source: trunk/src/STSideBandSep.cpp @ 2976

Last change on this file since 2976 was 2976, checked in by Kana Sugimoto, 10 years ago

New Development: No

JIRA Issue: Yes (CAS-5139)

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: No

Module(s): asap.sbseparator

Description: Fixed a bug for ifno=-1.
File size: 50.4 KB
Line 
1// C++ Interface: STSideBandSep
2//
3// Description:
4//    A class to invoke sideband separation of Scantable
5//
6// Author: Kana Sugimoto <kana.sugi@nao.ac.jp>, (C) 2012
7//
8// Copyright: See COPYING file that comes with this distribution
9//
10//
11
12// STL
13#include <ctype.h>
14
15// cascore
16#include <casa/OS/File.h>
17#include <casa/Logging/LogIO.h>
18#include <casa/Quanta/QuantumHolder.h>
19
20#include <measures/Measures/MFrequency.h>
21#include <measures/Measures/MCFrequency.h>
22
23#include <tables/Tables/TableRow.h>
24#include <tables/Tables/TableRecord.h>
25#include <tables/Tables/TableVector.h>
26
27// asap
28#include "STGrid.h"
29#include "STMath.h"
30#include "MathUtils.h"
31#include "STSideBandSep.h"
32
33using namespace std ;
34using namespace casa ;
35using namespace asap ;
36
37// #ifndef KS_DEBUG
38// #define KS_DEBUG
39// #endif
40
41namespace asap {
42
43// constructors
44STSideBandSep::STSideBandSep(const vector<string> &names)
45{
46  LogIO os(LogOrigin("STSideBandSep","STSideBandSep()", WHERE));
47  os << "Setting scantable names to process." << LogIO::POST ;
48  // Set file names
49  ntable_ = names.size();
50  infileList_.resize(ntable_);
51  for (unsigned int i = 0; i < ntable_; i++){
52    if (!checkFile(names[i], "d"))
53      throw( AipsError("File does not exist") );
54    infileList_[i] = names[i];
55  }
56  intabList_.resize(0);
57
58  init();
59
60  {// Summary
61    os << ntable_ << " files are set: [";
62    for (unsigned int i = 0; i < ntable_; i++) {
63      os << " '" << infileList_[i] << "' ";
64      if (i != ntable_-1) os << ",";
65    }
66    os << "] " << LogIO::POST;
67  }
68};
69
70STSideBandSep::STSideBandSep(const vector<ScantableWrapper> &tables)
71{
72  LogIO os(LogOrigin("STSideBandSep","STSideBandSep()", WHERE));
73  os << "Setting list of scantables to process." << LogIO::POST ;
74  // Set file names
75  ntable_ = tables.size();
76  intabList_.resize(ntable_);
77  for (unsigned int i = 0; i < ntable_; i++){
78    intabList_[i] = tables[i].getCP();
79  }
80  infileList_.resize(0);
81
82  init();
83  tp_ = intabList_[0]->table().tableType();
84
85  os << ntable_ << " tables are set." << LogIO::POST;
86};
87
88STSideBandSep::~STSideBandSep()
89{
90};
91
92void STSideBandSep::init()
93{
94  // frequency setup
95  sigIfno_= -1;
96  ftol_ = -1;
97  solFrame_ = MFrequency::N_Types;
98  // shifts
99  initshift();
100  // direction tolerance
101  xtol_ = ytol_ = 9.69627e-6; // 2arcsec
102  // solution parameters
103  otherside_ = false;
104  doboth_ = false;
105  rejlimit_ = 0.2;
106  // LO1 values
107  lo1Freq_ = -1;
108  loTime_ = -1;
109  loDir_ = "";
110  // Default LO frame is TOPO
111  loFrame_ = MFrequency::TOPO;
112  // scantable storage
113  tp_ = Table::Memory;
114};
115
116void STSideBandSep::initshift()
117{
118  // shifts
119  nshift_ = 0;
120  nchan_ = 0;
121  sigShift_.resize(0);
122  imgShift_.resize(0);
123  tableList_.resize(0);
124};
125
126void STSideBandSep::setFrequency(const int ifno,
127                                 const string freqtol,
128                                 const string frame)
129{
130  LogIO os(LogOrigin("STSideBandSep","setFrequency()", WHERE));
131
132  initshift();
133
134  // IFNO
135  sigIfno_ = ifno;
136
137  // Frequency tolerance
138  Quantum<Double> qftol;
139  readQuantity(qftol, String(freqtol));
140  if (!qftol.getUnit().empty()){
141    // make sure the quantity is frequency
142    if (qftol.getFullUnit().getValue() != Unit("Hz").getValue())
143      throw( AipsError("Invalid quantity for frequency tolerance.") );
144    qftol.convert("Hz");
145  }
146  ftol_ = qftol;
147
148  // Frequency Frame
149  if (!frame.empty()){
150    MFrequency::Types mft;
151    if (!MFrequency::getType(mft, frame))
152      throw( AipsError("Invalid frame type.") );
153    solFrame_ = mft;
154  } else {
155    solFrame_ = MFrequency::N_Types;
156  }
157
158  {// Summary
159    const String sframe = ( (solFrame_ == MFrequency::N_Types) ?
160                            "table frame" :
161                            MFrequency::showType(solFrame_) );
162    os << "Frequency setup to search IF group: "
163       << "IFNO of table[0] = " << sigIfno_
164       << " , Freq tolerance = " << ftol_.getValue() << " [ "
165       << (ftol_.getUnit().empty() ? "channel" : ftol_.getUnit() )
166       << " ] (in " << sframe <<")" << LogIO::POST;
167  }
168};
169
170
171void STSideBandSep::setDirTolerance(const vector<string> dirtol)
172{
173  LogIO os(LogOrigin("STSideBandSep","setDirTolerance()", WHERE));
174  Quantum<Double> qcell;
175  if ( (dirtol.size() == 1) && !dirtol[0].empty() ) {
176    readQuantity(qcell, String(dirtol[0]));
177    if (qcell.getFullUnit().getValue() == Unit("rad").getValue())
178      xtol_ = ytol_ = qcell.getValue("rad");
179    else
180      throw( AipsError("Invalid unit for direction tolerance.") );
181  }
182  else if (dirtol.size() > 1) {
183    if ( dirtol[0].empty() && dirtol[1].empty() )
184      throw( AipsError("Direction tolerance is empty.") );
185    if ( !dirtol[0].empty() ) {
186      readQuantity(qcell, String(dirtol[0]));
187      if (qcell.getFullUnit().getValue() == Unit("rad").getValue())
188        xtol_ = qcell.getValue("rad");
189      else
190        throw( AipsError("Invalid unit for direction tolerance.") );
191    }
192    if ( !dirtol[1].empty() ) {
193      readQuantity(qcell, String(dirtol[1]));
194      if (qcell.getFullUnit().getValue() == Unit("rad").getValue())
195        ytol_ = qcell.getValue("rad");
196      else
197        throw( AipsError("Invalid unit for direction tolerance.") );
198    }
199    else {
200      ytol_ = xtol_;
201    }
202  }
203  else throw( AipsError("Invalid direction tolerance.") );
204
205  os << "Direction tolerance: ( "
206     << xtol_ << " , " << ytol_ << " ) [rad]" << LogIO::POST;
207};
208
209void STSideBandSep::setShift(const vector<double> &shift)
210{
211  LogIO os(LogOrigin("STSideBandSep","setShift()", WHERE));
212  imgShift_.resize(shift.size());
213  for (unsigned int i = 0; i < shift.size(); i++)
214    imgShift_[i] = shift[i];
215
216  if (imgShift_.size() == 0) {
217    os << "Channel shifts are cleared." << LogIO::POST;
218  } else {
219    os << "Channel shifts of image sideband are set: ( ";
220    for (unsigned int i = 0; i < imgShift_.size(); i++) {
221      os << imgShift_[i];
222      if (i != imgShift_.size()-1) os << " , ";
223    }
224    os << " ) [channels]" << LogIO::POST;
225  }
226};
227
228void STSideBandSep::setThreshold(const double limit)
229{
230  LogIO os(LogOrigin("STSideBandSep","setThreshold()", WHERE));
231  if (limit < 0)
232    throw( AipsError("Rejection limit should be a positive number.") );
233
234  rejlimit_ = limit;
235  os << "Rejection limit is set to " << rejlimit_ << LogIO::POST;
236};
237
238void STSideBandSep::separate(string outname)
239{
240  LogIO os(LogOrigin("STSideBandSep","separate()", WHERE));
241  if (outname.empty())
242    outname = "sbseparated.asap";
243
244  // Set up a goup of IFNOs in the list of scantables within
245  // the frequency tolerance and make them a list.
246  nshift_ = setupShift();
247  if (nshift_ < 2)
248    throw( AipsError("At least 2 IFs are necessary for convolution.") );
249  // Grid scantable and generate output tables
250  ScantableWrapper gridst = gridTable();
251  sigTab_p = gridst.getCP();
252  if (doboth_)
253    imgTab_p = gridst.copy().getCP();
254  vector<unsigned int> remRowIds;
255  remRowIds.resize(0);
256  Matrix<float> specMat(nchan_, nshift_);
257  Matrix<bool> flagMat(nchan_, nshift_);
258  vector<float> sigSpec(nchan_), imgSpec(nchan_);
259  Vector<bool> flagVec(nchan_);
260  vector<uInt> tabIdvec;
261
262  //Generate FFTServer
263  fftsf.resize(IPosition(1, nchan_), FFTEnums::REALTOCOMPLEX);
264  fftsi.resize(IPosition(1, nchan_), FFTEnums::COMPLEXTOREAL);
265
266  /// Loop over sigTab_p and separate sideband
267  for (int irow = 0; irow < sigTab_p->nrow(); irow++){
268    tabIdvec.resize(0);
269    const int polId = sigTab_p->getPol(irow);
270    const int beamId = sigTab_p->getBeam(irow);
271    const vector<double> dir = sigTab_p->getDirectionVector(irow);
272    // Get a set of spectra to solve
273    if (!getSpectraToSolve(polId, beamId, dir[0], dir[1],
274                           specMat, flagMat, tabIdvec)){
275      remRowIds.push_back(irow);
276#ifdef KS_DEBUG
277      cout << "no matching row found. skipping row = " << irow << endl;
278#endif
279      continue;
280    }
281    // Solve signal sideband
282    sigSpec = solve(specMat, tabIdvec, true);
283    sigTab_p->setSpectrum(sigSpec, irow);
284    if (sigTab_p->isAllChannelsFlagged(irow)){
285      // unflag the spectrum since there should be some valid data
286      sigTab_p->flagRow(vector<uInt>(irow), true);
287      // need to unflag whole channels anyway
288      sigTab_p->flag(irow, vector<bool>(), true);
289    }
290    // apply channel flag
291    flagVec = collapseFlag(flagMat, tabIdvec, true);
292    //boolVec = !boolVec; // flag
293    vector<bool> tmpflag;
294    flagVec.tovector(tmpflag);
295    sigTab_p->flag(irow, tmpflag, false);
296
297    // Solve image sideband
298    if (doboth_) {
299      imgSpec = solve(specMat, tabIdvec, false);
300      imgTab_p->setSpectrum(imgSpec, irow);
301      if (imgTab_p->isAllChannelsFlagged(irow)){
302        // unflag the spectrum since there should be some valid data
303        imgTab_p->flagRow(vector<uInt>(irow), true);
304        // need to unflag whole channels anyway
305        imgTab_p->flag(irow, vector<bool>(), true);
306      }
307      // apply channel flag
308      flagVec = collapseFlag(flagMat, tabIdvec, false);
309      //boolVec = !boolVec; // flag
310      flagVec.tovector(tmpflag);
311      imgTab_p->flag(irow, tmpflag, false);
312    }
313  } // end of row loop
314
315  // Remove or flag rows without relevant data from gridded tables
316  if (remRowIds.size() > 0) {
317    const size_t nrem = remRowIds.size();
318    if ( sigTab_p->table().canRemoveRow() ) {
319      sigTab_p->table().removeRow(remRowIds);
320      os << "Removing " << nrem << " rows from the signal band table"
321         << LogIO::POST;
322    } else {
323      sigTab_p->flagRow(remRowIds, false);
324      os << "Cannot remove rows from the signal band table. Flagging "
325         << nrem << " rows" << LogIO::POST;
326    }
327
328    if (doboth_) {
329      if ( imgTab_p->table().canRemoveRow() ) {
330        imgTab_p->table().removeRow(remRowIds);
331        os << "Removing " << nrem << " rows from the image band table"
332           << LogIO::POST;
333      } else {
334        imgTab_p->flagRow(remRowIds, false);
335        os << "Cannot remove rows from the image band table. Flagging "
336           << nrem << " rows" << LogIO::POST;
337      }
338    }
339  }
340
341  // Finally, save tables on disk
342  if (outname.size() ==0)
343    outname = "sbseparated.asap";
344  const string sigName = outname + ".signalband";
345  os << "Saving SIGNAL sideband table: " << sigName << LogIO::POST;
346  sigTab_p->makePersistent(sigName);
347  if (doboth_) {
348    solveImageFrequency();
349    const string imgName = outname + ".imageband";
350    os << "Saving IMAGE sideband table: " << sigName << LogIO::POST;
351    imgTab_p->makePersistent(imgName);
352  }
353
354};
355
356unsigned int STSideBandSep::setupShift()
357{
358  LogIO os(LogOrigin("STSideBandSep","setupShift()", WHERE));
359  if (infileList_.size() == 0 && intabList_.size() == 0)
360    throw( AipsError("No scantable has been set. Set a list of scantables first.") );
361
362  const bool byname = (intabList_.size() == 0);
363  // Make sure sigIfno_ exists in the first table.
364  CountedPtr<Scantable> stab;
365  vector<string> coordsav;
366  vector<string> coordtmp(3);
367  os << "Checking IFNO in the first table." << LogIO::POST;
368  if (byname) {
369    if (!checkFile(infileList_[0], "d"))
370      os << LogIO::SEVERE << "Could not find scantable '" << infileList_[0]
371         << "'" << LogIO::EXCEPTION;
372    stab = CountedPtr<Scantable>(new Scantable(infileList_[0]));
373  } else {
374    stab = intabList_[0];
375  }
376  if (sigIfno_ < 0) {
377    sigIfno_ = (int) stab->getIF(0);
378    os << "IFNO to process has not been set. Using the first IF = "
379       << sigIfno_ << LogIO::POST;
380  }
381
382  unsigned int basench;
383  double basech0, baseinc, ftolval, inctolval;
384  coordsav = stab->getCoordInfo();
385  const string stfframe = coordsav[1];
386  coordtmp[0] = "Hz";
387  coordtmp[1] = ( (solFrame_ == MFrequency::N_Types) ?
388                  stfframe :
389                  MFrequency::showType(solFrame_) );
390  coordtmp[2] = coordsav[2];
391  stab->setCoordInfo(coordtmp);
392  if (!getFreqInfo(stab, (unsigned int) sigIfno_, basech0, baseinc, basench)) {
393    os << LogIO::SEVERE << "No data with IFNO=" << sigIfno_
394       << " found in the first table." << LogIO::EXCEPTION;
395  }
396  else {
397    os << "Found IFNO = " << sigIfno_
398       << " in the first table." << LogIO::POST;
399  }
400  if (ftol_.getUnit().empty()) {
401    // tolerance in unit of channels
402    ftolval = ftol_.getValue() * baseinc;
403  }
404  else {
405    ftolval = ftol_.getValue("Hz");
406  }
407  inctolval = abs(baseinc/(double) basench);
408  const string poltype0 = stab->getPolType();
409
410  // Initialize shift values
411  initshift();
412
413//   const bool setImg = ( doboth_ && (imgShift_.size() == 0) );
414  const bool setImg = (imgShift_.size() == 0);
415  // Select IFs
416  for (unsigned int itab = 0; itab < ntable_; itab++ ){
417    os << "Table " << itab << LogIO::POST;
418    if (itab > 0) {
419      if (byname) {
420        if (!checkFile(infileList_[itab], "d"))
421          os << LogIO::SEVERE << "Could not find scantable '"
422             << infileList_[itab] << "'" << LogIO::EXCEPTION;
423        stab = CountedPtr<Scantable>(new Scantable(infileList_[itab]));
424      } else {
425        stab = intabList_[itab];
426      }
427      //POLTYPE should be the same.
428      if (stab->getPolType() != poltype0 ) {
429        os << LogIO::WARN << "POLTYPE differs from the first table."
430           << " Skipping the table" << LogIO::POST;
431        continue;
432      }
433      // Multi beam data may not handled properly
434      if (stab->nbeam() > 1)
435        os <<  LogIO::WARN << "Table contains multiple beams. "
436           << "It may not be handled properly."  << LogIO::POST;
437
438      coordsav = stab->getCoordInfo();
439      coordtmp[2] = coordsav[2];
440      stab->setCoordInfo(coordtmp);
441    }
442    bool selected = false;
443    vector<uint> ifnos = stab->getIFNos();
444    vector<uint>::iterator iter;
445    const STSelector& basesel = stab->getSelection();
446    for (iter = ifnos.begin(); iter != ifnos.end(); iter++){
447      unsigned int nch;
448      double freq0, incr;
449      if ( getFreqInfo(stab, *iter, freq0, incr, nch) ){
450        if ( (nch == basench) && (abs(freq0-basech0) < ftolval)
451             && (abs(incr-baseinc) < inctolval) ){
452          //Found
453          STSelector sel(basesel);
454          sel.setIFs(vector<int>(1,(int) *iter));
455          stab->setSelection(sel);
456          CountedPtr<Scantable> seltab = ( new Scantable(*stab, false) );
457          stab->setSelection(basesel);
458          seltab->setCoordInfo(coordsav);
459          const double chShift = (freq0 - basech0) / baseinc;
460          tableList_.push_back(seltab);
461          sigShift_.push_back(-chShift);
462          if (setImg)
463            imgShift_.push_back(chShift);
464
465          selected = true;
466          os << "- IF" << *iter << " selected: sideband shift = "
467             << chShift << " channels" << LogIO::POST;
468        }
469      }
470    } // ifno loop
471    stab->setCoordInfo(coordsav);
472    if (!selected)
473      os << LogIO::WARN << "No data selected in Table "
474         << itab << LogIO::POST;
475  } // table loop
476  nchan_ = basench;
477
478  os << "Total number of IFs selected = " << tableList_.size()
479     << LogIO::POST;
480  if ( setImg && (sigShift_.size() != imgShift_.size()) ){
481      os << LogIO::SEVERE
482         << "User defined channel shift of image sideband has "
483         << imgShift_.size()
484         << " elements, while selected IFNOs are " << sigShift_.size()
485         << "\nThe frequency tolerance (freqtol) may be too small."
486         << LogIO::EXCEPTION;
487  }
488
489  return tableList_.size();
490};
491
492bool STSideBandSep::getFreqInfo(const CountedPtr<Scantable> &stab,
493                                const unsigned int &ifno,
494                                double &freq0, double &incr,
495                                unsigned int &nchan)
496{
497    vector<uint> ifnos = stab->getIFNos();
498    bool found = false;
499    vector<uint>::iterator iter;
500    for (iter = ifnos.begin(); iter != ifnos.end(); iter++){
501      if (*iter == ifno) {
502        found = true;
503        break;
504      }
505    }
506    if (!found)
507      return false;
508
509    const STSelector& basesel = stab->getSelection();
510    STSelector sel(basesel);
511    sel.setIFs(vector<int>(1,(int) ifno));
512    stab->setSelection(sel);
513    vector<double> freqs;
514    freqs = stab->getAbcissa(0);
515    freq0 = freqs[0];
516    incr = freqs[1] - freqs[0];
517    nchan = freqs.size();
518    stab->setSelection(basesel);
519    return true;
520};
521
522ScantableWrapper STSideBandSep::gridTable()
523{
524  LogIO os(LogOrigin("STSideBandSep","gridTable()", WHERE));
525  if (tableList_.size() == 0)
526    throw( AipsError("Internal error. No scantable has been set to grid.") );
527  Double xmin, xmax, ymin, ymax;
528  mapExtent(tableList_, xmin, xmax, ymin, ymax);
529  const Double centx = 0.5 * (xmin + xmax);
530  const Double centy = 0.5 * (ymin + ymax);
531  const int nx = max(1, (int) ceil( (xmax - xmin) * cos(centy) /xtol_ ) );
532  const int ny = max(1, (int) ceil( (ymax - ymin) / ytol_ ) );
533
534  string scellx, scelly;
535  {
536    ostringstream oss;
537    oss << xtol_ << "rad" ;
538    scellx = oss.str();
539  }
540  {
541    ostringstream oss;
542    oss << ytol_ << "rad" ;
543    scelly = oss.str();
544  }
545
546  ScantableWrapper stab0;
547  if (intabList_.size() > 0)
548    stab0 = ScantableWrapper(intabList_[0]);
549  else
550    stab0 = ScantableWrapper(infileList_[0]);
551
552  string scenter;
553  {
554    ostringstream oss;
555    oss << stab0.getCP()->getDirectionRefString() << " "
556        << centx << "rad" << " " << centy << "rad";
557    scenter = oss.str();
558  }
559 
560  STGrid2 gridder = STGrid2(stab0);
561  gridder.setIF(sigIfno_);
562  gridder.defineImage(nx, ny, scellx, scelly, scenter);
563  //  gridder.setFunc("box", 1); // convsupport=1 fails
564  gridder.setFunc("box");
565  gridder.setWeight("uniform");
566#ifdef KS_DEBUG
567  cout << "Grid parameter summary: " << endl;
568  cout << "- IF = " << sigIfno_ << endl;
569  cout << "- center = " << scenter << "\n"
570       << "- npix = (" << nx << ", " << ny << ")\n"
571       << "- cell = (" << scellx << ", " << scelly << ")" << endl;
572#endif
573  gridder.grid();
574  const int itp = (tp_ == Table::Memory ? 0 : 1);
575  ScantableWrapper gtab = gridder.getResultAsScantable(itp);
576  // WORKAROUND : Shift TIME for proper pointing resolution in future imaging.
577  shiftTimeInGriddedST(gtab.getCP());
578  return gtab;
579};
580
581void STSideBandSep::mapExtent(vector< CountedPtr<Scantable> > &tablist,
582                              Double &xmin, Double &xmax,
583                              Double &ymin, Double &ymax)
584{
585  ROArrayColumn<Double> dirCol_;
586  dirCol_.attach( tablist[0]->table(), "DIRECTION" );
587  Matrix<Double> direction = dirCol_.getColumn();
588  Vector<Double> ra( direction.row(0) );
589  mathutil::rotateRA(ra);
590  minMax( xmin, xmax, ra );
591  minMax( ymin, ymax, direction.row(1) );
592  Double amin, amax, bmin, bmax;
593  const uInt ntab = tablist.size();
594  for ( uInt i = 1 ; i < ntab ; i++ ) {
595    dirCol_.attach( tablist[i]->table(), "DIRECTION" );
596    direction.assign( dirCol_.getColumn() );
597    ra.assign( direction.row(0) );
598    mathutil::rotateRA(ra);
599    minMax( amin, amax, ra );
600    minMax( bmin, bmax, direction.row(1) );
601    xmin = min(xmin, amin);
602    xmax = max(xmax, amax);
603    ymin = min(ymin, bmin);
604    ymax = max(ymax, bmax);
605  }
606};
607
608// STGrid sets the identical time for all rows in scantable
609// which is reasonable thing to do in position based averaging.
610// However, this prevents CASA from finding proper pointing
611// per spectra once the gridded scantable is converted to
612// measurement set (MS). It is because MS does not
613// have ability to store per spectra pointing information.
614// MS stores pointing information in a subtable, POINTING,
615// with corresponding TIME when an antenna pointed the direction.
616// The pointing direction corresponding to a spectra is resolved
617// in MS by interpolating DIRECTION in POINTING subtable in TIME
618// the spectra is observed. If there are multiple match,
619// the first match is adopted. Therefore, gridded table (whose TIME
620// is set to a single value) is misunderstood in MS that all data
621// come from a single pointing.
622// The function workarounds this defect by artificially shifting
623// TIME by INTERVAL in each row.
624void STSideBandSep::shiftTimeInGriddedST(const CountedPtr<Scantable> &stab)
625{
626  LogIO os(LogOrigin("STSideBandSep", "shiftTimeInGriddedST()", WHERE));
627  // Gridded table usually has an IF and a BEAM.
628  {
629    std::vector<uint> bmnos = stab->getBeamNos();
630    if (bmnos.size() > 1)
631      throw( AipsError("Multiple BEAMNOs found in the scantable. This may not a gridded table") );
632    std::vector<uint> ifnos = stab->getIFNos();
633    if (ifnos.size() > 1)
634      throw( AipsError("Multiple IFNOs found in the scantable. This may not a gridded table") );
635  }
636  // Rows in gridded table usually sorted by DIRECTION
637  const Table& tab = stab->table();
638  ScalarColumn<Double> mjdCol( tab, "TIME");
639  ROScalarColumn<Double> intCol( tab, "INTERVAL");
640  ROArrayColumn<Double> dirCol( tab, "DIRECTION");
641  Matrix<Double> direction = dirCol.getColumn();
642  Vector<Double> ra( direction.row(0) );
643  Vector<Double> dec( direction.row(1) );
644  Double prevTime, prevInt, prevRA(ra[0]), prevDec(dec[0]);
645  mjdCol.get(0, prevTime);
646  intCol.get(0, prevInt);
647  Double currInt, currRA, currDec;
648  Double dx(xtol_*0.95), dy(ytol_*0.95);
649  Double secToDay(1./24./3600.);
650  for (int irow = 0; irow < stab->nrow(); ++irow){
651    currRA = ra[irow];
652    currDec = dec[irow];
653    if ((prevRA+dx-currRA)*(currRA-prevRA+dx)>=0 &&
654        (prevDec+dy-currDec)*(currDec-prevDec+dy)>=0) {
655      // the same time stamp as the previous row
656      mjdCol.put(irow, prevTime);
657      // remember the longest interval
658      intCol.get(irow, currInt);
659      if (currInt > prevInt) prevInt = currInt;
660    } else {
661      // a new direction. need to set new time stamp.
662      prevTime += prevInt*secToDay;
663      mjdCol.put(irow, prevTime);
664      // new interval and direction
665      intCol.get(irow, prevInt);
666      prevRA = currRA;
667      prevDec = currDec;
668    }
669  }
670};
671
672// bool STSideBandSep::getSpectraToSolve(const int polId, const int beamId,
673//                                    const double dirX, const double dirY,
674//                                    Matrix<float> &specMat, vector<uInt> &tabIdvec)
675bool STSideBandSep::getSpectraToSolve(const int polId, const int beamId,
676                                      const double dirX, const double dirY,
677                                      Matrix<float> &specMat,
678                                      Matrix<bool> &flagMat,
679                                      vector<uInt> &tabIdvec)
680{
681  LogIO os(LogOrigin("STSideBandSep","getSpectraToSolve()", WHERE));
682
683  tabIdvec.resize(0);
684  specMat.resize(nchan_, nshift_);
685  Vector<float> spec;
686  Vector<bool> boolVec;
687  uInt nspec = 0;
688  STMath stm(false); // insitu has no effect for average.
689  for (uInt itab = 0 ; itab < nshift_ ; itab++) {
690    CountedPtr<Scantable> currtab_p = tableList_[itab];
691    // Selection by POLNO and BEAMNO
692    const STSelector& basesel = currtab_p->getSelection();
693    STSelector sel(basesel);
694    sel.setPolarizations(vector<int>(1, polId));
695    sel.setBeams(vector<int>(1, beamId));
696    try {
697      currtab_p->setSelection(sel);
698    } catch (...) {
699#ifdef KS_DEBUG
700      cout << "Table " << itab << " - No spectrum found. skipping the table."
701           << endl;
702#endif
703      continue;
704    }
705    // Selection by direction;
706    vector<int> selrow(0);
707    vector<double> currDir(2, 0.);
708    const int nselrow = currtab_p->nrow();
709    for (int irow = 0 ; irow < nselrow ; irow++) {
710      currDir = currtab_p->getDirectionVector(irow);
711      if ( (abs(currDir[0]-dirX) > xtol_) ||
712           (abs(currDir[1]-dirY) > ytol_) )
713        continue;
714      // within direction tolerance
715      selrow.push_back(irow);
716    } // end of row loop
717
718    if (selrow.size() < 1) {
719      currtab_p->setSelection(basesel);
720
721#ifdef KS_DEBUG
722      cout << "Table " << itab << " - No spectrum found. skipping the table."
723           << endl;
724#endif
725
726      continue;
727    }
728
729    // At least a spectrum is selected in this table
730    CountedPtr<Scantable> seltab_p = ( new Scantable(*currtab_p, false) );
731    currtab_p->setSelection(basesel);
732    STSelector sel2(seltab_p->getSelection());
733    sel2.setRows(selrow);
734    seltab_p->setSelection(sel2);
735    CountedPtr<Scantable> avetab_p;
736    if (seltab_p->nrow() > 1) {
737      // STMath::average also merges FLAGTRA and FLAGROW
738      avetab_p = stm.average(vector< CountedPtr<Scantable> >(1, seltab_p),
739                             vector<bool>(), "TINTSYS", "NONE");
740#ifdef KS_DEBUG
741      cout << "Table " << itab << " - more than a spectrum is selected. averaging rows..."
742           << endl;
743#endif
744      if (avetab_p->nrow() > 1)
745        throw( AipsError("Averaged table has more than a row. Somethigs went wrong.") );
746    } else {
747      avetab_p = seltab_p;
748    }
749    // Check FLAGTRA and FLAGROW if there's any valid channel in the spectrum
750    if (avetab_p->getFlagRow(0) || avetab_p->isAllChannelsFlagged(0)) {
751#ifdef KS_DEBUG
752      cout << "Table " << itab << " - All data are flagged. skipping the table."
753           << endl;
754#endif
755      continue;
756    }
757    // Interpolate flagged channels of the spectrum.
758    Vector<Float> tmpSpec = avetab_p->getSpectrum(0);
759    // Mask is true if the data is valid (!flag)
760    vector<bool> mask = avetab_p->getMask(0);
761    mathutil::doZeroOrderInterpolation(tmpSpec, mask);
762    spec.reference(specMat.column(nspec));
763    spec = tmpSpec;
764    boolVec.reference(flagMat.column(nspec));
765    boolVec = mask; // cast std::vector to casa::Vector
766    boolVec = !boolVec;
767    tabIdvec.push_back((uInt) itab);
768    nspec++;
769    //Liberate from reference
770    spec.unique();
771    boolVec.unique();
772  } // end of table loop
773  // Check the number of selected spectra and resize matrix.
774  if (nspec != nshift_){
775    //shiftSpecmat.resize(nchan_, nspec, true);
776    specMat.resize(nchan_, nspec, true);
777    flagMat.resize(nchan_, nspec, true);
778#ifdef KS_DEBUG
779      cout << "Could not find corresponding rows in some tables."
780           << endl;
781      cout << "Number of spectra selected = " << nspec << endl;
782#endif
783  }
784  if (nspec < 2) {
785#ifdef KS_DEBUG
786      cout << "At least 2 spectra are necessary for convolution"
787           << endl;
788#endif
789      return false;
790  }
791  return true;
792};
793
794
795Vector<bool> STSideBandSep::collapseFlag(const Matrix<bool> &flagMat,
796                                         const vector<uInt> &tabIdvec,
797                                         const bool signal)
798{
799  LogIO os(LogOrigin("STSideBandSep","collapseFlag()", WHERE));
800  if (tabIdvec.size() == 0)
801    throw(AipsError("Internal error. Table index is not defined."));
802  if (flagMat.ncolumn() != tabIdvec.size())
803    throw(AipsError("Internal error. The row number of input matrix is not conformant."));
804  if (flagMat.nrow() != nchan_)
805    throw(AipsError("Internal error. The channel size of input matrix is not conformant."));
806 
807  const size_t nspec = tabIdvec.size();
808  vector<double> *thisShift;
809  if (signal == otherside_) {
810    // (solve signal && solveother = T) OR (solve image && solveother = F)
811    thisShift = &imgShift_;
812  } else {
813    // (solve signal && solveother = F) OR (solve image && solveother = T)
814    thisShift =  &sigShift_;
815 }
816
817  Vector<bool> outflag(nchan_, false);
818  double tempshift;
819  Vector<bool> shiftvec(nchan_, false);
820  Vector<bool> accflag(nchan_, false);
821  uInt shiftId;
822  for (uInt i = 0 ; i < nspec; ++i) {
823    shiftId = tabIdvec[i];
824    tempshift = - thisShift->at(shiftId);
825    shiftFlag(flagMat.column(i), tempshift, shiftvec);
826    // Now accumulate Flag
827    for (uInt j = 0 ; j < nchan_ ; ++j)
828      accflag[j] |= shiftvec[j];
829  }
830  outflag = accflag;
831  // Shift back Flag
832  //cout << "Shifting FLAG back to " << thisShift->at(0) << " channels" << endl;
833  //shiftFlag(accflag, thisShift->at(0), outflag);
834
835  return outflag;
836}
837
838
839vector<float> STSideBandSep::solve(const Matrix<float> &specmat,
840                                   const vector<uInt> &tabIdvec,
841                                   const bool signal)
842{
843  LogIO os(LogOrigin("STSideBandSep","solve()", WHERE));
844  if (tabIdvec.size() == 0)
845    throw(AipsError("Internal error. Table index is not defined."));
846  if (specmat.ncolumn() != tabIdvec.size())
847    throw(AipsError("Internal error. The row number of input matrix is not conformant."));
848  if (specmat.nrow() != nchan_)
849    throw(AipsError("Internal error. The channel size of input matrix is not conformant."));
850 
851
852#ifdef KS_DEBUG
853  cout << "Solving " << (signal ? "SIGNAL" : "IMAGE") << " sideband."
854     << endl;
855#endif
856
857  const size_t nspec = tabIdvec.size();
858  vector<double> *thisShift, *otherShift;
859  if (signal == otherside_) {
860    // (solve signal && solveother = T) OR (solve image && solveother = F)
861    thisShift = &imgShift_;
862    otherShift = &sigShift_;
863#ifdef KS_DEBUG
864    cout << "Image sideband will be deconvolved." << endl;
865#endif
866  } else {
867    // (solve signal && solveother = F) OR (solve image && solveother = T)
868    thisShift =  &sigShift_;
869    otherShift = &imgShift_;
870#ifdef KS_DEBUG
871    cout << "Signal sideband will be deconvolved." << endl;
872#endif
873 }
874
875  vector<double> spshift(nspec);
876  Matrix<float> shiftSpecmat(nchan_, nspec, 0.);
877  double tempshift;
878  Vector<float> shiftspvec;
879  uInt shiftId;
880  for (uInt i = 0 ; i < nspec; i++) {
881    shiftId = tabIdvec[i];
882    spshift[i] = otherShift->at(shiftId) - thisShift->at(shiftId);
883    tempshift = - thisShift->at(shiftId);
884    shiftspvec.reference(shiftSpecmat.column(i));
885    shiftSpectrum(specmat.column(i), tempshift, shiftspvec);
886  }
887
888  Matrix<float> convmat(nchan_, nspec*(nspec-1)/2, 0.);
889  vector<float> thisvec(nchan_, 0.);
890
891  float minval, maxval;
892  minMax(minval, maxval, shiftSpecmat);
893#ifdef KS_DEBUG
894  cout << "Max/Min of input Matrix = (max: " << maxval << ", min: " << minval << ")" << endl;
895#endif
896
897#ifdef KS_DEBUG
898  cout << "starting deconvolution" << endl;
899#endif
900  deconvolve(shiftSpecmat, spshift, rejlimit_, convmat);
901#ifdef KS_DEBUG
902  cout << "finished deconvolution" << endl;
903#endif
904
905  minMax(minval, maxval, convmat);
906#ifdef KS_DEBUG
907  cout << "Max/Min of output Matrix = (max: " << maxval << ", min: " << minval << ")" << endl;
908#endif
909
910  aggregateMat(convmat, thisvec);
911
912  if (!otherside_) return thisvec;
913
914  // subtract from the other side band.
915  vector<float> othervec(nchan_, 0.);
916  subtractFromOther(shiftSpecmat, thisvec, spshift, othervec);
917  return othervec;
918};
919
920
921void STSideBandSep::shiftSpectrum(const Vector<float> &invec,
922                                  double shift,
923                                  Vector<float> &outvec)
924{
925  LogIO os(LogOrigin("STSideBandSep","shiftSpectrum()", WHERE));
926  if (invec.size() != nchan_)
927    throw(AipsError("Internal error. The length of input vector differs from nchan_"));
928  if (outvec.size() != nchan_)
929    throw(AipsError("Internal error. The length of output vector differs from nchan_"));
930
931#ifdef KS_DEBUG
932  cout << "Start shifting spectrum for " << shift << " channels" << endl;
933#endif
934
935  // tweak shift to be in 0 ~ nchan_-1
936  if ( fabs(shift) > nchan_ ) shift = fmod(shift, nchan_);
937  if (shift < 0.) shift += nchan_;
938  double rweight = fmod(shift, 1.);
939  if (rweight < 0.) rweight += 1.;
940  double lweight = 1. - rweight;
941  uInt lchan, rchan;
942
943  outvec = 0;
944  for (uInt i = 0 ; i < nchan_ ; i++) {
945    lchan = uInt( floor( fmod( (i + shift), nchan_ ) ) );
946    if (lchan < 0.) lchan += nchan_;
947    rchan = ( (lchan + 1) % nchan_ );
948    outvec(lchan) += invec(i) * lweight;
949    outvec(rchan) += invec(i) * rweight;
950#ifdef KS_DEBUG
951    if (i == 2350 || i== 2930) {
952      cout << "Channel= " << i << " of input vector: " << endl;
953      cout << "L channel = " << lchan << endl;
954      cout << "R channel = " << rchan << endl;
955      cout << "L weight = " << lweight << endl;
956      cout << "R weight = " << rweight << endl;
957    }
958#endif
959  }
960};
961
962
963void STSideBandSep::shiftFlag(const Vector<bool> &invec,
964                                  double shift,
965                                  Vector<bool> &outvec)
966{
967  LogIO os(LogOrigin("STSideBandSep","shiftFlag()", WHERE));
968  if (invec.size() != nchan_)
969    throw(AipsError("Internal error. The length of input vector differs from nchan_"));
970  if (outvec.size() != nchan_)
971    throw(AipsError("Internal error. The length of output vector differs from nchan_"));
972
973#ifdef KS_DEBUG
974  cout << "Start shifting flag for " << shift << "channels" << endl;
975#endif
976
977  // shift is almost integer think it as int.
978  // tolerance should be in 0 - 1
979  double tolerance = 0.01;
980  // tweak shift to be in 0 ~ nchan_-1
981  if ( fabs(shift) > nchan_ ) shift = fmod(shift, nchan_);
982  if (shift < 0.) shift += nchan_;
983  double rweight = fmod(shift, 1.);
984  bool ruse(true), luse(true);
985  if (rweight < 0.) rweight += 1.;
986  if (rweight < tolerance){
987    // the shift is almost lchan
988    ruse = false;
989    luse = true;
990  }
991  if (rweight > 1-tolerance){
992    // the shift is almost rchan
993    ruse = true;
994    luse = false;
995  }
996  uInt lchan, rchan;
997
998  outvec = false;
999  for (uInt i = 0 ; i < nchan_ ; i++) {
1000    lchan = uInt( floor( fmod( (i + shift), nchan_ ) ) );
1001    if (lchan < 0.) lchan += nchan_;
1002    rchan = ( (lchan + 1) % nchan_ );
1003    outvec(lchan) |= (invec(i) && luse);
1004    outvec(rchan) |= (invec(i) && ruse);
1005#ifdef KS_DEBUG
1006    if (i == 2350 || i == 2930) {
1007      cout << "Channel= " << i << " of input vector: " << endl;
1008      cout << "L channel = " << lchan << endl;
1009      cout << "R channel = " << rchan << endl;
1010      cout << "L channel will be " << (luse ? "used" : "ignored") << endl;
1011      cout << "R channel will be " << (ruse ? "used" : "ignored") << endl;
1012    }
1013#endif
1014  }
1015};
1016
1017
1018void STSideBandSep::deconvolve(Matrix<float> &specmat,
1019                               const vector<double> shiftvec,
1020                               const double threshold,
1021                               Matrix<float> &outmat)
1022{
1023  LogIO os(LogOrigin("STSideBandSep","deconvolve()", WHERE));
1024  if (specmat.nrow() != nchan_)
1025    throw(AipsError("Internal error. The length of input matrix differs from nchan_"));
1026  if (specmat.ncolumn() != shiftvec.size())
1027    throw(AipsError("Internal error. The number of input shifts and spectrum  differs."));
1028
1029#ifdef KS_DEBUG
1030  float minval, maxval;
1031#endif
1032#ifdef KS_DEBUG
1033  minMax(minval, maxval, specmat);
1034  cout << "Max/Min of input Matrix = (max: " << maxval << ", min: " << minval << ")" << endl;
1035#endif
1036
1037  uInt ninsp = shiftvec.size();
1038  outmat.resize(nchan_, ninsp*(ninsp-1)/2, 0.);
1039  Matrix<Complex> fftspmat(nchan_/2+1, ninsp, 0.);
1040  Vector<float> rvecref(nchan_, 0.);
1041  Vector<Complex> cvecref(nchan_/2+1, 0.);
1042  uInt icol = 0;
1043  unsigned int nreject = 0;
1044
1045#ifdef KS_DEBUG
1046  cout << "Starting initial FFT. The number of input spectra = " << ninsp << endl;
1047  cout << "out matrix has ncolumn = " << outmat.ncolumn() << endl;
1048#endif
1049
1050  for (uInt isp = 0 ; isp < ninsp ; isp++) {
1051    rvecref.reference( specmat.column(isp) );
1052    cvecref.reference( fftspmat.column(isp) );
1053
1054#ifdef KS_DEBUG
1055    minMax(minval, maxval, rvecref);
1056    cout << "Max/Min of inv FFTed Matrix = (max: " << maxval << ", min: " << minval << ")" << endl;
1057#endif
1058
1059    fftsf.fft0(cvecref, rvecref, true);
1060
1061#ifdef KS_DEBUG
1062    double maxr=cvecref[0].real(), minr=cvecref[0].real(),
1063      maxi=cvecref[0].imag(), mini=cvecref[0].imag();
1064    for (uInt i = 1; i<cvecref.size();i++){
1065      maxr = max(maxr, cvecref[i].real());
1066      maxi = max(maxi, cvecref[i].imag());
1067      minr = min(minr, cvecref[i].real());
1068      mini = min(mini, cvecref[i].imag());
1069    }
1070    cout << "Max/Min of inv FFTed Matrix (size=" << cvecref.size() << ") = (max: " << maxr << " + " << maxi << "j , min: " << minr << " + " << mini << "j)" << endl;
1071#endif
1072  }
1073
1074  //Liberate from reference
1075  rvecref.unique();
1076
1077  Vector<Complex> cspec(nchan_/2+1, 0.);
1078  const double PI = 6.0 * asin(0.5);
1079  const double nchani = 1. / (float) nchan_;
1080  const Complex trans(0., 1.);
1081#ifdef KS_DEBUG
1082  cout << "starting actual deconvolution" << endl;
1083#endif
1084  for (uInt j = 0 ; j < ninsp ; j++) {
1085    for (uInt k = j+1 ; k < ninsp ; k++) {
1086      const double dx = (shiftvec[k] - shiftvec[j]) * 2. * PI * nchani;
1087
1088#ifdef KS_DEBUG
1089      cout << "icol = " << icol << endl;
1090#endif
1091
1092      for (uInt ichan = 0 ; ichan < cspec.size() ; ichan++){
1093        cspec[ichan] = ( fftspmat(ichan, j) + fftspmat(ichan, k) )*0.5;
1094        double phase = dx*ichan;
1095        if ( fabs( sin(phase) ) > threshold){
1096          cspec[ichan] += ( fftspmat(ichan, j) - fftspmat(ichan, k) ) * 0.5
1097            * trans * sin(phase) / ( 1. - cos(phase) );
1098        } else {
1099          nreject++;
1100        }
1101      } // end of channel loop
1102
1103#ifdef KS_DEBUG
1104      cout << "done calculation of cspec" << endl;
1105#endif
1106
1107      Vector<Float> rspec;
1108      rspec.reference( outmat.column(icol) );
1109
1110#ifdef KS_DEBUG
1111      cout << "Starting inverse FFT. icol = " << icol << endl;
1112      //cout << "- size of complex vector = " << cspec.size() << endl;
1113      double maxr=cspec[0].real(), minr=cspec[0].real(),
1114        maxi=cspec[0].imag(), mini=cspec[0].imag();
1115      for (uInt i = 1; i<cspec.size();i++){
1116        maxr = max(maxr, cspec[i].real());
1117        maxi = max(maxi, cspec[i].imag());
1118        minr = min(minr, cspec[i].real());
1119        mini = min(mini, cspec[i].imag());
1120      }
1121      cout << "Max/Min of conv vector (size=" << cspec.size() << ") = (max: " << maxr << " + " << maxi << "j , min: " << minr << " + " << mini << "j)" << endl;
1122#endif
1123
1124      fftsi.fft0(rspec, cspec, false);
1125
1126#ifdef KS_DEBUG
1127      //cout << "- size of inversed real vector = " << rspec.size() << endl;
1128      minMax(minval, maxval, rspec);
1129      cout << "Max/Min of inv FFTed Vector (size=" << rspec.size() << ") = (max: " << maxval << ", min: " << minval << ")" << endl;
1130      //cout << "Done inverse FFT. icol = " << icol << endl;
1131#endif
1132
1133      icol++;
1134    }
1135  }
1136
1137#ifdef KS_DEBUG
1138  minMax(minval, maxval, outmat);
1139  cout << "Max/Min of inv FFTed Matrix = (max: " << maxval << ", min: " << minval << ")" << endl;
1140#endif
1141
1142  os << "Threshold = " << threshold << ", Rejected channels = " << nreject << endl;
1143};
1144
1145
1146void STSideBandSep::aggregateMat(Matrix<float> &inmat,
1147                                 vector<float> &outvec)
1148{
1149  LogIO os(LogOrigin("STSideBandSep","aggregateMat()", WHERE));
1150  if (inmat.nrow() != nchan_)
1151    throw(AipsError("Internal error. The row numbers of input matrix differs from nchan_"));
1152//   if (outvec.size() != nchan_)
1153//     throw(AipsError("Internal error. The size of output vector should be equal to nchan_"));
1154
1155  os << "Averaging " << inmat.ncolumn() << " spectra in the input matrix."
1156     << LogIO::POST;
1157
1158  const uInt nspec = inmat.ncolumn();
1159  const double scale = 1./( (double) nspec );
1160  // initialize values with 0
1161  outvec.assign(nchan_, 0);
1162  for (uInt isp = 0 ; isp < nspec ; isp++) {
1163    for (uInt ich = 0 ; ich < nchan_ ; ich++) {
1164      outvec[ich] += inmat(ich, isp);
1165    }
1166  }
1167
1168  vector<float>::iterator iter;
1169  for (iter = outvec.begin(); iter != outvec.end(); iter++){
1170    *iter *= scale;
1171  }
1172};
1173
1174void STSideBandSep::subtractFromOther(const Matrix<float> &shiftmat,
1175                                      const vector<float> &invec,
1176                                      const vector<double> &shift,
1177                                      vector<float> &outvec)
1178{
1179  LogIO os(LogOrigin("STSideBandSep","subtractFromOther()", WHERE));
1180  if (shiftmat.nrow() != nchan_)
1181    throw(AipsError("Internal error. The row numbers of input matrix differs from nchan_"));
1182  if (invec.size() != nchan_)
1183    throw(AipsError("Internal error. The length of input vector should be nchan_"));
1184  if (shift.size() != shiftmat.ncolumn())
1185    throw(AipsError("Internal error. The column numbers of input matrix != the number of elements in shift"));
1186
1187  const uInt nspec = shiftmat.ncolumn();
1188  Vector<float> subsp(nchan_, 0.), shiftsub;
1189  Matrix<float> submat(nchan_, nspec, 0.);
1190  vector<float>::iterator iter;
1191  for (uInt isp = 0 ; isp < nspec ; isp++) {
1192    for (uInt ich = 0; ich < nchan_ ; ich++) {
1193      subsp(ich) = shiftmat(ich, isp) - invec[ich];
1194    }
1195    shiftsub.reference(submat.column(isp));
1196    shiftSpectrum(subsp, shift[isp], shiftsub);
1197  }
1198
1199  aggregateMat(submat, outvec);
1200};
1201
1202
1203void STSideBandSep::setLO1(const string lo1, const string frame,
1204                           const double reftime, const string refdir)
1205{
1206  Quantum<Double> qfreq;
1207  readQuantity(qfreq, String(lo1));
1208  lo1Freq_ = qfreq.getValue("Hz");
1209  MFrequency::getType(loFrame_, frame);
1210  loTime_ = reftime;
1211  loDir_ = refdir;
1212
1213#ifdef KS_DEBUG
1214  cout << "STSideBandSep::setLO1" << endl;
1215  if (lo1Freq_ > 0.)
1216    cout << "lo1 = " << lo1Freq_ << " [Hz] (" << frame << ")" << endl;
1217  if (loTime_ > 0.)
1218    cout << "ref time = " << loTime_ << " [day]" << endl;
1219  if (!loDir_.empty())
1220    cout << "ref direction = " << loDir_ << " [day]" << endl;
1221#endif
1222};
1223
1224void STSideBandSep::setLO1Root(string name)
1225{
1226   LogIO os(LogOrigin("STSideBandSep","setLO1Root()", WHERE));
1227   os << "Searching for '" << name << "'..." << LogIO::POST;
1228  // Check for existance of the file
1229  if (!checkFile(name)) {
1230     throw(AipsError("File does not exist"));
1231  }
1232  if (name[(name.size()-1)] == '/')
1233    name = name.substr(0,(name.size()-2));
1234
1235  if (checkFile(name+"/Receiver.xml", "file") &&
1236      checkFile(name+"/SpectralWindow.xml", "file")){
1237    os << "Found '" << name << "/Receiver.xml' ... got an ASDM name." << LogIO::POST;
1238    asdmName_ = name;
1239  } else if (checkFile(name+"/ASDM_RECEIVER") &&
1240             checkFile(name+"/ASDM_SPECTRALWINDOW")){
1241    os << "Found '" << name << "/ASDM_RECEIVER' ... got a Table name." << LogIO::POST;
1242    asisName_ = name;
1243  } else {
1244    throw(AipsError("Invalid file name. Set an MS or ASDM name."));
1245  }
1246
1247#ifdef KS_DEBUG
1248  cout << "STSideBandSep::setLO1Root" << endl;
1249  if (!asdmName_.empty())
1250    cout << "asdm name = " << asdmName_ << endl;
1251  if (!asisName_.empty())
1252    cout << "MS name = " << asisName_ << endl;
1253#endif
1254};
1255
1256
1257void STSideBandSep::solveImageFrequency()
1258{
1259  LogIO os(LogOrigin("STSideBandSep","solveImageFreqency()", WHERE));
1260  os << "Start calculating frequencies of image side band" << LogIO::POST;
1261
1262  if (imgTab_p.null())
1263    throw AipsError("STSideBandSep::solveImageFreqency - an image side band scantable should be set first");
1264
1265  // Convert frequency REFVAL to the value in frame of LO.
1266  // The code assumes that imgTab_p has only an IF and only a FREQ_ID
1267  // is associated to an IFNO
1268  // TODO: More complete Procedure would be
1269  // 1. Get freq IDs associated to sigIfno_
1270  // 2. Get freq information of the freq IDs
1271  // 3. For each freqIDs, get freq infromation in TOPO and an LO1
1272  //    frequency and calculate image band frequencies.
1273  STFrequencies freqTab_ = imgTab_p->frequencies();
1274  // get the base frame of table
1275  const MFrequency::Types tabframe = freqTab_.getFrame(true);
1276  TableVector<uInt> freqIdVec( imgTab_p->table(), "FREQ_ID" );
1277  // assuming single freqID per IFNO
1278  uInt freqid = freqIdVec(0);
1279  int nChan = imgTab_p->nchan(imgTab_p->getIF(0));
1280  double refpix, refval, increment ;
1281  freqTab_.getEntry(refpix, refval, increment, freqid);
1282  //MFrequency sigrefval = MFrequency(MVFrequency(refval),tabframe);
1283  // get freq infromation of sigIfno_ in loFrame_
1284  const MPosition mp = imgTab_p->getAntennaPosition();
1285  MEpoch me;
1286  MDirection md;
1287  if (loTime_ < 0.)
1288    me = imgTab_p->getEpoch(-1);
1289  else
1290    me = MEpoch(MVEpoch(loTime_));
1291  if (loDir_.empty()) {
1292    ArrayColumn<Double> srcdirCol_;
1293    srcdirCol_.attach(imgTab_p->table(), "SRCDIRECTION");
1294    // Assuming J2000 and SRCDIRECTION in unit of rad
1295    Quantum<Double> srcra = Quantum<Double>(srcdirCol_(0)(IPosition(1,0)), "rad");
1296    Quantum<Double> srcdec = Quantum<Double>(srcdirCol_(0)(IPosition(1,1)), "rad");
1297    md = MDirection(srcra, srcdec, MDirection::J2000);
1298    //imgTab_p->getDirection(0);
1299  } else {
1300    // parse direction string
1301    string::size_type pos0 = loDir_.find(" ");
1302   
1303    if (pos0 == string::npos) {
1304      throw AipsError("bad string format in LO1 direction");
1305    }
1306    string::size_type pos1 = loDir_.find(" ", pos0+1);
1307    String sepoch, sra, sdec;
1308    if (pos1 != string::npos) {
1309      sepoch = loDir_.substr(0, pos0);
1310      sra = loDir_.substr(pos0+1, pos1-pos0);
1311      sdec = loDir_.substr(pos1+1);
1312    }
1313    MDirection::Types epoch;
1314    MDirection::getType(epoch, sepoch);
1315    QuantumHolder qh ;
1316    String err ;
1317    qh.fromString( err, sra);
1318    Quantum<Double> ra = qh.asQuantumDouble() ;
1319    qh.fromString( err, sdec ) ;
1320    Quantum<Double> dec = qh.asQuantumDouble() ;
1321    //md = MDirection(ra.getValue("rad"), dec.getValue("rad"),epoch);
1322    md = MDirection(ra, dec, epoch);
1323  }
1324  MeasFrame mframe( me, mp, md );
1325  MFrequency::Convert tobframe(loFrame_, MFrequency::Ref(tabframe, mframe));
1326  MFrequency::Convert toloframe(tabframe, MFrequency::Ref(loFrame_, mframe));
1327  // Convert refval to loFrame_
1328  double sigrefval;
1329  if (tabframe == loFrame_)
1330    sigrefval = refval;
1331  else
1332    sigrefval = toloframe(Quantum<Double>(refval, "Hz")).get("Hz").getValue();
1333
1334  // Check for the availability of LO1
1335  if (lo1Freq_ > 0.) {
1336    os << "Using user defined LO1 frequency." << LogIO::POST;
1337  } else if (!asisName_.empty()) {
1338      // MS name is set.
1339    os << "Using user defined MS (asis): " << asisName_ << LogIO::POST;
1340    if (!getLo1FromAsisTab(asisName_, sigrefval, refpix, increment, nChan)) {
1341      throw AipsError("Failed to get LO1 frequency from MS");
1342    }
1343  } else if (!asdmName_.empty()) {
1344      // ASDM name is set.
1345    os << "Using user defined ASDM: " << asdmName_ << LogIO::POST;
1346    if (!getLo1FromAsdm(asdmName_, sigrefval, refpix, increment, nChan)) {
1347      throw AipsError("Failed to get LO1 frequency from ASDM");
1348    }
1349  } else {
1350    // Try getting ASDM name from scantable header
1351    os << "Try getting information from scantable header" << LogIO::POST;
1352    if (!getLo1FromScanTab(tableList_[0], sigrefval, refpix, increment, nChan)) {
1353      //throw AipsError("Failed to get LO1 frequency from asis table");
1354      os << LogIO::WARN << "Failed to get LO1 frequency using information in scantable." << LogIO::POST;
1355      os << LogIO::WARN << "Could not fill frequency information of IMAGE sideband properly." << LogIO::POST;
1356      os << LogIO::WARN << "Storing values of SIGNAL sideband in FREQUENCIES table" << LogIO::POST;
1357      return;
1358    }
1359  }
1360
1361  // LO1 should now be ready.
1362  if (lo1Freq_ < 0.)
1363    throw(AipsError("Got negative LO1 Frequency"));
1364
1365  // Print summary
1366  {
1367    // LO1
1368    Vector<Double> dirvec = md.getAngle(Unit(String("rad"))).getValue();
1369    os << "[LO1 settings]" << LogIO::POST;
1370    os << "- Frequency: " << lo1Freq_ << " [Hz] ("
1371       << MFrequency::showType(loFrame_) << ")" << LogIO::POST;
1372    os << "- Reference time: " << me.get(Unit(String("d"))).getValue()
1373       << " [day]" << LogIO::POST;
1374    os << "- Reference direction: [" << dirvec[0] << ", " << dirvec[1]
1375       << "] (" << md.getRefString() << ") " << LogIO::POST;
1376
1377    // signal sideband
1378    os << "[Signal side band]" << LogIO::POST;
1379    os << "- IFNO: " << imgTab_p->getIF(0) << " (FREQ_ID = " << freqid << ")"
1380       << LogIO::POST;
1381    os << "- Reference value: " << refval << " [Hz] ("
1382       << MFrequency::showType(tabframe) << ") = "
1383       << sigrefval << " [Hz] (" <<  MFrequency::showType(loFrame_)
1384       << ")" << LogIO::POST;
1385    os << "- Reference pixel: " << refpix  << LogIO::POST;
1386    os << "- Increment: " << increment << " [Hz]" << LogIO::POST;
1387  }
1388
1389  // Calculate image band incr and refval in loFrame_
1390  Double imgincr = -increment;
1391  Double imgrefval = 2 * lo1Freq_ - sigrefval;
1392  Double imgrefval_tab = imgrefval;
1393  // Convert imgrefval back to table base frame
1394  if (tabframe != loFrame_)
1395    imgrefval = tobframe(Quantum<Double>(imgrefval, "Hz")).get("Hz").getValue();
1396  // Set new frequencies table
1397  uInt fIDnew = freqTab_.addEntry(refpix, imgrefval, imgincr);
1398  // Update FREQ_ID in table.
1399  freqIdVec = fIDnew;
1400
1401  // Print summary (Image sideband)
1402  {
1403    os << "[Image side band]" << LogIO::POST;
1404    os << "- IFNO: " << imgTab_p->getIF(0) << " (FREQ_ID = " << freqIdVec(0)
1405       << ")" << LogIO::POST;
1406    os << "- Reference value: " << imgrefval << " [Hz] ("
1407       << MFrequency::showType(tabframe) << ") = "
1408       << imgrefval_tab << " [Hz] (" <<  MFrequency::showType(loFrame_)
1409       << ")" << LogIO::POST;
1410    os << "- Reference pixel: " << refpix  << LogIO::POST;
1411    os << "- Increment: " << imgincr << " [Hz]" << LogIO::POST;
1412  }
1413};
1414
1415Bool STSideBandSep::checkFile(const string name, string type)
1416{
1417  File file(name);
1418  if (!file.exists()){
1419    return false;
1420  } else if (type.empty()) {
1421    return true;
1422  } else {
1423    // Check for file type
1424    switch (tolower(type[0])) {
1425    case 'f':
1426      return file.isRegular(True);
1427    case 'd':
1428      return file.isDirectory(True);
1429    case 's':
1430      return file.isSymLink();
1431    default:
1432      throw AipsError("Invalid file type. Available types are 'file', 'directory', and 'symlink'.");
1433    }
1434  }
1435};
1436
1437bool STSideBandSep::getLo1FromAsdm(const string asdmname,
1438                                   const double /*refval*/,
1439                                   const double /*refpix*/,
1440                                   const double /*increment*/,
1441                                   const int /*nChan*/)
1442{
1443  // Check for relevant tables.
1444  string spwname = asdmname + "/SpectralWindow.xml";
1445  string recname = asdmname + "/Receiver.xml";
1446  if (!checkFile(spwname) || !checkFile(recname)) {
1447    throw(AipsError("Could not find subtables in ASDM"));
1448  }
1449
1450  return false;
1451
1452};
1453
1454
1455bool STSideBandSep::getLo1FromScanTab(CountedPtr< Scantable > &scantab,
1456                                      const double refval,
1457                                      const double refpix,
1458                                      const double increment,
1459                                      const int nChan)
1460{
1461  LogIO os(LogOrigin("STSideBandSep","getLo1FromScanTab()", WHERE));
1462  // Check for relevant tables.
1463  const TableRecord &rec = scantab->table().keywordSet() ;
1464  String spwname, recname;
1465  if (rec.isDefined("ASDM_SPECTRALWINDOW") && rec.isDefined("ASDM_RECEIVER")){
1466    spwname = rec.asString("ASDM_SPECTRALWINDOW");
1467    recname = rec.asString("ASDM_RECEIVER");
1468  }
1469  else {
1470    // keywords are not there
1471    os << LogIO::WARN
1472       << "Could not find necessary table names in scantable header."
1473       << LogIO::POST;
1474    return false;
1475  }
1476  if (!checkFile(spwname,"directory") || !checkFile(recname,"directory")) {
1477    throw(AipsError("Could not find relevant subtables in MS"));
1478  }
1479  // Get root MS name
1480  string msname;
1481  const String recsuff = "/ASDM_RECEIVER";
1482  String::size_type pos;
1483  pos = recname.size()-recsuff.size();
1484  if (recname.substr(pos) == recsuff)
1485    msname = recname.substr(0, pos);
1486  else
1487    throw(AipsError("Internal error in parsing table name from a scantable keyword."));
1488
1489  if (!checkFile(msname))
1490    throw(AipsError("Internal error in parsing MS name from a scantable keyword."));
1491
1492  return getLo1FromAsisTab(msname, refval, refpix, increment, nChan);
1493
1494};
1495
1496bool STSideBandSep::getLo1FromAsisTab(const string msname,
1497                                      const double refval,
1498                                      const double refpix,
1499                                      const double increment,
1500                                      const int nChan)
1501{
1502  LogIO os(LogOrigin("STSideBandSep","getLo1FromAsisTab()", WHERE));
1503  os << "Searching an LO1 frequency in '" << msname << "'" << LogIO::POST;
1504  // Check for relevant tables.
1505  const string spwname = msname + "/ASDM_SPECTRALWINDOW";
1506  const string recname = msname + "/ASDM_RECEIVER";
1507  if (!checkFile(spwname,"directory") || !checkFile(recname,"directory")) {
1508    throw(AipsError("Could not find relevant tables in MS"));
1509  }
1510
1511  Table spwtab_ = Table(spwname);
1512  String asdmSpw;
1513  ROTableRow spwrow(spwtab_);
1514  const Double rtol = 0.01;
1515  for (uInt idx = 0; idx < spwtab_.nrow(); idx++){
1516    const TableRecord& rec = spwrow.get(idx);
1517    // Compare nchan
1518    if (rec.asInt("numChan") != (Int) nChan)
1519      continue;
1520    // Compare increment
1521    Double asdminc;
1522    Array<Double> incarr = rec.asArrayDouble("chanWidthArray");
1523    if (incarr.size() > 0)
1524      asdminc = incarr(IPosition(1, (uInt) refpix));
1525    else
1526      asdminc = rec.asDouble("chanWidth");
1527    if (abs(asdminc - abs(increment)) > rtol * abs(increment))
1528      continue;
1529    // Compare refval
1530    Double asdmrefv;
1531    Array<Double> refvarr = rec.asArrayDouble("chanFreqArray");
1532    if (refvarr.size() > 0){
1533      const uInt iref = (uInt) refpix;
1534      const Double ratio = refpix - (Double) iref;
1535      asdmrefv = refvarr(IPosition(1, iref))*(1.-ratio)
1536        + refvarr(IPosition(1,iref+1))*ratio;
1537    }
1538    else {
1539      const Double ch0 = rec.asDouble("chanFreqStart");
1540      const Double chstep = rec.asDouble("chanFreqStep");
1541      asdmrefv = ch0 + chstep * refpix;
1542    }
1543    if (abs(asdmrefv - refval) < 0.5*abs(asdminc)){
1544      asdmSpw = rec.asString("spectralWindowId");
1545      break;
1546    }
1547  }
1548
1549  if (asdmSpw.empty()){
1550    os << LogIO::WARN << "Could not find relevant SPW ID in " << spwname << LogIO::POST;
1551    return false;
1552  }
1553  else {
1554    os << asdmSpw << " in " << spwname
1555       << " matches the freqeuncies of signal side band." << LogIO::POST;
1556  }
1557
1558  Table rectab_ = Table(recname);
1559  ROTableRow recrow(rectab_);
1560  for (uInt idx = 0; idx < rectab_.nrow(); idx++){
1561    const TableRecord& rec = recrow.get(idx);
1562    if (rec.asString("spectralWindowId") == asdmSpw){
1563      const Array<Double> loarr = rec.asArrayDouble("freqLO");
1564      lo1Freq_ = loarr(IPosition(1,0));
1565      os << "Found LO1 Frequency in " << recname << ": "
1566         << lo1Freq_ << " [Hz]" << LogIO::POST;
1567      return true;
1568    }
1569  }
1570  os << LogIO::WARN << "Could not find " << asdmSpw << " in " << recname
1571     << LogIO::POST;
1572  return false;
1573};
1574
1575} //namespace asap
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