source: branches/alma/src/STMath.cpp@ 2700

Last change on this file since 2700 was 1757, checked in by Kana Sugimoto, 14 years ago

New Development: Yes

JIRA Issue: Yes (CAS-2211)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: ASAP 3.0.0 interface changes

Test Programs:

Put in Release Notes: Yes

Module(s): all the CASA sd tools and tasks are affected.

Description: Merged ATNF-ASAP 3.0.0 developments to CASA (alma) branch.

Note you also need to update casa/code/atnf.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 164.2 KB
Line 
1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <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 "STSelector.h"
55
56#include "STMath.h"
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::W_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::W_NONE;
1955 lookup["TINT"] = asap::W_TINT;
1956 lookup["TINTSYS"] = asap::W_TINTSYS;
1957 lookup["TSYS"] = asap::W_TSYS;
1958 lookup["VAR"] = asap::W_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-1);
2003 coeff = coeffs;
2004 msg = String("user");
2005 } else {
2006 STAttr sdAttr;
2007 coeff = sdAttr.gainElevationPoly(inst);
2008 ppoly = new Polynomial<Float>(coeff.nelements()-1);
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 const std::vector<float>& tau )
2210{
2211 CountedPtr< Scantable > out = getScantable(in, false);
2212
2213 Table outtab = out->table();
2214
2215 const uInt ntau = uInt(tau.size());
2216 std::vector<float>::const_iterator tauit = tau.begin();
2217 AlwaysAssert((ntau == 1 || ntau == in->nif() || ntau == in->nif() * in->npol()),
2218 AipsError);
2219 TableIterator iiter(outtab, "IFNO");
2220 while ( !iiter.pastEnd() ) {
2221 Table itab = iiter.table();
2222 TableIterator piter(outtab, "POLNO");
2223 while ( !piter.pastEnd() ) {
2224 Table tab = piter.table();
2225 ROScalarColumn<Float> elev(tab, "ELEVATION");
2226 ArrayColumn<Float> specCol(tab, "SPECTRA");
2227 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2228 ArrayColumn<Float> tsysCol(tab, "TSYS");
2229 for ( uInt i=0; i<tab.nrow(); ++i) {
2230 Float zdist = Float(C::pi_2) - elev(i);
2231 Float factor = exp(*tauit/cos(zdist));
2232 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2233 ma *= factor;
2234 specCol.put(i, ma.getArray());
2235 flagCol.put(i, flagsFromMA(ma));
2236 Vector<Float> tsys;
2237 tsysCol.get(i, tsys);
2238 tsys *= factor;
2239 tsysCol.put(i, tsys);
2240 }
2241 if (ntau == in->nif()*in->npol() ) {
2242 tauit++;
2243 }
2244 piter++;
2245 }
2246 if (ntau >= in->nif() ) {
2247 tauit++;
2248 }
2249 iiter++;
2250 }
2251 return out;
2252}
2253
2254CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in,
2255 const std::string& kernel,
2256 float width, int order)
2257{
2258 CountedPtr< Scantable > out = getScantable(in, false);
2259 Table& table = out->table();
2260 ArrayColumn<Float> specCol(table, "SPECTRA");
2261 ArrayColumn<uChar> flagCol(table, "FLAGTRA");
2262 Vector<Float> spec;
2263 Vector<uChar> flag;
2264 for ( uInt i=0; i<table.nrow(); ++i) {
2265 specCol.get(i, spec);
2266 flagCol.get(i, flag);
2267 Vector<Bool> mask(flag.nelements());
2268 convertArray(mask, flag);
2269 Vector<Float> specout;
2270 Vector<Bool> maskout;
2271 if ( kernel == "hanning" ) {
2272 mathutil::hanning(specout, maskout, spec , !mask);
2273 convertArray(flag, !maskout);
2274 } else if ( kernel == "rmedian" ) {
2275 mathutil::runningMedian(specout, maskout, spec , mask, width);
2276 convertArray(flag, maskout);
2277 } else if ( kernel == "poly" ) {
2278 mathutil::polyfit(specout, maskout, spec, !mask, width, order);
2279 convertArray(flag, !maskout);
2280 }
2281 flagCol.put(i, flag);
2282 specCol.put(i, specout);
2283 }
2284 return out;
2285}
2286
2287CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
2288 const std::string& kernel, float width,
2289 int order)
2290{
2291 if (kernel == "rmedian" || kernel == "hanning" || kernel == "poly") {
2292 return smoothOther(in, kernel, width, order);
2293 }
2294 CountedPtr< Scantable > out = getScantable(in, false);
2295 Table& table = out->table();
2296 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
2297 // same IFNO should have same no of channels
2298 // this saves overhead
2299 TableIterator iter(table, "IFNO");
2300 while (!iter.pastEnd()) {
2301 Table tab = iter.table();
2302 ArrayColumn<Float> specCol(tab, "SPECTRA");
2303 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2304 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2305 uInt nchan = tmpspec.nelements();
2306 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
2307 Convolver<Float> conv(kvec, IPosition(1,nchan));
2308 Vector<Float> spec;
2309 Vector<uChar> flag;
2310 for ( uInt i=0; i<tab.nrow(); ++i) {
2311 specCol.get(i, spec);
2312 flagCol.get(i, flag);
2313 Vector<Bool> mask(flag.nelements());
2314 convertArray(mask, flag);
2315 Vector<Float> specout;
2316 mathutil::replaceMaskByZero(specout, mask);
2317 conv.linearConv(specout, spec);
2318 specCol.put(i, specout);
2319 }
2320 ++iter;
2321 }
2322 return out;
2323}
2324
2325CountedPtr< Scantable >
2326 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
2327{
2328 if ( in.size() < 2 ) {
2329 throw(AipsError("Need at least two scantables to perform a merge."));
2330 }
2331 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
2332 bool insitu = insitu_;
2333 setInsitu(false);
2334 CountedPtr< Scantable > out = getScantable(*it, false);
2335 setInsitu(insitu);
2336 Table& tout = out->table();
2337 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
2338 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
2339 // Renumber SCANNO to be 0-based
2340 Vector<uInt> scannos = scannocol.getColumn();
2341 uInt offset = min(scannos);
2342 scannos -= offset;
2343 scannocol.putColumn(scannos);
2344 uInt newscanno = max(scannos)+1;
2345 ++it;
2346 while ( it != in.end() ){
2347 if ( ! (*it)->conformant(*out) ) {
2348 // non conformant.
2349 //pushLog(String("Warning: Can't merge scantables as header info differs."));
2350 LogIO os( LogOrigin( "STMath", "merge()", WHERE ) ) ;
2351 os << LogIO::SEVERE << "Can't merge scantables as header informations (any one of AntennaName, Equinox, and FluxUnit) differ." << LogIO::EXCEPTION ;
2352 }
2353 out->appendToHistoryTable((*it)->history());
2354 const Table& tab = (*it)->table();
2355 TableIterator scanit(tab, "SCANNO");
2356 while (!scanit.pastEnd()) {
2357 TableIterator freqit(scanit.table(), "FREQ_ID");
2358 while ( !freqit.pastEnd() ) {
2359 Table thetab = freqit.table();
2360 uInt nrow = tout.nrow();
2361 tout.addRow(thetab.nrow());
2362 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
2363 ROTableRow row(thetab);
2364 for ( uInt i=0; i<thetab.nrow(); ++i) {
2365 uInt k = nrow+i;
2366 scannocol.put(k, newscanno);
2367 const TableRecord& rec = row.get(i);
2368 Double rv,rp,inc;
2369 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
2370 uInt id;
2371 id = out->frequencies().addEntry(rp, rv, inc);
2372 freqidcol.put(k,id);
2373 //String name,fname;Double rf;
2374 Vector<String> name,fname;Vector<Double> rf;
2375 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
2376 id = out->molecules().addEntry(rf, name, fname);
2377 molidcol.put(k, id);
2378 Float fpa,frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
2379 (*it)->focus().getEntry(fpa, fax, ftan, frot, fhand,
2380 fmount,fuser, fxy, fxyp,
2381 rec.asuInt("FOCUS_ID"));
2382 id = out->focus().addEntry(fpa, fax, ftan, frot, fhand,
2383 fmount,fuser, fxy, fxyp);
2384 focusidcol.put(k, id);
2385 }
2386 ++freqit;
2387 }
2388 ++newscanno;
2389 ++scanit;
2390 }
2391 ++it;
2392 }
2393 return out;
2394}
2395
2396CountedPtr< Scantable >
2397 STMath::invertPhase( const CountedPtr < Scantable >& in )
2398{
2399 return applyToPol(in, &STPol::invertPhase, Float(0.0));
2400}
2401
2402CountedPtr< Scantable >
2403 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
2404{
2405 return applyToPol(in, &STPol::rotatePhase, Float(phase));
2406}
2407
2408CountedPtr< Scantable >
2409 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
2410{
2411 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
2412}
2413
2414CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
2415 STPol::polOperation fptr,
2416 Float phase )
2417{
2418 CountedPtr< Scantable > out = getScantable(in, false);
2419 Table& tout = out->table();
2420 Block<String> cols(4);
2421 cols[0] = String("SCANNO");
2422 cols[1] = String("BEAMNO");
2423 cols[2] = String("IFNO");
2424 cols[3] = String("CYCLENO");
2425 TableIterator iter(tout, cols);
2426 CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
2427 out->getPolType() );
2428 while (!iter.pastEnd()) {
2429 Table t = iter.table();
2430 ArrayColumn<Float> speccol(t, "SPECTRA");
2431 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
2432 Matrix<Float> pols(speccol.getColumn());
2433 try {
2434 stpol->setSpectra(pols);
2435 Float fang,fhand;
2436 fang = in->focusTable_.getTotalAngle(focidcol(0));
2437 fhand = in->focusTable_.getFeedHand(focidcol(0));
2438 stpol->setPhaseCorrections(fang, fhand);
2439 // use a member function pointer in STPol. This only works on
2440 // the STPol pointer itself, not the Counted Pointer so
2441 // derefernce it.
2442 (&(*(stpol))->*fptr)(phase);
2443 speccol.putColumn(stpol->getSpectra());
2444 } catch (AipsError& e) {
2445 //delete stpol;stpol=0;
2446 throw(e);
2447 }
2448 ++iter;
2449 }
2450 //delete stpol;stpol=0;
2451 return out;
2452}
2453
2454CountedPtr< Scantable >
2455 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
2456{
2457 CountedPtr< Scantable > out = getScantable(in, false);
2458 Table& tout = out->table();
2459 Table t0 = tout(tout.col("POLNO") == 0);
2460 Table t1 = tout(tout.col("POLNO") == 1);
2461 if ( t0.nrow() != t1.nrow() )
2462 throw(AipsError("Inconsistent number of polarisations"));
2463 ArrayColumn<Float> speccol0(t0, "SPECTRA");
2464 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
2465 ArrayColumn<Float> speccol1(t1, "SPECTRA");
2466 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
2467 Matrix<Float> s0 = speccol0.getColumn();
2468 Matrix<uChar> f0 = flagcol0.getColumn();
2469 speccol0.putColumn(speccol1.getColumn());
2470 flagcol0.putColumn(flagcol1.getColumn());
2471 speccol1.putColumn(s0);
2472 flagcol1.putColumn(f0);
2473 return out;
2474}
2475
2476CountedPtr< Scantable >
2477 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
2478 const std::vector<bool>& mask,
2479 const std::string& weight )
2480{
2481 if (in->npol() < 2 )
2482 throw(AipsError("averagePolarisations can only be applied to two or more"
2483 "polarisations"));
2484 bool insitu = insitu_;
2485 setInsitu(false);
2486 CountedPtr< Scantable > pols = getScantable(in, true);
2487 setInsitu(insitu);
2488 Table& tout = pols->table();
2489 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
2490 Table tab = tableCommand(taql, in->table());
2491 if (tab.nrow() == 0 )
2492 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
2493 TableCopy::copyRows(tout, tab);
2494 TableVector<uInt> vec(tout, "POLNO");
2495 vec = 0;
2496 pols->table_.rwKeywordSet().define("nPol", Int(1));
2497 //pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
2498 pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
2499 std::vector<CountedPtr<Scantable> > vpols;
2500 vpols.push_back(pols);
2501 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
2502 return out;
2503}
2504
2505CountedPtr< Scantable >
2506 STMath::averageBeams( const CountedPtr< Scantable > & in,
2507 const std::vector<bool>& mask,
2508 const std::string& weight )
2509{
2510 bool insitu = insitu_;
2511 setInsitu(false);
2512 CountedPtr< Scantable > beams = getScantable(in, false);
2513 setInsitu(insitu);
2514 Table& tout = beams->table();
2515 // give all rows the same BEAMNO
2516 TableVector<uInt> vec(tout, "BEAMNO");
2517 vec = 0;
2518 beams->table_.rwKeywordSet().define("nBeam", Int(1));
2519 std::vector<CountedPtr<Scantable> > vbeams;
2520 vbeams.push_back(beams);
2521 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
2522 return out;
2523}
2524
2525
2526CountedPtr< Scantable >
2527 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
2528 const std::string & refTime,
2529 const std::string & method)
2530{
2531 // clone as this is not working insitu
2532 bool insitu = insitu_;
2533 setInsitu(false);
2534 CountedPtr< Scantable > out = getScantable(in, false);
2535 setInsitu(insitu);
2536 Table& tout = out->table();
2537 // Get reference Epoch to time of first row or given String
2538 Unit DAY(String("d"));
2539 MEpoch::Ref epochRef(in->getTimeReference());
2540 MEpoch refEpoch;
2541 if (refTime.length()>0) {
2542 Quantum<Double> qt;
2543 if (MVTime::read(qt,refTime)) {
2544 MVEpoch mv(qt);
2545 refEpoch = MEpoch(mv, epochRef);
2546 } else {
2547 throw(AipsError("Invalid format for Epoch string"));
2548 }
2549 } else {
2550 refEpoch = in->timeCol_(0);
2551 }
2552 MPosition refPos = in->getAntennaPosition();
2553
2554 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2555 /*
2556 // Comment from MV.
2557 // the following code has been commented out because different FREQ_IDs have to be aligned together even
2558 // if the frame doesn't change. So far, lack of this check didn't cause any problems.
2559 // test if user frame is different to base frame
2560 if ( in->frequencies().getFrameString(true)
2561 == in->frequencies().getFrameString(false) ) {
2562 throw(AipsError("Can't convert as no output frame has been set"
2563 " (use set_freqframe) or it is aligned already."));
2564 }
2565 */
2566 MFrequency::Types system = in->frequencies().getFrame();
2567 MVTime mvt(refEpoch.getValue());
2568 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
2569 ostringstream oss;
2570 oss << "Aligned at reference Epoch " << epochout
2571 << " in frame " << MFrequency::showType(system);
2572 pushLog(String(oss));
2573 // set up the iterator
2574 Block<String> cols(4);
2575 // select by constant direction
2576 cols[0] = String("SRCNAME");
2577 cols[1] = String("BEAMNO");
2578 // select by IF ( no of channels varies over this )
2579 cols[2] = String("IFNO");
2580 // select by restfrequency
2581 cols[3] = String("MOLECULE_ID");
2582 TableIterator iter(tout, cols);
2583 while ( !iter.pastEnd() ) {
2584 Table t = iter.table();
2585 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
2586 TableIterator fiter(t, "FREQ_ID");
2587 // determine nchan from the first row. This should work as
2588 // we are iterating over BEAMNO and IFNO // we should have constant direction
2589
2590 ROArrayColumn<Float> sCol(t, "SPECTRA");
2591 const MDirection direction = dirCol(0);
2592 const uInt nchan = sCol(0).nelements();
2593
2594 // skip operations if there is nothing to align
2595 if (fiter.pastEnd()) {
2596 continue;
2597 }
2598
2599 Table ftab = fiter.table();
2600 // align all frequency ids with respect to the first encountered id
2601 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
2602 // get the SpectralCoordinate for the freqid, which we are iterating over
2603 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
2604 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
2605 direction, refPos, system );
2606 // realign the SpectralCoordinate and put into the output Scantable
2607 Vector<String> units(1);
2608 units = String("Hz");
2609 Bool linear=True;
2610 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
2611 sc2.setWorldAxisUnits(units);
2612 const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
2613 sc2.referenceValue()[0],
2614 sc2.increment()[0]);
2615 while ( !fiter.pastEnd() ) {
2616 ftab = fiter.table();
2617 // spectral coordinate for the current FREQ_ID
2618 ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
2619 sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
2620 // create the "global" abcissa for alignment with same FREQ_ID
2621 Vector<Double> abc(nchan);
2622 for (uInt i=0; i<nchan; i++) {
2623 Double w;
2624 sC.toWorld(w,Double(i));
2625 abc[i] = w;
2626 }
2627 TableVector<uInt> tvec(ftab, "FREQ_ID");
2628 // assign new frequency id to all rows
2629 tvec = id;
2630 // cache abcissa for same time stamps, so iterate over those
2631 TableIterator timeiter(ftab, "TIME");
2632 while ( !timeiter.pastEnd() ) {
2633 Table tab = timeiter.table();
2634 ArrayColumn<Float> specCol(tab, "SPECTRA");
2635 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2636 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2637 // use align abcissa cache after the first row
2638 // these rows should be just be POLNO
2639 bool first = true;
2640 for (int i=0; i<int(tab.nrow()); ++i) {
2641 // input values
2642 Vector<uChar> flag = flagCol(i);
2643 Vector<Bool> mask(flag.shape());
2644 Vector<Float> specOut, spec;
2645 spec = specCol(i);
2646 Vector<Bool> maskOut;Vector<uChar> flagOut;
2647 convertArray(mask, flag);
2648 // alignment
2649 Bool ok = fa.align(specOut, maskOut, abc, spec,
2650 mask, timeCol(i), !first,
2651 interp, False);
2652 // back into scantable
2653 flagOut.resize(maskOut.nelements());
2654 convertArray(flagOut, maskOut);
2655 flagCol.put(i, flagOut);
2656 specCol.put(i, specOut);
2657 // start abcissa caching
2658 first = false;
2659 }
2660 // next timestamp
2661 ++timeiter;
2662 }
2663 // next FREQ_ID
2664 ++fiter;
2665 }
2666 // next aligner
2667 ++iter;
2668 }
2669 // set this afterwards to ensure we are doing insitu correctly.
2670 out->frequencies().setFrame(system, true);
2671 return out;
2672}
2673
2674CountedPtr<Scantable>
2675 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
2676 const std::string & newtype )
2677{
2678 if (in->npol() != 2 && in->npol() != 4)
2679 throw(AipsError("Can only convert two or four polarisations."));
2680 if ( in->getPolType() == newtype )
2681 throw(AipsError("No need to convert."));
2682 if ( ! in->selector_.empty() )
2683 throw(AipsError("Can only convert whole scantable. Unset the selection."));
2684 bool insitu = insitu_;
2685 setInsitu(false);
2686 CountedPtr< Scantable > out = getScantable(in, true);
2687 setInsitu(insitu);
2688 Table& tout = out->table();
2689 tout.rwKeywordSet().define("POLTYPE", String(newtype));
2690
2691 Block<String> cols(4);
2692 cols[0] = "SCANNO";
2693 cols[1] = "CYCLENO";
2694 cols[2] = "BEAMNO";
2695 cols[3] = "IFNO";
2696 TableIterator it(in->originalTable_, cols);
2697 String basetype = in->getPolType();
2698 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
2699 try {
2700 while ( !it.pastEnd() ) {
2701 Table tab = it.table();
2702 uInt row = tab.rowNumbers()[0];
2703 stpol->setSpectra(in->getPolMatrix(row));
2704 Float fang,fhand;
2705 fang = in->focusTable_.getTotalAngle(in->mfocusidCol_(row));
2706 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
2707 stpol->setPhaseCorrections(fang, fhand);
2708 Int npolout = 0;
2709 for (uInt i=0; i<tab.nrow(); ++i) {
2710 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
2711 if ( outvec.nelements() > 0 ) {
2712 tout.addRow();
2713 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
2714 ArrayColumn<Float> sCol(tout,"SPECTRA");
2715 ScalarColumn<uInt> pCol(tout,"POLNO");
2716 sCol.put(tout.nrow()-1 ,outvec);
2717 pCol.put(tout.nrow()-1 ,uInt(npolout));
2718 npolout++;
2719 }
2720 }
2721 tout.rwKeywordSet().define("nPol", npolout);
2722 ++it;
2723 }
2724 } catch (AipsError& e) {
2725 delete stpol;
2726 throw(e);
2727 }
2728 delete stpol;
2729 return out;
2730}
2731
2732CountedPtr< Scantable >
2733 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
2734 const std::string & scantype )
2735{
2736 bool insitu = insitu_;
2737 setInsitu(false);
2738 CountedPtr< Scantable > out = getScantable(in, true);
2739 setInsitu(insitu);
2740 Table& tout = out->table();
2741 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
2742 if (scantype == "on") {
2743 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
2744 }
2745 Table tab = tableCommand(taql, in->table());
2746 TableCopy::copyRows(tout, tab);
2747 if (scantype == "on") {
2748 // re-index SCANNO to 0
2749 TableVector<uInt> vec(tout, "SCANNO");
2750 vec = 0;
2751 }
2752 return out;
2753}
2754
2755CountedPtr< Scantable >
2756 asap::STMath::lagFlag( const CountedPtr< Scantable > & in,
2757 double start, double end,
2758 const std::string& mode)
2759{
2760 CountedPtr< Scantable > out = getScantable(in, false);
2761 Table& tout = out->table();
2762 TableIterator iter(tout, "FREQ_ID");
2763 FFTServer<Float,Complex> ffts;
2764 while ( !iter.pastEnd() ) {
2765 Table tab = iter.table();
2766 Double rp,rv,inc;
2767 ROTableRow row(tab);
2768 const TableRecord& rec = row.get(0);
2769 uInt freqid = rec.asuInt("FREQ_ID");
2770 out->frequencies().getEntry(rp, rv, inc, freqid);
2771 ArrayColumn<Float> specCol(tab, "SPECTRA");
2772 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2773 for (int i=0; i<int(tab.nrow()); ++i) {
2774 Vector<Float> spec = specCol(i);
2775 Vector<uChar> flag = flagCol(i);
2776 int fstart = -1;
2777 int fend = -1;
2778 for (unsigned int k=0; k < flag.nelements(); ++k ) {
2779 if (flag[k] > 0) {
2780 fstart = k;
2781 while (flag[k] > 0 && k < flag.nelements()) {
2782 fend = k;
2783 k++;
2784 }
2785 }
2786 Float interp = 0.0;
2787 if (fstart-1 > 0 ) {
2788 interp = spec[fstart-1];
2789 if (fend+1 < spec.nelements()) {
2790 interp = (interp+spec[fend+1])/2.0;
2791 }
2792 } else {
2793 interp = spec[fend+1];
2794 }
2795 if (fstart > -1 && fend > -1) {
2796 for (int j=fstart;j<=fend;++j) {
2797 spec[j] = interp;
2798 }
2799 }
2800 fstart =-1;
2801 fend = -1;
2802 }
2803 Vector<Complex> lags;
2804 ffts.fft0(lags, spec);
2805 Int lag0(start+0.5);
2806 Int lag1(end+0.5);
2807 if (mode == "frequency") {
2808 lag0 = Int(spec.nelements()*abs(inc)/(start)+0.5);
2809 lag1 = Int(spec.nelements()*abs(inc)/(end)+0.5);
2810 }
2811 Int lstart = max(0, lag0);
2812 Int lend = min(Int(lags.nelements()-1), lag1);
2813 if (lstart == lend) {
2814 lags[lstart] = Complex(0.0);
2815 } else {
2816 if (lstart > lend) {
2817 Int tmp = lend;
2818 lend = lstart;
2819 lstart = tmp;
2820 }
2821 for (int j=lstart; j <=lend ;++j) {
2822 lags[j] = Complex(0.0);
2823 }
2824 }
2825 ffts.fft0(spec, lags);
2826 specCol.put(i, spec);
2827 }
2828 ++iter;
2829 }
2830 return out;
2831}
2832
2833// Averaging spectra with different channel/resolution
2834CountedPtr<Scantable>
2835STMath::new_average( const std::vector<CountedPtr<Scantable> >& in,
2836 const bool& compel,
2837 const std::vector<bool>& mask,
2838 const std::string& weight,
2839 const std::string& avmode )
2840 throw ( casa::AipsError )
2841{
2842 LogIO os( LogOrigin( "STMath", "new_average()", WHERE ) ) ;
2843 if ( avmode == "SCAN" && in.size() != 1 )
2844 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
2845 "Use merge first."));
2846
2847 // check if OTF observation
2848 String obstype = in[0]->getHeader().obstype ;
2849 Double tol = 0.0 ;
2850 if ( obstype.find( "OTF" ) != String::npos ) {
2851 tol = TOL_OTF ;
2852 }
2853 else {
2854 tol = TOL_POINT ;
2855 }
2856
2857 CountedPtr<Scantable> out ; // processed result
2858 if ( compel ) {
2859 std::vector< CountedPtr<Scantable> > newin ; // input for average process
2860 uInt insize = in.size() ; // number of input scantables
2861
2862 // TEST: do normal average in each table before IF grouping
2863 os << "Do preliminary averaging" << LogIO::POST ;
2864 vector< CountedPtr<Scantable> > tmpin( insize ) ;
2865 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2866 vector< CountedPtr<Scantable> > v( 1, in[itable] ) ;
2867 tmpin[itable] = average( v, mask, weight, avmode ) ;
2868 }
2869
2870 // warning
2871 os << "Average spectra with different spectral resolution" << LogIO::POST ;
2872
2873 // temporarily set coordinfo
2874 vector<string> oldinfo( insize ) ;
2875 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2876 vector<string> coordinfo = in[itable]->getCoordInfo() ;
2877 oldinfo[itable] = coordinfo[0] ;
2878 coordinfo[0] = "Hz" ;
2879 tmpin[itable]->setCoordInfo( coordinfo ) ;
2880 }
2881
2882 // columns
2883 ScalarColumn<uInt> freqIDCol ;
2884 ScalarColumn<uInt> ifnoCol ;
2885 ScalarColumn<uInt> scannoCol ;
2886
2887
2888 // check IF frequency coverage
2889 // freqid: list of FREQ_ID, which is used, in each table
2890 // iffreq: list of minimum and maximum frequency for each FREQ_ID in
2891 // each table
2892 // freqid[insize][numIF]
2893 // freqid: [[id00, id01, ...],
2894 // [id10, id11, ...],
2895 // ...
2896 // [idn0, idn1, ...]]
2897 // iffreq[insize][numIF*2]
2898 // iffreq: [[min_id00, max_id00, min_id01, max_id01, ...],
2899 // [min_id10, max_id10, min_id11, max_id11, ...],
2900 // ...
2901 // [min_idn0, max_idn0, min_idn1, max_idn1, ...]]
2902 //os << "Check IF settings in each table" << LogIO::POST ;
2903 vector< vector<uInt> > freqid( insize );
2904 vector< vector<double> > iffreq( insize ) ;
2905 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2906 uInt rows = tmpin[itable]->nrow() ;
2907 uInt freqnrows = tmpin[itable]->frequencies().table().nrow() ;
2908 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
2909 if ( freqid[itable].size() == freqnrows ) {
2910 break ;
2911 }
2912 else {
2913 freqIDCol.attach( tmpin[itable]->table(), "FREQ_ID" ) ;
2914 ifnoCol.attach( tmpin[itable]->table(), "IFNO" ) ;
2915 uInt id = freqIDCol( irow ) ;
2916 if ( freqid[itable].size() == 0 || count( freqid[itable].begin(), freqid[itable].end(), id ) == 0 ) {
2917 //os << "itable = " << itable << ": IF " << id << " is included in the list" << LogIO::POST ;
2918 vector<double> abcissa = tmpin[itable]->getAbcissa( irow ) ;
2919 freqid[itable].push_back( id ) ;
2920 iffreq[itable].push_back( abcissa[0] - 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
2921 iffreq[itable].push_back( abcissa[abcissa.size()-1] + 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
2922 }
2923 }
2924 }
2925 }
2926
2927 // debug
2928 //os << "IF settings summary:" << endl ;
2929 //for ( uInt i = 0 ; i < freqid.size() ; i++ ) {
2930 //os << " Table" << i << endl ;
2931 //for ( uInt j = 0 ; j < freqid[i].size() ; j++ ) {
2932 //os << " id = " << freqid[i][j] << " (min,max) = (" << iffreq[i][2*j] << "," << iffreq[i][2*j+1] << ")" << endl ;
2933 //}
2934 //}
2935 //os << endl ;
2936 //os.post() ;
2937
2938 // IF grouping based on their frequency coverage
2939 // ifgrp: list of table index and FREQ_ID for all members in each IF group
2940 // ifgfreq: list of minimum and maximum frequency in each IF group
2941 // ifgrp[numgrp][nummember*2]
2942 // ifgrp: [[table00, freqrow00, table01, freqrow01, ...],
2943 // [table10, freqrow10, table11, freqrow11, ...],
2944 // ...
2945 // [tablen0, freqrown0, tablen1, freqrown1, ...]]
2946 // ifgfreq[numgrp*2]
2947 // ifgfreq: [min0_grp0, max0_grp0, min1_grp1, max1_grp1, ...]
2948 //os << "IF grouping based on their frequency coverage" << LogIO::POST ;
2949 vector< vector<uInt> > ifgrp ;
2950 vector<double> ifgfreq ;
2951
2952 // parameter for IF grouping
2953 // groupmode = OR retrieve all region
2954 // AND only retrieve overlaped region
2955 //string groupmode = "AND" ;
2956 string groupmode = "OR" ;
2957 uInt sizecr = 0 ;
2958 if ( groupmode == "AND" )
2959 sizecr = 2 ;
2960 else if ( groupmode == "OR" )
2961 sizecr = 0 ;
2962
2963 vector<double> sortedfreq ;
2964 for ( uInt i = 0 ; i < iffreq.size() ; i++ ) {
2965 for ( uInt j = 0 ; j < iffreq[i].size() ; j++ ) {
2966 if ( count( sortedfreq.begin(), sortedfreq.end(), iffreq[i][j] ) == 0 )
2967 sortedfreq.push_back( iffreq[i][j] ) ;
2968 }
2969 }
2970 sort( sortedfreq.begin(), sortedfreq.end() ) ;
2971 for ( vector<double>::iterator i = sortedfreq.begin() ; i != sortedfreq.end()-1 ; i++ ) {
2972 ifgfreq.push_back( *i ) ;
2973 ifgfreq.push_back( *(i+1) ) ;
2974 }
2975 ifgrp.resize( ifgfreq.size()/2 ) ;
2976 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
2977 for ( uInt iif = 0 ; iif < freqid[itable].size() ; iif++ ) {
2978 double range0 = iffreq[itable][2*iif] ;
2979 double range1 = iffreq[itable][2*iif+1] ;
2980 for ( uInt j = 0 ; j < ifgrp.size() ; j++ ) {
2981 double fmin = max( range0, ifgfreq[2*j] ) ;
2982 double fmax = min( range1, ifgfreq[2*j+1] ) ;
2983 if ( fmin < fmax ) {
2984 ifgrp[j].push_back( itable ) ;
2985 ifgrp[j].push_back( freqid[itable][iif] ) ;
2986 }
2987 }
2988 }
2989 }
2990 vector< vector<uInt> >::iterator fiter = ifgrp.begin() ;
2991 vector<double>::iterator giter = ifgfreq.begin() ;
2992 while( fiter != ifgrp.end() ) {
2993 if ( fiter->size() <= sizecr ) {
2994 fiter = ifgrp.erase( fiter ) ;
2995 giter = ifgfreq.erase( giter ) ;
2996 giter = ifgfreq.erase( giter ) ;
2997 }
2998 else {
2999 fiter++ ;
3000 advance( giter, 2 ) ;
3001 }
3002 }
3003
3004 // Grouping continuous IF groups (without frequency gap)
3005 // freqgrp: list of IF group indexes in each frequency group
3006 // freqrange: list of minimum and maximum frequency in each frequency group
3007 // freqgrp[numgrp][nummember]
3008 // freqgrp: [[ifgrp00, ifgrp01, ifgrp02, ...],
3009 // [ifgrp10, ifgrp11, ifgrp12, ...],
3010 // ...
3011 // [ifgrpn0, ifgrpn1, ifgrpn2, ...]]
3012 // freqrange[numgrp*2]
3013 // freqrange: [min_grp0, max_grp0, min_grp1, max_grp1, ...]
3014 vector< vector<uInt> > freqgrp ;
3015 double freqrange = 0.0 ;
3016 uInt grpnum = 0 ;
3017 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3018 // Assumed that ifgfreq was sorted
3019 if ( grpnum != 0 && freqrange == ifgfreq[2*i] ) {
3020 freqgrp[grpnum-1].push_back( i ) ;
3021 }
3022 else {
3023 vector<uInt> grp0( 1, i ) ;
3024 freqgrp.push_back( grp0 ) ;
3025 grpnum++ ;
3026 }
3027 freqrange = ifgfreq[2*i+1] ;
3028 }
3029
3030
3031 // print IF groups
3032 ostringstream oss ;
3033 oss << "IF Group summary: " << endl ;
3034 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3035 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3036 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3037 for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3038 oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3039 }
3040 oss << endl ;
3041 }
3042 oss << endl ;
3043 os << oss.str() << LogIO::POST ;
3044
3045 // print frequency group
3046 oss.str("") ;
3047 oss << "Frequency Group summary: " << endl ;
3048 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: IF_GROUP_ID" << endl ;
3049 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3050 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*freqgrp[i][0]] << "," << ifgfreq[2*freqgrp[i][freqgrp[i].size()-1]+1] << "]: " ;
3051 for ( uInt j = 0 ; j < freqgrp[i].size() ; j++ ) {
3052 oss << freqgrp[i][j] << " " ;
3053 }
3054 oss << endl ;
3055 }
3056 oss << endl ;
3057 os << oss.str() << LogIO::POST ;
3058
3059 // membership check
3060 // groups: list of IF group indexes whose frequency range overlaps with
3061 // that of each table and IF
3062 // groups[numtable][numIF][nummembership]
3063 // groups: [[[grp, grp,...], [grp, grp,...],...],
3064 // [[grp, grp,...], [grp, grp,...],...],
3065 // ...
3066 // [[grp, grp,...], [grp, grp,...],...]]
3067 vector< vector< vector<uInt> > > groups( insize ) ;
3068 for ( uInt i = 0 ; i < insize ; i++ ) {
3069 groups[i].resize( freqid[i].size() ) ;
3070 }
3071 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3072 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3073 uInt tableid = ifgrp[igrp][2*imem] ;
3074 vector<uInt>::iterator iter = find( freqid[tableid].begin(), freqid[tableid].end(), ifgrp[igrp][2*imem+1] ) ;
3075 if ( iter != freqid[tableid].end() ) {
3076 uInt rowid = distance( freqid[tableid].begin(), iter ) ;
3077 groups[tableid][rowid].push_back( igrp ) ;
3078 }
3079 }
3080 }
3081
3082 // print membership
3083 //oss.str("") ;
3084 //for ( uInt i = 0 ; i < insize ; i++ ) {
3085 //oss << "Table " << i << endl ;
3086 //for ( uInt j = 0 ; j < groups[i].size() ; j++ ) {
3087 //oss << " FREQ_ID " << setw( 2 ) << freqid[i][j] << ": " ;
3088 //for ( uInt k = 0 ; k < groups[i][j].size() ; k++ ) {
3089 //oss << setw( 2 ) << groups[i][j][k] << " " ;
3090 //}
3091 //oss << endl ;
3092 //}
3093 //}
3094 //os << oss.str() << LogIO::POST ;
3095
3096 // set back coordinfo
3097 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3098 vector<string> coordinfo = tmpin[itable]->getCoordInfo() ;
3099 coordinfo[0] = oldinfo[itable] ;
3100 tmpin[itable]->setCoordInfo( coordinfo ) ;
3101 }
3102
3103 // Create additional table if needed
3104 bool oldInsitu = insitu_ ;
3105 setInsitu( false ) ;
3106 vector< vector<uInt> > addrow( insize ) ;
3107 vector<uInt> addtable( insize, 0 ) ;
3108 vector<uInt> newtableids( insize ) ;
3109 vector<uInt> newifids( insize, 0 ) ;
3110 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3111 //os << "Table " << itable << ": " ;
3112 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3113 addrow[itable].push_back( groups[itable][ifrow].size()-1 ) ;
3114 //os << addrow[itable][ifrow] << " " ;
3115 }
3116 addtable[itable] = *max_element( addrow[itable].begin(), addrow[itable].end() ) ;
3117 //os << "(" << addtable[itable] << ")" << LogIO::POST ;
3118 }
3119 newin.resize( insize ) ;
3120 copy( tmpin.begin(), tmpin.end(), newin.begin() ) ;
3121 for ( uInt i = 0 ; i < insize ; i++ ) {
3122 newtableids[i] = i ;
3123 }
3124 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3125 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3126 CountedPtr<Scantable> add = getScantable( newin[itable], false ) ;
3127 vector<int> freqidlist ;
3128 for ( uInt i = 0 ; i < groups[itable].size() ; i++ ) {
3129 if ( groups[itable][i].size() > iadd + 1 ) {
3130 freqidlist.push_back( freqid[itable][i] ) ;
3131 }
3132 }
3133 stringstream taqlstream ;
3134 taqlstream << "SELECT FROM $1 WHERE FREQ_ID IN [" ;
3135 for ( uInt i = 0 ; i < freqidlist.size() ; i++ ) {
3136 taqlstream << i ;
3137 if ( i < freqidlist.size() - 1 )
3138 taqlstream << "," ;
3139 else
3140 taqlstream << "]" ;
3141 }
3142 string taql = taqlstream.str() ;
3143 //os << "taql = " << taql << LogIO::POST ;
3144 STSelector selector = STSelector() ;
3145 selector.setTaQL( taql ) ;
3146 add->setSelection( selector ) ;
3147 newin.push_back( add ) ;
3148 newtableids.push_back( itable ) ;
3149 newifids.push_back( iadd + 1 ) ;
3150 }
3151 }
3152
3153 // udpate ifgrp
3154 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3155 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3156 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3157 if ( groups[itable][ifrow].size() > iadd + 1 ) {
3158 uInt igrp = groups[itable][ifrow][iadd+1] ;
3159 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3160 if ( ifgrp[igrp][2*imem] == newtableids[iadd+insize] && ifgrp[igrp][2*imem+1] == freqid[newtableids[iadd+insize]][ifrow] ) {
3161 ifgrp[igrp][2*imem] = insize + iadd ;
3162 }
3163 }
3164 }
3165 }
3166 }
3167 }
3168
3169 // print IF groups again for debug
3170 //oss.str( "" ) ;
3171 //oss << "IF Group summary: " << endl ;
3172 //oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3173 //for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3174 //oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3175 //for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3176 //oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3177 //}
3178 //oss << endl ;
3179 //}
3180 //oss << endl ;
3181 //os << oss.str() << LogIO::POST ;
3182
3183 // reset SCANNO and IFNO/FREQ_ID: IF is reset by the result of sortation
3184 os << "All scan number is set to 0" << LogIO::POST ;
3185 //os << "All IF number is set to IF group index" << LogIO::POST ;
3186 insize = newin.size() ;
3187 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3188 uInt rows = newin[itable]->nrow() ;
3189 Table &tmpt = newin[itable]->table() ;
3190 freqIDCol.attach( tmpt, "FREQ_ID" ) ;
3191 scannoCol.attach( tmpt, "SCANNO" ) ;
3192 ifnoCol.attach( tmpt, "IFNO" ) ;
3193 for ( uInt irow=0 ; irow < rows ; irow++ ) {
3194 scannoCol.put( irow, 0 ) ;
3195 uInt freqID = freqIDCol( irow ) ;
3196 vector<uInt>::iterator iter = find( freqid[newtableids[itable]].begin(), freqid[newtableids[itable]].end(), freqID ) ;
3197 if ( iter != freqid[newtableids[itable]].end() ) {
3198 uInt index = distance( freqid[newtableids[itable]].begin(), iter ) ;
3199 ifnoCol.put( irow, groups[newtableids[itable]][index][newifids[itable]] ) ;
3200 }
3201 else {
3202 throw(AipsError("IF grouping was wrong in additional tables.")) ;
3203 }
3204 }
3205 }
3206 oldinfo.resize( insize ) ;
3207 setInsitu( oldInsitu ) ;
3208
3209 // temporarily set coordinfo
3210 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3211 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3212 oldinfo[itable] = coordinfo[0] ;
3213 coordinfo[0] = "Hz" ;
3214 newin[itable]->setCoordInfo( coordinfo ) ;
3215 }
3216
3217 // save column values in the vector
3218 vector< vector<uInt> > freqTableIdVec( insize ) ;
3219 vector< vector<uInt> > freqIdVec( insize ) ;
3220 vector< vector<uInt> > ifNoVec( insize ) ;
3221 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3222 ScalarColumn<uInt> freqIDs ;
3223 freqIDs.attach( newin[itable]->frequencies().table(), "ID" ) ;
3224 ifnoCol.attach( newin[itable]->table(), "IFNO" ) ;
3225 freqIDCol.attach( newin[itable]->table(), "FREQ_ID" ) ;
3226 for ( uInt irow = 0 ; irow < newin[itable]->frequencies().table().nrow() ; irow++ ) {
3227 freqTableIdVec[itable].push_back( freqIDs( irow ) ) ;
3228 }
3229 for ( uInt irow = 0 ; irow < newin[itable]->table().nrow() ; irow++ ) {
3230 freqIdVec[itable].push_back( freqIDCol( irow ) ) ;
3231 ifNoVec[itable].push_back( ifnoCol( irow ) ) ;
3232 }
3233 }
3234
3235 // reset spectra and flagtra: pick up common part of frequency coverage
3236 //os << "Pick common frequency range and align resolution" << LogIO::POST ;
3237 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3238 uInt rows = newin[itable]->nrow() ;
3239 int nminchan = -1 ;
3240 int nmaxchan = -1 ;
3241 vector<uInt> freqIdUpdate ;
3242 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3243 uInt ifno = ifNoVec[itable][irow] ; // IFNO is reset by group index
3244 double minfreq = ifgfreq[2*ifno] ;
3245 double maxfreq = ifgfreq[2*ifno+1] ;
3246 //os << "frequency range: [" << minfreq << "," << maxfreq << "]" << LogIO::POST ;
3247 vector<double> abcissa = newin[itable]->getAbcissa( irow ) ;
3248 int nchan = abcissa.size() ;
3249 double resol = abcissa[1] - abcissa[0] ;
3250 //os << "abcissa range : [" << abcissa[0] << "," << abcissa[nchan-1] << "]" << LogIO::POST ;
3251 if ( minfreq <= abcissa[0] )
3252 nminchan = 0 ;
3253 else {
3254 //double cfreq = ( minfreq - abcissa[0] ) / resol ;
3255 double cfreq = ( minfreq - abcissa[0] + 0.5 * resol ) / resol ;
3256 nminchan = int(cfreq) + ( ( cfreq - int(cfreq) <= 0.5 ) ? 0 : 1 ) ;
3257 }
3258 if ( maxfreq >= abcissa[abcissa.size()-1] )
3259 nmaxchan = abcissa.size() - 1 ;
3260 else {
3261 //double cfreq = ( abcissa[abcissa.size()-1] - maxfreq ) / resol ;
3262 double cfreq = ( abcissa[abcissa.size()-1] - maxfreq + 0.5 * resol ) / resol ;
3263 nmaxchan = abcissa.size() - 1 - int(cfreq) - ( ( cfreq - int(cfreq) >= 0.5 ) ? 1 : 0 ) ;
3264 }
3265 //os << "channel range (" << irow << "): [" << nminchan << "," << nmaxchan << "]" << LogIO::POST ;
3266 if ( nmaxchan > nminchan ) {
3267 newin[itable]->reshapeSpectrum( nminchan, nmaxchan, irow ) ;
3268 int newchan = nmaxchan - nminchan + 1 ;
3269 if ( count( freqIdUpdate.begin(), freqIdUpdate.end(), freqIdVec[itable][irow] ) == 0 && newchan < nchan )
3270 freqIdUpdate.push_back( freqIdVec[itable][irow] ) ;
3271 }
3272 else {
3273 throw(AipsError("Failed to pick up common part of frequency range.")) ;
3274 }
3275 }
3276 for ( uInt i = 0 ; i < freqIdUpdate.size() ; i++ ) {
3277 uInt freqId = freqIdUpdate[i] ;
3278 Double refpix ;
3279 Double refval ;
3280 Double increment ;
3281
3282 // update row
3283 newin[itable]->frequencies().getEntry( refpix, refval, increment, freqId ) ;
3284 refval = refval - ( refpix - nminchan ) * increment ;
3285 refpix = 0 ;
3286 newin[itable]->frequencies().setEntry( refpix, refval, increment, freqId ) ;
3287 }
3288 }
3289
3290
3291 // reset spectra and flagtra: align spectral resolution
3292 //os << "Align spectral resolution" << LogIO::POST ;
3293 // gmaxdnu: the coarsest frequency resolution in the frequency group
3294 // gmemid: member index that have a resolution equal to gmaxdnu
3295 // gmaxdnu[numfreqgrp]
3296 // gmaxdnu: [dnu0, dnu1, ...]
3297 // gmemid[numfreqgrp]
3298 // gmemid: [id0, id1, ...]
3299 vector<double> gmaxdnu( freqgrp.size(), 0.0 ) ;
3300 vector<uInt> gmemid( freqgrp.size(), 0 ) ;
3301 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3302 double maxdnu = 0.0 ; // maximum (coarsest) frequency resolution
3303 int minchan = INT_MAX ; // minimum channel number
3304 Double refpixref = -1 ; // reference of 'reference pixel'
3305 Double refvalref = -1 ; // reference of 'reference frequency'
3306 Double refinc = -1 ; // reference frequency resolution
3307 uInt refreqid ;
3308 uInt reftable = INT_MAX;
3309 // process only if group member > 1
3310 if ( ifgrp[igrp].size() > 2 ) {
3311 // find minchan and maxdnu in each group
3312 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3313 uInt tableid = ifgrp[igrp][2*imem] ;
3314 uInt rowid = ifgrp[igrp][2*imem+1] ;
3315 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3316 if ( iter != freqIdVec[tableid].end() ) {
3317 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3318 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3319 int nchan = abcissa.size() ;
3320 double dnu = abcissa[1] - abcissa[0] ;
3321 //os << "GROUP " << igrp << " (" << tableid << "," << rowid << "): nchan = " << nchan << " (minchan = " << minchan << ")" << LogIO::POST ;
3322 if ( nchan < minchan ) {
3323 minchan = nchan ;
3324 maxdnu = dnu ;
3325 newin[tableid]->frequencies().getEntry( refpixref, refvalref, refinc, rowid ) ;
3326 refreqid = rowid ;
3327 reftable = tableid ;
3328 }
3329 }
3330 }
3331 // regrid spectra in each group
3332 os << "GROUP " << igrp << endl ;
3333 os << " Channel number is adjusted to " << minchan << endl ;
3334 os << " Corresponding frequency resolution is " << maxdnu << "Hz" << LogIO::POST ;
3335 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3336 uInt tableid = ifgrp[igrp][2*imem] ;
3337 uInt rowid = ifgrp[igrp][2*imem+1] ;
3338 freqIDCol.attach( newin[tableid]->table(), "FREQ_ID" ) ;
3339 //os << "tableid = " << tableid << " rowid = " << rowid << ": " << LogIO::POST ;
3340 //os << " regridChannel applied to " ;
3341 if ( tableid != reftable )
3342 refreqid = newin[tableid]->frequencies().addEntry( refpixref, refvalref, refinc ) ;
3343 for ( uInt irow = 0 ; irow < newin[tableid]->table().nrow() ; irow++ ) {
3344 uInt tfreqid = freqIdVec[tableid][irow] ;
3345 if ( tfreqid == rowid ) {
3346 //os << irow << " " ;
3347 newin[tableid]->regridChannel( minchan, maxdnu, irow ) ;
3348 freqIDCol.put( irow, refreqid ) ;
3349 freqIdVec[tableid][irow] = refreqid ;
3350 }
3351 }
3352 //os << LogIO::POST ;
3353 }
3354 }
3355 else {
3356 uInt tableid = ifgrp[igrp][0] ;
3357 uInt rowid = ifgrp[igrp][1] ;
3358 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3359 if ( iter != freqIdVec[tableid].end() ) {
3360 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3361 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3362 minchan = abcissa.size() ;
3363 maxdnu = abcissa[1] - abcissa[0] ;
3364 }
3365 }
3366 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3367 if ( count( freqgrp[i].begin(), freqgrp[i].end(), igrp ) > 0 ) {
3368 if ( maxdnu > gmaxdnu[i] ) {
3369 gmaxdnu[i] = maxdnu ;
3370 gmemid[i] = igrp ;
3371 }
3372 break ;
3373 }
3374 }
3375 }
3376
3377 // set back coordinfo
3378 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3379 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3380 coordinfo[0] = oldinfo[itable] ;
3381 newin[itable]->setCoordInfo( coordinfo ) ;
3382 }
3383
3384 // accumulate all rows into the first table
3385 // NOTE: assumed in.size() = 1
3386 vector< CountedPtr<Scantable> > tmp( 1 ) ;
3387 if ( newin.size() == 1 )
3388 tmp[0] = newin[0] ;
3389 else
3390 tmp[0] = merge( newin ) ;
3391
3392 //return tmp[0] ;
3393
3394 // average
3395 CountedPtr<Scantable> tmpout = average( tmp, mask, weight, avmode ) ;
3396
3397 //return tmpout ;
3398
3399 // combine frequency group
3400 os << "Combine spectra based on frequency grouping" << LogIO::POST ;
3401 os << "IFNO is renumbered as frequency group ID (see above)" << LogIO::POST ;
3402 vector<string> coordinfo = tmpout->getCoordInfo() ;
3403 oldinfo[0] = coordinfo[0] ;
3404 coordinfo[0] = "Hz" ;
3405 tmpout->setCoordInfo( coordinfo ) ;
3406 // create proformas of output table
3407 stringstream taqlstream ;
3408 taqlstream << "SELECT FROM $1 WHERE IFNO IN [" ;
3409 for ( uInt i = 0 ; i < gmemid.size() ; i++ ) {
3410 taqlstream << gmemid[i] ;
3411 if ( i < gmemid.size() - 1 )
3412 taqlstream << "," ;
3413 else
3414 taqlstream << "]" ;
3415 }
3416 string taql = taqlstream.str() ;
3417 //os << "taql = " << taql << LogIO::POST ;
3418 STSelector selector = STSelector() ;
3419 selector.setTaQL( taql ) ;
3420 oldInsitu = insitu_ ;
3421 setInsitu( false ) ;
3422 out = getScantable( tmpout, false ) ;
3423 setInsitu( oldInsitu ) ;
3424 out->setSelection( selector ) ;
3425 // regrid rows
3426 ifnoCol.attach( tmpout->table(), "IFNO" ) ;
3427 for ( uInt irow = 0 ; irow < tmpout->table().nrow() ; irow++ ) {
3428 uInt ifno = ifnoCol( irow ) ;
3429 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3430 if ( count( freqgrp[igrp].begin(), freqgrp[igrp].end(), ifno ) > 0 ) {
3431 vector<double> abcissa = tmpout->getAbcissa( irow ) ;
3432 double bw = ( abcissa[1] - abcissa[0] ) * abcissa.size() ;
3433 int nchan = (int)( bw / gmaxdnu[igrp] ) ;
3434 tmpout->regridChannel( nchan, gmaxdnu[igrp], irow ) ;
3435 break ;
3436 }
3437 }
3438 }
3439 // combine spectra
3440 ArrayColumn<Float> specColOut ;
3441 specColOut.attach( out->table(), "SPECTRA" ) ;
3442 ArrayColumn<uChar> flagColOut ;
3443 flagColOut.attach( out->table(), "FLAGTRA" ) ;
3444 ScalarColumn<uInt> ifnoColOut ;
3445 ifnoColOut.attach( out->table(), "IFNO" ) ;
3446 ScalarColumn<uInt> polnoColOut ;
3447 polnoColOut.attach( out->table(), "POLNO" ) ;
3448 ScalarColumn<uInt> freqidColOut ;
3449 freqidColOut.attach( out->table(), "FREQ_ID" ) ;
3450 MDirection::ScalarColumn dirColOut ;
3451 dirColOut.attach( out->table(), "DIRECTION" ) ;
3452 Table &tab = tmpout->table() ;
3453 Block<String> cols(1);
3454 cols[0] = String("POLNO") ;
3455 TableIterator iter( tab, cols ) ;
3456 bool done = false ;
3457 vector< vector<uInt> > sizes( freqgrp.size() ) ;
3458 while( !iter.pastEnd() ) {
3459 vector< vector<Float> > specout( freqgrp.size() ) ;
3460 vector< vector<uChar> > flagout( freqgrp.size() ) ;
3461 ArrayColumn<Float> specCols ;
3462 specCols.attach( iter.table(), "SPECTRA" ) ;
3463 ArrayColumn<uChar> flagCols ;
3464 flagCols.attach( iter.table(), "FLAGTRA" ) ;
3465 ifnoCol.attach( iter.table(), "IFNO" ) ;
3466 ScalarColumn<uInt> polnos ;
3467 polnos.attach( iter.table(), "POLNO" ) ;
3468 MDirection::ScalarColumn dircol ;
3469 dircol.attach( iter.table(), "DIRECTION" ) ;
3470 uInt polno = polnos( 0 ) ;
3471 //os << "POLNO iteration: " << polno << LogIO::POST ;
3472// for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3473// sizes[igrp].resize( freqgrp[igrp].size() ) ;
3474// for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3475// for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3476// uInt ifno = ifnoCol( irow ) ;
3477// if ( ifno == freqgrp[igrp][imem] ) {
3478// Vector<Float> spec = specCols( irow ) ;
3479// Vector<uChar> flag = flagCols( irow ) ;
3480// vector<Float> svec ;
3481// spec.tovector( svec ) ;
3482// vector<uChar> fvec ;
3483// flag.tovector( fvec ) ;
3484// //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3485// specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3486// flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3487// //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3488// sizes[igrp][imem] = spec.nelements() ;
3489// }
3490// }
3491// }
3492// for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3493// uInt ifout = ifnoColOut( irow ) ;
3494// uInt polout = polnoColOut( irow ) ;
3495// if ( ifout == gmemid[igrp] && polout == polno ) {
3496// // set SPECTRA and FRAGTRA
3497// Vector<Float> newspec( specout[igrp] ) ;
3498// Vector<uChar> newflag( flagout[igrp] ) ;
3499// specColOut.put( irow, newspec ) ;
3500// flagColOut.put( irow, newflag ) ;
3501// // IFNO renumbering
3502// ifnoColOut.put( irow, igrp ) ;
3503// }
3504// }
3505// }
3506 // get a list of number of channels for each frequency group member
3507 if ( !done ) {
3508 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3509 sizes[igrp].resize( freqgrp[igrp].size() ) ;
3510 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3511 for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3512 uInt ifno = ifnoCol( irow ) ;
3513 if ( ifno == freqgrp[igrp][imem] ) {
3514 Vector<Float> spec = specCols( irow ) ;
3515 sizes[igrp][imem] = spec.nelements() ;
3516 break ;
3517 }
3518 }
3519 }
3520 }
3521 done = true ;
3522 }
3523 // combine spectra
3524 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3525 uInt polout = polnoColOut( irow ) ;
3526 if ( polout == polno ) {
3527 uInt ifout = ifnoColOut( irow ) ;
3528 Vector<Double> direction = dirColOut(irow).getAngle(Unit(String("rad"))).getValue() ;
3529 uInt igrp ;
3530 for ( uInt jgrp = 0 ; jgrp < freqgrp.size() ; jgrp++ ) {
3531 if ( ifout == gmemid[jgrp] ) {
3532 igrp = jgrp ;
3533 break ;
3534 }
3535 }
3536 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3537 for ( uInt jrow = 0 ; jrow < iter.table().nrow() ; jrow++ ) {
3538 uInt ifno = ifnoCol( jrow ) ;
3539 Vector<Double> tdir = dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
3540 //if ( ifno == freqgrp[igrp][imem] && allTrue( tdir == direction ) ) {
3541 Double dx = tdir[0] - direction[0] ;
3542 Double dy = tdir[1] - direction[1] ;
3543 Double dd = sqrt( dx * dx + dy * dy ) ;
3544 //if ( ifno == freqgrp[igrp][imem] && allNearAbs( tdir, direction, tol ) ) {
3545 if ( ifno == freqgrp[igrp][imem] && dd <= tol ) {
3546 Vector<Float> spec = specCols( jrow ) ;
3547 Vector<uChar> flag = flagCols( jrow ) ;
3548 vector<Float> svec ;
3549 spec.tovector( svec ) ;
3550 vector<uChar> fvec ;
3551 flag.tovector( fvec ) ;
3552 //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3553 specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3554 flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3555 //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3556 }
3557 }
3558 }
3559 // set SPECTRA and FRAGTRA
3560 Vector<Float> newspec( specout[igrp] ) ;
3561 Vector<uChar> newflag( flagout[igrp] ) ;
3562 specColOut.put( irow, newspec ) ;
3563 flagColOut.put( irow, newflag ) ;
3564 // IFNO renumbering
3565 ifnoColOut.put( irow, igrp ) ;
3566 }
3567 }
3568 iter++ ;
3569 }
3570 // update FREQUENCIES subtable
3571 vector<bool> updated( freqgrp.size(), false ) ;
3572 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3573 uInt index = 0 ;
3574 uInt pixShift = 0 ;
3575 while ( freqgrp[igrp][index] != gmemid[igrp] ) {
3576 pixShift += sizes[igrp][index++] ;
3577 }
3578 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3579 if ( ifnoColOut( irow ) == gmemid[igrp] && !updated[igrp] ) {
3580 uInt freqidOut = freqidColOut( irow ) ;
3581 //os << "freqgrp " << igrp << " freqidOut = " << freqidOut << LogIO::POST ;
3582 double refpix ;
3583 double refval ;
3584 double increm ;
3585 out->frequencies().getEntry( refpix, refval, increm, freqidOut ) ;
3586 refpix += pixShift ;
3587 out->frequencies().setEntry( refpix, refval, increm, freqidOut ) ;
3588 updated[igrp] = true ;
3589 }
3590 }
3591 }
3592
3593 //out = tmpout ;
3594
3595 coordinfo = tmpout->getCoordInfo() ;
3596 coordinfo[0] = oldinfo[0] ;
3597 tmpout->setCoordInfo( coordinfo ) ;
3598 }
3599 else {
3600 // simple average
3601 out = average( in, mask, weight, avmode ) ;
3602 }
3603
3604 return out ;
3605}
3606
3607CountedPtr<Scantable> STMath::cwcal( const CountedPtr<Scantable>& s,
3608 const String calmode,
3609 const String antname )
3610{
3611 // frequency switch
3612 if ( calmode == "fs" ) {
3613 return cwcalfs( s, antname ) ;
3614 }
3615 else {
3616 vector<bool> masks = s->getMask( 0 ) ;
3617 vector<int> types ;
3618
3619 // sky scan
3620 STSelector sel = STSelector() ;
3621 types.push_back( SrcType::SKY ) ;
3622 sel.setTypes( types ) ;
3623 s->setSelection( sel ) ;
3624 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3625 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
3626 s->unsetSelection() ;
3627 sel.reset() ;
3628 types.clear() ;
3629
3630 // hot scan
3631 types.push_back( SrcType::HOT ) ;
3632 sel.setTypes( types ) ;
3633 s->setSelection( sel ) ;
3634 tmp.clear() ;
3635 tmp.push_back( getScantable( s, false ) ) ;
3636 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
3637 s->unsetSelection() ;
3638 sel.reset() ;
3639 types.clear() ;
3640
3641 // cold scan
3642 CountedPtr<Scantable> acold ;
3643// types.push_back( SrcType::COLD ) ;
3644// sel.setTypes( types ) ;
3645// s->setSelection( sel ) ;
3646// tmp.clear() ;
3647// tmp.push_back( getScantable( s, false ) ) ;
3648// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCNAN" ) ;
3649// s->unsetSelection() ;
3650// sel.reset() ;
3651// types.clear() ;
3652
3653 // off scan
3654 types.push_back( SrcType::PSOFF ) ;
3655 sel.setTypes( types ) ;
3656 s->setSelection( sel ) ;
3657 tmp.clear() ;
3658 tmp.push_back( getScantable( s, false ) ) ;
3659 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
3660 s->unsetSelection() ;
3661 sel.reset() ;
3662 types.clear() ;
3663
3664 // on scan
3665 bool insitu = insitu_ ;
3666 insitu_ = false ;
3667 CountedPtr<Scantable> out = getScantable( s, true ) ;
3668 insitu_ = insitu ;
3669 types.push_back( SrcType::PSON ) ;
3670 sel.setTypes( types ) ;
3671 s->setSelection( sel ) ;
3672 TableCopy::copyRows( out->table(), s->table() ) ;
3673 s->unsetSelection() ;
3674 sel.reset() ;
3675 types.clear() ;
3676
3677 // process each on scan
3678 ArrayColumn<Float> tsysCol ;
3679 tsysCol.attach( out->table(), "TSYS" ) ;
3680 for ( int i = 0 ; i < out->nrow() ; i++ ) {
3681 vector<float> sp = getCalibratedSpectra( out, aoff, asky, ahot, acold, i, antname ) ;
3682 out->setSpectrum( sp, i ) ;
3683 string reftime = out->getTime( i ) ;
3684 vector<int> ii( 1, out->getIF( i ) ) ;
3685 vector<int> ib( 1, out->getBeam( i ) ) ;
3686 vector<int> ip( 1, out->getPol( i ) ) ;
3687 sel.setIFs( ii ) ;
3688 sel.setBeams( ib ) ;
3689 sel.setPolarizations( ip ) ;
3690 asky->setSelection( sel ) ;
3691 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
3692 const Vector<Float> Vtsys( sptsys ) ;
3693 tsysCol.put( i, Vtsys ) ;
3694 asky->unsetSelection() ;
3695 sel.reset() ;
3696 }
3697
3698 // flux unit
3699 out->setFluxUnit( "K" ) ;
3700
3701 return out ;
3702 }
3703}
3704
3705CountedPtr<Scantable> STMath::almacal( const CountedPtr<Scantable>& s,
3706 const String calmode )
3707{
3708 // frequency switch
3709 if ( calmode == "fs" ) {
3710 return almacalfs( s ) ;
3711 }
3712 else {
3713 vector<bool> masks = s->getMask( 0 ) ;
3714
3715 // off scan
3716 STSelector sel = STSelector() ;
3717 vector<int> types ;
3718 types.push_back( SrcType::PSOFF ) ;
3719 sel.setTypes( types ) ;
3720 s->setSelection( sel ) ;
3721 // TODO 2010/01/08 TN
3722 // Grouping by time should be needed before averaging.
3723 // Each group must have own unique SCANNO (should be renumbered).
3724 // See PIPELINE/SDCalibration.py
3725 CountedPtr<Scantable> soff = getScantable( s, false ) ;
3726 Table ttab = soff->table() ;
3727 ROScalarColumn<Double> timeCol( ttab, "TIME" ) ;
3728 uInt nrow = timeCol.nrow() ;
3729 Vector<Double> timeSep( nrow - 1 ) ;
3730 for ( uInt i = 0 ; i < nrow - 1 ; i++ ) {
3731 timeSep[i] = timeCol(i+1) - timeCol(i) ;
3732 }
3733 ScalarColumn<Double> intervalCol( ttab, "INTERVAL" ) ;
3734 Vector<Double> interval = intervalCol.getColumn() ;
3735 interval /= 86400.0 ;
3736 ScalarColumn<uInt> scanCol( ttab, "SCANNO" ) ;
3737 vector<uInt> glist ;
3738 for ( uInt i = 0 ; i < nrow - 1 ; i++ ) {
3739 double gap = 2.0 * timeSep[i] / ( interval[i] + interval[i+1] ) ;
3740 //cout << "gap[" << i << "]=" << setw(5) << gap << endl ;
3741 if ( gap > 1.1 ) {
3742 glist.push_back( i ) ;
3743 }
3744 }
3745 Vector<uInt> gaplist( glist ) ;
3746 //cout << "gaplist = " << gaplist << endl ;
3747 uInt newid = 0 ;
3748 for ( uInt i = 0 ; i < nrow ; i++ ) {
3749 scanCol.put( i, newid ) ;
3750 if ( i == gaplist[newid] ) {
3751 newid++ ;
3752 }
3753 }
3754 //cout << "new scancol = " << scanCol.getColumn() << endl ;
3755 vector< CountedPtr<Scantable> > tmp( 1, soff ) ;
3756 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
3757 //cout << "aoff.nrow = " << aoff->nrow() << endl ;
3758 s->unsetSelection() ;
3759 sel.reset() ;
3760 types.clear() ;
3761
3762 // on scan
3763 bool insitu = insitu_ ;
3764 insitu_ = false ;
3765 CountedPtr<Scantable> out = getScantable( s, true ) ;
3766 insitu_ = insitu ;
3767 types.push_back( SrcType::PSON ) ;
3768 sel.setTypes( types ) ;
3769 s->setSelection( sel ) ;
3770 TableCopy::copyRows( out->table(), s->table() ) ;
3771 s->unsetSelection() ;
3772 sel.reset() ;
3773 types.clear() ;
3774
3775 // process each on scan
3776 ArrayColumn<Float> tsysCol ;
3777 tsysCol.attach( out->table(), "TSYS" ) ;
3778 for ( int i = 0 ; i < out->nrow() ; i++ ) {
3779 vector<float> sp = getCalibratedSpectra( out, aoff, i ) ;
3780 out->setSpectrum( sp, i ) ;
3781 }
3782
3783 // flux unit
3784 out->setFluxUnit( "K" ) ;
3785
3786 return out ;
3787 }
3788}
3789
3790CountedPtr<Scantable> STMath::cwcalfs( const CountedPtr<Scantable>& s,
3791 const String antname )
3792{
3793 vector<int> types ;
3794
3795 // APEX calibration mode
3796 int apexcalmode = 1 ;
3797
3798 if ( antname.find( "APEX" ) != string::npos ) {
3799 // check if off scan exists or not
3800 STSelector sel = STSelector() ;
3801 //sel.setName( offstr1 ) ;
3802 types.push_back( SrcType::FLOOFF ) ;
3803 sel.setTypes( types ) ;
3804 try {
3805 s->setSelection( sel ) ;
3806 }
3807 catch ( AipsError &e ) {
3808 apexcalmode = 0 ;
3809 }
3810 sel.reset() ;
3811 }
3812 s->unsetSelection() ;
3813 types.clear() ;
3814
3815 vector<bool> masks = s->getMask( 0 ) ;
3816 CountedPtr<Scantable> ssig, sref ;
3817 CountedPtr<Scantable> out ;
3818
3819 if ( antname.find( "APEX" ) != string::npos ) {
3820 // APEX calibration
3821 // sky scan
3822 STSelector sel = STSelector() ;
3823 types.push_back( SrcType::FLOSKY ) ;
3824 sel.setTypes( types ) ;
3825 s->setSelection( sel ) ;
3826 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3827 CountedPtr<Scantable> askylo = average( tmp, masks, "TINT", "SCAN" ) ;
3828 s->unsetSelection() ;
3829 sel.reset() ;
3830 types.clear() ;
3831 types.push_back( SrcType::FHISKY ) ;
3832 sel.setTypes( types ) ;
3833 s->setSelection( sel ) ;
3834 tmp.clear() ;
3835 tmp.push_back( getScantable( s, false ) ) ;
3836 CountedPtr<Scantable> askyhi = average( tmp, masks, "TINT", "SCAN" ) ;
3837 s->unsetSelection() ;
3838 sel.reset() ;
3839 types.clear() ;
3840
3841 // hot scan
3842 types.push_back( SrcType::FLOHOT ) ;
3843 sel.setTypes( types ) ;
3844 s->setSelection( sel ) ;
3845 tmp.clear() ;
3846 tmp.push_back( getScantable( s, false ) ) ;
3847 CountedPtr<Scantable> ahotlo = average( tmp, masks, "TINT", "SCAN" ) ;
3848 s->unsetSelection() ;
3849 sel.reset() ;
3850 types.clear() ;
3851 types.push_back( SrcType::FHIHOT ) ;
3852 sel.setTypes( types ) ;
3853 s->setSelection( sel ) ;
3854 tmp.clear() ;
3855 tmp.push_back( getScantable( s, false ) ) ;
3856 CountedPtr<Scantable> ahothi = average( tmp, masks, "TINT", "SCAN" ) ;
3857 s->unsetSelection() ;
3858 sel.reset() ;
3859 types.clear() ;
3860
3861 // cold scan
3862 CountedPtr<Scantable> acoldlo, acoldhi ;
3863// types.push_back( SrcType::FLOCOLD ) ;
3864// sel.setTypes( types ) ;
3865// s->setSelection( sel ) ;
3866// tmp.clear() ;
3867// tmp.push_back( getScantable( s, false ) ) ;
3868// CountedPtr<Scantable> acoldlo = average( tmp, masks, "TINT", "SCAN" ) ;
3869// s->unsetSelection() ;
3870// sel.reset() ;
3871// types.clear() ;
3872// types.push_back( SrcType::FHICOLD ) ;
3873// sel.setTypes( types ) ;
3874// s->setSelection( sel ) ;
3875// tmp.clear() ;
3876// tmp.push_back( getScantable( s, false ) ) ;
3877// CountedPtr<Scantable> acoldhi = average( tmp, masks, "TINT", "SCAN" ) ;
3878// s->unsetSelection() ;
3879// sel.reset() ;
3880// types.clear() ;
3881
3882 // ref scan
3883 bool insitu = insitu_ ;
3884 insitu_ = false ;
3885 sref = getScantable( s, true ) ;
3886 insitu_ = insitu ;
3887 types.push_back( SrcType::FSLO ) ;
3888 sel.setTypes( types ) ;
3889 s->setSelection( sel ) ;
3890 TableCopy::copyRows( sref->table(), s->table() ) ;
3891 s->unsetSelection() ;
3892 sel.reset() ;
3893 types.clear() ;
3894
3895 // sig scan
3896 insitu_ = false ;
3897 ssig = getScantable( s, true ) ;
3898 insitu_ = insitu ;
3899 types.push_back( SrcType::FSHI ) ;
3900 sel.setTypes( types ) ;
3901 s->setSelection( sel ) ;
3902 TableCopy::copyRows( ssig->table(), s->table() ) ;
3903 s->unsetSelection() ;
3904 sel.reset() ;
3905 types.clear() ;
3906
3907 if ( apexcalmode == 0 ) {
3908 // APEX fs data without off scan
3909 // process each sig and ref scan
3910 ArrayColumn<Float> tsysCollo ;
3911 tsysCollo.attach( ssig->table(), "TSYS" ) ;
3912 ArrayColumn<Float> tsysColhi ;
3913 tsysColhi.attach( sref->table(), "TSYS" ) ;
3914 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
3915 vector< CountedPtr<Scantable> > sky( 2 ) ;
3916 sky[0] = askylo ;
3917 sky[1] = askyhi ;
3918 vector< CountedPtr<Scantable> > hot( 2 ) ;
3919 hot[0] = ahotlo ;
3920 hot[1] = ahothi ;
3921 vector< CountedPtr<Scantable> > cold( 2 ) ;
3922 //cold[0] = acoldlo ;
3923 //cold[1] = acoldhi ;
3924 vector<float> sp = getFSCalibratedSpectra( ssig, sref, sky, hot, cold, i ) ;
3925 ssig->setSpectrum( sp, i ) ;
3926 string reftime = ssig->getTime( i ) ;
3927 vector<int> ii( 1, ssig->getIF( i ) ) ;
3928 vector<int> ib( 1, ssig->getBeam( i ) ) ;
3929 vector<int> ip( 1, ssig->getPol( i ) ) ;
3930 sel.setIFs( ii ) ;
3931 sel.setBeams( ib ) ;
3932 sel.setPolarizations( ip ) ;
3933 askylo->setSelection( sel ) ;
3934 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
3935 const Vector<Float> Vtsyslo( sptsys ) ;
3936 tsysCollo.put( i, Vtsyslo ) ;
3937 askylo->unsetSelection() ;
3938 sel.reset() ;
3939 sky[0] = askyhi ;
3940 sky[1] = askylo ;
3941 hot[0] = ahothi ;
3942 hot[1] = ahotlo ;
3943 cold[0] = acoldhi ;
3944 cold[1] = acoldlo ;
3945 sp = getFSCalibratedSpectra( sref, ssig, sky, hot, cold, i ) ;
3946 sref->setSpectrum( sp, i ) ;
3947 reftime = sref->getTime( i ) ;
3948 ii[0] = sref->getIF( i ) ;
3949 ib[0] = sref->getBeam( i ) ;
3950 ip[0] = sref->getPol( i ) ;
3951 sel.setIFs( ii ) ;
3952 sel.setBeams( ib ) ;
3953 sel.setPolarizations( ip ) ;
3954 askyhi->setSelection( sel ) ;
3955 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
3956 const Vector<Float> Vtsyshi( sptsys ) ;
3957 tsysColhi.put( i, Vtsyshi ) ;
3958 askyhi->unsetSelection() ;
3959 sel.reset() ;
3960 }
3961 }
3962 else if ( apexcalmode == 1 ) {
3963 // APEX fs data with off scan
3964 // off scan
3965 types.push_back( SrcType::FLOOFF ) ;
3966 sel.setTypes( types ) ;
3967 s->setSelection( sel ) ;
3968 tmp.clear() ;
3969 tmp.push_back( getScantable( s, false ) ) ;
3970 CountedPtr<Scantable> aofflo = average( tmp, masks, "TINT", "SCAN" ) ;
3971 s->unsetSelection() ;
3972 sel.reset() ;
3973 types.clear() ;
3974 types.push_back( SrcType::FHIOFF ) ;
3975 sel.setTypes( types ) ;
3976 s->setSelection( sel ) ;
3977 tmp.clear() ;
3978 tmp.push_back( getScantable( s, false ) ) ;
3979 CountedPtr<Scantable> aoffhi = average( tmp, masks, "TINT", "SCAN" ) ;
3980 s->unsetSelection() ;
3981 sel.reset() ;
3982 types.clear() ;
3983
3984 // process each sig and ref scan
3985 ArrayColumn<Float> tsysCollo ;
3986 tsysCollo.attach( ssig->table(), "TSYS" ) ;
3987 ArrayColumn<Float> tsysColhi ;
3988 tsysColhi.attach( sref->table(), "TSYS" ) ;
3989 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
3990 vector<float> sp = getCalibratedSpectra( ssig, aofflo, askylo, ahotlo, acoldlo, i, antname ) ;
3991 ssig->setSpectrum( sp, i ) ;
3992 sp = getCalibratedSpectra( sref, aoffhi, askyhi, ahothi, acoldhi, i, antname ) ;
3993 string reftime = ssig->getTime( i ) ;
3994 vector<int> ii( 1, ssig->getIF( i ) ) ;
3995 vector<int> ib( 1, ssig->getBeam( i ) ) ;
3996 vector<int> ip( 1, ssig->getPol( i ) ) ;
3997 sel.setIFs( ii ) ;
3998 sel.setBeams( ib ) ;
3999 sel.setPolarizations( ip ) ;
4000 askylo->setSelection( sel ) ;
4001 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
4002 const Vector<Float> Vtsyslo( sptsys ) ;
4003 tsysCollo.put( i, Vtsyslo ) ;
4004 askylo->unsetSelection() ;
4005 sel.reset() ;
4006 sref->setSpectrum( sp, i ) ;
4007 reftime = sref->getTime( i ) ;
4008 ii[0] = sref->getIF( i ) ;
4009 ib[0] = sref->getBeam( i ) ;
4010 ip[0] = sref->getPol( i ) ;
4011 sel.setIFs( ii ) ;
4012 sel.setBeams( ib ) ;
4013 sel.setPolarizations( ip ) ;
4014 askyhi->setSelection( sel ) ;
4015 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
4016 const Vector<Float> Vtsyshi( sptsys ) ;
4017 tsysColhi.put( i, Vtsyshi ) ;
4018 askyhi->unsetSelection() ;
4019 sel.reset() ;
4020 }
4021 }
4022 }
4023 else {
4024 // non-APEX fs data
4025 // sky scan
4026 STSelector sel = STSelector() ;
4027 types.push_back( SrcType::SKY ) ;
4028 sel.setTypes( types ) ;
4029 s->setSelection( sel ) ;
4030 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
4031 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
4032 s->unsetSelection() ;
4033 sel.reset() ;
4034 types.clear() ;
4035
4036 // hot scan
4037 types.push_back( SrcType::HOT ) ;
4038 sel.setTypes( types ) ;
4039 s->setSelection( sel ) ;
4040 tmp.clear() ;
4041 tmp.push_back( getScantable( s, false ) ) ;
4042 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
4043 s->unsetSelection() ;
4044 sel.reset() ;
4045 types.clear() ;
4046
4047 // cold scan
4048 CountedPtr<Scantable> acold ;
4049// types.push_back( SrcType::COLD ) ;
4050// sel.setTypes( types ) ;
4051// s->setSelection( sel ) ;
4052// tmp.clear() ;
4053// tmp.push_back( getScantable( s, false ) ) ;
4054// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCAN" ) ;
4055// s->unsetSelection() ;
4056// sel.reset() ;
4057// types.clear() ;
4058
4059 // ref scan
4060 bool insitu = insitu_ ;
4061 insitu_ = false ;
4062 sref = getScantable( s, true ) ;
4063 insitu_ = insitu ;
4064 types.push_back( SrcType::FSOFF ) ;
4065 sel.setTypes( types ) ;
4066 s->setSelection( sel ) ;
4067 TableCopy::copyRows( sref->table(), s->table() ) ;
4068 s->unsetSelection() ;
4069 sel.reset() ;
4070 types.clear() ;
4071
4072 // sig scan
4073 insitu_ = false ;
4074 ssig = getScantable( s, true ) ;
4075 insitu_ = insitu ;
4076 types.push_back( SrcType::FSON ) ;
4077 sel.setTypes( types ) ;
4078 s->setSelection( sel ) ;
4079 TableCopy::copyRows( ssig->table(), s->table() ) ;
4080 s->unsetSelection() ;
4081 sel.reset() ;
4082 types.clear() ;
4083
4084 // process each sig and ref scan
4085 ArrayColumn<Float> tsysColsig ;
4086 tsysColsig.attach( ssig->table(), "TSYS" ) ;
4087 ArrayColumn<Float> tsysColref ;
4088 tsysColref.attach( ssig->table(), "TSYS" ) ;
4089 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4090 vector<float> sp = getFSCalibratedSpectra( ssig, sref, asky, ahot, acold, i ) ;
4091 ssig->setSpectrum( sp, i ) ;
4092 string reftime = ssig->getTime( i ) ;
4093 vector<int> ii( 1, ssig->getIF( i ) ) ;
4094 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4095 vector<int> ip( 1, ssig->getPol( i ) ) ;
4096 sel.setIFs( ii ) ;
4097 sel.setBeams( ib ) ;
4098 sel.setPolarizations( ip ) ;
4099 asky->setSelection( sel ) ;
4100 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
4101 const Vector<Float> Vtsys( sptsys ) ;
4102 tsysColsig.put( i, Vtsys ) ;
4103 asky->unsetSelection() ;
4104 sel.reset() ;
4105 sp = getFSCalibratedSpectra( sref, ssig, asky, ahot, acold, i ) ;
4106 sref->setSpectrum( sp, i ) ;
4107 tsysColref.put( i, Vtsys ) ;
4108 }
4109 }
4110
4111 // do folding if necessary
4112 Table sigtab = ssig->table() ;
4113 Table reftab = sref->table() ;
4114 ScalarColumn<uInt> sigifnoCol ;
4115 ScalarColumn<uInt> refifnoCol ;
4116 ScalarColumn<uInt> sigfidCol ;
4117 ScalarColumn<uInt> reffidCol ;
4118 Int nchan = (Int)ssig->nchan() ;
4119 sigifnoCol.attach( sigtab, "IFNO" ) ;
4120 refifnoCol.attach( reftab, "IFNO" ) ;
4121 sigfidCol.attach( sigtab, "FREQ_ID" ) ;
4122 reffidCol.attach( reftab, "FREQ_ID" ) ;
4123 Vector<uInt> sfids( sigfidCol.getColumn() ) ;
4124 Vector<uInt> rfids( reffidCol.getColumn() ) ;
4125 vector<uInt> sfids_unique ;
4126 vector<uInt> rfids_unique ;
4127 vector<uInt> sifno_unique ;
4128 vector<uInt> rifno_unique ;
4129 for ( uInt i = 0 ; i < sfids.nelements() ; i++ ) {
4130 if ( count( sfids_unique.begin(), sfids_unique.end(), sfids[i] ) == 0 ) {
4131 sfids_unique.push_back( sfids[i] ) ;
4132 sifno_unique.push_back( ssig->getIF( i ) ) ;
4133 }
4134 if ( count( rfids_unique.begin(), rfids_unique.end(), rfids[i] ) == 0 ) {
4135 rfids_unique.push_back( rfids[i] ) ;
4136 rifno_unique.push_back( sref->getIF( i ) ) ;
4137 }
4138 }
4139 double refpix_sig, refval_sig, increment_sig ;
4140 double refpix_ref, refval_ref, increment_ref ;
4141 vector< CountedPtr<Scantable> > tmp( sfids_unique.size() ) ;
4142 for ( uInt i = 0 ; i < sfids_unique.size() ; i++ ) {
4143 ssig->frequencies().getEntry( refpix_sig, refval_sig, increment_sig, sfids_unique[i] ) ;
4144 sref->frequencies().getEntry( refpix_ref, refval_ref, increment_ref, rfids_unique[i] ) ;
4145 if ( refpix_sig == refpix_ref ) {
4146 double foffset = refval_ref - refval_sig ;
4147 int choffset = static_cast<int>(foffset/increment_sig) ;
4148 double doffset = foffset / increment_sig ;
4149 if ( abs(choffset) >= nchan ) {
4150 LogIO os( LogOrigin( "STMath", "cwcalfs", WHERE ) ) ;
4151 os << "FREQ_ID=[" << sfids_unique[i] << "," << rfids_unique[i] << "]: out-band frequency switching, no folding" << LogIO::POST ;
4152 os << "Just return signal data" << LogIO::POST ;
4153 //std::vector< CountedPtr<Scantable> > tabs ;
4154 //tabs.push_back( ssig ) ;
4155 //tabs.push_back( sref ) ;
4156 //out = merge( tabs ) ;
4157 tmp[i] = ssig ;
4158 }
4159 else {
4160 STSelector sel = STSelector() ;
4161 vector<int> v( 1, sifno_unique[i] ) ;
4162 sel.setIFs( v ) ;
4163 ssig->setSelection( sel ) ;
4164 sel.reset() ;
4165 v[0] = rifno_unique[i] ;
4166 sel.setIFs( v ) ;
4167 sref->setSelection( sel ) ;
4168 sel.reset() ;
4169 if ( antname.find( "APEX" ) != string::npos ) {
4170 tmp[i] = dofold( ssig, sref, 0.5*doffset, -0.5*doffset ) ;
4171 //tmp[i] = dofold( ssig, sref, doffset ) ;
4172 }
4173 else {
4174 tmp[i] = dofold( ssig, sref, doffset ) ;
4175 }
4176 ssig->unsetSelection() ;
4177 sref->unsetSelection() ;
4178 }
4179 }
4180 }
4181
4182 if ( tmp.size() > 1 ) {
4183 out = merge( tmp ) ;
4184 }
4185 else {
4186 out = tmp[0] ;
4187 }
4188
4189 // flux unit
4190 out->setFluxUnit( "K" ) ;
4191
4192 return out ;
4193}
4194
4195CountedPtr<Scantable> STMath::almacalfs( const CountedPtr<Scantable>& s )
4196{
4197 CountedPtr<Scantable> out ;
4198
4199 return out ;
4200}
4201
4202vector<float> STMath::getSpectrumFromTime( string reftime,
4203 CountedPtr<Scantable>& s,
4204 string mode )
4205{
4206 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
4207 vector<float> sp ;
4208
4209 if ( s->nrow() == 0 ) {
4210 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
4211 return sp ;
4212 }
4213 else if ( s->nrow() == 1 ) {
4214 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
4215 return s->getSpectrum( 0 ) ;
4216 }
4217 else {
4218 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4219 if ( mode == "before" ) {
4220 int id = -1 ;
4221 if ( idx[0] != -1 ) {
4222 id = idx[0] ;
4223 }
4224 else if ( idx[1] != -1 ) {
4225 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4226 id = idx[1] ;
4227 }
4228 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4229 sp = s->getSpectrum( id ) ;
4230 }
4231 else if ( mode == "after" ) {
4232 int id = -1 ;
4233 if ( idx[1] != -1 ) {
4234 id = idx[1] ;
4235 }
4236 else if ( idx[0] != -1 ) {
4237 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4238 id = idx[1] ;
4239 }
4240 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4241 sp = s->getSpectrum( id ) ;
4242 }
4243 else if ( mode == "nearest" ) {
4244 int id = -1 ;
4245 if ( idx[0] == -1 ) {
4246 id = idx[1] ;
4247 }
4248 else if ( idx[1] == -1 ) {
4249 id = idx[0] ;
4250 }
4251 else if ( idx[0] == idx[1] ) {
4252 id = idx[0] ;
4253 }
4254 else {
4255 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4256 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4257 double tref = getMJD( reftime ) ;
4258 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4259 id = idx[1] ;
4260 }
4261 else {
4262 id = idx[0] ;
4263 }
4264 }
4265 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4266 sp = s->getSpectrum( id ) ;
4267 }
4268 else if ( mode == "linear" ) {
4269 if ( idx[0] == -1 ) {
4270 // use after
4271 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4272 int id = idx[1] ;
4273 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4274 sp = s->getSpectrum( id ) ;
4275 }
4276 else if ( idx[1] == -1 ) {
4277 // use before
4278 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4279 int id = idx[0] ;
4280 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4281 sp = s->getSpectrum( id ) ;
4282 }
4283 else if ( idx[0] == idx[1] ) {
4284 // use before
4285 //os << "No need to interporate." << LogIO::POST ;
4286 int id = idx[0] ;
4287 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4288 sp = s->getSpectrum( id ) ;
4289 }
4290 else {
4291 // do interpolation
4292 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4293 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4294 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4295 double tref = getMJD( reftime ) ;
4296 vector<float> sp0 = s->getSpectrum( idx[0] ) ;
4297 vector<float> sp1 = s->getSpectrum( idx[1] ) ;
4298 for ( unsigned int i = 0 ; i < sp0.size() ; i++ ) {
4299 float v = ( sp1[i] - sp0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + sp0[i] ;
4300 sp.push_back( v ) ;
4301 }
4302 }
4303 }
4304 else {
4305 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4306 }
4307 return sp ;
4308 }
4309}
4310
4311double STMath::getMJD( string strtime )
4312{
4313 if ( strtime.find("/") == string::npos ) {
4314 // MJD time string
4315 return atof( strtime.c_str() ) ;
4316 }
4317 else {
4318 // string in YYYY/MM/DD/HH:MM:SS format
4319 uInt year = atoi( strtime.substr( 0, 4 ).c_str() ) ;
4320 uInt month = atoi( strtime.substr( 5, 2 ).c_str() ) ;
4321 uInt day = atoi( strtime.substr( 8, 2 ).c_str() ) ;
4322 uInt hour = atoi( strtime.substr( 11, 2 ).c_str() ) ;
4323 uInt minute = atoi( strtime.substr( 14, 2 ).c_str() ) ;
4324 uInt sec = atoi( strtime.substr( 17, 2 ).c_str() ) ;
4325 Time t( year, month, day, hour, minute, sec ) ;
4326 return t.modifiedJulianDay() ;
4327 }
4328}
4329
4330vector<int> STMath::getRowIdFromTime( string reftime, CountedPtr<Scantable> &s )
4331{
4332 double reft = getMJD( reftime ) ;
4333 double dtmin = 1.0e100 ;
4334 double dtmax = -1.0e100 ;
4335 vector<double> dt ;
4336 int just_before = -1 ;
4337 int just_after = -1 ;
4338 for ( int i = 0 ; i < s->nrow() ; i++ ) {
4339 dt.push_back( getMJD( s->getTime( i ) ) - reft ) ;
4340 }
4341 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4342 if ( dt[i] > 0.0 ) {
4343 // after reftime
4344 if ( dt[i] < dtmin ) {
4345 just_after = i ;
4346 dtmin = dt[i] ;
4347 }
4348 }
4349 else if ( dt[i] < 0.0 ) {
4350 // before reftime
4351 if ( dt[i] > dtmax ) {
4352 just_before = i ;
4353 dtmax = dt[i] ;
4354 }
4355 }
4356 else {
4357 // just a reftime
4358 just_before = i ;
4359 just_after = i ;
4360 dtmax = 0 ;
4361 dtmin = 0 ;
4362 break ;
4363 }
4364 }
4365
4366 vector<int> v ;
4367 v.push_back( just_before ) ;
4368 v.push_back( just_after ) ;
4369
4370 return v ;
4371}
4372
4373vector<float> STMath::getTcalFromTime( string reftime,
4374 CountedPtr<Scantable>& s,
4375 string mode )
4376{
4377 LogIO os( LogOrigin( "STMath", "getTcalFromTime", WHERE ) ) ;
4378 vector<float> tcal ;
4379 STTcal tcalTable = s->tcal() ;
4380 String time ;
4381 Vector<Float> tcalval ;
4382 if ( s->nrow() == 0 ) {
4383 os << LogIO::SEVERE << "No row in the input scantable. Return empty tcal." << LogIO::POST ;
4384 return tcal ;
4385 }
4386 else if ( s->nrow() == 1 ) {
4387 uInt tcalid = s->getTcalId( 0 ) ;
4388 //os << "use row " << 0 << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4389 tcalTable.getEntry( time, tcalval, tcalid ) ;
4390 tcalval.tovector( tcal ) ;
4391 return tcal ;
4392 }
4393 else {
4394 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4395 if ( mode == "before" ) {
4396 int id = -1 ;
4397 if ( idx[0] != -1 ) {
4398 id = idx[0] ;
4399 }
4400 else if ( idx[1] != -1 ) {
4401 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4402 id = idx[1] ;
4403 }
4404 uInt tcalid = s->getTcalId( id ) ;
4405 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4406 tcalTable.getEntry( time, tcalval, tcalid ) ;
4407 tcalval.tovector( tcal ) ;
4408 }
4409 else if ( mode == "after" ) {
4410 int id = -1 ;
4411 if ( idx[1] != -1 ) {
4412 id = idx[1] ;
4413 }
4414 else if ( idx[0] != -1 ) {
4415 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4416 id = idx[1] ;
4417 }
4418 uInt tcalid = s->getTcalId( id ) ;
4419 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4420 tcalTable.getEntry( time, tcalval, tcalid ) ;
4421 tcalval.tovector( tcal ) ;
4422 }
4423 else if ( mode == "nearest" ) {
4424 int id = -1 ;
4425 if ( idx[0] == -1 ) {
4426 id = idx[1] ;
4427 }
4428 else if ( idx[1] == -1 ) {
4429 id = idx[0] ;
4430 }
4431 else if ( idx[0] == idx[1] ) {
4432 id = idx[0] ;
4433 }
4434 else {
4435 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4436 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4437 double tref = getMJD( reftime ) ;
4438 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4439 id = idx[1] ;
4440 }
4441 else {
4442 id = idx[0] ;
4443 }
4444 }
4445 uInt tcalid = s->getTcalId( id ) ;
4446 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4447 tcalTable.getEntry( time, tcalval, tcalid ) ;
4448 tcalval.tovector( tcal ) ;
4449 }
4450 else if ( mode == "linear" ) {
4451 if ( idx[0] == -1 ) {
4452 // use after
4453 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4454 int id = idx[1] ;
4455 uInt tcalid = s->getTcalId( id ) ;
4456 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4457 tcalTable.getEntry( time, tcalval, tcalid ) ;
4458 tcalval.tovector( tcal ) ;
4459 }
4460 else if ( idx[1] == -1 ) {
4461 // use before
4462 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4463 int id = idx[0] ;
4464 uInt tcalid = s->getTcalId( id ) ;
4465 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4466 tcalTable.getEntry( time, tcalval, tcalid ) ;
4467 tcalval.tovector( tcal ) ;
4468 }
4469 else if ( idx[0] == idx[1] ) {
4470 // use before
4471 //os << "No need to interporate." << LogIO::POST ;
4472 int id = idx[0] ;
4473 uInt tcalid = s->getTcalId( id ) ;
4474 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4475 tcalTable.getEntry( time, tcalval, tcalid ) ;
4476 tcalval.tovector( tcal ) ;
4477 }
4478 else {
4479 // do interpolation
4480 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4481 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4482 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4483 double tref = getMJD( reftime ) ;
4484 vector<float> tcal0 ;
4485 vector<float> tcal1 ;
4486 uInt tcalid0 = s->getTcalId( idx[0] ) ;
4487 uInt tcalid1 = s->getTcalId( idx[1] ) ;
4488 tcalTable.getEntry( time, tcalval, tcalid0 ) ;
4489 tcalval.tovector( tcal0 ) ;
4490 tcalTable.getEntry( time, tcalval, tcalid1 ) ;
4491 tcalval.tovector( tcal1 ) ;
4492 for ( unsigned int i = 0 ; i < tcal0.size() ; i++ ) {
4493 float v = ( tcal1[i] - tcal0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tcal0[i] ;
4494 tcal.push_back( v ) ;
4495 }
4496 }
4497 }
4498 else {
4499 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4500 }
4501 return tcal ;
4502 }
4503}
4504
4505vector<float> STMath::getTsysFromTime( string reftime,
4506 CountedPtr<Scantable>& s,
4507 string mode )
4508{
4509 LogIO os( LogOrigin( "STMath", "getTsysFromTime", WHERE ) ) ;
4510 ArrayColumn<Float> tsysCol ;
4511 tsysCol.attach( s->table(), "TSYS" ) ;
4512 vector<float> tsys ;
4513 String time ;
4514 Vector<Float> tsysval ;
4515 if ( s->nrow() == 0 ) {
4516 os << LogIO::SEVERE << "No row in the input scantable. Return empty tsys." << LogIO::POST ;
4517 return tsys ;
4518 }
4519 else if ( s->nrow() == 1 ) {
4520 //os << "use row " << 0 << LogIO::POST ;
4521 tsysval = tsysCol( 0 ) ;
4522 tsysval.tovector( tsys ) ;
4523 return tsys ;
4524 }
4525 else {
4526 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4527 if ( mode == "before" ) {
4528 int id = -1 ;
4529 if ( idx[0] != -1 ) {
4530 id = idx[0] ;
4531 }
4532 else if ( idx[1] != -1 ) {
4533 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4534 id = idx[1] ;
4535 }
4536 //os << "use row " << id << LogIO::POST ;
4537 tsysval = tsysCol( id ) ;
4538 tsysval.tovector( tsys ) ;
4539 }
4540 else if ( mode == "after" ) {
4541 int id = -1 ;
4542 if ( idx[1] != -1 ) {
4543 id = idx[1] ;
4544 }
4545 else if ( idx[0] != -1 ) {
4546 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4547 id = idx[1] ;
4548 }
4549 //os << "use row " << id << LogIO::POST ;
4550 tsysval = tsysCol( id ) ;
4551 tsysval.tovector( tsys ) ;
4552 }
4553 else if ( mode == "nearest" ) {
4554 int id = -1 ;
4555 if ( idx[0] == -1 ) {
4556 id = idx[1] ;
4557 }
4558 else if ( idx[1] == -1 ) {
4559 id = idx[0] ;
4560 }
4561 else if ( idx[0] == idx[1] ) {
4562 id = idx[0] ;
4563 }
4564 else {
4565 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4566 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4567 double tref = getMJD( reftime ) ;
4568 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4569 id = idx[1] ;
4570 }
4571 else {
4572 id = idx[0] ;
4573 }
4574 }
4575 //os << "use row " << id << LogIO::POST ;
4576 tsysval = tsysCol( id ) ;
4577 tsysval.tovector( tsys ) ;
4578 }
4579 else if ( mode == "linear" ) {
4580 if ( idx[0] == -1 ) {
4581 // use after
4582 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4583 int id = idx[1] ;
4584 //os << "use row " << id << LogIO::POST ;
4585 tsysval = tsysCol( id ) ;
4586 tsysval.tovector( tsys ) ;
4587 }
4588 else if ( idx[1] == -1 ) {
4589 // use before
4590 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4591 int id = idx[0] ;
4592 //os << "use row " << id << LogIO::POST ;
4593 tsysval = tsysCol( id ) ;
4594 tsysval.tovector( tsys ) ;
4595 }
4596 else if ( idx[0] == idx[1] ) {
4597 // use before
4598 //os << "No need to interporate." << LogIO::POST ;
4599 int id = idx[0] ;
4600 //os << "use row " << id << LogIO::POST ;
4601 tsysval = tsysCol( id ) ;
4602 tsysval.tovector( tsys ) ;
4603 }
4604 else {
4605 // do interpolation
4606 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4607 double t0 = getMJD( s->getTime( idx[0] ) ) ;
4608 double t1 = getMJD( s->getTime( idx[1] ) ) ;
4609 double tref = getMJD( reftime ) ;
4610 vector<float> tsys0 ;
4611 vector<float> tsys1 ;
4612 tsysval = tsysCol( idx[0] ) ;
4613 tsysval.tovector( tsys0 ) ;
4614 tsysval = tsysCol( idx[1] ) ;
4615 tsysval.tovector( tsys1 ) ;
4616 for ( unsigned int i = 0 ; i < tsys0.size() ; i++ ) {
4617 float v = ( tsys1[i] - tsys0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tsys0[i] ;
4618 tsys.push_back( v ) ;
4619 }
4620 }
4621 }
4622 else {
4623 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4624 }
4625 return tsys ;
4626 }
4627}
4628
4629vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
4630 CountedPtr<Scantable>& off,
4631 CountedPtr<Scantable>& sky,
4632 CountedPtr<Scantable>& hot,
4633 CountedPtr<Scantable>& cold,
4634 int index,
4635 string antname )
4636{
4637 string reftime = on->getTime( index ) ;
4638 vector<int> ii( 1, on->getIF( index ) ) ;
4639 vector<int> ib( 1, on->getBeam( index ) ) ;
4640 vector<int> ip( 1, on->getPol( index ) ) ;
4641 vector<int> ic( 1, on->getScan( index ) ) ;
4642 STSelector sel = STSelector() ;
4643 sel.setIFs( ii ) ;
4644 sel.setBeams( ib ) ;
4645 sel.setPolarizations( ip ) ;
4646 sky->setSelection( sel ) ;
4647 hot->setSelection( sel ) ;
4648 //cold->setSelection( sel ) ;
4649 off->setSelection( sel ) ;
4650 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
4651 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
4652 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
4653 vector<float> spoff = getSpectrumFromTime( reftime, off, "linear" ) ;
4654 vector<float> spec = on->getSpectrum( index ) ;
4655 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
4656 vector<float> sp( tcal.size() ) ;
4657 if ( antname.find( "APEX" ) != string::npos ) {
4658 // using gain array
4659 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4660 float v = ( ( spec[j] - spoff[j] ) / spoff[j] )
4661 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4662 sp[j] = v ;
4663 }
4664 }
4665 else {
4666 // Chopper-Wheel calibration (Ulich & Haas 1976)
4667 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4668 float v = ( spec[j] - spoff[j] ) / ( sphot[j] - spsky[j] ) * tcal[j] ;
4669 sp[j] = v ;
4670 }
4671 }
4672 sel.reset() ;
4673 sky->unsetSelection() ;
4674 hot->unsetSelection() ;
4675 //cold->unsetSelection() ;
4676 off->unsetSelection() ;
4677
4678 return sp ;
4679}
4680
4681vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
4682 CountedPtr<Scantable>& off,
4683 int index )
4684{
4685 string reftime = on->getTime( index ) ;
4686 vector<int> ii( 1, on->getIF( index ) ) ;
4687 vector<int> ib( 1, on->getBeam( index ) ) ;
4688 vector<int> ip( 1, on->getPol( index ) ) ;
4689 vector<int> ic( 1, on->getScan( index ) ) ;
4690 STSelector sel = STSelector() ;
4691 sel.setIFs( ii ) ;
4692 sel.setBeams( ib ) ;
4693 sel.setPolarizations( ip ) ;
4694 off->setSelection( sel ) ;
4695 vector<float> spoff = getSpectrumFromTime( reftime, off, "linear" ) ;
4696 vector<float> spec = on->getSpectrum( index ) ;
4697 //vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
4698 //vector<float> tsys = on->getTsysVec( index ) ;
4699 ArrayColumn<Float> tsysCol( on->table(), "TSYS" ) ;
4700 Vector<Float> tsys = tsysCol( index ) ;
4701 vector<float> sp( spec.size() ) ;
4702 // ALMA Calibration
4703 //
4704 // Ta* = Tsys * ( ON - OFF ) / OFF
4705 //
4706 // 2010/01/07 Takeshi Nakazato
4707 unsigned int tsyssize = tsys.nelements() ;
4708 unsigned int spsize = sp.size() ;
4709 for ( unsigned int j = 0 ; j < sp.size() ; j++ ) {
4710 float tscale = 0.0 ;
4711 if ( tsyssize == spsize )
4712 tscale = tsys[j] ;
4713 else
4714 tscale = tsys[0] ;
4715 float v = tscale * ( spec[j] - spoff[j] ) / spoff[j] ;
4716 sp[j] = v ;
4717 }
4718 sel.reset() ;
4719 off->unsetSelection() ;
4720
4721 return sp ;
4722}
4723
4724vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
4725 CountedPtr<Scantable>& ref,
4726 CountedPtr<Scantable>& sky,
4727 CountedPtr<Scantable>& hot,
4728 CountedPtr<Scantable>& cold,
4729 int index )
4730{
4731 string reftime = sig->getTime( index ) ;
4732 vector<int> ii( 1, sig->getIF( index ) ) ;
4733 vector<int> ib( 1, sig->getBeam( index ) ) ;
4734 vector<int> ip( 1, sig->getPol( index ) ) ;
4735 vector<int> ic( 1, sig->getScan( index ) ) ;
4736 STSelector sel = STSelector() ;
4737 sel.setIFs( ii ) ;
4738 sel.setBeams( ib ) ;
4739 sel.setPolarizations( ip ) ;
4740 sky->setSelection( sel ) ;
4741 hot->setSelection( sel ) ;
4742 //cold->setSelection( sel ) ;
4743 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
4744 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
4745 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
4746 vector<float> spref = ref->getSpectrum( index ) ;
4747 vector<float> spsig = sig->getSpectrum( index ) ;
4748 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
4749 vector<float> sp( tcal.size() ) ;
4750 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4751 float v = tcal[j] * spsky[j] / ( sphot[j] - spsky[j] ) * ( spsig[j] - spref[j] ) / spref[j] ;
4752 sp[j] = v ;
4753 }
4754 sel.reset() ;
4755 sky->unsetSelection() ;
4756 hot->unsetSelection() ;
4757 //cold->unsetSelection() ;
4758
4759 return sp ;
4760}
4761
4762vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
4763 CountedPtr<Scantable>& ref,
4764 vector< CountedPtr<Scantable> >& sky,
4765 vector< CountedPtr<Scantable> >& hot,
4766 vector< CountedPtr<Scantable> >& cold,
4767 int index )
4768{
4769 string reftime = sig->getTime( index ) ;
4770 vector<int> ii( 1, sig->getIF( index ) ) ;
4771 vector<int> ib( 1, sig->getBeam( index ) ) ;
4772 vector<int> ip( 1, sig->getPol( index ) ) ;
4773 vector<int> ic( 1, sig->getScan( index ) ) ;
4774 STSelector sel = STSelector() ;
4775 sel.setIFs( ii ) ;
4776 sel.setBeams( ib ) ;
4777 sel.setPolarizations( ip ) ;
4778 sky[0]->setSelection( sel ) ;
4779 hot[0]->setSelection( sel ) ;
4780 //cold[0]->setSelection( sel ) ;
4781 vector<float> spskys = getSpectrumFromTime( reftime, sky[0], "linear" ) ;
4782 vector<float> sphots = getSpectrumFromTime( reftime, hot[0], "linear" ) ;
4783 //vector<float> spcolds = getSpectrumFromTime( reftime, cold[0], "linear" ) ;
4784 vector<float> tcals = getTcalFromTime( reftime, sky[0], "linear" ) ;
4785 sel.reset() ;
4786 ii[0] = ref->getIF( index ) ;
4787 sel.setIFs( ii ) ;
4788 sel.setBeams( ib ) ;
4789 sel.setPolarizations( ip ) ;
4790 sky[1]->setSelection( sel ) ;
4791 hot[1]->setSelection( sel ) ;
4792 //cold[1]->setSelection( sel ) ;
4793 vector<float> spskyr = getSpectrumFromTime( reftime, sky[1], "linear" ) ;
4794 vector<float> sphotr = getSpectrumFromTime( reftime, hot[1], "linear" ) ;
4795 //vector<float> spcoldr = getSpectrumFromTime( reftime, cold[1], "linear" ) ;
4796 vector<float> tcalr = getTcalFromTime( reftime, sky[1], "linear" ) ;
4797 vector<float> spref = ref->getSpectrum( index ) ;
4798 vector<float> spsig = sig->getSpectrum( index ) ;
4799 vector<float> sp( tcals.size() ) ;
4800 for ( unsigned int j = 0 ; j < tcals.size() ; j++ ) {
4801 float v = tcals[j] * spsig[j] / ( sphots[j] - spskys[j] ) - tcalr[j] * spref[j] / ( sphotr[j] - spskyr[j] ) ;
4802 sp[j] = v ;
4803 }
4804 sel.reset() ;
4805 sky[0]->unsetSelection() ;
4806 hot[0]->unsetSelection() ;
4807 //cold[0]->unsetSelection() ;
4808 sky[1]->unsetSelection() ;
4809 hot[1]->unsetSelection() ;
4810 //cold[1]->unsetSelection() ;
4811
4812 return sp ;
4813}
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