source: branches/hpc33/src/STMath.cpp@ 2543

Last change on this file since 2543 was 2543, checked in by Takeshi Nakazato, 13 years ago

New Development: No

JIRA Issue: No

Ready for Test: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

Put in Release Notes: Yes/No

Module(s): Module Names change impacts.

Description: Describe your changes here...

Defiend STMath::copyRows that is able to skip to copy SPECTRA/FLAGTRA/TSYS
if they are not necessary to copy.


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File size: 185.2 KB
Line 
1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <sstream>
14
15#include <casa/iomanip.h>
16#include <casa/Arrays/MaskArrLogi.h>
17#include <casa/Arrays/MaskArrMath.h>
18#include <casa/Arrays/ArrayLogical.h>
19#include <casa/Arrays/ArrayMath.h>
20#include <casa/Arrays/Slice.h>
21#include <casa/Arrays/Slicer.h>
22#include <casa/BasicSL/String.h>
23#include <casa/Containers/Block.h>
24#include <casa/Containers/RecordField.h>
25#include <casa/Exceptions/Error.h>
26#include <casa/Logging/LogIO.h>
27
28#include <coordinates/Coordinates/CoordinateSystem.h>
29#include <coordinates/Coordinates/CoordinateUtil.h>
30#include <coordinates/Coordinates/FrequencyAligner.h>
31#include <coordinates/Coordinates/SpectralCoordinate.h>
32
33#include <lattices/Lattices/LatticeUtilities.h>
34
35#include <scimath/Functionals/Polynomial.h>
36#include <scimath/Mathematics/Convolver.h>
37#include <scimath/Mathematics/VectorKernel.h>
38
39#include <tables/Tables/ExprNode.h>
40#include <tables/Tables/ReadAsciiTable.h>
41#include <tables/Tables/TableCopy.h>
42#include <tables/Tables/TableIter.h>
43#include <tables/Tables/TableParse.h>
44#include <tables/Tables/TableRecord.h>
45#include <tables/Tables/TableRow.h>
46#include <tables/Tables/TableVector.h>
47#include <tables/Tables/TabVecMath.h>
48
49#include <atnf/PKSIO/SrcType.h>
50
51#include "RowAccumulator.h"
52#include "STAttr.h"
53#include "STMath.h"
54#include "STSelector.h"
55#include "Accelerator.h"
56#include "STIdxIter.h"
57
58using namespace casa;
59using namespace asap;
60
61
62// 2012/02/17 TN
63// Since STGrid is implemented, average doesn't consider direction
64// when accumulating
65// tolerance for direction comparison (rad)
66// #define TOL_OTF 1.0e-15
67// #define TOL_POINT 2.9088821e-4 // 1 arcmin
68
69STMath::STMath(bool insitu) :
70 insitu_(insitu)
71{
72}
73
74
75STMath::~STMath()
76{
77}
78
79CountedPtr<Scantable>
80STMath::average( const std::vector<CountedPtr<Scantable> >& in,
81 const std::vector<bool>& mask,
82 const std::string& weight,
83 const std::string& avmode)
84{
85// double t0, t1 ;
86// t0 = mathutil::gettimeofday_sec() ;
87
88 LogIO os( LogOrigin( "STMath", "average()", WHERE ) ) ;
89 if ( avmode == "SCAN" && in.size() != 1 )
90 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
91 "Use merge first."));
92 WeightType wtype = stringToWeight(weight);
93
94 // 2012/02/17 TN
95 // Since STGrid is implemented, average doesn't consider direction
96 // when accumulating
97 // check if OTF observation
98// String obstype = in[0]->getHeader().obstype ;
99// Double tol = 0.0 ;
100// if ( (obstype.find( "OTF" ) != String::npos) || (obstype.find( "OBSERVE_TARGET" ) != String::npos) ) {
101// tol = TOL_OTF ;
102// }
103// else {
104// tol = TOL_POINT ;
105// }
106
107 // output
108 // clone as this is non insitu
109 bool insitu = insitu_;
110 setInsitu(false);
111 CountedPtr< Scantable > out = getScantable(in[0], true);
112 setInsitu(insitu);
113 std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
114 ++stit;
115 while ( stit != in.end() ) {
116 out->appendToHistoryTable((*stit)->history());
117 ++stit;
118 }
119
120 Table& tout = out->table();
121
122 /// @todo check if all scantables are conformant
123
124 ArrayColumn<Float> specColOut(tout,"SPECTRA");
125 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
126 ArrayColumn<Float> tsysColOut(tout,"TSYS");
127 ScalarColumn<Double> mjdColOut(tout,"TIME");
128 ScalarColumn<Double> intColOut(tout,"INTERVAL");
129 ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
130 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
131
132 // set up the output table rows. These are based on the structure of the
133 // FIRST scantable in the vector
134 const Table& baset = in[0]->table();
135
136 RowAccumulator acc(wtype);
137 Vector<Bool> cmask(mask);
138 acc.setUserMask(cmask);
139// ROTableRow row(tout);
140 ROArrayColumn<Float> specCol, tsysCol;
141 ROArrayColumn<uChar> flagCol;
142 ROScalarColumn<Double> mjdCol, intCol;
143 ROScalarColumn<Int> scanIDCol;
144
145 Vector<uInt> rowstodelete;
146
147// Block<String> cols(3);
148 vector<string> cols(3) ;
149 cols[0] = String("BEAMNO");
150 cols[1] = String("IFNO");
151 cols[2] = String("POLNO");
152 if ( avmode == "SOURCE" ) {
153 cols.resize(4);
154 cols[3] = String("SRCNAME");
155 }
156 if ( avmode == "SCAN" && in.size() == 1) {
157 //cols.resize(4);
158 //cols[3] = String("SCANNO");
159 cols.resize(5);
160 cols[3] = String("SRCNAME");
161 cols[4] = String("SCANNO");
162 }
163 uInt outrowCount = 0;
164 // use STIdxIterExAcc instead of TableIterator
165 STIdxIterExAcc iter( in[0], cols ) ;
166// double t2 = 0 ;
167// double t3 = 0 ;
168// double t4 = 0 ;
169// double t5 = 0 ;
170// TableIterator iter(baset, cols);
171// int count = 0 ;
172 while (!iter.pastEnd()) {
173 Vector<uInt> rows = iter.getRows( SHARE ) ;
174 if ( rows.nelements() == 0 ) {
175 iter.next() ;
176 continue ;
177 }
178 Vector<uInt> current = iter.current() ;
179 String srcname = iter.getSrcName() ;
180 //Table subt = iter.table();
181 // copy the first row of this selection into the new table
182 tout.addRow();
183// t4 = mathutil::gettimeofday_sec() ;
184 //TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
185 //TableCopy::copyRows(tout, baset, outrowCount, rows[0], 1);
186 // skip to copy SPECTRA, FLAGTRA, and TSYS since those heavy columns are
187 // overwritten in the following process
188 copyRows( tout, baset, outrowCount, rows[0], 1, False, False, False ) ;
189// t5 += mathutil::gettimeofday_sec() - t4 ;
190 // re-index to 0
191 if ( avmode != "SCAN" && avmode != "SOURCE" ) {
192 scanColOut.put(outrowCount, uInt(0));
193 }
194
195 // 2012/02/17 TN
196 // Since STGrid is implemented, average doesn't consider direction
197 // when accumulating
198// MDirection::ScalarColumn dircol ;
199// dircol.attach( subt, "DIRECTION" ) ;
200// Int length = subt.nrow() ;
201// vector< Vector<Double> > dirs ;
202// vector<int> indexes ;
203// for ( Int i = 0 ; i < length ; i++ ) {
204// Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
205// //os << << count++ << ": " ;
206// //os << "[" << t[0] << "," << t[1] << "]" << LogIO::POST ;
207// bool adddir = true ;
208// for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
209// //if ( allTrue( t == dirs[j] ) ) {
210// Double dx = t[0] - dirs[j][0] ;
211// Double dy = t[1] - dirs[j][1] ;
212// Double dd = sqrt( dx * dx + dy * dy ) ;
213// //if ( allNearAbs( t, dirs[j], tol ) ) {
214// if ( dd <= tol ) {
215// adddir = false ;
216// break ;
217// }
218// }
219// if ( adddir ) {
220// dirs.push_back( t ) ;
221// indexes.push_back( i ) ;
222// }
223// }
224// uInt rowNum = dirs.size() ;
225// tout.addRow( rowNum ) ;
226// for ( uInt i = 0 ; i < rowNum ; i++ ) {
227// TableCopy::copyRows( tout, subt, outrowCount+i, indexes[i], 1 ) ;
228// // re-index to 0
229// if ( avmode != "SCAN" && avmode != "SOURCE" ) {
230// scanColOut.put(outrowCount+i, uInt(0));
231// }
232// }
233// outrowCount += rowNum ;
234
235// merge loop
236 uInt i = outrowCount ;
237// for (uInt i=0; i < tout.nrow(); ++i) {
238
239 // in[0] is already selected by TableItertor
240 specCol.attach(baset,"SPECTRA");
241 flagCol.attach(baset,"FLAGTRA");
242 tsysCol.attach(baset,"TSYS");
243 intCol.attach(baset,"INTERVAL");
244 mjdCol.attach(baset,"TIME");
245 Vector<Float> spec,tsys;
246 Vector<uChar> flag;
247 Double inter,time;
248// for (uInt k = 0; k < subt.nrow(); ++k ) {
249 for (uInt l = 0; l < rows.nelements(); ++l ) {
250 uInt k = rows[l] ;
251 flagCol.get(k, flag);
252 Vector<Bool> bflag(flag.shape());
253 convertArray(bflag, flag);
254 /*
255 if ( allEQ(bflag, True) ) {
256 continue;//don't accumulate
257 }
258 */
259 specCol.get(k, spec);
260 tsysCol.get(k, tsys);
261 intCol.get(k, inter);
262 mjdCol.get(k, time);
263 // spectrum has to be added last to enable weighting by the other values
264// t2 = mathutil::gettimeofday_sec() ;
265 acc.add(spec, !bflag, tsys, inter, time);
266// t3 += mathutil::gettimeofday_sec() - t2 ;
267
268 }
269
270
271 // in[0] is already selected by TableIterator so that index is
272 // started from 1
273 //for ( int j=0; j < int(in.size()); ++j ) {
274 for ( int j=1; j < int(in.size()); ++j ) {
275 const Table& tin = in[j]->table();
276 //const TableRecord& rec = row.get(i);
277 ROScalarColumn<Double> tmp(tin, "TIME");
278 Double td;tmp.get(0,td);
279
280#if 1
281 static char const*const colNames1[] = { "IFNO", "BEAMNO", "POLNO" };
282 //uInt const values1[] = { rec.asuInt("IFNO"), rec.asuInt("BEAMNO"), rec.asuInt("POLNO") };
283 uInt const values1[] = { current[1], current[0], current[2] };
284 SingleTypeEqPredicate<uInt, 3> myPred(tin, colNames1, values1);
285 CustomTableExprNodeRep myNodeRep(tin, myPred);
286 myNodeRep.link(); // to avoid automatic delete when myExpr is destructed.
287 CustomTableExprNode myExpr(myNodeRep);
288 Table basesubt = tin(myExpr);
289#else
290// Table basesubt = tin( tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
291// && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
292// && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
293 Table basesubt = tin( tin.col("BEAMNO") == current[0]
294 && tin.col("IFNO") == current[1]
295 && tin.col("POLNO") == current[2] );
296#endif
297 Table subt;
298 if ( avmode == "SOURCE") {
299// subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME"));
300 subt = basesubt( basesubt.col("SRCNAME") == srcname );
301
302 } else if (avmode == "SCAN") {
303// subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME")
304// && basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
305 subt = basesubt( basesubt.col("SRCNAME") == srcname
306 && basesubt.col("SCANNO") == current[4] );
307 } else {
308 subt = basesubt;
309 }
310
311 // 2012/02/17 TN
312 // Since STGrid is implemented, average doesn't consider direction
313 // when accumulating
314// vector<uInt> removeRows ;
315// uInt nrsubt = subt.nrow() ;
316// for ( uInt irow = 0 ; irow < nrsubt ; irow++ ) {
317// //if ( !allTrue((subt.col("DIRECTION").getArrayDouble(TableExprId(irow)))==rec.asArrayDouble("DIRECTION")) ) {
318// Vector<Double> x0 = (subt.col("DIRECTION").getArrayDouble(TableExprId(irow))) ;
319// Vector<Double> x1 = rec.asArrayDouble("DIRECTION") ;
320// double dx = x0[0] - x1[0];
321// double dy = x0[1] - x1[1];
322// Double dd = sqrt( dx * dx + dy * dy ) ;
323// //if ( !allNearAbs((subt.col("DIRECTION").getArrayDouble(TableExprId(irow))), rec.asArrayDouble("DIRECTION"), tol ) ) {
324// if ( dd > tol ) {
325// removeRows.push_back( irow ) ;
326// }
327// }
328// if ( removeRows.size() != 0 ) {
329// subt.removeRow( removeRows ) ;
330// }
331
332// if ( nrsubt == removeRows.size() )
333// throw(AipsError("Averaging data is empty.")) ;
334
335 specCol.attach(subt,"SPECTRA");
336 flagCol.attach(subt,"FLAGTRA");
337 tsysCol.attach(subt,"TSYS");
338 intCol.attach(subt,"INTERVAL");
339 mjdCol.attach(subt,"TIME");
340 for (uInt k = 0; k < subt.nrow(); ++k ) {
341 flagCol.get(k, flag);
342 Vector<Bool> bflag(flag.shape());
343 convertArray(bflag, flag);
344 /*
345 if ( allEQ(bflag, True) ) {
346 continue;//don't accumulate
347 }
348 */
349 specCol.get(k, spec);
350 tsysCol.get(k, tsys);
351 intCol.get(k, inter);
352 mjdCol.get(k, time);
353 // spectrum has to be added last to enable weighting by the other values
354// t2 = mathutil::gettimeofday_sec() ;
355 acc.add(spec, !bflag, tsys, inter, time);
356// t3 += mathutil::gettimeofday_sec() - t2 ;
357 }
358
359 }
360 const Vector<Bool>& msk = acc.getMask();
361 if ( allEQ(msk, False) ) {
362 uint n = rowstodelete.nelements();
363 rowstodelete.resize(n+1, True);
364 rowstodelete[n] = i;
365 continue;
366 }
367 //write out
368 if (acc.state()) {
369 // If there exists a channel at which all the input spectra are masked,
370 // spec has 'nan' values for that channel and it may affect the following
371 // processes. To avoid this, replacing 'nan' values in spec with
372 // weighted-mean of all spectra in the following line.
373 // (done for CAS-2776, 2011/04/07 by Wataru Kawasaki)
374 acc.replaceNaN();
375
376 Vector<uChar> flg(msk.shape());
377 convertArray(flg, !msk);
378 for (uInt k = 0; k < flg.nelements(); ++k) {
379 uChar userFlag = 1 << 7;
380 if (msk[k]==True) userFlag = 0 << 7;
381 flg(k) = userFlag;
382 }
383
384 flagColOut.put(i, flg);
385 specColOut.put(i, acc.getSpectrum());
386 tsysColOut.put(i, acc.getTsys());
387 intColOut.put(i, acc.getInterval());
388 mjdColOut.put(i, acc.getTime());
389 // we should only have one cycle now -> reset it to be 0
390 // frequency switched data has different CYCLENO for different IFNO
391 // which requires resetting this value
392 cycColOut.put(i, uInt(0));
393 } else {
394 ostringstream oss;
395 oss << "For output row="<<i<<", all input rows of data are flagged. no averaging" << endl;
396 pushLog(String(oss));
397 }
398 acc.reset();
399
400 // merge with while loop for preparing out table
401 ++outrowCount;
402// ++iter ;
403 iter.next() ;
404 }
405
406 if (rowstodelete.nelements() > 0) {
407 os << rowstodelete << LogIO::POST ;
408 tout.removeRow(rowstodelete);
409 if (tout.nrow() == 0) {
410 throw(AipsError("Can't average fully flagged data."));
411 }
412 }
413
414// t1 = mathutil::gettimeofday_sec() ;
415// cout << "elapsed time for average(): " << t1-t0 << " sec" << endl ;
416// cout << " elapsed time for acc.add(): " << t3 << " sec" << endl ;
417// cout << " elapsed time for copyRows(): " << t5 << " sec" << endl ;
418
419 return out;
420}
421
422CountedPtr< Scantable >
423STMath::averageChannel( const CountedPtr < Scantable > & in,
424 const std::string & mode,
425 const std::string& avmode )
426{
427 (void) mode; // currently unused
428 // 2012/02/17 TN
429 // Since STGrid is implemented, average doesn't consider direction
430 // when accumulating
431 // check if OTF observation
432// String obstype = in->getHeader().obstype ;
433// Double tol = 0.0 ;
434// if ( obstype.find( "OTF" ) != String::npos ) {
435// tol = TOL_OTF ;
436// }
437// else {
438// tol = TOL_POINT ;
439// }
440
441 // clone as this is non insitu
442 bool insitu = insitu_;
443 setInsitu(false);
444 CountedPtr< Scantable > out = getScantable(in, true);
445 setInsitu(insitu);
446 Table& tout = out->table();
447 ArrayColumn<Float> specColOut(tout,"SPECTRA");
448 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
449 ArrayColumn<Float> tsysColOut(tout,"TSYS");
450 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
451 ScalarColumn<Double> intColOut(tout, "INTERVAL");
452 Table tmp = in->table().sort("BEAMNO");
453 Block<String> cols(3);
454 cols[0] = String("BEAMNO");
455 cols[1] = String("IFNO");
456 cols[2] = String("POLNO");
457 if ( avmode == "SCAN") {
458 cols.resize(4);
459 cols[3] = String("SCANNO");
460 }
461 uInt outrowCount = 0;
462 uChar userflag = 1 << 7;
463 TableIterator iter(tmp, cols);
464 while (!iter.pastEnd()) {
465 Table subt = iter.table();
466 ROArrayColumn<Float> specCol, tsysCol;
467 ROArrayColumn<uChar> flagCol;
468 ROScalarColumn<Double> intCol(subt, "INTERVAL");
469 specCol.attach(subt,"SPECTRA");
470 flagCol.attach(subt,"FLAGTRA");
471 tsysCol.attach(subt,"TSYS");
472
473 tout.addRow();
474 TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
475 if ( avmode != "SCAN") {
476 scanColOut.put(outrowCount, uInt(0));
477 }
478 Vector<Float> tmp;
479 specCol.get(0, tmp);
480 uInt nchan = tmp.nelements();
481 // have to do channel by channel here as MaskedArrMath
482 // doesn't have partialMedians
483 Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
484 Vector<Float> outspec(nchan);
485 Vector<uChar> outflag(nchan,0);
486 Vector<Float> outtsys(1);/// @fixme when tsys is channel based
487 for (uInt i=0; i<nchan; ++i) {
488 Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
489 MaskedArray<Float> ma = maskedArray(specs,flags);
490 outspec[i] = median(ma);
491 if ( allEQ(ma.getMask(), False) )
492 outflag[i] = userflag;// flag data
493 }
494 outtsys[0] = median(tsysCol.getColumn());
495 specColOut.put(outrowCount, outspec);
496 flagColOut.put(outrowCount, outflag);
497 tsysColOut.put(outrowCount, outtsys);
498 Double intsum = sum(intCol.getColumn());
499 intColOut.put(outrowCount, intsum);
500 ++outrowCount;
501 ++iter;
502
503 // 2012/02/17 TN
504 // Since STGrid is implemented, average doesn't consider direction
505 // when accumulating
506// MDirection::ScalarColumn dircol ;
507// dircol.attach( subt, "DIRECTION" ) ;
508// Int length = subt.nrow() ;
509// vector< Vector<Double> > dirs ;
510// vector<int> indexes ;
511// // Handle MX mode averaging
512// if (in->nbeam() > 1 ) {
513// length = 1;
514// }
515// for ( Int i = 0 ; i < length ; i++ ) {
516// Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
517// bool adddir = true ;
518// for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
519// //if ( allTrue( t == dirs[j] ) ) {
520// Double dx = t[0] - dirs[j][0] ;
521// Double dy = t[1] - dirs[j][1] ;
522// Double dd = sqrt( dx * dx + dy * dy ) ;
523// //if ( allNearAbs( t, dirs[j], tol ) ) {
524// if ( dd <= tol ) {
525// adddir = false ;
526// break ;
527// }
528// }
529// if ( adddir ) {
530// dirs.push_back( t ) ;
531// indexes.push_back( i ) ;
532// }
533// }
534// uInt rowNum = dirs.size() ;
535// tout.addRow( rowNum );
536// for ( uInt i = 0 ; i < rowNum ; i++ ) {
537// TableCopy::copyRows(tout, subt, outrowCount+i, indexes[i], 1) ;
538// // Handle MX mode averaging
539// if ( avmode != "SCAN") {
540// scanColOut.put(outrowCount+i, uInt(0));
541// }
542// }
543// MDirection::ScalarColumn dircolOut ;
544// dircolOut.attach( tout, "DIRECTION" ) ;
545// for ( uInt irow = 0 ; irow < rowNum ; irow++ ) {
546// Vector<Double> t = \
547// dircolOut(outrowCount+irow).getAngle(Unit(String("rad"))).getValue() ;
548// Vector<Float> tmp;
549// specCol.get(0, tmp);
550// uInt nchan = tmp.nelements();
551// // have to do channel by channel here as MaskedArrMath
552// // doesn't have partialMedians
553// Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
554// // mask spectra for different DIRECTION
555// for ( uInt jrow = 0 ; jrow < subt.nrow() ; jrow++ ) {
556// Vector<Double> direction = \
557// dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
558// //if ( t[0] != direction[0] || t[1] != direction[1] ) {
559// Double dx = t[0] - direction[0];
560// Double dy = t[1] - direction[1];
561// Double dd = sqrt(dx*dx + dy*dy);
562// //if ( !allNearAbs( t, direction, tol ) ) {
563// if ( dd > tol && in->nbeam() < 2 ) {
564// flags[jrow] = userflag ;
565// }
566// }
567// Vector<Float> outspec(nchan);
568// Vector<uChar> outflag(nchan,0);
569// Vector<Float> outtsys(1);/// @fixme when tsys is channel based
570// for (uInt i=0; i<nchan; ++i) {
571// Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
572// MaskedArray<Float> ma = maskedArray(specs,flags);
573// outspec[i] = median(ma);
574// if ( allEQ(ma.getMask(), False) )
575// outflag[i] = userflag;// flag data
576// }
577// outtsys[0] = median(tsysCol.getColumn());
578// specColOut.put(outrowCount+irow, outspec);
579// flagColOut.put(outrowCount+irow, outflag);
580// tsysColOut.put(outrowCount+irow, outtsys);
581// Vector<Double> integ = intCol.getColumn() ;
582// MaskedArray<Double> mi = maskedArray( integ, flags ) ;
583// Double intsum = sum(mi);
584// intColOut.put(outrowCount+irow, intsum);
585// }
586// outrowCount += rowNum ;
587// ++iter;
588 }
589 return out;
590}
591
592CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
593 bool droprows)
594{
595 if (insitu_) {
596 return in;
597 }
598 else {
599 // clone
600 return CountedPtr<Scantable>(new Scantable(*in, Bool(droprows)));
601 }
602}
603
604CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
605 float val,
606 const std::string& mode,
607 bool tsys )
608{
609 CountedPtr< Scantable > out = getScantable(in, false);
610 Table& tab = out->table();
611 ArrayColumn<Float> specCol(tab,"SPECTRA");
612 ArrayColumn<Float> tsysCol(tab,"TSYS");
613 if (mode=="DIV") val = 1.0/val ;
614 else if (mode=="SUB") val *= -1.0 ;
615 for (uInt i=0; i<tab.nrow(); ++i) {
616 Vector<Float> spec;
617 Vector<Float> ts;
618 specCol.get(i, spec);
619 tsysCol.get(i, ts);
620 if (mode == "MUL" || mode == "DIV") {
621 //if (mode == "DIV") val = 1.0/val;
622 spec *= val;
623 specCol.put(i, spec);
624 if ( tsys ) {
625 ts *= val;
626 tsysCol.put(i, ts);
627 }
628 } else if ( mode == "ADD" || mode == "SUB") {
629 //if (mode == "SUB") val *= -1.0;
630 spec += val;
631 specCol.put(i, spec);
632 if ( tsys ) {
633 ts += val;
634 tsysCol.put(i, ts);
635 }
636 }
637 }
638 return out;
639}
640
641CountedPtr< Scantable > STMath::arrayOperate( const CountedPtr< Scantable >& in,
642 const std::vector<float> val,
643 const std::string& mode,
644 const std::string& opmode,
645 bool tsys )
646{
647 CountedPtr< Scantable > out ;
648 if ( opmode == "channel" ) {
649 out = arrayOperateChannel( in, val, mode, tsys ) ;
650 }
651 else if ( opmode == "row" ) {
652 out = arrayOperateRow( in, val, mode, tsys ) ;
653 }
654 else {
655 throw( AipsError( "Unknown array operation mode." ) ) ;
656 }
657 return out ;
658}
659
660CountedPtr< Scantable > STMath::arrayOperateChannel( const CountedPtr< Scantable >& in,
661 const std::vector<float> val,
662 const std::string& mode,
663 bool tsys )
664{
665 if ( val.size() == 1 ){
666 return unaryOperate( in, val[0], mode, tsys ) ;
667 }
668
669 // conformity of SPECTRA and TSYS
670 if ( tsys ) {
671 TableIterator titer(in->table(), "IFNO");
672 while ( !titer.pastEnd() ) {
673 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
674 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
675 Array<Float> spec = specCol.getColumn() ;
676 Array<Float> ts = tsysCol.getColumn() ;
677 if ( !spec.conform( ts ) ) {
678 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
679 }
680 titer.next() ;
681 }
682 }
683
684 // check if all spectra in the scantable have the same number of channel
685 vector<uInt> nchans;
686 vector<uInt> ifnos = in->getIFNos() ;
687 for ( uInt i = 0 ; i < ifnos.size() ; i++ ) {
688 nchans.push_back( in->nchan( ifnos[i] ) ) ;
689 }
690 Vector<uInt> mchans( nchans ) ;
691 if ( anyNE( mchans, mchans[0] ) ) {
692 throw( AipsError("All spectra in the input scantable must have the same number of channel for vector operation." ) ) ;
693 }
694
695 // check if vector size is equal to nchan
696 Vector<Float> fact( val ) ;
697 if ( fact.nelements() != mchans[0] ) {
698 throw( AipsError("Vector size must be 1 or be same as number of channel.") ) ;
699 }
700
701 // check divided by zero
702 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
703 throw( AipsError("Divided by zero is not recommended." ) ) ;
704 }
705
706 CountedPtr< Scantable > out = getScantable(in, false);
707 Table& tab = out->table();
708 ArrayColumn<Float> specCol(tab,"SPECTRA");
709 ArrayColumn<Float> tsysCol(tab,"TSYS");
710 if (mode == "DIV") fact = (float)1.0 / fact;
711 else if (mode == "SUB") fact *= (float)-1.0 ;
712 for (uInt i=0; i<tab.nrow(); ++i) {
713 Vector<Float> spec;
714 Vector<Float> ts;
715 specCol.get(i, spec);
716 tsysCol.get(i, ts);
717 if (mode == "MUL" || mode == "DIV") {
718 //if (mode == "DIV") fact = (float)1.0 / fact;
719 spec *= fact;
720 specCol.put(i, spec);
721 if ( tsys ) {
722 ts *= fact;
723 tsysCol.put(i, ts);
724 }
725 } else if ( mode == "ADD" || mode == "SUB") {
726 //if (mode == "SUB") fact *= (float)-1.0 ;
727 spec += fact;
728 specCol.put(i, spec);
729 if ( tsys ) {
730 ts += fact;
731 tsysCol.put(i, ts);
732 }
733 }
734 }
735 return out;
736}
737
738CountedPtr< Scantable > STMath::arrayOperateRow( const CountedPtr< Scantable >& in,
739 const std::vector<float> val,
740 const std::string& mode,
741 bool tsys )
742{
743 if ( val.size() == 1 ) {
744 return unaryOperate( in, val[0], mode, tsys ) ;
745 }
746
747 // conformity of SPECTRA and TSYS
748 if ( tsys ) {
749 TableIterator titer(in->table(), "IFNO");
750 while ( !titer.pastEnd() ) {
751 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
752 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
753 Array<Float> spec = specCol.getColumn() ;
754 Array<Float> ts = tsysCol.getColumn() ;
755 if ( !spec.conform( ts ) ) {
756 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
757 }
758 titer.next() ;
759 }
760 }
761
762 // check if vector size is equal to nrow
763 Vector<Float> fact( val ) ;
764 if (fact.nelements() != uInt(in->nrow())) {
765 throw( AipsError("Vector size must be 1 or be same as number of row.") ) ;
766 }
767
768 // check divided by zero
769 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
770 throw( AipsError("Divided by zero is not recommended." ) ) ;
771 }
772
773 CountedPtr< Scantable > out = getScantable(in, false);
774 Table& tab = out->table();
775 ArrayColumn<Float> specCol(tab,"SPECTRA");
776 ArrayColumn<Float> tsysCol(tab,"TSYS");
777 if (mode == "DIV") fact = (float)1.0 / fact;
778 if (mode == "SUB") fact *= (float)-1.0 ;
779 for (uInt i=0; i<tab.nrow(); ++i) {
780 Vector<Float> spec;
781 Vector<Float> ts;
782 specCol.get(i, spec);
783 tsysCol.get(i, ts);
784 if (mode == "MUL" || mode == "DIV") {
785 spec *= fact[i];
786 specCol.put(i, spec);
787 if ( tsys ) {
788 ts *= fact[i];
789 tsysCol.put(i, ts);
790 }
791 } else if ( mode == "ADD" || mode == "SUB") {
792 spec += fact[i];
793 specCol.put(i, spec);
794 if ( tsys ) {
795 ts += fact[i];
796 tsysCol.put(i, ts);
797 }
798 }
799 }
800 return out;
801}
802
803CountedPtr< Scantable > STMath::array2dOperate( const CountedPtr< Scantable >& in,
804 const std::vector< std::vector<float> > val,
805 const std::string& mode,
806 bool tsys )
807{
808 // conformity of SPECTRA and TSYS
809 if ( tsys ) {
810 TableIterator titer(in->table(), "IFNO");
811 while ( !titer.pastEnd() ) {
812 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
813 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
814 Array<Float> spec = specCol.getColumn() ;
815 Array<Float> ts = tsysCol.getColumn() ;
816 if ( !spec.conform( ts ) ) {
817 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
818 }
819 titer.next() ;
820 }
821 }
822
823 // some checks
824 vector<uInt> nchans;
825 for (Int i = 0 ; i < in->nrow() ; i++) {
826 nchans.push_back((in->getSpectrum(i)).size());
827 }
828 //Vector<uInt> mchans( nchans ) ;
829 vector< Vector<Float> > facts ;
830 for ( uInt i = 0 ; i < nchans.size() ; i++ ) {
831 Vector<Float> tmp( val[i] ) ;
832 // check divided by zero
833 if ( ( mode == "DIV" ) && anyEQ( tmp, (float)0.0 ) ) {
834 throw( AipsError("Divided by zero is not recommended." ) ) ;
835 }
836 // conformity check
837 if ( tmp.nelements() != nchans[i] ) {
838 stringstream ss ;
839 ss << "Row " << i << ": Vector size must be same as number of channel." ;
840 throw( AipsError( ss.str() ) ) ;
841 }
842 facts.push_back( tmp ) ;
843 }
844
845
846 CountedPtr< Scantable > out = getScantable(in, false);
847 Table& tab = out->table();
848 ArrayColumn<Float> specCol(tab,"SPECTRA");
849 ArrayColumn<Float> tsysCol(tab,"TSYS");
850 for (uInt i=0; i<tab.nrow(); ++i) {
851 Vector<Float> fact = facts[i] ;
852 Vector<Float> spec;
853 Vector<Float> ts;
854 specCol.get(i, spec);
855 tsysCol.get(i, ts);
856 if (mode == "MUL" || mode == "DIV") {
857 if (mode == "DIV") fact = (float)1.0 / fact;
858 spec *= fact;
859 specCol.put(i, spec);
860 if ( tsys ) {
861 ts *= fact;
862 tsysCol.put(i, ts);
863 }
864 } else if ( mode == "ADD" || mode == "SUB") {
865 if (mode == "SUB") fact *= (float)-1.0 ;
866 spec += fact;
867 specCol.put(i, spec);
868 if ( tsys ) {
869 ts += fact;
870 tsysCol.put(i, ts);
871 }
872 }
873 }
874 return out;
875}
876
877CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
878 const CountedPtr<Scantable>& right,
879 const std::string& mode)
880{
881 bool insitu = insitu_;
882 if ( ! left->conformant(*right) ) {
883 throw(AipsError("'left' and 'right' scantables are not conformant."));
884 }
885 setInsitu(false);
886 CountedPtr< Scantable > out = getScantable(left, false);
887 setInsitu(insitu);
888 Table& tout = out->table();
889 Block<String> coln(5);
890 coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO";
891 coln[3] = "IFNO"; coln[4] = "POLNO";
892 Table tmpl = tout.sort(coln);
893 Table tmpr = right->table().sort(coln);
894 ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
895 ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
896 ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
897 ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");
898
899 for (uInt i=0; i<tout.nrow(); ++i) {
900 Vector<Float> lspecvec, rspecvec;
901 Vector<uChar> lflagvec, rflagvec;
902 lspecvec = lspecCol(i); rspecvec = rspecCol(i);
903 lflagvec = lflagCol(i); rflagvec = rflagCol(i);
904 MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
905 MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
906 if (mode == "ADD") {
907 mleft += mright;
908 } else if ( mode == "SUB") {
909 mleft -= mright;
910 } else if ( mode == "MUL") {
911 mleft *= mright;
912 } else if ( mode == "DIV") {
913 mleft /= mright;
914 } else {
915 throw(AipsError("Illegal binary operator"));
916 }
917 lspecCol.put(i, mleft.getArray());
918 }
919 return out;
920}
921
922
923
924MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
925 const Vector<uChar>& f)
926{
927 Vector<Bool> mask;
928 mask.resize(f.shape());
929 convertArray(mask, f);
930 return MaskedArray<Float>(s,!mask);
931}
932
933MaskedArray<Double> STMath::maskedArray( const Vector<Double>& s,
934 const Vector<uChar>& f)
935{
936 Vector<Bool> mask;
937 mask.resize(f.shape());
938 convertArray(mask, f);
939 return MaskedArray<Double>(s,!mask);
940}
941
942Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
943{
944 const Vector<Bool>& m = ma.getMask();
945 Vector<uChar> flags(m.shape());
946 convertArray(flags, !m);
947 return flags;
948}
949
950CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
951 const std::string & mode,
952 bool preserve )
953{
954 /// @todo make other modes available
955 /// modes should be "nearest", "pair"
956 // make this operation non insitu
957 (void) mode; //currently unused
958 const Table& tin = in->table();
959 Table ons = tin(tin.col("SRCTYPE") == Int(SrcType::PSON));
960 Table offs = tin(tin.col("SRCTYPE") == Int(SrcType::PSOFF));
961 if ( offs.nrow() == 0 )
962 throw(AipsError("No 'off' scans present."));
963 // put all "on" scans into output table
964
965 bool insitu = insitu_;
966 setInsitu(false);
967 CountedPtr< Scantable > out = getScantable(in, true);
968 setInsitu(insitu);
969 Table& tout = out->table();
970
971 TableCopy::copyRows(tout, ons);
972 TableRow row(tout);
973 ROScalarColumn<Double> offtimeCol(offs, "TIME");
974 ArrayColumn<Float> outspecCol(tout, "SPECTRA");
975 ROArrayColumn<Float> outtsysCol(tout, "TSYS");
976 ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
977 for (uInt i=0; i < tout.nrow(); ++i) {
978 const TableRecord& rec = row.get(i);
979 Double ontime = rec.asDouble("TIME");
980 Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
981 && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
982 && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
983 ROScalarColumn<Double> offtimeCol(presel, "TIME");
984
985 Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
986 // Timestamp may vary within a cycle ???!!!
987 // increase this by 0.01 sec in case of rounding errors...
988 // There might be a better way to do this.
989 // fix to this fix. TIME is MJD, so 1.0d not 1.0s
990 mindeltat += 0.01/24./60./60.;
991 Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat);
992
993 if ( sel.nrow() < 1 ) {
994 throw(AipsError("No closest in time found... This could be a rounding "
995 "issue. Try quotient instead."));
996 }
997 TableRow offrow(sel);
998 const TableRecord& offrec = offrow.get(0);//should only be one row
999 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
1000 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
1001 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
1002 /// @fixme this assumes tsys is a scalar not vector
1003 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
1004 Vector<Float> specon, tsyson;
1005 outtsysCol.get(i, tsyson);
1006 outspecCol.get(i, specon);
1007 Vector<uChar> flagon;
1008 outflagCol.get(i, flagon);
1009 MaskedArray<Float> mon = maskedArray(specon, flagon);
1010 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
1011 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
1012 if (preserve) {
1013 quot -= tsysoffscalar;
1014 } else {
1015 quot -= tsyson[0];
1016 }
1017 outspecCol.put(i, quot.getArray());
1018 outflagCol.put(i, flagsFromMA(quot));
1019 }
1020 // renumber scanno
1021 TableIterator it(tout, "SCANNO");
1022 uInt i = 0;
1023 while ( !it.pastEnd() ) {
1024 Table t = it.table();
1025 TableVector<uInt> vec(t, "SCANNO");
1026 vec = i;
1027 ++i;
1028 ++it;
1029 }
1030 return out;
1031}
1032
1033
1034CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
1035 const CountedPtr< Scantable > & off,
1036 bool preserve )
1037{
1038 bool insitu = insitu_;
1039 if ( ! on->conformant(*off) ) {
1040 throw(AipsError("'on' and 'off' scantables are not conformant."));
1041 }
1042 setInsitu(false);
1043 CountedPtr< Scantable > out = getScantable(on, false);
1044 setInsitu(insitu);
1045 Table& tout = out->table();
1046 const Table& toff = off->table();
1047 TableIterator sit(tout, "SCANNO");
1048 TableIterator s2it(toff, "SCANNO");
1049 while ( !sit.pastEnd() ) {
1050 Table ton = sit.table();
1051 TableRow row(ton);
1052 Table t = s2it.table();
1053 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
1054 ROArrayColumn<Float> outtsysCol(ton, "TSYS");
1055 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
1056 for (uInt i=0; i < ton.nrow(); ++i) {
1057 const TableRecord& rec = row.get(i);
1058 Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1059 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
1060 && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
1061 if ( offsel.nrow() == 0 )
1062 throw AipsError("STMath::quotient: no matching off");
1063 TableRow offrow(offsel);
1064 const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
1065 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
1066 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
1067 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
1068 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
1069 Vector<Float> specon, tsyson;
1070 outtsysCol.get(i, tsyson);
1071 outspecCol.get(i, specon);
1072 Vector<uChar> flagon;
1073 outflagCol.get(i, flagon);
1074 MaskedArray<Float> mon = maskedArray(specon, flagon);
1075 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
1076 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
1077 if (preserve) {
1078 quot -= tsysoffscalar;
1079 } else {
1080 quot -= tsyson[0];
1081 }
1082 outspecCol.put(i, quot.getArray());
1083 outflagCol.put(i, flagsFromMA(quot));
1084 }
1085 ++sit;
1086 ++s2it;
1087 // take the first off for each on scan which doesn't have a
1088 // matching off scan
1089 // non <= noff: matching pairs, non > noff matching pairs then first off
1090 if ( s2it.pastEnd() ) s2it.reset();
1091 }
1092 return out;
1093}
1094
1095// dototalpower (migration of GBTIDL procedure dototalpower.pro)
1096// calibrate the CAL on-off pair. It calculate Tsys and average CAL on-off subintegrations
1097// do it for each cycles in a specific scan.
1098CountedPtr< Scantable > STMath::dototalpower( const CountedPtr< Scantable >& calon,
1099 const CountedPtr< Scantable >& caloff, Float tcal )
1100{
1101 if ( ! calon->conformant(*caloff) ) {
1102 throw(AipsError("'CAL on' and 'CAL off' scantables are not conformant."));
1103 }
1104 setInsitu(false);
1105 CountedPtr< Scantable > out = getScantable(caloff, false);
1106 Table& tout = out->table();
1107 const Table& tcon = calon->table();
1108 Vector<Float> tcalout;
1109
1110 std::map<uInt,uInt> tcalIdToRecNoMap;
1111 const Table& calOffTcalTable = caloff->tcal().table();
1112 {
1113 ROScalarColumn<uInt> calOffTcalTable_IDcol(calOffTcalTable, "ID");
1114 const Vector<uInt> tcalIds(calOffTcalTable_IDcol.getColumn());
1115 size_t tcalIdsEnd = tcalIds.nelements();
1116 for (uInt i = 0; i < tcalIdsEnd; i++) {
1117 tcalIdToRecNoMap[tcalIds[i]] = i;
1118 }
1119 }
1120 ROArrayColumn<Float> calOffTcalTable_TCALcol(calOffTcalTable, "TCAL");
1121
1122 if ( tout.nrow() != tcon.nrow() ) {
1123 throw(AipsError("Mismatch in number of rows to form cal on - off pair."));
1124 }
1125 // iteration by scanno or cycle no.
1126 TableIterator sit(tout, "SCANNO");
1127 TableIterator s2it(tcon, "SCANNO");
1128 while ( !sit.pastEnd() ) {
1129 Table toff = sit.table();
1130 TableRow row(toff);
1131 Table t = s2it.table();
1132 ScalarColumn<Double> outintCol(toff, "INTERVAL");
1133 ArrayColumn<Float> outspecCol(toff, "SPECTRA");
1134 ArrayColumn<Float> outtsysCol(toff, "TSYS");
1135 ArrayColumn<uChar> outflagCol(toff, "FLAGTRA");
1136 ROScalarColumn<uInt> outtcalIdCol(toff, "TCAL_ID");
1137 ROScalarColumn<uInt> outpolCol(toff, "POLNO");
1138 ROScalarColumn<Double> onintCol(t, "INTERVAL");
1139 ROArrayColumn<Float> onspecCol(t, "SPECTRA");
1140 ROArrayColumn<Float> ontsysCol(t, "TSYS");
1141 ROArrayColumn<uChar> onflagCol(t, "FLAGTRA");
1142 //ROScalarColumn<uInt> ontcalIdCol(t, "TCAL_ID");
1143
1144 for (uInt i=0; i < toff.nrow(); ++i) {
1145 //skip these checks -> assumes the data order are the same between the cal on off pairs
1146 //
1147 Vector<Float> specCalon, specCaloff;
1148 // to store scalar (mean) tsys
1149 Vector<Float> tsysout(1);
1150 uInt tcalId, polno;
1151 Double offint, onint;
1152 outpolCol.get(i, polno);
1153 outspecCol.get(i, specCaloff);
1154 onspecCol.get(i, specCalon);
1155 Vector<uChar> flagCaloff, flagCalon;
1156 outflagCol.get(i, flagCaloff);
1157 onflagCol.get(i, flagCalon);
1158 outtcalIdCol.get(i, tcalId);
1159 outintCol.get(i, offint);
1160 onintCol.get(i, onint);
1161 // caluculate mean Tsys
1162 uInt nchan = specCaloff.nelements();
1163 // percentage of edge cut off
1164 uInt pc = 10;
1165 uInt bchan = nchan/pc;
1166 uInt echan = nchan-bchan;
1167
1168 Slicer chansl(IPosition(1,bchan-1), IPosition(1,echan-1), IPosition(1,1),Slicer::endIsLast);
1169 Vector<Float> testsubsp = specCaloff(chansl);
1170 MaskedArray<Float> spoff = maskedArray( specCaloff(chansl),flagCaloff(chansl) );
1171 MaskedArray<Float> spon = maskedArray( specCalon(chansl),flagCalon(chansl) );
1172 MaskedArray<Float> spdiff = spon-spoff;
1173 uInt noff = spoff.nelementsValid();
1174 //uInt non = spon.nelementsValid();
1175 uInt ndiff = spdiff.nelementsValid();
1176 Float meantsys;
1177
1178/**
1179 Double subspec, subdiff;
1180 uInt usednchan;
1181 subspec = 0;
1182 subdiff = 0;
1183 usednchan = 0;
1184 for(uInt k=(bchan-1); k<echan; k++) {
1185 subspec += specCaloff[k];
1186 subdiff += static_cast<Double>(specCalon[k]-specCaloff[k]);
1187 ++usednchan;
1188 }
1189**/
1190 // get tcal if input tcal <= 0
1191 Float tcalUsed;
1192 tcalUsed = tcal;
1193 if ( tcal <= 0.0 ) {
1194 uInt tcalRecNo = tcalIdToRecNoMap[tcalId];
1195 calOffTcalTable_TCALcol.get(tcalRecNo, tcalout);
1196// if (polno<=3) {
1197// tcalUsed = tcalout[polno];
1198// }
1199// else {
1200// tcalUsed = tcalout[0];
1201// }
1202 if ( tcalout.size() == 1 )
1203 tcalUsed = tcalout[0] ;
1204 else if ( tcalout.size() == nchan )
1205 tcalUsed = mean(tcalout) ;
1206 else {
1207 uInt ipol = polno ;
1208 if ( ipol > 3 ) ipol = 0 ;
1209 tcalUsed = tcalout[ipol] ;
1210 }
1211 }
1212
1213 Float meanoff;
1214 Float meandiff;
1215 if (noff && ndiff) {
1216 //Debug
1217 //if(noff!=ndiff) cerr<<"noff and ndiff is not equal"<<endl;
1218 //LogIO os( LogOrigin( "STMath", "dototalpower()", WHERE ) ) ;
1219 //if(noff!=ndiff) os<<"noff and ndiff is not equal"<<LogIO::POST;
1220 meanoff = sum(spoff)/noff;
1221 meandiff = sum(spdiff)/ndiff;
1222 meantsys= (meanoff/meandiff )*tcalUsed + tcalUsed/2;
1223 }
1224 else {
1225 meantsys=1;
1226 }
1227
1228 tsysout[0] = Float(meantsys);
1229 MaskedArray<Float> mcaloff = maskedArray(specCaloff, flagCaloff);
1230 MaskedArray<Float> mcalon = maskedArray(specCalon, flagCalon);
1231 MaskedArray<Float> sig = Float(0.5) * (mcaloff + mcalon);
1232 //uInt ncaloff = mcaloff.nelementsValid();
1233 //uInt ncalon = mcalon.nelementsValid();
1234
1235 outintCol.put(i, offint+onint);
1236 outspecCol.put(i, sig.getArray());
1237 outflagCol.put(i, flagsFromMA(sig));
1238 outtsysCol.put(i, tsysout);
1239 }
1240 ++sit;
1241 ++s2it;
1242 }
1243 return out;
1244}
1245
1246//dosigref - migrated from GBT IDL's dosigref.pro, do calibration of position switch
1247// observatiions.
1248// input: sig and ref scantables, and an optional boxcar smoothing width(default width=0,
1249// no smoothing).
1250// output: resultant scantable [= (sig-ref/ref)*tsys]
1251CountedPtr< Scantable > STMath::dosigref( const CountedPtr < Scantable >& sig,
1252 const CountedPtr < Scantable >& ref,
1253 int smoothref,
1254 casa::Float tsysv,
1255 casa::Float tau )
1256{
1257if ( ! ref->conformant(*sig) ) {
1258 throw(AipsError("'sig' and 'ref' scantables are not conformant."));
1259 }
1260 setInsitu(false);
1261 CountedPtr< Scantable > out = getScantable(sig, false);
1262 CountedPtr< Scantable > smref;
1263 if ( smoothref > 1 ) {
1264 float fsmoothref = static_cast<float>(smoothref);
1265 std::string inkernel = "boxcar";
1266 smref = smooth(ref, inkernel, fsmoothref );
1267 ostringstream oss;
1268 oss<<"Applied smoothing of "<<fsmoothref<<" on the reference."<<endl;
1269 pushLog(String(oss));
1270 }
1271 else {
1272 smref = ref;
1273 }
1274 Table& tout = out->table();
1275 const Table& tref = smref->table();
1276 if ( tout.nrow() != tref.nrow() ) {
1277 throw(AipsError("Mismatch in number of rows to form on-source and reference pair."));
1278 }
1279 // iteration by scanno? or cycle no.
1280 TableIterator sit(tout, "SCANNO");
1281 TableIterator s2it(tref, "SCANNO");
1282 while ( !sit.pastEnd() ) {
1283 Table ton = sit.table();
1284 Table t = s2it.table();
1285 ScalarColumn<Double> outintCol(ton, "INTERVAL");
1286 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
1287 ArrayColumn<Float> outtsysCol(ton, "TSYS");
1288 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
1289 ArrayColumn<Float> refspecCol(t, "SPECTRA");
1290 ROScalarColumn<Double> refintCol(t, "INTERVAL");
1291 ROArrayColumn<Float> reftsysCol(t, "TSYS");
1292 ArrayColumn<uChar> refflagCol(t, "FLAGTRA");
1293 ROScalarColumn<Float> refelevCol(t, "ELEVATION");
1294 for (uInt i=0; i < ton.nrow(); ++i) {
1295
1296 Double onint, refint;
1297 Vector<Float> specon, specref;
1298 // to store scalar (mean) tsys
1299 Vector<Float> tsysref;
1300 outintCol.get(i, onint);
1301 refintCol.get(i, refint);
1302 outspecCol.get(i, specon);
1303 refspecCol.get(i, specref);
1304 Vector<uChar> flagref, flagon;
1305 outflagCol.get(i, flagon);
1306 refflagCol.get(i, flagref);
1307 reftsysCol.get(i, tsysref);
1308
1309 Float tsysrefscalar;
1310 if ( tsysv > 0.0 ) {
1311 ostringstream oss;
1312 Float elev;
1313 refelevCol.get(i, elev);
1314 oss << "user specified Tsys = " << tsysv;
1315 // do recalc elevation if EL = 0
1316 if ( elev == 0 ) {
1317 throw(AipsError("EL=0, elevation data is missing."));
1318 } else {
1319 if ( tau <= 0.0 ) {
1320 throw(AipsError("Valid tau is not supplied."));
1321 } else {
1322 tsysrefscalar = tsysv * exp(tau/elev);
1323 }
1324 }
1325 oss << ", corrected (for El) tsys= "<<tsysrefscalar;
1326 pushLog(String(oss));
1327 }
1328 else {
1329 tsysrefscalar = tsysref[0];
1330 }
1331 //get quotient spectrum
1332 MaskedArray<Float> mref = maskedArray(specref, flagref);
1333 MaskedArray<Float> mon = maskedArray(specon, flagon);
1334 MaskedArray<Float> specres = tsysrefscalar*((mon - mref)/mref);
1335 Double resint = onint*refint*smoothref/(onint+refint*smoothref);
1336
1337 //Debug
1338 //cerr<<"Tsys used="<<tsysrefscalar<<endl;
1339 //LogIO os( LogOrigin( "STMath", "dosigref", WHERE ) ) ;
1340 //os<<"Tsys used="<<tsysrefscalar<<LogIO::POST;
1341 // fill the result, replay signal tsys by reference tsys
1342 outintCol.put(i, resint);
1343 outspecCol.put(i, specres.getArray());
1344 outflagCol.put(i, flagsFromMA(specres));
1345 outtsysCol.put(i, tsysref);
1346 }
1347 ++sit;
1348 ++s2it;
1349 }
1350 return out;
1351}
1352
1353CountedPtr< Scantable > STMath::donod(const casa::CountedPtr<Scantable>& s,
1354 const std::vector<int>& scans,
1355 int smoothref,
1356 casa::Float tsysv,
1357 casa::Float tau,
1358 casa::Float tcal )
1359
1360{
1361 setInsitu(false);
1362 STSelector sel;
1363 std::vector<int> scan1, scan2, beams, types;
1364 std::vector< vector<int> > scanpair;
1365 //std::vector<string> calstate;
1366 std::vector<int> calstate;
1367 String msg;
1368
1369 CountedPtr< Scantable > s1b1on, s1b1off, s1b2on, s1b2off;
1370 CountedPtr< Scantable > s2b1on, s2b1off, s2b2on, s2b2off;
1371
1372 std::vector< CountedPtr< Scantable > > sctables;
1373 sctables.push_back(s1b1on);
1374 sctables.push_back(s1b1off);
1375 sctables.push_back(s1b2on);
1376 sctables.push_back(s1b2off);
1377 sctables.push_back(s2b1on);
1378 sctables.push_back(s2b1off);
1379 sctables.push_back(s2b2on);
1380 sctables.push_back(s2b2off);
1381
1382 //check scanlist
1383 int n=s->checkScanInfo(scans);
1384 if (n==1) {
1385 throw(AipsError("Incorrect scan pairs. "));
1386 }
1387
1388 // Assume scans contain only a pair of consecutive scan numbers.
1389 // It is assumed that first beam, b1, is on target.
1390 // There is no check if the first beam is on or not.
1391 if ( scans.size()==1 ) {
1392 scan1.push_back(scans[0]);
1393 scan2.push_back(scans[0]+1);
1394 } else if ( scans.size()==2 ) {
1395 scan1.push_back(scans[0]);
1396 scan2.push_back(scans[1]);
1397 } else {
1398 if ( scans.size()%2 == 0 ) {
1399 for (uInt i=0; i<scans.size(); i++) {
1400 if (i%2 == 0) {
1401 scan1.push_back(scans[i]);
1402 }
1403 else {
1404 scan2.push_back(scans[i]);
1405 }
1406 }
1407 } else {
1408 throw(AipsError("Odd numbers of scans, cannot form pairs."));
1409 }
1410 }
1411 scanpair.push_back(scan1);
1412 scanpair.push_back(scan2);
1413 //calstate.push_back("*calon");
1414 //calstate.push_back("*[^calon]");
1415 calstate.push_back(SrcType::NODCAL);
1416 calstate.push_back(SrcType::NOD);
1417 CountedPtr< Scantable > ws = getScantable(s, false);
1418 uInt l=0;
1419 while ( l < sctables.size() ) {
1420 for (uInt i=0; i < 2; i++) {
1421 for (uInt j=0; j < 2; j++) {
1422 for (uInt k=0; k < 2; k++) {
1423 sel.reset();
1424 sel.setScans(scanpair[i]);
1425 //sel.setName(calstate[k]);
1426 types.clear();
1427 types.push_back(calstate[k]);
1428 sel.setTypes(types);
1429 beams.clear();
1430 beams.push_back(j);
1431 sel.setBeams(beams);
1432 ws->setSelection(sel);
1433 sctables[l]= getScantable(ws, false);
1434 l++;
1435 }
1436 }
1437 }
1438 }
1439
1440 // replace here by splitData or getData functionality
1441 CountedPtr< Scantable > sig1;
1442 CountedPtr< Scantable > ref1;
1443 CountedPtr< Scantable > sig2;
1444 CountedPtr< Scantable > ref2;
1445 CountedPtr< Scantable > calb1;
1446 CountedPtr< Scantable > calb2;
1447
1448 msg=String("Processing dototalpower for subset of the data");
1449 ostringstream oss1;
1450 oss1 << msg << endl;
1451 pushLog(String(oss1));
1452 // Debug for IRC CS data
1453 //float tcal1=7.0;
1454 //float tcal2=4.0;
1455 sig1 = dototalpower(sctables[0], sctables[1], tcal=tcal);
1456 ref1 = dototalpower(sctables[2], sctables[3], tcal=tcal);
1457 ref2 = dototalpower(sctables[4], sctables[5], tcal=tcal);
1458 sig2 = dototalpower(sctables[6], sctables[7], tcal=tcal);
1459
1460 // correction of user-specified tsys for elevation here
1461
1462 // dosigref calibration
1463 msg=String("Processing dosigref for subset of the data");
1464 ostringstream oss2;
1465 oss2 << msg << endl;
1466 pushLog(String(oss2));
1467 calb1=dosigref(sig1,ref2,smoothref,tsysv,tau);
1468 calb2=dosigref(sig2,ref1,smoothref,tsysv,tau);
1469
1470 // iteration by scanno or cycle no.
1471 Table& tcalb1 = calb1->table();
1472 Table& tcalb2 = calb2->table();
1473 TableIterator sit(tcalb1, "SCANNO");
1474 TableIterator s2it(tcalb2, "SCANNO");
1475 while ( !sit.pastEnd() ) {
1476 Table t1 = sit.table();
1477 Table t2= s2it.table();
1478 ArrayColumn<Float> outspecCol(t1, "SPECTRA");
1479 ArrayColumn<Float> outtsysCol(t1, "TSYS");
1480 ArrayColumn<uChar> outflagCol(t1, "FLAGTRA");
1481 ScalarColumn<Double> outintCol(t1, "INTERVAL");
1482 ArrayColumn<Float> t2specCol(t2, "SPECTRA");
1483 ROArrayColumn<Float> t2tsysCol(t2, "TSYS");
1484 ArrayColumn<uChar> t2flagCol(t2, "FLAGTRA");
1485 ROScalarColumn<Double> t2intCol(t2, "INTERVAL");
1486 for (uInt i=0; i < t1.nrow(); ++i) {
1487 Vector<Float> spec1, spec2;
1488 // to store scalar (mean) tsys
1489 Vector<Float> tsys1, tsys2;
1490 Vector<uChar> flag1, flag2;
1491 Double tint1, tint2;
1492 outspecCol.get(i, spec1);
1493 t2specCol.get(i, spec2);
1494 outflagCol.get(i, flag1);
1495 t2flagCol.get(i, flag2);
1496 outtsysCol.get(i, tsys1);
1497 t2tsysCol.get(i, tsys2);
1498 outintCol.get(i, tint1);
1499 t2intCol.get(i, tint2);
1500 // average
1501 // assume scalar tsys for weights
1502 Float wt1, wt2, tsyssq1, tsyssq2;
1503 tsyssq1 = tsys1[0]*tsys1[0];
1504 tsyssq2 = tsys2[0]*tsys2[0];
1505 wt1 = Float(tint1)/tsyssq1;
1506 wt2 = Float(tint2)/tsyssq2;
1507 Float invsumwt=1/(wt1+wt2);
1508 MaskedArray<Float> mspec1 = maskedArray(spec1, flag1);
1509 MaskedArray<Float> mspec2 = maskedArray(spec2, flag2);
1510 MaskedArray<Float> avspec = invsumwt * (wt1*mspec1 + wt2*mspec2);
1511 //Array<Float> avtsys = Float(0.5) * (tsys1 + tsys2);
1512 // cerr<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<endl;
1513 // LogIO os( LogOrigin( "STMath", "donod", WHERE ) ) ;
1514 // os<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<LogIO::POST;
1515 tsys1[0] = sqrt(tsyssq1 + tsyssq2);
1516 Array<Float> avtsys = tsys1;
1517
1518 outspecCol.put(i, avspec.getArray());
1519 outflagCol.put(i, flagsFromMA(avspec));
1520 outtsysCol.put(i, avtsys);
1521 }
1522 ++sit;
1523 ++s2it;
1524 }
1525 return calb1;
1526}
1527
1528//GBTIDL version of frequency switched data calibration
1529CountedPtr< Scantable > STMath::dofs( const CountedPtr< Scantable >& s,
1530 const std::vector<int>& scans,
1531 int smoothref,
1532 casa::Float tsysv,
1533 casa::Float tau,
1534 casa::Float tcal )
1535{
1536
1537
1538 (void) scans; //currently unused
1539 STSelector sel;
1540 CountedPtr< Scantable > ws = getScantable(s, false);
1541 CountedPtr< Scantable > sig, sigwcal, ref, refwcal;
1542 CountedPtr< Scantable > calsig, calref, out, out1, out2;
1543 Bool nofold=False;
1544 vector<int> types ;
1545
1546 //split the data
1547 //sel.setName("*_fs");
1548 types.push_back( SrcType::FSON ) ;
1549 sel.setTypes( types ) ;
1550 ws->setSelection(sel);
1551 sig = getScantable(ws,false);
1552 sel.reset();
1553 types.clear() ;
1554 //sel.setName("*_fs_calon");
1555 types.push_back( SrcType::FONCAL ) ;
1556 sel.setTypes( types ) ;
1557 ws->setSelection(sel);
1558 sigwcal = getScantable(ws,false);
1559 sel.reset();
1560 types.clear() ;
1561 //sel.setName("*_fsr");
1562 types.push_back( SrcType::FSOFF ) ;
1563 sel.setTypes( types ) ;
1564 ws->setSelection(sel);
1565 ref = getScantable(ws,false);
1566 sel.reset();
1567 types.clear() ;
1568 //sel.setName("*_fsr_calon");
1569 types.push_back( SrcType::FOFFCAL ) ;
1570 sel.setTypes( types ) ;
1571 ws->setSelection(sel);
1572 refwcal = getScantable(ws,false);
1573 sel.reset() ;
1574 types.clear() ;
1575
1576 calsig = dototalpower(sigwcal, sig, tcal=tcal);
1577 calref = dototalpower(refwcal, ref, tcal=tcal);
1578
1579 out1=dosigref(calsig,calref,smoothref,tsysv,tau);
1580 out2=dosigref(calref,calsig,smoothref,tsysv,tau);
1581
1582 Table& tabout1=out1->table();
1583 Table& tabout2=out2->table();
1584 ROScalarColumn<uInt> freqidCol1(tabout1, "FREQ_ID");
1585 ScalarColumn<uInt> freqidCol2(tabout2, "FREQ_ID");
1586 ROArrayColumn<Float> specCol(tabout2, "SPECTRA");
1587 Vector<Float> spec; specCol.get(0, spec);
1588 uInt nchan = spec.nelements();
1589 uInt freqid1; freqidCol1.get(0,freqid1);
1590 uInt freqid2; freqidCol2.get(0,freqid2);
1591 Double rp1, rp2, rv1, rv2, inc1, inc2;
1592 out1->frequencies().getEntry(rp1, rv1, inc1, freqid1);
1593 out2->frequencies().getEntry(rp2, rv2, inc2, freqid2);
1594 //cerr << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << endl ;
1595 //LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1596 //os << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << LogIO::POST ;
1597 if (rp1==rp2) {
1598 Double foffset = rv1 - rv2;
1599 uInt choffset = static_cast<uInt>(foffset/abs(inc2));
1600 if (choffset >= nchan) {
1601 //cerr<<"out-band frequency switching, no folding"<<endl;
1602 LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1603 os<<"out-band frequency switching, no folding"<<LogIO::POST;
1604 nofold = True;
1605 }
1606 }
1607
1608 if (nofold) {
1609 std::vector< CountedPtr< Scantable > > tabs;
1610 tabs.push_back(out1);
1611 tabs.push_back(out2);
1612 out = merge(tabs);
1613 }
1614 else {
1615 //out = out1;
1616 Double choffset = ( rv1 - rv2 ) / inc2 ;
1617 out = dofold( out1, out2, choffset ) ;
1618 }
1619
1620 return out;
1621}
1622
1623CountedPtr<Scantable> STMath::dofold( const CountedPtr<Scantable> &sig,
1624 const CountedPtr<Scantable> &ref,
1625 Double choffset,
1626 Double choffset2 )
1627{
1628 LogIO os( LogOrigin( "STMath", "dofold", WHERE ) ) ;
1629 os << "choffset=" << choffset << " choffset2=" << choffset2 << LogIO::POST ;
1630
1631 // output scantable
1632 CountedPtr<Scantable> out = getScantable( sig, false ) ;
1633
1634 // separate choffset to integer part and decimal part
1635 Int ioffset = (Int)choffset ;
1636 Double doffset = choffset - ioffset ;
1637 Int ioffset2 = (Int)choffset2 ;
1638 Double doffset2 = choffset2 - ioffset2 ;
1639 os << "ioffset=" << ioffset << " doffset=" << doffset << LogIO::POST ;
1640 os << "ioffset2=" << ioffset2 << " doffset2=" << doffset2 << LogIO::POST ;
1641
1642 // get column
1643 ROArrayColumn<Float> specCol1( sig->table(), "SPECTRA" ) ;
1644 ROArrayColumn<Float> specCol2( ref->table(), "SPECTRA" ) ;
1645 ROArrayColumn<Float> tsysCol1( sig->table(), "TSYS" ) ;
1646 ROArrayColumn<Float> tsysCol2( ref->table(), "TSYS" ) ;
1647 ROArrayColumn<uChar> flagCol1( sig->table(), "FLAGTRA" ) ;
1648 ROArrayColumn<uChar> flagCol2( ref->table(), "FLAGTRA" ) ;
1649 ROScalarColumn<Double> mjdCol1( sig->table(), "TIME" ) ;
1650 ROScalarColumn<Double> mjdCol2( ref->table(), "TIME" ) ;
1651 ROScalarColumn<Double> intervalCol1( sig->table(), "INTERVAL" ) ;
1652 ROScalarColumn<Double> intervalCol2( ref->table(), "INTERVAL" ) ;
1653
1654 // check
1655 if ( ioffset == 0 ) {
1656 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1657 os << "channel offset is zero, no folding" << LogIO::POST ;
1658 return out ;
1659 }
1660 int nchan = ref->nchan() ;
1661 if ( abs(ioffset) >= nchan ) {
1662 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1663 os << "out-band frequency switching, no folding" << LogIO::POST ;
1664 return out ;
1665 }
1666
1667 // attach column for output scantable
1668 ArrayColumn<Float> specColOut( out->table(), "SPECTRA" ) ;
1669 ArrayColumn<uChar> flagColOut( out->table(), "FLAGTRA" ) ;
1670 ArrayColumn<Float> tsysColOut( out->table(), "TSYS" ) ;
1671 ScalarColumn<Double> mjdColOut( out->table(), "TIME" ) ;
1672 ScalarColumn<Double> intervalColOut( out->table(), "INTERVAL" ) ;
1673 ScalarColumn<uInt> fidColOut( out->table(), "FREQ_ID" ) ;
1674
1675 // for each row
1676 // assume that the data order are same between sig and ref
1677 RowAccumulator acc( asap::W_TINTSYS ) ;
1678 for ( int i = 0 ; i < sig->nrow() ; i++ ) {
1679 // get values
1680 Vector<Float> spsig ;
1681 specCol1.get( i, spsig ) ;
1682 Vector<Float> spref ;
1683 specCol2.get( i, spref ) ;
1684 Vector<Float> tsyssig ;
1685 tsysCol1.get( i, tsyssig ) ;
1686 Vector<Float> tsysref ;
1687 tsysCol2.get( i, tsysref ) ;
1688 Vector<uChar> flagsig ;
1689 flagCol1.get( i, flagsig ) ;
1690 Vector<uChar> flagref ;
1691 flagCol2.get( i, flagref ) ;
1692 Double timesig ;
1693 mjdCol1.get( i, timesig ) ;
1694 Double timeref ;
1695 mjdCol2.get( i, timeref ) ;
1696 Double intsig ;
1697 intervalCol1.get( i, intsig ) ;
1698 Double intref ;
1699 intervalCol2.get( i, intref ) ;
1700
1701 // shift reference spectra
1702 int refchan = spref.nelements() ;
1703 Vector<Float> sspref( spref.nelements() ) ;
1704 Vector<Float> stsysref( tsysref.nelements() ) ;
1705 Vector<uChar> sflagref( flagref.nelements() ) ;
1706 if ( ioffset > 0 ) {
1707 // SPECTRA and FLAGTRA
1708 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1709 sspref[j] = spref[j+ioffset] ;
1710 sflagref[j] = flagref[j+ioffset] ;
1711 }
1712 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1713 sspref[j] = spref[j-refchan+ioffset] ;
1714 sflagref[j] = flagref[j-refchan+ioffset] ;
1715 }
1716 spref = sspref.copy() ;
1717 flagref = sflagref.copy() ;
1718 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1719 sspref[j] = doffset * spref[j+1] + ( 1.0 - doffset ) * spref[j] ;
1720 sflagref[j] = flagref[j+1] + flagref[j] ;
1721 }
1722 sspref[refchan-1] = doffset * spref[0] + ( 1.0 - doffset ) * spref[refchan-1] ;
1723 sflagref[refchan-1] = flagref[0] + flagref[refchan-1] ;
1724
1725 // TSYS
1726 if ( spref.nelements() == tsysref.nelements() ) {
1727 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1728 stsysref[j] = tsysref[j+ioffset] ;
1729 }
1730 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1731 stsysref[j] = tsysref[j-refchan+ioffset] ;
1732 }
1733 tsysref = stsysref.copy() ;
1734 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1735 stsysref[j] = doffset * tsysref[j+1] + ( 1.0 - doffset ) * tsysref[j] ;
1736 }
1737 stsysref[refchan-1] = doffset * tsysref[0] + ( 1.0 - doffset ) * tsysref[refchan-1] ;
1738 }
1739 }
1740 else {
1741 // SPECTRA and FLAGTRA
1742 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1743 sspref[j] = spref[refchan+ioffset+j] ;
1744 sflagref[j] = flagref[refchan+ioffset+j] ;
1745 }
1746 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1747 sspref[j] = spref[j+ioffset] ;
1748 sflagref[j] = flagref[j+ioffset] ;
1749 }
1750 spref = sspref.copy() ;
1751 flagref = sflagref.copy() ;
1752 sspref[0] = doffset * spref[refchan-1] + ( 1.0 - doffset ) * spref[0] ;
1753 sflagref[0] = flagref[0] + flagref[refchan-1] ;
1754 for ( int j = 1 ; j < refchan ; j++ ) {
1755 sspref[j] = doffset * spref[j-1] + ( 1.0 - doffset ) * spref[j] ;
1756 sflagref[j] = flagref[j-1] + flagref[j] ;
1757 }
1758 // TSYS
1759 if ( spref.nelements() == tsysref.nelements() ) {
1760 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1761 stsysref[j] = tsysref[refchan+ioffset+j] ;
1762 }
1763 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1764 stsysref[j] = tsysref[j+ioffset] ;
1765 }
1766 tsysref = stsysref.copy() ;
1767 stsysref[0] = doffset * tsysref[refchan-1] + ( 1.0 - doffset ) * tsysref[0] ;
1768 for ( int j = 1 ; j < refchan ; j++ ) {
1769 stsysref[j] = doffset * tsysref[j-1] + ( 1.0 - doffset ) * tsysref[j] ;
1770 }
1771 }
1772 }
1773
1774 // shift signal spectra if necessary (only for APEX?)
1775 if ( choffset2 != 0.0 ) {
1776 int sigchan = spsig.nelements() ;
1777 Vector<Float> sspsig( spsig.nelements() ) ;
1778 Vector<Float> stsyssig( tsyssig.nelements() ) ;
1779 Vector<uChar> sflagsig( flagsig.nelements() ) ;
1780 if ( ioffset2 > 0 ) {
1781 // SPECTRA and FLAGTRA
1782 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1783 sspsig[j] = spsig[j+ioffset2] ;
1784 sflagsig[j] = flagsig[j+ioffset2] ;
1785 }
1786 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1787 sspsig[j] = spsig[j-sigchan+ioffset2] ;
1788 sflagsig[j] = flagsig[j-sigchan+ioffset2] ;
1789 }
1790 spsig = sspsig.copy() ;
1791 flagsig = sflagsig.copy() ;
1792 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1793 sspsig[j] = doffset2 * spsig[j+1] + ( 1.0 - doffset2 ) * spsig[j] ;
1794 sflagsig[j] = flagsig[j+1] || flagsig[j] ;
1795 }
1796 sspsig[sigchan-1] = doffset2 * spsig[0] + ( 1.0 - doffset2 ) * spsig[sigchan-1] ;
1797 sflagsig[sigchan-1] = flagsig[0] || flagsig[sigchan-1] ;
1798 // TSTS
1799 if ( spsig.nelements() == tsyssig.nelements() ) {
1800 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1801 stsyssig[j] = tsyssig[j+ioffset2] ;
1802 }
1803 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1804 stsyssig[j] = tsyssig[j-sigchan+ioffset2] ;
1805 }
1806 tsyssig = stsyssig.copy() ;
1807 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1808 stsyssig[j] = doffset2 * tsyssig[j+1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1809 }
1810 stsyssig[sigchan-1] = doffset2 * tsyssig[0] + ( 1.0 - doffset2 ) * tsyssig[sigchan-1] ;
1811 }
1812 }
1813 else {
1814 // SPECTRA and FLAGTRA
1815 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1816 sspsig[j] = spsig[sigchan+ioffset2+j] ;
1817 sflagsig[j] = flagsig[sigchan+ioffset2+j] ;
1818 }
1819 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1820 sspsig[j] = spsig[j+ioffset2] ;
1821 sflagsig[j] = flagsig[j+ioffset2] ;
1822 }
1823 spsig = sspsig.copy() ;
1824 flagsig = sflagsig.copy() ;
1825 sspsig[0] = doffset2 * spsig[sigchan-1] + ( 1.0 - doffset2 ) * spsig[0] ;
1826 sflagsig[0] = flagsig[0] + flagsig[sigchan-1] ;
1827 for ( int j = 1 ; j < sigchan ; j++ ) {
1828 sspsig[j] = doffset2 * spsig[j-1] + ( 1.0 - doffset2 ) * spsig[j] ;
1829 sflagsig[j] = flagsig[j-1] + flagsig[j] ;
1830 }
1831 // TSYS
1832 if ( spsig.nelements() == tsyssig.nelements() ) {
1833 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1834 stsyssig[j] = tsyssig[sigchan+ioffset2+j] ;
1835 }
1836 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1837 stsyssig[j] = tsyssig[j+ioffset2] ;
1838 }
1839 tsyssig = stsyssig.copy() ;
1840 stsyssig[0] = doffset2 * tsyssig[sigchan-1] + ( 1.0 - doffset2 ) * tsyssig[0] ;
1841 for ( int j = 1 ; j < sigchan ; j++ ) {
1842 stsyssig[j] = doffset2 * tsyssig[j-1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1843 }
1844 }
1845 }
1846 }
1847
1848 // folding
1849 acc.add( spsig, !flagsig, tsyssig, intsig, timesig ) ;
1850 acc.add( sspref, !sflagref, stsysref, intref, timeref ) ;
1851
1852 // put result
1853 specColOut.put( i, acc.getSpectrum() ) ;
1854 const Vector<Bool> &msk = acc.getMask() ;
1855 Vector<uChar> flg( msk.shape() ) ;
1856 convertArray( flg, !msk ) ;
1857 flagColOut.put( i, flg ) ;
1858 tsysColOut.put( i, acc.getTsys() ) ;
1859 intervalColOut.put( i, acc.getInterval() ) ;
1860 mjdColOut.put( i, acc.getTime() ) ;
1861 // change FREQ_ID to unshifted IF setting (only for APEX?)
1862 if ( choffset2 != 0.0 ) {
1863 uInt freqid = fidColOut( 0 ) ; // assume single-IF data
1864 double refpix, refval, increment ;
1865 out->frequencies().getEntry( refpix, refval, increment, freqid ) ;
1866 refval -= choffset * increment ;
1867 uInt newfreqid = out->frequencies().addEntry( refpix, refval, increment ) ;
1868 Vector<uInt> freqids = fidColOut.getColumn() ;
1869 for ( uInt j = 0 ; j < freqids.nelements() ; j++ ) {
1870 if ( freqids[j] == freqid )
1871 freqids[j] = newfreqid ;
1872 }
1873 fidColOut.putColumn( freqids ) ;
1874 }
1875
1876 acc.reset() ;
1877 }
1878
1879 return out ;
1880}
1881
1882
1883CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
1884{
1885 // make copy or reference
1886 CountedPtr< Scantable > out = getScantable(in, false);
1887 Table& tout = out->table();
1888 Block<String> cols(4);
1889 cols[0] = String("SCANNO");
1890 cols[1] = String("CYCLENO");
1891 cols[2] = String("BEAMNO");
1892 cols[3] = String("POLNO");
1893 TableIterator iter(tout, cols);
1894 while (!iter.pastEnd()) {
1895 Table subt = iter.table();
1896 // this should leave us with two rows for the two IFs....if not ignore
1897 if (subt.nrow() != 2 ) {
1898 continue;
1899 }
1900 ArrayColumn<Float> specCol(subt, "SPECTRA");
1901 ArrayColumn<Float> tsysCol(subt, "TSYS");
1902 ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
1903 Vector<Float> onspec,offspec, ontsys, offtsys;
1904 Vector<uChar> onflag, offflag;
1905 tsysCol.get(0, ontsys); tsysCol.get(1, offtsys);
1906 specCol.get(0, onspec); specCol.get(1, offspec);
1907 flagCol.get(0, onflag); flagCol.get(1, offflag);
1908 MaskedArray<Float> on = maskedArray(onspec, onflag);
1909 MaskedArray<Float> off = maskedArray(offspec, offflag);
1910 MaskedArray<Float> oncopy = on.copy();
1911
1912 on /= off; on -= 1.0f;
1913 on *= ontsys[0];
1914 off /= oncopy; off -= 1.0f;
1915 off *= offtsys[0];
1916 specCol.put(0, on.getArray());
1917 const Vector<Bool>& m0 = on.getMask();
1918 Vector<uChar> flags0(m0.shape());
1919 convertArray(flags0, !m0);
1920 flagCol.put(0, flags0);
1921
1922 specCol.put(1, off.getArray());
1923 const Vector<Bool>& m1 = off.getMask();
1924 Vector<uChar> flags1(m1.shape());
1925 convertArray(flags1, !m1);
1926 flagCol.put(1, flags1);
1927 ++iter;
1928 }
1929
1930 return out;
1931}
1932
1933std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
1934 const std::vector< bool > & mask,
1935 const std::string& which )
1936{
1937
1938 Vector<Bool> m(mask);
1939 const Table& tab = in->table();
1940 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1941 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1942 std::vector<float> out;
1943 for (uInt i=0; i < tab.nrow(); ++i ) {
1944 Vector<Float> spec; specCol.get(i, spec);
1945 Vector<uChar> flag; flagCol.get(i, flag);
1946 MaskedArray<Float> ma = maskedArray(spec, flag);
1947 float outstat = 0.0;
1948 if ( spec.nelements() == m.nelements() ) {
1949 outstat = mathutil::statistics(which, ma(m));
1950 } else {
1951 outstat = mathutil::statistics(which, ma);
1952 }
1953 out.push_back(outstat);
1954 }
1955 return out;
1956}
1957
1958std::vector< float > STMath::statisticRow( const CountedPtr< Scantable > & in,
1959 const std::vector< bool > & mask,
1960 const std::string& which,
1961 int row )
1962{
1963
1964 Vector<Bool> m(mask);
1965 const Table& tab = in->table();
1966 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1967 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1968 std::vector<float> out;
1969
1970 Vector<Float> spec; specCol.get(row, spec);
1971 Vector<uChar> flag; flagCol.get(row, flag);
1972 MaskedArray<Float> ma = maskedArray(spec, flag);
1973 float outstat = 0.0;
1974 if ( spec.nelements() == m.nelements() ) {
1975 outstat = mathutil::statistics(which, ma(m));
1976 } else {
1977 outstat = mathutil::statistics(which, ma);
1978 }
1979 out.push_back(outstat);
1980
1981 return out;
1982}
1983
1984std::vector< int > STMath::minMaxChan( const CountedPtr< Scantable > & in,
1985 const std::vector< bool > & mask,
1986 const std::string& which )
1987{
1988
1989 Vector<Bool> m(mask);
1990 const Table& tab = in->table();
1991 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1992 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1993 std::vector<int> out;
1994 for (uInt i=0; i < tab.nrow(); ++i ) {
1995 Vector<Float> spec; specCol.get(i, spec);
1996 Vector<uChar> flag; flagCol.get(i, flag);
1997 MaskedArray<Float> ma = maskedArray(spec, flag);
1998 if (ma.ndim() != 1) {
1999 throw (ArrayError(
2000 "std::vector<int> STMath::minMaxChan("
2001 "ContedPtr<Scantable> &in, std::vector<bool> &mask, "
2002 " std::string &which)"
2003 " - MaskedArray is not 1D"));
2004 }
2005 IPosition outpos(1,0);
2006 if ( spec.nelements() == m.nelements() ) {
2007 outpos = mathutil::minMaxPos(which, ma(m));
2008 } else {
2009 outpos = mathutil::minMaxPos(which, ma);
2010 }
2011 out.push_back(outpos[0]);
2012 }
2013 return out;
2014}
2015
2016CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
2017 int width )
2018{
2019 if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
2020 CountedPtr< Scantable > out = getScantable(in, false);
2021 Table& tout = out->table();
2022 out->frequencies().rescale(width, "BIN");
2023 ArrayColumn<Float> specCol(tout, "SPECTRA");
2024 ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
2025 for (uInt i=0; i < tout.nrow(); ++i ) {
2026 MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
2027 MaskedArray<Float> maout;
2028 LatticeUtilities::bin(maout, main, 0, Int(width));
2029 /// @todo implement channel based tsys binning
2030 specCol.put(i, maout.getArray());
2031 flagCol.put(i, flagsFromMA(maout));
2032 // take only the first binned spectrum's length for the deprecated
2033 // global header item nChan
2034 if (i==0) tout.rwKeywordSet().define(String("nChan"),
2035 Int(maout.getArray().nelements()));
2036 }
2037 return out;
2038}
2039
2040CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
2041 const std::string& method,
2042 float width )
2043//
2044// Should add the possibility of width being specified in km/s. This means
2045// that for each freqID (SpectralCoordinate) we will need to convert to an
2046// average channel width (say at the reference pixel). Then we would need
2047// to be careful to make sure each spectrum (of different freqID)
2048// is the same length.
2049//
2050{
2051 //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
2052 Int interpMethod(stringToIMethod(method));
2053
2054 CountedPtr< Scantable > out = getScantable(in, false);
2055 Table& tout = out->table();
2056
2057// Resample SpectralCoordinates (one per freqID)
2058 out->frequencies().rescale(width, "RESAMPLE");
2059 TableIterator iter(tout, "IFNO");
2060 TableRow row(tout);
2061 while ( !iter.pastEnd() ) {
2062 Table tab = iter.table();
2063 ArrayColumn<Float> specCol(tab, "SPECTRA");
2064 //ArrayColumn<Float> tsysCol(tout, "TSYS");
2065 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2066 Vector<Float> spec;
2067 Vector<uChar> flag;
2068 specCol.get(0,spec); // the number of channels should be constant per IF
2069 uInt nChanIn = spec.nelements();
2070 Vector<Float> xIn(nChanIn); indgen(xIn);
2071 Int fac = Int(nChanIn/width);
2072 Vector<Float> xOut(fac+10); // 10 to be safe - resize later
2073 uInt k = 0;
2074 Float x = 0.0;
2075 while (x < Float(nChanIn) ) {
2076 xOut(k) = x;
2077 k++;
2078 x += width;
2079 }
2080 uInt nChanOut = k;
2081 xOut.resize(nChanOut, True);
2082 // process all rows for this IFNO
2083 Vector<Float> specOut;
2084 Vector<Bool> maskOut;
2085 Vector<uChar> flagOut;
2086 for (uInt i=0; i < tab.nrow(); ++i) {
2087 specCol.get(i, spec);
2088 flagCol.get(i, flag);
2089 Vector<Bool> mask(flag.nelements());
2090 convertArray(mask, flag);
2091
2092 IPosition shapeIn(spec.shape());
2093 //sh.nchan = nChanOut;
2094 InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
2095 xIn, spec, mask,
2096 interpMethod, True, True);
2097 /// @todo do the same for channel based Tsys
2098 flagOut.resize(maskOut.nelements());
2099 convertArray(flagOut, maskOut);
2100 specCol.put(i, specOut);
2101 flagCol.put(i, flagOut);
2102 }
2103 ++iter;
2104 }
2105
2106 return out;
2107}
2108
2109STMath::imethod STMath::stringToIMethod(const std::string& in)
2110{
2111 static STMath::imap lookup;
2112
2113 // initialize the lookup table if necessary
2114 if ( lookup.empty() ) {
2115 lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
2116 lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
2117 lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
2118 lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
2119 }
2120
2121 STMath::imap::const_iterator iter = lookup.find(in);
2122
2123 if ( lookup.end() == iter ) {
2124 std::string message = in;
2125 message += " is not a valid interpolation mode";
2126 throw(AipsError(message));
2127 }
2128 return iter->second;
2129}
2130
2131WeightType STMath::stringToWeight(const std::string& in)
2132{
2133 static std::map<std::string, WeightType> lookup;
2134
2135 // initialize the lookup table if necessary
2136 if ( lookup.empty() ) {
2137 lookup["NONE"] = asap::W_NONE;
2138 lookup["TINT"] = asap::W_TINT;
2139 lookup["TINTSYS"] = asap::W_TINTSYS;
2140 lookup["TSYS"] = asap::W_TSYS;
2141 lookup["VAR"] = asap::W_VAR;
2142 }
2143
2144 std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
2145
2146 if ( lookup.end() == iter ) {
2147 std::string message = in;
2148 message += " is not a valid weighting mode";
2149 throw(AipsError(message));
2150 }
2151 return iter->second;
2152}
2153
2154CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
2155 const vector< float > & coeff,
2156 const std::string & filename,
2157 const std::string& method)
2158{
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 ostringstream oss;
2202 oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
2203 oss << " " << coeff;
2204 pushLog(String(oss));
2205 const uInt nrow = tab.nrow();
2206 Vector<Float> factor(nrow);
2207 for ( uInt i=0; i < nrow; ++i ) {
2208 factor[i] = 1.0 / (*ppoly)(x[i]);
2209 }
2210 delete ppoly;
2211 scaleByVector(tab, factor, true);
2212
2213 } else {
2214 // Read and correct
2215 pushLog("Making correction from ascii Table");
2216 scaleFromAsciiTable(tab, filename, method, x, true);
2217 }
2218 return out;
2219}
2220
2221void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
2222 const std::string& method,
2223 const Vector<Float>& xout, bool dotsys)
2224{
2225
2226// Read gain-elevation ascii file data into a Table.
2227
2228 String formatString;
2229 Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
2230 scaleFromTable(in, tbl, method, xout, dotsys);
2231}
2232
2233void STMath::scaleFromTable(Table& in,
2234 const Table& table,
2235 const std::string& method,
2236 const Vector<Float>& xout, bool dotsys)
2237{
2238
2239 ROScalarColumn<Float> geElCol(table, "ELEVATION");
2240 ROScalarColumn<Float> geFacCol(table, "FACTOR");
2241 Vector<Float> xin = geElCol.getColumn();
2242 Vector<Float> yin = geFacCol.getColumn();
2243 Vector<Bool> maskin(xin.nelements(),True);
2244
2245 // Interpolate (and extrapolate) with desired method
2246
2247 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2248
2249 Vector<Float> yout;
2250 Vector<Bool> maskout;
2251 InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
2252 xin, yin, maskin, interp,
2253 True, True);
2254
2255 scaleByVector(in, Float(1.0)/yout, dotsys);
2256}
2257
2258void STMath::scaleByVector( Table& in,
2259 const Vector< Float >& factor,
2260 bool dotsys )
2261{
2262 uInt nrow = in.nrow();
2263 if ( factor.nelements() != nrow ) {
2264 throw(AipsError("factors.nelements() != table.nelements()"));
2265 }
2266 ArrayColumn<Float> specCol(in, "SPECTRA");
2267 ArrayColumn<uChar> flagCol(in, "FLAGTRA");
2268 ArrayColumn<Float> tsysCol(in, "TSYS");
2269 for (uInt i=0; i < nrow; ++i) {
2270 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2271 ma *= factor[i];
2272 specCol.put(i, ma.getArray());
2273 flagCol.put(i, flagsFromMA(ma));
2274 if ( dotsys ) {
2275 Vector<Float> tsys = tsysCol(i);
2276 tsys *= factor[i];
2277 tsysCol.put(i,tsys);
2278 }
2279 }
2280}
2281
2282CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
2283 float d, float etaap,
2284 float jyperk )
2285{
2286 CountedPtr< Scantable > out = getScantable(in, false);
2287 Table& tab = in->table();
2288 Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
2289 Unit K(String("K"));
2290 Unit JY(String("Jy"));
2291
2292 bool tokelvin = true;
2293 Double cfac = 1.0;
2294
2295 if ( fluxUnit == JY ) {
2296 pushLog("Converting to K");
2297 Quantum<Double> t(1.0,fluxUnit);
2298 Quantum<Double> t2 = t.get(JY);
2299 cfac = (t2 / t).getValue(); // value to Jy
2300
2301 tokelvin = true;
2302 out->setFluxUnit("K");
2303 } else if ( fluxUnit == K ) {
2304 pushLog("Converting to Jy");
2305 Quantum<Double> t(1.0,fluxUnit);
2306 Quantum<Double> t2 = t.get(K);
2307 cfac = (t2 / t).getValue(); // value to K
2308
2309 tokelvin = false;
2310 out->setFluxUnit("Jy");
2311 } else {
2312 throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
2313 }
2314 // Make sure input values are converted to either Jy or K first...
2315 Float factor = cfac;
2316
2317 // Select method
2318 if (jyperk > 0.0) {
2319 factor *= jyperk;
2320 if ( tokelvin ) factor = 1.0 / jyperk;
2321 ostringstream oss;
2322 oss << "Jy/K = " << jyperk;
2323 pushLog(String(oss));
2324 Vector<Float> factors(tab.nrow(), factor);
2325 scaleByVector(tab,factors, false);
2326 } else if ( etaap > 0.0) {
2327 if (d < 0) {
2328 Instrument inst =
2329 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2330 True);
2331 STAttr sda;
2332 d = sda.diameter(inst);
2333 }
2334 jyperk = STAttr::findJyPerK(etaap, d);
2335 ostringstream oss;
2336 oss << "Jy/K = " << jyperk;
2337 pushLog(String(oss));
2338 factor *= jyperk;
2339 if ( tokelvin ) {
2340 factor = 1.0 / factor;
2341 }
2342 Vector<Float> factors(tab.nrow(), factor);
2343 scaleByVector(tab, factors, False);
2344 } else {
2345
2346 // OK now we must deal with automatic look up of values.
2347 // We must also deal with the fact that the factors need
2348 // to be computed per IF and may be different and may
2349 // change per integration.
2350
2351 pushLog("Looking up conversion factors");
2352 convertBrightnessUnits(out, tokelvin, cfac);
2353 }
2354
2355 return out;
2356}
2357
2358void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
2359 bool tokelvin, float cfac )
2360{
2361 Table& table = in->table();
2362 Instrument inst =
2363 STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
2364 TableIterator iter(table, "FREQ_ID");
2365 STFrequencies stfreqs = in->frequencies();
2366 STAttr sdAtt;
2367 while (!iter.pastEnd()) {
2368 Table tab = iter.table();
2369 ArrayColumn<Float> specCol(tab, "SPECTRA");
2370 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2371 ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
2372 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2373
2374 uInt freqid; freqidCol.get(0, freqid);
2375 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2376 // STAttr.JyPerK has a Vector interface... change sometime.
2377 Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
2378 for ( uInt i=0; i<tab.nrow(); ++i) {
2379 Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
2380 Float factor = cfac * jyperk;
2381 if ( tokelvin ) factor = Float(1.0) / factor;
2382 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2383 ma *= factor;
2384 specCol.put(i, ma.getArray());
2385 flagCol.put(i, flagsFromMA(ma));
2386 }
2387 ++iter;
2388 }
2389}
2390
2391CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
2392 const std::vector<float>& tau )
2393{
2394 CountedPtr< Scantable > out = getScantable(in, false);
2395
2396 Table outtab = out->table();
2397
2398 const Int ntau = uInt(tau.size());
2399 std::vector<float>::const_iterator tauit = tau.begin();
2400 AlwaysAssert((ntau == 1 || ntau == in->nif() || ntau == in->nif() * in->npol()),
2401 AipsError);
2402 TableIterator iiter(outtab, "IFNO");
2403 while ( !iiter.pastEnd() ) {
2404 Table itab = iiter.table();
2405 TableIterator piter(itab, "POLNO");
2406 while ( !piter.pastEnd() ) {
2407 Table tab = piter.table();
2408 ROScalarColumn<Float> elev(tab, "ELEVATION");
2409 ArrayColumn<Float> specCol(tab, "SPECTRA");
2410 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2411 ArrayColumn<Float> tsysCol(tab, "TSYS");
2412 for ( uInt i=0; i<tab.nrow(); ++i) {
2413 Float zdist = Float(C::pi_2) - elev(i);
2414 Float factor = exp(*tauit/cos(zdist));
2415 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2416 ma *= factor;
2417 specCol.put(i, ma.getArray());
2418 flagCol.put(i, flagsFromMA(ma));
2419 Vector<Float> tsys;
2420 tsysCol.get(i, tsys);
2421 tsys *= factor;
2422 tsysCol.put(i, tsys);
2423 }
2424 if (ntau == in->nif()*in->npol() ) {
2425 tauit++;
2426 }
2427 piter++;
2428 }
2429 if (ntau >= in->nif() ) {
2430 tauit++;
2431 }
2432 iiter++;
2433 }
2434 return out;
2435}
2436
2437CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in,
2438 const std::string& kernel,
2439 float width, int order)
2440{
2441 CountedPtr< Scantable > out = getScantable(in, false);
2442 Table table = out->table();
2443
2444 TableIterator iter(table, "IFNO");
2445 while (!iter.pastEnd()) {
2446 Table tab = iter.table();
2447 ArrayColumn<Float> specCol(tab, "SPECTRA");
2448 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2449 Vector<Float> spec;
2450 Vector<uChar> flag;
2451 for (uInt i = 0; i < tab.nrow(); ++i) {
2452 specCol.get(i, spec);
2453 flagCol.get(i, flag);
2454 Vector<Bool> mask(flag.nelements());
2455 convertArray(mask, flag);
2456 Vector<Float> specout;
2457 Vector<Bool> maskout;
2458 if (kernel == "hanning") {
2459 mathutil::hanning(specout, maskout, spec, !mask);
2460 convertArray(flag, !maskout);
2461 } else if (kernel == "rmedian") {
2462 mathutil::runningMedian(specout, maskout, spec , mask, width);
2463 convertArray(flag, maskout);
2464 } else if (kernel == "poly") {
2465 mathutil::polyfit(specout, maskout, spec, !mask, width, order);
2466 convertArray(flag, !maskout);
2467 }
2468
2469 for (uInt j = 0; j < flag.nelements(); ++j) {
2470 uChar userFlag = 1 << 7;
2471 if (maskout[j]==True) userFlag = 0 << 7;
2472 flag(j) = userFlag;
2473 }
2474
2475 flagCol.put(i, flag);
2476 specCol.put(i, specout);
2477 }
2478 ++iter;
2479 }
2480 return out;
2481}
2482
2483CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
2484 const std::string& kernel, float width,
2485 int order)
2486{
2487 if (kernel == "rmedian" || kernel == "hanning" || kernel == "poly") {
2488 return smoothOther(in, kernel, width, order);
2489 }
2490 CountedPtr< Scantable > out = getScantable(in, false);
2491 Table& table = out->table();
2492 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
2493 // same IFNO should have same no of channels
2494 // this saves overhead
2495 TableIterator iter(table, "IFNO");
2496 while (!iter.pastEnd()) {
2497 Table tab = iter.table();
2498 ArrayColumn<Float> specCol(tab, "SPECTRA");
2499 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2500 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2501 uInt nchan = tmpspec.nelements();
2502 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
2503 Convolver<Float> conv(kvec, IPosition(1,nchan));
2504 Vector<Float> spec;
2505 Vector<uChar> flag;
2506 for ( uInt i=0; i<tab.nrow(); ++i) {
2507 specCol.get(i, spec);
2508 flagCol.get(i, flag);
2509 Vector<Bool> mask(flag.nelements());
2510 convertArray(mask, flag);
2511 Vector<Float> specout;
2512 mathutil::replaceMaskByZero(specout, mask);
2513 conv.linearConv(specout, spec);
2514 specCol.put(i, specout);
2515 }
2516 ++iter;
2517 }
2518 return out;
2519}
2520
2521CountedPtr< Scantable >
2522 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
2523{
2524 if ( in.size() < 2 ) {
2525 throw(AipsError("Need at least two scantables to perform a merge."));
2526 }
2527 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
2528 bool insitu = insitu_;
2529 setInsitu(false);
2530 CountedPtr< Scantable > out = getScantable(*it, false);
2531 setInsitu(insitu);
2532 Table& tout = out->table();
2533 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
2534 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
2535 // Renumber SCANNO to be 0-based
2536 Vector<uInt> scannos = scannocol.getColumn();
2537 uInt offset = min(scannos);
2538 scannos -= offset;
2539 scannocol.putColumn(scannos);
2540 uInt newscanno = max(scannos)+1;
2541 ++it;
2542 while ( it != in.end() ){
2543 if ( ! (*it)->conformant(*out) ) {
2544 // non conformant.
2545 //pushLog(String("Warning: Can't merge scantables as header info differs."));
2546 LogIO os( LogOrigin( "STMath", "merge()", WHERE ) ) ;
2547 os << LogIO::SEVERE << "Can't merge scantables as header informations (any one of AntennaName, Equinox, and FluxUnit) differ." << LogIO::EXCEPTION ;
2548 }
2549 out->appendToHistoryTable((*it)->history());
2550 const Table& tab = (*it)->table();
2551
2552 Block<String> cols(3);
2553 cols[0] = String("FREQ_ID");
2554 cols[1] = String("MOLECULE_ID");
2555 cols[2] = String("FOCUS_ID");
2556
2557 TableIterator scanit(tab, "SCANNO");
2558 while (!scanit.pastEnd()) {
2559 ScalarColumn<uInt> thescannocol(scanit.table(),"SCANNO");
2560 Vector<uInt> thescannos(thescannocol.nrow(),newscanno);
2561 thescannocol.putColumn(thescannos);
2562 TableIterator subit(scanit.table(), cols);
2563 while ( !subit.pastEnd() ) {
2564 uInt nrow = tout.nrow();
2565 Table thetab = subit.table();
2566 ROTableRow row(thetab);
2567 Vector<uInt> thecolvals(thetab.nrow());
2568 ScalarColumn<uInt> thefreqidcol(thetab,"FREQ_ID");
2569 ScalarColumn<uInt> themolidcol(thetab, "MOLECULE_ID");
2570 ScalarColumn<uInt> thefocusidcol(thetab,"FOCUS_ID");
2571 // The selected subset of table should have
2572 // the equal FREQ_ID, MOLECULE_ID, and FOCUS_ID values.
2573 const TableRecord& rec = row.get(0);
2574 // Set the proper FREQ_ID
2575 Double rv,rp,inc;
2576 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
2577 uInt id;
2578 id = out->frequencies().addEntry(rp, rv, inc);
2579 thecolvals = id;
2580 thefreqidcol.putColumn(thecolvals);
2581 // Set the proper MOLECULE_ID
2582 Vector<String> name,fname;Vector<Double> rf;
2583 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
2584 id = out->molecules().addEntry(rf, name, fname);
2585 thecolvals = id;
2586 themolidcol.putColumn(thecolvals);
2587 // Set the proper FOCUS_ID
2588 Float fpa,frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
2589 (*it)->focus().getEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2590 fxy, fxyp, rec.asuInt("FOCUS_ID"));
2591 id = out->focus().addEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2592 fxy, fxyp);
2593 thecolvals = id;
2594 thefocusidcol.putColumn(thecolvals);
2595
2596 tout.addRow(thetab.nrow());
2597 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
2598
2599 ++subit;
2600 }
2601 ++newscanno;
2602 ++scanit;
2603 }
2604 ++it;
2605 }
2606 return out;
2607}
2608
2609CountedPtr< Scantable >
2610 STMath::invertPhase( const CountedPtr < Scantable >& in )
2611{
2612 return applyToPol(in, &STPol::invertPhase, Float(0.0));
2613}
2614
2615CountedPtr< Scantable >
2616 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
2617{
2618 return applyToPol(in, &STPol::rotatePhase, Float(phase));
2619}
2620
2621CountedPtr< Scantable >
2622 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
2623{
2624 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
2625}
2626
2627CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
2628 STPol::polOperation fptr,
2629 Float phase )
2630{
2631 CountedPtr< Scantable > out = getScantable(in, false);
2632 Table& tout = out->table();
2633 Block<String> cols(4);
2634 cols[0] = String("SCANNO");
2635 cols[1] = String("BEAMNO");
2636 cols[2] = String("IFNO");
2637 cols[3] = String("CYCLENO");
2638 TableIterator iter(tout, cols);
2639 CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
2640 out->getPolType() );
2641 while (!iter.pastEnd()) {
2642 Table t = iter.table();
2643 ArrayColumn<Float> speccol(t, "SPECTRA");
2644 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
2645 Matrix<Float> pols(speccol.getColumn());
2646 try {
2647 stpol->setSpectra(pols);
2648 Float fang,fhand;
2649 fang = in->focusTable_.getTotalAngle(focidcol(0));
2650 fhand = in->focusTable_.getFeedHand(focidcol(0));
2651 stpol->setPhaseCorrections(fang, fhand);
2652 // use a member function pointer in STPol. This only works on
2653 // the STPol pointer itself, not the Counted Pointer so
2654 // derefernce it.
2655 (&(*(stpol))->*fptr)(phase);
2656 speccol.putColumn(stpol->getSpectra());
2657 } catch (AipsError& e) {
2658 //delete stpol;stpol=0;
2659 throw(e);
2660 }
2661 ++iter;
2662 }
2663 //delete stpol;stpol=0;
2664 return out;
2665}
2666
2667CountedPtr< Scantable >
2668 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
2669{
2670 CountedPtr< Scantable > out = getScantable(in, false);
2671 Table& tout = out->table();
2672 Table t0 = tout(tout.col("POLNO") == 0);
2673 Table t1 = tout(tout.col("POLNO") == 1);
2674 if ( t0.nrow() != t1.nrow() )
2675 throw(AipsError("Inconsistent number of polarisations"));
2676 ArrayColumn<Float> speccol0(t0, "SPECTRA");
2677 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
2678 ArrayColumn<Float> speccol1(t1, "SPECTRA");
2679 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
2680 Matrix<Float> s0 = speccol0.getColumn();
2681 Matrix<uChar> f0 = flagcol0.getColumn();
2682 speccol0.putColumn(speccol1.getColumn());
2683 flagcol0.putColumn(flagcol1.getColumn());
2684 speccol1.putColumn(s0);
2685 flagcol1.putColumn(f0);
2686 return out;
2687}
2688
2689CountedPtr< Scantable >
2690 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
2691 const std::vector<bool>& mask,
2692 const std::string& weight )
2693{
2694 if (in->npol() < 2 )
2695 throw(AipsError("averagePolarisations can only be applied to two or more"
2696 "polarisations"));
2697 bool insitu = insitu_;
2698 setInsitu(false);
2699 CountedPtr< Scantable > pols = getScantable(in, true);
2700 setInsitu(insitu);
2701 Table& tout = pols->table();
2702 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
2703 Table tab = tableCommand(taql, in->table());
2704 if (tab.nrow() == 0 )
2705 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
2706 TableCopy::copyRows(tout, tab);
2707 TableVector<uInt> vec(tout, "POLNO");
2708 vec = 0;
2709 pols->table_.rwKeywordSet().define("nPol", Int(1));
2710 pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
2711 //pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
2712 std::vector<CountedPtr<Scantable> > vpols;
2713 vpols.push_back(pols);
2714 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
2715 return out;
2716}
2717
2718CountedPtr< Scantable >
2719 STMath::averageBeams( const CountedPtr< Scantable > & in,
2720 const std::vector<bool>& mask,
2721 const std::string& weight )
2722{
2723 bool insitu = insitu_;
2724 setInsitu(false);
2725 CountedPtr< Scantable > beams = getScantable(in, false);
2726 setInsitu(insitu);
2727 Table& tout = beams->table();
2728 // give all rows the same BEAMNO
2729 TableVector<uInt> vec(tout, "BEAMNO");
2730 vec = 0;
2731 beams->table_.rwKeywordSet().define("nBeam", Int(1));
2732 std::vector<CountedPtr<Scantable> > vbeams;
2733 vbeams.push_back(beams);
2734 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
2735 return out;
2736}
2737
2738
2739CountedPtr< Scantable >
2740 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
2741 const std::string & refTime,
2742 const std::string & method)
2743{
2744 // clone as this is not working insitu
2745 bool insitu = insitu_;
2746 setInsitu(false);
2747 CountedPtr< Scantable > out = getScantable(in, false);
2748 setInsitu(insitu);
2749 Table& tout = out->table();
2750 // Get reference Epoch to time of first row or given String
2751 Unit DAY(String("d"));
2752 MEpoch::Ref epochRef(in->getTimeReference());
2753 MEpoch refEpoch;
2754 if (refTime.length()>0) {
2755 Quantum<Double> qt;
2756 if (MVTime::read(qt,refTime)) {
2757 MVEpoch mv(qt);
2758 refEpoch = MEpoch(mv, epochRef);
2759 } else {
2760 throw(AipsError("Invalid format for Epoch string"));
2761 }
2762 } else {
2763 refEpoch = in->timeCol_(0);
2764 }
2765 MPosition refPos = in->getAntennaPosition();
2766
2767 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2768 /*
2769 // Comment from MV.
2770 // the following code has been commented out because different FREQ_IDs have to be aligned together even
2771 // if the frame doesn't change. So far, lack of this check didn't cause any problems.
2772 // test if user frame is different to base frame
2773 if ( in->frequencies().getFrameString(true)
2774 == in->frequencies().getFrameString(false) ) {
2775 throw(AipsError("Can't convert as no output frame has been set"
2776 " (use set_freqframe) or it is aligned already."));
2777 }
2778 */
2779 MFrequency::Types system = in->frequencies().getFrame();
2780 MVTime mvt(refEpoch.getValue());
2781 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
2782 ostringstream oss;
2783 oss << "Aligned at reference Epoch " << epochout
2784 << " in frame " << MFrequency::showType(system);
2785 pushLog(String(oss));
2786 // set up the iterator
2787 Block<String> cols(4);
2788 // select by constant direction
2789 cols[0] = String("SRCNAME");
2790 cols[1] = String("BEAMNO");
2791 // select by IF ( no of channels varies over this )
2792 cols[2] = String("IFNO");
2793 // select by restfrequency
2794 cols[3] = String("MOLECULE_ID");
2795 TableIterator iter(tout, cols);
2796 while ( !iter.pastEnd() ) {
2797 Table t = iter.table();
2798 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
2799 TableIterator fiter(t, "FREQ_ID");
2800 // determine nchan from the first row. This should work as
2801 // we are iterating over BEAMNO and IFNO // we should have constant direction
2802
2803 ROArrayColumn<Float> sCol(t, "SPECTRA");
2804 const MDirection direction = dirCol(0);
2805 const uInt nchan = sCol(0).nelements();
2806
2807 // skip operations if there is nothing to align
2808 if (fiter.pastEnd()) {
2809 continue;
2810 }
2811
2812 Table ftab = fiter.table();
2813 // align all frequency ids with respect to the first encountered id
2814 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
2815 // get the SpectralCoordinate for the freqid, which we are iterating over
2816 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
2817 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
2818 direction, refPos, system );
2819 // realign the SpectralCoordinate and put into the output Scantable
2820 Vector<String> units(1);
2821 units = String("Hz");
2822 Bool linear=True;
2823 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
2824 sc2.setWorldAxisUnits(units);
2825 const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
2826 sc2.referenceValue()[0],
2827 sc2.increment()[0]);
2828 while ( !fiter.pastEnd() ) {
2829 ftab = fiter.table();
2830 // spectral coordinate for the current FREQ_ID
2831 ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
2832 sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
2833 // create the "global" abcissa for alignment with same FREQ_ID
2834 Vector<Double> abc(nchan);
2835 for (uInt i=0; i<nchan; i++) {
2836 Double w;
2837 sC.toWorld(w,Double(i));
2838 abc[i] = w;
2839 }
2840 TableVector<uInt> tvec(ftab, "FREQ_ID");
2841 // assign new frequency id to all rows
2842 tvec = id;
2843 // cache abcissa for same time stamps, so iterate over those
2844 TableIterator timeiter(ftab, "TIME");
2845 while ( !timeiter.pastEnd() ) {
2846 Table tab = timeiter.table();
2847 ArrayColumn<Float> specCol(tab, "SPECTRA");
2848 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2849 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2850 // use align abcissa cache after the first row
2851 // these rows should be just be POLNO
2852 bool first = true;
2853 for (int i=0; i<int(tab.nrow()); ++i) {
2854 // input values
2855 Vector<uChar> flag = flagCol(i);
2856 Vector<Bool> mask(flag.shape());
2857 Vector<Float> specOut, spec;
2858 spec = specCol(i);
2859 Vector<Bool> maskOut;Vector<uChar> flagOut;
2860 convertArray(mask, flag);
2861 // alignment
2862 Bool ok = fa.align(specOut, maskOut, abc, spec,
2863 mask, timeCol(i), !first,
2864 interp, False);
2865 (void) ok; // unused stop compiler nagging
2866 // back into scantable
2867 flagOut.resize(maskOut.nelements());
2868 convertArray(flagOut, maskOut);
2869 flagCol.put(i, flagOut);
2870 specCol.put(i, specOut);
2871 // start abcissa caching
2872 first = false;
2873 }
2874 // next timestamp
2875 ++timeiter;
2876 }
2877 // next FREQ_ID
2878 ++fiter;
2879 }
2880 // next aligner
2881 ++iter;
2882 }
2883 // set this afterwards to ensure we are doing insitu correctly.
2884 out->frequencies().setFrame(system, true);
2885 return out;
2886}
2887
2888CountedPtr<Scantable>
2889 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
2890 const std::string & newtype )
2891{
2892 if (in->npol() != 2 && in->npol() != 4)
2893 throw(AipsError("Can only convert two or four polarisations."));
2894 if ( in->getPolType() == newtype )
2895 throw(AipsError("No need to convert."));
2896 if ( ! in->selector_.empty() )
2897 throw(AipsError("Can only convert whole scantable. Unset the selection."));
2898 bool insitu = insitu_;
2899 setInsitu(false);
2900 CountedPtr< Scantable > out = getScantable(in, true);
2901 setInsitu(insitu);
2902 Table& tout = out->table();
2903 tout.rwKeywordSet().define("POLTYPE", String(newtype));
2904
2905 Block<String> cols(4);
2906 cols[0] = "SCANNO";
2907 cols[1] = "CYCLENO";
2908 cols[2] = "BEAMNO";
2909 cols[3] = "IFNO";
2910 TableIterator it(in->originalTable_, cols);
2911 String basetype = in->getPolType();
2912 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
2913 try {
2914 while ( !it.pastEnd() ) {
2915 Table tab = it.table();
2916 uInt row = tab.rowNumbers()[0];
2917 stpol->setSpectra(in->getPolMatrix(row));
2918 Float fang,fhand;
2919 fang = in->focusTable_.getTotalAngle(in->mfocusidCol_(row));
2920 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
2921 stpol->setPhaseCorrections(fang, fhand);
2922 Int npolout = 0;
2923 for (uInt i=0; i<tab.nrow(); ++i) {
2924 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
2925 if ( outvec.nelements() > 0 ) {
2926 tout.addRow();
2927 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
2928 ArrayColumn<Float> sCol(tout,"SPECTRA");
2929 ScalarColumn<uInt> pCol(tout,"POLNO");
2930 sCol.put(tout.nrow()-1 ,outvec);
2931 pCol.put(tout.nrow()-1 ,uInt(npolout));
2932 npolout++;
2933 }
2934 }
2935 tout.rwKeywordSet().define("nPol", npolout);
2936 ++it;
2937 }
2938 } catch (AipsError& e) {
2939 delete stpol;
2940 throw(e);
2941 }
2942 delete stpol;
2943 return out;
2944}
2945
2946CountedPtr< Scantable >
2947 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
2948 const std::string & scantype )
2949{
2950 bool insitu = insitu_;
2951 setInsitu(false);
2952 CountedPtr< Scantable > out = getScantable(in, true);
2953 setInsitu(insitu);
2954 Table& tout = out->table();
2955 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
2956 if (scantype == "on") {
2957 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
2958 }
2959 Table tab = tableCommand(taql, in->table());
2960 TableCopy::copyRows(tout, tab);
2961 if (scantype == "on") {
2962 // re-index SCANNO to 0
2963 TableVector<uInt> vec(tout, "SCANNO");
2964 vec = 0;
2965 }
2966 return out;
2967}
2968
2969std::vector<float>
2970 asap::STMath::fft( const casa::CountedPtr< Scantable > & in,
2971 const std::vector<int>& whichrow,
2972 bool getRealImag )
2973{
2974 std::vector<float> res;
2975 Table tab = in->table();
2976 std::vector<bool> mask;
2977
2978 if (whichrow.size() < 1) { // for all rows (by default)
2979 int nrow = int(tab.nrow());
2980 for (int i = 0; i < nrow; ++i) {
2981 res = in->execFFT(i, mask, getRealImag);
2982 }
2983 } else { // for specified rows
2984 for (uInt i = 0; i < whichrow.size(); ++i) {
2985 res = in->execFFT(i, mask, getRealImag);
2986 }
2987 }
2988
2989 return res;
2990}
2991
2992
2993CountedPtr<Scantable>
2994 asap::STMath::lagFlag( const CountedPtr<Scantable>& in,
2995 double start, double end,
2996 const std::string& mode )
2997{
2998 CountedPtr<Scantable> out = getScantable(in, false);
2999 Table& tout = out->table();
3000 TableIterator iter(tout, "FREQ_ID");
3001 FFTServer<Float,Complex> ffts;
3002
3003 while ( !iter.pastEnd() ) {
3004 Table tab = iter.table();
3005 Double rp,rv,inc;
3006 ROTableRow row(tab);
3007 const TableRecord& rec = row.get(0);
3008 uInt freqid = rec.asuInt("FREQ_ID");
3009 out->frequencies().getEntry(rp, rv, inc, freqid);
3010 ArrayColumn<Float> specCol(tab, "SPECTRA");
3011 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
3012
3013 for (int i=0; i<int(tab.nrow()); ++i) {
3014 Vector<Float> spec = specCol(i);
3015 Vector<uChar> flag = flagCol(i);
3016 std::vector<bool> mask;
3017 for (uInt j = 0; j < flag.nelements(); ++j) {
3018 mask.push_back(!(flag[j]>0));
3019 }
3020 mathutil::doZeroOrderInterpolation(spec, mask);
3021
3022 Vector<Complex> lags;
3023 ffts.fft0(lags, spec);
3024
3025 Int lag0(start+0.5);
3026 Int lag1(end+0.5);
3027 if (mode == "frequency") {
3028 lag0 = Int(spec.nelements()*abs(inc)/(start)+0.5);
3029 lag1 = Int(spec.nelements()*abs(inc)/(end)+0.5);
3030 }
3031 Int lstart = max(0, lag0);
3032 Int lend = min(Int(lags.nelements()-1), lag1);
3033 if (lstart == lend) {
3034 lags[lstart] = Complex(0.0);
3035 } else {
3036 if (lstart > lend) {
3037 Int tmp = lend;
3038 lend = lstart;
3039 lstart = tmp;
3040 }
3041 for (int j=lstart; j <=lend ;++j) {
3042 lags[j] = Complex(0.0);
3043 }
3044 }
3045
3046 ffts.fft0(spec, lags);
3047
3048 specCol.put(i, spec);
3049 }
3050 ++iter;
3051 }
3052 return out;
3053}
3054
3055// Averaging spectra with different channel/resolution
3056CountedPtr<Scantable>
3057STMath::new_average( const std::vector<CountedPtr<Scantable> >& in,
3058 const bool& compel,
3059 const std::vector<bool>& mask,
3060 const std::string& weight,
3061 const std::string& avmode )
3062 throw ( casa::AipsError )
3063{
3064 LogIO os( LogOrigin( "STMath", "new_average()", WHERE ) ) ;
3065 if ( avmode == "SCAN" && in.size() != 1 )
3066 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
3067 "Use merge first."));
3068
3069 // 2012/02/17 TN
3070 // Since STGrid is implemented, average doesn't consider direction
3071 // when accumulating
3072 // check if OTF observation
3073// String obstype = in[0]->getHeader().obstype ;
3074// Double tol = 0.0 ;
3075// if ( obstype.find( "OTF" ) != String::npos ) {
3076// tol = TOL_OTF ;
3077// }
3078// else {
3079// tol = TOL_POINT ;
3080// }
3081
3082 CountedPtr<Scantable> out ; // processed result
3083 if ( compel ) {
3084 std::vector< CountedPtr<Scantable> > newin ; // input for average process
3085 uInt insize = in.size() ; // number of input scantables
3086
3087 // TEST: do normal average in each table before IF grouping
3088 os << "Do preliminary averaging" << LogIO::POST ;
3089 vector< CountedPtr<Scantable> > tmpin( insize ) ;
3090 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3091 vector< CountedPtr<Scantable> > v( 1, in[itable] ) ;
3092 tmpin[itable] = average( v, mask, weight, avmode ) ;
3093 }
3094
3095 // warning
3096 os << "Average spectra with different spectral resolution" << LogIO::POST ;
3097
3098 // temporarily set coordinfo
3099 vector<string> oldinfo( insize ) ;
3100 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3101 vector<string> coordinfo = in[itable]->getCoordInfo() ;
3102 oldinfo[itable] = coordinfo[0] ;
3103 coordinfo[0] = "Hz" ;
3104 tmpin[itable]->setCoordInfo( coordinfo ) ;
3105 }
3106
3107 // columns
3108 ScalarColumn<uInt> freqIDCol ;
3109 ScalarColumn<uInt> ifnoCol ;
3110 ScalarColumn<uInt> scannoCol ;
3111
3112
3113 // check IF frequency coverage
3114 // freqid: list of FREQ_ID, which is used, in each table
3115 // iffreq: list of minimum and maximum frequency for each FREQ_ID in
3116 // each table
3117 // freqid[insize][numIF]
3118 // freqid: [[id00, id01, ...],
3119 // [id10, id11, ...],
3120 // ...
3121 // [idn0, idn1, ...]]
3122 // iffreq[insize][numIF*2]
3123 // iffreq: [[min_id00, max_id00, min_id01, max_id01, ...],
3124 // [min_id10, max_id10, min_id11, max_id11, ...],
3125 // ...
3126 // [min_idn0, max_idn0, min_idn1, max_idn1, ...]]
3127 //os << "Check IF settings in each table" << LogIO::POST ;
3128 vector< vector<uInt> > freqid( insize );
3129 vector< vector<double> > iffreq( insize ) ;
3130 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3131 uInt rows = tmpin[itable]->nrow() ;
3132 uInt freqnrows = tmpin[itable]->frequencies().table().nrow() ;
3133 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3134 if ( freqid[itable].size() == freqnrows ) {
3135 break ;
3136 }
3137 else {
3138 freqIDCol.attach( tmpin[itable]->table(), "FREQ_ID" ) ;
3139 ifnoCol.attach( tmpin[itable]->table(), "IFNO" ) ;
3140 uInt id = freqIDCol( irow ) ;
3141 if ( freqid[itable].size() == 0 || count( freqid[itable].begin(), freqid[itable].end(), id ) == 0 ) {
3142 //os << "itable = " << itable << ": IF " << id << " is included in the list" << LogIO::POST ;
3143 vector<double> abcissa = tmpin[itable]->getAbcissa( irow ) ;
3144 freqid[itable].push_back( id ) ;
3145 iffreq[itable].push_back( abcissa[0] - 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
3146 iffreq[itable].push_back( abcissa[abcissa.size()-1] + 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
3147 }
3148 }
3149 }
3150 }
3151
3152 // debug
3153 //os << "IF settings summary:" << endl ;
3154 //for ( uInt i = 0 ; i < freqid.size() ; i++ ) {
3155 //os << " Table" << i << endl ;
3156 //for ( uInt j = 0 ; j < freqid[i].size() ; j++ ) {
3157 //os << " id = " << freqid[i][j] << " (min,max) = (" << iffreq[i][2*j] << "," << iffreq[i][2*j+1] << ")" << endl ;
3158 //}
3159 //}
3160 //os << endl ;
3161 //os.post() ;
3162
3163 // IF grouping based on their frequency coverage
3164 // ifgrp: list of table index and FREQ_ID for all members in each IF group
3165 // ifgfreq: list of minimum and maximum frequency in each IF group
3166 // ifgrp[numgrp][nummember*2]
3167 // ifgrp: [[table00, freqrow00, table01, freqrow01, ...],
3168 // [table10, freqrow10, table11, freqrow11, ...],
3169 // ...
3170 // [tablen0, freqrown0, tablen1, freqrown1, ...]]
3171 // ifgfreq[numgrp*2]
3172 // ifgfreq: [min0_grp0, max0_grp0, min1_grp1, max1_grp1, ...]
3173 //os << "IF grouping based on their frequency coverage" << LogIO::POST ;
3174 vector< vector<uInt> > ifgrp ;
3175 vector<double> ifgfreq ;
3176
3177 // parameter for IF grouping
3178 // groupmode = OR retrieve all region
3179 // AND only retrieve overlaped region
3180 //string groupmode = "AND" ;
3181 string groupmode = "OR" ;
3182 uInt sizecr = 0 ;
3183 if ( groupmode == "AND" )
3184 sizecr = 2 ;
3185 else if ( groupmode == "OR" )
3186 sizecr = 0 ;
3187
3188 vector<double> sortedfreq ;
3189 for ( uInt i = 0 ; i < iffreq.size() ; i++ ) {
3190 for ( uInt j = 0 ; j < iffreq[i].size() ; j++ ) {
3191 if ( count( sortedfreq.begin(), sortedfreq.end(), iffreq[i][j] ) == 0 )
3192 sortedfreq.push_back( iffreq[i][j] ) ;
3193 }
3194 }
3195 sort( sortedfreq.begin(), sortedfreq.end() ) ;
3196 for ( vector<double>::iterator i = sortedfreq.begin() ; i != sortedfreq.end()-1 ; i++ ) {
3197 ifgfreq.push_back( *i ) ;
3198 ifgfreq.push_back( *(i+1) ) ;
3199 }
3200 ifgrp.resize( ifgfreq.size()/2 ) ;
3201 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3202 for ( uInt iif = 0 ; iif < freqid[itable].size() ; iif++ ) {
3203 double range0 = iffreq[itable][2*iif] ;
3204 double range1 = iffreq[itable][2*iif+1] ;
3205 for ( uInt j = 0 ; j < ifgrp.size() ; j++ ) {
3206 double fmin = max( range0, ifgfreq[2*j] ) ;
3207 double fmax = min( range1, ifgfreq[2*j+1] ) ;
3208 if ( fmin < fmax ) {
3209 ifgrp[j].push_back( itable ) ;
3210 ifgrp[j].push_back( freqid[itable][iif] ) ;
3211 }
3212 }
3213 }
3214 }
3215 vector< vector<uInt> >::iterator fiter = ifgrp.begin() ;
3216 vector<double>::iterator giter = ifgfreq.begin() ;
3217 while( fiter != ifgrp.end() ) {
3218 if ( fiter->size() <= sizecr ) {
3219 fiter = ifgrp.erase( fiter ) ;
3220 giter = ifgfreq.erase( giter ) ;
3221 giter = ifgfreq.erase( giter ) ;
3222 }
3223 else {
3224 fiter++ ;
3225 advance( giter, 2 ) ;
3226 }
3227 }
3228
3229 // Grouping continuous IF groups (without frequency gap)
3230 // freqgrp: list of IF group indexes in each frequency group
3231 // freqrange: list of minimum and maximum frequency in each frequency group
3232 // freqgrp[numgrp][nummember]
3233 // freqgrp: [[ifgrp00, ifgrp01, ifgrp02, ...],
3234 // [ifgrp10, ifgrp11, ifgrp12, ...],
3235 // ...
3236 // [ifgrpn0, ifgrpn1, ifgrpn2, ...]]
3237 // freqrange[numgrp*2]
3238 // freqrange: [min_grp0, max_grp0, min_grp1, max_grp1, ...]
3239 vector< vector<uInt> > freqgrp ;
3240 double freqrange = 0.0 ;
3241 uInt grpnum = 0 ;
3242 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3243 // Assumed that ifgfreq was sorted
3244 if ( grpnum != 0 && freqrange == ifgfreq[2*i] ) {
3245 freqgrp[grpnum-1].push_back( i ) ;
3246 }
3247 else {
3248 vector<uInt> grp0( 1, i ) ;
3249 freqgrp.push_back( grp0 ) ;
3250 grpnum++ ;
3251 }
3252 freqrange = ifgfreq[2*i+1] ;
3253 }
3254
3255
3256 // print IF groups
3257 ostringstream oss ;
3258 oss << "IF Group summary: " << endl ;
3259 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3260 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3261 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3262 for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3263 oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3264 }
3265 oss << endl ;
3266 }
3267 oss << endl ;
3268 os << oss.str() << LogIO::POST ;
3269
3270 // print frequency group
3271 oss.str("") ;
3272 oss << "Frequency Group summary: " << endl ;
3273 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: IF_GROUP_ID" << endl ;
3274 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3275 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*freqgrp[i][0]] << "," << ifgfreq[2*freqgrp[i][freqgrp[i].size()-1]+1] << "]: " ;
3276 for ( uInt j = 0 ; j < freqgrp[i].size() ; j++ ) {
3277 oss << freqgrp[i][j] << " " ;
3278 }
3279 oss << endl ;
3280 }
3281 oss << endl ;
3282 os << oss.str() << LogIO::POST ;
3283
3284 // membership check
3285 // groups: list of IF group indexes whose frequency range overlaps with
3286 // that of each table and IF
3287 // groups[numtable][numIF][nummembership]
3288 // groups: [[[grp, grp,...], [grp, grp,...],...],
3289 // [[grp, grp,...], [grp, grp,...],...],
3290 // ...
3291 // [[grp, grp,...], [grp, grp,...],...]]
3292 vector< vector< vector<uInt> > > groups( insize ) ;
3293 for ( uInt i = 0 ; i < insize ; i++ ) {
3294 groups[i].resize( freqid[i].size() ) ;
3295 }
3296 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3297 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3298 uInt tableid = ifgrp[igrp][2*imem] ;
3299 vector<uInt>::iterator iter = find( freqid[tableid].begin(), freqid[tableid].end(), ifgrp[igrp][2*imem+1] ) ;
3300 if ( iter != freqid[tableid].end() ) {
3301 uInt rowid = distance( freqid[tableid].begin(), iter ) ;
3302 groups[tableid][rowid].push_back( igrp ) ;
3303 }
3304 }
3305 }
3306
3307 // print membership
3308 //oss.str("") ;
3309 //for ( uInt i = 0 ; i < insize ; i++ ) {
3310 //oss << "Table " << i << endl ;
3311 //for ( uInt j = 0 ; j < groups[i].size() ; j++ ) {
3312 //oss << " FREQ_ID " << setw( 2 ) << freqid[i][j] << ": " ;
3313 //for ( uInt k = 0 ; k < groups[i][j].size() ; k++ ) {
3314 //oss << setw( 2 ) << groups[i][j][k] << " " ;
3315 //}
3316 //oss << endl ;
3317 //}
3318 //}
3319 //os << oss.str() << LogIO::POST ;
3320
3321 // set back coordinfo
3322 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3323 vector<string> coordinfo = tmpin[itable]->getCoordInfo() ;
3324 coordinfo[0] = oldinfo[itable] ;
3325 tmpin[itable]->setCoordInfo( coordinfo ) ;
3326 }
3327
3328 // Create additional table if needed
3329 bool oldInsitu = insitu_ ;
3330 setInsitu( false ) ;
3331 vector< vector<uInt> > addrow( insize ) ;
3332 vector<uInt> addtable( insize, 0 ) ;
3333 vector<uInt> newtableids( insize ) ;
3334 vector<uInt> newifids( insize, 0 ) ;
3335 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3336 //os << "Table " << itable << ": " ;
3337 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3338 addrow[itable].push_back( groups[itable][ifrow].size()-1 ) ;
3339 //os << addrow[itable][ifrow] << " " ;
3340 }
3341 addtable[itable] = *max_element( addrow[itable].begin(), addrow[itable].end() ) ;
3342 //os << "(" << addtable[itable] << ")" << LogIO::POST ;
3343 }
3344 newin.resize( insize ) ;
3345 copy( tmpin.begin(), tmpin.end(), newin.begin() ) ;
3346 for ( uInt i = 0 ; i < insize ; i++ ) {
3347 newtableids[i] = i ;
3348 }
3349 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3350 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3351 CountedPtr<Scantable> add = getScantable( newin[itable], false ) ;
3352 vector<int> freqidlist ;
3353 for ( uInt i = 0 ; i < groups[itable].size() ; i++ ) {
3354 if ( groups[itable][i].size() > iadd + 1 ) {
3355 freqidlist.push_back( freqid[itable][i] ) ;
3356 }
3357 }
3358 stringstream taqlstream ;
3359 taqlstream << "SELECT FROM $1 WHERE FREQ_ID IN [" ;
3360 for ( uInt i = 0 ; i < freqidlist.size() ; i++ ) {
3361 taqlstream << freqidlist[i] ;
3362 if ( i < freqidlist.size() - 1 )
3363 taqlstream << "," ;
3364 else
3365 taqlstream << "]" ;
3366 }
3367 string taql = taqlstream.str() ;
3368 //os << "taql = " << taql << LogIO::POST ;
3369 STSelector selector = STSelector() ;
3370 selector.setTaQL( taql ) ;
3371 add->setSelection( selector ) ;
3372 newin.push_back( add ) ;
3373 newtableids.push_back( itable ) ;
3374 newifids.push_back( iadd + 1 ) ;
3375 }
3376 }
3377
3378 // udpate ifgrp
3379 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3380 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3381 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3382 if ( groups[itable][ifrow].size() > iadd + 1 ) {
3383 uInt igrp = groups[itable][ifrow][iadd+1] ;
3384 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3385 if ( ifgrp[igrp][2*imem] == newtableids[iadd+insize] && ifgrp[igrp][2*imem+1] == freqid[newtableids[iadd+insize]][ifrow] ) {
3386 ifgrp[igrp][2*imem] = insize + iadd ;
3387 }
3388 }
3389 }
3390 }
3391 }
3392 }
3393
3394 // print IF groups again for debug
3395 //oss.str( "" ) ;
3396 //oss << "IF Group summary: " << endl ;
3397 //oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3398 //for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3399 //oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3400 //for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3401 //oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3402 //}
3403 //oss << endl ;
3404 //}
3405 //oss << endl ;
3406 //os << oss.str() << LogIO::POST ;
3407
3408 // reset SCANNO and IFNO/FREQ_ID: IF is reset by the result of sortation
3409 os << "All scan number is set to 0" << LogIO::POST ;
3410 //os << "All IF number is set to IF group index" << LogIO::POST ;
3411 insize = newin.size() ;
3412 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3413 uInt rows = newin[itable]->nrow() ;
3414 Table &tmpt = newin[itable]->table() ;
3415 freqIDCol.attach( tmpt, "FREQ_ID" ) ;
3416 scannoCol.attach( tmpt, "SCANNO" ) ;
3417 ifnoCol.attach( tmpt, "IFNO" ) ;
3418 for ( uInt irow=0 ; irow < rows ; irow++ ) {
3419 scannoCol.put( irow, 0 ) ;
3420 uInt freqID = freqIDCol( irow ) ;
3421 vector<uInt>::iterator iter = find( freqid[newtableids[itable]].begin(), freqid[newtableids[itable]].end(), freqID ) ;
3422 if ( iter != freqid[newtableids[itable]].end() ) {
3423 uInt index = distance( freqid[newtableids[itable]].begin(), iter ) ;
3424 ifnoCol.put( irow, groups[newtableids[itable]][index][newifids[itable]] ) ;
3425 }
3426 else {
3427 throw(AipsError("IF grouping was wrong in additional tables.")) ;
3428 }
3429 }
3430 }
3431 oldinfo.resize( insize ) ;
3432 setInsitu( oldInsitu ) ;
3433
3434 // temporarily set coordinfo
3435 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3436 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3437 oldinfo[itable] = coordinfo[0] ;
3438 coordinfo[0] = "Hz" ;
3439 newin[itable]->setCoordInfo( coordinfo ) ;
3440 }
3441
3442 // save column values in the vector
3443 vector< vector<uInt> > freqTableIdVec( insize ) ;
3444 vector< vector<uInt> > freqIdVec( insize ) ;
3445 vector< vector<uInt> > ifNoVec( insize ) ;
3446 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3447 ScalarColumn<uInt> freqIDs ;
3448 freqIDs.attach( newin[itable]->frequencies().table(), "ID" ) ;
3449 ifnoCol.attach( newin[itable]->table(), "IFNO" ) ;
3450 freqIDCol.attach( newin[itable]->table(), "FREQ_ID" ) ;
3451 for ( uInt irow = 0 ; irow < newin[itable]->frequencies().table().nrow() ; irow++ ) {
3452 freqTableIdVec[itable].push_back( freqIDs( irow ) ) ;
3453 }
3454 for ( uInt irow = 0 ; irow < newin[itable]->table().nrow() ; irow++ ) {
3455 freqIdVec[itable].push_back( freqIDCol( irow ) ) ;
3456 ifNoVec[itable].push_back( ifnoCol( irow ) ) ;
3457 }
3458 }
3459
3460 // reset spectra and flagtra: pick up common part of frequency coverage
3461 //os << "Pick common frequency range and align resolution" << LogIO::POST ;
3462 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3463 uInt rows = newin[itable]->nrow() ;
3464 int nminchan = -1 ;
3465 int nmaxchan = -1 ;
3466 vector<uInt> freqIdUpdate ;
3467 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3468 uInt ifno = ifNoVec[itable][irow] ; // IFNO is reset by group index
3469 double minfreq = ifgfreq[2*ifno] ;
3470 double maxfreq = ifgfreq[2*ifno+1] ;
3471 //os << "frequency range: [" << minfreq << "," << maxfreq << "]" << LogIO::POST ;
3472 vector<double> abcissa = newin[itable]->getAbcissa( irow ) ;
3473 int nchan = abcissa.size() ;
3474 double resol = abcissa[1] - abcissa[0] ;
3475 //os << "abcissa range : [" << abcissa[0] << "," << abcissa[nchan-1] << "]" << LogIO::POST ;
3476 if ( minfreq <= abcissa[0] )
3477 nminchan = 0 ;
3478 else {
3479 //double cfreq = ( minfreq - abcissa[0] ) / resol ;
3480 double cfreq = ( minfreq - abcissa[0] + 0.5 * resol ) / resol ;
3481 nminchan = int(cfreq) + ( ( cfreq - int(cfreq) <= 0.5 ) ? 0 : 1 ) ;
3482 }
3483 if ( maxfreq >= abcissa[abcissa.size()-1] )
3484 nmaxchan = abcissa.size() - 1 ;
3485 else {
3486 //double cfreq = ( abcissa[abcissa.size()-1] - maxfreq ) / resol ;
3487 double cfreq = ( abcissa[abcissa.size()-1] - maxfreq + 0.5 * resol ) / resol ;
3488 nmaxchan = abcissa.size() - 1 - int(cfreq) - ( ( cfreq - int(cfreq) >= 0.5 ) ? 1 : 0 ) ;
3489 }
3490 //os << "channel range (" << irow << "): [" << nminchan << "," << nmaxchan << "]" << LogIO::POST ;
3491 if ( nmaxchan > nminchan ) {
3492 newin[itable]->reshapeSpectrum( nminchan, nmaxchan, irow ) ;
3493 int newchan = nmaxchan - nminchan + 1 ;
3494 if ( count( freqIdUpdate.begin(), freqIdUpdate.end(), freqIdVec[itable][irow] ) == 0 && newchan < nchan )
3495 freqIdUpdate.push_back( freqIdVec[itable][irow] ) ;
3496 }
3497 else {
3498 throw(AipsError("Failed to pick up common part of frequency range.")) ;
3499 }
3500 }
3501 for ( uInt i = 0 ; i < freqIdUpdate.size() ; i++ ) {
3502 uInt freqId = freqIdUpdate[i] ;
3503 Double refpix ;
3504 Double refval ;
3505 Double increment ;
3506
3507 // update row
3508 newin[itable]->frequencies().getEntry( refpix, refval, increment, freqId ) ;
3509 refval = refval - ( refpix - nminchan ) * increment ;
3510 refpix = 0 ;
3511 newin[itable]->frequencies().setEntry( refpix, refval, increment, freqId ) ;
3512 }
3513 }
3514
3515
3516 // reset spectra and flagtra: align spectral resolution
3517 //os << "Align spectral resolution" << LogIO::POST ;
3518 // gmaxdnu: the coarsest frequency resolution in the frequency group
3519 // gmemid: member index that have a resolution equal to gmaxdnu
3520 // gmaxdnu[numfreqgrp]
3521 // gmaxdnu: [dnu0, dnu1, ...]
3522 // gmemid[numfreqgrp]
3523 // gmemid: [id0, id1, ...]
3524 vector<double> gmaxdnu( freqgrp.size(), 0.0 ) ;
3525 vector<uInt> gmemid( freqgrp.size(), 0 ) ;
3526 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3527 double maxdnu = 0.0 ; // maximum (coarsest) frequency resolution
3528 int minchan = INT_MAX ; // minimum channel number
3529 Double refpixref = -1 ; // reference of 'reference pixel'
3530 Double refvalref = -1 ; // reference of 'reference frequency'
3531 Double refinc = -1 ; // reference frequency resolution
3532 uInt refreqid ;
3533 uInt reftable = INT_MAX;
3534 // process only if group member > 1
3535 if ( ifgrp[igrp].size() > 2 ) {
3536 // find minchan and maxdnu in each group
3537 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3538 uInt tableid = ifgrp[igrp][2*imem] ;
3539 uInt rowid = ifgrp[igrp][2*imem+1] ;
3540 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3541 if ( iter != freqIdVec[tableid].end() ) {
3542 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3543 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3544 int nchan = abcissa.size() ;
3545 double dnu = abcissa[1] - abcissa[0] ;
3546 //os << "GROUP " << igrp << " (" << tableid << "," << rowid << "): nchan = " << nchan << " (minchan = " << minchan << ")" << LogIO::POST ;
3547 if ( nchan < minchan ) {
3548 minchan = nchan ;
3549 maxdnu = dnu ;
3550 newin[tableid]->frequencies().getEntry( refpixref, refvalref, refinc, rowid ) ;
3551 refreqid = rowid ;
3552 reftable = tableid ;
3553 }
3554 }
3555 }
3556 // regrid spectra in each group
3557 os << "GROUP " << igrp << endl ;
3558 os << " Channel number is adjusted to " << minchan << endl ;
3559 os << " Corresponding frequency resolution is " << maxdnu << "Hz" << LogIO::POST ;
3560 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3561 uInt tableid = ifgrp[igrp][2*imem] ;
3562 uInt rowid = ifgrp[igrp][2*imem+1] ;
3563 freqIDCol.attach( newin[tableid]->table(), "FREQ_ID" ) ;
3564 //os << "tableid = " << tableid << " rowid = " << rowid << ": " << LogIO::POST ;
3565 //os << " regridChannel applied to " ;
3566 //if ( tableid != reftable )
3567 refreqid = newin[tableid]->frequencies().addEntry( refpixref, refvalref, refinc ) ;
3568 for ( uInt irow = 0 ; irow < newin[tableid]->table().nrow() ; irow++ ) {
3569 uInt tfreqid = freqIdVec[tableid][irow] ;
3570 if ( tfreqid == rowid ) {
3571 //os << irow << " " ;
3572 newin[tableid]->regridChannel( minchan, maxdnu, irow ) ;
3573 freqIDCol.put( irow, refreqid ) ;
3574 freqIdVec[tableid][irow] = refreqid ;
3575 }
3576 }
3577 //os << LogIO::POST ;
3578 }
3579 }
3580 else {
3581 uInt tableid = ifgrp[igrp][0] ;
3582 uInt rowid = ifgrp[igrp][1] ;
3583 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3584 if ( iter != freqIdVec[tableid].end() ) {
3585 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3586 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3587 minchan = abcissa.size() ;
3588 maxdnu = abcissa[1] - abcissa[0] ;
3589 }
3590 }
3591 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3592 if ( count( freqgrp[i].begin(), freqgrp[i].end(), igrp ) > 0 ) {
3593 if ( maxdnu > gmaxdnu[i] ) {
3594 gmaxdnu[i] = maxdnu ;
3595 gmemid[i] = igrp ;
3596 }
3597 break ;
3598 }
3599 }
3600 }
3601
3602 // set back coordinfo
3603 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3604 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3605 coordinfo[0] = oldinfo[itable] ;
3606 newin[itable]->setCoordInfo( coordinfo ) ;
3607 }
3608
3609 // accumulate all rows into the first table
3610 // NOTE: assumed in.size() = 1
3611 vector< CountedPtr<Scantable> > tmp( 1 ) ;
3612 if ( newin.size() == 1 )
3613 tmp[0] = newin[0] ;
3614 else
3615 tmp[0] = merge( newin ) ;
3616
3617 //return tmp[0] ;
3618
3619 // average
3620 CountedPtr<Scantable> tmpout = average( tmp, mask, weight, avmode ) ;
3621
3622 //return tmpout ;
3623
3624 // combine frequency group
3625 os << "Combine spectra based on frequency grouping" << LogIO::POST ;
3626 os << "IFNO is renumbered as frequency group ID (see above)" << LogIO::POST ;
3627 vector<string> coordinfo = tmpout->getCoordInfo() ;
3628 oldinfo[0] = coordinfo[0] ;
3629 coordinfo[0] = "Hz" ;
3630 tmpout->setCoordInfo( coordinfo ) ;
3631 // create proformas of output table
3632 stringstream taqlstream ;
3633 taqlstream << "SELECT FROM $1 WHERE IFNO IN [" ;
3634 for ( uInt i = 0 ; i < gmemid.size() ; i++ ) {
3635 taqlstream << gmemid[i] ;
3636 if ( i < gmemid.size() - 1 )
3637 taqlstream << "," ;
3638 else
3639 taqlstream << "]" ;
3640 }
3641 string taql = taqlstream.str() ;
3642 //os << "taql = " << taql << LogIO::POST ;
3643 STSelector selector = STSelector() ;
3644 selector.setTaQL( taql ) ;
3645 oldInsitu = insitu_ ;
3646 setInsitu( false ) ;
3647 out = getScantable( tmpout, false ) ;
3648 setInsitu( oldInsitu ) ;
3649 out->setSelection( selector ) ;
3650 // regrid rows
3651 ifnoCol.attach( tmpout->table(), "IFNO" ) ;
3652 for ( uInt irow = 0 ; irow < tmpout->table().nrow() ; irow++ ) {
3653 uInt ifno = ifnoCol( irow ) ;
3654 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3655 if ( count( freqgrp[igrp].begin(), freqgrp[igrp].end(), ifno ) > 0 ) {
3656 vector<double> abcissa = tmpout->getAbcissa( irow ) ;
3657 double bw = ( abcissa[1] - abcissa[0] ) * abcissa.size() ;
3658 int nchan = (int)( bw / gmaxdnu[igrp] ) ;
3659 tmpout->regridChannel( nchan, gmaxdnu[igrp], irow ) ;
3660 break ;
3661 }
3662 }
3663 }
3664 // combine spectra
3665 ArrayColumn<Float> specColOut ;
3666 specColOut.attach( out->table(), "SPECTRA" ) ;
3667 ArrayColumn<uChar> flagColOut ;
3668 flagColOut.attach( out->table(), "FLAGTRA" ) ;
3669 ScalarColumn<uInt> ifnoColOut ;
3670 ifnoColOut.attach( out->table(), "IFNO" ) ;
3671 ScalarColumn<uInt> polnoColOut ;
3672 polnoColOut.attach( out->table(), "POLNO" ) ;
3673 ScalarColumn<uInt> freqidColOut ;
3674 freqidColOut.attach( out->table(), "FREQ_ID" ) ;
3675// MDirection::ScalarColumn dirColOut ;
3676// dirColOut.attach( out->table(), "DIRECTION" ) ;
3677 Table &tab = tmpout->table() ;
3678 Block<String> cols(1);
3679 cols[0] = String("POLNO") ;
3680 TableIterator iter( tab, cols ) ;
3681 bool done = false ;
3682 vector< vector<uInt> > sizes( freqgrp.size() ) ;
3683 while( !iter.pastEnd() ) {
3684 vector< vector<Float> > specout( freqgrp.size() ) ;
3685 vector< vector<uChar> > flagout( freqgrp.size() ) ;
3686 ArrayColumn<Float> specCols ;
3687 specCols.attach( iter.table(), "SPECTRA" ) ;
3688 ArrayColumn<uChar> flagCols ;
3689 flagCols.attach( iter.table(), "FLAGTRA" ) ;
3690 ifnoCol.attach( iter.table(), "IFNO" ) ;
3691 ScalarColumn<uInt> polnos ;
3692 polnos.attach( iter.table(), "POLNO" ) ;
3693// MDirection::ScalarColumn dircol ;
3694// dircol.attach( iter.table(), "DIRECTION" ) ;
3695 uInt polno = polnos( 0 ) ;
3696 //os << "POLNO iteration: " << polno << LogIO::POST ;
3697// for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3698// sizes[igrp].resize( freqgrp[igrp].size() ) ;
3699// for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3700// for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3701// uInt ifno = ifnoCol( irow ) ;
3702// if ( ifno == freqgrp[igrp][imem] ) {
3703// Vector<Float> spec = specCols( irow ) ;
3704// Vector<uChar> flag = flagCols( irow ) ;
3705// vector<Float> svec ;
3706// spec.tovector( svec ) ;
3707// vector<uChar> fvec ;
3708// flag.tovector( fvec ) ;
3709// //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3710// specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3711// flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3712// //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3713// sizes[igrp][imem] = spec.nelements() ;
3714// }
3715// }
3716// }
3717// for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3718// uInt ifout = ifnoColOut( irow ) ;
3719// uInt polout = polnoColOut( irow ) ;
3720// if ( ifout == gmemid[igrp] && polout == polno ) {
3721// // set SPECTRA and FRAGTRA
3722// Vector<Float> newspec( specout[igrp] ) ;
3723// Vector<uChar> newflag( flagout[igrp] ) ;
3724// specColOut.put( irow, newspec ) ;
3725// flagColOut.put( irow, newflag ) ;
3726// // IFNO renumbering
3727// ifnoColOut.put( irow, igrp ) ;
3728// }
3729// }
3730// }
3731 // get a list of number of channels for each frequency group member
3732 if ( !done ) {
3733 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3734 sizes[igrp].resize( freqgrp[igrp].size() ) ;
3735 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3736 for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3737 uInt ifno = ifnoCol( irow ) ;
3738 if ( ifno == freqgrp[igrp][imem] ) {
3739 Vector<Float> spec = specCols( irow ) ;
3740 sizes[igrp][imem] = spec.nelements() ;
3741 break ;
3742 }
3743 }
3744 }
3745 }
3746 done = true ;
3747 }
3748 // combine spectra
3749 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3750 uInt polout = polnoColOut( irow ) ;
3751 if ( polout == polno ) {
3752 uInt ifout = ifnoColOut( irow ) ;
3753// Vector<Double> direction = dirColOut(irow).getAngle(Unit(String("rad"))).getValue() ;
3754 uInt igrp ;
3755 for ( uInt jgrp = 0 ; jgrp < freqgrp.size() ; jgrp++ ) {
3756 if ( ifout == gmemid[jgrp] ) {
3757 igrp = jgrp ;
3758 break ;
3759 }
3760 }
3761 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3762 for ( uInt jrow = 0 ; jrow < iter.table().nrow() ; jrow++ ) {
3763 uInt ifno = ifnoCol( jrow ) ;
3764 // 2012/02/17 TN
3765 // Since STGrid is implemented, average doesn't consider direction
3766 // when accumulating
3767// Vector<Double> tdir = dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
3768// //if ( ifno == freqgrp[igrp][imem] && allTrue( tdir == direction ) ) {
3769// Double dx = tdir[0] - direction[0] ;
3770// Double dy = tdir[1] - direction[1] ;
3771// Double dd = sqrt( dx * dx + dy * dy ) ;
3772 //if ( ifno == freqgrp[igrp][imem] && allNearAbs( tdir, direction, tol ) ) {
3773// if ( ifno == freqgrp[igrp][imem] && dd <= tol ) {
3774 if ( ifno == freqgrp[igrp][imem] ) {
3775 Vector<Float> spec = specCols( jrow ) ;
3776 Vector<uChar> flag = flagCols( jrow ) ;
3777 vector<Float> svec ;
3778 spec.tovector( svec ) ;
3779 vector<uChar> fvec ;
3780 flag.tovector( fvec ) ;
3781 //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3782 specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3783 flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3784 //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3785 }
3786 }
3787 }
3788 // set SPECTRA and FRAGTRA
3789 Vector<Float> newspec( specout[igrp] ) ;
3790 Vector<uChar> newflag( flagout[igrp] ) ;
3791 specColOut.put( irow, newspec ) ;
3792 flagColOut.put( irow, newflag ) ;
3793 // IFNO renumbering
3794 ifnoColOut.put( irow, igrp ) ;
3795 }
3796 }
3797 iter++ ;
3798 }
3799 // update FREQUENCIES subtable
3800 vector<bool> updated( freqgrp.size(), false ) ;
3801 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3802 uInt index = 0 ;
3803 uInt pixShift = 0 ;
3804 while ( freqgrp[igrp][index] != gmemid[igrp] ) {
3805 pixShift += sizes[igrp][index++] ;
3806 }
3807 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3808 if ( ifnoColOut( irow ) == gmemid[igrp] && !updated[igrp] ) {
3809 uInt freqidOut = freqidColOut( irow ) ;
3810 //os << "freqgrp " << igrp << " freqidOut = " << freqidOut << LogIO::POST ;
3811 double refpix ;
3812 double refval ;
3813 double increm ;
3814 out->frequencies().getEntry( refpix, refval, increm, freqidOut ) ;
3815 refpix += pixShift ;
3816 out->frequencies().setEntry( refpix, refval, increm, freqidOut ) ;
3817 updated[igrp] = true ;
3818 }
3819 }
3820 }
3821
3822 //out = tmpout ;
3823
3824 coordinfo = tmpout->getCoordInfo() ;
3825 coordinfo[0] = oldinfo[0] ;
3826 tmpout->setCoordInfo( coordinfo ) ;
3827 }
3828 else {
3829 // simple average
3830 out = average( in, mask, weight, avmode ) ;
3831 }
3832
3833 return out;
3834}
3835
3836CountedPtr<Scantable> STMath::cwcal( const CountedPtr<Scantable>& s,
3837 const String calmode,
3838 const String antname )
3839{
3840 // frequency switch
3841 if ( calmode == "fs" ) {
3842 return cwcalfs( s, antname ) ;
3843 }
3844 else {
3845 vector<bool> masks = s->getMask( 0 ) ;
3846 vector<int> types ;
3847
3848 // sky scan
3849 STSelector sel = STSelector() ;
3850 types.push_back( SrcType::SKY ) ;
3851 sel.setTypes( types ) ;
3852 s->setSelection( sel ) ;
3853 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3854 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
3855 s->unsetSelection() ;
3856 sel.reset() ;
3857 types.clear() ;
3858
3859 // hot scan
3860 types.push_back( SrcType::HOT ) ;
3861 sel.setTypes( types ) ;
3862 s->setSelection( sel ) ;
3863 tmp.clear() ;
3864 tmp.push_back( getScantable( s, false ) ) ;
3865 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
3866 s->unsetSelection() ;
3867 sel.reset() ;
3868 types.clear() ;
3869
3870 // cold scan
3871 CountedPtr<Scantable> acold ;
3872// types.push_back( SrcType::COLD ) ;
3873// sel.setTypes( types ) ;
3874// s->setSelection( sel ) ;
3875// tmp.clear() ;
3876// tmp.push_back( getScantable( s, false ) ) ;
3877// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCNAN" ) ;
3878// s->unsetSelection() ;
3879// sel.reset() ;
3880// types.clear() ;
3881
3882 // off scan
3883 types.push_back( SrcType::PSOFF ) ;
3884 sel.setTypes( types ) ;
3885 s->setSelection( sel ) ;
3886 tmp.clear() ;
3887 tmp.push_back( getScantable( s, false ) ) ;
3888 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
3889 s->unsetSelection() ;
3890 sel.reset() ;
3891 types.clear() ;
3892
3893 // on scan
3894 bool insitu = insitu_ ;
3895 insitu_ = false ;
3896 CountedPtr<Scantable> out = getScantable( s, true ) ;
3897 insitu_ = insitu ;
3898 types.push_back( SrcType::PSON ) ;
3899 sel.setTypes( types ) ;
3900 s->setSelection( sel ) ;
3901 TableCopy::copyRows( out->table(), s->table() ) ;
3902 s->unsetSelection() ;
3903 sel.reset() ;
3904 types.clear() ;
3905
3906 // process each on scan
3907 ArrayColumn<Float> tsysCol ;
3908 tsysCol.attach( out->table(), "TSYS" ) ;
3909 for ( int i = 0 ; i < out->nrow() ; i++ ) {
3910 vector<float> sp = getCalibratedSpectra( out, aoff, asky, ahot, acold, i, antname ) ;
3911 out->setSpectrum( sp, i ) ;
3912 string reftime = out->getTime( i ) ;
3913 vector<int> ii( 1, out->getIF( i ) ) ;
3914 vector<int> ib( 1, out->getBeam( i ) ) ;
3915 vector<int> ip( 1, out->getPol( i ) ) ;
3916 sel.setIFs( ii ) ;
3917 sel.setBeams( ib ) ;
3918 sel.setPolarizations( ip ) ;
3919 asky->setSelection( sel ) ;
3920 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
3921 const Vector<Float> Vtsys( sptsys ) ;
3922 tsysCol.put( i, Vtsys ) ;
3923 asky->unsetSelection() ;
3924 sel.reset() ;
3925 }
3926
3927 // flux unit
3928 out->setFluxUnit( "K" ) ;
3929
3930 return out ;
3931 }
3932}
3933
3934CountedPtr<Scantable> STMath::almacal( const CountedPtr<Scantable>& s,
3935 const String calmode )
3936{
3937 // frequency switch
3938 if ( calmode == "fs" ) {
3939 return almacalfs( s ) ;
3940 }
3941 else {
3942 // double t0, t1 ;
3943 // t0 = mathutil::gettimeofday_sec() ;
3944 vector<bool> masks = s->getMask( 0 ) ;
3945
3946 // off scan
3947 STSelector sel = STSelector() ;
3948 vector<int> types( 1, SrcType::PSOFF ) ;
3949 //types.push_back( SrcType::PSOFF ) ;
3950 sel.setTypes( types ) ;
3951 s->setSelection( sel ) ;
3952 // TODO 2010/01/08 TN
3953 // Grouping by time should be needed before averaging.
3954 // Each group must have own unique SCANNO (should be renumbered).
3955 // See PIPELINE/SDCalibration.py
3956 CountedPtr<Scantable> soff = getScantable( s, false ) ;
3957 Table ttab = soff->table() ;
3958// String tmpname = File::newUniqueName( "./", "temp" ).baseName() ;
3959// Table ttab = s->table().copyToMemoryTable( tmpname, False ) ;
3960 ROScalarColumn<Double> *timeCol = new ROScalarColumn<Double>( ttab, "TIME" ) ;
3961 uInt nrow = timeCol->nrow() ;
3962 Vector<Double> timeSep = timeCol->getColumn() ;
3963 delete timeCol ;
3964 for ( uInt i = nrow-2 ; i > 0 ; i-- ) {
3965 timeSep[i] -= timeSep[i-1] ;
3966 }
3967 Vector<Double> interval = soff->integrCol_.getColumn() ;
3968 interval /= 86400.0 ;
3969 Block<uInt> gaplist( 100 ) ;
3970 uInt glidx = 0 ;
3971 uInt glsize = gaplist.size() ;
3972 for ( uInt i = 0 ; i < nrow - 1 ; i++ ) {
3973 double gap = 2.0 * timeSep[i+1] / ( interval[i] + interval[i+1] ) ;
3974 //cout << "gap[" << i << "]=" << setw(5) << gap << endl ;
3975 if ( gap > 1.1 ) {
3976// cout << "detected gap between " << i << " and " << i+1 << endl ;
3977 gaplist[glidx] = i ;
3978 glidx++ ;
3979 }
3980 if ( glidx >= glsize ) {
3981// cout << "resize gaplist" << endl ;
3982 glsize += 100 ;
3983 gaplist.resize( glsize ) ;
3984 }
3985 }
3986 gaplist[glidx] = nrow - 1 ;
3987 glidx++ ;
3988// cout << "gaplist = " << Vector<uInt>(IPosition(1,glidx),gaplist.storage()) << endl ;
3989 uInt newid = 0 ;
3990 Vector<uInt> newscanno( nrow, 0 ) ;
3991 uInt *p = newscanno.data() ;
3992 IPosition pos( 1 ) ;
3993 for ( uInt i = 1 ; i < glidx ; i++ ) {
3994 pos[0] = gaplist[i] - gaplist[i-1] ;
3995 Vector<uInt> scnslice( pos, p+gaplist[i-1]+1, SHARE ) ;
3996 scnslice = i ;
3997 }
3998 soff->scanCol_.putColumn( newscanno ) ;
3999// cout << "new scancol = " << soff->scanCol_.getColumn() << endl ;
4000// double t2 = mathutil::gettimeofday_sec() ;
4001 vector< CountedPtr<Scantable> > tmp( 1, soff ) ;
4002 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
4003 // double t3 = mathutil::gettimeofday_sec() ;
4004 //cout << "aoff.nrow = " << aoff->nrow() << endl ;
4005 s->unsetSelection() ;
4006 sel.reset() ;
4007 // t1 = mathutil::gettimeofday_sec() ;
4008 // cout << "elapsed time for off averaging: " << t1-t0 << " sec" << endl ;
4009 // cout << " elapsed time for average(): " << t3-t2 << " sec" << endl ;
4010
4011 // on scan
4012 // t0 = mathutil::gettimeofday_sec() ;
4013 bool insitu = insitu_ ;
4014 insitu_ = false ;
4015 CountedPtr<Scantable> out = getScantable( s, true ) ;
4016 insitu_ = insitu ;
4017 types[0] = SrcType::PSON ;
4018 sel.setTypes( types ) ;
4019 s->setSelection( sel ) ;
4020 TableCopy::copyRows( out->table(), s->table() ) ;
4021 s->unsetSelection() ;
4022 sel.reset() ;
4023 // t1 = mathutil::gettimeofday_sec() ;
4024 // cout << "elapsed time for preparing output table: " << t1-t0 << " sec" << endl ;
4025
4026 // process each on scan
4027 // t0 = mathutil::gettimeofday_sec() ;
4028// for ( int i = 0 ; i < out->nrow() ; i++ ) {
4029// vector<float> sp = getCalibratedSpectra( out, aoff, i ) ;
4030// out->setSpectrum( sp, i ) ;
4031// }
4032
4033 // using STIdxIterAcc
4034 vector<string> cols( 3 ) ;
4035 cols[0] = "BEAMNO" ;
4036 cols[1] = "POLNO" ;
4037 cols[2] = "IFNO" ;
4038 STIdxIter *iter = new STIdxIterAcc( out, cols ) ;
4039 while ( !iter->pastEnd() ) {
4040 Vector<uInt> ids = iter->current() ;
4041 stringstream ss ;
4042 ss << "SELECT FROM $1 WHERE "
4043 << "BEAMNO==" << ids[0] << "&&"
4044 << "POLNO==" << ids[1] << "&&"
4045 << "IFNO==" << ids[2] ;
4046 sel.setTaQL( ss.str() ) ;
4047 aoff->setSelection( sel ) ;
4048 Vector<uInt> rows = iter->getRows( SHARE ) ;
4049 calibrateALMA( out, aoff, rows ) ;
4050 aoff->unsetSelection() ;
4051 sel.reset() ;
4052 iter->next() ;
4053 }
4054 delete iter ;
4055
4056 // t1 = mathutil::gettimeofday_sec() ;
4057 // cout << "elapsed time for calibration: " << t1-t0 << " sec" << endl ;
4058
4059 // flux unit
4060 out->setFluxUnit( "K" ) ;
4061
4062 return out ;
4063 }
4064}
4065
4066CountedPtr<Scantable> STMath::cwcalfs( const CountedPtr<Scantable>& s,
4067 const String antname )
4068{
4069 vector<int> types ;
4070
4071 // APEX calibration mode
4072 int apexcalmode = 1 ;
4073
4074 if ( antname.find( "APEX" ) != string::npos ) {
4075 // check if off scan exists or not
4076 STSelector sel = STSelector() ;
4077 //sel.setName( offstr1 ) ;
4078 types.push_back( SrcType::FLOOFF ) ;
4079 sel.setTypes( types ) ;
4080 try {
4081 s->setSelection( sel ) ;
4082 }
4083 catch ( AipsError &e ) {
4084 apexcalmode = 0 ;
4085 }
4086 sel.reset() ;
4087 }
4088 s->unsetSelection() ;
4089 types.clear() ;
4090
4091 vector<bool> masks = s->getMask( 0 ) ;
4092 CountedPtr<Scantable> ssig, sref ;
4093 CountedPtr<Scantable> out ;
4094
4095 if ( antname.find( "APEX" ) != string::npos ) {
4096 // APEX calibration
4097 // sky scan
4098 STSelector sel = STSelector() ;
4099 types.push_back( SrcType::FLOSKY ) ;
4100 sel.setTypes( types ) ;
4101 s->setSelection( sel ) ;
4102 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
4103 CountedPtr<Scantable> askylo = average( tmp, masks, "TINT", "SCAN" ) ;
4104 s->unsetSelection() ;
4105 sel.reset() ;
4106 types.clear() ;
4107 types.push_back( SrcType::FHISKY ) ;
4108 sel.setTypes( types ) ;
4109 s->setSelection( sel ) ;
4110 tmp.clear() ;
4111 tmp.push_back( getScantable( s, false ) ) ;
4112 CountedPtr<Scantable> askyhi = average( tmp, masks, "TINT", "SCAN" ) ;
4113 s->unsetSelection() ;
4114 sel.reset() ;
4115 types.clear() ;
4116
4117 // hot scan
4118 types.push_back( SrcType::FLOHOT ) ;
4119 sel.setTypes( types ) ;
4120 s->setSelection( sel ) ;
4121 tmp.clear() ;
4122 tmp.push_back( getScantable( s, false ) ) ;
4123 CountedPtr<Scantable> ahotlo = average( tmp, masks, "TINT", "SCAN" ) ;
4124 s->unsetSelection() ;
4125 sel.reset() ;
4126 types.clear() ;
4127 types.push_back( SrcType::FHIHOT ) ;
4128 sel.setTypes( types ) ;
4129 s->setSelection( sel ) ;
4130 tmp.clear() ;
4131 tmp.push_back( getScantable( s, false ) ) ;
4132 CountedPtr<Scantable> ahothi = average( tmp, masks, "TINT", "SCAN" ) ;
4133 s->unsetSelection() ;
4134 sel.reset() ;
4135 types.clear() ;
4136
4137 // cold scan
4138 CountedPtr<Scantable> acoldlo, acoldhi ;
4139// types.push_back( SrcType::FLOCOLD ) ;
4140// sel.setTypes( types ) ;
4141// s->setSelection( sel ) ;
4142// tmp.clear() ;
4143// tmp.push_back( getScantable( s, false ) ) ;
4144// CountedPtr<Scantable> acoldlo = average( tmp, masks, "TINT", "SCAN" ) ;
4145// s->unsetSelection() ;
4146// sel.reset() ;
4147// types.clear() ;
4148// types.push_back( SrcType::FHICOLD ) ;
4149// sel.setTypes( types ) ;
4150// s->setSelection( sel ) ;
4151// tmp.clear() ;
4152// tmp.push_back( getScantable( s, false ) ) ;
4153// CountedPtr<Scantable> acoldhi = average( tmp, masks, "TINT", "SCAN" ) ;
4154// s->unsetSelection() ;
4155// sel.reset() ;
4156// types.clear() ;
4157
4158 // ref scan
4159 bool insitu = insitu_ ;
4160 insitu_ = false ;
4161 sref = getScantable( s, true ) ;
4162 insitu_ = insitu ;
4163 types.push_back( SrcType::FSLO ) ;
4164 sel.setTypes( types ) ;
4165 s->setSelection( sel ) ;
4166 TableCopy::copyRows( sref->table(), s->table() ) ;
4167 s->unsetSelection() ;
4168 sel.reset() ;
4169 types.clear() ;
4170
4171 // sig scan
4172 insitu_ = false ;
4173 ssig = getScantable( s, true ) ;
4174 insitu_ = insitu ;
4175 types.push_back( SrcType::FSHI ) ;
4176 sel.setTypes( types ) ;
4177 s->setSelection( sel ) ;
4178 TableCopy::copyRows( ssig->table(), s->table() ) ;
4179 s->unsetSelection() ;
4180 sel.reset() ;
4181 types.clear() ;
4182
4183 if ( apexcalmode == 0 ) {
4184 // APEX fs data without off scan
4185 // process each sig and ref scan
4186 ArrayColumn<Float> tsysCollo ;
4187 tsysCollo.attach( ssig->table(), "TSYS" ) ;
4188 ArrayColumn<Float> tsysColhi ;
4189 tsysColhi.attach( sref->table(), "TSYS" ) ;
4190 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4191 vector< CountedPtr<Scantable> > sky( 2 ) ;
4192 sky[0] = askylo ;
4193 sky[1] = askyhi ;
4194 vector< CountedPtr<Scantable> > hot( 2 ) ;
4195 hot[0] = ahotlo ;
4196 hot[1] = ahothi ;
4197 vector< CountedPtr<Scantable> > cold( 2 ) ;
4198 //cold[0] = acoldlo ;
4199 //cold[1] = acoldhi ;
4200 vector<float> sp = getFSCalibratedSpectra( ssig, sref, sky, hot, cold, i ) ;
4201 ssig->setSpectrum( sp, i ) ;
4202 string reftime = ssig->getTime( i ) ;
4203 vector<int> ii( 1, ssig->getIF( i ) ) ;
4204 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4205 vector<int> ip( 1, ssig->getPol( i ) ) ;
4206 sel.setIFs( ii ) ;
4207 sel.setBeams( ib ) ;
4208 sel.setPolarizations( ip ) ;
4209 askylo->setSelection( sel ) ;
4210 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
4211 const Vector<Float> Vtsyslo( sptsys ) ;
4212 tsysCollo.put( i, Vtsyslo ) ;
4213 askylo->unsetSelection() ;
4214 sel.reset() ;
4215 sky[0] = askyhi ;
4216 sky[1] = askylo ;
4217 hot[0] = ahothi ;
4218 hot[1] = ahotlo ;
4219 cold[0] = acoldhi ;
4220 cold[1] = acoldlo ;
4221 sp = getFSCalibratedSpectra( sref, ssig, sky, hot, cold, i ) ;
4222 sref->setSpectrum( sp, i ) ;
4223 reftime = sref->getTime( i ) ;
4224 ii[0] = sref->getIF( i ) ;
4225 ib[0] = sref->getBeam( i ) ;
4226 ip[0] = sref->getPol( i ) ;
4227 sel.setIFs( ii ) ;
4228 sel.setBeams( ib ) ;
4229 sel.setPolarizations( ip ) ;
4230 askyhi->setSelection( sel ) ;
4231 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
4232 const Vector<Float> Vtsyshi( sptsys ) ;
4233 tsysColhi.put( i, Vtsyshi ) ;
4234 askyhi->unsetSelection() ;
4235 sel.reset() ;
4236 }
4237 }
4238 else if ( apexcalmode == 1 ) {
4239 // APEX fs data with off scan
4240 // off scan
4241 types.push_back( SrcType::FLOOFF ) ;
4242 sel.setTypes( types ) ;
4243 s->setSelection( sel ) ;
4244 tmp.clear() ;
4245 tmp.push_back( getScantable( s, false ) ) ;
4246 CountedPtr<Scantable> aofflo = average( tmp, masks, "TINT", "SCAN" ) ;
4247 s->unsetSelection() ;
4248 sel.reset() ;
4249 types.clear() ;
4250 types.push_back( SrcType::FHIOFF ) ;
4251 sel.setTypes( types ) ;
4252 s->setSelection( sel ) ;
4253 tmp.clear() ;
4254 tmp.push_back( getScantable( s, false ) ) ;
4255 CountedPtr<Scantable> aoffhi = average( tmp, masks, "TINT", "SCAN" ) ;
4256 s->unsetSelection() ;
4257 sel.reset() ;
4258 types.clear() ;
4259
4260 // process each sig and ref scan
4261 ArrayColumn<Float> tsysCollo ;
4262 tsysCollo.attach( ssig->table(), "TSYS" ) ;
4263 ArrayColumn<Float> tsysColhi ;
4264 tsysColhi.attach( sref->table(), "TSYS" ) ;
4265 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4266 vector<float> sp = getCalibratedSpectra( ssig, aofflo, askylo, ahotlo, acoldlo, i, antname ) ;
4267 ssig->setSpectrum( sp, i ) ;
4268 sp = getCalibratedSpectra( sref, aoffhi, askyhi, ahothi, acoldhi, i, antname ) ;
4269 string reftime = ssig->getTime( i ) ;
4270 vector<int> ii( 1, ssig->getIF( i ) ) ;
4271 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4272 vector<int> ip( 1, ssig->getPol( i ) ) ;
4273 sel.setIFs( ii ) ;
4274 sel.setBeams( ib ) ;
4275 sel.setPolarizations( ip ) ;
4276 askylo->setSelection( sel ) ;
4277 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
4278 const Vector<Float> Vtsyslo( sptsys ) ;
4279 tsysCollo.put( i, Vtsyslo ) ;
4280 askylo->unsetSelection() ;
4281 sel.reset() ;
4282 sref->setSpectrum( sp, i ) ;
4283 reftime = sref->getTime( i ) ;
4284 ii[0] = sref->getIF( i ) ;
4285 ib[0] = sref->getBeam( i ) ;
4286 ip[0] = sref->getPol( i ) ;
4287 sel.setIFs( ii ) ;
4288 sel.setBeams( ib ) ;
4289 sel.setPolarizations( ip ) ;
4290 askyhi->setSelection( sel ) ;
4291 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
4292 const Vector<Float> Vtsyshi( sptsys ) ;
4293 tsysColhi.put( i, Vtsyshi ) ;
4294 askyhi->unsetSelection() ;
4295 sel.reset() ;
4296 }
4297 }
4298 }
4299 else {
4300 // non-APEX fs data
4301 // sky scan
4302 STSelector sel = STSelector() ;
4303 types.push_back( SrcType::SKY ) ;
4304 sel.setTypes( types ) ;
4305 s->setSelection( sel ) ;
4306 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
4307 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
4308 s->unsetSelection() ;
4309 sel.reset() ;
4310 types.clear() ;
4311
4312 // hot scan
4313 types.push_back( SrcType::HOT ) ;
4314 sel.setTypes( types ) ;
4315 s->setSelection( sel ) ;
4316 tmp.clear() ;
4317 tmp.push_back( getScantable( s, false ) ) ;
4318 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
4319 s->unsetSelection() ;
4320 sel.reset() ;
4321 types.clear() ;
4322
4323 // cold scan
4324 CountedPtr<Scantable> acold ;
4325// types.push_back( SrcType::COLD ) ;
4326// sel.setTypes( types ) ;
4327// s->setSelection( sel ) ;
4328// tmp.clear() ;
4329// tmp.push_back( getScantable( s, false ) ) ;
4330// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCAN" ) ;
4331// s->unsetSelection() ;
4332// sel.reset() ;
4333// types.clear() ;
4334
4335 // ref scan
4336 bool insitu = insitu_ ;
4337 insitu_ = false ;
4338 sref = getScantable( s, true ) ;
4339 insitu_ = insitu ;
4340 types.push_back( SrcType::FSOFF ) ;
4341 sel.setTypes( types ) ;
4342 s->setSelection( sel ) ;
4343 TableCopy::copyRows( sref->table(), s->table() ) ;
4344 s->unsetSelection() ;
4345 sel.reset() ;
4346 types.clear() ;
4347
4348 // sig scan
4349 insitu_ = false ;
4350 ssig = getScantable( s, true ) ;
4351 insitu_ = insitu ;
4352 types.push_back( SrcType::FSON ) ;
4353 sel.setTypes( types ) ;
4354 s->setSelection( sel ) ;
4355 TableCopy::copyRows( ssig->table(), s->table() ) ;
4356 s->unsetSelection() ;
4357 sel.reset() ;
4358 types.clear() ;
4359
4360 // process each sig and ref scan
4361 ArrayColumn<Float> tsysColsig ;
4362 tsysColsig.attach( ssig->table(), "TSYS" ) ;
4363 ArrayColumn<Float> tsysColref ;
4364 tsysColref.attach( ssig->table(), "TSYS" ) ;
4365 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4366 vector<float> sp = getFSCalibratedSpectra( ssig, sref, asky, ahot, acold, i ) ;
4367 ssig->setSpectrum( sp, i ) ;
4368 string reftime = ssig->getTime( i ) ;
4369 vector<int> ii( 1, ssig->getIF( i ) ) ;
4370 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4371 vector<int> ip( 1, ssig->getPol( i ) ) ;
4372 sel.setIFs( ii ) ;
4373 sel.setBeams( ib ) ;
4374 sel.setPolarizations( ip ) ;
4375 asky->setSelection( sel ) ;
4376 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
4377 const Vector<Float> Vtsys( sptsys ) ;
4378 tsysColsig.put( i, Vtsys ) ;
4379 asky->unsetSelection() ;
4380 sel.reset() ;
4381 sp = getFSCalibratedSpectra( sref, ssig, asky, ahot, acold, i ) ;
4382 sref->setSpectrum( sp, i ) ;
4383 tsysColref.put( i, Vtsys ) ;
4384 }
4385 }
4386
4387 // do folding if necessary
4388 Table sigtab = ssig->table() ;
4389 Table reftab = sref->table() ;
4390 ScalarColumn<uInt> sigifnoCol ;
4391 ScalarColumn<uInt> refifnoCol ;
4392 ScalarColumn<uInt> sigfidCol ;
4393 ScalarColumn<uInt> reffidCol ;
4394 Int nchan = (Int)ssig->nchan() ;
4395 sigifnoCol.attach( sigtab, "IFNO" ) ;
4396 refifnoCol.attach( reftab, "IFNO" ) ;
4397 sigfidCol.attach( sigtab, "FREQ_ID" ) ;
4398 reffidCol.attach( reftab, "FREQ_ID" ) ;
4399 Vector<uInt> sfids( sigfidCol.getColumn() ) ;
4400 Vector<uInt> rfids( reffidCol.getColumn() ) ;
4401 vector<uInt> sfids_unique ;
4402 vector<uInt> rfids_unique ;
4403 vector<uInt> sifno_unique ;
4404 vector<uInt> rifno_unique ;
4405 for ( uInt i = 0 ; i < sfids.nelements() ; i++ ) {
4406 if ( count( sfids_unique.begin(), sfids_unique.end(), sfids[i] ) == 0 ) {
4407 sfids_unique.push_back( sfids[i] ) ;
4408 sifno_unique.push_back( ssig->getIF( i ) ) ;
4409 }
4410 if ( count( rfids_unique.begin(), rfids_unique.end(), rfids[i] ) == 0 ) {
4411 rfids_unique.push_back( rfids[i] ) ;
4412 rifno_unique.push_back( sref->getIF( i ) ) ;
4413 }
4414 }
4415 double refpix_sig, refval_sig, increment_sig ;
4416 double refpix_ref, refval_ref, increment_ref ;
4417 vector< CountedPtr<Scantable> > tmp( sfids_unique.size() ) ;
4418 for ( uInt i = 0 ; i < sfids_unique.size() ; i++ ) {
4419 ssig->frequencies().getEntry( refpix_sig, refval_sig, increment_sig, sfids_unique[i] ) ;
4420 sref->frequencies().getEntry( refpix_ref, refval_ref, increment_ref, rfids_unique[i] ) ;
4421 if ( refpix_sig == refpix_ref ) {
4422 double foffset = refval_ref - refval_sig ;
4423 int choffset = static_cast<int>(foffset/increment_sig) ;
4424 double doffset = foffset / increment_sig ;
4425 if ( abs(choffset) >= nchan ) {
4426 LogIO os( LogOrigin( "STMath", "cwcalfs", WHERE ) ) ;
4427 os << "FREQ_ID=[" << sfids_unique[i] << "," << rfids_unique[i] << "]: out-band frequency switching, no folding" << LogIO::POST ;
4428 os << "Just return signal data" << LogIO::POST ;
4429 //std::vector< CountedPtr<Scantable> > tabs ;
4430 //tabs.push_back( ssig ) ;
4431 //tabs.push_back( sref ) ;
4432 //out = merge( tabs ) ;
4433 tmp[i] = ssig ;
4434 }
4435 else {
4436 STSelector sel = STSelector() ;
4437 vector<int> v( 1, sifno_unique[i] ) ;
4438 sel.setIFs( v ) ;
4439 ssig->setSelection( sel ) ;
4440 sel.reset() ;
4441 v[0] = rifno_unique[i] ;
4442 sel.setIFs( v ) ;
4443 sref->setSelection( sel ) ;
4444 sel.reset() ;
4445 if ( antname.find( "APEX" ) != string::npos ) {
4446 tmp[i] = dofold( ssig, sref, 0.5*doffset, -0.5*doffset ) ;
4447 //tmp[i] = dofold( ssig, sref, doffset ) ;
4448 }
4449 else {
4450 tmp[i] = dofold( ssig, sref, doffset ) ;
4451 }
4452 ssig->unsetSelection() ;
4453 sref->unsetSelection() ;
4454 }
4455 }
4456 }
4457
4458 if ( tmp.size() > 1 ) {
4459 out = merge( tmp ) ;
4460 }
4461 else {
4462 out = tmp[0] ;
4463 }
4464
4465 // flux unit
4466 out->setFluxUnit( "K" ) ;
4467
4468 return out ;
4469}
4470
4471CountedPtr<Scantable> STMath::almacalfs( const CountedPtr<Scantable>& s )
4472{
4473 (void) s; //currently unused
4474 CountedPtr<Scantable> out ;
4475
4476 return out ;
4477}
4478
4479vector<float> STMath::getSpectrumFromTime( string reftime,
4480 CountedPtr<Scantable>& s,
4481 string mode )
4482{
4483 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
4484 vector<float> sp ;
4485
4486 if ( s->nrow() == 0 ) {
4487 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
4488 return sp ;
4489 }
4490 else if ( s->nrow() == 1 ) {
4491 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
4492 return s->getSpectrum( 0 ) ;
4493 }
4494 else {
4495 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4496 if ( mode == "before" ) {
4497 int id = -1 ;
4498 if ( idx[0] != -1 ) {
4499 id = idx[0] ;
4500 }
4501 else if ( idx[1] != -1 ) {
4502 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4503 id = idx[1] ;
4504 }
4505 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4506 sp = s->getSpectrum( id ) ;
4507 }
4508 else if ( mode == "after" ) {
4509 int id = -1 ;
4510 if ( idx[1] != -1 ) {
4511 id = idx[1] ;
4512 }
4513 else if ( idx[0] != -1 ) {
4514 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4515 id = idx[1] ;
4516 }
4517 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4518 sp = s->getSpectrum( id ) ;
4519 }
4520 else if ( mode == "nearest" ) {
4521 int id = -1 ;
4522 if ( idx[0] == -1 ) {
4523 id = idx[1] ;
4524 }
4525 else if ( idx[1] == -1 ) {
4526 id = idx[0] ;
4527 }
4528 else if ( idx[0] == idx[1] ) {
4529 id = idx[0] ;
4530 }
4531 else {
4532 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4533 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4534 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4535 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4536 double tref = getMJD( reftime ) ;
4537 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4538 id = idx[1] ;
4539 }
4540 else {
4541 id = idx[0] ;
4542 }
4543 }
4544 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4545 sp = s->getSpectrum( id ) ;
4546 }
4547 else if ( mode == "linear" ) {
4548 if ( idx[0] == -1 ) {
4549 // use after
4550 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4551 int id = idx[1] ;
4552 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4553 sp = s->getSpectrum( id ) ;
4554 }
4555 else if ( idx[1] == -1 ) {
4556 // use before
4557 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4558 int id = idx[0] ;
4559 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4560 sp = s->getSpectrum( id ) ;
4561 }
4562 else if ( idx[0] == idx[1] ) {
4563 // use before
4564 //os << "No need to interporate." << LogIO::POST ;
4565 int id = idx[0] ;
4566 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4567 sp = s->getSpectrum( id ) ;
4568 }
4569 else {
4570 // do interpolation
4571 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4572 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4573 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4574 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4575 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4576 double tref = getMJD( reftime ) ;
4577 vector<float> sp0 = s->getSpectrum( idx[0] ) ;
4578 vector<float> sp1 = s->getSpectrum( idx[1] ) ;
4579 for ( unsigned int i = 0 ; i < sp0.size() ; i++ ) {
4580 float v = ( sp1[i] - sp0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + sp0[i] ;
4581 sp.push_back( v ) ;
4582 }
4583 }
4584 }
4585 else {
4586 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4587 }
4588 return sp ;
4589 }
4590}
4591
4592vector<float> STMath::getSpectrumFromTime( double reftime,
4593 Vector<Double> &timeVec,
4594 CountedPtr<Scantable>& s,
4595 string mode )
4596{
4597 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
4598 vector<float> sp ;
4599
4600 if ( s->nrow() == 0 ) {
4601 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
4602 return sp ;
4603 }
4604 else if ( s->nrow() == 1 ) {
4605 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
4606 return s->getSpectrum( 0 ) ;
4607 }
4608 else {
4609 //ROScalarColumn<Double> timeCol( s->table(), "TIME" ) ;
4610 //Vector<Double> timeVec = timeCol.getColumn() ;
4611 vector<int> idx = getRowIdFromTime( reftime, timeVec ) ;
4612 if ( mode == "before" ) {
4613 int id = -1 ;
4614 if ( idx[0] != -1 ) {
4615 id = idx[0] ;
4616 }
4617 else if ( idx[1] != -1 ) {
4618 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4619 id = idx[1] ;
4620 }
4621 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4622 sp = s->getSpectrum( id ) ;
4623 }
4624 else if ( mode == "after" ) {
4625 int id = -1 ;
4626 if ( idx[1] != -1 ) {
4627 id = idx[1] ;
4628 }
4629 else if ( idx[0] != -1 ) {
4630 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4631 id = idx[1] ;
4632 }
4633 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4634 sp = s->getSpectrum( id ) ;
4635 }
4636 else if ( mode == "nearest" ) {
4637 int id = -1 ;
4638 if ( idx[0] == -1 ) {
4639 id = idx[1] ;
4640 }
4641 else if ( idx[1] == -1 ) {
4642 id = idx[0] ;
4643 }
4644 else if ( idx[0] == idx[1] ) {
4645 id = idx[0] ;
4646 }
4647 else {
4648 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4649 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4650// double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4651// double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4652 double t0 = timeVec[idx[0]] ;
4653 double t1 = timeVec[idx[1]] ;
4654// cout << "t0-t0c=" << t0-t0c << endl ;
4655// cout << "t1-t1c=" << t1-t1c << endl ;
4656// double tref = getMJD( reftime ) ;
4657 double tref = reftime ;
4658 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4659 id = idx[1] ;
4660 }
4661 else {
4662 id = idx[0] ;
4663 }
4664 }
4665 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4666 sp = s->getSpectrum( id ) ;
4667 }
4668 else if ( mode == "linear" ) {
4669 if ( idx[0] == -1 ) {
4670 // use after
4671 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4672 int id = idx[1] ;
4673 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4674 sp = s->getSpectrum( id ) ;
4675 }
4676 else if ( idx[1] == -1 ) {
4677 // use before
4678 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4679 int id = idx[0] ;
4680 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4681 sp = s->getSpectrum( id ) ;
4682 }
4683 else if ( idx[0] == idx[1] ) {
4684 // use before
4685 //os << "No need to interporate." << LogIO::POST ;
4686 int id = idx[0] ;
4687 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4688 sp = s->getSpectrum( id ) ;
4689 }
4690 else {
4691 // do interpolation
4692 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4693 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4694 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4695// double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4696// double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4697 double t0 = timeVec[idx[0]] ;
4698 double t1 = timeVec[idx[1]] ;
4699// cout << "t0-t0c=" << t0-t0c << endl ;
4700// cout << "t1-t1c=" << t1-t1c << endl ;
4701// double tref = getMJD( reftime ) ;
4702 double tref = reftime ;
4703 sp = s->getSpectrum( idx[0] ) ;
4704 vector<float> sp1 = s->getSpectrum( idx[1] ) ;
4705 double tfactor = ( tref - t0 ) / ( t1 - t0 ) ;
4706 for ( unsigned int i = 0 ; i < sp.size() ; i++ ) {
4707 sp[i] = ( sp1[i] - sp[i] ) * tfactor + sp[i] ;
4708 }
4709 }
4710 }
4711 else {
4712 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4713 }
4714 return sp ;
4715 }
4716}
4717
4718double STMath::getMJD( string strtime )
4719{
4720 if ( strtime.find("/") == string::npos ) {
4721 // MJD time string
4722 return atof( strtime.c_str() ) ;
4723 }
4724 else {
4725 // string in YYYY/MM/DD/HH:MM:SS format
4726 uInt year = atoi( strtime.substr( 0, 4 ).c_str() ) ;
4727 uInt month = atoi( strtime.substr( 5, 2 ).c_str() ) ;
4728 uInt day = atoi( strtime.substr( 8, 2 ).c_str() ) ;
4729 uInt hour = atoi( strtime.substr( 11, 2 ).c_str() ) ;
4730 uInt minute = atoi( strtime.substr( 14, 2 ).c_str() ) ;
4731 uInt sec = atoi( strtime.substr( 17, 2 ).c_str() ) ;
4732 Time t( year, month, day, hour, minute, sec ) ;
4733 return t.modifiedJulianDay() ;
4734 }
4735}
4736
4737vector<int> STMath::getRowIdFromTime( string reftime, CountedPtr<Scantable> &s )
4738{
4739 double reft = getMJD( reftime ) ;
4740 double dtmin = 1.0e100 ;
4741 double dtmax = -1.0e100 ;
4742 vector<double> dt ;
4743 int just_before = -1 ;
4744 int just_after = -1 ;
4745 for ( int i = 0 ; i < s->nrow() ; i++ ) {
4746 dt.push_back( getMJD( s->getTime( i ) ) - reft ) ;
4747 }
4748 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4749 if ( dt[i] > 0.0 ) {
4750 // after reftime
4751 if ( dt[i] < dtmin ) {
4752 just_after = i ;
4753 dtmin = dt[i] ;
4754 }
4755 }
4756 else if ( dt[i] < 0.0 ) {
4757 // before reftime
4758 if ( dt[i] > dtmax ) {
4759 just_before = i ;
4760 dtmax = dt[i] ;
4761 }
4762 }
4763 else {
4764 // just a reftime
4765 just_before = i ;
4766 just_after = i ;
4767 dtmax = 0 ;
4768 dtmin = 0 ;
4769 break ;
4770 }
4771 }
4772
4773 vector<int> v ;
4774 v.push_back( just_before ) ;
4775 v.push_back( just_after ) ;
4776
4777 return v ;
4778}
4779
4780vector<int> STMath::getRowIdFromTime( double reftime, Vector<Double> &t )
4781{
4782// double reft = reftime ;
4783 double dtmin = 1.0e100 ;
4784 double dtmax = -1.0e100 ;
4785// vector<double> dt ;
4786 int just_before = -1 ;
4787 int just_after = -1 ;
4788 //cout << setprecision(24) << reft << endl ;
4789// ROScalarColumn<Double> timeCol( s->table(), "TIME" ) ;
4790// for ( int i = 0 ; i < s->nrow() ; i++ ) {
4791// cout << setprecision(24) << timeCol(i) << endl ;
4792// //dt.push_back( getMJD( s->getTime( i ) ) - reft ) ;
4793// dt.push_back( timeCol(i) - reft ) ;
4794// }
4795 Vector<Double> dt = t - reftime ;
4796 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4797 if ( dt[i] > 0.0 ) {
4798 // after reftime
4799 if ( dt[i] < dtmin ) {
4800 just_after = i ;
4801 dtmin = dt[i] ;
4802 }
4803 }
4804 else if ( dt[i] < 0.0 ) {
4805 // before reftime
4806 if ( dt[i] > dtmax ) {
4807 just_before = i ;
4808 dtmax = dt[i] ;
4809 }
4810 }
4811 else {
4812 // just a reftime
4813 just_before = i ;
4814 just_after = i ;
4815 dtmax = 0 ;
4816 dtmin = 0 ;
4817 break ;
4818 }
4819 }
4820
4821 vector<int> v(2) ;
4822 v[0] = just_before ;
4823 v[1] = just_after ;
4824
4825 return v ;
4826}
4827
4828vector<float> STMath::getTcalFromTime( string reftime,
4829 CountedPtr<Scantable>& s,
4830 string mode )
4831{
4832 LogIO os( LogOrigin( "STMath", "getTcalFromTime", WHERE ) ) ;
4833 vector<float> tcal ;
4834 STTcal tcalTable = s->tcal() ;
4835 String time ;
4836 Vector<Float> tcalval ;
4837 if ( s->nrow() == 0 ) {
4838 os << LogIO::SEVERE << "No row in the input scantable. Return empty tcal." << LogIO::POST ;
4839 return tcal ;
4840 }
4841 else if ( s->nrow() == 1 ) {
4842 uInt tcalid = s->getTcalId( 0 ) ;
4843 //os << "use row " << 0 << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4844 tcalTable.getEntry( time, tcalval, tcalid ) ;
4845 tcalval.tovector( tcal ) ;
4846 return tcal ;
4847 }
4848 else {
4849 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4850 if ( mode == "before" ) {
4851 int id = -1 ;
4852 if ( idx[0] != -1 ) {
4853 id = idx[0] ;
4854 }
4855 else if ( idx[1] != -1 ) {
4856 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4857 id = idx[1] ;
4858 }
4859 uInt tcalid = s->getTcalId( id ) ;
4860 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4861 tcalTable.getEntry( time, tcalval, tcalid ) ;
4862 tcalval.tovector( tcal ) ;
4863 }
4864 else if ( mode == "after" ) {
4865 int id = -1 ;
4866 if ( idx[1] != -1 ) {
4867 id = idx[1] ;
4868 }
4869 else if ( idx[0] != -1 ) {
4870 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4871 id = idx[1] ;
4872 }
4873 uInt tcalid = s->getTcalId( id ) ;
4874 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4875 tcalTable.getEntry( time, tcalval, tcalid ) ;
4876 tcalval.tovector( tcal ) ;
4877 }
4878 else if ( mode == "nearest" ) {
4879 int id = -1 ;
4880 if ( idx[0] == -1 ) {
4881 id = idx[1] ;
4882 }
4883 else if ( idx[1] == -1 ) {
4884 id = idx[0] ;
4885 }
4886 else if ( idx[0] == idx[1] ) {
4887 id = idx[0] ;
4888 }
4889 else {
4890 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4891 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4892 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4893 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4894 double tref = getMJD( reftime ) ;
4895 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4896 id = idx[1] ;
4897 }
4898 else {
4899 id = idx[0] ;
4900 }
4901 }
4902 uInt tcalid = s->getTcalId( id ) ;
4903 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4904 tcalTable.getEntry( time, tcalval, tcalid ) ;
4905 tcalval.tovector( tcal ) ;
4906 }
4907 else if ( mode == "linear" ) {
4908 if ( idx[0] == -1 ) {
4909 // use after
4910 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4911 int id = idx[1] ;
4912 uInt tcalid = s->getTcalId( id ) ;
4913 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4914 tcalTable.getEntry( time, tcalval, tcalid ) ;
4915 tcalval.tovector( tcal ) ;
4916 }
4917 else if ( idx[1] == -1 ) {
4918 // use before
4919 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4920 int id = idx[0] ;
4921 uInt tcalid = s->getTcalId( id ) ;
4922 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4923 tcalTable.getEntry( time, tcalval, tcalid ) ;
4924 tcalval.tovector( tcal ) ;
4925 }
4926 else if ( idx[0] == idx[1] ) {
4927 // use before
4928 //os << "No need to interporate." << LogIO::POST ;
4929 int id = idx[0] ;
4930 uInt tcalid = s->getTcalId( id ) ;
4931 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4932 tcalTable.getEntry( time, tcalval, tcalid ) ;
4933 tcalval.tovector( tcal ) ;
4934 }
4935 else {
4936 // do interpolation
4937 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4938 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4939 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4940 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4941 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4942 double tref = getMJD( reftime ) ;
4943 vector<float> tcal0 ;
4944 vector<float> tcal1 ;
4945 uInt tcalid0 = s->getTcalId( idx[0] ) ;
4946 uInt tcalid1 = s->getTcalId( idx[1] ) ;
4947 tcalTable.getEntry( time, tcalval, tcalid0 ) ;
4948 tcalval.tovector( tcal0 ) ;
4949 tcalTable.getEntry( time, tcalval, tcalid1 ) ;
4950 tcalval.tovector( tcal1 ) ;
4951 for ( unsigned int i = 0 ; i < tcal0.size() ; i++ ) {
4952 float v = ( tcal1[i] - tcal0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tcal0[i] ;
4953 tcal.push_back( v ) ;
4954 }
4955 }
4956 }
4957 else {
4958 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4959 }
4960 return tcal ;
4961 }
4962}
4963
4964vector<float> STMath::getTsysFromTime( string reftime,
4965 CountedPtr<Scantable>& s,
4966 string mode )
4967{
4968 LogIO os( LogOrigin( "STMath", "getTsysFromTime", WHERE ) ) ;
4969 ArrayColumn<Float> tsysCol ;
4970 tsysCol.attach( s->table(), "TSYS" ) ;
4971 vector<float> tsys ;
4972 String time ;
4973 Vector<Float> tsysval ;
4974 if ( s->nrow() == 0 ) {
4975 os << LogIO::SEVERE << "No row in the input scantable. Return empty tsys." << LogIO::POST ;
4976 return tsys ;
4977 }
4978 else if ( s->nrow() == 1 ) {
4979 //os << "use row " << 0 << LogIO::POST ;
4980 tsysval = tsysCol( 0 ) ;
4981 tsysval.tovector( tsys ) ;
4982 return tsys ;
4983 }
4984 else {
4985 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4986 if ( mode == "before" ) {
4987 int id = -1 ;
4988 if ( idx[0] != -1 ) {
4989 id = idx[0] ;
4990 }
4991 else if ( idx[1] != -1 ) {
4992 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4993 id = idx[1] ;
4994 }
4995 //os << "use row " << id << LogIO::POST ;
4996 tsysval = tsysCol( id ) ;
4997 tsysval.tovector( tsys ) ;
4998 }
4999 else if ( mode == "after" ) {
5000 int id = -1 ;
5001 if ( idx[1] != -1 ) {
5002 id = idx[1] ;
5003 }
5004 else if ( idx[0] != -1 ) {
5005 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
5006 id = idx[1] ;
5007 }
5008 //os << "use row " << id << LogIO::POST ;
5009 tsysval = tsysCol( id ) ;
5010 tsysval.tovector( tsys ) ;
5011 }
5012 else if ( mode == "nearest" ) {
5013 int id = -1 ;
5014 if ( idx[0] == -1 ) {
5015 id = idx[1] ;
5016 }
5017 else if ( idx[1] == -1 ) {
5018 id = idx[0] ;
5019 }
5020 else if ( idx[0] == idx[1] ) {
5021 id = idx[0] ;
5022 }
5023 else {
5024 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
5025 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
5026 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
5027 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
5028 double tref = getMJD( reftime ) ;
5029 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
5030 id = idx[1] ;
5031 }
5032 else {
5033 id = idx[0] ;
5034 }
5035 }
5036 //os << "use row " << id << LogIO::POST ;
5037 tsysval = tsysCol( id ) ;
5038 tsysval.tovector( tsys ) ;
5039 }
5040 else if ( mode == "linear" ) {
5041 if ( idx[0] == -1 ) {
5042 // use after
5043 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
5044 int id = idx[1] ;
5045 //os << "use row " << id << LogIO::POST ;
5046 tsysval = tsysCol( id ) ;
5047 tsysval.tovector( tsys ) ;
5048 }
5049 else if ( idx[1] == -1 ) {
5050 // use before
5051 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
5052 int id = idx[0] ;
5053 //os << "use row " << id << LogIO::POST ;
5054 tsysval = tsysCol( id ) ;
5055 tsysval.tovector( tsys ) ;
5056 }
5057 else if ( idx[0] == idx[1] ) {
5058 // use before
5059 //os << "No need to interporate." << LogIO::POST ;
5060 int id = idx[0] ;
5061 //os << "use row " << id << LogIO::POST ;
5062 tsysval = tsysCol( id ) ;
5063 tsysval.tovector( tsys ) ;
5064 }
5065 else {
5066 // do interpolation
5067 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
5068 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
5069 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
5070 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
5071 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
5072 double tref = getMJD( reftime ) ;
5073 vector<float> tsys0 ;
5074 vector<float> tsys1 ;
5075 tsysval = tsysCol( idx[0] ) ;
5076 tsysval.tovector( tsys0 ) ;
5077 tsysval = tsysCol( idx[1] ) ;
5078 tsysval.tovector( tsys1 ) ;
5079 for ( unsigned int i = 0 ; i < tsys0.size() ; i++ ) {
5080 float v = ( tsys1[i] - tsys0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tsys0[i] ;
5081 tsys.push_back( v ) ;
5082 }
5083 }
5084 }
5085 else {
5086 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
5087 }
5088 return tsys ;
5089 }
5090}
5091
5092vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
5093 CountedPtr<Scantable>& off,
5094 CountedPtr<Scantable>& sky,
5095 CountedPtr<Scantable>& hot,
5096 CountedPtr<Scantable>& cold,
5097 int index,
5098 string antname )
5099{
5100 (void) cold; //currently unused
5101 string reftime = on->getTime( index ) ;
5102 vector<int> ii( 1, on->getIF( index ) ) ;
5103 vector<int> ib( 1, on->getBeam( index ) ) ;
5104 vector<int> ip( 1, on->getPol( index ) ) ;
5105 STSelector sel = STSelector() ;
5106 sel.setIFs( ii ) ;
5107 sel.setBeams( ib ) ;
5108 sel.setPolarizations( ip ) ;
5109 sky->setSelection( sel ) ;
5110 hot->setSelection( sel ) ;
5111 //cold->setSelection( sel ) ;
5112 off->setSelection( sel ) ;
5113 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
5114 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
5115 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
5116 vector<float> spoff = getSpectrumFromTime( reftime, off, "linear" ) ;
5117 vector<float> spec = on->getSpectrum( index ) ;
5118 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
5119 vector<float> sp( tcal.size() ) ;
5120 if ( antname.find( "APEX" ) != string::npos ) {
5121 // using gain array
5122 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
5123 float v = ( ( spec[j] - spoff[j] ) / spoff[j] )
5124 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
5125 sp[j] = v ;
5126 }
5127 }
5128 else {
5129 // Chopper-Wheel calibration (Ulich & Haas 1976)
5130 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
5131 float v = ( spec[j] - spoff[j] ) / ( sphot[j] - spsky[j] ) * tcal[j] ;
5132 sp[j] = v ;
5133 }
5134 }
5135 sel.reset() ;
5136 sky->unsetSelection() ;
5137 hot->unsetSelection() ;
5138 //cold->unsetSelection() ;
5139 off->unsetSelection() ;
5140
5141 return sp ;
5142}
5143
5144vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
5145 CountedPtr<Scantable>& off,
5146 int index )
5147{
5148// string reftime = on->getTime( index ) ;
5149 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
5150 Vector<Double> timeVec = timeCol.getColumn() ;
5151 //ROTableColumn timeCol( on->table(), "TIME" ) ;
5152 timeCol.attach( on->table(), "TIME" ) ;
5153 double reftime = timeCol.asdouble(index) ;
5154 vector<int> ii( 1, on->getIF( index ) ) ;
5155 vector<int> ib( 1, on->getBeam( index ) ) ;
5156 vector<int> ip( 1, on->getPol( index ) ) ;
5157 STSelector sel = STSelector() ;
5158 sel.setIFs( ii ) ;
5159 sel.setBeams( ib ) ;
5160 sel.setPolarizations( ip ) ;
5161 off->setSelection( sel ) ;
5162 vector<float> spoff = getSpectrumFromTime( reftime, timeVec, off, "linear" ) ;
5163 vector<float> spec = on->getSpectrum( index ) ;
5164 //vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
5165 //vector<float> tsys = on->getTsysVec( index ) ;
5166 ArrayColumn<Float> tsysCol( on->table(), "TSYS" ) ;
5167 Vector<Float> tsys = tsysCol( index ) ;
5168 vector<float> sp( spec.size() ) ;
5169 // ALMA Calibration
5170 //
5171 // Ta* = Tsys * ( ON - OFF ) / OFF
5172 //
5173 // 2010/01/07 Takeshi Nakazato
5174 unsigned int tsyssize = tsys.nelements() ;
5175 unsigned int spsize = sp.size() ;
5176 for ( unsigned int j = 0 ; j < sp.size() ; j++ ) {
5177 float tscale = 0.0 ;
5178 if ( tsyssize == spsize )
5179 tscale = tsys[j] ;
5180 else
5181 tscale = tsys[0] ;
5182 float v = tscale * ( spec[j] - spoff[j] ) / spoff[j] ;
5183 sp[j] = v ;
5184 }
5185 sel.reset() ;
5186 off->unsetSelection() ;
5187
5188 return sp ;
5189}
5190
5191void STMath::calibrateALMA( CountedPtr<Scantable>& on,
5192 CountedPtr<Scantable>& off )
5193{
5194 if ( on->nrow() == 0 )
5195 return ;
5196 // string reftime = on->getTime( index ) ;
5197 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
5198 Vector<Double> timeVec = timeCol.getColumn() ;
5199 //ROTableColumn timeCol( on->table(), "TIME" ) ;
5200 timeCol.attach( on->table(), "TIME" ) ;
5201 ArrayColumn<Float> tsysCol( on->table(), "TSYS" ) ;
5202 vector<float> sp( on->nchan( on->getIF(0) ) ) ;
5203 unsigned int spsize = sp.size() ;
5204 for ( int index = 0 ; index < on->nrow() ; index++ ) {
5205 double reftime = timeCol.asdouble(index) ;
5206 vector<float> spoff = getSpectrumFromTime( reftime, timeVec, off, "linear" ) ;
5207 vector<float> spec = on->getSpectrum( index ) ;
5208 Vector<Float> tsys = tsysCol( index ) ;
5209 // ALMA Calibration
5210 //
5211 // Ta* = Tsys * ( ON - OFF ) / OFF
5212 //
5213 // 2010/01/07 Takeshi Nakazato
5214 unsigned int tsyssize = tsys.nelements() ;
5215 for ( unsigned int j = 0 ; j < sp.size() ; j++ ) {
5216 float tscale = 0.0 ;
5217 if ( tsyssize == spsize )
5218 tscale = tsys[j] ;
5219 else
5220 tscale = tsys[0] ;
5221 float v = tscale * ( spec[j] - spoff[j] ) / spoff[j] ;
5222 sp[j] = v ;
5223 }
5224 on->setSpectrum( sp, index ) ;
5225 }
5226}
5227
5228void STMath::calibrateALMA( CountedPtr<Scantable>& on,
5229 CountedPtr<Scantable>& off,
5230 Vector<uInt>& rows )
5231{
5232 // if rows is empty, just return
5233 if ( rows.nelements() == 0 )
5234 return ;
5235// string reftime = on->getTime( index ) ;
5236 ROScalarColumn<Double> timeCol( off->table(), "TIME" ) ;
5237 Vector<Double> timeVec = timeCol.getColumn() ;
5238 //ROTableColumn timeCol( on->table(), "TIME" ) ;
5239 timeCol.attach( on->table(), "TIME" ) ;
5240 ArrayColumn<Float> tsysCol( on->table(), "TSYS" ) ;
5241 vector<float> sp( on->nchan( on->getIF(rows[0]) ) ) ;
5242 unsigned int spsize = sp.size() ;
5243 // I know that the data is contiguous
5244 const uInt *p = rows.data() ;
5245 for ( int irow = 0 ; irow < rows.nelements() ; irow++ ) {
5246 //int index = rows[irow] ;
5247 //double reftime = timeCol.asdouble(index) ;
5248 double reftime = timeCol.asdouble(*p) ;
5249 vector<float> spoff = getSpectrumFromTime( reftime, timeVec, off, "linear" ) ;
5250 //vector<float> spec = on->getSpectrum( index ) ;
5251 //Vector<Float> tsys = tsysCol( index ) ;
5252 vector<float> spec = on->getSpectrum( *p ) ;
5253 Vector<Float> tsys = tsysCol( *p ) ;
5254 // ALMA Calibration
5255 //
5256 // Ta* = Tsys * ( ON - OFF ) / OFF
5257 //
5258 // 2010/01/07 Takeshi Nakazato
5259 unsigned int tsyssize = tsys.nelements() ;
5260 for ( unsigned int j = 0 ; j < sp.size() ; j++ ) {
5261 float tscale = 0.0 ;
5262 if ( tsyssize == spsize )
5263 tscale = tsys[j] ;
5264 else
5265 tscale = tsys[0] ;
5266 float v = tscale * ( spec[j] - spoff[j] ) / spoff[j] ;
5267 sp[j] = v ;
5268 }
5269 //on->setSpectrum( sp, index ) ;
5270 on->setSpectrum( sp, *p ) ;
5271 p++ ;
5272 }
5273}
5274
5275vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
5276 CountedPtr<Scantable>& ref,
5277 CountedPtr<Scantable>& sky,
5278 CountedPtr<Scantable>& hot,
5279 CountedPtr<Scantable>& cold,
5280 int index )
5281{
5282 (void) cold; //currently unused
5283 string reftime = sig->getTime( index ) ;
5284 vector<int> ii( 1, sig->getIF( index ) ) ;
5285 vector<int> ib( 1, sig->getBeam( index ) ) ;
5286 vector<int> ip( 1, sig->getPol( index ) ) ;
5287 vector<int> ic( 1, sig->getScan( index ) ) ;
5288 STSelector sel = STSelector() ;
5289 sel.setIFs( ii ) ;
5290 sel.setBeams( ib ) ;
5291 sel.setPolarizations( ip ) ;
5292 sky->setSelection( sel ) ;
5293 hot->setSelection( sel ) ;
5294 //cold->setSelection( sel ) ;
5295 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
5296 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
5297 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
5298 vector<float> spref = ref->getSpectrum( index ) ;
5299 vector<float> spsig = sig->getSpectrum( index ) ;
5300 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
5301 vector<float> sp( tcal.size() ) ;
5302 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
5303 float v = tcal[j] * spsky[j] / ( sphot[j] - spsky[j] ) * ( spsig[j] - spref[j] ) / spref[j] ;
5304 sp[j] = v ;
5305 }
5306 sel.reset() ;
5307 sky->unsetSelection() ;
5308 hot->unsetSelection() ;
5309 //cold->unsetSelection() ;
5310
5311 return sp ;
5312}
5313
5314vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
5315 CountedPtr<Scantable>& ref,
5316 vector< CountedPtr<Scantable> >& sky,
5317 vector< CountedPtr<Scantable> >& hot,
5318 vector< CountedPtr<Scantable> >& cold,
5319 int index )
5320{
5321 (void) cold; //currently unused
5322 string reftime = sig->getTime( index ) ;
5323 vector<int> ii( 1, sig->getIF( index ) ) ;
5324 vector<int> ib( 1, sig->getBeam( index ) ) ;
5325 vector<int> ip( 1, sig->getPol( index ) ) ;
5326 vector<int> ic( 1, sig->getScan( index ) ) ;
5327 STSelector sel = STSelector() ;
5328 sel.setIFs( ii ) ;
5329 sel.setBeams( ib ) ;
5330 sel.setPolarizations( ip ) ;
5331 sky[0]->setSelection( sel ) ;
5332 hot[0]->setSelection( sel ) ;
5333 //cold[0]->setSelection( sel ) ;
5334 vector<float> spskys = getSpectrumFromTime( reftime, sky[0], "linear" ) ;
5335 vector<float> sphots = getSpectrumFromTime( reftime, hot[0], "linear" ) ;
5336 //vector<float> spcolds = getSpectrumFromTime( reftime, cold[0], "linear" ) ;
5337 vector<float> tcals = getTcalFromTime( reftime, sky[0], "linear" ) ;
5338 sel.reset() ;
5339 ii[0] = ref->getIF( index ) ;
5340 sel.setIFs( ii ) ;
5341 sel.setBeams( ib ) ;
5342 sel.setPolarizations( ip ) ;
5343 sky[1]->setSelection( sel ) ;
5344 hot[1]->setSelection( sel ) ;
5345 //cold[1]->setSelection( sel ) ;
5346 vector<float> spskyr = getSpectrumFromTime( reftime, sky[1], "linear" ) ;
5347 vector<float> sphotr = getSpectrumFromTime( reftime, hot[1], "linear" ) ;
5348 //vector<float> spcoldr = getSpectrumFromTime( reftime, cold[1], "linear" ) ;
5349 vector<float> tcalr = getTcalFromTime( reftime, sky[1], "linear" ) ;
5350 vector<float> spref = ref->getSpectrum( index ) ;
5351 vector<float> spsig = sig->getSpectrum( index ) ;
5352 vector<float> sp( tcals.size() ) ;
5353 for ( unsigned int j = 0 ; j < tcals.size() ; j++ ) {
5354 float v = tcals[j] * spsig[j] / ( sphots[j] - spskys[j] ) - tcalr[j] * spref[j] / ( sphotr[j] - spskyr[j] ) ;
5355 sp[j] = v ;
5356 }
5357 sel.reset() ;
5358 sky[0]->unsetSelection() ;
5359 hot[0]->unsetSelection() ;
5360 //cold[0]->unsetSelection() ;
5361 sky[1]->unsetSelection() ;
5362 hot[1]->unsetSelection() ;
5363 //cold[1]->unsetSelection() ;
5364
5365 return sp ;
5366}
5367
5368void STMath::copyRows( Table &out,
5369 const Table &in,
5370 uInt startout,
5371 uInt startin,
5372 uInt nrow,
5373 Bool copySpectra,
5374 Bool copyFlagtra,
5375 Bool copyTsys )
5376{
5377 uInt nexclude = 0 ;
5378 Block<String> excludeColsBlock( 3 ) ;
5379 if ( !copySpectra ) {
5380 excludeColsBlock[nexclude] = "SPECTRA" ;
5381 nexclude++ ;
5382 }
5383 if ( !copyFlagtra ) {
5384 excludeColsBlock[nexclude] = "FLAGTRA" ;
5385 nexclude++ ;
5386 }
5387 if ( !copyTsys ) {
5388 excludeColsBlock[nexclude] = "TSYS" ;
5389 nexclude++ ;
5390 }
5391 // if ( nexclude < 3 ) {
5392 // excludeCols.resize( nexclude, True ) ;
5393 // }
5394 Vector<String> excludeCols( IPosition(1,nexclude),
5395 excludeColsBlock.storage(),
5396 SHARE ) ;
5397// cout << "excludeCols=" << excludeCols << endl ;
5398 TableRow rowout( out, excludeCols, True ) ;
5399 ROTableRow rowin( in, excludeCols, True ) ;
5400 uInt rin = startin ;
5401 uInt rout = startout ;
5402 for ( uInt i = 0 ; i < nrow ; i++ ) {
5403 rowin.get( rin ) ;
5404 rowout.putMatchingFields( rout, rowin.record() ) ;
5405 rin++ ;
5406 rout++ ;
5407 }
5408}
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