//
// C++ Implementation: STMath
//
// Description:
//
//
// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
//
// Copyright: See COPYING file that comes with this distribution
//
//

#include <casa/iomanip.h>
#include <casa/Exceptions/Error.h>
#include <casa/Containers/Block.h>
#include <casa/BasicSL/String.h>
#include <casa/Arrays/MaskArrLogi.h>
#include <casa/Arrays/MaskArrMath.h>
#include <casa/Arrays/ArrayLogical.h>
#include <casa/Arrays/ArrayMath.h>
#include <casa/Arrays/Slice.h>
#include <casa/Arrays/Slicer.h>
#include <casa/Containers/RecordField.h>
#include <tables/Tables/TableRow.h>
#include <tables/Tables/TableVector.h>
#include <tables/Tables/TabVecMath.h>
#include <tables/Tables/ExprNode.h>
#include <tables/Tables/TableRecord.h>
#include <tables/Tables/TableParse.h>
#include <tables/Tables/ReadAsciiTable.h>
#include <tables/Tables/TableIter.h>
#include <tables/Tables/TableCopy.h>
#include <scimath/Mathematics/FFTServer.h>

#include <lattices/Lattices/LatticeUtilities.h>

#include <coordinates/Coordinates/SpectralCoordinate.h>
#include <coordinates/Coordinates/CoordinateSystem.h>
#include <coordinates/Coordinates/CoordinateUtil.h>
#include <coordinates/Coordinates/FrequencyAligner.h>

#include <scimath/Mathematics/VectorKernel.h>
#include <scimath/Mathematics/Convolver.h>
#include <scimath/Functionals/Polynomial.h>

#include <casa/Logging/LogIO.h>

#include "MathUtils.h"
#include "RowAccumulator.h"
#include "STAttr.h"
#include "STSelector.h"

#include "STMath.h"
using namespace casa;

using namespace asap;

STMath::STMath(bool insitu) :
  insitu_(insitu)
{
}


STMath::~STMath()
{
}

CountedPtr<Scantable>
STMath::average( const std::vector<CountedPtr<Scantable> >& in,
                 const std::vector<bool>& mask,
                 const std::string& weight,
                 const std::string& avmode)
{
  if ( avmode == "SCAN" && in.size() != 1 )
    throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
                    "Use merge first."));
  WeightType wtype = stringToWeight(weight);
  LogIO os( LogOrigin( "STMath", "average()", WHERE ) ) ;
  os << "test" << LogIO::POST ;

  // output
  // clone as this is non insitu
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(in[0], true);
  setInsitu(insitu);
  std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
  ++stit;
  while ( stit != in.end() ) {
    out->appendToHistoryTable((*stit)->history());
    ++stit;
  }

  Table& tout = out->table();

  /// @todo check if all scantables are conformant

  ArrayColumn<Float> specColOut(tout,"SPECTRA");
  ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
  ArrayColumn<Float> tsysColOut(tout,"TSYS");
  ScalarColumn<Double> mjdColOut(tout,"TIME");
  ScalarColumn<Double> intColOut(tout,"INTERVAL");
  ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
  ScalarColumn<uInt> scanColOut(tout,"SCANNO");

  // set up the output table rows. These are based on the structure of the
  // FIRST scantable in the vector
  const Table& baset = in[0]->table();

  Block<String> cols(3);
  cols[0] = String("BEAMNO");
  cols[1] = String("IFNO");
  cols[2] = String("POLNO");
  if ( avmode == "SOURCE" ) {
    cols.resize(4);
    cols[3] = String("SRCNAME");
  }
  if ( avmode == "SCAN"  && in.size() == 1) {
    cols.resize(4);
    cols[3] = String("SCANNO");
  }
  uInt outrowCount = 0;
  TableIterator iter(baset, cols);
  while (!iter.pastEnd()) {
    Table subt = iter.table();
    // copy the first row of this selection into the new table
    tout.addRow();
    TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
    // re-index to 0
    if ( avmode != "SCAN" && avmode != "SOURCE" ) {
      scanColOut.put(outrowCount, uInt(0));
    }
    ++outrowCount;
    ++iter;
  }

  RowAccumulator acc(wtype);
  Vector<Bool> cmask(mask);
  acc.setUserMask(cmask);
  ROTableRow row(tout);
  ROArrayColumn<Float> specCol, tsysCol;
  ROArrayColumn<uChar> flagCol;
  ROScalarColumn<Double> mjdCol, intCol;
  ROScalarColumn<Int> scanIDCol;

  Vector<uInt> rowstodelete;

  for (uInt i=0; i < tout.nrow(); ++i) {
    for ( int j=0; j < int(in.size()); ++j ) {
      const Table& tin = in[j]->table();
      const TableRecord& rec = row.get(i);
      ROScalarColumn<Double> tmp(tin, "TIME");
      Double td;tmp.get(0,td);
      Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
                       && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
                       && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
      Table subt;
      if ( avmode == "SOURCE") {
        subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
      } else if (avmode == "SCAN") {
        subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
      } else {
        subt = basesubt;
      }
      specCol.attach(subt,"SPECTRA");
      flagCol.attach(subt,"FLAGTRA");
      tsysCol.attach(subt,"TSYS");
      intCol.attach(subt,"INTERVAL");
      mjdCol.attach(subt,"TIME");
      Vector<Float> spec,tsys;
      Vector<uChar> flag;
      Double inter,time;
      for (uInt k = 0; k < subt.nrow(); ++k ) {
        flagCol.get(k, flag);
        Vector<Bool> bflag(flag.shape());
        convertArray(bflag, flag);
	/*
        if ( allEQ(bflag, True) ) {
	continue;//don't accumulate
        }
	*/
        specCol.get(k, spec);
        tsysCol.get(k, tsys);
        intCol.get(k, inter);
        mjdCol.get(k, time);
        // spectrum has to be added last to enable weighting by the other values
        acc.add(spec, !bflag, tsys, inter, time);
      }
    }
    const Vector<Bool>& msk = acc.getMask();
    if ( allEQ(msk, False) ) {
      uint n = rowstodelete.nelements();
      rowstodelete.resize(n+1, True);
      rowstodelete[n] = i;
      continue;
    }
    //write out
    Vector<uChar> flg(msk.shape());
    convertArray(flg, !msk);
    flagColOut.put(i, flg);
    specColOut.put(i, acc.getSpectrum());
    tsysColOut.put(i, acc.getTsys());
    intColOut.put(i, acc.getInterval());
    mjdColOut.put(i, acc.getTime());
    // we should only have one cycle now -> reset it to be 0
    // frequency switched data has different CYCLENO for different IFNO
    // which requires resetting this value
    cycColOut.put(i, uInt(0));
    acc.reset();
  }
  if (rowstodelete.nelements() > 0) {
    tout.removeRow(rowstodelete);
    if (tout.nrow() == 0) {
      throw(AipsError("Can't average fully flagged data."));
    }
  }
  return out;
}

CountedPtr< Scantable >
  STMath::averageChannel( const CountedPtr < Scantable > & in,
                          const std::string & mode,
                          const std::string& avmode )
{
  // clone as this is non insitu
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(in, true);
  setInsitu(insitu);
  Table& tout = out->table();
  ArrayColumn<Float> specColOut(tout,"SPECTRA");
  ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
  ArrayColumn<Float> tsysColOut(tout,"TSYS");
  ScalarColumn<uInt> scanColOut(tout,"SCANNO");
  ScalarColumn<Double> intColOut(tout, "INTERVAL");
  Table tmp = in->table().sort("BEAMNO");
  Block<String> cols(3);
  cols[0] = String("BEAMNO");
  cols[1] = String("IFNO");
  cols[2] = String("POLNO");
  if ( avmode == "SCAN") {
    cols.resize(4);
    cols[3] = String("SCANNO");
  }
  uInt outrowCount = 0;
  uChar userflag = 1 << 7;
  TableIterator iter(tmp, cols);
  while (!iter.pastEnd()) {
    Table subt = iter.table();
    ROArrayColumn<Float> specCol, tsysCol;
    ROArrayColumn<uChar> flagCol;
    ROScalarColumn<Double> intCol(subt, "INTERVAL");
    specCol.attach(subt,"SPECTRA");
    flagCol.attach(subt,"FLAGTRA");
    tsysCol.attach(subt,"TSYS");
    tout.addRow();
    TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
    if ( avmode != "SCAN") {
      scanColOut.put(outrowCount, uInt(0));
    }
    Vector<Float> tmp;
    specCol.get(0, tmp);
    uInt nchan = tmp.nelements();
    // have to do channel by channel here as MaskedArrMath
    // doesn't have partialMedians
    Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
    Vector<Float> outspec(nchan);
    Vector<uChar> outflag(nchan,0);
    Vector<Float> outtsys(1);/// @fixme when tsys is channel based
    for (uInt i=0; i<nchan; ++i) {
      Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
      MaskedArray<Float> ma = maskedArray(specs,flags);
      outspec[i] = median(ma);
      if ( allEQ(ma.getMask(), False) )
        outflag[i] = userflag;// flag data
    }
    outtsys[0] = median(tsysCol.getColumn());
    specColOut.put(outrowCount, outspec);
    flagColOut.put(outrowCount, outflag);
    tsysColOut.put(outrowCount, outtsys);
    Double intsum = sum(intCol.getColumn());
    intColOut.put(outrowCount, intsum);
    ++outrowCount;
    ++iter;
  }
  return out;
}

CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
                                             bool droprows)
{
  if (insitu_) {
    return in;
  }
  else {
    // clone
    return CountedPtr<Scantable>(new Scantable(*in, Bool(droprows)));
  }
}

CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
                                              float val,
                                              const std::string& mode,
                                              bool tsys )
{
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tab = out->table();
  ArrayColumn<Float> specCol(tab,"SPECTRA");
  ArrayColumn<Float> tsysCol(tab,"TSYS");
  for (uInt i=0; i<tab.nrow(); ++i) {
    Vector<Float> spec;
    Vector<Float> ts;
    specCol.get(i, spec);
    tsysCol.get(i, ts);
    if (mode == "MUL" || mode == "DIV") {
      if (mode == "DIV") val = 1.0/val;
      spec *= val;
      specCol.put(i, spec);
      if ( tsys ) {
        ts *= val;
        tsysCol.put(i, ts);
      }
    } else if ( mode == "ADD"  || mode == "SUB") {
      if (mode == "SUB") val *= -1.0;
      spec += val;
      specCol.put(i, spec);
      if ( tsys ) {
        ts += val;
        tsysCol.put(i, ts);
      }
    }
  }
  return out;
}

CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
					    const CountedPtr<Scantable>& right,
					    const std::string& mode)
{
  bool insitu = insitu_;
  if ( ! left->conformant(*right) ) {
    throw(AipsError("'left' and 'right' scantables are not conformant."));
  }
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(left, false);
  setInsitu(insitu);
  Table& tout = out->table();
  Block<String> coln(5);
  coln[0] = "SCANNO";  coln[1] = "CYCLENO";  coln[2] = "BEAMNO";
  coln[3] = "IFNO";  coln[4] = "POLNO";
  Table tmpl = tout.sort(coln);
  Table tmpr = right->table().sort(coln);
  ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
  ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
  ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
  ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");

  for (uInt i=0; i<tout.nrow(); ++i) {
    Vector<Float> lspecvec, rspecvec;
    Vector<uChar> lflagvec, rflagvec;
    lspecvec = lspecCol(i);    rspecvec = rspecCol(i);
    lflagvec = lflagCol(i);    rflagvec = rflagCol(i);
    MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
    MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
    if (mode == "ADD") {
      mleft += mright;
    } else if ( mode == "SUB") {
      mleft -= mright;
    } else if ( mode == "MUL") {
      mleft *= mright;
    } else if ( mode == "DIV") {
      mleft /= mright;
    } else {
      throw(AipsError("Illegal binary operator"));
    }
    lspecCol.put(i, mleft.getArray());
  }
  return out;
}



MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
                                        const Vector<uChar>& f)
{
  Vector<Bool> mask;
  mask.resize(f.shape());
  convertArray(mask, f);
  return MaskedArray<Float>(s,!mask);
}

Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
{
  const Vector<Bool>& m = ma.getMask();
  Vector<uChar> flags(m.shape());
  convertArray(flags, !m);
  return flags;
}

CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
                                              const std::string & mode,
                                              bool preserve )
{
  /// @todo make other modes available
  /// modes should be "nearest", "pair"
  // make this operation non insitu
  const Table& tin = in->table();
  Table ons = tin(tin.col("SRCTYPE") == Int(0));
  Table offs = tin(tin.col("SRCTYPE") == Int(1));
  if ( offs.nrow() == 0 )
    throw(AipsError("No 'off' scans present."));
  // put all "on" scans into output table

  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(in, true);
  setInsitu(insitu);
  Table& tout = out->table();

  TableCopy::copyRows(tout, ons);
  TableRow row(tout);
  ROScalarColumn<Double> offtimeCol(offs, "TIME");
  ArrayColumn<Float> outspecCol(tout, "SPECTRA");
  ROArrayColumn<Float> outtsysCol(tout, "TSYS");
  ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
  for (uInt i=0; i < tout.nrow(); ++i) {
    const TableRecord& rec = row.get(i);
    Double ontime = rec.asDouble("TIME");
    Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
			&& offs.col("IFNO") == Int(rec.asuInt("IFNO"))
			&& offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
    ROScalarColumn<Double> offtimeCol(presel, "TIME");

    Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
    // Timestamp may vary within a cycle ???!!!
    // increase this by 0.01 sec in case of rounding errors...
    // There might be a better way to do this.
    // fix to this fix. TIME is MJD, so 1.0d not 1.0s
    mindeltat += 0.01/24./60./60.;
    Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat);

    if ( sel.nrow() < 1 )  {
      throw(AipsError("No closest in time found... This could be a rounding "
                      "issue. Try quotient instead."));
    }
    TableRow offrow(sel);
    const TableRecord& offrec = offrow.get(0);//should only be one row
    RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
    RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
    RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
    /// @fixme this assumes tsys is a scalar not vector
    Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
    Vector<Float> specon, tsyson;
    outtsysCol.get(i, tsyson);
    outspecCol.get(i, specon);
    Vector<uChar> flagon;
    outflagCol.get(i, flagon);
    MaskedArray<Float> mon = maskedArray(specon, flagon);
    MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
    MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
    if (preserve) {
      quot -= tsysoffscalar;
    } else {
      quot -= tsyson[0];
    }
    outspecCol.put(i, quot.getArray());
    outflagCol.put(i, flagsFromMA(quot));
  }
  // renumber scanno
  TableIterator it(tout, "SCANNO");
  uInt i = 0;
  while ( !it.pastEnd() ) {
    Table t = it.table();
    TableVector<uInt> vec(t, "SCANNO");
    vec = i;
    ++i;
    ++it;
  }
  return out;
}


CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
                                          const CountedPtr< Scantable > & off,
                                          bool preserve )
{
  bool insitu = insitu_;
  if ( ! on->conformant(*off) ) {
    throw(AipsError("'on' and 'off' scantables are not conformant."));
  }
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(on, false);
  setInsitu(insitu);
  Table& tout = out->table();
  const Table& toff = off->table();
  TableIterator sit(tout, "SCANNO");
  TableIterator s2it(toff, "SCANNO");
  while ( !sit.pastEnd() ) {
    Table ton = sit.table();
    TableRow row(ton);
    Table t = s2it.table();
    ArrayColumn<Float> outspecCol(ton, "SPECTRA");
    ROArrayColumn<Float> outtsysCol(ton, "TSYS");
    ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
    for (uInt i=0; i < ton.nrow(); ++i) {
      const TableRecord& rec = row.get(i);
      Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
                          && t.col("IFNO") == Int(rec.asuInt("IFNO"))
                          && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
      if ( offsel.nrow() == 0 )
        throw AipsError("STMath::quotient: no matching off");
      TableRow offrow(offsel);
      const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
      RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
      RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
      RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
      Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
      Vector<Float> specon, tsyson;
      outtsysCol.get(i, tsyson);
      outspecCol.get(i, specon);
      Vector<uChar> flagon;
      outflagCol.get(i, flagon);
      MaskedArray<Float> mon = maskedArray(specon, flagon);
      MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
      MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
      if (preserve) {
        quot -= tsysoffscalar;
      } else {
        quot -= tsyson[0];
      }
      outspecCol.put(i, quot.getArray());
      outflagCol.put(i, flagsFromMA(quot));
    }
    ++sit;
    ++s2it;
    // take the first off for each on scan which doesn't have a
    // matching off scan
    // non <= noff:  matching pairs, non > noff matching pairs then first off
    if ( s2it.pastEnd() ) s2it.reset();
  }
  return out;
}

// dototalpower (migration of GBTIDL procedure dototalpower.pro)
// calibrate the CAL on-off pair. It calculate Tsys and average CAL on-off subintegrations
// do it for each cycles in a specific scan.
CountedPtr< Scantable > STMath::dototalpower( const CountedPtr< Scantable >& calon,
                                              const CountedPtr< Scantable >& caloff, Float tcal )
{
if ( ! calon->conformant(*caloff) ) {
    throw(AipsError("'CAL on' and 'CAL off' scantables are not conformant."));
  }
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(caloff, false);
  Table& tout = out->table();
  const Table& tcon = calon->table();
  Vector<Float> tcalout;
  Vector<Float> tcalout2;  //debug

  if ( tout.nrow() != tcon.nrow() ) {
    throw(AipsError("Mismatch in number of rows to form cal on - off pair."));
  }
  // iteration by scanno or cycle no.
  TableIterator sit(tout, "SCANNO");
  TableIterator s2it(tcon, "SCANNO");
  while ( !sit.pastEnd() ) {
    Table toff = sit.table();
    TableRow row(toff);
    Table t = s2it.table();
    ScalarColumn<Double> outintCol(toff, "INTERVAL");
    ArrayColumn<Float> outspecCol(toff, "SPECTRA");
    ArrayColumn<Float> outtsysCol(toff, "TSYS");
    ArrayColumn<uChar> outflagCol(toff, "FLAGTRA");
    ROScalarColumn<uInt> outtcalIdCol(toff, "TCAL_ID");
    ROScalarColumn<uInt> outpolCol(toff, "POLNO");
    ROScalarColumn<Double> onintCol(t, "INTERVAL");
    ROArrayColumn<Float> onspecCol(t, "SPECTRA");
    ROArrayColumn<Float> ontsysCol(t, "TSYS");
    ROArrayColumn<uChar> onflagCol(t, "FLAGTRA");
    //ROScalarColumn<uInt> ontcalIdCol(t, "TCAL_ID");

    for (uInt i=0; i < toff.nrow(); ++i) {
      //skip these checks -> assumes the data order are the same between the cal on off pairs
      //
      Vector<Float> specCalon, specCaloff;
      // to store scalar (mean) tsys
      Vector<Float> tsysout(1);
      uInt tcalId, polno;
      Double offint, onint;
      outpolCol.get(i, polno);
      outspecCol.get(i, specCaloff);
      onspecCol.get(i, specCalon);
      Vector<uChar> flagCaloff, flagCalon;
      outflagCol.get(i, flagCaloff);
      onflagCol.get(i, flagCalon);
      outtcalIdCol.get(i, tcalId);
      outintCol.get(i, offint);
      onintCol.get(i, onint);
      // caluculate mean Tsys
      uInt nchan = specCaloff.nelements();
      // percentage of edge cut off
      uInt pc = 10;
      uInt bchan = nchan/pc;
      uInt echan = nchan-bchan;

      Slicer chansl(IPosition(1,bchan-1), IPosition(1,echan-1), IPosition(1,1),Slicer::endIsLast);
      Vector<Float> testsubsp = specCaloff(chansl);
      MaskedArray<Float> spoff = maskedArray( specCaloff(chansl),flagCaloff(chansl) );
      MaskedArray<Float> spon = maskedArray( specCalon(chansl),flagCalon(chansl) );
      MaskedArray<Float> spdiff = spon-spoff;
      uInt noff = spoff.nelementsValid();
      //uInt non = spon.nelementsValid();
      uInt ndiff = spdiff.nelementsValid();
      Float meantsys;

/**
      Double subspec, subdiff;
      uInt usednchan;
      subspec = 0;
      subdiff = 0;
      usednchan = 0;
      for(uInt k=(bchan-1); k<echan; k++) {
        subspec += specCaloff[k];
        subdiff += static_cast<Double>(specCalon[k]-specCaloff[k]);
        ++usednchan;
      }
**/
      // get tcal if input tcal <= 0
      String tcalt;
      Float tcalUsed;
      tcalUsed = tcal;
      if ( tcal <= 0.0 ) {
        caloff->tcal().getEntry(tcalt, tcalout, tcalId);
        if (polno<=3) {
          tcalUsed = tcalout[polno];
        }
        else {
          tcalUsed = tcalout[0];
        }
      }

      Float meanoff;
      Float meandiff;
      if (noff && ndiff) {
         //Debug
         //if(noff!=ndiff) cerr<<"noff and ndiff is not equal"<<endl;
         meanoff = sum(spoff)/noff;
         meandiff = sum(spdiff)/ndiff;
         meantsys= (meanoff/meandiff )*tcalUsed + tcalUsed/2;
      }
      else {
         meantsys=1;
      }

      tsysout[0] = Float(meantsys);
      MaskedArray<Float> mcaloff = maskedArray(specCaloff, flagCaloff);
      MaskedArray<Float> mcalon = maskedArray(specCalon, flagCalon);
      MaskedArray<Float> sig =   Float(0.5) * (mcaloff + mcalon);
      //uInt ncaloff = mcaloff.nelementsValid();
      //uInt ncalon = mcalon.nelementsValid();

      outintCol.put(i, offint+onint);
      outspecCol.put(i, sig.getArray());
      outflagCol.put(i, flagsFromMA(sig));
      outtsysCol.put(i, tsysout);
    }
    ++sit;
    ++s2it;
  }
  return out;
}

//dosigref - migrated from GBT IDL's dosigref.pro, do calibration of position switch
// observatiions.
// input: sig and ref scantables, and an optional boxcar smoothing width(default width=0,
//        no smoothing).
// output: resultant scantable [= (sig-ref/ref)*tsys]
CountedPtr< Scantable > STMath::dosigref( const CountedPtr < Scantable >& sig,
                                          const CountedPtr < Scantable >& ref,
                                          int smoothref,
                                          casa::Float tsysv,
                                          casa::Float tau )
{
if ( ! ref->conformant(*sig) ) {
    throw(AipsError("'sig' and 'ref' scantables are not conformant."));
  }
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(sig, false);
  CountedPtr< Scantable > smref;
  if ( smoothref > 1 ) {
    float fsmoothref = static_cast<float>(smoothref);
    std::string inkernel = "boxcar";
    smref = smooth(ref, inkernel, fsmoothref );
    ostringstream oss;
    oss<<"Applied smoothing of "<<fsmoothref<<" on the reference."<<endl;
    pushLog(String(oss));
  }
  else {
    smref = ref;
  }
  Table& tout = out->table();
  const Table& tref = smref->table();
  if ( tout.nrow() != tref.nrow() ) {
    throw(AipsError("Mismatch in number of rows to form on-source and reference pair."));
  }
  // iteration by scanno? or cycle no.
  TableIterator sit(tout, "SCANNO");
  TableIterator s2it(tref, "SCANNO");
  while ( !sit.pastEnd() ) {
    Table ton = sit.table();
    Table t = s2it.table();
    ScalarColumn<Double> outintCol(ton, "INTERVAL");
    ArrayColumn<Float> outspecCol(ton, "SPECTRA");
    ArrayColumn<Float> outtsysCol(ton, "TSYS");
    ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
    ArrayColumn<Float> refspecCol(t, "SPECTRA");
    ROScalarColumn<Double> refintCol(t, "INTERVAL");
    ROArrayColumn<Float> reftsysCol(t, "TSYS");
    ArrayColumn<uChar> refflagCol(t, "FLAGTRA");
    ROScalarColumn<Float> refelevCol(t, "ELEVATION");
    for (uInt i=0; i < ton.nrow(); ++i) {

      Double onint, refint;
      Vector<Float> specon, specref;
      // to store scalar (mean) tsys
      Vector<Float> tsysref;
      outintCol.get(i, onint);
      refintCol.get(i, refint);
      outspecCol.get(i, specon);
      refspecCol.get(i, specref);
      Vector<uChar> flagref, flagon;
      outflagCol.get(i, flagon);
      refflagCol.get(i, flagref);
      reftsysCol.get(i, tsysref);

      Float tsysrefscalar;
      if ( tsysv > 0.0 ) {
        ostringstream oss;
        Float elev;
        refelevCol.get(i, elev);
        oss << "user specified Tsys = " << tsysv;
        // do recalc elevation if EL = 0
        if ( elev == 0 ) {
          throw(AipsError("EL=0, elevation data is missing."));
        } else {
          if ( tau <= 0.0 ) {
            throw(AipsError("Valid tau is not supplied."));
          } else {
            tsysrefscalar = tsysv * exp(tau/elev);
          }
        }
        oss << ", corrected (for El) tsys= "<<tsysrefscalar;
        pushLog(String(oss));
      }
      else {
        tsysrefscalar = tsysref[0];
      }
      //get quotient spectrum
      MaskedArray<Float> mref = maskedArray(specref, flagref);
      MaskedArray<Float> mon = maskedArray(specon, flagon);
      MaskedArray<Float> specres =   tsysrefscalar*((mon - mref)/mref);
      Double resint = onint*refint*smoothref/(onint+refint*smoothref);

      //Debug
      //cerr<<"Tsys used="<<tsysrefscalar<<endl;
      // fill the result, replay signal tsys by reference tsys
      outintCol.put(i, resint);
      outspecCol.put(i, specres.getArray());
      outflagCol.put(i, flagsFromMA(specres));
      outtsysCol.put(i, tsysref);
    }
    ++sit;
    ++s2it;
  }
  return out;
}

CountedPtr< Scantable > STMath::donod(const casa::CountedPtr<Scantable>& s,
                                     const std::vector<int>& scans,
                                     int smoothref,
                                     casa::Float tsysv,
                                     casa::Float tau,
                                     casa::Float tcal )

{
  setInsitu(false);
  STSelector sel;
  std::vector<int> scan1, scan2, beams;
  std::vector< vector<int> > scanpair;
  std::vector<string> calstate;
  String msg;

  CountedPtr< Scantable > s1b1on, s1b1off, s1b2on, s1b2off;
  CountedPtr< Scantable > s2b1on, s2b1off, s2b2on, s2b2off;

  std::vector< CountedPtr< Scantable > > sctables;
  sctables.push_back(s1b1on);
  sctables.push_back(s1b1off);
  sctables.push_back(s1b2on);
  sctables.push_back(s1b2off);
  sctables.push_back(s2b1on);
  sctables.push_back(s2b1off);
  sctables.push_back(s2b2on);
  sctables.push_back(s2b2off);

  //check scanlist
  int n=s->checkScanInfo(scans);
  if (n==1) {
     throw(AipsError("Incorrect scan pairs. "));
  }

  // Assume scans contain only a pair of consecutive scan numbers.
  // It is assumed that first beam, b1,  is on target.
  // There is no check if the first beam is on or not.
  if ( scans.size()==1 ) {
    scan1.push_back(scans[0]);
    scan2.push_back(scans[0]+1);
  } else if ( scans.size()==2 ) {
   scan1.push_back(scans[0]);
   scan2.push_back(scans[1]);
  } else {
    if ( scans.size()%2 == 0 ) {
      for (uInt i=0; i<scans.size(); i++) {
        if (i%2 == 0) {
          scan1.push_back(scans[i]);
        }
        else {
          scan2.push_back(scans[i]);
        }
      }
    } else {
      throw(AipsError("Odd numbers of scans, cannot form pairs."));
    }
  }
  scanpair.push_back(scan1);
  scanpair.push_back(scan2);
  calstate.push_back("*calon");
  calstate.push_back("*[^calon]");
  CountedPtr< Scantable > ws = getScantable(s, false);
  uInt l=0;
  while ( l < sctables.size() ) {
    for (uInt i=0; i < 2; i++) {
      for (uInt j=0; j < 2; j++) {
        for (uInt k=0; k < 2; k++) {
          sel.reset();
          sel.setScans(scanpair[i]);
          sel.setName(calstate[k]);
          beams.clear();
          beams.push_back(j);
          sel.setBeams(beams);
          ws->setSelection(sel);
          sctables[l]= getScantable(ws, false);
          l++;
        }
      }
    }
  }

  // replace here by splitData or getData functionality
  CountedPtr< Scantable > sig1;
  CountedPtr< Scantable > ref1;
  CountedPtr< Scantable > sig2;
  CountedPtr< Scantable > ref2;
  CountedPtr< Scantable > calb1;
  CountedPtr< Scantable > calb2;

  msg=String("Processing dototalpower for subset of the data");
  ostringstream oss1;
  oss1 << msg  << endl;
  pushLog(String(oss1));
  // Debug for IRC CS data
  //float tcal1=7.0;
  //float tcal2=4.0;
  sig1 = dototalpower(sctables[0], sctables[1], tcal=tcal);
  ref1 = dototalpower(sctables[2], sctables[3], tcal=tcal);
  ref2 = dototalpower(sctables[4], sctables[5], tcal=tcal);
  sig2 = dototalpower(sctables[6], sctables[7], tcal=tcal);

  // correction of user-specified tsys for elevation here

  // dosigref calibration
  msg=String("Processing dosigref for subset of the data");
  ostringstream oss2;
  oss2 << msg  << endl;
  pushLog(String(oss2));
  calb1=dosigref(sig1,ref2,smoothref,tsysv,tau);
  calb2=dosigref(sig2,ref1,smoothref,tsysv,tau);

  // iteration by scanno or cycle no.
  Table& tcalb1 = calb1->table();
  Table& tcalb2 = calb2->table();
  TableIterator sit(tcalb1, "SCANNO");
  TableIterator s2it(tcalb2, "SCANNO");
  while ( !sit.pastEnd() ) {
    Table t1 = sit.table();
    Table t2= s2it.table();
    ArrayColumn<Float> outspecCol(t1, "SPECTRA");
    ArrayColumn<Float> outtsysCol(t1, "TSYS");
    ArrayColumn<uChar> outflagCol(t1, "FLAGTRA");
    ScalarColumn<Double> outintCol(t1, "INTERVAL");
    ArrayColumn<Float> t2specCol(t2, "SPECTRA");
    ROArrayColumn<Float> t2tsysCol(t2, "TSYS");
    ArrayColumn<uChar> t2flagCol(t2, "FLAGTRA");
    ROScalarColumn<Double> t2intCol(t2, "INTERVAL");
    for (uInt i=0; i < t1.nrow(); ++i) {
      Vector<Float> spec1, spec2;
      // to store scalar (mean) tsys
      Vector<Float> tsys1, tsys2;
      Vector<uChar> flag1, flag2;
      Double tint1, tint2;
      outspecCol.get(i, spec1);
      t2specCol.get(i, spec2);
      outflagCol.get(i, flag1);
      t2flagCol.get(i, flag2);
      outtsysCol.get(i, tsys1);
      t2tsysCol.get(i, tsys2);
      outintCol.get(i, tint1);
      t2intCol.get(i, tint2);
      // average
      // assume scalar tsys for weights
      Float wt1, wt2, tsyssq1, tsyssq2;
      tsyssq1 = tsys1[0]*tsys1[0];
      tsyssq2 = tsys2[0]*tsys2[0];
      wt1 = Float(tint1)/tsyssq1;
      wt2 = Float(tint2)/tsyssq2;
      Float invsumwt=1/(wt1+wt2);
      MaskedArray<Float> mspec1 = maskedArray(spec1, flag1);
      MaskedArray<Float> mspec2 = maskedArray(spec2, flag2);
      MaskedArray<Float> avspec =  invsumwt * (wt1*mspec1 + wt2*mspec2);
      //Array<Float> avtsys =  Float(0.5) * (tsys1 + tsys2);
      // cerr<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<endl;
      tsys1[0] = sqrt(tsyssq1 + tsyssq2);
      Array<Float> avtsys =  tsys1;

      outspecCol.put(i, avspec.getArray());
      outflagCol.put(i, flagsFromMA(avspec));
      outtsysCol.put(i, avtsys);
    }
    ++sit;
    ++s2it;
  }
  return calb1;
}

//GBTIDL version of frequency switched data calibration
CountedPtr< Scantable > STMath::dofs( const CountedPtr< Scantable >& s,
                                      const std::vector<int>& scans,
                                      int smoothref,
                                      casa::Float tsysv,
                                      casa::Float tau,
                                      casa::Float tcal )
{


  STSelector sel;
  CountedPtr< Scantable > ws = getScantable(s, false);
  CountedPtr< Scantable > sig, sigwcal, ref, refwcal;
  CountedPtr< Scantable > calsig, calref, out;

  //split the data
  sel.setName("*_fs");
  ws->setSelection(sel);
  sig = getScantable(ws,false);
  sel.reset();
  sel.setName("*_fs_calon");
  ws->setSelection(sel);
  sigwcal = getScantable(ws,false);
  sel.reset();
  sel.setName("*_fsr");
  ws->setSelection(sel);
  ref = getScantable(ws,false);
  sel.reset();
  sel.setName("*_fsr_calon");
  ws->setSelection(sel);
  refwcal = getScantable(ws,false);

  calsig = dototalpower(sigwcal, sig, tcal=tcal);
  calref = dototalpower(refwcal, ref, tcal=tcal);

  out=dosigref(calsig,calref,smoothref,tsysv,tau);

  return out;
}


CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
{
  // make copy or reference
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tout = out->table();
  Block<String> cols(4);
  cols[0] = String("SCANNO");
  cols[1] = String("CYCLENO");
  cols[2] = String("BEAMNO");
  cols[3] = String("POLNO");
  TableIterator iter(tout, cols);
  while (!iter.pastEnd()) {
    Table subt = iter.table();
    // this should leave us with two rows for the two IFs....if not ignore
    if (subt.nrow() != 2 ) {
      continue;
    }
    ArrayColumn<Float> specCol(subt, "SPECTRA");
    ArrayColumn<Float> tsysCol(subt, "TSYS");
    ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
    Vector<Float> onspec,offspec, ontsys, offtsys;
    Vector<uChar> onflag, offflag;
    tsysCol.get(0, ontsys);   tsysCol.get(1, offtsys);
    specCol.get(0, onspec);   specCol.get(1, offspec);
    flagCol.get(0, onflag);   flagCol.get(1, offflag);
    MaskedArray<Float> on  = maskedArray(onspec, onflag);
    MaskedArray<Float> off = maskedArray(offspec, offflag);
    MaskedArray<Float> oncopy = on.copy();

    on /= off; on -= 1.0f;
    on *= ontsys[0];
    off /= oncopy; off -= 1.0f;
    off *= offtsys[0];
    specCol.put(0, on.getArray());
    const Vector<Bool>& m0 = on.getMask();
    Vector<uChar> flags0(m0.shape());
    convertArray(flags0, !m0);
    flagCol.put(0, flags0);

    specCol.put(1, off.getArray());
    const Vector<Bool>& m1 = off.getMask();
    Vector<uChar> flags1(m1.shape());
    convertArray(flags1, !m1);
    flagCol.put(1, flags1);
    ++iter;
  }

  return out;
}

std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
                                        const std::vector< bool > & mask,
                                        const std::string& which )
{

  Vector<Bool> m(mask);
  const Table& tab = in->table();
  ROArrayColumn<Float> specCol(tab, "SPECTRA");
  ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
  std::vector<float> out;
  for (uInt i=0; i < tab.nrow(); ++i ) {
    Vector<Float> spec; specCol.get(i, spec);
    Vector<uChar> flag; flagCol.get(i, flag);
    MaskedArray<Float> ma  = maskedArray(spec, flag);
    float outstat = 0.0;
    if ( spec.nelements() == m.nelements() ) {
      outstat = mathutil::statistics(which, ma(m));
    } else {
      outstat = mathutil::statistics(which, ma);
    }
    out.push_back(outstat);
  }
  return out;
}

CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
                                     int width )
{
  if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tout = out->table();
  out->frequencies().rescale(width, "BIN");
  ArrayColumn<Float> specCol(tout, "SPECTRA");
  ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
  for (uInt i=0; i < tout.nrow(); ++i ) {
    MaskedArray<Float> main  = maskedArray(specCol(i), flagCol(i));
    MaskedArray<Float> maout;
    LatticeUtilities::bin(maout, main, 0, Int(width));
    /// @todo implement channel based tsys binning
    specCol.put(i, maout.getArray());
    flagCol.put(i, flagsFromMA(maout));
    // take only the first binned spectrum's length for the deprecated
    // global header item nChan
    if (i==0) tout.rwKeywordSet().define(String("nChan"),
                                       Int(maout.getArray().nelements()));
  }
  return out;
}

CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
                                          const std::string& method,
                                          float width )
//
// Should add the possibility of width being specified in km/s. This means
// that for each freqID (SpectralCoordinate) we will need to convert to an
// average channel width (say at the reference pixel).  Then we would need
// to be careful to make sure each spectrum (of different freqID)
// is the same length.
//
{
  //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
  Int interpMethod(stringToIMethod(method));

  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tout = out->table();

// Resample SpectralCoordinates (one per freqID)
  out->frequencies().rescale(width, "RESAMPLE");
  TableIterator iter(tout, "IFNO");
  TableRow row(tout);
  while ( !iter.pastEnd() ) {
    Table tab = iter.table();
    ArrayColumn<Float> specCol(tab, "SPECTRA");
    //ArrayColumn<Float> tsysCol(tout, "TSYS");
    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
    Vector<Float> spec;
    Vector<uChar> flag;
    specCol.get(0,spec); // the number of channels should be constant per IF
    uInt nChanIn = spec.nelements();
    Vector<Float> xIn(nChanIn); indgen(xIn);
    Int fac =  Int(nChanIn/width);
    Vector<Float> xOut(fac+10); // 10 to be safe - resize later
    uInt k = 0;
    Float x = 0.0;
    while (x < Float(nChanIn) ) {
      xOut(k) = x;
      k++;
      x += width;
    }
    uInt nChanOut = k;
    xOut.resize(nChanOut, True);
    // process all rows for this IFNO
    Vector<Float> specOut;
    Vector<Bool> maskOut;
    Vector<uChar> flagOut;
    for (uInt i=0; i < tab.nrow(); ++i) {
      specCol.get(i, spec);
      flagCol.get(i, flag);
      Vector<Bool> mask(flag.nelements());
      convertArray(mask, flag);

      IPosition shapeIn(spec.shape());
      //sh.nchan = nChanOut;
      InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
                                                   xIn, spec, mask,
                                                   interpMethod, True, True);
      /// @todo do the same for channel based Tsys
      flagOut.resize(maskOut.nelements());
      convertArray(flagOut, maskOut);
      specCol.put(i, specOut);
      flagCol.put(i, flagOut);
    }
    ++iter;
  }

  return out;
}

STMath::imethod STMath::stringToIMethod(const std::string& in)
{
  static STMath::imap lookup;

  // initialize the lookup table if necessary
  if ( lookup.empty() ) {
    lookup["nearest"]   = InterpolateArray1D<Double,Float>::nearestNeighbour;
    lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
    lookup["cubic"]  = InterpolateArray1D<Double,Float>::cubic;
    lookup["spline"]  = InterpolateArray1D<Double,Float>::spline;
  }

  STMath::imap::const_iterator iter = lookup.find(in);

  if ( lookup.end() == iter ) {
    std::string message = in;
    message += " is not a valid interpolation mode";
    throw(AipsError(message));
  }
  return iter->second;
}

WeightType STMath::stringToWeight(const std::string& in)
{
  static std::map<std::string, WeightType> lookup;

  // initialize the lookup table if necessary
  if ( lookup.empty() ) {
    lookup["NONE"]   = asap::W_NONE;
    lookup["TINT"] = asap::W_TINT;
    lookup["TINTSYS"]  = asap::W_TINTSYS;
    lookup["TSYS"]  = asap::W_TSYS;
    lookup["VAR"]  = asap::W_VAR;
  }

  std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);

  if ( lookup.end() == iter ) {
    std::string message = in;
    message += " is not a valid weighting mode";
    throw(AipsError(message));
  }
  return iter->second;
}

CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
                                               const vector< float > & coeff,
                                               const std::string & filename,
                                               const std::string& method)
{
  // Get elevation data from Scantable and convert to degrees
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tab = out->table();
  ROScalarColumn<Float> elev(tab, "ELEVATION");
  Vector<Float> x = elev.getColumn();
  x *= Float(180 / C::pi);                        // Degrees

  Vector<Float> coeffs(coeff);
  const uInt nc = coeffs.nelements();
  if ( filename.length() > 0 && nc > 0 ) {
    throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
  }

  // Correct
  if ( nc > 0 || filename.length() == 0 ) {
    // Find instrument
    Bool throwit = True;
    Instrument inst =
      STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
                                throwit);

    // Set polynomial
    Polynomial<Float>* ppoly = 0;
    Vector<Float> coeff;
    String msg;
    if ( nc > 0 ) {
      ppoly = new Polynomial<Float>(nc-1);
      coeff = coeffs;
      msg = String("user");
    } else {
      STAttr sdAttr;
      coeff = sdAttr.gainElevationPoly(inst);
      ppoly = new Polynomial<Float>(coeff.nelements()-1);
      msg = String("built in");
    }

    if ( coeff.nelements() > 0 ) {
      ppoly->setCoefficients(coeff);
    } else {
      delete ppoly;
      throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
    }
    ostringstream oss;
    oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
    oss << "   " <<  coeff;
    pushLog(String(oss));
    const uInt nrow = tab.nrow();
    Vector<Float> factor(nrow);
    for ( uInt i=0; i < nrow; ++i ) {
      factor[i] = 1.0 / (*ppoly)(x[i]);
    }
    delete ppoly;
    scaleByVector(tab, factor, true);

  } else {
    // Read and correct
    pushLog("Making correction from ascii Table");
    scaleFromAsciiTable(tab, filename, method, x, true);
  }
  return out;
}

void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
                                 const std::string& method,
                                 const Vector<Float>& xout, bool dotsys)
{

// Read gain-elevation ascii file data into a Table.

  String formatString;
  Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
  scaleFromTable(in, tbl, method, xout, dotsys);
}

void STMath::scaleFromTable(Table& in,
                            const Table& table,
                            const std::string& method,
                            const Vector<Float>& xout, bool dotsys)
{

  ROScalarColumn<Float> geElCol(table, "ELEVATION");
  ROScalarColumn<Float> geFacCol(table, "FACTOR");
  Vector<Float> xin = geElCol.getColumn();
  Vector<Float> yin = geFacCol.getColumn();
  Vector<Bool> maskin(xin.nelements(),True);

  // Interpolate (and extrapolate) with desired method

  InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);

   Vector<Float> yout;
   Vector<Bool> maskout;
   InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
                                                xin, yin, maskin, interp,
                                                True, True);

   scaleByVector(in, Float(1.0)/yout, dotsys);
}

void STMath::scaleByVector( Table& in,
                            const Vector< Float >& factor,
                            bool dotsys )
{
  uInt nrow = in.nrow();
  if ( factor.nelements() != nrow ) {
    throw(AipsError("factors.nelements() != table.nelements()"));
  }
  ArrayColumn<Float> specCol(in, "SPECTRA");
  ArrayColumn<uChar> flagCol(in, "FLAGTRA");
  ArrayColumn<Float> tsysCol(in, "TSYS");
  for (uInt i=0; i < nrow; ++i) {
    MaskedArray<Float> ma  = maskedArray(specCol(i), flagCol(i));
    ma *= factor[i];
    specCol.put(i, ma.getArray());
    flagCol.put(i, flagsFromMA(ma));
    if ( dotsys ) {
      Vector<Float> tsys = tsysCol(i);
      tsys *= factor[i];
      tsysCol.put(i,tsys);
    }
  }
}

CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
                                             float d, float etaap,
                                             float jyperk )
{
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tab = in->table();
  Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
  Unit K(String("K"));
  Unit JY(String("Jy"));

  bool tokelvin = true;
  Double cfac = 1.0;

  if ( fluxUnit == JY ) {
    pushLog("Converting to K");
    Quantum<Double> t(1.0,fluxUnit);
    Quantum<Double> t2 = t.get(JY);
    cfac = (t2 / t).getValue();               // value to Jy

    tokelvin = true;
    out->setFluxUnit("K");
  } else if ( fluxUnit == K ) {
    pushLog("Converting to Jy");
    Quantum<Double> t(1.0,fluxUnit);
    Quantum<Double> t2 = t.get(K);
    cfac = (t2 / t).getValue();              // value to K

    tokelvin = false;
    out->setFluxUnit("Jy");
  } else {
    throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
  }
  // Make sure input values are converted to either Jy or K first...
  Float factor = cfac;

  // Select method
  if (jyperk > 0.0) {
    factor *= jyperk;
    if ( tokelvin ) factor = 1.0 / jyperk;
    ostringstream oss;
    oss << "Jy/K = " << jyperk;
    pushLog(String(oss));
    Vector<Float> factors(tab.nrow(), factor);
    scaleByVector(tab,factors, false);
  } else if ( etaap > 0.0) {
    if (d < 0) {
      Instrument inst =
	STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
				  True);
      STAttr sda;
      d = sda.diameter(inst);
    }
    jyperk = STAttr::findJyPerK(etaap, d);
    ostringstream oss;
    oss << "Jy/K = " << jyperk;
    pushLog(String(oss));
    factor *= jyperk;
    if ( tokelvin ) {
      factor = 1.0 / factor;
    }
    Vector<Float> factors(tab.nrow(), factor);
    scaleByVector(tab, factors, False);
  } else {

    // OK now we must deal with automatic look up of values.
    // We must also deal with the fact that the factors need
    // to be computed per IF and may be different and may
    // change per integration.

    pushLog("Looking up conversion factors");
    convertBrightnessUnits(out, tokelvin, cfac);
  }

  return out;
}

void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
                                     bool tokelvin, float cfac )
{
  Table& table = in->table();
  Instrument inst =
    STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
  TableIterator iter(table, "FREQ_ID");
  STFrequencies stfreqs = in->frequencies();
  STAttr sdAtt;
  while (!iter.pastEnd()) {
    Table tab = iter.table();
    ArrayColumn<Float> specCol(tab, "SPECTRA");
    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
    ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
    MEpoch::ROScalarColumn timeCol(tab, "TIME");

    uInt freqid; freqidCol.get(0, freqid);
    Vector<Float> tmpspec; specCol.get(0, tmpspec);
    // STAttr.JyPerK has a Vector interface... change sometime.
    Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
    for ( uInt i=0; i<tab.nrow(); ++i) {
      Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
      Float factor = cfac * jyperk;
      if ( tokelvin ) factor = Float(1.0) / factor;
      MaskedArray<Float> ma  = maskedArray(specCol(i), flagCol(i));
      ma *= factor;
      specCol.put(i, ma.getArray());
      flagCol.put(i, flagsFromMA(ma));
    }
  ++iter;
  }
}

CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
                                         const std::vector<float>& tau )
{
  CountedPtr< Scantable > out = getScantable(in, false);

  Table outtab = out->table();

  const uInt ntau = uInt(tau.size());
  std::vector<float>::const_iterator tauit = tau.begin();
  AlwaysAssert((ntau == 1 || ntau == in->nif() || ntau == in->nif() * in->npol()),
               AipsError);
  TableIterator iiter(outtab, "IFNO");
  while ( !iiter.pastEnd() ) {
    Table itab = iiter.table();
    TableIterator piter(outtab, "POLNO");
    while ( !piter.pastEnd() ) {
      Table tab = piter.table();
      ROScalarColumn<Float> elev(tab, "ELEVATION");
      ArrayColumn<Float> specCol(tab, "SPECTRA");
      ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
      ArrayColumn<Float> tsysCol(tab, "TSYS");
      for ( uInt i=0; i<tab.nrow(); ++i) {
        Float zdist = Float(C::pi_2) - elev(i);
        Float factor = exp(*tauit/cos(zdist));
        MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
        ma *= factor;
        specCol.put(i, ma.getArray());
        flagCol.put(i, flagsFromMA(ma));
        Vector<Float> tsys;
        tsysCol.get(i, tsys);
        tsys *= factor;
        tsysCol.put(i, tsys);
      }
      if (ntau == in->nif()*in->npol() ) {
        tauit++;
      }
      piter++;
    }
    if (ntau >= in->nif() ) {
      tauit++;
    }
    iiter++;
  }
  return out;
}

CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in,
                                             const std::string& kernel,
                                             float width, int order)
{
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& table = out->table();
  ArrayColumn<Float> specCol(table, "SPECTRA");
  ArrayColumn<uChar> flagCol(table, "FLAGTRA");
  Vector<Float> spec;
  Vector<uChar> flag;
  for ( uInt i=0; i<table.nrow(); ++i) {
    specCol.get(i, spec);
    flagCol.get(i, flag);
    Vector<Bool> mask(flag.nelements());
    convertArray(mask, flag);
    Vector<Float> specout;
    Vector<Bool> maskout;
    if ( kernel == "hanning" ) {
      mathutil::hanning(specout, maskout, spec , !mask);
      convertArray(flag, !maskout);
    } else if (  kernel == "rmedian" ) {
      mathutil::runningMedian(specout, maskout, spec , mask, width);
      convertArray(flag, maskout);
    } else if ( kernel == "poly" ) {
      mathutil::polyfit(specout, maskout, spec, !mask, width, order);
      convertArray(flag, !maskout);
    }
    flagCol.put(i, flag);
    specCol.put(i, specout);
  }
  return out;
}

CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
                                        const std::string& kernel, float width,
                                        int order)
{
  if (kernel == "rmedian"  || kernel == "hanning" || kernel == "poly") {
    return smoothOther(in, kernel, width, order);
  }
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& table = out->table();
  VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
  // same IFNO should have same no of channels
  // this saves overhead
  TableIterator iter(table, "IFNO");
  while (!iter.pastEnd()) {
    Table tab = iter.table();
    ArrayColumn<Float> specCol(tab, "SPECTRA");
    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
    Vector<Float> tmpspec; specCol.get(0, tmpspec);
    uInt nchan = tmpspec.nelements();
    Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
    Convolver<Float> conv(kvec, IPosition(1,nchan));
    Vector<Float> spec;
    Vector<uChar> flag;
    for ( uInt i=0; i<tab.nrow(); ++i) {
      specCol.get(i, spec);
      flagCol.get(i, flag);
      Vector<Bool> mask(flag.nelements());
      convertArray(mask, flag);
      Vector<Float> specout;
      mathutil::replaceMaskByZero(specout, mask);
      conv.linearConv(specout, spec);
      specCol.put(i, specout);
    }
    ++iter;
  }
  return out;
}

CountedPtr< Scantable >
  STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
{
  if ( in.size() < 2 ) {
    throw(AipsError("Need at least two scantables to perform a merge."));
  }
  std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(*it, false);
  setInsitu(insitu);
  Table& tout = out->table();
  ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
  ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
  // Renumber SCANNO to be 0-based
  Vector<uInt> scannos = scannocol.getColumn();
  uInt offset = min(scannos);
  scannos -= offset;
  scannocol.putColumn(scannos);
  uInt newscanno = max(scannos)+1;
  ++it;
  while ( it != in.end() ){
    if ( ! (*it)->conformant(*out) ) {
      // non conformant.
      pushLog(String("Warning: Can't merge scantables as header info differs."));
    }
    out->appendToHistoryTable((*it)->history());
    const Table& tab = (*it)->table();
    TableIterator scanit(tab, "SCANNO");
    while (!scanit.pastEnd()) {
      TableIterator freqit(scanit.table(), "FREQ_ID");
      while ( !freqit.pastEnd() ) {
        Table thetab = freqit.table();
        uInt nrow = tout.nrow();
        tout.addRow(thetab.nrow());
        TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
        ROTableRow row(thetab);
        for ( uInt i=0; i<thetab.nrow(); ++i) {
          uInt k = nrow+i;
          scannocol.put(k, newscanno);
          const TableRecord& rec = row.get(i);
          Double rv,rp,inc;
          (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
          uInt id;
          id = out->frequencies().addEntry(rp, rv, inc);
          freqidcol.put(k,id);
          String name,fname;Double rf;
          (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
          id = out->molecules().addEntry(rf, name, fname);
          molidcol.put(k, id);
          Float fpa,frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
          (*it)->focus().getEntry(fpa, fax, ftan, frot, fhand,
                                  fmount,fuser, fxy, fxyp,
                                  rec.asuInt("FOCUS_ID"));
          id = out->focus().addEntry(fpa, fax, ftan, frot, fhand,
                                     fmount,fuser, fxy, fxyp);
          focusidcol.put(k, id);
        }
        ++freqit;
      }
      ++newscanno;
      ++scanit;
    }
    ++it;
  }
  return out;
}

CountedPtr< Scantable >
  STMath::invertPhase( const CountedPtr < Scantable >& in )
{
  return applyToPol(in, &STPol::invertPhase, Float(0.0));
}

CountedPtr< Scantable >
  STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
{
   return applyToPol(in, &STPol::rotatePhase, Float(phase));
}

CountedPtr< Scantable >
  STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
{
  return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
}

CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
                                             STPol::polOperation fptr,
                                             Float phase )
{
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tout = out->table();
  Block<String> cols(4);
  cols[0] = String("SCANNO");
  cols[1] = String("BEAMNO");
  cols[2] = String("IFNO");
  cols[3] = String("CYCLENO");
  TableIterator iter(tout, cols);
  CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
                                               out->getPolType() );
  while (!iter.pastEnd()) {
    Table t = iter.table();
    ArrayColumn<Float> speccol(t, "SPECTRA");
    ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
    Matrix<Float> pols(speccol.getColumn());
    try {
      stpol->setSpectra(pols);
      Float fang,fhand;
      fang = in->focusTable_.getTotalAngle(focidcol(0));
      fhand = in->focusTable_.getFeedHand(focidcol(0));
      stpol->setPhaseCorrections(fang, fhand);
      // use a member function pointer in STPol.  This only works on
      // the STPol pointer itself, not the Counted Pointer so
      // derefernce it.
      (&(*(stpol))->*fptr)(phase);
      speccol.putColumn(stpol->getSpectra());
    } catch (AipsError& e) {
      //delete stpol;stpol=0;
      throw(e);
    }
    ++iter;
  }
  //delete stpol;stpol=0;
  return out;
}

CountedPtr< Scantable >
  STMath::swapPolarisations( const CountedPtr< Scantable > & in )
{
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tout = out->table();
  Table t0 = tout(tout.col("POLNO") == 0);
  Table t1 = tout(tout.col("POLNO") == 1);
  if ( t0.nrow() != t1.nrow() )
    throw(AipsError("Inconsistent number of polarisations"));
  ArrayColumn<Float> speccol0(t0, "SPECTRA");
  ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
  ArrayColumn<Float> speccol1(t1, "SPECTRA");
  ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
  Matrix<Float> s0 = speccol0.getColumn();
  Matrix<uChar> f0 = flagcol0.getColumn();
  speccol0.putColumn(speccol1.getColumn());
  flagcol0.putColumn(flagcol1.getColumn());
  speccol1.putColumn(s0);
  flagcol1.putColumn(f0);
  return out;
}

CountedPtr< Scantable >
  STMath::averagePolarisations( const CountedPtr< Scantable > & in,
                                const std::vector<bool>& mask,
                                const std::string& weight )
{
  if (in->npol() < 2 )
    throw(AipsError("averagePolarisations can only be applied to two or more"
                    "polarisations"));
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > pols = getScantable(in, true);
  setInsitu(insitu);
  Table& tout = pols->table();
  std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
  Table tab = tableCommand(taql, in->table());
  if (tab.nrow() == 0 )
    throw(AipsError("Could not find  any rows with POLNO==0 and POLNO==1"));
  TableCopy::copyRows(tout, tab);
  TableVector<uInt> vec(tout, "POLNO");
  vec = 0;
  pols->table_.rwKeywordSet().define("nPol", Int(1));
  //pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
  pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
  std::vector<CountedPtr<Scantable> > vpols;
  vpols.push_back(pols);
  CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
  return out;
}

CountedPtr< Scantable >
  STMath::averageBeams( const CountedPtr< Scantable > & in,
                        const std::vector<bool>& mask,
                        const std::string& weight )
{
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > beams = getScantable(in, false);
  setInsitu(insitu);
  Table& tout = beams->table();
  // give all rows the same BEAMNO
  TableVector<uInt> vec(tout, "BEAMNO");
  vec = 0;
  beams->table_.rwKeywordSet().define("nBeam", Int(1));
  std::vector<CountedPtr<Scantable> > vbeams;
  vbeams.push_back(beams);
  CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
  return out;
}


CountedPtr< Scantable >
  asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
                                const std::string & refTime,
                                const std::string & method)
{
  // clone as this is not working insitu
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(in, false);
  setInsitu(insitu);
  Table& tout = out->table();
  // Get reference Epoch to time of first row or given String
  Unit DAY(String("d"));
  MEpoch::Ref epochRef(in->getTimeReference());
  MEpoch refEpoch;
  if (refTime.length()>0) {
    Quantum<Double> qt;
    if (MVTime::read(qt,refTime)) {
      MVEpoch mv(qt);
      refEpoch = MEpoch(mv, epochRef);
   } else {
      throw(AipsError("Invalid format for Epoch string"));
   }
  } else {
    refEpoch = in->timeCol_(0);
  }
  MPosition refPos = in->getAntennaPosition();

  InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
  /*
  // Comment from MV.
  // the following code has been commented out because different FREQ_IDs have to be aligned together even
  // if the frame doesn't change. So far, lack of this check didn't cause any problems.
  // test if user frame is different to base frame
  if ( in->frequencies().getFrameString(true)
       == in->frequencies().getFrameString(false) ) {
    throw(AipsError("Can't convert as no output frame has been set"
                    " (use set_freqframe) or it is aligned already."));
  }
  */
  MFrequency::Types system = in->frequencies().getFrame();
  MVTime mvt(refEpoch.getValue());
  String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
  ostringstream oss;
  oss << "Aligned at reference Epoch " << epochout
      << " in frame " << MFrequency::showType(system);
  pushLog(String(oss));
  // set up the iterator
  Block<String> cols(4);
  // select by constant direction
  cols[0] = String("SRCNAME");
  cols[1] = String("BEAMNO");
  // select by IF ( no of channels varies over this )
  cols[2] = String("IFNO");
  // select by restfrequency
  cols[3] = String("MOLECULE_ID");
  TableIterator iter(tout, cols);
  while ( !iter.pastEnd() ) {
    Table t = iter.table();
    MDirection::ROScalarColumn dirCol(t, "DIRECTION");
    TableIterator fiter(t, "FREQ_ID");
    // determine nchan from the first row. This should work as
    // we are iterating over BEAMNO and IFNO    // we should have constant direction

    ROArrayColumn<Float> sCol(t, "SPECTRA");
    const MDirection direction = dirCol(0);
    const uInt nchan = sCol(0).nelements();

    // skip operations if there is nothing to align
    if (fiter.pastEnd()) {
        continue;
    }

    Table ftab = fiter.table();
    // align all frequency ids with respect to the first encountered id
    ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
    // get the SpectralCoordinate for the freqid, which we are iterating over
    SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
    FrequencyAligner<Float> fa( sC, nchan, refEpoch,
                                direction, refPos, system );
    // realign the SpectralCoordinate and put into the output Scantable
    Vector<String> units(1);
    units = String("Hz");
    Bool linear=True;
    SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
    sc2.setWorldAxisUnits(units);
    const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
                                                sc2.referenceValue()[0],
                                                sc2.increment()[0]);
    while ( !fiter.pastEnd() ) {
      ftab = fiter.table();
      // spectral coordinate for the current FREQ_ID
      ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
      sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
      // create the "global" abcissa for alignment with same FREQ_ID
      Vector<Double> abc(nchan);
      for (uInt i=0; i<nchan; i++) {
           Double w;
           sC.toWorld(w,Double(i));
           abc[i] = w;
      }
      TableVector<uInt> tvec(ftab, "FREQ_ID");
      // assign new frequency id to all rows
      tvec = id;
      // cache abcissa for same time stamps, so iterate over those
      TableIterator timeiter(ftab, "TIME");
      while ( !timeiter.pastEnd() ) {
        Table tab = timeiter.table();
        ArrayColumn<Float> specCol(tab, "SPECTRA");
        ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
        MEpoch::ROScalarColumn timeCol(tab, "TIME");
        // use align abcissa cache after the first row
        // these rows should be just be POLNO
        bool first = true;
        for (int i=0; i<int(tab.nrow()); ++i) {
          // input values
          Vector<uChar> flag = flagCol(i);
          Vector<Bool> mask(flag.shape());
          Vector<Float> specOut, spec;
          spec  = specCol(i);
          Vector<Bool> maskOut;Vector<uChar> flagOut;
          convertArray(mask, flag);
          // alignment
          Bool ok = fa.align(specOut, maskOut, abc, spec,
                             mask, timeCol(i), !first,
                             interp, False);
          // back into scantable
          flagOut.resize(maskOut.nelements());
          convertArray(flagOut, maskOut);
          flagCol.put(i, flagOut);
          specCol.put(i, specOut);
          // start abcissa caching
          first = false;
        }
        // next timestamp
        ++timeiter;
      }
      // next FREQ_ID
      ++fiter;
    }
    // next aligner
    ++iter;
  }
  // set this afterwards to ensure we are doing insitu correctly.
  out->frequencies().setFrame(system, true);
  return out;
}

CountedPtr<Scantable>
  asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
                                     const std::string & newtype )
{
  if (in->npol() != 2 && in->npol() != 4)
    throw(AipsError("Can only convert two or four polarisations."));
  if ( in->getPolType() == newtype )
    throw(AipsError("No need to convert."));
  if ( ! in->selector_.empty() )
    throw(AipsError("Can only convert whole scantable. Unset the selection."));
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(in, true);
  setInsitu(insitu);
  Table& tout = out->table();
  tout.rwKeywordSet().define("POLTYPE", String(newtype));

  Block<String> cols(4);
  cols[0] = "SCANNO";
  cols[1] = "CYCLENO";
  cols[2] = "BEAMNO";
  cols[3] = "IFNO";
  TableIterator it(in->originalTable_, cols);
  String basetype = in->getPolType();
  STPol* stpol = STPol::getPolClass(in->factories_, basetype);
  try {
    while ( !it.pastEnd() ) {
      Table tab = it.table();
      uInt row = tab.rowNumbers()[0];
      stpol->setSpectra(in->getPolMatrix(row));
      Float fang,fhand;
      fang = in->focusTable_.getTotalAngle(in->mfocusidCol_(row));
      fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
      stpol->setPhaseCorrections(fang, fhand);
      Int npolout = 0;
      for (uInt i=0; i<tab.nrow(); ++i) {
        Vector<Float> outvec = stpol->getSpectrum(i, newtype);
        if ( outvec.nelements() > 0 ) {
          tout.addRow();
          TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
          ArrayColumn<Float> sCol(tout,"SPECTRA");
          ScalarColumn<uInt> pCol(tout,"POLNO");
          sCol.put(tout.nrow()-1 ,outvec);
          pCol.put(tout.nrow()-1 ,uInt(npolout));
          npolout++;
       }
      }
      tout.rwKeywordSet().define("nPol", npolout);
      ++it;
    }
  } catch (AipsError& e) {
    delete stpol;
    throw(e);
  }
  delete stpol;
  return out;
}

CountedPtr< Scantable >
  asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
                           const std::string & scantype )
{
  bool insitu = insitu_;
  setInsitu(false);
  CountedPtr< Scantable > out = getScantable(in, true);
  setInsitu(insitu);
  Table& tout = out->table();
  std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
  if (scantype == "on") {
    taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
  }
  Table tab = tableCommand(taql, in->table());
  TableCopy::copyRows(tout, tab);
  if (scantype == "on") {
    // re-index SCANNO to 0
    TableVector<uInt> vec(tout, "SCANNO");
    vec = 0;
  }
  return out;
}

CountedPtr< Scantable >
  asap::STMath::lagFlag( const CountedPtr< Scantable > & in,
                         double start, double end,
                         const std::string& mode)
{
  CountedPtr< Scantable > out = getScantable(in, false);
  Table& tout = out->table();
  TableIterator iter(tout, "FREQ_ID");
  FFTServer<Float,Complex> ffts;
  while ( !iter.pastEnd() ) {
    Table tab = iter.table();
    Double rp,rv,inc;
    ROTableRow row(tab);
    const TableRecord& rec = row.get(0);
    uInt freqid = rec.asuInt("FREQ_ID");
    out->frequencies().getEntry(rp, rv, inc, freqid);
    ArrayColumn<Float> specCol(tab, "SPECTRA");
    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
    for (int i=0; i<int(tab.nrow()); ++i) {
      Vector<Float> spec = specCol(i);
      Vector<uChar> flag = flagCol(i);
      int fstart = -1;
      int fend = -1;
      for (int k=0; k < flag.nelements(); ++k ) {
        if (flag[k] > 0) {
          fstart = k;
          while (flag[k] > 0 && k < flag.nelements()) {
            fend = k;
            k++;
          }
        }
        Float interp = 0.0;
        if (fstart-1 > 0 ) {
          interp = spec[fstart-1];
          if (fend+1 < spec.nelements()) {
            interp = (interp+spec[fend+1])/2.0;
          }
        } else {
          interp = spec[fend+1];
        }
        if (fstart > -1 && fend > -1) {
          for (int j=fstart;j<=fend;++j) {
            spec[j] = interp;
          }
        }
        fstart =-1;
        fend = -1;
      }
      Vector<Complex> lags;
      ffts.fft0(lags, spec);
      Int lag0(start+0.5);
      Int lag1(end+0.5);
      if (mode == "frequency") {
        lag0 = Int(spec.nelements()*abs(inc)/(start)+0.5);
        lag1 = Int(spec.nelements()*abs(inc)/(end)+0.5);
      }
      Int lstart =  max(0, lag0);
      Int lend =  min(Int(lags.nelements()-1), lag1);
      if (lstart == lend) {
        lags[lstart] = Complex(0.0);
      } else {
        if (lstart > lend) {
          Int tmp = lend;
          lend = lstart;
          lstart = tmp;
        }
        for (int j=lstart; j <=lend ;++j) {
          lags[j] = Complex(0.0);
        }
      }
      ffts.fft0(spec, lags);
      specCol.put(i, spec);
    }
    ++iter;
  }
  return out;
}