source: trunk/src/STMath.cpp@ 2676

Last change on this file since 2676 was 2670, checked in by Malte Marquarding, 12 years ago

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