source: branches/alma/src/STMath.cpp@ 1734

Last change on this file since 1734 was 1719, checked in by Takeshi Nakazato, 15 years ago

New Development: No

JIRA Issue: Yes CAS-1809

Ready to Release: For 3.0.2

Interface Changes: No

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Module(s): Module Names change impacts.

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1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <casa/iomanip.h>
14#include <casa/Exceptions/Error.h>
15#include <casa/Containers/Block.h>
16#include <casa/BasicSL/String.h>
17#include <casa/Arrays/MaskArrLogi.h>
18#include <casa/Arrays/MaskArrMath.h>
19#include <casa/Arrays/ArrayLogical.h>
20#include <casa/Arrays/ArrayMath.h>
21#include <casa/Arrays/Slice.h>
22#include <casa/Arrays/Slicer.h>
23#include <casa/Containers/RecordField.h>
24#include <tables/Tables/TableRow.h>
25#include <tables/Tables/TableVector.h>
26#include <tables/Tables/TabVecMath.h>
27#include <tables/Tables/ExprNode.h>
28#include <tables/Tables/TableRecord.h>
29#include <tables/Tables/TableParse.h>
30#include <tables/Tables/ReadAsciiTable.h>
31#include <tables/Tables/TableIter.h>
32#include <tables/Tables/TableCopy.h>
33#include <scimath/Mathematics/FFTServer.h>
34
35#include <lattices/Lattices/LatticeUtilities.h>
36
37#include <coordinates/Coordinates/SpectralCoordinate.h>
38#include <coordinates/Coordinates/CoordinateSystem.h>
39#include <coordinates/Coordinates/CoordinateUtil.h>
40#include <coordinates/Coordinates/FrequencyAligner.h>
41
42#include <scimath/Mathematics/VectorKernel.h>
43#include <scimath/Mathematics/Convolver.h>
44#include <scimath/Functionals/Polynomial.h>
45
46#include <atnf/PKSIO/SrcType.h>
47
48#include <casa/Logging/LogIO.h>
49#include <sstream>
50
51#include "MathUtils.h"
52#include "RowAccumulator.h"
53#include "STAttr.h"
54#include "STMath.h"
55#include "STSelector.h"
56
57using namespace casa;
58
59using namespace asap;
60
61// tolerance for direction comparison (rad)
62#define TOL_OTF 1.0e-15
63#define TOL_POINT 2.9088821e-4 // 1 arcmin
64
65STMath::STMath(bool insitu) :
66 insitu_(insitu)
67{
68}
69
70
71STMath::~STMath()
72{
73}
74
75CountedPtr<Scantable>
76STMath::average( const std::vector<CountedPtr<Scantable> >& in,
77 const std::vector<bool>& mask,
78 const std::string& weight,
79 const std::string& avmode)
80{
81 LogIO os( LogOrigin( "STMath", "average()", WHERE ) ) ;
82 if ( avmode == "SCAN" && in.size() != 1 )
83 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
84 "Use merge first."));
85 WeightType wtype = stringToWeight(weight);
86
87 // check if OTF observation
88 String obstype = in[0]->getHeader().obstype ;
89 Double tol = 0.0 ;
90 if ( (obstype.find( "OTF" ) != String::npos) || (obstype.find( "OBSERVE_TARGET" ) != String::npos) ) {
91 tol = TOL_OTF ;
92 }
93 else {
94 tol = TOL_POINT ;
95 }
96
97 // output
98 // clone as this is non insitu
99 bool insitu = insitu_;
100 setInsitu(false);
101 CountedPtr< Scantable > out = getScantable(in[0], true);
102 setInsitu(insitu);
103 std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
104 ++stit;
105 while ( stit != in.end() ) {
106 out->appendToHistoryTable((*stit)->history());
107 ++stit;
108 }
109
110 Table& tout = out->table();
111
112 /// @todo check if all scantables are conformant
113
114 ArrayColumn<Float> specColOut(tout,"SPECTRA");
115 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
116 ArrayColumn<Float> tsysColOut(tout,"TSYS");
117 ScalarColumn<Double> mjdColOut(tout,"TIME");
118 ScalarColumn<Double> intColOut(tout,"INTERVAL");
119 ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
120 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
121
122 // set up the output table rows. These are based on the structure of the
123 // FIRST scantable in the vector
124 const Table& baset = in[0]->table();
125
126 Block<String> cols(3);
127 cols[0] = String("BEAMNO");
128 cols[1] = String("IFNO");
129 cols[2] = String("POLNO");
130 if ( avmode == "SOURCE" ) {
131 cols.resize(4);
132 cols[3] = String("SRCNAME");
133 }
134 if ( avmode == "SCAN" && in.size() == 1) {
135 //cols.resize(4);
136 //cols[3] = String("SCANNO");
137 cols.resize(5);
138 cols[3] = String("SRCNAME");
139 cols[4] = String("SCANNO");
140 }
141 uInt outrowCount = 0;
142 TableIterator iter(baset, cols);
143// int count = 0 ;
144 while (!iter.pastEnd()) {
145 Table subt = iter.table();
146// // copy the first row of this selection into the new table
147// tout.addRow();
148// TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
149// // re-index to 0
150// if ( avmode != "SCAN" && avmode != "SOURCE" ) {
151// scanColOut.put(outrowCount, uInt(0));
152// }
153// ++outrowCount;
154 MDirection::ScalarColumn dircol ;
155 dircol.attach( subt, "DIRECTION" ) ;
156 Int length = subt.nrow() ;
157 vector< Vector<Double> > dirs ;
158 vector<int> indexes ;
159 for ( Int i = 0 ; i < length ; i++ ) {
160 Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
161 //os << << count++ << ": " ;
162 //os << "[" << t[0] << "," << t[1] << "]" << LogIO::POST ;
163 bool adddir = true ;
164 for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
165 //if ( allTrue( t == dirs[j] ) ) {
166 Double dx = t[0] - dirs[j][0] ;
167 Double dy = t[1] - dirs[j][1] ;
168 Double dd = sqrt( dx * dx + dy * dy ) ;
169 //if ( allNearAbs( t, dirs[j], tol ) ) {
170 if ( dd <= tol ) {
171 adddir = false ;
172 break ;
173 }
174 }
175 if ( adddir ) {
176 dirs.push_back( t ) ;
177 indexes.push_back( i ) ;
178 }
179 }
180 uInt rowNum = dirs.size() ;
181 tout.addRow( rowNum ) ;
182 for ( uInt i = 0 ; i < rowNum ; i++ ) {
183 TableCopy::copyRows( tout, subt, outrowCount+i, indexes[i], 1 ) ;
184 // re-index to 0
185 if ( avmode != "SCAN" && avmode != "SOURCE" ) {
186 scanColOut.put(outrowCount+i, uInt(0));
187 }
188 }
189 outrowCount += rowNum ;
190 ++iter;
191 }
192 RowAccumulator acc(wtype);
193 Vector<Bool> cmask(mask);
194 acc.setUserMask(cmask);
195 ROTableRow row(tout);
196 ROArrayColumn<Float> specCol, tsysCol;
197 ROArrayColumn<uChar> flagCol;
198 ROScalarColumn<Double> mjdCol, intCol;
199 ROScalarColumn<Int> scanIDCol;
200
201 Vector<uInt> rowstodelete;
202
203 for (uInt i=0; i < tout.nrow(); ++i) {
204 for ( int j=0; j < int(in.size()); ++j ) {
205 const Table& tin = in[j]->table();
206 const TableRecord& rec = row.get(i);
207 ROScalarColumn<Double> tmp(tin, "TIME");
208 Double td;tmp.get(0,td);
209 Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
210 && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
211 && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
212 Table subt;
213 if ( avmode == "SOURCE") {
214 subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
215 } else if (avmode == "SCAN") {
216 //subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
217 subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO"))
218 && basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
219 } else {
220 subt = basesubt;
221 }
222
223 vector<uInt> removeRows ;
224 uInt nrsubt = subt.nrow() ;
225 for ( uInt irow = 0 ; irow < nrsubt ; irow++ ) {
226 //if ( !allTrue((subt.col("DIRECTION").getArrayDouble(TableExprId(irow)))==rec.asArrayDouble("DIRECTION")) ) {
227 Vector<Double> x0 = (subt.col("DIRECTION").getArrayDouble(TableExprId(irow))) ;
228 Vector<Double> x1 = rec.asArrayDouble("DIRECTION") ;
229 double dx = x0[0] - x1[0] ;
230 double dy = x0[0] - x1[0] ;
231 Double dd = sqrt( dx * dx + dy * dy ) ;
232 //if ( !allNearAbs((subt.col("DIRECTION").getArrayDouble(TableExprId(irow))), rec.asArrayDouble("DIRECTION"), tol ) ) {
233 if ( dd > tol ) {
234 removeRows.push_back( irow ) ;
235 }
236 }
237 if ( removeRows.size() != 0 ) {
238 subt.removeRow( removeRows ) ;
239 }
240
241 if ( nrsubt == removeRows.size() )
242 throw(AipsError("Averaging data is empty.")) ;
243
244 specCol.attach(subt,"SPECTRA");
245 flagCol.attach(subt,"FLAGTRA");
246 tsysCol.attach(subt,"TSYS");
247 intCol.attach(subt,"INTERVAL");
248 mjdCol.attach(subt,"TIME");
249 Vector<Float> spec,tsys;
250 Vector<uChar> flag;
251 Double inter,time;
252 for (uInt k = 0; k < subt.nrow(); ++k ) {
253 flagCol.get(k, flag);
254 Vector<Bool> bflag(flag.shape());
255 convertArray(bflag, flag);
256 /*
257 if ( allEQ(bflag, True) ) {
258 continue;//don't accumulate
259 }
260 */
261 specCol.get(k, spec);
262 tsysCol.get(k, tsys);
263 intCol.get(k, inter);
264 mjdCol.get(k, time);
265 // spectrum has to be added last to enable weighting by the other values
266 acc.add(spec, !bflag, tsys, inter, time);
267 }
268 }
269 const Vector<Bool>& msk = acc.getMask();
270 if ( allEQ(msk, False) ) {
271 uint n = rowstodelete.nelements();
272 rowstodelete.resize(n+1, True);
273 rowstodelete[n] = i;
274 continue;
275 }
276 //write out
277 if (acc.state()) {
278 Vector<uChar> flg(msk.shape());
279 convertArray(flg, !msk);
280 flagColOut.put(i, flg);
281 specColOut.put(i, acc.getSpectrum());
282 tsysColOut.put(i, acc.getTsys());
283 intColOut.put(i, acc.getInterval());
284 mjdColOut.put(i, acc.getTime());
285 // we should only have one cycle now -> reset it to be 0
286 // frequency switched data has different CYCLENO for different IFNO
287 // which requires resetting this value
288 cycColOut.put(i, uInt(0));
289 } else {
290 ostringstream oss;
291 oss << "For output row="<<i<<", all input rows of data are flagged. no averaging" << endl;
292 pushLog(String(oss));
293 }
294 acc.reset();
295 }
296 if (rowstodelete.nelements() > 0) {
297 //cout << rowstodelete << endl;
298 os << rowstodelete << LogIO::POST ;
299 tout.removeRow(rowstodelete);
300 if (tout.nrow() == 0) {
301 throw(AipsError("Can't average fully flagged data."));
302 }
303 }
304 return out;
305}
306
307CountedPtr< Scantable >
308 STMath::averageChannel( const CountedPtr < Scantable > & in,
309 const std::string & mode,
310 const std::string& avmode )
311{
312 // check if OTF observation
313 String obstype = in->getHeader().obstype ;
314 Double tol = 0.0 ;
315 if ( obstype.find( "OTF" ) != String::npos ) {
316 tol = TOL_OTF ;
317 }
318 else {
319 tol = TOL_POINT ;
320 }
321
322 // clone as this is non insitu
323 bool insitu = insitu_;
324 setInsitu(false);
325 CountedPtr< Scantable > out = getScantable(in, true);
326 setInsitu(insitu);
327 Table& tout = out->table();
328 ArrayColumn<Float> specColOut(tout,"SPECTRA");
329 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
330 ArrayColumn<Float> tsysColOut(tout,"TSYS");
331 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
332 ScalarColumn<Double> intColOut(tout, "INTERVAL");
333 Table tmp = in->table().sort("BEAMNO");
334 Block<String> cols(3);
335 cols[0] = String("BEAMNO");
336 cols[1] = String("IFNO");
337 cols[2] = String("POLNO");
338 if ( avmode == "SCAN") {
339 cols.resize(4);
340 cols[3] = String("SCANNO");
341 }
342 uInt outrowCount = 0;
343 uChar userflag = 1 << 7;
344 TableIterator iter(tmp, cols);
345 while (!iter.pastEnd()) {
346 Table subt = iter.table();
347 ROArrayColumn<Float> specCol, tsysCol;
348 ROArrayColumn<uChar> flagCol;
349 ROScalarColumn<Double> intCol(subt, "INTERVAL");
350 specCol.attach(subt,"SPECTRA");
351 flagCol.attach(subt,"FLAGTRA");
352 tsysCol.attach(subt,"TSYS");
353// tout.addRow();
354// TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
355// if ( avmode != "SCAN") {
356// scanColOut.put(outrowCount, uInt(0));
357// }
358// Vector<Float> tmp;
359// specCol.get(0, tmp);
360// uInt nchan = tmp.nelements();
361// // have to do channel by channel here as MaskedArrMath
362// // doesn't have partialMedians
363// Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
364// Vector<Float> outspec(nchan);
365// Vector<uChar> outflag(nchan,0);
366// Vector<Float> outtsys(1);/// @fixme when tsys is channel based
367// for (uInt i=0; i<nchan; ++i) {
368// Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
369// MaskedArray<Float> ma = maskedArray(specs,flags);
370// outspec[i] = median(ma);
371// if ( allEQ(ma.getMask(), False) )
372// outflag[i] = userflag;// flag data
373// }
374// outtsys[0] = median(tsysCol.getColumn());
375// specColOut.put(outrowCount, outspec);
376// flagColOut.put(outrowCount, outflag);
377// tsysColOut.put(outrowCount, outtsys);
378// Double intsum = sum(intCol.getColumn());
379// intColOut.put(outrowCount, intsum);
380// ++outrowCount;
381// ++iter;
382 MDirection::ScalarColumn dircol ;
383 dircol.attach( subt, "DIRECTION" ) ;
384 Int length = subt.nrow() ;
385 vector< Vector<Double> > dirs ;
386 vector<int> indexes ;
387 for ( Int i = 0 ; i < length ; i++ ) {
388 Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
389 bool adddir = true ;
390 for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
391 //if ( allTrue( t == dirs[j] ) ) {
392 Double dx = t[0] - dirs[j][0] ;
393 Double dy = t[1] - dirs[j][1] ;
394 Double dd = sqrt( dx * dx + dy * dy ) ;
395 //if ( allNearAbs( t, dirs[j], tol ) ) {
396 if ( dd <= tol ) {
397 adddir = false ;
398 break ;
399 }
400 }
401 if ( adddir ) {
402 dirs.push_back( t ) ;
403 indexes.push_back( i ) ;
404 }
405 }
406 uInt rowNum = dirs.size() ;
407 tout.addRow( rowNum );
408 for ( uInt i = 0 ; i < rowNum ; i++ ) {
409 TableCopy::copyRows(tout, subt, outrowCount+i, indexes[i], 1) ;
410 if ( avmode != "SCAN") {
411 //scanColOut.put(outrowCount+i, uInt(0));
412 }
413 }
414 MDirection::ScalarColumn dircolOut ;
415 dircolOut.attach( tout, "DIRECTION" ) ;
416 for ( uInt irow = 0 ; irow < rowNum ; irow++ ) {
417 Vector<Double> t = dircolOut(outrowCount+irow).getAngle(Unit(String("rad"))).getValue() ;
418 Vector<Float> tmp;
419 specCol.get(0, tmp);
420 uInt nchan = tmp.nelements();
421 // have to do channel by channel here as MaskedArrMath
422 // doesn't have partialMedians
423 Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
424 // mask spectra for different DIRECTION
425 for ( uInt jrow = 0 ; jrow < subt.nrow() ; jrow++ ) {
426 Vector<Double> direction = dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
427 //if ( t[0] != direction[0] || t[1] != direction[1] ) {
428 Double dx = t[0] - direction[0] ;
429 Double dy = t[1] - direction[1] ;
430 Double dd = sqrt( dx * dx + dy * dy ) ;
431 //if ( !allNearAbs( t, direction, tol ) ) {
432 if ( dd > tol ) {
433 flags[jrow] = userflag ;
434 }
435 }
436 Vector<Float> outspec(nchan);
437 Vector<uChar> outflag(nchan,0);
438 Vector<Float> outtsys(1);/// @fixme when tsys is channel based
439 for (uInt i=0; i<nchan; ++i) {
440 Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
441 MaskedArray<Float> ma = maskedArray(specs,flags);
442 outspec[i] = median(ma);
443 if ( allEQ(ma.getMask(), False) )
444 outflag[i] = userflag;// flag data
445 }
446 outtsys[0] = median(tsysCol.getColumn());
447 specColOut.put(outrowCount+irow, outspec);
448 flagColOut.put(outrowCount+irow, outflag);
449 tsysColOut.put(outrowCount+irow, outtsys);
450 Vector<Double> integ = intCol.getColumn() ;
451 MaskedArray<Double> mi = maskedArray( integ, flags ) ;
452 Double intsum = sum(mi);
453 intColOut.put(outrowCount+irow, intsum);
454 }
455 outrowCount += rowNum ;
456 ++iter;
457 }
458 return out;
459}
460
461CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
462 bool droprows)
463{
464 if (insitu_) {
465 return in;
466 }
467 else {
468 // clone
469 return CountedPtr<Scantable>(new Scantable(*in, Bool(droprows)));
470 }
471}
472
473CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
474 float val,
475 const std::string& mode,
476 bool tsys )
477{
478 CountedPtr< Scantable > out = getScantable(in, false);
479 Table& tab = out->table();
480 ArrayColumn<Float> specCol(tab,"SPECTRA");
481 ArrayColumn<Float> tsysCol(tab,"TSYS");
482 for (uInt i=0; i<tab.nrow(); ++i) {
483 Vector<Float> spec;
484 Vector<Float> ts;
485 specCol.get(i, spec);
486 tsysCol.get(i, ts);
487 if (mode == "MUL" || mode == "DIV") {
488 if (mode == "DIV") val = 1.0/val;
489 spec *= val;
490 specCol.put(i, spec);
491 if ( tsys ) {
492 ts *= val;
493 tsysCol.put(i, ts);
494 }
495 } else if ( mode == "ADD" || mode == "SUB") {
496 if (mode == "SUB") val *= -1.0;
497 spec += val;
498 specCol.put(i, spec);
499 if ( tsys ) {
500 ts += val;
501 tsysCol.put(i, ts);
502 }
503 }
504 }
505 return out;
506}
507
508CountedPtr< Scantable > STMath::arrayOperate( const CountedPtr< Scantable >& in,
509 const std::vector<float> val,
510 const std::string& mode,
511 const std::string& opmode,
512 bool tsys )
513{
514 CountedPtr< Scantable > out ;
515 if ( opmode == "channel" ) {
516 out = arrayOperateChannel( in, val, mode, tsys ) ;
517 }
518 else if ( opmode == "row" ) {
519 out = arrayOperateRow( in, val, mode, tsys ) ;
520 }
521 else {
522 throw( AipsError( "Unknown array operation mode." ) ) ;
523 }
524 return out ;
525}
526
527CountedPtr< Scantable > STMath::arrayOperateChannel( const CountedPtr< Scantable >& in,
528 const std::vector<float> val,
529 const std::string& mode,
530 bool tsys )
531{
532 if ( val.size() == 1 ){
533 return unaryOperate( in, val[0], mode, tsys ) ;
534 }
535
536 // conformity of SPECTRA and TSYS
537 if ( tsys ) {
538 TableIterator titer(in->table(), "IFNO");
539 while ( !titer.pastEnd() ) {
540 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
541 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
542 Array<Float> spec = specCol.getColumn() ;
543 Array<Float> ts = tsysCol.getColumn() ;
544 if ( !spec.conform( ts ) ) {
545 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
546 }
547 titer.next() ;
548 }
549 }
550
551 // check if all spectra in the scantable have the same number of channel
552 vector<uInt> nchans;
553 vector<uInt> ifnos = in->getIFNos() ;
554 for ( uInt i = 0 ; i < ifnos.size() ; i++ ) {
555 nchans.push_back( in->nchan( ifnos[i] ) ) ;
556 }
557 Vector<uInt> mchans( nchans ) ;
558 if ( anyNE( mchans, mchans[0] ) ) {
559 throw( AipsError("All spectra in the input scantable must have the same number of channel for vector operation." ) ) ;
560 }
561
562 // check if vector size is equal to nchan
563 Vector<Float> fact( val ) ;
564 if ( fact.nelements() != mchans[0] ) {
565 throw( AipsError("Vector size must be 1 or be same as number of channel.") ) ;
566 }
567
568 // check divided by zero
569 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
570 throw( AipsError("Divided by zero is not recommended." ) ) ;
571 }
572
573 CountedPtr< Scantable > out = getScantable(in, false);
574 Table& tab = out->table();
575 ArrayColumn<Float> specCol(tab,"SPECTRA");
576 ArrayColumn<Float> tsysCol(tab,"TSYS");
577 for (uInt i=0; i<tab.nrow(); ++i) {
578 Vector<Float> spec;
579 Vector<Float> ts;
580 specCol.get(i, spec);
581 tsysCol.get(i, ts);
582 if (mode == "MUL" || mode == "DIV") {
583 if (mode == "DIV") fact = (float)1.0 / fact;
584 spec *= fact;
585 specCol.put(i, spec);
586 if ( tsys ) {
587 ts *= fact;
588 tsysCol.put(i, ts);
589 }
590 } else if ( mode == "ADD" || mode == "SUB") {
591 if (mode == "SUB") fact *= (float)-1.0 ;
592 spec += fact;
593 specCol.put(i, spec);
594 if ( tsys ) {
595 ts += fact;
596 tsysCol.put(i, ts);
597 }
598 }
599 }
600 return out;
601}
602
603CountedPtr< Scantable > STMath::arrayOperateRow( const CountedPtr< Scantable >& in,
604 const std::vector<float> val,
605 const std::string& mode,
606 bool tsys )
607{
608 if ( val.size() == 1 ) {
609 return unaryOperate( in, val[0], mode, tsys ) ;
610 }
611
612 // conformity of SPECTRA and TSYS
613 if ( tsys ) {
614 TableIterator titer(in->table(), "IFNO");
615 while ( !titer.pastEnd() ) {
616 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
617 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
618 Array<Float> spec = specCol.getColumn() ;
619 Array<Float> ts = tsysCol.getColumn() ;
620 if ( !spec.conform( ts ) ) {
621 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
622 }
623 titer.next() ;
624 }
625 }
626
627 // check if vector size is equal to nrow
628 Vector<Float> fact( val ) ;
629 if ( fact.nelements() != in->nrow() ) {
630 throw( AipsError("Vector size must be 1 or be same as number of row.") ) ;
631 }
632
633 // check divided by zero
634 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
635 throw( AipsError("Divided by zero is not recommended." ) ) ;
636 }
637
638 CountedPtr< Scantable > out = getScantable(in, false);
639 Table& tab = out->table();
640 ArrayColumn<Float> specCol(tab,"SPECTRA");
641 ArrayColumn<Float> tsysCol(tab,"TSYS");
642 if (mode == "DIV") fact = (float)1.0 / fact;
643 if (mode == "SUB") fact *= (float)-1.0 ;
644 for (uInt i=0; i<tab.nrow(); ++i) {
645 Vector<Float> spec;
646 Vector<Float> ts;
647 specCol.get(i, spec);
648 tsysCol.get(i, ts);
649 if (mode == "MUL" || mode == "DIV") {
650 spec *= fact[i];
651 specCol.put(i, spec);
652 if ( tsys ) {
653 ts *= fact[i];
654 tsysCol.put(i, ts);
655 }
656 } else if ( mode == "ADD" || mode == "SUB") {
657 spec += fact[i];
658 specCol.put(i, spec);
659 if ( tsys ) {
660 ts += fact[i];
661 tsysCol.put(i, ts);
662 }
663 }
664 }
665 return out;
666}
667
668CountedPtr< Scantable > STMath::array2dOperate( const CountedPtr< Scantable >& in,
669 const std::vector< std::vector<float> > val,
670 const std::string& mode,
671 bool tsys )
672{
673 // conformity of SPECTRA and TSYS
674 if ( tsys ) {
675 TableIterator titer(in->table(), "IFNO");
676 while ( !titer.pastEnd() ) {
677 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
678 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
679 Array<Float> spec = specCol.getColumn() ;
680 Array<Float> ts = tsysCol.getColumn() ;
681 if ( !spec.conform( ts ) ) {
682 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
683 }
684 titer.next() ;
685 }
686 }
687
688 // some checks
689 vector<uInt> nchans;
690 for ( uInt i = 0 ; i < in->nrow() ; i++ ) {
691 nchans.push_back( (in->getSpectrum( i )).size() ) ;
692 }
693 //Vector<uInt> mchans( nchans ) ;
694 vector< Vector<Float> > facts ;
695 for ( uInt i = 0 ; i < nchans.size() ; i++ ) {
696 Vector<Float> tmp( val[i] ) ;
697 // check divided by zero
698 if ( ( mode == "DIV" ) && anyEQ( tmp, (float)0.0 ) ) {
699 throw( AipsError("Divided by zero is not recommended." ) ) ;
700 }
701 // conformity check
702 if ( tmp.nelements() != nchans[i] ) {
703 stringstream ss ;
704 ss << "Row " << i << ": Vector size must be same as number of channel." ;
705 throw( AipsError( ss.str() ) ) ;
706 }
707 facts.push_back( tmp ) ;
708 }
709
710
711 CountedPtr< Scantable > out = getScantable(in, false);
712 Table& tab = out->table();
713 ArrayColumn<Float> specCol(tab,"SPECTRA");
714 ArrayColumn<Float> tsysCol(tab,"TSYS");
715 for (uInt i=0; i<tab.nrow(); ++i) {
716 Vector<Float> fact = facts[i] ;
717 Vector<Float> spec;
718 Vector<Float> ts;
719 specCol.get(i, spec);
720 tsysCol.get(i, ts);
721 if (mode == "MUL" || mode == "DIV") {
722 if (mode == "DIV") fact = (float)1.0 / fact;
723 spec *= fact;
724 specCol.put(i, spec);
725 if ( tsys ) {
726 ts *= fact;
727 tsysCol.put(i, ts);
728 }
729 } else if ( mode == "ADD" || mode == "SUB") {
730 if (mode == "SUB") fact *= (float)-1.0 ;
731 spec += fact;
732 specCol.put(i, spec);
733 if ( tsys ) {
734 ts += fact;
735 tsysCol.put(i, ts);
736 }
737 }
738 }
739 return out;
740}
741
742CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
743 const CountedPtr<Scantable>& right,
744 const std::string& mode)
745{
746 bool insitu = insitu_;
747 if ( ! left->conformant(*right) ) {
748 throw(AipsError("'left' and 'right' scantables are not conformant."));
749 }
750 setInsitu(false);
751 CountedPtr< Scantable > out = getScantable(left, false);
752 setInsitu(insitu);
753 Table& tout = out->table();
754 Block<String> coln(5);
755 coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO";
756 coln[3] = "IFNO"; coln[4] = "POLNO";
757 Table tmpl = tout.sort(coln);
758 Table tmpr = right->table().sort(coln);
759 ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
760 ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
761 ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
762 ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");
763
764 for (uInt i=0; i<tout.nrow(); ++i) {
765 Vector<Float> lspecvec, rspecvec;
766 Vector<uChar> lflagvec, rflagvec;
767 lspecvec = lspecCol(i); rspecvec = rspecCol(i);
768 lflagvec = lflagCol(i); rflagvec = rflagCol(i);
769 MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
770 MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
771 if (mode == "ADD") {
772 mleft += mright;
773 } else if ( mode == "SUB") {
774 mleft -= mright;
775 } else if ( mode == "MUL") {
776 mleft *= mright;
777 } else if ( mode == "DIV") {
778 mleft /= mright;
779 } else {
780 throw(AipsError("Illegal binary operator"));
781 }
782 lspecCol.put(i, mleft.getArray());
783 }
784 return out;
785}
786
787
788
789MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
790 const Vector<uChar>& f)
791{
792 Vector<Bool> mask;
793 mask.resize(f.shape());
794 convertArray(mask, f);
795 return MaskedArray<Float>(s,!mask);
796}
797
798MaskedArray<Double> STMath::maskedArray( const Vector<Double>& s,
799 const Vector<uChar>& f)
800{
801 Vector<Bool> mask;
802 mask.resize(f.shape());
803 convertArray(mask, f);
804 return MaskedArray<Double>(s,!mask);
805}
806
807Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
808{
809 const Vector<Bool>& m = ma.getMask();
810 Vector<uChar> flags(m.shape());
811 convertArray(flags, !m);
812 return flags;
813}
814
815CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
816 const std::string & mode,
817 bool preserve )
818{
819 /// @todo make other modes available
820 /// modes should be "nearest", "pair"
821 // make this operation non insitu
822 const Table& tin = in->table();
823 Table ons = tin(tin.col("SRCTYPE") == Int(SrcType::PSON));
824 Table offs = tin(tin.col("SRCTYPE") == Int(SrcType::PSOFF));
825 if ( offs.nrow() == 0 )
826 throw(AipsError("No 'off' scans present."));
827 // put all "on" scans into output table
828
829 bool insitu = insitu_;
830 setInsitu(false);
831 CountedPtr< Scantable > out = getScantable(in, true);
832 setInsitu(insitu);
833 Table& tout = out->table();
834
835 TableCopy::copyRows(tout, ons);
836 TableRow row(tout);
837 ROScalarColumn<Double> offtimeCol(offs, "TIME");
838 ArrayColumn<Float> outspecCol(tout, "SPECTRA");
839 ROArrayColumn<Float> outtsysCol(tout, "TSYS");
840 ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
841 for (uInt i=0; i < tout.nrow(); ++i) {
842 const TableRecord& rec = row.get(i);
843 Double ontime = rec.asDouble("TIME");
844 Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
845 && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
846 && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
847 ROScalarColumn<Double> offtimeCol(presel, "TIME");
848
849 Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
850 // Timestamp may vary within a cycle ???!!!
851 // increase this by 0.01 sec in case of rounding errors...
852 // There might be a better way to do this.
853 // fix to this fix. TIME is MJD, so 1.0d not 1.0s
854 mindeltat += 0.01/24./60./60.;
855 Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat);
856
857 if ( sel.nrow() < 1 ) {
858 throw(AipsError("No closest in time found... This could be a rounding "
859 "issue. Try quotient instead."));
860 }
861 TableRow offrow(sel);
862 const TableRecord& offrec = offrow.get(0);//should only be one row
863 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
864 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
865 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
866 /// @fixme this assumes tsys is a scalar not vector
867 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
868 Vector<Float> specon, tsyson;
869 outtsysCol.get(i, tsyson);
870 outspecCol.get(i, specon);
871 Vector<uChar> flagon;
872 outflagCol.get(i, flagon);
873 MaskedArray<Float> mon = maskedArray(specon, flagon);
874 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
875 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
876 if (preserve) {
877 quot -= tsysoffscalar;
878 } else {
879 quot -= tsyson[0];
880 }
881 outspecCol.put(i, quot.getArray());
882 outflagCol.put(i, flagsFromMA(quot));
883 }
884 // renumber scanno
885 TableIterator it(tout, "SCANNO");
886 uInt i = 0;
887 while ( !it.pastEnd() ) {
888 Table t = it.table();
889 TableVector<uInt> vec(t, "SCANNO");
890 vec = i;
891 ++i;
892 ++it;
893 }
894 return out;
895}
896
897
898CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
899 const CountedPtr< Scantable > & off,
900 bool preserve )
901{
902 bool insitu = insitu_;
903 if ( ! on->conformant(*off) ) {
904 throw(AipsError("'on' and 'off' scantables are not conformant."));
905 }
906 setInsitu(false);
907 CountedPtr< Scantable > out = getScantable(on, false);
908 setInsitu(insitu);
909 Table& tout = out->table();
910 const Table& toff = off->table();
911 TableIterator sit(tout, "SCANNO");
912 TableIterator s2it(toff, "SCANNO");
913 while ( !sit.pastEnd() ) {
914 Table ton = sit.table();
915 TableRow row(ton);
916 Table t = s2it.table();
917 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
918 ROArrayColumn<Float> outtsysCol(ton, "TSYS");
919 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
920 for (uInt i=0; i < ton.nrow(); ++i) {
921 const TableRecord& rec = row.get(i);
922 Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
923 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
924 && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
925 if ( offsel.nrow() == 0 )
926 throw AipsError("STMath::quotient: no matching off");
927 TableRow offrow(offsel);
928 const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
929 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
930 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
931 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
932 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
933 Vector<Float> specon, tsyson;
934 outtsysCol.get(i, tsyson);
935 outspecCol.get(i, specon);
936 Vector<uChar> flagon;
937 outflagCol.get(i, flagon);
938 MaskedArray<Float> mon = maskedArray(specon, flagon);
939 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
940 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
941 if (preserve) {
942 quot -= tsysoffscalar;
943 } else {
944 quot -= tsyson[0];
945 }
946 outspecCol.put(i, quot.getArray());
947 outflagCol.put(i, flagsFromMA(quot));
948 }
949 ++sit;
950 ++s2it;
951 // take the first off for each on scan which doesn't have a
952 // matching off scan
953 // non <= noff: matching pairs, non > noff matching pairs then first off
954 if ( s2it.pastEnd() ) s2it.reset();
955 }
956 return out;
957}
958
959// dototalpower (migration of GBTIDL procedure dototalpower.pro)
960// calibrate the CAL on-off pair. It calculate Tsys and average CAL on-off subintegrations
961// do it for each cycles in a specific scan.
962CountedPtr< Scantable > STMath::dototalpower( const CountedPtr< Scantable >& calon,
963 const CountedPtr< Scantable >& caloff, Float tcal )
964{
965if ( ! calon->conformant(*caloff) ) {
966 throw(AipsError("'CAL on' and 'CAL off' scantables are not conformant."));
967 }
968 setInsitu(false);
969 CountedPtr< Scantable > out = getScantable(caloff, false);
970 Table& tout = out->table();
971 const Table& tcon = calon->table();
972 Vector<Float> tcalout;
973 Vector<Float> tcalout2; //debug
974
975 if ( tout.nrow() != tcon.nrow() ) {
976 throw(AipsError("Mismatch in number of rows to form cal on - off pair."));
977 }
978 // iteration by scanno or cycle no.
979 TableIterator sit(tout, "SCANNO");
980 TableIterator s2it(tcon, "SCANNO");
981 while ( !sit.pastEnd() ) {
982 Table toff = sit.table();
983 TableRow row(toff);
984 Table t = s2it.table();
985 ScalarColumn<Double> outintCol(toff, "INTERVAL");
986 ArrayColumn<Float> outspecCol(toff, "SPECTRA");
987 ArrayColumn<Float> outtsysCol(toff, "TSYS");
988 ArrayColumn<uChar> outflagCol(toff, "FLAGTRA");
989 ROScalarColumn<uInt> outtcalIdCol(toff, "TCAL_ID");
990 ROScalarColumn<uInt> outpolCol(toff, "POLNO");
991 ROScalarColumn<Double> onintCol(t, "INTERVAL");
992 ROArrayColumn<Float> onspecCol(t, "SPECTRA");
993 ROArrayColumn<Float> ontsysCol(t, "TSYS");
994 ROArrayColumn<uChar> onflagCol(t, "FLAGTRA");
995 //ROScalarColumn<uInt> ontcalIdCol(t, "TCAL_ID");
996
997 for (uInt i=0; i < toff.nrow(); ++i) {
998 //skip these checks -> assumes the data order are the same between the cal on off pairs
999 //
1000 Vector<Float> specCalon, specCaloff;
1001 // to store scalar (mean) tsys
1002 Vector<Float> tsysout(1);
1003 uInt tcalId, polno;
1004 Double offint, onint;
1005 outpolCol.get(i, polno);
1006 outspecCol.get(i, specCaloff);
1007 onspecCol.get(i, specCalon);
1008 Vector<uChar> flagCaloff, flagCalon;
1009 outflagCol.get(i, flagCaloff);
1010 onflagCol.get(i, flagCalon);
1011 outtcalIdCol.get(i, tcalId);
1012 outintCol.get(i, offint);
1013 onintCol.get(i, onint);
1014 // caluculate mean Tsys
1015 uInt nchan = specCaloff.nelements();
1016 // percentage of edge cut off
1017 uInt pc = 10;
1018 uInt bchan = nchan/pc;
1019 uInt echan = nchan-bchan;
1020
1021 Slicer chansl(IPosition(1,bchan-1), IPosition(1,echan-1), IPosition(1,1),Slicer::endIsLast);
1022 Vector<Float> testsubsp = specCaloff(chansl);
1023 MaskedArray<Float> spoff = maskedArray( specCaloff(chansl),flagCaloff(chansl) );
1024 MaskedArray<Float> spon = maskedArray( specCalon(chansl),flagCalon(chansl) );
1025 MaskedArray<Float> spdiff = spon-spoff;
1026 uInt noff = spoff.nelementsValid();
1027 //uInt non = spon.nelementsValid();
1028 uInt ndiff = spdiff.nelementsValid();
1029 Float meantsys;
1030
1031/**
1032 Double subspec, subdiff;
1033 uInt usednchan;
1034 subspec = 0;
1035 subdiff = 0;
1036 usednchan = 0;
1037 for(uInt k=(bchan-1); k<echan; k++) {
1038 subspec += specCaloff[k];
1039 subdiff += static_cast<Double>(specCalon[k]-specCaloff[k]);
1040 ++usednchan;
1041 }
1042**/
1043 // get tcal if input tcal <= 0
1044 String tcalt;
1045 Float tcalUsed;
1046 tcalUsed = tcal;
1047 if ( tcal <= 0.0 ) {
1048 caloff->tcal().getEntry(tcalt, tcalout, tcalId);
1049 if (polno<=3) {
1050 tcalUsed = tcalout[polno];
1051 }
1052 else {
1053 tcalUsed = tcalout[0];
1054 }
1055 }
1056
1057 Float meanoff;
1058 Float meandiff;
1059 if (noff && ndiff) {
1060 //Debug
1061 //if(noff!=ndiff) cerr<<"noff and ndiff is not equal"<<endl;
1062 //LogIO os( LogOrigin( "STMath", "dototalpower()", WHERE ) ) ;
1063 //if(noff!=ndiff) os<<"noff and ndiff is not equal"<<LogIO::POST;
1064 meanoff = sum(spoff)/noff;
1065 meandiff = sum(spdiff)/ndiff;
1066 meantsys= (meanoff/meandiff )*tcalUsed + tcalUsed/2;
1067 }
1068 else {
1069 meantsys=1;
1070 }
1071
1072 tsysout[0] = Float(meantsys);
1073 MaskedArray<Float> mcaloff = maskedArray(specCaloff, flagCaloff);
1074 MaskedArray<Float> mcalon = maskedArray(specCalon, flagCalon);
1075 MaskedArray<Float> sig = Float(0.5) * (mcaloff + mcalon);
1076 //uInt ncaloff = mcaloff.nelementsValid();
1077 //uInt ncalon = mcalon.nelementsValid();
1078
1079 outintCol.put(i, offint+onint);
1080 outspecCol.put(i, sig.getArray());
1081 outflagCol.put(i, flagsFromMA(sig));
1082 outtsysCol.put(i, tsysout);
1083 }
1084 ++sit;
1085 ++s2it;
1086 }
1087 return out;
1088}
1089
1090//dosigref - migrated from GBT IDL's dosigref.pro, do calibration of position switch
1091// observatiions.
1092// input: sig and ref scantables, and an optional boxcar smoothing width(default width=0,
1093// no smoothing).
1094// output: resultant scantable [= (sig-ref/ref)*tsys]
1095CountedPtr< Scantable > STMath::dosigref( const CountedPtr < Scantable >& sig,
1096 const CountedPtr < Scantable >& ref,
1097 int smoothref,
1098 casa::Float tsysv,
1099 casa::Float tau )
1100{
1101if ( ! ref->conformant(*sig) ) {
1102 throw(AipsError("'sig' and 'ref' scantables are not conformant."));
1103 }
1104 setInsitu(false);
1105 CountedPtr< Scantable > out = getScantable(sig, false);
1106 CountedPtr< Scantable > smref;
1107 if ( smoothref > 1 ) {
1108 float fsmoothref = static_cast<float>(smoothref);
1109 std::string inkernel = "boxcar";
1110 smref = smooth(ref, inkernel, fsmoothref );
1111 ostringstream oss;
1112 oss<<"Applied smoothing of "<<fsmoothref<<" on the reference."<<endl;
1113 pushLog(String(oss));
1114 }
1115 else {
1116 smref = ref;
1117 }
1118 Table& tout = out->table();
1119 const Table& tref = smref->table();
1120 if ( tout.nrow() != tref.nrow() ) {
1121 throw(AipsError("Mismatch in number of rows to form on-source and reference pair."));
1122 }
1123 // iteration by scanno? or cycle no.
1124 TableIterator sit(tout, "SCANNO");
1125 TableIterator s2it(tref, "SCANNO");
1126 while ( !sit.pastEnd() ) {
1127 Table ton = sit.table();
1128 Table t = s2it.table();
1129 ScalarColumn<Double> outintCol(ton, "INTERVAL");
1130 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
1131 ArrayColumn<Float> outtsysCol(ton, "TSYS");
1132 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
1133 ArrayColumn<Float> refspecCol(t, "SPECTRA");
1134 ROScalarColumn<Double> refintCol(t, "INTERVAL");
1135 ROArrayColumn<Float> reftsysCol(t, "TSYS");
1136 ArrayColumn<uChar> refflagCol(t, "FLAGTRA");
1137 ROScalarColumn<Float> refelevCol(t, "ELEVATION");
1138 for (uInt i=0; i < ton.nrow(); ++i) {
1139
1140 Double onint, refint;
1141 Vector<Float> specon, specref;
1142 // to store scalar (mean) tsys
1143 Vector<Float> tsysref;
1144 outintCol.get(i, onint);
1145 refintCol.get(i, refint);
1146 outspecCol.get(i, specon);
1147 refspecCol.get(i, specref);
1148 Vector<uChar> flagref, flagon;
1149 outflagCol.get(i, flagon);
1150 refflagCol.get(i, flagref);
1151 reftsysCol.get(i, tsysref);
1152
1153 Float tsysrefscalar;
1154 if ( tsysv > 0.0 ) {
1155 ostringstream oss;
1156 Float elev;
1157 refelevCol.get(i, elev);
1158 oss << "user specified Tsys = " << tsysv;
1159 // do recalc elevation if EL = 0
1160 if ( elev == 0 ) {
1161 throw(AipsError("EL=0, elevation data is missing."));
1162 } else {
1163 if ( tau <= 0.0 ) {
1164 throw(AipsError("Valid tau is not supplied."));
1165 } else {
1166 tsysrefscalar = tsysv * exp(tau/elev);
1167 }
1168 }
1169 oss << ", corrected (for El) tsys= "<<tsysrefscalar;
1170 pushLog(String(oss));
1171 }
1172 else {
1173 tsysrefscalar = tsysref[0];
1174 }
1175 //get quotient spectrum
1176 MaskedArray<Float> mref = maskedArray(specref, flagref);
1177 MaskedArray<Float> mon = maskedArray(specon, flagon);
1178 MaskedArray<Float> specres = tsysrefscalar*((mon - mref)/mref);
1179 Double resint = onint*refint*smoothref/(onint+refint*smoothref);
1180
1181 //Debug
1182 //cerr<<"Tsys used="<<tsysrefscalar<<endl;
1183 //LogIO os( LogOrigin( "STMath", "dosigref", WHERE ) ) ;
1184 //os<<"Tsys used="<<tsysrefscalar<<LogIO::POST;
1185 // fill the result, replay signal tsys by reference tsys
1186 outintCol.put(i, resint);
1187 outspecCol.put(i, specres.getArray());
1188 outflagCol.put(i, flagsFromMA(specres));
1189 outtsysCol.put(i, tsysref);
1190 }
1191 ++sit;
1192 ++s2it;
1193 }
1194 return out;
1195}
1196
1197CountedPtr< Scantable > STMath::donod(const casa::CountedPtr<Scantable>& s,
1198 const std::vector<int>& scans,
1199 int smoothref,
1200 casa::Float tsysv,
1201 casa::Float tau,
1202 casa::Float tcal )
1203
1204{
1205 setInsitu(false);
1206 STSelector sel;
1207 std::vector<int> scan1, scan2, beams, types;
1208 std::vector< vector<int> > scanpair;
1209 //std::vector<string> calstate;
1210 std::vector<int> calstate;
1211 String msg;
1212
1213 CountedPtr< Scantable > s1b1on, s1b1off, s1b2on, s1b2off;
1214 CountedPtr< Scantable > s2b1on, s2b1off, s2b2on, s2b2off;
1215
1216 std::vector< CountedPtr< Scantable > > sctables;
1217 sctables.push_back(s1b1on);
1218 sctables.push_back(s1b1off);
1219 sctables.push_back(s1b2on);
1220 sctables.push_back(s1b2off);
1221 sctables.push_back(s2b1on);
1222 sctables.push_back(s2b1off);
1223 sctables.push_back(s2b2on);
1224 sctables.push_back(s2b2off);
1225
1226 //check scanlist
1227 int n=s->checkScanInfo(scans);
1228 if (n==1) {
1229 throw(AipsError("Incorrect scan pairs. "));
1230 }
1231
1232 // Assume scans contain only a pair of consecutive scan numbers.
1233 // It is assumed that first beam, b1, is on target.
1234 // There is no check if the first beam is on or not.
1235 if ( scans.size()==1 ) {
1236 scan1.push_back(scans[0]);
1237 scan2.push_back(scans[0]+1);
1238 } else if ( scans.size()==2 ) {
1239 scan1.push_back(scans[0]);
1240 scan2.push_back(scans[1]);
1241 } else {
1242 if ( scans.size()%2 == 0 ) {
1243 for (uInt i=0; i<scans.size(); i++) {
1244 if (i%2 == 0) {
1245 scan1.push_back(scans[i]);
1246 }
1247 else {
1248 scan2.push_back(scans[i]);
1249 }
1250 }
1251 } else {
1252 throw(AipsError("Odd numbers of scans, cannot form pairs."));
1253 }
1254 }
1255 scanpair.push_back(scan1);
1256 scanpair.push_back(scan2);
1257 //calstate.push_back("*calon");
1258 //calstate.push_back("*[^calon]");
1259 calstate.push_back(SrcType::NODCAL);
1260 calstate.push_back(SrcType::NOD);
1261 CountedPtr< Scantable > ws = getScantable(s, false);
1262 uInt l=0;
1263 while ( l < sctables.size() ) {
1264 for (uInt i=0; i < 2; i++) {
1265 for (uInt j=0; j < 2; j++) {
1266 for (uInt k=0; k < 2; k++) {
1267 sel.reset();
1268 sel.setScans(scanpair[i]);
1269 //sel.setName(calstate[k]);
1270 types.clear();
1271 types.push_back(calstate[k]);
1272 sel.setTypes(types);
1273 beams.clear();
1274 beams.push_back(j);
1275 sel.setBeams(beams);
1276 ws->setSelection(sel);
1277 sctables[l]= getScantable(ws, false);
1278 l++;
1279 }
1280 }
1281 }
1282 }
1283
1284 // replace here by splitData or getData functionality
1285 CountedPtr< Scantable > sig1;
1286 CountedPtr< Scantable > ref1;
1287 CountedPtr< Scantable > sig2;
1288 CountedPtr< Scantable > ref2;
1289 CountedPtr< Scantable > calb1;
1290 CountedPtr< Scantable > calb2;
1291
1292 msg=String("Processing dototalpower for subset of the data");
1293 ostringstream oss1;
1294 oss1 << msg << endl;
1295 pushLog(String(oss1));
1296 // Debug for IRC CS data
1297 //float tcal1=7.0;
1298 //float tcal2=4.0;
1299 sig1 = dototalpower(sctables[0], sctables[1], tcal=tcal);
1300 ref1 = dototalpower(sctables[2], sctables[3], tcal=tcal);
1301 ref2 = dototalpower(sctables[4], sctables[5], tcal=tcal);
1302 sig2 = dototalpower(sctables[6], sctables[7], tcal=tcal);
1303
1304 // correction of user-specified tsys for elevation here
1305
1306 // dosigref calibration
1307 msg=String("Processing dosigref for subset of the data");
1308 ostringstream oss2;
1309 oss2 << msg << endl;
1310 pushLog(String(oss2));
1311 calb1=dosigref(sig1,ref2,smoothref,tsysv,tau);
1312 calb2=dosigref(sig2,ref1,smoothref,tsysv,tau);
1313
1314 // iteration by scanno or cycle no.
1315 Table& tcalb1 = calb1->table();
1316 Table& tcalb2 = calb2->table();
1317 TableIterator sit(tcalb1, "SCANNO");
1318 TableIterator s2it(tcalb2, "SCANNO");
1319 while ( !sit.pastEnd() ) {
1320 Table t1 = sit.table();
1321 Table t2= s2it.table();
1322 ArrayColumn<Float> outspecCol(t1, "SPECTRA");
1323 ArrayColumn<Float> outtsysCol(t1, "TSYS");
1324 ArrayColumn<uChar> outflagCol(t1, "FLAGTRA");
1325 ScalarColumn<Double> outintCol(t1, "INTERVAL");
1326 ArrayColumn<Float> t2specCol(t2, "SPECTRA");
1327 ROArrayColumn<Float> t2tsysCol(t2, "TSYS");
1328 ArrayColumn<uChar> t2flagCol(t2, "FLAGTRA");
1329 ROScalarColumn<Double> t2intCol(t2, "INTERVAL");
1330 for (uInt i=0; i < t1.nrow(); ++i) {
1331 Vector<Float> spec1, spec2;
1332 // to store scalar (mean) tsys
1333 Vector<Float> tsys1, tsys2;
1334 Vector<uChar> flag1, flag2;
1335 Double tint1, tint2;
1336 outspecCol.get(i, spec1);
1337 t2specCol.get(i, spec2);
1338 outflagCol.get(i, flag1);
1339 t2flagCol.get(i, flag2);
1340 outtsysCol.get(i, tsys1);
1341 t2tsysCol.get(i, tsys2);
1342 outintCol.get(i, tint1);
1343 t2intCol.get(i, tint2);
1344 // average
1345 // assume scalar tsys for weights
1346 Float wt1, wt2, tsyssq1, tsyssq2;
1347 tsyssq1 = tsys1[0]*tsys1[0];
1348 tsyssq2 = tsys2[0]*tsys2[0];
1349 wt1 = Float(tint1)/tsyssq1;
1350 wt2 = Float(tint2)/tsyssq2;
1351 Float invsumwt=1/(wt1+wt2);
1352 MaskedArray<Float> mspec1 = maskedArray(spec1, flag1);
1353 MaskedArray<Float> mspec2 = maskedArray(spec2, flag2);
1354 MaskedArray<Float> avspec = invsumwt * (wt1*mspec1 + wt2*mspec2);
1355 //Array<Float> avtsys = Float(0.5) * (tsys1 + tsys2);
1356 // cerr<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<endl;
1357 // LogIO os( LogOrigin( "STMath", "donod", WHERE ) ) ;
1358 // os<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<LogIO::POST;
1359 tsys1[0] = sqrt(tsyssq1 + tsyssq2);
1360 Array<Float> avtsys = tsys1;
1361
1362 outspecCol.put(i, avspec.getArray());
1363 outflagCol.put(i, flagsFromMA(avspec));
1364 outtsysCol.put(i, avtsys);
1365 }
1366 ++sit;
1367 ++s2it;
1368 }
1369 return calb1;
1370}
1371
1372//GBTIDL version of frequency switched data calibration
1373CountedPtr< Scantable > STMath::dofs( const CountedPtr< Scantable >& s,
1374 const std::vector<int>& scans,
1375 int smoothref,
1376 casa::Float tsysv,
1377 casa::Float tau,
1378 casa::Float tcal )
1379{
1380
1381
1382 STSelector sel;
1383 CountedPtr< Scantable > ws = getScantable(s, false);
1384 CountedPtr< Scantable > sig, sigwcal, ref, refwcal;
1385 CountedPtr< Scantable > calsig, calref, out, out1, out2;
1386 Bool nofold=False;
1387 vector<int> types ;
1388
1389 //split the data
1390 //sel.setName("*_fs");
1391 types.push_back( SrcType::FSON ) ;
1392 sel.setTypes( types ) ;
1393 ws->setSelection(sel);
1394 sig = getScantable(ws,false);
1395 sel.reset();
1396 types.clear() ;
1397 //sel.setName("*_fs_calon");
1398 types.push_back( SrcType::FONCAL ) ;
1399 sel.setTypes( types ) ;
1400 ws->setSelection(sel);
1401 sigwcal = getScantable(ws,false);
1402 sel.reset();
1403 types.clear() ;
1404 //sel.setName("*_fsr");
1405 types.push_back( SrcType::FSOFF ) ;
1406 sel.setTypes( types ) ;
1407 ws->setSelection(sel);
1408 ref = getScantable(ws,false);
1409 sel.reset();
1410 types.clear() ;
1411 //sel.setName("*_fsr_calon");
1412 types.push_back( SrcType::FOFFCAL ) ;
1413 sel.setTypes( types ) ;
1414 ws->setSelection(sel);
1415 refwcal = getScantable(ws,false);
1416 sel.reset() ;
1417 types.clear() ;
1418
1419 calsig = dototalpower(sigwcal, sig, tcal=tcal);
1420 calref = dototalpower(refwcal, ref, tcal=tcal);
1421
1422 out1=dosigref(calsig,calref,smoothref,tsysv,tau);
1423 out2=dosigref(calref,calsig,smoothref,tsysv,tau);
1424
1425 Table& tabout1=out1->table();
1426 Table& tabout2=out2->table();
1427 ROScalarColumn<uInt> freqidCol1(tabout1, "FREQ_ID");
1428 ScalarColumn<uInt> freqidCol2(tabout2, "FREQ_ID");
1429 ROArrayColumn<Float> specCol(tabout2, "SPECTRA");
1430 Vector<Float> spec; specCol.get(0, spec);
1431 uInt nchan = spec.nelements();
1432 uInt freqid1; freqidCol1.get(0,freqid1);
1433 uInt freqid2; freqidCol2.get(0,freqid2);
1434 Double rp1, rp2, rv1, rv2, inc1, inc2;
1435 out1->frequencies().getEntry(rp1, rv1, inc1, freqid1);
1436 out2->frequencies().getEntry(rp2, rv2, inc2, freqid2);
1437 //cerr << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << endl ;
1438 //LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1439 //os << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << LogIO::POST ;
1440 if (rp1==rp2) {
1441 Double foffset = rv1 - rv2;
1442 uInt choffset = static_cast<uInt>(foffset/abs(inc2));
1443 if (choffset >= nchan) {
1444 //cerr<<"out-band frequency switching, no folding"<<endl;
1445 LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1446 os<<"out-band frequency switching, no folding"<<LogIO::POST;
1447 nofold = True;
1448 }
1449 }
1450
1451 if (nofold) {
1452 std::vector< CountedPtr< Scantable > > tabs;
1453 tabs.push_back(out1);
1454 tabs.push_back(out2);
1455 out = merge(tabs);
1456 }
1457 else {
1458 //out = out1;
1459 Double choffset = ( rv1 - rv2 ) / inc2 ;
1460 out = dofold( out1, out2, choffset ) ;
1461 }
1462
1463 return out;
1464}
1465
1466CountedPtr<Scantable> STMath::dofold( const CountedPtr<Scantable> &sig,
1467 const CountedPtr<Scantable> &ref,
1468 Double choffset,
1469 Double choffset2 )
1470{
1471 LogIO os( LogOrigin( "STMath", "dofold", WHERE ) ) ;
1472 os << "choffset=" << choffset << " choffset2=" << choffset2 << LogIO::POST ;
1473
1474 // output scantable
1475 CountedPtr<Scantable> out = getScantable( sig, false ) ;
1476
1477 // separate choffset to integer part and decimal part
1478 Int ioffset = (Int)choffset ;
1479 Double doffset = choffset - ioffset ;
1480 Int ioffset2 = (Int)choffset2 ;
1481 Double doffset2 = choffset2 - ioffset2 ;
1482 os << "ioffset=" << ioffset << " doffset=" << doffset << LogIO::POST ;
1483 os << "ioffset2=" << ioffset2 << " doffset2=" << doffset2 << LogIO::POST ;
1484
1485 // get column
1486 ROArrayColumn<Float> specCol1( sig->table(), "SPECTRA" ) ;
1487 ROArrayColumn<Float> specCol2( ref->table(), "SPECTRA" ) ;
1488 ROArrayColumn<Float> tsysCol1( sig->table(), "TSYS" ) ;
1489 ROArrayColumn<Float> tsysCol2( ref->table(), "TSYS" ) ;
1490 ROArrayColumn<uChar> flagCol1( sig->table(), "FLAGTRA" ) ;
1491 ROArrayColumn<uChar> flagCol2( ref->table(), "FLAGTRA" ) ;
1492 ROScalarColumn<Double> mjdCol1( sig->table(), "TIME" ) ;
1493 ROScalarColumn<Double> mjdCol2( ref->table(), "TIME" ) ;
1494 ROScalarColumn<Double> intervalCol1( sig->table(), "INTERVAL" ) ;
1495 ROScalarColumn<Double> intervalCol2( ref->table(), "INTERVAL" ) ;
1496
1497 // check
1498 if ( ioffset == 0 ) {
1499 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1500 os << "channel offset is zero, no folding" << LogIO::POST ;
1501 return out ;
1502 }
1503 int nchan = ref->nchan() ;
1504 if ( abs(ioffset) >= nchan ) {
1505 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1506 os << "out-band frequency switching, no folding" << LogIO::POST ;
1507 return out ;
1508 }
1509
1510 // attach column for output scantable
1511 ArrayColumn<Float> specColOut( out->table(), "SPECTRA" ) ;
1512 ArrayColumn<uChar> flagColOut( out->table(), "FLAGTRA" ) ;
1513 ArrayColumn<Float> tsysColOut( out->table(), "TSYS" ) ;
1514 ScalarColumn<Double> mjdColOut( out->table(), "TIME" ) ;
1515 ScalarColumn<Double> intervalColOut( out->table(), "INTERVAL" ) ;
1516 ScalarColumn<uInt> fidColOut( out->table(), "FREQ_ID" ) ;
1517
1518 // for each row
1519 // assume that the data order are same between sig and ref
1520 RowAccumulator acc( asap::TINTSYS ) ;
1521 for ( int i = 0 ; i < sig->nrow() ; i++ ) {
1522 // get values
1523 Vector<Float> spsig ;
1524 specCol1.get( i, spsig ) ;
1525 Vector<Float> spref ;
1526 specCol2.get( i, spref ) ;
1527 Vector<Float> tsyssig ;
1528 tsysCol1.get( i, tsyssig ) ;
1529 Vector<Float> tsysref ;
1530 tsysCol2.get( i, tsysref ) ;
1531 Vector<uChar> flagsig ;
1532 flagCol1.get( i, flagsig ) ;
1533 Vector<uChar> flagref ;
1534 flagCol2.get( i, flagref ) ;
1535 Double timesig ;
1536 mjdCol1.get( i, timesig ) ;
1537 Double timeref ;
1538 mjdCol2.get( i, timeref ) ;
1539 Double intsig ;
1540 intervalCol1.get( i, intsig ) ;
1541 Double intref ;
1542 intervalCol2.get( i, intref ) ;
1543
1544 // shift reference spectra
1545 int refchan = spref.nelements() ;
1546 Vector<Float> sspref( spref.nelements() ) ;
1547 Vector<Float> stsysref( tsysref.nelements() ) ;
1548 Vector<uChar> sflagref( flagref.nelements() ) ;
1549 if ( ioffset > 0 ) {
1550 // SPECTRA and FLAGTRA
1551 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1552 sspref[j] = spref[j+ioffset] ;
1553 sflagref[j] = flagref[j+ioffset] ;
1554 }
1555 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1556 sspref[j] = spref[j-refchan+ioffset] ;
1557 sflagref[j] = flagref[j-refchan+ioffset] ;
1558 }
1559 spref = sspref.copy() ;
1560 flagref = sflagref.copy() ;
1561 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1562 sspref[j] = doffset * spref[j+1] + ( 1.0 - doffset ) * spref[j] ;
1563 sflagref[j] = flagref[j+1] + flagref[j] ;
1564 }
1565 sspref[refchan-1] = doffset * spref[0] + ( 1.0 - doffset ) * spref[refchan-1] ;
1566 sflagref[refchan-1] = flagref[0] + flagref[refchan-1] ;
1567
1568 // TSYS
1569 if ( spref.nelements() == tsysref.nelements() ) {
1570 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1571 stsysref[j] = tsysref[j+ioffset] ;
1572 }
1573 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1574 stsysref[j] = tsysref[j-refchan+ioffset] ;
1575 }
1576 tsysref = stsysref.copy() ;
1577 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1578 stsysref[j] = doffset * tsysref[j+1] + ( 1.0 - doffset ) * tsysref[j] ;
1579 }
1580 stsysref[refchan-1] = doffset * tsysref[0] + ( 1.0 - doffset ) * tsysref[refchan-1] ;
1581 }
1582 }
1583 else {
1584 // SPECTRA and FLAGTRA
1585 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1586 sspref[j] = spref[refchan+ioffset+j] ;
1587 sflagref[j] = flagref[refchan+ioffset+j] ;
1588 }
1589 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1590 sspref[j] = spref[j+ioffset] ;
1591 sflagref[j] = flagref[j+ioffset] ;
1592 }
1593 spref = sspref.copy() ;
1594 flagref = sflagref.copy() ;
1595 sspref[0] = doffset * spref[refchan-1] + ( 1.0 - doffset ) * spref[0] ;
1596 sflagref[0] = flagref[0] + flagref[refchan-1] ;
1597 for ( int j = 1 ; j < refchan ; j++ ) {
1598 sspref[j] = doffset * spref[j-1] + ( 1.0 - doffset ) * spref[j] ;
1599 sflagref[j] = flagref[j-1] + flagref[j] ;
1600 }
1601 // TSYS
1602 if ( spref.nelements() == tsysref.nelements() ) {
1603 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1604 stsysref[j] = tsysref[refchan+ioffset+j] ;
1605 }
1606 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1607 stsysref[j] = tsysref[j+ioffset] ;
1608 }
1609 tsysref = stsysref.copy() ;
1610 stsysref[0] = doffset * tsysref[refchan-1] + ( 1.0 - doffset ) * tsysref[0] ;
1611 for ( int j = 1 ; j < refchan ; j++ ) {
1612 stsysref[j] = doffset * tsysref[j-1] + ( 1.0 - doffset ) * tsysref[j] ;
1613 }
1614 }
1615 }
1616
1617 // shift signal spectra if necessary (only for APEX?)
1618 if ( choffset2 != 0.0 ) {
1619 int sigchan = spsig.nelements() ;
1620 Vector<Float> sspsig( spsig.nelements() ) ;
1621 Vector<Float> stsyssig( tsyssig.nelements() ) ;
1622 Vector<uChar> sflagsig( flagsig.nelements() ) ;
1623 if ( ioffset2 > 0 ) {
1624 // SPECTRA and FLAGTRA
1625 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1626 sspsig[j] = spsig[j+ioffset2] ;
1627 sflagsig[j] = flagsig[j+ioffset2] ;
1628 }
1629 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1630 sspsig[j] = spsig[j-sigchan+ioffset2] ;
1631 sflagsig[j] = flagsig[j-sigchan+ioffset2] ;
1632 }
1633 spsig = sspsig.copy() ;
1634 flagsig = sflagsig.copy() ;
1635 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1636 sspsig[j] = doffset2 * spsig[j+1] + ( 1.0 - doffset2 ) * spsig[j] ;
1637 sflagsig[j] = flagsig[j+1] || flagsig[j] ;
1638 }
1639 sspsig[sigchan-1] = doffset2 * spsig[0] + ( 1.0 - doffset2 ) * spsig[sigchan-1] ;
1640 sflagsig[sigchan-1] = flagsig[0] || flagsig[sigchan-1] ;
1641 // TSTS
1642 if ( spsig.nelements() == tsyssig.nelements() ) {
1643 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1644 stsyssig[j] = tsyssig[j+ioffset2] ;
1645 }
1646 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1647 stsyssig[j] = tsyssig[j-sigchan+ioffset2] ;
1648 }
1649 tsyssig = stsyssig.copy() ;
1650 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1651 stsyssig[j] = doffset2 * tsyssig[j+1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1652 }
1653 stsyssig[sigchan-1] = doffset2 * tsyssig[0] + ( 1.0 - doffset2 ) * tsyssig[sigchan-1] ;
1654 }
1655 }
1656 else {
1657 // SPECTRA and FLAGTRA
1658 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1659 sspsig[j] = spsig[sigchan+ioffset2+j] ;
1660 sflagsig[j] = flagsig[sigchan+ioffset2+j] ;
1661 }
1662 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1663 sspsig[j] = spsig[j+ioffset2] ;
1664 sflagsig[j] = flagsig[j+ioffset2] ;
1665 }
1666 spsig = sspsig.copy() ;
1667 flagsig = sflagsig.copy() ;
1668 sspsig[0] = doffset2 * spsig[sigchan-1] + ( 1.0 - doffset2 ) * spsig[0] ;
1669 sflagsig[0] = flagsig[0] + flagsig[sigchan-1] ;
1670 for ( int j = 1 ; j < sigchan ; j++ ) {
1671 sspsig[j] = doffset2 * spsig[j-1] + ( 1.0 - doffset2 ) * spsig[j] ;
1672 sflagsig[j] = flagsig[j-1] + flagsig[j] ;
1673 }
1674 // TSYS
1675 if ( spsig.nelements() == tsyssig.nelements() ) {
1676 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1677 stsyssig[j] = tsyssig[sigchan+ioffset2+j] ;
1678 }
1679 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1680 stsyssig[j] = tsyssig[j+ioffset2] ;
1681 }
1682 tsyssig = stsyssig.copy() ;
1683 stsyssig[0] = doffset2 * tsyssig[sigchan-1] + ( 1.0 - doffset2 ) * tsyssig[0] ;
1684 for ( int j = 1 ; j < sigchan ; j++ ) {
1685 stsyssig[j] = doffset2 * tsyssig[j-1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1686 }
1687 }
1688 }
1689 }
1690
1691 // folding
1692 acc.add( spsig, !flagsig, tsyssig, intsig, timesig ) ;
1693 acc.add( sspref, !sflagref, stsysref, intref, timeref ) ;
1694
1695 // put result
1696 specColOut.put( i, acc.getSpectrum() ) ;
1697 const Vector<Bool> &msk = acc.getMask() ;
1698 Vector<uChar> flg( msk.shape() ) ;
1699 convertArray( flg, !msk ) ;
1700 flagColOut.put( i, flg ) ;
1701 tsysColOut.put( i, acc.getTsys() ) ;
1702 intervalColOut.put( i, acc.getInterval() ) ;
1703 mjdColOut.put( i, acc.getTime() ) ;
1704 // change FREQ_ID to unshifted IF setting (only for APEX?)
1705 if ( choffset2 != 0.0 ) {
1706 uInt freqid = fidColOut( 0 ) ; // assume single-IF data
1707 double refpix, refval, increment ;
1708 out->frequencies().getEntry( refpix, refval, increment, freqid ) ;
1709 refval -= choffset * increment ;
1710 uInt newfreqid = out->frequencies().addEntry( refpix, refval, increment ) ;
1711 Vector<uInt> freqids = fidColOut.getColumn() ;
1712 for ( uInt j = 0 ; j < freqids.nelements() ; j++ ) {
1713 if ( freqids[j] == freqid )
1714 freqids[j] = newfreqid ;
1715 }
1716 fidColOut.putColumn( freqids ) ;
1717 }
1718
1719 acc.reset() ;
1720 }
1721
1722 return out ;
1723}
1724
1725
1726CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
1727{
1728 // make copy or reference
1729 CountedPtr< Scantable > out = getScantable(in, false);
1730 Table& tout = out->table();
1731 Block<String> cols(4);
1732 cols[0] = String("SCANNO");
1733 cols[1] = String("CYCLENO");
1734 cols[2] = String("BEAMNO");
1735 cols[3] = String("POLNO");
1736 TableIterator iter(tout, cols);
1737 while (!iter.pastEnd()) {
1738 Table subt = iter.table();
1739 // this should leave us with two rows for the two IFs....if not ignore
1740 if (subt.nrow() != 2 ) {
1741 continue;
1742 }
1743 ArrayColumn<Float> specCol(subt, "SPECTRA");
1744 ArrayColumn<Float> tsysCol(subt, "TSYS");
1745 ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
1746 Vector<Float> onspec,offspec, ontsys, offtsys;
1747 Vector<uChar> onflag, offflag;
1748 tsysCol.get(0, ontsys); tsysCol.get(1, offtsys);
1749 specCol.get(0, onspec); specCol.get(1, offspec);
1750 flagCol.get(0, onflag); flagCol.get(1, offflag);
1751 MaskedArray<Float> on = maskedArray(onspec, onflag);
1752 MaskedArray<Float> off = maskedArray(offspec, offflag);
1753 MaskedArray<Float> oncopy = on.copy();
1754
1755 on /= off; on -= 1.0f;
1756 on *= ontsys[0];
1757 off /= oncopy; off -= 1.0f;
1758 off *= offtsys[0];
1759 specCol.put(0, on.getArray());
1760 const Vector<Bool>& m0 = on.getMask();
1761 Vector<uChar> flags0(m0.shape());
1762 convertArray(flags0, !m0);
1763 flagCol.put(0, flags0);
1764
1765 specCol.put(1, off.getArray());
1766 const Vector<Bool>& m1 = off.getMask();
1767 Vector<uChar> flags1(m1.shape());
1768 convertArray(flags1, !m1);
1769 flagCol.put(1, flags1);
1770 ++iter;
1771 }
1772
1773 return out;
1774}
1775
1776std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
1777 const std::vector< bool > & mask,
1778 const std::string& which )
1779{
1780
1781 Vector<Bool> m(mask);
1782 const Table& tab = in->table();
1783 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1784 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1785 std::vector<float> out;
1786 for (uInt i=0; i < tab.nrow(); ++i ) {
1787 Vector<Float> spec; specCol.get(i, spec);
1788 Vector<uChar> flag; flagCol.get(i, flag);
1789 MaskedArray<Float> ma = maskedArray(spec, flag);
1790 float outstat = 0.0;
1791 if ( spec.nelements() == m.nelements() ) {
1792 outstat = mathutil::statistics(which, ma(m));
1793 } else {
1794 outstat = mathutil::statistics(which, ma);
1795 }
1796 out.push_back(outstat);
1797 }
1798 return out;
1799}
1800
1801std::vector< int > STMath::minMaxChan( const CountedPtr< Scantable > & in,
1802 const std::vector< bool > & mask,
1803 const std::string& which )
1804{
1805
1806 Vector<Bool> m(mask);
1807 const Table& tab = in->table();
1808 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1809 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1810 std::vector<int> out;
1811 for (uInt i=0; i < tab.nrow(); ++i ) {
1812 Vector<Float> spec; specCol.get(i, spec);
1813 Vector<uChar> flag; flagCol.get(i, flag);
1814 MaskedArray<Float> ma = maskedArray(spec, flag);
1815 if (ma.ndim() != 1) {
1816 throw (ArrayError(
1817 "std::vector<int> STMath::minMaxChan("
1818 "ContedPtr<Scantable> &in, std::vector<bool> &mask, "
1819 " std::string &which)"
1820 " - MaskedArray is not 1D"));
1821 }
1822 IPosition outpos(1,0);
1823 if ( spec.nelements() == m.nelements() ) {
1824 outpos = mathutil::minMaxPos(which, ma(m));
1825 } else {
1826 outpos = mathutil::minMaxPos(which, ma);
1827 }
1828 out.push_back(outpos[0]);
1829 }
1830 return out;
1831}
1832
1833CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
1834 int width )
1835{
1836 if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
1837 CountedPtr< Scantable > out = getScantable(in, false);
1838 Table& tout = out->table();
1839 out->frequencies().rescale(width, "BIN");
1840 ArrayColumn<Float> specCol(tout, "SPECTRA");
1841 ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
1842 for (uInt i=0; i < tout.nrow(); ++i ) {
1843 MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
1844 MaskedArray<Float> maout;
1845 LatticeUtilities::bin(maout, main, 0, Int(width));
1846 /// @todo implement channel based tsys binning
1847 specCol.put(i, maout.getArray());
1848 flagCol.put(i, flagsFromMA(maout));
1849 // take only the first binned spectrum's length for the deprecated
1850 // global header item nChan
1851 if (i==0) tout.rwKeywordSet().define(String("nChan"),
1852 Int(maout.getArray().nelements()));
1853 }
1854 return out;
1855}
1856
1857CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
1858 const std::string& method,
1859 float width )
1860//
1861// Should add the possibility of width being specified in km/s. This means
1862// that for each freqID (SpectralCoordinate) we will need to convert to an
1863// average channel width (say at the reference pixel). Then we would need
1864// to be careful to make sure each spectrum (of different freqID)
1865// is the same length.
1866//
1867{
1868 //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
1869 Int interpMethod(stringToIMethod(method));
1870
1871 CountedPtr< Scantable > out = getScantable(in, false);
1872 Table& tout = out->table();
1873
1874// Resample SpectralCoordinates (one per freqID)
1875 out->frequencies().rescale(width, "RESAMPLE");
1876 TableIterator iter(tout, "IFNO");
1877 TableRow row(tout);
1878 while ( !iter.pastEnd() ) {
1879 Table tab = iter.table();
1880 ArrayColumn<Float> specCol(tab, "SPECTRA");
1881 //ArrayColumn<Float> tsysCol(tout, "TSYS");
1882 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1883 Vector<Float> spec;
1884 Vector<uChar> flag;
1885 specCol.get(0,spec); // the number of channels should be constant per IF
1886 uInt nChanIn = spec.nelements();
1887 Vector<Float> xIn(nChanIn); indgen(xIn);
1888 Int fac = Int(nChanIn/width);
1889 Vector<Float> xOut(fac+10); // 10 to be safe - resize later
1890 uInt k = 0;
1891 Float x = 0.0;
1892 while (x < Float(nChanIn) ) {
1893 xOut(k) = x;
1894 k++;
1895 x += width;
1896 }
1897 uInt nChanOut = k;
1898 xOut.resize(nChanOut, True);
1899 // process all rows for this IFNO
1900 Vector<Float> specOut;
1901 Vector<Bool> maskOut;
1902 Vector<uChar> flagOut;
1903 for (uInt i=0; i < tab.nrow(); ++i) {
1904 specCol.get(i, spec);
1905 flagCol.get(i, flag);
1906 Vector<Bool> mask(flag.nelements());
1907 convertArray(mask, flag);
1908
1909 IPosition shapeIn(spec.shape());
1910 //sh.nchan = nChanOut;
1911 InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
1912 xIn, spec, mask,
1913 interpMethod, True, True);
1914 /// @todo do the same for channel based Tsys
1915 flagOut.resize(maskOut.nelements());
1916 convertArray(flagOut, maskOut);
1917 specCol.put(i, specOut);
1918 flagCol.put(i, flagOut);
1919 }
1920 ++iter;
1921 }
1922
1923 return out;
1924}
1925
1926STMath::imethod STMath::stringToIMethod(const std::string& in)
1927{
1928 static STMath::imap lookup;
1929
1930 // initialize the lookup table if necessary
1931 if ( lookup.empty() ) {
1932 lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
1933 lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
1934 lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
1935 lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
1936 }
1937
1938 STMath::imap::const_iterator iter = lookup.find(in);
1939
1940 if ( lookup.end() == iter ) {
1941 std::string message = in;
1942 message += " is not a valid interpolation mode";
1943 throw(AipsError(message));
1944 }
1945 return iter->second;
1946}
1947
1948WeightType STMath::stringToWeight(const std::string& in)
1949{
1950 static std::map<std::string, WeightType> lookup;
1951
1952 // initialize the lookup table if necessary
1953 if ( lookup.empty() ) {
1954 lookup["NONE"] = asap::NONE;
1955 lookup["TINT"] = asap::TINT;
1956 lookup["TINTSYS"] = asap::TINTSYS;
1957 lookup["TSYS"] = asap::TSYS;
1958 lookup["VAR"] = asap::VAR;
1959 }
1960
1961 std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
1962
1963 if ( lookup.end() == iter ) {
1964 std::string message = in;
1965 message += " is not a valid weighting mode";
1966 throw(AipsError(message));
1967 }
1968 return iter->second;
1969}
1970
1971CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
1972 const vector< float > & coeff,
1973 const std::string & filename,
1974 const std::string& method)
1975{
1976 // Get elevation data from Scantable and convert to degrees
1977 CountedPtr< Scantable > out = getScantable(in, false);
1978 Table& tab = out->table();
1979 ROScalarColumn<Float> elev(tab, "ELEVATION");
1980 Vector<Float> x = elev.getColumn();
1981 x *= Float(180 / C::pi); // Degrees
1982
1983 Vector<Float> coeffs(coeff);
1984 const uInt nc = coeffs.nelements();
1985 if ( filename.length() > 0 && nc > 0 ) {
1986 throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
1987 }
1988
1989 // Correct
1990 if ( nc > 0 || filename.length() == 0 ) {
1991 // Find instrument
1992 Bool throwit = True;
1993 Instrument inst =
1994 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
1995 throwit);
1996
1997 // Set polynomial
1998 Polynomial<Float>* ppoly = 0;
1999 Vector<Float> coeff;
2000 String msg;
2001 if ( nc > 0 ) {
2002 ppoly = new Polynomial<Float>(nc);
2003 coeff = coeffs;
2004 msg = String("user");
2005 } else {
2006 STAttr sdAttr;
2007 coeff = sdAttr.gainElevationPoly(inst);
2008 ppoly = new Polynomial<Float>(3);
2009 msg = String("built in");
2010 }
2011
2012 if ( coeff.nelements() > 0 ) {
2013 ppoly->setCoefficients(coeff);
2014 } else {
2015 delete ppoly;
2016 throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
2017 }
2018 ostringstream oss;
2019 oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
2020 oss << " " << coeff;
2021 pushLog(String(oss));
2022 const uInt nrow = tab.nrow();
2023 Vector<Float> factor(nrow);
2024 for ( uInt i=0; i < nrow; ++i ) {
2025 factor[i] = 1.0 / (*ppoly)(x[i]);
2026 }
2027 delete ppoly;
2028 scaleByVector(tab, factor, true);
2029
2030 } else {
2031 // Read and correct
2032 pushLog("Making correction from ascii Table");
2033 scaleFromAsciiTable(tab, filename, method, x, true);
2034 }
2035 return out;
2036}
2037
2038void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
2039 const std::string& method,
2040 const Vector<Float>& xout, bool dotsys)
2041{
2042
2043// Read gain-elevation ascii file data into a Table.
2044
2045 String formatString;
2046 Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
2047 scaleFromTable(in, tbl, method, xout, dotsys);
2048}
2049
2050void STMath::scaleFromTable(Table& in,
2051 const Table& table,
2052 const std::string& method,
2053 const Vector<Float>& xout, bool dotsys)
2054{
2055
2056 ROScalarColumn<Float> geElCol(table, "ELEVATION");
2057 ROScalarColumn<Float> geFacCol(table, "FACTOR");
2058 Vector<Float> xin = geElCol.getColumn();
2059 Vector<Float> yin = geFacCol.getColumn();
2060 Vector<Bool> maskin(xin.nelements(),True);
2061
2062 // Interpolate (and extrapolate) with desired method
2063
2064 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2065
2066 Vector<Float> yout;
2067 Vector<Bool> maskout;
2068 InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
2069 xin, yin, maskin, interp,
2070 True, True);
2071
2072 scaleByVector(in, Float(1.0)/yout, dotsys);
2073}
2074
2075void STMath::scaleByVector( Table& in,
2076 const Vector< Float >& factor,
2077 bool dotsys )
2078{
2079 uInt nrow = in.nrow();
2080 if ( factor.nelements() != nrow ) {
2081 throw(AipsError("factors.nelements() != table.nelements()"));
2082 }
2083 ArrayColumn<Float> specCol(in, "SPECTRA");
2084 ArrayColumn<uChar> flagCol(in, "FLAGTRA");
2085 ArrayColumn<Float> tsysCol(in, "TSYS");
2086 for (uInt i=0; i < nrow; ++i) {
2087 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2088 ma *= factor[i];
2089 specCol.put(i, ma.getArray());
2090 flagCol.put(i, flagsFromMA(ma));
2091 if ( dotsys ) {
2092 Vector<Float> tsys = tsysCol(i);
2093 tsys *= factor[i];
2094 tsysCol.put(i,tsys);
2095 }
2096 }
2097}
2098
2099CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
2100 float d, float etaap,
2101 float jyperk )
2102{
2103 CountedPtr< Scantable > out = getScantable(in, false);
2104 Table& tab = in->table();
2105 Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
2106 Unit K(String("K"));
2107 Unit JY(String("Jy"));
2108
2109 bool tokelvin = true;
2110 Double cfac = 1.0;
2111
2112 if ( fluxUnit == JY ) {
2113 pushLog("Converting to K");
2114 Quantum<Double> t(1.0,fluxUnit);
2115 Quantum<Double> t2 = t.get(JY);
2116 cfac = (t2 / t).getValue(); // value to Jy
2117
2118 tokelvin = true;
2119 out->setFluxUnit("K");
2120 } else if ( fluxUnit == K ) {
2121 pushLog("Converting to Jy");
2122 Quantum<Double> t(1.0,fluxUnit);
2123 Quantum<Double> t2 = t.get(K);
2124 cfac = (t2 / t).getValue(); // value to K
2125
2126 tokelvin = false;
2127 out->setFluxUnit("Jy");
2128 } else {
2129 throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
2130 }
2131 // Make sure input values are converted to either Jy or K first...
2132 Float factor = cfac;
2133
2134 // Select method
2135 if (jyperk > 0.0) {
2136 factor *= jyperk;
2137 if ( tokelvin ) factor = 1.0 / jyperk;
2138 ostringstream oss;
2139 oss << "Jy/K = " << jyperk;
2140 pushLog(String(oss));
2141 Vector<Float> factors(tab.nrow(), factor);
2142 scaleByVector(tab,factors, false);
2143 } else if ( etaap > 0.0) {
2144 if (d < 0) {
2145 Instrument inst =
2146 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2147 True);
2148 STAttr sda;
2149 d = sda.diameter(inst);
2150 }
2151 jyperk = STAttr::findJyPerK(etaap, d);
2152 ostringstream oss;
2153 oss << "Jy/K = " << jyperk;
2154 pushLog(String(oss));
2155 factor *= jyperk;
2156 if ( tokelvin ) {
2157 factor = 1.0 / factor;
2158 }
2159 Vector<Float> factors(tab.nrow(), factor);
2160 scaleByVector(tab, factors, False);
2161 } else {
2162
2163 // OK now we must deal with automatic look up of values.
2164 // We must also deal with the fact that the factors need
2165 // to be computed per IF and may be different and may
2166 // change per integration.
2167
2168 pushLog("Looking up conversion factors");
2169 convertBrightnessUnits(out, tokelvin, cfac);
2170 }
2171
2172 return out;
2173}
2174
2175void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
2176 bool tokelvin, float cfac )
2177{
2178 Table& table = in->table();
2179 Instrument inst =
2180 STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
2181 TableIterator iter(table, "FREQ_ID");
2182 STFrequencies stfreqs = in->frequencies();
2183 STAttr sdAtt;
2184 while (!iter.pastEnd()) {
2185 Table tab = iter.table();
2186 ArrayColumn<Float> specCol(tab, "SPECTRA");
2187 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2188 ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
2189 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2190
2191 uInt freqid; freqidCol.get(0, freqid);
2192 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2193 // STAttr.JyPerK has a Vector interface... change sometime.
2194 Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
2195 for ( uInt i=0; i<tab.nrow(); ++i) {
2196 Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
2197 Float factor = cfac * jyperk;
2198 if ( tokelvin ) factor = Float(1.0) / factor;
2199 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2200 ma *= factor;
2201 specCol.put(i, ma.getArray());
2202 flagCol.put(i, flagsFromMA(ma));
2203 }
2204 ++iter;
2205 }
2206}
2207
2208CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
2209 float tau )
2210{
2211 CountedPtr< Scantable > out = getScantable(in, false);
2212
2213 Table tab = out->table();
2214 ROScalarColumn<Float> elev(tab, "ELEVATION");
2215 ArrayColumn<Float> specCol(tab, "SPECTRA");
2216 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2217 ArrayColumn<Float> tsysCol(tab, "TSYS");
2218 for ( uInt i=0; i<tab.nrow(); ++i) {
2219 Float zdist = Float(C::pi_2) - elev(i);
2220 Float factor = exp(tau/cos(zdist));
2221 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2222 ma *= factor;
2223 specCol.put(i, ma.getArray());
2224 flagCol.put(i, flagsFromMA(ma));
2225 Vector<Float> tsys;
2226 tsysCol.get(i, tsys);
2227 tsys *= factor;
2228 tsysCol.put(i, tsys);
2229 }
2230 return out;
2231}
2232
2233CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in,
2234 const std::string& kernel,
2235 float width )
2236{
2237 CountedPtr< Scantable > out = getScantable(in, false);
2238 Table& table = out->table();
2239 ArrayColumn<Float> specCol(table, "SPECTRA");
2240 ArrayColumn<uChar> flagCol(table, "FLAGTRA");
2241 Vector<Float> spec;
2242 Vector<uChar> flag;
2243 for ( uInt i=0; i<table.nrow(); ++i) {
2244 specCol.get(i, spec);
2245 flagCol.get(i, flag);
2246 Vector<Bool> mask(flag.nelements());
2247 convertArray(mask, flag);
2248 Vector<Float> specout;
2249 Vector<Bool> maskout;
2250 if ( kernel == "hanning" ) {
2251 mathutil::hanning(specout, maskout, spec , !mask);
2252 convertArray(flag, !maskout);
2253 } else if ( kernel == "rmedian" ) {
2254 mathutil::runningMedian(specout, maskout, spec , mask, width);
2255 convertArray(flag, maskout);
2256 }
2257 flagCol.put(i, flag);
2258 specCol.put(i, specout);
2259 }
2260 return out;
2261}
2262
2263CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
2264 const std::string& kernel, float width )
2265{
2266 if (kernel == "rmedian" || kernel == "hanning") {
2267 return smoothOther(in, kernel, width);
2268 }
2269 CountedPtr< Scantable > out = getScantable(in, false);
2270 Table& table = out->table();
2271 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
2272 // same IFNO should have same no of channels
2273 // this saves overhead
2274 TableIterator iter(table, "IFNO");
2275 while (!iter.pastEnd()) {
2276 Table tab = iter.table();
2277 ArrayColumn<Float> specCol(tab, "SPECTRA");
2278 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2279 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2280 uInt nchan = tmpspec.nelements();
2281 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
2282 Convolver<Float> conv(kvec, IPosition(1,nchan));
2283 Vector<Float> spec;
2284 Vector<uChar> flag;
2285 for ( uInt i=0; i<tab.nrow(); ++i) {
2286 specCol.get(i, spec);
2287 flagCol.get(i, flag);
2288 Vector<Bool> mask(flag.nelements());
2289 convertArray(mask, flag);
2290 Vector<Float> specout;
2291 mathutil::replaceMaskByZero(specout, mask);
2292 conv.linearConv(specout, spec);
2293 specCol.put(i, specout);
2294 }
2295 ++iter;
2296 }
2297 return out;
2298}
2299
2300CountedPtr< Scantable >
2301 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
2302{
2303 if ( in.size() < 2 ) {
2304 throw(AipsError("Need at least two scantables to perform a merge."));
2305 }
2306 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
2307 bool insitu = insitu_;
2308 setInsitu(false);
2309 CountedPtr< Scantable > out = getScantable(*it, false);
2310 setInsitu(insitu);
2311 Table& tout = out->table();
2312 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
2313 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
2314 // Renumber SCANNO to be 0-based
2315 Vector<uInt> scannos = scannocol.getColumn();
2316 uInt offset = min(scannos);
2317 scannos -= offset;
2318 scannocol.putColumn(scannos);
2319 uInt newscanno = max(scannos)+1;
2320 ++it;
2321 while ( it != in.end() ){
2322 if ( ! (*it)->conformant(*out) ) {
2323 // non conformant.
2324 //pushLog(String("Warning: Can't merge scantables as header info differs."));
2325 LogIO os( LogOrigin( "STMath", "merge()", WHERE ) ) ;
2326 os << LogIO::SEVERE << "Can't merge scantables as header informations (any one of AntennaName, Equinox, and FluxUnit) differ." << LogIO::EXCEPTION ;
2327 }
2328 out->appendToHistoryTable((*it)->history());
2329 const Table& tab = (*it)->table();
2330 TableIterator scanit(tab, "SCANNO");
2331 while (!scanit.pastEnd()) {
2332 TableIterator freqit(scanit.table(), "FREQ_ID");
2333 while ( !freqit.pastEnd() ) {
2334 Table thetab = freqit.table();
2335 uInt nrow = tout.nrow();
2336 tout.addRow(thetab.nrow());
2337 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
2338 ROTableRow row(thetab);
2339 for ( uInt i=0; i<thetab.nrow(); ++i) {
2340 uInt k = nrow+i;
2341 scannocol.put(k, newscanno);
2342 const TableRecord& rec = row.get(i);
2343 Double rv,rp,inc;
2344 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
2345 uInt id;
2346 id = out->frequencies().addEntry(rp, rv, inc);
2347 freqidcol.put(k,id);
2348 //String name,fname;Double rf;
2349 Vector<String> name,fname;Vector<Double> rf;
2350 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
2351 id = out->molecules().addEntry(rf, name, fname);
2352 molidcol.put(k, id);
2353 Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
2354 (*it)->focus().getEntry(fax, ftan, frot, fhand,
2355 fmount,fuser, fxy, fxyp,
2356 rec.asuInt("FOCUS_ID"));
2357 id = out->focus().addEntry(fax, ftan, frot, fhand,
2358 fmount,fuser, fxy, fxyp);
2359 focusidcol.put(k, id);
2360 }
2361 ++freqit;
2362 }
2363 ++newscanno;
2364 ++scanit;
2365 }
2366 ++it;
2367 }
2368 return out;
2369}
2370
2371CountedPtr< Scantable >
2372 STMath::invertPhase( const CountedPtr < Scantable >& in )
2373{
2374 return applyToPol(in, &STPol::invertPhase, Float(0.0));
2375}
2376
2377CountedPtr< Scantable >
2378 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
2379{
2380 return applyToPol(in, &STPol::rotatePhase, Float(phase));
2381}
2382
2383CountedPtr< Scantable >
2384 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
2385{
2386 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
2387}
2388
2389CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
2390 STPol::polOperation fptr,
2391 Float phase )
2392{
2393 CountedPtr< Scantable > out = getScantable(in, false);
2394 Table& tout = out->table();
2395 Block<String> cols(4);
2396 cols[0] = String("SCANNO");
2397 cols[1] = String("BEAMNO");
2398 cols[2] = String("IFNO");
2399 cols[3] = String("CYCLENO");
2400 TableIterator iter(tout, cols);
2401 CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
2402 out->getPolType() );
2403 while (!iter.pastEnd()) {
2404 Table t = iter.table();
2405 ArrayColumn<Float> speccol(t, "SPECTRA");
2406 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
2407 ScalarColumn<Float> parancol(t, "PARANGLE");
2408 Matrix<Float> pols(speccol.getColumn());
2409 try {
2410 stpol->setSpectra(pols);
2411 Float fang,fhand,parang;
2412 fang = in->focusTable_.getTotalFeedAngle(focidcol(0));
2413 fhand = in->focusTable_.getFeedHand(focidcol(0));
2414 parang = parancol(0);
2415 /// @todo re-enable this
2416 // disable total feed angle to support paralactifying Caswell style
2417 stpol->setPhaseCorrections(parang, -parang, fhand);
2418 // use a member function pointer in STPol. This only works on
2419 // the STPol pointer itself, not the Counted Pointer so
2420 // derefernce it.
2421 (&(*(stpol))->*fptr)(phase);
2422 speccol.putColumn(stpol->getSpectra());
2423 } catch (AipsError& e) {
2424 //delete stpol;stpol=0;
2425 throw(e);
2426 }
2427 ++iter;
2428 }
2429 //delete stpol;stpol=0;
2430 return out;
2431}
2432
2433CountedPtr< Scantable >
2434 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
2435{
2436 CountedPtr< Scantable > out = getScantable(in, false);
2437 Table& tout = out->table();
2438 Table t0 = tout(tout.col("POLNO") == 0);
2439 Table t1 = tout(tout.col("POLNO") == 1);
2440 if ( t0.nrow() != t1.nrow() )
2441 throw(AipsError("Inconsistent number of polarisations"));
2442 ArrayColumn<Float> speccol0(t0, "SPECTRA");
2443 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
2444 ArrayColumn<Float> speccol1(t1, "SPECTRA");
2445 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
2446 Matrix<Float> s0 = speccol0.getColumn();
2447 Matrix<uChar> f0 = flagcol0.getColumn();
2448 speccol0.putColumn(speccol1.getColumn());
2449 flagcol0.putColumn(flagcol1.getColumn());
2450 speccol1.putColumn(s0);
2451 flagcol1.putColumn(f0);
2452 return out;
2453}
2454
2455CountedPtr< Scantable >
2456 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
2457 const std::vector<bool>& mask,
2458 const std::string& weight )
2459{
2460 if (in->npol() < 2 )
2461 throw(AipsError("averagePolarisations can only be applied to two or more"
2462 "polarisations"));
2463 bool insitu = insitu_;
2464 setInsitu(false);
2465 CountedPtr< Scantable > pols = getScantable(in, true);
2466 setInsitu(insitu);
2467 Table& tout = pols->table();
2468 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
2469 Table tab = tableCommand(taql, in->table());
2470 if (tab.nrow() == 0 )
2471 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
2472 TableCopy::copyRows(tout, tab);
2473 TableVector<uInt> vec(tout, "POLNO");
2474 vec = 0;
2475 pols->table_.rwKeywordSet().define("nPol", Int(1));
2476 //pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
2477 pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
2478 std::vector<CountedPtr<Scantable> > vpols;
2479 vpols.push_back(pols);
2480 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
2481 return out;
2482}
2483
2484CountedPtr< Scantable >
2485 STMath::averageBeams( const CountedPtr< Scantable > & in,
2486 const std::vector<bool>& mask,
2487 const std::string& weight )
2488{
2489 bool insitu = insitu_;
2490 setInsitu(false);
2491 CountedPtr< Scantable > beams = getScantable(in, false);
2492 setInsitu(insitu);
2493 Table& tout = beams->table();
2494 // give all rows the same BEAMNO
2495 TableVector<uInt> vec(tout, "BEAMNO");
2496 vec = 0;
2497 beams->table_.rwKeywordSet().define("nBeam", Int(1));
2498 std::vector<CountedPtr<Scantable> > vbeams;
2499 vbeams.push_back(beams);
2500 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
2501 return out;
2502}
2503
2504
2505CountedPtr< Scantable >
2506 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
2507 const std::string & refTime,
2508 const std::string & method)
2509{
2510 // clone as this is not working insitu
2511 bool insitu = insitu_;
2512 setInsitu(false);
2513 CountedPtr< Scantable > out = getScantable(in, false);
2514 setInsitu(insitu);
2515 Table& tout = out->table();
2516 // Get reference Epoch to time of first row or given String
2517 Unit DAY(String("d"));
2518 MEpoch::Ref epochRef(in->getTimeReference());
2519 MEpoch refEpoch;
2520 if (refTime.length()>0) {
2521 Quantum<Double> qt;
2522 if (MVTime::read(qt,refTime)) {
2523 MVEpoch mv(qt);
2524 refEpoch = MEpoch(mv, epochRef);
2525 } else {
2526 throw(AipsError("Invalid format for Epoch string"));
2527 }
2528 } else {
2529 refEpoch = in->timeCol_(0);
2530 }
2531 MPosition refPos = in->getAntennaPosition();
2532
2533 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2534 /*
2535 // Comment from MV.
2536 // the following code has been commented out because different FREQ_IDs have to be aligned together even
2537 // if the frame doesn't change. So far, lack of this check didn't cause any problems.
2538 // test if user frame is different to base frame
2539 if ( in->frequencies().getFrameString(true)
2540 == in->frequencies().getFrameString(false) ) {
2541 throw(AipsError("Can't convert as no output frame has been set"
2542 " (use set_freqframe) or it is aligned already."));
2543 }
2544 */
2545 MFrequency::Types system = in->frequencies().getFrame();
2546 MVTime mvt(refEpoch.getValue());
2547 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
2548 ostringstream oss;
2549 oss << "Aligned at reference Epoch " << epochout
2550 << " in frame " << MFrequency::showType(system);
2551 pushLog(String(oss));
2552 // set up the iterator
2553 Block<String> cols(4);
2554 // select by constant direction
2555 cols[0] = String("SRCNAME");
2556 cols[1] = String("BEAMNO");
2557 // select by IF ( no of channels varies over this )
2558 cols[2] = String("IFNO");
2559 // select by restfrequency
2560 cols[3] = String("MOLECULE_ID");
2561 TableIterator iter(tout, cols);
2562 while ( !iter.pastEnd() ) {
2563 Table t = iter.table();
2564 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
2565 TableIterator fiter(t, "FREQ_ID");
2566 // determine nchan from the first row. This should work as
2567 // we are iterating over BEAMNO and IFNO // we should have constant direction
2568
2569 ROArrayColumn<Float> sCol(t, "SPECTRA");
2570 const MDirection direction = dirCol(0);
2571 const uInt nchan = sCol(0).nelements();
2572
2573 // skip operations if there is nothing to align
2574 if (fiter.pastEnd()) {
2575 continue;
2576 }
2577
2578 Table ftab = fiter.table();
2579 // align all frequency ids with respect to the first encountered id
2580 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
2581 // get the SpectralCoordinate for the freqid, which we are iterating over
2582 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
2583 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
2584 direction, refPos, system );
2585 // realign the SpectralCoordinate and put into the output Scantable
2586 Vector<String> units(1);
2587 units = String("Hz");
2588 Bool linear=True;
2589 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
2590 sc2.setWorldAxisUnits(units);
2591 const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
2592 sc2.referenceValue()[0],
2593 sc2.increment()[0]);
2594 while ( !fiter.pastEnd() ) {
2595 ftab = fiter.table();
2596 // spectral coordinate for the current FREQ_ID
2597 ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
2598 sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
2599 // create the "global" abcissa for alignment with same FREQ_ID
2600 Vector<Double> abc(nchan);
2601 for (uInt i=0; i<nchan; i++) {
2602 Double w;
2603 sC.toWorld(w,Double(i));
2604 abc[i] = w;
2605 }
2606 TableVector<uInt> tvec(ftab, "FREQ_ID");
2607 // assign new frequency id to all rows
2608 tvec = id;
2609 // cache abcissa for same time stamps, so iterate over those
2610 TableIterator timeiter(ftab, "TIME");
2611 while ( !timeiter.pastEnd() ) {
2612 Table tab = timeiter.table();
2613 ArrayColumn<Float> specCol(tab, "SPECTRA");
2614 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2615 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2616 // use align abcissa cache after the first row
2617 // these rows should be just be POLNO
2618 bool first = true;
2619 for (int i=0; i<int(tab.nrow()); ++i) {
2620 // input values
2621 Vector<uChar> flag = flagCol(i);
2622 Vector<Bool> mask(flag.shape());
2623 Vector<Float> specOut, spec;
2624 spec = specCol(i);
2625 Vector<Bool> maskOut;Vector<uChar> flagOut;
2626 convertArray(mask, flag);
2627 // alignment
2628 Bool ok = fa.align(specOut, maskOut, abc, spec,
2629 mask, timeCol(i), !first,
2630 interp, False);
2631 // back into scantable
2632 flagOut.resize(maskOut.nelements());
2633 convertArray(flagOut, maskOut);
2634 flagCol.put(i, flagOut);
2635 specCol.put(i, specOut);
2636 // start abcissa caching
2637 first = false;
2638 }
2639 // next timestamp
2640 ++timeiter;
2641 }
2642 // next FREQ_ID
2643 ++fiter;
2644 }
2645 // next aligner
2646 ++iter;
2647 }
2648 // set this afterwards to ensure we are doing insitu correctly.
2649 out->frequencies().setFrame(system, true);
2650 return out;
2651}
2652
2653CountedPtr<Scantable>
2654 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
2655 const std::string & newtype )
2656{
2657 if (in->npol() != 2 && in->npol() != 4)
2658 throw(AipsError("Can only convert two or four polarisations."));
2659 if ( in->getPolType() == newtype )
2660 throw(AipsError("No need to convert."));
2661 if ( ! in->selector_.empty() )
2662 throw(AipsError("Can only convert whole scantable. Unset the selection."));
2663 bool insitu = insitu_;
2664 setInsitu(false);
2665 CountedPtr< Scantable > out = getScantable(in, true);
2666 setInsitu(insitu);
2667 Table& tout = out->table();
2668 tout.rwKeywordSet().define("POLTYPE", String(newtype));
2669
2670 Block<String> cols(4);
2671 cols[0] = "SCANNO";
2672 cols[1] = "CYCLENO";
2673 cols[2] = "BEAMNO";
2674 cols[3] = "IFNO";
2675 TableIterator it(in->originalTable_, cols);
2676 String basetype = in->getPolType();
2677 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
2678 try {
2679 while ( !it.pastEnd() ) {
2680 Table tab = it.table();
2681 uInt row = tab.rowNumbers()[0];
2682 stpol->setSpectra(in->getPolMatrix(row));
2683 Float fang,fhand,parang;
2684 fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row));
2685 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
2686 parang = in->paraCol_(row);
2687 /// @todo re-enable this
2688 // disable total feed angle to support paralactifying Caswell style
2689 stpol->setPhaseCorrections(parang, -parang, fhand);
2690 Int npolout = 0;
2691 for (uInt i=0; i<tab.nrow(); ++i) {
2692 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
2693 if ( outvec.nelements() > 0 ) {
2694 tout.addRow();
2695 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
2696 ArrayColumn<Float> sCol(tout,"SPECTRA");
2697 ScalarColumn<uInt> pCol(tout,"POLNO");
2698 sCol.put(tout.nrow()-1 ,outvec);
2699 pCol.put(tout.nrow()-1 ,uInt(npolout));
2700 npolout++;
2701 }
2702 }
2703 tout.rwKeywordSet().define("nPol", npolout);
2704 ++it;
2705 }
2706 } catch (AipsError& e) {
2707 delete stpol;
2708 throw(e);
2709 }
2710 delete stpol;
2711 return out;
2712}
2713
2714CountedPtr< Scantable >
2715 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
2716 const std::string & scantype )
2717{
2718 bool insitu = insitu_;
2719 setInsitu(false);
2720 CountedPtr< Scantable > out = getScantable(in, true);
2721 setInsitu(insitu);
2722 Table& tout = out->table();
2723 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
2724 if (scantype == "on") {
2725 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
2726 }
2727 Table tab = tableCommand(taql, in->table());
2728 TableCopy::copyRows(tout, tab);
2729 if (scantype == "on") {
2730 // re-index SCANNO to 0
2731 TableVector<uInt> vec(tout, "SCANNO");
2732 vec = 0;
2733 }
2734 return out;
2735}
2736
2737CountedPtr< Scantable >
2738 asap::STMath::lagFlag( const CountedPtr< Scantable > & in,
2739 double frequency, double width )
2740{
2741 CountedPtr< Scantable > out = getScantable(in, false);
2742 Table& tout = out->table();
2743 TableIterator iter(tout, "FREQ_ID");
2744 FFTServer<Float,Complex> ffts;
2745 while ( !iter.pastEnd() ) {
2746 Table tab = iter.table();
2747 Double rp,rv,inc;
2748 ROTableRow row(tab);
2749 const TableRecord& rec = row.get(0);
2750 uInt freqid = rec.asuInt("FREQ_ID");
2751 out->frequencies().getEntry(rp, rv, inc, freqid);
2752 ArrayColumn<Float> specCol(tab, "SPECTRA");
2753 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2754 for (int i=0; i<int(tab.nrow()); ++i) {
2755 Vector<Float> spec = specCol(i);
2756 Vector<uChar> flag = flagCol(i);
2757 Int lag0 = Int(spec.nelements()*abs(inc)/(frequency+width)+0.5);
2758 Int lag1 = Int(spec.nelements()*abs(inc)/(frequency-width)+0.5);
2759 for (unsigned int k=0; k < flag.nelements(); ++k ) {
2760 if (flag[k] > 0) {
2761 spec[k] = 0.0;
2762 }
2763 }
2764 Vector<Complex> lags;
2765 ffts.fft0(lags, spec);
2766 Int start = max(0, lag0);
2767 Int end = min(Int(lags.nelements()-1), lag1);
2768 if (start == end) {
2769 lags[start] = Complex(0.0);
2770 } else {
2771 for (int j=start; j <=end ;++j) {
2772 lags[j] = Complex(0.0);
2773 }
2774 }
2775 ffts.fft0(spec, lags);
2776 specCol.put(i, spec);
2777 }
2778 ++iter;
2779 }
2780 return out;
2781}
2782
2783// Averaging spectra with different channel/resolution
2784CountedPtr<Scantable>
2785STMath::new_average( const std::vector<CountedPtr<Scantable> >& in,
2786 const bool& compel,
2787 const std::vector<bool>& mask,
2788 const std::string& weight,
2789 const std::string& avmode )
2790 throw ( casa::AipsError )
2791{
2792 LogIO os( LogOrigin( "STMath", "new_average()", WHERE ) ) ;
2793 if ( avmode == "SCAN" && in.size() != 1 )
2794 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
2795 "Use merge first."));
2796
2797 // check if OTF observation
2798 String obstype = in[0]->getHeader().obstype ;
2799 Double tol = 0.0 ;
2800 if ( obstype.find( "OTF" ) != String::npos ) {
2801 tol = TOL_OTF ;
2802 }
2803 else {
2804 tol = TOL_POINT ;
2805 }
2806
2807 CountedPtr<Scantable> out ; // processed result
2808 if ( compel ) {
2809 std::vector< CountedPtr<Scantable> > newin ; // input for average process
2810 uInt insize = in.size() ; // number of input scantables
2811
2812 // TEST: do normal average in each table before IF grouping
2813 os << "Do preliminary averaging" << LogIO::POST ;
2814 vector< CountedPtr<Scantable> > tmpin( insize ) ;
2815 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2816 vector< CountedPtr<Scantable> > v( 1, in[itable] ) ;
2817 tmpin[itable] = average( v, mask, weight, avmode ) ;
2818 }
2819
2820 // warning
2821 os << "Average spectra with different spectral resolution" << LogIO::POST ;
2822
2823 // temporarily set coordinfo
2824 vector<string> oldinfo( insize ) ;
2825 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2826 vector<string> coordinfo = in[itable]->getCoordInfo() ;
2827 oldinfo[itable] = coordinfo[0] ;
2828 coordinfo[0] = "Hz" ;
2829 tmpin[itable]->setCoordInfo( coordinfo ) ;
2830 }
2831
2832 // columns
2833 ScalarColumn<uInt> freqIDCol ;
2834 ScalarColumn<uInt> ifnoCol ;
2835 ScalarColumn<uInt> scannoCol ;
2836
2837
2838 // check IF frequency coverage
2839 // freqid: list of FREQ_ID, which is used, in each table
2840 // iffreq: list of minimum and maximum frequency for each FREQ_ID in
2841 // each table
2842 // freqid[insize][numIF]
2843 // freqid: [[id00, id01, ...],
2844 // [id10, id11, ...],
2845 // ...
2846 // [idn0, idn1, ...]]
2847 // iffreq[insize][numIF*2]
2848 // iffreq: [[min_id00, max_id00, min_id01, max_id01, ...],
2849 // [min_id10, max_id10, min_id11, max_id11, ...],
2850 // ...
2851 // [min_idn0, max_idn0, min_idn1, max_idn1, ...]]
2852 //os << "Check IF settings in each table" << LogIO::POST ;
2853 vector< vector<uInt> > freqid( insize );
2854 vector< vector<double> > iffreq( insize ) ;
2855 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2856 uInt rows = tmpin[itable]->nrow() ;
2857 uInt freqnrows = tmpin[itable]->frequencies().table().nrow() ;
2858 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
2859 if ( freqid[itable].size() == freqnrows ) {
2860 break ;
2861 }
2862 else {
2863 freqIDCol.attach( tmpin[itable]->table(), "FREQ_ID" ) ;
2864 ifnoCol.attach( tmpin[itable]->table(), "IFNO" ) ;
2865 uInt id = freqIDCol( irow ) ;
2866 if ( freqid[itable].size() == 0 || count( freqid[itable].begin(), freqid[itable].end(), id ) == 0 ) {
2867 //os << "itable = " << itable << ": IF " << id << " is included in the list" << LogIO::POST ;
2868 vector<double> abcissa = tmpin[itable]->getAbcissa( irow ) ;
2869 freqid[itable].push_back( id ) ;
2870 iffreq[itable].push_back( abcissa[0] - 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
2871 iffreq[itable].push_back( abcissa[abcissa.size()-1] + 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
2872 }
2873 }
2874 }
2875 }
2876
2877 // debug
2878 //os << "IF settings summary:" << endl ;
2879 //for ( uInt i = 0 ; i < freqid.size() ; i++ ) {
2880 //os << " Table" << i << endl ;
2881 //for ( uInt j = 0 ; j < freqid[i].size() ; j++ ) {
2882 //os << " id = " << freqid[i][j] << " (min,max) = (" << iffreq[i][2*j] << "," << iffreq[i][2*j+1] << ")" << endl ;
2883 //}
2884 //}
2885 //os << endl ;
2886 //os.post() ;
2887
2888 // IF grouping based on their frequency coverage
2889 // ifgrp: list of table index and FREQ_ID for all members in each IF group
2890 // ifgfreq: list of minimum and maximum frequency in each IF group
2891 // ifgrp[numgrp][nummember*2]
2892 // ifgrp: [[table00, freqrow00, table01, freqrow01, ...],
2893 // [table10, freqrow10, table11, freqrow11, ...],
2894 // ...
2895 // [tablen0, freqrown0, tablen1, freqrown1, ...]]
2896 // ifgfreq[numgrp*2]
2897 // ifgfreq: [min0_grp0, max0_grp0, min1_grp1, max1_grp1, ...]
2898 //os << "IF grouping based on their frequency coverage" << LogIO::POST ;
2899 vector< vector<uInt> > ifgrp ;
2900 vector<double> ifgfreq ;
2901
2902 // parameter for IF grouping
2903 // groupmode = OR retrieve all region
2904 // AND only retrieve overlaped region
2905 //string groupmode = "AND" ;
2906 string groupmode = "OR" ;
2907 uInt sizecr = 0 ;
2908 if ( groupmode == "AND" )
2909 sizecr = 2 ;
2910 else if ( groupmode == "OR" )
2911 sizecr = 0 ;
2912
2913 vector<double> sortedfreq ;
2914 for ( uInt i = 0 ; i < iffreq.size() ; i++ ) {
2915 for ( uInt j = 0 ; j < iffreq[i].size() ; j++ ) {
2916 if ( count( sortedfreq.begin(), sortedfreq.end(), iffreq[i][j] ) == 0 )
2917 sortedfreq.push_back( iffreq[i][j] ) ;
2918 }
2919 }
2920 sort( sortedfreq.begin(), sortedfreq.end() ) ;
2921 for ( vector<double>::iterator i = sortedfreq.begin() ; i != sortedfreq.end()-1 ; i++ ) {
2922 ifgfreq.push_back( *i ) ;
2923 ifgfreq.push_back( *(i+1) ) ;
2924 }
2925 ifgrp.resize( ifgfreq.size()/2 ) ;
2926 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2927 for ( uInt iif = 0 ; iif < freqid[itable].size() ; iif++ ) {
2928 double range0 = iffreq[itable][2*iif] ;
2929 double range1 = iffreq[itable][2*iif+1] ;
2930 for ( uInt j = 0 ; j < ifgrp.size() ; j++ ) {
2931 double fmin = max( range0, ifgfreq[2*j] ) ;
2932 double fmax = min( range1, ifgfreq[2*j+1] ) ;
2933 if ( fmin < fmax ) {
2934 ifgrp[j].push_back( itable ) ;
2935 ifgrp[j].push_back( freqid[itable][iif] ) ;
2936 }
2937 }
2938 }
2939 }
2940 vector< vector<uInt> >::iterator fiter = ifgrp.begin() ;
2941 vector<double>::iterator giter = ifgfreq.begin() ;
2942 while( fiter != ifgrp.end() ) {
2943 if ( fiter->size() <= sizecr ) {
2944 fiter = ifgrp.erase( fiter ) ;
2945 giter = ifgfreq.erase( giter ) ;
2946 giter = ifgfreq.erase( giter ) ;
2947 }
2948 else {
2949 fiter++ ;
2950 advance( giter, 2 ) ;
2951 }
2952 }
2953
2954 // Grouping continuous IF groups (without frequency gap)
2955 // freqgrp: list of IF group indexes in each frequency group
2956 // freqrange: list of minimum and maximum frequency in each frequency group
2957 // freqgrp[numgrp][nummember]
2958 // freqgrp: [[ifgrp00, ifgrp01, ifgrp02, ...],
2959 // [ifgrp10, ifgrp11, ifgrp12, ...],
2960 // ...
2961 // [ifgrpn0, ifgrpn1, ifgrpn2, ...]]
2962 // freqrange[numgrp*2]
2963 // freqrange: [min_grp0, max_grp0, min_grp1, max_grp1, ...]
2964 vector< vector<uInt> > freqgrp ;
2965 double freqrange = 0.0 ;
2966 uInt grpnum = 0 ;
2967 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
2968 // Assumed that ifgfreq was sorted
2969 if ( grpnum != 0 && freqrange == ifgfreq[2*i] ) {
2970 freqgrp[grpnum-1].push_back( i ) ;
2971 }
2972 else {
2973 vector<uInt> grp0( 1, i ) ;
2974 freqgrp.push_back( grp0 ) ;
2975 grpnum++ ;
2976 }
2977 freqrange = ifgfreq[2*i+1] ;
2978 }
2979
2980
2981 // print IF groups
2982 ostringstream oss ;
2983 oss << "IF Group summary: " << endl ;
2984 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
2985 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
2986 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
2987 for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
2988 oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
2989 }
2990 oss << endl ;
2991 }
2992 oss << endl ;
2993 os << oss.str() << LogIO::POST ;
2994
2995 // print frequency group
2996 oss.str("") ;
2997 oss << "Frequency Group summary: " << endl ;
2998 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: IF_GROUP_ID" << endl ;
2999 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3000 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*freqgrp[i][0]] << "," << ifgfreq[2*freqgrp[i][freqgrp[i].size()-1]+1] << "]: " ;
3001 for ( uInt j = 0 ; j < freqgrp[i].size() ; j++ ) {
3002 oss << freqgrp[i][j] << " " ;
3003 }
3004 oss << endl ;
3005 }
3006 oss << endl ;
3007 os << oss.str() << LogIO::POST ;
3008
3009 // membership check
3010 // groups: list of IF group indexes whose frequency range overlaps with
3011 // that of each table and IF
3012 // groups[numtable][numIF][nummembership]
3013 // groups: [[[grp, grp,...], [grp, grp,...],...],
3014 // [[grp, grp,...], [grp, grp,...],...],
3015 // ...
3016 // [[grp, grp,...], [grp, grp,...],...]]
3017 vector< vector< vector<uInt> > > groups( insize ) ;
3018 for ( uInt i = 0 ; i < insize ; i++ ) {
3019 groups[i].resize( freqid[i].size() ) ;
3020 }
3021 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3022 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3023 uInt tableid = ifgrp[igrp][2*imem] ;
3024 vector<uInt>::iterator iter = find( freqid[tableid].begin(), freqid[tableid].end(), ifgrp[igrp][2*imem+1] ) ;
3025 if ( iter != freqid[tableid].end() ) {
3026 uInt rowid = distance( freqid[tableid].begin(), iter ) ;
3027 groups[tableid][rowid].push_back( igrp ) ;
3028 }
3029 }
3030 }
3031
3032 // print membership
3033 //oss.str("") ;
3034 //for ( uInt i = 0 ; i < insize ; i++ ) {
3035 //oss << "Table " << i << endl ;
3036 //for ( uInt j = 0 ; j < groups[i].size() ; j++ ) {
3037 //oss << " FREQ_ID " << setw( 2 ) << freqid[i][j] << ": " ;
3038 //for ( uInt k = 0 ; k < groups[i][j].size() ; k++ ) {
3039 //oss << setw( 2 ) << groups[i][j][k] << " " ;
3040 //}
3041 //oss << endl ;
3042 //}
3043 //}
3044 //os << oss.str() << LogIO::POST ;
3045
3046 // set back coordinfo
3047 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3048 vector<string> coordinfo = tmpin[itable]->getCoordInfo() ;
3049 coordinfo[0] = oldinfo[itable] ;
3050 tmpin[itable]->setCoordInfo( coordinfo ) ;
3051 }
3052
3053 // Create additional table if needed
3054 bool oldInsitu = insitu_ ;
3055 setInsitu( false ) ;
3056 vector< vector<uInt> > addrow( insize ) ;
3057 vector<uInt> addtable( insize, 0 ) ;
3058 vector<uInt> newtableids( insize ) ;
3059 vector<uInt> newifids( insize, 0 ) ;
3060 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3061 //os << "Table " << itable << ": " ;
3062 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3063 addrow[itable].push_back( groups[itable][ifrow].size()-1 ) ;
3064 //os << addrow[itable][ifrow] << " " ;
3065 }
3066 addtable[itable] = *max_element( addrow[itable].begin(), addrow[itable].end() ) ;
3067 //os << "(" << addtable[itable] << ")" << LogIO::POST ;
3068 }
3069 newin.resize( insize ) ;
3070 copy( tmpin.begin(), tmpin.end(), newin.begin() ) ;
3071 for ( uInt i = 0 ; i < insize ; i++ ) {
3072 newtableids[i] = i ;
3073 }
3074 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3075 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3076 CountedPtr<Scantable> add = getScantable( newin[itable], false ) ;
3077 vector<int> freqidlist ;
3078 for ( uInt i = 0 ; i < groups[itable].size() ; i++ ) {
3079 if ( groups[itable][i].size() > iadd + 1 ) {
3080 freqidlist.push_back( freqid[itable][i] ) ;
3081 }
3082 }
3083 stringstream taqlstream ;
3084 taqlstream << "SELECT FROM $1 WHERE FREQ_ID IN [" ;
3085 for ( uInt i = 0 ; i < freqidlist.size() ; i++ ) {
3086 taqlstream << i ;
3087 if ( i < freqidlist.size() - 1 )
3088 taqlstream << "," ;
3089 else
3090 taqlstream << "]" ;
3091 }
3092 string taql = taqlstream.str() ;
3093 //os << "taql = " << taql << LogIO::POST ;
3094 STSelector selector = STSelector() ;
3095 selector.setTaQL( taql ) ;
3096 add->setSelection( selector ) ;
3097 newin.push_back( add ) ;
3098 newtableids.push_back( itable ) ;
3099 newifids.push_back( iadd + 1 ) ;
3100 }
3101 }
3102
3103 // udpate ifgrp
3104 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3105 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3106 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3107 if ( groups[itable][ifrow].size() > iadd + 1 ) {
3108 uInt igrp = groups[itable][ifrow][iadd+1] ;
3109 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3110 if ( ifgrp[igrp][2*imem] == newtableids[iadd+insize] && ifgrp[igrp][2*imem+1] == freqid[newtableids[iadd+insize]][ifrow] ) {
3111 ifgrp[igrp][2*imem] = insize + iadd ;
3112 }
3113 }
3114 }
3115 }
3116 }
3117 }
3118
3119 // print IF groups again for debug
3120 //oss.str( "" ) ;
3121 //oss << "IF Group summary: " << endl ;
3122 //oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3123 //for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3124 //oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3125 //for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3126 //oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3127 //}
3128 //oss << endl ;
3129 //}
3130 //oss << endl ;
3131 //os << oss.str() << LogIO::POST ;
3132
3133 // reset SCANNO and IFNO/FREQ_ID: IF is reset by the result of sortation
3134 os << "All scan number is set to 0" << LogIO::POST ;
3135 //os << "All IF number is set to IF group index" << LogIO::POST ;
3136 insize = newin.size() ;
3137 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3138 uInt rows = newin[itable]->nrow() ;
3139 Table &tmpt = newin[itable]->table() ;
3140 freqIDCol.attach( tmpt, "FREQ_ID" ) ;
3141 scannoCol.attach( tmpt, "SCANNO" ) ;
3142 ifnoCol.attach( tmpt, "IFNO" ) ;
3143 for ( uInt irow=0 ; irow < rows ; irow++ ) {
3144 scannoCol.put( irow, 0 ) ;
3145 uInt freqID = freqIDCol( irow ) ;
3146 vector<uInt>::iterator iter = find( freqid[newtableids[itable]].begin(), freqid[newtableids[itable]].end(), freqID ) ;
3147 if ( iter != freqid[newtableids[itable]].end() ) {
3148 uInt index = distance( freqid[newtableids[itable]].begin(), iter ) ;
3149 ifnoCol.put( irow, groups[newtableids[itable]][index][newifids[itable]] ) ;
3150 }
3151 else {
3152 throw(AipsError("IF grouping was wrong in additional tables.")) ;
3153 }
3154 }
3155 }
3156 oldinfo.resize( insize ) ;
3157 setInsitu( oldInsitu ) ;
3158
3159 // temporarily set coordinfo
3160 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3161 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3162 oldinfo[itable] = coordinfo[0] ;
3163 coordinfo[0] = "Hz" ;
3164 newin[itable]->setCoordInfo( coordinfo ) ;
3165 }
3166
3167 // save column values in the vector
3168 vector< vector<uInt> > freqTableIdVec( insize ) ;
3169 vector< vector<uInt> > freqIdVec( insize ) ;
3170 vector< vector<uInt> > ifNoVec( insize ) ;
3171 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3172 ScalarColumn<uInt> freqIDs ;
3173 freqIDs.attach( newin[itable]->frequencies().table(), "ID" ) ;
3174 ifnoCol.attach( newin[itable]->table(), "IFNO" ) ;
3175 freqIDCol.attach( newin[itable]->table(), "FREQ_ID" ) ;
3176 for ( uInt irow = 0 ; irow < newin[itable]->frequencies().table().nrow() ; irow++ ) {
3177 freqTableIdVec[itable].push_back( freqIDs( irow ) ) ;
3178 }
3179 for ( uInt irow = 0 ; irow < newin[itable]->table().nrow() ; irow++ ) {
3180 freqIdVec[itable].push_back( freqIDCol( irow ) ) ;
3181 ifNoVec[itable].push_back( ifnoCol( irow ) ) ;
3182 }
3183 }
3184
3185 // reset spectra and flagtra: pick up common part of frequency coverage
3186 //os << "Pick common frequency range and align resolution" << LogIO::POST ;
3187 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3188 uInt rows = newin[itable]->nrow() ;
3189 int nminchan = -1 ;
3190 int nmaxchan = -1 ;
3191 vector<uInt> freqIdUpdate ;
3192 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3193 uInt ifno = ifNoVec[itable][irow] ; // IFNO is reset by group index
3194 double minfreq = ifgfreq[2*ifno] ;
3195 double maxfreq = ifgfreq[2*ifno+1] ;
3196 //os << "frequency range: [" << minfreq << "," << maxfreq << "]" << LogIO::POST ;
3197 vector<double> abcissa = newin[itable]->getAbcissa( irow ) ;
3198 int nchan = abcissa.size() ;
3199 double resol = abcissa[1] - abcissa[0] ;
3200 //os << "abcissa range : [" << abcissa[0] << "," << abcissa[nchan-1] << "]" << LogIO::POST ;
3201 if ( minfreq <= abcissa[0] )
3202 nminchan = 0 ;
3203 else {
3204 //double cfreq = ( minfreq - abcissa[0] ) / resol ;
3205 double cfreq = ( minfreq - abcissa[0] + 0.5 * resol ) / resol ;
3206 nminchan = int(cfreq) + ( ( cfreq - int(cfreq) <= 0.5 ) ? 0 : 1 ) ;
3207 }
3208 if ( maxfreq >= abcissa[abcissa.size()-1] )
3209 nmaxchan = abcissa.size() - 1 ;
3210 else {
3211 //double cfreq = ( abcissa[abcissa.size()-1] - maxfreq ) / resol ;
3212 double cfreq = ( abcissa[abcissa.size()-1] - maxfreq + 0.5 * resol ) / resol ;
3213 nmaxchan = abcissa.size() - 1 - int(cfreq) - ( ( cfreq - int(cfreq) >= 0.5 ) ? 1 : 0 ) ;
3214 }
3215 //os << "channel range (" << irow << "): [" << nminchan << "," << nmaxchan << "]" << LogIO::POST ;
3216 if ( nmaxchan > nminchan ) {
3217 newin[itable]->reshapeSpectrum( nminchan, nmaxchan, irow ) ;
3218 int newchan = nmaxchan - nminchan + 1 ;
3219 if ( count( freqIdUpdate.begin(), freqIdUpdate.end(), freqIdVec[itable][irow] ) == 0 && newchan < nchan )
3220 freqIdUpdate.push_back( freqIdVec[itable][irow] ) ;
3221 }
3222 else {
3223 throw(AipsError("Failed to pick up common part of frequency range.")) ;
3224 }
3225 }
3226 for ( uInt i = 0 ; i < freqIdUpdate.size() ; i++ ) {
3227 uInt freqId = freqIdUpdate[i] ;
3228 Double refpix ;
3229 Double refval ;
3230 Double increment ;
3231
3232 // update row
3233 newin[itable]->frequencies().getEntry( refpix, refval, increment, freqId ) ;
3234 refval = refval - ( refpix - nminchan ) * increment ;
3235 refpix = 0 ;
3236 newin[itable]->frequencies().setEntry( refpix, refval, increment, freqId ) ;
3237 }
3238 }
3239
3240
3241 // reset spectra and flagtra: align spectral resolution
3242 //os << "Align spectral resolution" << LogIO::POST ;
3243 // gmaxdnu: the coarsest frequency resolution in the frequency group
3244 // gmemid: member index that have a resolution equal to gmaxdnu
3245 // gmaxdnu[numfreqgrp]
3246 // gmaxdnu: [dnu0, dnu1, ...]
3247 // gmemid[numfreqgrp]
3248 // gmemid: [id0, id1, ...]
3249 vector<double> gmaxdnu( freqgrp.size(), 0.0 ) ;
3250 vector<uInt> gmemid( freqgrp.size(), 0 ) ;
3251 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3252 double maxdnu = 0.0 ; // maximum (coarsest) frequency resolution
3253 int minchan = INT_MAX ; // minimum channel number
3254 Double refpixref = -1 ; // reference of 'reference pixel'
3255 Double refvalref = -1 ; // reference of 'reference frequency'
3256 Double refinc = -1 ; // reference frequency resolution
3257 uInt refreqid ;
3258 uInt reftable = INT_MAX;
3259 // process only if group member > 1
3260 if ( ifgrp[igrp].size() > 2 ) {
3261 // find minchan and maxdnu in each group
3262 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3263 uInt tableid = ifgrp[igrp][2*imem] ;
3264 uInt rowid = ifgrp[igrp][2*imem+1] ;
3265 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3266 if ( iter != freqIdVec[tableid].end() ) {
3267 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3268 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3269 int nchan = abcissa.size() ;
3270 double dnu = abcissa[1] - abcissa[0] ;
3271 //os << "GROUP " << igrp << " (" << tableid << "," << rowid << "): nchan = " << nchan << " (minchan = " << minchan << ")" << LogIO::POST ;
3272 if ( nchan < minchan ) {
3273 minchan = nchan ;
3274 maxdnu = dnu ;
3275 newin[tableid]->frequencies().getEntry( refpixref, refvalref, refinc, rowid ) ;
3276 refreqid = rowid ;
3277 reftable = tableid ;
3278 }
3279 }
3280 }
3281 // regrid spectra in each group
3282 os << "GROUP " << igrp << endl ;
3283 os << " Channel number is adjusted to " << minchan << endl ;
3284 os << " Corresponding frequency resolution is " << maxdnu << "Hz" << LogIO::POST ;
3285 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3286 uInt tableid = ifgrp[igrp][2*imem] ;
3287 uInt rowid = ifgrp[igrp][2*imem+1] ;
3288 freqIDCol.attach( newin[tableid]->table(), "FREQ_ID" ) ;
3289 //os << "tableid = " << tableid << " rowid = " << rowid << ": " << LogIO::POST ;
3290 //os << " regridChannel applied to " ;
3291 if ( tableid != reftable )
3292 refreqid = newin[tableid]->frequencies().addEntry( refpixref, refvalref, refinc ) ;
3293 for ( uInt irow = 0 ; irow < newin[tableid]->table().nrow() ; irow++ ) {
3294 uInt tfreqid = freqIdVec[tableid][irow] ;
3295 if ( tfreqid == rowid ) {
3296 //os << irow << " " ;
3297 newin[tableid]->regridChannel( minchan, maxdnu, irow ) ;
3298 freqIDCol.put( irow, refreqid ) ;
3299 freqIdVec[tableid][irow] = refreqid ;
3300 }
3301 }
3302 //os << LogIO::POST ;
3303 }
3304 }
3305 else {
3306 uInt tableid = ifgrp[igrp][0] ;
3307 uInt rowid = ifgrp[igrp][1] ;
3308 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3309 if ( iter != freqIdVec[tableid].end() ) {
3310 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3311 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3312 minchan = abcissa.size() ;
3313 maxdnu = abcissa[1] - abcissa[0] ;
3314 }
3315 }
3316 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3317 if ( count( freqgrp[i].begin(), freqgrp[i].end(), igrp ) > 0 ) {
3318 if ( maxdnu > gmaxdnu[i] ) {
3319 gmaxdnu[i] = maxdnu ;
3320 gmemid[i] = igrp ;
3321 }
3322 break ;
3323 }
3324 }
3325 }
3326
3327 // set back coordinfo
3328 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3329 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3330 coordinfo[0] = oldinfo[itable] ;
3331 newin[itable]->setCoordInfo( coordinfo ) ;
3332 }
3333
3334 // accumulate all rows into the first table
3335 // NOTE: assumed in.size() = 1
3336 vector< CountedPtr<Scantable> > tmp( 1 ) ;
3337 if ( newin.size() == 1 )
3338 tmp[0] = newin[0] ;
3339 else
3340 tmp[0] = merge( newin ) ;
3341
3342 //return tmp[0] ;
3343
3344 // average
3345 CountedPtr<Scantable> tmpout = average( tmp, mask, weight, avmode ) ;
3346
3347 //return tmpout ;
3348
3349 // combine frequency group
3350 os << "Combine spectra based on frequency grouping" << LogIO::POST ;
3351 os << "IFNO is renumbered as frequency group ID (see above)" << LogIO::POST ;
3352 vector<string> coordinfo = tmpout->getCoordInfo() ;
3353 oldinfo[0] = coordinfo[0] ;
3354 coordinfo[0] = "Hz" ;
3355 tmpout->setCoordInfo( coordinfo ) ;
3356 // create proformas of output table
3357 stringstream taqlstream ;
3358 taqlstream << "SELECT FROM $1 WHERE IFNO IN [" ;
3359 for ( uInt i = 0 ; i < gmemid.size() ; i++ ) {
3360 taqlstream << gmemid[i] ;
3361 if ( i < gmemid.size() - 1 )
3362 taqlstream << "," ;
3363 else
3364 taqlstream << "]" ;
3365 }
3366 string taql = taqlstream.str() ;
3367 //os << "taql = " << taql << LogIO::POST ;
3368 STSelector selector = STSelector() ;
3369 selector.setTaQL( taql ) ;
3370 oldInsitu = insitu_ ;
3371 setInsitu( false ) ;
3372 out = getScantable( tmpout, false ) ;
3373 setInsitu( oldInsitu ) ;
3374 out->setSelection( selector ) ;
3375 // regrid rows
3376 ifnoCol.attach( tmpout->table(), "IFNO" ) ;
3377 for ( uInt irow = 0 ; irow < tmpout->table().nrow() ; irow++ ) {
3378 uInt ifno = ifnoCol( irow ) ;
3379 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3380 if ( count( freqgrp[igrp].begin(), freqgrp[igrp].end(), ifno ) > 0 ) {
3381 vector<double> abcissa = tmpout->getAbcissa( irow ) ;
3382 double bw = ( abcissa[1] - abcissa[0] ) * abcissa.size() ;
3383 int nchan = (int)( bw / gmaxdnu[igrp] ) ;
3384 tmpout->regridChannel( nchan, gmaxdnu[igrp], irow ) ;
3385 break ;
3386 }
3387 }
3388 }
3389 // combine spectra
3390 ArrayColumn<Float> specColOut ;
3391 specColOut.attach( out->table(), "SPECTRA" ) ;
3392 ArrayColumn<uChar> flagColOut ;
3393 flagColOut.attach( out->table(), "FLAGTRA" ) ;
3394 ScalarColumn<uInt> ifnoColOut ;
3395 ifnoColOut.attach( out->table(), "IFNO" ) ;
3396 ScalarColumn<uInt> polnoColOut ;
3397 polnoColOut.attach( out->table(), "POLNO" ) ;
3398 ScalarColumn<uInt> freqidColOut ;
3399 freqidColOut.attach( out->table(), "FREQ_ID" ) ;
3400 MDirection::ScalarColumn dirColOut ;
3401 dirColOut.attach( out->table(), "DIRECTION" ) ;
3402 Table &tab = tmpout->table() ;
3403 Block<String> cols(1);
3404 cols[0] = String("POLNO") ;
3405 TableIterator iter( tab, cols ) ;
3406 bool done = false ;
3407 vector< vector<uInt> > sizes( freqgrp.size() ) ;
3408 while( !iter.pastEnd() ) {
3409 vector< vector<Float> > specout( freqgrp.size() ) ;
3410 vector< vector<uChar> > flagout( freqgrp.size() ) ;
3411 ArrayColumn<Float> specCols ;
3412 specCols.attach( iter.table(), "SPECTRA" ) ;
3413 ArrayColumn<uChar> flagCols ;
3414 flagCols.attach( iter.table(), "FLAGTRA" ) ;
3415 ifnoCol.attach( iter.table(), "IFNO" ) ;
3416 ScalarColumn<uInt> polnos ;
3417 polnos.attach( iter.table(), "POLNO" ) ;
3418 MDirection::ScalarColumn dircol ;
3419 dircol.attach( iter.table(), "DIRECTION" ) ;
3420 uInt polno = polnos( 0 ) ;
3421 //os << "POLNO iteration: " << polno << LogIO::POST ;
3422// for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3423// sizes[igrp].resize( freqgrp[igrp].size() ) ;
3424// for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3425// for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3426// uInt ifno = ifnoCol( irow ) ;
3427// if ( ifno == freqgrp[igrp][imem] ) {
3428// Vector<Float> spec = specCols( irow ) ;
3429// Vector<uChar> flag = flagCols( irow ) ;
3430// vector<Float> svec ;
3431// spec.tovector( svec ) ;
3432// vector<uChar> fvec ;
3433// flag.tovector( fvec ) ;
3434// //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3435// specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3436// flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3437// //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3438// sizes[igrp][imem] = spec.nelements() ;
3439// }
3440// }
3441// }
3442// for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3443// uInt ifout = ifnoColOut( irow ) ;
3444// uInt polout = polnoColOut( irow ) ;
3445// if ( ifout == gmemid[igrp] && polout == polno ) {
3446// // set SPECTRA and FRAGTRA
3447// Vector<Float> newspec( specout[igrp] ) ;
3448// Vector<uChar> newflag( flagout[igrp] ) ;
3449// specColOut.put( irow, newspec ) ;
3450// flagColOut.put( irow, newflag ) ;
3451// // IFNO renumbering
3452// ifnoColOut.put( irow, igrp ) ;
3453// }
3454// }
3455// }
3456 // get a list of number of channels for each frequency group member
3457 if ( !done ) {
3458 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3459 sizes[igrp].resize( freqgrp[igrp].size() ) ;
3460 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3461 for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3462 uInt ifno = ifnoCol( irow ) ;
3463 if ( ifno == freqgrp[igrp][imem] ) {
3464 Vector<Float> spec = specCols( irow ) ;
3465 sizes[igrp][imem] = spec.nelements() ;
3466 break ;
3467 }
3468 }
3469 }
3470 }
3471 done = true ;
3472 }
3473 // combine spectra
3474 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3475 uInt polout = polnoColOut( irow ) ;
3476 if ( polout == polno ) {
3477 uInt ifout = ifnoColOut( irow ) ;
3478 Vector<Double> direction = dirColOut(irow).getAngle(Unit(String("rad"))).getValue() ;
3479 uInt igrp ;
3480 for ( uInt jgrp = 0 ; jgrp < freqgrp.size() ; jgrp++ ) {
3481 if ( ifout == gmemid[jgrp] ) {
3482 igrp = jgrp ;
3483 break ;
3484 }
3485 }
3486 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3487 for ( uInt jrow = 0 ; jrow < iter.table().nrow() ; jrow++ ) {
3488 uInt ifno = ifnoCol( jrow ) ;
3489 Vector<Double> tdir = dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
3490 //if ( ifno == freqgrp[igrp][imem] && allTrue( tdir == direction ) ) {
3491 Double dx = tdir[0] - direction[0] ;
3492 Double dy = tdir[1] - direction[1] ;
3493 Double dd = sqrt( dx * dx + dy * dy ) ;
3494 //if ( ifno == freqgrp[igrp][imem] && allNearAbs( tdir, direction, tol ) ) {
3495 if ( ifno == freqgrp[igrp][imem] && dd <= tol ) {
3496 Vector<Float> spec = specCols( jrow ) ;
3497 Vector<uChar> flag = flagCols( jrow ) ;
3498 vector<Float> svec ;
3499 spec.tovector( svec ) ;
3500 vector<uChar> fvec ;
3501 flag.tovector( fvec ) ;
3502 //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3503 specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3504 flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3505 //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3506 }
3507 }
3508 }
3509 // set SPECTRA and FRAGTRA
3510 Vector<Float> newspec( specout[igrp] ) ;
3511 Vector<uChar> newflag( flagout[igrp] ) ;
3512 specColOut.put( irow, newspec ) ;
3513 flagColOut.put( irow, newflag ) ;
3514 // IFNO renumbering
3515 ifnoColOut.put( irow, igrp ) ;
3516 }
3517 }
3518 iter++ ;
3519 }
3520 // update FREQUENCIES subtable
3521 vector<bool> updated( freqgrp.size(), false ) ;
3522 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3523 uInt index = 0 ;
3524 uInt pixShift = 0 ;
3525 while ( freqgrp[igrp][index] != gmemid[igrp] ) {
3526 pixShift += sizes[igrp][index++] ;
3527 }
3528 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3529 if ( ifnoColOut( irow ) == gmemid[igrp] && !updated[igrp] ) {
3530 uInt freqidOut = freqidColOut( irow ) ;
3531 //os << "freqgrp " << igrp << " freqidOut = " << freqidOut << LogIO::POST ;
3532 double refpix ;
3533 double refval ;
3534 double increm ;
3535 out->frequencies().getEntry( refpix, refval, increm, freqidOut ) ;
3536 refpix += pixShift ;
3537 out->frequencies().setEntry( refpix, refval, increm, freqidOut ) ;
3538 updated[igrp] = true ;
3539 }
3540 }
3541 }
3542
3543 //out = tmpout ;
3544
3545 coordinfo = tmpout->getCoordInfo() ;
3546 coordinfo[0] = oldinfo[0] ;
3547 tmpout->setCoordInfo( coordinfo ) ;
3548 }
3549 else {
3550 // simple average
3551 out = average( in, mask, weight, avmode ) ;
3552 }
3553
3554 return out ;
3555}
3556
3557CountedPtr<Scantable> STMath::cwcal( const CountedPtr<Scantable>& s,
3558 const String calmode,
3559 const String antname )
3560{
3561 // frequency switch
3562 if ( calmode == "fs" ) {
3563 return cwcalfs( s, antname ) ;
3564 }
3565 else {
3566 vector<bool> masks = s->getMask( 0 ) ;
3567 vector<int> types ;
3568
3569 // sky scan
3570 STSelector sel = STSelector() ;
3571 types.push_back( SrcType::SKY ) ;
3572 sel.setTypes( types ) ;
3573 s->setSelection( sel ) ;
3574 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3575 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
3576 s->unsetSelection() ;
3577 sel.reset() ;
3578 types.clear() ;
3579
3580 // hot scan
3581 types.push_back( SrcType::HOT ) ;
3582 sel.setTypes( types ) ;
3583 s->setSelection( sel ) ;
3584 tmp.clear() ;
3585 tmp.push_back( getScantable( s, false ) ) ;
3586 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
3587 s->unsetSelection() ;
3588 sel.reset() ;
3589 types.clear() ;
3590
3591 // cold scan
3592 CountedPtr<Scantable> acold ;
3593// types.push_back( SrcType::COLD ) ;
3594// sel.setTypes( types ) ;
3595// s->setSelection( sel ) ;
3596// tmp.clear() ;
3597// tmp.push_back( getScantable( s, false ) ) ;
3598// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCNAN" ) ;
3599// s->unsetSelection() ;
3600// sel.reset() ;
3601// types.clear() ;
3602
3603 // off scan
3604 types.push_back( SrcType::PSOFF ) ;
3605 sel.setTypes( types ) ;
3606 s->setSelection( sel ) ;
3607 tmp.clear() ;
3608 tmp.push_back( getScantable( s, false ) ) ;
3609 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
3610 s->unsetSelection() ;
3611 sel.reset() ;
3612 types.clear() ;
3613
3614 // on scan
3615 bool insitu = insitu_ ;
3616 insitu_ = false ;
3617 CountedPtr<Scantable> out = getScantable( s, true ) ;
3618 insitu_ = insitu ;
3619 types.push_back( SrcType::PSON ) ;
3620 sel.setTypes( types ) ;
3621 s->setSelection( sel ) ;
3622 TableCopy::copyRows( out->table(), s->table() ) ;
3623 s->unsetSelection() ;
3624 sel.reset() ;
3625 types.clear() ;
3626
3627 // process each on scan
3628 ArrayColumn<Float> tsysCol ;
3629 tsysCol.attach( out->table(), "TSYS" ) ;
3630 for ( int i = 0 ; i < out->nrow() ; i++ ) {
3631 vector<float> sp = getCalibratedSpectra( out, aoff, asky, ahot, acold, i, antname ) ;
3632 out->setSpectrum( sp, i ) ;
3633 string reftime = out->getTime( i ) ;
3634 vector<int> ii( 1, out->getIF( i ) ) ;
3635 vector<int> ib( 1, out->getBeam( i ) ) ;
3636 vector<int> ip( 1, out->getPol( i ) ) ;
3637 sel.setIFs( ii ) ;
3638 sel.setBeams( ib ) ;
3639 sel.setPolarizations( ip ) ;
3640 asky->setSelection( sel ) ;
3641 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
3642 const Vector<Float> Vtsys( sptsys ) ;
3643 tsysCol.put( i, Vtsys ) ;
3644 asky->unsetSelection() ;
3645 sel.reset() ;
3646 }
3647
3648 // flux unit
3649 out->setFluxUnit( "K" ) ;
3650
3651 return out ;
3652 }
3653}
3654
3655CountedPtr<Scantable> STMath::almacal( const CountedPtr<Scantable>& s,
3656 const String calmode )
3657{
3658 // frequency switch
3659 if ( calmode == "fs" ) {
3660 return almacalfs( s ) ;
3661 }
3662 else {
3663 vector<bool> masks = s->getMask( 0 ) ;
3664
3665 // off scan
3666 STSelector sel = STSelector() ;
3667 vector<int> types ;
3668 types.push_back( SrcType::PSOFF ) ;
3669 sel.setTypes( types ) ;
3670 s->setSelection( sel ) ;
3671 // TODO 2010/01/08 TN
3672 // Grouping by time should be needed before averaging.
3673 // Each group must have own unique SCANNO (should be renumbered).
3674 // See PIPELINE/SDCalibration.py
3675 CountedPtr<Scantable> soff = getScantable( s, false ) ;
3676 Table ttab = soff->table() ;
3677 ROScalarColumn<Double> timeCol( ttab, "TIME" ) ;
3678 uInt nrow = timeCol.nrow() ;
3679 Vector<Double> timeSep( nrow - 1 ) ;
3680 for ( uInt i = 0 ; i < nrow - 1 ; i++ ) {
3681 timeSep[i] = timeCol(i+1) - timeCol(i) ;
3682 }
3683 ScalarColumn<Double> intervalCol( ttab, "INTERVAL" ) ;
3684 Vector<Double> interval = intervalCol.getColumn() ;
3685 interval /= 86400.0 ;
3686 ScalarColumn<uInt> scanCol( ttab, "SCANNO" ) ;
3687 vector<uInt> glist ;
3688 for ( uInt i = 0 ; i < nrow - 1 ; i++ ) {
3689 double gap = 2.0 * timeSep[i] / ( interval[i] + interval[i+1] ) ;
3690 //cout << "gap[" << i << "]=" << setw(5) << gap << endl ;
3691 if ( gap > 1.1 ) {
3692 glist.push_back( i ) ;
3693 }
3694 }
3695 Vector<uInt> gaplist( glist ) ;
3696 //cout << "gaplist = " << gaplist << endl ;
3697 uInt newid = 0 ;
3698 for ( uInt i = 0 ; i < nrow ; i++ ) {
3699 scanCol.put( i, newid ) ;
3700 if ( i == gaplist[newid] ) {
3701 newid++ ;
3702 }
3703 }
3704 //cout << "new scancol = " << scanCol.getColumn() << endl ;
3705 vector< CountedPtr<Scantable> > tmp( 1, soff ) ;
3706 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
3707 //cout << "aoff.nrow = " << aoff->nrow() << endl ;
3708 s->unsetSelection() ;
3709 sel.reset() ;
3710 types.clear() ;
3711
3712 // on scan
3713 bool insitu = insitu_ ;
3714 insitu_ = false ;
3715 CountedPtr<Scantable> out = getScantable( s, true ) ;
3716 insitu_ = insitu ;
3717 types.push_back( SrcType::PSON ) ;
3718 sel.setTypes( types ) ;
3719 s->setSelection( sel ) ;
3720 TableCopy::copyRows( out->table(), s->table() ) ;
3721 s->unsetSelection() ;
3722 sel.reset() ;
3723 types.clear() ;
3724
3725 // process each on scan
3726 ArrayColumn<Float> tsysCol ;
3727 tsysCol.attach( out->table(), "TSYS" ) ;
3728 for ( int i = 0 ; i < out->nrow() ; i++ ) {
3729 vector<float> sp = getCalibratedSpectra( out, aoff, i ) ;
3730 out->setSpectrum( sp, i ) ;
3731 }
3732
3733 // flux unit
3734 out->setFluxUnit( "K" ) ;
3735
3736 return out ;
3737 }
3738}
3739
3740CountedPtr<Scantable> STMath::cwcalfs( const CountedPtr<Scantable>& s,
3741 const String antname )
3742{
3743 vector<int> types ;
3744
3745 // APEX calibration mode
3746 int apexcalmode = 1 ;
3747
3748 if ( antname.find( "APEX" ) != string::npos ) {
3749 // check if off scan exists or not
3750 STSelector sel = STSelector() ;
3751 //sel.setName( offstr1 ) ;
3752 types.push_back( SrcType::FLOOFF ) ;
3753 sel.setTypes( types ) ;
3754 try {
3755 s->setSelection( sel ) ;
3756 }
3757 catch ( AipsError &e ) {
3758 apexcalmode = 0 ;
3759 }
3760 sel.reset() ;
3761 }
3762 s->unsetSelection() ;
3763 types.clear() ;
3764
3765 vector<bool> masks = s->getMask( 0 ) ;
3766 CountedPtr<Scantable> ssig, sref ;
3767 CountedPtr<Scantable> out ;
3768
3769 if ( antname.find( "APEX" ) != string::npos ) {
3770 // APEX calibration
3771 // sky scan
3772 STSelector sel = STSelector() ;
3773 types.push_back( SrcType::FLOSKY ) ;
3774 sel.setTypes( types ) ;
3775 s->setSelection( sel ) ;
3776 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3777 CountedPtr<Scantable> askylo = average( tmp, masks, "TINT", "SCAN" ) ;
3778 s->unsetSelection() ;
3779 sel.reset() ;
3780 types.clear() ;
3781 types.push_back( SrcType::FHISKY ) ;
3782 sel.setTypes( types ) ;
3783 s->setSelection( sel ) ;
3784 tmp.clear() ;
3785 tmp.push_back( getScantable( s, false ) ) ;
3786 CountedPtr<Scantable> askyhi = average( tmp, masks, "TINT", "SCAN" ) ;
3787 s->unsetSelection() ;
3788 sel.reset() ;
3789 types.clear() ;
3790
3791 // hot scan
3792 types.push_back( SrcType::FLOHOT ) ;
3793 sel.setTypes( types ) ;
3794 s->setSelection( sel ) ;
3795 tmp.clear() ;
3796 tmp.push_back( getScantable( s, false ) ) ;
3797 CountedPtr<Scantable> ahotlo = average( tmp, masks, "TINT", "SCAN" ) ;
3798 s->unsetSelection() ;
3799 sel.reset() ;
3800 types.clear() ;
3801 types.push_back( SrcType::FHIHOT ) ;
3802 sel.setTypes( types ) ;
3803 s->setSelection( sel ) ;
3804 tmp.clear() ;
3805 tmp.push_back( getScantable( s, false ) ) ;
3806 CountedPtr<Scantable> ahothi = average( tmp, masks, "TINT", "SCAN" ) ;
3807 s->unsetSelection() ;
3808 sel.reset() ;
3809 types.clear() ;
3810
3811 // cold scan
3812 CountedPtr<Scantable> acoldlo, acoldhi ;
3813// types.push_back( SrcType::FLOCOLD ) ;
3814// sel.setTypes( types ) ;
3815// s->setSelection( sel ) ;
3816// tmp.clear() ;
3817// tmp.push_back( getScantable( s, false ) ) ;
3818// CountedPtr<Scantable> acoldlo = average( tmp, masks, "TINT", "SCAN" ) ;
3819// s->unsetSelection() ;
3820// sel.reset() ;
3821// types.clear() ;
3822// types.push_back( SrcType::FHICOLD ) ;
3823// sel.setTypes( types ) ;
3824// s->setSelection( sel ) ;
3825// tmp.clear() ;
3826// tmp.push_back( getScantable( s, false ) ) ;
3827// CountedPtr<Scantable> acoldhi = average( tmp, masks, "TINT", "SCAN" ) ;
3828// s->unsetSelection() ;
3829// sel.reset() ;
3830// types.clear() ;
3831
3832 // ref scan
3833 bool insitu = insitu_ ;
3834 insitu_ = false ;
3835 sref = getScantable( s, true ) ;
3836 insitu_ = insitu ;
3837 types.push_back( SrcType::FSLO ) ;
3838 sel.setTypes( types ) ;
3839 s->setSelection( sel ) ;
3840 TableCopy::copyRows( sref->table(), s->table() ) ;
3841 s->unsetSelection() ;
3842 sel.reset() ;
3843 types.clear() ;
3844
3845 // sig scan
3846 insitu_ = false ;
3847 ssig = getScantable( s, true ) ;
3848 insitu_ = insitu ;
3849 types.push_back( SrcType::FSHI ) ;
3850 sel.setTypes( types ) ;
3851 s->setSelection( sel ) ;
3852 TableCopy::copyRows( ssig->table(), s->table() ) ;
3853 s->unsetSelection() ;
3854 sel.reset() ;
3855 types.clear() ;
3856
3857 if ( apexcalmode == 0 ) {
3858 // APEX fs data without off scan
3859 // process each sig and ref scan
3860 ArrayColumn<Float> tsysCollo ;
3861 tsysCollo.attach( ssig->table(), "TSYS" ) ;
3862 ArrayColumn<Float> tsysColhi ;
3863 tsysColhi.attach( sref->table(), "TSYS" ) ;
3864 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
3865 vector< CountedPtr<Scantable> > sky( 2 ) ;
3866 sky[0] = askylo ;
3867 sky[1] = askyhi ;
3868 vector< CountedPtr<Scantable> > hot( 2 ) ;
3869 hot[0] = ahotlo ;
3870 hot[1] = ahothi ;
3871 vector< CountedPtr<Scantable> > cold( 2 ) ;
3872 //cold[0] = acoldlo ;
3873 //cold[1] = acoldhi ;
3874 vector<float> sp = getFSCalibratedSpectra( ssig, sref, sky, hot, cold, i ) ;
3875 ssig->setSpectrum( sp, i ) ;
3876 string reftime = ssig->getTime( i ) ;
3877 vector<int> ii( 1, ssig->getIF( i ) ) ;
3878 vector<int> ib( 1, ssig->getBeam( i ) ) ;
3879 vector<int> ip( 1, ssig->getPol( i ) ) ;
3880 sel.setIFs( ii ) ;
3881 sel.setBeams( ib ) ;
3882 sel.setPolarizations( ip ) ;
3883 askylo->setSelection( sel ) ;
3884 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
3885 const Vector<Float> Vtsyslo( sptsys ) ;
3886 tsysCollo.put( i, Vtsyslo ) ;
3887 askylo->unsetSelection() ;
3888 sel.reset() ;
3889 sky[0] = askyhi ;
3890 sky[1] = askylo ;
3891 hot[0] = ahothi ;
3892 hot[1] = ahotlo ;
3893 cold[0] = acoldhi ;
3894 cold[1] = acoldlo ;
3895 sp = getFSCalibratedSpectra( sref, ssig, sky, hot, cold, i ) ;
3896 sref->setSpectrum( sp, i ) ;
3897 reftime = sref->getTime( i ) ;
3898 ii[0] = sref->getIF( i ) ;
3899 ib[0] = sref->getBeam( i ) ;
3900 ip[0] = sref->getPol( i ) ;
3901 sel.setIFs( ii ) ;
3902 sel.setBeams( ib ) ;
3903 sel.setPolarizations( ip ) ;
3904 askyhi->setSelection( sel ) ;
3905 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
3906 const Vector<Float> Vtsyshi( sptsys ) ;
3907 tsysColhi.put( i, Vtsyshi ) ;
3908 askyhi->unsetSelection() ;
3909 sel.reset() ;
3910 }
3911 }
3912 else if ( apexcalmode == 1 ) {
3913 // APEX fs data with off scan
3914 // off scan
3915 types.push_back( SrcType::FLOOFF ) ;
3916 sel.setTypes( types ) ;
3917 s->setSelection( sel ) ;
3918 tmp.clear() ;
3919 tmp.push_back( getScantable( s, false ) ) ;
3920 CountedPtr<Scantable> aofflo = average( tmp, masks, "TINT", "SCAN" ) ;
3921 s->unsetSelection() ;
3922 sel.reset() ;
3923 types.clear() ;
3924 types.push_back( SrcType::FHIOFF ) ;
3925 sel.setTypes( types ) ;
3926 s->setSelection( sel ) ;
3927 tmp.clear() ;
3928 tmp.push_back( getScantable( s, false ) ) ;
3929 CountedPtr<Scantable> aoffhi = average( tmp, masks, "TINT", "SCAN" ) ;
3930 s->unsetSelection() ;
3931 sel.reset() ;
3932 types.clear() ;
3933
3934 // process each sig and ref scan
3935 ArrayColumn<Float> tsysCollo ;
3936 tsysCollo.attach( ssig->table(), "TSYS" ) ;
3937 ArrayColumn<Float> tsysColhi ;
3938 tsysColhi.attach( sref->table(), "TSYS" ) ;
3939 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
3940 vector<float> sp = getCalibratedSpectra( ssig, aofflo, askylo, ahotlo, acoldlo, i, antname ) ;
3941 ssig->setSpectrum( sp, i ) ;
3942 sp = getCalibratedSpectra( sref, aoffhi, askyhi, ahothi, acoldhi, i, antname ) ;
3943 string reftime = ssig->getTime( i ) ;
3944 vector<int> ii( 1, ssig->getIF( i ) ) ;
3945 vector<int> ib( 1, ssig->getBeam( i ) ) ;
3946 vector<int> ip( 1, ssig->getPol( i ) ) ;
3947 sel.setIFs( ii ) ;
3948 sel.setBeams( ib ) ;
3949 sel.setPolarizations( ip ) ;
3950 askylo->setSelection( sel ) ;
3951 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
3952 const Vector<Float> Vtsyslo( sptsys ) ;
3953 tsysCollo.put( i, Vtsyslo ) ;
3954 askylo->unsetSelection() ;
3955 sel.reset() ;
3956 sref->setSpectrum( sp, i ) ;
3957 reftime = sref->getTime( i ) ;
3958 ii[0] = sref->getIF( i ) ;
3959 ib[0] = sref->getBeam( i ) ;
3960 ip[0] = sref->getPol( i ) ;
3961 sel.setIFs( ii ) ;
3962 sel.setBeams( ib ) ;
3963 sel.setPolarizations( ip ) ;
3964 askyhi->setSelection( sel ) ;
3965 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
3966 const Vector<Float> Vtsyshi( sptsys ) ;
3967 tsysColhi.put( i, Vtsyshi ) ;
3968 askyhi->unsetSelection() ;
3969 sel.reset() ;
3970 }
3971 }
3972 }
3973 else {
3974 // non-APEX fs data
3975 // sky scan
3976 STSelector sel = STSelector() ;
3977 types.push_back( SrcType::SKY ) ;
3978 sel.setTypes( types ) ;
3979 s->setSelection( sel ) ;
3980 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3981 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
3982 s->unsetSelection() ;
3983 sel.reset() ;
3984 types.clear() ;
3985
3986 // hot scan
3987 types.push_back( SrcType::HOT ) ;
3988 sel.setTypes( types ) ;
3989 s->setSelection( sel ) ;
3990 tmp.clear() ;
3991 tmp.push_back( getScantable( s, false ) ) ;
3992 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
3993 s->unsetSelection() ;
3994 sel.reset() ;
3995 types.clear() ;
3996
3997 // cold scan
3998 CountedPtr<Scantable> acold ;
3999// types.push_back( SrcType::COLD ) ;
4000// sel.setTypes( types ) ;
4001// s->setSelection( sel ) ;
4002// tmp.clear() ;
4003// tmp.push_back( getScantable( s, false ) ) ;
4004// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCAN" ) ;
4005// s->unsetSelection() ;
4006// sel.reset() ;
4007// types.clear() ;
4008
4009 // ref scan
4010 bool insitu = insitu_ ;
4011 insitu_ = false ;
4012 sref = getScantable( s, true ) ;
4013 insitu_ = insitu ;
4014 types.push_back( SrcType::FSOFF ) ;
4015 sel.setTypes( types ) ;
4016 s->setSelection( sel ) ;
4017 TableCopy::copyRows( sref->table(), s->table() ) ;
4018 s->unsetSelection() ;
4019 sel.reset() ;
4020 types.clear() ;
4021
4022 // sig scan
4023 insitu_ = false ;
4024 ssig = getScantable( s, true ) ;
4025 insitu_ = insitu ;
4026 types.push_back( SrcType::FSON ) ;
4027 sel.setTypes( types ) ;
4028 s->setSelection( sel ) ;
4029 TableCopy::copyRows( ssig->table(), s->table() ) ;
4030 s->unsetSelection() ;
4031 sel.reset() ;
4032 types.clear() ;
4033
4034 // process each sig and ref scan
4035 ArrayColumn<Float> tsysColsig ;
4036 tsysColsig.attach( ssig->table(), "TSYS" ) ;
4037 ArrayColumn<Float> tsysColref ;
4038 tsysColref.attach( ssig->table(), "TSYS" ) ;
4039 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4040 vector<float> sp = getFSCalibratedSpectra( ssig, sref, asky, ahot, acold, i ) ;
4041 ssig->setSpectrum( sp, i ) ;
4042 string reftime = ssig->getTime( i ) ;
4043 vector<int> ii( 1, ssig->getIF( i ) ) ;
4044 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4045 vector<int> ip( 1, ssig->getPol( i ) ) ;
4046 sel.setIFs( ii ) ;
4047 sel.setBeams( ib ) ;
4048 sel.setPolarizations( ip ) ;
4049 asky->setSelection( sel ) ;
4050 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
4051 const Vector<Float> Vtsys( sptsys ) ;
4052 tsysColsig.put( i, Vtsys ) ;
4053 asky->unsetSelection() ;
4054 sel.reset() ;
4055 sp = getFSCalibratedSpectra( sref, ssig, asky, ahot, acold, i ) ;
4056 sref->setSpectrum( sp, i ) ;
4057 tsysColref.put( i, Vtsys ) ;
4058 }
4059 }
4060
4061 // do folding if necessary
4062 Table sigtab = ssig->table() ;
4063 Table reftab = sref->table() ;
4064 ScalarColumn<uInt> sigifnoCol ;
4065 ScalarColumn<uInt> refifnoCol ;
4066 ScalarColumn<uInt> sigfidCol ;
4067 ScalarColumn<uInt> reffidCol ;
4068 Int nchan = (Int)ssig->nchan() ;
4069 sigifnoCol.attach( sigtab, "IFNO" ) ;
4070 refifnoCol.attach( reftab, "IFNO" ) ;
4071 sigfidCol.attach( sigtab, "FREQ_ID" ) ;
4072 reffidCol.attach( reftab, "FREQ_ID" ) ;
4073 Vector<uInt> sfids( sigfidCol.getColumn() ) ;
4074 Vector<uInt> rfids( reffidCol.getColumn() ) ;
4075 vector<uInt> sfids_unique ;
4076 vector<uInt> rfids_unique ;
4077 vector<uInt> sifno_unique ;
4078 vector<uInt> rifno_unique ;
4079 for ( uInt i = 0 ; i < sfids.nelements() ; i++ ) {
4080 if ( count( sfids_unique.begin(), sfids_unique.end(), sfids[i] ) == 0 ) {
4081 sfids_unique.push_back( sfids[i] ) ;
4082 sifno_unique.push_back( ssig->getIF( i ) ) ;
4083 }
4084 if ( count( rfids_unique.begin(), rfids_unique.end(), rfids[i] ) == 0 ) {
4085 rfids_unique.push_back( rfids[i] ) ;
4086 rifno_unique.push_back( sref->getIF( i ) ) ;
4087 }
4088 }
4089 double refpix_sig, refval_sig, increment_sig ;
4090 double refpix_ref, refval_ref, increment_ref ;
4091 vector< CountedPtr<Scantable> > tmp( sfids_unique.size() ) ;
4092 for ( uInt i = 0 ; i < sfids_unique.size() ; i++ ) {
4093 ssig->frequencies().getEntry( refpix_sig, refval_sig, increment_sig, sfids_unique[i] ) ;
4094 sref->frequencies().getEntry( refpix_ref, refval_ref, increment_ref, rfids_unique[i] ) ;
4095 if ( refpix_sig == refpix_ref ) {
4096 double foffset = refval_ref - refval_sig ;
4097 int choffset = static_cast<int>(foffset/increment_sig) ;
4098 double doffset = foffset / increment_sig ;
4099 if ( abs(choffset) >= nchan ) {
4100 LogIO os( LogOrigin( "STMath", "cwcalfs", WHERE ) ) ;
4101 os << "FREQ_ID=[" << sfids_unique[i] << "," << rfids_unique[i] << "]: out-band frequency switching, no folding" << LogIO::POST ;
4102 os << "Just return signal data" << LogIO::POST ;
4103 //std::vector< CountedPtr<Scantable> > tabs ;
4104 //tabs.push_back( ssig ) ;
4105 //tabs.push_back( sref ) ;
4106 //out = merge( tabs ) ;
4107 tmp[i] = ssig ;
4108 }
4109 else {
4110 STSelector sel = STSelector() ;
4111 vector<int> v( 1, sifno_unique[i] ) ;
4112 sel.setIFs( v ) ;
4113 ssig->setSelection( sel ) ;
4114 sel.reset() ;
4115 v[0] = rifno_unique[i] ;
4116 sel.setIFs( v ) ;
4117 sref->setSelection( sel ) ;
4118 sel.reset() ;
4119 if ( antname.find( "APEX" ) != string::npos ) {
4120 tmp[i] = dofold( ssig, sref, 0.5*doffset, -0.5*doffset ) ;
4121 //tmp[i] = dofold( ssig, sref, doffset ) ;
4122 }
4123 else {
4124 tmp[i] = dofold( ssig, sref, doffset ) ;
4125 }
4126 ssig->unsetSelection() ;
4127 sref->unsetSelection() ;
4128 }
4129 }
4130 }
4131
4132 if ( tmp.size() > 1 ) {
4133 out = merge( tmp ) ;
4134 }
4135 else {
4136 out = tmp[0] ;
4137 }
4138
4139 // flux unit
4140 out->setFluxUnit( "K" ) ;
4141
4142 return out ;
4143}
4144
4145CountedPtr<Scantable> STMath::almacalfs( const CountedPtr<Scantable>& s )
4146{
4147 CountedPtr<Scantable> out ;
4148
4149 return out ;
4150}
4151
4152vector<float> STMath::getSpectrumFromTime( string reftime,
4153 CountedPtr<Scantable>& s,
4154 string mode )
4155{
4156 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
4157 vector<float> sp ;
4158
4159 if ( s->nrow() == 0 ) {
4160 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
4161 return sp ;
4162 }
4163 else if ( s->nrow() == 1 ) {
4164 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
4165 return s->getSpectrum( 0 ) ;
4166 }
4167 else {
4168 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4169 if ( mode == "before" ) {
4170 int id = -1 ;
4171 if ( idx[0] != -1 ) {
4172 id = idx[0] ;
4173 }
4174 else if ( idx[1] != -1 ) {
4175 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4176 id = idx[1] ;
4177 }
4178 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4179 sp = s->getSpectrum( id ) ;
4180 }
4181 else if ( mode == "after" ) {
4182 int id = -1 ;
4183 if ( idx[1] != -1 ) {
4184 id = idx[1] ;
4185 }
4186 else if ( idx[0] != -1 ) {
4187 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4188 id = idx[1] ;
4189 }
4190 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4191 sp = s->getSpectrum( id ) ;
4192 }
4193 else if ( mode == "nearest" ) {
4194 int id = -1 ;
4195 if ( idx[0] == -1 ) {
4196 id = idx[1] ;
4197 }
4198 else if ( idx[1] == -1 ) {
4199 id = idx[0] ;
4200 }
4201 else if ( idx[0] == idx[1] ) {
4202 id = idx[0] ;
4203 }
4204 else {
4205 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4206 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4207 double tref = getMJD( reftime ) ;
4208 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4209 id = idx[1] ;
4210 }
4211 else {
4212 id = idx[0] ;
4213 }
4214 }
4215 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4216 sp = s->getSpectrum( id ) ;
4217 }
4218 else if ( mode == "linear" ) {
4219 if ( idx[0] == -1 ) {
4220 // use after
4221 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4222 int id = idx[1] ;
4223 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4224 sp = s->getSpectrum( id ) ;
4225 }
4226 else if ( idx[1] == -1 ) {
4227 // use before
4228 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4229 int id = idx[0] ;
4230 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4231 sp = s->getSpectrum( id ) ;
4232 }
4233 else if ( idx[0] == idx[1] ) {
4234 // use before
4235 //os << "No need to interporate." << LogIO::POST ;
4236 int id = idx[0] ;
4237 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4238 sp = s->getSpectrum( id ) ;
4239 }
4240 else {
4241 // do interpolation
4242 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4243 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4244 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4245 double tref = getMJD( reftime ) ;
4246 vector<float> sp0 = s->getSpectrum( idx[0] ) ;
4247 vector<float> sp1 = s->getSpectrum( idx[1] ) ;
4248 for ( unsigned int i = 0 ; i < sp0.size() ; i++ ) {
4249 float v = ( sp1[i] - sp0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + sp0[i] ;
4250 sp.push_back( v ) ;
4251 }
4252 }
4253 }
4254 else {
4255 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4256 }
4257 return sp ;
4258 }
4259}
4260
4261double STMath::getMJD( string strtime )
4262{
4263 if ( strtime.find("/") == string::npos ) {
4264 // MJD time string
4265 return atof( strtime.c_str() ) ;
4266 }
4267 else {
4268 // string in YYYY/MM/DD/HH:MM:SS format
4269 uInt year = atoi( strtime.substr( 0, 4 ).c_str() ) ;
4270 uInt month = atoi( strtime.substr( 5, 2 ).c_str() ) ;
4271 uInt day = atoi( strtime.substr( 8, 2 ).c_str() ) ;
4272 uInt hour = atoi( strtime.substr( 11, 2 ).c_str() ) ;
4273 uInt minute = atoi( strtime.substr( 14, 2 ).c_str() ) ;
4274 uInt sec = atoi( strtime.substr( 17, 2 ).c_str() ) ;
4275 Time t( year, month, day, hour, minute, sec ) ;
4276 return t.modifiedJulianDay() ;
4277 }
4278}
4279
4280vector<int> STMath::getRowIdFromTime( string reftime, CountedPtr<Scantable> &s )
4281{
4282 double reft = getMJD( reftime ) ;
4283 double dtmin = 1.0e100 ;
4284 double dtmax = -1.0e100 ;
4285 vector<double> dt ;
4286 int just_before = -1 ;
4287 int just_after = -1 ;
4288 for ( int i = 0 ; i < s->nrow() ; i++ ) {
4289 dt.push_back( getMJD( s->getTime( i ) ) - reft ) ;
4290 }
4291 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4292 if ( dt[i] > 0.0 ) {
4293 // after reftime
4294 if ( dt[i] < dtmin ) {
4295 just_after = i ;
4296 dtmin = dt[i] ;
4297 }
4298 }
4299 else if ( dt[i] < 0.0 ) {
4300 // before reftime
4301 if ( dt[i] > dtmax ) {
4302 just_before = i ;
4303 dtmax = dt[i] ;
4304 }
4305 }
4306 else {
4307 // just a reftime
4308 just_before = i ;
4309 just_after = i ;
4310 dtmax = 0 ;
4311 dtmin = 0 ;
4312 break ;
4313 }
4314 }
4315
4316 vector<int> v ;
4317 v.push_back( just_before ) ;
4318 v.push_back( just_after ) ;
4319
4320 return v ;
4321}
4322
4323vector<float> STMath::getTcalFromTime( string reftime,
4324 CountedPtr<Scantable>& s,
4325 string mode )
4326{
4327 LogIO os( LogOrigin( "STMath", "getTcalFromTime", WHERE ) ) ;
4328 vector<float> tcal ;
4329 STTcal tcalTable = s->tcal() ;
4330 String time ;
4331 Vector<Float> tcalval ;
4332 if ( s->nrow() == 0 ) {
4333 os << LogIO::SEVERE << "No row in the input scantable. Return empty tcal." << LogIO::POST ;
4334 return tcal ;
4335 }
4336 else if ( s->nrow() == 1 ) {
4337 uInt tcalid = s->getTcalId( 0 ) ;
4338 //os << "use row " << 0 << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4339 tcalTable.getEntry( time, tcalval, tcalid ) ;
4340 tcalval.tovector( tcal ) ;
4341 return tcal ;
4342 }
4343 else {
4344 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4345 if ( mode == "before" ) {
4346 int id = -1 ;
4347 if ( idx[0] != -1 ) {
4348 id = idx[0] ;
4349 }
4350 else if ( idx[1] != -1 ) {
4351 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4352 id = idx[1] ;
4353 }
4354 uInt tcalid = s->getTcalId( id ) ;
4355 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4356 tcalTable.getEntry( time, tcalval, tcalid ) ;
4357 tcalval.tovector( tcal ) ;
4358 }
4359 else if ( mode == "after" ) {
4360 int id = -1 ;
4361 if ( idx[1] != -1 ) {
4362 id = idx[1] ;
4363 }
4364 else if ( idx[0] != -1 ) {
4365 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4366 id = idx[1] ;
4367 }
4368 uInt tcalid = s->getTcalId( id ) ;
4369 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4370 tcalTable.getEntry( time, tcalval, tcalid ) ;
4371 tcalval.tovector( tcal ) ;
4372 }
4373 else if ( mode == "nearest" ) {
4374 int id = -1 ;
4375 if ( idx[0] == -1 ) {
4376 id = idx[1] ;
4377 }
4378 else if ( idx[1] == -1 ) {
4379 id = idx[0] ;
4380 }
4381 else if ( idx[0] == idx[1] ) {
4382 id = idx[0] ;
4383 }
4384 else {
4385 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4386 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4387 double tref = getMJD( reftime ) ;
4388 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4389 id = idx[1] ;
4390 }
4391 else {
4392 id = idx[0] ;
4393 }
4394 }
4395 uInt tcalid = s->getTcalId( id ) ;
4396 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4397 tcalTable.getEntry( time, tcalval, tcalid ) ;
4398 tcalval.tovector( tcal ) ;
4399 }
4400 else if ( mode == "linear" ) {
4401 if ( idx[0] == -1 ) {
4402 // use after
4403 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4404 int id = idx[1] ;
4405 uInt tcalid = s->getTcalId( id ) ;
4406 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4407 tcalTable.getEntry( time, tcalval, tcalid ) ;
4408 tcalval.tovector( tcal ) ;
4409 }
4410 else if ( idx[1] == -1 ) {
4411 // use before
4412 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4413 int id = idx[0] ;
4414 uInt tcalid = s->getTcalId( id ) ;
4415 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4416 tcalTable.getEntry( time, tcalval, tcalid ) ;
4417 tcalval.tovector( tcal ) ;
4418 }
4419 else if ( idx[0] == idx[1] ) {
4420 // use before
4421 //os << "No need to interporate." << LogIO::POST ;
4422 int id = idx[0] ;
4423 uInt tcalid = s->getTcalId( id ) ;
4424 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4425 tcalTable.getEntry( time, tcalval, tcalid ) ;
4426 tcalval.tovector( tcal ) ;
4427 }
4428 else {
4429 // do interpolation
4430 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4431 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4432 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4433 double tref = getMJD( reftime ) ;
4434 vector<float> tcal0 ;
4435 vector<float> tcal1 ;
4436 uInt tcalid0 = s->getTcalId( idx[0] ) ;
4437 uInt tcalid1 = s->getTcalId( idx[1] ) ;
4438 tcalTable.getEntry( time, tcalval, tcalid0 ) ;
4439 tcalval.tovector( tcal0 ) ;
4440 tcalTable.getEntry( time, tcalval, tcalid1 ) ;
4441 tcalval.tovector( tcal1 ) ;
4442 for ( unsigned int i = 0 ; i < tcal0.size() ; i++ ) {
4443 float v = ( tcal1[i] - tcal0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tcal0[i] ;
4444 tcal.push_back( v ) ;
4445 }
4446 }
4447 }
4448 else {
4449 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4450 }
4451 return tcal ;
4452 }
4453}
4454
4455vector<float> STMath::getTsysFromTime( string reftime,
4456 CountedPtr<Scantable>& s,
4457 string mode )
4458{
4459 LogIO os( LogOrigin( "STMath", "getTsysFromTime", WHERE ) ) ;
4460 ArrayColumn<Float> tsysCol ;
4461 tsysCol.attach( s->table(), "TSYS" ) ;
4462 vector<float> tsys ;
4463 String time ;
4464 Vector<Float> tsysval ;
4465 if ( s->nrow() == 0 ) {
4466 os << LogIO::SEVERE << "No row in the input scantable. Return empty tsys." << LogIO::POST ;
4467 return tsys ;
4468 }
4469 else if ( s->nrow() == 1 ) {
4470 //os << "use row " << 0 << LogIO::POST ;
4471 tsysval = tsysCol( 0 ) ;
4472 tsysval.tovector( tsys ) ;
4473 return tsys ;
4474 }
4475 else {
4476 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4477 if ( mode == "before" ) {
4478 int id = -1 ;
4479 if ( idx[0] != -1 ) {
4480 id = idx[0] ;
4481 }
4482 else if ( idx[1] != -1 ) {
4483 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4484 id = idx[1] ;
4485 }
4486 //os << "use row " << id << LogIO::POST ;
4487 tsysval = tsysCol( id ) ;
4488 tsysval.tovector( tsys ) ;
4489 }
4490 else if ( mode == "after" ) {
4491 int id = -1 ;
4492 if ( idx[1] != -1 ) {
4493 id = idx[1] ;
4494 }
4495 else if ( idx[0] != -1 ) {
4496 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4497 id = idx[1] ;
4498 }
4499 //os << "use row " << id << LogIO::POST ;
4500 tsysval = tsysCol( id ) ;
4501 tsysval.tovector( tsys ) ;
4502 }
4503 else if ( mode == "nearest" ) {
4504 int id = -1 ;
4505 if ( idx[0] == -1 ) {
4506 id = idx[1] ;
4507 }
4508 else if ( idx[1] == -1 ) {
4509 id = idx[0] ;
4510 }
4511 else if ( idx[0] == idx[1] ) {
4512 id = idx[0] ;
4513 }
4514 else {
4515 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4516 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4517 double tref = getMJD( reftime ) ;
4518 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4519 id = idx[1] ;
4520 }
4521 else {
4522 id = idx[0] ;
4523 }
4524 }
4525 //os << "use row " << id << LogIO::POST ;
4526 tsysval = tsysCol( id ) ;
4527 tsysval.tovector( tsys ) ;
4528 }
4529 else if ( mode == "linear" ) {
4530 if ( idx[0] == -1 ) {
4531 // use after
4532 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4533 int id = idx[1] ;
4534 //os << "use row " << id << LogIO::POST ;
4535 tsysval = tsysCol( id ) ;
4536 tsysval.tovector( tsys ) ;
4537 }
4538 else if ( idx[1] == -1 ) {
4539 // use before
4540 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4541 int id = idx[0] ;
4542 //os << "use row " << id << LogIO::POST ;
4543 tsysval = tsysCol( id ) ;
4544 tsysval.tovector( tsys ) ;
4545 }
4546 else if ( idx[0] == idx[1] ) {
4547 // use before
4548 //os << "No need to interporate." << LogIO::POST ;
4549 int id = idx[0] ;
4550 //os << "use row " << id << LogIO::POST ;
4551 tsysval = tsysCol( id ) ;
4552 tsysval.tovector( tsys ) ;
4553 }
4554 else {
4555 // do interpolation
4556 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4557 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4558 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4559 double tref = getMJD( reftime ) ;
4560 vector<float> tsys0 ;
4561 vector<float> tsys1 ;
4562 tsysval = tsysCol( idx[0] ) ;
4563 tsysval.tovector( tsys0 ) ;
4564 tsysval = tsysCol( idx[1] ) ;
4565 tsysval.tovector( tsys1 ) ;
4566 for ( unsigned int i = 0 ; i < tsys0.size() ; i++ ) {
4567 float v = ( tsys1[i] - tsys0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tsys0[i] ;
4568 tsys.push_back( v ) ;
4569 }
4570 }
4571 }
4572 else {
4573 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4574 }
4575 return tsys ;
4576 }
4577}
4578
4579vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
4580 CountedPtr<Scantable>& off,
4581 CountedPtr<Scantable>& sky,
4582 CountedPtr<Scantable>& hot,
4583 CountedPtr<Scantable>& cold,
4584 int index,
4585 string antname )
4586{
4587 string reftime = on->getTime( index ) ;
4588 vector<int> ii( 1, on->getIF( index ) ) ;
4589 vector<int> ib( 1, on->getBeam( index ) ) ;
4590 vector<int> ip( 1, on->getPol( index ) ) ;
4591 vector<int> ic( 1, on->getScan( index ) ) ;
4592 STSelector sel = STSelector() ;
4593 sel.setIFs( ii ) ;
4594 sel.setBeams( ib ) ;
4595 sel.setPolarizations( ip ) ;
4596 sky->setSelection( sel ) ;
4597 hot->setSelection( sel ) ;
4598 //cold->setSelection( sel ) ;
4599 off->setSelection( sel ) ;
4600 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
4601 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
4602 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
4603 vector<float> spoff = getSpectrumFromTime( reftime, off, "linear" ) ;
4604 vector<float> spec = on->getSpectrum( index ) ;
4605 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
4606 vector<float> sp( tcal.size() ) ;
4607 if ( antname.find( "APEX" ) != string::npos ) {
4608 // using gain array
4609 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4610 float v = ( ( spec[j] - spoff[j] ) / spoff[j] )
4611 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4612 sp[j] = v ;
4613 }
4614 }
4615 else {
4616 // Chopper-Wheel calibration (Ulich & Haas 1976)
4617 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4618 float v = ( spec[j] - spoff[j] ) / ( sphot[j] - spsky[j] ) * tcal[j] ;
4619 sp[j] = v ;
4620 }
4621 }
4622 sel.reset() ;
4623 sky->unsetSelection() ;
4624 hot->unsetSelection() ;
4625 //cold->unsetSelection() ;
4626 off->unsetSelection() ;
4627
4628 return sp ;
4629}
4630
4631vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
4632 CountedPtr<Scantable>& off,
4633 int index )
4634{
4635 string reftime = on->getTime( index ) ;
4636 vector<int> ii( 1, on->getIF( index ) ) ;
4637 vector<int> ib( 1, on->getBeam( index ) ) ;
4638 vector<int> ip( 1, on->getPol( index ) ) ;
4639 vector<int> ic( 1, on->getScan( index ) ) ;
4640 STSelector sel = STSelector() ;
4641 sel.setIFs( ii ) ;
4642 sel.setBeams( ib ) ;
4643 sel.setPolarizations( ip ) ;
4644 off->setSelection( sel ) ;
4645 vector<float> spoff = getSpectrumFromTime( reftime, off, "linear" ) ;
4646 vector<float> spec = on->getSpectrum( index ) ;
4647 //vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
4648 //vector<float> tsys = on->getTsysVec( index ) ;
4649 ArrayColumn<Float> tsysCol( on->table(), "TSYS" ) ;
4650 Vector<Float> tsys = tsysCol( index ) ;
4651 vector<float> sp( spec.size() ) ;
4652 // ALMA Calibration
4653 //
4654 // Ta* = Tsys * ( ON - OFF ) / OFF
4655 //
4656 // 2010/01/07 Takeshi Nakazato
4657 unsigned int tsyssize = tsys.nelements() ;
4658 unsigned int spsize = sp.size() ;
4659 for ( unsigned int j = 0 ; j < sp.size() ; j++ ) {
4660 float tscale = 0.0 ;
4661 if ( tsyssize == spsize )
4662 tscale = tsys[j] ;
4663 else
4664 tscale = tsys[0] ;
4665 float v = tscale * ( spec[j] - spoff[j] ) / spoff[j] ;
4666 sp[j] = v ;
4667 }
4668 sel.reset() ;
4669 off->unsetSelection() ;
4670
4671 return sp ;
4672}
4673
4674vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
4675 CountedPtr<Scantable>& ref,
4676 CountedPtr<Scantable>& sky,
4677 CountedPtr<Scantable>& hot,
4678 CountedPtr<Scantable>& cold,
4679 int index )
4680{
4681 string reftime = sig->getTime( index ) ;
4682 vector<int> ii( 1, sig->getIF( index ) ) ;
4683 vector<int> ib( 1, sig->getBeam( index ) ) ;
4684 vector<int> ip( 1, sig->getPol( index ) ) ;
4685 vector<int> ic( 1, sig->getScan( index ) ) ;
4686 STSelector sel = STSelector() ;
4687 sel.setIFs( ii ) ;
4688 sel.setBeams( ib ) ;
4689 sel.setPolarizations( ip ) ;
4690 sky->setSelection( sel ) ;
4691 hot->setSelection( sel ) ;
4692 //cold->setSelection( sel ) ;
4693 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
4694 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
4695 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
4696 vector<float> spref = ref->getSpectrum( index ) ;
4697 vector<float> spsig = sig->getSpectrum( index ) ;
4698 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
4699 vector<float> sp( tcal.size() ) ;
4700 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4701 float v = tcal[j] * spsky[j] / ( sphot[j] - spsky[j] ) * ( spsig[j] - spref[j] ) / spref[j] ;
4702 sp[j] = v ;
4703 }
4704 sel.reset() ;
4705 sky->unsetSelection() ;
4706 hot->unsetSelection() ;
4707 //cold->unsetSelection() ;
4708
4709 return sp ;
4710}
4711
4712vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
4713 CountedPtr<Scantable>& ref,
4714 vector< CountedPtr<Scantable> >& sky,
4715 vector< CountedPtr<Scantable> >& hot,
4716 vector< CountedPtr<Scantable> >& cold,
4717 int index )
4718{
4719 string reftime = sig->getTime( index ) ;
4720 vector<int> ii( 1, sig->getIF( index ) ) ;
4721 vector<int> ib( 1, sig->getBeam( index ) ) ;
4722 vector<int> ip( 1, sig->getPol( index ) ) ;
4723 vector<int> ic( 1, sig->getScan( index ) ) ;
4724 STSelector sel = STSelector() ;
4725 sel.setIFs( ii ) ;
4726 sel.setBeams( ib ) ;
4727 sel.setPolarizations( ip ) ;
4728 sky[0]->setSelection( sel ) ;
4729 hot[0]->setSelection( sel ) ;
4730 //cold[0]->setSelection( sel ) ;
4731 vector<float> spskys = getSpectrumFromTime( reftime, sky[0], "linear" ) ;
4732 vector<float> sphots = getSpectrumFromTime( reftime, hot[0], "linear" ) ;
4733 //vector<float> spcolds = getSpectrumFromTime( reftime, cold[0], "linear" ) ;
4734 vector<float> tcals = getTcalFromTime( reftime, sky[0], "linear" ) ;
4735 sel.reset() ;
4736 ii[0] = ref->getIF( index ) ;
4737 sel.setIFs( ii ) ;
4738 sel.setBeams( ib ) ;
4739 sel.setPolarizations( ip ) ;
4740 sky[1]->setSelection( sel ) ;
4741 hot[1]->setSelection( sel ) ;
4742 //cold[1]->setSelection( sel ) ;
4743 vector<float> spskyr = getSpectrumFromTime( reftime, sky[1], "linear" ) ;
4744 vector<float> sphotr = getSpectrumFromTime( reftime, hot[1], "linear" ) ;
4745 //vector<float> spcoldr = getSpectrumFromTime( reftime, cold[1], "linear" ) ;
4746 vector<float> tcalr = getTcalFromTime( reftime, sky[1], "linear" ) ;
4747 vector<float> spref = ref->getSpectrum( index ) ;
4748 vector<float> spsig = sig->getSpectrum( index ) ;
4749 vector<float> sp( tcals.size() ) ;
4750 for ( unsigned int j = 0 ; j < tcals.size() ; j++ ) {
4751 float v = tcals[j] * spsig[j] / ( sphots[j] - spskys[j] ) - tcalr[j] * spref[j] / ( sphotr[j] - spskyr[j] ) ;
4752 sp[j] = v ;
4753 }
4754 sel.reset() ;
4755 sky[0]->unsetSelection() ;
4756 hot[0]->unsetSelection() ;
4757 //cold[0]->unsetSelection() ;
4758 sky[1]->unsetSelection() ;
4759 hot[1]->unsetSelection() ;
4760 //cold[1]->unsetSelection() ;
4761
4762 return sp ;
4763}
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