source: trunk/src/STMath.cpp@ 2643

Last change on this file since 2643 was 2643, checked in by ShinnosukeKawakami, 12 years ago

hpc34 to trunk 24th Aug. 2012
  • Property svn:eol-style set to native
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File size: 162.6 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 <sstream>
14
15#include <casa/iomanip.h>
16#include <casa/Arrays/MaskArrLogi.h>
17#include <casa/Arrays/MaskArrMath.h>
18#include <casa/Arrays/ArrayLogical.h>
19#include <casa/Arrays/ArrayMath.h>
20#include <casa/Arrays/Slice.h>
21#include <casa/Arrays/Slicer.h>
22#include <casa/BasicSL/String.h>
23#include <casa/Containers/Block.h>
24#include <casa/Containers/RecordField.h>
25#include <casa/Exceptions/Error.h>
26#include <casa/Logging/LogIO.h>
27
28#include <coordinates/Coordinates/CoordinateSystem.h>
29#include <coordinates/Coordinates/CoordinateUtil.h>
30#include <coordinates/Coordinates/FrequencyAligner.h>
31#include <coordinates/Coordinates/SpectralCoordinate.h>
32
33#include <lattices/Lattices/LatticeUtilities.h>
34
35#include <scimath/Functionals/Polynomial.h>
36#include <scimath/Mathematics/Convolver.h>
37#include <scimath/Mathematics/VectorKernel.h>
38
39#include <tables/Tables/ExprNode.h>
40#include <tables/Tables/ReadAsciiTable.h>
41#include <tables/Tables/TableCopy.h>
42#include <tables/Tables/TableIter.h>
43#include <tables/Tables/TableParse.h>
44#include <tables/Tables/TableRecord.h>
45#include <tables/Tables/TableRow.h>
46#include <tables/Tables/TableVector.h>
47#include <tables/Tables/TabVecMath.h>
48
49#include <atnf/PKSIO/SrcType.h>
50
51#include "RowAccumulator.h"
52#include "STAttr.h"
53#include "STMath.h"
54#include "STSelector.h"
55#include "Accelerator.h"
56#include "STIdxIter.h"
57
58using namespace casa;
59using namespace asap;
60
61// 2012/02/17 TN
62// Since STGrid is implemented, average doesn't consider direction
63// when accumulating
64// tolerance for direction comparison (rad)
65// #define TOL_OTF 1.0e-15
66// #define TOL_POINT 2.9088821e-4 // 1 arcmin
67
68STMath::STMath(bool insitu) :
69 insitu_(insitu)
70{
71}
72
73
74STMath::~STMath()
75{
76}
77
78CountedPtr<Scantable>
79STMath::average( const std::vector<CountedPtr<Scantable> >& in,
80 const std::vector<bool>& mask,
81 const std::string& weight,
82 const std::string& avmode)
83{
84// double t0, t1 ;
85// t0 = mathutil::gettimeofday_sec() ;
86
87 LogIO os( LogOrigin( "STMath", "average()", WHERE ) ) ;
88 if ( avmode == "SCAN" && in.size() != 1 )
89 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
90 "Use merge first."));
91 WeightType wtype = stringToWeight(weight);
92
93 // 2012/02/17 TN
94 // Since STGrid is implemented, average doesn't consider direction
95 // when accumulating
96 // check if OTF observation
97// String obstype = in[0]->getHeader().obstype ;
98// Double tol = 0.0 ;
99// if ( (obstype.find( "OTF" ) != String::npos) || (obstype.find( "OBSERVE_TARGET" ) != String::npos) ) {
100// tol = TOL_OTF ;
101// }
102// else {
103// tol = TOL_POINT ;
104// }
105
106 // output
107 // clone as this is non insitu
108 bool insitu = insitu_;
109 setInsitu(false);
110 CountedPtr< Scantable > out = getScantable(in[0], true);
111 setInsitu(insitu);
112 std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
113 ++stit;
114 while ( stit != in.end() ) {
115 out->appendToHistoryTable((*stit)->history());
116 ++stit;
117 }
118
119 Table& tout = out->table();
120
121 /// @todo check if all scantables are conformant
122
123 ArrayColumn<Float> specColOut(tout,"SPECTRA");
124 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
125 ArrayColumn<Float> tsysColOut(tout,"TSYS");
126 ScalarColumn<Double> mjdColOut(tout,"TIME");
127 ScalarColumn<Double> intColOut(tout,"INTERVAL");
128 ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
129 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
130
131 // set up the output table rows. These are based on the structure of the
132 // FIRST scantable in the vector
133 const Table& baset = in[0]->table();
134
135 RowAccumulator acc(wtype);
136 Vector<Bool> cmask(mask);
137 acc.setUserMask(cmask);
138// ROTableRow row(tout);
139 ROArrayColumn<Float> specCol, tsysCol;
140 ROArrayColumn<uChar> flagCol;
141 ROScalarColumn<Double> mjdCol, intCol;
142 ROScalarColumn<Int> scanIDCol;
143
144 //Vector<uInt> rowstodelete;
145 Block<uInt> rowstodelB( in[0]->nrow() ) ;
146 uInt nrowdel = 0 ;
147
148// Block<String> cols(3);
149 vector<string> cols(3) ;
150 cols[0] = String("BEAMNO");
151 cols[1] = String("IFNO");
152 cols[2] = String("POLNO");
153 if ( avmode == "SOURCE" ) {
154 cols.resize(4);
155 cols[3] = String("SRCNAME");
156 }
157 if ( avmode == "SCAN" && in.size() == 1) {
158 //cols.resize(4);
159 //cols[3] = String("SCANNO");
160 cols.resize(5);
161 cols[3] = String("SRCNAME");
162 cols[4] = String("SCANNO");
163 }
164 uInt outrowCount = 0;
165 // use STIdxIterExAcc instead of TableIterator
166 STIdxIterExAcc iter( in[0], cols ) ;
167// double t2 = 0 ;
168// double t3 = 0 ;
169// double t4 = 0 ;
170// double t5 = 0 ;
171// TableIterator iter(baset, cols);
172// int count = 0 ;
173 while (!iter.pastEnd()) {
174 Vector<uInt> rows = iter.getRows( SHARE ) ;
175 if ( rows.nelements() == 0 ) {
176 iter.next() ;
177 continue ;
178 }
179 Vector<uInt> current = iter.current() ;
180 String srcname = iter.getSrcName() ;
181 //Table subt = iter.table();
182 // copy the first row of this selection into the new table
183 tout.addRow();
184// t4 = mathutil::gettimeofday_sec() ;
185 // skip to copy SPECTRA, FLAGTRA, and TSYS since those heavy columns are
186 // overwritten in the following process
187 copyRows( tout, baset, outrowCount, rows[0], 1, False, False, False ) ;
188// t5 += mathutil::gettimeofday_sec() - t4 ;
189 // re-index to 0
190 if ( avmode != "SCAN" && avmode != "SOURCE" ) {
191 scanColOut.put(outrowCount, uInt(0));
192 }
193
194 // 2012/02/17 TN
195 // Since STGrid is implemented, average doesn't consider direction
196 // when accumulating
197// MDirection::ScalarColumn dircol ;
198// dircol.attach( subt, "DIRECTION" ) ;
199// Int length = subt.nrow() ;
200// vector< Vector<Double> > dirs ;
201// vector<int> indexes ;
202// for ( Int i = 0 ; i < length ; i++ ) {
203// Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
204// //os << << count++ << ": " ;
205// //os << "[" << t[0] << "," << t[1] << "]" << LogIO::POST ;
206// bool adddir = true ;
207// for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
208// //if ( allTrue( t == dirs[j] ) ) {
209// Double dx = t[0] - dirs[j][0] ;
210// Double dy = t[1] - dirs[j][1] ;
211// Double dd = sqrt( dx * dx + dy * dy ) ;
212// //if ( allNearAbs( t, dirs[j], tol ) ) {
213// if ( dd <= tol ) {
214// adddir = false ;
215// break ;
216// }
217// }
218// if ( adddir ) {
219// dirs.push_back( t ) ;
220// indexes.push_back( i ) ;
221// }
222// }
223// uInt rowNum = dirs.size() ;
224// tout.addRow( rowNum ) ;
225// for ( uInt i = 0 ; i < rowNum ; i++ ) {
226// TableCopy::copyRows( tout, subt, outrowCount+i, indexes[i], 1 ) ;
227// // re-index to 0
228// if ( avmode != "SCAN" && avmode != "SOURCE" ) {
229// scanColOut.put(outrowCount+i, uInt(0));
230// }
231// }
232// outrowCount += rowNum ;
233
234 // merge loop
235 uInt i = outrowCount ;
236 // in[0] is already selected by iterator
237 specCol.attach(baset,"SPECTRA");
238 flagCol.attach(baset,"FLAGTRA");
239 tsysCol.attach(baset,"TSYS");
240 intCol.attach(baset,"INTERVAL");
241 mjdCol.attach(baset,"TIME");
242 Vector<Float> spec,tsys;
243 Vector<uChar> flag;
244 Double inter,time;
245
246 for (uInt l = 0; l < rows.nelements(); ++l ) {
247 uInt k = rows[l] ;
248 flagCol.get(k, flag);
249 Vector<Bool> bflag(flag.shape());
250 convertArray(bflag, flag);
251 /*
252 if ( allEQ(bflag, True) ) {
253 continue;//don't accumulate
254 }
255 */
256 specCol.get(k, spec);
257 tsysCol.get(k, tsys);
258 intCol.get(k, inter);
259 mjdCol.get(k, time);
260 // spectrum has to be added last to enable weighting by the other values
261// t2 = mathutil::gettimeofday_sec() ;
262 acc.add(spec, !bflag, tsys, inter, time);
263// t3 += mathutil::gettimeofday_sec() - t2 ;
264
265 }
266
267
268 // in[0] is already selected by TableIterator so that index is
269 // started from 1
270 for ( int j=1; j < int(in.size()); ++j ) {
271 const Table& tin = in[j]->table();
272 //const TableRecord& rec = row.get(i);
273 ROScalarColumn<Double> tmp(tin, "TIME");
274 Double td;tmp.get(0,td);
275
276#if 1
277 static char const*const colNames1[] = { "IFNO", "BEAMNO", "POLNO" };
278 //uInt const values1[] = { rec.asuInt("IFNO"), rec.asuInt("BEAMNO"), rec.asuInt("POLNO") };
279 uInt const values1[] = { current[1], current[0], current[2] };
280 SingleTypeEqPredicate<uInt, 3> myPred(tin, colNames1, values1);
281 CustomTableExprNodeRep myNodeRep(tin, myPred);
282 myNodeRep.link(); // to avoid automatic delete when myExpr is destructed.
283 CustomTableExprNode myExpr(myNodeRep);
284 Table basesubt = tin(myExpr);
285#else
286// Table basesubt = tin( tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
287// && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
288// && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
289 Table basesubt = tin( tin.col("BEAMNO") == current[0]
290 && tin.col("IFNO") == current[1]
291 && tin.col("POLNO") == current[2] );
292#endif
293 Table subt;
294 if ( avmode == "SOURCE") {
295// subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME"));
296 subt = basesubt( basesubt.col("SRCNAME") == srcname );
297
298 } else if (avmode == "SCAN") {
299// subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME")
300// && basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
301 subt = basesubt( basesubt.col("SRCNAME") == srcname
302 && basesubt.col("SCANNO") == current[4] );
303 } else {
304 subt = basesubt;
305 }
306
307 // 2012/02/17 TN
308 // Since STGrid is implemented, average doesn't consider direction
309 // when accumulating
310// vector<uInt> removeRows ;
311// uInt nrsubt = subt.nrow() ;
312// for ( uInt irow = 0 ; irow < nrsubt ; irow++ ) {
313// //if ( !allTrue((subt.col("DIRECTION").getArrayDouble(TableExprId(irow)))==rec.asArrayDouble("DIRECTION")) ) {
314// Vector<Double> x0 = (subt.col("DIRECTION").getArrayDouble(TableExprId(irow))) ;
315// Vector<Double> x1 = rec.asArrayDouble("DIRECTION") ;
316// double dx = x0[0] - x1[0];
317// double dy = x0[1] - x1[1];
318// Double dd = sqrt( dx * dx + dy * dy ) ;
319// //if ( !allNearAbs((subt.col("DIRECTION").getArrayDouble(TableExprId(irow))), rec.asArrayDouble("DIRECTION"), tol ) ) {
320// if ( dd > tol ) {
321// removeRows.push_back( irow ) ;
322// }
323// }
324// if ( removeRows.size() != 0 ) {
325// subt.removeRow( removeRows ) ;
326// }
327
328// if ( nrsubt == removeRows.size() )
329// throw(AipsError("Averaging data is empty.")) ;
330
331 specCol.attach(subt,"SPECTRA");
332 flagCol.attach(subt,"FLAGTRA");
333 tsysCol.attach(subt,"TSYS");
334 intCol.attach(subt,"INTERVAL");
335 mjdCol.attach(subt,"TIME");
336 for (uInt k = 0; k < subt.nrow(); ++k ) {
337 flagCol.get(k, flag);
338 Vector<Bool> bflag(flag.shape());
339 convertArray(bflag, flag);
340 /*
341 if ( allEQ(bflag, True) ) {
342 continue;//don't accumulate
343 }
344 */
345 specCol.get(k, spec);
346 //tsysCol.get(k, tsys);
347 tsys.assign( tsysCol(k) );
348 intCol.get(k, inter);
349 mjdCol.get(k, time);
350 // spectrum has to be added last to enable weighting by the other values
351// t2 = mathutil::gettimeofday_sec() ;
352 acc.add(spec, !bflag, tsys, inter, time);
353// t3 += mathutil::gettimeofday_sec() - t2 ;
354 }
355
356 }
357 const Vector<Bool>& msk = acc.getMask();
358 if ( allEQ(msk, False) ) {
359 rowstodelB[nrowdel] = i ;
360 nrowdel++ ;
361 continue;
362 }
363 //write out
364 if (acc.state()) {
365 // If there exists a channel at which all the input spectra are masked,
366 // spec has 'nan' values for that channel and it may affect the following
367 // processes. To avoid this, replacing 'nan' values in spec with
368 // weighted-mean of all spectra in the following line.
369 // (done for CAS-2776, 2011/04/07 by Wataru Kawasaki)
370 acc.replaceNaN();
371
372 Vector<uChar> flg(msk.shape());
373 convertArray(flg, !msk);
374 for (uInt k = 0; k < flg.nelements(); ++k) {
375 uChar userFlag = 1 << 7;
376 if (msk[k]==True) userFlag = 0 << 7;
377 flg(k) = userFlag;
378 }
379
380 flagColOut.put(i, flg);
381 specColOut.put(i, acc.getSpectrum());
382 tsysColOut.put(i, acc.getTsys());
383 intColOut.put(i, acc.getInterval());
384 mjdColOut.put(i, acc.getTime());
385 // we should only have one cycle now -> reset it to be 0
386 // frequency switched data has different CYCLENO for different IFNO
387 // which requires resetting this value
388 cycColOut.put(i, uInt(0));
389 } else {
390 ostringstream oss;
391 oss << "For output row="<<i<<", all input rows of data are flagged. no averaging" << endl;
392 pushLog(String(oss));
393 }
394 acc.reset();
395
396 // merge with while loop for preparing out table
397 ++outrowCount;
398// ++iter ;
399 iter.next() ;
400 }
401
402 if ( nrowdel > 0 ) {
403 Vector<uInt> rowstodelete( IPosition(1,nrowdel), rowstodelB.storage(), SHARE ) ;
404 os << rowstodelete << LogIO::POST ;
405 tout.removeRow(rowstodelete);
406 if (tout.nrow() == 0) {
407 throw(AipsError("Can't average fully flagged data."));
408 }
409 }
410
411// t1 = mathutil::gettimeofday_sec() ;
412// cout << "elapsed time for average(): " << t1-t0 << " sec" << endl ;
413// cout << " elapsed time for acc.add(): " << t3 << " sec" << endl ;
414// cout << " elapsed time for copyRows(): " << t5 << " sec" << endl ;
415
416 return out;
417}
418
419CountedPtr< Scantable >
420STMath::averageChannel( const CountedPtr < Scantable > & in,
421 const std::string & mode,
422 const std::string& avmode )
423{
424 (void) mode; // currently unused
425 // 2012/02/17 TN
426 // Since STGrid is implemented, average doesn't consider direction
427 // when accumulating
428 // check if OTF observation
429// String obstype = in->getHeader().obstype ;
430// Double tol = 0.0 ;
431// if ( obstype.find( "OTF" ) != String::npos ) {
432// tol = TOL_OTF ;
433// }
434// else {
435// tol = TOL_POINT ;
436// }
437
438 // clone as this is non insitu
439 bool insitu = insitu_;
440 setInsitu(false);
441 CountedPtr< Scantable > out = getScantable(in, true);
442 setInsitu(insitu);
443 Table& tout = out->table();
444 ArrayColumn<Float> specColOut(tout,"SPECTRA");
445 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
446 ArrayColumn<Float> tsysColOut(tout,"TSYS");
447 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
448 ScalarColumn<Double> intColOut(tout, "INTERVAL");
449 Table tmp = in->table().sort("BEAMNO");
450 Block<String> cols(3);
451 cols[0] = String("BEAMNO");
452 cols[1] = String("IFNO");
453 cols[2] = String("POLNO");
454 if ( avmode == "SCAN") {
455 cols.resize(4);
456 cols[3] = String("SCANNO");
457 }
458 uInt outrowCount = 0;
459 uChar userflag = 1 << 7;
460 TableIterator iter(tmp, cols);
461 while (!iter.pastEnd()) {
462 Table subt = iter.table();
463 ROArrayColumn<Float> specCol, tsysCol;
464 ROArrayColumn<uChar> flagCol;
465 ROScalarColumn<Double> intCol(subt, "INTERVAL");
466 specCol.attach(subt,"SPECTRA");
467 flagCol.attach(subt,"FLAGTRA");
468 tsysCol.attach(subt,"TSYS");
469
470 tout.addRow();
471 TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
472 if ( avmode != "SCAN") {
473 scanColOut.put(outrowCount, uInt(0));
474 }
475 Vector<Float> tmp;
476 specCol.get(0, tmp);
477 uInt nchan = tmp.nelements();
478 // have to do channel by channel here as MaskedArrMath
479 // doesn't have partialMedians
480 Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
481 Vector<Float> outspec(nchan);
482 Vector<uChar> outflag(nchan,0);
483 Vector<Float> outtsys(1);/// @fixme when tsys is channel based
484 for (uInt i=0; i<nchan; ++i) {
485 Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
486 MaskedArray<Float> ma = maskedArray(specs,flags);
487 outspec[i] = median(ma);
488 if ( allEQ(ma.getMask(), False) )
489 outflag[i] = userflag;// flag data
490 }
491 outtsys[0] = median(tsysCol.getColumn());
492 specColOut.put(outrowCount, outspec);
493 flagColOut.put(outrowCount, outflag);
494 tsysColOut.put(outrowCount, outtsys);
495 Double intsum = sum(intCol.getColumn());
496 intColOut.put(outrowCount, intsum);
497 ++outrowCount;
498 ++iter;
499
500 // 2012/02/17 TN
501 // Since STGrid is implemented, average doesn't consider direction
502 // when accumulating
503// MDirection::ScalarColumn dircol ;
504// dircol.attach( subt, "DIRECTION" ) ;
505// Int length = subt.nrow() ;
506// vector< Vector<Double> > dirs ;
507// vector<int> indexes ;
508// // Handle MX mode averaging
509// if (in->nbeam() > 1 ) {
510// length = 1;
511// }
512// for ( Int i = 0 ; i < length ; i++ ) {
513// Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
514// bool adddir = true ;
515// for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
516// //if ( allTrue( t == dirs[j] ) ) {
517// Double dx = t[0] - dirs[j][0] ;
518// Double dy = t[1] - dirs[j][1] ;
519// Double dd = sqrt( dx * dx + dy * dy ) ;
520// //if ( allNearAbs( t, dirs[j], tol ) ) {
521// if ( dd <= tol ) {
522// adddir = false ;
523// break ;
524// }
525// }
526// if ( adddir ) {
527// dirs.push_back( t ) ;
528// indexes.push_back( i ) ;
529// }
530// }
531// uInt rowNum = dirs.size() ;
532// tout.addRow( rowNum );
533// for ( uInt i = 0 ; i < rowNum ; i++ ) {
534// TableCopy::copyRows(tout, subt, outrowCount+i, indexes[i], 1) ;
535// // Handle MX mode averaging
536// if ( avmode != "SCAN") {
537// scanColOut.put(outrowCount+i, uInt(0));
538// }
539// }
540// MDirection::ScalarColumn dircolOut ;
541// dircolOut.attach( tout, "DIRECTION" ) ;
542// for ( uInt irow = 0 ; irow < rowNum ; irow++ ) {
543// Vector<Double> t = \
544// dircolOut(outrowCount+irow).getAngle(Unit(String("rad"))).getValue() ;
545// Vector<Float> tmp;
546// specCol.get(0, tmp);
547// uInt nchan = tmp.nelements();
548// // have to do channel by channel here as MaskedArrMath
549// // doesn't have partialMedians
550// Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
551// // mask spectra for different DIRECTION
552// for ( uInt jrow = 0 ; jrow < subt.nrow() ; jrow++ ) {
553// Vector<Double> direction = \
554// dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
555// //if ( t[0] != direction[0] || t[1] != direction[1] ) {
556// Double dx = t[0] - direction[0];
557// Double dy = t[1] - direction[1];
558// Double dd = sqrt(dx*dx + dy*dy);
559// //if ( !allNearAbs( t, direction, tol ) ) {
560// if ( dd > tol && in->nbeam() < 2 ) {
561// flags[jrow] = userflag ;
562// }
563// }
564// Vector<Float> outspec(nchan);
565// Vector<uChar> outflag(nchan,0);
566// Vector<Float> outtsys(1);/// @fixme when tsys is channel based
567// for (uInt i=0; i<nchan; ++i) {
568// Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
569// MaskedArray<Float> ma = maskedArray(specs,flags);
570// outspec[i] = median(ma);
571// if ( allEQ(ma.getMask(), False) )
572// outflag[i] = userflag;// flag data
573// }
574// outtsys[0] = median(tsysCol.getColumn());
575// specColOut.put(outrowCount+irow, outspec);
576// flagColOut.put(outrowCount+irow, outflag);
577// tsysColOut.put(outrowCount+irow, outtsys);
578// Vector<Double> integ = intCol.getColumn() ;
579// MaskedArray<Double> mi = maskedArray( integ, flags ) ;
580// Double intsum = sum(mi);
581// intColOut.put(outrowCount+irow, intsum);
582// }
583// outrowCount += rowNum ;
584// ++iter;
585 }
586 return out;
587}
588
589CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
590 bool droprows)
591{
592 if (insitu_) {
593 return in;
594 }
595 else {
596 // clone
597 return CountedPtr<Scantable>(new Scantable(*in, Bool(droprows)));
598 }
599}
600
601CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
602 float val,
603 const std::string& mode,
604 bool tsys )
605{
606 CountedPtr< Scantable > out = getScantable(in, false);
607 Table& tab = out->table();
608 ArrayColumn<Float> specCol(tab,"SPECTRA");
609 ArrayColumn<Float> tsysCol(tab,"TSYS");
610 if (mode=="DIV") val = 1.0/val ;
611 else if (mode=="SUB") val *= -1.0 ;
612 for (uInt i=0; i<tab.nrow(); ++i) {
613 Vector<Float> spec;
614 Vector<Float> ts;
615 specCol.get(i, spec);
616 tsysCol.get(i, ts);
617 if (mode == "MUL" || mode == "DIV") {
618 //if (mode == "DIV") val = 1.0/val;
619 spec *= val;
620 specCol.put(i, spec);
621 if ( tsys ) {
622 ts *= val;
623 tsysCol.put(i, ts);
624 }
625 } else if ( mode == "ADD" || mode == "SUB") {
626 //if (mode == "SUB") val *= -1.0;
627 spec += val;
628 specCol.put(i, spec);
629 if ( tsys ) {
630 ts += val;
631 tsysCol.put(i, ts);
632 }
633 }
634 }
635 return out;
636}
637
638CountedPtr< Scantable > STMath::arrayOperate( const CountedPtr< Scantable >& in,
639 const std::vector<float> val,
640 const std::string& mode,
641 const std::string& opmode,
642 bool tsys )
643{
644 CountedPtr< Scantable > out ;
645 if ( opmode == "channel" ) {
646 out = arrayOperateChannel( in, val, mode, tsys ) ;
647 }
648 else if ( opmode == "row" ) {
649 out = arrayOperateRow( in, val, mode, tsys ) ;
650 }
651 else {
652 throw( AipsError( "Unknown array operation mode." ) ) ;
653 }
654 return out ;
655}
656
657CountedPtr< Scantable > STMath::arrayOperateChannel( const CountedPtr< Scantable >& in,
658 const std::vector<float> val,
659 const std::string& mode,
660 bool tsys )
661{
662 if ( val.size() == 1 ){
663 return unaryOperate( in, val[0], mode, tsys ) ;
664 }
665
666 // conformity of SPECTRA and TSYS
667 if ( tsys ) {
668 TableIterator titer(in->table(), "IFNO");
669 while ( !titer.pastEnd() ) {
670 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
671 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
672 Array<Float> spec = specCol.getColumn() ;
673 Array<Float> ts = tsysCol.getColumn() ;
674 if ( !spec.conform( ts ) ) {
675 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
676 }
677 titer.next() ;
678 }
679 }
680
681 // check if all spectra in the scantable have the same number of channel
682 vector<uInt> nchans;
683 vector<uInt> ifnos = in->getIFNos() ;
684 for ( uInt i = 0 ; i < ifnos.size() ; i++ ) {
685 nchans.push_back( in->nchan( ifnos[i] ) ) ;
686 }
687 Vector<uInt> mchans( nchans ) ;
688 if ( anyNE( mchans, mchans[0] ) ) {
689 throw( AipsError("All spectra in the input scantable must have the same number of channel for vector operation." ) ) ;
690 }
691
692 // check if vector size is equal to nchan
693 Vector<Float> fact( val ) ;
694 if ( fact.nelements() != mchans[0] ) {
695 throw( AipsError("Vector size must be 1 or be same as number of channel.") ) ;
696 }
697
698 // check divided by zero
699 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
700 throw( AipsError("Divided by zero is not recommended." ) ) ;
701 }
702
703 CountedPtr< Scantable > out = getScantable(in, false);
704 Table& tab = out->table();
705 ArrayColumn<Float> specCol(tab,"SPECTRA");
706 ArrayColumn<Float> tsysCol(tab,"TSYS");
707 if (mode == "DIV") fact = (float)1.0 / fact;
708 else if (mode == "SUB") fact *= (float)-1.0 ;
709 for (uInt i=0; i<tab.nrow(); ++i) {
710 Vector<Float> spec;
711 Vector<Float> ts;
712 specCol.get(i, spec);
713 tsysCol.get(i, ts);
714 if (mode == "MUL" || mode == "DIV") {
715 //if (mode == "DIV") fact = (float)1.0 / fact;
716 spec *= fact;
717 specCol.put(i, spec);
718 if ( tsys ) {
719 ts *= fact;
720 tsysCol.put(i, ts);
721 }
722 } else if ( mode == "ADD" || mode == "SUB") {
723 //if (mode == "SUB") fact *= (float)-1.0 ;
724 spec += fact;
725 specCol.put(i, spec);
726 if ( tsys ) {
727 ts += fact;
728 tsysCol.put(i, ts);
729 }
730 }
731 }
732 return out;
733}
734
735CountedPtr< Scantable > STMath::arrayOperateRow( const CountedPtr< Scantable >& in,
736 const std::vector<float> val,
737 const std::string& mode,
738 bool tsys )
739{
740 if ( val.size() == 1 ) {
741 return unaryOperate( in, val[0], mode, tsys ) ;
742 }
743
744 // conformity of SPECTRA and TSYS
745 if ( tsys ) {
746 TableIterator titer(in->table(), "IFNO");
747 while ( !titer.pastEnd() ) {
748 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
749 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
750 Array<Float> spec = specCol.getColumn() ;
751 Array<Float> ts = tsysCol.getColumn() ;
752 if ( !spec.conform( ts ) ) {
753 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
754 }
755 titer.next() ;
756 }
757 }
758
759 // check if vector size is equal to nrow
760 Vector<Float> fact( val ) ;
761 if (fact.nelements() != uInt(in->nrow())) {
762 throw( AipsError("Vector size must be 1 or be same as number of row.") ) ;
763 }
764
765 // check divided by zero
766 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
767 throw( AipsError("Divided by zero is not recommended." ) ) ;
768 }
769
770 CountedPtr< Scantable > out = getScantable(in, false);
771 Table& tab = out->table();
772 ArrayColumn<Float> specCol(tab,"SPECTRA");
773 ArrayColumn<Float> tsysCol(tab,"TSYS");
774 if (mode == "DIV") fact = (float)1.0 / fact;
775 if (mode == "SUB") fact *= (float)-1.0 ;
776 for (uInt i=0; i<tab.nrow(); ++i) {
777 Vector<Float> spec;
778 Vector<Float> ts;
779 specCol.get(i, spec);
780 tsysCol.get(i, ts);
781 if (mode == "MUL" || mode == "DIV") {
782 spec *= fact[i];
783 specCol.put(i, spec);
784 if ( tsys ) {
785 ts *= fact[i];
786 tsysCol.put(i, ts);
787 }
788 } else if ( mode == "ADD" || mode == "SUB") {
789 spec += fact[i];
790 specCol.put(i, spec);
791 if ( tsys ) {
792 ts += fact[i];
793 tsysCol.put(i, ts);
794 }
795 }
796 }
797 return out;
798}
799
800CountedPtr< Scantable > STMath::array2dOperate( const CountedPtr< Scantable >& in,
801 const std::vector< std::vector<float> > val,
802 const std::string& mode,
803 bool tsys )
804{
805 // conformity of SPECTRA and TSYS
806 if ( tsys ) {
807 TableIterator titer(in->table(), "IFNO");
808 while ( !titer.pastEnd() ) {
809 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
810 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
811 Array<Float> spec = specCol.getColumn() ;
812 Array<Float> ts = tsysCol.getColumn() ;
813 if ( !spec.conform( ts ) ) {
814 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
815 }
816 titer.next() ;
817 }
818 }
819
820 // some checks
821 vector<uInt> nchans;
822 for (Int i = 0 ; i < in->nrow() ; i++) {
823 nchans.push_back((in->getSpectrum(i)).size());
824 }
825 //Vector<uInt> mchans( nchans ) ;
826 vector< Vector<Float> > facts ;
827 for ( uInt i = 0 ; i < nchans.size() ; i++ ) {
828 Vector<Float> tmp( val[i] ) ;
829 // check divided by zero
830 if ( ( mode == "DIV" ) && anyEQ( tmp, (float)0.0 ) ) {
831 throw( AipsError("Divided by zero is not recommended." ) ) ;
832 }
833 // conformity check
834 if ( tmp.nelements() != nchans[i] ) {
835 stringstream ss ;
836 ss << "Row " << i << ": Vector size must be same as number of channel." ;
837 throw( AipsError( ss.str() ) ) ;
838 }
839 facts.push_back( tmp ) ;
840 }
841
842
843 CountedPtr< Scantable > out = getScantable(in, false);
844 Table& tab = out->table();
845 ArrayColumn<Float> specCol(tab,"SPECTRA");
846 ArrayColumn<Float> tsysCol(tab,"TSYS");
847 for (uInt i=0; i<tab.nrow(); ++i) {
848 Vector<Float> fact = facts[i] ;
849 Vector<Float> spec;
850 Vector<Float> ts;
851 specCol.get(i, spec);
852 tsysCol.get(i, ts);
853 if (mode == "MUL" || mode == "DIV") {
854 if (mode == "DIV") fact = (float)1.0 / fact;
855 spec *= fact;
856 specCol.put(i, spec);
857 if ( tsys ) {
858 ts *= fact;
859 tsysCol.put(i, ts);
860 }
861 } else if ( mode == "ADD" || mode == "SUB") {
862 if (mode == "SUB") fact *= (float)-1.0 ;
863 spec += fact;
864 specCol.put(i, spec);
865 if ( tsys ) {
866 ts += fact;
867 tsysCol.put(i, ts);
868 }
869 }
870 }
871 return out;
872}
873
874CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
875 const CountedPtr<Scantable>& right,
876 const std::string& mode)
877{
878 bool insitu = insitu_;
879 if ( ! left->conformant(*right) ) {
880 throw(AipsError("'left' and 'right' scantables are not conformant."));
881 }
882 setInsitu(false);
883 CountedPtr< Scantable > out = getScantable(left, false);
884 setInsitu(insitu);
885 Table& tout = out->table();
886 Block<String> coln(5);
887 coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO";
888 coln[3] = "IFNO"; coln[4] = "POLNO";
889 Table tmpl = tout.sort(coln);
890 Table tmpr = right->table().sort(coln);
891 ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
892 ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
893 ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
894 ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");
895
896 for (uInt i=0; i<tout.nrow(); ++i) {
897 Vector<Float> lspecvec, rspecvec;
898 Vector<uChar> lflagvec, rflagvec;
899 lspecvec = lspecCol(i); rspecvec = rspecCol(i);
900 lflagvec = lflagCol(i); rflagvec = rflagCol(i);
901 MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
902 MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
903 if (mode == "ADD") {
904 mleft += mright;
905 } else if ( mode == "SUB") {
906 mleft -= mright;
907 } else if ( mode == "MUL") {
908 mleft *= mright;
909 } else if ( mode == "DIV") {
910 mleft /= mright;
911 } else {
912 throw(AipsError("Illegal binary operator"));
913 }
914 lspecCol.put(i, mleft.getArray());
915 }
916 return out;
917}
918
919
920
921MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
922 const Vector<uChar>& f)
923{
924 Vector<Bool> mask;
925 mask.resize(f.shape());
926 convertArray(mask, f);
927 return MaskedArray<Float>(s,!mask);
928}
929
930MaskedArray<Double> STMath::maskedArray( const Vector<Double>& s,
931 const Vector<uChar>& f)
932{
933 Vector<Bool> mask;
934 mask.resize(f.shape());
935 convertArray(mask, f);
936 return MaskedArray<Double>(s,!mask);
937}
938
939Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
940{
941 const Vector<Bool>& m = ma.getMask();
942 Vector<uChar> flags(m.shape());
943 convertArray(flags, !m);
944 return flags;
945}
946
947CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
948 const std::string & mode,
949 bool preserve )
950{
951 /// @todo make other modes available
952 /// modes should be "nearest", "pair"
953 // make this operation non insitu
954 (void) mode; //currently unused
955 const Table& tin = in->table();
956 Table ons = tin(tin.col("SRCTYPE") == Int(SrcType::PSON));
957 Table offs = tin(tin.col("SRCTYPE") == Int(SrcType::PSOFF));
958 if ( offs.nrow() == 0 )
959 throw(AipsError("No 'off' scans present."));
960 // put all "on" scans into output table
961
962 bool insitu = insitu_;
963 setInsitu(false);
964 CountedPtr< Scantable > out = getScantable(in, true);
965 setInsitu(insitu);
966 Table& tout = out->table();
967
968 TableCopy::copyRows(tout, ons);
969 TableRow row(tout);
970 ROScalarColumn<Double> offtimeCol(offs, "TIME");
971 ArrayColumn<Float> outspecCol(tout, "SPECTRA");
972 ROArrayColumn<Float> outtsysCol(tout, "TSYS");
973 ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
974 for (uInt i=0; i < tout.nrow(); ++i) {
975 const TableRecord& rec = row.get(i);
976 Double ontime = rec.asDouble("TIME");
977 Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
978 && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
979 && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
980 ROScalarColumn<Double> offtimeCol(presel, "TIME");
981
982 Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
983 // Timestamp may vary within a cycle ???!!!
984 // increase this by 0.01 sec in case of rounding errors...
985 // There might be a better way to do this.
986 // fix to this fix. TIME is MJD, so 1.0d not 1.0s
987 mindeltat += 0.01/24./60./60.;
988 Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat);
989
990 if ( sel.nrow() < 1 ) {
991 throw(AipsError("No closest in time found... This could be a rounding "
992 "issue. Try quotient instead."));
993 }
994 TableRow offrow(sel);
995 const TableRecord& offrec = offrow.get(0);//should only be one row
996 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
997 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
998 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
999 /// @fixme this assumes tsys is a scalar not vector
1000 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
1001 Vector<Float> specon, tsyson;
1002 outtsysCol.get(i, tsyson);
1003 outspecCol.get(i, specon);
1004 Vector<uChar> flagon;
1005 outflagCol.get(i, flagon);
1006 MaskedArray<Float> mon = maskedArray(specon, flagon);
1007 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
1008 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
1009 if (preserve) {
1010 quot -= tsysoffscalar;
1011 } else {
1012 quot -= tsyson[0];
1013 }
1014 outspecCol.put(i, quot.getArray());
1015 outflagCol.put(i, flagsFromMA(quot));
1016 }
1017 // renumber scanno
1018 TableIterator it(tout, "SCANNO");
1019 uInt i = 0;
1020 while ( !it.pastEnd() ) {
1021 Table t = it.table();
1022 TableVector<uInt> vec(t, "SCANNO");
1023 vec = i;
1024 ++i;
1025 ++it;
1026 }
1027 return out;
1028}
1029
1030
1031CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
1032 const CountedPtr< Scantable > & off,
1033 bool preserve )
1034{
1035 bool insitu = insitu_;
1036 if ( ! on->conformant(*off) ) {
1037 throw(AipsError("'on' and 'off' scantables are not conformant."));
1038 }
1039 setInsitu(false);
1040 CountedPtr< Scantable > out = getScantable(on, false);
1041 setInsitu(insitu);
1042 Table& tout = out->table();
1043 const Table& toff = off->table();
1044 TableIterator sit(tout, "SCANNO");
1045 TableIterator s2it(toff, "SCANNO");
1046 while ( !sit.pastEnd() ) {
1047 Table ton = sit.table();
1048 TableRow row(ton);
1049 Table t = s2it.table();
1050 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
1051 ROArrayColumn<Float> outtsysCol(ton, "TSYS");
1052 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
1053 for (uInt i=0; i < ton.nrow(); ++i) {
1054 const TableRecord& rec = row.get(i);
1055 Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1056 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
1057 && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
1058 if ( offsel.nrow() == 0 )
1059 throw AipsError("STMath::quotient: no matching off");
1060 TableRow offrow(offsel);
1061 const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
1062 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
1063 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
1064 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
1065 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
1066 Vector<Float> specon, tsyson;
1067 outtsysCol.get(i, tsyson);
1068 outspecCol.get(i, specon);
1069 Vector<uChar> flagon;
1070 outflagCol.get(i, flagon);
1071 MaskedArray<Float> mon = maskedArray(specon, flagon);
1072 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
1073 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
1074 if (preserve) {
1075 quot -= tsysoffscalar;
1076 } else {
1077 quot -= tsyson[0];
1078 }
1079 outspecCol.put(i, quot.getArray());
1080 outflagCol.put(i, flagsFromMA(quot));
1081 }
1082 ++sit;
1083 ++s2it;
1084 // take the first off for each on scan which doesn't have a
1085 // matching off scan
1086 // non <= noff: matching pairs, non > noff matching pairs then first off
1087 if ( s2it.pastEnd() ) s2it.reset();
1088 }
1089 return out;
1090}
1091
1092// dototalpower (migration of GBTIDL procedure dototalpower.pro)
1093// calibrate the CAL on-off pair. It calculate Tsys and average CAL on-off subintegrations
1094// do it for each cycles in a specific scan.
1095CountedPtr< Scantable > STMath::dototalpower( const CountedPtr< Scantable >& calon,
1096 const CountedPtr< Scantable >& caloff, Float tcal )
1097{
1098 if ( ! calon->conformant(*caloff) ) {
1099 throw(AipsError("'CAL on' and 'CAL off' scantables are not conformant."));
1100 }
1101 setInsitu(false);
1102 CountedPtr< Scantable > out = getScantable(caloff, false);
1103 Table& tout = out->table();
1104 const Table& tcon = calon->table();
1105 Vector<Float> tcalout;
1106
1107 std::map<uInt,uInt> tcalIdToRecNoMap;
1108 const Table& calOffTcalTable = caloff->tcal().table();
1109 {
1110 ROScalarColumn<uInt> calOffTcalTable_IDcol(calOffTcalTable, "ID");
1111 const Vector<uInt> tcalIds(calOffTcalTable_IDcol.getColumn());
1112 size_t tcalIdsEnd = tcalIds.nelements();
1113 for (uInt i = 0; i < tcalIdsEnd; i++) {
1114 tcalIdToRecNoMap[tcalIds[i]] = i;
1115 }
1116 }
1117 ROArrayColumn<Float> calOffTcalTable_TCALcol(calOffTcalTable, "TCAL");
1118
1119 if ( tout.nrow() != tcon.nrow() ) {
1120 throw(AipsError("Mismatch in number of rows to form cal on - off pair."));
1121 }
1122 // iteration by scanno or cycle no.
1123 TableIterator sit(tout, "SCANNO");
1124 TableIterator s2it(tcon, "SCANNO");
1125 while ( !sit.pastEnd() ) {
1126 Table toff = sit.table();
1127 TableRow row(toff);
1128 Table t = s2it.table();
1129 ScalarColumn<Double> outintCol(toff, "INTERVAL");
1130 ArrayColumn<Float> outspecCol(toff, "SPECTRA");
1131 ArrayColumn<Float> outtsysCol(toff, "TSYS");
1132 ArrayColumn<uChar> outflagCol(toff, "FLAGTRA");
1133 ROScalarColumn<uInt> outtcalIdCol(toff, "TCAL_ID");
1134 ROScalarColumn<uInt> outpolCol(toff, "POLNO");
1135 ROScalarColumn<Double> onintCol(t, "INTERVAL");
1136 ROArrayColumn<Float> onspecCol(t, "SPECTRA");
1137 ROArrayColumn<Float> ontsysCol(t, "TSYS");
1138 ROArrayColumn<uChar> onflagCol(t, "FLAGTRA");
1139 //ROScalarColumn<uInt> ontcalIdCol(t, "TCAL_ID");
1140
1141 for (uInt i=0; i < toff.nrow(); ++i) {
1142 //skip these checks -> assumes the data order are the same between the cal on off pairs
1143 //
1144 Vector<Float> specCalon, specCaloff;
1145 // to store scalar (mean) tsys
1146 Vector<Float> tsysout(1);
1147 uInt tcalId, polno;
1148 Double offint, onint;
1149 outpolCol.get(i, polno);
1150 outspecCol.get(i, specCaloff);
1151 onspecCol.get(i, specCalon);
1152 Vector<uChar> flagCaloff, flagCalon;
1153 outflagCol.get(i, flagCaloff);
1154 onflagCol.get(i, flagCalon);
1155 outtcalIdCol.get(i, tcalId);
1156 outintCol.get(i, offint);
1157 onintCol.get(i, onint);
1158 // caluculate mean Tsys
1159 uInt nchan = specCaloff.nelements();
1160 // percentage of edge cut off
1161 uInt pc = 10;
1162 uInt bchan = nchan/pc;
1163 uInt echan = nchan-bchan;
1164
1165 Slicer chansl(IPosition(1,bchan-1), IPosition(1,echan-1), IPosition(1,1),Slicer::endIsLast);
1166 Vector<Float> testsubsp = specCaloff(chansl);
1167 MaskedArray<Float> spoff = maskedArray( specCaloff(chansl),flagCaloff(chansl) );
1168 MaskedArray<Float> spon = maskedArray( specCalon(chansl),flagCalon(chansl) );
1169 MaskedArray<Float> spdiff = spon-spoff;
1170 uInt noff = spoff.nelementsValid();
1171 //uInt non = spon.nelementsValid();
1172 uInt ndiff = spdiff.nelementsValid();
1173 Float meantsys;
1174
1175/**
1176 Double subspec, subdiff;
1177 uInt usednchan;
1178 subspec = 0;
1179 subdiff = 0;
1180 usednchan = 0;
1181 for(uInt k=(bchan-1); k<echan; k++) {
1182 subspec += specCaloff[k];
1183 subdiff += static_cast<Double>(specCalon[k]-specCaloff[k]);
1184 ++usednchan;
1185 }
1186**/
1187 // get tcal if input tcal <= 0
1188 Float tcalUsed;
1189 tcalUsed = tcal;
1190 if ( tcal <= 0.0 ) {
1191 uInt tcalRecNo = tcalIdToRecNoMap[tcalId];
1192 calOffTcalTable_TCALcol.get(tcalRecNo, tcalout);
1193// if (polno<=3) {
1194// tcalUsed = tcalout[polno];
1195// }
1196// else {
1197// tcalUsed = tcalout[0];
1198// }
1199 if ( tcalout.size() == 1 )
1200 tcalUsed = tcalout[0] ;
1201 else if ( tcalout.size() == nchan )
1202 tcalUsed = mean(tcalout) ;
1203 else {
1204 uInt ipol = polno ;
1205 if ( ipol > 3 ) ipol = 0 ;
1206 tcalUsed = tcalout[ipol] ;
1207 }
1208 }
1209
1210 Float meanoff;
1211 Float meandiff;
1212 if (noff && ndiff) {
1213 //Debug
1214 //if(noff!=ndiff) cerr<<"noff and ndiff is not equal"<<endl;
1215 //LogIO os( LogOrigin( "STMath", "dototalpower()", WHERE ) ) ;
1216 //if(noff!=ndiff) os<<"noff and ndiff is not equal"<<LogIO::POST;
1217 meanoff = sum(spoff)/noff;
1218 meandiff = sum(spdiff)/ndiff;
1219 meantsys= (meanoff/meandiff )*tcalUsed + tcalUsed/2;
1220 }
1221 else {
1222 meantsys=1;
1223 }
1224
1225 tsysout[0] = Float(meantsys);
1226 MaskedArray<Float> mcaloff = maskedArray(specCaloff, flagCaloff);
1227 MaskedArray<Float> mcalon = maskedArray(specCalon, flagCalon);
1228 MaskedArray<Float> sig = Float(0.5) * (mcaloff + mcalon);
1229 //uInt ncaloff = mcaloff.nelementsValid();
1230 //uInt ncalon = mcalon.nelementsValid();
1231
1232 outintCol.put(i, offint+onint);
1233 outspecCol.put(i, sig.getArray());
1234 outflagCol.put(i, flagsFromMA(sig));
1235 outtsysCol.put(i, tsysout);
1236 }
1237 ++sit;
1238 ++s2it;
1239 }
1240 return out;
1241}
1242
1243//dosigref - migrated from GBT IDL's dosigref.pro, do calibration of position switch
1244// observatiions.
1245// input: sig and ref scantables, and an optional boxcar smoothing width(default width=0,
1246// no smoothing).
1247// output: resultant scantable [= (sig-ref/ref)*tsys]
1248CountedPtr< Scantable > STMath::dosigref( const CountedPtr < Scantable >& sig,
1249 const CountedPtr < Scantable >& ref,
1250 int smoothref,
1251 casa::Float tsysv,
1252 casa::Float tau )
1253{
1254if ( ! ref->conformant(*sig) ) {
1255 throw(AipsError("'sig' and 'ref' scantables are not conformant."));
1256 }
1257 setInsitu(false);
1258 CountedPtr< Scantable > out = getScantable(sig, false);
1259 CountedPtr< Scantable > smref;
1260 if ( smoothref > 1 ) {
1261 float fsmoothref = static_cast<float>(smoothref);
1262 std::string inkernel = "boxcar";
1263 smref = smooth(ref, inkernel, fsmoothref );
1264 ostringstream oss;
1265 oss<<"Applied smoothing of "<<fsmoothref<<" on the reference."<<endl;
1266 pushLog(String(oss));
1267 }
1268 else {
1269 smref = ref;
1270 }
1271 Table& tout = out->table();
1272 const Table& tref = smref->table();
1273 if ( tout.nrow() != tref.nrow() ) {
1274 throw(AipsError("Mismatch in number of rows to form on-source and reference pair."));
1275 }
1276 // iteration by scanno? or cycle no.
1277 TableIterator sit(tout, "SCANNO");
1278 TableIterator s2it(tref, "SCANNO");
1279 while ( !sit.pastEnd() ) {
1280 Table ton = sit.table();
1281 Table t = s2it.table();
1282 ScalarColumn<Double> outintCol(ton, "INTERVAL");
1283 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
1284 ArrayColumn<Float> outtsysCol(ton, "TSYS");
1285 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
1286 ArrayColumn<Float> refspecCol(t, "SPECTRA");
1287 ROScalarColumn<Double> refintCol(t, "INTERVAL");
1288 ROArrayColumn<Float> reftsysCol(t, "TSYS");
1289 ArrayColumn<uChar> refflagCol(t, "FLAGTRA");
1290 ROScalarColumn<Float> refelevCol(t, "ELEVATION");
1291 for (uInt i=0; i < ton.nrow(); ++i) {
1292
1293 Double onint, refint;
1294 Vector<Float> specon, specref;
1295 // to store scalar (mean) tsys
1296 Vector<Float> tsysref;
1297 outintCol.get(i, onint);
1298 refintCol.get(i, refint);
1299 outspecCol.get(i, specon);
1300 refspecCol.get(i, specref);
1301 Vector<uChar> flagref, flagon;
1302 outflagCol.get(i, flagon);
1303 refflagCol.get(i, flagref);
1304 reftsysCol.get(i, tsysref);
1305
1306 Float tsysrefscalar;
1307 if ( tsysv > 0.0 ) {
1308 ostringstream oss;
1309 Float elev;
1310 refelevCol.get(i, elev);
1311 oss << "user specified Tsys = " << tsysv;
1312 // do recalc elevation if EL = 0
1313 if ( elev == 0 ) {
1314 throw(AipsError("EL=0, elevation data is missing."));
1315 } else {
1316 if ( tau <= 0.0 ) {
1317 throw(AipsError("Valid tau is not supplied."));
1318 } else {
1319 tsysrefscalar = tsysv * exp(tau/elev);
1320 }
1321 }
1322 oss << ", corrected (for El) tsys= "<<tsysrefscalar;
1323 pushLog(String(oss));
1324 }
1325 else {
1326 tsysrefscalar = tsysref[0];
1327 }
1328 //get quotient spectrum
1329 MaskedArray<Float> mref = maskedArray(specref, flagref);
1330 MaskedArray<Float> mon = maskedArray(specon, flagon);
1331 MaskedArray<Float> specres = tsysrefscalar*((mon - mref)/mref);
1332 Double resint = onint*refint*smoothref/(onint+refint*smoothref);
1333
1334 //Debug
1335 //cerr<<"Tsys used="<<tsysrefscalar<<endl;
1336 //LogIO os( LogOrigin( "STMath", "dosigref", WHERE ) ) ;
1337 //os<<"Tsys used="<<tsysrefscalar<<LogIO::POST;
1338 // fill the result, replay signal tsys by reference tsys
1339 outintCol.put(i, resint);
1340 outspecCol.put(i, specres.getArray());
1341 outflagCol.put(i, flagsFromMA(specres));
1342 outtsysCol.put(i, tsysref);
1343 }
1344 ++sit;
1345 ++s2it;
1346 }
1347 return out;
1348}
1349
1350CountedPtr< Scantable > STMath::donod(const casa::CountedPtr<Scantable>& s,
1351 const std::vector<int>& scans,
1352 int smoothref,
1353 casa::Float tsysv,
1354 casa::Float tau,
1355 casa::Float tcal )
1356
1357{
1358 setInsitu(false);
1359 STSelector sel;
1360 std::vector<int> scan1, scan2, beams, types;
1361 std::vector< vector<int> > scanpair;
1362 //std::vector<string> calstate;
1363 std::vector<int> calstate;
1364 String msg;
1365
1366 CountedPtr< Scantable > s1b1on, s1b1off, s1b2on, s1b2off;
1367 CountedPtr< Scantable > s2b1on, s2b1off, s2b2on, s2b2off;
1368
1369 std::vector< CountedPtr< Scantable > > sctables;
1370 sctables.push_back(s1b1on);
1371 sctables.push_back(s1b1off);
1372 sctables.push_back(s1b2on);
1373 sctables.push_back(s1b2off);
1374 sctables.push_back(s2b1on);
1375 sctables.push_back(s2b1off);
1376 sctables.push_back(s2b2on);
1377 sctables.push_back(s2b2off);
1378
1379 //check scanlist
1380 int n=s->checkScanInfo(scans);
1381 if (n==1) {
1382 throw(AipsError("Incorrect scan pairs. "));
1383 }
1384
1385 // Assume scans contain only a pair of consecutive scan numbers.
1386 // It is assumed that first beam, b1, is on target.
1387 // There is no check if the first beam is on or not.
1388 if ( scans.size()==1 ) {
1389 scan1.push_back(scans[0]);
1390 scan2.push_back(scans[0]+1);
1391 } else if ( scans.size()==2 ) {
1392 scan1.push_back(scans[0]);
1393 scan2.push_back(scans[1]);
1394 } else {
1395 if ( scans.size()%2 == 0 ) {
1396 for (uInt i=0; i<scans.size(); i++) {
1397 if (i%2 == 0) {
1398 scan1.push_back(scans[i]);
1399 }
1400 else {
1401 scan2.push_back(scans[i]);
1402 }
1403 }
1404 } else {
1405 throw(AipsError("Odd numbers of scans, cannot form pairs."));
1406 }
1407 }
1408 scanpair.push_back(scan1);
1409 scanpair.push_back(scan2);
1410 //calstate.push_back("*calon");
1411 //calstate.push_back("*[^calon]");
1412 calstate.push_back(SrcType::NODCAL);
1413 calstate.push_back(SrcType::NOD);
1414 CountedPtr< Scantable > ws = getScantable(s, false);
1415 uInt l=0;
1416 while ( l < sctables.size() ) {
1417 for (uInt i=0; i < 2; i++) {
1418 for (uInt j=0; j < 2; j++) {
1419 for (uInt k=0; k < 2; k++) {
1420 sel.reset();
1421 sel.setScans(scanpair[i]);
1422 //sel.setName(calstate[k]);
1423 types.clear();
1424 types.push_back(calstate[k]);
1425 sel.setTypes(types);
1426 beams.clear();
1427 beams.push_back(j);
1428 sel.setBeams(beams);
1429 ws->setSelection(sel);
1430 sctables[l]= getScantable(ws, false);
1431 l++;
1432 }
1433 }
1434 }
1435 }
1436
1437 // replace here by splitData or getData functionality
1438 CountedPtr< Scantable > sig1;
1439 CountedPtr< Scantable > ref1;
1440 CountedPtr< Scantable > sig2;
1441 CountedPtr< Scantable > ref2;
1442 CountedPtr< Scantable > calb1;
1443 CountedPtr< Scantable > calb2;
1444
1445 msg=String("Processing dototalpower for subset of the data");
1446 ostringstream oss1;
1447 oss1 << msg << endl;
1448 pushLog(String(oss1));
1449 // Debug for IRC CS data
1450 //float tcal1=7.0;
1451 //float tcal2=4.0;
1452 sig1 = dototalpower(sctables[0], sctables[1], tcal=tcal);
1453 ref1 = dototalpower(sctables[2], sctables[3], tcal=tcal);
1454 ref2 = dototalpower(sctables[4], sctables[5], tcal=tcal);
1455 sig2 = dototalpower(sctables[6], sctables[7], tcal=tcal);
1456
1457 // correction of user-specified tsys for elevation here
1458
1459 // dosigref calibration
1460 msg=String("Processing dosigref for subset of the data");
1461 ostringstream oss2;
1462 oss2 << msg << endl;
1463 pushLog(String(oss2));
1464 calb1=dosigref(sig1,ref2,smoothref,tsysv,tau);
1465 calb2=dosigref(sig2,ref1,smoothref,tsysv,tau);
1466
1467 // iteration by scanno or cycle no.
1468 Table& tcalb1 = calb1->table();
1469 Table& tcalb2 = calb2->table();
1470 TableIterator sit(tcalb1, "SCANNO");
1471 TableIterator s2it(tcalb2, "SCANNO");
1472 while ( !sit.pastEnd() ) {
1473 Table t1 = sit.table();
1474 Table t2= s2it.table();
1475 ArrayColumn<Float> outspecCol(t1, "SPECTRA");
1476 ArrayColumn<Float> outtsysCol(t1, "TSYS");
1477 ArrayColumn<uChar> outflagCol(t1, "FLAGTRA");
1478 ScalarColumn<Double> outintCol(t1, "INTERVAL");
1479 ArrayColumn<Float> t2specCol(t2, "SPECTRA");
1480 ROArrayColumn<Float> t2tsysCol(t2, "TSYS");
1481 ArrayColumn<uChar> t2flagCol(t2, "FLAGTRA");
1482 ROScalarColumn<Double> t2intCol(t2, "INTERVAL");
1483 for (uInt i=0; i < t1.nrow(); ++i) {
1484 Vector<Float> spec1, spec2;
1485 // to store scalar (mean) tsys
1486 Vector<Float> tsys1, tsys2;
1487 Vector<uChar> flag1, flag2;
1488 Double tint1, tint2;
1489 outspecCol.get(i, spec1);
1490 t2specCol.get(i, spec2);
1491 outflagCol.get(i, flag1);
1492 t2flagCol.get(i, flag2);
1493 outtsysCol.get(i, tsys1);
1494 t2tsysCol.get(i, tsys2);
1495 outintCol.get(i, tint1);
1496 t2intCol.get(i, tint2);
1497 // average
1498 // assume scalar tsys for weights
1499 Float wt1, wt2, tsyssq1, tsyssq2;
1500 tsyssq1 = tsys1[0]*tsys1[0];
1501 tsyssq2 = tsys2[0]*tsys2[0];
1502 wt1 = Float(tint1)/tsyssq1;
1503 wt2 = Float(tint2)/tsyssq2;
1504 Float invsumwt=1/(wt1+wt2);
1505 MaskedArray<Float> mspec1 = maskedArray(spec1, flag1);
1506 MaskedArray<Float> mspec2 = maskedArray(spec2, flag2);
1507 MaskedArray<Float> avspec = invsumwt * (wt1*mspec1 + wt2*mspec2);
1508 //Array<Float> avtsys = Float(0.5) * (tsys1 + tsys2);
1509 // cerr<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<endl;
1510 // LogIO os( LogOrigin( "STMath", "donod", WHERE ) ) ;
1511 // os<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<LogIO::POST;
1512 tsys1[0] = sqrt(tsyssq1 + tsyssq2);
1513 Array<Float> avtsys = tsys1;
1514
1515 outspecCol.put(i, avspec.getArray());
1516 outflagCol.put(i, flagsFromMA(avspec));
1517 outtsysCol.put(i, avtsys);
1518 }
1519 ++sit;
1520 ++s2it;
1521 }
1522 return calb1;
1523}
1524
1525//GBTIDL version of frequency switched data calibration
1526CountedPtr< Scantable > STMath::dofs( const CountedPtr< Scantable >& s,
1527 const std::vector<int>& scans,
1528 int smoothref,
1529 casa::Float tsysv,
1530 casa::Float tau,
1531 casa::Float tcal )
1532{
1533
1534
1535 (void) scans; //currently unused
1536 STSelector sel;
1537 CountedPtr< Scantable > ws = getScantable(s, false);
1538 CountedPtr< Scantable > sig, sigwcal, ref, refwcal;
1539 CountedPtr< Scantable > calsig, calref, out, out1, out2;
1540 Bool nofold=False;
1541 vector<int> types ;
1542
1543 //split the data
1544 //sel.setName("*_fs");
1545 types.push_back( SrcType::FSON ) ;
1546 sel.setTypes( types ) ;
1547 ws->setSelection(sel);
1548 sig = getScantable(ws,false);
1549 sel.reset();
1550 types.clear() ;
1551 //sel.setName("*_fs_calon");
1552 types.push_back( SrcType::FONCAL ) ;
1553 sel.setTypes( types ) ;
1554 ws->setSelection(sel);
1555 sigwcal = getScantable(ws,false);
1556 sel.reset();
1557 types.clear() ;
1558 //sel.setName("*_fsr");
1559 types.push_back( SrcType::FSOFF ) ;
1560 sel.setTypes( types ) ;
1561 ws->setSelection(sel);
1562 ref = getScantable(ws,false);
1563 sel.reset();
1564 types.clear() ;
1565 //sel.setName("*_fsr_calon");
1566 types.push_back( SrcType::FOFFCAL ) ;
1567 sel.setTypes( types ) ;
1568 ws->setSelection(sel);
1569 refwcal = getScantable(ws,false);
1570 sel.reset() ;
1571 types.clear() ;
1572
1573 calsig = dototalpower(sigwcal, sig, tcal=tcal);
1574 calref = dototalpower(refwcal, ref, tcal=tcal);
1575
1576 out1=dosigref(calsig,calref,smoothref,tsysv,tau);
1577 out2=dosigref(calref,calsig,smoothref,tsysv,tau);
1578
1579 Table& tabout1=out1->table();
1580 Table& tabout2=out2->table();
1581 ROScalarColumn<uInt> freqidCol1(tabout1, "FREQ_ID");
1582 ScalarColumn<uInt> freqidCol2(tabout2, "FREQ_ID");
1583 ROArrayColumn<Float> specCol(tabout2, "SPECTRA");
1584 Vector<Float> spec; specCol.get(0, spec);
1585 uInt nchan = spec.nelements();
1586 uInt freqid1; freqidCol1.get(0,freqid1);
1587 uInt freqid2; freqidCol2.get(0,freqid2);
1588 Double rp1, rp2, rv1, rv2, inc1, inc2;
1589 out1->frequencies().getEntry(rp1, rv1, inc1, freqid1);
1590 out2->frequencies().getEntry(rp2, rv2, inc2, freqid2);
1591 //cerr << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << endl ;
1592 //LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1593 //os << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << LogIO::POST ;
1594 if (rp1==rp2) {
1595 Double foffset = rv1 - rv2;
1596 uInt choffset = static_cast<uInt>(foffset/abs(inc2));
1597 if (choffset >= nchan) {
1598 //cerr<<"out-band frequency switching, no folding"<<endl;
1599 LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1600 os<<"out-band frequency switching, no folding"<<LogIO::POST;
1601 nofold = True;
1602 }
1603 }
1604
1605 if (nofold) {
1606 std::vector< CountedPtr< Scantable > > tabs;
1607 tabs.push_back(out1);
1608 tabs.push_back(out2);
1609 out = merge(tabs);
1610 }
1611 else {
1612 //out = out1;
1613 Double choffset = ( rv1 - rv2 ) / inc2 ;
1614 out = dofold( out1, out2, choffset ) ;
1615 }
1616
1617 return out;
1618}
1619
1620CountedPtr<Scantable> STMath::dofold( const CountedPtr<Scantable> &sig,
1621 const CountedPtr<Scantable> &ref,
1622 Double choffset,
1623 Double choffset2 )
1624{
1625 LogIO os( LogOrigin( "STMath", "dofold", WHERE ) ) ;
1626 os << "choffset=" << choffset << " choffset2=" << choffset2 << LogIO::POST ;
1627
1628 // output scantable
1629 CountedPtr<Scantable> out = getScantable( sig, false ) ;
1630
1631 // separate choffset to integer part and decimal part
1632 Int ioffset = (Int)choffset ;
1633 Double doffset = choffset - ioffset ;
1634 Int ioffset2 = (Int)choffset2 ;
1635 Double doffset2 = choffset2 - ioffset2 ;
1636 os << "ioffset=" << ioffset << " doffset=" << doffset << LogIO::POST ;
1637 os << "ioffset2=" << ioffset2 << " doffset2=" << doffset2 << LogIO::POST ;
1638
1639 // get column
1640 ROArrayColumn<Float> specCol1( sig->table(), "SPECTRA" ) ;
1641 ROArrayColumn<Float> specCol2( ref->table(), "SPECTRA" ) ;
1642 ROArrayColumn<Float> tsysCol1( sig->table(), "TSYS" ) ;
1643 ROArrayColumn<Float> tsysCol2( ref->table(), "TSYS" ) ;
1644 ROArrayColumn<uChar> flagCol1( sig->table(), "FLAGTRA" ) ;
1645 ROArrayColumn<uChar> flagCol2( ref->table(), "FLAGTRA" ) ;
1646 ROScalarColumn<Double> mjdCol1( sig->table(), "TIME" ) ;
1647 ROScalarColumn<Double> mjdCol2( ref->table(), "TIME" ) ;
1648 ROScalarColumn<Double> intervalCol1( sig->table(), "INTERVAL" ) ;
1649 ROScalarColumn<Double> intervalCol2( ref->table(), "INTERVAL" ) ;
1650
1651 // check
1652 if ( ioffset == 0 ) {
1653 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1654 os << "channel offset is zero, no folding" << LogIO::POST ;
1655 return out ;
1656 }
1657 int nchan = ref->nchan() ;
1658 if ( abs(ioffset) >= nchan ) {
1659 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1660 os << "out-band frequency switching, no folding" << LogIO::POST ;
1661 return out ;
1662 }
1663
1664 // attach column for output scantable
1665 ArrayColumn<Float> specColOut( out->table(), "SPECTRA" ) ;
1666 ArrayColumn<uChar> flagColOut( out->table(), "FLAGTRA" ) ;
1667 ArrayColumn<Float> tsysColOut( out->table(), "TSYS" ) ;
1668 ScalarColumn<Double> mjdColOut( out->table(), "TIME" ) ;
1669 ScalarColumn<Double> intervalColOut( out->table(), "INTERVAL" ) ;
1670 ScalarColumn<uInt> fidColOut( out->table(), "FREQ_ID" ) ;
1671
1672 // for each row
1673 // assume that the data order are same between sig and ref
1674 RowAccumulator acc( asap::W_TINTSYS ) ;
1675 for ( int i = 0 ; i < sig->nrow() ; i++ ) {
1676 // get values
1677 Vector<Float> spsig ;
1678 specCol1.get( i, spsig ) ;
1679 Vector<Float> spref ;
1680 specCol2.get( i, spref ) ;
1681 Vector<Float> tsyssig ;
1682 tsysCol1.get( i, tsyssig ) ;
1683 Vector<Float> tsysref ;
1684 tsysCol2.get( i, tsysref ) ;
1685 Vector<uChar> flagsig ;
1686 flagCol1.get( i, flagsig ) ;
1687 Vector<uChar> flagref ;
1688 flagCol2.get( i, flagref ) ;
1689 Double timesig ;
1690 mjdCol1.get( i, timesig ) ;
1691 Double timeref ;
1692 mjdCol2.get( i, timeref ) ;
1693 Double intsig ;
1694 intervalCol1.get( i, intsig ) ;
1695 Double intref ;
1696 intervalCol2.get( i, intref ) ;
1697
1698 // shift reference spectra
1699 int refchan = spref.nelements() ;
1700 Vector<Float> sspref( spref.nelements() ) ;
1701 Vector<Float> stsysref( tsysref.nelements() ) ;
1702 Vector<uChar> sflagref( flagref.nelements() ) ;
1703 if ( ioffset > 0 ) {
1704 // SPECTRA and FLAGTRA
1705 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1706 sspref[j] = spref[j+ioffset] ;
1707 sflagref[j] = flagref[j+ioffset] ;
1708 }
1709 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1710 sspref[j] = spref[j-refchan+ioffset] ;
1711 sflagref[j] = flagref[j-refchan+ioffset] ;
1712 }
1713 spref = sspref.copy() ;
1714 flagref = sflagref.copy() ;
1715 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1716 sspref[j] = doffset * spref[j+1] + ( 1.0 - doffset ) * spref[j] ;
1717 sflagref[j] = flagref[j+1] + flagref[j] ;
1718 }
1719 sspref[refchan-1] = doffset * spref[0] + ( 1.0 - doffset ) * spref[refchan-1] ;
1720 sflagref[refchan-1] = flagref[0] + flagref[refchan-1] ;
1721
1722 // TSYS
1723 if ( spref.nelements() == tsysref.nelements() ) {
1724 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1725 stsysref[j] = tsysref[j+ioffset] ;
1726 }
1727 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1728 stsysref[j] = tsysref[j-refchan+ioffset] ;
1729 }
1730 tsysref = stsysref.copy() ;
1731 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1732 stsysref[j] = doffset * tsysref[j+1] + ( 1.0 - doffset ) * tsysref[j] ;
1733 }
1734 stsysref[refchan-1] = doffset * tsysref[0] + ( 1.0 - doffset ) * tsysref[refchan-1] ;
1735 }
1736 }
1737 else {
1738 // SPECTRA and FLAGTRA
1739 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1740 sspref[j] = spref[refchan+ioffset+j] ;
1741 sflagref[j] = flagref[refchan+ioffset+j] ;
1742 }
1743 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1744 sspref[j] = spref[j+ioffset] ;
1745 sflagref[j] = flagref[j+ioffset] ;
1746 }
1747 spref = sspref.copy() ;
1748 flagref = sflagref.copy() ;
1749 sspref[0] = doffset * spref[refchan-1] + ( 1.0 - doffset ) * spref[0] ;
1750 sflagref[0] = flagref[0] + flagref[refchan-1] ;
1751 for ( int j = 1 ; j < refchan ; j++ ) {
1752 sspref[j] = doffset * spref[j-1] + ( 1.0 - doffset ) * spref[j] ;
1753 sflagref[j] = flagref[j-1] + flagref[j] ;
1754 }
1755 // TSYS
1756 if ( spref.nelements() == tsysref.nelements() ) {
1757 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1758 stsysref[j] = tsysref[refchan+ioffset+j] ;
1759 }
1760 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1761 stsysref[j] = tsysref[j+ioffset] ;
1762 }
1763 tsysref = stsysref.copy() ;
1764 stsysref[0] = doffset * tsysref[refchan-1] + ( 1.0 - doffset ) * tsysref[0] ;
1765 for ( int j = 1 ; j < refchan ; j++ ) {
1766 stsysref[j] = doffset * tsysref[j-1] + ( 1.0 - doffset ) * tsysref[j] ;
1767 }
1768 }
1769 }
1770
1771 // shift signal spectra if necessary (only for APEX?)
1772 if ( choffset2 != 0.0 ) {
1773 int sigchan = spsig.nelements() ;
1774 Vector<Float> sspsig( spsig.nelements() ) ;
1775 Vector<Float> stsyssig( tsyssig.nelements() ) ;
1776 Vector<uChar> sflagsig( flagsig.nelements() ) ;
1777 if ( ioffset2 > 0 ) {
1778 // SPECTRA and FLAGTRA
1779 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1780 sspsig[j] = spsig[j+ioffset2] ;
1781 sflagsig[j] = flagsig[j+ioffset2] ;
1782 }
1783 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1784 sspsig[j] = spsig[j-sigchan+ioffset2] ;
1785 sflagsig[j] = flagsig[j-sigchan+ioffset2] ;
1786 }
1787 spsig = sspsig.copy() ;
1788 flagsig = sflagsig.copy() ;
1789 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1790 sspsig[j] = doffset2 * spsig[j+1] + ( 1.0 - doffset2 ) * spsig[j] ;
1791 sflagsig[j] = flagsig[j+1] || flagsig[j] ;
1792 }
1793 sspsig[sigchan-1] = doffset2 * spsig[0] + ( 1.0 - doffset2 ) * spsig[sigchan-1] ;
1794 sflagsig[sigchan-1] = flagsig[0] || flagsig[sigchan-1] ;
1795 // TSTS
1796 if ( spsig.nelements() == tsyssig.nelements() ) {
1797 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1798 stsyssig[j] = tsyssig[j+ioffset2] ;
1799 }
1800 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1801 stsyssig[j] = tsyssig[j-sigchan+ioffset2] ;
1802 }
1803 tsyssig = stsyssig.copy() ;
1804 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1805 stsyssig[j] = doffset2 * tsyssig[j+1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1806 }
1807 stsyssig[sigchan-1] = doffset2 * tsyssig[0] + ( 1.0 - doffset2 ) * tsyssig[sigchan-1] ;
1808 }
1809 }
1810 else {
1811 // SPECTRA and FLAGTRA
1812 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1813 sspsig[j] = spsig[sigchan+ioffset2+j] ;
1814 sflagsig[j] = flagsig[sigchan+ioffset2+j] ;
1815 }
1816 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1817 sspsig[j] = spsig[j+ioffset2] ;
1818 sflagsig[j] = flagsig[j+ioffset2] ;
1819 }
1820 spsig = sspsig.copy() ;
1821 flagsig = sflagsig.copy() ;
1822 sspsig[0] = doffset2 * spsig[sigchan-1] + ( 1.0 - doffset2 ) * spsig[0] ;
1823 sflagsig[0] = flagsig[0] + flagsig[sigchan-1] ;
1824 for ( int j = 1 ; j < sigchan ; j++ ) {
1825 sspsig[j] = doffset2 * spsig[j-1] + ( 1.0 - doffset2 ) * spsig[j] ;
1826 sflagsig[j] = flagsig[j-1] + flagsig[j] ;
1827 }
1828 // TSYS
1829 if ( spsig.nelements() == tsyssig.nelements() ) {
1830 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1831 stsyssig[j] = tsyssig[sigchan+ioffset2+j] ;
1832 }
1833 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1834 stsyssig[j] = tsyssig[j+ioffset2] ;
1835 }
1836 tsyssig = stsyssig.copy() ;
1837 stsyssig[0] = doffset2 * tsyssig[sigchan-1] + ( 1.0 - doffset2 ) * tsyssig[0] ;
1838 for ( int j = 1 ; j < sigchan ; j++ ) {
1839 stsyssig[j] = doffset2 * tsyssig[j-1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1840 }
1841 }
1842 }
1843 }
1844
1845 // folding
1846 acc.add( spsig, !flagsig, tsyssig, intsig, timesig ) ;
1847 acc.add( sspref, !sflagref, stsysref, intref, timeref ) ;
1848
1849 // put result
1850 specColOut.put( i, acc.getSpectrum() ) ;
1851 const Vector<Bool> &msk = acc.getMask() ;
1852 Vector<uChar> flg( msk.shape() ) ;
1853 convertArray( flg, !msk ) ;
1854 flagColOut.put( i, flg ) ;
1855 tsysColOut.put( i, acc.getTsys() ) ;
1856 intervalColOut.put( i, acc.getInterval() ) ;
1857 mjdColOut.put( i, acc.getTime() ) ;
1858 // change FREQ_ID to unshifted IF setting (only for APEX?)
1859 if ( choffset2 != 0.0 ) {
1860 uInt freqid = fidColOut( 0 ) ; // assume single-IF data
1861 double refpix, refval, increment ;
1862 out->frequencies().getEntry( refpix, refval, increment, freqid ) ;
1863 refval -= choffset * increment ;
1864 uInt newfreqid = out->frequencies().addEntry( refpix, refval, increment ) ;
1865 Vector<uInt> freqids = fidColOut.getColumn() ;
1866 for ( uInt j = 0 ; j < freqids.nelements() ; j++ ) {
1867 if ( freqids[j] == freqid )
1868 freqids[j] = newfreqid ;
1869 }
1870 fidColOut.putColumn( freqids ) ;
1871 }
1872
1873 acc.reset() ;
1874 }
1875
1876 return out ;
1877}
1878
1879
1880CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
1881{
1882 // make copy or reference
1883 CountedPtr< Scantable > out = getScantable(in, false);
1884 Table& tout = out->table();
1885 Block<String> cols(4);
1886 cols[0] = String("SCANNO");
1887 cols[1] = String("CYCLENO");
1888 cols[2] = String("BEAMNO");
1889 cols[3] = String("POLNO");
1890 TableIterator iter(tout, cols);
1891 while (!iter.pastEnd()) {
1892 Table subt = iter.table();
1893 // this should leave us with two rows for the two IFs....if not ignore
1894 if (subt.nrow() != 2 ) {
1895 continue;
1896 }
1897 ArrayColumn<Float> specCol(subt, "SPECTRA");
1898 ArrayColumn<Float> tsysCol(subt, "TSYS");
1899 ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
1900 Vector<Float> onspec,offspec, ontsys, offtsys;
1901 Vector<uChar> onflag, offflag;
1902 tsysCol.get(0, ontsys); tsysCol.get(1, offtsys);
1903 specCol.get(0, onspec); specCol.get(1, offspec);
1904 flagCol.get(0, onflag); flagCol.get(1, offflag);
1905 MaskedArray<Float> on = maskedArray(onspec, onflag);
1906 MaskedArray<Float> off = maskedArray(offspec, offflag);
1907 MaskedArray<Float> oncopy = on.copy();
1908
1909 on /= off; on -= 1.0f;
1910 on *= ontsys[0];
1911 off /= oncopy; off -= 1.0f;
1912 off *= offtsys[0];
1913 specCol.put(0, on.getArray());
1914 const Vector<Bool>& m0 = on.getMask();
1915 Vector<uChar> flags0(m0.shape());
1916 convertArray(flags0, !m0);
1917 flagCol.put(0, flags0);
1918
1919 specCol.put(1, off.getArray());
1920 const Vector<Bool>& m1 = off.getMask();
1921 Vector<uChar> flags1(m1.shape());
1922 convertArray(flags1, !m1);
1923 flagCol.put(1, flags1);
1924 ++iter;
1925 }
1926
1927 return out;
1928}
1929
1930std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
1931 const std::vector< bool > & mask,
1932 const std::string& which )
1933{
1934
1935 Vector<Bool> m(mask);
1936 const Table& tab = in->table();
1937 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1938 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1939 std::vector<float> out;
1940 for (uInt i=0; i < tab.nrow(); ++i ) {
1941 Vector<Float> spec; specCol.get(i, spec);
1942 Vector<uChar> flag; flagCol.get(i, flag);
1943 MaskedArray<Float> ma = maskedArray(spec, flag);
1944 float outstat = 0.0;
1945 if ( spec.nelements() == m.nelements() ) {
1946 outstat = mathutil::statistics(which, ma(m));
1947 } else {
1948 outstat = mathutil::statistics(which, ma);
1949 }
1950 out.push_back(outstat);
1951 }
1952 return out;
1953}
1954
1955std::vector< float > STMath::statisticRow( const CountedPtr< Scantable > & in,
1956 const std::vector< bool > & mask,
1957 const std::string& which,
1958 int row )
1959{
1960
1961 Vector<Bool> m(mask);
1962 const Table& tab = in->table();
1963 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1964 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1965 std::vector<float> out;
1966
1967 Vector<Float> spec; specCol.get(row, spec);
1968 Vector<uChar> flag; flagCol.get(row, flag);
1969 MaskedArray<Float> ma = maskedArray(spec, flag);
1970 float outstat = 0.0;
1971 if ( spec.nelements() == m.nelements() ) {
1972 outstat = mathutil::statistics(which, ma(m));
1973 } else {
1974 outstat = mathutil::statistics(which, ma);
1975 }
1976 out.push_back(outstat);
1977
1978 return out;
1979}
1980
1981std::vector< int > STMath::minMaxChan( const CountedPtr< Scantable > & in,
1982 const std::vector< bool > & mask,
1983 const std::string& which )
1984{
1985
1986 Vector<Bool> m(mask);
1987 const Table& tab = in->table();
1988 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1989 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1990 std::vector<int> out;
1991 for (uInt i=0; i < tab.nrow(); ++i ) {
1992 Vector<Float> spec; specCol.get(i, spec);
1993 Vector<uChar> flag; flagCol.get(i, flag);
1994 MaskedArray<Float> ma = maskedArray(spec, flag);
1995 if (ma.ndim() != 1) {
1996 throw (ArrayError(
1997 "std::vector<int> STMath::minMaxChan("
1998 "ContedPtr<Scantable> &in, std::vector<bool> &mask, "
1999 " std::string &which)"
2000 " - MaskedArray is not 1D"));
2001 }
2002 IPosition outpos(1,0);
2003 if ( spec.nelements() == m.nelements() ) {
2004 outpos = mathutil::minMaxPos(which, ma(m));
2005 } else {
2006 outpos = mathutil::minMaxPos(which, ma);
2007 }
2008 out.push_back(outpos[0]);
2009 }
2010 return out;
2011}
2012
2013CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
2014 int width )
2015{
2016 if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
2017 CountedPtr< Scantable > out = getScantable(in, false);
2018 Table& tout = out->table();
2019 out->frequencies().rescale(width, "BIN");
2020 ArrayColumn<Float> specCol(tout, "SPECTRA");
2021 ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
2022 ArrayColumn<Float> tsysCol(tout, "TSYS");
2023
2024 for (uInt i=0; i < tout.nrow(); ++i ) {
2025 MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
2026 MaskedArray<Float> maout;
2027 LatticeUtilities::bin(maout, main, 0, Int(width));
2028 specCol.put(i, maout.getArray());
2029 flagCol.put(i, flagsFromMA(maout));
2030 if (tsysCol(i).nelements() == specCol(i).nelements()) {
2031 MaskedArray<Float> matsysin = maskedArray(tsysCol(i), flagCol(i));
2032 MaskedArray<Float> matsysout;
2033 LatticeUtilities::bin(matsysout, matsysin, 0, Int(width));
2034 tsysCol.put(i, matsysout.getArray());
2035 }
2036 // take only the first binned spectrum's length for the deprecated
2037 // global header item nChan
2038 if (i==0) tout.rwKeywordSet().define(String("nChan"),
2039 Int(maout.getArray().nelements()));
2040 }
2041 return out;
2042}
2043
2044CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
2045 const std::string& method,
2046 float width )
2047//
2048// Should add the possibility of width being specified in km/s. This means
2049// that for each freqID (SpectralCoordinate) we will need to convert to an
2050// average channel width (say at the reference pixel). Then we would need
2051// to be careful to make sure each spectrum (of different freqID)
2052// is the same length.
2053//
2054{
2055 //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
2056 Int interpMethod(stringToIMethod(method));
2057
2058 CountedPtr< Scantable > out = getScantable(in, false);
2059 Table& tout = out->table();
2060
2061// Resample SpectralCoordinates (one per freqID)
2062 out->frequencies().rescale(width, "RESAMPLE");
2063 TableIterator iter(tout, "IFNO");
2064 TableRow row(tout);
2065 while ( !iter.pastEnd() ) {
2066 Table tab = iter.table();
2067 ArrayColumn<Float> specCol(tab, "SPECTRA");
2068 //ArrayColumn<Float> tsysCol(tout, "TSYS");
2069 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2070 Vector<Float> spec;
2071 Vector<uChar> flag;
2072 specCol.get(0,spec); // the number of channels should be constant per IF
2073 uInt nChanIn = spec.nelements();
2074 Vector<Float> xIn(nChanIn); indgen(xIn);
2075 Int fac = Int(nChanIn/width);
2076 Vector<Float> xOut(fac+10); // 10 to be safe - resize later
2077 uInt k = 0;
2078 Float x = 0.0;
2079 while (x < Float(nChanIn) ) {
2080 xOut(k) = x;
2081 k++;
2082 x += width;
2083 }
2084 uInt nChanOut = k;
2085 xOut.resize(nChanOut, True);
2086 // process all rows for this IFNO
2087 Vector<Float> specOut;
2088 Vector<Bool> maskOut;
2089 Vector<uChar> flagOut;
2090 for (uInt i=0; i < tab.nrow(); ++i) {
2091 specCol.get(i, spec);
2092 flagCol.get(i, flag);
2093 Vector<Bool> mask(flag.nelements());
2094 convertArray(mask, flag);
2095
2096 IPosition shapeIn(spec.shape());
2097 //sh.nchan = nChanOut;
2098 InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
2099 xIn, spec, mask,
2100 interpMethod, True, True);
2101 /// @todo do the same for channel based Tsys
2102 flagOut.resize(maskOut.nelements());
2103 convertArray(flagOut, maskOut);
2104 specCol.put(i, specOut);
2105 flagCol.put(i, flagOut);
2106 }
2107 ++iter;
2108 }
2109
2110 return out;
2111}
2112
2113STMath::imethod STMath::stringToIMethod(const std::string& in)
2114{
2115 static STMath::imap lookup;
2116
2117 // initialize the lookup table if necessary
2118 if ( lookup.empty() ) {
2119 lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
2120 lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
2121 lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
2122 lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
2123 }
2124
2125 STMath::imap::const_iterator iter = lookup.find(in);
2126
2127 if ( lookup.end() == iter ) {
2128 std::string message = in;
2129 message += " is not a valid interpolation mode";
2130 throw(AipsError(message));
2131 }
2132 return iter->second;
2133}
2134
2135WeightType STMath::stringToWeight(const std::string& in)
2136{
2137 static std::map<std::string, WeightType> lookup;
2138
2139 // initialize the lookup table if necessary
2140 if ( lookup.empty() ) {
2141 lookup["NONE"] = asap::W_NONE;
2142 lookup["TINT"] = asap::W_TINT;
2143 lookup["TINTSYS"] = asap::W_TINTSYS;
2144 lookup["TSYS"] = asap::W_TSYS;
2145 lookup["VAR"] = asap::W_VAR;
2146 }
2147
2148 std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
2149
2150 if ( lookup.end() == iter ) {
2151 std::string message = in;
2152 message += " is not a valid weighting mode";
2153 throw(AipsError(message));
2154 }
2155 return iter->second;
2156}
2157
2158CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
2159 const vector< float > & coeff,
2160 const std::string & filename,
2161 const std::string& method)
2162{
2163 // Get elevation data from Scantable and convert to degrees
2164 CountedPtr< Scantable > out = getScantable(in, false);
2165 Table& tab = out->table();
2166 ROScalarColumn<Float> elev(tab, "ELEVATION");
2167 Vector<Float> x = elev.getColumn();
2168 x *= Float(180 / C::pi); // Degrees
2169
2170 Vector<Float> coeffs(coeff);
2171 const uInt nc = coeffs.nelements();
2172 if ( filename.length() > 0 && nc > 0 ) {
2173 throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
2174 }
2175
2176 // Correct
2177 if ( nc > 0 || filename.length() == 0 ) {
2178 // Find instrument
2179 Bool throwit = True;
2180 Instrument inst =
2181 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2182 throwit);
2183
2184 // Set polynomial
2185 Polynomial<Float>* ppoly = 0;
2186 Vector<Float> coeff;
2187 String msg;
2188 if ( nc > 0 ) {
2189 ppoly = new Polynomial<Float>(nc-1);
2190 coeff = coeffs;
2191 msg = String("user");
2192 } else {
2193 STAttr sdAttr;
2194 coeff = sdAttr.gainElevationPoly(inst);
2195 ppoly = new Polynomial<Float>(coeff.nelements()-1);
2196 msg = String("built in");
2197 }
2198
2199 if ( coeff.nelements() > 0 ) {
2200 ppoly->setCoefficients(coeff);
2201 } else {
2202 delete ppoly;
2203 throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
2204 }
2205 ostringstream oss;
2206 oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
2207 oss << " " << coeff;
2208 pushLog(String(oss));
2209 const uInt nrow = tab.nrow();
2210 Vector<Float> factor(nrow);
2211 for ( uInt i=0; i < nrow; ++i ) {
2212 factor[i] = 1.0 / (*ppoly)(x[i]);
2213 }
2214 delete ppoly;
2215 scaleByVector(tab, factor, true);
2216
2217 } else {
2218 // Read and correct
2219 pushLog("Making correction from ascii Table");
2220 scaleFromAsciiTable(tab, filename, method, x, true);
2221 }
2222 return out;
2223}
2224
2225void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
2226 const std::string& method,
2227 const Vector<Float>& xout, bool dotsys)
2228{
2229
2230// Read gain-elevation ascii file data into a Table.
2231
2232 String formatString;
2233 Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
2234 scaleFromTable(in, tbl, method, xout, dotsys);
2235}
2236
2237void STMath::scaleFromTable(Table& in,
2238 const Table& table,
2239 const std::string& method,
2240 const Vector<Float>& xout, bool dotsys)
2241{
2242
2243 ROScalarColumn<Float> geElCol(table, "ELEVATION");
2244 ROScalarColumn<Float> geFacCol(table, "FACTOR");
2245 Vector<Float> xin = geElCol.getColumn();
2246 Vector<Float> yin = geFacCol.getColumn();
2247 Vector<Bool> maskin(xin.nelements(),True);
2248
2249 // Interpolate (and extrapolate) with desired method
2250
2251 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2252
2253 Vector<Float> yout;
2254 Vector<Bool> maskout;
2255 InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
2256 xin, yin, maskin, interp,
2257 True, True);
2258
2259 scaleByVector(in, Float(1.0)/yout, dotsys);
2260}
2261
2262void STMath::scaleByVector( Table& in,
2263 const Vector< Float >& factor,
2264 bool dotsys )
2265{
2266 uInt nrow = in.nrow();
2267 if ( factor.nelements() != nrow ) {
2268 throw(AipsError("factors.nelements() != table.nelements()"));
2269 }
2270 ArrayColumn<Float> specCol(in, "SPECTRA");
2271 ArrayColumn<uChar> flagCol(in, "FLAGTRA");
2272 ArrayColumn<Float> tsysCol(in, "TSYS");
2273 for (uInt i=0; i < nrow; ++i) {
2274 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2275 ma *= factor[i];
2276 specCol.put(i, ma.getArray());
2277 flagCol.put(i, flagsFromMA(ma));
2278 if ( dotsys ) {
2279 Vector<Float> tsys = tsysCol(i);
2280 tsys *= factor[i];
2281 tsysCol.put(i,tsys);
2282 }
2283 }
2284}
2285
2286CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
2287 float d, float etaap,
2288 float jyperk )
2289{
2290 CountedPtr< Scantable > out = getScantable(in, false);
2291 Table& tab = in->table();
2292 Table& outtab = out->table();
2293 Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
2294 Unit K(String("K"));
2295 Unit JY(String("Jy"));
2296
2297 bool tokelvin = true;
2298 Double cfac = 1.0;
2299
2300 if ( fluxUnit == JY ) {
2301 pushLog("Converting to K");
2302 Quantum<Double> t(1.0,fluxUnit);
2303 Quantum<Double> t2 = t.get(JY);
2304 cfac = (t2 / t).getValue(); // value to Jy
2305
2306 tokelvin = true;
2307 out->setFluxUnit("K");
2308 } else if ( fluxUnit == K ) {
2309 pushLog("Converting to Jy");
2310 Quantum<Double> t(1.0,fluxUnit);
2311 Quantum<Double> t2 = t.get(K);
2312 cfac = (t2 / t).getValue(); // value to K
2313
2314 tokelvin = false;
2315 out->setFluxUnit("Jy");
2316 } else {
2317 throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
2318 }
2319 // Make sure input values are converted to either Jy or K first...
2320 Float factor = cfac;
2321
2322 // Select method
2323 if (jyperk > 0.0) {
2324 factor *= jyperk;
2325 if ( tokelvin ) factor = 1.0 / jyperk;
2326 ostringstream oss;
2327 oss << "Jy/K = " << jyperk;
2328 pushLog(String(oss));
2329 Vector<Float> factors(outtab.nrow(), factor);
2330 scaleByVector(outtab,factors, false);
2331 } else if ( etaap > 0.0) {
2332 if (d < 0) {
2333 Instrument inst =
2334 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2335 True);
2336 STAttr sda;
2337 d = sda.diameter(inst);
2338 }
2339 jyperk = STAttr::findJyPerK(etaap, d);
2340 ostringstream oss;
2341 oss << "Jy/K = " << jyperk;
2342 pushLog(String(oss));
2343 factor *= jyperk;
2344 if ( tokelvin ) {
2345 factor = 1.0 / factor;
2346 }
2347 Vector<Float> factors(outtab.nrow(), factor);
2348 scaleByVector(outtab, factors, False);
2349 } else {
2350
2351 // OK now we must deal with automatic look up of values.
2352 // We must also deal with the fact that the factors need
2353 // to be computed per IF and may be different and may
2354 // change per integration.
2355
2356 pushLog("Looking up conversion factors");
2357 convertBrightnessUnits(out, tokelvin, cfac);
2358 }
2359
2360 return out;
2361}
2362
2363void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
2364 bool tokelvin, float cfac )
2365{
2366 Table& table = in->table();
2367 Instrument inst =
2368 STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
2369 TableIterator iter(table, "FREQ_ID");
2370 STFrequencies stfreqs = in->frequencies();
2371 STAttr sdAtt;
2372 while (!iter.pastEnd()) {
2373 Table tab = iter.table();
2374 ArrayColumn<Float> specCol(tab, "SPECTRA");
2375 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2376 ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
2377 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2378
2379 uInt freqid; freqidCol.get(0, freqid);
2380 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2381 // STAttr.JyPerK has a Vector interface... change sometime.
2382 Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
2383 for ( uInt i=0; i<tab.nrow(); ++i) {
2384 Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
2385 Float factor = cfac * jyperk;
2386 if ( tokelvin ) factor = Float(1.0) / factor;
2387 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2388 ma *= factor;
2389 specCol.put(i, ma.getArray());
2390 flagCol.put(i, flagsFromMA(ma));
2391 }
2392 ++iter;
2393 }
2394}
2395
2396CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
2397 const std::vector<float>& tau )
2398{
2399 CountedPtr< Scantable > out = getScantable(in, false);
2400
2401 Table outtab = out->table();
2402
2403 const Int ntau = uInt(tau.size());
2404 std::vector<float>::const_iterator tauit = tau.begin();
2405 AlwaysAssert((ntau == 1 || ntau == in->nif() || ntau == in->nif() * in->npol()),
2406 AipsError);
2407 TableIterator iiter(outtab, "IFNO");
2408 while ( !iiter.pastEnd() ) {
2409 Table itab = iiter.table();
2410 TableIterator piter(itab, "POLNO");
2411 while ( !piter.pastEnd() ) {
2412 Table tab = piter.table();
2413 ROScalarColumn<Float> elev(tab, "ELEVATION");
2414 ArrayColumn<Float> specCol(tab, "SPECTRA");
2415 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2416 ArrayColumn<Float> tsysCol(tab, "TSYS");
2417 for ( uInt i=0; i<tab.nrow(); ++i) {
2418 Float zdist = Float(C::pi_2) - elev(i);
2419 Float factor = exp(*tauit/cos(zdist));
2420 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2421 ma *= factor;
2422 specCol.put(i, ma.getArray());
2423 flagCol.put(i, flagsFromMA(ma));
2424 Vector<Float> tsys;
2425 tsysCol.get(i, tsys);
2426 tsys *= factor;
2427 tsysCol.put(i, tsys);
2428 }
2429 if (ntau == in->nif()*in->npol() ) {
2430 tauit++;
2431 }
2432 piter++;
2433 }
2434 if (ntau >= in->nif() ) {
2435 tauit++;
2436 }
2437 iiter++;
2438 }
2439 return out;
2440}
2441
2442CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in,
2443 const std::string& kernel,
2444 float width, int order)
2445{
2446 CountedPtr< Scantable > out = getScantable(in, false);
2447 Table table = out->table();
2448
2449 TableIterator iter(table, "IFNO");
2450 while (!iter.pastEnd()) {
2451 Table tab = iter.table();
2452 ArrayColumn<Float> specCol(tab, "SPECTRA");
2453 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2454 Vector<Float> spec;
2455 Vector<uChar> flag;
2456 for (uInt i = 0; i < tab.nrow(); ++i) {
2457 specCol.get(i, spec);
2458 flagCol.get(i, flag);
2459 Vector<Bool> mask(flag.nelements());
2460 convertArray(mask, flag);
2461 Vector<Float> specout;
2462 Vector<Bool> maskout;
2463 if (kernel == "hanning") {
2464 mathutil::hanning(specout, maskout, spec, !mask);
2465 convertArray(flag, !maskout);
2466 } else if (kernel == "rmedian") {
2467 mathutil::runningMedian(specout, maskout, spec , mask, width);
2468 convertArray(flag, maskout);
2469 } else if (kernel == "poly") {
2470 mathutil::polyfit(specout, maskout, spec, !mask, width, order);
2471 convertArray(flag, !maskout);
2472 }
2473
2474 for (uInt j = 0; j < flag.nelements(); ++j) {
2475 uChar userFlag = 1 << 7;
2476 if (maskout[j]==True) userFlag = 0 << 7;
2477 flag(j) = userFlag;
2478 }
2479
2480 flagCol.put(i, flag);
2481 specCol.put(i, specout);
2482 }
2483 ++iter;
2484 }
2485 return out;
2486}
2487
2488CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
2489 const std::string& kernel, float width,
2490 int order)
2491{
2492 if (kernel == "rmedian" || kernel == "hanning" || kernel == "poly") {
2493 return smoothOther(in, kernel, width, order);
2494 }
2495 CountedPtr< Scantable > out = getScantable(in, false);
2496 Table& table = out->table();
2497 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
2498 // same IFNO should have same no of channels
2499 // this saves overhead
2500 TableIterator iter(table, "IFNO");
2501 while (!iter.pastEnd()) {
2502 Table tab = iter.table();
2503 ArrayColumn<Float> specCol(tab, "SPECTRA");
2504 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2505 Vector<Float> spec = specCol( 0 );
2506 uInt nchan = spec.nelements();
2507 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
2508 Convolver<Float> conv(kvec, IPosition(1,nchan));
2509 Vector<uChar> flag;
2510 Vector<Bool> mask(nchan);
2511 for ( uInt i=0; i<tab.nrow(); ++i) {
2512 specCol.get(i, spec);
2513 flagCol.get(i, flag);
2514 convertArray(mask, flag);
2515 Vector<Float> specout;
2516 mathutil::replaceMaskByZero(specout, mask);
2517 conv.linearConv(specout, spec);
2518 specCol.put(i, specout);
2519 }
2520 ++iter;
2521 }
2522 return out;
2523}
2524
2525CountedPtr< Scantable >
2526 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
2527{
2528 if ( in.size() < 2 ) {
2529 throw(AipsError("Need at least two scantables to perform a merge."));
2530 }
2531 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
2532 bool insitu = insitu_;
2533 setInsitu(false);
2534 CountedPtr< Scantable > out = getScantable(*it, false);
2535 setInsitu(insitu);
2536 Table& tout = out->table();
2537 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
2538 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
2539 // Renumber SCANNO to be 0-based
2540 Vector<uInt> scannos = scannocol.getColumn();
2541 uInt offset = min(scannos);
2542 scannos -= offset;
2543 scannocol.putColumn(scannos);
2544 uInt newscanno = max(scannos)+1;
2545 ++it;
2546 while ( it != in.end() ){
2547 if ( ! (*it)->conformant(*out) ) {
2548 // non conformant.
2549 //pushLog(String("Warning: Can't merge scantables as header info differs."));
2550 LogIO os( LogOrigin( "STMath", "merge()", WHERE ) ) ;
2551 os << LogIO::SEVERE << "Can't merge scantables as header informations (any one of AntennaName, Equinox, and FluxUnit) differ." << LogIO::EXCEPTION ;
2552 }
2553 out->appendToHistoryTable((*it)->history());
2554 const Table& tab = (*it)->table();
2555
2556 Block<String> cols(3);
2557 cols[0] = String("FREQ_ID");
2558 cols[1] = String("MOLECULE_ID");
2559 cols[2] = String("FOCUS_ID");
2560
2561 TableIterator scanit(tab, "SCANNO");
2562 while (!scanit.pastEnd()) {
2563 ScalarColumn<uInt> thescannocol(scanit.table(),"SCANNO");
2564 Vector<uInt> thescannos(thescannocol.nrow(),newscanno);
2565 thescannocol.putColumn(thescannos);
2566 TableIterator subit(scanit.table(), cols);
2567 while ( !subit.pastEnd() ) {
2568 uInt nrow = tout.nrow();
2569 Table thetab = subit.table();
2570 ROTableRow row(thetab);
2571 Vector<uInt> thecolvals(thetab.nrow());
2572 ScalarColumn<uInt> thefreqidcol(thetab,"FREQ_ID");
2573 ScalarColumn<uInt> themolidcol(thetab, "MOLECULE_ID");
2574 ScalarColumn<uInt> thefocusidcol(thetab,"FOCUS_ID");
2575 // The selected subset of table should have
2576 // the equal FREQ_ID, MOLECULE_ID, and FOCUS_ID values.
2577 const TableRecord& rec = row.get(0);
2578 // Set the proper FREQ_ID
2579 Double rv,rp,inc;
2580 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
2581 uInt id;
2582 id = out->frequencies().addEntry(rp, rv, inc);
2583 thecolvals = id;
2584 thefreqidcol.putColumn(thecolvals);
2585 // Set the proper MOLECULE_ID
2586 Vector<String> name,fname;Vector<Double> rf;
2587 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
2588 id = out->molecules().addEntry(rf, name, fname);
2589 thecolvals = id;
2590 themolidcol.putColumn(thecolvals);
2591 // Set the proper FOCUS_ID
2592 Float fpa,frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
2593 (*it)->focus().getEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2594 fxy, fxyp, rec.asuInt("FOCUS_ID"));
2595 id = out->focus().addEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2596 fxy, fxyp);
2597 thecolvals = id;
2598 thefocusidcol.putColumn(thecolvals);
2599
2600 tout.addRow(thetab.nrow());
2601 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
2602
2603 ++subit;
2604 }
2605 ++newscanno;
2606 ++scanit;
2607 }
2608 ++it;
2609 }
2610 return out;
2611}
2612
2613CountedPtr< Scantable >
2614 STMath::invertPhase( const CountedPtr < Scantable >& in )
2615{
2616 return applyToPol(in, &STPol::invertPhase, Float(0.0));
2617}
2618
2619CountedPtr< Scantable >
2620 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
2621{
2622 return applyToPol(in, &STPol::rotatePhase, Float(phase));
2623}
2624
2625CountedPtr< Scantable >
2626 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
2627{
2628 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
2629}
2630
2631CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
2632 STPol::polOperation fptr,
2633 Float phase )
2634{
2635 CountedPtr< Scantable > out = getScantable(in, false);
2636 Table& tout = out->table();
2637 Block<String> cols(4);
2638 cols[0] = String("SCANNO");
2639 cols[1] = String("BEAMNO");
2640 cols[2] = String("IFNO");
2641 cols[3] = String("CYCLENO");
2642 TableIterator iter(tout, cols);
2643 CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
2644 out->getPolType() );
2645 while (!iter.pastEnd()) {
2646 Table t = iter.table();
2647 ArrayColumn<Float> speccol(t, "SPECTRA");
2648 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
2649 Matrix<Float> pols(speccol.getColumn());
2650 try {
2651 stpol->setSpectra(pols);
2652 Float fang,fhand;
2653 fang = in->focusTable_.getTotalAngle(focidcol(0));
2654 fhand = in->focusTable_.getFeedHand(focidcol(0));
2655 stpol->setPhaseCorrections(fang, fhand);
2656 // use a member function pointer in STPol. This only works on
2657 // the STPol pointer itself, not the Counted Pointer so
2658 // derefernce it.
2659 (&(*(stpol))->*fptr)(phase);
2660 speccol.putColumn(stpol->getSpectra());
2661 } catch (AipsError& e) {
2662 //delete stpol;stpol=0;
2663 throw(e);
2664 }
2665 ++iter;
2666 }
2667 //delete stpol;stpol=0;
2668 return out;
2669}
2670
2671CountedPtr< Scantable >
2672 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
2673{
2674 CountedPtr< Scantable > out = getScantable(in, false);
2675 Table& tout = out->table();
2676 Table t0 = tout(tout.col("POLNO") == 0);
2677 Table t1 = tout(tout.col("POLNO") == 1);
2678 if ( t0.nrow() != t1.nrow() )
2679 throw(AipsError("Inconsistent number of polarisations"));
2680 ArrayColumn<Float> speccol0(t0, "SPECTRA");
2681 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
2682 ArrayColumn<Float> speccol1(t1, "SPECTRA");
2683 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
2684 Matrix<Float> s0 = speccol0.getColumn();
2685 Matrix<uChar> f0 = flagcol0.getColumn();
2686 speccol0.putColumn(speccol1.getColumn());
2687 flagcol0.putColumn(flagcol1.getColumn());
2688 speccol1.putColumn(s0);
2689 flagcol1.putColumn(f0);
2690 return out;
2691}
2692
2693CountedPtr< Scantable >
2694 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
2695 const std::vector<bool>& mask,
2696 const std::string& weight )
2697{
2698 if (in->npol() < 2 )
2699 throw(AipsError("averagePolarisations can only be applied to two or more"
2700 "polarisations"));
2701 bool insitu = insitu_;
2702 setInsitu(false);
2703 CountedPtr< Scantable > pols = getScantable(in, true);
2704 setInsitu(insitu);
2705 Table& tout = pols->table();
2706 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
2707 Table tab = tableCommand(taql, in->table());
2708 if (tab.nrow() == 0 )
2709 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
2710 TableCopy::copyRows(tout, tab);
2711 TableVector<uInt> vec(tout, "POLNO");
2712 vec = 0;
2713 pols->table_.rwKeywordSet().define("nPol", Int(1));
2714 pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
2715 //pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
2716 std::vector<CountedPtr<Scantable> > vpols;
2717 vpols.push_back(pols);
2718 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
2719 return out;
2720}
2721
2722CountedPtr< Scantable >
2723 STMath::averageBeams( const CountedPtr< Scantable > & in,
2724 const std::vector<bool>& mask,
2725 const std::string& weight )
2726{
2727 bool insitu = insitu_;
2728 setInsitu(false);
2729 CountedPtr< Scantable > beams = getScantable(in, false);
2730 setInsitu(insitu);
2731 Table& tout = beams->table();
2732 // give all rows the same BEAMNO
2733 TableVector<uInt> vec(tout, "BEAMNO");
2734 vec = 0;
2735 beams->table_.rwKeywordSet().define("nBeam", Int(1));
2736 std::vector<CountedPtr<Scantable> > vbeams;
2737 vbeams.push_back(beams);
2738 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
2739 return out;
2740}
2741
2742
2743CountedPtr< Scantable >
2744 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
2745 const std::string & refTime,
2746 const std::string & method)
2747{
2748 // clone as this is not working insitu
2749 bool insitu = insitu_;
2750 setInsitu(false);
2751 CountedPtr< Scantable > out = getScantable(in, false);
2752 setInsitu(insitu);
2753 Table& tout = out->table();
2754 // Get reference Epoch to time of first row or given String
2755 Unit DAY(String("d"));
2756 MEpoch::Ref epochRef(in->getTimeReference());
2757 MEpoch refEpoch;
2758 if (refTime.length()>0) {
2759 Quantum<Double> qt;
2760 if (MVTime::read(qt,refTime)) {
2761 MVEpoch mv(qt);
2762 refEpoch = MEpoch(mv, epochRef);
2763 } else {
2764 throw(AipsError("Invalid format for Epoch string"));
2765 }
2766 } else {
2767 refEpoch = in->timeCol_(0);
2768 }
2769 MPosition refPos = in->getAntennaPosition();
2770
2771 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2772 /*
2773 // Comment from MV.
2774 // the following code has been commented out because different FREQ_IDs have to be aligned together even
2775 // if the frame doesn't change. So far, lack of this check didn't cause any problems.
2776 // test if user frame is different to base frame
2777 if ( in->frequencies().getFrameString(true)
2778 == in->frequencies().getFrameString(false) ) {
2779 throw(AipsError("Can't convert as no output frame has been set"
2780 " (use set_freqframe) or it is aligned already."));
2781 }
2782 */
2783 MFrequency::Types system = in->frequencies().getFrame();
2784 MVTime mvt(refEpoch.getValue());
2785 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
2786 ostringstream oss;
2787 oss << "Aligned at reference Epoch " << epochout
2788 << " in frame " << MFrequency::showType(system);
2789 pushLog(String(oss));
2790 // set up the iterator
2791 Block<String> cols(4);
2792 // select by constant direction
2793 cols[0] = String("SRCNAME");
2794 cols[1] = String("BEAMNO");
2795 // select by IF ( no of channels varies over this )
2796 cols[2] = String("IFNO");
2797 // select by restfrequency
2798 cols[3] = String("MOLECULE_ID");
2799 TableIterator iter(tout, cols);
2800 while ( !iter.pastEnd() ) {
2801 Table t = iter.table();
2802 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
2803 TableIterator fiter(t, "FREQ_ID");
2804 // determine nchan from the first row. This should work as
2805 // we are iterating over BEAMNO and IFNO // we should have constant direction
2806
2807 ROArrayColumn<Float> sCol(t, "SPECTRA");
2808 const MDirection direction = dirCol(0);
2809 const uInt nchan = sCol(0).nelements();
2810
2811 // skip operations if there is nothing to align
2812 if (fiter.pastEnd()) {
2813 continue;
2814 }
2815
2816 Table ftab = fiter.table();
2817 // align all frequency ids with respect to the first encountered id
2818 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
2819 // get the SpectralCoordinate for the freqid, which we are iterating over
2820 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
2821 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
2822 direction, refPos, system );
2823 // realign the SpectralCoordinate and put into the output Scantable
2824 Vector<String> units(1);
2825 units = String("Hz");
2826 Bool linear=True;
2827 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
2828 sc2.setWorldAxisUnits(units);
2829 const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
2830 sc2.referenceValue()[0],
2831 sc2.increment()[0]);
2832 while ( !fiter.pastEnd() ) {
2833 ftab = fiter.table();
2834 // spectral coordinate for the current FREQ_ID
2835 ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
2836 sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
2837 // create the "global" abcissa for alignment with same FREQ_ID
2838 Vector<Double> abc(nchan);
2839 for (uInt i=0; i<nchan; i++) {
2840 Double w;
2841 sC.toWorld(w,Double(i));
2842 abc[i] = w;
2843 }
2844 TableVector<uInt> tvec(ftab, "FREQ_ID");
2845 // assign new frequency id to all rows
2846 tvec = id;
2847 // cache abcissa for same time stamps, so iterate over those
2848 TableIterator timeiter(ftab, "TIME");
2849 while ( !timeiter.pastEnd() ) {
2850 Table tab = timeiter.table();
2851 ArrayColumn<Float> specCol(tab, "SPECTRA");
2852 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2853 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2854 // use align abcissa cache after the first row
2855 // these rows should be just be POLNO
2856 bool first = true;
2857 for (int i=0; i<int(tab.nrow()); ++i) {
2858 // input values
2859 Vector<uChar> flag = flagCol(i);
2860 Vector<Bool> mask(flag.shape());
2861 Vector<Float> specOut, spec;
2862 spec = specCol(i);
2863 Vector<Bool> maskOut;Vector<uChar> flagOut;
2864 convertArray(mask, flag);
2865 // alignment
2866 Bool ok = fa.align(specOut, maskOut, abc, spec,
2867 mask, timeCol(i), !first,
2868 interp, False);
2869 (void) ok; // unused stop compiler nagging
2870 // back into scantable
2871 flagOut.resize(maskOut.nelements());
2872 convertArray(flagOut, maskOut);
2873 flagCol.put(i, flagOut);
2874 specCol.put(i, specOut);
2875 // start abcissa caching
2876 first = false;
2877 }
2878 // next timestamp
2879 ++timeiter;
2880 }
2881 // next FREQ_ID
2882 ++fiter;
2883 }
2884 // next aligner
2885 ++iter;
2886 }
2887 // set this afterwards to ensure we are doing insitu correctly.
2888 out->frequencies().setFrame(system, true);
2889 return out;
2890}
2891
2892CountedPtr<Scantable>
2893 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
2894 const std::string & newtype )
2895{
2896 if (in->npol() != 2 && in->npol() != 4)
2897 throw(AipsError("Can only convert two or four polarisations."));
2898 if ( in->getPolType() == newtype )
2899 throw(AipsError("No need to convert."));
2900 if ( ! in->selector_.empty() )
2901 throw(AipsError("Can only convert whole scantable. Unset the selection."));
2902 bool insitu = insitu_;
2903 setInsitu(false);
2904 CountedPtr< Scantable > out = getScantable(in, true);
2905 setInsitu(insitu);
2906 Table& tout = out->table();
2907 tout.rwKeywordSet().define("POLTYPE", String(newtype));
2908
2909 Block<String> cols(4);
2910 cols[0] = "SCANNO";
2911 cols[1] = "CYCLENO";
2912 cols[2] = "BEAMNO";
2913 cols[3] = "IFNO";
2914 TableIterator it(in->originalTable_, cols);
2915 String basetype = in->getPolType();
2916 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
2917 try {
2918 while ( !it.pastEnd() ) {
2919 Table tab = it.table();
2920 uInt row = tab.rowNumbers()[0];
2921 stpol->setSpectra(in->getPolMatrix(row));
2922 Float fang,fhand;
2923 fang = in->focusTable_.getTotalAngle(in->mfocusidCol_(row));
2924 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
2925 stpol->setPhaseCorrections(fang, fhand);
2926 Int npolout = 0;
2927 for (uInt i=0; i<tab.nrow(); ++i) {
2928 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
2929 if ( outvec.nelements() > 0 ) {
2930 tout.addRow();
2931 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
2932 ArrayColumn<Float> sCol(tout,"SPECTRA");
2933 ScalarColumn<uInt> pCol(tout,"POLNO");
2934 sCol.put(tout.nrow()-1 ,outvec);
2935 pCol.put(tout.nrow()-1 ,uInt(npolout));
2936 npolout++;
2937 }
2938 }
2939 tout.rwKeywordSet().define("nPol", npolout);
2940 ++it;
2941 }
2942 } catch (AipsError& e) {
2943 delete stpol;
2944 throw(e);
2945 }
2946 delete stpol;
2947 return out;
2948}
2949
2950CountedPtr< Scantable >
2951 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
2952 const std::string & scantype )
2953{
2954 bool insitu = insitu_;
2955 setInsitu(false);
2956 CountedPtr< Scantable > out = getScantable(in, true);
2957 setInsitu(insitu);
2958 Table& tout = out->table();
2959 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
2960 if (scantype == "on") {
2961 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
2962 }
2963 Table tab = tableCommand(taql, in->table());
2964 TableCopy::copyRows(tout, tab);
2965 if (scantype == "on") {
2966 // re-index SCANNO to 0
2967 TableVector<uInt> vec(tout, "SCANNO");
2968 vec = 0;
2969 }
2970 return out;
2971}
2972
2973std::vector<float>
2974 asap::STMath::fft( const casa::CountedPtr< Scantable > & in,
2975 const std::vector<int>& whichrow,
2976 bool getRealImag )
2977{
2978 std::vector<float> res;
2979 Table tab = in->table();
2980 std::vector<bool> mask;
2981
2982 if (whichrow.size() < 1) { // for all rows (by default)
2983 int nrow = int(tab.nrow());
2984 for (int i = 0; i < nrow; ++i) {
2985 res = in->execFFT(i, mask, getRealImag);
2986 }
2987 } else { // for specified rows
2988 for (uInt i = 0; i < whichrow.size(); ++i) {
2989 res = in->execFFT(i, mask, getRealImag);
2990 }
2991 }
2992
2993 return res;
2994}
2995
2996
2997CountedPtr<Scantable>
2998 asap::STMath::lagFlag( const CountedPtr<Scantable>& in,
2999 double start, double end,
3000 const std::string& mode )
3001{
3002 CountedPtr<Scantable> out = getScantable(in, false);
3003 Table& tout = out->table();
3004 TableIterator iter(tout, "FREQ_ID");
3005 FFTServer<Float,Complex> ffts;
3006
3007 while ( !iter.pastEnd() ) {
3008 Table tab = iter.table();
3009 Double rp,rv,inc;
3010 ROTableRow row(tab);
3011 const TableRecord& rec = row.get(0);
3012 uInt freqid = rec.asuInt("FREQ_ID");
3013 out->frequencies().getEntry(rp, rv, inc, freqid);
3014 ArrayColumn<Float> specCol(tab, "SPECTRA");
3015 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
3016
3017 for (int i=0; i<int(tab.nrow()); ++i) {
3018 Vector<Float> spec = specCol(i);
3019 Vector<uChar> flag = flagCol(i);
3020 std::vector<bool> mask;
3021 for (uInt j = 0; j < flag.nelements(); ++j) {
3022 mask.push_back(!(flag[j]>0));
3023 }
3024 mathutil::doZeroOrderInterpolation(spec, mask);
3025
3026 Vector<Complex> lags;
3027 ffts.fft0(lags, spec);
3028
3029 Int lag0(start+0.5);
3030 Int lag1(end+0.5);
3031 if (mode == "frequency") {
3032 lag0 = Int(spec.nelements()*abs(inc)/(start)+0.5);
3033 lag1 = Int(spec.nelements()*abs(inc)/(end)+0.5);
3034 }
3035 Int lstart = max(0, lag0);
3036 Int lend = min(Int(lags.nelements()-1), lag1);
3037 if (lstart == lend) {
3038 lags[lstart] = Complex(0.0);
3039 } else {
3040 if (lstart > lend) {
3041 Int tmp = lend;
3042 lend = lstart;
3043 lstart = tmp;
3044 }
3045 for (int j=lstart; j <=lend ;++j) {
3046 lags[j] = Complex(0.0);
3047 }
3048 }
3049
3050 ffts.fft0(spec, lags);
3051
3052 specCol.put(i, spec);
3053 }
3054 ++iter;
3055 }
3056 return out;
3057}
3058
3059// Averaging spectra with different channel/resolution
3060CountedPtr<Scantable>
3061STMath::new_average( const std::vector<CountedPtr<Scantable> >& in,
3062 const bool& compel,
3063 const std::vector<bool>& mask,
3064 const std::string& weight,
3065 const std::string& avmode )
3066 throw ( casa::AipsError )
3067{
3068 LogIO os( LogOrigin( "STMath", "new_average()", WHERE ) ) ;
3069 if ( avmode == "SCAN" && in.size() != 1 )
3070 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
3071 "Use merge first."));
3072
3073 CountedPtr<Scantable> out ; // processed result
3074 if ( compel ) {
3075 std::vector< CountedPtr<Scantable> > newin ; // input for average process
3076 uInt insize = in.size() ; // number of input scantables
3077
3078 // setup newin
3079 bool oldInsitu = insitu_ ;
3080 setInsitu( false ) ;
3081 newin.resize( insize ) ;
3082 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3083 newin[itable] = getScantable( in[itable], false ) ;
3084 }
3085 setInsitu( oldInsitu ) ;
3086
3087 // warning
3088 os << "Average spectra with different spectral resolution" << LogIO::POST ;
3089
3090 // temporarily set coordinfo
3091 vector<string> oldinfo( insize ) ;
3092 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3093 vector<string> coordinfo = in[itable]->getCoordInfo() ;
3094 oldinfo[itable] = coordinfo[0] ;
3095 coordinfo[0] = "Hz" ;
3096 newin[itable]->setCoordInfo( coordinfo ) ;
3097 }
3098
3099 ostringstream oss ;
3100
3101 // check IF frequency coverage
3102 // freqid: list of FREQ_ID, which is used, in each table
3103 // iffreq: list of minimum and maximum frequency for each FREQ_ID in
3104 // each table
3105 // freqid[insize][numIF]
3106 // freqid: [[id00, id01, ...],
3107 // [id10, id11, ...],
3108 // ...
3109 // [idn0, idn1, ...]]
3110 // iffreq[insize][numIF*2]
3111 // iffreq: [[min_id00, max_id00, min_id01, max_id01, ...],
3112 // [min_id10, max_id10, min_id11, max_id11, ...],
3113 // ...
3114 // [min_idn0, max_idn0, min_idn1, max_idn1, ...]]
3115 //os << "Check IF settings in each table" << LogIO::POST ;
3116 vector< vector<uInt> > freqid( insize );
3117 vector< vector<double> > iffreq( insize ) ;
3118 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3119 Vector<uInt> freqIds = newin[itable]->mfreqidCol_.getColumn() ;
3120 vector<uInt> uniqueFreqId = newin[itable]->getNumbers(newin[itable]->mfreqidCol_) ;
3121 for ( vector<uInt>::iterator i = uniqueFreqId.begin() ;
3122 i != uniqueFreqId.end() ; i++ ) {
3123 //os << "itable = " << itable << ": IF " << id << " is included in the list" << LogIO::POST ;
3124 uInt target = 0 ;
3125 while ( freqIds[target] != *i )
3126 target++ ;
3127 vector<double> abcissa = newin[itable]->getAbcissa( target ) ;
3128 freqid[itable].push_back( *i ) ;
3129 double incr = abs( abcissa[1] - abcissa[0] ) ;
3130 iffreq[itable].push_back( (*min_element(abcissa.begin(),abcissa.end()))-0.5*incr ) ;
3131 iffreq[itable].push_back( (*max_element(abcissa.begin(),abcissa.end()))+0.5*incr ) ;
3132 }
3133 }
3134
3135 // debug
3136// os << "IF settings summary:" << endl ;
3137// for ( uInt i = 0 ; i < freqid.size() ; i++ ) {
3138// os << " Table" << i << endl ;
3139// for ( uInt j = 0 ; j < freqid[i].size() ; j++ ) {
3140// os << " id = " << freqid[i][j] << " (min,max) = (" << iffreq[i][2*j] << "," << iffreq[i][2*j+1] << ")" << endl ;
3141// }
3142// }
3143// os << endl ;
3144// os.post() ;
3145
3146 // IF grouping based on their frequency coverage
3147 // ifgrp: number of member in each IF group
3148 // ifgrp[numgrp]
3149 // ifgrp: [n0, n1, ...]
3150 //os << "IF grouping based on their frequency coverage" << LogIO::POST ;
3151
3152 // parameter for IF grouping
3153 // groupmode = OR retrieve all region
3154 // AND only retrieve overlaped region
3155 //string groupmode = "AND" ;
3156 string groupmode = "OR" ;
3157 uInt sizecr = 0 ;
3158 if ( groupmode == "AND" )
3159 sizecr = 1 ;
3160 else if ( groupmode == "OR" )
3161 sizecr = 0 ;
3162
3163 vector<double> sortedfreq ;
3164 for ( uInt i = 0 ; i < iffreq.size() ; i++ ) {
3165 for ( uInt j = 0 ; j < iffreq[i].size() ; j++ ) {
3166 if ( count( sortedfreq.begin(), sortedfreq.end(), iffreq[i][j] ) == 0 )
3167 sortedfreq.push_back( iffreq[i][j] ) ;
3168 }
3169 }
3170 sort( sortedfreq.begin(), sortedfreq.end() ) ;
3171 vector<uInt> ifgrp( sortedfreq.size()-1, 0 ) ;
3172 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3173 for ( uInt iif = 0 ; iif < freqid[itable].size() ; iif++ ) {
3174 double range0 = iffreq[itable][2*iif] ;
3175 double range1 = iffreq[itable][2*iif+1] ;
3176 for ( uInt j = 0 ; j < sortedfreq.size()-1 ; j++ ) {
3177 double fmin = max( range0, sortedfreq[j] ) ;
3178 double fmax = min( range1, sortedfreq[j+1] ) ;
3179 if ( fmin < fmax ) {
3180 ifgrp[j]++ ;
3181 }
3182 }
3183 }
3184 }
3185
3186 // Grouping continuous IF groups (without frequency gap)
3187 // freqgrp: list of IF group indexes in each frequency group
3188 // freqgrp[numgrp][nummember]
3189 // freqgrp: [[ifgrp00, ifgrp01, ifgrp02, ...],
3190 // [ifgrp10, ifgrp11, ifgrp12, ...],
3191 // ...
3192 // [ifgrpn0, ifgrpn1, ifgrpn2, ...]]
3193 // grprange[2*numgrp]
3194 // grprange: [fmin0,fmax0,fmin1,fmax1,...]
3195 vector< vector<uInt> > freqgrp ;
3196 vector<double> grprange ;
3197 vector<uInt> grpedge ;
3198 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3199 if ( ifgrp[igrp] <= sizecr ) {
3200 grpedge.push_back( igrp ) ;
3201 }
3202 }
3203 grpedge.push_back( ifgrp.size() ) ;
3204 uInt itmp = 0 ;
3205 for ( uInt i = 0 ; i < grpedge.size() ; i++ ) {
3206 int n = grpedge[i] - itmp ;
3207 if ( n > 0 ) {
3208 vector<uInt> members( n ) ;
3209 for ( int j = 0 ; j < n ; j++ ) {
3210 members[j] = itmp+j ;
3211 }
3212 freqgrp.push_back( members ) ;
3213 grprange.push_back( sortedfreq[itmp] ) ;
3214 grprange.push_back( sortedfreq[grpedge[i]] ) ;
3215 }
3216 itmp += n + 1 ;
3217 }
3218
3219 // print frequency group
3220 oss.str("") ;
3221 oss << "Frequency Group summary: " << endl ;
3222 oss << " GROUP_ID: [FREQ_MIN, FREQ_MAX]" << endl ;
3223 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3224 oss << " GROUP " << setw( 2 ) << i << ": [" << grprange[2*i] << "," << grprange[2*i+1] << "]" ;
3225 oss << endl ;
3226 }
3227 oss << endl ;
3228 os << oss.str() << LogIO::POST ;
3229
3230 // groups: list of frequency group index whose frequency range overlaps
3231 // with that of each table and IF
3232 // groups[numtable][numIF]
3233 // groups: [[grpx, grpy,...],
3234 // [grpa, grpb,...],
3235 // ...
3236 // [grpk, grpm,...]]
3237 vector< vector<uInt> > groups( insize ) ;
3238 for ( uInt i = 0 ; i < insize ; i++ ) {
3239 groups[i].resize( freqid[i].size() ) ;
3240 }
3241 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3242 for ( uInt ifreq = 0 ; ifreq < freqid[itable].size() ; ifreq++ ) {
3243 double minf = iffreq[itable][2*ifreq] ;
3244 uInt groupid ;
3245 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3246 vector<uInt> memberlist = freqgrp[igrp] ;
3247 if ( (minf >= grprange[2*igrp]) && (minf <= grprange[2*igrp+1]) ) {
3248 groupid = igrp ;
3249 break ;
3250 }
3251 }
3252 groups[itable][ifreq] = groupid ;
3253 }
3254 }
3255
3256
3257 // print membership
3258 oss.str("") ;
3259 for ( uInt i = 0 ; i < insize ; i++ ) {
3260 oss << "Table " << i << endl ;
3261 for ( uInt j = 0 ; j < groups[i].size() ; j++ ) {
3262 oss << " FREQ_ID " << setw( 2 ) << freqid[i][j] << ": " ;
3263 oss << setw( 2 ) << groups[i][j] ;
3264 oss << endl ;
3265 }
3266 }
3267 os << oss.str() << LogIO::POST ;
3268
3269 // reset SCANNO and IFNO/FREQ_ID: IF is reset by the result of sortation
3270 //os << "All IF number is set to IF group index" << LogIO::POST ;
3271 // reset SCANNO only when avmode != "SCAN"
3272 if ( avmode != "SCAN" ) {
3273 os << "All scan number is set to 0" << LogIO::POST ;
3274 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3275 uInt nrow = newin[itable]->nrow() ;
3276 Vector<uInt> resetScan( nrow, 0 ) ;
3277 newin[itable]->scanCol_.putColumn( resetScan ) ;
3278 }
3279 }
3280
3281 // reset spectra and flagtra: align spectral resolution
3282 //os << "Align spectral resolution" << LogIO::POST ;
3283 // gmaxdnu: the coarsest frequency resolution in the frequency group
3284 // gminfreq: lower frequency edge of the frequency group
3285 // gnchan: number of channels for the frequency group
3286 vector<double> gmaxdnu( freqgrp.size(), 0.0 ) ;
3287 vector<double> gminfreq( freqgrp.size() ) ;
3288 vector<double> gnchan( freqgrp.size() ) ;
3289 for ( uInt i = 0 ; i < insize ; i++ ) {
3290 vector<uInt> members = groups[i] ;
3291 for ( uInt j = 0 ; j < members.size() ; j++ ) {
3292 uInt groupid = members[j] ;
3293 Double rp,rv,ic ;
3294 newin[i]->frequencies().getEntry( rp, rv, ic, j ) ;
3295 if ( abs(ic) > abs(gmaxdnu[groupid]) )
3296 gmaxdnu[groupid] = ic ;
3297 }
3298 }
3299 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3300 gminfreq[igrp] = grprange[2*igrp] ;
3301 double maxfreq = grprange[2*igrp+1] ;
3302 gnchan[igrp] = (int)(abs((maxfreq-gminfreq[igrp])/gmaxdnu[igrp])+0.9) ;
3303 }
3304
3305 // regrid spectral data and update frequency info
3306 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3307 Vector<uInt> oldFreqId = newin[itable]->mfreqidCol_.getColumn() ;
3308 Vector<uInt> newFreqId( oldFreqId.nelements() ) ;
3309
3310 // update MAIN
3311 for ( uInt irow = 0 ; irow < newin[itable]->nrow() ; irow++ ) {
3312 uInt groupid = groups[itable][oldFreqId[irow]] ;
3313 newFreqId[irow] = groupid ;
3314 newin[itable]->regridChannel( gnchan[groupid],
3315 gmaxdnu[groupid],
3316 gminfreq[groupid],
3317 irow ) ;
3318 }
3319 newin[itable]->mfreqidCol_.putColumn( newFreqId ) ;
3320 newin[itable]->ifCol_.putColumn( newFreqId ) ;
3321
3322 // update FREQUENCIES
3323 Table tab = newin[itable]->frequencies().table() ;
3324 ScalarColumn<uInt> fIdCol( tab, "ID" ) ;
3325 ScalarColumn<Double> fRefPixCol( tab, "REFPIX" ) ;
3326 ScalarColumn<Double> fRefValCol( tab, "REFVAL" ) ;
3327 ScalarColumn<Double> fIncrCol( tab, "INCREMENT" ) ;
3328 if ( freqgrp.size() > tab.nrow() ) {
3329 tab.addRow( freqgrp.size()-tab.nrow() ) ;
3330 }
3331 for ( uInt irow = 0 ; irow < freqgrp.size() ; irow++ ) {
3332 Double refval = gminfreq[irow] + 0.5 * abs(gmaxdnu[irow]) ;
3333 Double refpix = (gmaxdnu[irow] > 0.0) ? 0 : gnchan[irow]-1 ;
3334 Double increment = gmaxdnu[irow] ;
3335 fIdCol.put( irow, irow ) ;
3336 fRefPixCol.put( irow, refpix ) ;
3337 fRefValCol.put( irow, refval ) ;
3338 fIncrCol.put( irow, increment ) ;
3339 }
3340 }
3341
3342 // set back coordinfo
3343 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3344 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3345 coordinfo[0] = oldinfo[itable] ;
3346 newin[itable]->setCoordInfo( coordinfo ) ;
3347 }
3348
3349 // average
3350 out = average( newin, mask, weight, avmode ) ;
3351 }
3352 else {
3353 // simple average
3354 out = average( in, mask, weight, avmode ) ;
3355 }
3356
3357 return out;
3358}
3359
3360CountedPtr<Scantable> STMath::cwcal( const CountedPtr<Scantable>& s,
3361 const String calmode,
3362 const String antname )
3363{
3364 // frequency switch
3365 if ( calmode == "fs" ) {
3366 return cwcalfs( s, antname ) ;
3367 }
3368 else {
3369 vector<bool> masks = s->getMask( 0 ) ;
3370 vector<int> types ;
3371
3372 // save original table selection
3373 Table torg = s->table_ ;
3374
3375 // sky scan
3376 bool insitu = insitu_ ;
3377 insitu_ = false ;
3378 // share calibration scans before average with out
3379 CountedPtr<Scantable> out = getScantable( s, true ) ;
3380 insitu_ = insitu ;
3381 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::SKY ) ;
3382 out->attach() ;
3383 CountedPtr<Scantable> asky = averageWithinSession( out,
3384 masks,
3385 "TINT" ) ;
3386 // hot scan
3387 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::HOT ) ;
3388 out->attach() ;
3389 CountedPtr<Scantable> ahot = averageWithinSession( out,
3390 masks,
3391 "TINT" ) ;
3392 // cold scan
3393 CountedPtr<Scantable> acold ;
3394// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::COLD ) ;
3395// out->attach() ;
3396// CountedPtr<Scantable> acold = averageWithinSession( out,
3397// masks,
3398// "TINT" ) ;
3399
3400 // off scan
3401 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3402 out->attach() ;
3403 CountedPtr<Scantable> aoff = averageWithinSession( out,
3404 masks,
3405 "TINT" ) ;
3406
3407 // on scan
3408 s->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3409 s->attach() ;
3410 out->table_ = out->originalTable_ ;
3411 out->attach() ;
3412 out->table().addRow( s->nrow() ) ;
3413 copyRows( out->table(), s->table(), 0, 0, s->nrow(), False, True, False ) ;
3414
3415 // process each on scan
3416 STSelector sel ;
3417 vector<string> cols( 3 ) ;
3418 cols[0] = "BEAMNO" ;
3419 cols[1] = "POLNO" ;
3420 cols[2] = "IFNO" ;
3421 STIdxIter *iter = new STIdxIterAcc( out, cols ) ;
3422 while ( !iter->pastEnd() ) {
3423 Vector<uInt> ids = iter->current() ;
3424 stringstream ss ;
3425 ss << "SELECT FROM $1 WHERE "
3426 << "BEAMNO==" << ids[0] << "&&"
3427 << "POLNO==" << ids[1] << "&&"
3428 << "IFNO==" << ids[2] ;
3429 //cout << "TaQL string: " << ss.str() << endl ;
3430 sel.setTaQL( ss.str() ) ;
3431 aoff->setSelection( sel ) ;
3432 ahot->setSelection( sel ) ;
3433 asky->setSelection( sel ) ;
3434 Vector<uInt> rows = iter->getRows( SHARE ) ;
3435 // out should be an exact copy of s except that SPECTRA column is empty
3436 calibrateCW( out, s, aoff, asky, ahot, acold, rows, antname ) ;
3437 aoff->unsetSelection() ;
3438 ahot->unsetSelection() ;
3439 asky->unsetSelection() ;
3440 sel.reset() ;
3441 iter->next() ;
3442 }
3443 delete iter ;
3444 s->table_ = torg ;
3445 s->attach() ;
3446
3447 // flux unit
3448 out->setFluxUnit( "K" ) ;
3449
3450 return out ;
3451 }
3452}
3453
3454CountedPtr<Scantable> STMath::almacal( const CountedPtr<Scantable>& s,
3455 const String calmode )
3456{
3457 // frequency switch
3458 if ( calmode == "fs" ) {
3459 return almacalfs( s ) ;
3460 }
3461 else {
3462// double t0, t1 ;
3463// t0 = mathutil::gettimeofday_sec() ;
3464 vector<bool> masks = s->getMask( 0 ) ;
3465
3466 // save original table selection
3467 Table torg = s->table_ ;
3468
3469 // off scan
3470 // TODO 2010/01/08 TN
3471 // Grouping by time should be needed before averaging.
3472 // Each group must have own unique SCANNO (should be renumbered).
3473 // See PIPELINE/SDCalibration.py
3474 bool insitu = insitu_ ;
3475 insitu_ = false ;
3476 // share off scan before average with out
3477 CountedPtr<Scantable> out = getScantable( s, true ) ;
3478 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3479 out->attach() ;
3480 insitu_ = insitu ;
3481 CountedPtr<Scantable> aoff = averageWithinSession( out,
3482 masks,
3483 "TINT" ) ;
3484
3485 // on scan
3486// t0 = mathutil::gettimeofday_sec() ;
3487 s->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3488 s->attach() ;
3489 out->table_ = out->originalTable_ ;
3490 out->attach() ;
3491 out->table().addRow( s->nrow() ) ;
3492 copyRows( out->table(), s->table(), 0, 0, s->nrow(), False ) ;
3493// t1 = mathutil::gettimeofday_sec() ;
3494// cout << "elapsed time for preparing output table: " << t1-t0 << " sec" << endl ;
3495
3496 // process each on scan
3497// t0 = mathutil::gettimeofday_sec() ;
3498
3499 // using STIdxIterAcc
3500 vector<string> cols( 3 ) ;
3501 cols[0] = "BEAMNO" ;
3502 cols[1] = "POLNO" ;
3503 cols[2] = "IFNO" ;
3504 STIdxIter *iter = new STIdxIterAcc( out, cols ) ;
3505 STSelector sel ;
3506 while ( !iter->pastEnd() ) {
3507 Vector<uInt> ids = iter->current() ;
3508 stringstream ss ;
3509 ss << "SELECT FROM $1 WHERE "
3510 << "BEAMNO==" << ids[0] << "&&"
3511 << "POLNO==" << ids[1] << "&&"
3512 << "IFNO==" << ids[2] ;
3513 //cout << "TaQL string: " << ss.str() << endl ;
3514 sel.setTaQL( ss.str() ) ;
3515 aoff->setSelection( sel ) ;
3516 Vector<uInt> rows = iter->getRows( SHARE ) ;
3517 // out should be an exact copy of s except that SPECTRA column is empty
3518 calibrateALMA( out, s, aoff, rows ) ;
3519 aoff->unsetSelection() ;
3520 sel.reset() ;
3521 iter->next() ;
3522 }
3523 delete iter ;
3524 s->table_ = torg ;
3525 s->attach() ;
3526
3527// t1 = mathutil::gettimeofday_sec() ;
3528// cout << "elapsed time for calibration: " << t1-t0 << " sec" << endl ;
3529
3530 // flux unit
3531 out->setFluxUnit( "K" ) ;
3532
3533 return out ;
3534 }
3535}
3536
3537CountedPtr<Scantable> STMath::cwcalfs( const CountedPtr<Scantable>& s,
3538 const String antname )
3539{
3540 vector<int> types ;
3541
3542 // APEX calibration mode
3543 int apexcalmode = 1 ;
3544
3545 if ( antname.find( "APEX" ) != string::npos ) {
3546 // check if off scan exists or not
3547 STSelector sel = STSelector() ;
3548 //sel.setName( offstr1 ) ;
3549 types.push_back( SrcType::FLOOFF ) ;
3550 sel.setTypes( types ) ;
3551 try {
3552 s->setSelection( sel ) ;
3553 }
3554 catch ( AipsError &e ) {
3555 apexcalmode = 0 ;
3556 }
3557 sel.reset() ;
3558 }
3559 s->unsetSelection() ;
3560 types.clear() ;
3561
3562 vector<bool> masks = s->getMask( 0 ) ;
3563 CountedPtr<Scantable> ssig, sref ;
3564 //CountedPtr<Scantable> out ;
3565 bool insitu = insitu_ ;
3566 insitu_ = False ;
3567 CountedPtr<Scantable> out = getScantable( s, true ) ;
3568 insitu_ = insitu ;
3569
3570 if ( antname.find( "APEX" ) != string::npos ) {
3571 // APEX calibration
3572 // sky scan
3573 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOSKY ) ;
3574 out->attach() ;
3575 CountedPtr<Scantable> askylo = averageWithinSession( out,
3576 masks,
3577 "TINT" ) ;
3578 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHISKY ) ;
3579 out->attach() ;
3580 CountedPtr<Scantable> askyhi = averageWithinSession( out,
3581 masks,
3582 "TINT" ) ;
3583
3584 // hot scan
3585 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOHOT ) ;
3586 out->attach() ;
3587 CountedPtr<Scantable> ahotlo = averageWithinSession( out,
3588 masks,
3589 "TINT" ) ;
3590 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHIHOT ) ;
3591 out->attach() ;
3592 CountedPtr<Scantable> ahothi = averageWithinSession( out,
3593 masks,
3594 "TINT" ) ;
3595
3596 // cold scan
3597 CountedPtr<Scantable> acoldlo, acoldhi ;
3598// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOCOLD ) ;
3599// out->attach() ;
3600// CountedPtr<Scantable> acoldlo = averageWithinSession( out,
3601// masks,
3602// "TINT" ) ;
3603// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHICOLD ) ;
3604// out->attach() ;
3605// CountedPtr<Scantable> acoldhi = averageWithinSession( out,
3606// masks,
3607// "TINT" ) ;
3608
3609 // ref scan
3610 insitu_ = false ;
3611 sref = getScantable( s, true ) ;
3612 CountedPtr<Scantable> rref = getScantable( s, true ) ;
3613 insitu_ = insitu ;
3614 rref->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FSLO ) ;
3615 rref->attach() ;
3616 copyRows( sref->table_, rref->table_, 0, 0, rref->nrow(), False, True, False ) ;
3617
3618 // sig scan
3619 insitu_ = false ;
3620 ssig = getScantable( s, true ) ;
3621 CountedPtr<Scantable> rsig = getScantable( s, true ) ;
3622 insitu_ = insitu ;
3623 rsig->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FSHI ) ;
3624 rsig->attach() ;
3625 copyRows( ssig->table_, rsig->table_, 0, 0, rsig->nrow(), False, True, False ) ;
3626
3627 if ( apexcalmode == 0 ) {
3628 // using STIdxIterAcc
3629 vector<string> cols( 3 ) ;
3630 cols[0] = "BEAMNO" ;
3631 cols[1] = "POLNO" ;
3632 cols[2] = "IFNO" ;
3633 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
3634 STSelector sel ;
3635 vector< CountedPtr<Scantable> > on( 2 ) ;
3636 on[0] = rsig ;
3637 on[1] = rref ;
3638 vector< CountedPtr<Scantable> > sky( 2 ) ;
3639 sky[0] = askylo ;
3640 sky[1] = askyhi ;
3641 vector< CountedPtr<Scantable> > hot( 2 ) ;
3642 hot[0] = ahotlo ;
3643 hot[1] = ahothi ;
3644 vector< CountedPtr<Scantable> > cold( 2 ) ;
3645 while ( !iter->pastEnd() ) {
3646 Vector<uInt> ids = iter->current() ;
3647 stringstream ss ;
3648 ss << "SELECT FROM $1 WHERE "
3649 << "BEAMNO==" << ids[0] << "&&"
3650 << "POLNO==" << ids[1] << "&&"
3651 << "IFNO==" << ids[2] ;
3652 //cout << "TaQL string: " << ss.str() << endl ;
3653 sel.setTaQL( ss.str() ) ;
3654 sky[0]->setSelection( sel ) ;
3655 sky[1]->setSelection( sel ) ;
3656 hot[0]->setSelection( sel ) ;
3657 hot[1]->setSelection( sel ) ;
3658 Vector<uInt> rows = iter->getRows( SHARE ) ;
3659 calibrateAPEXFS( ssig, sref, on, sky, hot, cold, rows ) ;
3660 sky[0]->unsetSelection() ;
3661 sky[1]->unsetSelection() ;
3662 hot[0]->unsetSelection() ;
3663 hot[1]->unsetSelection() ;
3664 sel.reset() ;
3665 iter->next() ;
3666 }
3667 delete iter ;
3668
3669 }
3670 else if ( apexcalmode == 1 ) {
3671 // APEX fs data with off scan
3672 // off scan
3673 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOOFF ) ;
3674 out->attach() ;
3675 CountedPtr<Scantable> aofflo = averageWithinSession( out,
3676 masks,
3677 "TINT" ) ;
3678 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHIOFF ) ;
3679 out->attach() ;
3680 CountedPtr<Scantable> aoffhi = averageWithinSession( out,
3681 masks,
3682 "TINT" ) ;
3683
3684 // process each sig and ref scan
3685// STSelector sel ;
3686 vector<string> cols( 3 ) ;
3687 cols[0] = "BEAMNO" ;
3688 cols[1] = "POLNO" ;
3689 cols[2] = "IFNO" ;
3690 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
3691 STSelector sel ;
3692 while ( !iter->pastEnd() ) {
3693 Vector<uInt> ids = iter->current() ;
3694 stringstream ss ;
3695 ss << "SELECT FROM $1 WHERE "
3696 << "BEAMNO==" << ids[0] << "&&"
3697 << "POLNO==" << ids[1] << "&&"
3698 << "IFNO==" << ids[2] ;
3699 //cout << "TaQL string: " << ss.str() << endl ;
3700 sel.setTaQL( ss.str() ) ;
3701 aofflo->setSelection( sel ) ;
3702 ahotlo->setSelection( sel ) ;
3703 askylo->setSelection( sel ) ;
3704 Vector<uInt> rows = iter->getRows( SHARE ) ;
3705 calibrateCW( ssig, rsig, aofflo, askylo, ahotlo, acoldlo, rows, antname ) ;
3706 aofflo->unsetSelection() ;
3707 ahotlo->unsetSelection() ;
3708 askylo->unsetSelection() ;
3709 sel.reset() ;
3710 iter->next() ;
3711 }
3712 delete iter ;
3713 iter = new STIdxIterAcc( sref, cols ) ;
3714 while ( !iter->pastEnd() ) {
3715 Vector<uInt> ids = iter->current() ;
3716 stringstream ss ;
3717 ss << "SELECT FROM $1 WHERE "
3718 << "BEAMNO==" << ids[0] << "&&"
3719 << "POLNO==" << ids[1] << "&&"
3720 << "IFNO==" << ids[2] ;
3721 //cout << "TaQL string: " << ss.str() << endl ;
3722 sel.setTaQL( ss.str() ) ;
3723 aoffhi->setSelection( sel ) ;
3724 ahothi->setSelection( sel ) ;
3725 askyhi->setSelection( sel ) ;
3726 Vector<uInt> rows = iter->getRows( SHARE ) ;
3727 calibrateCW( sref, rref, aoffhi, askyhi, ahothi, acoldhi, rows, antname ) ;
3728 aoffhi->unsetSelection() ;
3729 ahothi->unsetSelection() ;
3730 askyhi->unsetSelection() ;
3731 sel.reset() ;
3732 iter->next() ;
3733 }
3734 delete iter ;
3735 }
3736 }
3737 else {
3738 // non-APEX fs data
3739 // sky scan
3740 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::SKY ) ;
3741 out->attach() ;
3742 CountedPtr<Scantable> asky = averageWithinSession( out,
3743 masks,
3744 "TINT" ) ;
3745 STSelector sel = STSelector() ;
3746
3747 // hot scan
3748 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::HOT ) ;
3749 out->attach() ;
3750 CountedPtr<Scantable> ahot = averageWithinSession( out,
3751 masks,
3752 "TINT" ) ;
3753
3754 // cold scan
3755 CountedPtr<Scantable> acold ;
3756// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::COLD ) ;
3757// out->attach() ;
3758// CountedPtr<Scantable> acold = averageWithinSession( out,
3759// masks,
3760// "TINT" ) ;
3761
3762 // ref scan
3763 bool insitu = insitu_ ;
3764 insitu_ = false ;
3765 sref = getScantable( s, true ) ;
3766 CountedPtr<Scantable> rref = getScantable( s, true ) ;
3767 insitu_ = insitu ;
3768 rref->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3769 rref->attach() ;
3770 copyRows( sref->table_, rref->table_, 0, 0, rref->nrow(), False, True, False ) ;
3771
3772 // sig scan
3773 insitu_ = false ;
3774 ssig = getScantable( s, true ) ;
3775 CountedPtr<Scantable> rsig = getScantable( s, true ) ;
3776 insitu_ = insitu ;
3777 rsig->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3778 rsig->attach() ;
3779 copyRows( ssig->table_, rsig->table_, 0, 0, rsig->nrow(), False, True, False ) ;
3780
3781 // process each sig and ref scan
3782 vector<string> cols( 3 ) ;
3783 cols[0] = "BEAMNO" ;
3784 cols[1] = "POLNO" ;
3785 cols[2] = "IFNO" ;
3786 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
3787 while ( !iter->pastEnd() ) {
3788 Vector<uInt> ids = iter->current() ;
3789 stringstream ss ;
3790 ss << "SELECT FROM $1 WHERE "
3791 << "BEAMNO==" << ids[0] << "&&"
3792 << "POLNO==" << ids[1] << "&&"
3793 << "IFNO==" << ids[2] ;
3794 //cout << "TaQL string: " << ss.str() << endl ;
3795 sel.setTaQL( ss.str() ) ;
3796 ahot->setSelection( sel ) ;
3797 asky->setSelection( sel ) ;
3798 Vector<uInt> rows = iter->getRows( SHARE ) ;
3799 // out should be an exact copy of s except that SPECTRA column is empty
3800 calibrateFS( ssig, sref, rsig, rref, asky, ahot, acold, rows ) ;
3801 ahot->unsetSelection() ;
3802 asky->unsetSelection() ;
3803 sel.reset() ;
3804 iter->next() ;
3805 }
3806 delete iter ;
3807 }
3808
3809 // do folding if necessary
3810 Table sigtab = ssig->table() ;
3811 Table reftab = sref->table() ;
3812 ScalarColumn<uInt> reffidCol ;
3813 Int nchan = (Int)ssig->nchan() ;
3814 reffidCol.attach( reftab, "FREQ_ID" ) ;
3815 Vector<uInt> sfids = ssig->mfreqidCol_.getColumn() ;
3816 Vector<uInt> rfids = sref->mfreqidCol_.getColumn() ;
3817 vector<uInt> sfids_unique ;
3818 vector<uInt> rfids_unique ;
3819 vector<uInt> sifno_unique ;
3820 vector<uInt> rifno_unique ;
3821 for ( uInt i = 0 ; i < sfids.nelements() ; i++ ) {
3822 if ( count( sfids_unique.begin(), sfids_unique.end(), sfids[i] ) == 0 ) {
3823 sfids_unique.push_back( sfids[i] ) ;
3824 sifno_unique.push_back( ssig->getIF( i ) ) ;
3825 }
3826 if ( count( rfids_unique.begin(), rfids_unique.end(), rfids[i] ) == 0 ) {
3827 rfids_unique.push_back( rfids[i] ) ;
3828 rifno_unique.push_back( sref->getIF( i ) ) ;
3829 }
3830 }
3831 double refpix_sig, refval_sig, increment_sig ;
3832 double refpix_ref, refval_ref, increment_ref ;
3833 vector< CountedPtr<Scantable> > tmp( sfids_unique.size() ) ;
3834 for ( uInt i = 0 ; i < sfids_unique.size() ; i++ ) {
3835 ssig->frequencies().getEntry( refpix_sig, refval_sig, increment_sig, sfids_unique[i] ) ;
3836 sref->frequencies().getEntry( refpix_ref, refval_ref, increment_ref, rfids_unique[i] ) ;
3837 if ( refpix_sig == refpix_ref ) {
3838 double foffset = refval_ref - refval_sig ;
3839 int choffset = static_cast<int>(foffset/increment_sig) ;
3840 double doffset = foffset / increment_sig ;
3841 if ( abs(choffset) >= nchan ) {
3842 LogIO os( LogOrigin( "STMath", "cwcalfs", WHERE ) ) ;
3843 os << "FREQ_ID=[" << sfids_unique[i] << "," << rfids_unique[i] << "]: out-band frequency switching, no folding" << LogIO::POST ;
3844 os << "Just return signal data" << LogIO::POST ;
3845 //std::vector< CountedPtr<Scantable> > tabs ;
3846 //tabs.push_back( ssig ) ;
3847 //tabs.push_back( sref ) ;
3848 //out = merge( tabs ) ;
3849 tmp[i] = ssig ;
3850 }
3851 else {
3852 STSelector sel = STSelector() ;
3853 vector<int> v( 1, sifno_unique[i] ) ;
3854 sel.setIFs( v ) ;
3855 ssig->setSelection( sel ) ;
3856 sel.reset() ;
3857 v[0] = rifno_unique[i] ;
3858 sel.setIFs( v ) ;
3859 sref->setSelection( sel ) ;
3860 sel.reset() ;
3861 if ( antname.find( "APEX" ) != string::npos ) {
3862 tmp[i] = dofold( ssig, sref, 0.5*doffset, -0.5*doffset ) ;
3863 //tmp[i] = dofold( ssig, sref, doffset ) ;
3864 }
3865 else {
3866 tmp[i] = dofold( ssig, sref, doffset ) ;
3867 }
3868 ssig->unsetSelection() ;
3869 sref->unsetSelection() ;
3870 }
3871 }
3872 }
3873
3874 if ( tmp.size() > 1 ) {
3875 out = merge( tmp ) ;
3876 }
3877 else {
3878 out = tmp[0] ;
3879 }
3880
3881 // flux unit
3882 out->setFluxUnit( "K" ) ;
3883
3884 return out ;
3885}
3886
3887CountedPtr<Scantable> STMath::almacalfs( const CountedPtr<Scantable>& s )
3888{
3889 (void) s; //currently unused
3890 CountedPtr<Scantable> out ;
3891
3892 return out ;
3893}
3894
3895Vector<Float> STMath::getSpectrumFromTime( double reftime,
3896 const Vector<Double> &timeVec,
3897 const vector<int> &idx,
3898 const Matrix<Float>& spectra,
3899 string mode )
3900{
3901 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
3902 Vector<Float> sp ;
3903 uInt ncol = spectra.ncolumn() ;
3904
3905 if ( ncol == 0 ) {
3906 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
3907 return sp ;
3908 }
3909 else if ( ncol == 1 ) {
3910 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
3911 sp.reference( spectra.column( 0 ) ) ;
3912 return sp ;
3913 }
3914 else {
3915 if ( mode == "before" ) {
3916 int id = -1 ;
3917 if ( idx[0] != -1 ) {
3918 id = idx[0] ;
3919 }
3920 else if ( idx[1] != -1 ) {
3921 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
3922 id = idx[1] ;
3923 }
3924 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3925 sp.reference( spectra.column( id ) ) ;
3926 }
3927 else if ( mode == "after" ) {
3928 int id = -1 ;
3929 if ( idx[1] != -1 ) {
3930 id = idx[1] ;
3931 }
3932 else if ( idx[0] != -1 ) {
3933 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
3934 id = idx[1] ;
3935 }
3936 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3937 sp.reference( spectra.column( id ) ) ;
3938 }
3939 else if ( mode == "nearest" ) {
3940 int id = -1 ;
3941 if ( idx[0] == -1 ) {
3942 id = idx[1] ;
3943 }
3944 else if ( idx[1] == -1 ) {
3945 id = idx[0] ;
3946 }
3947 else if ( idx[0] == idx[1] ) {
3948 id = idx[0] ;
3949 }
3950 else {
3951 double t0 = timeVec[idx[0]] ;
3952 double t1 = timeVec[idx[1]] ;
3953 double tref = reftime ;
3954 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
3955 id = idx[1] ;
3956 }
3957 else {
3958 id = idx[0] ;
3959 }
3960 }
3961 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3962 sp.reference( spectra.column( id ) ) ;
3963 }
3964 else if ( mode == "linear" ) {
3965 if ( idx[0] == -1 ) {
3966 // use after
3967 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
3968 int id = idx[1] ;
3969 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3970 sp.reference( spectra.column( id ) ) ;
3971 }
3972 else if ( idx[1] == -1 ) {
3973 // use before
3974 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
3975 int id = idx[0] ;
3976 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3977 sp.reference( spectra.column( id ) ) ;
3978 }
3979 else if ( idx[0] == idx[1] ) {
3980 // use before
3981 //os << "No need to interporate." << LogIO::POST ;
3982 int id = idx[0] ;
3983 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3984 sp.reference( spectra.column( id ) ) ;
3985 }
3986 else {
3987 // do interpolation
3988 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
3989 double t0 = timeVec[idx[0]] ;
3990 double t1 = timeVec[idx[1]] ;
3991 double tref = reftime ;
3992 sp = spectra.column( idx[0] ).copy() ;
3993 Vector<Float> sp1( spectra.column( idx[1] ) ) ;
3994 double tfactor = ( tref - t0 ) / ( t1 - t0 ) ;
3995 for ( unsigned int i = 0 ; i < sp.size() ; i++ ) {
3996 sp[i] = ( sp1[i] - sp[i] ) * tfactor + sp[i] ;
3997 }
3998 }
3999 }
4000 else {
4001 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4002 }
4003 return sp ;
4004 }
4005}
4006
4007vector<int> STMath::getRowIdFromTime( double reftime, const Vector<Double> &t )
4008{
4009// double reft = reftime ;
4010 double dtmin = 1.0e100 ;
4011 double dtmax = -1.0e100 ;
4012// vector<double> dt ;
4013 int just_before = -1 ;
4014 int just_after = -1 ;
4015 Vector<Double> dt = t - reftime ;
4016 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4017 if ( dt[i] > 0.0 ) {
4018 // after reftime
4019 if ( dt[i] < dtmin ) {
4020 just_after = i ;
4021 dtmin = dt[i] ;
4022 }
4023 }
4024 else if ( dt[i] < 0.0 ) {
4025 // before reftime
4026 if ( dt[i] > dtmax ) {
4027 just_before = i ;
4028 dtmax = dt[i] ;
4029 }
4030 }
4031 else {
4032 // just a reftime
4033 just_before = i ;
4034 just_after = i ;
4035 dtmax = 0 ;
4036 dtmin = 0 ;
4037 break ;
4038 }
4039 }
4040
4041 vector<int> v(2) ;
4042 v[0] = just_before ;
4043 v[1] = just_after ;
4044
4045 return v ;
4046}
4047
4048Vector<Float> STMath::getTcalFromTime( double reftime,
4049 const Vector<Double> &timeVec,
4050 const vector<int> &idx,
4051 const CountedPtr<Scantable>& s,
4052 string mode )
4053{
4054 LogIO os( LogOrigin( "STMath", "getTcalFromTime", WHERE ) ) ;
4055 STTcal tcalTable = s->tcal() ;
4056 String time ;
4057 Vector<Float> tcalval ;
4058 if ( s->nrow() == 0 ) {
4059 os << LogIO::SEVERE << "No row in the input scantable. Return empty tcal." << LogIO::POST ;
4060 return tcalval ;
4061 }
4062 else if ( s->nrow() == 1 ) {
4063 uInt tcalid = s->getTcalId( 0 ) ;
4064 //os << "use row " << 0 << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4065 tcalTable.getEntry( time, tcalval, tcalid ) ;
4066 return tcalval ;
4067 }
4068 else {
4069 if ( mode == "before" ) {
4070 int id = -1 ;
4071 if ( idx[0] != -1 ) {
4072 id = idx[0] ;
4073 }
4074 else if ( idx[1] != -1 ) {
4075 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4076 id = idx[1] ;
4077 }
4078 uInt tcalid = s->getTcalId( id ) ;
4079 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4080 tcalTable.getEntry( time, tcalval, tcalid ) ;
4081 }
4082 else if ( mode == "after" ) {
4083 int id = -1 ;
4084 if ( idx[1] != -1 ) {
4085 id = idx[1] ;
4086 }
4087 else if ( idx[0] != -1 ) {
4088 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4089 id = idx[1] ;
4090 }
4091 uInt tcalid = s->getTcalId( id ) ;
4092 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4093 tcalTable.getEntry( time, tcalval, tcalid ) ;
4094 }
4095 else if ( mode == "nearest" ) {
4096 int id = -1 ;
4097 if ( idx[0] == -1 ) {
4098 id = idx[1] ;
4099 }
4100 else if ( idx[1] == -1 ) {
4101 id = idx[0] ;
4102 }
4103 else if ( idx[0] == idx[1] ) {
4104 id = idx[0] ;
4105 }
4106 else {
4107 double t0 = timeVec[idx[0]] ;
4108 double t1 = timeVec[idx[1]] ;
4109 if ( abs( t0 - reftime ) > abs( t1 - reftime ) ) {
4110 id = idx[1] ;
4111 }
4112 else {
4113 id = idx[0] ;
4114 }
4115 }
4116 uInt tcalid = s->getTcalId( id ) ;
4117 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4118 tcalTable.getEntry( time, tcalval, tcalid ) ;
4119 }
4120 else if ( mode == "linear" ) {
4121 if ( idx[0] == -1 ) {
4122 // use after
4123 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4124 int id = idx[1] ;
4125 uInt tcalid = s->getTcalId( id ) ;
4126 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4127 tcalTable.getEntry( time, tcalval, tcalid ) ;
4128 }
4129 else if ( idx[1] == -1 ) {
4130 // use before
4131 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4132 int id = idx[0] ;
4133 uInt tcalid = s->getTcalId( id ) ;
4134 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4135 tcalTable.getEntry( time, tcalval, tcalid ) ;
4136 }
4137 else if ( idx[0] == idx[1] ) {
4138 // use before
4139 //os << "No need to interporate." << LogIO::POST ;
4140 int id = idx[0] ;
4141 uInt tcalid = s->getTcalId( id ) ;
4142 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4143 tcalTable.getEntry( time, tcalval, tcalid ) ;
4144 }
4145 else {
4146 // do interpolation
4147 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4148 double t0 = timeVec[idx[0]] ;
4149 double t1 = timeVec[idx[1]] ;
4150 Vector<Float> tcal0 ;
4151 uInt tcalid0 = s->getTcalId( idx[0] ) ;
4152 uInt tcalid1 = s->getTcalId( idx[1] ) ;
4153 tcalTable.getEntry( time, tcal0, tcalid0 ) ;
4154 tcalTable.getEntry( time, tcalval, tcalid1 ) ;
4155 double tfactor = (reftime - t0) / (t1 - t0) ;
4156 for ( unsigned int i = 0 ; i < tcal0.size() ; i++ ) {
4157 tcalval[i] = ( tcalval[i] - tcal0[i] ) * tfactor + tcal0[i] ;
4158 }
4159 }
4160 }
4161 else {
4162 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4163 }
4164 return tcalval ;
4165 }
4166}
4167
4168Vector<Float> STMath::getTsysFromTime( double reftime,
4169 const Vector<Double> &timeVec,
4170 const vector<int> &idx,
4171 const CountedPtr<Scantable> &s,
4172 string mode )
4173{
4174 LogIO os( LogOrigin( "STMath", "getTsysFromTime", WHERE ) ) ;
4175 ArrayColumn<Float> tsysCol ;
4176 tsysCol.attach( s->table(), "TSYS" ) ;
4177 Vector<Float> tsysval ;
4178 if ( s->nrow() == 0 ) {
4179 os << LogIO::SEVERE << "No row in the input scantable. Return empty tsys." << LogIO::POST ;
4180 return tsysval ;
4181 }
4182 else if ( s->nrow() == 1 ) {
4183 //os << "use row " << 0 << LogIO::POST ;
4184 tsysval = tsysCol( 0 ) ;
4185 return tsysval ;
4186 }
4187 else {
4188 if ( mode == "before" ) {
4189 int id = -1 ;
4190 if ( idx[0] != -1 ) {
4191 id = idx[0] ;
4192 }
4193 else if ( idx[1] != -1 ) {
4194 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4195 id = idx[1] ;
4196 }
4197 //os << "use row " << id << LogIO::POST ;
4198 tsysval = tsysCol( id ) ;
4199 }
4200 else if ( mode == "after" ) {
4201 int id = -1 ;
4202 if ( idx[1] != -1 ) {
4203 id = idx[1] ;
4204 }
4205 else if ( idx[0] != -1 ) {
4206 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4207 id = idx[1] ;
4208 }
4209 //os << "use row " << id << LogIO::POST ;
4210 tsysval = tsysCol( id ) ;
4211 }
4212 else if ( mode == "nearest" ) {
4213 int id = -1 ;
4214 if ( idx[0] == -1 ) {
4215 id = idx[1] ;
4216 }
4217 else if ( idx[1] == -1 ) {
4218 id = idx[0] ;
4219 }
4220 else if ( idx[0] == idx[1] ) {
4221 id = idx[0] ;
4222 }
4223 else {
4224 double t0 = timeVec[idx[0]] ;
4225 double t1 = timeVec[idx[1]] ;
4226 if ( abs( t0 - reftime ) > abs( t1 - reftime ) ) {
4227 id = idx[1] ;
4228 }
4229 else {
4230 id = idx[0] ;
4231 }
4232 }
4233 //os << "use row " << id << LogIO::POST ;
4234 tsysval = tsysCol( id ) ;
4235 }
4236 else if ( mode == "linear" ) {
4237 if ( idx[0] == -1 ) {
4238 // use after
4239 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4240 int id = idx[1] ;
4241 //os << "use row " << id << LogIO::POST ;
4242 tsysval = tsysCol( id ) ;
4243 }
4244 else if ( idx[1] == -1 ) {
4245 // use before
4246 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4247 int id = idx[0] ;
4248 //os << "use row " << id << LogIO::POST ;
4249 tsysval = tsysCol( id ) ;
4250 }
4251 else if ( idx[0] == idx[1] ) {
4252 // use before
4253 //os << "No need to interporate." << LogIO::POST ;
4254 int id = idx[0] ;
4255 //os << "use row " << id << LogIO::POST ;
4256 tsysval = tsysCol( id ) ;
4257 }
4258 else {
4259 // do interpolation
4260 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4261 double t0 = timeVec[idx[0]] ;
4262 double t1 = timeVec[idx[1]] ;
4263 Vector<Float> tsys0 ;
4264 tsys0 = tsysCol( idx[0] ) ;
4265 tsysval = tsysCol( idx[1] ) ;
4266 double tfactor = (reftime - t0) / (t1 - t0) ;
4267 for ( unsigned int i = 0 ; i < tsys0.size() ; i++ ) {
4268 tsysval[i] = ( tsysval[i] - tsys0[i] ) * tfactor + tsys0[i] ;
4269 }
4270 }
4271 }
4272 else {
4273 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4274 }
4275 return tsysval ;
4276 }
4277}
4278
4279void STMath::calibrateCW( CountedPtr<Scantable> &out,
4280 const CountedPtr<Scantable>& on,
4281 const CountedPtr<Scantable>& off,
4282 const CountedPtr<Scantable>& sky,
4283 const CountedPtr<Scantable>& hot,
4284 const CountedPtr<Scantable>& cold,
4285 const Vector<uInt> &rows,
4286 const String &antname )
4287{
4288 // 2012/05/22 TN
4289 // Assume that out has empty SPECTRA column
4290
4291 // if rows is empty, just return
4292 if ( rows.nelements() == 0 )
4293 return ;
4294 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
4295 Vector<Double> timeOff = timeCol.getColumn() ;
4296 timeCol.attach( sky->table(), "TIME" ) ;
4297 Vector<Double> timeSky = timeCol.getColumn() ;
4298 timeCol.attach( hot->table(), "TIME" ) ;
4299 Vector<Double> timeHot = timeCol.getColumn() ;
4300 timeCol.attach( on->table(), "TIME" ) ;
4301 ROArrayColumn<Float> arrayFloatCol( off->table(), "SPECTRA" ) ;
4302 Matrix<Float> offspectra = arrayFloatCol.getColumn() ;
4303 arrayFloatCol.attach( sky->table(), "SPECTRA" ) ;
4304 Matrix<Float> skyspectra = arrayFloatCol.getColumn() ;
4305 arrayFloatCol.attach( hot->table(), "SPECTRA" ) ;
4306 Matrix<Float> hotspectra = arrayFloatCol.getColumn() ;
4307 unsigned int spsize = on->nchan( on->getIF(rows[0]) ) ;
4308 // I know that the data is contiguous
4309 const uInt *p = rows.data() ;
4310 vector<int> ids( 2 ) ;
4311 Block<uInt> flagchan( spsize ) ;
4312 uInt nflag = 0 ;
4313 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4314 double reftime = timeCol.asdouble(*p) ;
4315 ids = getRowIdFromTime( reftime, timeOff ) ;
4316 Vector<Float> spoff = getSpectrumFromTime( reftime, timeOff, ids, offspectra, "linear" ) ;
4317 ids = getRowIdFromTime( reftime, timeSky ) ;
4318 Vector<Float> spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
4319 Vector<Float> tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4320 Vector<Float> tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4321 ids = getRowIdFromTime( reftime, timeHot ) ;
4322 Vector<Float> sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra, "linear" ) ;
4323 Vector<Float> spec = on->specCol_( *p ) ;
4324 if ( antname.find( "APEX" ) != String::npos ) {
4325 // using gain array
4326 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4327 if ( spoff[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
4328 spec[j] = 0.0 ;
4329 flagchan[nflag++] = j ;
4330 }
4331 else {
4332 spec[j] = ( ( spec[j] - spoff[j] ) / spoff[j] )
4333 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4334 }
4335 }
4336 }
4337 else {
4338 // Chopper-Wheel calibration (Ulich & Haas 1976)
4339 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4340 if ( (sphot[j]-spsky[j]) == 0.0 ) {
4341 spec[j] = 0.0 ;
4342 flagchan[nflag++] = j ;
4343 }
4344 else {
4345 spec[j] = ( spec[j] - spoff[j] ) / ( sphot[j] - spsky[j] ) * tcal[j] ;
4346 }
4347 }
4348 }
4349 out->specCol_.put( *p, spec ) ;
4350 out->tsysCol_.put( *p, tsys ) ;
4351 if ( nflag > 0 ) {
4352 Vector<uChar> fl = out->flagsCol_( *p ) ;
4353 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4354 fl[flagchan[j]] = (uChar)True ;
4355 }
4356 out->flagsCol_.put( *p, fl ) ;
4357 }
4358 nflag = 0 ;
4359 p++ ;
4360 }
4361}
4362
4363void STMath::calibrateALMA( CountedPtr<Scantable>& out,
4364 const CountedPtr<Scantable>& on,
4365 const CountedPtr<Scantable>& off,
4366 const Vector<uInt>& rows )
4367{
4368 // 2012/05/22 TN
4369 // Assume that out has empty SPECTRA column
4370
4371 // if rows is empty, just return
4372 if ( rows.nelements() == 0 )
4373 return ;
4374 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
4375 Vector<Double> timeVec = timeCol.getColumn() ;
4376 timeCol.attach( on->table(), "TIME" ) ;
4377 ROArrayColumn<Float> arrayFloatCol( off->table(), "SPECTRA" ) ;
4378 Matrix<Float> offspectra = arrayFloatCol.getColumn() ;
4379 unsigned int spsize = on->nchan( on->getIF(rows[0]) ) ;
4380 // I know that the data is contiguous
4381 const uInt *p = rows.data() ;
4382 vector<int> ids( 2 ) ;
4383 Block<uInt> flagchan( spsize ) ;
4384 uInt nflag = 0 ;
4385 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4386 double reftime = timeCol.asdouble(*p) ;
4387 ids = getRowIdFromTime( reftime, timeVec ) ;
4388 Vector<Float> spoff = getSpectrumFromTime( reftime, timeVec, ids, offspectra, "linear" ) ;
4389 //Vector<Float> spoff = getSpectrumFromTime( reftime, timeVec, off, "linear" ) ;
4390 Vector<Float> spec = on->specCol_( *p ) ;
4391 Vector<Float> tsys = on->tsysCol_( *p ) ;
4392 // ALMA Calibration
4393 //
4394 // Ta* = Tsys * ( ON - OFF ) / OFF
4395 //
4396 // 2010/01/07 Takeshi Nakazato
4397 unsigned int tsyssize = tsys.nelements() ;
4398 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4399 if ( spoff[j] == 0.0 ) {
4400 spec[j] = 0.0 ;
4401 flagchan[nflag++] = j ;
4402 }
4403 else {
4404 spec[j] = ( spec[j] - spoff[j] ) / spoff[j] ;
4405 }
4406 if ( tsyssize == spsize )
4407 spec[j] *= tsys[j] ;
4408 else
4409 spec[j] *= tsys[0] ;
4410 }
4411 out->specCol_.put( *p, spec ) ;
4412 if ( nflag > 0 ) {
4413 Vector<uChar> fl = out->flagsCol_( *p ) ;
4414 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4415 fl[flagchan[j]] = (uChar)True ;
4416 }
4417 out->flagsCol_.put( *p, fl ) ;
4418 }
4419 nflag = 0 ;
4420 p++ ;
4421 }
4422}
4423
4424void STMath::calibrateAPEXFS( CountedPtr<Scantable> &sig,
4425 CountedPtr<Scantable> &ref,
4426 const vector< CountedPtr<Scantable> >& on,
4427 const vector< CountedPtr<Scantable> >& sky,
4428 const vector< CountedPtr<Scantable> >& hot,
4429 const vector< CountedPtr<Scantable> >& cold,
4430 const Vector<uInt> &rows )
4431{
4432 // if rows is empty, just return
4433 if ( rows.nelements() == 0 )
4434 return ;
4435 ROScalarColumn<Double> timeCol( sky[0]->table(), "TIME" ) ;
4436 Vector<Double> timeSkyS = timeCol.getColumn() ;
4437 timeCol.attach( sky[1]->table(), "TIME" ) ;
4438 Vector<Double> timeSkyR = timeCol.getColumn() ;
4439 timeCol.attach( hot[0]->table(), "TIME" ) ;
4440 Vector<Double> timeHotS = timeCol.getColumn() ;
4441 timeCol.attach( hot[1]->table(), "TIME" ) ;
4442 Vector<Double> timeHotR = timeCol.getColumn() ;
4443 timeCol.attach( sig->table(), "TIME" ) ;
4444 ROScalarColumn<Double> timeCol2( ref->table(), "TIME" ) ;
4445 ROArrayColumn<Float> arrayFloatCol( sky[0]->table(), "SPECTRA" ) ;
4446 Matrix<Float> skyspectraS = arrayFloatCol.getColumn() ;
4447 arrayFloatCol.attach( sky[1]->table(), "SPECTRA" ) ;
4448 Matrix<Float> skyspectraR = arrayFloatCol.getColumn() ;
4449 arrayFloatCol.attach( hot[0]->table(), "SPECTRA" ) ;
4450 Matrix<Float> hotspectraS = arrayFloatCol.getColumn() ;
4451 arrayFloatCol.attach( hot[1]->table(), "SPECTRA" ) ;
4452 Matrix<Float> hotspectraR = arrayFloatCol.getColumn() ;
4453 unsigned int spsize = sig->nchan( sig->getIF(rows[0]) ) ;
4454 Vector<Float> spec( spsize ) ;
4455 // I know that the data is contiguous
4456 const uInt *p = rows.data() ;
4457 vector<int> ids( 2 ) ;
4458 Block<uInt> flagchan( spsize ) ;
4459 uInt nflag = 0 ;
4460 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4461 double reftime = timeCol.asdouble(*p) ;
4462 ids = getRowIdFromTime( reftime, timeSkyS ) ;
4463 Vector<Float> spskyS = getSpectrumFromTime( reftime, timeSkyS, ids, skyspectraS, "linear" ) ;
4464 Vector<Float> tcalS = getTcalFromTime( reftime, timeSkyS, ids, sky[0], "linear" ) ;
4465 Vector<Float> tsysS = getTsysFromTime( reftime, timeSkyS, ids, sky[0], "linear" ) ;
4466 ids = getRowIdFromTime( reftime, timeHotS ) ;
4467 Vector<Float> sphotS = getSpectrumFromTime( reftime, timeHotS, ids, hotspectraS ) ;
4468 reftime = timeCol2.asdouble(*p) ;
4469 ids = getRowIdFromTime( reftime, timeSkyR ) ;
4470 Vector<Float> spskyR = getSpectrumFromTime( reftime, timeSkyR, ids, skyspectraR, "linear" ) ;
4471 Vector<Float> tcalR = getTcalFromTime( reftime, timeSkyR, ids, sky[1], "linear" ) ;
4472 Vector<Float> tsysR = getTsysFromTime( reftime, timeSkyR, ids, sky[1], "linear" ) ;
4473 ids = getRowIdFromTime( reftime, timeHotR ) ;
4474 Vector<Float> sphotR = getSpectrumFromTime( reftime, timeHotR, ids, hotspectraR ) ;
4475 Vector<Float> spsig = on[0]->specCol_( *p ) ;
4476 Vector<Float> spref = on[1]->specCol_( *p ) ;
4477 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4478 if ( (sphotS[j]-spskyS[j]) == 0.0 || (sphotR[j]-spskyR[j]) == 0.0 ) {
4479 spec[j] = 0.0 ;
4480 flagchan[nflag++] = j ;
4481 }
4482 else {
4483 spec[j] = tcalS[j] * spsig[j] / ( sphotS[j] - spskyS[j] )
4484 - tcalR[j] * spref[j] / ( sphotR[j] - spskyR[j] ) ;
4485 }
4486 }
4487 sig->specCol_.put( *p, spec ) ;
4488 sig->tsysCol_.put( *p, tsysS ) ;
4489 spec *= (Float)-1.0 ;
4490 ref->specCol_.put( *p, spec ) ;
4491 ref->tsysCol_.put( *p, tsysR ) ;
4492 if ( nflag > 0 ) {
4493 Vector<uChar> flsig = sig->flagsCol_( *p ) ;
4494 Vector<uChar> flref = ref->flagsCol_( *p ) ;
4495 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4496 flsig[flagchan[j]] = (uChar)True ;
4497 flref[flagchan[j]] = (uChar)True ;
4498 }
4499 sig->flagsCol_.put( *p, flsig ) ;
4500 ref->flagsCol_.put( *p, flref ) ;
4501 }
4502 nflag = 0 ;
4503 p++ ;
4504 }
4505}
4506
4507void STMath::calibrateFS( CountedPtr<Scantable> &sig,
4508 CountedPtr<Scantable> &ref,
4509 const CountedPtr<Scantable>& rsig,
4510 const CountedPtr<Scantable>& rref,
4511 const CountedPtr<Scantable>& sky,
4512 const CountedPtr<Scantable>& hot,
4513 const CountedPtr<Scantable>& cold,
4514 const Vector<uInt> &rows )
4515{
4516 // if rows is empty, just return
4517 if ( rows.nelements() == 0 )
4518 return ;
4519 ROScalarColumn<Double> timeCol( sky->table(), "TIME" ) ;
4520 Vector<Double> timeSky = timeCol.getColumn() ;
4521 timeCol.attach( hot->table(), "TIME" ) ;
4522 Vector<Double> timeHot = timeCol.getColumn() ;
4523 timeCol.attach( sig->table(), "TIME" ) ;
4524 ROScalarColumn<Double> timeCol2( ref->table(), "TIME" ) ;
4525 ROArrayColumn<Float> arrayFloatCol( sky->table(), "SPECTRA" ) ;
4526 Matrix<Float> skyspectra = arrayFloatCol.getColumn() ;
4527 arrayFloatCol.attach( hot->table(), "SPECTRA" ) ;
4528 Matrix<Float> hotspectra = arrayFloatCol.getColumn() ;
4529 unsigned int spsize = sig->nchan( sig->getIF(rows[0]) ) ;
4530 Vector<Float> spec( spsize ) ;
4531 // I know that the data is contiguous
4532 const uInt *p = rows.data() ;
4533 vector<int> ids( 2 ) ;
4534 Block<uInt> flagchan( spsize ) ;
4535 uInt nflag = 0 ;
4536 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4537 double reftime = timeCol.asdouble(*p) ;
4538 ids = getRowIdFromTime( reftime, timeSky ) ;
4539 Vector<Float> spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
4540 Vector<Float> tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4541 Vector<Float> tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4542 ids = getRowIdFromTime( reftime, timeHot ) ;
4543 Vector<Float> sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra ) ;
4544 Vector<Float> spsig = rsig->specCol_( *p ) ;
4545 Vector<Float> spref = rref->specCol_( *p ) ;
4546 // using gain array
4547 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4548 if ( spref[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
4549 spec[j] = 0.0 ;
4550 flagchan[nflag++] = j ;
4551 }
4552 else {
4553 spec[j] = ( ( spsig[j] - spref[j] ) / spref[j] )
4554 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4555 }
4556 }
4557 sig->specCol_.put( *p, spec ) ;
4558 sig->tsysCol_.put( *p, tsys ) ;
4559 if ( nflag > 0 ) {
4560 Vector<uChar> fl = sig->flagsCol_( *p ) ;
4561 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4562 fl[flagchan[j]] = (uChar)True ;
4563 }
4564 sig->flagsCol_.put( *p, fl ) ;
4565 }
4566 nflag = 0 ;
4567
4568 reftime = timeCol2.asdouble(*p) ;
4569 spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
4570 tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4571 tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4572 ids = getRowIdFromTime( reftime, timeHot ) ;
4573 sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra ) ;
4574 // using gain array
4575 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4576 if ( spsig[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
4577 spec[j] = 0.0 ;
4578 flagchan[nflag++] = j ;
4579 }
4580 else {
4581 spec[j] = ( ( spref[j] - spsig[j] ) / spsig[j] )
4582 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4583 }
4584 }
4585 ref->specCol_.put( *p, spec ) ;
4586 ref->tsysCol_.put( *p, tsys ) ;
4587 if ( nflag > 0 ) {
4588 Vector<uChar> fl = ref->flagsCol_( *p ) ;
4589 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4590 fl[flagchan[j]] = (uChar)True ;
4591 }
4592 ref->flagsCol_.put( *p, fl ) ;
4593 }
4594 nflag = 0 ;
4595 p++ ;
4596 }
4597}
4598
4599void STMath::copyRows( Table &out,
4600 const Table &in,
4601 uInt startout,
4602 uInt startin,
4603 uInt nrow,
4604 Bool copySpectra,
4605 Bool copyFlagtra,
4606 Bool copyTsys )
4607{
4608 uInt nexclude = 0 ;
4609 Block<String> excludeColsBlock( 3 ) ;
4610 if ( !copySpectra ) {
4611 excludeColsBlock[nexclude] = "SPECTRA" ;
4612 nexclude++ ;
4613 }
4614 if ( !copyFlagtra ) {
4615 excludeColsBlock[nexclude] = "FLAGTRA" ;
4616 nexclude++ ;
4617 }
4618 if ( !copyTsys ) {
4619 excludeColsBlock[nexclude] = "TSYS" ;
4620 nexclude++ ;
4621 }
4622 // if ( nexclude < 3 ) {
4623 // excludeCols.resize( nexclude, True ) ;
4624 // }
4625 Vector<String> excludeCols( IPosition(1,nexclude),
4626 excludeColsBlock.storage(),
4627 SHARE ) ;
4628// cout << "excludeCols=" << excludeCols << endl ;
4629 TableRow rowout( out, excludeCols, True ) ;
4630 ROTableRow rowin( in, excludeCols, True ) ;
4631 uInt rin = startin ;
4632 uInt rout = startout ;
4633 for ( uInt i = 0 ; i < nrow ; i++ ) {
4634 rowin.get( rin ) ;
4635 rowout.putMatchingFields( rout, rowin.record() ) ;
4636 rin++ ;
4637 rout++ ;
4638 }
4639}
4640
4641CountedPtr<Scantable> STMath::averageWithinSession( CountedPtr<Scantable> &s,
4642 vector<bool> &mask,
4643 string weight )
4644{
4645 // prepare output table
4646 bool insitu = insitu_ ;
4647 insitu_ = false ;
4648 CountedPtr<Scantable> a = getScantable( s, true ) ;
4649 insitu_ = insitu ;
4650 Table &atab = a->table() ;
4651 ScalarColumn<Double> timeColOut( atab, "TIME" ) ;
4652
4653 if ( s->nrow() == 0 )
4654 return a ;
4655
4656 // setup RowAccumulator
4657 WeightType wtype = stringToWeight( weight ) ;
4658 RowAccumulator acc( wtype ) ;
4659 Vector<Bool> cmask( mask ) ;
4660 acc.setUserMask( cmask ) ;
4661
4662 vector<string> cols( 3 ) ;
4663 cols[0] = "IFNO" ;
4664 cols[1] = "POLNO" ;
4665 cols[2] = "BEAMNO" ;
4666 STIdxIterAcc iter( s, cols ) ;
4667
4668 Table ttab = s->table() ;
4669 ROScalarColumn<Double> *timeCol = new ROScalarColumn<Double>( ttab, "TIME" ) ;
4670 Vector<Double> timeVec = timeCol->getColumn() ;
4671 delete timeCol ;
4672 Vector<Double> interval = s->integrCol_.getColumn() ;
4673 uInt nrow = timeVec.nelements() ;
4674 uInt outrow = 0 ;
4675
4676 while( !iter.pastEnd() ) {
4677
4678 Vector<uInt> rows = iter.getRows( SHARE ) ;
4679 uInt len = rows.nelements() ;
4680
4681 if ( len == 0 ) {
4682 iter.next() ;
4683 continue ;
4684 }
4685
4686 uInt nchan = s->nchan(s->getIF(rows[0])) ;
4687 Vector<uChar> flag( nchan ) ;
4688 Vector<Bool> bflag( nchan ) ;
4689 Vector<Float> spec( nchan ) ;
4690 Vector<Float> tsys( nchan ) ;
4691
4692 Vector<Double> timeSep( len-1 ) ;
4693 for ( uInt i = 0 ; i < len-1 ; i++ ) {
4694 timeSep[i] = timeVec[rows[i+1]] - timeVec[rows[i]] ;
4695 }
4696
4697 uInt irow ;
4698 uInt jrow ;
4699 for ( uInt i = 0 ; i < len-1 ; i++ ) {
4700 irow = rows[i] ;
4701 jrow = rows[i+1] ;
4702 // accumulate data
4703 s->flagsCol_.get( irow, flag ) ;
4704 convertArray( bflag, flag ) ;
4705 s->specCol_.get( irow, spec ) ;
4706 tsys.assign( s->tsysCol_( irow ) ) ;
4707 if ( !allEQ(bflag,True) )
4708 acc.add( spec, !bflag, tsys, interval[irow], timeVec[irow] ) ;
4709 double gap = 2.0 * 86400.0 * timeSep[i] / ( interval[jrow] + interval[irow] ) ;
4710 //cout << "gap[" << i << "]=" << setw(5) << gap << endl ;
4711 if ( gap > 1.1 ) {
4712 //cout << "detected gap between " << i << " and " << i+1 << endl ;
4713 // put data to output table
4714 // reset RowAccumulator
4715 if ( acc.state() ) {
4716 atab.addRow() ;
4717 copyRows( atab, ttab, outrow, irow, 1, False, False, False ) ;
4718 acc.replaceNaN() ;
4719 const Vector<Bool> &msk = acc.getMask() ;
4720 convertArray( flag, !msk ) ;
4721 for (uInt k = 0; k < nchan; ++k) {
4722 uChar userFlag = 1 << 7;
4723 if (msk[k]==True) userFlag = 0 << 7;
4724 flag(k) = userFlag;
4725 }
4726 a->flagsCol_.put( outrow, flag ) ;
4727 a->specCol_.put( outrow, acc.getSpectrum() ) ;
4728 a->tsysCol_.put( outrow, acc.getTsys() ) ;
4729 a->integrCol_.put( outrow, acc.getInterval() ) ;
4730 timeColOut.put( outrow, acc.getTime() ) ;
4731 a->cycleCol_.put( outrow, 0 ) ;
4732 }
4733 acc.reset() ;
4734 outrow++ ;
4735 }
4736 }
4737
4738 // accumulate and add last data
4739 irow = rows[len-1] ;
4740 s->flagsCol_.get( irow, flag ) ;
4741 convertArray( bflag, flag ) ;
4742 s->specCol_.get( irow, spec ) ;
4743 tsys.assign( s->tsysCol_( irow ) ) ;
4744 if (!allEQ(bflag,True) )
4745 acc.add( spec, !bflag, tsys, interval[irow], timeVec[irow] ) ;
4746 if ( acc.state() ) {
4747 atab.addRow() ;
4748 copyRows( atab, ttab, outrow, irow, 1, False, False, False ) ;
4749 acc.replaceNaN() ;
4750 const Vector<Bool> &msk = acc.getMask() ;
4751 convertArray( flag, !msk ) ;
4752 for (uInt k = 0; k < nchan; ++k) {
4753 uChar userFlag = 1 << 7;
4754 if (msk[k]==True) userFlag = 0 << 7;
4755 flag(k) = userFlag;
4756 }
4757 a->flagsCol_.put( outrow, flag ) ;
4758 a->specCol_.put( outrow, acc.getSpectrum() ) ;
4759 a->tsysCol_.put( outrow, acc.getTsys() ) ;
4760 a->integrCol_.put( outrow, acc.getInterval() ) ;
4761 timeColOut.put( outrow, acc.getTime() ) ;
4762 a->cycleCol_.put( outrow, 0 ) ;
4763 }
4764 acc.reset() ;
4765 outrow++ ;
4766
4767 iter.next() ;
4768 }
4769
4770 return a ;
4771}
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