source: trunk/src/STMath.cpp@ 2665

Last change on this file since 2665 was 2658, checked in by Malte Marquarding, 12 years ago

Ticket #199: Excised Logger::pushLog; now everything is using LogIO
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File size: 162.5 KB
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1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <sstream>
14
15#include <casa/iomanip.h>
16#include <casa/Arrays/MaskArrLogi.h>
17#include <casa/Arrays/MaskArrMath.h>
18#include <casa/Arrays/ArrayLogical.h>
19#include <casa/Arrays/ArrayMath.h>
20#include <casa/Arrays/Slice.h>
21#include <casa/Arrays/Slicer.h>
22#include <casa/BasicSL/String.h>
23#include <casa/Containers/Block.h>
24#include <casa/Containers/RecordField.h>
25#include <casa/Exceptions/Error.h>
26#include <casa/Logging/LogIO.h>
27
28#include <coordinates/Coordinates/CoordinateSystem.h>
29#include <coordinates/Coordinates/CoordinateUtil.h>
30#include <coordinates/Coordinates/FrequencyAligner.h>
31#include <coordinates/Coordinates/SpectralCoordinate.h>
32
33#include <lattices/Lattices/LatticeUtilities.h>
34
35#include <scimath/Functionals/Polynomial.h>
36#include <scimath/Mathematics/Convolver.h>
37#include <scimath/Mathematics/VectorKernel.h>
38
39#include <tables/Tables/ExprNode.h>
40#include <tables/Tables/ReadAsciiTable.h>
41#include <tables/Tables/TableCopy.h>
42#include <tables/Tables/TableIter.h>
43#include <tables/Tables/TableParse.h>
44#include <tables/Tables/TableRecord.h>
45#include <tables/Tables/TableRow.h>
46#include <tables/Tables/TableVector.h>
47#include <tables/Tables/TabVecMath.h>
48
49#include <atnf/PKSIO/SrcType.h>
50
51#include "RowAccumulator.h"
52#include "STAttr.h"
53#include "STMath.h"
54#include "STSelector.h"
55#include "Accelerator.h"
56#include "STIdxIter.h"
57
58using namespace casa;
59using namespace asap;
60
61// 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 convertArray(flag, !maskout);
2458 } else if (kernel == "rmedian") {
2459 mathutil::runningMedian(specout, maskout, spec , mask, width);
2460 convertArray(flag, maskout);
2461 } else if (kernel == "poly") {
2462 mathutil::polyfit(specout, maskout, spec, !mask, width, order);
2463 convertArray(flag, !maskout);
2464 }
2465
2466 for (uInt j = 0; j < flag.nelements(); ++j) {
2467 uChar userFlag = 1 << 7;
2468 if (maskout[j]==True) userFlag = 0 << 7;
2469 flag(j) = userFlag;
2470 }
2471
2472 flagCol.put(i, flag);
2473 specCol.put(i, specout);
2474 }
2475 ++iter;
2476 }
2477 return out;
2478}
2479
2480CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
2481 const std::string& kernel, float width,
2482 int order)
2483{
2484 if (kernel == "rmedian" || kernel == "hanning" || kernel == "poly") {
2485 return smoothOther(in, kernel, width, order);
2486 }
2487 CountedPtr< Scantable > out = getScantable(in, false);
2488 Table& table = out->table();
2489 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
2490 // same IFNO should have same no of channels
2491 // this saves overhead
2492 TableIterator iter(table, "IFNO");
2493 while (!iter.pastEnd()) {
2494 Table tab = iter.table();
2495 ArrayColumn<Float> specCol(tab, "SPECTRA");
2496 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2497 Vector<Float> spec = specCol( 0 );
2498 uInt nchan = spec.nelements();
2499 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
2500 Convolver<Float> conv(kvec, IPosition(1,nchan));
2501 Vector<uChar> flag;
2502 Vector<Bool> mask(nchan);
2503 for ( uInt i=0; i<tab.nrow(); ++i) {
2504 specCol.get(i, spec);
2505 flagCol.get(i, flag);
2506 convertArray(mask, flag);
2507 Vector<Float> specout;
2508 mathutil::replaceMaskByZero(specout, mask);
2509 conv.linearConv(specout, spec);
2510 specCol.put(i, specout);
2511 }
2512 ++iter;
2513 }
2514 return out;
2515}
2516
2517CountedPtr< Scantable >
2518 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
2519{
2520 if ( in.size() < 2 ) {
2521 throw(AipsError("Need at least two scantables to perform a merge."));
2522 }
2523 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
2524 bool insitu = insitu_;
2525 setInsitu(false);
2526 CountedPtr< Scantable > out = getScantable(*it, false);
2527 setInsitu(insitu);
2528 Table& tout = out->table();
2529 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
2530 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
2531 // Renumber SCANNO to be 0-based
2532 Vector<uInt> scannos = scannocol.getColumn();
2533 uInt offset = min(scannos);
2534 scannos -= offset;
2535 scannocol.putColumn(scannos);
2536 uInt newscanno = max(scannos)+1;
2537 ++it;
2538 while ( it != in.end() ){
2539 if ( ! (*it)->conformant(*out) ) {
2540 // non conformant.
2541 LogIO os( LogOrigin( "STMath", "merge()", WHERE ) ) ;
2542 os << LogIO::SEVERE << "Can't merge scantables as header informations (any one of AntennaName, Equinox, and FluxUnit) differ." << LogIO::EXCEPTION ;
2543 }
2544 out->appendToHistoryTable((*it)->history());
2545 const Table& tab = (*it)->table();
2546
2547 Block<String> cols(3);
2548 cols[0] = String("FREQ_ID");
2549 cols[1] = String("MOLECULE_ID");
2550 cols[2] = String("FOCUS_ID");
2551
2552 TableIterator scanit(tab, "SCANNO");
2553 while (!scanit.pastEnd()) {
2554 ScalarColumn<uInt> thescannocol(scanit.table(),"SCANNO");
2555 Vector<uInt> thescannos(thescannocol.nrow(),newscanno);
2556 thescannocol.putColumn(thescannos);
2557 TableIterator subit(scanit.table(), cols);
2558 while ( !subit.pastEnd() ) {
2559 uInt nrow = tout.nrow();
2560 Table thetab = subit.table();
2561 ROTableRow row(thetab);
2562 Vector<uInt> thecolvals(thetab.nrow());
2563 ScalarColumn<uInt> thefreqidcol(thetab,"FREQ_ID");
2564 ScalarColumn<uInt> themolidcol(thetab, "MOLECULE_ID");
2565 ScalarColumn<uInt> thefocusidcol(thetab,"FOCUS_ID");
2566 // The selected subset of table should have
2567 // the equal FREQ_ID, MOLECULE_ID, and FOCUS_ID values.
2568 const TableRecord& rec = row.get(0);
2569 // Set the proper FREQ_ID
2570 Double rv,rp,inc;
2571 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
2572 uInt id;
2573 id = out->frequencies().addEntry(rp, rv, inc);
2574 thecolvals = id;
2575 thefreqidcol.putColumn(thecolvals);
2576 // Set the proper MOLECULE_ID
2577 Vector<String> name,fname;Vector<Double> rf;
2578 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
2579 id = out->molecules().addEntry(rf, name, fname);
2580 thecolvals = id;
2581 themolidcol.putColumn(thecolvals);
2582 // Set the proper FOCUS_ID
2583 Float fpa,frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
2584 (*it)->focus().getEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2585 fxy, fxyp, rec.asuInt("FOCUS_ID"));
2586 id = out->focus().addEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2587 fxy, fxyp);
2588 thecolvals = id;
2589 thefocusidcol.putColumn(thecolvals);
2590
2591 tout.addRow(thetab.nrow());
2592 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
2593
2594 ++subit;
2595 }
2596 ++newscanno;
2597 ++scanit;
2598 }
2599 ++it;
2600 }
2601 return out;
2602}
2603
2604CountedPtr< Scantable >
2605 STMath::invertPhase( const CountedPtr < Scantable >& in )
2606{
2607 return applyToPol(in, &STPol::invertPhase, Float(0.0));
2608}
2609
2610CountedPtr< Scantable >
2611 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
2612{
2613 return applyToPol(in, &STPol::rotatePhase, Float(phase));
2614}
2615
2616CountedPtr< Scantable >
2617 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
2618{
2619 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
2620}
2621
2622CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
2623 STPol::polOperation fptr,
2624 Float phase )
2625{
2626 CountedPtr< Scantable > out = getScantable(in, false);
2627 Table& tout = out->table();
2628 Block<String> cols(4);
2629 cols[0] = String("SCANNO");
2630 cols[1] = String("BEAMNO");
2631 cols[2] = String("IFNO");
2632 cols[3] = String("CYCLENO");
2633 TableIterator iter(tout, cols);
2634 CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
2635 out->getPolType() );
2636 while (!iter.pastEnd()) {
2637 Table t = iter.table();
2638 ArrayColumn<Float> speccol(t, "SPECTRA");
2639 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
2640 Matrix<Float> pols(speccol.getColumn());
2641 try {
2642 stpol->setSpectra(pols);
2643 Float fang,fhand;
2644 fang = in->focusTable_.getTotalAngle(focidcol(0));
2645 fhand = in->focusTable_.getFeedHand(focidcol(0));
2646 stpol->setPhaseCorrections(fang, fhand);
2647 // use a member function pointer in STPol. This only works on
2648 // the STPol pointer itself, not the Counted Pointer so
2649 // derefernce it.
2650 (&(*(stpol))->*fptr)(phase);
2651 speccol.putColumn(stpol->getSpectra());
2652 } catch (AipsError& e) {
2653 //delete stpol;stpol=0;
2654 throw(e);
2655 }
2656 ++iter;
2657 }
2658 //delete stpol;stpol=0;
2659 return out;
2660}
2661
2662CountedPtr< Scantable >
2663 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
2664{
2665 CountedPtr< Scantable > out = getScantable(in, false);
2666 Table& tout = out->table();
2667 Table t0 = tout(tout.col("POLNO") == 0);
2668 Table t1 = tout(tout.col("POLNO") == 1);
2669 if ( t0.nrow() != t1.nrow() )
2670 throw(AipsError("Inconsistent number of polarisations"));
2671 ArrayColumn<Float> speccol0(t0, "SPECTRA");
2672 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
2673 ArrayColumn<Float> speccol1(t1, "SPECTRA");
2674 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
2675 Matrix<Float> s0 = speccol0.getColumn();
2676 Matrix<uChar> f0 = flagcol0.getColumn();
2677 speccol0.putColumn(speccol1.getColumn());
2678 flagcol0.putColumn(flagcol1.getColumn());
2679 speccol1.putColumn(s0);
2680 flagcol1.putColumn(f0);
2681 return out;
2682}
2683
2684CountedPtr< Scantable >
2685 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
2686 const std::vector<bool>& mask,
2687 const std::string& weight )
2688{
2689 if (in->npol() < 2 )
2690 throw(AipsError("averagePolarisations can only be applied to two or more"
2691 "polarisations"));
2692 bool insitu = insitu_;
2693 setInsitu(false);
2694 CountedPtr< Scantable > pols = getScantable(in, true);
2695 setInsitu(insitu);
2696 Table& tout = pols->table();
2697 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
2698 Table tab = tableCommand(taql, in->table());
2699 if (tab.nrow() == 0 )
2700 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
2701 TableCopy::copyRows(tout, tab);
2702 TableVector<uInt> vec(tout, "POLNO");
2703 vec = 0;
2704 pols->table_.rwKeywordSet().define("nPol", Int(1));
2705 pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
2706 //pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
2707 std::vector<CountedPtr<Scantable> > vpols;
2708 vpols.push_back(pols);
2709 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
2710 return out;
2711}
2712
2713CountedPtr< Scantable >
2714 STMath::averageBeams( const CountedPtr< Scantable > & in,
2715 const std::vector<bool>& mask,
2716 const std::string& weight )
2717{
2718 bool insitu = insitu_;
2719 setInsitu(false);
2720 CountedPtr< Scantable > beams = getScantable(in, false);
2721 setInsitu(insitu);
2722 Table& tout = beams->table();
2723 // give all rows the same BEAMNO
2724 TableVector<uInt> vec(tout, "BEAMNO");
2725 vec = 0;
2726 beams->table_.rwKeywordSet().define("nBeam", Int(1));
2727 std::vector<CountedPtr<Scantable> > vbeams;
2728 vbeams.push_back(beams);
2729 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
2730 return out;
2731}
2732
2733
2734CountedPtr< Scantable >
2735 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
2736 const std::string & refTime,
2737 const std::string & method)
2738{
2739 LogIO os( casa::LogOrigin("STMath", "frequencyAlign()", WHERE));
2740 // clone as this is not working insitu
2741 bool insitu = insitu_;
2742 setInsitu(false);
2743 CountedPtr< Scantable > out = getScantable(in, false);
2744 setInsitu(insitu);
2745 Table& tout = out->table();
2746 // Get reference Epoch to time of first row or given String
2747 Unit DAY(String("d"));
2748 MEpoch::Ref epochRef(in->getTimeReference());
2749 MEpoch refEpoch;
2750 if (refTime.length()>0) {
2751 Quantum<Double> qt;
2752 if (MVTime::read(qt,refTime)) {
2753 MVEpoch mv(qt);
2754 refEpoch = MEpoch(mv, epochRef);
2755 } else {
2756 throw(AipsError("Invalid format for Epoch string"));
2757 }
2758 } else {
2759 refEpoch = in->timeCol_(0);
2760 }
2761 MPosition refPos = in->getAntennaPosition();
2762
2763 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2764 /*
2765 // Comment from MV.
2766 // the following code has been commented out because different FREQ_IDs have to be aligned together even
2767 // if the frame doesn't change. So far, lack of this check didn't cause any problems.
2768 // test if user frame is different to base frame
2769 if ( in->frequencies().getFrameString(true)
2770 == in->frequencies().getFrameString(false) ) {
2771 throw(AipsError("Can't convert as no output frame has been set"
2772 " (use set_freqframe) or it is aligned already."));
2773 }
2774 */
2775 MFrequency::Types system = in->frequencies().getFrame();
2776 MVTime mvt(refEpoch.getValue());
2777 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
2778 os << "Aligned at reference Epoch " << epochout
2779 << " in frame " << MFrequency::showType(system) << LogIO::POST;
2780 // set up the iterator
2781 Block<String> cols(4);
2782 // select by constant direction
2783 cols[0] = String("SRCNAME");
2784 cols[1] = String("BEAMNO");
2785 // select by IF ( no of channels varies over this )
2786 cols[2] = String("IFNO");
2787 // select by restfrequency
2788 cols[3] = String("MOLECULE_ID");
2789 TableIterator iter(tout, cols);
2790 while ( !iter.pastEnd() ) {
2791 Table t = iter.table();
2792 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
2793 TableIterator fiter(t, "FREQ_ID");
2794 // determine nchan from the first row. This should work as
2795 // we are iterating over BEAMNO and IFNO // we should have constant direction
2796
2797 ROArrayColumn<Float> sCol(t, "SPECTRA");
2798 const MDirection direction = dirCol(0);
2799 const uInt nchan = sCol(0).nelements();
2800
2801 // skip operations if there is nothing to align
2802 if (fiter.pastEnd()) {
2803 continue;
2804 }
2805
2806 Table ftab = fiter.table();
2807 // align all frequency ids with respect to the first encountered id
2808 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
2809 // get the SpectralCoordinate for the freqid, which we are iterating over
2810 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
2811 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
2812 direction, refPos, system );
2813 // realign the SpectralCoordinate and put into the output Scantable
2814 Vector<String> units(1);
2815 units = String("Hz");
2816 Bool linear=True;
2817 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
2818 sc2.setWorldAxisUnits(units);
2819 const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
2820 sc2.referenceValue()[0],
2821 sc2.increment()[0]);
2822 while ( !fiter.pastEnd() ) {
2823 ftab = fiter.table();
2824 // spectral coordinate for the current FREQ_ID
2825 ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
2826 sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
2827 // create the "global" abcissa for alignment with same FREQ_ID
2828 Vector<Double> abc(nchan);
2829 for (uInt i=0; i<nchan; i++) {
2830 Double w;
2831 sC.toWorld(w,Double(i));
2832 abc[i] = w;
2833 }
2834 TableVector<uInt> tvec(ftab, "FREQ_ID");
2835 // assign new frequency id to all rows
2836 tvec = id;
2837 // cache abcissa for same time stamps, so iterate over those
2838 TableIterator timeiter(ftab, "TIME");
2839 while ( !timeiter.pastEnd() ) {
2840 Table tab = timeiter.table();
2841 ArrayColumn<Float> specCol(tab, "SPECTRA");
2842 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2843 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2844 // use align abcissa cache after the first row
2845 // these rows should be just be POLNO
2846 bool first = true;
2847 for (int i=0; i<int(tab.nrow()); ++i) {
2848 // input values
2849 Vector<uChar> flag = flagCol(i);
2850 Vector<Bool> mask(flag.shape());
2851 Vector<Float> specOut, spec;
2852 spec = specCol(i);
2853 Vector<Bool> maskOut;Vector<uChar> flagOut;
2854 convertArray(mask, flag);
2855 // alignment
2856 Bool ok = fa.align(specOut, maskOut, abc, spec,
2857 mask, timeCol(i), !first,
2858 interp, False);
2859 (void) ok; // unused stop compiler nagging
2860 // back into scantable
2861 flagOut.resize(maskOut.nelements());
2862 convertArray(flagOut, maskOut);
2863 flagCol.put(i, flagOut);
2864 specCol.put(i, specOut);
2865 // start abcissa caching
2866 first = false;
2867 }
2868 // next timestamp
2869 ++timeiter;
2870 }
2871 // next FREQ_ID
2872 ++fiter;
2873 }
2874 // next aligner
2875 ++iter;
2876 }
2877 // set this afterwards to ensure we are doing insitu correctly.
2878 out->frequencies().setFrame(system, true);
2879 return out;
2880}
2881
2882CountedPtr<Scantable>
2883 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
2884 const std::string & newtype )
2885{
2886 if (in->npol() != 2 && in->npol() != 4)
2887 throw(AipsError("Can only convert two or four polarisations."));
2888 if ( in->getPolType() == newtype )
2889 throw(AipsError("No need to convert."));
2890 if ( ! in->selector_.empty() )
2891 throw(AipsError("Can only convert whole scantable. Unset the selection."));
2892 bool insitu = insitu_;
2893 setInsitu(false);
2894 CountedPtr< Scantable > out = getScantable(in, true);
2895 setInsitu(insitu);
2896 Table& tout = out->table();
2897 tout.rwKeywordSet().define("POLTYPE", String(newtype));
2898
2899 Block<String> cols(4);
2900 cols[0] = "SCANNO";
2901 cols[1] = "CYCLENO";
2902 cols[2] = "BEAMNO";
2903 cols[3] = "IFNO";
2904 TableIterator it(in->originalTable_, cols);
2905 String basetype = in->getPolType();
2906 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
2907 try {
2908 while ( !it.pastEnd() ) {
2909 Table tab = it.table();
2910 uInt row = tab.rowNumbers()[0];
2911 stpol->setSpectra(in->getPolMatrix(row));
2912 Float fang,fhand;
2913 fang = in->focusTable_.getTotalAngle(in->mfocusidCol_(row));
2914 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
2915 stpol->setPhaseCorrections(fang, fhand);
2916 Int npolout = 0;
2917 for (uInt i=0; i<tab.nrow(); ++i) {
2918 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
2919 if ( outvec.nelements() > 0 ) {
2920 tout.addRow();
2921 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
2922 ArrayColumn<Float> sCol(tout,"SPECTRA");
2923 ScalarColumn<uInt> pCol(tout,"POLNO");
2924 sCol.put(tout.nrow()-1 ,outvec);
2925 pCol.put(tout.nrow()-1 ,uInt(npolout));
2926 npolout++;
2927 }
2928 }
2929 tout.rwKeywordSet().define("nPol", npolout);
2930 ++it;
2931 }
2932 } catch (AipsError& e) {
2933 delete stpol;
2934 throw(e);
2935 }
2936 delete stpol;
2937 return out;
2938}
2939
2940CountedPtr< Scantable >
2941 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
2942 const std::string & scantype )
2943{
2944 bool insitu = insitu_;
2945 setInsitu(false);
2946 CountedPtr< Scantable > out = getScantable(in, true);
2947 setInsitu(insitu);
2948 Table& tout = out->table();
2949 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
2950 if (scantype == "on") {
2951 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
2952 }
2953 Table tab = tableCommand(taql, in->table());
2954 TableCopy::copyRows(tout, tab);
2955 if (scantype == "on") {
2956 // re-index SCANNO to 0
2957 TableVector<uInt> vec(tout, "SCANNO");
2958 vec = 0;
2959 }
2960 return out;
2961}
2962
2963std::vector<float>
2964 asap::STMath::fft( const casa::CountedPtr< Scantable > & in,
2965 const std::vector<int>& whichrow,
2966 bool getRealImag )
2967{
2968 std::vector<float> res;
2969 Table tab = in->table();
2970 std::vector<bool> mask;
2971
2972 if (whichrow.size() < 1) { // for all rows (by default)
2973 int nrow = int(tab.nrow());
2974 for (int i = 0; i < nrow; ++i) {
2975 res = in->execFFT(i, mask, getRealImag);
2976 }
2977 } else { // for specified rows
2978 for (uInt i = 0; i < whichrow.size(); ++i) {
2979 res = in->execFFT(i, mask, getRealImag);
2980 }
2981 }
2982
2983 return res;
2984}
2985
2986
2987CountedPtr<Scantable>
2988 asap::STMath::lagFlag( const CountedPtr<Scantable>& in,
2989 double start, double end,
2990 const std::string& mode )
2991{
2992 CountedPtr<Scantable> out = getScantable(in, false);
2993 Table& tout = out->table();
2994 TableIterator iter(tout, "FREQ_ID");
2995 FFTServer<Float,Complex> ffts;
2996
2997 while ( !iter.pastEnd() ) {
2998 Table tab = iter.table();
2999 Double rp,rv,inc;
3000 ROTableRow row(tab);
3001 const TableRecord& rec = row.get(0);
3002 uInt freqid = rec.asuInt("FREQ_ID");
3003 out->frequencies().getEntry(rp, rv, inc, freqid);
3004 ArrayColumn<Float> specCol(tab, "SPECTRA");
3005 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
3006
3007 for (int i=0; i<int(tab.nrow()); ++i) {
3008 Vector<Float> spec = specCol(i);
3009 Vector<uChar> flag = flagCol(i);
3010 std::vector<bool> mask;
3011 for (uInt j = 0; j < flag.nelements(); ++j) {
3012 mask.push_back(!(flag[j]>0));
3013 }
3014 mathutil::doZeroOrderInterpolation(spec, mask);
3015
3016 Vector<Complex> lags;
3017 ffts.fft0(lags, spec);
3018
3019 Int lag0(start+0.5);
3020 Int lag1(end+0.5);
3021 if (mode == "frequency") {
3022 lag0 = Int(spec.nelements()*abs(inc)/(start)+0.5);
3023 lag1 = Int(spec.nelements()*abs(inc)/(end)+0.5);
3024 }
3025 Int lstart = max(0, lag0);
3026 Int lend = min(Int(lags.nelements()-1), lag1);
3027 if (lstart == lend) {
3028 lags[lstart] = Complex(0.0);
3029 } else {
3030 if (lstart > lend) {
3031 Int tmp = lend;
3032 lend = lstart;
3033 lstart = tmp;
3034 }
3035 for (int j=lstart; j <=lend ;++j) {
3036 lags[j] = Complex(0.0);
3037 }
3038 }
3039
3040 ffts.fft0(spec, lags);
3041
3042 specCol.put(i, spec);
3043 }
3044 ++iter;
3045 }
3046 return out;
3047}
3048
3049// Averaging spectra with different channel/resolution
3050CountedPtr<Scantable>
3051STMath::new_average( const std::vector<CountedPtr<Scantable> >& in,
3052 const bool& compel,
3053 const std::vector<bool>& mask,
3054 const std::string& weight,
3055 const std::string& avmode )
3056 throw ( casa::AipsError )
3057{
3058 LogIO os( LogOrigin( "STMath", "new_average()", WHERE ) ) ;
3059 if ( avmode == "SCAN" && in.size() != 1 )
3060 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
3061 "Use merge first."));
3062
3063 CountedPtr<Scantable> out ; // processed result
3064 if ( compel ) {
3065 std::vector< CountedPtr<Scantable> > newin ; // input for average process
3066 uInt insize = in.size() ; // number of input scantables
3067
3068 // setup newin
3069 bool oldInsitu = insitu_ ;
3070 setInsitu( false ) ;
3071 newin.resize( insize ) ;
3072 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3073 newin[itable] = getScantable( in[itable], false ) ;
3074 }
3075 setInsitu( oldInsitu ) ;
3076
3077 // warning
3078 os << "Average spectra with different spectral resolution" << LogIO::POST ;
3079
3080 // temporarily set coordinfo
3081 vector<string> oldinfo( insize ) ;
3082 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3083 vector<string> coordinfo = in[itable]->getCoordInfo() ;
3084 oldinfo[itable] = coordinfo[0] ;
3085 coordinfo[0] = "Hz" ;
3086 newin[itable]->setCoordInfo( coordinfo ) ;
3087 }
3088
3089 ostringstream oss ;
3090
3091 // check IF frequency coverage
3092 // freqid: list of FREQ_ID, which is used, in each table
3093 // iffreq: list of minimum and maximum frequency for each FREQ_ID in
3094 // each table
3095 // freqid[insize][numIF]
3096 // freqid: [[id00, id01, ...],
3097 // [id10, id11, ...],
3098 // ...
3099 // [idn0, idn1, ...]]
3100 // iffreq[insize][numIF*2]
3101 // iffreq: [[min_id00, max_id00, min_id01, max_id01, ...],
3102 // [min_id10, max_id10, min_id11, max_id11, ...],
3103 // ...
3104 // [min_idn0, max_idn0, min_idn1, max_idn1, ...]]
3105 //os << "Check IF settings in each table" << LogIO::POST ;
3106 vector< vector<uInt> > freqid( insize );
3107 vector< vector<double> > iffreq( insize ) ;
3108 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3109 Vector<uInt> freqIds = newin[itable]->mfreqidCol_.getColumn() ;
3110 vector<uInt> uniqueFreqId = newin[itable]->getNumbers(newin[itable]->mfreqidCol_) ;
3111 for ( vector<uInt>::iterator i = uniqueFreqId.begin() ;
3112 i != uniqueFreqId.end() ; i++ ) {
3113 //os << "itable = " << itable << ": IF " << id << " is included in the list" << LogIO::POST ;
3114 uInt target = 0 ;
3115 while ( freqIds[target] != *i )
3116 target++ ;
3117 vector<double> abcissa = newin[itable]->getAbcissa( target ) ;
3118 freqid[itable].push_back( *i ) ;
3119 double incr = abs( abcissa[1] - abcissa[0] ) ;
3120 iffreq[itable].push_back( (*min_element(abcissa.begin(),abcissa.end()))-0.5*incr ) ;
3121 iffreq[itable].push_back( (*max_element(abcissa.begin(),abcissa.end()))+0.5*incr ) ;
3122 }
3123 }
3124
3125 // debug
3126// os << "IF settings summary:" << endl ;
3127// for ( uInt i = 0 ; i < freqid.size() ; i++ ) {
3128// os << " Table" << i << endl ;
3129// for ( uInt j = 0 ; j < freqid[i].size() ; j++ ) {
3130// os << " id = " << freqid[i][j] << " (min,max) = (" << iffreq[i][2*j] << "," << iffreq[i][2*j+1] << ")" << endl ;
3131// }
3132// }
3133// os << endl ;
3134// os.post() ;
3135
3136 // IF grouping based on their frequency coverage
3137 // ifgrp: number of member in each IF group
3138 // ifgrp[numgrp]
3139 // ifgrp: [n0, n1, ...]
3140 //os << "IF grouping based on their frequency coverage" << LogIO::POST ;
3141
3142 // parameter for IF grouping
3143 // groupmode = OR retrieve all region
3144 // AND only retrieve overlaped region
3145 //string groupmode = "AND" ;
3146 string groupmode = "OR" ;
3147 uInt sizecr = 0 ;
3148 if ( groupmode == "AND" )
3149 sizecr = 1 ;
3150 else if ( groupmode == "OR" )
3151 sizecr = 0 ;
3152
3153 vector<double> sortedfreq ;
3154 for ( uInt i = 0 ; i < iffreq.size() ; i++ ) {
3155 for ( uInt j = 0 ; j < iffreq[i].size() ; j++ ) {
3156 if ( count( sortedfreq.begin(), sortedfreq.end(), iffreq[i][j] ) == 0 )
3157 sortedfreq.push_back( iffreq[i][j] ) ;
3158 }
3159 }
3160 sort( sortedfreq.begin(), sortedfreq.end() ) ;
3161 vector<uInt> ifgrp( sortedfreq.size()-1, 0 ) ;
3162 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3163 for ( uInt iif = 0 ; iif < freqid[itable].size() ; iif++ ) {
3164 double range0 = iffreq[itable][2*iif] ;
3165 double range1 = iffreq[itable][2*iif+1] ;
3166 for ( uInt j = 0 ; j < sortedfreq.size()-1 ; j++ ) {
3167 double fmin = max( range0, sortedfreq[j] ) ;
3168 double fmax = min( range1, sortedfreq[j+1] ) ;
3169 if ( fmin < fmax ) {
3170 ifgrp[j]++ ;
3171 }
3172 }
3173 }
3174 }
3175
3176 // Grouping continuous IF groups (without frequency gap)
3177 // freqgrp: list of IF group indexes in each frequency group
3178 // freqgrp[numgrp][nummember]
3179 // freqgrp: [[ifgrp00, ifgrp01, ifgrp02, ...],
3180 // [ifgrp10, ifgrp11, ifgrp12, ...],
3181 // ...
3182 // [ifgrpn0, ifgrpn1, ifgrpn2, ...]]
3183 // grprange[2*numgrp]
3184 // grprange: [fmin0,fmax0,fmin1,fmax1,...]
3185 vector< vector<uInt> > freqgrp ;
3186 vector<double> grprange ;
3187 vector<uInt> grpedge ;
3188 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3189 if ( ifgrp[igrp] <= sizecr ) {
3190 grpedge.push_back( igrp ) ;
3191 }
3192 }
3193 grpedge.push_back( ifgrp.size() ) ;
3194 uInt itmp = 0 ;
3195 for ( uInt i = 0 ; i < grpedge.size() ; i++ ) {
3196 int n = grpedge[i] - itmp ;
3197 if ( n > 0 ) {
3198 vector<uInt> members( n ) ;
3199 for ( int j = 0 ; j < n ; j++ ) {
3200 members[j] = itmp+j ;
3201 }
3202 freqgrp.push_back( members ) ;
3203 grprange.push_back( sortedfreq[itmp] ) ;
3204 grprange.push_back( sortedfreq[grpedge[i]] ) ;
3205 }
3206 itmp += n + 1 ;
3207 }
3208
3209 // print frequency group
3210 oss.str("") ;
3211 oss << "Frequency Group summary: " << endl ;
3212 oss << " GROUP_ID: [FREQ_MIN, FREQ_MAX]" << endl ;
3213 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3214 oss << " GROUP " << setw( 2 ) << i << ": [" << grprange[2*i] << "," << grprange[2*i+1] << "]" ;
3215 oss << endl ;
3216 }
3217 oss << endl ;
3218 os << oss.str() << LogIO::POST ;
3219
3220 // groups: list of frequency group index whose frequency range overlaps
3221 // with that of each table and IF
3222 // groups[numtable][numIF]
3223 // groups: [[grpx, grpy,...],
3224 // [grpa, grpb,...],
3225 // ...
3226 // [grpk, grpm,...]]
3227 vector< vector<uInt> > groups( insize ) ;
3228 for ( uInt i = 0 ; i < insize ; i++ ) {
3229 groups[i].resize( freqid[i].size() ) ;
3230 }
3231 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3232 for ( uInt ifreq = 0 ; ifreq < freqid[itable].size() ; ifreq++ ) {
3233 double minf = iffreq[itable][2*ifreq] ;
3234 uInt groupid ;
3235 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3236 vector<uInt> memberlist = freqgrp[igrp] ;
3237 if ( (minf >= grprange[2*igrp]) && (minf <= grprange[2*igrp+1]) ) {
3238 groupid = igrp ;
3239 break ;
3240 }
3241 }
3242 groups[itable][ifreq] = groupid ;
3243 }
3244 }
3245
3246
3247 // print membership
3248 oss.str("") ;
3249 for ( uInt i = 0 ; i < insize ; i++ ) {
3250 oss << "Table " << i << endl ;
3251 for ( uInt j = 0 ; j < groups[i].size() ; j++ ) {
3252 oss << " FREQ_ID " << setw( 2 ) << freqid[i][j] << ": " ;
3253 oss << setw( 2 ) << groups[i][j] ;
3254 oss << endl ;
3255 }
3256 }
3257 os << oss.str() << LogIO::POST ;
3258
3259 // reset SCANNO and IFNO/FREQ_ID: IF is reset by the result of sortation
3260 //os << "All IF number is set to IF group index" << LogIO::POST ;
3261 // reset SCANNO only when avmode != "SCAN"
3262 if ( avmode != "SCAN" ) {
3263 os << "All scan number is set to 0" << LogIO::POST ;
3264 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3265 uInt nrow = newin[itable]->nrow() ;
3266 Vector<uInt> resetScan( nrow, 0 ) ;
3267 newin[itable]->scanCol_.putColumn( resetScan ) ;
3268 }
3269 }
3270
3271 // reset spectra and flagtra: align spectral resolution
3272 //os << "Align spectral resolution" << LogIO::POST ;
3273 // gmaxdnu: the coarsest frequency resolution in the frequency group
3274 // gminfreq: lower frequency edge of the frequency group
3275 // gnchan: number of channels for the frequency group
3276 vector<double> gmaxdnu( freqgrp.size(), 0.0 ) ;
3277 vector<double> gminfreq( freqgrp.size() ) ;
3278 vector<double> gnchan( freqgrp.size() ) ;
3279 for ( uInt i = 0 ; i < insize ; i++ ) {
3280 vector<uInt> members = groups[i] ;
3281 for ( uInt j = 0 ; j < members.size() ; j++ ) {
3282 uInt groupid = members[j] ;
3283 Double rp,rv,ic ;
3284 newin[i]->frequencies().getEntry( rp, rv, ic, j ) ;
3285 if ( abs(ic) > abs(gmaxdnu[groupid]) )
3286 gmaxdnu[groupid] = ic ;
3287 }
3288 }
3289 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3290 gminfreq[igrp] = grprange[2*igrp] ;
3291 double maxfreq = grprange[2*igrp+1] ;
3292 gnchan[igrp] = (int)(abs((maxfreq-gminfreq[igrp])/gmaxdnu[igrp])+0.9) ;
3293 }
3294
3295 // regrid spectral data and update frequency info
3296 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3297 Vector<uInt> oldFreqId = newin[itable]->mfreqidCol_.getColumn() ;
3298 Vector<uInt> newFreqId( oldFreqId.nelements() ) ;
3299
3300 // update MAIN
3301 for ( uInt irow = 0 ; irow < newin[itable]->nrow() ; irow++ ) {
3302 uInt groupid = groups[itable][oldFreqId[irow]] ;
3303 newFreqId[irow] = groupid ;
3304 newin[itable]->regridChannel( gnchan[groupid],
3305 gmaxdnu[groupid],
3306 gminfreq[groupid],
3307 irow ) ;
3308 }
3309 newin[itable]->mfreqidCol_.putColumn( newFreqId ) ;
3310 newin[itable]->ifCol_.putColumn( newFreqId ) ;
3311
3312 // update FREQUENCIES
3313 Table tab = newin[itable]->frequencies().table() ;
3314 ScalarColumn<uInt> fIdCol( tab, "ID" ) ;
3315 ScalarColumn<Double> fRefPixCol( tab, "REFPIX" ) ;
3316 ScalarColumn<Double> fRefValCol( tab, "REFVAL" ) ;
3317 ScalarColumn<Double> fIncrCol( tab, "INCREMENT" ) ;
3318 if ( freqgrp.size() > tab.nrow() ) {
3319 tab.addRow( freqgrp.size()-tab.nrow() ) ;
3320 }
3321 for ( uInt irow = 0 ; irow < freqgrp.size() ; irow++ ) {
3322 Double refval = gminfreq[irow] + 0.5 * abs(gmaxdnu[irow]) ;
3323 Double refpix = (gmaxdnu[irow] > 0.0) ? 0 : gnchan[irow]-1 ;
3324 Double increment = gmaxdnu[irow] ;
3325 fIdCol.put( irow, irow ) ;
3326 fRefPixCol.put( irow, refpix ) ;
3327 fRefValCol.put( irow, refval ) ;
3328 fIncrCol.put( irow, increment ) ;
3329 }
3330 }
3331
3332 // set back coordinfo
3333 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3334 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3335 coordinfo[0] = oldinfo[itable] ;
3336 newin[itable]->setCoordInfo( coordinfo ) ;
3337 }
3338
3339 // average
3340 out = average( newin, mask, weight, avmode ) ;
3341 }
3342 else {
3343 // simple average
3344 out = average( in, mask, weight, avmode ) ;
3345 }
3346
3347 return out;
3348}
3349
3350CountedPtr<Scantable> STMath::cwcal( const CountedPtr<Scantable>& s,
3351 const String calmode,
3352 const String antname )
3353{
3354 // frequency switch
3355 if ( calmode == "fs" ) {
3356 return cwcalfs( s, antname ) ;
3357 }
3358 else {
3359 vector<bool> masks = s->getMask( 0 ) ;
3360 vector<int> types ;
3361
3362 // save original table selection
3363 Table torg = s->table_ ;
3364
3365 // sky scan
3366 bool insitu = insitu_ ;
3367 insitu_ = false ;
3368 // share calibration scans before average with out
3369 CountedPtr<Scantable> out = getScantable( s, true ) ;
3370 insitu_ = insitu ;
3371 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::SKY ) ;
3372 out->attach() ;
3373 CountedPtr<Scantable> asky = averageWithinSession( out,
3374 masks,
3375 "TINT" ) ;
3376 // hot scan
3377 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::HOT ) ;
3378 out->attach() ;
3379 CountedPtr<Scantable> ahot = averageWithinSession( out,
3380 masks,
3381 "TINT" ) ;
3382 // cold scan
3383 CountedPtr<Scantable> acold ;
3384// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::COLD ) ;
3385// out->attach() ;
3386// CountedPtr<Scantable> acold = averageWithinSession( out,
3387// masks,
3388// "TINT" ) ;
3389
3390 // off scan
3391 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3392 out->attach() ;
3393 CountedPtr<Scantable> aoff = averageWithinSession( out,
3394 masks,
3395 "TINT" ) ;
3396
3397 // on scan
3398 s->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3399 s->attach() ;
3400 out->table_ = out->originalTable_ ;
3401 out->attach() ;
3402 out->table().addRow( s->nrow() ) ;
3403 copyRows( out->table(), s->table(), 0, 0, s->nrow(), False, True, False ) ;
3404
3405 // process each on scan
3406 STSelector sel ;
3407 vector<string> cols( 3 ) ;
3408 cols[0] = "BEAMNO" ;
3409 cols[1] = "POLNO" ;
3410 cols[2] = "IFNO" ;
3411 STIdxIter *iter = new STIdxIterAcc( out, cols ) ;
3412 while ( !iter->pastEnd() ) {
3413 Vector<uInt> ids = iter->current() ;
3414 stringstream ss ;
3415 ss << "SELECT FROM $1 WHERE "
3416 << "BEAMNO==" << ids[0] << "&&"
3417 << "POLNO==" << ids[1] << "&&"
3418 << "IFNO==" << ids[2] ;
3419 //cout << "TaQL string: " << ss.str() << endl ;
3420 sel.setTaQL( ss.str() ) ;
3421 aoff->setSelection( sel ) ;
3422 ahot->setSelection( sel ) ;
3423 asky->setSelection( sel ) ;
3424 Vector<uInt> rows = iter->getRows( SHARE ) ;
3425 // out should be an exact copy of s except that SPECTRA column is empty
3426 calibrateCW( out, s, aoff, asky, ahot, acold, rows, antname ) ;
3427 aoff->unsetSelection() ;
3428 ahot->unsetSelection() ;
3429 asky->unsetSelection() ;
3430 sel.reset() ;
3431 iter->next() ;
3432 }
3433 delete iter ;
3434 s->table_ = torg ;
3435 s->attach() ;
3436
3437 // flux unit
3438 out->setFluxUnit( "K" ) ;
3439
3440 return out ;
3441 }
3442}
3443
3444CountedPtr<Scantable> STMath::almacal( const CountedPtr<Scantable>& s,
3445 const String calmode )
3446{
3447 // frequency switch
3448 if ( calmode == "fs" ) {
3449 return almacalfs( s ) ;
3450 }
3451 else {
3452// double t0, t1 ;
3453// t0 = mathutil::gettimeofday_sec() ;
3454 vector<bool> masks = s->getMask( 0 ) ;
3455
3456 // save original table selection
3457 Table torg = s->table_ ;
3458
3459 // off scan
3460 // TODO 2010/01/08 TN
3461 // Grouping by time should be needed before averaging.
3462 // Each group must have own unique SCANNO (should be renumbered).
3463 // See PIPELINE/SDCalibration.py
3464 bool insitu = insitu_ ;
3465 insitu_ = false ;
3466 // share off scan before average with out
3467 CountedPtr<Scantable> out = getScantable( s, true ) ;
3468 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3469 out->attach() ;
3470 insitu_ = insitu ;
3471 CountedPtr<Scantable> aoff = averageWithinSession( out,
3472 masks,
3473 "TINT" ) ;
3474
3475 // on scan
3476// t0 = mathutil::gettimeofday_sec() ;
3477 s->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3478 s->attach() ;
3479 out->table_ = out->originalTable_ ;
3480 out->attach() ;
3481 out->table().addRow( s->nrow() ) ;
3482 copyRows( out->table(), s->table(), 0, 0, s->nrow(), False ) ;
3483// t1 = mathutil::gettimeofday_sec() ;
3484// cout << "elapsed time for preparing output table: " << t1-t0 << " sec" << endl ;
3485
3486 // process each on scan
3487// t0 = mathutil::gettimeofday_sec() ;
3488
3489 // using STIdxIterAcc
3490 vector<string> cols( 3 ) ;
3491 cols[0] = "BEAMNO" ;
3492 cols[1] = "POLNO" ;
3493 cols[2] = "IFNO" ;
3494 STIdxIter *iter = new STIdxIterAcc( out, cols ) ;
3495 STSelector sel ;
3496 while ( !iter->pastEnd() ) {
3497 Vector<uInt> ids = iter->current() ;
3498 stringstream ss ;
3499 ss << "SELECT FROM $1 WHERE "
3500 << "BEAMNO==" << ids[0] << "&&"
3501 << "POLNO==" << ids[1] << "&&"
3502 << "IFNO==" << ids[2] ;
3503 //cout << "TaQL string: " << ss.str() << endl ;
3504 sel.setTaQL( ss.str() ) ;
3505 aoff->setSelection( sel ) ;
3506 Vector<uInt> rows = iter->getRows( SHARE ) ;
3507 // out should be an exact copy of s except that SPECTRA column is empty
3508 calibrateALMA( out, s, aoff, rows ) ;
3509 aoff->unsetSelection() ;
3510 sel.reset() ;
3511 iter->next() ;
3512 }
3513 delete iter ;
3514 s->table_ = torg ;
3515 s->attach() ;
3516
3517// t1 = mathutil::gettimeofday_sec() ;
3518// cout << "elapsed time for calibration: " << t1-t0 << " sec" << endl ;
3519
3520 // flux unit
3521 out->setFluxUnit( "K" ) ;
3522
3523 return out ;
3524 }
3525}
3526
3527CountedPtr<Scantable> STMath::cwcalfs( const CountedPtr<Scantable>& s,
3528 const String antname )
3529{
3530 vector<int> types ;
3531
3532 // APEX calibration mode
3533 int apexcalmode = 1 ;
3534
3535 if ( antname.find( "APEX" ) != string::npos ) {
3536 // check if off scan exists or not
3537 STSelector sel = STSelector() ;
3538 //sel.setName( offstr1 ) ;
3539 types.push_back( SrcType::FLOOFF ) ;
3540 sel.setTypes( types ) ;
3541 try {
3542 s->setSelection( sel ) ;
3543 }
3544 catch ( AipsError &e ) {
3545 apexcalmode = 0 ;
3546 }
3547 sel.reset() ;
3548 }
3549 s->unsetSelection() ;
3550 types.clear() ;
3551
3552 vector<bool> masks = s->getMask( 0 ) ;
3553 CountedPtr<Scantable> ssig, sref ;
3554 //CountedPtr<Scantable> out ;
3555 bool insitu = insitu_ ;
3556 insitu_ = False ;
3557 CountedPtr<Scantable> out = getScantable( s, true ) ;
3558 insitu_ = insitu ;
3559
3560 if ( antname.find( "APEX" ) != string::npos ) {
3561 // APEX calibration
3562 // sky scan
3563 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOSKY ) ;
3564 out->attach() ;
3565 CountedPtr<Scantable> askylo = averageWithinSession( out,
3566 masks,
3567 "TINT" ) ;
3568 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHISKY ) ;
3569 out->attach() ;
3570 CountedPtr<Scantable> askyhi = averageWithinSession( out,
3571 masks,
3572 "TINT" ) ;
3573
3574 // hot scan
3575 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOHOT ) ;
3576 out->attach() ;
3577 CountedPtr<Scantable> ahotlo = averageWithinSession( out,
3578 masks,
3579 "TINT" ) ;
3580 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHIHOT ) ;
3581 out->attach() ;
3582 CountedPtr<Scantable> ahothi = averageWithinSession( out,
3583 masks,
3584 "TINT" ) ;
3585
3586 // cold scan
3587 CountedPtr<Scantable> acoldlo, acoldhi ;
3588// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOCOLD ) ;
3589// out->attach() ;
3590// CountedPtr<Scantable> acoldlo = averageWithinSession( out,
3591// masks,
3592// "TINT" ) ;
3593// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHICOLD ) ;
3594// out->attach() ;
3595// CountedPtr<Scantable> acoldhi = averageWithinSession( out,
3596// masks,
3597// "TINT" ) ;
3598
3599 // ref scan
3600 insitu_ = false ;
3601 sref = getScantable( s, true ) ;
3602 CountedPtr<Scantable> rref = getScantable( s, true ) ;
3603 insitu_ = insitu ;
3604 rref->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FSLO ) ;
3605 rref->attach() ;
3606 copyRows( sref->table_, rref->table_, 0, 0, rref->nrow(), False, True, False ) ;
3607
3608 // sig scan
3609 insitu_ = false ;
3610 ssig = getScantable( s, true ) ;
3611 CountedPtr<Scantable> rsig = getScantable( s, true ) ;
3612 insitu_ = insitu ;
3613 rsig->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FSHI ) ;
3614 rsig->attach() ;
3615 copyRows( ssig->table_, rsig->table_, 0, 0, rsig->nrow(), False, True, False ) ;
3616
3617 if ( apexcalmode == 0 ) {
3618 // using STIdxIterAcc
3619 vector<string> cols( 3 ) ;
3620 cols[0] = "BEAMNO" ;
3621 cols[1] = "POLNO" ;
3622 cols[2] = "IFNO" ;
3623 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
3624 STSelector sel ;
3625 vector< CountedPtr<Scantable> > on( 2 ) ;
3626 on[0] = rsig ;
3627 on[1] = rref ;
3628 vector< CountedPtr<Scantable> > sky( 2 ) ;
3629 sky[0] = askylo ;
3630 sky[1] = askyhi ;
3631 vector< CountedPtr<Scantable> > hot( 2 ) ;
3632 hot[0] = ahotlo ;
3633 hot[1] = ahothi ;
3634 vector< CountedPtr<Scantable> > cold( 2 ) ;
3635 while ( !iter->pastEnd() ) {
3636 Vector<uInt> ids = iter->current() ;
3637 stringstream ss ;
3638 ss << "SELECT FROM $1 WHERE "
3639 << "BEAMNO==" << ids[0] << "&&"
3640 << "POLNO==" << ids[1] << "&&"
3641 << "IFNO==" << ids[2] ;
3642 //cout << "TaQL string: " << ss.str() << endl ;
3643 sel.setTaQL( ss.str() ) ;
3644 sky[0]->setSelection( sel ) ;
3645 sky[1]->setSelection( sel ) ;
3646 hot[0]->setSelection( sel ) ;
3647 hot[1]->setSelection( sel ) ;
3648 Vector<uInt> rows = iter->getRows( SHARE ) ;
3649 calibrateAPEXFS( ssig, sref, on, sky, hot, cold, rows ) ;
3650 sky[0]->unsetSelection() ;
3651 sky[1]->unsetSelection() ;
3652 hot[0]->unsetSelection() ;
3653 hot[1]->unsetSelection() ;
3654 sel.reset() ;
3655 iter->next() ;
3656 }
3657 delete iter ;
3658
3659 }
3660 else if ( apexcalmode == 1 ) {
3661 // APEX fs data with off scan
3662 // off scan
3663 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FLOOFF ) ;
3664 out->attach() ;
3665 CountedPtr<Scantable> aofflo = averageWithinSession( out,
3666 masks,
3667 "TINT" ) ;
3668 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::FHIOFF ) ;
3669 out->attach() ;
3670 CountedPtr<Scantable> aoffhi = averageWithinSession( out,
3671 masks,
3672 "TINT" ) ;
3673
3674 // process each sig and ref scan
3675// STSelector sel ;
3676 vector<string> cols( 3 ) ;
3677 cols[0] = "BEAMNO" ;
3678 cols[1] = "POLNO" ;
3679 cols[2] = "IFNO" ;
3680 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
3681 STSelector sel ;
3682 while ( !iter->pastEnd() ) {
3683 Vector<uInt> ids = iter->current() ;
3684 stringstream ss ;
3685 ss << "SELECT FROM $1 WHERE "
3686 << "BEAMNO==" << ids[0] << "&&"
3687 << "POLNO==" << ids[1] << "&&"
3688 << "IFNO==" << ids[2] ;
3689 //cout << "TaQL string: " << ss.str() << endl ;
3690 sel.setTaQL( ss.str() ) ;
3691 aofflo->setSelection( sel ) ;
3692 ahotlo->setSelection( sel ) ;
3693 askylo->setSelection( sel ) ;
3694 Vector<uInt> rows = iter->getRows( SHARE ) ;
3695 calibrateCW( ssig, rsig, aofflo, askylo, ahotlo, acoldlo, rows, antname ) ;
3696 aofflo->unsetSelection() ;
3697 ahotlo->unsetSelection() ;
3698 askylo->unsetSelection() ;
3699 sel.reset() ;
3700 iter->next() ;
3701 }
3702 delete iter ;
3703 iter = new STIdxIterAcc( sref, cols ) ;
3704 while ( !iter->pastEnd() ) {
3705 Vector<uInt> ids = iter->current() ;
3706 stringstream ss ;
3707 ss << "SELECT FROM $1 WHERE "
3708 << "BEAMNO==" << ids[0] << "&&"
3709 << "POLNO==" << ids[1] << "&&"
3710 << "IFNO==" << ids[2] ;
3711 //cout << "TaQL string: " << ss.str() << endl ;
3712 sel.setTaQL( ss.str() ) ;
3713 aoffhi->setSelection( sel ) ;
3714 ahothi->setSelection( sel ) ;
3715 askyhi->setSelection( sel ) ;
3716 Vector<uInt> rows = iter->getRows( SHARE ) ;
3717 calibrateCW( sref, rref, aoffhi, askyhi, ahothi, acoldhi, rows, antname ) ;
3718 aoffhi->unsetSelection() ;
3719 ahothi->unsetSelection() ;
3720 askyhi->unsetSelection() ;
3721 sel.reset() ;
3722 iter->next() ;
3723 }
3724 delete iter ;
3725 }
3726 }
3727 else {
3728 // non-APEX fs data
3729 // sky scan
3730 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::SKY ) ;
3731 out->attach() ;
3732 CountedPtr<Scantable> asky = averageWithinSession( out,
3733 masks,
3734 "TINT" ) ;
3735 STSelector sel = STSelector() ;
3736
3737 // hot scan
3738 out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::HOT ) ;
3739 out->attach() ;
3740 CountedPtr<Scantable> ahot = averageWithinSession( out,
3741 masks,
3742 "TINT" ) ;
3743
3744 // cold scan
3745 CountedPtr<Scantable> acold ;
3746// out->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::COLD ) ;
3747// out->attach() ;
3748// CountedPtr<Scantable> acold = averageWithinSession( out,
3749// masks,
3750// "TINT" ) ;
3751
3752 // ref scan
3753 bool insitu = insitu_ ;
3754 insitu_ = false ;
3755 sref = getScantable( s, true ) ;
3756 CountedPtr<Scantable> rref = getScantable( s, true ) ;
3757 insitu_ = insitu ;
3758 rref->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSOFF ) ;
3759 rref->attach() ;
3760 copyRows( sref->table_, rref->table_, 0, 0, rref->nrow(), False, True, False ) ;
3761
3762 // sig scan
3763 insitu_ = false ;
3764 ssig = getScantable( s, true ) ;
3765 CountedPtr<Scantable> rsig = getScantable( s, true ) ;
3766 insitu_ = insitu ;
3767 rsig->table_ = s->table_( s->table_.col("SRCTYPE") == (Int)SrcType::PSON ) ;
3768 rsig->attach() ;
3769 copyRows( ssig->table_, rsig->table_, 0, 0, rsig->nrow(), False, True, False ) ;
3770
3771 // process each sig and ref scan
3772 vector<string> cols( 3 ) ;
3773 cols[0] = "BEAMNO" ;
3774 cols[1] = "POLNO" ;
3775 cols[2] = "IFNO" ;
3776 STIdxIter *iter = new STIdxIterAcc( ssig, cols ) ;
3777 while ( !iter->pastEnd() ) {
3778 Vector<uInt> ids = iter->current() ;
3779 stringstream ss ;
3780 ss << "SELECT FROM $1 WHERE "
3781 << "BEAMNO==" << ids[0] << "&&"
3782 << "POLNO==" << ids[1] << "&&"
3783 << "IFNO==" << ids[2] ;
3784 //cout << "TaQL string: " << ss.str() << endl ;
3785 sel.setTaQL( ss.str() ) ;
3786 ahot->setSelection( sel ) ;
3787 asky->setSelection( sel ) ;
3788 Vector<uInt> rows = iter->getRows( SHARE ) ;
3789 // out should be an exact copy of s except that SPECTRA column is empty
3790 calibrateFS( ssig, sref, rsig, rref, asky, ahot, acold, rows ) ;
3791 ahot->unsetSelection() ;
3792 asky->unsetSelection() ;
3793 sel.reset() ;
3794 iter->next() ;
3795 }
3796 delete iter ;
3797 }
3798
3799 // do folding if necessary
3800 Table sigtab = ssig->table() ;
3801 Table reftab = sref->table() ;
3802 ScalarColumn<uInt> reffidCol ;
3803 Int nchan = (Int)ssig->nchan() ;
3804 reffidCol.attach( reftab, "FREQ_ID" ) ;
3805 Vector<uInt> sfids = ssig->mfreqidCol_.getColumn() ;
3806 Vector<uInt> rfids = sref->mfreqidCol_.getColumn() ;
3807 vector<uInt> sfids_unique ;
3808 vector<uInt> rfids_unique ;
3809 vector<uInt> sifno_unique ;
3810 vector<uInt> rifno_unique ;
3811 for ( uInt i = 0 ; i < sfids.nelements() ; i++ ) {
3812 if ( count( sfids_unique.begin(), sfids_unique.end(), sfids[i] ) == 0 ) {
3813 sfids_unique.push_back( sfids[i] ) ;
3814 sifno_unique.push_back( ssig->getIF( i ) ) ;
3815 }
3816 if ( count( rfids_unique.begin(), rfids_unique.end(), rfids[i] ) == 0 ) {
3817 rfids_unique.push_back( rfids[i] ) ;
3818 rifno_unique.push_back( sref->getIF( i ) ) ;
3819 }
3820 }
3821 double refpix_sig, refval_sig, increment_sig ;
3822 double refpix_ref, refval_ref, increment_ref ;
3823 vector< CountedPtr<Scantable> > tmp( sfids_unique.size() ) ;
3824 for ( uInt i = 0 ; i < sfids_unique.size() ; i++ ) {
3825 ssig->frequencies().getEntry( refpix_sig, refval_sig, increment_sig, sfids_unique[i] ) ;
3826 sref->frequencies().getEntry( refpix_ref, refval_ref, increment_ref, rfids_unique[i] ) ;
3827 if ( refpix_sig == refpix_ref ) {
3828 double foffset = refval_ref - refval_sig ;
3829 int choffset = static_cast<int>(foffset/increment_sig) ;
3830 double doffset = foffset / increment_sig ;
3831 if ( abs(choffset) >= nchan ) {
3832 LogIO os( LogOrigin( "STMath", "cwcalfs", WHERE ) ) ;
3833 os << "FREQ_ID=[" << sfids_unique[i] << "," << rfids_unique[i] << "]: out-band frequency switching, no folding" << LogIO::POST ;
3834 os << "Just return signal data" << LogIO::POST ;
3835 //std::vector< CountedPtr<Scantable> > tabs ;
3836 //tabs.push_back( ssig ) ;
3837 //tabs.push_back( sref ) ;
3838 //out = merge( tabs ) ;
3839 tmp[i] = ssig ;
3840 }
3841 else {
3842 STSelector sel = STSelector() ;
3843 vector<int> v( 1, sifno_unique[i] ) ;
3844 sel.setIFs( v ) ;
3845 ssig->setSelection( sel ) ;
3846 sel.reset() ;
3847 v[0] = rifno_unique[i] ;
3848 sel.setIFs( v ) ;
3849 sref->setSelection( sel ) ;
3850 sel.reset() ;
3851 if ( antname.find( "APEX" ) != string::npos ) {
3852 tmp[i] = dofold( ssig, sref, 0.5*doffset, -0.5*doffset ) ;
3853 //tmp[i] = dofold( ssig, sref, doffset ) ;
3854 }
3855 else {
3856 tmp[i] = dofold( ssig, sref, doffset ) ;
3857 }
3858 ssig->unsetSelection() ;
3859 sref->unsetSelection() ;
3860 }
3861 }
3862 }
3863
3864 if ( tmp.size() > 1 ) {
3865 out = merge( tmp ) ;
3866 }
3867 else {
3868 out = tmp[0] ;
3869 }
3870
3871 // flux unit
3872 out->setFluxUnit( "K" ) ;
3873
3874 return out ;
3875}
3876
3877CountedPtr<Scantable> STMath::almacalfs( const CountedPtr<Scantable>& s )
3878{
3879 (void) s; //currently unused
3880 CountedPtr<Scantable> out ;
3881
3882 return out ;
3883}
3884
3885Vector<Float> STMath::getSpectrumFromTime( double reftime,
3886 const Vector<Double> &timeVec,
3887 const vector<int> &idx,
3888 const Matrix<Float>& spectra,
3889 string mode )
3890{
3891 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
3892 Vector<Float> sp ;
3893 uInt ncol = spectra.ncolumn() ;
3894
3895 if ( ncol == 0 ) {
3896 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
3897 return sp ;
3898 }
3899 else if ( ncol == 1 ) {
3900 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
3901 sp.reference( spectra.column( 0 ) ) ;
3902 return sp ;
3903 }
3904 else {
3905 if ( mode == "before" ) {
3906 int id = -1 ;
3907 if ( idx[0] != -1 ) {
3908 id = idx[0] ;
3909 }
3910 else if ( idx[1] != -1 ) {
3911 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
3912 id = idx[1] ;
3913 }
3914 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3915 sp.reference( spectra.column( id ) ) ;
3916 }
3917 else if ( mode == "after" ) {
3918 int id = -1 ;
3919 if ( idx[1] != -1 ) {
3920 id = idx[1] ;
3921 }
3922 else if ( idx[0] != -1 ) {
3923 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
3924 id = idx[1] ;
3925 }
3926 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3927 sp.reference( spectra.column( id ) ) ;
3928 }
3929 else if ( mode == "nearest" ) {
3930 int id = -1 ;
3931 if ( idx[0] == -1 ) {
3932 id = idx[1] ;
3933 }
3934 else if ( idx[1] == -1 ) {
3935 id = idx[0] ;
3936 }
3937 else if ( idx[0] == idx[1] ) {
3938 id = idx[0] ;
3939 }
3940 else {
3941 double t0 = timeVec[idx[0]] ;
3942 double t1 = timeVec[idx[1]] ;
3943 double tref = reftime ;
3944 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
3945 id = idx[1] ;
3946 }
3947 else {
3948 id = idx[0] ;
3949 }
3950 }
3951 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3952 sp.reference( spectra.column( id ) ) ;
3953 }
3954 else if ( mode == "linear" ) {
3955 if ( idx[0] == -1 ) {
3956 // use after
3957 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
3958 int id = idx[1] ;
3959 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3960 sp.reference( spectra.column( id ) ) ;
3961 }
3962 else if ( idx[1] == -1 ) {
3963 // use before
3964 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
3965 int id = idx[0] ;
3966 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3967 sp.reference( spectra.column( id ) ) ;
3968 }
3969 else if ( idx[0] == idx[1] ) {
3970 // use before
3971 //os << "No need to interporate." << LogIO::POST ;
3972 int id = idx[0] ;
3973 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
3974 sp.reference( spectra.column( id ) ) ;
3975 }
3976 else {
3977 // do interpolation
3978 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
3979 double t0 = timeVec[idx[0]] ;
3980 double t1 = timeVec[idx[1]] ;
3981 double tref = reftime ;
3982 sp = spectra.column( idx[0] ).copy() ;
3983 Vector<Float> sp1( spectra.column( idx[1] ) ) ;
3984 double tfactor = ( tref - t0 ) / ( t1 - t0 ) ;
3985 for ( unsigned int i = 0 ; i < sp.size() ; i++ ) {
3986 sp[i] = ( sp1[i] - sp[i] ) * tfactor + sp[i] ;
3987 }
3988 }
3989 }
3990 else {
3991 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
3992 }
3993 return sp ;
3994 }
3995}
3996
3997vector<int> STMath::getRowIdFromTime( double reftime, const Vector<Double> &t )
3998{
3999// double reft = reftime ;
4000 double dtmin = 1.0e100 ;
4001 double dtmax = -1.0e100 ;
4002// vector<double> dt ;
4003 int just_before = -1 ;
4004 int just_after = -1 ;
4005 Vector<Double> dt = t - reftime ;
4006 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4007 if ( dt[i] > 0.0 ) {
4008 // after reftime
4009 if ( dt[i] < dtmin ) {
4010 just_after = i ;
4011 dtmin = dt[i] ;
4012 }
4013 }
4014 else if ( dt[i] < 0.0 ) {
4015 // before reftime
4016 if ( dt[i] > dtmax ) {
4017 just_before = i ;
4018 dtmax = dt[i] ;
4019 }
4020 }
4021 else {
4022 // just a reftime
4023 just_before = i ;
4024 just_after = i ;
4025 dtmax = 0 ;
4026 dtmin = 0 ;
4027 break ;
4028 }
4029 }
4030
4031 vector<int> v(2) ;
4032 v[0] = just_before ;
4033 v[1] = just_after ;
4034
4035 return v ;
4036}
4037
4038Vector<Float> STMath::getTcalFromTime( double reftime,
4039 const Vector<Double> &timeVec,
4040 const vector<int> &idx,
4041 const CountedPtr<Scantable>& s,
4042 string mode )
4043{
4044 LogIO os( LogOrigin( "STMath", "getTcalFromTime", WHERE ) ) ;
4045 STTcal tcalTable = s->tcal() ;
4046 String time ;
4047 Vector<Float> tcalval ;
4048 if ( s->nrow() == 0 ) {
4049 os << LogIO::SEVERE << "No row in the input scantable. Return empty tcal." << LogIO::POST ;
4050 return tcalval ;
4051 }
4052 else if ( s->nrow() == 1 ) {
4053 uInt tcalid = s->getTcalId( 0 ) ;
4054 //os << "use row " << 0 << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4055 tcalTable.getEntry( time, tcalval, tcalid ) ;
4056 return tcalval ;
4057 }
4058 else {
4059 if ( mode == "before" ) {
4060 int id = -1 ;
4061 if ( idx[0] != -1 ) {
4062 id = idx[0] ;
4063 }
4064 else if ( idx[1] != -1 ) {
4065 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4066 id = idx[1] ;
4067 }
4068 uInt tcalid = s->getTcalId( id ) ;
4069 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4070 tcalTable.getEntry( time, tcalval, tcalid ) ;
4071 }
4072 else if ( mode == "after" ) {
4073 int id = -1 ;
4074 if ( idx[1] != -1 ) {
4075 id = idx[1] ;
4076 }
4077 else if ( idx[0] != -1 ) {
4078 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4079 id = idx[1] ;
4080 }
4081 uInt tcalid = s->getTcalId( id ) ;
4082 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4083 tcalTable.getEntry( time, tcalval, tcalid ) ;
4084 }
4085 else if ( mode == "nearest" ) {
4086 int id = -1 ;
4087 if ( idx[0] == -1 ) {
4088 id = idx[1] ;
4089 }
4090 else if ( idx[1] == -1 ) {
4091 id = idx[0] ;
4092 }
4093 else if ( idx[0] == idx[1] ) {
4094 id = idx[0] ;
4095 }
4096 else {
4097 double t0 = timeVec[idx[0]] ;
4098 double t1 = timeVec[idx[1]] ;
4099 if ( abs( t0 - reftime ) > abs( t1 - reftime ) ) {
4100 id = idx[1] ;
4101 }
4102 else {
4103 id = idx[0] ;
4104 }
4105 }
4106 uInt tcalid = s->getTcalId( id ) ;
4107 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4108 tcalTable.getEntry( time, tcalval, tcalid ) ;
4109 }
4110 else if ( mode == "linear" ) {
4111 if ( idx[0] == -1 ) {
4112 // use after
4113 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4114 int id = idx[1] ;
4115 uInt tcalid = s->getTcalId( id ) ;
4116 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4117 tcalTable.getEntry( time, tcalval, tcalid ) ;
4118 }
4119 else if ( idx[1] == -1 ) {
4120 // use before
4121 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4122 int id = idx[0] ;
4123 uInt tcalid = s->getTcalId( id ) ;
4124 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4125 tcalTable.getEntry( time, tcalval, tcalid ) ;
4126 }
4127 else if ( idx[0] == idx[1] ) {
4128 // use before
4129 //os << "No need to interporate." << LogIO::POST ;
4130 int id = idx[0] ;
4131 uInt tcalid = s->getTcalId( id ) ;
4132 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4133 tcalTable.getEntry( time, tcalval, tcalid ) ;
4134 }
4135 else {
4136 // do interpolation
4137 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4138 double t0 = timeVec[idx[0]] ;
4139 double t1 = timeVec[idx[1]] ;
4140 Vector<Float> tcal0 ;
4141 uInt tcalid0 = s->getTcalId( idx[0] ) ;
4142 uInt tcalid1 = s->getTcalId( idx[1] ) ;
4143 tcalTable.getEntry( time, tcal0, tcalid0 ) ;
4144 tcalTable.getEntry( time, tcalval, tcalid1 ) ;
4145 double tfactor = (reftime - t0) / (t1 - t0) ;
4146 for ( unsigned int i = 0 ; i < tcal0.size() ; i++ ) {
4147 tcalval[i] = ( tcalval[i] - tcal0[i] ) * tfactor + tcal0[i] ;
4148 }
4149 }
4150 }
4151 else {
4152 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4153 }
4154 return tcalval ;
4155 }
4156}
4157
4158Vector<Float> STMath::getTsysFromTime( double reftime,
4159 const Vector<Double> &timeVec,
4160 const vector<int> &idx,
4161 const CountedPtr<Scantable> &s,
4162 string mode )
4163{
4164 LogIO os( LogOrigin( "STMath", "getTsysFromTime", WHERE ) ) ;
4165 ArrayColumn<Float> tsysCol ;
4166 tsysCol.attach( s->table(), "TSYS" ) ;
4167 Vector<Float> tsysval ;
4168 if ( s->nrow() == 0 ) {
4169 os << LogIO::SEVERE << "No row in the input scantable. Return empty tsys." << LogIO::POST ;
4170 return tsysval ;
4171 }
4172 else if ( s->nrow() == 1 ) {
4173 //os << "use row " << 0 << LogIO::POST ;
4174 tsysval = tsysCol( 0 ) ;
4175 return tsysval ;
4176 }
4177 else {
4178 if ( mode == "before" ) {
4179 int id = -1 ;
4180 if ( idx[0] != -1 ) {
4181 id = idx[0] ;
4182 }
4183 else if ( idx[1] != -1 ) {
4184 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4185 id = idx[1] ;
4186 }
4187 //os << "use row " << id << LogIO::POST ;
4188 tsysval = tsysCol( id ) ;
4189 }
4190 else if ( mode == "after" ) {
4191 int id = -1 ;
4192 if ( idx[1] != -1 ) {
4193 id = idx[1] ;
4194 }
4195 else if ( idx[0] != -1 ) {
4196 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4197 id = idx[1] ;
4198 }
4199 //os << "use row " << id << LogIO::POST ;
4200 tsysval = tsysCol( id ) ;
4201 }
4202 else if ( mode == "nearest" ) {
4203 int id = -1 ;
4204 if ( idx[0] == -1 ) {
4205 id = idx[1] ;
4206 }
4207 else if ( idx[1] == -1 ) {
4208 id = idx[0] ;
4209 }
4210 else if ( idx[0] == idx[1] ) {
4211 id = idx[0] ;
4212 }
4213 else {
4214 double t0 = timeVec[idx[0]] ;
4215 double t1 = timeVec[idx[1]] ;
4216 if ( abs( t0 - reftime ) > abs( t1 - reftime ) ) {
4217 id = idx[1] ;
4218 }
4219 else {
4220 id = idx[0] ;
4221 }
4222 }
4223 //os << "use row " << id << LogIO::POST ;
4224 tsysval = tsysCol( id ) ;
4225 }
4226 else if ( mode == "linear" ) {
4227 if ( idx[0] == -1 ) {
4228 // use after
4229 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4230 int id = idx[1] ;
4231 //os << "use row " << id << LogIO::POST ;
4232 tsysval = tsysCol( id ) ;
4233 }
4234 else if ( idx[1] == -1 ) {
4235 // use before
4236 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4237 int id = idx[0] ;
4238 //os << "use row " << id << LogIO::POST ;
4239 tsysval = tsysCol( id ) ;
4240 }
4241 else if ( idx[0] == idx[1] ) {
4242 // use before
4243 //os << "No need to interporate." << LogIO::POST ;
4244 int id = idx[0] ;
4245 //os << "use row " << id << LogIO::POST ;
4246 tsysval = tsysCol( id ) ;
4247 }
4248 else {
4249 // do interpolation
4250 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4251 double t0 = timeVec[idx[0]] ;
4252 double t1 = timeVec[idx[1]] ;
4253 Vector<Float> tsys0 ;
4254 tsys0 = tsysCol( idx[0] ) ;
4255 tsysval = tsysCol( idx[1] ) ;
4256 double tfactor = (reftime - t0) / (t1 - t0) ;
4257 for ( unsigned int i = 0 ; i < tsys0.size() ; i++ ) {
4258 tsysval[i] = ( tsysval[i] - tsys0[i] ) * tfactor + tsys0[i] ;
4259 }
4260 }
4261 }
4262 else {
4263 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4264 }
4265 return tsysval ;
4266 }
4267}
4268
4269void STMath::calibrateCW( CountedPtr<Scantable> &out,
4270 const CountedPtr<Scantable>& on,
4271 const CountedPtr<Scantable>& off,
4272 const CountedPtr<Scantable>& sky,
4273 const CountedPtr<Scantable>& hot,
4274 const CountedPtr<Scantable>& cold,
4275 const Vector<uInt> &rows,
4276 const String &antname )
4277{
4278 // 2012/05/22 TN
4279 // Assume that out has empty SPECTRA column
4280
4281 // if rows is empty, just return
4282 if ( rows.nelements() == 0 )
4283 return ;
4284 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
4285 Vector<Double> timeOff = timeCol.getColumn() ;
4286 timeCol.attach( sky->table(), "TIME" ) ;
4287 Vector<Double> timeSky = timeCol.getColumn() ;
4288 timeCol.attach( hot->table(), "TIME" ) ;
4289 Vector<Double> timeHot = timeCol.getColumn() ;
4290 timeCol.attach( on->table(), "TIME" ) ;
4291 ROArrayColumn<Float> arrayFloatCol( off->table(), "SPECTRA" ) ;
4292 Matrix<Float> offspectra = arrayFloatCol.getColumn() ;
4293 arrayFloatCol.attach( sky->table(), "SPECTRA" ) ;
4294 Matrix<Float> skyspectra = arrayFloatCol.getColumn() ;
4295 arrayFloatCol.attach( hot->table(), "SPECTRA" ) ;
4296 Matrix<Float> hotspectra = arrayFloatCol.getColumn() ;
4297 unsigned int spsize = on->nchan( on->getIF(rows[0]) ) ;
4298 // I know that the data is contiguous
4299 const uInt *p = rows.data() ;
4300 vector<int> ids( 2 ) ;
4301 Block<uInt> flagchan( spsize ) ;
4302 uInt nflag = 0 ;
4303 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4304 double reftime = timeCol.asdouble(*p) ;
4305 ids = getRowIdFromTime( reftime, timeOff ) ;
4306 Vector<Float> spoff = getSpectrumFromTime( reftime, timeOff, ids, offspectra, "linear" ) ;
4307 ids = getRowIdFromTime( reftime, timeSky ) ;
4308 Vector<Float> spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
4309 Vector<Float> tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4310 Vector<Float> tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4311 ids = getRowIdFromTime( reftime, timeHot ) ;
4312 Vector<Float> sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra, "linear" ) ;
4313 Vector<Float> spec = on->specCol_( *p ) ;
4314 if ( antname.find( "APEX" ) != String::npos ) {
4315 // using gain array
4316 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4317 if ( spoff[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
4318 spec[j] = 0.0 ;
4319 flagchan[nflag++] = j ;
4320 }
4321 else {
4322 spec[j] = ( ( spec[j] - spoff[j] ) / spoff[j] )
4323 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4324 }
4325 }
4326 }
4327 else {
4328 // Chopper-Wheel calibration (Ulich & Haas 1976)
4329 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4330 if ( (sphot[j]-spsky[j]) == 0.0 ) {
4331 spec[j] = 0.0 ;
4332 flagchan[nflag++] = j ;
4333 }
4334 else {
4335 spec[j] = ( spec[j] - spoff[j] ) / ( sphot[j] - spsky[j] ) * tcal[j] ;
4336 }
4337 }
4338 }
4339 out->specCol_.put( *p, spec ) ;
4340 out->tsysCol_.put( *p, tsys ) ;
4341 if ( nflag > 0 ) {
4342 Vector<uChar> fl = out->flagsCol_( *p ) ;
4343 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4344 fl[flagchan[j]] = (uChar)True ;
4345 }
4346 out->flagsCol_.put( *p, fl ) ;
4347 }
4348 nflag = 0 ;
4349 p++ ;
4350 }
4351}
4352
4353void STMath::calibrateALMA( CountedPtr<Scantable>& out,
4354 const CountedPtr<Scantable>& on,
4355 const CountedPtr<Scantable>& off,
4356 const Vector<uInt>& rows )
4357{
4358 // 2012/05/22 TN
4359 // Assume that out has empty SPECTRA column
4360
4361 // if rows is empty, just return
4362 if ( rows.nelements() == 0 )
4363 return ;
4364 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
4365 Vector<Double> timeVec = timeCol.getColumn() ;
4366 timeCol.attach( on->table(), "TIME" ) ;
4367 ROArrayColumn<Float> arrayFloatCol( off->table(), "SPECTRA" ) ;
4368 Matrix<Float> offspectra = arrayFloatCol.getColumn() ;
4369 unsigned int spsize = on->nchan( on->getIF(rows[0]) ) ;
4370 // I know that the data is contiguous
4371 const uInt *p = rows.data() ;
4372 vector<int> ids( 2 ) ;
4373 Block<uInt> flagchan( spsize ) ;
4374 uInt nflag = 0 ;
4375 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4376 double reftime = timeCol.asdouble(*p) ;
4377 ids = getRowIdFromTime( reftime, timeVec ) ;
4378 Vector<Float> spoff = getSpectrumFromTime( reftime, timeVec, ids, offspectra, "linear" ) ;
4379 //Vector<Float> spoff = getSpectrumFromTime( reftime, timeVec, off, "linear" ) ;
4380 Vector<Float> spec = on->specCol_( *p ) ;
4381 Vector<Float> tsys = on->tsysCol_( *p ) ;
4382 // ALMA Calibration
4383 //
4384 // Ta* = Tsys * ( ON - OFF ) / OFF
4385 //
4386 // 2010/01/07 Takeshi Nakazato
4387 unsigned int tsyssize = tsys.nelements() ;
4388 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4389 if ( spoff[j] == 0.0 ) {
4390 spec[j] = 0.0 ;
4391 flagchan[nflag++] = j ;
4392 }
4393 else {
4394 spec[j] = ( spec[j] - spoff[j] ) / spoff[j] ;
4395 }
4396 if ( tsyssize == spsize )
4397 spec[j] *= tsys[j] ;
4398 else
4399 spec[j] *= tsys[0] ;
4400 }
4401 out->specCol_.put( *p, spec ) ;
4402 if ( nflag > 0 ) {
4403 Vector<uChar> fl = out->flagsCol_( *p ) ;
4404 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4405 fl[flagchan[j]] = (uChar)True ;
4406 }
4407 out->flagsCol_.put( *p, fl ) ;
4408 }
4409 nflag = 0 ;
4410 p++ ;
4411 }
4412}
4413
4414void STMath::calibrateAPEXFS( CountedPtr<Scantable> &sig,
4415 CountedPtr<Scantable> &ref,
4416 const vector< CountedPtr<Scantable> >& on,
4417 const vector< CountedPtr<Scantable> >& sky,
4418 const vector< CountedPtr<Scantable> >& hot,
4419 const vector< CountedPtr<Scantable> >& cold,
4420 const Vector<uInt> &rows )
4421{
4422 // if rows is empty, just return
4423 if ( rows.nelements() == 0 )
4424 return ;
4425 ROScalarColumn<Double> timeCol( sky[0]->table(), "TIME" ) ;
4426 Vector<Double> timeSkyS = timeCol.getColumn() ;
4427 timeCol.attach( sky[1]->table(), "TIME" ) ;
4428 Vector<Double> timeSkyR = timeCol.getColumn() ;
4429 timeCol.attach( hot[0]->table(), "TIME" ) ;
4430 Vector<Double> timeHotS = timeCol.getColumn() ;
4431 timeCol.attach( hot[1]->table(), "TIME" ) ;
4432 Vector<Double> timeHotR = timeCol.getColumn() ;
4433 timeCol.attach( sig->table(), "TIME" ) ;
4434 ROScalarColumn<Double> timeCol2( ref->table(), "TIME" ) ;
4435 ROArrayColumn<Float> arrayFloatCol( sky[0]->table(), "SPECTRA" ) ;
4436 Matrix<Float> skyspectraS = arrayFloatCol.getColumn() ;
4437 arrayFloatCol.attach( sky[1]->table(), "SPECTRA" ) ;
4438 Matrix<Float> skyspectraR = arrayFloatCol.getColumn() ;
4439 arrayFloatCol.attach( hot[0]->table(), "SPECTRA" ) ;
4440 Matrix<Float> hotspectraS = arrayFloatCol.getColumn() ;
4441 arrayFloatCol.attach( hot[1]->table(), "SPECTRA" ) ;
4442 Matrix<Float> hotspectraR = arrayFloatCol.getColumn() ;
4443 unsigned int spsize = sig->nchan( sig->getIF(rows[0]) ) ;
4444 Vector<Float> spec( spsize ) ;
4445 // I know that the data is contiguous
4446 const uInt *p = rows.data() ;
4447 vector<int> ids( 2 ) ;
4448 Block<uInt> flagchan( spsize ) ;
4449 uInt nflag = 0 ;
4450 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4451 double reftime = timeCol.asdouble(*p) ;
4452 ids = getRowIdFromTime( reftime, timeSkyS ) ;
4453 Vector<Float> spskyS = getSpectrumFromTime( reftime, timeSkyS, ids, skyspectraS, "linear" ) ;
4454 Vector<Float> tcalS = getTcalFromTime( reftime, timeSkyS, ids, sky[0], "linear" ) ;
4455 Vector<Float> tsysS = getTsysFromTime( reftime, timeSkyS, ids, sky[0], "linear" ) ;
4456 ids = getRowIdFromTime( reftime, timeHotS ) ;
4457 Vector<Float> sphotS = getSpectrumFromTime( reftime, timeHotS, ids, hotspectraS ) ;
4458 reftime = timeCol2.asdouble(*p) ;
4459 ids = getRowIdFromTime( reftime, timeSkyR ) ;
4460 Vector<Float> spskyR = getSpectrumFromTime( reftime, timeSkyR, ids, skyspectraR, "linear" ) ;
4461 Vector<Float> tcalR = getTcalFromTime( reftime, timeSkyR, ids, sky[1], "linear" ) ;
4462 Vector<Float> tsysR = getTsysFromTime( reftime, timeSkyR, ids, sky[1], "linear" ) ;
4463 ids = getRowIdFromTime( reftime, timeHotR ) ;
4464 Vector<Float> sphotR = getSpectrumFromTime( reftime, timeHotR, ids, hotspectraR ) ;
4465 Vector<Float> spsig = on[0]->specCol_( *p ) ;
4466 Vector<Float> spref = on[1]->specCol_( *p ) ;
4467 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4468 if ( (sphotS[j]-spskyS[j]) == 0.0 || (sphotR[j]-spskyR[j]) == 0.0 ) {
4469 spec[j] = 0.0 ;
4470 flagchan[nflag++] = j ;
4471 }
4472 else {
4473 spec[j] = tcalS[j] * spsig[j] / ( sphotS[j] - spskyS[j] )
4474 - tcalR[j] * spref[j] / ( sphotR[j] - spskyR[j] ) ;
4475 }
4476 }
4477 sig->specCol_.put( *p, spec ) ;
4478 sig->tsysCol_.put( *p, tsysS ) ;
4479 spec *= (Float)-1.0 ;
4480 ref->specCol_.put( *p, spec ) ;
4481 ref->tsysCol_.put( *p, tsysR ) ;
4482 if ( nflag > 0 ) {
4483 Vector<uChar> flsig = sig->flagsCol_( *p ) ;
4484 Vector<uChar> flref = ref->flagsCol_( *p ) ;
4485 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4486 flsig[flagchan[j]] = (uChar)True ;
4487 flref[flagchan[j]] = (uChar)True ;
4488 }
4489 sig->flagsCol_.put( *p, flsig ) ;
4490 ref->flagsCol_.put( *p, flref ) ;
4491 }
4492 nflag = 0 ;
4493 p++ ;
4494 }
4495}
4496
4497void STMath::calibrateFS( CountedPtr<Scantable> &sig,
4498 CountedPtr<Scantable> &ref,
4499 const CountedPtr<Scantable>& rsig,
4500 const CountedPtr<Scantable>& rref,
4501 const CountedPtr<Scantable>& sky,
4502 const CountedPtr<Scantable>& hot,
4503 const CountedPtr<Scantable>& cold,
4504 const Vector<uInt> &rows )
4505{
4506 // if rows is empty, just return
4507 if ( rows.nelements() == 0 )
4508 return ;
4509 ROScalarColumn<Double> timeCol( sky->table(), "TIME" ) ;
4510 Vector<Double> timeSky = timeCol.getColumn() ;
4511 timeCol.attach( hot->table(), "TIME" ) ;
4512 Vector<Double> timeHot = timeCol.getColumn() ;
4513 timeCol.attach( sig->table(), "TIME" ) ;
4514 ROScalarColumn<Double> timeCol2( ref->table(), "TIME" ) ;
4515 ROArrayColumn<Float> arrayFloatCol( sky->table(), "SPECTRA" ) ;
4516 Matrix<Float> skyspectra = arrayFloatCol.getColumn() ;
4517 arrayFloatCol.attach( hot->table(), "SPECTRA" ) ;
4518 Matrix<Float> hotspectra = arrayFloatCol.getColumn() ;
4519 unsigned int spsize = sig->nchan( sig->getIF(rows[0]) ) ;
4520 Vector<Float> spec( spsize ) ;
4521 // I know that the data is contiguous
4522 const uInt *p = rows.data() ;
4523 vector<int> ids( 2 ) ;
4524 Block<uInt> flagchan( spsize ) ;
4525 uInt nflag = 0 ;
4526 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
4527 double reftime = timeCol.asdouble(*p) ;
4528 ids = getRowIdFromTime( reftime, timeSky ) ;
4529 Vector<Float> spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
4530 Vector<Float> tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4531 Vector<Float> tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4532 ids = getRowIdFromTime( reftime, timeHot ) ;
4533 Vector<Float> sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra ) ;
4534 Vector<Float> spsig = rsig->specCol_( *p ) ;
4535 Vector<Float> spref = rref->specCol_( *p ) ;
4536 // using gain array
4537 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4538 if ( spref[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
4539 spec[j] = 0.0 ;
4540 flagchan[nflag++] = j ;
4541 }
4542 else {
4543 spec[j] = ( ( spsig[j] - spref[j] ) / spref[j] )
4544 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4545 }
4546 }
4547 sig->specCol_.put( *p, spec ) ;
4548 sig->tsysCol_.put( *p, tsys ) ;
4549 if ( nflag > 0 ) {
4550 Vector<uChar> fl = sig->flagsCol_( *p ) ;
4551 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4552 fl[flagchan[j]] = (uChar)True ;
4553 }
4554 sig->flagsCol_.put( *p, fl ) ;
4555 }
4556 nflag = 0 ;
4557
4558 reftime = timeCol2.asdouble(*p) ;
4559 spsky = getSpectrumFromTime( reftime, timeSky, ids, skyspectra, "linear" ) ;
4560 tcal = getTcalFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4561 tsys = getTsysFromTime( reftime, timeSky, ids, sky, "linear" ) ;
4562 ids = getRowIdFromTime( reftime, timeHot ) ;
4563 sphot = getSpectrumFromTime( reftime, timeHot, ids, hotspectra ) ;
4564 // using gain array
4565 for ( unsigned int j = 0 ; j < spsize ; j++ ) {
4566 if ( spsig[j] == 0.0 || (sphot[j]-spsky[j]) == 0.0 ) {
4567 spec[j] = 0.0 ;
4568 flagchan[nflag++] = j ;
4569 }
4570 else {
4571 spec[j] = ( ( spref[j] - spsig[j] ) / spsig[j] )
4572 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4573 }
4574 }
4575 ref->specCol_.put( *p, spec ) ;
4576 ref->tsysCol_.put( *p, tsys ) ;
4577 if ( nflag > 0 ) {
4578 Vector<uChar> fl = ref->flagsCol_( *p ) ;
4579 for ( unsigned int j = 0 ; j < nflag ; j++ ) {
4580 fl[flagchan[j]] = (uChar)True ;
4581 }
4582 ref->flagsCol_.put( *p, fl ) ;
4583 }
4584 nflag = 0 ;
4585 p++ ;
4586 }
4587}
4588
4589void STMath::copyRows( Table &out,
4590 const Table &in,
4591 uInt startout,
4592 uInt startin,
4593 uInt nrow,
4594 Bool copySpectra,
4595 Bool copyFlagtra,
4596 Bool copyTsys )
4597{
4598 uInt nexclude = 0 ;
4599 Block<String> excludeColsBlock( 3 ) ;
4600 if ( !copySpectra ) {
4601 excludeColsBlock[nexclude] = "SPECTRA" ;
4602 nexclude++ ;
4603 }
4604 if ( !copyFlagtra ) {
4605 excludeColsBlock[nexclude] = "FLAGTRA" ;
4606 nexclude++ ;
4607 }
4608 if ( !copyTsys ) {
4609 excludeColsBlock[nexclude] = "TSYS" ;
4610 nexclude++ ;
4611 }
4612 // if ( nexclude < 3 ) {
4613 // excludeCols.resize( nexclude, True ) ;
4614 // }
4615 Vector<String> excludeCols( IPosition(1,nexclude),
4616 excludeColsBlock.storage(),
4617 SHARE ) ;
4618// cout << "excludeCols=" << excludeCols << endl ;
4619 TableRow rowout( out, excludeCols, True ) ;
4620 ROTableRow rowin( in, excludeCols, True ) ;
4621 uInt rin = startin ;
4622 uInt rout = startout ;
4623 for ( uInt i = 0 ; i < nrow ; i++ ) {
4624 rowin.get( rin ) ;
4625 rowout.putMatchingFields( rout, rowin.record() ) ;
4626 rin++ ;
4627 rout++ ;
4628 }
4629}
4630
4631CountedPtr<Scantable> STMath::averageWithinSession( CountedPtr<Scantable> &s,
4632 vector<bool> &mask,
4633 string weight )
4634{
4635 // prepare output table
4636 bool insitu = insitu_ ;
4637 insitu_ = false ;
4638 CountedPtr<Scantable> a = getScantable( s, true ) ;
4639 insitu_ = insitu ;
4640 Table &atab = a->table() ;
4641 ScalarColumn<Double> timeColOut( atab, "TIME" ) ;
4642
4643 if ( s->nrow() == 0 )
4644 return a ;
4645
4646 // setup RowAccumulator
4647 WeightType wtype = stringToWeight( weight ) ;
4648 RowAccumulator acc( wtype ) ;
4649 Vector<Bool> cmask( mask ) ;
4650 acc.setUserMask( cmask ) ;
4651
4652 vector<string> cols( 3 ) ;
4653 cols[0] = "IFNO" ;
4654 cols[1] = "POLNO" ;
4655 cols[2] = "BEAMNO" ;
4656 STIdxIterAcc iter( s, cols ) ;
4657
4658 Table ttab = s->table() ;
4659 ROScalarColumn<Double> *timeCol = new ROScalarColumn<Double>( ttab, "TIME" ) ;
4660 Vector<Double> timeVec = timeCol->getColumn() ;
4661 delete timeCol ;
4662 Vector<Double> interval = s->integrCol_.getColumn() ;
4663 uInt nrow = timeVec.nelements() ;
4664 uInt outrow = 0 ;
4665
4666 while( !iter.pastEnd() ) {
4667
4668 Vector<uInt> rows = iter.getRows( SHARE ) ;
4669 uInt len = rows.nelements() ;
4670
4671 if ( len == 0 ) {
4672 iter.next() ;
4673 continue ;
4674 }
4675
4676 uInt nchan = s->nchan(s->getIF(rows[0])) ;
4677 Vector<uChar> flag( nchan ) ;
4678 Vector<Bool> bflag( nchan ) ;
4679 Vector<Float> spec( nchan ) ;
4680 Vector<Float> tsys( nchan ) ;
4681
4682 Vector<Double> timeSep( len-1 ) ;
4683 for ( uInt i = 0 ; i < len-1 ; i++ ) {
4684 timeSep[i] = timeVec[rows[i+1]] - timeVec[rows[i]] ;
4685 }
4686
4687 uInt irow ;
4688 uInt jrow ;
4689 for ( uInt i = 0 ; i < len-1 ; i++ ) {
4690 irow = rows[i] ;
4691 jrow = rows[i+1] ;
4692 // accumulate data
4693 s->flagsCol_.get( irow, flag ) ;
4694 convertArray( bflag, flag ) ;
4695 s->specCol_.get( irow, spec ) ;
4696 tsys.assign( s->tsysCol_( irow ) ) ;
4697 if ( !allEQ(bflag,True) )
4698 acc.add( spec, !bflag, tsys, interval[irow], timeVec[irow] ) ;
4699 double gap = 2.0 * 86400.0 * timeSep[i] / ( interval[jrow] + interval[irow] ) ;
4700 //cout << "gap[" << i << "]=" << setw(5) << gap << endl ;
4701 if ( gap > 1.1 ) {
4702 //cout << "detected gap between " << i << " and " << i+1 << endl ;
4703 // put data to output table
4704 // reset RowAccumulator
4705 if ( acc.state() ) {
4706 atab.addRow() ;
4707 copyRows( atab, ttab, outrow, irow, 1, False, False, False ) ;
4708 acc.replaceNaN() ;
4709 const Vector<Bool> &msk = acc.getMask() ;
4710 convertArray( flag, !msk ) ;
4711 for (uInt k = 0; k < nchan; ++k) {
4712 uChar userFlag = 1 << 7;
4713 if (msk[k]==True) userFlag = 0 << 7;
4714 flag(k) = userFlag;
4715 }
4716 a->flagsCol_.put( outrow, flag ) ;
4717 a->specCol_.put( outrow, acc.getSpectrum() ) ;
4718 a->tsysCol_.put( outrow, acc.getTsys() ) ;
4719 a->integrCol_.put( outrow, acc.getInterval() ) ;
4720 timeColOut.put( outrow, acc.getTime() ) ;
4721 a->cycleCol_.put( outrow, 0 ) ;
4722 }
4723 acc.reset() ;
4724 outrow++ ;
4725 }
4726 }
4727
4728 // accumulate and add last data
4729 irow = rows[len-1] ;
4730 s->flagsCol_.get( irow, flag ) ;
4731 convertArray( bflag, flag ) ;
4732 s->specCol_.get( irow, spec ) ;
4733 tsys.assign( s->tsysCol_( irow ) ) ;
4734 if (!allEQ(bflag,True) )
4735 acc.add( spec, !bflag, tsys, interval[irow], timeVec[irow] ) ;
4736 if ( acc.state() ) {
4737 atab.addRow() ;
4738 copyRows( atab, ttab, outrow, irow, 1, False, False, False ) ;
4739 acc.replaceNaN() ;
4740 const Vector<Bool> &msk = acc.getMask() ;
4741 convertArray( flag, !msk ) ;
4742 for (uInt k = 0; k < nchan; ++k) {
4743 uChar userFlag = 1 << 7;
4744 if (msk[k]==True) userFlag = 0 << 7;
4745 flag(k) = userFlag;
4746 }
4747 a->flagsCol_.put( outrow, flag ) ;
4748 a->specCol_.put( outrow, acc.getSpectrum() ) ;
4749 a->tsysCol_.put( outrow, acc.getTsys() ) ;
4750 a->integrCol_.put( outrow, acc.getInterval() ) ;
4751 timeColOut.put( outrow, acc.getTime() ) ;
4752 a->cycleCol_.put( outrow, 0 ) ;
4753 }
4754 acc.reset() ;
4755 outrow++ ;
4756
4757 iter.next() ;
4758 }
4759
4760 return a ;
4761}
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