source: branches/Release2.1.2/src/STMath.cpp @ 1320

Last change on this file since 1320 was 1320, checked in by mar637, 17 years ago

merge from trunk, to get most recent bug fixes
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File size: 49.0 KB
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1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <casa/iomanip.h>
14#include <casa/Exceptions/Error.h>
15#include <casa/Containers/Block.h>
16#include <casa/BasicSL/String.h>
17#include <casa/Arrays/MaskArrLogi.h>
18#include <casa/Arrays/MaskArrMath.h>
19#include <casa/Arrays/ArrayLogical.h>
20#include <casa/Arrays/ArrayMath.h>
21#include <casa/Arrays/Slice.h>
22#include <casa/Arrays/Slicer.h>
23#include <casa/Containers/RecordField.h>
24#include <tables/Tables/TableRow.h>
25#include <tables/Tables/TableVector.h>
26#include <tables/Tables/TabVecMath.h>
27#include <tables/Tables/ExprNode.h>
28#include <tables/Tables/TableRecord.h>
29#include <tables/Tables/TableParse.h>
30#include <tables/Tables/ReadAsciiTable.h>
31#include <tables/Tables/TableIter.h>
32#include <tables/Tables/TableCopy.h>
33#include <scimath/Mathematics/FFTServer.h>
34
35#include <lattices/Lattices/LatticeUtilities.h>
36
37#include <coordinates/Coordinates/SpectralCoordinate.h>
38#include <coordinates/Coordinates/CoordinateSystem.h>
39#include <coordinates/Coordinates/CoordinateUtil.h>
40#include <coordinates/Coordinates/FrequencyAligner.h>
41
42#include <scimath/Mathematics/VectorKernel.h>
43#include <scimath/Mathematics/Convolver.h>
44#include <scimath/Functionals/Polynomial.h>
45
46#include "MathUtils.h"
47#include "RowAccumulator.h"
48#include "STAttr.h"
49#include "STMath.h"
50
51using namespace casa;
52
53using namespace asap;
54
55STMath::STMath(bool insitu) :
56  insitu_(insitu)
57{
58}
59
60
61STMath::~STMath()
62{
63}
64
65CountedPtr<Scantable>
66STMath::average( const std::vector<CountedPtr<Scantable> >& in,
67                 const std::vector<bool>& mask,
68                 const std::string& weight,
69                 const std::string& avmode)
70{
71  if ( avmode == "SCAN" && in.size() != 1 )
72    throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
73                    "Use merge first."));
74  WeightType wtype = stringToWeight(weight);
75
76  // output
77  // clone as this is non insitu
78  bool insitu = insitu_;
79  setInsitu(false);
80  CountedPtr< Scantable > out = getScantable(in[0], true);
81  setInsitu(insitu);
82  std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
83  ++stit;
84  while ( stit != in.end() ) {
85    out->appendToHistoryTable((*stit)->history());
86    ++stit;
87  }
88
89  Table& tout = out->table();
90
91  /// @todo check if all scantables are conformant
92
93  ArrayColumn<Float> specColOut(tout,"SPECTRA");
94  ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
95  ArrayColumn<Float> tsysColOut(tout,"TSYS");
96  ScalarColumn<Double> mjdColOut(tout,"TIME");
97  ScalarColumn<Double> intColOut(tout,"INTERVAL");
98  ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
99  ScalarColumn<uInt> scanColOut(tout,"SCANNO");
100
101  // set up the output table rows. These are based on the structure of the
102  // FIRST scantable in the vector
103  const Table& baset = in[0]->table();
104
105  Block<String> cols(3);
106  cols[0] = String("BEAMNO");
107  cols[1] = String("IFNO");
108  cols[2] = String("POLNO");
109  if ( avmode == "SOURCE" ) {
110    cols.resize(4);
111    cols[3] = String("SRCNAME");
112  }
113  if ( avmode == "SCAN"  && in.size() == 1) {
114    cols.resize(4);
115    cols[3] = String("SCANNO");
116  }
117  uInt outrowCount = 0;
118  TableIterator iter(baset, cols);
119  while (!iter.pastEnd()) {
120    Table subt = iter.table();
121    // copy the first row of this selection into the new table
122    tout.addRow();
123    TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
124    // re-index to 0
125    if ( avmode != "SCAN" && avmode != "SOURCE" ) {
126      scanColOut.put(outrowCount, uInt(0));
127    }
128    ++outrowCount;
129    ++iter;
130  }
131  RowAccumulator acc(wtype);
132  Vector<Bool> cmask(mask);
133  acc.setUserMask(cmask);
134  ROTableRow row(tout);
135  ROArrayColumn<Float> specCol, tsysCol;
136  ROArrayColumn<uChar> flagCol;
137  ROScalarColumn<Double> mjdCol, intCol;
138  ROScalarColumn<Int> scanIDCol;
139
140  for (uInt i=0; i < tout.nrow(); ++i) {
141    for ( int j=0; j < int(in.size()); ++j ) {
142      const Table& tin = in[j]->table();
143      const TableRecord& rec = row.get(i);
144      ROScalarColumn<Double> tmp(tin, "TIME");
145      Double td;tmp.get(0,td);
146      Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
147                       && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
148                       && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
149      Table subt;
150      if ( avmode == "SOURCE") {
151        subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
152      } else if (avmode == "SCAN") {
153        subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
154      } else {
155        subt = basesubt;
156      }
157      specCol.attach(subt,"SPECTRA");
158      flagCol.attach(subt,"FLAGTRA");
159      tsysCol.attach(subt,"TSYS");
160      intCol.attach(subt,"INTERVAL");
161      mjdCol.attach(subt,"TIME");
162      Vector<Float> spec,tsys;
163      Vector<uChar> flag;
164      Double inter,time;
165      for (uInt k = 0; k < subt.nrow(); ++k ) {
166        flagCol.get(k, flag);
167        Vector<Bool> bflag(flag.shape());
168        convertArray(bflag, flag);
169        /*
170        if ( allEQ(bflag, True) ) {
171        continue;//don't accumulate
172        }
173        */
174        specCol.get(k, spec);
175        tsysCol.get(k, tsys);
176        intCol.get(k, inter);
177        mjdCol.get(k, time);
178        // spectrum has to be added last to enable weighting by the other values
179        acc.add(spec, !bflag, tsys, inter, time);
180      }
181    }
182    //write out
183    specColOut.put(i, acc.getSpectrum());
184    const Vector<Bool>& msk = acc.getMask();
185    Vector<uChar> flg(msk.shape());
186    convertArray(flg, !msk);
187    flagColOut.put(i, flg);
188    tsysColOut.put(i, acc.getTsys());
189    intColOut.put(i, acc.getInterval());
190    mjdColOut.put(i, acc.getTime());
191    // we should only have one cycle now -> reset it to be 0
192    // frequency switched data has different CYCLENO for different IFNO
193    // which requires resetting this value
194    cycColOut.put(i, uInt(0));
195    acc.reset();
196  }
197  return out;
198}
199
200CountedPtr< Scantable >
201  STMath::averageChannel( const CountedPtr < Scantable > & in,
202                          const std::string & mode,
203                          const std::string& avmode )
204{
205  // clone as this is non insitu
206  bool insitu = insitu_;
207  setInsitu(false);
208  CountedPtr< Scantable > out = getScantable(in, true);
209  setInsitu(insitu);
210  Table& tout = out->table();
211  ArrayColumn<Float> specColOut(tout,"SPECTRA");
212  ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
213  ArrayColumn<Float> tsysColOut(tout,"TSYS");
214  ScalarColumn<uInt> scanColOut(tout,"SCANNO");
215  ScalarColumn<Double> intColOut(tout, "INTERVAL");
216  Table tmp = in->table().sort("BEAMNO");
217  Block<String> cols(3);
218  cols[0] = String("BEAMNO");
219  cols[1] = String("IFNO");
220  cols[2] = String("POLNO");
221  if ( avmode == "SCAN") {
222    cols.resize(4);
223    cols[3] = String("SCANNO");
224  }
225  uInt outrowCount = 0;
226  uChar userflag = 1 << 7;
227  TableIterator iter(tmp, cols);
228  while (!iter.pastEnd()) {
229    Table subt = iter.table();
230    ROArrayColumn<Float> specCol, tsysCol;
231    ROArrayColumn<uChar> flagCol;
232    ROScalarColumn<Double> intCol(subt, "INTERVAL");
233    specCol.attach(subt,"SPECTRA");
234    flagCol.attach(subt,"FLAGTRA");
235    tsysCol.attach(subt,"TSYS");
236    tout.addRow();
237    TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
238    if ( avmode != "SCAN") {
239      scanColOut.put(outrowCount, uInt(0));
240    }
241    Vector<Float> tmp;
242    specCol.get(0, tmp);
243    uInt nchan = tmp.nelements();
244    // have to do channel by channel here as MaskedArrMath
245    // doesn't have partialMedians
246    Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
247    Vector<Float> outspec(nchan);
248    Vector<uChar> outflag(nchan,0);
249    Vector<Float> outtsys(1);/// @fixme when tsys is channel based
250    for (uInt i=0; i<nchan; ++i) {
251      Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
252      MaskedArray<Float> ma = maskedArray(specs,flags);
253      outspec[i] = median(ma);
254      if ( allEQ(ma.getMask(), False) )
255        outflag[i] = userflag;// flag data
256    }
257    outtsys[0] = median(tsysCol.getColumn());
258    specColOut.put(outrowCount, outspec);
259    flagColOut.put(outrowCount, outflag);
260    tsysColOut.put(outrowCount, outtsys);
261    Double intsum = sum(intCol.getColumn());
262    intColOut.put(outrowCount, intsum);
263    ++outrowCount;
264    ++iter;
265  }
266  return out;
267}
268
269CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
270                                             bool droprows)
271{
272  if (insitu_) return in;
273  else {
274    // clone
275    Scantable* tabp = new Scantable(*in, Bool(droprows));
276    return CountedPtr<Scantable>(tabp);
277  }
278}
279
280CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
281                                              float val,
282                                              const std::string& mode,
283                                              bool tsys )
284{
285  CountedPtr< Scantable > out = getScantable(in, false);
286  Table& tab = out->table();
287  ArrayColumn<Float> specCol(tab,"SPECTRA");
288  ArrayColumn<Float> tsysCol(tab,"TSYS");
289  for (uInt i=0; i<tab.nrow(); ++i) {
290    Vector<Float> spec;
291    Vector<Float> ts;
292    specCol.get(i, spec);
293    tsysCol.get(i, ts);
294    if (mode == "MUL" || mode == "DIV") {
295      if (mode == "DIV") val = 1.0/val;
296      spec *= val;
297      specCol.put(i, spec);
298      if ( tsys ) {
299        ts *= val;
300        tsysCol.put(i, ts);
301      }
302    } else if ( mode == "ADD"  || mode == "SUB") {
303      if (mode == "SUB") val *= -1.0;
304      spec += val;
305      specCol.put(i, spec);
306      if ( tsys ) {
307        ts += val;
308        tsysCol.put(i, ts);
309      }
310    }
311  }
312  return out;
313}
314
315CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
316                                            const CountedPtr<Scantable>& right,
317                                            const std::string& mode)
318{
319  bool insitu = insitu_;
320  if ( ! left->conformant(*right) ) {
321    throw(AipsError("'left' and 'right' scantables are not conformant."));
322  }
323  setInsitu(false);
324  CountedPtr< Scantable > out = getScantable(left, false);
325  setInsitu(insitu);
326  Table& tout = out->table();
327  Block<String> coln(5);
328  coln[0] = "SCANNO";  coln[1] = "CYCLENO";  coln[2] = "BEAMNO";
329  coln[3] = "IFNO";  coln[4] = "POLNO";
330  Table tmpl = tout.sort(coln);
331  Table tmpr = right->table().sort(coln);
332  ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
333  ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
334  ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
335  ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");
336
337  for (uInt i=0; i<tout.nrow(); ++i) {
338    Vector<Float> lspecvec, rspecvec;
339    Vector<uChar> lflagvec, rflagvec;
340    lspecvec = lspecCol(i);    rspecvec = rspecCol(i);
341    lflagvec = lflagCol(i);    rflagvec = rflagCol(i);
342    MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
343    MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
344    if (mode == "ADD") {
345      mleft += mright;
346    } else if ( mode == "SUB") {
347      mleft -= mright;
348    } else if ( mode == "MUL") {
349      mleft *= mright;
350    } else if ( mode == "DIV") {
351      mleft /= mright;
352    } else {
353      throw(AipsError("Illegal binary operator"));
354    }
355    lspecCol.put(i, mleft.getArray());
356  }
357  return out;
358}
359
360
361
362MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
363                                        const Vector<uChar>& f)
364{
365  Vector<Bool> mask;
366  mask.resize(f.shape());
367  convertArray(mask, f);
368  return MaskedArray<Float>(s,!mask);
369}
370
371Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
372{
373  const Vector<Bool>& m = ma.getMask();
374  Vector<uChar> flags(m.shape());
375  convertArray(flags, !m);
376  return flags;
377}
378
379CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
380                                              const std::string & mode,
381                                              bool preserve )
382{
383  /// @todo make other modes available
384  /// modes should be "nearest", "pair"
385  // make this operation non insitu
386  const Table& tin = in->table();
387  Table ons = tin(tin.col("SRCTYPE") == Int(0));
388  Table offs = tin(tin.col("SRCTYPE") == Int(1));
389  if ( offs.nrow() == 0 )
390    throw(AipsError("No 'off' scans present."));
391  // put all "on" scans into output table
392
393  bool insitu = insitu_;
394  setInsitu(false);
395  CountedPtr< Scantable > out = getScantable(in, true);
396  setInsitu(insitu);
397  Table& tout = out->table();
398
399  TableCopy::copyRows(tout, ons);
400  TableRow row(tout);
401  ROScalarColumn<Double> offtimeCol(offs, "TIME");
402  ArrayColumn<Float> outspecCol(tout, "SPECTRA");
403  ROArrayColumn<Float> outtsysCol(tout, "TSYS");
404  ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
405  for (uInt i=0; i < tout.nrow(); ++i) {
406    const TableRecord& rec = row.get(i);
407    Double ontime = rec.asDouble("TIME");
408    ROScalarColumn<Double> offtimeCol(offs, "TIME");
409    Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
410    // Timestamp may vary within a cycle ???!!!
411    // increase this by 0.5 sec in case of rounding errors...
412    // There might be a better way to do this.
413    mindeltat += 0.5;
414    Table sel = offs( abs(offs.col("TIME")-ontime) <= (mindeltat+0.5)
415                       && offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
416                       && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
417                       && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
418
419    if ( sel.nrow() < 1 )  {
420      throw(AipsError("No closest in time found... This could be a rounding "
421                      "issue. Try quotient instead."));
422    }
423    TableRow offrow(sel);
424    const TableRecord& offrec = offrow.get(0);//should only be one row
425    RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
426    RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
427    RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
428    /// @fixme this assumes tsys is a scalar not vector
429    Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
430    Vector<Float> specon, tsyson;
431    outtsysCol.get(i, tsyson);
432    outspecCol.get(i, specon);
433    Vector<uChar> flagon;
434    outflagCol.get(i, flagon);
435    MaskedArray<Float> mon = maskedArray(specon, flagon);
436    MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
437    MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
438    if (preserve) {
439      quot -= tsysoffscalar;
440    } else {
441      quot -= tsyson[0];
442    }
443    outspecCol.put(i, quot.getArray());
444    outflagCol.put(i, flagsFromMA(quot));
445  }
446  // renumber scanno
447  TableIterator it(tout, "SCANNO");
448  uInt i = 0;
449  while ( !it.pastEnd() ) {
450    Table t = it.table();
451    TableVector<uInt> vec(t, "SCANNO");
452    vec = i;
453    ++i;
454    ++it;
455  }
456  return out;
457}
458
459
460CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
461                                          const CountedPtr< Scantable > & off,
462                                          bool preserve )
463{
464  bool insitu = insitu_;
465  if ( ! on->conformant(*off) ) {
466    throw(AipsError("'on' and 'off' scantables are not conformant."));
467  }
468  setInsitu(false);
469  CountedPtr< Scantable > out = getScantable(on, false);
470  setInsitu(insitu);
471  Table& tout = out->table();
472  const Table& toff = off->table();
473  TableIterator sit(tout, "SCANNO");
474  TableIterator s2it(toff, "SCANNO");
475  while ( !sit.pastEnd() ) {
476    Table ton = sit.table();
477    TableRow row(ton);
478    Table t = s2it.table();
479    ArrayColumn<Float> outspecCol(ton, "SPECTRA");
480    ROArrayColumn<Float> outtsysCol(ton, "TSYS");
481    ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
482    for (uInt i=0; i < ton.nrow(); ++i) {
483      const TableRecord& rec = row.get(i);
484      Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
485                          && t.col("IFNO") == Int(rec.asuInt("IFNO"))
486                          && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
487      if ( offsel.nrow() == 0 )
488        throw AipsError("STMath::quotient: no matching off");
489      TableRow offrow(offsel);
490      const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
491      RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
492      RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
493      RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
494      Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
495      Vector<Float> specon, tsyson;
496      outtsysCol.get(i, tsyson);
497      outspecCol.get(i, specon);
498      Vector<uChar> flagon;
499      outflagCol.get(i, flagon);
500      MaskedArray<Float> mon = maskedArray(specon, flagon);
501      MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
502      MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
503      if (preserve) {
504        quot -= tsysoffscalar;
505      } else {
506        quot -= tsyson[0];
507      }
508      outspecCol.put(i, quot.getArray());
509      outflagCol.put(i, flagsFromMA(quot));
510    }
511    ++sit;
512    ++s2it;
513    // take the first off for each on scan which doesn't have a
514    // matching off scan
515    // non <= noff:  matching pairs, non > noff matching pairs then first off
516    if ( s2it.pastEnd() ) s2it.reset();
517  }
518  return out;
519}
520
521
522CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
523{
524  // make copy or reference
525  CountedPtr< Scantable > out = getScantable(in, false);
526  Table& tout = out->table();
527  Block<String> cols(4);
528  cols[0] = String("SCANNO");
529  cols[1] = String("CYCLENO");
530  cols[2] = String("BEAMNO");
531  cols[3] = String("POLNO");
532  TableIterator iter(tout, cols);
533  while (!iter.pastEnd()) {
534    Table subt = iter.table();
535    // this should leave us with two rows for the two IFs....if not ignore
536    if (subt.nrow() != 2 ) {
537      continue;
538    }
539    ArrayColumn<Float> specCol(subt, "SPECTRA");
540    ArrayColumn<Float> tsysCol(subt, "TSYS");
541    ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
542    Vector<Float> onspec,offspec, ontsys, offtsys;
543    Vector<uChar> onflag, offflag;
544    tsysCol.get(0, ontsys);   tsysCol.get(1, offtsys);
545    specCol.get(0, onspec);   specCol.get(1, offspec);
546    flagCol.get(0, onflag);   flagCol.get(1, offflag);
547    MaskedArray<Float> on  = maskedArray(onspec, onflag);
548    MaskedArray<Float> off = maskedArray(offspec, offflag);
549    MaskedArray<Float> oncopy = on.copy();
550
551    on /= off; on -= 1.0f;
552    on *= ontsys[0];
553    off /= oncopy; off -= 1.0f;
554    off *= offtsys[0];
555    specCol.put(0, on.getArray());
556    const Vector<Bool>& m0 = on.getMask();
557    Vector<uChar> flags0(m0.shape());
558    convertArray(flags0, !m0);
559    flagCol.put(0, flags0);
560
561    specCol.put(1, off.getArray());
562    const Vector<Bool>& m1 = off.getMask();
563    Vector<uChar> flags1(m1.shape());
564    convertArray(flags1, !m1);
565    flagCol.put(1, flags1);
566    ++iter;
567  }
568
569  return out;
570}
571
572std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
573                                        const std::vector< bool > & mask,
574                                        const std::string& which )
575{
576
577  Vector<Bool> m(mask);
578  const Table& tab = in->table();
579  ROArrayColumn<Float> specCol(tab, "SPECTRA");
580  ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
581  std::vector<float> out;
582  for (uInt i=0; i < tab.nrow(); ++i ) {
583    Vector<Float> spec; specCol.get(i, spec);
584    Vector<uChar> flag; flagCol.get(i, flag);
585    MaskedArray<Float> ma  = maskedArray(spec, flag);
586    float outstat = 0.0;
587    if ( spec.nelements() == m.nelements() ) {
588      outstat = mathutil::statistics(which, ma(m));
589    } else {
590      outstat = mathutil::statistics(which, ma);
591    }
592    out.push_back(outstat);
593  }
594  return out;
595}
596
597CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
598                                     int width )
599{
600  if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
601  CountedPtr< Scantable > out = getScantable(in, false);
602  Table& tout = out->table();
603  out->frequencies().rescale(width, "BIN");
604  ArrayColumn<Float> specCol(tout, "SPECTRA");
605  ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
606  for (uInt i=0; i < tout.nrow(); ++i ) {
607    MaskedArray<Float> main  = maskedArray(specCol(i), flagCol(i));
608    MaskedArray<Float> maout;
609    LatticeUtilities::bin(maout, main, 0, Int(width));
610    /// @todo implement channel based tsys binning
611    specCol.put(i, maout.getArray());
612    flagCol.put(i, flagsFromMA(maout));
613    // take only the first binned spectrum's length for the deprecated
614    // global header item nChan
615    if (i==0) tout.rwKeywordSet().define(String("nChan"),
616                                       Int(maout.getArray().nelements()));
617  }
618  return out;
619}
620
621CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
622                                          const std::string& method,
623                                          float width )
624//
625// Should add the possibility of width being specified in km/s. This means
626// that for each freqID (SpectralCoordinate) we will need to convert to an
627// average channel width (say at the reference pixel).  Then we would need
628// to be careful to make sure each spectrum (of different freqID)
629// is the same length.
630//
631{
632  //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
633  Int interpMethod(stringToIMethod(method));
634
635  CountedPtr< Scantable > out = getScantable(in, false);
636  Table& tout = out->table();
637
638// Resample SpectralCoordinates (one per freqID)
639  out->frequencies().rescale(width, "RESAMPLE");
640  TableIterator iter(tout, "IFNO");
641  TableRow row(tout);
642  while ( !iter.pastEnd() ) {
643    Table tab = iter.table();
644    ArrayColumn<Float> specCol(tab, "SPECTRA");
645    //ArrayColumn<Float> tsysCol(tout, "TSYS");
646    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
647    Vector<Float> spec;
648    Vector<uChar> flag;
649    specCol.get(0,spec); // the number of channels should be constant per IF
650    uInt nChanIn = spec.nelements();
651    Vector<Float> xIn(nChanIn); indgen(xIn);
652    Int fac =  Int(nChanIn/width);
653    Vector<Float> xOut(fac+10); // 10 to be safe - resize later
654    uInt k = 0;
655    Float x = 0.0;
656    while (x < Float(nChanIn) ) {
657      xOut(k) = x;
658      k++;
659      x += width;
660    }
661    uInt nChanOut = k;
662    xOut.resize(nChanOut, True);
663    // process all rows for this IFNO
664    Vector<Float> specOut;
665    Vector<Bool> maskOut;
666    Vector<uChar> flagOut;
667    for (uInt i=0; i < tab.nrow(); ++i) {
668      specCol.get(i, spec);
669      flagCol.get(i, flag);
670      Vector<Bool> mask(flag.nelements());
671      convertArray(mask, flag);
672
673      IPosition shapeIn(spec.shape());
674      //sh.nchan = nChanOut;
675      InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
676                                                   xIn, spec, mask,
677                                                   interpMethod, True, True);
678      /// @todo do the same for channel based Tsys
679      flagOut.resize(maskOut.nelements());
680      convertArray(flagOut, maskOut);
681      specCol.put(i, specOut);
682      flagCol.put(i, flagOut);
683    }
684    ++iter;
685  }
686
687  return out;
688}
689
690STMath::imethod STMath::stringToIMethod(const std::string& in)
691{
692  static STMath::imap lookup;
693
694  // initialize the lookup table if necessary
695  if ( lookup.empty() ) {
696    lookup["nearest"]   = InterpolateArray1D<Double,Float>::nearestNeighbour;
697    lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
698    lookup["cubic"]  = InterpolateArray1D<Double,Float>::cubic;
699    lookup["spline"]  = InterpolateArray1D<Double,Float>::spline;
700  }
701
702  STMath::imap::const_iterator iter = lookup.find(in);
703
704  if ( lookup.end() == iter ) {
705    std::string message = in;
706    message += " is not a valid interpolation mode";
707    throw(AipsError(message));
708  }
709  return iter->second;
710}
711
712WeightType STMath::stringToWeight(const std::string& in)
713{
714  static std::map<std::string, WeightType> lookup;
715
716  // initialize the lookup table if necessary
717  if ( lookup.empty() ) {
718    lookup["NONE"]   = asap::NONE;
719    lookup["TINT"] = asap::TINT;
720    lookup["TINTSYS"]  = asap::TINTSYS;
721    lookup["TSYS"]  = asap::TSYS;
722    lookup["VAR"]  = asap::VAR;
723  }
724
725  std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
726
727  if ( lookup.end() == iter ) {
728    std::string message = in;
729    message += " is not a valid weighting mode";
730    throw(AipsError(message));
731  }
732  return iter->second;
733}
734
735CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
736                                               const vector< float > & coeff,
737                                               const std::string & filename,
738                                               const std::string& method)
739{
740  // Get elevation data from Scantable and convert to degrees
741  CountedPtr< Scantable > out = getScantable(in, false);
742  Table& tab = out->table();
743  ROScalarColumn<Float> elev(tab, "ELEVATION");
744  Vector<Float> x = elev.getColumn();
745  x *= Float(180 / C::pi);                        // Degrees
746
747  Vector<Float> coeffs(coeff);
748  const uInt nc = coeffs.nelements();
749  if ( filename.length() > 0 && nc > 0 ) {
750    throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
751  }
752
753  // Correct
754  if ( nc > 0 || filename.length() == 0 ) {
755    // Find instrument
756    Bool throwit = True;
757    Instrument inst =
758      STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
759                                throwit);
760
761    // Set polynomial
762    Polynomial<Float>* ppoly = 0;
763    Vector<Float> coeff;
764    String msg;
765    if ( nc > 0 ) {
766      ppoly = new Polynomial<Float>(nc);
767      coeff = coeffs;
768      msg = String("user");
769    } else {
770      STAttr sdAttr;
771      coeff = sdAttr.gainElevationPoly(inst);
772      ppoly = new Polynomial<Float>(3);
773      msg = String("built in");
774    }
775
776    if ( coeff.nelements() > 0 ) {
777      ppoly->setCoefficients(coeff);
778    } else {
779      delete ppoly;
780      throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
781    }
782    ostringstream oss;
783    oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
784    oss << "   " <<  coeff;
785    pushLog(String(oss));
786    const uInt nrow = tab.nrow();
787    Vector<Float> factor(nrow);
788    for ( uInt i=0; i < nrow; ++i ) {
789      factor[i] = 1.0 / (*ppoly)(x[i]);
790    }
791    delete ppoly;
792    scaleByVector(tab, factor, true);
793
794  } else {
795    // Read and correct
796    pushLog("Making correction from ascii Table");
797    scaleFromAsciiTable(tab, filename, method, x, true);
798  }
799  return out;
800}
801
802void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
803                                 const std::string& method,
804                                 const Vector<Float>& xout, bool dotsys)
805{
806
807// Read gain-elevation ascii file data into a Table.
808
809  String formatString;
810  Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
811  scaleFromTable(in, tbl, method, xout, dotsys);
812}
813
814void STMath::scaleFromTable(Table& in,
815                            const Table& table,
816                            const std::string& method,
817                            const Vector<Float>& xout, bool dotsys)
818{
819
820  ROScalarColumn<Float> geElCol(table, "ELEVATION");
821  ROScalarColumn<Float> geFacCol(table, "FACTOR");
822  Vector<Float> xin = geElCol.getColumn();
823  Vector<Float> yin = geFacCol.getColumn();
824  Vector<Bool> maskin(xin.nelements(),True);
825
826  // Interpolate (and extrapolate) with desired method
827
828  InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
829
830   Vector<Float> yout;
831   Vector<Bool> maskout;
832   InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
833                                                xin, yin, maskin, interp,
834                                                True, True);
835
836   scaleByVector(in, Float(1.0)/yout, dotsys);
837}
838
839void STMath::scaleByVector( Table& in,
840                            const Vector< Float >& factor,
841                            bool dotsys )
842{
843  uInt nrow = in.nrow();
844  if ( factor.nelements() != nrow ) {
845    throw(AipsError("factors.nelements() != table.nelements()"));
846  }
847  ArrayColumn<Float> specCol(in, "SPECTRA");
848  ArrayColumn<uChar> flagCol(in, "FLAGTRA");
849  ArrayColumn<Float> tsysCol(in, "TSYS");
850  for (uInt i=0; i < nrow; ++i) {
851    MaskedArray<Float> ma  = maskedArray(specCol(i), flagCol(i));
852    ma *= factor[i];
853    specCol.put(i, ma.getArray());
854    flagCol.put(i, flagsFromMA(ma));
855    if ( dotsys ) {
856      Vector<Float> tsys = tsysCol(i);
857      tsys *= factor[i];
858      tsysCol.put(i,tsys);
859    }
860  }
861}
862
863CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
864                                             float d, float etaap,
865                                             float jyperk )
866{
867  CountedPtr< Scantable > out = getScantable(in, false);
868  Table& tab = in->table();
869  Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
870  Unit K(String("K"));
871  Unit JY(String("Jy"));
872
873  bool tokelvin = true;
874  Double cfac = 1.0;
875
876  if ( fluxUnit == JY ) {
877    pushLog("Converting to K");
878    Quantum<Double> t(1.0,fluxUnit);
879    Quantum<Double> t2 = t.get(JY);
880    cfac = (t2 / t).getValue();               // value to Jy
881
882    tokelvin = true;
883    out->setFluxUnit("K");
884  } else if ( fluxUnit == K ) {
885    pushLog("Converting to Jy");
886    Quantum<Double> t(1.0,fluxUnit);
887    Quantum<Double> t2 = t.get(K);
888    cfac = (t2 / t).getValue();              // value to K
889
890    tokelvin = false;
891    out->setFluxUnit("Jy");
892  } else {
893    throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
894  }
895  // Make sure input values are converted to either Jy or K first...
896  Float factor = cfac;
897
898  // Select method
899  if (jyperk > 0.0) {
900    factor *= jyperk;
901    if ( tokelvin ) factor = 1.0 / jyperk;
902    ostringstream oss;
903    oss << "Jy/K = " << jyperk;
904    pushLog(String(oss));
905    Vector<Float> factors(tab.nrow(), factor);
906    scaleByVector(tab,factors, false);
907  } else if ( etaap > 0.0) {
908    if (d < 0) {
909      Instrument inst =
910        STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
911                                  True);
912      STAttr sda;
913      d = sda.diameter(inst);
914    }
915    jyperk = STAttr::findJyPerK(etaap, d);
916    ostringstream oss;
917    oss << "Jy/K = " << jyperk;
918    pushLog(String(oss));
919    factor *= jyperk;
920    if ( tokelvin ) {
921      factor = 1.0 / factor;
922    }
923    Vector<Float> factors(tab.nrow(), factor);
924    scaleByVector(tab, factors, False);
925  } else {
926
927    // OK now we must deal with automatic look up of values.
928    // We must also deal with the fact that the factors need
929    // to be computed per IF and may be different and may
930    // change per integration.
931
932    pushLog("Looking up conversion factors");
933    convertBrightnessUnits(out, tokelvin, cfac);
934  }
935
936  return out;
937}
938
939void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
940                                     bool tokelvin, float cfac )
941{
942  Table& table = in->table();
943  Instrument inst =
944    STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
945  TableIterator iter(table, "FREQ_ID");
946  STFrequencies stfreqs = in->frequencies();
947  STAttr sdAtt;
948  while (!iter.pastEnd()) {
949    Table tab = iter.table();
950    ArrayColumn<Float> specCol(tab, "SPECTRA");
951    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
952    ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
953    MEpoch::ROScalarColumn timeCol(tab, "TIME");
954
955    uInt freqid; freqidCol.get(0, freqid);
956    Vector<Float> tmpspec; specCol.get(0, tmpspec);
957    // STAttr.JyPerK has a Vector interface... change sometime.
958    Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
959    for ( uInt i=0; i<tab.nrow(); ++i) {
960      Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
961      Float factor = cfac * jyperk;
962      if ( tokelvin ) factor = Float(1.0) / factor;
963      MaskedArray<Float> ma  = maskedArray(specCol(i), flagCol(i));
964      ma *= factor;
965      specCol.put(i, ma.getArray());
966      flagCol.put(i, flagsFromMA(ma));
967    }
968  ++iter;
969  }
970}
971
972CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
973                                         float tau )
974{
975  CountedPtr< Scantable > out = getScantable(in, false);
976
977  Table tab = out->table();
978  ROScalarColumn<Float> elev(tab, "ELEVATION");
979  ArrayColumn<Float> specCol(tab, "SPECTRA");
980  ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
981  for ( uInt i=0; i<tab.nrow(); ++i) {
982    Float zdist = Float(C::pi_2) - elev(i);
983    Float factor = exp(tau/cos(zdist));
984    MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
985    ma *= factor;
986    specCol.put(i, ma.getArray());
987    flagCol.put(i, flagsFromMA(ma));
988  }
989  return out;
990}
991
992CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
993                                        const std::string& kernel, float width )
994{
995  CountedPtr< Scantable > out = getScantable(in, false);
996  Table& table = out->table();
997  VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
998  // same IFNO should have same no of channels
999  // this saves overhead
1000  TableIterator iter(table, "IFNO");
1001  while (!iter.pastEnd()) {
1002    Table tab = iter.table();
1003    ArrayColumn<Float> specCol(tab, "SPECTRA");
1004    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1005    Vector<Float> tmpspec; specCol.get(0, tmpspec);
1006    uInt nchan = tmpspec.nelements();
1007    Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
1008    Convolver<Float> conv(kvec, IPosition(1,nchan));
1009    Vector<Float> spec;
1010    Vector<uChar> flag;
1011    for ( uInt i=0; i<tab.nrow(); ++i) {
1012      specCol.get(i, spec);
1013      flagCol.get(i, flag);
1014      Vector<Bool> mask(flag.nelements());
1015      convertArray(mask, flag);
1016      Vector<Float> specout;
1017      if ( type == VectorKernel::HANNING ) {
1018        Vector<Bool> maskout;
1019        mathutil::hanning(specout, maskout, spec , !mask);
1020        convertArray(flag, !maskout);
1021        flagCol.put(i, flag);
1022        specCol.put(i, specout);
1023     } else {
1024        mathutil::replaceMaskByZero(specout, mask);
1025        conv.linearConv(specout, spec);
1026        specCol.put(i, specout);
1027      }
1028    }
1029    ++iter;
1030  }
1031  return out;
1032}
1033
1034CountedPtr< Scantable >
1035  STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
1036{
1037  if ( in.size() < 2 ) {
1038    throw(AipsError("Need at least two scantables to perform a merge."));
1039  }
1040  std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
1041  bool insitu = insitu_;
1042  setInsitu(false);
1043  CountedPtr< Scantable > out = getScantable(*it, false);
1044  setInsitu(insitu);
1045  Table& tout = out->table();
1046  ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
1047  ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
1048  // Renumber SCANNO to be 0-based
1049  Vector<uInt> scannos = scannocol.getColumn();
1050  uInt offset = min(scannos);
1051  scannos -= offset;
1052  scannocol.putColumn(scannos);
1053  uInt newscanno = max(scannos)+1;
1054  ++it;
1055  while ( it != in.end() ){
1056    if ( ! (*it)->conformant(*out) ) {
1057      // log message: "ignoring scantable i, as it isn't
1058      // conformant with the other(s)"
1059      cerr << "oh oh" << endl;
1060      ++it;
1061      continue;
1062    }
1063    out->appendToHistoryTable((*it)->history());
1064    const Table& tab = (*it)->table();
1065    TableIterator scanit(tab, "SCANNO");
1066    while (!scanit.pastEnd()) {
1067      TableIterator freqit(scanit.table(), "FREQ_ID");
1068      while ( !freqit.pastEnd() ) {
1069        Table thetab = freqit.table();
1070        uInt nrow = tout.nrow();
1071        //tout.addRow(thetab.nrow());
1072        TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
1073        ROTableRow row(thetab);
1074        for ( uInt i=0; i<thetab.nrow(); ++i) {
1075          uInt k = nrow+i;
1076          scannocol.put(k, newscanno);
1077          const TableRecord& rec = row.get(i);
1078          Double rv,rp,inc;
1079          (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
1080          uInt id;
1081          id = out->frequencies().addEntry(rp, rv, inc);
1082          freqidcol.put(k,id);
1083          String name,fname;Double rf;
1084          (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
1085          id = out->molecules().addEntry(rf, name, fname);
1086          molidcol.put(k, id);
1087          Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
1088          (*it)->focus().getEntry(fax, ftan, frot, fhand,
1089                                  fmount,fuser, fxy, fxyp,
1090                                  rec.asuInt("FOCUS_ID"));
1091          id = out->focus().addEntry(fax, ftan, frot, fhand,
1092                                     fmount,fuser, fxy, fxyp);
1093          focusidcol.put(k, id);
1094        }
1095        ++freqit;
1096      }
1097      ++newscanno;
1098      ++scanit;
1099    }
1100    ++it;
1101  }
1102  return out;
1103}
1104
1105CountedPtr< Scantable >
1106  STMath::invertPhase( const CountedPtr < Scantable >& in )
1107{
1108  return applyToPol(in, &STPol::invertPhase, Float(0.0));
1109}
1110
1111CountedPtr< Scantable >
1112  STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
1113{
1114   return applyToPol(in, &STPol::rotatePhase, Float(phase));
1115}
1116
1117CountedPtr< Scantable >
1118  STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
1119{
1120  return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
1121}
1122
1123CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
1124                                             STPol::polOperation fptr,
1125                                             Float phase )
1126{
1127  CountedPtr< Scantable > out = getScantable(in, false);
1128  Table& tout = out->table();
1129  Block<String> cols(4);
1130  cols[0] = String("SCANNO");
1131  cols[1] = String("BEAMNO");
1132  cols[2] = String("IFNO");
1133  cols[3] = String("CYCLENO");
1134  TableIterator iter(tout, cols);
1135  STPol* stpol = STPol::getPolClass(out->factories_, out->getPolType() );
1136  while (!iter.pastEnd()) {
1137    Table t = iter.table();
1138    ArrayColumn<Float> speccol(t, "SPECTRA");
1139    ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
1140    ScalarColumn<Float> parancol(t, "PARANGLE");
1141    Matrix<Float> pols = speccol.getColumn();
1142    try {
1143      stpol->setSpectra(pols);
1144      Float fang,fhand,parang;
1145      fang = in->focusTable_.getTotalFeedAngle(focidcol(0));
1146      fhand = in->focusTable_.getFeedHand(focidcol(0));
1147      parang = parancol(0);
1148      /// @todo re-enable this
1149      // disable total feed angle to support paralactifying Caswell style
1150      stpol->setPhaseCorrections(parang, -parang, fhand);
1151      (stpol->*fptr)(phase);
1152      speccol.putColumn(stpol->getSpectra());
1153      Matrix<Float> tmp = stpol->getSpectra();
1154    } catch (AipsError& e) {
1155      delete stpol;stpol=0;
1156      throw(e);
1157    }
1158    ++iter;
1159  }
1160  delete stpol;stpol=0;
1161  return out;
1162}
1163
1164CountedPtr< Scantable >
1165  STMath::swapPolarisations( const CountedPtr< Scantable > & in )
1166{
1167  CountedPtr< Scantable > out = getScantable(in, false);
1168  Table& tout = out->table();
1169  Table t0 = tout(tout.col("POLNO") == 0);
1170  Table t1 = tout(tout.col("POLNO") == 1);
1171  if ( t0.nrow() != t1.nrow() )
1172    throw(AipsError("Inconsistent number of polarisations"));
1173  ArrayColumn<Float> speccol0(t0, "SPECTRA");
1174  ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
1175  ArrayColumn<Float> speccol1(t1, "SPECTRA");
1176  ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
1177  Matrix<Float> s0 = speccol0.getColumn();
1178  Matrix<uChar> f0 = flagcol0.getColumn();
1179  speccol0.putColumn(speccol1.getColumn());
1180  flagcol0.putColumn(flagcol1.getColumn());
1181  speccol1.putColumn(s0);
1182  flagcol1.putColumn(f0);
1183  return out;
1184}
1185
1186CountedPtr< Scantable >
1187  STMath::averagePolarisations( const CountedPtr< Scantable > & in,
1188                                const std::vector<bool>& mask,
1189                                const std::string& weight )
1190{
1191  if (in->npol() < 2 )
1192    throw(AipsError("averagePolarisations can only be applied to two or more"
1193                    "polarisations"));
1194  bool insitu = insitu_;
1195  setInsitu(false);
1196  CountedPtr< Scantable > pols = getScantable(in, true);
1197  setInsitu(insitu);
1198  Table& tout = pols->table();
1199  std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
1200  Table tab = tableCommand(taql, in->table());
1201  if (tab.nrow() == 0 )
1202    throw(AipsError("Could not find  any rows with POLNO==0 and POLNO==1"));
1203  TableCopy::copyRows(tout, tab);
1204  TableVector<uInt> vec(tout, "POLNO");
1205  vec = 0;
1206  pols->table_.rwKeywordSet().define("nPol", Int(1));
1207  pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
1208  std::vector<CountedPtr<Scantable> > vpols;
1209  vpols.push_back(pols);
1210  CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
1211  return out;
1212}
1213
1214CountedPtr< Scantable >
1215  STMath::averageBeams( const CountedPtr< Scantable > & in,
1216                        const std::vector<bool>& mask,
1217                        const std::string& weight )
1218{
1219  bool insitu = insitu_;
1220  setInsitu(false);
1221  CountedPtr< Scantable > beams = getScantable(in, false);
1222  setInsitu(insitu);
1223  Table& tout = beams->table();
1224  // give all rows the same BEAMNO
1225  TableVector<uInt> vec(tout, "BEAMNO");
1226  vec = 0;
1227  beams->table_.rwKeywordSet().define("nBeam", Int(1));
1228  std::vector<CountedPtr<Scantable> > vbeams;
1229  vbeams.push_back(beams);
1230  CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
1231  return out;
1232}
1233
1234
1235CountedPtr< Scantable >
1236  asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
1237                                const std::string & refTime,
1238                                const std::string & method)
1239{
1240  // clone as this is not working insitu
1241  bool insitu = insitu_;
1242  setInsitu(false);
1243  CountedPtr< Scantable > out = getScantable(in, false);
1244  setInsitu(insitu);
1245  Table& tout = out->table();
1246  // Get reference Epoch to time of first row or given String
1247  Unit DAY(String("d"));
1248  MEpoch::Ref epochRef(in->getTimeReference());
1249  MEpoch refEpoch;
1250  if (refTime.length()>0) {
1251    Quantum<Double> qt;
1252    if (MVTime::read(qt,refTime)) {
1253      MVEpoch mv(qt);
1254      refEpoch = MEpoch(mv, epochRef);
1255   } else {
1256      throw(AipsError("Invalid format for Epoch string"));
1257   }
1258  } else {
1259    refEpoch = in->timeCol_(0);
1260  }
1261  MPosition refPos = in->getAntennaPosition();
1262
1263  InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
1264  // test if user frame is different to base frame
1265  if ( in->frequencies().getFrameString(true)
1266       == in->frequencies().getFrameString(false) ) {
1267    throw(AipsError("Can't convert as no output frame has been set"
1268                    " (use set_freqframe) or it is aligned already."));
1269  }
1270  MFrequency::Types system = in->frequencies().getFrame();
1271  MVTime mvt(refEpoch.getValue());
1272  String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
1273  ostringstream oss;
1274  oss << "Aligned at reference Epoch " << epochout
1275      << " in frame " << MFrequency::showType(system);
1276  pushLog(String(oss));
1277  // set up the iterator
1278  Block<String> cols(4);
1279  // select by constant direction
1280  cols[0] = String("SRCNAME");
1281  cols[1] = String("BEAMNO");
1282  // select by IF ( no of channels varies over this )
1283  cols[2] = String("IFNO");
1284  // select by restfrequency
1285  cols[3] = String("MOLECULE_ID");
1286  TableIterator iter(tout, cols);
1287  while ( !iter.pastEnd() ) {
1288    Table t = iter.table();
1289    MDirection::ROScalarColumn dirCol(t, "DIRECTION");
1290    TableIterator fiter(t, "FREQ_ID");
1291    // determine nchan from the first row. This should work as
1292    // we are iterating over BEAMNO and IFNO    // we should have constant direction
1293
1294    ROArrayColumn<Float> sCol(t, "SPECTRA");
1295    MDirection direction = dirCol(0);
1296    uInt nchan = sCol(0).nelements();
1297    while ( !fiter.pastEnd() ) {
1298      Table ftab = fiter.table();
1299      ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
1300      // get the SpectralCoordinate for the freqid, which we are iterating over
1301      SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
1302      FrequencyAligner<Float> fa( sC, nchan, refEpoch,
1303                                  direction, refPos, system );
1304      // realign the SpectralCoordinate and put into the output Scantable
1305      Vector<String> units(1);
1306      units = String("Hz");
1307      Bool linear=True;
1308      SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
1309      sc2.setWorldAxisUnits(units);
1310      uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
1311                                            sc2.referenceValue()[0],
1312                                            sc2.increment()[0]);
1313      TableVector<uInt> tvec(ftab, "FREQ_ID");
1314      tvec = id;
1315      // create the "global" abcissa for alignment with same FREQ_ID
1316      Vector<Double> abc(nchan);
1317      Double w;
1318      for (uInt i=0; i<nchan; i++) {
1319        sC.toWorld(w,Double(i));
1320        abc[i] = w;
1321      }
1322      // cache abcissa for same time stamps, so iterate over those
1323      TableIterator timeiter(ftab, "TIME");
1324      while ( !timeiter.pastEnd() ) {
1325        Table tab = timeiter.table();
1326        ArrayColumn<Float> specCol(tab, "SPECTRA");
1327        ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1328        MEpoch::ROScalarColumn timeCol(tab, "TIME");
1329        // use align abcissa cache after the first row
1330        bool first = true;
1331        // these rows should be just be POLNO
1332        for (int i=0; i<int(tab.nrow()); ++i) {
1333          // input values
1334          Vector<uChar> flag = flagCol(i);
1335          Vector<Bool> mask(flag.shape());
1336          Vector<Float> specOut, spec;
1337          spec  = specCol(i);
1338          Vector<Bool> maskOut;Vector<uChar> flagOut;
1339          convertArray(mask, flag);
1340          // alignment
1341          Bool ok = fa.align(specOut, maskOut, abc, spec,
1342                             mask, timeCol(i), !first,
1343                             interp, False);
1344          // back into scantable
1345          flagOut.resize(maskOut.nelements());
1346          convertArray(flagOut, maskOut);
1347          flagCol.put(i, flagOut);
1348          specCol.put(i, specOut);
1349          // start abcissa caching
1350          first = false;
1351        }
1352        // next timestamp
1353        ++timeiter;
1354      }
1355      // next FREQ_ID
1356      ++fiter;
1357    }
1358    // next aligner
1359    ++iter;
1360  }
1361  // set this afterwards to ensure we are doing insitu correctly.
1362  out->frequencies().setFrame(system, true);
1363  return out;
1364}
1365
1366CountedPtr<Scantable>
1367  asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
1368                                     const std::string & newtype )
1369{
1370  if (in->npol() != 2 && in->npol() != 4)
1371    throw(AipsError("Can only convert two or four polarisations."));
1372  if ( in->getPolType() == newtype )
1373    throw(AipsError("No need to convert."));
1374  if ( ! in->selector_.empty() )
1375    throw(AipsError("Can only convert whole scantable. Unset the selection."));
1376  bool insitu = insitu_;
1377  setInsitu(false);
1378  CountedPtr< Scantable > out = getScantable(in, true);
1379  setInsitu(insitu);
1380  Table& tout = out->table();
1381  tout.rwKeywordSet().define("POLTYPE", String(newtype));
1382
1383  Block<String> cols(4);
1384  cols[0] = "SCANNO";
1385  cols[1] = "CYCLENO";
1386  cols[2] = "BEAMNO";
1387  cols[3] = "IFNO";
1388  TableIterator it(in->originalTable_, cols);
1389  String basetype = in->getPolType();
1390  STPol* stpol = STPol::getPolClass(in->factories_, basetype);
1391  try {
1392    while ( !it.pastEnd() ) {
1393      Table tab = it.table();
1394      uInt row = tab.rowNumbers()[0];
1395      stpol->setSpectra(in->getPolMatrix(row));
1396      Float fang,fhand,parang;
1397      fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row));
1398      fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
1399      parang = in->paraCol_(row);
1400      /// @todo re-enable this
1401      // disable total feed angle to support paralactifying Caswell style
1402      stpol->setPhaseCorrections(parang, -parang, fhand);
1403      Int npolout = 0;
1404      for (uInt i=0; i<tab.nrow(); ++i) {
1405        Vector<Float> outvec = stpol->getSpectrum(i, newtype);
1406        if ( outvec.nelements() > 0 ) {
1407          tout.addRow();
1408          TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
1409          ArrayColumn<Float> sCol(tout,"SPECTRA");
1410          ScalarColumn<uInt> pCol(tout,"POLNO");
1411          sCol.put(tout.nrow()-1 ,outvec);
1412          pCol.put(tout.nrow()-1 ,uInt(npolout));
1413          npolout++;
1414       }
1415      }
1416      tout.rwKeywordSet().define("nPol", npolout);
1417      ++it;
1418    }
1419  } catch (AipsError& e) {
1420    delete stpol;
1421    throw(e);
1422  }
1423  delete stpol;
1424  return out;
1425}
1426
1427CountedPtr< Scantable >
1428  asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
1429                           const std::string & scantype )
1430{
1431  bool insitu = insitu_;
1432  setInsitu(false);
1433  CountedPtr< Scantable > out = getScantable(in, true);
1434  setInsitu(insitu);
1435  Table& tout = out->table();
1436  std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
1437  if (scantype == "on") {
1438    taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
1439  }
1440  Table tab = tableCommand(taql, in->table());
1441  TableCopy::copyRows(tout, tab);
1442  if (scantype == "on") {
1443    // re-index SCANNO to 0
1444    TableVector<uInt> vec(tout, "SCANNO");
1445    vec = 0;
1446  }
1447  return out;
1448}
1449
1450CountedPtr< Scantable >
1451  asap::STMath::lagFlag( const CountedPtr< Scantable > & in,
1452                          double frequency, double width )
1453{
1454  CountedPtr< Scantable > out = getScantable(in, false);
1455  Table& tout = out->table();
1456  TableIterator iter(tout, "FREQ_ID");
1457  FFTServer<Float,Complex> ffts;
1458  while ( !iter.pastEnd() ) {
1459    Table tab = iter.table();
1460    Double rp,rv,inc;
1461    ROTableRow row(tab);
1462    const TableRecord& rec = row.get(0);
1463    uInt freqid = rec.asuInt("FREQ_ID");
1464    out->frequencies().getEntry(rp, rv, inc, freqid);
1465    ArrayColumn<Float> specCol(tab, "SPECTRA");
1466    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1467    for (int i=0; i<int(tab.nrow()); ++i) {
1468      Vector<Float> spec = specCol(i);
1469      Vector<uChar> flag = flagCol(i);
1470      Int lag0 = Int(spec.nelements()*abs(inc)/(frequency+width)+0.5);
1471      Int lag1 = Int(spec.nelements()*abs(inc)/(frequency-width)+0.5);
1472      for (int k=0; k < flag.nelements(); ++k ) {
1473        if (flag[k] > 0) {
1474          spec[k] = 0.0;
1475        }
1476      }
1477      Vector<Complex> lags;
1478      ffts.fft0(lags, spec);
1479      Int start =  max(0, lag0);
1480      Int end =  min(Int(lags.nelements()-1), lag1);
1481      if (start == end) {
1482        lags[start] = Complex(0.0);
1483      } else {
1484        for (int j=start; j <=end ;++j) {
1485          lags[j] = Complex(0.0);
1486        }
1487      }
1488      ffts.fft0(spec, lags);
1489      specCol.put(i, spec);
1490    }
1491    ++iter;
1492  }
1493  return out;
1494}
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