source: tags/hpctags/hpc33/src/STMath.cpp@ 3008

Last change on this file since 3008 was 2572, checked in by Takeshi Nakazato, 12 years ago

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JIRA Issue: no

Ready for Test: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

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Module(s): Module Names change impacts.

Description: Describe your changes here...

Bug fix on averageWithinSession
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File size: 181.0 KB
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1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <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
62// 2012/02/17 TN
63// Since STGrid is implemented, average doesn't consider direction
64// when accumulating
65// tolerance for direction comparison (rad)
66// #define TOL_OTF 1.0e-15
67// #define TOL_POINT 2.9088821e-4 // 1 arcmin
68
69STMath::STMath(bool insitu) :
70 insitu_(insitu)
71{
72}
73
74
75STMath::~STMath()
76{
77}
78
79CountedPtr<Scantable>
80STMath::average( const std::vector<CountedPtr<Scantable> >& in,
81 const std::vector<bool>& mask,
82 const std::string& weight,
83 const std::string& avmode)
84{
85// double t0, t1 ;
86// t0 = mathutil::gettimeofday_sec() ;
87
88 LogIO os( LogOrigin( "STMath", "average()", WHERE ) ) ;
89 if ( avmode == "SCAN" && in.size() != 1 )
90 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
91 "Use merge first."));
92 WeightType wtype = stringToWeight(weight);
93
94 // 2012/02/17 TN
95 // Since STGrid is implemented, average doesn't consider direction
96 // when accumulating
97 // check if OTF observation
98// String obstype = in[0]->getHeader().obstype ;
99// Double tol = 0.0 ;
100// if ( (obstype.find( "OTF" ) != String::npos) || (obstype.find( "OBSERVE_TARGET" ) != String::npos) ) {
101// tol = TOL_OTF ;
102// }
103// else {
104// tol = TOL_POINT ;
105// }
106
107 // output
108 // clone as this is non insitu
109 bool insitu = insitu_;
110 setInsitu(false);
111 CountedPtr< Scantable > out = getScantable(in[0], true);
112 setInsitu(insitu);
113 std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
114 ++stit;
115 while ( stit != in.end() ) {
116 out->appendToHistoryTable((*stit)->history());
117 ++stit;
118 }
119
120 Table& tout = out->table();
121
122 /// @todo check if all scantables are conformant
123
124 ArrayColumn<Float> specColOut(tout,"SPECTRA");
125 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
126 ArrayColumn<Float> tsysColOut(tout,"TSYS");
127 ScalarColumn<Double> mjdColOut(tout,"TIME");
128 ScalarColumn<Double> intColOut(tout,"INTERVAL");
129 ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
130 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
131
132 // set up the output table rows. These are based on the structure of the
133 // FIRST scantable in the vector
134 const Table& baset = in[0]->table();
135
136 RowAccumulator acc(wtype);
137 Vector<Bool> cmask(mask);
138 acc.setUserMask(cmask);
139// ROTableRow row(tout);
140 ROArrayColumn<Float> specCol, tsysCol;
141 ROArrayColumn<uChar> flagCol;
142 ROScalarColumn<Double> mjdCol, intCol;
143 ROScalarColumn<Int> scanIDCol;
144
145 //Vector<uInt> rowstodelete;
146 Block<uInt> rowstodelB( in[0]->nrow() ) ;
147 uInt nrowdel = 0 ;
148
149// Block<String> cols(3);
150 vector<string> cols(3) ;
151 cols[0] = String("BEAMNO");
152 cols[1] = String("IFNO");
153 cols[2] = String("POLNO");
154 if ( avmode == "SOURCE" ) {
155 cols.resize(4);
156 cols[3] = String("SRCNAME");
157 }
158 if ( avmode == "SCAN" && in.size() == 1) {
159 //cols.resize(4);
160 //cols[3] = String("SCANNO");
161 cols.resize(5);
162 cols[3] = String("SRCNAME");
163 cols[4] = String("SCANNO");
164 }
165 uInt outrowCount = 0;
166 // use STIdxIterExAcc instead of TableIterator
167 STIdxIterExAcc iter( in[0], cols ) ;
168// double t2 = 0 ;
169// double t3 = 0 ;
170// double t4 = 0 ;
171// double t5 = 0 ;
172// TableIterator iter(baset, cols);
173// int count = 0 ;
174 while (!iter.pastEnd()) {
175 Vector<uInt> rows = iter.getRows( SHARE ) ;
176 if ( rows.nelements() == 0 ) {
177 iter.next() ;
178 continue ;
179 }
180 Vector<uInt> current = iter.current() ;
181 String srcname = iter.getSrcName() ;
182 //Table subt = iter.table();
183 // copy the first row of this selection into the new table
184 tout.addRow();
185// t4 = mathutil::gettimeofday_sec() ;
186 // skip to copy SPECTRA, FLAGTRA, and TSYS since those heavy columns are
187 // overwritten in the following process
188 copyRows( tout, baset, outrowCount, rows[0], 1, False, False, False ) ;
189// t5 += mathutil::gettimeofday_sec() - t4 ;
190 // re-index to 0
191 if ( avmode != "SCAN" && avmode != "SOURCE" ) {
192 scanColOut.put(outrowCount, uInt(0));
193 }
194
195 // 2012/02/17 TN
196 // Since STGrid is implemented, average doesn't consider direction
197 // when accumulating
198// MDirection::ScalarColumn dircol ;
199// dircol.attach( subt, "DIRECTION" ) ;
200// Int length = subt.nrow() ;
201// vector< Vector<Double> > dirs ;
202// vector<int> indexes ;
203// for ( Int i = 0 ; i < length ; i++ ) {
204// Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
205// //os << << count++ << ": " ;
206// //os << "[" << t[0] << "," << t[1] << "]" << LogIO::POST ;
207// bool adddir = true ;
208// for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
209// //if ( allTrue( t == dirs[j] ) ) {
210// Double dx = t[0] - dirs[j][0] ;
211// Double dy = t[1] - dirs[j][1] ;
212// Double dd = sqrt( dx * dx + dy * dy ) ;
213// //if ( allNearAbs( t, dirs[j], tol ) ) {
214// if ( dd <= tol ) {
215// adddir = false ;
216// break ;
217// }
218// }
219// if ( adddir ) {
220// dirs.push_back( t ) ;
221// indexes.push_back( i ) ;
222// }
223// }
224// uInt rowNum = dirs.size() ;
225// tout.addRow( rowNum ) ;
226// for ( uInt i = 0 ; i < rowNum ; i++ ) {
227// TableCopy::copyRows( tout, subt, outrowCount+i, indexes[i], 1 ) ;
228// // re-index to 0
229// if ( avmode != "SCAN" && avmode != "SOURCE" ) {
230// scanColOut.put(outrowCount+i, uInt(0));
231// }
232// }
233// outrowCount += rowNum ;
234
235 // merge loop
236 uInt i = outrowCount ;
237 // in[0] is already selected by iterator
238 specCol.attach(baset,"SPECTRA");
239 flagCol.attach(baset,"FLAGTRA");
240 tsysCol.attach(baset,"TSYS");
241 intCol.attach(baset,"INTERVAL");
242 mjdCol.attach(baset,"TIME");
243 Vector<Float> spec,tsys;
244 Vector<uChar> flag;
245 Double inter,time;
246
247 for (uInt l = 0; l < rows.nelements(); ++l ) {
248 uInt k = rows[l] ;
249 flagCol.get(k, flag);
250 Vector<Bool> bflag(flag.shape());
251 convertArray(bflag, flag);
252 /*
253 if ( allEQ(bflag, True) ) {
254 continue;//don't accumulate
255 }
256 */
257 specCol.get(k, spec);
258 tsysCol.get(k, tsys);
259 intCol.get(k, inter);
260 mjdCol.get(k, time);
261 // spectrum has to be added last to enable weighting by the other values
262// t2 = mathutil::gettimeofday_sec() ;
263 acc.add(spec, !bflag, tsys, inter, time);
264// t3 += mathutil::gettimeofday_sec() - t2 ;
265
266 }
267
268
269 // in[0] is already selected by TableIterator so that index is
270 // started from 1
271 for ( int j=1; j < int(in.size()); ++j ) {
272 const Table& tin = in[j]->table();
273 //const TableRecord& rec = row.get(i);
274 ROScalarColumn<Double> tmp(tin, "TIME");
275 Double td;tmp.get(0,td);
276
277#if 1
278 static char const*const colNames1[] = { "IFNO", "BEAMNO", "POLNO" };
279 //uInt const values1[] = { rec.asuInt("IFNO"), rec.asuInt("BEAMNO"), rec.asuInt("POLNO") };
280 uInt const values1[] = { current[1], current[0], current[2] };
281 SingleTypeEqPredicate<uInt, 3> myPred(tin, colNames1, values1);
282 CustomTableExprNodeRep myNodeRep(tin, myPred);
283 myNodeRep.link(); // to avoid automatic delete when myExpr is destructed.
284 CustomTableExprNode myExpr(myNodeRep);
285 Table basesubt = tin(myExpr);
286#else
287// Table basesubt = tin( tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
288// && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
289// && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
290 Table basesubt = tin( tin.col("BEAMNO") == current[0]
291 && tin.col("IFNO") == current[1]
292 && tin.col("POLNO") == current[2] );
293#endif
294 Table subt;
295 if ( avmode == "SOURCE") {
296// subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME"));
297 subt = basesubt( basesubt.col("SRCNAME") == srcname );
298
299 } else if (avmode == "SCAN") {
300// subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME")
301// && basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
302 subt = basesubt( basesubt.col("SRCNAME") == srcname
303 && basesubt.col("SCANNO") == current[4] );
304 } else {
305 subt = basesubt;
306 }
307
308 // 2012/02/17 TN
309 // Since STGrid is implemented, average doesn't consider direction
310 // when accumulating
311// vector<uInt> removeRows ;
312// uInt nrsubt = subt.nrow() ;
313// for ( uInt irow = 0 ; irow < nrsubt ; irow++ ) {
314// //if ( !allTrue((subt.col("DIRECTION").getArrayDouble(TableExprId(irow)))==rec.asArrayDouble("DIRECTION")) ) {
315// Vector<Double> x0 = (subt.col("DIRECTION").getArrayDouble(TableExprId(irow))) ;
316// Vector<Double> x1 = rec.asArrayDouble("DIRECTION") ;
317// double dx = x0[0] - x1[0];
318// double dy = x0[1] - x1[1];
319// Double dd = sqrt( dx * dx + dy * dy ) ;
320// //if ( !allNearAbs((subt.col("DIRECTION").getArrayDouble(TableExprId(irow))), rec.asArrayDouble("DIRECTION"), tol ) ) {
321// if ( dd > tol ) {
322// removeRows.push_back( irow ) ;
323// }
324// }
325// if ( removeRows.size() != 0 ) {
326// subt.removeRow( removeRows ) ;
327// }
328
329// if ( nrsubt == removeRows.size() )
330// throw(AipsError("Averaging data is empty.")) ;
331
332 specCol.attach(subt,"SPECTRA");
333 flagCol.attach(subt,"FLAGTRA");
334 tsysCol.attach(subt,"TSYS");
335 intCol.attach(subt,"INTERVAL");
336 mjdCol.attach(subt,"TIME");
337 for (uInt k = 0; k < subt.nrow(); ++k ) {
338 flagCol.get(k, flag);
339 Vector<Bool> bflag(flag.shape());
340 convertArray(bflag, flag);
341 /*
342 if ( allEQ(bflag, True) ) {
343 continue;//don't accumulate
344 }
345 */
346 specCol.get(k, spec);
347 tsysCol.get(k, tsys);
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 for (uInt i=0; i < tout.nrow(); ++i ) {
2023 MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
2024 MaskedArray<Float> maout;
2025 LatticeUtilities::bin(maout, main, 0, Int(width));
2026 /// @todo implement channel based tsys binning
2027 specCol.put(i, maout.getArray());
2028 flagCol.put(i, flagsFromMA(maout));
2029 // take only the first binned spectrum's length for the deprecated
2030 // global header item nChan
2031 if (i==0) tout.rwKeywordSet().define(String("nChan"),
2032 Int(maout.getArray().nelements()));
2033 }
2034 return out;
2035}
2036
2037CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
2038 const std::string& method,
2039 float width )
2040//
2041// Should add the possibility of width being specified in km/s. This means
2042// that for each freqID (SpectralCoordinate) we will need to convert to an
2043// average channel width (say at the reference pixel). Then we would need
2044// to be careful to make sure each spectrum (of different freqID)
2045// is the same length.
2046//
2047{
2048 //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
2049 Int interpMethod(stringToIMethod(method));
2050
2051 CountedPtr< Scantable > out = getScantable(in, false);
2052 Table& tout = out->table();
2053
2054// Resample SpectralCoordinates (one per freqID)
2055 out->frequencies().rescale(width, "RESAMPLE");
2056 TableIterator iter(tout, "IFNO");
2057 TableRow row(tout);
2058 while ( !iter.pastEnd() ) {
2059 Table tab = iter.table();
2060 ArrayColumn<Float> specCol(tab, "SPECTRA");
2061 //ArrayColumn<Float> tsysCol(tout, "TSYS");
2062 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2063 Vector<Float> spec;
2064 Vector<uChar> flag;
2065 specCol.get(0,spec); // the number of channels should be constant per IF
2066 uInt nChanIn = spec.nelements();
2067 Vector<Float> xIn(nChanIn); indgen(xIn);
2068 Int fac = Int(nChanIn/width);
2069 Vector<Float> xOut(fac+10); // 10 to be safe - resize later
2070 uInt k = 0;
2071 Float x = 0.0;
2072 while (x < Float(nChanIn) ) {
2073 xOut(k) = x;
2074 k++;
2075 x += width;
2076 }
2077 uInt nChanOut = k;
2078 xOut.resize(nChanOut, True);
2079 // process all rows for this IFNO
2080 Vector<Float> specOut;
2081 Vector<Bool> maskOut;
2082 Vector<uChar> flagOut;
2083 for (uInt i=0; i < tab.nrow(); ++i) {
2084 specCol.get(i, spec);
2085 flagCol.get(i, flag);
2086 Vector<Bool> mask(flag.nelements());
2087 convertArray(mask, flag);
2088
2089 IPosition shapeIn(spec.shape());
2090 //sh.nchan = nChanOut;
2091 InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
2092 xIn, spec, mask,
2093 interpMethod, True, True);
2094 /// @todo do the same for channel based Tsys
2095 flagOut.resize(maskOut.nelements());
2096 convertArray(flagOut, maskOut);
2097 specCol.put(i, specOut);
2098 flagCol.put(i, flagOut);
2099 }
2100 ++iter;
2101 }
2102
2103 return out;
2104}
2105
2106STMath::imethod STMath::stringToIMethod(const std::string& in)
2107{
2108 static STMath::imap lookup;
2109
2110 // initialize the lookup table if necessary
2111 if ( lookup.empty() ) {
2112 lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
2113 lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
2114 lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
2115 lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
2116 }
2117
2118 STMath::imap::const_iterator iter = lookup.find(in);
2119
2120 if ( lookup.end() == iter ) {
2121 std::string message = in;
2122 message += " is not a valid interpolation mode";
2123 throw(AipsError(message));
2124 }
2125 return iter->second;
2126}
2127
2128WeightType STMath::stringToWeight(const std::string& in)
2129{
2130 static std::map<std::string, WeightType> lookup;
2131
2132 // initialize the lookup table if necessary
2133 if ( lookup.empty() ) {
2134 lookup["NONE"] = asap::W_NONE;
2135 lookup["TINT"] = asap::W_TINT;
2136 lookup["TINTSYS"] = asap::W_TINTSYS;
2137 lookup["TSYS"] = asap::W_TSYS;
2138 lookup["VAR"] = asap::W_VAR;
2139 }
2140
2141 std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
2142
2143 if ( lookup.end() == iter ) {
2144 std::string message = in;
2145 message += " is not a valid weighting mode";
2146 throw(AipsError(message));
2147 }
2148 return iter->second;
2149}
2150
2151CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
2152 const vector< float > & coeff,
2153 const std::string & filename,
2154 const std::string& method)
2155{
2156 // Get elevation data from Scantable and convert to degrees
2157 CountedPtr< Scantable > out = getScantable(in, false);
2158 Table& tab = out->table();
2159 ROScalarColumn<Float> elev(tab, "ELEVATION");
2160 Vector<Float> x = elev.getColumn();
2161 x *= Float(180 / C::pi); // Degrees
2162
2163 Vector<Float> coeffs(coeff);
2164 const uInt nc = coeffs.nelements();
2165 if ( filename.length() > 0 && nc > 0 ) {
2166 throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
2167 }
2168
2169 // Correct
2170 if ( nc > 0 || filename.length() == 0 ) {
2171 // Find instrument
2172 Bool throwit = True;
2173 Instrument inst =
2174 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2175 throwit);
2176
2177 // Set polynomial
2178 Polynomial<Float>* ppoly = 0;
2179 Vector<Float> coeff;
2180 String msg;
2181 if ( nc > 0 ) {
2182 ppoly = new Polynomial<Float>(nc-1);
2183 coeff = coeffs;
2184 msg = String("user");
2185 } else {
2186 STAttr sdAttr;
2187 coeff = sdAttr.gainElevationPoly(inst);
2188 ppoly = new Polynomial<Float>(coeff.nelements()-1);
2189 msg = String("built in");
2190 }
2191
2192 if ( coeff.nelements() > 0 ) {
2193 ppoly->setCoefficients(coeff);
2194 } else {
2195 delete ppoly;
2196 throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
2197 }
2198 ostringstream oss;
2199 oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
2200 oss << " " << coeff;
2201 pushLog(String(oss));
2202 const uInt nrow = tab.nrow();
2203 Vector<Float> factor(nrow);
2204 for ( uInt i=0; i < nrow; ++i ) {
2205 factor[i] = 1.0 / (*ppoly)(x[i]);
2206 }
2207 delete ppoly;
2208 scaleByVector(tab, factor, true);
2209
2210 } else {
2211 // Read and correct
2212 pushLog("Making correction from ascii Table");
2213 scaleFromAsciiTable(tab, filename, method, x, true);
2214 }
2215 return out;
2216}
2217
2218void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
2219 const std::string& method,
2220 const Vector<Float>& xout, bool dotsys)
2221{
2222
2223// Read gain-elevation ascii file data into a Table.
2224
2225 String formatString;
2226 Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
2227 scaleFromTable(in, tbl, method, xout, dotsys);
2228}
2229
2230void STMath::scaleFromTable(Table& in,
2231 const Table& table,
2232 const std::string& method,
2233 const Vector<Float>& xout, bool dotsys)
2234{
2235
2236 ROScalarColumn<Float> geElCol(table, "ELEVATION");
2237 ROScalarColumn<Float> geFacCol(table, "FACTOR");
2238 Vector<Float> xin = geElCol.getColumn();
2239 Vector<Float> yin = geFacCol.getColumn();
2240 Vector<Bool> maskin(xin.nelements(),True);
2241
2242 // Interpolate (and extrapolate) with desired method
2243
2244 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2245
2246 Vector<Float> yout;
2247 Vector<Bool> maskout;
2248 InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
2249 xin, yin, maskin, interp,
2250 True, True);
2251
2252 scaleByVector(in, Float(1.0)/yout, dotsys);
2253}
2254
2255void STMath::scaleByVector( Table& in,
2256 const Vector< Float >& factor,
2257 bool dotsys )
2258{
2259 uInt nrow = in.nrow();
2260 if ( factor.nelements() != nrow ) {
2261 throw(AipsError("factors.nelements() != table.nelements()"));
2262 }
2263 ArrayColumn<Float> specCol(in, "SPECTRA");
2264 ArrayColumn<uChar> flagCol(in, "FLAGTRA");
2265 ArrayColumn<Float> tsysCol(in, "TSYS");
2266 for (uInt i=0; i < nrow; ++i) {
2267 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2268 ma *= factor[i];
2269 specCol.put(i, ma.getArray());
2270 flagCol.put(i, flagsFromMA(ma));
2271 if ( dotsys ) {
2272 Vector<Float> tsys = tsysCol(i);
2273 tsys *= factor[i];
2274 tsysCol.put(i,tsys);
2275 }
2276 }
2277}
2278
2279CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
2280 float d, float etaap,
2281 float jyperk )
2282{
2283 CountedPtr< Scantable > out = getScantable(in, false);
2284 Table& tab = in->table();
2285 Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
2286 Unit K(String("K"));
2287 Unit JY(String("Jy"));
2288
2289 bool tokelvin = true;
2290 Double cfac = 1.0;
2291
2292 if ( fluxUnit == JY ) {
2293 pushLog("Converting to K");
2294 Quantum<Double> t(1.0,fluxUnit);
2295 Quantum<Double> t2 = t.get(JY);
2296 cfac = (t2 / t).getValue(); // value to Jy
2297
2298 tokelvin = true;
2299 out->setFluxUnit("K");
2300 } else if ( fluxUnit == K ) {
2301 pushLog("Converting to Jy");
2302 Quantum<Double> t(1.0,fluxUnit);
2303 Quantum<Double> t2 = t.get(K);
2304 cfac = (t2 / t).getValue(); // value to K
2305
2306 tokelvin = false;
2307 out->setFluxUnit("Jy");
2308 } else {
2309 throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
2310 }
2311 // Make sure input values are converted to either Jy or K first...
2312 Float factor = cfac;
2313
2314 // Select method
2315 if (jyperk > 0.0) {
2316 factor *= jyperk;
2317 if ( tokelvin ) factor = 1.0 / jyperk;
2318 ostringstream oss;
2319 oss << "Jy/K = " << jyperk;
2320 pushLog(String(oss));
2321 Vector<Float> factors(tab.nrow(), factor);
2322 scaleByVector(tab,factors, false);
2323 } else if ( etaap > 0.0) {
2324 if (d < 0) {
2325 Instrument inst =
2326 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2327 True);
2328 STAttr sda;
2329 d = sda.diameter(inst);
2330 }
2331 jyperk = STAttr::findJyPerK(etaap, d);
2332 ostringstream oss;
2333 oss << "Jy/K = " << jyperk;
2334 pushLog(String(oss));
2335 factor *= jyperk;
2336 if ( tokelvin ) {
2337 factor = 1.0 / factor;
2338 }
2339 Vector<Float> factors(tab.nrow(), factor);
2340 scaleByVector(tab, factors, False);
2341 } else {
2342
2343 // OK now we must deal with automatic look up of values.
2344 // We must also deal with the fact that the factors need
2345 // to be computed per IF and may be different and may
2346 // change per integration.
2347
2348 pushLog("Looking up conversion factors");
2349 convertBrightnessUnits(out, tokelvin, cfac);
2350 }
2351
2352 return out;
2353}
2354
2355void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
2356 bool tokelvin, float cfac )
2357{
2358 Table& table = in->table();
2359 Instrument inst =
2360 STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
2361 TableIterator iter(table, "FREQ_ID");
2362 STFrequencies stfreqs = in->frequencies();
2363 STAttr sdAtt;
2364 while (!iter.pastEnd()) {
2365 Table tab = iter.table();
2366 ArrayColumn<Float> specCol(tab, "SPECTRA");
2367 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2368 ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
2369 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2370
2371 uInt freqid; freqidCol.get(0, freqid);
2372 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2373 // STAttr.JyPerK has a Vector interface... change sometime.
2374 Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
2375 for ( uInt i=0; i<tab.nrow(); ++i) {
2376 Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
2377 Float factor = cfac * jyperk;
2378 if ( tokelvin ) factor = Float(1.0) / factor;
2379 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2380 ma *= factor;
2381 specCol.put(i, ma.getArray());
2382 flagCol.put(i, flagsFromMA(ma));
2383 }
2384 ++iter;
2385 }
2386}
2387
2388CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
2389 const std::vector<float>& tau )
2390{
2391 CountedPtr< Scantable > out = getScantable(in, false);
2392
2393 Table outtab = out->table();
2394
2395 const Int ntau = uInt(tau.size());
2396 std::vector<float>::const_iterator tauit = tau.begin();
2397 AlwaysAssert((ntau == 1 || ntau == in->nif() || ntau == in->nif() * in->npol()),
2398 AipsError);
2399 TableIterator iiter(outtab, "IFNO");
2400 while ( !iiter.pastEnd() ) {
2401 Table itab = iiter.table();
2402 TableIterator piter(itab, "POLNO");
2403 while ( !piter.pastEnd() ) {
2404 Table tab = piter.table();
2405 ROScalarColumn<Float> elev(tab, "ELEVATION");
2406 ArrayColumn<Float> specCol(tab, "SPECTRA");
2407 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2408 ArrayColumn<Float> tsysCol(tab, "TSYS");
2409 for ( uInt i=0; i<tab.nrow(); ++i) {
2410 Float zdist = Float(C::pi_2) - elev(i);
2411 Float factor = exp(*tauit/cos(zdist));
2412 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2413 ma *= factor;
2414 specCol.put(i, ma.getArray());
2415 flagCol.put(i, flagsFromMA(ma));
2416 Vector<Float> tsys;
2417 tsysCol.get(i, tsys);
2418 tsys *= factor;
2419 tsysCol.put(i, tsys);
2420 }
2421 if (ntau == in->nif()*in->npol() ) {
2422 tauit++;
2423 }
2424 piter++;
2425 }
2426 if (ntau >= in->nif() ) {
2427 tauit++;
2428 }
2429 iiter++;
2430 }
2431 return out;
2432}
2433
2434CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in,
2435 const std::string& kernel,
2436 float width, int order)
2437{
2438 CountedPtr< Scantable > out = getScantable(in, false);
2439 Table table = out->table();
2440
2441 TableIterator iter(table, "IFNO");
2442 while (!iter.pastEnd()) {
2443 Table tab = iter.table();
2444 ArrayColumn<Float> specCol(tab, "SPECTRA");
2445 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2446 Vector<Float> spec;
2447 Vector<uChar> flag;
2448 for (uInt i = 0; i < tab.nrow(); ++i) {
2449 specCol.get(i, spec);
2450 flagCol.get(i, flag);
2451 Vector<Bool> mask(flag.nelements());
2452 convertArray(mask, flag);
2453 Vector<Float> specout;
2454 Vector<Bool> maskout;
2455 if (kernel == "hanning") {
2456 mathutil::hanning(specout, maskout, spec, !mask);
2457 convertArray(flag, !maskout);
2458 } else if (kernel == "rmedian") {
2459 mathutil::runningMedian(specout, maskout, spec , mask, width);
2460 convertArray(flag, maskout);
2461 } else if (kernel == "poly") {
2462 mathutil::polyfit(specout, maskout, spec, !mask, width, order);
2463 convertArray(flag, !maskout);
2464 }
2465
2466 for (uInt j = 0; j < flag.nelements(); ++j) {
2467 uChar userFlag = 1 << 7;
2468 if (maskout[j]==True) userFlag = 0 << 7;
2469 flag(j) = userFlag;
2470 }
2471
2472 flagCol.put(i, flag);
2473 specCol.put(i, specout);
2474 }
2475 ++iter;
2476 }
2477 return out;
2478}
2479
2480CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
2481 const std::string& kernel, float width,
2482 int order)
2483{
2484 if (kernel == "rmedian" || kernel == "hanning" || kernel == "poly") {
2485 return smoothOther(in, kernel, width, order);
2486 }
2487 CountedPtr< Scantable > out = getScantable(in, false);
2488 Table& table = out->table();
2489 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
2490 // same IFNO should have same no of channels
2491 // this saves overhead
2492 TableIterator iter(table, "IFNO");
2493 while (!iter.pastEnd()) {
2494 Table tab = iter.table();
2495 ArrayColumn<Float> specCol(tab, "SPECTRA");
2496 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2497 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2498 uInt nchan = tmpspec.nelements();
2499 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
2500 Convolver<Float> conv(kvec, IPosition(1,nchan));
2501 Vector<Float> spec;
2502 Vector<uChar> flag;
2503 for ( uInt i=0; i<tab.nrow(); ++i) {
2504 specCol.get(i, spec);
2505 flagCol.get(i, flag);
2506 Vector<Bool> mask(flag.nelements());
2507 convertArray(mask, flag);
2508 Vector<Float> specout;
2509 mathutil::replaceMaskByZero(specout, mask);
2510 conv.linearConv(specout, spec);
2511 specCol.put(i, specout);
2512 }
2513 ++iter;
2514 }
2515 return out;
2516}
2517
2518CountedPtr< Scantable >
2519 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
2520{
2521 if ( in.size() < 2 ) {
2522 throw(AipsError("Need at least two scantables to perform a merge."));
2523 }
2524 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
2525 bool insitu = insitu_;
2526 setInsitu(false);
2527 CountedPtr< Scantable > out = getScantable(*it, false);
2528 setInsitu(insitu);
2529 Table& tout = out->table();
2530 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
2531 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
2532 // Renumber SCANNO to be 0-based
2533 Vector<uInt> scannos = scannocol.getColumn();
2534 uInt offset = min(scannos);
2535 scannos -= offset;
2536 scannocol.putColumn(scannos);
2537 uInt newscanno = max(scannos)+1;
2538 ++it;
2539 while ( it != in.end() ){
2540 if ( ! (*it)->conformant(*out) ) {
2541 // non conformant.
2542 //pushLog(String("Warning: Can't merge scantables as header info differs."));
2543 LogIO os( LogOrigin( "STMath", "merge()", WHERE ) ) ;
2544 os << LogIO::SEVERE << "Can't merge scantables as header informations (any one of AntennaName, Equinox, and FluxUnit) differ." << LogIO::EXCEPTION ;
2545 }
2546 out->appendToHistoryTable((*it)->history());
2547 const Table& tab = (*it)->table();
2548
2549 Block<String> cols(3);
2550 cols[0] = String("FREQ_ID");
2551 cols[1] = String("MOLECULE_ID");
2552 cols[2] = String("FOCUS_ID");
2553
2554 TableIterator scanit(tab, "SCANNO");
2555 while (!scanit.pastEnd()) {
2556 ScalarColumn<uInt> thescannocol(scanit.table(),"SCANNO");
2557 Vector<uInt> thescannos(thescannocol.nrow(),newscanno);
2558 thescannocol.putColumn(thescannos);
2559 TableIterator subit(scanit.table(), cols);
2560 while ( !subit.pastEnd() ) {
2561 uInt nrow = tout.nrow();
2562 Table thetab = subit.table();
2563 ROTableRow row(thetab);
2564 Vector<uInt> thecolvals(thetab.nrow());
2565 ScalarColumn<uInt> thefreqidcol(thetab,"FREQ_ID");
2566 ScalarColumn<uInt> themolidcol(thetab, "MOLECULE_ID");
2567 ScalarColumn<uInt> thefocusidcol(thetab,"FOCUS_ID");
2568 // The selected subset of table should have
2569 // the equal FREQ_ID, MOLECULE_ID, and FOCUS_ID values.
2570 const TableRecord& rec = row.get(0);
2571 // Set the proper FREQ_ID
2572 Double rv,rp,inc;
2573 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
2574 uInt id;
2575 id = out->frequencies().addEntry(rp, rv, inc);
2576 thecolvals = id;
2577 thefreqidcol.putColumn(thecolvals);
2578 // Set the proper MOLECULE_ID
2579 Vector<String> name,fname;Vector<Double> rf;
2580 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
2581 id = out->molecules().addEntry(rf, name, fname);
2582 thecolvals = id;
2583 themolidcol.putColumn(thecolvals);
2584 // Set the proper FOCUS_ID
2585 Float fpa,frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
2586 (*it)->focus().getEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2587 fxy, fxyp, rec.asuInt("FOCUS_ID"));
2588 id = out->focus().addEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2589 fxy, fxyp);
2590 thecolvals = id;
2591 thefocusidcol.putColumn(thecolvals);
2592
2593 tout.addRow(thetab.nrow());
2594 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
2595
2596 ++subit;
2597 }
2598 ++newscanno;
2599 ++scanit;
2600 }
2601 ++it;
2602 }
2603 return out;
2604}
2605
2606CountedPtr< Scantable >
2607 STMath::invertPhase( const CountedPtr < Scantable >& in )
2608{
2609 return applyToPol(in, &STPol::invertPhase, Float(0.0));
2610}
2611
2612CountedPtr< Scantable >
2613 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
2614{
2615 return applyToPol(in, &STPol::rotatePhase, Float(phase));
2616}
2617
2618CountedPtr< Scantable >
2619 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
2620{
2621 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
2622}
2623
2624CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
2625 STPol::polOperation fptr,
2626 Float phase )
2627{
2628 CountedPtr< Scantable > out = getScantable(in, false);
2629 Table& tout = out->table();
2630 Block<String> cols(4);
2631 cols[0] = String("SCANNO");
2632 cols[1] = String("BEAMNO");
2633 cols[2] = String("IFNO");
2634 cols[3] = String("CYCLENO");
2635 TableIterator iter(tout, cols);
2636 CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
2637 out->getPolType() );
2638 while (!iter.pastEnd()) {
2639 Table t = iter.table();
2640 ArrayColumn<Float> speccol(t, "SPECTRA");
2641 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
2642 Matrix<Float> pols(speccol.getColumn());
2643 try {
2644 stpol->setSpectra(pols);
2645 Float fang,fhand;
2646 fang = in->focusTable_.getTotalAngle(focidcol(0));
2647 fhand = in->focusTable_.getFeedHand(focidcol(0));
2648 stpol->setPhaseCorrections(fang, fhand);
2649 // use a member function pointer in STPol. This only works on
2650 // the STPol pointer itself, not the Counted Pointer so
2651 // derefernce it.
2652 (&(*(stpol))->*fptr)(phase);
2653 speccol.putColumn(stpol->getSpectra());
2654 } catch (AipsError& e) {
2655 //delete stpol;stpol=0;
2656 throw(e);
2657 }
2658 ++iter;
2659 }
2660 //delete stpol;stpol=0;
2661 return out;
2662}
2663
2664CountedPtr< Scantable >
2665 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
2666{
2667 CountedPtr< Scantable > out = getScantable(in, false);
2668 Table& tout = out->table();
2669 Table t0 = tout(tout.col("POLNO") == 0);
2670 Table t1 = tout(tout.col("POLNO") == 1);
2671 if ( t0.nrow() != t1.nrow() )
2672 throw(AipsError("Inconsistent number of polarisations"));
2673 ArrayColumn<Float> speccol0(t0, "SPECTRA");
2674 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
2675 ArrayColumn<Float> speccol1(t1, "SPECTRA");
2676 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
2677 Matrix<Float> s0 = speccol0.getColumn();
2678 Matrix<uChar> f0 = flagcol0.getColumn();
2679 speccol0.putColumn(speccol1.getColumn());
2680 flagcol0.putColumn(flagcol1.getColumn());
2681 speccol1.putColumn(s0);
2682 flagcol1.putColumn(f0);
2683 return out;
2684}
2685
2686CountedPtr< Scantable >
2687 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
2688 const std::vector<bool>& mask,
2689 const std::string& weight )
2690{
2691 if (in->npol() < 2 )
2692 throw(AipsError("averagePolarisations can only be applied to two or more"
2693 "polarisations"));
2694 bool insitu = insitu_;
2695 setInsitu(false);
2696 CountedPtr< Scantable > pols = getScantable(in, true);
2697 setInsitu(insitu);
2698 Table& tout = pols->table();
2699 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
2700 Table tab = tableCommand(taql, in->table());
2701 if (tab.nrow() == 0 )
2702 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
2703 TableCopy::copyRows(tout, tab);
2704 TableVector<uInt> vec(tout, "POLNO");
2705 vec = 0;
2706 pols->table_.rwKeywordSet().define("nPol", Int(1));
2707 pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
2708 //pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
2709 std::vector<CountedPtr<Scantable> > vpols;
2710 vpols.push_back(pols);
2711 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
2712 return out;
2713}
2714
2715CountedPtr< Scantable >
2716 STMath::averageBeams( const CountedPtr< Scantable > & in,
2717 const std::vector<bool>& mask,
2718 const std::string& weight )
2719{
2720 bool insitu = insitu_;
2721 setInsitu(false);
2722 CountedPtr< Scantable > beams = getScantable(in, false);
2723 setInsitu(insitu);
2724 Table& tout = beams->table();
2725 // give all rows the same BEAMNO
2726 TableVector<uInt> vec(tout, "BEAMNO");
2727 vec = 0;
2728 beams->table_.rwKeywordSet().define("nBeam", Int(1));
2729 std::vector<CountedPtr<Scantable> > vbeams;
2730 vbeams.push_back(beams);
2731 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
2732 return out;
2733}
2734
2735
2736CountedPtr< Scantable >
2737 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
2738 const std::string & refTime,
2739 const std::string & method)
2740{
2741 // clone as this is not working insitu
2742 bool insitu = insitu_;
2743 setInsitu(false);
2744 CountedPtr< Scantable > out = getScantable(in, false);
2745 setInsitu(insitu);
2746 Table& tout = out->table();
2747 // Get reference Epoch to time of first row or given String
2748 Unit DAY(String("d"));
2749 MEpoch::Ref epochRef(in->getTimeReference());
2750 MEpoch refEpoch;
2751 if (refTime.length()>0) {
2752 Quantum<Double> qt;
2753 if (MVTime::read(qt,refTime)) {
2754 MVEpoch mv(qt);
2755 refEpoch = MEpoch(mv, epochRef);
2756 } else {
2757 throw(AipsError("Invalid format for Epoch string"));
2758 }
2759 } else {
2760 refEpoch = in->timeCol_(0);
2761 }
2762 MPosition refPos = in->getAntennaPosition();
2763
2764 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2765 /*
2766 // Comment from MV.
2767 // the following code has been commented out because different FREQ_IDs have to be aligned together even
2768 // if the frame doesn't change. So far, lack of this check didn't cause any problems.
2769 // test if user frame is different to base frame
2770 if ( in->frequencies().getFrameString(true)
2771 == in->frequencies().getFrameString(false) ) {
2772 throw(AipsError("Can't convert as no output frame has been set"
2773 " (use set_freqframe) or it is aligned already."));
2774 }
2775 */
2776 MFrequency::Types system = in->frequencies().getFrame();
2777 MVTime mvt(refEpoch.getValue());
2778 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
2779 ostringstream oss;
2780 oss << "Aligned at reference Epoch " << epochout
2781 << " in frame " << MFrequency::showType(system);
2782 pushLog(String(oss));
2783 // set up the iterator
2784 Block<String> cols(4);
2785 // select by constant direction
2786 cols[0] = String("SRCNAME");
2787 cols[1] = String("BEAMNO");
2788 // select by IF ( no of channels varies over this )
2789 cols[2] = String("IFNO");
2790 // select by restfrequency
2791 cols[3] = String("MOLECULE_ID");
2792 TableIterator iter(tout, cols);
2793 while ( !iter.pastEnd() ) {
2794 Table t = iter.table();
2795 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
2796 TableIterator fiter(t, "FREQ_ID");
2797 // determine nchan from the first row. This should work as
2798 // we are iterating over BEAMNO and IFNO // we should have constant direction
2799
2800 ROArrayColumn<Float> sCol(t, "SPECTRA");
2801 const MDirection direction = dirCol(0);
2802 const uInt nchan = sCol(0).nelements();
2803
2804 // skip operations if there is nothing to align
2805 if (fiter.pastEnd()) {
2806 continue;
2807 }
2808
2809 Table ftab = fiter.table();
2810 // align all frequency ids with respect to the first encountered id
2811 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
2812 // get the SpectralCoordinate for the freqid, which we are iterating over
2813 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
2814 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
2815 direction, refPos, system );
2816 // realign the SpectralCoordinate and put into the output Scantable
2817 Vector<String> units(1);
2818 units = String("Hz");
2819 Bool linear=True;
2820 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
2821 sc2.setWorldAxisUnits(units);
2822 const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
2823 sc2.referenceValue()[0],
2824 sc2.increment()[0]);
2825 while ( !fiter.pastEnd() ) {
2826 ftab = fiter.table();
2827 // spectral coordinate for the current FREQ_ID
2828 ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
2829 sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
2830 // create the "global" abcissa for alignment with same FREQ_ID
2831 Vector<Double> abc(nchan);
2832 for (uInt i=0; i<nchan; i++) {
2833 Double w;
2834 sC.toWorld(w,Double(i));
2835 abc[i] = w;
2836 }
2837 TableVector<uInt> tvec(ftab, "FREQ_ID");
2838 // assign new frequency id to all rows
2839 tvec = id;
2840 // cache abcissa for same time stamps, so iterate over those
2841 TableIterator timeiter(ftab, "TIME");
2842 while ( !timeiter.pastEnd() ) {
2843 Table tab = timeiter.table();
2844 ArrayColumn<Float> specCol(tab, "SPECTRA");
2845 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2846 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2847 // use align abcissa cache after the first row
2848 // these rows should be just be POLNO
2849 bool first = true;
2850 for (int i=0; i<int(tab.nrow()); ++i) {
2851 // input values
2852 Vector<uChar> flag = flagCol(i);
2853 Vector<Bool> mask(flag.shape());
2854 Vector<Float> specOut, spec;
2855 spec = specCol(i);
2856 Vector<Bool> maskOut;Vector<uChar> flagOut;
2857 convertArray(mask, flag);
2858 // alignment
2859 Bool ok = fa.align(specOut, maskOut, abc, spec,
2860 mask, timeCol(i), !first,
2861 interp, False);
2862 (void) ok; // unused stop compiler nagging
2863 // back into scantable
2864 flagOut.resize(maskOut.nelements());
2865 convertArray(flagOut, maskOut);
2866 flagCol.put(i, flagOut);
2867 specCol.put(i, specOut);
2868 // start abcissa caching
2869 first = false;
2870 }
2871 // next timestamp
2872 ++timeiter;
2873 }
2874 // next FREQ_ID
2875 ++fiter;
2876 }
2877 // next aligner
2878 ++iter;
2879 }
2880 // set this afterwards to ensure we are doing insitu correctly.
2881 out->frequencies().setFrame(system, true);
2882 return out;
2883}
2884
2885CountedPtr<Scantable>
2886 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
2887 const std::string & newtype )
2888{
2889 if (in->npol() != 2 && in->npol() != 4)
2890 throw(AipsError("Can only convert two or four polarisations."));
2891 if ( in->getPolType() == newtype )
2892 throw(AipsError("No need to convert."));
2893 if ( ! in->selector_.empty() )
2894 throw(AipsError("Can only convert whole scantable. Unset the selection."));
2895 bool insitu = insitu_;
2896 setInsitu(false);
2897 CountedPtr< Scantable > out = getScantable(in, true);
2898 setInsitu(insitu);
2899 Table& tout = out->table();
2900 tout.rwKeywordSet().define("POLTYPE", String(newtype));
2901
2902 Block<String> cols(4);
2903 cols[0] = "SCANNO";
2904 cols[1] = "CYCLENO";
2905 cols[2] = "BEAMNO";
2906 cols[3] = "IFNO";
2907 TableIterator it(in->originalTable_, cols);
2908 String basetype = in->getPolType();
2909 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
2910 try {
2911 while ( !it.pastEnd() ) {
2912 Table tab = it.table();
2913 uInt row = tab.rowNumbers()[0];
2914 stpol->setSpectra(in->getPolMatrix(row));
2915 Float fang,fhand;
2916 fang = in->focusTable_.getTotalAngle(in->mfocusidCol_(row));
2917 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
2918 stpol->setPhaseCorrections(fang, fhand);
2919 Int npolout = 0;
2920 for (uInt i=0; i<tab.nrow(); ++i) {
2921 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
2922 if ( outvec.nelements() > 0 ) {
2923 tout.addRow();
2924 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
2925 ArrayColumn<Float> sCol(tout,"SPECTRA");
2926 ScalarColumn<uInt> pCol(tout,"POLNO");
2927 sCol.put(tout.nrow()-1 ,outvec);
2928 pCol.put(tout.nrow()-1 ,uInt(npolout));
2929 npolout++;
2930 }
2931 }
2932 tout.rwKeywordSet().define("nPol", npolout);
2933 ++it;
2934 }
2935 } catch (AipsError& e) {
2936 delete stpol;
2937 throw(e);
2938 }
2939 delete stpol;
2940 return out;
2941}
2942
2943CountedPtr< Scantable >
2944 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
2945 const std::string & scantype )
2946{
2947 bool insitu = insitu_;
2948 setInsitu(false);
2949 CountedPtr< Scantable > out = getScantable(in, true);
2950 setInsitu(insitu);
2951 Table& tout = out->table();
2952 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
2953 if (scantype == "on") {
2954 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
2955 }
2956 Table tab = tableCommand(taql, in->table());
2957 TableCopy::copyRows(tout, tab);
2958 if (scantype == "on") {
2959 // re-index SCANNO to 0
2960 TableVector<uInt> vec(tout, "SCANNO");
2961 vec = 0;
2962 }
2963 return out;
2964}
2965
2966std::vector<float>
2967 asap::STMath::fft( const casa::CountedPtr< Scantable > & in,
2968 const std::vector<int>& whichrow,
2969 bool getRealImag )
2970{
2971 std::vector<float> res;
2972 Table tab = in->table();
2973 std::vector<bool> mask;
2974
2975 if (whichrow.size() < 1) { // for all rows (by default)
2976 int nrow = int(tab.nrow());
2977 for (int i = 0; i < nrow; ++i) {
2978 res = in->execFFT(i, mask, getRealImag);
2979 }
2980 } else { // for specified rows
2981 for (uInt i = 0; i < whichrow.size(); ++i) {
2982 res = in->execFFT(i, mask, getRealImag);
2983 }
2984 }
2985
2986 return res;
2987}
2988
2989
2990CountedPtr<Scantable>
2991 asap::STMath::lagFlag( const CountedPtr<Scantable>& in,
2992 double start, double end,
2993 const std::string& mode )
2994{
2995 CountedPtr<Scantable> out = getScantable(in, false);
2996 Table& tout = out->table();
2997 TableIterator iter(tout, "FREQ_ID");
2998 FFTServer<Float,Complex> ffts;
2999
3000 while ( !iter.pastEnd() ) {
3001 Table tab = iter.table();
3002 Double rp,rv,inc;
3003 ROTableRow row(tab);
3004 const TableRecord& rec = row.get(0);
3005 uInt freqid = rec.asuInt("FREQ_ID");
3006 out->frequencies().getEntry(rp, rv, inc, freqid);
3007 ArrayColumn<Float> specCol(tab, "SPECTRA");
3008 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
3009
3010 for (int i=0; i<int(tab.nrow()); ++i) {
3011 Vector<Float> spec = specCol(i);
3012 Vector<uChar> flag = flagCol(i);
3013 std::vector<bool> mask;
3014 for (uInt j = 0; j < flag.nelements(); ++j) {
3015 mask.push_back(!(flag[j]>0));
3016 }
3017 mathutil::doZeroOrderInterpolation(spec, mask);
3018
3019 Vector<Complex> lags;
3020 ffts.fft0(lags, spec);
3021
3022 Int lag0(start+0.5);
3023 Int lag1(end+0.5);
3024 if (mode == "frequency") {
3025 lag0 = Int(spec.nelements()*abs(inc)/(start)+0.5);
3026 lag1 = Int(spec.nelements()*abs(inc)/(end)+0.5);
3027 }
3028 Int lstart = max(0, lag0);
3029 Int lend = min(Int(lags.nelements()-1), lag1);
3030 if (lstart == lend) {
3031 lags[lstart] = Complex(0.0);
3032 } else {
3033 if (lstart > lend) {
3034 Int tmp = lend;
3035 lend = lstart;
3036 lstart = tmp;
3037 }
3038 for (int j=lstart; j <=lend ;++j) {
3039 lags[j] = Complex(0.0);
3040 }
3041 }
3042
3043 ffts.fft0(spec, lags);
3044
3045 specCol.put(i, spec);
3046 }
3047 ++iter;
3048 }
3049 return out;
3050}
3051
3052// Averaging spectra with different channel/resolution
3053CountedPtr<Scantable>
3054STMath::new_average( const std::vector<CountedPtr<Scantable> >& in,
3055 const bool& compel,
3056 const std::vector<bool>& mask,
3057 const std::string& weight,
3058 const std::string& avmode )
3059 throw ( casa::AipsError )
3060{
3061 LogIO os( LogOrigin( "STMath", "new_average()", WHERE ) ) ;
3062 if ( avmode == "SCAN" && in.size() != 1 )
3063 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
3064 "Use merge first."));
3065
3066 // 2012/02/17 TN
3067 // Since STGrid is implemented, average doesn't consider direction
3068 // when accumulating
3069 // check if OTF observation
3070// String obstype = in[0]->getHeader().obstype ;
3071// Double tol = 0.0 ;
3072// if ( obstype.find( "OTF" ) != String::npos ) {
3073// tol = TOL_OTF ;
3074// }
3075// else {
3076// tol = TOL_POINT ;
3077// }
3078
3079 CountedPtr<Scantable> out ; // processed result
3080 if ( compel ) {
3081 std::vector< CountedPtr<Scantable> > newin ; // input for average process
3082 uInt insize = in.size() ; // number of input scantables
3083
3084 // TEST: do normal average in each table before IF grouping
3085 os << "Do preliminary averaging" << LogIO::POST ;
3086 vector< CountedPtr<Scantable> > tmpin( insize ) ;
3087 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3088 vector< CountedPtr<Scantable> > v( 1, in[itable] ) ;
3089 tmpin[itable] = average( v, mask, weight, avmode ) ;
3090 }
3091
3092 // warning
3093 os << "Average spectra with different spectral resolution" << LogIO::POST ;
3094
3095 // temporarily set coordinfo
3096 vector<string> oldinfo( insize ) ;
3097 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3098 vector<string> coordinfo = in[itable]->getCoordInfo() ;
3099 oldinfo[itable] = coordinfo[0] ;
3100 coordinfo[0] = "Hz" ;
3101 tmpin[itable]->setCoordInfo( coordinfo ) ;
3102 }
3103
3104 // columns
3105 ScalarColumn<uInt> freqIDCol ;
3106 ScalarColumn<uInt> ifnoCol ;
3107 ScalarColumn<uInt> scannoCol ;
3108
3109
3110 // check IF frequency coverage
3111 // freqid: list of FREQ_ID, which is used, in each table
3112 // iffreq: list of minimum and maximum frequency for each FREQ_ID in
3113 // each table
3114 // freqid[insize][numIF]
3115 // freqid: [[id00, id01, ...],
3116 // [id10, id11, ...],
3117 // ...
3118 // [idn0, idn1, ...]]
3119 // iffreq[insize][numIF*2]
3120 // iffreq: [[min_id00, max_id00, min_id01, max_id01, ...],
3121 // [min_id10, max_id10, min_id11, max_id11, ...],
3122 // ...
3123 // [min_idn0, max_idn0, min_idn1, max_idn1, ...]]
3124 //os << "Check IF settings in each table" << LogIO::POST ;
3125 vector< vector<uInt> > freqid( insize );
3126 vector< vector<double> > iffreq( insize ) ;
3127 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3128 uInt rows = tmpin[itable]->nrow() ;
3129 uInt freqnrows = tmpin[itable]->frequencies().table().nrow() ;
3130 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3131 if ( freqid[itable].size() == freqnrows ) {
3132 break ;
3133 }
3134 else {
3135 freqIDCol.attach( tmpin[itable]->table(), "FREQ_ID" ) ;
3136 ifnoCol.attach( tmpin[itable]->table(), "IFNO" ) ;
3137 uInt id = freqIDCol( irow ) ;
3138 if ( freqid[itable].size() == 0 || count( freqid[itable].begin(), freqid[itable].end(), id ) == 0 ) {
3139 //os << "itable = " << itable << ": IF " << id << " is included in the list" << LogIO::POST ;
3140 vector<double> abcissa = tmpin[itable]->getAbcissa( irow ) ;
3141 freqid[itable].push_back( id ) ;
3142 iffreq[itable].push_back( abcissa[0] - 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
3143 iffreq[itable].push_back( abcissa[abcissa.size()-1] + 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
3144 }
3145 }
3146 }
3147 }
3148
3149 // debug
3150 //os << "IF settings summary:" << endl ;
3151 //for ( uInt i = 0 ; i < freqid.size() ; i++ ) {
3152 //os << " Table" << i << endl ;
3153 //for ( uInt j = 0 ; j < freqid[i].size() ; j++ ) {
3154 //os << " id = " << freqid[i][j] << " (min,max) = (" << iffreq[i][2*j] << "," << iffreq[i][2*j+1] << ")" << endl ;
3155 //}
3156 //}
3157 //os << endl ;
3158 //os.post() ;
3159
3160 // IF grouping based on their frequency coverage
3161 // ifgrp: list of table index and FREQ_ID for all members in each IF group
3162 // ifgfreq: list of minimum and maximum frequency in each IF group
3163 // ifgrp[numgrp][nummember*2]
3164 // ifgrp: [[table00, freqrow00, table01, freqrow01, ...],
3165 // [table10, freqrow10, table11, freqrow11, ...],
3166 // ...
3167 // [tablen0, freqrown0, tablen1, freqrown1, ...]]
3168 // ifgfreq[numgrp*2]
3169 // ifgfreq: [min0_grp0, max0_grp0, min1_grp1, max1_grp1, ...]
3170 //os << "IF grouping based on their frequency coverage" << LogIO::POST ;
3171 vector< vector<uInt> > ifgrp ;
3172 vector<double> ifgfreq ;
3173
3174 // parameter for IF grouping
3175 // groupmode = OR retrieve all region
3176 // AND only retrieve overlaped region
3177 //string groupmode = "AND" ;
3178 string groupmode = "OR" ;
3179 uInt sizecr = 0 ;
3180 if ( groupmode == "AND" )
3181 sizecr = 2 ;
3182 else if ( groupmode == "OR" )
3183 sizecr = 0 ;
3184
3185 vector<double> sortedfreq ;
3186 for ( uInt i = 0 ; i < iffreq.size() ; i++ ) {
3187 for ( uInt j = 0 ; j < iffreq[i].size() ; j++ ) {
3188 if ( count( sortedfreq.begin(), sortedfreq.end(), iffreq[i][j] ) == 0 )
3189 sortedfreq.push_back( iffreq[i][j] ) ;
3190 }
3191 }
3192 sort( sortedfreq.begin(), sortedfreq.end() ) ;
3193 for ( vector<double>::iterator i = sortedfreq.begin() ; i != sortedfreq.end()-1 ; i++ ) {
3194 ifgfreq.push_back( *i ) ;
3195 ifgfreq.push_back( *(i+1) ) ;
3196 }
3197 ifgrp.resize( ifgfreq.size()/2 ) ;
3198 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3199 for ( uInt iif = 0 ; iif < freqid[itable].size() ; iif++ ) {
3200 double range0 = iffreq[itable][2*iif] ;
3201 double range1 = iffreq[itable][2*iif+1] ;
3202 for ( uInt j = 0 ; j < ifgrp.size() ; j++ ) {
3203 double fmin = max( range0, ifgfreq[2*j] ) ;
3204 double fmax = min( range1, ifgfreq[2*j+1] ) ;
3205 if ( fmin < fmax ) {
3206 ifgrp[j].push_back( itable ) ;
3207 ifgrp[j].push_back( freqid[itable][iif] ) ;
3208 }
3209 }
3210 }
3211 }
3212 vector< vector<uInt> >::iterator fiter = ifgrp.begin() ;
3213 vector<double>::iterator giter = ifgfreq.begin() ;
3214 while( fiter != ifgrp.end() ) {
3215 if ( fiter->size() <= sizecr ) {
3216 fiter = ifgrp.erase( fiter ) ;
3217 giter = ifgfreq.erase( giter ) ;
3218 giter = ifgfreq.erase( giter ) ;
3219 }
3220 else {
3221 fiter++ ;
3222 advance( giter, 2 ) ;
3223 }
3224 }
3225
3226 // Grouping continuous IF groups (without frequency gap)
3227 // freqgrp: list of IF group indexes in each frequency group
3228 // freqrange: list of minimum and maximum frequency in each frequency group
3229 // freqgrp[numgrp][nummember]
3230 // freqgrp: [[ifgrp00, ifgrp01, ifgrp02, ...],
3231 // [ifgrp10, ifgrp11, ifgrp12, ...],
3232 // ...
3233 // [ifgrpn0, ifgrpn1, ifgrpn2, ...]]
3234 // freqrange[numgrp*2]
3235 // freqrange: [min_grp0, max_grp0, min_grp1, max_grp1, ...]
3236 vector< vector<uInt> > freqgrp ;
3237 double freqrange = 0.0 ;
3238 uInt grpnum = 0 ;
3239 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3240 // Assumed that ifgfreq was sorted
3241 if ( grpnum != 0 && freqrange == ifgfreq[2*i] ) {
3242 freqgrp[grpnum-1].push_back( i ) ;
3243 }
3244 else {
3245 vector<uInt> grp0( 1, i ) ;
3246 freqgrp.push_back( grp0 ) ;
3247 grpnum++ ;
3248 }
3249 freqrange = ifgfreq[2*i+1] ;
3250 }
3251
3252
3253 // print IF groups
3254 ostringstream oss ;
3255 oss << "IF Group summary: " << endl ;
3256 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3257 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3258 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3259 for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3260 oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3261 }
3262 oss << endl ;
3263 }
3264 oss << endl ;
3265 os << oss.str() << LogIO::POST ;
3266
3267 // print frequency group
3268 oss.str("") ;
3269 oss << "Frequency Group summary: " << endl ;
3270 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: IF_GROUP_ID" << endl ;
3271 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3272 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*freqgrp[i][0]] << "," << ifgfreq[2*freqgrp[i][freqgrp[i].size()-1]+1] << "]: " ;
3273 for ( uInt j = 0 ; j < freqgrp[i].size() ; j++ ) {
3274 oss << freqgrp[i][j] << " " ;
3275 }
3276 oss << endl ;
3277 }
3278 oss << endl ;
3279 os << oss.str() << LogIO::POST ;
3280
3281 // membership check
3282 // groups: list of IF group indexes whose frequency range overlaps with
3283 // that of each table and IF
3284 // groups[numtable][numIF][nummembership]
3285 // groups: [[[grp, grp,...], [grp, grp,...],...],
3286 // [[grp, grp,...], [grp, grp,...],...],
3287 // ...
3288 // [[grp, grp,...], [grp, grp,...],...]]
3289 vector< vector< vector<uInt> > > groups( insize ) ;
3290 for ( uInt i = 0 ; i < insize ; i++ ) {
3291 groups[i].resize( freqid[i].size() ) ;
3292 }
3293 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3294 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3295 uInt tableid = ifgrp[igrp][2*imem] ;
3296 vector<uInt>::iterator iter = find( freqid[tableid].begin(), freqid[tableid].end(), ifgrp[igrp][2*imem+1] ) ;
3297 if ( iter != freqid[tableid].end() ) {
3298 uInt rowid = distance( freqid[tableid].begin(), iter ) ;
3299 groups[tableid][rowid].push_back( igrp ) ;
3300 }
3301 }
3302 }
3303
3304 // print membership
3305 //oss.str("") ;
3306 //for ( uInt i = 0 ; i < insize ; i++ ) {
3307 //oss << "Table " << i << endl ;
3308 //for ( uInt j = 0 ; j < groups[i].size() ; j++ ) {
3309 //oss << " FREQ_ID " << setw( 2 ) << freqid[i][j] << ": " ;
3310 //for ( uInt k = 0 ; k < groups[i][j].size() ; k++ ) {
3311 //oss << setw( 2 ) << groups[i][j][k] << " " ;
3312 //}
3313 //oss << endl ;
3314 //}
3315 //}
3316 //os << oss.str() << LogIO::POST ;
3317
3318 // set back coordinfo
3319 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3320 vector<string> coordinfo = tmpin[itable]->getCoordInfo() ;
3321 coordinfo[0] = oldinfo[itable] ;
3322 tmpin[itable]->setCoordInfo( coordinfo ) ;
3323 }
3324
3325 // Create additional table if needed
3326 bool oldInsitu = insitu_ ;
3327 setInsitu( false ) ;
3328 vector< vector<uInt> > addrow( insize ) ;
3329 vector<uInt> addtable( insize, 0 ) ;
3330 vector<uInt> newtableids( insize ) ;
3331 vector<uInt> newifids( insize, 0 ) ;
3332 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3333 //os << "Table " << itable << ": " ;
3334 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3335 addrow[itable].push_back( groups[itable][ifrow].size()-1 ) ;
3336 //os << addrow[itable][ifrow] << " " ;
3337 }
3338 addtable[itable] = *max_element( addrow[itable].begin(), addrow[itable].end() ) ;
3339 //os << "(" << addtable[itable] << ")" << LogIO::POST ;
3340 }
3341 newin.resize( insize ) ;
3342 copy( tmpin.begin(), tmpin.end(), newin.begin() ) ;
3343 for ( uInt i = 0 ; i < insize ; i++ ) {
3344 newtableids[i] = i ;
3345 }
3346 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3347 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3348 CountedPtr<Scantable> add = getScantable( newin[itable], false ) ;
3349 vector<int> freqidlist ;
3350 for ( uInt i = 0 ; i < groups[itable].size() ; i++ ) {
3351 if ( groups[itable][i].size() > iadd + 1 ) {
3352 freqidlist.push_back( freqid[itable][i] ) ;
3353 }
3354 }
3355 stringstream taqlstream ;
3356 taqlstream << "SELECT FROM $1 WHERE FREQ_ID IN [" ;
3357 for ( uInt i = 0 ; i < freqidlist.size() ; i++ ) {
3358 taqlstream << freqidlist[i] ;
3359 if ( i < freqidlist.size() - 1 )
3360 taqlstream << "," ;
3361 else
3362 taqlstream << "]" ;
3363 }
3364 string taql = taqlstream.str() ;
3365 //os << "taql = " << taql << LogIO::POST ;
3366 STSelector selector = STSelector() ;
3367 selector.setTaQL( taql ) ;
3368 add->setSelection( selector ) ;
3369 newin.push_back( add ) ;
3370 newtableids.push_back( itable ) ;
3371 newifids.push_back( iadd + 1 ) ;
3372 }
3373 }
3374
3375 // udpate ifgrp
3376 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3377 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3378 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3379 if ( groups[itable][ifrow].size() > iadd + 1 ) {
3380 uInt igrp = groups[itable][ifrow][iadd+1] ;
3381 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3382 if ( ifgrp[igrp][2*imem] == newtableids[iadd+insize] && ifgrp[igrp][2*imem+1] == freqid[newtableids[iadd+insize]][ifrow] ) {
3383 ifgrp[igrp][2*imem] = insize + iadd ;
3384 }
3385 }
3386 }
3387 }
3388 }
3389 }
3390
3391 // print IF groups again for debug
3392 //oss.str( "" ) ;
3393 //oss << "IF Group summary: " << endl ;
3394 //oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3395 //for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3396 //oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3397 //for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3398 //oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3399 //}
3400 //oss << endl ;
3401 //}
3402 //oss << endl ;
3403 //os << oss.str() << LogIO::POST ;
3404
3405 // reset SCANNO and IFNO/FREQ_ID: IF is reset by the result of sortation
3406 os << "All scan number is set to 0" << LogIO::POST ;
3407 //os << "All IF number is set to IF group index" << LogIO::POST ;
3408 insize = newin.size() ;
3409 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3410 uInt rows = newin[itable]->nrow() ;
3411 Table &tmpt = newin[itable]->table() ;
3412 freqIDCol.attach( tmpt, "FREQ_ID" ) ;
3413 scannoCol.attach( tmpt, "SCANNO" ) ;
3414 ifnoCol.attach( tmpt, "IFNO" ) ;
3415 for ( uInt irow=0 ; irow < rows ; irow++ ) {
3416 scannoCol.put( irow, 0 ) ;
3417 uInt freqID = freqIDCol( irow ) ;
3418 vector<uInt>::iterator iter = find( freqid[newtableids[itable]].begin(), freqid[newtableids[itable]].end(), freqID ) ;
3419 if ( iter != freqid[newtableids[itable]].end() ) {
3420 uInt index = distance( freqid[newtableids[itable]].begin(), iter ) ;
3421 ifnoCol.put( irow, groups[newtableids[itable]][index][newifids[itable]] ) ;
3422 }
3423 else {
3424 throw(AipsError("IF grouping was wrong in additional tables.")) ;
3425 }
3426 }
3427 }
3428 oldinfo.resize( insize ) ;
3429 setInsitu( oldInsitu ) ;
3430
3431 // temporarily set coordinfo
3432 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3433 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3434 oldinfo[itable] = coordinfo[0] ;
3435 coordinfo[0] = "Hz" ;
3436 newin[itable]->setCoordInfo( coordinfo ) ;
3437 }
3438
3439 // save column values in the vector
3440 vector< vector<uInt> > freqTableIdVec( insize ) ;
3441 vector< vector<uInt> > freqIdVec( insize ) ;
3442 vector< vector<uInt> > ifNoVec( insize ) ;
3443 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3444 ScalarColumn<uInt> freqIDs ;
3445 freqIDs.attach( newin[itable]->frequencies().table(), "ID" ) ;
3446 ifnoCol.attach( newin[itable]->table(), "IFNO" ) ;
3447 freqIDCol.attach( newin[itable]->table(), "FREQ_ID" ) ;
3448 for ( uInt irow = 0 ; irow < newin[itable]->frequencies().table().nrow() ; irow++ ) {
3449 freqTableIdVec[itable].push_back( freqIDs( irow ) ) ;
3450 }
3451 for ( uInt irow = 0 ; irow < newin[itable]->table().nrow() ; irow++ ) {
3452 freqIdVec[itable].push_back( freqIDCol( irow ) ) ;
3453 ifNoVec[itable].push_back( ifnoCol( irow ) ) ;
3454 }
3455 }
3456
3457 // reset spectra and flagtra: pick up common part of frequency coverage
3458 //os << "Pick common frequency range and align resolution" << LogIO::POST ;
3459 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3460 uInt rows = newin[itable]->nrow() ;
3461 int nminchan = -1 ;
3462 int nmaxchan = -1 ;
3463 vector<uInt> freqIdUpdate ;
3464 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3465 uInt ifno = ifNoVec[itable][irow] ; // IFNO is reset by group index
3466 double minfreq = ifgfreq[2*ifno] ;
3467 double maxfreq = ifgfreq[2*ifno+1] ;
3468 //os << "frequency range: [" << minfreq << "," << maxfreq << "]" << LogIO::POST ;
3469 vector<double> abcissa = newin[itable]->getAbcissa( irow ) ;
3470 int nchan = abcissa.size() ;
3471 double resol = abcissa[1] - abcissa[0] ;
3472 //os << "abcissa range : [" << abcissa[0] << "," << abcissa[nchan-1] << "]" << LogIO::POST ;
3473 if ( minfreq <= abcissa[0] )
3474 nminchan = 0 ;
3475 else {
3476 //double cfreq = ( minfreq - abcissa[0] ) / resol ;
3477 double cfreq = ( minfreq - abcissa[0] + 0.5 * resol ) / resol ;
3478 nminchan = int(cfreq) + ( ( cfreq - int(cfreq) <= 0.5 ) ? 0 : 1 ) ;
3479 }
3480 if ( maxfreq >= abcissa[abcissa.size()-1] )
3481 nmaxchan = abcissa.size() - 1 ;
3482 else {
3483 //double cfreq = ( abcissa[abcissa.size()-1] - maxfreq ) / resol ;
3484 double cfreq = ( abcissa[abcissa.size()-1] - maxfreq + 0.5 * resol ) / resol ;
3485 nmaxchan = abcissa.size() - 1 - int(cfreq) - ( ( cfreq - int(cfreq) >= 0.5 ) ? 1 : 0 ) ;
3486 }
3487 //os << "channel range (" << irow << "): [" << nminchan << "," << nmaxchan << "]" << LogIO::POST ;
3488 if ( nmaxchan > nminchan ) {
3489 newin[itable]->reshapeSpectrum( nminchan, nmaxchan, irow ) ;
3490 int newchan = nmaxchan - nminchan + 1 ;
3491 if ( count( freqIdUpdate.begin(), freqIdUpdate.end(), freqIdVec[itable][irow] ) == 0 && newchan < nchan )
3492 freqIdUpdate.push_back( freqIdVec[itable][irow] ) ;
3493 }
3494 else {
3495 throw(AipsError("Failed to pick up common part of frequency range.")) ;
3496 }
3497 }
3498 for ( uInt i = 0 ; i < freqIdUpdate.size() ; i++ ) {
3499 uInt freqId = freqIdUpdate[i] ;
3500 Double refpix ;
3501 Double refval ;
3502 Double increment ;
3503
3504 // update row
3505 newin[itable]->frequencies().getEntry( refpix, refval, increment, freqId ) ;
3506 refval = refval - ( refpix - nminchan ) * increment ;
3507 refpix = 0 ;
3508 newin[itable]->frequencies().setEntry( refpix, refval, increment, freqId ) ;
3509 }
3510 }
3511
3512
3513 // reset spectra and flagtra: align spectral resolution
3514 //os << "Align spectral resolution" << LogIO::POST ;
3515 // gmaxdnu: the coarsest frequency resolution in the frequency group
3516 // gmemid: member index that have a resolution equal to gmaxdnu
3517 // gmaxdnu[numfreqgrp]
3518 // gmaxdnu: [dnu0, dnu1, ...]
3519 // gmemid[numfreqgrp]
3520 // gmemid: [id0, id1, ...]
3521 vector<double> gmaxdnu( freqgrp.size(), 0.0 ) ;
3522 vector<uInt> gmemid( freqgrp.size(), 0 ) ;
3523 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3524 double maxdnu = 0.0 ; // maximum (coarsest) frequency resolution
3525 int minchan = INT_MAX ; // minimum channel number
3526 Double refpixref = -1 ; // reference of 'reference pixel'
3527 Double refvalref = -1 ; // reference of 'reference frequency'
3528 Double refinc = -1 ; // reference frequency resolution
3529 uInt refreqid ;
3530 uInt reftable = INT_MAX;
3531 // process only if group member > 1
3532 if ( ifgrp[igrp].size() > 2 ) {
3533 // find minchan and maxdnu in each group
3534 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3535 uInt tableid = ifgrp[igrp][2*imem] ;
3536 uInt rowid = ifgrp[igrp][2*imem+1] ;
3537 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3538 if ( iter != freqIdVec[tableid].end() ) {
3539 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3540 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3541 int nchan = abcissa.size() ;
3542 double dnu = abcissa[1] - abcissa[0] ;
3543 //os << "GROUP " << igrp << " (" << tableid << "," << rowid << "): nchan = " << nchan << " (minchan = " << minchan << ")" << LogIO::POST ;
3544 if ( nchan < minchan ) {
3545 minchan = nchan ;
3546 maxdnu = dnu ;
3547 newin[tableid]->frequencies().getEntry( refpixref, refvalref, refinc, rowid ) ;
3548 refreqid = rowid ;
3549 reftable = tableid ;
3550 }
3551 }
3552 }
3553 // regrid spectra in each group
3554 os << "GROUP " << igrp << endl ;
3555 os << " Channel number is adjusted to " << minchan << endl ;
3556 os << " Corresponding frequency resolution is " << maxdnu << "Hz" << LogIO::POST ;
3557 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3558 uInt tableid = ifgrp[igrp][2*imem] ;
3559 uInt rowid = ifgrp[igrp][2*imem+1] ;
3560 freqIDCol.attach( newin[tableid]->table(), "FREQ_ID" ) ;
3561 //os << "tableid = " << tableid << " rowid = " << rowid << ": " << LogIO::POST ;
3562 //os << " regridChannel applied to " ;
3563 //if ( tableid != reftable )
3564 refreqid = newin[tableid]->frequencies().addEntry( refpixref, refvalref, refinc ) ;
3565 for ( uInt irow = 0 ; irow < newin[tableid]->table().nrow() ; irow++ ) {
3566 uInt tfreqid = freqIdVec[tableid][irow] ;
3567 if ( tfreqid == rowid ) {
3568 //os << irow << " " ;
3569 newin[tableid]->regridChannel( minchan, maxdnu, irow ) ;
3570 freqIDCol.put( irow, refreqid ) ;
3571 freqIdVec[tableid][irow] = refreqid ;
3572 }
3573 }
3574 //os << LogIO::POST ;
3575 }
3576 }
3577 else {
3578 uInt tableid = ifgrp[igrp][0] ;
3579 uInt rowid = ifgrp[igrp][1] ;
3580 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3581 if ( iter != freqIdVec[tableid].end() ) {
3582 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3583 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3584 minchan = abcissa.size() ;
3585 maxdnu = abcissa[1] - abcissa[0] ;
3586 }
3587 }
3588 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3589 if ( count( freqgrp[i].begin(), freqgrp[i].end(), igrp ) > 0 ) {
3590 if ( maxdnu > gmaxdnu[i] ) {
3591 gmaxdnu[i] = maxdnu ;
3592 gmemid[i] = igrp ;
3593 }
3594 break ;
3595 }
3596 }
3597 }
3598
3599 // set back coordinfo
3600 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3601 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3602 coordinfo[0] = oldinfo[itable] ;
3603 newin[itable]->setCoordInfo( coordinfo ) ;
3604 }
3605
3606 // accumulate all rows into the first table
3607 // NOTE: assumed in.size() = 1
3608 vector< CountedPtr<Scantable> > tmp( 1 ) ;
3609 if ( newin.size() == 1 )
3610 tmp[0] = newin[0] ;
3611 else
3612 tmp[0] = merge( newin ) ;
3613
3614 //return tmp[0] ;
3615
3616 // average
3617 CountedPtr<Scantable> tmpout = average( tmp, mask, weight, avmode ) ;
3618
3619 //return tmpout ;
3620
3621 // combine frequency group
3622 os << "Combine spectra based on frequency grouping" << LogIO::POST ;
3623 os << "IFNO is renumbered as frequency group ID (see above)" << LogIO::POST ;
3624 vector<string> coordinfo = tmpout->getCoordInfo() ;
3625 oldinfo[0] = coordinfo[0] ;
3626 coordinfo[0] = "Hz" ;
3627 tmpout->setCoordInfo( coordinfo ) ;
3628 // create proformas of output table
3629 stringstream taqlstream ;
3630 taqlstream << "SELECT FROM $1 WHERE IFNO IN [" ;
3631 for ( uInt i = 0 ; i < gmemid.size() ; i++ ) {
3632 taqlstream << gmemid[i] ;
3633 if ( i < gmemid.size() - 1 )
3634 taqlstream << "," ;
3635 else
3636 taqlstream << "]" ;
3637 }
3638 string taql = taqlstream.str() ;
3639 //os << "taql = " << taql << LogIO::POST ;
3640 STSelector selector = STSelector() ;
3641 selector.setTaQL( taql ) ;
3642 oldInsitu = insitu_ ;
3643 setInsitu( false ) ;
3644 out = getScantable( tmpout, false ) ;
3645 setInsitu( oldInsitu ) ;
3646 out->setSelection( selector ) ;
3647 // regrid rows
3648 ifnoCol.attach( tmpout->table(), "IFNO" ) ;
3649 for ( uInt irow = 0 ; irow < tmpout->table().nrow() ; irow++ ) {
3650 uInt ifno = ifnoCol( irow ) ;
3651 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3652 if ( count( freqgrp[igrp].begin(), freqgrp[igrp].end(), ifno ) > 0 ) {
3653 vector<double> abcissa = tmpout->getAbcissa( irow ) ;
3654 double bw = ( abcissa[1] - abcissa[0] ) * abcissa.size() ;
3655 int nchan = (int)( bw / gmaxdnu[igrp] ) ;
3656 tmpout->regridChannel( nchan, gmaxdnu[igrp], irow ) ;
3657 break ;
3658 }
3659 }
3660 }
3661 // combine spectra
3662 ArrayColumn<Float> specColOut ;
3663 specColOut.attach( out->table(), "SPECTRA" ) ;
3664 ArrayColumn<uChar> flagColOut ;
3665 flagColOut.attach( out->table(), "FLAGTRA" ) ;
3666 ScalarColumn<uInt> ifnoColOut ;
3667 ifnoColOut.attach( out->table(), "IFNO" ) ;
3668 ScalarColumn<uInt> polnoColOut ;
3669 polnoColOut.attach( out->table(), "POLNO" ) ;
3670 ScalarColumn<uInt> freqidColOut ;
3671 freqidColOut.attach( out->table(), "FREQ_ID" ) ;
3672// MDirection::ScalarColumn dirColOut ;
3673// dirColOut.attach( out->table(), "DIRECTION" ) ;
3674 Table &tab = tmpout->table() ;
3675 Block<String> cols(1);
3676 cols[0] = String("POLNO") ;
3677 TableIterator iter( tab, cols ) ;
3678 bool done = false ;
3679 vector< vector<uInt> > sizes( freqgrp.size() ) ;
3680 while( !iter.pastEnd() ) {
3681 vector< vector<Float> > specout( freqgrp.size() ) ;
3682 vector< vector<uChar> > flagout( freqgrp.size() ) ;
3683 ArrayColumn<Float> specCols ;
3684 specCols.attach( iter.table(), "SPECTRA" ) ;
3685 ArrayColumn<uChar> flagCols ;
3686 flagCols.attach( iter.table(), "FLAGTRA" ) ;
3687 ifnoCol.attach( iter.table(), "IFNO" ) ;
3688 ScalarColumn<uInt> polnos ;
3689 polnos.attach( iter.table(), "POLNO" ) ;
3690// MDirection::ScalarColumn dircol ;
3691// dircol.attach( iter.table(), "DIRECTION" ) ;
3692 uInt polno = polnos( 0 ) ;
3693 //os << "POLNO iteration: " << polno << LogIO::POST ;
3694// for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3695// sizes[igrp].resize( freqgrp[igrp].size() ) ;
3696// for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3697// for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3698// uInt ifno = ifnoCol( irow ) ;
3699// if ( ifno == freqgrp[igrp][imem] ) {
3700// Vector<Float> spec = specCols( irow ) ;
3701// Vector<uChar> flag = flagCols( irow ) ;
3702// vector<Float> svec ;
3703// spec.tovector( svec ) ;
3704// vector<uChar> fvec ;
3705// flag.tovector( fvec ) ;
3706// //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3707// specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3708// flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3709// //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3710// sizes[igrp][imem] = spec.nelements() ;
3711// }
3712// }
3713// }
3714// for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3715// uInt ifout = ifnoColOut( irow ) ;
3716// uInt polout = polnoColOut( irow ) ;
3717// if ( ifout == gmemid[igrp] && polout == polno ) {
3718// // set SPECTRA and FRAGTRA
3719// Vector<Float> newspec( specout[igrp] ) ;
3720// Vector<uChar> newflag( flagout[igrp] ) ;
3721// specColOut.put( irow, newspec ) ;
3722// flagColOut.put( irow, newflag ) ;
3723// // IFNO renumbering
3724// ifnoColOut.put( irow, igrp ) ;
3725// }
3726// }
3727// }
3728 // get a list of number of channels for each frequency group member
3729 if ( !done ) {
3730 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3731 sizes[igrp].resize( freqgrp[igrp].size() ) ;
3732 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3733 for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3734 uInt ifno = ifnoCol( irow ) ;
3735 if ( ifno == freqgrp[igrp][imem] ) {
3736 Vector<Float> spec = specCols( irow ) ;
3737 sizes[igrp][imem] = spec.nelements() ;
3738 break ;
3739 }
3740 }
3741 }
3742 }
3743 done = true ;
3744 }
3745 // combine spectra
3746 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3747 uInt polout = polnoColOut( irow ) ;
3748 if ( polout == polno ) {
3749 uInt ifout = ifnoColOut( irow ) ;
3750// Vector<Double> direction = dirColOut(irow).getAngle(Unit(String("rad"))).getValue() ;
3751 uInt igrp ;
3752 for ( uInt jgrp = 0 ; jgrp < freqgrp.size() ; jgrp++ ) {
3753 if ( ifout == gmemid[jgrp] ) {
3754 igrp = jgrp ;
3755 break ;
3756 }
3757 }
3758 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3759 for ( uInt jrow = 0 ; jrow < iter.table().nrow() ; jrow++ ) {
3760 uInt ifno = ifnoCol( jrow ) ;
3761 // 2012/02/17 TN
3762 // Since STGrid is implemented, average doesn't consider direction
3763 // when accumulating
3764// Vector<Double> tdir = dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
3765// //if ( ifno == freqgrp[igrp][imem] && allTrue( tdir == direction ) ) {
3766// Double dx = tdir[0] - direction[0] ;
3767// Double dy = tdir[1] - direction[1] ;
3768// Double dd = sqrt( dx * dx + dy * dy ) ;
3769 //if ( ifno == freqgrp[igrp][imem] && allNearAbs( tdir, direction, tol ) ) {
3770// if ( ifno == freqgrp[igrp][imem] && dd <= tol ) {
3771 if ( ifno == freqgrp[igrp][imem] ) {
3772 Vector<Float> spec = specCols( jrow ) ;
3773 Vector<uChar> flag = flagCols( jrow ) ;
3774 vector<Float> svec ;
3775 spec.tovector( svec ) ;
3776 vector<uChar> fvec ;
3777 flag.tovector( fvec ) ;
3778 //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3779 specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3780 flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3781 //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3782 }
3783 }
3784 }
3785 // set SPECTRA and FRAGTRA
3786 Vector<Float> newspec( specout[igrp] ) ;
3787 Vector<uChar> newflag( flagout[igrp] ) ;
3788 specColOut.put( irow, newspec ) ;
3789 flagColOut.put( irow, newflag ) ;
3790 // IFNO renumbering
3791 ifnoColOut.put( irow, igrp ) ;
3792 }
3793 }
3794 iter++ ;
3795 }
3796 // update FREQUENCIES subtable
3797 vector<bool> updated( freqgrp.size(), false ) ;
3798 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3799 uInt index = 0 ;
3800 uInt pixShift = 0 ;
3801 while ( freqgrp[igrp][index] != gmemid[igrp] ) {
3802 pixShift += sizes[igrp][index++] ;
3803 }
3804 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3805 if ( ifnoColOut( irow ) == gmemid[igrp] && !updated[igrp] ) {
3806 uInt freqidOut = freqidColOut( irow ) ;
3807 //os << "freqgrp " << igrp << " freqidOut = " << freqidOut << LogIO::POST ;
3808 double refpix ;
3809 double refval ;
3810 double increm ;
3811 out->frequencies().getEntry( refpix, refval, increm, freqidOut ) ;
3812 refpix += pixShift ;
3813 out->frequencies().setEntry( refpix, refval, increm, freqidOut ) ;
3814 updated[igrp] = true ;
3815 }
3816 }
3817 }
3818
3819 //out = tmpout ;
3820
3821 coordinfo = tmpout->getCoordInfo() ;
3822 coordinfo[0] = oldinfo[0] ;
3823 tmpout->setCoordInfo( coordinfo ) ;
3824 }
3825 else {
3826 // simple average
3827 out = average( in, mask, weight, avmode ) ;
3828 }
3829
3830 return out;
3831}
3832
3833CountedPtr<Scantable> STMath::cwcal( const CountedPtr<Scantable>& s,
3834 const String calmode,
3835 const String antname )
3836{
3837 // frequency switch
3838 if ( calmode == "fs" ) {
3839 return cwcalfs( s, antname ) ;
3840 }
3841 else {
3842 vector<bool> masks = s->getMask( 0 ) ;
3843 vector<int> types ;
3844
3845 // save original table selection
3846 Table torg = s->table_ ;
3847
3848 // sky scan
3849 bool insitu = insitu_ ;
3850 insitu_ = false ;
3851 // share calibration scans before average with out
3852 CountedPtr<Scantable> out = getScantable( s, true ) ;
3853 insitu_ = insitu ;
3854 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::SKY ) ;
3855 out->attach() ;
3856 CountedPtr<Scantable> asky = averageWithinSession( out,
3857 masks,
3858 "TINT" ) ;
3859 // hot scan
3860 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::HOT ) ;
3861 out->attach() ;
3862 CountedPtr<Scantable> ahot = averageWithinSession( out,
3863 masks,
3864 "TINT" ) ;
3865 // cold scan
3866 CountedPtr<Scantable> acold ;
3867// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::COLD ) ;
3868// out->attach() ;
3869// CountedPtr<Scantable> acold = averageWithinSession( out,
3870// masks,
3871// "TINT" ) ;
3872
3873 // off scan
3874 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3875 out->attach() ;
3876 CountedPtr<Scantable> aoff = averageWithinSession( out,
3877 masks,
3878 "TINT" ) ;
3879
3880 // on scan
3881 s->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3882 s->attach() ;
3883 out->table_ = out->originalTable_ ;
3884 out->attach() ;
3885 out->table().addRow( s->nrow() ) ;
3886 copyRows( out->table(), s->table(), 0, 0, s->nrow(), False, True, False ) ;
3887
3888 // process each on scan
3889 STSelector sel ;
3890 vector<string> cols( 3 ) ;
3891 cols[0] = "BEAMNO" ;
3892 cols[1] = "POLNO" ;
3893 cols[2] = "IFNO" ;
3894 STIdxIter *iter = new STIdxIterAcc( out, cols ) ;
3895 while ( !iter->pastEnd() ) {
3896 Vector<uInt> ids = iter->current() ;
3897 stringstream ss ;
3898 ss << "SELECT FROM $1 WHERE "
3899 << "BEAMNO==" << ids[0] << "&&"
3900 << "POLNO==" << ids[1] << "&&"
3901 << "IFNO==" << ids[2] ;
3902 //cout << "TaQL string: " << ss.str() << endl ;
3903 sel.setTaQL( ss.str() ) ;
3904 aoff->setSelection( sel ) ;
3905 ahot->setSelection( sel ) ;
3906 asky->setSelection( sel ) ;
3907 Vector<uInt> rows = iter->getRows( SHARE ) ;
3908 // out should be an exact copy of s except that SPECTRA column is empty
3909 calibrateCW( out, s, aoff, asky, ahot, acold, rows, antname ) ;
3910 aoff->unsetSelection() ;
3911 ahot->unsetSelection() ;
3912 asky->unsetSelection() ;
3913 sel.reset() ;
3914 iter->next() ;
3915 }
3916 delete iter ;
3917 s->table_ = torg ;
3918 s->attach() ;
3919
3920 // flux unit
3921 out->setFluxUnit( "K" ) ;
3922
3923 return out ;
3924 }
3925}
3926
3927CountedPtr<Scantable> STMath::almacal( const CountedPtr<Scantable>& s,
3928 const String calmode )
3929{
3930 // frequency switch
3931 if ( calmode == "fs" ) {
3932 return almacalfs( s ) ;
3933 }
3934 else {
3935// double t0, t1 ;
3936// t0 = mathutil::gettimeofday_sec() ;
3937 vector<bool> masks = s->getMask( 0 ) ;
3938
3939 // save original table selection
3940 Table torg = s->table_ ;
3941
3942 // off scan
3943 // TODO 2010/01/08 TN
3944 // Grouping by time should be needed before averaging.
3945 // Each group must have own unique SCANNO (should be renumbered).
3946 // See PIPELINE/SDCalibration.py
3947 bool insitu = insitu_ ;
3948 insitu_ = false ;
3949 // share off scan before average with out
3950 CountedPtr<Scantable> out = getScantable( s, true ) ;
3951 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3952 out->attach() ;
3953 insitu_ = insitu ;
3954 CountedPtr<Scantable> aoff = averageWithinSession( out,
3955 masks,
3956 "TINT" ) ;
3957
3958 // on scan
3959// t0 = mathutil::gettimeofday_sec() ;
3960 s->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3961 s->attach() ;
3962 out->table_ = out->originalTable_ ;
3963 out->attach() ;
3964 out->table().addRow( s->nrow() ) ;
3965 copyRows( out->table(), s->table(), 0, 0, s->nrow(), False ) ;
3966// t1 = mathutil::gettimeofday_sec() ;
3967// cout << "elapsed time for preparing output table: " << t1-t0 << " sec" << endl ;
3968
3969 // process each on scan
3970// t0 = mathutil::gettimeofday_sec() ;
3971
3972 // using STIdxIterAcc
3973 vector<string> cols( 3 ) ;
3974 cols[0] = "BEAMNO" ;
3975 cols[1] = "POLNO" ;
3976 cols[2] = "IFNO" ;
3977 STIdxIter *iter = new STIdxIterAcc( out, cols ) ;
3978 STSelector sel ;
3979 while ( !iter->pastEnd() ) {
3980 Vector<uInt> ids = iter->current() ;
3981 stringstream ss ;
3982 ss << "SELECT FROM $1 WHERE "
3983 << "BEAMNO==" << ids[0] << "&&"
3984 << "POLNO==" << ids[1] << "&&"
3985 << "IFNO==" << ids[2] ;
3986 //cout << "TaQL string: " << ss.str() << endl ;
3987 sel.setTaQL( ss.str() ) ;
3988 aoff->setSelection( sel ) ;
3989 Vector<uInt> rows = iter->getRows( SHARE ) ;
3990 // out should be an exact copy of s except that SPECTRA column is empty
3991 calibrateALMA( out, s, aoff, rows ) ;
3992 aoff->unsetSelection() ;
3993 sel.reset() ;
3994 iter->next() ;
3995 }
3996 delete iter ;
3997 s->table_ = torg ;
3998 s->attach() ;
3999
4000// t1 = mathutil::gettimeofday_sec() ;
4001// cout << "elapsed time for calibration: " << t1-t0 << " sec" << endl ;
4002
4003 // flux unit
4004 out->setFluxUnit( "K" ) ;
4005
4006 return out ;
4007 }
4008}
4009
4010CountedPtr<Scantable> STMath::cwcalfs( const CountedPtr<Scantable>& s,
4011 const String antname )
4012{
4013 vector<int> types ;
4014
4015 // APEX calibration mode
4016 int apexcalmode = 1 ;
4017
4018 if ( antname.find( "APEX" ) != string::npos ) {
4019 // check if off scan exists or not
4020 STSelector sel = STSelector() ;
4021 //sel.setName( offstr1 ) ;
4022 types.push_back( SrcType::FLOOFF ) ;
4023 sel.setTypes( types ) ;
4024 try {
4025 s->setSelection( sel ) ;
4026 }
4027 catch ( AipsError &e ) {
4028 apexcalmode = 0 ;
4029 }
4030 sel.reset() ;
4031 }
4032 s->unsetSelection() ;
4033 types.clear() ;
4034
4035 vector<bool> masks = s->getMask( 0 ) ;
4036 CountedPtr<Scantable> ssig, sref ;
4037 //CountedPtr<Scantable> out ;
4038 bool insitu = insitu_ ;
4039 insitu_ = False ;
4040 CountedPtr<Scantable> out = getScantable( s, true ) ;
4041 insitu_ = insitu ;
4042
4043 if ( antname.find( "APEX" ) != string::npos ) {
4044 // APEX calibration
4045 // sky scan
4046 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOSKY ) ;
4047 out->attach() ;
4048 CountedPtr<Scantable> askylo = averageWithinSession( out,
4049 masks,
4050 "TINT" ) ;
4051 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHISKY ) ;
4052 out->attach() ;
4053 CountedPtr<Scantable> askyhi = averageWithinSession( out,
4054 masks,
4055 "TINT" ) ;
4056
4057 // hot scan
4058 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOHOT ) ;
4059 out->attach() ;
4060 CountedPtr<Scantable> ahotlo = averageWithinSession( out,
4061 masks,
4062 "TINT" ) ;
4063 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHIHOT ) ;
4064 out->attach() ;
4065 CountedPtr<Scantable> ahothi = averageWithinSession( out,
4066 masks,
4067 "TINT" ) ;
4068
4069 // cold scan
4070 CountedPtr<Scantable> acoldlo, acoldhi ;
4071// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOCOLD ) ;
4072// out->attach() ;
4073// CountedPtr<Scantable> acoldlo = averageWithinSession( out,
4074// masks,
4075// "TINT" ) ;
4076// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHICOLD ) ;
4077// out->attach() ;
4078// CountedPtr<Scantable> acoldhi = averageWithinSession( out,
4079// masks,
4080// "TINT" ) ;
4081
4082 // ref scan
4083 insitu_ = false ;
4084 sref = getScantable( s, true ) ;
4085 CountedPtr<Scantable> rref = getScantable( s, true ) ;
4086 insitu_ = insitu ;
4087 rref->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FSLO ) ;
4088 rref->attach() ;
4089 copyRows( sref->table_, rref->table_, 0, 0, rref->nrow(), False, True, False ) ;
4090
4091 // sig scan
4092 insitu_ = false ;
4093 ssig = getScantable( s, true ) ;
4094 CountedPtr<Scantable> rsig = getScantable( s, true ) ;
4095 insitu_ = insitu ;
4096 rsig->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FSHI ) ;
4097 rsig->attach() ;
4098 copyRows( ssig->table_, rsig->table_, 0, 0, rsig->nrow(), False, True, False ) ;
4099
4100 if ( apexcalmode == 0 ) {
4101 // using STIdxIterAcc
4102 vector<string> cols( 3 ) ;
4103 cols[0] = "BEAMNO" ;
4104 cols[1] = "POLNO" ;
4105 cols[2] = "IFNO" ;
4106 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
4107 STSelector sel ;
4108 vector< CountedPtr<Scantable> > on( 2 ) ;
4109 on[0] = rsig ;
4110 on[1] = rref ;
4111 vector< CountedPtr<Scantable> > sky( 2 ) ;
4112 sky[0] = askylo ;
4113 sky[1] = askyhi ;
4114 vector< CountedPtr<Scantable> > hot( 2 ) ;
4115 hot[0] = ahotlo ;
4116 hot[1] = ahothi ;
4117 vector< CountedPtr<Scantable> > cold( 2 ) ;
4118 while ( !iter->pastEnd() ) {
4119 Vector<uInt> ids = iter->current() ;
4120 stringstream ss ;
4121 ss << "SELECT FROM $1 WHERE "
4122 << "BEAMNO==" << ids[0] << "&&"
4123 << "POLNO==" << ids[1] << "&&"
4124 << "IFNO==" << ids[2] ;
4125 //cout << "TaQL string: " << ss.str() << endl ;
4126 sel.setTaQL( ss.str() ) ;
4127 sky[0]->setSelection( sel ) ;
4128 sky[1]->setSelection( sel ) ;
4129 hot[0]->setSelection( sel ) ;
4130 hot[1]->setSelection( sel ) ;
4131 Vector<uInt> rows = iter->getRows( SHARE ) ;
4132 calibrateAPEXFS( ssig, sref, on, sky, hot, cold, rows ) ;
4133 sky[0]->unsetSelection() ;
4134 sky[1]->unsetSelection() ;
4135 hot[0]->unsetSelection() ;
4136 hot[1]->unsetSelection() ;
4137 sel.reset() ;
4138 iter->next() ;
4139 }
4140 delete iter ;
4141
4142 }
4143 else if ( apexcalmode == 1 ) {
4144 // APEX fs data with off scan
4145 // off scan
4146 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOOFF ) ;
4147 out->attach() ;
4148 CountedPtr<Scantable> aofflo = averageWithinSession( out,
4149 masks,
4150 "TINT" ) ;
4151 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHIOFF ) ;
4152 out->attach() ;
4153 CountedPtr<Scantable> aoffhi = averageWithinSession( out,
4154 masks,
4155 "TINT" ) ;
4156
4157 // process each sig and ref scan
4158// STSelector sel ;
4159 vector<string> cols( 3 ) ;
4160 cols[0] = "BEAMNO" ;
4161 cols[1] = "POLNO" ;
4162 cols[2] = "IFNO" ;
4163 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
4164 STSelector sel ;
4165 while ( !iter->pastEnd() ) {
4166 Vector<uInt> ids = iter->current() ;
4167 stringstream ss ;
4168 ss << "SELECT FROM $1 WHERE "
4169 << "BEAMNO==" << ids[0] << "&&"
4170 << "POLNO==" << ids[1] << "&&"
4171 << "IFNO==" << ids[2] ;
4172 //cout << "TaQL string: " << ss.str() << endl ;
4173 sel.setTaQL( ss.str() ) ;
4174 aofflo->setSelection( sel ) ;
4175 ahotlo->setSelection( sel ) ;
4176 askylo->setSelection( sel ) ;
4177 Vector<uInt> rows = iter->getRows( SHARE ) ;
4178 calibrateCW( ssig, rsig, aofflo, askylo, ahotlo, acoldlo, rows, antname ) ;
4179 aofflo->unsetSelection() ;
4180 ahotlo->unsetSelection() ;
4181 askylo->unsetSelection() ;
4182 sel.reset() ;
4183 iter->next() ;
4184 }
4185 delete iter ;
4186 iter = new STIdxIterAcc( sref, cols ) ;
4187 while ( !iter->pastEnd() ) {
4188 Vector<uInt> ids = iter->current() ;
4189 stringstream ss ;
4190 ss << "SELECT FROM $1 WHERE "
4191 << "BEAMNO==" << ids[0] << "&&"
4192 << "POLNO==" << ids[1] << "&&"
4193 << "IFNO==" << ids[2] ;
4194 //cout << "TaQL string: " << ss.str() << endl ;
4195 sel.setTaQL( ss.str() ) ;
4196 aoffhi->setSelection( sel ) ;
4197 ahothi->setSelection( sel ) ;
4198 askyhi->setSelection( sel ) ;
4199 Vector<uInt> rows = iter->getRows( SHARE ) ;
4200 calibrateCW( sref, rref, aoffhi, askyhi, ahothi, acoldhi, rows, antname ) ;
4201 aoffhi->unsetSelection() ;
4202 ahothi->unsetSelection() ;
4203 askyhi->unsetSelection() ;
4204 sel.reset() ;
4205 iter->next() ;
4206 }
4207 delete iter ;
4208 }
4209 }
4210 else {
4211 // non-APEX fs data
4212 // sky scan
4213 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::SKY ) ;
4214 out->attach() ;
4215 CountedPtr<Scantable> asky = averageWithinSession( out,
4216 masks,
4217 "TINT" ) ;
4218 STSelector sel = STSelector() ;
4219
4220 // hot scan
4221 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::HOT ) ;
4222 out->attach() ;
4223 CountedPtr<Scantable> ahot = averageWithinSession( out,
4224 masks,
4225 "TINT" ) ;
4226
4227 // cold scan
4228 CountedPtr<Scantable> acold ;
4229// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::COLD ) ;
4230// out->attach() ;
4231// CountedPtr<Scantable> acold = averageWithinSession( out,
4232// masks,
4233// "TINT" ) ;
4234
4235 // ref scan
4236 bool insitu = insitu_ ;
4237 insitu_ = false ;
4238 sref = getScantable( s, true ) ;
4239 CountedPtr<Scantable> rref = getScantable( s, true ) ;
4240 insitu_ = insitu ;
4241 rref->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
4242 rref->attach() ;
4243 copyRows( sref->table_, rref->table_, 0, 0, rref->nrow(), False, True, False ) ;
4244
4245 // sig scan
4246 insitu_ = false ;
4247 ssig = getScantable( s, true ) ;
4248 CountedPtr<Scantable> rsig = getScantable( s, true ) ;
4249 insitu_ = insitu ;
4250 rsig->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
4251 rsig->attach() ;
4252 copyRows( ssig->table_, rsig->table_, 0, 0, rsig->nrow(), False, True, False ) ;
4253
4254 // process each sig and ref scan
4255 vector<string> cols( 3 ) ;
4256 cols[0] = "BEAMNO" ;
4257 cols[1] = "POLNO" ;
4258 cols[2] = "IFNO" ;
4259 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
4260 while ( !iter->pastEnd() ) {
4261 Vector<uInt> ids = iter->current() ;
4262 stringstream ss ;
4263 ss << "SELECT FROM $1 WHERE "
4264 << "BEAMNO==" << ids[0] << "&&"
4265 << "POLNO==" << ids[1] << "&&"
4266 << "IFNO==" << ids[2] ;
4267 //cout << "TaQL string: " << ss.str() << endl ;
4268 sel.setTaQL( ss.str() ) ;
4269 ahot->setSelection( sel ) ;
4270 asky->setSelection( sel ) ;
4271 Vector<uInt> rows = iter->getRows( SHARE ) ;
4272 // out should be an exact copy of s except that SPECTRA column is empty
4273 calibrateFS( ssig, sref, rsig, rref, asky, ahot, acold, rows ) ;
4274 ahot->unsetSelection() ;
4275 asky->unsetSelection() ;
4276 sel.reset() ;
4277 iter->next() ;
4278 }
4279 delete iter ;
4280 }
4281
4282 // do folding if necessary
4283 Table sigtab = ssig->table() ;
4284 Table reftab = sref->table() ;
4285 ScalarColumn<uInt> reffidCol ;
4286 Int nchan = (Int)ssig->nchan() ;
4287 reffidCol.attach( reftab, "FREQ_ID" ) ;
4288 Vector<uInt> sfids = ssig->mfreqidCol_.getColumn() ;
4289 Vector<uInt> rfids = sref->mfreqidCol_.getColumn() ;
4290 vector<uInt> sfids_unique ;
4291 vector<uInt> rfids_unique ;
4292 vector<uInt> sifno_unique ;
4293 vector<uInt> rifno_unique ;
4294 for ( uInt i = 0 ; i < sfids.nelements() ; i++ ) {
4295 if ( count( sfids_unique.begin(), sfids_unique.end(), sfids[i] ) == 0 ) {
4296 sfids_unique.push_back( sfids[i] ) ;
4297 sifno_unique.push_back( ssig->getIF( i ) ) ;
4298 }
4299 if ( count( rfids_unique.begin(), rfids_unique.end(), rfids[i] ) == 0 ) {
4300 rfids_unique.push_back( rfids[i] ) ;
4301 rifno_unique.push_back( sref->getIF( i ) ) ;
4302 }
4303 }
4304 double refpix_sig, refval_sig, increment_sig ;
4305 double refpix_ref, refval_ref, increment_ref ;
4306 vector< CountedPtr<Scantable> > tmp( sfids_unique.size() ) ;
4307 for ( uInt i = 0 ; i < sfids_unique.size() ; i++ ) {
4308 ssig->frequencies().getEntry( refpix_sig, refval_sig, increment_sig, sfids_unique[i] ) ;
4309 sref->frequencies().getEntry( refpix_ref, refval_ref, increment_ref, rfids_unique[i] ) ;
4310 if ( refpix_sig == refpix_ref ) {
4311 double foffset = refval_ref - refval_sig ;
4312 int choffset = static_cast<int>(foffset/increment_sig) ;
4313 double doffset = foffset / increment_sig ;
4314 if ( abs(choffset) >= nchan ) {
4315 LogIO os( LogOrigin( "STMath", "cwcalfs", WHERE ) ) ;
4316 os << "FREQ_ID=[" << sfids_unique[i] << "," << rfids_unique[i] << "]: out-band frequency switching, no folding" << LogIO::POST ;
4317 os << "Just return signal data" << LogIO::POST ;
4318 //std::vector< CountedPtr<Scantable> > tabs ;
4319 //tabs.push_back( ssig ) ;
4320 //tabs.push_back( sref ) ;
4321 //out = merge( tabs ) ;
4322 tmp[i] = ssig ;
4323 }
4324 else {
4325 STSelector sel = STSelector() ;
4326 vector<int> v( 1, sifno_unique[i] ) ;
4327 sel.setIFs( v ) ;
4328 ssig->setSelection( sel ) ;
4329 sel.reset() ;
4330 v[0] = rifno_unique[i] ;
4331 sel.setIFs( v ) ;
4332 sref->setSelection( sel ) ;
4333 sel.reset() ;
4334 if ( antname.find( "APEX" ) != string::npos ) {
4335 tmp[i] = dofold( ssig, sref, 0.5*doffset, -0.5*doffset ) ;
4336 //tmp[i] = dofold( ssig, sref, doffset ) ;
4337 }
4338 else {
4339 tmp[i] = dofold( ssig, sref, doffset ) ;
4340 }
4341 ssig->unsetSelection() ;
4342 sref->unsetSelection() ;
4343 }
4344 }
4345 }
4346
4347 if ( tmp.size() > 1 ) {
4348 out = merge( tmp ) ;
4349 }
4350 else {
4351 out = tmp[0] ;
4352 }
4353
4354 // flux unit
4355 out->setFluxUnit( "K" ) ;
4356
4357 return out ;
4358}
4359
4360CountedPtr<Scantable> STMath::almacalfs( const CountedPtr<Scantable>& s )
4361{
4362 (void) s; //currently unused
4363 CountedPtr<Scantable> out ;
4364
4365 return out ;
4366}
4367
4368Vector<Float> STMath::getSpectrumFromTime( double reftime,
4369 const Vector<Double> &timeVec,
4370 const vector<int> &idx,
4371 const Matrix<Float>& spectra,
4372 string mode )
4373{
4374 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
4375 Vector<Float> sp ;
4376 uInt ncol = spectra.ncolumn() ;
4377
4378 if ( ncol == 0 ) {
4379 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
4380 return sp ;
4381 }
4382 else if ( ncol == 1 ) {
4383 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
4384 sp.reference( spectra.column( 0 ) ) ;
4385 return sp ;
4386 }
4387 else {
4388 if ( mode == "before" ) {
4389 int id = -1 ;
4390 if ( idx[0] != -1 ) {
4391 id = idx[0] ;
4392 }
4393 else if ( idx[1] != -1 ) {
4394 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4395 id = idx[1] ;
4396 }
4397 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4398 sp.reference( spectra.column( id ) ) ;
4399 }
4400 else if ( mode == "after" ) {
4401 int id = -1 ;
4402 if ( idx[1] != -1 ) {
4403 id = idx[1] ;
4404 }
4405 else if ( idx[0] != -1 ) {
4406 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4407 id = idx[1] ;
4408 }
4409 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4410 sp.reference( spectra.column( id ) ) ;
4411 }
4412 else if ( mode == "nearest" ) {
4413 int id = -1 ;
4414 if ( idx[0] == -1 ) {
4415 id = idx[1] ;
4416 }
4417 else if ( idx[1] == -1 ) {
4418 id = idx[0] ;
4419 }
4420 else if ( idx[0] == idx[1] ) {
4421 id = idx[0] ;
4422 }
4423 else {
4424 double t0 = timeVec[idx[0]] ;
4425 double t1 = timeVec[idx[1]] ;
4426 double tref = reftime ;
4427 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4428 id = idx[1] ;
4429 }
4430 else {
4431 id = idx[0] ;
4432 }
4433 }
4434 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4435 sp.reference( spectra.column( id ) ) ;
4436 }
4437 else if ( mode == "linear" ) {
4438 if ( idx[0] == -1 ) {
4439 // use after
4440 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4441 int id = idx[1] ;
4442 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4443 sp.reference( spectra.column( id ) ) ;
4444 }
4445 else if ( idx[1] == -1 ) {
4446 // use before
4447 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4448 int id = idx[0] ;
4449 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4450 sp.reference( spectra.column( id ) ) ;
4451 }
4452 else if ( idx[0] == idx[1] ) {
4453 // use before
4454 //os << "No need to interporate." << LogIO::POST ;
4455 int id = idx[0] ;
4456 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4457 sp.reference( spectra.column( id ) ) ;
4458 }
4459 else {
4460 // do interpolation
4461 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4462 double t0 = timeVec[idx[0]] ;
4463 double t1 = timeVec[idx[1]] ;
4464 double tref = reftime ;
4465 sp = spectra.column( idx[0] ).copy() ;
4466 Vector<Float> sp1( spectra.column( idx[1] ) ) ;
4467 double tfactor = ( tref - t0 ) / ( t1 - t0 ) ;
4468 for ( unsigned int i = 0 ; i < sp.size() ; i++ ) {
4469 sp[i] = ( sp1[i] - sp[i] ) * tfactor + sp[i] ;
4470 }
4471 }
4472 }
4473 else {
4474 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4475 }
4476 return sp ;
4477 }
4478}
4479
4480vector<int> STMath::getRowIdFromTime( double reftime, const Vector<Double> &t )
4481{
4482// double reft = reftime ;
4483 double dtmin = 1.0e100 ;
4484 double dtmax = -1.0e100 ;
4485// vector<double> dt ;
4486 int just_before = -1 ;
4487 int just_after = -1 ;
4488 Vector<Double> dt = t - reftime ;
4489 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4490 if ( dt[i] > 0.0 ) {
4491 // after reftime
4492 if ( dt[i] < dtmin ) {
4493 just_after = i ;
4494 dtmin = dt[i] ;
4495 }
4496 }
4497 else if ( dt[i] < 0.0 ) {
4498 // before reftime
4499 if ( dt[i] > dtmax ) {
4500 just_before = i ;
4501 dtmax = dt[i] ;
4502 }
4503 }
4504 else {
4505 // just a reftime
4506 just_before = i ;
4507 just_after = i ;
4508 dtmax = 0 ;
4509 dtmin = 0 ;
4510 break ;
4511 }
4512 }
4513
4514 vector<int> v(2) ;
4515 v[0] = just_before ;
4516 v[1] = just_after ;
4517
4518 return v ;
4519}
4520
4521Vector<Float> STMath::getTcalFromTime( double reftime,
4522 const Vector<Double> &timeVec,
4523 const vector<int> &idx,
4524 const CountedPtr<Scantable>& s,
4525 string mode )
4526{
4527 LogIO os( LogOrigin( "STMath", "getTcalFromTime", WHERE ) ) ;
4528 STTcal tcalTable = s->tcal() ;
4529 String time ;
4530 Vector<Float> tcalval ;
4531 if ( s->nrow() == 0 ) {
4532 os << LogIO::SEVERE << "No row in the input scantable. Return empty tcal." << LogIO::POST ;
4533 return tcalval ;
4534 }
4535 else if ( s->nrow() == 1 ) {
4536 uInt tcalid = s->getTcalId( 0 ) ;
4537 //os << "use row " << 0 << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4538 tcalTable.getEntry( time, tcalval, tcalid ) ;
4539 return tcalval ;
4540 }
4541 else {
4542 if ( mode == "before" ) {
4543 int id = -1 ;
4544 if ( idx[0] != -1 ) {
4545 id = idx[0] ;
4546 }
4547 else if ( idx[1] != -1 ) {
4548 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4549 id = idx[1] ;
4550 }
4551 uInt tcalid = s->getTcalId( id ) ;
4552 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4553 tcalTable.getEntry( time, tcalval, tcalid ) ;
4554 }
4555 else if ( mode == "after" ) {
4556 int id = -1 ;
4557 if ( idx[1] != -1 ) {
4558 id = idx[1] ;
4559 }
4560 else if ( idx[0] != -1 ) {
4561 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4562 id = idx[1] ;
4563 }
4564 uInt tcalid = s->getTcalId( id ) ;
4565 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4566 tcalTable.getEntry( time, tcalval, tcalid ) ;
4567 }
4568 else if ( mode == "nearest" ) {
4569 int id = -1 ;
4570 if ( idx[0] == -1 ) {
4571 id = idx[1] ;
4572 }
4573 else if ( idx[1] == -1 ) {
4574 id = idx[0] ;
4575 }
4576 else if ( idx[0] == idx[1] ) {
4577 id = idx[0] ;
4578 }
4579 else {
4580 double t0 = timeVec[idx[0]] ;
4581 double t1 = timeVec[idx[1]] ;
4582 if ( abs( t0 - reftime ) > abs( t1 - reftime ) ) {
4583 id = idx[1] ;
4584 }
4585 else {
4586 id = idx[0] ;
4587 }
4588 }
4589 uInt tcalid = s->getTcalId( id ) ;
4590 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4591 tcalTable.getEntry( time, tcalval, tcalid ) ;
4592 }
4593 else if ( mode == "linear" ) {
4594 if ( idx[0] == -1 ) {
4595 // use after
4596 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4597 int id = idx[1] ;
4598 uInt tcalid = s->getTcalId( id ) ;
4599 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4600 tcalTable.getEntry( time, tcalval, tcalid ) ;
4601 }
4602 else if ( idx[1] == -1 ) {
4603 // use before
4604 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4605 int id = idx[0] ;
4606 uInt tcalid = s->getTcalId( id ) ;
4607 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4608 tcalTable.getEntry( time, tcalval, tcalid ) ;
4609 }
4610 else if ( idx[0] == idx[1] ) {
4611 // use before
4612 //os << "No need to interporate." << LogIO::POST ;
4613 int id = idx[0] ;
4614 uInt tcalid = s->getTcalId( id ) ;
4615 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4616 tcalTable.getEntry( time, tcalval, tcalid ) ;
4617 }
4618 else {
4619 // do interpolation
4620 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4621 double t0 = timeVec[idx[0]] ;
4622 double t1 = timeVec[idx[1]] ;
4623 Vector<Float> tcal0 ;
4624 uInt tcalid0 = s->getTcalId( idx[0] ) ;
4625 uInt tcalid1 = s->getTcalId( idx[1] ) ;
4626 tcalTable.getEntry( time, tcal0, tcalid0 ) ;
4627 tcalTable.getEntry( time, tcalval, tcalid1 ) ;
4628 double tfactor = (reftime - t0) / (t1 - t0) ;
4629 for ( unsigned int i = 0 ; i < tcal0.size() ; i++ ) {
4630 tcalval[i] = ( tcalval[i] - tcal0[i] ) * tfactor + tcal0[i] ;
4631 }
4632 }
4633 }
4634 else {
4635 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4636 }
4637 return tcalval ;
4638 }
4639}
4640
4641Vector<Float> STMath::getTsysFromTime( double reftime,
4642 const Vector<Double> &timeVec,
4643 const vector<int> &idx,
4644 const CountedPtr<Scantable> &s,
4645 string mode )
4646{
4647 LogIO os( LogOrigin( "STMath", "getTsysFromTime", WHERE ) ) ;
4648 ArrayColumn<Float> tsysCol ;
4649 tsysCol.attach( s->table(), "TSYS" ) ;
4650 Vector<Float> tsysval ;
4651 if ( s->nrow() == 0 ) {
4652 os << LogIO::SEVERE << "No row in the input scantable. Return empty tsys." << LogIO::POST ;
4653 return tsysval ;
4654 }
4655 else if ( s->nrow() == 1 ) {
4656 //os << "use row " << 0 << LogIO::POST ;
4657 tsysval = tsysCol( 0 ) ;
4658 return tsysval ;
4659 }
4660 else {
4661 if ( mode == "before" ) {
4662 int id = -1 ;
4663 if ( idx[0] != -1 ) {
4664 id = idx[0] ;
4665 }
4666 else if ( idx[1] != -1 ) {
4667 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4668 id = idx[1] ;
4669 }
4670 //os << "use row " << id << LogIO::POST ;
4671 tsysval = tsysCol( id ) ;
4672 }
4673 else if ( mode == "after" ) {
4674 int id = -1 ;
4675 if ( idx[1] != -1 ) {
4676 id = idx[1] ;
4677 }
4678 else if ( idx[0] != -1 ) {
4679 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4680 id = idx[1] ;
4681 }
4682 //os << "use row " << id << LogIO::POST ;
4683 tsysval = tsysCol( id ) ;
4684 }
4685 else if ( mode == "nearest" ) {
4686 int id = -1 ;
4687 if ( idx[0] == -1 ) {
4688 id = idx[1] ;
4689 }
4690 else if ( idx[1] == -1 ) {
4691 id = idx[0] ;
4692 }
4693 else if ( idx[0] == idx[1] ) {
4694 id = idx[0] ;
4695 }
4696 else {
4697 double t0 = timeVec[idx[0]] ;
4698 double t1 = timeVec[idx[1]] ;
4699 if ( abs( t0 - reftime ) > abs( t1 - reftime ) ) {
4700 id = idx[1] ;
4701 }
4702 else {
4703 id = idx[0] ;
4704 }
4705 }
4706 //os << "use row " << id << LogIO::POST ;
4707 tsysval = tsysCol( id ) ;
4708 }
4709 else if ( mode == "linear" ) {
4710 if ( idx[0] == -1 ) {
4711 // use after
4712 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4713 int id = idx[1] ;
4714 //os << "use row " << id << LogIO::POST ;
4715 tsysval = tsysCol( id ) ;
4716 }
4717 else if ( idx[1] == -1 ) {
4718 // use before
4719 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4720 int id = idx[0] ;
4721 //os << "use row " << id << LogIO::POST ;
4722 tsysval = tsysCol( id ) ;
4723 }
4724 else if ( idx[0] == idx[1] ) {
4725 // use before
4726 //os << "No need to interporate." << LogIO::POST ;
4727 int id = idx[0] ;
4728 //os << "use row " << id << LogIO::POST ;
4729 tsysval = tsysCol( id ) ;
4730 }
4731 else {
4732 // do interpolation
4733 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4734 double t0 = timeVec[idx[0]] ;
4735 double t1 = timeVec[idx[1]] ;
4736 Vector<Float> tsys0 ;
4737 tsys0 = tsysCol( idx[0] ) ;
4738 tsysval = tsysCol( idx[1] ) ;
4739 double tfactor = (reftime - t0) / (t1 - t0) ;
4740 for ( unsigned int i = 0 ; i < tsys0.size() ; i++ ) {
4741 tsysval[i] = ( tsysval[i] - tsys0[i] ) * tfactor + tsys0[i] ;
4742 }
4743 }
4744 }
4745 else {
4746 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4747 }
4748 return tsysval ;
4749 }
4750}
4751
4752void STMath::calibrateCW( CountedPtr<Scantable> &out,
4753 const CountedPtr<Scantable>& on,
4754 const CountedPtr<Scantable>& off,
4755 const CountedPtr<Scantable>& sky,
4756 const CountedPtr<Scantable>& hot,
4757 const CountedPtr<Scantable>& cold,
4758 const Vector<uInt> &rows,
4759 const String &antname )
4760{
4761 // 2012/05/22 TN
4762 // Assume that out has empty SPECTRA column
4763
4764 // if rows is empty, just return
4765 if ( rows.nelements() == 0 )
4766 return ;
4767 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
4768 Vector<Double> timeOff = timeCol.getColumn() ;
4769 timeCol.attach( sky->table(), "TIME" ) ;
4770 Vector<Double> timeSky = timeCol.getColumn() ;
4771 timeCol.attach( hot->table(), "TIME" ) ;
4772 Vector<Double> timeHot = timeCol.getColumn() ;
4773 timeCol.attach( on->table(), "TIME" ) ;
4774 ROArrayColumn<Float> arrayFloatCol( off->table(), "SPECTRA" ) ;
4775 Matrix<Float> offspectra = arrayFloatCol.getColumn() ;
4776 arrayFloatCol.attach( sky->table(), "SPECTRA" ) ;
4777 Matrix<Float> skyspectra = arrayFloatCol.getColumn() ;
4778 arrayFloatCol.attach( hot->table(), "SPECTRA" ) ;
4779 Matrix<Float> hotspectra = arrayFloatCol.getColumn() ;
4780 unsigned int spsize = on->nchan( on->getIF(rows[0]) ) ;
4781 // I know that the data is contiguous
4782 const uInt *p = rows.data() ;
4783 vector<int> ids( 2 ) ;
4784 Block<uInt> flagchan( spsize ) ;
4785 uInt nflag = 0 ;
4786 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4787 double reftime = timeCol.asdouble(*p) ;
4788 ids = getRowIdFromTime( reftime, timeOff ) ;
4789 Vector<Float> spoff = getSpectrumFromTime( reftime, timeOff, ids, offspectra, "linear" ) ;
4790 ids = getRowIdFromTime( reftime, timeSky ) ;
4791 Vector<Float> spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
4792 Vector<Float> tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4793 Vector<Float> tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4794 ids = getRowIdFromTime( reftime, timeHot ) ;
4795 Vector<Float> sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra, "linear" ) ;
4796 Vector<Float> spec = on->specCol_( *p ) ;
4797 if ( antname.find( "APEX" ) != String::npos ) {
4798 // using gain array
4799 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4800 if ( spoff[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
4801 spec[j] = 0.0 ;
4802 flagchan[nflag++] = j ;
4803 }
4804 else {
4805 spec[j] = ( ( spec[j] - spoff[j] ) / spoff[j] )
4806 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4807 }
4808 }
4809 }
4810 else {
4811 // Chopper-Wheel calibration (Ulich & Haas 1976)
4812 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4813 if ( (sphot[j]-spsky[j]) == 0.0 ) {
4814 spec[j] = 0.0 ;
4815 flagchan[nflag++] = j ;
4816 }
4817 else {
4818 spec[j] = ( spec[j] - spoff[j] ) / ( sphot[j] - spsky[j] ) * tcal[j] ;
4819 }
4820 }
4821 }
4822 out->specCol_.put( *p, spec ) ;
4823 out->tsysCol_.put( *p, tsys ) ;
4824 if ( nflag > 0 ) {
4825 Vector<uChar> fl = out->flagsCol_( *p ) ;
4826 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4827 fl[flagchan[j]] = (uChar)True ;
4828 }
4829 out->flagsCol_.put( *p, fl ) ;
4830 }
4831 nflag = 0 ;
4832 p++ ;
4833 }
4834}
4835
4836void STMath::calibrateALMA( CountedPtr<Scantable>& out,
4837 const CountedPtr<Scantable>& on,
4838 const CountedPtr<Scantable>& off,
4839 const Vector<uInt>& rows )
4840{
4841 // 2012/05/22 TN
4842 // Assume that out has empty SPECTRA column
4843
4844 // if rows is empty, just return
4845 if ( rows.nelements() == 0 )
4846 return ;
4847 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
4848 Vector<Double> timeVec = timeCol.getColumn() ;
4849 timeCol.attach( on->table(), "TIME" ) ;
4850 ROArrayColumn<Float> arrayFloatCol( off->table(), "SPECTRA" ) ;
4851 Matrix<Float> offspectra = arrayFloatCol.getColumn() ;
4852 unsigned int spsize = on->nchan( on->getIF(rows[0]) ) ;
4853 // I know that the data is contiguous
4854 const uInt *p = rows.data() ;
4855 vector<int> ids( 2 ) ;
4856 Block<uInt> flagchan( spsize ) ;
4857 uInt nflag = 0 ;
4858 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4859 double reftime = timeCol.asdouble(*p) ;
4860 ids = getRowIdFromTime( reftime, timeVec ) ;
4861 Vector<Float> spoff = getSpectrumFromTime( reftime, timeVec, ids, offspectra, "linear" ) ;
4862 //Vector<Float> spoff = getSpectrumFromTime( reftime, timeVec, off, "linear" ) ;
4863 Vector<Float> spec = on->specCol_( *p ) ;
4864 Vector<Float> tsys = on->tsysCol_( *p ) ;
4865 // ALMA Calibration
4866 //
4867 // Ta* = Tsys * ( ON - OFF ) / OFF
4868 //
4869 // 2010/01/07 Takeshi Nakazato
4870 unsigned int tsyssize = tsys.nelements() ;
4871 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4872 if ( spoff[j] == 0.0 ) {
4873 spec[j] = 0.0 ;
4874 flagchan[nflag++] = j ;
4875 }
4876 else {
4877 spec[j] = ( spec[j] - spoff[j] ) / spoff[j] ;
4878 }
4879 if ( tsyssize == spsize )
4880 spec[j] *= tsys[j] ;
4881 else
4882 spec[j] *= tsys[0] ;
4883 }
4884 out->specCol_.put( *p, spec ) ;
4885 if ( nflag > 0 ) {
4886 Vector<uChar> fl = out->flagsCol_( *p ) ;
4887 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4888 fl[flagchan[j]] = (uChar)True ;
4889 }
4890 out->flagsCol_.put( *p, fl ) ;
4891 }
4892 nflag = 0 ;
4893 p++ ;
4894 }
4895}
4896
4897void STMath::calibrateAPEXFS( CountedPtr<Scantable> &sig,
4898 CountedPtr<Scantable> &ref,
4899 const vector< CountedPtr<Scantable> >& on,
4900 const vector< CountedPtr<Scantable> >& sky,
4901 const vector< CountedPtr<Scantable> >& hot,
4902 const vector< CountedPtr<Scantable> >& cold,
4903 const Vector<uInt> &rows )
4904{
4905 // if rows is empty, just return
4906 if ( rows.nelements() == 0 )
4907 return ;
4908 ROScalarColumn<Double> timeCol( sky[0]->table(), "TIME" ) ;
4909 Vector<Double> timeSkyS = timeCol.getColumn() ;
4910 timeCol.attach( sky[1]->table(), "TIME" ) ;
4911 Vector<Double> timeSkyR = timeCol.getColumn() ;
4912 timeCol.attach( hot[0]->table(), "TIME" ) ;
4913 Vector<Double> timeHotS = timeCol.getColumn() ;
4914 timeCol.attach( hot[1]->table(), "TIME" ) ;
4915 Vector<Double> timeHotR = timeCol.getColumn() ;
4916 timeCol.attach( sig->table(), "TIME" ) ;
4917 ROScalarColumn<Double> timeCol2( ref->table(), "TIME" ) ;
4918 ROArrayColumn<Float> arrayFloatCol( sky[0]->table(), "SPECTRA" ) ;
4919 Matrix<Float> skyspectraS = arrayFloatCol.getColumn() ;
4920 arrayFloatCol.attach( sky[1]->table(), "SPECTRA" ) ;
4921 Matrix<Float> skyspectraR = arrayFloatCol.getColumn() ;
4922 arrayFloatCol.attach( hot[0]->table(), "SPECTRA" ) ;
4923 Matrix<Float> hotspectraS = arrayFloatCol.getColumn() ;
4924 arrayFloatCol.attach( hot[1]->table(), "SPECTRA" ) ;
4925 Matrix<Float> hotspectraR = arrayFloatCol.getColumn() ;
4926 unsigned int spsize = sig->nchan( sig->getIF(rows[0]) ) ;
4927 Vector<Float> spec( spsize ) ;
4928 // I know that the data is contiguous
4929 const uInt *p = rows.data() ;
4930 vector<int> ids( 2 ) ;
4931 Block<uInt> flagchan( spsize ) ;
4932 uInt nflag = 0 ;
4933 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4934 double reftime = timeCol.asdouble(*p) ;
4935 ids = getRowIdFromTime( reftime, timeSkyS ) ;
4936 Vector<Float> spskyS = getSpectrumFromTime( reftime, timeSkyS, ids, skyspectraS, "linear" ) ;
4937 Vector<Float> tcalS = getTcalFromTime( reftime, timeSkyS, ids, sky[0], "linear" ) ;
4938 Vector<Float> tsysS = getTsysFromTime( reftime, timeSkyS, ids, sky[0], "linear" ) ;
4939 ids = getRowIdFromTime( reftime, timeHotS ) ;
4940 Vector<Float> sphotS = getSpectrumFromTime( reftime, timeHotS, ids, hotspectraS ) ;
4941 reftime = timeCol2.asdouble(*p) ;
4942 ids = getRowIdFromTime( reftime, timeSkyR ) ;
4943 Vector<Float> spskyR = getSpectrumFromTime( reftime, timeSkyR, ids, skyspectraR, "linear" ) ;
4944 Vector<Float> tcalR = getTcalFromTime( reftime, timeSkyR, ids, sky[1], "linear" ) ;
4945 Vector<Float> tsysR = getTsysFromTime( reftime, timeSkyR, ids, sky[1], "linear" ) ;
4946 ids = getRowIdFromTime( reftime, timeHotR ) ;
4947 Vector<Float> sphotR = getSpectrumFromTime( reftime, timeHotR, ids, hotspectraR ) ;
4948 Vector<Float> spsig = on[0]->specCol_( *p ) ;
4949 Vector<Float> spref = on[1]->specCol_( *p ) ;
4950 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4951 if ( (sphotS[j]-spskyS[j]) == 0.0 || (sphotR[j]-spskyR[j]) == 0.0 ) {
4952 spec[j] = 0.0 ;
4953 flagchan[nflag++] = j ;
4954 }
4955 else {
4956 spec[j] = tcalS[j] * spsig[j] / ( sphotS[j] - spskyS[j] )
4957 - tcalR[j] * spref[j] / ( sphotR[j] - spskyR[j] ) ;
4958 }
4959 }
4960 sig->specCol_.put( *p, spec ) ;
4961 sig->tsysCol_.put( *p, tsysS ) ;
4962 spec *= (Float)-1.0 ;
4963 ref->specCol_.put( *p, spec ) ;
4964 ref->tsysCol_.put( *p, tsysR ) ;
4965 if ( nflag > 0 ) {
4966 Vector<uChar> flsig = sig->flagsCol_( *p ) ;
4967 Vector<uChar> flref = ref->flagsCol_( *p ) ;
4968 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4969 flsig[flagchan[j]] = (uChar)True ;
4970 flref[flagchan[j]] = (uChar)True ;
4971 }
4972 sig->flagsCol_.put( *p, flsig ) ;
4973 ref->flagsCol_.put( *p, flref ) ;
4974 }
4975 nflag = 0 ;
4976 p++ ;
4977 }
4978}
4979
4980void STMath::calibrateFS( CountedPtr<Scantable> &sig,
4981 CountedPtr<Scantable> &ref,
4982 const CountedPtr<Scantable>& rsig,
4983 const CountedPtr<Scantable>& rref,
4984 const CountedPtr<Scantable>& sky,
4985 const CountedPtr<Scantable>& hot,
4986 const CountedPtr<Scantable>& cold,
4987 const Vector<uInt> &rows )
4988{
4989 // if rows is empty, just return
4990 if ( rows.nelements() == 0 )
4991 return ;
4992 ROScalarColumn<Double> timeCol( sky->table(), "TIME" ) ;
4993 Vector<Double> timeSky = timeCol.getColumn() ;
4994 timeCol.attach( hot->table(), "TIME" ) ;
4995 Vector<Double> timeHot = timeCol.getColumn() ;
4996 timeCol.attach( sig->table(), "TIME" ) ;
4997 ROScalarColumn<Double> timeCol2( ref->table(), "TIME" ) ;
4998 ROArrayColumn<Float> arrayFloatCol( sky->table(), "SPECTRA" ) ;
4999 Matrix<Float> skyspectra = arrayFloatCol.getColumn() ;
5000 arrayFloatCol.attach( hot->table(), "SPECTRA" ) ;
5001 Matrix<Float> hotspectra = arrayFloatCol.getColumn() ;
5002 unsigned int spsize = sig->nchan( sig->getIF(rows[0]) ) ;
5003 Vector<Float> spec( spsize ) ;
5004 // I know that the data is contiguous
5005 const uInt *p = rows.data() ;
5006 vector<int> ids( 2 ) ;
5007 Block<uInt> flagchan( spsize ) ;
5008 uInt nflag = 0 ;
5009 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
5010 double reftime = timeCol.asdouble(*p) ;
5011 ids = getRowIdFromTime( reftime, timeSky ) ;
5012 Vector<Float> spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
5013 Vector<Float> tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
5014 Vector<Float> tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
5015 ids = getRowIdFromTime( reftime, timeHot ) ;
5016 Vector<Float> sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra ) ;
5017 Vector<Float> spsig = rsig->specCol_( *p ) ;
5018 Vector<Float> spref = rref->specCol_( *p ) ;
5019 // using gain array
5020 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
5021 if ( spref[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
5022 spec[j] = 0.0 ;
5023 flagchan[nflag++] = j ;
5024 }
5025 else {
5026 spec[j] = ( ( spsig[j] - spref[j] ) / spref[j] )
5027 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
5028 }
5029 }
5030 sig->specCol_.put( *p, spec ) ;
5031 sig->tsysCol_.put( *p, tsys ) ;
5032 if ( nflag > 0 ) {
5033 Vector<uChar> fl = sig->flagsCol_( *p ) ;
5034 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
5035 fl[flagchan[j]] = (uChar)True ;
5036 }
5037 sig->flagsCol_.put( *p, fl ) ;
5038 }
5039 nflag = 0 ;
5040
5041 reftime = timeCol2.asdouble(*p) ;
5042 spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
5043 tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
5044 tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
5045 ids = getRowIdFromTime( reftime, timeHot ) ;
5046 sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra ) ;
5047 // using gain array
5048 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
5049 if ( spsig[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
5050 spec[j] = 0.0 ;
5051 flagchan[nflag++] = j ;
5052 }
5053 else {
5054 spec[j] = ( ( spref[j] - spsig[j] ) / spsig[j] )
5055 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
5056 }
5057 }
5058 ref->specCol_.put( *p, spec ) ;
5059 ref->tsysCol_.put( *p, tsys ) ;
5060 if ( nflag > 0 ) {
5061 Vector<uChar> fl = ref->flagsCol_( *p ) ;
5062 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
5063 fl[flagchan[j]] = (uChar)True ;
5064 }
5065 ref->flagsCol_.put( *p, fl ) ;
5066 }
5067 nflag = 0 ;
5068 p++ ;
5069 }
5070}
5071
5072void STMath::copyRows( Table &out,
5073 const Table &in,
5074 uInt startout,
5075 uInt startin,
5076 uInt nrow,
5077 Bool copySpectra,
5078 Bool copyFlagtra,
5079 Bool copyTsys )
5080{
5081 uInt nexclude = 0 ;
5082 Block<String> excludeColsBlock( 3 ) ;
5083 if ( !copySpectra ) {
5084 excludeColsBlock[nexclude] = "SPECTRA" ;
5085 nexclude++ ;
5086 }
5087 if ( !copyFlagtra ) {
5088 excludeColsBlock[nexclude] = "FLAGTRA" ;
5089 nexclude++ ;
5090 }
5091 if ( !copyTsys ) {
5092 excludeColsBlock[nexclude] = "TSYS" ;
5093 nexclude++ ;
5094 }
5095 // if ( nexclude < 3 ) {
5096 // excludeCols.resize( nexclude, True ) ;
5097 // }
5098 Vector<String> excludeCols( IPosition(1,nexclude),
5099 excludeColsBlock.storage(),
5100 SHARE ) ;
5101// cout << "excludeCols=" << excludeCols << endl ;
5102 TableRow rowout( out, excludeCols, True ) ;
5103 ROTableRow rowin( in, excludeCols, True ) ;
5104 uInt rin = startin ;
5105 uInt rout = startout ;
5106 for ( uInt i = 0 ; i < nrow ; i++ ) {
5107 rowin.get( rin ) ;
5108 rowout.putMatchingFields( rout, rowin.record() ) ;
5109 rin++ ;
5110 rout++ ;
5111 }
5112}
5113
5114CountedPtr<Scantable> STMath::averageWithinSession( CountedPtr<Scantable> &s,
5115 vector<bool> &mask,
5116 string weight )
5117{
5118 // prepare output table
5119 bool insitu = insitu_ ;
5120 insitu_ = false ;
5121 CountedPtr<Scantable> a = getScantable( s, true ) ;
5122 insitu_ = insitu ;
5123 Table &atab = a->table() ;
5124 ScalarColumn<Double> timeColOut( atab, "TIME" ) ;
5125
5126 if ( s->nrow() == 0 )
5127 return a ;
5128
5129 // setup RowAccumulator
5130 WeightType wtype = stringToWeight( weight ) ;
5131 RowAccumulator acc( wtype ) ;
5132 Vector<Bool> cmask( mask ) ;
5133 acc.setUserMask( cmask ) ;
5134
5135 vector<string> cols( 3 ) ;
5136 cols[0] = "IFNO" ;
5137 cols[1] = "POLNO" ;
5138 cols[2] = "BEAMNO" ;
5139 STIdxIterAcc iter( s, cols ) ;
5140
5141 Table ttab = s->table() ;
5142 ROScalarColumn<Double> *timeCol = new ROScalarColumn<Double>( ttab, "TIME" ) ;
5143 Vector<Double> timeVec = timeCol->getColumn() ;
5144 delete timeCol ;
5145 Vector<Double> interval = s->integrCol_.getColumn() ;
5146 uInt nrow = timeVec.nelements() ;
5147 uInt outrow = 0 ;
5148
5149 while( !iter.pastEnd() ) {
5150
5151 Vector<uInt> rows = iter.getRows( SHARE ) ;
5152
5153 uInt nchan = s->nchan(s->getIF(rows[0])) ;
5154 Vector<uChar> flag( nchan ) ;
5155 Vector<Bool> bflag( nchan ) ;
5156 Vector<Float> spec( nchan ) ;
5157 Vector<Float> tsys( nchan ) ;
5158
5159 uInt len = rows.nelements() ;
5160
5161 Vector<Double> timeSep( len-1 ) ;
5162 for ( uInt i = 0 ; i < len-1 ; i++ ) {
5163 timeSep[i] = timeVec[rows[i+1]] - timeVec[rows[i]] ;
5164 }
5165
5166 uInt irow ;
5167 uInt jrow ;
5168 for ( uInt i = 0 ; i < len-1 ; i++ ) {
5169 irow = rows[i] ;
5170 jrow = rows[i+1] ;
5171 // accumulate data
5172 s->flagsCol_.get( irow, flag ) ;
5173 convertArray( bflag, flag ) ;
5174 s->specCol_.get( irow, spec ) ;
5175 tsys.assign( s->tsysCol_( irow ) ) ;
5176 if ( !allEQ(bflag,True) )
5177 acc.add( spec, !bflag, tsys, interval[irow], timeVec[irow] ) ;
5178 double gap = 2.0 * 86400.0 * timeSep[i] / ( interval[jrow] + interval[irow] ) ;
5179 //cout << "gap[" << i << "]=" << setw(5) << gap << endl ;
5180 if ( gap > 1.1 ) {
5181 //cout << "detected gap between " << i << " and " << i+1 << endl ;
5182 // put data to output table
5183 // reset RowAccumulator
5184 if ( acc.state() ) {
5185 atab.addRow() ;
5186 copyRows( atab, ttab, outrow, irow, 1, False, False, False ) ;
5187 acc.replaceNaN() ;
5188 const Vector<Bool> &msk = acc.getMask() ;
5189 convertArray( flag, !msk ) ;
5190 for (uInt k = 0; k < nchan; ++k) {
5191 uChar userFlag = 1 << 7;
5192 if (msk[k]==True) userFlag = 0 << 7;
5193 flag(k) = userFlag;
5194 }
5195 a->flagsCol_.put( outrow, flag ) ;
5196 a->specCol_.put( outrow, acc.getSpectrum() ) ;
5197 a->tsysCol_.put( outrow, acc.getTsys() ) ;
5198 a->integrCol_.put( outrow, acc.getInterval() ) ;
5199 timeColOut.put( outrow, acc.getTime() ) ;
5200 a->cycleCol_.put( outrow, 0 ) ;
5201 }
5202 acc.reset() ;
5203 outrow++ ;
5204 }
5205 }
5206
5207 // accumulate and add last data
5208 irow = rows[len-1] ;
5209 s->flagsCol_.get( irow, flag ) ;
5210 convertArray( bflag, flag ) ;
5211 s->specCol_.get( irow, spec ) ;
5212 tsys.assign( s->tsysCol_( irow ) ) ;
5213 if (!allEQ(bflag,True) )
5214 acc.add( spec, !bflag, tsys, interval[irow], timeVec[irow] ) ;
5215 if ( acc.state() ) {
5216 atab.addRow() ;
5217 copyRows( atab, ttab, outrow, irow, 1, False, False, False ) ;
5218 acc.replaceNaN() ;
5219 const Vector<Bool> &msk = acc.getMask() ;
5220 convertArray( flag, !msk ) ;
5221 for (uInt k = 0; k < nchan; ++k) {
5222 uChar userFlag = 1 << 7;
5223 if (msk[k]==True) userFlag = 0 << 7;
5224 flag(k) = userFlag;
5225 }
5226 a->flagsCol_.put( outrow, flag ) ;
5227 a->specCol_.put( outrow, acc.getSpectrum() ) ;
5228 a->tsysCol_.put( outrow, acc.getTsys() ) ;
5229 a->integrCol_.put( outrow, acc.getInterval() ) ;
5230 timeColOut.put( outrow, acc.getTime() ) ;
5231 a->cycleCol_.put( outrow, 0 ) ;
5232 }
5233 acc.reset() ;
5234 outrow++ ;
5235
5236 iter.next() ;
5237 }
5238
5239 return a ;
5240}
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