source: tags/asap2beta/src/STMath.cpp

Last change on this file was 1010, checked in by mar637, 18 years ago

Fix to Ticket #17 - average_pol not working.
  • Property svn:eol-style set to native
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File size: 38.7 KB
Line 
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 <tables/Tables/TableIter.h>
18#include <tables/Tables/TableCopy.h>
19#include <casa/Arrays/MaskArrLogi.h>
20#include <casa/Arrays/MaskArrMath.h>
21#include <casa/Arrays/ArrayLogical.h>
22#include <casa/Arrays/ArrayMath.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/ReadAsciiTable.h>
30
31#include <lattices/Lattices/LatticeUtilities.h>
32
33#include <coordinates/Coordinates/SpectralCoordinate.h>
34#include <coordinates/Coordinates/CoordinateSystem.h>
35#include <coordinates/Coordinates/CoordinateUtil.h>
36#include <coordinates/Coordinates/FrequencyAligner.h>
37
38#include <scimath/Mathematics/VectorKernel.h>
39#include <scimath/Mathematics/Convolver.h>
40#include <scimath/Functionals/Polynomial.h>
41
42#include "MathUtils.h"
43#include "RowAccumulator.h"
44#include "STAttr.h"
45#include "STMath.h"
46
47using namespace casa;
48
49using namespace asap;
50
51STMath::STMath(bool insitu) :
52  insitu_(insitu)
53{
54}
55
56
57STMath::~STMath()
58{
59}
60
61CountedPtr<Scantable>
62STMath::average( const std::vector<CountedPtr<Scantable> >& in,
63                 const std::vector<bool>& mask,
64                 const std::string& weight,
65                 const std::string& avmode)
66{
67  if ( avmode == "SCAN" && in.size() != 1 )
68    throw(AipsError("Can't perform 'SCAN' averaging on multiple tables"));
69  WeightType wtype = stringToWeight(weight);
70
71  // output
72  // clone as this is non insitu
73  bool insitu = insitu_;
74  setInsitu(false);
75  CountedPtr< Scantable > out = getScantable(in[0], true);
76  setInsitu(insitu);
77  std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
78  ++stit;
79  while ( stit != in.end() ) {
80    out->appendToHistoryTable((*stit)->history());
81    ++stit;
82  }
83
84  Table& tout = out->table();
85
86  /// @todo check if all scantables are conformant
87
88  ArrayColumn<Float> specColOut(tout,"SPECTRA");
89  ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
90  ArrayColumn<Float> tsysColOut(tout,"TSYS");
91  ScalarColumn<Double> mjdColOut(tout,"TIME");
92  ScalarColumn<Double> intColOut(tout,"INTERVAL");
93  ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
94
95  // set up the output table rows. These are based on the structure of the
96  // FIRST scantable in the vector
97  const Table& baset = in[0]->table();
98
99  Block<String> cols(3);
100  cols[0] = String("BEAMNO");
101  cols[1] = String("IFNO");
102  cols[2] = String("POLNO");
103  if ( avmode == "SOURCE" ) {
104    cols.resize(4);
105    cols[3] = String("SRCNAME");
106  }
107  if ( avmode == "SCAN"  && in.size() == 1) {
108    cols.resize(4);
109    cols[3] = String("SCANNO");
110  }
111  uInt outrowCount = 0;
112  TableIterator iter(baset, cols);
113  while (!iter.pastEnd()) {
114    Table subt = iter.table();
115    // copy the first row of this selection into the new table
116    tout.addRow();
117    TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
118    ++outrowCount;
119    ++iter;
120  }
121  RowAccumulator acc(wtype);
122  Vector<Bool> cmask(mask);
123  acc.setUserMask(cmask);
124  ROTableRow row(tout);
125  ROArrayColumn<Float> specCol, tsysCol;
126  ROArrayColumn<uChar> flagCol;
127  ROScalarColumn<Double> mjdCol, intCol;
128  ROScalarColumn<Int> scanIDCol;
129
130  for (uInt i=0; i < tout.nrow(); ++i) {
131    for ( int j=0; j < int(in.size()); ++j ) {
132      const Table& tin = in[j]->table();
133      const TableRecord& rec = row.get(i);
134      ROScalarColumn<Double> tmp(tin, "TIME");
135      Double td;tmp.get(0,td);
136      Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
137                       && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
138                       && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
139      Table subt;
140      if ( avmode == "SOURCE") {
141        subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
142      } else if (avmode == "SCAN") {
143        subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
144      } else {
145        subt = basesubt;
146      }
147      specCol.attach(subt,"SPECTRA");
148      flagCol.attach(subt,"FLAGTRA");
149      tsysCol.attach(subt,"TSYS");
150      intCol.attach(subt,"INTERVAL");
151      mjdCol.attach(subt,"TIME");
152      Vector<Float> spec,tsys;
153      Vector<uChar> flag;
154      Double inter,time;
155      cout << rec.asuInt("POLNO") << endl;
156      for (uInt k = 0; k < subt.nrow(); ++k ) {
157        flagCol.get(k, flag);
158        Vector<Bool> bflag(flag.shape());
159        convertArray(bflag, flag);
160        if ( allEQ(bflag, True) ) {
161          continue;//don't accumulate
162        }
163        specCol.get(k, spec);
164        tsysCol.get(k, tsys);
165        intCol.get(k, inter);
166        mjdCol.get(k, time);
167        // spectrum has to be added last to enable weighting by the other values
168        acc.add(spec, !bflag, tsys, inter, time);
169      }
170    }
171    //write out
172    specColOut.put(i, acc.getSpectrum());
173    const Vector<Bool>& msk = acc.getMask();
174    Vector<uChar> flg(msk.shape());
175    convertArray(flg, !msk);
176    flagColOut.put(i, flg);
177    tsysColOut.put(i, acc.getTsys());
178    intColOut.put(i, acc.getInterval());
179    mjdColOut.put(i, acc.getTime());
180    // we should only have one cycle now -> reset it to be 0
181    // frequency switched data has different CYCLENO for different IFNO
182    // which requires resetting this value
183    cycColOut.put(i, uInt(0));
184    acc.reset();
185  }
186  return out;
187}
188
189CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
190                                             bool droprows)
191{
192  if (insitu_) return in;
193  else {
194    // clone
195    Scantable* tabp = new Scantable(*in, Bool(droprows));
196    return CountedPtr<Scantable>(tabp);
197  }
198}
199
200CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
201                                              float val,
202                                              const std::string& mode,
203                                              bool tsys )
204{
205  // modes are "ADD" and "MUL"
206  CountedPtr< Scantable > out = getScantable(in, false);
207  Table& tab = out->table();
208  ArrayColumn<Float> specCol(tab,"SPECTRA");
209  ArrayColumn<Float> tsysCol(tab,"TSYS");
210  for (uInt i=0; i<tab.nrow(); ++i) {
211    Vector<Float> spec;
212    Vector<Float> ts;
213    specCol.get(i, spec);
214    tsysCol.get(i, ts);
215    if (mode == "MUL") {
216      spec *= val;
217      specCol.put(i, spec);
218      if ( tsys ) {
219        ts *= val;
220        tsysCol.put(i, ts);
221      }
222    } else if ( mode == "ADD" ) {
223      spec += val;
224      specCol.put(i, spec);
225      if ( tsys ) {
226        ts += val;
227        tsysCol.put(i, ts);
228      }
229    }
230  }
231  return out;
232}
233
234MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
235                                        const Vector<uChar>& f)
236{
237  Vector<Bool> mask;
238  mask.resize(f.shape());
239  convertArray(mask, f);
240  return MaskedArray<Float>(s,!mask);
241}
242
243Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
244{
245  const Vector<Bool>& m = ma.getMask();
246  Vector<uChar> flags(m.shape());
247  convertArray(flags, !m);
248  return flags;
249}
250
251CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable >& in,
252                                          const std::string & mode,
253                                          bool preserve )
254{
255  /// @todo make other modes available
256  /// modes should be "nearest", "pair"
257  // make this operation non insitu
258  const Table& tin = in->table();
259  Table ons = tin(tin.col("SRCTYPE") == Int(0));
260  Table offs = tin(tin.col("SRCTYPE") == Int(1));
261  if ( offs.nrow() == 0 )
262    throw(AipsError("No 'off' scans present."));
263  // put all "on" scans into output table
264
265  bool insitu = insitu_;
266  setInsitu(false);
267  CountedPtr< Scantable > out = getScantable(in, true);
268  setInsitu(insitu);
269  Table& tout = out->table();
270
271  TableCopy::copyRows(tout, ons);
272  TableRow row(tout);
273  ROScalarColumn<Double> offtimeCol(offs, "TIME");
274
275  ArrayColumn<Float> outspecCol(tout, "SPECTRA");
276  ROArrayColumn<Float> outtsysCol(tout, "TSYS");
277  ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
278  for (uInt i=0; i < tout.nrow(); ++i) {
279    const TableRecord& rec = row.get(i);
280    Double ontime = rec.asDouble("TIME");
281    ROScalarColumn<Double> offtimeCol(offs, "TIME");
282    Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
283    Table sel = offs( abs(offs.col("TIME")-ontime) <= mindeltat
284                       && offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
285                       && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
286                       && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
287
288    TableRow offrow(sel);
289    const TableRecord& offrec = offrow.get(0);//should only be one row
290    RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
291    RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
292    RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
293    /// @fixme this assumes tsys is a scalar not vector
294    Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
295    Vector<Float> specon, tsyson;
296    outtsysCol.get(i, tsyson);
297    outspecCol.get(i, specon);
298    Vector<uChar> flagon;
299    outflagCol.get(i, flagon);
300    MaskedArray<Float> mon = maskedArray(specon, flagon);
301    MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
302    MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
303    if (preserve) {
304      quot -= tsysoffscalar;
305    } else {
306      quot -= tsyson[0];
307    }
308    outspecCol.put(i, quot.getArray());
309    outflagCol.put(i, flagsFromMA(quot));
310  }
311  // renumber scanno
312  TableIterator it(tout, "SCANNO");
313  uInt i = 0;
314  while ( !it.pastEnd() ) {
315    Table t = it.table();
316    TableVector<uInt> vec(t, "SCANNO");
317    vec = i;
318    ++i;
319    ++it;
320  }
321  return out;
322}
323
324CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
325{
326  // make copy or reference
327  CountedPtr< Scantable > out = getScantable(in, false);
328  Table& tout = out->table();
329  Block<String> cols(4);
330  cols[0] = String("SCANNO");
331  cols[1] = String("CYCLENO");
332  cols[2] = String("BEAMNO");
333  cols[3] = String("POLNO");
334  TableIterator iter(tout, cols);
335  while (!iter.pastEnd()) {
336    Table subt = iter.table();
337    // this should leave us with two rows for the two IFs....if not ignore
338    if (subt.nrow() != 2 ) {
339      continue;
340    }
341    ArrayColumn<Float> specCol(subt, "SPECTRA");
342    ArrayColumn<Float> tsysCol(subt, "TSYS");
343    ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
344    Vector<Float> onspec,offspec, ontsys, offtsys;
345    Vector<uChar> onflag, offflag;
346    tsysCol.get(0, ontsys);   tsysCol.get(1, offtsys);
347    specCol.get(0, onspec);   specCol.get(1, offspec);
348    flagCol.get(0, onflag);   flagCol.get(1, offflag);
349    MaskedArray<Float> on  = maskedArray(onspec, onflag);
350    MaskedArray<Float> off = maskedArray(offspec, offflag);
351    MaskedArray<Float> oncopy = on.copy();
352
353    on /= off; on -= 1.0f;
354    on *= ontsys[0];
355    off /= oncopy; off -= 1.0f;
356    off *= offtsys[0];
357    specCol.put(0, on.getArray());
358    const Vector<Bool>& m0 = on.getMask();
359    Vector<uChar> flags0(m0.shape());
360    convertArray(flags0, !m0);
361    flagCol.put(0, flags0);
362
363    specCol.put(1, off.getArray());
364    const Vector<Bool>& m1 = off.getMask();
365    Vector<uChar> flags1(m1.shape());
366    convertArray(flags1, !m1);
367    flagCol.put(1, flags1);
368    ++iter;
369  }
370
371  return out;
372}
373
374std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
375                                        const std::vector< bool > & mask,
376                                        const std::string& which )
377{
378
379  Vector<Bool> m(mask);
380  const Table& tab = in->table();
381  ROArrayColumn<Float> specCol(tab, "SPECTRA");
382  ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
383  std::vector<float> out;
384  for (uInt i=0; i < tab.nrow(); ++i ) {
385    Vector<Float> spec; specCol.get(i, spec);
386    Vector<uChar> flag; flagCol.get(i, flag);
387    MaskedArray<Float> ma  = maskedArray(spec, flag);
388    float outstat = 0.0;
389    if ( spec.nelements() == m.nelements() ) {
390      outstat = mathutil::statistics(which, ma(m));
391    } else {
392      outstat = mathutil::statistics(which, ma);
393    }
394    out.push_back(outstat);
395  }
396  return out;
397}
398
399CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
400                                     int width )
401{
402  if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
403  CountedPtr< Scantable > out = getScantable(in, false);
404  Table& tout = out->table();
405  out->frequencies().rescale(width, "BIN");
406  ArrayColumn<Float> specCol(tout, "SPECTRA");
407  ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
408  for (uInt i=0; i < tout.nrow(); ++i ) {
409    MaskedArray<Float> main  = maskedArray(specCol(i), flagCol(i));
410    MaskedArray<Float> maout;
411    LatticeUtilities::bin(maout, main, 0, Int(width));
412    /// @todo implement channel based tsys binning
413    specCol.put(i, maout.getArray());
414    flagCol.put(i, flagsFromMA(maout));
415    // take only the first binned spectrum's length for the deprecated
416    // global header item nChan
417    if (i==0) tout.rwKeywordSet().define(String("nChan"),
418                                       Int(maout.getArray().nelements()));
419  }
420  return out;
421}
422
423CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
424                                          const std::string& method,
425                                          float width )
426//
427// Should add the possibility of width being specified in km/s. This means
428// that for each freqID (SpectralCoordinate) we will need to convert to an
429// average channel width (say at the reference pixel).  Then we would need
430// to be careful to make sure each spectrum (of different freqID)
431// is the same length.
432//
433{
434  //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
435  Int interpMethod(stringToIMethod(method));
436
437  CountedPtr< Scantable > out = getScantable(in, false);
438  Table& tout = out->table();
439
440// Resample SpectralCoordinates (one per freqID)
441  out->frequencies().rescale(width, "RESAMPLE");
442  TableIterator iter(tout, "IFNO");
443  TableRow row(tout);
444  while ( !iter.pastEnd() ) {
445    Table tab = iter.table();
446    ArrayColumn<Float> specCol(tab, "SPECTRA");
447    //ArrayColumn<Float> tsysCol(tout, "TSYS");
448    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
449    Vector<Float> spec;
450    Vector<uChar> flag;
451    specCol.get(0,spec); // the number of channels should be constant per IF
452    uInt nChanIn = spec.nelements();
453    Vector<Float> xIn(nChanIn); indgen(xIn);
454    Int fac =  Int(nChanIn/width);
455    Vector<Float> xOut(fac+10); // 10 to be safe - resize later
456    uInt k = 0;
457    Float x = 0.0;
458    while (x < Float(nChanIn) ) {
459      xOut(k) = x;
460      k++;
461      x += width;
462    }
463    uInt nChanOut = k;
464    xOut.resize(nChanOut, True);
465    // process all rows for this IFNO
466    Vector<Float> specOut;
467    Vector<Bool> maskOut;
468    Vector<uChar> flagOut;
469    for (uInt i=0; i < tab.nrow(); ++i) {
470      specCol.get(i, spec);
471      flagCol.get(i, flag);
472      Vector<Bool> mask(flag.nelements());
473      convertArray(mask, flag);
474
475      IPosition shapeIn(spec.shape());
476      //sh.nchan = nChanOut;
477      InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
478                                                   xIn, spec, mask,
479                                                   interpMethod, True, True);
480      /// @todo do the same for channel based Tsys
481      flagOut.resize(maskOut.nelements());
482      convertArray(flagOut, maskOut);
483      specCol.put(i, specOut);
484      flagCol.put(i, flagOut);
485    }
486    ++iter;
487  }
488
489  return out;
490}
491
492STMath::imethod STMath::stringToIMethod(const std::string& in)
493{
494  static STMath::imap lookup;
495
496  // initialize the lookup table if necessary
497  if ( lookup.empty() ) {
498    lookup["nearest"]   = InterpolateArray1D<Double,Float>::nearestNeighbour;
499    lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
500    lookup["cubic"]  = InterpolateArray1D<Double,Float>::cubic;
501    lookup["spline"]  = InterpolateArray1D<Double,Float>::spline;
502  }
503
504  STMath::imap::const_iterator iter = lookup.find(in);
505
506  if ( lookup.end() == iter ) {
507    std::string message = in;
508    message += " is not a valid interpolation mode";
509    throw(AipsError(message));
510  }
511  return iter->second;
512}
513
514WeightType STMath::stringToWeight(const std::string& in)
515{
516  static std::map<std::string, WeightType> lookup;
517
518  // initialize the lookup table if necessary
519  if ( lookup.empty() ) {
520    lookup["NONE"]   = asap::NONE;
521    lookup["TINT"] = asap::TINT;
522    lookup["TINTSYS"]  = asap::TINTSYS;
523    lookup["TSYS"]  = asap::TSYS;
524    lookup["VAR"]  = asap::VAR;
525  }
526
527  std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
528
529  if ( lookup.end() == iter ) {
530    std::string message = in;
531    message += " is not a valid weighting mode";
532    throw(AipsError(message));
533  }
534  return iter->second;
535}
536
537CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
538                                               const vector< float > & coeff,
539                                               const std::string & filename,
540                                               const std::string& method)
541{
542  // Get elevation data from Scantable and convert to degrees
543  CountedPtr< Scantable > out = getScantable(in, false);
544  Table& tab = out->table();
545  ROScalarColumn<Float> elev(tab, "ELEVATION");
546  Vector<Float> x = elev.getColumn();
547  x *= Float(180 / C::pi);                        // Degrees
548
549  Vector<Float> coeffs(coeff);
550  const uInt nc = coeffs.nelements();
551  if ( filename.length() > 0 && nc > 0 ) {
552    throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
553  }
554
555  // Correct
556  if ( nc > 0 || filename.length() == 0 ) {
557    // Find instrument
558    Bool throwit = True;
559    Instrument inst =
560      STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
561                                throwit);
562
563    // Set polynomial
564    Polynomial<Float>* ppoly = 0;
565    Vector<Float> coeff;
566    String msg;
567    if ( nc > 0 ) {
568      ppoly = new Polynomial<Float>(nc);
569      coeff = coeffs;
570      msg = String("user");
571    } else {
572      STAttr sdAttr;
573      coeff = sdAttr.gainElevationPoly(inst);
574      ppoly = new Polynomial<Float>(3);
575      msg = String("built in");
576    }
577
578    if ( coeff.nelements() > 0 ) {
579      ppoly->setCoefficients(coeff);
580    } else {
581      delete ppoly;
582      throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
583    }
584    ostringstream oss;
585    oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
586    oss << "   " <<  coeff;
587    pushLog(String(oss));
588    const uInt nrow = tab.nrow();
589    Vector<Float> factor(nrow);
590    for ( uInt i=0; i < nrow; ++i ) {
591      factor[i] = 1.0 / (*ppoly)(x[i]);
592    }
593    delete ppoly;
594    scaleByVector(tab, factor, true);
595
596  } else {
597    // Read and correct
598    pushLog("Making correction from ascii Table");
599    scaleFromAsciiTable(tab, filename, method, x, true);
600  }
601  return out;
602}
603
604void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
605                                 const std::string& method,
606                                 const Vector<Float>& xout, bool dotsys)
607{
608
609// Read gain-elevation ascii file data into a Table.
610
611  String formatString;
612  Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
613  scaleFromTable(in, tbl, method, xout, dotsys);
614}
615
616void STMath::scaleFromTable(Table& in,
617                            const Table& table,
618                            const std::string& method,
619                            const Vector<Float>& xout, bool dotsys)
620{
621
622  ROScalarColumn<Float> geElCol(table, "ELEVATION");
623  ROScalarColumn<Float> geFacCol(table, "FACTOR");
624  Vector<Float> xin = geElCol.getColumn();
625  Vector<Float> yin = geFacCol.getColumn();
626  Vector<Bool> maskin(xin.nelements(),True);
627
628  // Interpolate (and extrapolate) with desired method
629
630  InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
631
632   Vector<Float> yout;
633   Vector<Bool> maskout;
634   InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
635                                                xin, yin, maskin, interp,
636                                                True, True);
637
638   scaleByVector(in, Float(1.0)/yout, dotsys);
639}
640
641void STMath::scaleByVector( Table& in,
642                            const Vector< Float >& factor,
643                            bool dotsys )
644{
645  uInt nrow = in.nrow();
646  if ( factor.nelements() != nrow ) {
647    throw(AipsError("factors.nelements() != table.nelements()"));
648  }
649  ArrayColumn<Float> specCol(in, "SPECTRA");
650  ArrayColumn<uChar> flagCol(in, "FLAGTRA");
651  ArrayColumn<Float> tsysCol(in, "TSYS");
652  for (uInt i=0; i < nrow; ++i) {
653    MaskedArray<Float> ma  = maskedArray(specCol(i), flagCol(i));
654    ma *= factor[i];
655    specCol.put(i, ma.getArray());
656    flagCol.put(i, flagsFromMA(ma));
657    if ( dotsys ) {
658      Vector<Float> tsys = tsysCol(i);
659      tsys *= factor[i];
660      tsysCol.put(i,tsys);
661    }
662  }
663}
664
665CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
666                                             float d, float etaap,
667                                             float jyperk )
668{
669  CountedPtr< Scantable > out = getScantable(in, false);
670  Table& tab = in->table();
671  Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
672  Unit K(String("K"));
673  Unit JY(String("Jy"));
674
675  bool tokelvin = true;
676  Double cfac = 1.0;
677
678  if ( fluxUnit == JY ) {
679    pushLog("Converting to K");
680    Quantum<Double> t(1.0,fluxUnit);
681    Quantum<Double> t2 = t.get(JY);
682    cfac = (t2 / t).getValue();               // value to Jy
683
684    tokelvin = true;
685    out->setFluxUnit("K");
686  } else if ( fluxUnit == K ) {
687    pushLog("Converting to Jy");
688    Quantum<Double> t(1.0,fluxUnit);
689    Quantum<Double> t2 = t.get(K);
690    cfac = (t2 / t).getValue();              // value to K
691
692    tokelvin = false;
693    out->setFluxUnit("Jy");
694  } else {
695    throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
696  }
697  // Make sure input values are converted to either Jy or K first...
698  Float factor = cfac;
699
700  // Select method
701  if (jyperk > 0.0) {
702    factor *= jyperk;
703    if ( tokelvin ) factor = 1.0 / jyperk;
704    ostringstream oss;
705    oss << "Jy/K = " << jyperk;
706    pushLog(String(oss));
707    Vector<Float> factors(tab.nrow(), factor);
708    scaleByVector(tab,factors, false);
709  } else if ( etaap > 0.0) {
710    Instrument inst =
711      STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True);
712    STAttr sda;
713    if (d < 0) d = sda.diameter(inst);
714    jyperk = STAttr::findJyPerK(etaap, d);
715    ostringstream oss;
716    oss << "Jy/K = " << jyperk;
717    pushLog(String(oss));
718    factor *= jyperk;
719    if ( tokelvin ) {
720      factor = 1.0 / factor;
721    }
722    Vector<Float> factors(tab.nrow(), factor);
723    scaleByVector(tab, factors, False);
724  } else {
725
726    // OK now we must deal with automatic look up of values.
727    // We must also deal with the fact that the factors need
728    // to be computed per IF and may be different and may
729    // change per integration.
730
731    pushLog("Looking up conversion factors");
732    convertBrightnessUnits(out, tokelvin, cfac);
733  }
734
735  return out;
736}
737
738void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
739                                     bool tokelvin, float cfac )
740{
741  Table& table = in->table();
742  Instrument inst =
743    STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
744  TableIterator iter(table, "FREQ_ID");
745  STFrequencies stfreqs = in->frequencies();
746  STAttr sdAtt;
747  while (!iter.pastEnd()) {
748    Table tab = iter.table();
749    ArrayColumn<Float> specCol(tab, "SPECTRA");
750    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
751    ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
752    MEpoch::ROScalarColumn timeCol(tab, "TIME");
753
754    uInt freqid; freqidCol.get(0, freqid);
755    Vector<Float> tmpspec; specCol.get(0, tmpspec);
756    // STAttr.JyPerK has a Vector interface... change sometime.
757    Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
758    for ( uInt i=0; i<tab.nrow(); ++i) {
759      Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
760      Float factor = cfac * jyperk;
761      if ( tokelvin ) factor = Float(1.0) / factor;
762      MaskedArray<Float> ma  = maskedArray(specCol(i), flagCol(i));
763      ma *= factor;
764      specCol.put(i, ma.getArray());
765      flagCol.put(i, flagsFromMA(ma));
766    }
767  ++iter;
768  }
769}
770
771CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
772                                         float tau )
773{
774  CountedPtr< Scantable > out = getScantable(in, false);
775
776  Table tab = out->table();
777  ROScalarColumn<Float> elev(tab, "ELEVATION");
778  ArrayColumn<Float> specCol(tab, "SPECTRA");
779  ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
780  for ( uInt i=0; i<tab.nrow(); ++i) {
781    Float zdist = Float(C::pi_2) - elev(i);
782    Float factor = exp(tau)/cos(zdist);
783    MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
784    ma *= factor;
785    specCol.put(i, ma.getArray());
786    flagCol.put(i, flagsFromMA(ma));
787  }
788  return out;
789}
790
791CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
792                                        const std::string& kernel, float width )
793{
794  CountedPtr< Scantable > out = getScantable(in, false);
795  Table& table = in->table();
796  VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
797  // same IFNO should have same no of channels
798  // this saves overhead
799  TableIterator iter(table, "IFNO");
800  while (!iter.pastEnd()) {
801    Table tab = iter.table();
802    ArrayColumn<Float> specCol(tab, "SPECTRA");
803    ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
804    Vector<Float> tmpspec; specCol.get(0, tmpspec);
805    uInt nchan = tmpspec.nelements();
806    Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
807    Convolver<Float> conv(kvec, IPosition(1,nchan));
808    Vector<Float> spec;
809    Vector<uChar> flag;
810    for ( uInt i=0; i<tab.nrow(); ++i) {
811      specCol.get(i, spec);
812      flagCol.get(i, flag);
813      Vector<Bool> mask(flag.nelements());
814      convertArray(mask, flag);
815      Vector<Float> specout;
816      if ( type == VectorKernel::HANNING ) {
817        Vector<Bool> maskout;
818        mathutil::hanning(specout, maskout, spec , mask);
819        convertArray(flag, maskout);
820        flagCol.put(i, flag);
821      } else {
822        mathutil::replaceMaskByZero(specout, mask);
823        conv.linearConv(specout, spec);
824      }
825      specCol.put(i, specout);
826    }
827    ++iter;
828  }
829  return out;
830}
831
832CountedPtr< Scantable >
833  STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
834{
835  if ( in.size() < 2 ) {
836    throw(AipsError("Need at least two scantables to perform a merge."));
837  }
838  std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
839  bool insitu = insitu_;
840  setInsitu(false);
841  CountedPtr< Scantable > out = getScantable(*it, false);
842  setInsitu(insitu);
843  Table& tout = out->table();
844  ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
845  ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
846  // Renumber SCANNO to be 0-based
847  Vector<uInt> scannos = scannocol.getColumn();
848  uInt offset = min(scannos);
849  scannos -= offset;
850  scannocol.putColumn(scannos);
851  uInt newscanno = max(scannos)+1;
852  ++it;
853  while ( it != in.end() ){
854    if ( ! (*it)->conformant(*out) ) {
855      // log message: "ignoring scantable i, as it isn't
856      // conformant with the other(s)"
857      cerr << "oh oh" << endl;
858      ++it;
859      continue;
860    }
861    out->appendToHistoryTable((*it)->history());
862    const Table& tab = (*it)->table();
863    TableIterator scanit(tab, "SCANNO");
864    while (!scanit.pastEnd()) {
865      TableIterator freqit(scanit.table(), "FREQ_ID");
866      while ( !freqit.pastEnd() ) {
867        Table thetab = freqit.table();
868        uInt nrow = tout.nrow();
869        //tout.addRow(thetab.nrow());
870        TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
871        ROTableRow row(thetab);
872        for ( uInt i=0; i<thetab.nrow(); ++i) {
873          uInt k = nrow+i;
874          scannocol.put(k, newscanno);
875          const TableRecord& rec = row.get(i);
876          Double rv,rp,inc;
877          (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
878          uInt id;
879          id = out->frequencies().addEntry(rp, rv, inc);
880          freqidcol.put(k,id);
881          String name,fname;Double rf;
882          (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
883          id = out->molecules().addEntry(rf, name, fname);
884          molidcol.put(k, id);
885          Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
886          (*it)->focus().getEntry(fax, ftan, frot, fhand,
887                                  fmount,fuser, fxy, fxyp,
888                                  rec.asuInt("FOCUS_ID"));
889          id = out->focus().addEntry(fax, ftan, frot, fhand,
890                                     fmount,fuser, fxy, fxyp);
891          focusidcol.put(k, id);
892        }
893        ++freqit;
894      }
895      ++newscanno;
896      ++scanit;
897    }
898    ++it;
899  }
900  return out;
901}
902
903CountedPtr< Scantable >
904  STMath::invertPhase( const CountedPtr < Scantable >& in )
905{
906  return applyToPol(in, &STPol::invertPhase, Float(0.0));
907}
908
909CountedPtr< Scantable >
910  STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
911{
912   return applyToPol(in, &STPol::rotatePhase, Float(phase));
913}
914
915CountedPtr< Scantable >
916  STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
917{
918  return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
919}
920
921CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
922                                             STPol::polOperation fptr,
923                                             Float phase )
924{
925  CountedPtr< Scantable > out = getScantable(in, false);
926  Table& tout = out->table();
927  Block<String> cols(4);
928  cols[0] = String("SCANNO");
929  cols[1] = String("BEAMNO");
930  cols[2] = String("IFNO");
931  cols[3] = String("CYCLENO");
932  TableIterator iter(tout, cols);
933  STPol* stpol = NULL;
934  stpol =STPol::getPolClass(out->factories_, out->getPolType() );
935  while (!iter.pastEnd()) {
936    Table t = iter.table();
937    ArrayColumn<Float> speccol(t, "SPECTRA");
938    Matrix<Float> pols = speccol.getColumn();
939    try {
940      stpol->setSpectra(pols);
941      (stpol->*fptr)(phase);
942      speccol.putColumn(stpol->getSpectra());
943    } catch (AipsError& e) {
944      delete stpol;stpol=0;
945      throw(e);
946    }
947    ++iter;
948  }
949  delete stpol;stpol=0;
950  return out;
951}
952
953CountedPtr< Scantable >
954  STMath::swapPolarisations( const CountedPtr< Scantable > & in )
955{
956  CountedPtr< Scantable > out = getScantable(in, false);
957  Table& tout = out->table();
958  Table t0 = tout(tout.col("POLNO") == 0);
959  Table t1 = tout(tout.col("POLNO") == 1);
960  if ( t0.nrow() != t1.nrow() )
961    throw(AipsError("Inconsistent number of polarisations"));
962  ArrayColumn<Float> speccol0(t0, "SPECTRA");
963  ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
964  ArrayColumn<Float> speccol1(t1, "SPECTRA");
965  ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
966  Matrix<Float> s0 = speccol0.getColumn();
967  Matrix<uChar> f0 = flagcol0.getColumn();
968  speccol0.putColumn(speccol1.getColumn());
969  flagcol0.putColumn(flagcol1.getColumn());
970  speccol1.putColumn(s0);
971  flagcol1.putColumn(f0);
972  return out;
973}
974
975CountedPtr< Scantable >
976  STMath::averagePolarisations( const CountedPtr< Scantable > & in,
977                                const std::vector<bool>& mask,
978                                const std::string& weight )
979{
980  if (in->getPolType() != "linear"  || in->npol() != 2 )
981    throw(AipsError("averagePolarisations can only be applied to two linear polarisations."));
982  bool insitu = insitu_;
983  setInsitu(false);
984  CountedPtr< Scantable > pols = getScantable(in, false);
985  setInsitu(insitu);
986  Table& tout = pols->table();
987  // give all rows the same POLNO
988  TableVector<uInt> vec(tout,"POLNO");
989  vec = 0;
990  pols->table_.rwKeywordSet().define("nPol",Int(1));
991  std::vector<CountedPtr<Scantable> > vpols;
992  vpols.push_back(pols);
993  CountedPtr< Scantable > out = average(vpols, mask, weight, "NONE");
994  return out;
995}
996
997
998CountedPtr< Scantable >
999  asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
1000                                const std::string & refTime,
1001                                const std::string & method)
1002{
1003  // clone as this is not working insitu
1004  bool insitu = insitu_;
1005  setInsitu(false);
1006  CountedPtr< Scantable > out = getScantable(in, false);
1007  setInsitu(insitu);
1008  Table& tout = out->table();
1009  // Get reference Epoch to time of first row or given String
1010  Unit DAY(String("d"));
1011  MEpoch::Ref epochRef(in->getTimeReference());
1012  MEpoch refEpoch;
1013  if (refTime.length()>0) {
1014    Quantum<Double> qt;
1015    if (MVTime::read(qt,refTime)) {
1016      MVEpoch mv(qt);
1017      refEpoch = MEpoch(mv, epochRef);
1018   } else {
1019      throw(AipsError("Invalid format for Epoch string"));
1020   }
1021  } else {
1022    refEpoch = in->timeCol_(0);
1023  }
1024  MPosition refPos = in->getAntennaPosition();
1025
1026  InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
1027  // test if user frame is different to base frame
1028  if ( in->frequencies().getFrameString(true)
1029       == in->frequencies().getFrameString(false) ) {
1030    throw(AipsError("Can't convert as no output frame has been set"
1031                    " (use set_freqframe) or it is aligned already."));
1032  }
1033  MFrequency::Types system = in->frequencies().getFrame();
1034  MVTime mvt(refEpoch.getValue());
1035  String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
1036  ostringstream oss;
1037  oss << "Aligned at reference Epoch " << epochout
1038      << " in frame " << MFrequency::showType(system);
1039  pushLog(String(oss));
1040  // set up the iterator
1041  Block<String> cols(4);
1042  // select by constant direction
1043  cols[0] = String("SRCNAME");
1044  cols[1] = String("BEAMNO");
1045  // select by IF ( no of channels varies over this )
1046  cols[2] = String("IFNO");
1047  // select by restfrequency
1048  cols[3] = String("MOLECULE_ID");
1049  TableIterator iter(tout, cols);
1050  while ( !iter.pastEnd() ) {
1051    Table t = iter.table();
1052    MDirection::ROScalarColumn dirCol(t, "DIRECTION");
1053    TableIterator fiter(t, "FREQ_ID");
1054    // determine nchan from the first row. This should work as
1055    // we are iterating over BEAMNO and IFNO    // we should have constant direction
1056
1057    ROArrayColumn<Float> sCol(t, "SPECTRA");
1058    MDirection direction = dirCol(0);
1059    uInt nchan = sCol(0).nelements();
1060    while ( !fiter.pastEnd() ) {
1061      Table ftab = fiter.table();
1062      ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
1063      // get the SpectralCoordinate for the freqid, which we are iterating over
1064      SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
1065      FrequencyAligner<Float> fa( sC, nchan, refEpoch,
1066                                  direction, refPos, system );
1067      // realign the SpectralCoordinate and put into the output Scantable
1068      Vector<String> units(1);
1069      units = String("Hz");
1070      Bool linear=True;
1071      SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
1072      sc2.setWorldAxisUnits(units);
1073      uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
1074                                            sc2.referenceValue()[0],
1075                                            sc2.increment()[0]);
1076      TableVector<uInt> tvec(ftab, "FREQ_ID");
1077      tvec = id;
1078      // create the "global" abcissa for alignment with same FREQ_ID
1079      Vector<Double> abc(nchan);
1080      Double w;
1081      for (uInt i=0; i<nchan; i++) {
1082        sC.toWorld(w,Double(i));
1083        abc[i] = w;
1084      }
1085      // cache abcissa for same time stamps, so iterate over those
1086      TableIterator timeiter(ftab, "TIME");
1087      while ( !timeiter.pastEnd() ) {
1088        Table tab = timeiter.table();
1089        ArrayColumn<Float> specCol(tab, "SPECTRA");
1090        ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1091        MEpoch::ROScalarColumn timeCol(tab, "TIME");
1092        // use align abcissa cache after the first row
1093        bool first = true;
1094        // these rows should be just be POLNO
1095        for (int i=0; i<int(tab.nrow()); ++i) {
1096          // input values
1097          Vector<uChar> flag = flagCol(i);
1098          Vector<Bool> mask(flag.shape());
1099          Vector<Float> specOut, spec;
1100          spec  = specCol(i);
1101          Vector<Bool> maskOut;Vector<uChar> flagOut;
1102          convertArray(mask, flag);
1103          // alignment
1104          Bool ok = fa.align(specOut, maskOut, abc, spec,
1105                             mask, timeCol(i), !first,
1106                             interp, False);
1107          // back into scantable
1108          flagOut.resize(maskOut.nelements());
1109          convertArray(flagOut, maskOut);
1110          flagCol.put(i, flagOut);
1111          specCol.put(i, specOut);
1112          // start abcissa caching
1113          first = false;
1114        }
1115        // next timestamp
1116        ++timeiter;
1117      }
1118      // next FREQ_ID
1119      ++fiter;
1120    }
1121    // next aligner
1122    ++iter;
1123  }
1124  // set this afterwards to ensure we are doing insitu correctly.
1125  out->frequencies().setFrame(system, true);
1126  return out;
1127}
1128
1129CountedPtr<Scantable>
1130  asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
1131                                     const std::string & newtype )
1132{
1133  if (in->npol() != 2 && in->npol() != 4)
1134    throw(AipsError("Can only convert two or four polarisations."));
1135  if ( in->getPolType() == newtype )
1136    throw(AipsError("No need to convert."));
1137  if ( ! in->selector_.empty() )
1138    throw(AipsError("Can only convert whole scantable. Unset the selection."));
1139  bool insitu = insitu_;
1140  setInsitu(false);
1141  CountedPtr< Scantable > out = getScantable(in, true);
1142  setInsitu(insitu);
1143  Table& tout = out->table();
1144  tout.rwKeywordSet().define("POLTYPE", String(newtype));
1145
1146  Block<String> cols(4);
1147  cols[0] = "SCANNO";
1148  cols[1] = "CYCLENO";
1149  cols[2] = "BEAMNO";
1150  cols[3] = "IFNO";
1151  TableIterator it(in->originalTable_, cols);
1152  String basetype = in->getPolType();
1153  STPol* stpol = STPol::getPolClass(in->factories_, basetype);
1154  try {
1155    while ( !it.pastEnd() ) {
1156      Table tab = it.table();
1157      uInt row = tab.rowNumbers()[0];
1158      stpol->setSpectra(in->getPolMatrix(row));
1159      Float fang,fhand,parang;
1160      fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row));
1161      fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
1162      parang = in->paraCol_(row);
1163      /// @todo re-enable this
1164      // disable total feed angle to support paralactifying Caswell style
1165      stpol->setPhaseCorrections(parang, -parang, fhand);
1166      Int npolout = 0;
1167      for (uInt i=0; i<tab.nrow(); ++i) {
1168        Vector<Float> outvec = stpol->getSpectrum(i, newtype);
1169        if ( outvec.nelements() > 0 ) {
1170          tout.addRow();
1171          TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
1172          ArrayColumn<Float> sCol(tout,"SPECTRA");
1173          ScalarColumn<uInt> pCol(tout,"POLNO");
1174          sCol.put(tout.nrow()-1 ,outvec);
1175          pCol.put(tout.nrow()-1 ,uInt(npolout));
1176          npolout++;
1177       }
1178      }
1179      tout.rwKeywordSet().define("nPol", npolout);
1180      ++it;
1181    }
1182  } catch (AipsError& e) {
1183    delete stpol;
1184    throw(e);
1185  }
1186  delete stpol;
1187  return out;
1188}
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