|
|---|
| 876 | TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
|
|---|
| 877 | ROTableRow row(thetab);
|
|---|
| 878 | for ( uInt i=0; i<thetab.nrow(); ++i) {
|
|---|
| 879 | uInt k = nrow+i;
|
|---|
| 880 | scannocol.put(k, newscanno);
|
|---|
| 881 | const TableRecord& rec = row.get(i);
|
|---|
| 882 | Double rv,rp,inc;
|
|---|
| 883 | (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
|
|---|
| 884 | uInt id;
|
|---|
| 885 | id = out->frequencies().addEntry(rp, rv, inc);
|
|---|
| 886 | freqidcol.put(k,id);
|
|---|
| 887 | String name,fname;Double rf;
|
|---|
| 888 | (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
|
|---|
| 889 | id = out->molecules().addEntry(rf, name, fname);
|
|---|
| 890 | molidcol.put(k, id);
|
|---|
| 891 | Float frot,fang,ftan;
|
|---|
| 892 | (*it)->focus().getEntry(frot, fang, ftan, rec.asuInt("FOCUS_ID"));
|
|---|
| 893 | id = out->focus().addEntry(frot, fang, ftan);
|
|---|
| 894 | focusidcol.put(k, id);
|
|---|
| 895 | }
|
|---|
| 896 | ++freqit;
|
|---|
| 897 | }
|
|---|
| 898 | ++newscanno;
|
|---|
| 899 | ++scanit;
|
|---|
| 900 | }
|
|---|
| 901 | ++it;
|
|---|
| 902 | }
|
|---|
| 903 | return out;
|
|---|
| 904 | }
|
|---|
| 905 |
|
|---|
| 906 | CountedPtr< Scantable >
|
|---|
| 907 | STMath::invertPhase( const CountedPtr < Scantable >& in )
|
|---|
| 908 | {
|
|---|
| 909 | applyToPol(in, &STPol::invertPhase, Float(0.0));
|
|---|
| 910 | }
|
|---|
| 911 |
|
|---|
| 912 | CountedPtr< Scantable >
|
|---|
| 913 | STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
|
|---|
| 914 | {
|
|---|
| 915 | return applyToPol(in, &STPol::rotatePhase, Float(phase));
|
|---|
| 916 | }
|
|---|
| 917 |
|
|---|
| 918 | CountedPtr< Scantable >
|
|---|
| 919 | STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
|
|---|
| 920 | {
|
|---|
| 921 | return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
|
|---|
| 922 | }
|
|---|
| 923 |
|
|---|
| 924 | CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
|
|---|
| 925 | STPol::polOperation fptr,
|
|---|
| 926 | Float phase )
|
|---|
| 927 | {
|
|---|
| 928 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 929 | Table& tout = out->table();
|
|---|
| 930 | Block<String> cols(4);
|
|---|
| 931 | cols[0] = String("SCANNO");
|
|---|
| 932 | cols[1] = String("BEAMNO");
|
|---|
| 933 | cols[2] = String("IFNO");
|
|---|
| 934 | cols[3] = String("CYCLENO");
|
|---|
| 935 | TableIterator iter(tout, cols);
|
|---|
| 936 | STPol* stpol = NULL;
|
|---|
| 937 | stpol =STPol::getPolClass(out->factories_, out->getPolType() );
|
|---|
| 938 | while (!iter.pastEnd()) {
|
|---|
| 939 | Table t = iter.table();
|
|---|
| 940 | ArrayColumn<Float> speccol(t, "SPECTRA");
|
|---|
| 941 | Matrix<Float> pols = speccol.getColumn();
|
|---|
| 942 | Matrix<Float> out;
|
|---|
| 943 | try {
|
|---|
| 944 | stpol->setSpectra(pols);
|
|---|
| 945 | (stpol->*fptr)(phase);
|
|---|
| 946 | speccol.putColumn(stpol->getSpectra());
|
|---|
| 947 | delete stpol;stpol=0;
|
|---|
| 948 | } catch (AipsError& e) {
|
|---|
| 949 | delete stpol;stpol=0;
|
|---|
| 950 | throw(e);
|
|---|
| 951 | }
|
|---|
| 952 | ++iter;
|
|---|
| 953 | }
|
|---|
| 954 | return out;
|
|---|
| 955 | }
|
|---|
| 956 |
|
|---|
| 957 | CountedPtr< Scantable >
|
|---|
| 958 | STMath::swapPolarisations( const CountedPtr< Scantable > & in )
|
|---|
| 959 | {
|
|---|
| 960 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 961 | Table& tout = out->table();
|
|---|
| 962 | Table t0 = tout(tout.col("POLNO") == 0);
|
|---|
| 963 | Table t1 = tout(tout.col("POLNO") == 1);
|
|---|
| 964 | if ( t0.nrow() != t1.nrow() )
|
|---|
| 965 | throw(AipsError("Inconsistent number of polarisations"));
|
|---|
| 966 | ArrayColumn<Float> speccol0(t0, "SPECTRA");
|
|---|
| 967 | ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
|
|---|
| 968 | ArrayColumn<Float> speccol1(t1, "SPECTRA");
|
|---|
| 969 | ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
|
|---|
| 970 | Matrix<Float> s0 = speccol0.getColumn();
|
|---|
| 971 | Matrix<uChar> f0 = flagcol0.getColumn();
|
|---|
| 972 | speccol0.putColumn(speccol1.getColumn());
|
|---|
| 973 | flagcol0.putColumn(flagcol1.getColumn());
|
|---|
| 974 | speccol1.putColumn(s0);
|
|---|
| 975 | flagcol1.putColumn(f0);
|
|---|
| 976 | return out;
|
|---|
| 977 | }
|
|---|
| 978 |
|
|---|
| 979 | CountedPtr< Scantable >
|
|---|
| 980 | asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
|
|---|
| 981 | const std::string & refTime,
|
|---|
| 982 | const std::string & method)
|
|---|
| 983 | {
|
|---|
| 984 | CountedPtr< Scantable > out = getScantable(in, false);
|
|---|
| 985 | Table& tout = out->table();
|
|---|
| 986 | // clear ouput frequency table
|
|---|
| 987 | Table ftable = out->frequencies().table();
|
|---|
| 988 | ftable.removeRow(ftable.rowNumbers());
|
|---|
| 989 | // Get reference Epoch to time of first row or given String
|
|---|
| 990 | Unit DAY(String("d"));
|
|---|
| 991 | MEpoch::Ref epochRef(in->getTimeReference());
|
|---|
| 992 | MEpoch refEpoch;
|
|---|
| 993 | if (refTime.length()>0) {
|
|---|
| 994 | Quantum<Double> qt;
|
|---|
| 995 | if (MVTime::read(qt,refTime)) {
|
|---|
| 996 | MVEpoch mv(qt);
|
|---|
| 997 | refEpoch = MEpoch(mv, epochRef);
|
|---|
| 998 | } else {
|
|---|
| 999 | throw(AipsError("Invalid format for Epoch string"));
|
|---|
| 1000 | }
|
|---|
| 1001 | } else {
|
|---|
| 1002 | refEpoch = in->timeCol_(0);
|
|---|
| 1003 | }
|
|---|
| 1004 | MPosition refPos = in->getAntennaPosition();
|
|---|
| 1005 | /* ostringstream oss;
|
|---|
| 1006 | oss << "Aligned at reference Epoch " << formatEpoch(refEpoch)
|
|---|
| 1007 | << " in frame " << MFrequency::showType(freqSystem);
|
|---|
| 1008 | pushLog(String(oss));
|
|---|
| 1009 | */
|
|---|
| 1010 | InterpolateArray1D<Double,Float>::InterpolationMethod interp;
|
|---|
| 1011 | Int interpMethod(stringToIMethod(method));
|
|---|
| 1012 | // test if user frame is different to base frame
|
|---|
| 1013 | if ( in->frequencies().getFrameString(true)
|
|---|
| 1014 | == in->frequencies().getFrameString(false) ) {
|
|---|
| 1015 | throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe"));
|
|---|
| 1016 | }
|
|---|
| 1017 | MFrequency::Types system = in->frequencies().getFrame();
|
|---|
| 1018 | out->frequencies().setFrame(system);
|
|---|
| 1019 | // set up the iterator
|
|---|
| 1020 | Block<String> cols(4);
|
|---|
| 1021 | // select by constant direction
|
|---|
| 1022 | cols[0] = String("SRCNAME");
|
|---|
| 1023 | cols[1] = String("BEAMNO");
|
|---|
| 1024 | // select by IF ( no of channels varies over this )
|
|---|
| 1025 | cols[2] = String("IFNO");
|
|---|
| 1026 | // select by restfrequency
|
|---|
| 1027 | cols[3] = String("MOLECULE_ID");
|
|---|
| 1028 | TableIterator iter(tout, cols);
|
|---|
| 1029 | while ( !iter.pastEnd() ) {
|
|---|
| 1030 | Table t = iter.table();
|
|---|
| 1031 | MDirection::ROScalarColumn dirCol(t, "DIRECTION");
|
|---|
| 1032 | TableIterator fiter(t, "FREQ_ID");
|
|---|
| 1033 | // determine nchan from the first row. This should work as
|
|---|
| 1034 | // we are iterating over BEAMNO and IFNO // we should have constant direction
|
|---|
| 1035 |
|
|---|
| 1036 | ROArrayColumn<Float> sCol(t, "SPECTRA");
|
|---|
| 1037 | MDirection direction = dirCol(0);
|
|---|
| 1038 | uInt nchan = sCol(0).nelements();
|
|---|
| 1039 | while ( !fiter.pastEnd() ) {
|
|---|
| 1040 | Table ftab = fiter.table();
|
|---|
| 1041 | ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
|
|---|
| 1042 | // get the SpectralCoordinate for the freqid, which we are iterating over
|
|---|
| 1043 | cout << freqidCol.getColumn() << endl;
|
|---|
| 1044 | SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
|
|---|
| 1045 | FrequencyAligner<Float> fa( sC, nchan, refEpoch,
|
|---|
| 1046 | direction, refPos, system );
|
|---|
| 1047 | // realign the SpectralCoordinate and put into the output Scantable
|
|---|
| 1048 | Vector<String> units(1);
|
|---|
| 1049 | units = String("Hz");
|
|---|
| 1050 | Bool linear=True;
|
|---|
| 1051 | SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
|
|---|
| 1052 | sc2.setWorldAxisUnits(units);
|
|---|
| 1053 | out->frequencies().addEntry(sc2.referencePixel()[0],
|
|---|
| 1054 | sc2.referenceValue()[0],
|
|---|
| 1055 | sc2.increment()[0]);
|
|---|
| 1056 | // create the "global" abcissa for alignment with same FREQ_ID
|
|---|
| 1057 | Vector<Double> abc(nchan);
|
|---|
| 1058 | Double w;
|
|---|
| 1059 | for (uInt i=0; i<nchan; i++) {
|
|---|
| 1060 | sC.toWorld(w,Double(i));
|
|---|
| 1061 | abc[i] = w;
|
|---|
| 1062 | }
|
|---|
| 1063 | // cache abcissa for same time stamps, so iterate over those
|
|---|
| 1064 | TableIterator timeiter(ftab, "TIME");
|
|---|
| 1065 | while ( !timeiter.pastEnd() ) {
|
|---|
| 1066 | Table tab = timeiter.table();
|
|---|
| 1067 | ArrayColumn<Float> specCol(tab, "SPECTRA");
|
|---|
| 1068 | ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
|
|---|
| 1069 | MEpoch::ROScalarColumn timeCol(tab, "TIME");
|
|---|
| 1070 | // use align abcissa cache after the first row
|
|---|
| 1071 | bool first = true;
|
|---|
| 1072 | // these rows should be just be POLNO
|
|---|
| 1073 | for (int i=0; i<tab.nrow(); ++i) {
|
|---|
| 1074 | // input values
|
|---|
| 1075 | Vector<uChar> flag = flagCol(i);
|
|---|
| 1076 | Vector<Bool> mask(flag.shape());
|
|---|
| 1077 | Vector<Float> specOut, spec;
|
|---|
| 1078 | spec = specCol(i);
|
|---|
| 1079 | Vector<Bool> maskOut;Vector<uChar> flagOut;
|
|---|
| 1080 | convertArray(mask, flag);
|
|---|
| 1081 | // alignment
|
|---|
| 1082 | Bool ok = fa.align(specOut, maskOut, abc, spec,
|
|---|
| 1083 | mask, timeCol(i), !first,
|
|---|
| 1084 | interp, False);
|
|---|
| 1085 | // back into scantable
|
|---|
| 1086 | cout << spec[spec.nelements()/2] << " --- " << specOut[specOut.nelements()/2] << endl;
|
|---|
| 1087 | flagOut.resize(maskOut.nelements());
|
|---|
| 1088 | convertArray(flagOut, maskOut);
|
|---|
| 1089 | flagCol.put(i, flagOut);
|
|---|
| 1090 | specCol.put(i, specOut);
|
|---|
| 1091 | // start abcissa caching
|
|---|
| 1092 | first = false;
|
|---|
| 1093 | }
|
|---|
| 1094 | // next timestamp
|
|---|
| 1095 | ++timeiter;
|
|---|
| 1096 | }
|
|---|
| 1097 | // nect FREQ_ID
|
|---|
| 1098 | ++fiter;
|
|---|
| 1099 | }
|
|---|
| 1100 | // next aligner
|
|---|
| 1101 | ++iter;
|
|---|
| 1102 | }
|
|---|
| 1103 | return out;
|
|---|
| 1104 | }
|
|---|
