source: branches/hpc33/src/STMath.cpp@ 2497

Last change on this file since 2497 was 2473, checked in by KohjiNakamura, 13 years ago

remove debug code
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 175.9 KB
Line 
1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <sstream>
14
15#include <casa/iomanip.h>
16#include <casa/Arrays/MaskArrLogi.h>
17#include <casa/Arrays/MaskArrMath.h>
18#include <casa/Arrays/ArrayLogical.h>
19#include <casa/Arrays/ArrayMath.h>
20#include <casa/Arrays/Slice.h>
21#include <casa/Arrays/Slicer.h>
22#include <casa/BasicSL/String.h>
23#include <casa/Containers/Block.h>
24#include <casa/Containers/RecordField.h>
25#include <casa/Exceptions/Error.h>
26#include <casa/Logging/LogIO.h>
27
28#include <coordinates/Coordinates/CoordinateSystem.h>
29#include <coordinates/Coordinates/CoordinateUtil.h>
30#include <coordinates/Coordinates/FrequencyAligner.h>
31#include <coordinates/Coordinates/SpectralCoordinate.h>
32
33#include <lattices/Lattices/LatticeUtilities.h>
34
35#include <scimath/Functionals/Polynomial.h>
36#include <scimath/Mathematics/Convolver.h>
37#include <scimath/Mathematics/VectorKernel.h>
38
39#include <tables/Tables/ExprNode.h>
40#include <tables/Tables/ReadAsciiTable.h>
41#include <tables/Tables/TableCopy.h>
42#include <tables/Tables/TableIter.h>
43#include <tables/Tables/TableParse.h>
44#include <tables/Tables/TableRecord.h>
45#include <tables/Tables/TableRow.h>
46#include <tables/Tables/TableVector.h>
47#include <tables/Tables/TabVecMath.h>
48
49#include <atnf/PKSIO/SrcType.h>
50
51#include "RowAccumulator.h"
52#include "STAttr.h"
53#include "STMath.h"
54#include "STSelector.h"
55#include "Accelerator.h"
56
57using namespace casa;
58using namespace asap;
59
60
61// 2012/02/17 TN
62// Since STGrid is implemented, average doesn't consider direction
63// when accumulating
64// tolerance for direction comparison (rad)
65// #define TOL_OTF 1.0e-15
66// #define TOL_POINT 2.9088821e-4 // 1 arcmin
67
68STMath::STMath(bool insitu) :
69 insitu_(insitu)
70{
71}
72
73
74STMath::~STMath()
75{
76}
77
78CountedPtr<Scantable>
79STMath::average( const std::vector<CountedPtr<Scantable> >& in,
80 const std::vector<bool>& mask,
81 const std::string& weight,
82 const std::string& avmode)
83{
84 LogIO os( LogOrigin( "STMath", "average()", WHERE ) ) ;
85 if ( avmode == "SCAN" && in.size() != 1 )
86 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
87 "Use merge first."));
88 WeightType wtype = stringToWeight(weight);
89
90 // 2012/02/17 TN
91 // Since STGrid is implemented, average doesn't consider direction
92 // when accumulating
93 // check if OTF observation
94// String obstype = in[0]->getHeader().obstype ;
95// Double tol = 0.0 ;
96// if ( (obstype.find( "OTF" ) != String::npos) || (obstype.find( "OBSERVE_TARGET" ) != String::npos) ) {
97// tol = TOL_OTF ;
98// }
99// else {
100// tol = TOL_POINT ;
101// }
102
103 // output
104 // clone as this is non insitu
105 bool insitu = insitu_;
106 setInsitu(false);
107 CountedPtr< Scantable > out = getScantable(in[0], true);
108 setInsitu(insitu);
109 std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
110 ++stit;
111 while ( stit != in.end() ) {
112 out->appendToHistoryTable((*stit)->history());
113 ++stit;
114 }
115
116 Table& tout = out->table();
117
118 /// @todo check if all scantables are conformant
119
120 ArrayColumn<Float> specColOut(tout,"SPECTRA");
121 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
122 ArrayColumn<Float> tsysColOut(tout,"TSYS");
123 ScalarColumn<Double> mjdColOut(tout,"TIME");
124 ScalarColumn<Double> intColOut(tout,"INTERVAL");
125 ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
126 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
127
128 // set up the output table rows. These are based on the structure of the
129 // FIRST scantable in the vector
130 const Table& baset = in[0]->table();
131
132 Block<String> cols(3);
133 cols[0] = String("BEAMNO");
134 cols[1] = String("IFNO");
135 cols[2] = String("POLNO");
136 if ( avmode == "SOURCE" ) {
137 cols.resize(4);
138 cols[3] = String("SRCNAME");
139 }
140 if ( avmode == "SCAN" && in.size() == 1) {
141 //cols.resize(4);
142 //cols[3] = String("SCANNO");
143 cols.resize(5);
144 cols[3] = String("SRCNAME");
145 cols[4] = String("SCANNO");
146 }
147 uInt outrowCount = 0;
148 TableIterator iter(baset, cols);
149// int count = 0 ;
150 while (!iter.pastEnd()) {
151 Table subt = iter.table();
152 // copy the first row of this selection into the new table
153 tout.addRow();
154 TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
155 // re-index to 0
156 if ( avmode != "SCAN" && avmode != "SOURCE" ) {
157 scanColOut.put(outrowCount, uInt(0));
158 }
159 ++outrowCount;
160 // 2012/02/17 TN
161 // Since STGrid is implemented, average doesn't consider direction
162 // when accumulating
163// MDirection::ScalarColumn dircol ;
164// dircol.attach( subt, "DIRECTION" ) ;
165// Int length = subt.nrow() ;
166// vector< Vector<Double> > dirs ;
167// vector<int> indexes ;
168// for ( Int i = 0 ; i < length ; i++ ) {
169// Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
170// //os << << count++ << ": " ;
171// //os << "[" << t[0] << "," << t[1] << "]" << LogIO::POST ;
172// bool adddir = true ;
173// for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
174// //if ( allTrue( t == dirs[j] ) ) {
175// Double dx = t[0] - dirs[j][0] ;
176// Double dy = t[1] - dirs[j][1] ;
177// Double dd = sqrt( dx * dx + dy * dy ) ;
178// //if ( allNearAbs( t, dirs[j], tol ) ) {
179// if ( dd <= tol ) {
180// adddir = false ;
181// break ;
182// }
183// }
184// if ( adddir ) {
185// dirs.push_back( t ) ;
186// indexes.push_back( i ) ;
187// }
188// }
189// uInt rowNum = dirs.size() ;
190// tout.addRow( rowNum ) ;
191// for ( uInt i = 0 ; i < rowNum ; i++ ) {
192// TableCopy::copyRows( tout, subt, outrowCount+i, indexes[i], 1 ) ;
193// // re-index to 0
194// if ( avmode != "SCAN" && avmode != "SOURCE" ) {
195// scanColOut.put(outrowCount+i, uInt(0));
196// }
197// }
198// outrowCount += rowNum ;
199 ++iter;
200 }
201 RowAccumulator acc(wtype);
202 Vector<Bool> cmask(mask);
203 acc.setUserMask(cmask);
204 ROTableRow row(tout);
205 ROArrayColumn<Float> specCol, tsysCol;
206 ROArrayColumn<uChar> flagCol;
207 ROScalarColumn<Double> mjdCol, intCol;
208 ROScalarColumn<Int> scanIDCol;
209
210 Vector<uInt> rowstodelete;
211
212 for (uInt i=0; i < tout.nrow(); ++i) {
213 for ( int j=0; j < int(in.size()); ++j ) {
214 const Table& tin = in[j]->table();
215 const TableRecord& rec = row.get(i);
216 ROScalarColumn<Double> tmp(tin, "TIME");
217 Double td;tmp.get(0,td);
218
219#if 1
220 static char const*const colNames1[] = { "IFNO", "BEAMNO", "POLNO" };
221 uInt const values1[] = { rec.asuInt("IFNO"), rec.asuInt("BEAMNO"), rec.asuInt("POLNO") };
222 SingleTypeEqPredicate<uInt, 3> myPred(tin, colNames1, values1);
223 CustomTableExprNodeRep myNodeRep(tin, myPred);
224 myNodeRep.link(); // to avoid automatic delete when myExpr is destructed.
225 CustomTableExprNode myExpr(myNodeRep);
226 Table basesubt = tin(myExpr);
227#else
228 Table basesubt = tin( tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
229 && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
230 && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
231#endif
232 Table subt;
233 if ( avmode == "SOURCE") {
234 subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME"));
235 } else if (avmode == "SCAN") {
236 subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME")
237 && basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
238 } else {
239 subt = basesubt;
240 }
241
242 // 2012/02/17 TN
243 // Since STGrid is implemented, average doesn't consider direction
244 // when accumulating
245// vector<uInt> removeRows ;
246// uInt nrsubt = subt.nrow() ;
247// for ( uInt irow = 0 ; irow < nrsubt ; irow++ ) {
248// //if ( !allTrue((subt.col("DIRECTION").getArrayDouble(TableExprId(irow)))==rec.asArrayDouble("DIRECTION")) ) {
249// Vector<Double> x0 = (subt.col("DIRECTION").getArrayDouble(TableExprId(irow))) ;
250// Vector<Double> x1 = rec.asArrayDouble("DIRECTION") ;
251// double dx = x0[0] - x1[0];
252// double dy = x0[1] - x1[1];
253// Double dd = sqrt( dx * dx + dy * dy ) ;
254// //if ( !allNearAbs((subt.col("DIRECTION").getArrayDouble(TableExprId(irow))), rec.asArrayDouble("DIRECTION"), tol ) ) {
255// if ( dd > tol ) {
256// removeRows.push_back( irow ) ;
257// }
258// }
259// if ( removeRows.size() != 0 ) {
260// subt.removeRow( removeRows ) ;
261// }
262
263// if ( nrsubt == removeRows.size() )
264// throw(AipsError("Averaging data is empty.")) ;
265
266 specCol.attach(subt,"SPECTRA");
267 flagCol.attach(subt,"FLAGTRA");
268 tsysCol.attach(subt,"TSYS");
269 intCol.attach(subt,"INTERVAL");
270 mjdCol.attach(subt,"TIME");
271 Vector<Float> spec,tsys;
272 Vector<uChar> flag;
273 Double inter,time;
274 for (uInt k = 0; k < subt.nrow(); ++k ) {
275 flagCol.get(k, flag);
276 Vector<Bool> bflag(flag.shape());
277 convertArray(bflag, flag);
278 /*
279 if ( allEQ(bflag, True) ) {
280 continue;//don't accumulate
281 }
282 */
283 specCol.get(k, spec);
284 tsysCol.get(k, tsys);
285 intCol.get(k, inter);
286 mjdCol.get(k, time);
287 // spectrum has to be added last to enable weighting by the other values
288 acc.add(spec, !bflag, tsys, inter, time);
289 }
290
291 // If there exists a channel at which all the input spectra are masked,
292 // spec has 'nan' values for that channel and it may affect the following
293 // processes. To avoid this, replacing 'nan' values in spec with
294 // weighted-mean of all spectra in the following line.
295 // (done for CAS-2776, 2011/04/07 by Wataru Kawasaki)
296 acc.replaceNaN();
297 }
298 const Vector<Bool>& msk = acc.getMask();
299 if ( allEQ(msk, False) ) {
300 uint n = rowstodelete.nelements();
301 rowstodelete.resize(n+1, True);
302 rowstodelete[n] = i;
303 continue;
304 }
305 //write out
306 if (acc.state()) {
307 Vector<uChar> flg(msk.shape());
308 convertArray(flg, !msk);
309 for (uInt k = 0; k < flg.nelements(); ++k) {
310 uChar userFlag = 1 << 7;
311 if (msk[k]==True) userFlag = 0 << 7;
312 flg(k) = userFlag;
313 }
314
315 flagColOut.put(i, flg);
316 specColOut.put(i, acc.getSpectrum());
317 tsysColOut.put(i, acc.getTsys());
318 intColOut.put(i, acc.getInterval());
319 mjdColOut.put(i, acc.getTime());
320 // we should only have one cycle now -> reset it to be 0
321 // frequency switched data has different CYCLENO for different IFNO
322 // which requires resetting this value
323 cycColOut.put(i, uInt(0));
324 } else {
325 ostringstream oss;
326 oss << "For output row="<<i<<", all input rows of data are flagged. no averaging" << endl;
327 pushLog(String(oss));
328 }
329 acc.reset();
330 }
331
332 if (rowstodelete.nelements() > 0) {
333 os << rowstodelete << LogIO::POST ;
334 tout.removeRow(rowstodelete);
335 if (tout.nrow() == 0) {
336 throw(AipsError("Can't average fully flagged data."));
337 }
338 }
339 return out;
340}
341
342CountedPtr< Scantable >
343STMath::averageChannel( const CountedPtr < Scantable > & in,
344 const std::string & mode,
345 const std::string& avmode )
346{
347 (void) mode; // currently unused
348 // 2012/02/17 TN
349 // Since STGrid is implemented, average doesn't consider direction
350 // when accumulating
351 // check if OTF observation
352// String obstype = in->getHeader().obstype ;
353// Double tol = 0.0 ;
354// if ( obstype.find( "OTF" ) != String::npos ) {
355// tol = TOL_OTF ;
356// }
357// else {
358// tol = TOL_POINT ;
359// }
360
361 // clone as this is non insitu
362 bool insitu = insitu_;
363 setInsitu(false);
364 CountedPtr< Scantable > out = getScantable(in, true);
365 setInsitu(insitu);
366 Table& tout = out->table();
367 ArrayColumn<Float> specColOut(tout,"SPECTRA");
368 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
369 ArrayColumn<Float> tsysColOut(tout,"TSYS");
370 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
371 ScalarColumn<Double> intColOut(tout, "INTERVAL");
372 Table tmp = in->table().sort("BEAMNO");
373 Block<String> cols(3);
374 cols[0] = String("BEAMNO");
375 cols[1] = String("IFNO");
376 cols[2] = String("POLNO");
377 if ( avmode == "SCAN") {
378 cols.resize(4);
379 cols[3] = String("SCANNO");
380 }
381 uInt outrowCount = 0;
382 uChar userflag = 1 << 7;
383 TableIterator iter(tmp, cols);
384 while (!iter.pastEnd()) {
385 Table subt = iter.table();
386 ROArrayColumn<Float> specCol, tsysCol;
387 ROArrayColumn<uChar> flagCol;
388 ROScalarColumn<Double> intCol(subt, "INTERVAL");
389 specCol.attach(subt,"SPECTRA");
390 flagCol.attach(subt,"FLAGTRA");
391 tsysCol.attach(subt,"TSYS");
392
393 tout.addRow();
394 TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
395 if ( avmode != "SCAN") {
396 scanColOut.put(outrowCount, uInt(0));
397 }
398 Vector<Float> tmp;
399 specCol.get(0, tmp);
400 uInt nchan = tmp.nelements();
401 // have to do channel by channel here as MaskedArrMath
402 // doesn't have partialMedians
403 Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
404 Vector<Float> outspec(nchan);
405 Vector<uChar> outflag(nchan,0);
406 Vector<Float> outtsys(1);/// @fixme when tsys is channel based
407 for (uInt i=0; i<nchan; ++i) {
408 Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
409 MaskedArray<Float> ma = maskedArray(specs,flags);
410 outspec[i] = median(ma);
411 if ( allEQ(ma.getMask(), False) )
412 outflag[i] = userflag;// flag data
413 }
414 outtsys[0] = median(tsysCol.getColumn());
415 specColOut.put(outrowCount, outspec);
416 flagColOut.put(outrowCount, outflag);
417 tsysColOut.put(outrowCount, outtsys);
418 Double intsum = sum(intCol.getColumn());
419 intColOut.put(outrowCount, intsum);
420 ++outrowCount;
421 ++iter;
422
423 // 2012/02/17 TN
424 // Since STGrid is implemented, average doesn't consider direction
425 // when accumulating
426// MDirection::ScalarColumn dircol ;
427// dircol.attach( subt, "DIRECTION" ) ;
428// Int length = subt.nrow() ;
429// vector< Vector<Double> > dirs ;
430// vector<int> indexes ;
431// // Handle MX mode averaging
432// if (in->nbeam() > 1 ) {
433// length = 1;
434// }
435// for ( Int i = 0 ; i < length ; i++ ) {
436// Vector<Double> t = dircol(i).getAngle(Unit(String("rad"))).getValue() ;
437// bool adddir = true ;
438// for ( uInt j = 0 ; j < dirs.size() ; j++ ) {
439// //if ( allTrue( t == dirs[j] ) ) {
440// Double dx = t[0] - dirs[j][0] ;
441// Double dy = t[1] - dirs[j][1] ;
442// Double dd = sqrt( dx * dx + dy * dy ) ;
443// //if ( allNearAbs( t, dirs[j], tol ) ) {
444// if ( dd <= tol ) {
445// adddir = false ;
446// break ;
447// }
448// }
449// if ( adddir ) {
450// dirs.push_back( t ) ;
451// indexes.push_back( i ) ;
452// }
453// }
454// uInt rowNum = dirs.size() ;
455// tout.addRow( rowNum );
456// for ( uInt i = 0 ; i < rowNum ; i++ ) {
457// TableCopy::copyRows(tout, subt, outrowCount+i, indexes[i], 1) ;
458// // Handle MX mode averaging
459// if ( avmode != "SCAN") {
460// scanColOut.put(outrowCount+i, uInt(0));
461// }
462// }
463// MDirection::ScalarColumn dircolOut ;
464// dircolOut.attach( tout, "DIRECTION" ) ;
465// for ( uInt irow = 0 ; irow < rowNum ; irow++ ) {
466// Vector<Double> t = \
467// dircolOut(outrowCount+irow).getAngle(Unit(String("rad"))).getValue() ;
468// Vector<Float> tmp;
469// specCol.get(0, tmp);
470// uInt nchan = tmp.nelements();
471// // have to do channel by channel here as MaskedArrMath
472// // doesn't have partialMedians
473// Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
474// // mask spectra for different DIRECTION
475// for ( uInt jrow = 0 ; jrow < subt.nrow() ; jrow++ ) {
476// Vector<Double> direction = \
477// dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
478// //if ( t[0] != direction[0] || t[1] != direction[1] ) {
479// Double dx = t[0] - direction[0];
480// Double dy = t[1] - direction[1];
481// Double dd = sqrt(dx*dx + dy*dy);
482// //if ( !allNearAbs( t, direction, tol ) ) {
483// if ( dd > tol && in->nbeam() < 2 ) {
484// flags[jrow] = userflag ;
485// }
486// }
487// Vector<Float> outspec(nchan);
488// Vector<uChar> outflag(nchan,0);
489// Vector<Float> outtsys(1);/// @fixme when tsys is channel based
490// for (uInt i=0; i<nchan; ++i) {
491// Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
492// MaskedArray<Float> ma = maskedArray(specs,flags);
493// outspec[i] = median(ma);
494// if ( allEQ(ma.getMask(), False) )
495// outflag[i] = userflag;// flag data
496// }
497// outtsys[0] = median(tsysCol.getColumn());
498// specColOut.put(outrowCount+irow, outspec);
499// flagColOut.put(outrowCount+irow, outflag);
500// tsysColOut.put(outrowCount+irow, outtsys);
501// Vector<Double> integ = intCol.getColumn() ;
502// MaskedArray<Double> mi = maskedArray( integ, flags ) ;
503// Double intsum = sum(mi);
504// intColOut.put(outrowCount+irow, intsum);
505// }
506// outrowCount += rowNum ;
507// ++iter;
508 }
509 return out;
510}
511
512CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
513 bool droprows)
514{
515 if (insitu_) {
516 return in;
517 }
518 else {
519 // clone
520 return CountedPtr<Scantable>(new Scantable(*in, Bool(droprows)));
521 }
522}
523
524CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
525 float val,
526 const std::string& mode,
527 bool tsys )
528{
529 CountedPtr< Scantable > out = getScantable(in, false);
530 Table& tab = out->table();
531 ArrayColumn<Float> specCol(tab,"SPECTRA");
532 ArrayColumn<Float> tsysCol(tab,"TSYS");
533 if (mode=="DIV") val = 1.0/val ;
534 else if (mode=="SUB") val *= -1.0 ;
535 for (uInt i=0; i<tab.nrow(); ++i) {
536 Vector<Float> spec;
537 Vector<Float> ts;
538 specCol.get(i, spec);
539 tsysCol.get(i, ts);
540 if (mode == "MUL" || mode == "DIV") {
541 //if (mode == "DIV") val = 1.0/val;
542 spec *= val;
543 specCol.put(i, spec);
544 if ( tsys ) {
545 ts *= val;
546 tsysCol.put(i, ts);
547 }
548 } else if ( mode == "ADD" || mode == "SUB") {
549 //if (mode == "SUB") val *= -1.0;
550 spec += val;
551 specCol.put(i, spec);
552 if ( tsys ) {
553 ts += val;
554 tsysCol.put(i, ts);
555 }
556 }
557 }
558 return out;
559}
560
561CountedPtr< Scantable > STMath::arrayOperate( const CountedPtr< Scantable >& in,
562 const std::vector<float> val,
563 const std::string& mode,
564 const std::string& opmode,
565 bool tsys )
566{
567 CountedPtr< Scantable > out ;
568 if ( opmode == "channel" ) {
569 out = arrayOperateChannel( in, val, mode, tsys ) ;
570 }
571 else if ( opmode == "row" ) {
572 out = arrayOperateRow( in, val, mode, tsys ) ;
573 }
574 else {
575 throw( AipsError( "Unknown array operation mode." ) ) ;
576 }
577 return out ;
578}
579
580CountedPtr< Scantable > STMath::arrayOperateChannel( const CountedPtr< Scantable >& in,
581 const std::vector<float> val,
582 const std::string& mode,
583 bool tsys )
584{
585 if ( val.size() == 1 ){
586 return unaryOperate( in, val[0], mode, tsys ) ;
587 }
588
589 // conformity of SPECTRA and TSYS
590 if ( tsys ) {
591 TableIterator titer(in->table(), "IFNO");
592 while ( !titer.pastEnd() ) {
593 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
594 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
595 Array<Float> spec = specCol.getColumn() ;
596 Array<Float> ts = tsysCol.getColumn() ;
597 if ( !spec.conform( ts ) ) {
598 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
599 }
600 titer.next() ;
601 }
602 }
603
604 // check if all spectra in the scantable have the same number of channel
605 vector<uInt> nchans;
606 vector<uInt> ifnos = in->getIFNos() ;
607 for ( uInt i = 0 ; i < ifnos.size() ; i++ ) {
608 nchans.push_back( in->nchan( ifnos[i] ) ) ;
609 }
610 Vector<uInt> mchans( nchans ) ;
611 if ( anyNE( mchans, mchans[0] ) ) {
612 throw( AipsError("All spectra in the input scantable must have the same number of channel for vector operation." ) ) ;
613 }
614
615 // check if vector size is equal to nchan
616 Vector<Float> fact( val ) ;
617 if ( fact.nelements() != mchans[0] ) {
618 throw( AipsError("Vector size must be 1 or be same as number of channel.") ) ;
619 }
620
621 // check divided by zero
622 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
623 throw( AipsError("Divided by zero is not recommended." ) ) ;
624 }
625
626 CountedPtr< Scantable > out = getScantable(in, false);
627 Table& tab = out->table();
628 ArrayColumn<Float> specCol(tab,"SPECTRA");
629 ArrayColumn<Float> tsysCol(tab,"TSYS");
630 if (mode == "DIV") fact = (float)1.0 / fact;
631 else if (mode == "SUB") fact *= (float)-1.0 ;
632 for (uInt i=0; i<tab.nrow(); ++i) {
633 Vector<Float> spec;
634 Vector<Float> ts;
635 specCol.get(i, spec);
636 tsysCol.get(i, ts);
637 if (mode == "MUL" || mode == "DIV") {
638 //if (mode == "DIV") fact = (float)1.0 / fact;
639 spec *= fact;
640 specCol.put(i, spec);
641 if ( tsys ) {
642 ts *= fact;
643 tsysCol.put(i, ts);
644 }
645 } else if ( mode == "ADD" || mode == "SUB") {
646 //if (mode == "SUB") fact *= (float)-1.0 ;
647 spec += fact;
648 specCol.put(i, spec);
649 if ( tsys ) {
650 ts += fact;
651 tsysCol.put(i, ts);
652 }
653 }
654 }
655 return out;
656}
657
658CountedPtr< Scantable > STMath::arrayOperateRow( const CountedPtr< Scantable >& in,
659 const std::vector<float> val,
660 const std::string& mode,
661 bool tsys )
662{
663 if ( val.size() == 1 ) {
664 return unaryOperate( in, val[0], mode, tsys ) ;
665 }
666
667 // conformity of SPECTRA and TSYS
668 if ( tsys ) {
669 TableIterator titer(in->table(), "IFNO");
670 while ( !titer.pastEnd() ) {
671 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
672 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
673 Array<Float> spec = specCol.getColumn() ;
674 Array<Float> ts = tsysCol.getColumn() ;
675 if ( !spec.conform( ts ) ) {
676 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
677 }
678 titer.next() ;
679 }
680 }
681
682 // check if vector size is equal to nrow
683 Vector<Float> fact( val ) ;
684 if (fact.nelements() != uInt(in->nrow())) {
685 throw( AipsError("Vector size must be 1 or be same as number of row.") ) ;
686 }
687
688 // check divided by zero
689 if ( ( mode == "DIV" ) && anyEQ( fact, (float)0.0 ) ) {
690 throw( AipsError("Divided by zero is not recommended." ) ) ;
691 }
692
693 CountedPtr< Scantable > out = getScantable(in, false);
694 Table& tab = out->table();
695 ArrayColumn<Float> specCol(tab,"SPECTRA");
696 ArrayColumn<Float> tsysCol(tab,"TSYS");
697 if (mode == "DIV") fact = (float)1.0 / fact;
698 if (mode == "SUB") fact *= (float)-1.0 ;
699 for (uInt i=0; i<tab.nrow(); ++i) {
700 Vector<Float> spec;
701 Vector<Float> ts;
702 specCol.get(i, spec);
703 tsysCol.get(i, ts);
704 if (mode == "MUL" || mode == "DIV") {
705 spec *= fact[i];
706 specCol.put(i, spec);
707 if ( tsys ) {
708 ts *= fact[i];
709 tsysCol.put(i, ts);
710 }
711 } else if ( mode == "ADD" || mode == "SUB") {
712 spec += fact[i];
713 specCol.put(i, spec);
714 if ( tsys ) {
715 ts += fact[i];
716 tsysCol.put(i, ts);
717 }
718 }
719 }
720 return out;
721}
722
723CountedPtr< Scantable > STMath::array2dOperate( const CountedPtr< Scantable >& in,
724 const std::vector< std::vector<float> > val,
725 const std::string& mode,
726 bool tsys )
727{
728 // conformity of SPECTRA and TSYS
729 if ( tsys ) {
730 TableIterator titer(in->table(), "IFNO");
731 while ( !titer.pastEnd() ) {
732 ArrayColumn<Float> specCol( in->table(), "SPECTRA" ) ;
733 ArrayColumn<Float> tsysCol( in->table(), "TSYS" ) ;
734 Array<Float> spec = specCol.getColumn() ;
735 Array<Float> ts = tsysCol.getColumn() ;
736 if ( !spec.conform( ts ) ) {
737 throw( AipsError( "SPECTRA and TSYS must conform in shape if you want to apply operation on Tsys." ) ) ;
738 }
739 titer.next() ;
740 }
741 }
742
743 // some checks
744 vector<uInt> nchans;
745 for (Int i = 0 ; i < in->nrow() ; i++) {
746 nchans.push_back((in->getSpectrum(i)).size());
747 }
748 //Vector<uInt> mchans( nchans ) ;
749 vector< Vector<Float> > facts ;
750 for ( uInt i = 0 ; i < nchans.size() ; i++ ) {
751 Vector<Float> tmp( val[i] ) ;
752 // check divided by zero
753 if ( ( mode == "DIV" ) && anyEQ( tmp, (float)0.0 ) ) {
754 throw( AipsError("Divided by zero is not recommended." ) ) ;
755 }
756 // conformity check
757 if ( tmp.nelements() != nchans[i] ) {
758 stringstream ss ;
759 ss << "Row " << i << ": Vector size must be same as number of channel." ;
760 throw( AipsError( ss.str() ) ) ;
761 }
762 facts.push_back( tmp ) ;
763 }
764
765
766 CountedPtr< Scantable > out = getScantable(in, false);
767 Table& tab = out->table();
768 ArrayColumn<Float> specCol(tab,"SPECTRA");
769 ArrayColumn<Float> tsysCol(tab,"TSYS");
770 for (uInt i=0; i<tab.nrow(); ++i) {
771 Vector<Float> fact = facts[i] ;
772 Vector<Float> spec;
773 Vector<Float> ts;
774 specCol.get(i, spec);
775 tsysCol.get(i, ts);
776 if (mode == "MUL" || mode == "DIV") {
777 if (mode == "DIV") fact = (float)1.0 / fact;
778 spec *= fact;
779 specCol.put(i, spec);
780 if ( tsys ) {
781 ts *= fact;
782 tsysCol.put(i, ts);
783 }
784 } else if ( mode == "ADD" || mode == "SUB") {
785 if (mode == "SUB") fact *= (float)-1.0 ;
786 spec += fact;
787 specCol.put(i, spec);
788 if ( tsys ) {
789 ts += fact;
790 tsysCol.put(i, ts);
791 }
792 }
793 }
794 return out;
795}
796
797CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
798 const CountedPtr<Scantable>& right,
799 const std::string& mode)
800{
801 bool insitu = insitu_;
802 if ( ! left->conformant(*right) ) {
803 throw(AipsError("'left' and 'right' scantables are not conformant."));
804 }
805 setInsitu(false);
806 CountedPtr< Scantable > out = getScantable(left, false);
807 setInsitu(insitu);
808 Table& tout = out->table();
809 Block<String> coln(5);
810 coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO";
811 coln[3] = "IFNO"; coln[4] = "POLNO";
812 Table tmpl = tout.sort(coln);
813 Table tmpr = right->table().sort(coln);
814 ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
815 ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
816 ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
817 ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");
818
819 for (uInt i=0; i<tout.nrow(); ++i) {
820 Vector<Float> lspecvec, rspecvec;
821 Vector<uChar> lflagvec, rflagvec;
822 lspecvec = lspecCol(i); rspecvec = rspecCol(i);
823 lflagvec = lflagCol(i); rflagvec = rflagCol(i);
824 MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
825 MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
826 if (mode == "ADD") {
827 mleft += mright;
828 } else if ( mode == "SUB") {
829 mleft -= mright;
830 } else if ( mode == "MUL") {
831 mleft *= mright;
832 } else if ( mode == "DIV") {
833 mleft /= mright;
834 } else {
835 throw(AipsError("Illegal binary operator"));
836 }
837 lspecCol.put(i, mleft.getArray());
838 }
839 return out;
840}
841
842
843
844MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
845 const Vector<uChar>& f)
846{
847 Vector<Bool> mask;
848 mask.resize(f.shape());
849 convertArray(mask, f);
850 return MaskedArray<Float>(s,!mask);
851}
852
853MaskedArray<Double> STMath::maskedArray( const Vector<Double>& s,
854 const Vector<uChar>& f)
855{
856 Vector<Bool> mask;
857 mask.resize(f.shape());
858 convertArray(mask, f);
859 return MaskedArray<Double>(s,!mask);
860}
861
862Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
863{
864 const Vector<Bool>& m = ma.getMask();
865 Vector<uChar> flags(m.shape());
866 convertArray(flags, !m);
867 return flags;
868}
869
870CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
871 const std::string & mode,
872 bool preserve )
873{
874 /// @todo make other modes available
875 /// modes should be "nearest", "pair"
876 // make this operation non insitu
877 (void) mode; //currently unused
878 const Table& tin = in->table();
879 Table ons = tin(tin.col("SRCTYPE") == Int(SrcType::PSON));
880 Table offs = tin(tin.col("SRCTYPE") == Int(SrcType::PSOFF));
881 if ( offs.nrow() == 0 )
882 throw(AipsError("No 'off' scans present."));
883 // put all "on" scans into output table
884
885 bool insitu = insitu_;
886 setInsitu(false);
887 CountedPtr< Scantable > out = getScantable(in, true);
888 setInsitu(insitu);
889 Table& tout = out->table();
890
891 TableCopy::copyRows(tout, ons);
892 TableRow row(tout);
893 ROScalarColumn<Double> offtimeCol(offs, "TIME");
894 ArrayColumn<Float> outspecCol(tout, "SPECTRA");
895 ROArrayColumn<Float> outtsysCol(tout, "TSYS");
896 ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
897 for (uInt i=0; i < tout.nrow(); ++i) {
898 const TableRecord& rec = row.get(i);
899 Double ontime = rec.asDouble("TIME");
900 Table presel = offs(offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
901 && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
902 && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
903 ROScalarColumn<Double> offtimeCol(presel, "TIME");
904
905 Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
906 // Timestamp may vary within a cycle ???!!!
907 // increase this by 0.01 sec in case of rounding errors...
908 // There might be a better way to do this.
909 // fix to this fix. TIME is MJD, so 1.0d not 1.0s
910 mindeltat += 0.01/24./60./60.;
911 Table sel = presel( abs(presel.col("TIME")-ontime) <= mindeltat);
912
913 if ( sel.nrow() < 1 ) {
914 throw(AipsError("No closest in time found... This could be a rounding "
915 "issue. Try quotient instead."));
916 }
917 TableRow offrow(sel);
918 const TableRecord& offrec = offrow.get(0);//should only be one row
919 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
920 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
921 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
922 /// @fixme this assumes tsys is a scalar not vector
923 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
924 Vector<Float> specon, tsyson;
925 outtsysCol.get(i, tsyson);
926 outspecCol.get(i, specon);
927 Vector<uChar> flagon;
928 outflagCol.get(i, flagon);
929 MaskedArray<Float> mon = maskedArray(specon, flagon);
930 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
931 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
932 if (preserve) {
933 quot -= tsysoffscalar;
934 } else {
935 quot -= tsyson[0];
936 }
937 outspecCol.put(i, quot.getArray());
938 outflagCol.put(i, flagsFromMA(quot));
939 }
940 // renumber scanno
941 TableIterator it(tout, "SCANNO");
942 uInt i = 0;
943 while ( !it.pastEnd() ) {
944 Table t = it.table();
945 TableVector<uInt> vec(t, "SCANNO");
946 vec = i;
947 ++i;
948 ++it;
949 }
950 return out;
951}
952
953
954CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
955 const CountedPtr< Scantable > & off,
956 bool preserve )
957{
958 bool insitu = insitu_;
959 if ( ! on->conformant(*off) ) {
960 throw(AipsError("'on' and 'off' scantables are not conformant."));
961 }
962 setInsitu(false);
963 CountedPtr< Scantable > out = getScantable(on, false);
964 setInsitu(insitu);
965 Table& tout = out->table();
966 const Table& toff = off->table();
967 TableIterator sit(tout, "SCANNO");
968 TableIterator s2it(toff, "SCANNO");
969 while ( !sit.pastEnd() ) {
970 Table ton = sit.table();
971 TableRow row(ton);
972 Table t = s2it.table();
973 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
974 ROArrayColumn<Float> outtsysCol(ton, "TSYS");
975 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
976 for (uInt i=0; i < ton.nrow(); ++i) {
977 const TableRecord& rec = row.get(i);
978 Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
979 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
980 && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
981 if ( offsel.nrow() == 0 )
982 throw AipsError("STMath::quotient: no matching off");
983 TableRow offrow(offsel);
984 const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
985 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
986 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
987 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
988 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
989 Vector<Float> specon, tsyson;
990 outtsysCol.get(i, tsyson);
991 outspecCol.get(i, specon);
992 Vector<uChar> flagon;
993 outflagCol.get(i, flagon);
994 MaskedArray<Float> mon = maskedArray(specon, flagon);
995 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
996 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
997 if (preserve) {
998 quot -= tsysoffscalar;
999 } else {
1000 quot -= tsyson[0];
1001 }
1002 outspecCol.put(i, quot.getArray());
1003 outflagCol.put(i, flagsFromMA(quot));
1004 }
1005 ++sit;
1006 ++s2it;
1007 // take the first off for each on scan which doesn't have a
1008 // matching off scan
1009 // non <= noff: matching pairs, non > noff matching pairs then first off
1010 if ( s2it.pastEnd() ) s2it.reset();
1011 }
1012 return out;
1013}
1014
1015// dototalpower (migration of GBTIDL procedure dototalpower.pro)
1016// calibrate the CAL on-off pair. It calculate Tsys and average CAL on-off subintegrations
1017// do it for each cycles in a specific scan.
1018CountedPtr< Scantable > STMath::dototalpower( const CountedPtr< Scantable >& calon,
1019 const CountedPtr< Scantable >& caloff, Float tcal )
1020{
1021 if ( ! calon->conformant(*caloff) ) {
1022 throw(AipsError("'CAL on' and 'CAL off' scantables are not conformant."));
1023 }
1024 setInsitu(false);
1025 CountedPtr< Scantable > out = getScantable(caloff, false);
1026 Table& tout = out->table();
1027 const Table& tcon = calon->table();
1028 Vector<Float> tcalout;
1029
1030 std::map<uInt,uInt> tcalIdToRecNoMap;
1031 const Table& calOffTcalTable = caloff->tcal().table();
1032 {
1033 ROScalarColumn<uInt> calOffTcalTable_IDcol(calOffTcalTable, "ID");
1034 const Vector<uInt> tcalIds(calOffTcalTable_IDcol.getColumn());
1035 size_t tcalIdsEnd = tcalIds.nelements();
1036 for (uInt i = 0; i < tcalIdsEnd; i++) {
1037 tcalIdToRecNoMap[tcalIds[i]] = i;
1038 }
1039 }
1040 ROArrayColumn<Float> calOffTcalTable_TCALcol(calOffTcalTable, "TCAL");
1041
1042 if ( tout.nrow() != tcon.nrow() ) {
1043 throw(AipsError("Mismatch in number of rows to form cal on - off pair."));
1044 }
1045 // iteration by scanno or cycle no.
1046 TableIterator sit(tout, "SCANNO");
1047 TableIterator s2it(tcon, "SCANNO");
1048 while ( !sit.pastEnd() ) {
1049 Table toff = sit.table();
1050 TableRow row(toff);
1051 Table t = s2it.table();
1052 ScalarColumn<Double> outintCol(toff, "INTERVAL");
1053 ArrayColumn<Float> outspecCol(toff, "SPECTRA");
1054 ArrayColumn<Float> outtsysCol(toff, "TSYS");
1055 ArrayColumn<uChar> outflagCol(toff, "FLAGTRA");
1056 ROScalarColumn<uInt> outtcalIdCol(toff, "TCAL_ID");
1057 ROScalarColumn<uInt> outpolCol(toff, "POLNO");
1058 ROScalarColumn<Double> onintCol(t, "INTERVAL");
1059 ROArrayColumn<Float> onspecCol(t, "SPECTRA");
1060 ROArrayColumn<Float> ontsysCol(t, "TSYS");
1061 ROArrayColumn<uChar> onflagCol(t, "FLAGTRA");
1062 //ROScalarColumn<uInt> ontcalIdCol(t, "TCAL_ID");
1063
1064 for (uInt i=0; i < toff.nrow(); ++i) {
1065 //skip these checks -> assumes the data order are the same between the cal on off pairs
1066 //
1067 Vector<Float> specCalon, specCaloff;
1068 // to store scalar (mean) tsys
1069 Vector<Float> tsysout(1);
1070 uInt tcalId, polno;
1071 Double offint, onint;
1072 outpolCol.get(i, polno);
1073 outspecCol.get(i, specCaloff);
1074 onspecCol.get(i, specCalon);
1075 Vector<uChar> flagCaloff, flagCalon;
1076 outflagCol.get(i, flagCaloff);
1077 onflagCol.get(i, flagCalon);
1078 outtcalIdCol.get(i, tcalId);
1079 outintCol.get(i, offint);
1080 onintCol.get(i, onint);
1081 // caluculate mean Tsys
1082 uInt nchan = specCaloff.nelements();
1083 // percentage of edge cut off
1084 uInt pc = 10;
1085 uInt bchan = nchan/pc;
1086 uInt echan = nchan-bchan;
1087
1088 Slicer chansl(IPosition(1,bchan-1), IPosition(1,echan-1), IPosition(1,1),Slicer::endIsLast);
1089 Vector<Float> testsubsp = specCaloff(chansl);
1090 MaskedArray<Float> spoff = maskedArray( specCaloff(chansl),flagCaloff(chansl) );
1091 MaskedArray<Float> spon = maskedArray( specCalon(chansl),flagCalon(chansl) );
1092 MaskedArray<Float> spdiff = spon-spoff;
1093 uInt noff = spoff.nelementsValid();
1094 //uInt non = spon.nelementsValid();
1095 uInt ndiff = spdiff.nelementsValid();
1096 Float meantsys;
1097
1098/**
1099 Double subspec, subdiff;
1100 uInt usednchan;
1101 subspec = 0;
1102 subdiff = 0;
1103 usednchan = 0;
1104 for(uInt k=(bchan-1); k<echan; k++) {
1105 subspec += specCaloff[k];
1106 subdiff += static_cast<Double>(specCalon[k]-specCaloff[k]);
1107 ++usednchan;
1108 }
1109**/
1110 // get tcal if input tcal <= 0
1111 Float tcalUsed;
1112 tcalUsed = tcal;
1113 if ( tcal <= 0.0 ) {
1114 uInt tcalRecNo = tcalIdToRecNoMap[tcalId];
1115 calOffTcalTable_TCALcol.get(tcalRecNo, tcalout);
1116// if (polno<=3) {
1117// tcalUsed = tcalout[polno];
1118// }
1119// else {
1120// tcalUsed = tcalout[0];
1121// }
1122 if ( tcalout.size() == 1 )
1123 tcalUsed = tcalout[0] ;
1124 else if ( tcalout.size() == nchan )
1125 tcalUsed = mean(tcalout) ;
1126 else {
1127 uInt ipol = polno ;
1128 if ( ipol > 3 ) ipol = 0 ;
1129 tcalUsed = tcalout[ipol] ;
1130 }
1131 }
1132
1133 Float meanoff;
1134 Float meandiff;
1135 if (noff && ndiff) {
1136 //Debug
1137 //if(noff!=ndiff) cerr<<"noff and ndiff is not equal"<<endl;
1138 //LogIO os( LogOrigin( "STMath", "dototalpower()", WHERE ) ) ;
1139 //if(noff!=ndiff) os<<"noff and ndiff is not equal"<<LogIO::POST;
1140 meanoff = sum(spoff)/noff;
1141 meandiff = sum(spdiff)/ndiff;
1142 meantsys= (meanoff/meandiff )*tcalUsed + tcalUsed/2;
1143 }
1144 else {
1145 meantsys=1;
1146 }
1147
1148 tsysout[0] = Float(meantsys);
1149 MaskedArray<Float> mcaloff = maskedArray(specCaloff, flagCaloff);
1150 MaskedArray<Float> mcalon = maskedArray(specCalon, flagCalon);
1151 MaskedArray<Float> sig = Float(0.5) * (mcaloff + mcalon);
1152 //uInt ncaloff = mcaloff.nelementsValid();
1153 //uInt ncalon = mcalon.nelementsValid();
1154
1155 outintCol.put(i, offint+onint);
1156 outspecCol.put(i, sig.getArray());
1157 outflagCol.put(i, flagsFromMA(sig));
1158 outtsysCol.put(i, tsysout);
1159 }
1160 ++sit;
1161 ++s2it;
1162 }
1163 return out;
1164}
1165
1166//dosigref - migrated from GBT IDL's dosigref.pro, do calibration of position switch
1167// observatiions.
1168// input: sig and ref scantables, and an optional boxcar smoothing width(default width=0,
1169// no smoothing).
1170// output: resultant scantable [= (sig-ref/ref)*tsys]
1171CountedPtr< Scantable > STMath::dosigref( const CountedPtr < Scantable >& sig,
1172 const CountedPtr < Scantable >& ref,
1173 int smoothref,
1174 casa::Float tsysv,
1175 casa::Float tau )
1176{
1177if ( ! ref->conformant(*sig) ) {
1178 throw(AipsError("'sig' and 'ref' scantables are not conformant."));
1179 }
1180 setInsitu(false);
1181 CountedPtr< Scantable > out = getScantable(sig, false);
1182 CountedPtr< Scantable > smref;
1183 if ( smoothref > 1 ) {
1184 float fsmoothref = static_cast<float>(smoothref);
1185 std::string inkernel = "boxcar";
1186 smref = smooth(ref, inkernel, fsmoothref );
1187 ostringstream oss;
1188 oss<<"Applied smoothing of "<<fsmoothref<<" on the reference."<<endl;
1189 pushLog(String(oss));
1190 }
1191 else {
1192 smref = ref;
1193 }
1194 Table& tout = out->table();
1195 const Table& tref = smref->table();
1196 if ( tout.nrow() != tref.nrow() ) {
1197 throw(AipsError("Mismatch in number of rows to form on-source and reference pair."));
1198 }
1199 // iteration by scanno? or cycle no.
1200 TableIterator sit(tout, "SCANNO");
1201 TableIterator s2it(tref, "SCANNO");
1202 while ( !sit.pastEnd() ) {
1203 Table ton = sit.table();
1204 Table t = s2it.table();
1205 ScalarColumn<Double> outintCol(ton, "INTERVAL");
1206 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
1207 ArrayColumn<Float> outtsysCol(ton, "TSYS");
1208 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
1209 ArrayColumn<Float> refspecCol(t, "SPECTRA");
1210 ROScalarColumn<Double> refintCol(t, "INTERVAL");
1211 ROArrayColumn<Float> reftsysCol(t, "TSYS");
1212 ArrayColumn<uChar> refflagCol(t, "FLAGTRA");
1213 ROScalarColumn<Float> refelevCol(t, "ELEVATION");
1214 for (uInt i=0; i < ton.nrow(); ++i) {
1215
1216 Double onint, refint;
1217 Vector<Float> specon, specref;
1218 // to store scalar (mean) tsys
1219 Vector<Float> tsysref;
1220 outintCol.get(i, onint);
1221 refintCol.get(i, refint);
1222 outspecCol.get(i, specon);
1223 refspecCol.get(i, specref);
1224 Vector<uChar> flagref, flagon;
1225 outflagCol.get(i, flagon);
1226 refflagCol.get(i, flagref);
1227 reftsysCol.get(i, tsysref);
1228
1229 Float tsysrefscalar;
1230 if ( tsysv > 0.0 ) {
1231 ostringstream oss;
1232 Float elev;
1233 refelevCol.get(i, elev);
1234 oss << "user specified Tsys = " << tsysv;
1235 // do recalc elevation if EL = 0
1236 if ( elev == 0 ) {
1237 throw(AipsError("EL=0, elevation data is missing."));
1238 } else {
1239 if ( tau <= 0.0 ) {
1240 throw(AipsError("Valid tau is not supplied."));
1241 } else {
1242 tsysrefscalar = tsysv * exp(tau/elev);
1243 }
1244 }
1245 oss << ", corrected (for El) tsys= "<<tsysrefscalar;
1246 pushLog(String(oss));
1247 }
1248 else {
1249 tsysrefscalar = tsysref[0];
1250 }
1251 //get quotient spectrum
1252 MaskedArray<Float> mref = maskedArray(specref, flagref);
1253 MaskedArray<Float> mon = maskedArray(specon, flagon);
1254 MaskedArray<Float> specres = tsysrefscalar*((mon - mref)/mref);
1255 Double resint = onint*refint*smoothref/(onint+refint*smoothref);
1256
1257 //Debug
1258 //cerr<<"Tsys used="<<tsysrefscalar<<endl;
1259 //LogIO os( LogOrigin( "STMath", "dosigref", WHERE ) ) ;
1260 //os<<"Tsys used="<<tsysrefscalar<<LogIO::POST;
1261 // fill the result, replay signal tsys by reference tsys
1262 outintCol.put(i, resint);
1263 outspecCol.put(i, specres.getArray());
1264 outflagCol.put(i, flagsFromMA(specres));
1265 outtsysCol.put(i, tsysref);
1266 }
1267 ++sit;
1268 ++s2it;
1269 }
1270 return out;
1271}
1272
1273CountedPtr< Scantable > STMath::donod(const casa::CountedPtr<Scantable>& s,
1274 const std::vector<int>& scans,
1275 int smoothref,
1276 casa::Float tsysv,
1277 casa::Float tau,
1278 casa::Float tcal )
1279
1280{
1281 setInsitu(false);
1282 STSelector sel;
1283 std::vector<int> scan1, scan2, beams, types;
1284 std::vector< vector<int> > scanpair;
1285 //std::vector<string> calstate;
1286 std::vector<int> calstate;
1287 String msg;
1288
1289 CountedPtr< Scantable > s1b1on, s1b1off, s1b2on, s1b2off;
1290 CountedPtr< Scantable > s2b1on, s2b1off, s2b2on, s2b2off;
1291
1292 std::vector< CountedPtr< Scantable > > sctables;
1293 sctables.push_back(s1b1on);
1294 sctables.push_back(s1b1off);
1295 sctables.push_back(s1b2on);
1296 sctables.push_back(s1b2off);
1297 sctables.push_back(s2b1on);
1298 sctables.push_back(s2b1off);
1299 sctables.push_back(s2b2on);
1300 sctables.push_back(s2b2off);
1301
1302 //check scanlist
1303 int n=s->checkScanInfo(scans);
1304 if (n==1) {
1305 throw(AipsError("Incorrect scan pairs. "));
1306 }
1307
1308 // Assume scans contain only a pair of consecutive scan numbers.
1309 // It is assumed that first beam, b1, is on target.
1310 // There is no check if the first beam is on or not.
1311 if ( scans.size()==1 ) {
1312 scan1.push_back(scans[0]);
1313 scan2.push_back(scans[0]+1);
1314 } else if ( scans.size()==2 ) {
1315 scan1.push_back(scans[0]);
1316 scan2.push_back(scans[1]);
1317 } else {
1318 if ( scans.size()%2 == 0 ) {
1319 for (uInt i=0; i<scans.size(); i++) {
1320 if (i%2 == 0) {
1321 scan1.push_back(scans[i]);
1322 }
1323 else {
1324 scan2.push_back(scans[i]);
1325 }
1326 }
1327 } else {
1328 throw(AipsError("Odd numbers of scans, cannot form pairs."));
1329 }
1330 }
1331 scanpair.push_back(scan1);
1332 scanpair.push_back(scan2);
1333 //calstate.push_back("*calon");
1334 //calstate.push_back("*[^calon]");
1335 calstate.push_back(SrcType::NODCAL);
1336 calstate.push_back(SrcType::NOD);
1337 CountedPtr< Scantable > ws = getScantable(s, false);
1338 uInt l=0;
1339 while ( l < sctables.size() ) {
1340 for (uInt i=0; i < 2; i++) {
1341 for (uInt j=0; j < 2; j++) {
1342 for (uInt k=0; k < 2; k++) {
1343 sel.reset();
1344 sel.setScans(scanpair[i]);
1345 //sel.setName(calstate[k]);
1346 types.clear();
1347 types.push_back(calstate[k]);
1348 sel.setTypes(types);
1349 beams.clear();
1350 beams.push_back(j);
1351 sel.setBeams(beams);
1352 ws->setSelection(sel);
1353 sctables[l]= getScantable(ws, false);
1354 l++;
1355 }
1356 }
1357 }
1358 }
1359
1360 // replace here by splitData or getData functionality
1361 CountedPtr< Scantable > sig1;
1362 CountedPtr< Scantable > ref1;
1363 CountedPtr< Scantable > sig2;
1364 CountedPtr< Scantable > ref2;
1365 CountedPtr< Scantable > calb1;
1366 CountedPtr< Scantable > calb2;
1367
1368 msg=String("Processing dototalpower for subset of the data");
1369 ostringstream oss1;
1370 oss1 << msg << endl;
1371 pushLog(String(oss1));
1372 // Debug for IRC CS data
1373 //float tcal1=7.0;
1374 //float tcal2=4.0;
1375 sig1 = dototalpower(sctables[0], sctables[1], tcal=tcal);
1376 ref1 = dototalpower(sctables[2], sctables[3], tcal=tcal);
1377 ref2 = dototalpower(sctables[4], sctables[5], tcal=tcal);
1378 sig2 = dototalpower(sctables[6], sctables[7], tcal=tcal);
1379
1380 // correction of user-specified tsys for elevation here
1381
1382 // dosigref calibration
1383 msg=String("Processing dosigref for subset of the data");
1384 ostringstream oss2;
1385 oss2 << msg << endl;
1386 pushLog(String(oss2));
1387 calb1=dosigref(sig1,ref2,smoothref,tsysv,tau);
1388 calb2=dosigref(sig2,ref1,smoothref,tsysv,tau);
1389
1390 // iteration by scanno or cycle no.
1391 Table& tcalb1 = calb1->table();
1392 Table& tcalb2 = calb2->table();
1393 TableIterator sit(tcalb1, "SCANNO");
1394 TableIterator s2it(tcalb2, "SCANNO");
1395 while ( !sit.pastEnd() ) {
1396 Table t1 = sit.table();
1397 Table t2= s2it.table();
1398 ArrayColumn<Float> outspecCol(t1, "SPECTRA");
1399 ArrayColumn<Float> outtsysCol(t1, "TSYS");
1400 ArrayColumn<uChar> outflagCol(t1, "FLAGTRA");
1401 ScalarColumn<Double> outintCol(t1, "INTERVAL");
1402 ArrayColumn<Float> t2specCol(t2, "SPECTRA");
1403 ROArrayColumn<Float> t2tsysCol(t2, "TSYS");
1404 ArrayColumn<uChar> t2flagCol(t2, "FLAGTRA");
1405 ROScalarColumn<Double> t2intCol(t2, "INTERVAL");
1406 for (uInt i=0; i < t1.nrow(); ++i) {
1407 Vector<Float> spec1, spec2;
1408 // to store scalar (mean) tsys
1409 Vector<Float> tsys1, tsys2;
1410 Vector<uChar> flag1, flag2;
1411 Double tint1, tint2;
1412 outspecCol.get(i, spec1);
1413 t2specCol.get(i, spec2);
1414 outflagCol.get(i, flag1);
1415 t2flagCol.get(i, flag2);
1416 outtsysCol.get(i, tsys1);
1417 t2tsysCol.get(i, tsys2);
1418 outintCol.get(i, tint1);
1419 t2intCol.get(i, tint2);
1420 // average
1421 // assume scalar tsys for weights
1422 Float wt1, wt2, tsyssq1, tsyssq2;
1423 tsyssq1 = tsys1[0]*tsys1[0];
1424 tsyssq2 = tsys2[0]*tsys2[0];
1425 wt1 = Float(tint1)/tsyssq1;
1426 wt2 = Float(tint2)/tsyssq2;
1427 Float invsumwt=1/(wt1+wt2);
1428 MaskedArray<Float> mspec1 = maskedArray(spec1, flag1);
1429 MaskedArray<Float> mspec2 = maskedArray(spec2, flag2);
1430 MaskedArray<Float> avspec = invsumwt * (wt1*mspec1 + wt2*mspec2);
1431 //Array<Float> avtsys = Float(0.5) * (tsys1 + tsys2);
1432 // cerr<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<endl;
1433 // LogIO os( LogOrigin( "STMath", "donod", WHERE ) ) ;
1434 // os<< "Tsys1="<<tsys1<<" Tsys2="<<tsys2<<LogIO::POST;
1435 tsys1[0] = sqrt(tsyssq1 + tsyssq2);
1436 Array<Float> avtsys = tsys1;
1437
1438 outspecCol.put(i, avspec.getArray());
1439 outflagCol.put(i, flagsFromMA(avspec));
1440 outtsysCol.put(i, avtsys);
1441 }
1442 ++sit;
1443 ++s2it;
1444 }
1445 return calb1;
1446}
1447
1448//GBTIDL version of frequency switched data calibration
1449CountedPtr< Scantable > STMath::dofs( const CountedPtr< Scantable >& s,
1450 const std::vector<int>& scans,
1451 int smoothref,
1452 casa::Float tsysv,
1453 casa::Float tau,
1454 casa::Float tcal )
1455{
1456
1457
1458 (void) scans; //currently unused
1459 STSelector sel;
1460 CountedPtr< Scantable > ws = getScantable(s, false);
1461 CountedPtr< Scantable > sig, sigwcal, ref, refwcal;
1462 CountedPtr< Scantable > calsig, calref, out, out1, out2;
1463 Bool nofold=False;
1464 vector<int> types ;
1465
1466 //split the data
1467 //sel.setName("*_fs");
1468 types.push_back( SrcType::FSON ) ;
1469 sel.setTypes( types ) ;
1470 ws->setSelection(sel);
1471 sig = getScantable(ws,false);
1472 sel.reset();
1473 types.clear() ;
1474 //sel.setName("*_fs_calon");
1475 types.push_back( SrcType::FONCAL ) ;
1476 sel.setTypes( types ) ;
1477 ws->setSelection(sel);
1478 sigwcal = getScantable(ws,false);
1479 sel.reset();
1480 types.clear() ;
1481 //sel.setName("*_fsr");
1482 types.push_back( SrcType::FSOFF ) ;
1483 sel.setTypes( types ) ;
1484 ws->setSelection(sel);
1485 ref = getScantable(ws,false);
1486 sel.reset();
1487 types.clear() ;
1488 //sel.setName("*_fsr_calon");
1489 types.push_back( SrcType::FOFFCAL ) ;
1490 sel.setTypes( types ) ;
1491 ws->setSelection(sel);
1492 refwcal = getScantable(ws,false);
1493 sel.reset() ;
1494 types.clear() ;
1495
1496 calsig = dototalpower(sigwcal, sig, tcal=tcal);
1497 calref = dototalpower(refwcal, ref, tcal=tcal);
1498
1499 out1=dosigref(calsig,calref,smoothref,tsysv,tau);
1500 out2=dosigref(calref,calsig,smoothref,tsysv,tau);
1501
1502 Table& tabout1=out1->table();
1503 Table& tabout2=out2->table();
1504 ROScalarColumn<uInt> freqidCol1(tabout1, "FREQ_ID");
1505 ScalarColumn<uInt> freqidCol2(tabout2, "FREQ_ID");
1506 ROArrayColumn<Float> specCol(tabout2, "SPECTRA");
1507 Vector<Float> spec; specCol.get(0, spec);
1508 uInt nchan = spec.nelements();
1509 uInt freqid1; freqidCol1.get(0,freqid1);
1510 uInt freqid2; freqidCol2.get(0,freqid2);
1511 Double rp1, rp2, rv1, rv2, inc1, inc2;
1512 out1->frequencies().getEntry(rp1, rv1, inc1, freqid1);
1513 out2->frequencies().getEntry(rp2, rv2, inc2, freqid2);
1514 //cerr << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << endl ;
1515 //LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1516 //os << out1->frequencies().table().nrow() << " " << out2->frequencies().table().nrow() << LogIO::POST ;
1517 if (rp1==rp2) {
1518 Double foffset = rv1 - rv2;
1519 uInt choffset = static_cast<uInt>(foffset/abs(inc2));
1520 if (choffset >= nchan) {
1521 //cerr<<"out-band frequency switching, no folding"<<endl;
1522 LogIO os( LogOrigin( "STMath", "dofs()", WHERE ) ) ;
1523 os<<"out-band frequency switching, no folding"<<LogIO::POST;
1524 nofold = True;
1525 }
1526 }
1527
1528 if (nofold) {
1529 std::vector< CountedPtr< Scantable > > tabs;
1530 tabs.push_back(out1);
1531 tabs.push_back(out2);
1532 out = merge(tabs);
1533 }
1534 else {
1535 //out = out1;
1536 Double choffset = ( rv1 - rv2 ) / inc2 ;
1537 out = dofold( out1, out2, choffset ) ;
1538 }
1539
1540 return out;
1541}
1542
1543CountedPtr<Scantable> STMath::dofold( const CountedPtr<Scantable> &sig,
1544 const CountedPtr<Scantable> &ref,
1545 Double choffset,
1546 Double choffset2 )
1547{
1548 LogIO os( LogOrigin( "STMath", "dofold", WHERE ) ) ;
1549 os << "choffset=" << choffset << " choffset2=" << choffset2 << LogIO::POST ;
1550
1551 // output scantable
1552 CountedPtr<Scantable> out = getScantable( sig, false ) ;
1553
1554 // separate choffset to integer part and decimal part
1555 Int ioffset = (Int)choffset ;
1556 Double doffset = choffset - ioffset ;
1557 Int ioffset2 = (Int)choffset2 ;
1558 Double doffset2 = choffset2 - ioffset2 ;
1559 os << "ioffset=" << ioffset << " doffset=" << doffset << LogIO::POST ;
1560 os << "ioffset2=" << ioffset2 << " doffset2=" << doffset2 << LogIO::POST ;
1561
1562 // get column
1563 ROArrayColumn<Float> specCol1( sig->table(), "SPECTRA" ) ;
1564 ROArrayColumn<Float> specCol2( ref->table(), "SPECTRA" ) ;
1565 ROArrayColumn<Float> tsysCol1( sig->table(), "TSYS" ) ;
1566 ROArrayColumn<Float> tsysCol2( ref->table(), "TSYS" ) ;
1567 ROArrayColumn<uChar> flagCol1( sig->table(), "FLAGTRA" ) ;
1568 ROArrayColumn<uChar> flagCol2( ref->table(), "FLAGTRA" ) ;
1569 ROScalarColumn<Double> mjdCol1( sig->table(), "TIME" ) ;
1570 ROScalarColumn<Double> mjdCol2( ref->table(), "TIME" ) ;
1571 ROScalarColumn<Double> intervalCol1( sig->table(), "INTERVAL" ) ;
1572 ROScalarColumn<Double> intervalCol2( ref->table(), "INTERVAL" ) ;
1573
1574 // check
1575 if ( ioffset == 0 ) {
1576 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1577 os << "channel offset is zero, no folding" << LogIO::POST ;
1578 return out ;
1579 }
1580 int nchan = ref->nchan() ;
1581 if ( abs(ioffset) >= nchan ) {
1582 LogIO os( LogOrigin( "STMath", "dofold()", WHERE ) ) ;
1583 os << "out-band frequency switching, no folding" << LogIO::POST ;
1584 return out ;
1585 }
1586
1587 // attach column for output scantable
1588 ArrayColumn<Float> specColOut( out->table(), "SPECTRA" ) ;
1589 ArrayColumn<uChar> flagColOut( out->table(), "FLAGTRA" ) ;
1590 ArrayColumn<Float> tsysColOut( out->table(), "TSYS" ) ;
1591 ScalarColumn<Double> mjdColOut( out->table(), "TIME" ) ;
1592 ScalarColumn<Double> intervalColOut( out->table(), "INTERVAL" ) ;
1593 ScalarColumn<uInt> fidColOut( out->table(), "FREQ_ID" ) ;
1594
1595 // for each row
1596 // assume that the data order are same between sig and ref
1597 RowAccumulator acc( asap::W_TINTSYS ) ;
1598 for ( int i = 0 ; i < sig->nrow() ; i++ ) {
1599 // get values
1600 Vector<Float> spsig ;
1601 specCol1.get( i, spsig ) ;
1602 Vector<Float> spref ;
1603 specCol2.get( i, spref ) ;
1604 Vector<Float> tsyssig ;
1605 tsysCol1.get( i, tsyssig ) ;
1606 Vector<Float> tsysref ;
1607 tsysCol2.get( i, tsysref ) ;
1608 Vector<uChar> flagsig ;
1609 flagCol1.get( i, flagsig ) ;
1610 Vector<uChar> flagref ;
1611 flagCol2.get( i, flagref ) ;
1612 Double timesig ;
1613 mjdCol1.get( i, timesig ) ;
1614 Double timeref ;
1615 mjdCol2.get( i, timeref ) ;
1616 Double intsig ;
1617 intervalCol1.get( i, intsig ) ;
1618 Double intref ;
1619 intervalCol2.get( i, intref ) ;
1620
1621 // shift reference spectra
1622 int refchan = spref.nelements() ;
1623 Vector<Float> sspref( spref.nelements() ) ;
1624 Vector<Float> stsysref( tsysref.nelements() ) ;
1625 Vector<uChar> sflagref( flagref.nelements() ) ;
1626 if ( ioffset > 0 ) {
1627 // SPECTRA and FLAGTRA
1628 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1629 sspref[j] = spref[j+ioffset] ;
1630 sflagref[j] = flagref[j+ioffset] ;
1631 }
1632 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1633 sspref[j] = spref[j-refchan+ioffset] ;
1634 sflagref[j] = flagref[j-refchan+ioffset] ;
1635 }
1636 spref = sspref.copy() ;
1637 flagref = sflagref.copy() ;
1638 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1639 sspref[j] = doffset * spref[j+1] + ( 1.0 - doffset ) * spref[j] ;
1640 sflagref[j] = flagref[j+1] + flagref[j] ;
1641 }
1642 sspref[refchan-1] = doffset * spref[0] + ( 1.0 - doffset ) * spref[refchan-1] ;
1643 sflagref[refchan-1] = flagref[0] + flagref[refchan-1] ;
1644
1645 // TSYS
1646 if ( spref.nelements() == tsysref.nelements() ) {
1647 for ( int j = 0 ; j < refchan-ioffset ; j++ ) {
1648 stsysref[j] = tsysref[j+ioffset] ;
1649 }
1650 for ( int j = refchan-ioffset ; j < refchan ; j++ ) {
1651 stsysref[j] = tsysref[j-refchan+ioffset] ;
1652 }
1653 tsysref = stsysref.copy() ;
1654 for ( int j = 0 ; j < refchan - 1 ; j++ ) {
1655 stsysref[j] = doffset * tsysref[j+1] + ( 1.0 - doffset ) * tsysref[j] ;
1656 }
1657 stsysref[refchan-1] = doffset * tsysref[0] + ( 1.0 - doffset ) * tsysref[refchan-1] ;
1658 }
1659 }
1660 else {
1661 // SPECTRA and FLAGTRA
1662 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1663 sspref[j] = spref[refchan+ioffset+j] ;
1664 sflagref[j] = flagref[refchan+ioffset+j] ;
1665 }
1666 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1667 sspref[j] = spref[j+ioffset] ;
1668 sflagref[j] = flagref[j+ioffset] ;
1669 }
1670 spref = sspref.copy() ;
1671 flagref = sflagref.copy() ;
1672 sspref[0] = doffset * spref[refchan-1] + ( 1.0 - doffset ) * spref[0] ;
1673 sflagref[0] = flagref[0] + flagref[refchan-1] ;
1674 for ( int j = 1 ; j < refchan ; j++ ) {
1675 sspref[j] = doffset * spref[j-1] + ( 1.0 - doffset ) * spref[j] ;
1676 sflagref[j] = flagref[j-1] + flagref[j] ;
1677 }
1678 // TSYS
1679 if ( spref.nelements() == tsysref.nelements() ) {
1680 for ( int j = 0 ; j < abs(ioffset) ; j++ ) {
1681 stsysref[j] = tsysref[refchan+ioffset+j] ;
1682 }
1683 for ( int j = abs(ioffset) ; j < refchan ; j++ ) {
1684 stsysref[j] = tsysref[j+ioffset] ;
1685 }
1686 tsysref = stsysref.copy() ;
1687 stsysref[0] = doffset * tsysref[refchan-1] + ( 1.0 - doffset ) * tsysref[0] ;
1688 for ( int j = 1 ; j < refchan ; j++ ) {
1689 stsysref[j] = doffset * tsysref[j-1] + ( 1.0 - doffset ) * tsysref[j] ;
1690 }
1691 }
1692 }
1693
1694 // shift signal spectra if necessary (only for APEX?)
1695 if ( choffset2 != 0.0 ) {
1696 int sigchan = spsig.nelements() ;
1697 Vector<Float> sspsig( spsig.nelements() ) ;
1698 Vector<Float> stsyssig( tsyssig.nelements() ) ;
1699 Vector<uChar> sflagsig( flagsig.nelements() ) ;
1700 if ( ioffset2 > 0 ) {
1701 // SPECTRA and FLAGTRA
1702 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1703 sspsig[j] = spsig[j+ioffset2] ;
1704 sflagsig[j] = flagsig[j+ioffset2] ;
1705 }
1706 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1707 sspsig[j] = spsig[j-sigchan+ioffset2] ;
1708 sflagsig[j] = flagsig[j-sigchan+ioffset2] ;
1709 }
1710 spsig = sspsig.copy() ;
1711 flagsig = sflagsig.copy() ;
1712 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1713 sspsig[j] = doffset2 * spsig[j+1] + ( 1.0 - doffset2 ) * spsig[j] ;
1714 sflagsig[j] = flagsig[j+1] || flagsig[j] ;
1715 }
1716 sspsig[sigchan-1] = doffset2 * spsig[0] + ( 1.0 - doffset2 ) * spsig[sigchan-1] ;
1717 sflagsig[sigchan-1] = flagsig[0] || flagsig[sigchan-1] ;
1718 // TSTS
1719 if ( spsig.nelements() == tsyssig.nelements() ) {
1720 for ( int j = 0 ; j < sigchan-ioffset2 ; j++ ) {
1721 stsyssig[j] = tsyssig[j+ioffset2] ;
1722 }
1723 for ( int j = sigchan-ioffset2 ; j < sigchan ; j++ ) {
1724 stsyssig[j] = tsyssig[j-sigchan+ioffset2] ;
1725 }
1726 tsyssig = stsyssig.copy() ;
1727 for ( int j = 0 ; j < sigchan - 1 ; j++ ) {
1728 stsyssig[j] = doffset2 * tsyssig[j+1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1729 }
1730 stsyssig[sigchan-1] = doffset2 * tsyssig[0] + ( 1.0 - doffset2 ) * tsyssig[sigchan-1] ;
1731 }
1732 }
1733 else {
1734 // SPECTRA and FLAGTRA
1735 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1736 sspsig[j] = spsig[sigchan+ioffset2+j] ;
1737 sflagsig[j] = flagsig[sigchan+ioffset2+j] ;
1738 }
1739 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1740 sspsig[j] = spsig[j+ioffset2] ;
1741 sflagsig[j] = flagsig[j+ioffset2] ;
1742 }
1743 spsig = sspsig.copy() ;
1744 flagsig = sflagsig.copy() ;
1745 sspsig[0] = doffset2 * spsig[sigchan-1] + ( 1.0 - doffset2 ) * spsig[0] ;
1746 sflagsig[0] = flagsig[0] + flagsig[sigchan-1] ;
1747 for ( int j = 1 ; j < sigchan ; j++ ) {
1748 sspsig[j] = doffset2 * spsig[j-1] + ( 1.0 - doffset2 ) * spsig[j] ;
1749 sflagsig[j] = flagsig[j-1] + flagsig[j] ;
1750 }
1751 // TSYS
1752 if ( spsig.nelements() == tsyssig.nelements() ) {
1753 for ( int j = 0 ; j < abs(ioffset2) ; j++ ) {
1754 stsyssig[j] = tsyssig[sigchan+ioffset2+j] ;
1755 }
1756 for ( int j = abs(ioffset2) ; j < sigchan ; j++ ) {
1757 stsyssig[j] = tsyssig[j+ioffset2] ;
1758 }
1759 tsyssig = stsyssig.copy() ;
1760 stsyssig[0] = doffset2 * tsyssig[sigchan-1] + ( 1.0 - doffset2 ) * tsyssig[0] ;
1761 for ( int j = 1 ; j < sigchan ; j++ ) {
1762 stsyssig[j] = doffset2 * tsyssig[j-1] + ( 1.0 - doffset2 ) * tsyssig[j] ;
1763 }
1764 }
1765 }
1766 }
1767
1768 // folding
1769 acc.add( spsig, !flagsig, tsyssig, intsig, timesig ) ;
1770 acc.add( sspref, !sflagref, stsysref, intref, timeref ) ;
1771
1772 // put result
1773 specColOut.put( i, acc.getSpectrum() ) ;
1774 const Vector<Bool> &msk = acc.getMask() ;
1775 Vector<uChar> flg( msk.shape() ) ;
1776 convertArray( flg, !msk ) ;
1777 flagColOut.put( i, flg ) ;
1778 tsysColOut.put( i, acc.getTsys() ) ;
1779 intervalColOut.put( i, acc.getInterval() ) ;
1780 mjdColOut.put( i, acc.getTime() ) ;
1781 // change FREQ_ID to unshifted IF setting (only for APEX?)
1782 if ( choffset2 != 0.0 ) {
1783 uInt freqid = fidColOut( 0 ) ; // assume single-IF data
1784 double refpix, refval, increment ;
1785 out->frequencies().getEntry( refpix, refval, increment, freqid ) ;
1786 refval -= choffset * increment ;
1787 uInt newfreqid = out->frequencies().addEntry( refpix, refval, increment ) ;
1788 Vector<uInt> freqids = fidColOut.getColumn() ;
1789 for ( uInt j = 0 ; j < freqids.nelements() ; j++ ) {
1790 if ( freqids[j] == freqid )
1791 freqids[j] = newfreqid ;
1792 }
1793 fidColOut.putColumn( freqids ) ;
1794 }
1795
1796 acc.reset() ;
1797 }
1798
1799 return out ;
1800}
1801
1802
1803CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
1804{
1805 // make copy or reference
1806 CountedPtr< Scantable > out = getScantable(in, false);
1807 Table& tout = out->table();
1808 Block<String> cols(4);
1809 cols[0] = String("SCANNO");
1810 cols[1] = String("CYCLENO");
1811 cols[2] = String("BEAMNO");
1812 cols[3] = String("POLNO");
1813 TableIterator iter(tout, cols);
1814 while (!iter.pastEnd()) {
1815 Table subt = iter.table();
1816 // this should leave us with two rows for the two IFs....if not ignore
1817 if (subt.nrow() != 2 ) {
1818 continue;
1819 }
1820 ArrayColumn<Float> specCol(subt, "SPECTRA");
1821 ArrayColumn<Float> tsysCol(subt, "TSYS");
1822 ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
1823 Vector<Float> onspec,offspec, ontsys, offtsys;
1824 Vector<uChar> onflag, offflag;
1825 tsysCol.get(0, ontsys); tsysCol.get(1, offtsys);
1826 specCol.get(0, onspec); specCol.get(1, offspec);
1827 flagCol.get(0, onflag); flagCol.get(1, offflag);
1828 MaskedArray<Float> on = maskedArray(onspec, onflag);
1829 MaskedArray<Float> off = maskedArray(offspec, offflag);
1830 MaskedArray<Float> oncopy = on.copy();
1831
1832 on /= off; on -= 1.0f;
1833 on *= ontsys[0];
1834 off /= oncopy; off -= 1.0f;
1835 off *= offtsys[0];
1836 specCol.put(0, on.getArray());
1837 const Vector<Bool>& m0 = on.getMask();
1838 Vector<uChar> flags0(m0.shape());
1839 convertArray(flags0, !m0);
1840 flagCol.put(0, flags0);
1841
1842 specCol.put(1, off.getArray());
1843 const Vector<Bool>& m1 = off.getMask();
1844 Vector<uChar> flags1(m1.shape());
1845 convertArray(flags1, !m1);
1846 flagCol.put(1, flags1);
1847 ++iter;
1848 }
1849
1850 return out;
1851}
1852
1853std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
1854 const std::vector< bool > & mask,
1855 const std::string& which )
1856{
1857
1858 Vector<Bool> m(mask);
1859 const Table& tab = in->table();
1860 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1861 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1862 std::vector<float> out;
1863 for (uInt i=0; i < tab.nrow(); ++i ) {
1864 Vector<Float> spec; specCol.get(i, spec);
1865 Vector<uChar> flag; flagCol.get(i, flag);
1866 MaskedArray<Float> ma = maskedArray(spec, flag);
1867 float outstat = 0.0;
1868 if ( spec.nelements() == m.nelements() ) {
1869 outstat = mathutil::statistics(which, ma(m));
1870 } else {
1871 outstat = mathutil::statistics(which, ma);
1872 }
1873 out.push_back(outstat);
1874 }
1875 return out;
1876}
1877
1878std::vector< float > STMath::statisticRow( const CountedPtr< Scantable > & in,
1879 const std::vector< bool > & mask,
1880 const std::string& which,
1881 int row )
1882{
1883
1884 Vector<Bool> m(mask);
1885 const Table& tab = in->table();
1886 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1887 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1888 std::vector<float> out;
1889
1890 Vector<Float> spec; specCol.get(row, spec);
1891 Vector<uChar> flag; flagCol.get(row, flag);
1892 MaskedArray<Float> ma = maskedArray(spec, flag);
1893 float outstat = 0.0;
1894 if ( spec.nelements() == m.nelements() ) {
1895 outstat = mathutil::statistics(which, ma(m));
1896 } else {
1897 outstat = mathutil::statistics(which, ma);
1898 }
1899 out.push_back(outstat);
1900
1901 return out;
1902}
1903
1904std::vector< int > STMath::minMaxChan( const CountedPtr< Scantable > & in,
1905 const std::vector< bool > & mask,
1906 const std::string& which )
1907{
1908
1909 Vector<Bool> m(mask);
1910 const Table& tab = in->table();
1911 ROArrayColumn<Float> specCol(tab, "SPECTRA");
1912 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1913 std::vector<int> out;
1914 for (uInt i=0; i < tab.nrow(); ++i ) {
1915 Vector<Float> spec; specCol.get(i, spec);
1916 Vector<uChar> flag; flagCol.get(i, flag);
1917 MaskedArray<Float> ma = maskedArray(spec, flag);
1918 if (ma.ndim() != 1) {
1919 throw (ArrayError(
1920 "std::vector<int> STMath::minMaxChan("
1921 "ContedPtr<Scantable> &in, std::vector<bool> &mask, "
1922 " std::string &which)"
1923 " - MaskedArray is not 1D"));
1924 }
1925 IPosition outpos(1,0);
1926 if ( spec.nelements() == m.nelements() ) {
1927 outpos = mathutil::minMaxPos(which, ma(m));
1928 } else {
1929 outpos = mathutil::minMaxPos(which, ma);
1930 }
1931 out.push_back(outpos[0]);
1932 }
1933 return out;
1934}
1935
1936CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
1937 int width )
1938{
1939 if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
1940 CountedPtr< Scantable > out = getScantable(in, false);
1941 Table& tout = out->table();
1942 out->frequencies().rescale(width, "BIN");
1943 ArrayColumn<Float> specCol(tout, "SPECTRA");
1944 ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
1945 for (uInt i=0; i < tout.nrow(); ++i ) {
1946 MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
1947 MaskedArray<Float> maout;
1948 LatticeUtilities::bin(maout, main, 0, Int(width));
1949 /// @todo implement channel based tsys binning
1950 specCol.put(i, maout.getArray());
1951 flagCol.put(i, flagsFromMA(maout));
1952 // take only the first binned spectrum's length for the deprecated
1953 // global header item nChan
1954 if (i==0) tout.rwKeywordSet().define(String("nChan"),
1955 Int(maout.getArray().nelements()));
1956 }
1957 return out;
1958}
1959
1960CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
1961 const std::string& method,
1962 float width )
1963//
1964// Should add the possibility of width being specified in km/s. This means
1965// that for each freqID (SpectralCoordinate) we will need to convert to an
1966// average channel width (say at the reference pixel). Then we would need
1967// to be careful to make sure each spectrum (of different freqID)
1968// is the same length.
1969//
1970{
1971 //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
1972 Int interpMethod(stringToIMethod(method));
1973
1974 CountedPtr< Scantable > out = getScantable(in, false);
1975 Table& tout = out->table();
1976
1977// Resample SpectralCoordinates (one per freqID)
1978 out->frequencies().rescale(width, "RESAMPLE");
1979 TableIterator iter(tout, "IFNO");
1980 TableRow row(tout);
1981 while ( !iter.pastEnd() ) {
1982 Table tab = iter.table();
1983 ArrayColumn<Float> specCol(tab, "SPECTRA");
1984 //ArrayColumn<Float> tsysCol(tout, "TSYS");
1985 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1986 Vector<Float> spec;
1987 Vector<uChar> flag;
1988 specCol.get(0,spec); // the number of channels should be constant per IF
1989 uInt nChanIn = spec.nelements();
1990 Vector<Float> xIn(nChanIn); indgen(xIn);
1991 Int fac = Int(nChanIn/width);
1992 Vector<Float> xOut(fac+10); // 10 to be safe - resize later
1993 uInt k = 0;
1994 Float x = 0.0;
1995 while (x < Float(nChanIn) ) {
1996 xOut(k) = x;
1997 k++;
1998 x += width;
1999 }
2000 uInt nChanOut = k;
2001 xOut.resize(nChanOut, True);
2002 // process all rows for this IFNO
2003 Vector<Float> specOut;
2004 Vector<Bool> maskOut;
2005 Vector<uChar> flagOut;
2006 for (uInt i=0; i < tab.nrow(); ++i) {
2007 specCol.get(i, spec);
2008 flagCol.get(i, flag);
2009 Vector<Bool> mask(flag.nelements());
2010 convertArray(mask, flag);
2011
2012 IPosition shapeIn(spec.shape());
2013 //sh.nchan = nChanOut;
2014 InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
2015 xIn, spec, mask,
2016 interpMethod, True, True);
2017 /// @todo do the same for channel based Tsys
2018 flagOut.resize(maskOut.nelements());
2019 convertArray(flagOut, maskOut);
2020 specCol.put(i, specOut);
2021 flagCol.put(i, flagOut);
2022 }
2023 ++iter;
2024 }
2025
2026 return out;
2027}
2028
2029STMath::imethod STMath::stringToIMethod(const std::string& in)
2030{
2031 static STMath::imap lookup;
2032
2033 // initialize the lookup table if necessary
2034 if ( lookup.empty() ) {
2035 lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
2036 lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
2037 lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
2038 lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
2039 }
2040
2041 STMath::imap::const_iterator iter = lookup.find(in);
2042
2043 if ( lookup.end() == iter ) {
2044 std::string message = in;
2045 message += " is not a valid interpolation mode";
2046 throw(AipsError(message));
2047 }
2048 return iter->second;
2049}
2050
2051WeightType STMath::stringToWeight(const std::string& in)
2052{
2053 static std::map<std::string, WeightType> lookup;
2054
2055 // initialize the lookup table if necessary
2056 if ( lookup.empty() ) {
2057 lookup["NONE"] = asap::W_NONE;
2058 lookup["TINT"] = asap::W_TINT;
2059 lookup["TINTSYS"] = asap::W_TINTSYS;
2060 lookup["TSYS"] = asap::W_TSYS;
2061 lookup["VAR"] = asap::W_VAR;
2062 }
2063
2064 std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
2065
2066 if ( lookup.end() == iter ) {
2067 std::string message = in;
2068 message += " is not a valid weighting mode";
2069 throw(AipsError(message));
2070 }
2071 return iter->second;
2072}
2073
2074CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
2075 const vector< float > & coeff,
2076 const std::string & filename,
2077 const std::string& method)
2078{
2079 // Get elevation data from Scantable and convert to degrees
2080 CountedPtr< Scantable > out = getScantable(in, false);
2081 Table& tab = out->table();
2082 ROScalarColumn<Float> elev(tab, "ELEVATION");
2083 Vector<Float> x = elev.getColumn();
2084 x *= Float(180 / C::pi); // Degrees
2085
2086 Vector<Float> coeffs(coeff);
2087 const uInt nc = coeffs.nelements();
2088 if ( filename.length() > 0 && nc > 0 ) {
2089 throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
2090 }
2091
2092 // Correct
2093 if ( nc > 0 || filename.length() == 0 ) {
2094 // Find instrument
2095 Bool throwit = True;
2096 Instrument inst =
2097 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2098 throwit);
2099
2100 // Set polynomial
2101 Polynomial<Float>* ppoly = 0;
2102 Vector<Float> coeff;
2103 String msg;
2104 if ( nc > 0 ) {
2105 ppoly = new Polynomial<Float>(nc-1);
2106 coeff = coeffs;
2107 msg = String("user");
2108 } else {
2109 STAttr sdAttr;
2110 coeff = sdAttr.gainElevationPoly(inst);
2111 ppoly = new Polynomial<Float>(coeff.nelements()-1);
2112 msg = String("built in");
2113 }
2114
2115 if ( coeff.nelements() > 0 ) {
2116 ppoly->setCoefficients(coeff);
2117 } else {
2118 delete ppoly;
2119 throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
2120 }
2121 ostringstream oss;
2122 oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
2123 oss << " " << coeff;
2124 pushLog(String(oss));
2125 const uInt nrow = tab.nrow();
2126 Vector<Float> factor(nrow);
2127 for ( uInt i=0; i < nrow; ++i ) {
2128 factor[i] = 1.0 / (*ppoly)(x[i]);
2129 }
2130 delete ppoly;
2131 scaleByVector(tab, factor, true);
2132
2133 } else {
2134 // Read and correct
2135 pushLog("Making correction from ascii Table");
2136 scaleFromAsciiTable(tab, filename, method, x, true);
2137 }
2138 return out;
2139}
2140
2141void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
2142 const std::string& method,
2143 const Vector<Float>& xout, bool dotsys)
2144{
2145
2146// Read gain-elevation ascii file data into a Table.
2147
2148 String formatString;
2149 Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
2150 scaleFromTable(in, tbl, method, xout, dotsys);
2151}
2152
2153void STMath::scaleFromTable(Table& in,
2154 const Table& table,
2155 const std::string& method,
2156 const Vector<Float>& xout, bool dotsys)
2157{
2158
2159 ROScalarColumn<Float> geElCol(table, "ELEVATION");
2160 ROScalarColumn<Float> geFacCol(table, "FACTOR");
2161 Vector<Float> xin = geElCol.getColumn();
2162 Vector<Float> yin = geFacCol.getColumn();
2163 Vector<Bool> maskin(xin.nelements(),True);
2164
2165 // Interpolate (and extrapolate) with desired method
2166
2167 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2168
2169 Vector<Float> yout;
2170 Vector<Bool> maskout;
2171 InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
2172 xin, yin, maskin, interp,
2173 True, True);
2174
2175 scaleByVector(in, Float(1.0)/yout, dotsys);
2176}
2177
2178void STMath::scaleByVector( Table& in,
2179 const Vector< Float >& factor,
2180 bool dotsys )
2181{
2182 uInt nrow = in.nrow();
2183 if ( factor.nelements() != nrow ) {
2184 throw(AipsError("factors.nelements() != table.nelements()"));
2185 }
2186 ArrayColumn<Float> specCol(in, "SPECTRA");
2187 ArrayColumn<uChar> flagCol(in, "FLAGTRA");
2188 ArrayColumn<Float> tsysCol(in, "TSYS");
2189 for (uInt i=0; i < nrow; ++i) {
2190 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2191 ma *= factor[i];
2192 specCol.put(i, ma.getArray());
2193 flagCol.put(i, flagsFromMA(ma));
2194 if ( dotsys ) {
2195 Vector<Float> tsys = tsysCol(i);
2196 tsys *= factor[i];
2197 tsysCol.put(i,tsys);
2198 }
2199 }
2200}
2201
2202CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
2203 float d, float etaap,
2204 float jyperk )
2205{
2206 CountedPtr< Scantable > out = getScantable(in, false);
2207 Table& tab = in->table();
2208 Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
2209 Unit K(String("K"));
2210 Unit JY(String("Jy"));
2211
2212 bool tokelvin = true;
2213 Double cfac = 1.0;
2214
2215 if ( fluxUnit == JY ) {
2216 pushLog("Converting to K");
2217 Quantum<Double> t(1.0,fluxUnit);
2218 Quantum<Double> t2 = t.get(JY);
2219 cfac = (t2 / t).getValue(); // value to Jy
2220
2221 tokelvin = true;
2222 out->setFluxUnit("K");
2223 } else if ( fluxUnit == K ) {
2224 pushLog("Converting to Jy");
2225 Quantum<Double> t(1.0,fluxUnit);
2226 Quantum<Double> t2 = t.get(K);
2227 cfac = (t2 / t).getValue(); // value to K
2228
2229 tokelvin = false;
2230 out->setFluxUnit("Jy");
2231 } else {
2232 throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
2233 }
2234 // Make sure input values are converted to either Jy or K first...
2235 Float factor = cfac;
2236
2237 // Select method
2238 if (jyperk > 0.0) {
2239 factor *= jyperk;
2240 if ( tokelvin ) factor = 1.0 / jyperk;
2241 ostringstream oss;
2242 oss << "Jy/K = " << jyperk;
2243 pushLog(String(oss));
2244 Vector<Float> factors(tab.nrow(), factor);
2245 scaleByVector(tab,factors, false);
2246 } else if ( etaap > 0.0) {
2247 if (d < 0) {
2248 Instrument inst =
2249 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
2250 True);
2251 STAttr sda;
2252 d = sda.diameter(inst);
2253 }
2254 jyperk = STAttr::findJyPerK(etaap, d);
2255 ostringstream oss;
2256 oss << "Jy/K = " << jyperk;
2257 pushLog(String(oss));
2258 factor *= jyperk;
2259 if ( tokelvin ) {
2260 factor = 1.0 / factor;
2261 }
2262 Vector<Float> factors(tab.nrow(), factor);
2263 scaleByVector(tab, factors, False);
2264 } else {
2265
2266 // OK now we must deal with automatic look up of values.
2267 // We must also deal with the fact that the factors need
2268 // to be computed per IF and may be different and may
2269 // change per integration.
2270
2271 pushLog("Looking up conversion factors");
2272 convertBrightnessUnits(out, tokelvin, cfac);
2273 }
2274
2275 return out;
2276}
2277
2278void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
2279 bool tokelvin, float cfac )
2280{
2281 Table& table = in->table();
2282 Instrument inst =
2283 STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
2284 TableIterator iter(table, "FREQ_ID");
2285 STFrequencies stfreqs = in->frequencies();
2286 STAttr sdAtt;
2287 while (!iter.pastEnd()) {
2288 Table tab = iter.table();
2289 ArrayColumn<Float> specCol(tab, "SPECTRA");
2290 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2291 ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
2292 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2293
2294 uInt freqid; freqidCol.get(0, freqid);
2295 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2296 // STAttr.JyPerK has a Vector interface... change sometime.
2297 Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
2298 for ( uInt i=0; i<tab.nrow(); ++i) {
2299 Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
2300 Float factor = cfac * jyperk;
2301 if ( tokelvin ) factor = Float(1.0) / factor;
2302 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2303 ma *= factor;
2304 specCol.put(i, ma.getArray());
2305 flagCol.put(i, flagsFromMA(ma));
2306 }
2307 ++iter;
2308 }
2309}
2310
2311CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
2312 const std::vector<float>& tau )
2313{
2314 CountedPtr< Scantable > out = getScantable(in, false);
2315
2316 Table outtab = out->table();
2317
2318 const Int ntau = uInt(tau.size());
2319 std::vector<float>::const_iterator tauit = tau.begin();
2320 AlwaysAssert((ntau == 1 || ntau == in->nif() || ntau == in->nif() * in->npol()),
2321 AipsError);
2322 TableIterator iiter(outtab, "IFNO");
2323 while ( !iiter.pastEnd() ) {
2324 Table itab = iiter.table();
2325 TableIterator piter(itab, "POLNO");
2326 while ( !piter.pastEnd() ) {
2327 Table tab = piter.table();
2328 ROScalarColumn<Float> elev(tab, "ELEVATION");
2329 ArrayColumn<Float> specCol(tab, "SPECTRA");
2330 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2331 ArrayColumn<Float> tsysCol(tab, "TSYS");
2332 for ( uInt i=0; i<tab.nrow(); ++i) {
2333 Float zdist = Float(C::pi_2) - elev(i);
2334 Float factor = exp(*tauit/cos(zdist));
2335 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
2336 ma *= factor;
2337 specCol.put(i, ma.getArray());
2338 flagCol.put(i, flagsFromMA(ma));
2339 Vector<Float> tsys;
2340 tsysCol.get(i, tsys);
2341 tsys *= factor;
2342 tsysCol.put(i, tsys);
2343 }
2344 if (ntau == in->nif()*in->npol() ) {
2345 tauit++;
2346 }
2347 piter++;
2348 }
2349 if (ntau >= in->nif() ) {
2350 tauit++;
2351 }
2352 iiter++;
2353 }
2354 return out;
2355}
2356
2357CountedPtr< Scantable > STMath::smoothOther( const CountedPtr< Scantable >& in,
2358 const std::string& kernel,
2359 float width, int order)
2360{
2361 CountedPtr< Scantable > out = getScantable(in, false);
2362 Table table = out->table();
2363
2364 TableIterator iter(table, "IFNO");
2365 while (!iter.pastEnd()) {
2366 Table tab = iter.table();
2367 ArrayColumn<Float> specCol(tab, "SPECTRA");
2368 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2369 Vector<Float> spec;
2370 Vector<uChar> flag;
2371 for (uInt i = 0; i < tab.nrow(); ++i) {
2372 specCol.get(i, spec);
2373 flagCol.get(i, flag);
2374 Vector<Bool> mask(flag.nelements());
2375 convertArray(mask, flag);
2376 Vector<Float> specout;
2377 Vector<Bool> maskout;
2378 if (kernel == "hanning") {
2379 mathutil::hanning(specout, maskout, spec, !mask);
2380 convertArray(flag, !maskout);
2381 } else if (kernel == "rmedian") {
2382 mathutil::runningMedian(specout, maskout, spec , mask, width);
2383 convertArray(flag, maskout);
2384 } else if (kernel == "poly") {
2385 mathutil::polyfit(specout, maskout, spec, !mask, width, order);
2386 convertArray(flag, !maskout);
2387 }
2388
2389 for (uInt j = 0; j < flag.nelements(); ++j) {
2390 uChar userFlag = 1 << 7;
2391 if (maskout[j]==True) userFlag = 0 << 7;
2392 flag(j) = userFlag;
2393 }
2394
2395 flagCol.put(i, flag);
2396 specCol.put(i, specout);
2397 }
2398 ++iter;
2399 }
2400 return out;
2401}
2402
2403CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
2404 const std::string& kernel, float width,
2405 int order)
2406{
2407 if (kernel == "rmedian" || kernel == "hanning" || kernel == "poly") {
2408 return smoothOther(in, kernel, width, order);
2409 }
2410 CountedPtr< Scantable > out = getScantable(in, false);
2411 Table& table = out->table();
2412 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
2413 // same IFNO should have same no of channels
2414 // this saves overhead
2415 TableIterator iter(table, "IFNO");
2416 while (!iter.pastEnd()) {
2417 Table tab = iter.table();
2418 ArrayColumn<Float> specCol(tab, "SPECTRA");
2419 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2420 Vector<Float> tmpspec; specCol.get(0, tmpspec);
2421 uInt nchan = tmpspec.nelements();
2422 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
2423 Convolver<Float> conv(kvec, IPosition(1,nchan));
2424 Vector<Float> spec;
2425 Vector<uChar> flag;
2426 for ( uInt i=0; i<tab.nrow(); ++i) {
2427 specCol.get(i, spec);
2428 flagCol.get(i, flag);
2429 Vector<Bool> mask(flag.nelements());
2430 convertArray(mask, flag);
2431 Vector<Float> specout;
2432 mathutil::replaceMaskByZero(specout, mask);
2433 conv.linearConv(specout, spec);
2434 specCol.put(i, specout);
2435 }
2436 ++iter;
2437 }
2438 return out;
2439}
2440
2441CountedPtr< Scantable >
2442 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
2443{
2444 if ( in.size() < 2 ) {
2445 throw(AipsError("Need at least two scantables to perform a merge."));
2446 }
2447 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
2448 bool insitu = insitu_;
2449 setInsitu(false);
2450 CountedPtr< Scantable > out = getScantable(*it, false);
2451 setInsitu(insitu);
2452 Table& tout = out->table();
2453 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
2454 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
2455 // Renumber SCANNO to be 0-based
2456 Vector<uInt> scannos = scannocol.getColumn();
2457 uInt offset = min(scannos);
2458 scannos -= offset;
2459 scannocol.putColumn(scannos);
2460 uInt newscanno = max(scannos)+1;
2461 ++it;
2462 while ( it != in.end() ){
2463 if ( ! (*it)->conformant(*out) ) {
2464 // non conformant.
2465 //pushLog(String("Warning: Can't merge scantables as header info differs."));
2466 LogIO os( LogOrigin( "STMath", "merge()", WHERE ) ) ;
2467 os << LogIO::SEVERE << "Can't merge scantables as header informations (any one of AntennaName, Equinox, and FluxUnit) differ." << LogIO::EXCEPTION ;
2468 }
2469 out->appendToHistoryTable((*it)->history());
2470 const Table& tab = (*it)->table();
2471
2472 Block<String> cols(3);
2473 cols[0] = String("FREQ_ID");
2474 cols[1] = String("MOLECULE_ID");
2475 cols[2] = String("FOCUS_ID");
2476
2477 TableIterator scanit(tab, "SCANNO");
2478 while (!scanit.pastEnd()) {
2479 ScalarColumn<uInt> thescannocol(scanit.table(),"SCANNO");
2480 Vector<uInt> thescannos(thescannocol.nrow(),newscanno);
2481 thescannocol.putColumn(thescannos);
2482 TableIterator subit(scanit.table(), cols);
2483 while ( !subit.pastEnd() ) {
2484 uInt nrow = tout.nrow();
2485 Table thetab = subit.table();
2486 ROTableRow row(thetab);
2487 Vector<uInt> thecolvals(thetab.nrow());
2488 ScalarColumn<uInt> thefreqidcol(thetab,"FREQ_ID");
2489 ScalarColumn<uInt> themolidcol(thetab, "MOLECULE_ID");
2490 ScalarColumn<uInt> thefocusidcol(thetab,"FOCUS_ID");
2491 // The selected subset of table should have
2492 // the equal FREQ_ID, MOLECULE_ID, and FOCUS_ID values.
2493 const TableRecord& rec = row.get(0);
2494 // Set the proper FREQ_ID
2495 Double rv,rp,inc;
2496 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
2497 uInt id;
2498 id = out->frequencies().addEntry(rp, rv, inc);
2499 thecolvals = id;
2500 thefreqidcol.putColumn(thecolvals);
2501 // Set the proper MOLECULE_ID
2502 Vector<String> name,fname;Vector<Double> rf;
2503 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
2504 id = out->molecules().addEntry(rf, name, fname);
2505 thecolvals = id;
2506 themolidcol.putColumn(thecolvals);
2507 // Set the proper FOCUS_ID
2508 Float fpa,frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
2509 (*it)->focus().getEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2510 fxy, fxyp, rec.asuInt("FOCUS_ID"));
2511 id = out->focus().addEntry(fpa, fax, ftan, frot, fhand, fmount,fuser,
2512 fxy, fxyp);
2513 thecolvals = id;
2514 thefocusidcol.putColumn(thecolvals);
2515
2516 tout.addRow(thetab.nrow());
2517 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
2518
2519 ++subit;
2520 }
2521 ++newscanno;
2522 ++scanit;
2523 }
2524 ++it;
2525 }
2526 return out;
2527}
2528
2529CountedPtr< Scantable >
2530 STMath::invertPhase( const CountedPtr < Scantable >& in )
2531{
2532 return applyToPol(in, &STPol::invertPhase, Float(0.0));
2533}
2534
2535CountedPtr< Scantable >
2536 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
2537{
2538 return applyToPol(in, &STPol::rotatePhase, Float(phase));
2539}
2540
2541CountedPtr< Scantable >
2542 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
2543{
2544 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
2545}
2546
2547CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
2548 STPol::polOperation fptr,
2549 Float phase )
2550{
2551 CountedPtr< Scantable > out = getScantable(in, false);
2552 Table& tout = out->table();
2553 Block<String> cols(4);
2554 cols[0] = String("SCANNO");
2555 cols[1] = String("BEAMNO");
2556 cols[2] = String("IFNO");
2557 cols[3] = String("CYCLENO");
2558 TableIterator iter(tout, cols);
2559 CountedPtr<STPol> stpol = STPol::getPolClass(out->factories_,
2560 out->getPolType() );
2561 while (!iter.pastEnd()) {
2562 Table t = iter.table();
2563 ArrayColumn<Float> speccol(t, "SPECTRA");
2564 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
2565 Matrix<Float> pols(speccol.getColumn());
2566 try {
2567 stpol->setSpectra(pols);
2568 Float fang,fhand;
2569 fang = in->focusTable_.getTotalAngle(focidcol(0));
2570 fhand = in->focusTable_.getFeedHand(focidcol(0));
2571 stpol->setPhaseCorrections(fang, fhand);
2572 // use a member function pointer in STPol. This only works on
2573 // the STPol pointer itself, not the Counted Pointer so
2574 // derefernce it.
2575 (&(*(stpol))->*fptr)(phase);
2576 speccol.putColumn(stpol->getSpectra());
2577 } catch (AipsError& e) {
2578 //delete stpol;stpol=0;
2579 throw(e);
2580 }
2581 ++iter;
2582 }
2583 //delete stpol;stpol=0;
2584 return out;
2585}
2586
2587CountedPtr< Scantable >
2588 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
2589{
2590 CountedPtr< Scantable > out = getScantable(in, false);
2591 Table& tout = out->table();
2592 Table t0 = tout(tout.col("POLNO") == 0);
2593 Table t1 = tout(tout.col("POLNO") == 1);
2594 if ( t0.nrow() != t1.nrow() )
2595 throw(AipsError("Inconsistent number of polarisations"));
2596 ArrayColumn<Float> speccol0(t0, "SPECTRA");
2597 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
2598 ArrayColumn<Float> speccol1(t1, "SPECTRA");
2599 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
2600 Matrix<Float> s0 = speccol0.getColumn();
2601 Matrix<uChar> f0 = flagcol0.getColumn();
2602 speccol0.putColumn(speccol1.getColumn());
2603 flagcol0.putColumn(flagcol1.getColumn());
2604 speccol1.putColumn(s0);
2605 flagcol1.putColumn(f0);
2606 return out;
2607}
2608
2609CountedPtr< Scantable >
2610 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
2611 const std::vector<bool>& mask,
2612 const std::string& weight )
2613{
2614 if (in->npol() < 2 )
2615 throw(AipsError("averagePolarisations can only be applied to two or more"
2616 "polarisations"));
2617 bool insitu = insitu_;
2618 setInsitu(false);
2619 CountedPtr< Scantable > pols = getScantable(in, true);
2620 setInsitu(insitu);
2621 Table& tout = pols->table();
2622 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
2623 Table tab = tableCommand(taql, in->table());
2624 if (tab.nrow() == 0 )
2625 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
2626 TableCopy::copyRows(tout, tab);
2627 TableVector<uInt> vec(tout, "POLNO");
2628 vec = 0;
2629 pols->table_.rwKeywordSet().define("nPol", Int(1));
2630 pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
2631 //pols->table_.rwKeywordSet().define("POLTYPE", in->getPolType());
2632 std::vector<CountedPtr<Scantable> > vpols;
2633 vpols.push_back(pols);
2634 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
2635 return out;
2636}
2637
2638CountedPtr< Scantable >
2639 STMath::averageBeams( const CountedPtr< Scantable > & in,
2640 const std::vector<bool>& mask,
2641 const std::string& weight )
2642{
2643 bool insitu = insitu_;
2644 setInsitu(false);
2645 CountedPtr< Scantable > beams = getScantable(in, false);
2646 setInsitu(insitu);
2647 Table& tout = beams->table();
2648 // give all rows the same BEAMNO
2649 TableVector<uInt> vec(tout, "BEAMNO");
2650 vec = 0;
2651 beams->table_.rwKeywordSet().define("nBeam", Int(1));
2652 std::vector<CountedPtr<Scantable> > vbeams;
2653 vbeams.push_back(beams);
2654 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
2655 return out;
2656}
2657
2658
2659CountedPtr< Scantable >
2660 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
2661 const std::string & refTime,
2662 const std::string & method)
2663{
2664 // clone as this is not working insitu
2665 bool insitu = insitu_;
2666 setInsitu(false);
2667 CountedPtr< Scantable > out = getScantable(in, false);
2668 setInsitu(insitu);
2669 Table& tout = out->table();
2670 // Get reference Epoch to time of first row or given String
2671 Unit DAY(String("d"));
2672 MEpoch::Ref epochRef(in->getTimeReference());
2673 MEpoch refEpoch;
2674 if (refTime.length()>0) {
2675 Quantum<Double> qt;
2676 if (MVTime::read(qt,refTime)) {
2677 MVEpoch mv(qt);
2678 refEpoch = MEpoch(mv, epochRef);
2679 } else {
2680 throw(AipsError("Invalid format for Epoch string"));
2681 }
2682 } else {
2683 refEpoch = in->timeCol_(0);
2684 }
2685 MPosition refPos = in->getAntennaPosition();
2686
2687 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
2688 /*
2689 // Comment from MV.
2690 // the following code has been commented out because different FREQ_IDs have to be aligned together even
2691 // if the frame doesn't change. So far, lack of this check didn't cause any problems.
2692 // test if user frame is different to base frame
2693 if ( in->frequencies().getFrameString(true)
2694 == in->frequencies().getFrameString(false) ) {
2695 throw(AipsError("Can't convert as no output frame has been set"
2696 " (use set_freqframe) or it is aligned already."));
2697 }
2698 */
2699 MFrequency::Types system = in->frequencies().getFrame();
2700 MVTime mvt(refEpoch.getValue());
2701 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
2702 ostringstream oss;
2703 oss << "Aligned at reference Epoch " << epochout
2704 << " in frame " << MFrequency::showType(system);
2705 pushLog(String(oss));
2706 // set up the iterator
2707 Block<String> cols(4);
2708 // select by constant direction
2709 cols[0] = String("SRCNAME");
2710 cols[1] = String("BEAMNO");
2711 // select by IF ( no of channels varies over this )
2712 cols[2] = String("IFNO");
2713 // select by restfrequency
2714 cols[3] = String("MOLECULE_ID");
2715 TableIterator iter(tout, cols);
2716 while ( !iter.pastEnd() ) {
2717 Table t = iter.table();
2718 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
2719 TableIterator fiter(t, "FREQ_ID");
2720 // determine nchan from the first row. This should work as
2721 // we are iterating over BEAMNO and IFNO // we should have constant direction
2722
2723 ROArrayColumn<Float> sCol(t, "SPECTRA");
2724 const MDirection direction = dirCol(0);
2725 const uInt nchan = sCol(0).nelements();
2726
2727 // skip operations if there is nothing to align
2728 if (fiter.pastEnd()) {
2729 continue;
2730 }
2731
2732 Table ftab = fiter.table();
2733 // align all frequency ids with respect to the first encountered id
2734 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
2735 // get the SpectralCoordinate for the freqid, which we are iterating over
2736 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
2737 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
2738 direction, refPos, system );
2739 // realign the SpectralCoordinate and put into the output Scantable
2740 Vector<String> units(1);
2741 units = String("Hz");
2742 Bool linear=True;
2743 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
2744 sc2.setWorldAxisUnits(units);
2745 const uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
2746 sc2.referenceValue()[0],
2747 sc2.increment()[0]);
2748 while ( !fiter.pastEnd() ) {
2749 ftab = fiter.table();
2750 // spectral coordinate for the current FREQ_ID
2751 ScalarColumn<uInt> freqidCol2(ftab, "FREQ_ID");
2752 sC = in->frequencies().getSpectralCoordinate(freqidCol2(0));
2753 // create the "global" abcissa for alignment with same FREQ_ID
2754 Vector<Double> abc(nchan);
2755 for (uInt i=0; i<nchan; i++) {
2756 Double w;
2757 sC.toWorld(w,Double(i));
2758 abc[i] = w;
2759 }
2760 TableVector<uInt> tvec(ftab, "FREQ_ID");
2761 // assign new frequency id to all rows
2762 tvec = id;
2763 // cache abcissa for same time stamps, so iterate over those
2764 TableIterator timeiter(ftab, "TIME");
2765 while ( !timeiter.pastEnd() ) {
2766 Table tab = timeiter.table();
2767 ArrayColumn<Float> specCol(tab, "SPECTRA");
2768 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2769 MEpoch::ROScalarColumn timeCol(tab, "TIME");
2770 // use align abcissa cache after the first row
2771 // these rows should be just be POLNO
2772 bool first = true;
2773 for (int i=0; i<int(tab.nrow()); ++i) {
2774 // input values
2775 Vector<uChar> flag = flagCol(i);
2776 Vector<Bool> mask(flag.shape());
2777 Vector<Float> specOut, spec;
2778 spec = specCol(i);
2779 Vector<Bool> maskOut;Vector<uChar> flagOut;
2780 convertArray(mask, flag);
2781 // alignment
2782 Bool ok = fa.align(specOut, maskOut, abc, spec,
2783 mask, timeCol(i), !first,
2784 interp, False);
2785 (void) ok; // unused stop compiler nagging
2786 // back into scantable
2787 flagOut.resize(maskOut.nelements());
2788 convertArray(flagOut, maskOut);
2789 flagCol.put(i, flagOut);
2790 specCol.put(i, specOut);
2791 // start abcissa caching
2792 first = false;
2793 }
2794 // next timestamp
2795 ++timeiter;
2796 }
2797 // next FREQ_ID
2798 ++fiter;
2799 }
2800 // next aligner
2801 ++iter;
2802 }
2803 // set this afterwards to ensure we are doing insitu correctly.
2804 out->frequencies().setFrame(system, true);
2805 return out;
2806}
2807
2808CountedPtr<Scantable>
2809 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
2810 const std::string & newtype )
2811{
2812 if (in->npol() != 2 && in->npol() != 4)
2813 throw(AipsError("Can only convert two or four polarisations."));
2814 if ( in->getPolType() == newtype )
2815 throw(AipsError("No need to convert."));
2816 if ( ! in->selector_.empty() )
2817 throw(AipsError("Can only convert whole scantable. Unset the selection."));
2818 bool insitu = insitu_;
2819 setInsitu(false);
2820 CountedPtr< Scantable > out = getScantable(in, true);
2821 setInsitu(insitu);
2822 Table& tout = out->table();
2823 tout.rwKeywordSet().define("POLTYPE", String(newtype));
2824
2825 Block<String> cols(4);
2826 cols[0] = "SCANNO";
2827 cols[1] = "CYCLENO";
2828 cols[2] = "BEAMNO";
2829 cols[3] = "IFNO";
2830 TableIterator it(in->originalTable_, cols);
2831 String basetype = in->getPolType();
2832 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
2833 try {
2834 while ( !it.pastEnd() ) {
2835 Table tab = it.table();
2836 uInt row = tab.rowNumbers()[0];
2837 stpol->setSpectra(in->getPolMatrix(row));
2838 Float fang,fhand;
2839 fang = in->focusTable_.getTotalAngle(in->mfocusidCol_(row));
2840 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
2841 stpol->setPhaseCorrections(fang, fhand);
2842 Int npolout = 0;
2843 for (uInt i=0; i<tab.nrow(); ++i) {
2844 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
2845 if ( outvec.nelements() > 0 ) {
2846 tout.addRow();
2847 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
2848 ArrayColumn<Float> sCol(tout,"SPECTRA");
2849 ScalarColumn<uInt> pCol(tout,"POLNO");
2850 sCol.put(tout.nrow()-1 ,outvec);
2851 pCol.put(tout.nrow()-1 ,uInt(npolout));
2852 npolout++;
2853 }
2854 }
2855 tout.rwKeywordSet().define("nPol", npolout);
2856 ++it;
2857 }
2858 } catch (AipsError& e) {
2859 delete stpol;
2860 throw(e);
2861 }
2862 delete stpol;
2863 return out;
2864}
2865
2866CountedPtr< Scantable >
2867 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
2868 const std::string & scantype )
2869{
2870 bool insitu = insitu_;
2871 setInsitu(false);
2872 CountedPtr< Scantable > out = getScantable(in, true);
2873 setInsitu(insitu);
2874 Table& tout = out->table();
2875 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
2876 if (scantype == "on") {
2877 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
2878 }
2879 Table tab = tableCommand(taql, in->table());
2880 TableCopy::copyRows(tout, tab);
2881 if (scantype == "on") {
2882 // re-index SCANNO to 0
2883 TableVector<uInt> vec(tout, "SCANNO");
2884 vec = 0;
2885 }
2886 return out;
2887}
2888
2889std::vector<float>
2890 asap::STMath::fft( const casa::CountedPtr< Scantable > & in,
2891 const std::vector<int>& whichrow,
2892 bool getRealImag )
2893{
2894 std::vector<float> res;
2895 Table tab = in->table();
2896 std::vector<bool> mask;
2897
2898 if (whichrow.size() < 1) { // for all rows (by default)
2899 int nrow = int(tab.nrow());
2900 for (int i = 0; i < nrow; ++i) {
2901 res = in->execFFT(i, mask, getRealImag);
2902 }
2903 } else { // for specified rows
2904 for (uInt i = 0; i < whichrow.size(); ++i) {
2905 res = in->execFFT(i, mask, getRealImag);
2906 }
2907 }
2908
2909 return res;
2910}
2911
2912
2913CountedPtr<Scantable>
2914 asap::STMath::lagFlag( const CountedPtr<Scantable>& in,
2915 double start, double end,
2916 const std::string& mode )
2917{
2918 CountedPtr<Scantable> out = getScantable(in, false);
2919 Table& tout = out->table();
2920 TableIterator iter(tout, "FREQ_ID");
2921 FFTServer<Float,Complex> ffts;
2922
2923 while ( !iter.pastEnd() ) {
2924 Table tab = iter.table();
2925 Double rp,rv,inc;
2926 ROTableRow row(tab);
2927 const TableRecord& rec = row.get(0);
2928 uInt freqid = rec.asuInt("FREQ_ID");
2929 out->frequencies().getEntry(rp, rv, inc, freqid);
2930 ArrayColumn<Float> specCol(tab, "SPECTRA");
2931 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
2932
2933 for (int i=0; i<int(tab.nrow()); ++i) {
2934 Vector<Float> spec = specCol(i);
2935 Vector<uChar> flag = flagCol(i);
2936 std::vector<bool> mask;
2937 for (uInt j = 0; j < flag.nelements(); ++j) {
2938 mask.push_back(!(flag[j]>0));
2939 }
2940 mathutil::doZeroOrderInterpolation(spec, mask);
2941
2942 Vector<Complex> lags;
2943 ffts.fft0(lags, spec);
2944
2945 Int lag0(start+0.5);
2946 Int lag1(end+0.5);
2947 if (mode == "frequency") {
2948 lag0 = Int(spec.nelements()*abs(inc)/(start)+0.5);
2949 lag1 = Int(spec.nelements()*abs(inc)/(end)+0.5);
2950 }
2951 Int lstart = max(0, lag0);
2952 Int lend = min(Int(lags.nelements()-1), lag1);
2953 if (lstart == lend) {
2954 lags[lstart] = Complex(0.0);
2955 } else {
2956 if (lstart > lend) {
2957 Int tmp = lend;
2958 lend = lstart;
2959 lstart = tmp;
2960 }
2961 for (int j=lstart; j <=lend ;++j) {
2962 lags[j] = Complex(0.0);
2963 }
2964 }
2965
2966 ffts.fft0(spec, lags);
2967
2968 specCol.put(i, spec);
2969 }
2970 ++iter;
2971 }
2972 return out;
2973}
2974
2975// Averaging spectra with different channel/resolution
2976CountedPtr<Scantable>
2977STMath::new_average( const std::vector<CountedPtr<Scantable> >& in,
2978 const bool& compel,
2979 const std::vector<bool>& mask,
2980 const std::string& weight,
2981 const std::string& avmode )
2982 throw ( casa::AipsError )
2983{
2984 LogIO os( LogOrigin( "STMath", "new_average()", WHERE ) ) ;
2985 if ( avmode == "SCAN" && in.size() != 1 )
2986 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
2987 "Use merge first."));
2988
2989 // 2012/02/17 TN
2990 // Since STGrid is implemented, average doesn't consider direction
2991 // when accumulating
2992 // check if OTF observation
2993// String obstype = in[0]->getHeader().obstype ;
2994// Double tol = 0.0 ;
2995// if ( obstype.find( "OTF" ) != String::npos ) {
2996// tol = TOL_OTF ;
2997// }
2998// else {
2999// tol = TOL_POINT ;
3000// }
3001
3002 CountedPtr<Scantable> out ; // processed result
3003 if ( compel ) {
3004 std::vector< CountedPtr<Scantable> > newin ; // input for average process
3005 uInt insize = in.size() ; // number of input scantables
3006
3007 // TEST: do normal average in each table before IF grouping
3008 os << "Do preliminary averaging" << LogIO::POST ;
3009 vector< CountedPtr<Scantable> > tmpin( insize ) ;
3010 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3011 vector< CountedPtr<Scantable> > v( 1, in[itable] ) ;
3012 tmpin[itable] = average( v, mask, weight, avmode ) ;
3013 }
3014
3015 // warning
3016 os << "Average spectra with different spectral resolution" << LogIO::POST ;
3017
3018 // temporarily set coordinfo
3019 vector<string> oldinfo( insize ) ;
3020 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3021 vector<string> coordinfo = in[itable]->getCoordInfo() ;
3022 oldinfo[itable] = coordinfo[0] ;
3023 coordinfo[0] = "Hz" ;
3024 tmpin[itable]->setCoordInfo( coordinfo ) ;
3025 }
3026
3027 // columns
3028 ScalarColumn<uInt> freqIDCol ;
3029 ScalarColumn<uInt> ifnoCol ;
3030 ScalarColumn<uInt> scannoCol ;
3031
3032
3033 // check IF frequency coverage
3034 // freqid: list of FREQ_ID, which is used, in each table
3035 // iffreq: list of minimum and maximum frequency for each FREQ_ID in
3036 // each table
3037 // freqid[insize][numIF]
3038 // freqid: [[id00, id01, ...],
3039 // [id10, id11, ...],
3040 // ...
3041 // [idn0, idn1, ...]]
3042 // iffreq[insize][numIF*2]
3043 // iffreq: [[min_id00, max_id00, min_id01, max_id01, ...],
3044 // [min_id10, max_id10, min_id11, max_id11, ...],
3045 // ...
3046 // [min_idn0, max_idn0, min_idn1, max_idn1, ...]]
3047 //os << "Check IF settings in each table" << LogIO::POST ;
3048 vector< vector<uInt> > freqid( insize );
3049 vector< vector<double> > iffreq( insize ) ;
3050 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3051 uInt rows = tmpin[itable]->nrow() ;
3052 uInt freqnrows = tmpin[itable]->frequencies().table().nrow() ;
3053 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3054 if ( freqid[itable].size() == freqnrows ) {
3055 break ;
3056 }
3057 else {
3058 freqIDCol.attach( tmpin[itable]->table(), "FREQ_ID" ) ;
3059 ifnoCol.attach( tmpin[itable]->table(), "IFNO" ) ;
3060 uInt id = freqIDCol( irow ) ;
3061 if ( freqid[itable].size() == 0 || count( freqid[itable].begin(), freqid[itable].end(), id ) == 0 ) {
3062 //os << "itable = " << itable << ": IF " << id << " is included in the list" << LogIO::POST ;
3063 vector<double> abcissa = tmpin[itable]->getAbcissa( irow ) ;
3064 freqid[itable].push_back( id ) ;
3065 iffreq[itable].push_back( abcissa[0] - 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
3066 iffreq[itable].push_back( abcissa[abcissa.size()-1] + 0.5 * ( abcissa[1] - abcissa[0] ) ) ;
3067 }
3068 }
3069 }
3070 }
3071
3072 // debug
3073 //os << "IF settings summary:" << endl ;
3074 //for ( uInt i = 0 ; i < freqid.size() ; i++ ) {
3075 //os << " Table" << i << endl ;
3076 //for ( uInt j = 0 ; j < freqid[i].size() ; j++ ) {
3077 //os << " id = " << freqid[i][j] << " (min,max) = (" << iffreq[i][2*j] << "," << iffreq[i][2*j+1] << ")" << endl ;
3078 //}
3079 //}
3080 //os << endl ;
3081 //os.post() ;
3082
3083 // IF grouping based on their frequency coverage
3084 // ifgrp: list of table index and FREQ_ID for all members in each IF group
3085 // ifgfreq: list of minimum and maximum frequency in each IF group
3086 // ifgrp[numgrp][nummember*2]
3087 // ifgrp: [[table00, freqrow00, table01, freqrow01, ...],
3088 // [table10, freqrow10, table11, freqrow11, ...],
3089 // ...
3090 // [tablen0, freqrown0, tablen1, freqrown1, ...]]
3091 // ifgfreq[numgrp*2]
3092 // ifgfreq: [min0_grp0, max0_grp0, min1_grp1, max1_grp1, ...]
3093 //os << "IF grouping based on their frequency coverage" << LogIO::POST ;
3094 vector< vector<uInt> > ifgrp ;
3095 vector<double> ifgfreq ;
3096
3097 // parameter for IF grouping
3098 // groupmode = OR retrieve all region
3099 // AND only retrieve overlaped region
3100 //string groupmode = "AND" ;
3101 string groupmode = "OR" ;
3102 uInt sizecr = 0 ;
3103 if ( groupmode == "AND" )
3104 sizecr = 2 ;
3105 else if ( groupmode == "OR" )
3106 sizecr = 0 ;
3107
3108 vector<double> sortedfreq ;
3109 for ( uInt i = 0 ; i < iffreq.size() ; i++ ) {
3110 for ( uInt j = 0 ; j < iffreq[i].size() ; j++ ) {
3111 if ( count( sortedfreq.begin(), sortedfreq.end(), iffreq[i][j] ) == 0 )
3112 sortedfreq.push_back( iffreq[i][j] ) ;
3113 }
3114 }
3115 sort( sortedfreq.begin(), sortedfreq.end() ) ;
3116 for ( vector<double>::iterator i = sortedfreq.begin() ; i != sortedfreq.end()-1 ; i++ ) {
3117 ifgfreq.push_back( *i ) ;
3118 ifgfreq.push_back( *(i+1) ) ;
3119 }
3120 ifgrp.resize( ifgfreq.size()/2 ) ;
3121 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3122 for ( uInt iif = 0 ; iif < freqid[itable].size() ; iif++ ) {
3123 double range0 = iffreq[itable][2*iif] ;
3124 double range1 = iffreq[itable][2*iif+1] ;
3125 for ( uInt j = 0 ; j < ifgrp.size() ; j++ ) {
3126 double fmin = max( range0, ifgfreq[2*j] ) ;
3127 double fmax = min( range1, ifgfreq[2*j+1] ) ;
3128 if ( fmin < fmax ) {
3129 ifgrp[j].push_back( itable ) ;
3130 ifgrp[j].push_back( freqid[itable][iif] ) ;
3131 }
3132 }
3133 }
3134 }
3135 vector< vector<uInt> >::iterator fiter = ifgrp.begin() ;
3136 vector<double>::iterator giter = ifgfreq.begin() ;
3137 while( fiter != ifgrp.end() ) {
3138 if ( fiter->size() <= sizecr ) {
3139 fiter = ifgrp.erase( fiter ) ;
3140 giter = ifgfreq.erase( giter ) ;
3141 giter = ifgfreq.erase( giter ) ;
3142 }
3143 else {
3144 fiter++ ;
3145 advance( giter, 2 ) ;
3146 }
3147 }
3148
3149 // Grouping continuous IF groups (without frequency gap)
3150 // freqgrp: list of IF group indexes in each frequency group
3151 // freqrange: list of minimum and maximum frequency in each frequency group
3152 // freqgrp[numgrp][nummember]
3153 // freqgrp: [[ifgrp00, ifgrp01, ifgrp02, ...],
3154 // [ifgrp10, ifgrp11, ifgrp12, ...],
3155 // ...
3156 // [ifgrpn0, ifgrpn1, ifgrpn2, ...]]
3157 // freqrange[numgrp*2]
3158 // freqrange: [min_grp0, max_grp0, min_grp1, max_grp1, ...]
3159 vector< vector<uInt> > freqgrp ;
3160 double freqrange = 0.0 ;
3161 uInt grpnum = 0 ;
3162 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3163 // Assumed that ifgfreq was sorted
3164 if ( grpnum != 0 && freqrange == ifgfreq[2*i] ) {
3165 freqgrp[grpnum-1].push_back( i ) ;
3166 }
3167 else {
3168 vector<uInt> grp0( 1, i ) ;
3169 freqgrp.push_back( grp0 ) ;
3170 grpnum++ ;
3171 }
3172 freqrange = ifgfreq[2*i+1] ;
3173 }
3174
3175
3176 // print IF groups
3177 ostringstream oss ;
3178 oss << "IF Group summary: " << endl ;
3179 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3180 for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3181 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3182 for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3183 oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3184 }
3185 oss << endl ;
3186 }
3187 oss << endl ;
3188 os << oss.str() << LogIO::POST ;
3189
3190 // print frequency group
3191 oss.str("") ;
3192 oss << "Frequency Group summary: " << endl ;
3193 oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: IF_GROUP_ID" << endl ;
3194 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3195 oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*freqgrp[i][0]] << "," << ifgfreq[2*freqgrp[i][freqgrp[i].size()-1]+1] << "]: " ;
3196 for ( uInt j = 0 ; j < freqgrp[i].size() ; j++ ) {
3197 oss << freqgrp[i][j] << " " ;
3198 }
3199 oss << endl ;
3200 }
3201 oss << endl ;
3202 os << oss.str() << LogIO::POST ;
3203
3204 // membership check
3205 // groups: list of IF group indexes whose frequency range overlaps with
3206 // that of each table and IF
3207 // groups[numtable][numIF][nummembership]
3208 // groups: [[[grp, grp,...], [grp, grp,...],...],
3209 // [[grp, grp,...], [grp, grp,...],...],
3210 // ...
3211 // [[grp, grp,...], [grp, grp,...],...]]
3212 vector< vector< vector<uInt> > > groups( insize ) ;
3213 for ( uInt i = 0 ; i < insize ; i++ ) {
3214 groups[i].resize( freqid[i].size() ) ;
3215 }
3216 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3217 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3218 uInt tableid = ifgrp[igrp][2*imem] ;
3219 vector<uInt>::iterator iter = find( freqid[tableid].begin(), freqid[tableid].end(), ifgrp[igrp][2*imem+1] ) ;
3220 if ( iter != freqid[tableid].end() ) {
3221 uInt rowid = distance( freqid[tableid].begin(), iter ) ;
3222 groups[tableid][rowid].push_back( igrp ) ;
3223 }
3224 }
3225 }
3226
3227 // print membership
3228 //oss.str("") ;
3229 //for ( uInt i = 0 ; i < insize ; i++ ) {
3230 //oss << "Table " << i << endl ;
3231 //for ( uInt j = 0 ; j < groups[i].size() ; j++ ) {
3232 //oss << " FREQ_ID " << setw( 2 ) << freqid[i][j] << ": " ;
3233 //for ( uInt k = 0 ; k < groups[i][j].size() ; k++ ) {
3234 //oss << setw( 2 ) << groups[i][j][k] << " " ;
3235 //}
3236 //oss << endl ;
3237 //}
3238 //}
3239 //os << oss.str() << LogIO::POST ;
3240
3241 // set back coordinfo
3242 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3243 vector<string> coordinfo = tmpin[itable]->getCoordInfo() ;
3244 coordinfo[0] = oldinfo[itable] ;
3245 tmpin[itable]->setCoordInfo( coordinfo ) ;
3246 }
3247
3248 // Create additional table if needed
3249 bool oldInsitu = insitu_ ;
3250 setInsitu( false ) ;
3251 vector< vector<uInt> > addrow( insize ) ;
3252 vector<uInt> addtable( insize, 0 ) ;
3253 vector<uInt> newtableids( insize ) ;
3254 vector<uInt> newifids( insize, 0 ) ;
3255 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3256 //os << "Table " << itable << ": " ;
3257 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3258 addrow[itable].push_back( groups[itable][ifrow].size()-1 ) ;
3259 //os << addrow[itable][ifrow] << " " ;
3260 }
3261 addtable[itable] = *max_element( addrow[itable].begin(), addrow[itable].end() ) ;
3262 //os << "(" << addtable[itable] << ")" << LogIO::POST ;
3263 }
3264 newin.resize( insize ) ;
3265 copy( tmpin.begin(), tmpin.end(), newin.begin() ) ;
3266 for ( uInt i = 0 ; i < insize ; i++ ) {
3267 newtableids[i] = i ;
3268 }
3269 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3270 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3271 CountedPtr<Scantable> add = getScantable( newin[itable], false ) ;
3272 vector<int> freqidlist ;
3273 for ( uInt i = 0 ; i < groups[itable].size() ; i++ ) {
3274 if ( groups[itable][i].size() > iadd + 1 ) {
3275 freqidlist.push_back( freqid[itable][i] ) ;
3276 }
3277 }
3278 stringstream taqlstream ;
3279 taqlstream << "SELECT FROM $1 WHERE FREQ_ID IN [" ;
3280 for ( uInt i = 0 ; i < freqidlist.size() ; i++ ) {
3281 taqlstream << freqidlist[i] ;
3282 if ( i < freqidlist.size() - 1 )
3283 taqlstream << "," ;
3284 else
3285 taqlstream << "]" ;
3286 }
3287 string taql = taqlstream.str() ;
3288 //os << "taql = " << taql << LogIO::POST ;
3289 STSelector selector = STSelector() ;
3290 selector.setTaQL( taql ) ;
3291 add->setSelection( selector ) ;
3292 newin.push_back( add ) ;
3293 newtableids.push_back( itable ) ;
3294 newifids.push_back( iadd + 1 ) ;
3295 }
3296 }
3297
3298 // udpate ifgrp
3299 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3300 for ( uInt iadd = 0 ; iadd < addtable[itable] ; iadd++ ) {
3301 for ( uInt ifrow = 0 ; ifrow < groups[itable].size() ; ifrow++ ) {
3302 if ( groups[itable][ifrow].size() > iadd + 1 ) {
3303 uInt igrp = groups[itable][ifrow][iadd+1] ;
3304 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3305 if ( ifgrp[igrp][2*imem] == newtableids[iadd+insize] && ifgrp[igrp][2*imem+1] == freqid[newtableids[iadd+insize]][ifrow] ) {
3306 ifgrp[igrp][2*imem] = insize + iadd ;
3307 }
3308 }
3309 }
3310 }
3311 }
3312 }
3313
3314 // print IF groups again for debug
3315 //oss.str( "" ) ;
3316 //oss << "IF Group summary: " << endl ;
3317 //oss << " GROUP_ID [FREQ_MIN, FREQ_MAX]: (TABLE_ID, FREQ_ID)" << endl ;
3318 //for ( uInt i = 0 ; i < ifgrp.size() ; i++ ) {
3319 //oss << " GROUP " << setw( 2 ) << i << " [" << ifgfreq[2*i] << "," << ifgfreq[2*i+1] << "]: " ;
3320 //for ( uInt j = 0 ; j < ifgrp[i].size()/2 ; j++ ) {
3321 //oss << "(" << ifgrp[i][2*j] << "," << ifgrp[i][2*j+1] << ") " ;
3322 //}
3323 //oss << endl ;
3324 //}
3325 //oss << endl ;
3326 //os << oss.str() << LogIO::POST ;
3327
3328 // reset SCANNO and IFNO/FREQ_ID: IF is reset by the result of sortation
3329 os << "All scan number is set to 0" << LogIO::POST ;
3330 //os << "All IF number is set to IF group index" << LogIO::POST ;
3331 insize = newin.size() ;
3332 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3333 uInt rows = newin[itable]->nrow() ;
3334 Table &tmpt = newin[itable]->table() ;
3335 freqIDCol.attach( tmpt, "FREQ_ID" ) ;
3336 scannoCol.attach( tmpt, "SCANNO" ) ;
3337 ifnoCol.attach( tmpt, "IFNO" ) ;
3338 for ( uInt irow=0 ; irow < rows ; irow++ ) {
3339 scannoCol.put( irow, 0 ) ;
3340 uInt freqID = freqIDCol( irow ) ;
3341 vector<uInt>::iterator iter = find( freqid[newtableids[itable]].begin(), freqid[newtableids[itable]].end(), freqID ) ;
3342 if ( iter != freqid[newtableids[itable]].end() ) {
3343 uInt index = distance( freqid[newtableids[itable]].begin(), iter ) ;
3344 ifnoCol.put( irow, groups[newtableids[itable]][index][newifids[itable]] ) ;
3345 }
3346 else {
3347 throw(AipsError("IF grouping was wrong in additional tables.")) ;
3348 }
3349 }
3350 }
3351 oldinfo.resize( insize ) ;
3352 setInsitu( oldInsitu ) ;
3353
3354 // temporarily set coordinfo
3355 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3356 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3357 oldinfo[itable] = coordinfo[0] ;
3358 coordinfo[0] = "Hz" ;
3359 newin[itable]->setCoordInfo( coordinfo ) ;
3360 }
3361
3362 // save column values in the vector
3363 vector< vector<uInt> > freqTableIdVec( insize ) ;
3364 vector< vector<uInt> > freqIdVec( insize ) ;
3365 vector< vector<uInt> > ifNoVec( insize ) ;
3366 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3367 ScalarColumn<uInt> freqIDs ;
3368 freqIDs.attach( newin[itable]->frequencies().table(), "ID" ) ;
3369 ifnoCol.attach( newin[itable]->table(), "IFNO" ) ;
3370 freqIDCol.attach( newin[itable]->table(), "FREQ_ID" ) ;
3371 for ( uInt irow = 0 ; irow < newin[itable]->frequencies().table().nrow() ; irow++ ) {
3372 freqTableIdVec[itable].push_back( freqIDs( irow ) ) ;
3373 }
3374 for ( uInt irow = 0 ; irow < newin[itable]->table().nrow() ; irow++ ) {
3375 freqIdVec[itable].push_back( freqIDCol( irow ) ) ;
3376 ifNoVec[itable].push_back( ifnoCol( irow ) ) ;
3377 }
3378 }
3379
3380 // reset spectra and flagtra: pick up common part of frequency coverage
3381 //os << "Pick common frequency range and align resolution" << LogIO::POST ;
3382 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3383 uInt rows = newin[itable]->nrow() ;
3384 int nminchan = -1 ;
3385 int nmaxchan = -1 ;
3386 vector<uInt> freqIdUpdate ;
3387 for ( uInt irow = 0 ; irow < rows ; irow++ ) {
3388 uInt ifno = ifNoVec[itable][irow] ; // IFNO is reset by group index
3389 double minfreq = ifgfreq[2*ifno] ;
3390 double maxfreq = ifgfreq[2*ifno+1] ;
3391 //os << "frequency range: [" << minfreq << "," << maxfreq << "]" << LogIO::POST ;
3392 vector<double> abcissa = newin[itable]->getAbcissa( irow ) ;
3393 int nchan = abcissa.size() ;
3394 double resol = abcissa[1] - abcissa[0] ;
3395 //os << "abcissa range : [" << abcissa[0] << "," << abcissa[nchan-1] << "]" << LogIO::POST ;
3396 if ( minfreq <= abcissa[0] )
3397 nminchan = 0 ;
3398 else {
3399 //double cfreq = ( minfreq - abcissa[0] ) / resol ;
3400 double cfreq = ( minfreq - abcissa[0] + 0.5 * resol ) / resol ;
3401 nminchan = int(cfreq) + ( ( cfreq - int(cfreq) <= 0.5 ) ? 0 : 1 ) ;
3402 }
3403 if ( maxfreq >= abcissa[abcissa.size()-1] )
3404 nmaxchan = abcissa.size() - 1 ;
3405 else {
3406 //double cfreq = ( abcissa[abcissa.size()-1] - maxfreq ) / resol ;
3407 double cfreq = ( abcissa[abcissa.size()-1] - maxfreq + 0.5 * resol ) / resol ;
3408 nmaxchan = abcissa.size() - 1 - int(cfreq) - ( ( cfreq - int(cfreq) >= 0.5 ) ? 1 : 0 ) ;
3409 }
3410 //os << "channel range (" << irow << "): [" << nminchan << "," << nmaxchan << "]" << LogIO::POST ;
3411 if ( nmaxchan > nminchan ) {
3412 newin[itable]->reshapeSpectrum( nminchan, nmaxchan, irow ) ;
3413 int newchan = nmaxchan - nminchan + 1 ;
3414 if ( count( freqIdUpdate.begin(), freqIdUpdate.end(), freqIdVec[itable][irow] ) == 0 && newchan < nchan )
3415 freqIdUpdate.push_back( freqIdVec[itable][irow] ) ;
3416 }
3417 else {
3418 throw(AipsError("Failed to pick up common part of frequency range.")) ;
3419 }
3420 }
3421 for ( uInt i = 0 ; i < freqIdUpdate.size() ; i++ ) {
3422 uInt freqId = freqIdUpdate[i] ;
3423 Double refpix ;
3424 Double refval ;
3425 Double increment ;
3426
3427 // update row
3428 newin[itable]->frequencies().getEntry( refpix, refval, increment, freqId ) ;
3429 refval = refval - ( refpix - nminchan ) * increment ;
3430 refpix = 0 ;
3431 newin[itable]->frequencies().setEntry( refpix, refval, increment, freqId ) ;
3432 }
3433 }
3434
3435
3436 // reset spectra and flagtra: align spectral resolution
3437 //os << "Align spectral resolution" << LogIO::POST ;
3438 // gmaxdnu: the coarsest frequency resolution in the frequency group
3439 // gmemid: member index that have a resolution equal to gmaxdnu
3440 // gmaxdnu[numfreqgrp]
3441 // gmaxdnu: [dnu0, dnu1, ...]
3442 // gmemid[numfreqgrp]
3443 // gmemid: [id0, id1, ...]
3444 vector<double> gmaxdnu( freqgrp.size(), 0.0 ) ;
3445 vector<uInt> gmemid( freqgrp.size(), 0 ) ;
3446 for ( uInt igrp = 0 ; igrp < ifgrp.size() ; igrp++ ) {
3447 double maxdnu = 0.0 ; // maximum (coarsest) frequency resolution
3448 int minchan = INT_MAX ; // minimum channel number
3449 Double refpixref = -1 ; // reference of 'reference pixel'
3450 Double refvalref = -1 ; // reference of 'reference frequency'
3451 Double refinc = -1 ; // reference frequency resolution
3452 uInt refreqid ;
3453 uInt reftable = INT_MAX;
3454 // process only if group member > 1
3455 if ( ifgrp[igrp].size() > 2 ) {
3456 // find minchan and maxdnu in each group
3457 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3458 uInt tableid = ifgrp[igrp][2*imem] ;
3459 uInt rowid = ifgrp[igrp][2*imem+1] ;
3460 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3461 if ( iter != freqIdVec[tableid].end() ) {
3462 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3463 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3464 int nchan = abcissa.size() ;
3465 double dnu = abcissa[1] - abcissa[0] ;
3466 //os << "GROUP " << igrp << " (" << tableid << "," << rowid << "): nchan = " << nchan << " (minchan = " << minchan << ")" << LogIO::POST ;
3467 if ( nchan < minchan ) {
3468 minchan = nchan ;
3469 maxdnu = dnu ;
3470 newin[tableid]->frequencies().getEntry( refpixref, refvalref, refinc, rowid ) ;
3471 refreqid = rowid ;
3472 reftable = tableid ;
3473 }
3474 }
3475 }
3476 // regrid spectra in each group
3477 os << "GROUP " << igrp << endl ;
3478 os << " Channel number is adjusted to " << minchan << endl ;
3479 os << " Corresponding frequency resolution is " << maxdnu << "Hz" << LogIO::POST ;
3480 for ( uInt imem = 0 ; imem < ifgrp[igrp].size()/2 ; imem++ ) {
3481 uInt tableid = ifgrp[igrp][2*imem] ;
3482 uInt rowid = ifgrp[igrp][2*imem+1] ;
3483 freqIDCol.attach( newin[tableid]->table(), "FREQ_ID" ) ;
3484 //os << "tableid = " << tableid << " rowid = " << rowid << ": " << LogIO::POST ;
3485 //os << " regridChannel applied to " ;
3486 //if ( tableid != reftable )
3487 refreqid = newin[tableid]->frequencies().addEntry( refpixref, refvalref, refinc ) ;
3488 for ( uInt irow = 0 ; irow < newin[tableid]->table().nrow() ; irow++ ) {
3489 uInt tfreqid = freqIdVec[tableid][irow] ;
3490 if ( tfreqid == rowid ) {
3491 //os << irow << " " ;
3492 newin[tableid]->regridChannel( minchan, maxdnu, irow ) ;
3493 freqIDCol.put( irow, refreqid ) ;
3494 freqIdVec[tableid][irow] = refreqid ;
3495 }
3496 }
3497 //os << LogIO::POST ;
3498 }
3499 }
3500 else {
3501 uInt tableid = ifgrp[igrp][0] ;
3502 uInt rowid = ifgrp[igrp][1] ;
3503 vector<uInt>::iterator iter = find( freqIdVec[tableid].begin(), freqIdVec[tableid].end(), rowid ) ;
3504 if ( iter != freqIdVec[tableid].end() ) {
3505 uInt index = distance( freqIdVec[tableid].begin(), iter ) ;
3506 vector<double> abcissa = newin[tableid]->getAbcissa( index ) ;
3507 minchan = abcissa.size() ;
3508 maxdnu = abcissa[1] - abcissa[0] ;
3509 }
3510 }
3511 for ( uInt i = 0 ; i < freqgrp.size() ; i++ ) {
3512 if ( count( freqgrp[i].begin(), freqgrp[i].end(), igrp ) > 0 ) {
3513 if ( maxdnu > gmaxdnu[i] ) {
3514 gmaxdnu[i] = maxdnu ;
3515 gmemid[i] = igrp ;
3516 }
3517 break ;
3518 }
3519 }
3520 }
3521
3522 // set back coordinfo
3523 for ( uInt itable = 0 ; itable < insize ; itable++ ) {
3524 vector<string> coordinfo = newin[itable]->getCoordInfo() ;
3525 coordinfo[0] = oldinfo[itable] ;
3526 newin[itable]->setCoordInfo( coordinfo ) ;
3527 }
3528
3529 // accumulate all rows into the first table
3530 // NOTE: assumed in.size() = 1
3531 vector< CountedPtr<Scantable> > tmp( 1 ) ;
3532 if ( newin.size() == 1 )
3533 tmp[0] = newin[0] ;
3534 else
3535 tmp[0] = merge( newin ) ;
3536
3537 //return tmp[0] ;
3538
3539 // average
3540 CountedPtr<Scantable> tmpout = average( tmp, mask, weight, avmode ) ;
3541
3542 //return tmpout ;
3543
3544 // combine frequency group
3545 os << "Combine spectra based on frequency grouping" << LogIO::POST ;
3546 os << "IFNO is renumbered as frequency group ID (see above)" << LogIO::POST ;
3547 vector<string> coordinfo = tmpout->getCoordInfo() ;
3548 oldinfo[0] = coordinfo[0] ;
3549 coordinfo[0] = "Hz" ;
3550 tmpout->setCoordInfo( coordinfo ) ;
3551 // create proformas of output table
3552 stringstream taqlstream ;
3553 taqlstream << "SELECT FROM $1 WHERE IFNO IN [" ;
3554 for ( uInt i = 0 ; i < gmemid.size() ; i++ ) {
3555 taqlstream << gmemid[i] ;
3556 if ( i < gmemid.size() - 1 )
3557 taqlstream << "," ;
3558 else
3559 taqlstream << "]" ;
3560 }
3561 string taql = taqlstream.str() ;
3562 //os << "taql = " << taql << LogIO::POST ;
3563 STSelector selector = STSelector() ;
3564 selector.setTaQL( taql ) ;
3565 oldInsitu = insitu_ ;
3566 setInsitu( false ) ;
3567 out = getScantable( tmpout, false ) ;
3568 setInsitu( oldInsitu ) ;
3569 out->setSelection( selector ) ;
3570 // regrid rows
3571 ifnoCol.attach( tmpout->table(), "IFNO" ) ;
3572 for ( uInt irow = 0 ; irow < tmpout->table().nrow() ; irow++ ) {
3573 uInt ifno = ifnoCol( irow ) ;
3574 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3575 if ( count( freqgrp[igrp].begin(), freqgrp[igrp].end(), ifno ) > 0 ) {
3576 vector<double> abcissa = tmpout->getAbcissa( irow ) ;
3577 double bw = ( abcissa[1] - abcissa[0] ) * abcissa.size() ;
3578 int nchan = (int)( bw / gmaxdnu[igrp] ) ;
3579 tmpout->regridChannel( nchan, gmaxdnu[igrp], irow ) ;
3580 break ;
3581 }
3582 }
3583 }
3584 // combine spectra
3585 ArrayColumn<Float> specColOut ;
3586 specColOut.attach( out->table(), "SPECTRA" ) ;
3587 ArrayColumn<uChar> flagColOut ;
3588 flagColOut.attach( out->table(), "FLAGTRA" ) ;
3589 ScalarColumn<uInt> ifnoColOut ;
3590 ifnoColOut.attach( out->table(), "IFNO" ) ;
3591 ScalarColumn<uInt> polnoColOut ;
3592 polnoColOut.attach( out->table(), "POLNO" ) ;
3593 ScalarColumn<uInt> freqidColOut ;
3594 freqidColOut.attach( out->table(), "FREQ_ID" ) ;
3595// MDirection::ScalarColumn dirColOut ;
3596// dirColOut.attach( out->table(), "DIRECTION" ) ;
3597 Table &tab = tmpout->table() ;
3598 Block<String> cols(1);
3599 cols[0] = String("POLNO") ;
3600 TableIterator iter( tab, cols ) ;
3601 bool done = false ;
3602 vector< vector<uInt> > sizes( freqgrp.size() ) ;
3603 while( !iter.pastEnd() ) {
3604 vector< vector<Float> > specout( freqgrp.size() ) ;
3605 vector< vector<uChar> > flagout( freqgrp.size() ) ;
3606 ArrayColumn<Float> specCols ;
3607 specCols.attach( iter.table(), "SPECTRA" ) ;
3608 ArrayColumn<uChar> flagCols ;
3609 flagCols.attach( iter.table(), "FLAGTRA" ) ;
3610 ifnoCol.attach( iter.table(), "IFNO" ) ;
3611 ScalarColumn<uInt> polnos ;
3612 polnos.attach( iter.table(), "POLNO" ) ;
3613// MDirection::ScalarColumn dircol ;
3614// dircol.attach( iter.table(), "DIRECTION" ) ;
3615 uInt polno = polnos( 0 ) ;
3616 //os << "POLNO iteration: " << polno << LogIO::POST ;
3617// for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3618// sizes[igrp].resize( freqgrp[igrp].size() ) ;
3619// for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3620// for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3621// uInt ifno = ifnoCol( irow ) ;
3622// if ( ifno == freqgrp[igrp][imem] ) {
3623// Vector<Float> spec = specCols( irow ) ;
3624// Vector<uChar> flag = flagCols( irow ) ;
3625// vector<Float> svec ;
3626// spec.tovector( svec ) ;
3627// vector<uChar> fvec ;
3628// flag.tovector( fvec ) ;
3629// //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3630// specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3631// flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3632// //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3633// sizes[igrp][imem] = spec.nelements() ;
3634// }
3635// }
3636// }
3637// for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3638// uInt ifout = ifnoColOut( irow ) ;
3639// uInt polout = polnoColOut( irow ) ;
3640// if ( ifout == gmemid[igrp] && polout == polno ) {
3641// // set SPECTRA and FRAGTRA
3642// Vector<Float> newspec( specout[igrp] ) ;
3643// Vector<uChar> newflag( flagout[igrp] ) ;
3644// specColOut.put( irow, newspec ) ;
3645// flagColOut.put( irow, newflag ) ;
3646// // IFNO renumbering
3647// ifnoColOut.put( irow, igrp ) ;
3648// }
3649// }
3650// }
3651 // get a list of number of channels for each frequency group member
3652 if ( !done ) {
3653 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3654 sizes[igrp].resize( freqgrp[igrp].size() ) ;
3655 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3656 for ( uInt irow = 0 ; irow < iter.table().nrow() ; irow++ ) {
3657 uInt ifno = ifnoCol( irow ) ;
3658 if ( ifno == freqgrp[igrp][imem] ) {
3659 Vector<Float> spec = specCols( irow ) ;
3660 sizes[igrp][imem] = spec.nelements() ;
3661 break ;
3662 }
3663 }
3664 }
3665 }
3666 done = true ;
3667 }
3668 // combine spectra
3669 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3670 uInt polout = polnoColOut( irow ) ;
3671 if ( polout == polno ) {
3672 uInt ifout = ifnoColOut( irow ) ;
3673// Vector<Double> direction = dirColOut(irow).getAngle(Unit(String("rad"))).getValue() ;
3674 uInt igrp ;
3675 for ( uInt jgrp = 0 ; jgrp < freqgrp.size() ; jgrp++ ) {
3676 if ( ifout == gmemid[jgrp] ) {
3677 igrp = jgrp ;
3678 break ;
3679 }
3680 }
3681 for ( uInt imem = 0 ; imem < freqgrp[igrp].size() ; imem++ ) {
3682 for ( uInt jrow = 0 ; jrow < iter.table().nrow() ; jrow++ ) {
3683 uInt ifno = ifnoCol( jrow ) ;
3684 // 2012/02/17 TN
3685 // Since STGrid is implemented, average doesn't consider direction
3686 // when accumulating
3687// Vector<Double> tdir = dircol(jrow).getAngle(Unit(String("rad"))).getValue() ;
3688// //if ( ifno == freqgrp[igrp][imem] && allTrue( tdir == direction ) ) {
3689// Double dx = tdir[0] - direction[0] ;
3690// Double dy = tdir[1] - direction[1] ;
3691// Double dd = sqrt( dx * dx + dy * dy ) ;
3692 //if ( ifno == freqgrp[igrp][imem] && allNearAbs( tdir, direction, tol ) ) {
3693// if ( ifno == freqgrp[igrp][imem] && dd <= tol ) {
3694 if ( ifno == freqgrp[igrp][imem] ) {
3695 Vector<Float> spec = specCols( jrow ) ;
3696 Vector<uChar> flag = flagCols( jrow ) ;
3697 vector<Float> svec ;
3698 spec.tovector( svec ) ;
3699 vector<uChar> fvec ;
3700 flag.tovector( fvec ) ;
3701 //os << "spec.size() = " << svec.size() << " fvec.size() = " << fvec.size() << LogIO::POST ;
3702 specout[igrp].insert( specout[igrp].end(), svec.begin(), svec.end() ) ;
3703 flagout[igrp].insert( flagout[igrp].end(), fvec.begin(), fvec.end() ) ;
3704 //os << "specout[" << igrp << "].size() = " << specout[igrp].size() << LogIO::POST ;
3705 }
3706 }
3707 }
3708 // set SPECTRA and FRAGTRA
3709 Vector<Float> newspec( specout[igrp] ) ;
3710 Vector<uChar> newflag( flagout[igrp] ) ;
3711 specColOut.put( irow, newspec ) ;
3712 flagColOut.put( irow, newflag ) ;
3713 // IFNO renumbering
3714 ifnoColOut.put( irow, igrp ) ;
3715 }
3716 }
3717 iter++ ;
3718 }
3719 // update FREQUENCIES subtable
3720 vector<bool> updated( freqgrp.size(), false ) ;
3721 for ( uInt igrp = 0 ; igrp < freqgrp.size() ; igrp++ ) {
3722 uInt index = 0 ;
3723 uInt pixShift = 0 ;
3724 while ( freqgrp[igrp][index] != gmemid[igrp] ) {
3725 pixShift += sizes[igrp][index++] ;
3726 }
3727 for ( uInt irow = 0 ; irow < out->table().nrow() ; irow++ ) {
3728 if ( ifnoColOut( irow ) == gmemid[igrp] && !updated[igrp] ) {
3729 uInt freqidOut = freqidColOut( irow ) ;
3730 //os << "freqgrp " << igrp << " freqidOut = " << freqidOut << LogIO::POST ;
3731 double refpix ;
3732 double refval ;
3733 double increm ;
3734 out->frequencies().getEntry( refpix, refval, increm, freqidOut ) ;
3735 refpix += pixShift ;
3736 out->frequencies().setEntry( refpix, refval, increm, freqidOut ) ;
3737 updated[igrp] = true ;
3738 }
3739 }
3740 }
3741
3742 //out = tmpout ;
3743
3744 coordinfo = tmpout->getCoordInfo() ;
3745 coordinfo[0] = oldinfo[0] ;
3746 tmpout->setCoordInfo( coordinfo ) ;
3747 }
3748 else {
3749 // simple average
3750 out = average( in, mask, weight, avmode ) ;
3751 }
3752
3753 return out;
3754}
3755
3756CountedPtr<Scantable> STMath::cwcal( const CountedPtr<Scantable>& s,
3757 const String calmode,
3758 const String antname )
3759{
3760 // frequency switch
3761 if ( calmode == "fs" ) {
3762 return cwcalfs( s, antname ) ;
3763 }
3764 else {
3765 vector<bool> masks = s->getMask( 0 ) ;
3766 vector<int> types ;
3767
3768 // sky scan
3769 STSelector sel = STSelector() ;
3770 types.push_back( SrcType::SKY ) ;
3771 sel.setTypes( types ) ;
3772 s->setSelection( sel ) ;
3773 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3774 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
3775 s->unsetSelection() ;
3776 sel.reset() ;
3777 types.clear() ;
3778
3779 // hot scan
3780 types.push_back( SrcType::HOT ) ;
3781 sel.setTypes( types ) ;
3782 s->setSelection( sel ) ;
3783 tmp.clear() ;
3784 tmp.push_back( getScantable( s, false ) ) ;
3785 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
3786 s->unsetSelection() ;
3787 sel.reset() ;
3788 types.clear() ;
3789
3790 // cold scan
3791 CountedPtr<Scantable> acold ;
3792// types.push_back( SrcType::COLD ) ;
3793// sel.setTypes( types ) ;
3794// s->setSelection( sel ) ;
3795// tmp.clear() ;
3796// tmp.push_back( getScantable( s, false ) ) ;
3797// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCNAN" ) ;
3798// s->unsetSelection() ;
3799// sel.reset() ;
3800// types.clear() ;
3801
3802 // off scan
3803 types.push_back( SrcType::PSOFF ) ;
3804 sel.setTypes( types ) ;
3805 s->setSelection( sel ) ;
3806 tmp.clear() ;
3807 tmp.push_back( getScantable( s, false ) ) ;
3808 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
3809 s->unsetSelection() ;
3810 sel.reset() ;
3811 types.clear() ;
3812
3813 // on scan
3814 bool insitu = insitu_ ;
3815 insitu_ = false ;
3816 CountedPtr<Scantable> out = getScantable( s, true ) ;
3817 insitu_ = insitu ;
3818 types.push_back( SrcType::PSON ) ;
3819 sel.setTypes( types ) ;
3820 s->setSelection( sel ) ;
3821 TableCopy::copyRows( out->table(), s->table() ) ;
3822 s->unsetSelection() ;
3823 sel.reset() ;
3824 types.clear() ;
3825
3826 // process each on scan
3827 ArrayColumn<Float> tsysCol ;
3828 tsysCol.attach( out->table(), "TSYS" ) ;
3829 for ( int i = 0 ; i < out->nrow() ; i++ ) {
3830 vector<float> sp = getCalibratedSpectra( out, aoff, asky, ahot, acold, i, antname ) ;
3831 out->setSpectrum( sp, i ) ;
3832 string reftime = out->getTime( i ) ;
3833 vector<int> ii( 1, out->getIF( i ) ) ;
3834 vector<int> ib( 1, out->getBeam( i ) ) ;
3835 vector<int> ip( 1, out->getPol( i ) ) ;
3836 sel.setIFs( ii ) ;
3837 sel.setBeams( ib ) ;
3838 sel.setPolarizations( ip ) ;
3839 asky->setSelection( sel ) ;
3840 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
3841 const Vector<Float> Vtsys( sptsys ) ;
3842 tsysCol.put( i, Vtsys ) ;
3843 asky->unsetSelection() ;
3844 sel.reset() ;
3845 }
3846
3847 // flux unit
3848 out->setFluxUnit( "K" ) ;
3849
3850 return out ;
3851 }
3852}
3853
3854CountedPtr<Scantable> STMath::almacal( const CountedPtr<Scantable>& s,
3855 const String calmode )
3856{
3857 // frequency switch
3858 if ( calmode == "fs" ) {
3859 return almacalfs( s ) ;
3860 }
3861 else {
3862 vector<bool> masks = s->getMask( 0 ) ;
3863
3864 // off scan
3865 STSelector sel = STSelector() ;
3866 vector<int> types ;
3867 types.push_back( SrcType::PSOFF ) ;
3868 sel.setTypes( types ) ;
3869 s->setSelection( sel ) ;
3870 // TODO 2010/01/08 TN
3871 // Grouping by time should be needed before averaging.
3872 // Each group must have own unique SCANNO (should be renumbered).
3873 // See PIPELINE/SDCalibration.py
3874 CountedPtr<Scantable> soff = getScantable( s, false ) ;
3875 Table ttab = soff->table() ;
3876 ROScalarColumn<Double> timeCol( ttab, "TIME" ) ;
3877 uInt nrow = timeCol.nrow() ;
3878 Vector<Double> timeSep( nrow - 1 ) ;
3879 for ( uInt i = 0 ; i < nrow - 1 ; i++ ) {
3880 timeSep[i] = timeCol(i+1) - timeCol(i) ;
3881 }
3882 ScalarColumn<Double> intervalCol( ttab, "INTERVAL" ) ;
3883 Vector<Double> interval = intervalCol.getColumn() ;
3884 interval /= 86400.0 ;
3885 ScalarColumn<uInt> scanCol( ttab, "SCANNO" ) ;
3886 vector<uInt> glist ;
3887 for ( uInt i = 0 ; i < nrow - 1 ; i++ ) {
3888 double gap = 2.0 * timeSep[i] / ( interval[i] + interval[i+1] ) ;
3889 //cout << "gap[" << i << "]=" << setw(5) << gap << endl ;
3890 if ( gap > 1.1 ) {
3891 glist.push_back( i ) ;
3892 }
3893 }
3894 Vector<uInt> gaplist( glist ) ;
3895 //cout << "gaplist = " << gaplist << endl ;
3896 uInt newid = 0 ;
3897 for ( uInt i = 0 ; i < nrow ; i++ ) {
3898 scanCol.put( i, newid ) ;
3899 if ( i == gaplist[newid] ) {
3900 newid++ ;
3901 }
3902 }
3903 //cout << "new scancol = " << scanCol.getColumn() << endl ;
3904 vector< CountedPtr<Scantable> > tmp( 1, soff ) ;
3905 CountedPtr<Scantable> aoff = average( tmp, masks, "TINT", "SCAN" ) ;
3906 //cout << "aoff.nrow = " << aoff->nrow() << endl ;
3907 s->unsetSelection() ;
3908 sel.reset() ;
3909 types.clear() ;
3910
3911 // on scan
3912 bool insitu = insitu_ ;
3913 insitu_ = false ;
3914 CountedPtr<Scantable> out = getScantable( s, true ) ;
3915 insitu_ = insitu ;
3916 types.push_back( SrcType::PSON ) ;
3917 sel.setTypes( types ) ;
3918 s->setSelection( sel ) ;
3919 TableCopy::copyRows( out->table(), s->table() ) ;
3920 s->unsetSelection() ;
3921 sel.reset() ;
3922 types.clear() ;
3923
3924 // process each on scan
3925 ArrayColumn<Float> tsysCol ;
3926 tsysCol.attach( out->table(), "TSYS" ) ;
3927 for ( int i = 0 ; i < out->nrow() ; i++ ) {
3928 vector<float> sp = getCalibratedSpectra( out, aoff, i ) ;
3929 out->setSpectrum( sp, i ) ;
3930 }
3931
3932 // flux unit
3933 out->setFluxUnit( "K" ) ;
3934
3935 return out ;
3936 }
3937}
3938
3939CountedPtr<Scantable> STMath::cwcalfs( const CountedPtr<Scantable>& s,
3940 const String antname )
3941{
3942 vector<int> types ;
3943
3944 // APEX calibration mode
3945 int apexcalmode = 1 ;
3946
3947 if ( antname.find( "APEX" ) != string::npos ) {
3948 // check if off scan exists or not
3949 STSelector sel = STSelector() ;
3950 //sel.setName( offstr1 ) ;
3951 types.push_back( SrcType::FLOOFF ) ;
3952 sel.setTypes( types ) ;
3953 try {
3954 s->setSelection( sel ) ;
3955 }
3956 catch ( AipsError &e ) {
3957 apexcalmode = 0 ;
3958 }
3959 sel.reset() ;
3960 }
3961 s->unsetSelection() ;
3962 types.clear() ;
3963
3964 vector<bool> masks = s->getMask( 0 ) ;
3965 CountedPtr<Scantable> ssig, sref ;
3966 CountedPtr<Scantable> out ;
3967
3968 if ( antname.find( "APEX" ) != string::npos ) {
3969 // APEX calibration
3970 // sky scan
3971 STSelector sel = STSelector() ;
3972 types.push_back( SrcType::FLOSKY ) ;
3973 sel.setTypes( types ) ;
3974 s->setSelection( sel ) ;
3975 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
3976 CountedPtr<Scantable> askylo = average( tmp, masks, "TINT", "SCAN" ) ;
3977 s->unsetSelection() ;
3978 sel.reset() ;
3979 types.clear() ;
3980 types.push_back( SrcType::FHISKY ) ;
3981 sel.setTypes( types ) ;
3982 s->setSelection( sel ) ;
3983 tmp.clear() ;
3984 tmp.push_back( getScantable( s, false ) ) ;
3985 CountedPtr<Scantable> askyhi = average( tmp, masks, "TINT", "SCAN" ) ;
3986 s->unsetSelection() ;
3987 sel.reset() ;
3988 types.clear() ;
3989
3990 // hot scan
3991 types.push_back( SrcType::FLOHOT ) ;
3992 sel.setTypes( types ) ;
3993 s->setSelection( sel ) ;
3994 tmp.clear() ;
3995 tmp.push_back( getScantable( s, false ) ) ;
3996 CountedPtr<Scantable> ahotlo = average( tmp, masks, "TINT", "SCAN" ) ;
3997 s->unsetSelection() ;
3998 sel.reset() ;
3999 types.clear() ;
4000 types.push_back( SrcType::FHIHOT ) ;
4001 sel.setTypes( types ) ;
4002 s->setSelection( sel ) ;
4003 tmp.clear() ;
4004 tmp.push_back( getScantable( s, false ) ) ;
4005 CountedPtr<Scantable> ahothi = average( tmp, masks, "TINT", "SCAN" ) ;
4006 s->unsetSelection() ;
4007 sel.reset() ;
4008 types.clear() ;
4009
4010 // cold scan
4011 CountedPtr<Scantable> acoldlo, acoldhi ;
4012// types.push_back( SrcType::FLOCOLD ) ;
4013// sel.setTypes( types ) ;
4014// s->setSelection( sel ) ;
4015// tmp.clear() ;
4016// tmp.push_back( getScantable( s, false ) ) ;
4017// CountedPtr<Scantable> acoldlo = average( tmp, masks, "TINT", "SCAN" ) ;
4018// s->unsetSelection() ;
4019// sel.reset() ;
4020// types.clear() ;
4021// types.push_back( SrcType::FHICOLD ) ;
4022// sel.setTypes( types ) ;
4023// s->setSelection( sel ) ;
4024// tmp.clear() ;
4025// tmp.push_back( getScantable( s, false ) ) ;
4026// CountedPtr<Scantable> acoldhi = average( tmp, masks, "TINT", "SCAN" ) ;
4027// s->unsetSelection() ;
4028// sel.reset() ;
4029// types.clear() ;
4030
4031 // ref scan
4032 bool insitu = insitu_ ;
4033 insitu_ = false ;
4034 sref = getScantable( s, true ) ;
4035 insitu_ = insitu ;
4036 types.push_back( SrcType::FSLO ) ;
4037 sel.setTypes( types ) ;
4038 s->setSelection( sel ) ;
4039 TableCopy::copyRows( sref->table(), s->table() ) ;
4040 s->unsetSelection() ;
4041 sel.reset() ;
4042 types.clear() ;
4043
4044 // sig scan
4045 insitu_ = false ;
4046 ssig = getScantable( s, true ) ;
4047 insitu_ = insitu ;
4048 types.push_back( SrcType::FSHI ) ;
4049 sel.setTypes( types ) ;
4050 s->setSelection( sel ) ;
4051 TableCopy::copyRows( ssig->table(), s->table() ) ;
4052 s->unsetSelection() ;
4053 sel.reset() ;
4054 types.clear() ;
4055
4056 if ( apexcalmode == 0 ) {
4057 // APEX fs data without off scan
4058 // process each sig and ref scan
4059 ArrayColumn<Float> tsysCollo ;
4060 tsysCollo.attach( ssig->table(), "TSYS" ) ;
4061 ArrayColumn<Float> tsysColhi ;
4062 tsysColhi.attach( sref->table(), "TSYS" ) ;
4063 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4064 vector< CountedPtr<Scantable> > sky( 2 ) ;
4065 sky[0] = askylo ;
4066 sky[1] = askyhi ;
4067 vector< CountedPtr<Scantable> > hot( 2 ) ;
4068 hot[0] = ahotlo ;
4069 hot[1] = ahothi ;
4070 vector< CountedPtr<Scantable> > cold( 2 ) ;
4071 //cold[0] = acoldlo ;
4072 //cold[1] = acoldhi ;
4073 vector<float> sp = getFSCalibratedSpectra( ssig, sref, sky, hot, cold, i ) ;
4074 ssig->setSpectrum( sp, i ) ;
4075 string reftime = ssig->getTime( i ) ;
4076 vector<int> ii( 1, ssig->getIF( i ) ) ;
4077 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4078 vector<int> ip( 1, ssig->getPol( i ) ) ;
4079 sel.setIFs( ii ) ;
4080 sel.setBeams( ib ) ;
4081 sel.setPolarizations( ip ) ;
4082 askylo->setSelection( sel ) ;
4083 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
4084 const Vector<Float> Vtsyslo( sptsys ) ;
4085 tsysCollo.put( i, Vtsyslo ) ;
4086 askylo->unsetSelection() ;
4087 sel.reset() ;
4088 sky[0] = askyhi ;
4089 sky[1] = askylo ;
4090 hot[0] = ahothi ;
4091 hot[1] = ahotlo ;
4092 cold[0] = acoldhi ;
4093 cold[1] = acoldlo ;
4094 sp = getFSCalibratedSpectra( sref, ssig, sky, hot, cold, i ) ;
4095 sref->setSpectrum( sp, i ) ;
4096 reftime = sref->getTime( i ) ;
4097 ii[0] = sref->getIF( i ) ;
4098 ib[0] = sref->getBeam( i ) ;
4099 ip[0] = sref->getPol( i ) ;
4100 sel.setIFs( ii ) ;
4101 sel.setBeams( ib ) ;
4102 sel.setPolarizations( ip ) ;
4103 askyhi->setSelection( sel ) ;
4104 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
4105 const Vector<Float> Vtsyshi( sptsys ) ;
4106 tsysColhi.put( i, Vtsyshi ) ;
4107 askyhi->unsetSelection() ;
4108 sel.reset() ;
4109 }
4110 }
4111 else if ( apexcalmode == 1 ) {
4112 // APEX fs data with off scan
4113 // off scan
4114 types.push_back( SrcType::FLOOFF ) ;
4115 sel.setTypes( types ) ;
4116 s->setSelection( sel ) ;
4117 tmp.clear() ;
4118 tmp.push_back( getScantable( s, false ) ) ;
4119 CountedPtr<Scantable> aofflo = average( tmp, masks, "TINT", "SCAN" ) ;
4120 s->unsetSelection() ;
4121 sel.reset() ;
4122 types.clear() ;
4123 types.push_back( SrcType::FHIOFF ) ;
4124 sel.setTypes( types ) ;
4125 s->setSelection( sel ) ;
4126 tmp.clear() ;
4127 tmp.push_back( getScantable( s, false ) ) ;
4128 CountedPtr<Scantable> aoffhi = average( tmp, masks, "TINT", "SCAN" ) ;
4129 s->unsetSelection() ;
4130 sel.reset() ;
4131 types.clear() ;
4132
4133 // process each sig and ref scan
4134 ArrayColumn<Float> tsysCollo ;
4135 tsysCollo.attach( ssig->table(), "TSYS" ) ;
4136 ArrayColumn<Float> tsysColhi ;
4137 tsysColhi.attach( sref->table(), "TSYS" ) ;
4138 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4139 vector<float> sp = getCalibratedSpectra( ssig, aofflo, askylo, ahotlo, acoldlo, i, antname ) ;
4140 ssig->setSpectrum( sp, i ) ;
4141 sp = getCalibratedSpectra( sref, aoffhi, askyhi, ahothi, acoldhi, i, antname ) ;
4142 string reftime = ssig->getTime( i ) ;
4143 vector<int> ii( 1, ssig->getIF( i ) ) ;
4144 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4145 vector<int> ip( 1, ssig->getPol( i ) ) ;
4146 sel.setIFs( ii ) ;
4147 sel.setBeams( ib ) ;
4148 sel.setPolarizations( ip ) ;
4149 askylo->setSelection( sel ) ;
4150 vector<float> sptsys = getTsysFromTime( reftime, askylo, "linear" ) ;
4151 const Vector<Float> Vtsyslo( sptsys ) ;
4152 tsysCollo.put( i, Vtsyslo ) ;
4153 askylo->unsetSelection() ;
4154 sel.reset() ;
4155 sref->setSpectrum( sp, i ) ;
4156 reftime = sref->getTime( i ) ;
4157 ii[0] = sref->getIF( i ) ;
4158 ib[0] = sref->getBeam( i ) ;
4159 ip[0] = sref->getPol( i ) ;
4160 sel.setIFs( ii ) ;
4161 sel.setBeams( ib ) ;
4162 sel.setPolarizations( ip ) ;
4163 askyhi->setSelection( sel ) ;
4164 sptsys = getTsysFromTime( reftime, askyhi, "linear" ) ;
4165 const Vector<Float> Vtsyshi( sptsys ) ;
4166 tsysColhi.put( i, Vtsyshi ) ;
4167 askyhi->unsetSelection() ;
4168 sel.reset() ;
4169 }
4170 }
4171 }
4172 else {
4173 // non-APEX fs data
4174 // sky scan
4175 STSelector sel = STSelector() ;
4176 types.push_back( SrcType::SKY ) ;
4177 sel.setTypes( types ) ;
4178 s->setSelection( sel ) ;
4179 vector< CountedPtr<Scantable> > tmp( 1, getScantable( s, false ) ) ;
4180 CountedPtr<Scantable> asky = average( tmp, masks, "TINT", "SCAN" ) ;
4181 s->unsetSelection() ;
4182 sel.reset() ;
4183 types.clear() ;
4184
4185 // hot scan
4186 types.push_back( SrcType::HOT ) ;
4187 sel.setTypes( types ) ;
4188 s->setSelection( sel ) ;
4189 tmp.clear() ;
4190 tmp.push_back( getScantable( s, false ) ) ;
4191 CountedPtr<Scantable> ahot = average( tmp, masks, "TINT", "SCAN" ) ;
4192 s->unsetSelection() ;
4193 sel.reset() ;
4194 types.clear() ;
4195
4196 // cold scan
4197 CountedPtr<Scantable> acold ;
4198// types.push_back( SrcType::COLD ) ;
4199// sel.setTypes( types ) ;
4200// s->setSelection( sel ) ;
4201// tmp.clear() ;
4202// tmp.push_back( getScantable( s, false ) ) ;
4203// CountedPtr<Scantable> acold = average( tmp, masks, "TINT", "SCAN" ) ;
4204// s->unsetSelection() ;
4205// sel.reset() ;
4206// types.clear() ;
4207
4208 // ref scan
4209 bool insitu = insitu_ ;
4210 insitu_ = false ;
4211 sref = getScantable( s, true ) ;
4212 insitu_ = insitu ;
4213 types.push_back( SrcType::FSOFF ) ;
4214 sel.setTypes( types ) ;
4215 s->setSelection( sel ) ;
4216 TableCopy::copyRows( sref->table(), s->table() ) ;
4217 s->unsetSelection() ;
4218 sel.reset() ;
4219 types.clear() ;
4220
4221 // sig scan
4222 insitu_ = false ;
4223 ssig = getScantable( s, true ) ;
4224 insitu_ = insitu ;
4225 types.push_back( SrcType::FSON ) ;
4226 sel.setTypes( types ) ;
4227 s->setSelection( sel ) ;
4228 TableCopy::copyRows( ssig->table(), s->table() ) ;
4229 s->unsetSelection() ;
4230 sel.reset() ;
4231 types.clear() ;
4232
4233 // process each sig and ref scan
4234 ArrayColumn<Float> tsysColsig ;
4235 tsysColsig.attach( ssig->table(), "TSYS" ) ;
4236 ArrayColumn<Float> tsysColref ;
4237 tsysColref.attach( ssig->table(), "TSYS" ) ;
4238 for ( int i = 0 ; i < ssig->nrow() ; i++ ) {
4239 vector<float> sp = getFSCalibratedSpectra( ssig, sref, asky, ahot, acold, i ) ;
4240 ssig->setSpectrum( sp, i ) ;
4241 string reftime = ssig->getTime( i ) ;
4242 vector<int> ii( 1, ssig->getIF( i ) ) ;
4243 vector<int> ib( 1, ssig->getBeam( i ) ) ;
4244 vector<int> ip( 1, ssig->getPol( i ) ) ;
4245 sel.setIFs( ii ) ;
4246 sel.setBeams( ib ) ;
4247 sel.setPolarizations( ip ) ;
4248 asky->setSelection( sel ) ;
4249 vector<float> sptsys = getTsysFromTime( reftime, asky, "linear" ) ;
4250 const Vector<Float> Vtsys( sptsys ) ;
4251 tsysColsig.put( i, Vtsys ) ;
4252 asky->unsetSelection() ;
4253 sel.reset() ;
4254 sp = getFSCalibratedSpectra( sref, ssig, asky, ahot, acold, i ) ;
4255 sref->setSpectrum( sp, i ) ;
4256 tsysColref.put( i, Vtsys ) ;
4257 }
4258 }
4259
4260 // do folding if necessary
4261 Table sigtab = ssig->table() ;
4262 Table reftab = sref->table() ;
4263 ScalarColumn<uInt> sigifnoCol ;
4264 ScalarColumn<uInt> refifnoCol ;
4265 ScalarColumn<uInt> sigfidCol ;
4266 ScalarColumn<uInt> reffidCol ;
4267 Int nchan = (Int)ssig->nchan() ;
4268 sigifnoCol.attach( sigtab, "IFNO" ) ;
4269 refifnoCol.attach( reftab, "IFNO" ) ;
4270 sigfidCol.attach( sigtab, "FREQ_ID" ) ;
4271 reffidCol.attach( reftab, "FREQ_ID" ) ;
4272 Vector<uInt> sfids( sigfidCol.getColumn() ) ;
4273 Vector<uInt> rfids( reffidCol.getColumn() ) ;
4274 vector<uInt> sfids_unique ;
4275 vector<uInt> rfids_unique ;
4276 vector<uInt> sifno_unique ;
4277 vector<uInt> rifno_unique ;
4278 for ( uInt i = 0 ; i < sfids.nelements() ; i++ ) {
4279 if ( count( sfids_unique.begin(), sfids_unique.end(), sfids[i] ) == 0 ) {
4280 sfids_unique.push_back( sfids[i] ) ;
4281 sifno_unique.push_back( ssig->getIF( i ) ) ;
4282 }
4283 if ( count( rfids_unique.begin(), rfids_unique.end(), rfids[i] ) == 0 ) {
4284 rfids_unique.push_back( rfids[i] ) ;
4285 rifno_unique.push_back( sref->getIF( i ) ) ;
4286 }
4287 }
4288 double refpix_sig, refval_sig, increment_sig ;
4289 double refpix_ref, refval_ref, increment_ref ;
4290 vector< CountedPtr<Scantable> > tmp( sfids_unique.size() ) ;
4291 for ( uInt i = 0 ; i < sfids_unique.size() ; i++ ) {
4292 ssig->frequencies().getEntry( refpix_sig, refval_sig, increment_sig, sfids_unique[i] ) ;
4293 sref->frequencies().getEntry( refpix_ref, refval_ref, increment_ref, rfids_unique[i] ) ;
4294 if ( refpix_sig == refpix_ref ) {
4295 double foffset = refval_ref - refval_sig ;
4296 int choffset = static_cast<int>(foffset/increment_sig) ;
4297 double doffset = foffset / increment_sig ;
4298 if ( abs(choffset) >= nchan ) {
4299 LogIO os( LogOrigin( "STMath", "cwcalfs", WHERE ) ) ;
4300 os << "FREQ_ID=[" << sfids_unique[i] << "," << rfids_unique[i] << "]: out-band frequency switching, no folding" << LogIO::POST ;
4301 os << "Just return signal data" << LogIO::POST ;
4302 //std::vector< CountedPtr<Scantable> > tabs ;
4303 //tabs.push_back( ssig ) ;
4304 //tabs.push_back( sref ) ;
4305 //out = merge( tabs ) ;
4306 tmp[i] = ssig ;
4307 }
4308 else {
4309 STSelector sel = STSelector() ;
4310 vector<int> v( 1, sifno_unique[i] ) ;
4311 sel.setIFs( v ) ;
4312 ssig->setSelection( sel ) ;
4313 sel.reset() ;
4314 v[0] = rifno_unique[i] ;
4315 sel.setIFs( v ) ;
4316 sref->setSelection( sel ) ;
4317 sel.reset() ;
4318 if ( antname.find( "APEX" ) != string::npos ) {
4319 tmp[i] = dofold( ssig, sref, 0.5*doffset, -0.5*doffset ) ;
4320 //tmp[i] = dofold( ssig, sref, doffset ) ;
4321 }
4322 else {
4323 tmp[i] = dofold( ssig, sref, doffset ) ;
4324 }
4325 ssig->unsetSelection() ;
4326 sref->unsetSelection() ;
4327 }
4328 }
4329 }
4330
4331 if ( tmp.size() > 1 ) {
4332 out = merge( tmp ) ;
4333 }
4334 else {
4335 out = tmp[0] ;
4336 }
4337
4338 // flux unit
4339 out->setFluxUnit( "K" ) ;
4340
4341 return out ;
4342}
4343
4344CountedPtr<Scantable> STMath::almacalfs( const CountedPtr<Scantable>& s )
4345{
4346 (void) s; //currently unused
4347 CountedPtr<Scantable> out ;
4348
4349 return out ;
4350}
4351
4352vector<float> STMath::getSpectrumFromTime( string reftime,
4353 CountedPtr<Scantable>& s,
4354 string mode )
4355{
4356 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
4357 vector<float> sp ;
4358
4359 if ( s->nrow() == 0 ) {
4360 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
4361 return sp ;
4362 }
4363 else if ( s->nrow() == 1 ) {
4364 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
4365 return s->getSpectrum( 0 ) ;
4366 }
4367 else {
4368 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4369 if ( mode == "before" ) {
4370 int id = -1 ;
4371 if ( idx[0] != -1 ) {
4372 id = idx[0] ;
4373 }
4374 else if ( idx[1] != -1 ) {
4375 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4376 id = idx[1] ;
4377 }
4378 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4379 sp = s->getSpectrum( id ) ;
4380 }
4381 else if ( mode == "after" ) {
4382 int id = -1 ;
4383 if ( idx[1] != -1 ) {
4384 id = idx[1] ;
4385 }
4386 else if ( idx[0] != -1 ) {
4387 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4388 id = idx[1] ;
4389 }
4390 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4391 sp = s->getSpectrum( id ) ;
4392 }
4393 else if ( mode == "nearest" ) {
4394 int id = -1 ;
4395 if ( idx[0] == -1 ) {
4396 id = idx[1] ;
4397 }
4398 else if ( idx[1] == -1 ) {
4399 id = idx[0] ;
4400 }
4401 else if ( idx[0] == idx[1] ) {
4402 id = idx[0] ;
4403 }
4404 else {
4405 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4406 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4407 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4408 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4409 double tref = getMJD( reftime ) ;
4410 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4411 id = idx[1] ;
4412 }
4413 else {
4414 id = idx[0] ;
4415 }
4416 }
4417 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4418 sp = s->getSpectrum( id ) ;
4419 }
4420 else if ( mode == "linear" ) {
4421 if ( idx[0] == -1 ) {
4422 // use after
4423 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4424 int id = idx[1] ;
4425 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4426 sp = s->getSpectrum( id ) ;
4427 }
4428 else if ( idx[1] == -1 ) {
4429 // use before
4430 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4431 int id = idx[0] ;
4432 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4433 sp = s->getSpectrum( id ) ;
4434 }
4435 else if ( idx[0] == idx[1] ) {
4436 // use before
4437 //os << "No need to interporate." << LogIO::POST ;
4438 int id = idx[0] ;
4439 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4440 sp = s->getSpectrum( id ) ;
4441 }
4442 else {
4443 // do interpolation
4444 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4445 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4446 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4447 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4448 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4449 double tref = getMJD( reftime ) ;
4450 vector<float> sp0 = s->getSpectrum( idx[0] ) ;
4451 vector<float> sp1 = s->getSpectrum( idx[1] ) ;
4452 for ( unsigned int i = 0 ; i < sp0.size() ; i++ ) {
4453 float v = ( sp1[i] - sp0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + sp0[i] ;
4454 sp.push_back( v ) ;
4455 }
4456 }
4457 }
4458 else {
4459 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4460 }
4461 return sp ;
4462 }
4463}
4464
4465vector<float> STMath::getSpectrumFromTime( double reftime,
4466 CountedPtr<Scantable>& s,
4467 string mode )
4468{
4469 LogIO os( LogOrigin( "STMath", "getSpectrumFromTime", WHERE ) ) ;
4470 vector<float> sp ;
4471
4472 if ( s->nrow() == 0 ) {
4473 os << LogIO::SEVERE << "No spectra in the input scantable. Return empty spectrum." << LogIO::POST ;
4474 return sp ;
4475 }
4476 else if ( s->nrow() == 1 ) {
4477 //os << "use row " << 0 << " (scanno = " << s->getScan( 0 ) << ")" << LogIO::POST ;
4478 return s->getSpectrum( 0 ) ;
4479 }
4480 else {
4481 ROScalarColumn<Double> timeCol( s->table(), "TIME" ) ;
4482 Vector<Double> timeVec = timeCol.getColumn() ;
4483 vector<int> idx = getRowIdFromTime( reftime, timeVec ) ;
4484 if ( mode == "before" ) {
4485 int id = -1 ;
4486 if ( idx[0] != -1 ) {
4487 id = idx[0] ;
4488 }
4489 else if ( idx[1] != -1 ) {
4490 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4491 id = idx[1] ;
4492 }
4493 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4494 sp = s->getSpectrum( id ) ;
4495 }
4496 else if ( mode == "after" ) {
4497 int id = -1 ;
4498 if ( idx[1] != -1 ) {
4499 id = idx[1] ;
4500 }
4501 else if ( idx[0] != -1 ) {
4502 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4503 id = idx[1] ;
4504 }
4505 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4506 sp = s->getSpectrum( id ) ;
4507 }
4508 else if ( mode == "nearest" ) {
4509 int id = -1 ;
4510 if ( idx[0] == -1 ) {
4511 id = idx[1] ;
4512 }
4513 else if ( idx[1] == -1 ) {
4514 id = idx[0] ;
4515 }
4516 else if ( idx[0] == idx[1] ) {
4517 id = idx[0] ;
4518 }
4519 else {
4520 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4521 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4522// double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4523// double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4524 double t0 = timeVec[idx[0]] ;
4525 double t1 = timeVec[idx[1]] ;
4526// cout << "t0-t0c=" << t0-t0c << endl ;
4527// cout << "t1-t1c=" << t1-t1c << endl ;
4528// double tref = getMJD( reftime ) ;
4529 double tref = reftime ;
4530 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4531 id = idx[1] ;
4532 }
4533 else {
4534 id = idx[0] ;
4535 }
4536 }
4537 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4538 sp = s->getSpectrum( id ) ;
4539 }
4540 else if ( mode == "linear" ) {
4541 if ( idx[0] == -1 ) {
4542 // use after
4543 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4544 int id = idx[1] ;
4545 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4546 sp = s->getSpectrum( id ) ;
4547 }
4548 else if ( idx[1] == -1 ) {
4549 // use before
4550 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4551 int id = idx[0] ;
4552 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4553 sp = s->getSpectrum( id ) ;
4554 }
4555 else if ( idx[0] == idx[1] ) {
4556 // use before
4557 //os << "No need to interporate." << LogIO::POST ;
4558 int id = idx[0] ;
4559 //os << "use row " << id << " (scanno = " << s->getScan( id ) << ")" << LogIO::POST ;
4560 sp = s->getSpectrum( id ) ;
4561 }
4562 else {
4563 // do interpolation
4564 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4565 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4566 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4567// double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4568// double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4569 double t0 = timeVec[idx[0]] ;
4570 double t1 = timeVec[idx[1]] ;
4571// cout << "t0-t0c=" << t0-t0c << endl ;
4572// cout << "t1-t1c=" << t1-t1c << endl ;
4573// double tref = getMJD( reftime ) ;
4574 double tref = reftime ;
4575 vector<float> sp0 = s->getSpectrum( idx[0] ) ;
4576 vector<float> sp1 = s->getSpectrum( idx[1] ) ;
4577 for ( unsigned int i = 0 ; i < sp0.size() ; i++ ) {
4578 float v = ( sp1[i] - sp0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + sp0[i] ;
4579 sp.push_back( v ) ;
4580 }
4581 }
4582 }
4583 else {
4584 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4585 }
4586 return sp ;
4587 }
4588}
4589
4590double STMath::getMJD( string strtime )
4591{
4592 if ( strtime.find("/") == string::npos ) {
4593 // MJD time string
4594 return atof( strtime.c_str() ) ;
4595 }
4596 else {
4597 // string in YYYY/MM/DD/HH:MM:SS format
4598 uInt year = atoi( strtime.substr( 0, 4 ).c_str() ) ;
4599 uInt month = atoi( strtime.substr( 5, 2 ).c_str() ) ;
4600 uInt day = atoi( strtime.substr( 8, 2 ).c_str() ) ;
4601 uInt hour = atoi( strtime.substr( 11, 2 ).c_str() ) ;
4602 uInt minute = atoi( strtime.substr( 14, 2 ).c_str() ) ;
4603 uInt sec = atoi( strtime.substr( 17, 2 ).c_str() ) ;
4604 Time t( year, month, day, hour, minute, sec ) ;
4605 return t.modifiedJulianDay() ;
4606 }
4607}
4608
4609vector<int> STMath::getRowIdFromTime( string reftime, CountedPtr<Scantable> &s )
4610{
4611 double reft = getMJD( reftime ) ;
4612 double dtmin = 1.0e100 ;
4613 double dtmax = -1.0e100 ;
4614 vector<double> dt ;
4615 int just_before = -1 ;
4616 int just_after = -1 ;
4617 for ( int i = 0 ; i < s->nrow() ; i++ ) {
4618 dt.push_back( getMJD( s->getTime( i ) ) - reft ) ;
4619 }
4620 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4621 if ( dt[i] > 0.0 ) {
4622 // after reftime
4623 if ( dt[i] < dtmin ) {
4624 just_after = i ;
4625 dtmin = dt[i] ;
4626 }
4627 }
4628 else if ( dt[i] < 0.0 ) {
4629 // before reftime
4630 if ( dt[i] > dtmax ) {
4631 just_before = i ;
4632 dtmax = dt[i] ;
4633 }
4634 }
4635 else {
4636 // just a reftime
4637 just_before = i ;
4638 just_after = i ;
4639 dtmax = 0 ;
4640 dtmin = 0 ;
4641 break ;
4642 }
4643 }
4644
4645 vector<int> v ;
4646 v.push_back( just_before ) ;
4647 v.push_back( just_after ) ;
4648
4649 return v ;
4650}
4651
4652vector<int> STMath::getRowIdFromTime( double reftime, Vector<Double> &t )
4653{
4654// double reft = reftime ;
4655 double dtmin = 1.0e100 ;
4656 double dtmax = -1.0e100 ;
4657// vector<double> dt ;
4658 int just_before = -1 ;
4659 int just_after = -1 ;
4660 //cout << setprecision(24) << reft << endl ;
4661// ROScalarColumn<Double> timeCol( s->table(), "TIME" ) ;
4662// for ( int i = 0 ; i < s->nrow() ; i++ ) {
4663// cout << setprecision(24) << timeCol(i) << endl ;
4664// //dt.push_back( getMJD( s->getTime( i ) ) - reft ) ;
4665// dt.push_back( timeCol(i) - reft ) ;
4666// }
4667 Vector<Double> dt = t - reftime ;
4668 for ( unsigned int i = 0 ; i < dt.size() ; i++ ) {
4669 if ( dt[i] > 0.0 ) {
4670 // after reftime
4671 if ( dt[i] < dtmin ) {
4672 just_after = i ;
4673 dtmin = dt[i] ;
4674 }
4675 }
4676 else if ( dt[i] < 0.0 ) {
4677 // before reftime
4678 if ( dt[i] > dtmax ) {
4679 just_before = i ;
4680 dtmax = dt[i] ;
4681 }
4682 }
4683 else {
4684 // just a reftime
4685 just_before = i ;
4686 just_after = i ;
4687 dtmax = 0 ;
4688 dtmin = 0 ;
4689 break ;
4690 }
4691 }
4692
4693 vector<int> v(2) ;
4694 v[0] = just_before ;
4695 v[1] = just_after ;
4696
4697 return v ;
4698}
4699
4700vector<float> STMath::getTcalFromTime( string reftime,
4701 CountedPtr<Scantable>& s,
4702 string mode )
4703{
4704 LogIO os( LogOrigin( "STMath", "getTcalFromTime", WHERE ) ) ;
4705 vector<float> tcal ;
4706 STTcal tcalTable = s->tcal() ;
4707 String time ;
4708 Vector<Float> tcalval ;
4709 if ( s->nrow() == 0 ) {
4710 os << LogIO::SEVERE << "No row in the input scantable. Return empty tcal." << LogIO::POST ;
4711 return tcal ;
4712 }
4713 else if ( s->nrow() == 1 ) {
4714 uInt tcalid = s->getTcalId( 0 ) ;
4715 //os << "use row " << 0 << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4716 tcalTable.getEntry( time, tcalval, tcalid ) ;
4717 tcalval.tovector( tcal ) ;
4718 return tcal ;
4719 }
4720 else {
4721 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4722 if ( mode == "before" ) {
4723 int id = -1 ;
4724 if ( idx[0] != -1 ) {
4725 id = idx[0] ;
4726 }
4727 else if ( idx[1] != -1 ) {
4728 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4729 id = idx[1] ;
4730 }
4731 uInt tcalid = s->getTcalId( id ) ;
4732 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4733 tcalTable.getEntry( time, tcalval, tcalid ) ;
4734 tcalval.tovector( tcal ) ;
4735 }
4736 else if ( mode == "after" ) {
4737 int id = -1 ;
4738 if ( idx[1] != -1 ) {
4739 id = idx[1] ;
4740 }
4741 else if ( idx[0] != -1 ) {
4742 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4743 id = idx[1] ;
4744 }
4745 uInt tcalid = s->getTcalId( id ) ;
4746 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4747 tcalTable.getEntry( time, tcalval, tcalid ) ;
4748 tcalval.tovector( tcal ) ;
4749 }
4750 else if ( mode == "nearest" ) {
4751 int id = -1 ;
4752 if ( idx[0] == -1 ) {
4753 id = idx[1] ;
4754 }
4755 else if ( idx[1] == -1 ) {
4756 id = idx[0] ;
4757 }
4758 else if ( idx[0] == idx[1] ) {
4759 id = idx[0] ;
4760 }
4761 else {
4762 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4763 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4764 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4765 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4766 double tref = getMJD( reftime ) ;
4767 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4768 id = idx[1] ;
4769 }
4770 else {
4771 id = idx[0] ;
4772 }
4773 }
4774 uInt tcalid = s->getTcalId( id ) ;
4775 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4776 tcalTable.getEntry( time, tcalval, tcalid ) ;
4777 tcalval.tovector( tcal ) ;
4778 }
4779 else if ( mode == "linear" ) {
4780 if ( idx[0] == -1 ) {
4781 // use after
4782 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4783 int id = idx[1] ;
4784 uInt tcalid = s->getTcalId( id ) ;
4785 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4786 tcalTable.getEntry( time, tcalval, tcalid ) ;
4787 tcalval.tovector( tcal ) ;
4788 }
4789 else if ( idx[1] == -1 ) {
4790 // use before
4791 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4792 int id = idx[0] ;
4793 uInt tcalid = s->getTcalId( id ) ;
4794 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4795 tcalTable.getEntry( time, tcalval, tcalid ) ;
4796 tcalval.tovector( tcal ) ;
4797 }
4798 else if ( idx[0] == idx[1] ) {
4799 // use before
4800 //os << "No need to interporate." << LogIO::POST ;
4801 int id = idx[0] ;
4802 uInt tcalid = s->getTcalId( id ) ;
4803 //os << "use row " << id << " (tcalid = " << tcalid << ")" << LogIO::POST ;
4804 tcalTable.getEntry( time, tcalval, tcalid ) ;
4805 tcalval.tovector( tcal ) ;
4806 }
4807 else {
4808 // do interpolation
4809 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4810 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4811 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4812 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4813 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4814 double tref = getMJD( reftime ) ;
4815 vector<float> tcal0 ;
4816 vector<float> tcal1 ;
4817 uInt tcalid0 = s->getTcalId( idx[0] ) ;
4818 uInt tcalid1 = s->getTcalId( idx[1] ) ;
4819 tcalTable.getEntry( time, tcalval, tcalid0 ) ;
4820 tcalval.tovector( tcal0 ) ;
4821 tcalTable.getEntry( time, tcalval, tcalid1 ) ;
4822 tcalval.tovector( tcal1 ) ;
4823 for ( unsigned int i = 0 ; i < tcal0.size() ; i++ ) {
4824 float v = ( tcal1[i] - tcal0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tcal0[i] ;
4825 tcal.push_back( v ) ;
4826 }
4827 }
4828 }
4829 else {
4830 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4831 }
4832 return tcal ;
4833 }
4834}
4835
4836vector<float> STMath::getTsysFromTime( string reftime,
4837 CountedPtr<Scantable>& s,
4838 string mode )
4839{
4840 LogIO os( LogOrigin( "STMath", "getTsysFromTime", WHERE ) ) ;
4841 ArrayColumn<Float> tsysCol ;
4842 tsysCol.attach( s->table(), "TSYS" ) ;
4843 vector<float> tsys ;
4844 String time ;
4845 Vector<Float> tsysval ;
4846 if ( s->nrow() == 0 ) {
4847 os << LogIO::SEVERE << "No row in the input scantable. Return empty tsys." << LogIO::POST ;
4848 return tsys ;
4849 }
4850 else if ( s->nrow() == 1 ) {
4851 //os << "use row " << 0 << LogIO::POST ;
4852 tsysval = tsysCol( 0 ) ;
4853 tsysval.tovector( tsys ) ;
4854 return tsys ;
4855 }
4856 else {
4857 vector<int> idx = getRowIdFromTime( reftime, s ) ;
4858 if ( mode == "before" ) {
4859 int id = -1 ;
4860 if ( idx[0] != -1 ) {
4861 id = idx[0] ;
4862 }
4863 else if ( idx[1] != -1 ) {
4864 os << LogIO::WARN << "Failed to find a scan before reftime. return a spectrum just after the reftime." << LogIO::POST ;
4865 id = idx[1] ;
4866 }
4867 //os << "use row " << id << LogIO::POST ;
4868 tsysval = tsysCol( id ) ;
4869 tsysval.tovector( tsys ) ;
4870 }
4871 else if ( mode == "after" ) {
4872 int id = -1 ;
4873 if ( idx[1] != -1 ) {
4874 id = idx[1] ;
4875 }
4876 else if ( idx[0] != -1 ) {
4877 os << LogIO::WARN << "Failed to find a scan after reftime. return a spectrum just before the reftime." << LogIO::POST ;
4878 id = idx[1] ;
4879 }
4880 //os << "use row " << id << LogIO::POST ;
4881 tsysval = tsysCol( id ) ;
4882 tsysval.tovector( tsys ) ;
4883 }
4884 else if ( mode == "nearest" ) {
4885 int id = -1 ;
4886 if ( idx[0] == -1 ) {
4887 id = idx[1] ;
4888 }
4889 else if ( idx[1] == -1 ) {
4890 id = idx[0] ;
4891 }
4892 else if ( idx[0] == idx[1] ) {
4893 id = idx[0] ;
4894 }
4895 else {
4896 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4897 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4898 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4899 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4900 double tref = getMJD( reftime ) ;
4901 if ( abs( t0 - tref ) > abs( t1 - tref ) ) {
4902 id = idx[1] ;
4903 }
4904 else {
4905 id = idx[0] ;
4906 }
4907 }
4908 //os << "use row " << id << LogIO::POST ;
4909 tsysval = tsysCol( id ) ;
4910 tsysval.tovector( tsys ) ;
4911 }
4912 else if ( mode == "linear" ) {
4913 if ( idx[0] == -1 ) {
4914 // use after
4915 os << LogIO::WARN << "Failed to interpolate. return a spectrum just after the reftime." << LogIO::POST ;
4916 int id = idx[1] ;
4917 //os << "use row " << id << LogIO::POST ;
4918 tsysval = tsysCol( id ) ;
4919 tsysval.tovector( tsys ) ;
4920 }
4921 else if ( idx[1] == -1 ) {
4922 // use before
4923 os << LogIO::WARN << "Failed to interpolate. return a spectrum just before the reftime." << LogIO::POST ;
4924 int id = idx[0] ;
4925 //os << "use row " << id << LogIO::POST ;
4926 tsysval = tsysCol( id ) ;
4927 tsysval.tovector( tsys ) ;
4928 }
4929 else if ( idx[0] == idx[1] ) {
4930 // use before
4931 //os << "No need to interporate." << LogIO::POST ;
4932 int id = idx[0] ;
4933 //os << "use row " << id << LogIO::POST ;
4934 tsysval = tsysCol( id ) ;
4935 tsysval.tovector( tsys ) ;
4936 }
4937 else {
4938 // do interpolation
4939 //os << "interpolate between " << idx[0] << " and " << idx[1] << " (scanno: " << s->getScan( idx[0] ) << ", " << s->getScan( idx[1] ) << ")" << LogIO::POST ;
4940 //double t0 = getMJD( s->getTime( idx[0] ) ) ;
4941 //double t1 = getMJD( s->getTime( idx[1] ) ) ;
4942 double t0 = s->getEpoch( idx[0] ).get( Unit( "d" ) ).getValue() ;
4943 double t1 = s->getEpoch( idx[1] ).get( Unit( "d" ) ).getValue() ;
4944 double tref = getMJD( reftime ) ;
4945 vector<float> tsys0 ;
4946 vector<float> tsys1 ;
4947 tsysval = tsysCol( idx[0] ) ;
4948 tsysval.tovector( tsys0 ) ;
4949 tsysval = tsysCol( idx[1] ) ;
4950 tsysval.tovector( tsys1 ) ;
4951 for ( unsigned int i = 0 ; i < tsys0.size() ; i++ ) {
4952 float v = ( tsys1[i] - tsys0[i] ) / ( t1 - t0 ) * ( tref - t0 ) + tsys0[i] ;
4953 tsys.push_back( v ) ;
4954 }
4955 }
4956 }
4957 else {
4958 os << LogIO::SEVERE << "Unknown mode" << LogIO::POST ;
4959 }
4960 return tsys ;
4961 }
4962}
4963
4964vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
4965 CountedPtr<Scantable>& off,
4966 CountedPtr<Scantable>& sky,
4967 CountedPtr<Scantable>& hot,
4968 CountedPtr<Scantable>& cold,
4969 int index,
4970 string antname )
4971{
4972 (void) cold; //currently unused
4973 string reftime = on->getTime( index ) ;
4974 vector<int> ii( 1, on->getIF( index ) ) ;
4975 vector<int> ib( 1, on->getBeam( index ) ) ;
4976 vector<int> ip( 1, on->getPol( index ) ) ;
4977 vector<int> ic( 1, on->getScan( index ) ) ;
4978 STSelector sel = STSelector() ;
4979 sel.setIFs( ii ) ;
4980 sel.setBeams( ib ) ;
4981 sel.setPolarizations( ip ) ;
4982 sky->setSelection( sel ) ;
4983 hot->setSelection( sel ) ;
4984 //cold->setSelection( sel ) ;
4985 off->setSelection( sel ) ;
4986 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
4987 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
4988 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
4989 vector<float> spoff = getSpectrumFromTime( reftime, off, "linear" ) ;
4990 vector<float> spec = on->getSpectrum( index ) ;
4991 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
4992 vector<float> sp( tcal.size() ) ;
4993 if ( antname.find( "APEX" ) != string::npos ) {
4994 // using gain array
4995 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
4996 float v = ( ( spec[j] - spoff[j] ) / spoff[j] )
4997 * ( spsky[j] / ( sphot[j] - spsky[j] ) ) * tcal[j] ;
4998 sp[j] = v ;
4999 }
5000 }
5001 else {
5002 // Chopper-Wheel calibration (Ulich & Haas 1976)
5003 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
5004 float v = ( spec[j] - spoff[j] ) / ( sphot[j] - spsky[j] ) * tcal[j] ;
5005 sp[j] = v ;
5006 }
5007 }
5008 sel.reset() ;
5009 sky->unsetSelection() ;
5010 hot->unsetSelection() ;
5011 //cold->unsetSelection() ;
5012 off->unsetSelection() ;
5013
5014 return sp ;
5015}
5016
5017vector<float> STMath::getCalibratedSpectra( CountedPtr<Scantable>& on,
5018 CountedPtr<Scantable>& off,
5019 int index )
5020{
5021// string reftime = on->getTime( index ) ;
5022 ROTableColumn timeCol( on->table(), "TIME" ) ;
5023 double reftime = timeCol.asdouble(index) ;
5024 vector<int> ii( 1, on->getIF( index ) ) ;
5025 vector<int> ib( 1, on->getBeam( index ) ) ;
5026 vector<int> ip( 1, on->getPol( index ) ) ;
5027 vector<int> ic( 1, on->getScan( index ) ) ;
5028 STSelector sel = STSelector() ;
5029 sel.setIFs( ii ) ;
5030 sel.setBeams( ib ) ;
5031 sel.setPolarizations( ip ) ;
5032 off->setSelection( sel ) ;
5033 vector<float> spoff = getSpectrumFromTime( reftime, off, "linear" ) ;
5034 vector<float> spec = on->getSpectrum( index ) ;
5035 //vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
5036 //vector<float> tsys = on->getTsysVec( index ) ;
5037 ArrayColumn<Float> tsysCol( on->table(), "TSYS" ) ;
5038 Vector<Float> tsys = tsysCol( index ) ;
5039 vector<float> sp( spec.size() ) ;
5040 // ALMA Calibration
5041 //
5042 // Ta* = Tsys * ( ON - OFF ) / OFF
5043 //
5044 // 2010/01/07 Takeshi Nakazato
5045 unsigned int tsyssize = tsys.nelements() ;
5046 unsigned int spsize = sp.size() ;
5047 for ( unsigned int j = 0 ; j < sp.size() ; j++ ) {
5048 float tscale = 0.0 ;
5049 if ( tsyssize == spsize )
5050 tscale = tsys[j] ;
5051 else
5052 tscale = tsys[0] ;
5053 float v = tscale * ( spec[j] - spoff[j] ) / spoff[j] ;
5054 sp[j] = v ;
5055 }
5056 sel.reset() ;
5057 off->unsetSelection() ;
5058
5059 return sp ;
5060}
5061
5062vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
5063 CountedPtr<Scantable>& ref,
5064 CountedPtr<Scantable>& sky,
5065 CountedPtr<Scantable>& hot,
5066 CountedPtr<Scantable>& cold,
5067 int index )
5068{
5069 (void) cold; //currently unused
5070 string reftime = sig->getTime( index ) ;
5071 vector<int> ii( 1, sig->getIF( index ) ) ;
5072 vector<int> ib( 1, sig->getBeam( index ) ) ;
5073 vector<int> ip( 1, sig->getPol( index ) ) ;
5074 vector<int> ic( 1, sig->getScan( index ) ) ;
5075 STSelector sel = STSelector() ;
5076 sel.setIFs( ii ) ;
5077 sel.setBeams( ib ) ;
5078 sel.setPolarizations( ip ) ;
5079 sky->setSelection( sel ) ;
5080 hot->setSelection( sel ) ;
5081 //cold->setSelection( sel ) ;
5082 vector<float> spsky = getSpectrumFromTime( reftime, sky, "linear" ) ;
5083 vector<float> sphot = getSpectrumFromTime( reftime, hot, "linear" ) ;
5084 //vector<float> spcold = getSpectrumFromTime( reftime, cold, "linear" ) ;
5085 vector<float> spref = ref->getSpectrum( index ) ;
5086 vector<float> spsig = sig->getSpectrum( index ) ;
5087 vector<float> tcal = getTcalFromTime( reftime, sky, "linear" ) ;
5088 vector<float> sp( tcal.size() ) ;
5089 for ( unsigned int j = 0 ; j < tcal.size() ; j++ ) {
5090 float v = tcal[j] * spsky[j] / ( sphot[j] - spsky[j] ) * ( spsig[j] - spref[j] ) / spref[j] ;
5091 sp[j] = v ;
5092 }
5093 sel.reset() ;
5094 sky->unsetSelection() ;
5095 hot->unsetSelection() ;
5096 //cold->unsetSelection() ;
5097
5098 return sp ;
5099}
5100
5101vector<float> STMath::getFSCalibratedSpectra( CountedPtr<Scantable>& sig,
5102 CountedPtr<Scantable>& ref,
5103 vector< CountedPtr<Scantable> >& sky,
5104 vector< CountedPtr<Scantable> >& hot,
5105 vector< CountedPtr<Scantable> >& cold,
5106 int index )
5107{
5108 (void) cold; //currently unused
5109 string reftime = sig->getTime( index ) ;
5110 vector<int> ii( 1, sig->getIF( index ) ) ;
5111 vector<int> ib( 1, sig->getBeam( index ) ) ;
5112 vector<int> ip( 1, sig->getPol( index ) ) ;
5113 vector<int> ic( 1, sig->getScan( index ) ) ;
5114 STSelector sel = STSelector() ;
5115 sel.setIFs( ii ) ;
5116 sel.setBeams( ib ) ;
5117 sel.setPolarizations( ip ) ;
5118 sky[0]->setSelection( sel ) ;
5119 hot[0]->setSelection( sel ) ;
5120 //cold[0]->setSelection( sel ) ;
5121 vector<float> spskys = getSpectrumFromTime( reftime, sky[0], "linear" ) ;
5122 vector<float> sphots = getSpectrumFromTime( reftime, hot[0], "linear" ) ;
5123 //vector<float> spcolds = getSpectrumFromTime( reftime, cold[0], "linear" ) ;
5124 vector<float> tcals = getTcalFromTime( reftime, sky[0], "linear" ) ;
5125 sel.reset() ;
5126 ii[0] = ref->getIF( index ) ;
5127 sel.setIFs( ii ) ;
5128 sel.setBeams( ib ) ;
5129 sel.setPolarizations( ip ) ;
5130 sky[1]->setSelection( sel ) ;
5131 hot[1]->setSelection( sel ) ;
5132 //cold[1]->setSelection( sel ) ;
5133 vector<float> spskyr = getSpectrumFromTime( reftime, sky[1], "linear" ) ;
5134 vector<float> sphotr = getSpectrumFromTime( reftime, hot[1], "linear" ) ;
5135 //vector<float> spcoldr = getSpectrumFromTime( reftime, cold[1], "linear" ) ;
5136 vector<float> tcalr = getTcalFromTime( reftime, sky[1], "linear" ) ;
5137 vector<float> spref = ref->getSpectrum( index ) ;
5138 vector<float> spsig = sig->getSpectrum( index ) ;
5139 vector<float> sp( tcals.size() ) ;
5140 for ( unsigned int j = 0 ; j < tcals.size() ; j++ ) {
5141 float v = tcals[j] * spsig[j] / ( sphots[j] - spskys[j] ) - tcalr[j] * spref[j] / ( sphotr[j] - spskyr[j] ) ;
5142 sp[j] = v ;
5143 }
5144 sel.reset() ;
5145 sky[0]->unsetSelection() ;
5146 hot[0]->unsetSelection() ;
5147 //cold[0]->unsetSelection() ;
5148 sky[1]->unsetSelection() ;
5149 hot[1]->unsetSelection() ;
5150 //cold[1]->unsetSelection() ;
5151
5152 return sp ;
5153}
Note: See TracBrowser for help on using the repository browser.