source: trunk/src/STMath.cpp@ 1318

Last change on this file since 1318 was 1318, checked in by mar637, 18 years ago

Fix for Ticket #97; corrected opacity formula. Forgot to check this in
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File size: 49.0 KB
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1//
2// C++ Implementation: STMath
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12
13#include <casa/iomanip.h>
14#include <casa/Exceptions/Error.h>
15#include <casa/Containers/Block.h>
16#include <casa/BasicSL/String.h>
17#include <casa/Arrays/MaskArrLogi.h>
18#include <casa/Arrays/MaskArrMath.h>
19#include <casa/Arrays/ArrayLogical.h>
20#include <casa/Arrays/ArrayMath.h>
21#include <casa/Arrays/Slice.h>
22#include <casa/Arrays/Slicer.h>
23#include <casa/Containers/RecordField.h>
24#include <tables/Tables/TableRow.h>
25#include <tables/Tables/TableVector.h>
26#include <tables/Tables/TabVecMath.h>
27#include <tables/Tables/ExprNode.h>
28#include <tables/Tables/TableRecord.h>
29#include <tables/Tables/TableParse.h>
30#include <tables/Tables/ReadAsciiTable.h>
31#include <tables/Tables/TableIter.h>
32#include <tables/Tables/TableCopy.h>
33#include <scimath/Mathematics/FFTServer.h>
34
35#include <lattices/Lattices/LatticeUtilities.h>
36
37#include <coordinates/Coordinates/SpectralCoordinate.h>
38#include <coordinates/Coordinates/CoordinateSystem.h>
39#include <coordinates/Coordinates/CoordinateUtil.h>
40#include <coordinates/Coordinates/FrequencyAligner.h>
41
42#include <scimath/Mathematics/VectorKernel.h>
43#include <scimath/Mathematics/Convolver.h>
44#include <scimath/Functionals/Polynomial.h>
45
46#include "MathUtils.h"
47#include "RowAccumulator.h"
48#include "STAttr.h"
49#include "STMath.h"
50
51using namespace casa;
52
53using namespace asap;
54
55STMath::STMath(bool insitu) :
56 insitu_(insitu)
57{
58}
59
60
61STMath::~STMath()
62{
63}
64
65CountedPtr<Scantable>
66STMath::average( const std::vector<CountedPtr<Scantable> >& in,
67 const std::vector<bool>& mask,
68 const std::string& weight,
69 const std::string& avmode)
70{
71 if ( avmode == "SCAN" && in.size() != 1 )
72 throw(AipsError("Can't perform 'SCAN' averaging on multiple tables.\n"
73 "Use merge first."));
74 WeightType wtype = stringToWeight(weight);
75
76 // output
77 // clone as this is non insitu
78 bool insitu = insitu_;
79 setInsitu(false);
80 CountedPtr< Scantable > out = getScantable(in[0], true);
81 setInsitu(insitu);
82 std::vector<CountedPtr<Scantable> >::const_iterator stit = in.begin();
83 ++stit;
84 while ( stit != in.end() ) {
85 out->appendToHistoryTable((*stit)->history());
86 ++stit;
87 }
88
89 Table& tout = out->table();
90
91 /// @todo check if all scantables are conformant
92
93 ArrayColumn<Float> specColOut(tout,"SPECTRA");
94 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
95 ArrayColumn<Float> tsysColOut(tout,"TSYS");
96 ScalarColumn<Double> mjdColOut(tout,"TIME");
97 ScalarColumn<Double> intColOut(tout,"INTERVAL");
98 ScalarColumn<uInt> cycColOut(tout,"CYCLENO");
99 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
100
101 // set up the output table rows. These are based on the structure of the
102 // FIRST scantable in the vector
103 const Table& baset = in[0]->table();
104
105 Block<String> cols(3);
106 cols[0] = String("BEAMNO");
107 cols[1] = String("IFNO");
108 cols[2] = String("POLNO");
109 if ( avmode == "SOURCE" ) {
110 cols.resize(4);
111 cols[3] = String("SRCNAME");
112 }
113 if ( avmode == "SCAN" && in.size() == 1) {
114 cols.resize(4);
115 cols[3] = String("SCANNO");
116 }
117 uInt outrowCount = 0;
118 TableIterator iter(baset, cols);
119 while (!iter.pastEnd()) {
120 Table subt = iter.table();
121 // copy the first row of this selection into the new table
122 tout.addRow();
123 TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
124 // re-index to 0
125 if ( avmode != "SCAN" && avmode != "SOURCE" ) {
126 scanColOut.put(outrowCount, uInt(0));
127 }
128 ++outrowCount;
129 ++iter;
130 }
131 RowAccumulator acc(wtype);
132 Vector<Bool> cmask(mask);
133 acc.setUserMask(cmask);
134 ROTableRow row(tout);
135 ROArrayColumn<Float> specCol, tsysCol;
136 ROArrayColumn<uChar> flagCol;
137 ROScalarColumn<Double> mjdCol, intCol;
138 ROScalarColumn<Int> scanIDCol;
139
140 for (uInt i=0; i < tout.nrow(); ++i) {
141 for ( int j=0; j < int(in.size()); ++j ) {
142 const Table& tin = in[j]->table();
143 const TableRecord& rec = row.get(i);
144 ROScalarColumn<Double> tmp(tin, "TIME");
145 Double td;tmp.get(0,td);
146 Table basesubt = tin(tin.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
147 && tin.col("IFNO") == Int(rec.asuInt("IFNO"))
148 && tin.col("POLNO") == Int(rec.asuInt("POLNO")) );
149 Table subt;
150 if ( avmode == "SOURCE") {
151 subt = basesubt( basesubt.col("SRCNAME") == rec.asString("SRCNAME") );
152 } else if (avmode == "SCAN") {
153 subt = basesubt( basesubt.col("SCANNO") == Int(rec.asuInt("SCANNO")) );
154 } else {
155 subt = basesubt;
156 }
157 specCol.attach(subt,"SPECTRA");
158 flagCol.attach(subt,"FLAGTRA");
159 tsysCol.attach(subt,"TSYS");
160 intCol.attach(subt,"INTERVAL");
161 mjdCol.attach(subt,"TIME");
162 Vector<Float> spec,tsys;
163 Vector<uChar> flag;
164 Double inter,time;
165 for (uInt k = 0; k < subt.nrow(); ++k ) {
166 flagCol.get(k, flag);
167 Vector<Bool> bflag(flag.shape());
168 convertArray(bflag, flag);
169 /*
170 if ( allEQ(bflag, True) ) {
171 continue;//don't accumulate
172 }
173 */
174 specCol.get(k, spec);
175 tsysCol.get(k, tsys);
176 intCol.get(k, inter);
177 mjdCol.get(k, time);
178 // spectrum has to be added last to enable weighting by the other values
179 acc.add(spec, !bflag, tsys, inter, time);
180 }
181 }
182 //write out
183 specColOut.put(i, acc.getSpectrum());
184 const Vector<Bool>& msk = acc.getMask();
185 Vector<uChar> flg(msk.shape());
186 convertArray(flg, !msk);
187 flagColOut.put(i, flg);
188 tsysColOut.put(i, acc.getTsys());
189 intColOut.put(i, acc.getInterval());
190 mjdColOut.put(i, acc.getTime());
191 // we should only have one cycle now -> reset it to be 0
192 // frequency switched data has different CYCLENO for different IFNO
193 // which requires resetting this value
194 cycColOut.put(i, uInt(0));
195 acc.reset();
196 }
197 return out;
198}
199
200CountedPtr< Scantable >
201 STMath::averageChannel( const CountedPtr < Scantable > & in,
202 const std::string & mode,
203 const std::string& avmode )
204{
205 // clone as this is non insitu
206 bool insitu = insitu_;
207 setInsitu(false);
208 CountedPtr< Scantable > out = getScantable(in, true);
209 setInsitu(insitu);
210 Table& tout = out->table();
211 ArrayColumn<Float> specColOut(tout,"SPECTRA");
212 ArrayColumn<uChar> flagColOut(tout,"FLAGTRA");
213 ArrayColumn<Float> tsysColOut(tout,"TSYS");
214 ScalarColumn<uInt> scanColOut(tout,"SCANNO");
215 ScalarColumn<Double> intColOut(tout, "INTERVAL");
216 Table tmp = in->table().sort("BEAMNO");
217 Block<String> cols(3);
218 cols[0] = String("BEAMNO");
219 cols[1] = String("IFNO");
220 cols[2] = String("POLNO");
221 if ( avmode == "SCAN") {
222 cols.resize(4);
223 cols[3] = String("SCANNO");
224 }
225 uInt outrowCount = 0;
226 uChar userflag = 1 << 7;
227 TableIterator iter(tmp, cols);
228 while (!iter.pastEnd()) {
229 Table subt = iter.table();
230 ROArrayColumn<Float> specCol, tsysCol;
231 ROArrayColumn<uChar> flagCol;
232 ROScalarColumn<Double> intCol(subt, "INTERVAL");
233 specCol.attach(subt,"SPECTRA");
234 flagCol.attach(subt,"FLAGTRA");
235 tsysCol.attach(subt,"TSYS");
236 tout.addRow();
237 TableCopy::copyRows(tout, subt, outrowCount, 0, 1);
238 if ( avmode != "SCAN") {
239 scanColOut.put(outrowCount, uInt(0));
240 }
241 Vector<Float> tmp;
242 specCol.get(0, tmp);
243 uInt nchan = tmp.nelements();
244 // have to do channel by channel here as MaskedArrMath
245 // doesn't have partialMedians
246 Vector<uChar> flags = flagCol.getColumn(Slicer(Slice(0)));
247 Vector<Float> outspec(nchan);
248 Vector<uChar> outflag(nchan,0);
249 Vector<Float> outtsys(1);/// @fixme when tsys is channel based
250 for (uInt i=0; i<nchan; ++i) {
251 Vector<Float> specs = specCol.getColumn(Slicer(Slice(i)));
252 MaskedArray<Float> ma = maskedArray(specs,flags);
253 outspec[i] = median(ma);
254 if ( allEQ(ma.getMask(), False) )
255 outflag[i] = userflag;// flag data
256 }
257 outtsys[0] = median(tsysCol.getColumn());
258 specColOut.put(outrowCount, outspec);
259 flagColOut.put(outrowCount, outflag);
260 tsysColOut.put(outrowCount, outtsys);
261 Double intsum = sum(intCol.getColumn());
262 intColOut.put(outrowCount, intsum);
263 ++outrowCount;
264 ++iter;
265 }
266 return out;
267}
268
269CountedPtr< Scantable > STMath::getScantable(const CountedPtr< Scantable >& in,
270 bool droprows)
271{
272 if (insitu_) return in;
273 else {
274 // clone
275 Scantable* tabp = new Scantable(*in, Bool(droprows));
276 return CountedPtr<Scantable>(tabp);
277 }
278}
279
280CountedPtr< Scantable > STMath::unaryOperate( const CountedPtr< Scantable >& in,
281 float val,
282 const std::string& mode,
283 bool tsys )
284{
285 CountedPtr< Scantable > out = getScantable(in, false);
286 Table& tab = out->table();
287 ArrayColumn<Float> specCol(tab,"SPECTRA");
288 ArrayColumn<Float> tsysCol(tab,"TSYS");
289 for (uInt i=0; i<tab.nrow(); ++i) {
290 Vector<Float> spec;
291 Vector<Float> ts;
292 specCol.get(i, spec);
293 tsysCol.get(i, ts);
294 if (mode == "MUL" || mode == "DIV") {
295 if (mode == "DIV") val = 1.0/val;
296 spec *= val;
297 specCol.put(i, spec);
298 if ( tsys ) {
299 ts *= val;
300 tsysCol.put(i, ts);
301 }
302 } else if ( mode == "ADD" || mode == "SUB") {
303 if (mode == "SUB") val *= -1.0;
304 spec += val;
305 specCol.put(i, spec);
306 if ( tsys ) {
307 ts += val;
308 tsysCol.put(i, ts);
309 }
310 }
311 }
312 return out;
313}
314
315CountedPtr<Scantable> STMath::binaryOperate(const CountedPtr<Scantable>& left,
316 const CountedPtr<Scantable>& right,
317 const std::string& mode)
318{
319 bool insitu = insitu_;
320 if ( ! left->conformant(*right) ) {
321 throw(AipsError("'left' and 'right' scantables are not conformant."));
322 }
323 setInsitu(false);
324 CountedPtr< Scantable > out = getScantable(left, false);
325 setInsitu(insitu);
326 Table& tout = out->table();
327 Block<String> coln(5);
328 coln[0] = "SCANNO"; coln[1] = "CYCLENO"; coln[2] = "BEAMNO";
329 coln[3] = "IFNO"; coln[4] = "POLNO";
330 Table tmpl = tout.sort(coln);
331 Table tmpr = right->table().sort(coln);
332 ArrayColumn<Float> lspecCol(tmpl,"SPECTRA");
333 ROArrayColumn<Float> rspecCol(tmpr,"SPECTRA");
334 ArrayColumn<uChar> lflagCol(tmpl,"FLAGTRA");
335 ROArrayColumn<uChar> rflagCol(tmpr,"FLAGTRA");
336
337 for (uInt i=0; i<tout.nrow(); ++i) {
338 Vector<Float> lspecvec, rspecvec;
339 Vector<uChar> lflagvec, rflagvec;
340 lspecvec = lspecCol(i); rspecvec = rspecCol(i);
341 lflagvec = lflagCol(i); rflagvec = rflagCol(i);
342 MaskedArray<Float> mleft = maskedArray(lspecvec, lflagvec);
343 MaskedArray<Float> mright = maskedArray(rspecvec, rflagvec);
344 if (mode == "ADD") {
345 mleft += mright;
346 } else if ( mode == "SUB") {
347 mleft -= mright;
348 } else if ( mode == "MUL") {
349 mleft *= mright;
350 } else if ( mode == "DIV") {
351 mleft /= mright;
352 } else {
353 throw(AipsError("Illegal binary operator"));
354 }
355 lspecCol.put(i, mleft.getArray());
356 }
357 return out;
358}
359
360
361
362MaskedArray<Float> STMath::maskedArray( const Vector<Float>& s,
363 const Vector<uChar>& f)
364{
365 Vector<Bool> mask;
366 mask.resize(f.shape());
367 convertArray(mask, f);
368 return MaskedArray<Float>(s,!mask);
369}
370
371Vector<uChar> STMath::flagsFromMA(const MaskedArray<Float>& ma)
372{
373 const Vector<Bool>& m = ma.getMask();
374 Vector<uChar> flags(m.shape());
375 convertArray(flags, !m);
376 return flags;
377}
378
379CountedPtr< Scantable > STMath::autoQuotient( const CountedPtr< Scantable >& in,
380 const std::string & mode,
381 bool preserve )
382{
383 /// @todo make other modes available
384 /// modes should be "nearest", "pair"
385 // make this operation non insitu
386 const Table& tin = in->table();
387 Table ons = tin(tin.col("SRCTYPE") == Int(0));
388 Table offs = tin(tin.col("SRCTYPE") == Int(1));
389 if ( offs.nrow() == 0 )
390 throw(AipsError("No 'off' scans present."));
391 // put all "on" scans into output table
392
393 bool insitu = insitu_;
394 setInsitu(false);
395 CountedPtr< Scantable > out = getScantable(in, true);
396 setInsitu(insitu);
397 Table& tout = out->table();
398
399 TableCopy::copyRows(tout, ons);
400 TableRow row(tout);
401 ROScalarColumn<Double> offtimeCol(offs, "TIME");
402 ArrayColumn<Float> outspecCol(tout, "SPECTRA");
403 ROArrayColumn<Float> outtsysCol(tout, "TSYS");
404 ArrayColumn<uChar> outflagCol(tout, "FLAGTRA");
405 for (uInt i=0; i < tout.nrow(); ++i) {
406 const TableRecord& rec = row.get(i);
407 Double ontime = rec.asDouble("TIME");
408 ROScalarColumn<Double> offtimeCol(offs, "TIME");
409 Double mindeltat = min(abs(offtimeCol.getColumn() - ontime));
410 // Timestamp may vary within a cycle ???!!!
411 // increase this by 0.5 sec in case of rounding errors...
412 // There might be a better way to do this.
413 mindeltat += 0.5;
414 Table sel = offs( abs(offs.col("TIME")-ontime) <= (mindeltat+0.5)
415 && offs.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
416 && offs.col("IFNO") == Int(rec.asuInt("IFNO"))
417 && offs.col("POLNO") == Int(rec.asuInt("POLNO")) );
418
419 if ( sel.nrow() < 1 ) {
420 throw(AipsError("No closest in time found... This could be a rounding "
421 "issue. Try quotient instead."));
422 }
423 TableRow offrow(sel);
424 const TableRecord& offrec = offrow.get(0);//should only be one row
425 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
426 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
427 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
428 /// @fixme this assumes tsys is a scalar not vector
429 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
430 Vector<Float> specon, tsyson;
431 outtsysCol.get(i, tsyson);
432 outspecCol.get(i, specon);
433 Vector<uChar> flagon;
434 outflagCol.get(i, flagon);
435 MaskedArray<Float> mon = maskedArray(specon, flagon);
436 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
437 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
438 if (preserve) {
439 quot -= tsysoffscalar;
440 } else {
441 quot -= tsyson[0];
442 }
443 outspecCol.put(i, quot.getArray());
444 outflagCol.put(i, flagsFromMA(quot));
445 }
446 // renumber scanno
447 TableIterator it(tout, "SCANNO");
448 uInt i = 0;
449 while ( !it.pastEnd() ) {
450 Table t = it.table();
451 TableVector<uInt> vec(t, "SCANNO");
452 vec = i;
453 ++i;
454 ++it;
455 }
456 return out;
457}
458
459
460CountedPtr< Scantable > STMath::quotient( const CountedPtr< Scantable > & on,
461 const CountedPtr< Scantable > & off,
462 bool preserve )
463{
464 bool insitu = insitu_;
465 if ( ! on->conformant(*off) ) {
466 throw(AipsError("'on' and 'off' scantables are not conformant."));
467 }
468 setInsitu(false);
469 CountedPtr< Scantable > out = getScantable(on, false);
470 setInsitu(insitu);
471 Table& tout = out->table();
472 const Table& toff = off->table();
473 TableIterator sit(tout, "SCANNO");
474 TableIterator s2it(toff, "SCANNO");
475 while ( !sit.pastEnd() ) {
476 Table ton = sit.table();
477 TableRow row(ton);
478 Table t = s2it.table();
479 ArrayColumn<Float> outspecCol(ton, "SPECTRA");
480 ROArrayColumn<Float> outtsysCol(ton, "TSYS");
481 ArrayColumn<uChar> outflagCol(ton, "FLAGTRA");
482 for (uInt i=0; i < ton.nrow(); ++i) {
483 const TableRecord& rec = row.get(i);
484 Table offsel = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
485 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
486 && t.col("POLNO") == Int(rec.asuInt("POLNO")) );
487 if ( offsel.nrow() == 0 )
488 throw AipsError("STMath::quotient: no matching off");
489 TableRow offrow(offsel);
490 const TableRecord& offrec = offrow.get(0);//should be ncycles - take first
491 RORecordFieldPtr< Array<Float> > specoff(offrec, "SPECTRA");
492 RORecordFieldPtr< Array<Float> > tsysoff(offrec, "TSYS");
493 RORecordFieldPtr< Array<uChar> > flagoff(offrec, "FLAGTRA");
494 Float tsysoffscalar = (*tsysoff)(IPosition(1,0));
495 Vector<Float> specon, tsyson;
496 outtsysCol.get(i, tsyson);
497 outspecCol.get(i, specon);
498 Vector<uChar> flagon;
499 outflagCol.get(i, flagon);
500 MaskedArray<Float> mon = maskedArray(specon, flagon);
501 MaskedArray<Float> moff = maskedArray(*specoff, *flagoff);
502 MaskedArray<Float> quot = (tsysoffscalar * mon / moff);
503 if (preserve) {
504 quot -= tsysoffscalar;
505 } else {
506 quot -= tsyson[0];
507 }
508 outspecCol.put(i, quot.getArray());
509 outflagCol.put(i, flagsFromMA(quot));
510 }
511 ++sit;
512 ++s2it;
513 // take the first off for each on scan which doesn't have a
514 // matching off scan
515 // non <= noff: matching pairs, non > noff matching pairs then first off
516 if ( s2it.pastEnd() ) s2it.reset();
517 }
518 return out;
519}
520
521
522CountedPtr< Scantable > STMath::freqSwitch( const CountedPtr< Scantable >& in )
523{
524 // make copy or reference
525 CountedPtr< Scantable > out = getScantable(in, false);
526 Table& tout = out->table();
527 Block<String> cols(4);
528 cols[0] = String("SCANNO");
529 cols[1] = String("CYCLENO");
530 cols[2] = String("BEAMNO");
531 cols[3] = String("POLNO");
532 TableIterator iter(tout, cols);
533 while (!iter.pastEnd()) {
534 Table subt = iter.table();
535 // this should leave us with two rows for the two IFs....if not ignore
536 if (subt.nrow() != 2 ) {
537 continue;
538 }
539 ArrayColumn<Float> specCol(subt, "SPECTRA");
540 ArrayColumn<Float> tsysCol(subt, "TSYS");
541 ArrayColumn<uChar> flagCol(subt, "FLAGTRA");
542 Vector<Float> onspec,offspec, ontsys, offtsys;
543 Vector<uChar> onflag, offflag;
544 tsysCol.get(0, ontsys); tsysCol.get(1, offtsys);
545 specCol.get(0, onspec); specCol.get(1, offspec);
546 flagCol.get(0, onflag); flagCol.get(1, offflag);
547 MaskedArray<Float> on = maskedArray(onspec, onflag);
548 MaskedArray<Float> off = maskedArray(offspec, offflag);
549 MaskedArray<Float> oncopy = on.copy();
550
551 on /= off; on -= 1.0f;
552 on *= ontsys[0];
553 off /= oncopy; off -= 1.0f;
554 off *= offtsys[0];
555 specCol.put(0, on.getArray());
556 const Vector<Bool>& m0 = on.getMask();
557 Vector<uChar> flags0(m0.shape());
558 convertArray(flags0, !m0);
559 flagCol.put(0, flags0);
560
561 specCol.put(1, off.getArray());
562 const Vector<Bool>& m1 = off.getMask();
563 Vector<uChar> flags1(m1.shape());
564 convertArray(flags1, !m1);
565 flagCol.put(1, flags1);
566 ++iter;
567 }
568
569 return out;
570}
571
572std::vector< float > STMath::statistic( const CountedPtr< Scantable > & in,
573 const std::vector< bool > & mask,
574 const std::string& which )
575{
576
577 Vector<Bool> m(mask);
578 const Table& tab = in->table();
579 ROArrayColumn<Float> specCol(tab, "SPECTRA");
580 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
581 std::vector<float> out;
582 for (uInt i=0; i < tab.nrow(); ++i ) {
583 Vector<Float> spec; specCol.get(i, spec);
584 Vector<uChar> flag; flagCol.get(i, flag);
585 MaskedArray<Float> ma = maskedArray(spec, flag);
586 float outstat = 0.0;
587 if ( spec.nelements() == m.nelements() ) {
588 outstat = mathutil::statistics(which, ma(m));
589 } else {
590 outstat = mathutil::statistics(which, ma);
591 }
592 out.push_back(outstat);
593 }
594 return out;
595}
596
597CountedPtr< Scantable > STMath::bin( const CountedPtr< Scantable > & in,
598 int width )
599{
600 if ( !in->getSelection().empty() ) throw(AipsError("Can't bin subset of the data."));
601 CountedPtr< Scantable > out = getScantable(in, false);
602 Table& tout = out->table();
603 out->frequencies().rescale(width, "BIN");
604 ArrayColumn<Float> specCol(tout, "SPECTRA");
605 ArrayColumn<uChar> flagCol(tout, "FLAGTRA");
606 for (uInt i=0; i < tout.nrow(); ++i ) {
607 MaskedArray<Float> main = maskedArray(specCol(i), flagCol(i));
608 MaskedArray<Float> maout;
609 LatticeUtilities::bin(maout, main, 0, Int(width));
610 /// @todo implement channel based tsys binning
611 specCol.put(i, maout.getArray());
612 flagCol.put(i, flagsFromMA(maout));
613 // take only the first binned spectrum's length for the deprecated
614 // global header item nChan
615 if (i==0) tout.rwKeywordSet().define(String("nChan"),
616 Int(maout.getArray().nelements()));
617 }
618 return out;
619}
620
621CountedPtr< Scantable > STMath::resample( const CountedPtr< Scantable >& in,
622 const std::string& method,
623 float width )
624//
625// Should add the possibility of width being specified in km/s. This means
626// that for each freqID (SpectralCoordinate) we will need to convert to an
627// average channel width (say at the reference pixel). Then we would need
628// to be careful to make sure each spectrum (of different freqID)
629// is the same length.
630//
631{
632 //InterpolateArray1D<Double,Float>::InterpolationMethod interp;
633 Int interpMethod(stringToIMethod(method));
634
635 CountedPtr< Scantable > out = getScantable(in, false);
636 Table& tout = out->table();
637
638// Resample SpectralCoordinates (one per freqID)
639 out->frequencies().rescale(width, "RESAMPLE");
640 TableIterator iter(tout, "IFNO");
641 TableRow row(tout);
642 while ( !iter.pastEnd() ) {
643 Table tab = iter.table();
644 ArrayColumn<Float> specCol(tab, "SPECTRA");
645 //ArrayColumn<Float> tsysCol(tout, "TSYS");
646 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
647 Vector<Float> spec;
648 Vector<uChar> flag;
649 specCol.get(0,spec); // the number of channels should be constant per IF
650 uInt nChanIn = spec.nelements();
651 Vector<Float> xIn(nChanIn); indgen(xIn);
652 Int fac = Int(nChanIn/width);
653 Vector<Float> xOut(fac+10); // 10 to be safe - resize later
654 uInt k = 0;
655 Float x = 0.0;
656 while (x < Float(nChanIn) ) {
657 xOut(k) = x;
658 k++;
659 x += width;
660 }
661 uInt nChanOut = k;
662 xOut.resize(nChanOut, True);
663 // process all rows for this IFNO
664 Vector<Float> specOut;
665 Vector<Bool> maskOut;
666 Vector<uChar> flagOut;
667 for (uInt i=0; i < tab.nrow(); ++i) {
668 specCol.get(i, spec);
669 flagCol.get(i, flag);
670 Vector<Bool> mask(flag.nelements());
671 convertArray(mask, flag);
672
673 IPosition shapeIn(spec.shape());
674 //sh.nchan = nChanOut;
675 InterpolateArray1D<Float,Float>::interpolate(specOut, maskOut, xOut,
676 xIn, spec, mask,
677 interpMethod, True, True);
678 /// @todo do the same for channel based Tsys
679 flagOut.resize(maskOut.nelements());
680 convertArray(flagOut, maskOut);
681 specCol.put(i, specOut);
682 flagCol.put(i, flagOut);
683 }
684 ++iter;
685 }
686
687 return out;
688}
689
690STMath::imethod STMath::stringToIMethod(const std::string& in)
691{
692 static STMath::imap lookup;
693
694 // initialize the lookup table if necessary
695 if ( lookup.empty() ) {
696 lookup["nearest"] = InterpolateArray1D<Double,Float>::nearestNeighbour;
697 lookup["linear"] = InterpolateArray1D<Double,Float>::linear;
698 lookup["cubic"] = InterpolateArray1D<Double,Float>::cubic;
699 lookup["spline"] = InterpolateArray1D<Double,Float>::spline;
700 }
701
702 STMath::imap::const_iterator iter = lookup.find(in);
703
704 if ( lookup.end() == iter ) {
705 std::string message = in;
706 message += " is not a valid interpolation mode";
707 throw(AipsError(message));
708 }
709 return iter->second;
710}
711
712WeightType STMath::stringToWeight(const std::string& in)
713{
714 static std::map<std::string, WeightType> lookup;
715
716 // initialize the lookup table if necessary
717 if ( lookup.empty() ) {
718 lookup["NONE"] = asap::NONE;
719 lookup["TINT"] = asap::TINT;
720 lookup["TINTSYS"] = asap::TINTSYS;
721 lookup["TSYS"] = asap::TSYS;
722 lookup["VAR"] = asap::VAR;
723 }
724
725 std::map<std::string, WeightType>::const_iterator iter = lookup.find(in);
726
727 if ( lookup.end() == iter ) {
728 std::string message = in;
729 message += " is not a valid weighting mode";
730 throw(AipsError(message));
731 }
732 return iter->second;
733}
734
735CountedPtr< Scantable > STMath::gainElevation( const CountedPtr< Scantable >& in,
736 const vector< float > & coeff,
737 const std::string & filename,
738 const std::string& method)
739{
740 // Get elevation data from Scantable and convert to degrees
741 CountedPtr< Scantable > out = getScantable(in, false);
742 Table& tab = out->table();
743 ROScalarColumn<Float> elev(tab, "ELEVATION");
744 Vector<Float> x = elev.getColumn();
745 x *= Float(180 / C::pi); // Degrees
746
747 Vector<Float> coeffs(coeff);
748 const uInt nc = coeffs.nelements();
749 if ( filename.length() > 0 && nc > 0 ) {
750 throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
751 }
752
753 // Correct
754 if ( nc > 0 || filename.length() == 0 ) {
755 // Find instrument
756 Bool throwit = True;
757 Instrument inst =
758 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"),
759 throwit);
760
761 // Set polynomial
762 Polynomial<Float>* ppoly = 0;
763 Vector<Float> coeff;
764 String msg;
765 if ( nc > 0 ) {
766 ppoly = new Polynomial<Float>(nc);
767 coeff = coeffs;
768 msg = String("user");
769 } else {
770 STAttr sdAttr;
771 coeff = sdAttr.gainElevationPoly(inst);
772 ppoly = new Polynomial<Float>(3);
773 msg = String("built in");
774 }
775
776 if ( coeff.nelements() > 0 ) {
777 ppoly->setCoefficients(coeff);
778 } else {
779 delete ppoly;
780 throw(AipsError("There is no known gain-elevation polynomial known for this instrument"));
781 }
782 ostringstream oss;
783 oss << "Making polynomial correction with " << msg << " coefficients:" << endl;
784 oss << " " << coeff;
785 pushLog(String(oss));
786 const uInt nrow = tab.nrow();
787 Vector<Float> factor(nrow);
788 for ( uInt i=0; i < nrow; ++i ) {
789 factor[i] = 1.0 / (*ppoly)(x[i]);
790 }
791 delete ppoly;
792 scaleByVector(tab, factor, true);
793
794 } else {
795 // Read and correct
796 pushLog("Making correction from ascii Table");
797 scaleFromAsciiTable(tab, filename, method, x, true);
798 }
799 return out;
800}
801
802void STMath::scaleFromAsciiTable(Table& in, const std::string& filename,
803 const std::string& method,
804 const Vector<Float>& xout, bool dotsys)
805{
806
807// Read gain-elevation ascii file data into a Table.
808
809 String formatString;
810 Table tbl = readAsciiTable(formatString, Table::Memory, filename, "", "", False);
811 scaleFromTable(in, tbl, method, xout, dotsys);
812}
813
814void STMath::scaleFromTable(Table& in,
815 const Table& table,
816 const std::string& method,
817 const Vector<Float>& xout, bool dotsys)
818{
819
820 ROScalarColumn<Float> geElCol(table, "ELEVATION");
821 ROScalarColumn<Float> geFacCol(table, "FACTOR");
822 Vector<Float> xin = geElCol.getColumn();
823 Vector<Float> yin = geFacCol.getColumn();
824 Vector<Bool> maskin(xin.nelements(),True);
825
826 // Interpolate (and extrapolate) with desired method
827
828 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
829
830 Vector<Float> yout;
831 Vector<Bool> maskout;
832 InterpolateArray1D<Float,Float>::interpolate(yout, maskout, xout,
833 xin, yin, maskin, interp,
834 True, True);
835
836 scaleByVector(in, Float(1.0)/yout, dotsys);
837}
838
839void STMath::scaleByVector( Table& in,
840 const Vector< Float >& factor,
841 bool dotsys )
842{
843 uInt nrow = in.nrow();
844 if ( factor.nelements() != nrow ) {
845 throw(AipsError("factors.nelements() != table.nelements()"));
846 }
847 ArrayColumn<Float> specCol(in, "SPECTRA");
848 ArrayColumn<uChar> flagCol(in, "FLAGTRA");
849 ArrayColumn<Float> tsysCol(in, "TSYS");
850 for (uInt i=0; i < nrow; ++i) {
851 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
852 ma *= factor[i];
853 specCol.put(i, ma.getArray());
854 flagCol.put(i, flagsFromMA(ma));
855 if ( dotsys ) {
856 Vector<Float> tsys = tsysCol(i);
857 tsys *= factor[i];
858 tsysCol.put(i,tsys);
859 }
860 }
861}
862
863CountedPtr< Scantable > STMath::convertFlux( const CountedPtr< Scantable >& in,
864 float d, float etaap,
865 float jyperk )
866{
867 CountedPtr< Scantable > out = getScantable(in, false);
868 Table& tab = in->table();
869 Unit fluxUnit(tab.keywordSet().asString("FluxUnit"));
870 Unit K(String("K"));
871 Unit JY(String("Jy"));
872
873 bool tokelvin = true;
874 Double cfac = 1.0;
875
876 if ( fluxUnit == JY ) {
877 pushLog("Converting to K");
878 Quantum<Double> t(1.0,fluxUnit);
879 Quantum<Double> t2 = t.get(JY);
880 cfac = (t2 / t).getValue(); // value to Jy
881
882 tokelvin = true;
883 out->setFluxUnit("K");
884 } else if ( fluxUnit == K ) {
885 pushLog("Converting to Jy");
886 Quantum<Double> t(1.0,fluxUnit);
887 Quantum<Double> t2 = t.get(K);
888 cfac = (t2 / t).getValue(); // value to K
889
890 tokelvin = false;
891 out->setFluxUnit("Jy");
892 } else {
893 throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
894 }
895 // Make sure input values are converted to either Jy or K first...
896 Float factor = cfac;
897
898 // Select method
899 if (jyperk > 0.0) {
900 factor *= jyperk;
901 if ( tokelvin ) factor = 1.0 / jyperk;
902 ostringstream oss;
903 oss << "Jy/K = " << jyperk;
904 pushLog(String(oss));
905 Vector<Float> factors(tab.nrow(), factor);
906 scaleByVector(tab,factors, false);
907 } else if ( etaap > 0.0) {
908 Instrument inst =
909 STAttr::convertInstrument(tab.keywordSet().asString("AntennaName"), True);
910 STAttr sda;
911 if (d < 0) d = sda.diameter(inst);
912 jyperk = STAttr::findJyPerK(etaap, d);
913 ostringstream oss;
914 oss << "Jy/K = " << jyperk;
915 pushLog(String(oss));
916 factor *= jyperk;
917 if ( tokelvin ) {
918 factor = 1.0 / factor;
919 }
920 Vector<Float> factors(tab.nrow(), factor);
921 scaleByVector(tab, factors, False);
922 } else {
923
924 // OK now we must deal with automatic look up of values.
925 // We must also deal with the fact that the factors need
926 // to be computed per IF and may be different and may
927 // change per integration.
928
929 pushLog("Looking up conversion factors");
930 convertBrightnessUnits(out, tokelvin, cfac);
931 }
932
933 return out;
934}
935
936void STMath::convertBrightnessUnits( CountedPtr<Scantable>& in,
937 bool tokelvin, float cfac )
938{
939 Table& table = in->table();
940 Instrument inst =
941 STAttr::convertInstrument(table.keywordSet().asString("AntennaName"), True);
942 TableIterator iter(table, "FREQ_ID");
943 STFrequencies stfreqs = in->frequencies();
944 STAttr sdAtt;
945 while (!iter.pastEnd()) {
946 Table tab = iter.table();
947 ArrayColumn<Float> specCol(tab, "SPECTRA");
948 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
949 ROScalarColumn<uInt> freqidCol(tab, "FREQ_ID");
950 MEpoch::ROScalarColumn timeCol(tab, "TIME");
951
952 uInt freqid; freqidCol.get(0, freqid);
953 Vector<Float> tmpspec; specCol.get(0, tmpspec);
954 // STAttr.JyPerK has a Vector interface... change sometime.
955 Vector<Float> freqs(1,stfreqs.getRefFreq(freqid, tmpspec.nelements()));
956 for ( uInt i=0; i<tab.nrow(); ++i) {
957 Float jyperk = (sdAtt.JyPerK(inst, timeCol(i), freqs))[0];
958 Float factor = cfac * jyperk;
959 if ( tokelvin ) factor = Float(1.0) / factor;
960 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
961 ma *= factor;
962 specCol.put(i, ma.getArray());
963 flagCol.put(i, flagsFromMA(ma));
964 }
965 ++iter;
966 }
967}
968
969CountedPtr< Scantable > STMath::opacity( const CountedPtr< Scantable > & in,
970 float tau )
971{
972 CountedPtr< Scantable > out = getScantable(in, false);
973
974 Table tab = out->table();
975 ROScalarColumn<Float> elev(tab, "ELEVATION");
976 ArrayColumn<Float> specCol(tab, "SPECTRA");
977 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
978 for ( uInt i=0; i<tab.nrow(); ++i) {
979 Float zdist = Float(C::pi_2) - elev(i);
980 Float factor = exp(tau/cos(zdist));
981 MaskedArray<Float> ma = maskedArray(specCol(i), flagCol(i));
982 ma *= factor;
983 specCol.put(i, ma.getArray());
984 flagCol.put(i, flagsFromMA(ma));
985 }
986 return out;
987}
988
989CountedPtr< Scantable > STMath::smooth( const CountedPtr< Scantable >& in,
990 const std::string& kernel, float width )
991{
992 CountedPtr< Scantable > out = getScantable(in, false);
993 Table& table = out->table();
994 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernel);
995 // same IFNO should have same no of channels
996 // this saves overhead
997 TableIterator iter(table, "IFNO");
998 while (!iter.pastEnd()) {
999 Table tab = iter.table();
1000 ArrayColumn<Float> specCol(tab, "SPECTRA");
1001 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1002 Vector<Float> tmpspec; specCol.get(0, tmpspec);
1003 uInt nchan = tmpspec.nelements();
1004 Vector<Float> kvec = VectorKernel::make(type, width, nchan, True, False);
1005 Convolver<Float> conv(kvec, IPosition(1,nchan));
1006 Vector<Float> spec;
1007 Vector<uChar> flag;
1008 for ( uInt i=0; i<tab.nrow(); ++i) {
1009 specCol.get(i, spec);
1010 flagCol.get(i, flag);
1011 Vector<Bool> mask(flag.nelements());
1012 convertArray(mask, flag);
1013 Vector<Float> specout;
1014 if ( type == VectorKernel::HANNING ) {
1015 Vector<Bool> maskout;
1016 mathutil::hanning(specout, maskout, spec , !mask);
1017 convertArray(flag, !maskout);
1018 flagCol.put(i, flag);
1019 specCol.put(i, specout);
1020 } else {
1021 mathutil::replaceMaskByZero(specout, mask);
1022 conv.linearConv(specout, spec);
1023 specCol.put(i, specout);
1024 }
1025 }
1026 ++iter;
1027 }
1028 return out;
1029}
1030
1031CountedPtr< Scantable >
1032 STMath::merge( const std::vector< CountedPtr < Scantable > >& in )
1033{
1034 if ( in.size() < 2 ) {
1035 throw(AipsError("Need at least two scantables to perform a merge."));
1036 }
1037 std::vector<CountedPtr < Scantable > >::const_iterator it = in.begin();
1038 bool insitu = insitu_;
1039 setInsitu(false);
1040 CountedPtr< Scantable > out = getScantable(*it, false);
1041 setInsitu(insitu);
1042 Table& tout = out->table();
1043 ScalarColumn<uInt> freqidcol(tout,"FREQ_ID"), molidcol(tout, "MOLECULE_ID");
1044 ScalarColumn<uInt> scannocol(tout,"SCANNO"), focusidcol(tout,"FOCUS_ID");
1045 // Renumber SCANNO to be 0-based
1046 Vector<uInt> scannos = scannocol.getColumn();
1047 uInt offset = min(scannos);
1048 scannos -= offset;
1049 scannocol.putColumn(scannos);
1050 uInt newscanno = max(scannos)+1;
1051 ++it;
1052 while ( it != in.end() ){
1053 if ( ! (*it)->conformant(*out) ) {
1054 // log message: "ignoring scantable i, as it isn't
1055 // conformant with the other(s)"
1056 cerr << "oh oh" << endl;
1057 ++it;
1058 continue;
1059 }
1060 out->appendToHistoryTable((*it)->history());
1061 const Table& tab = (*it)->table();
1062 TableIterator scanit(tab, "SCANNO");
1063 while (!scanit.pastEnd()) {
1064 TableIterator freqit(scanit.table(), "FREQ_ID");
1065 while ( !freqit.pastEnd() ) {
1066 Table thetab = freqit.table();
1067 uInt nrow = tout.nrow();
1068 //tout.addRow(thetab.nrow());
1069 TableCopy::copyRows(tout, thetab, nrow, 0, thetab.nrow());
1070 ROTableRow row(thetab);
1071 for ( uInt i=0; i<thetab.nrow(); ++i) {
1072 uInt k = nrow+i;
1073 scannocol.put(k, newscanno);
1074 const TableRecord& rec = row.get(i);
1075 Double rv,rp,inc;
1076 (*it)->frequencies().getEntry(rp, rv, inc, rec.asuInt("FREQ_ID"));
1077 uInt id;
1078 id = out->frequencies().addEntry(rp, rv, inc);
1079 freqidcol.put(k,id);
1080 String name,fname;Double rf;
1081 (*it)->molecules().getEntry(rf, name, fname, rec.asuInt("MOLECULE_ID"));
1082 id = out->molecules().addEntry(rf, name, fname);
1083 molidcol.put(k, id);
1084 Float frot,fax,ftan,fhand,fmount,fuser, fxy, fxyp;
1085 (*it)->focus().getEntry(fax, ftan, frot, fhand,
1086 fmount,fuser, fxy, fxyp,
1087 rec.asuInt("FOCUS_ID"));
1088 id = out->focus().addEntry(fax, ftan, frot, fhand,
1089 fmount,fuser, fxy, fxyp);
1090 focusidcol.put(k, id);
1091 }
1092 ++freqit;
1093 }
1094 ++newscanno;
1095 ++scanit;
1096 }
1097 ++it;
1098 }
1099 return out;
1100}
1101
1102CountedPtr< Scantable >
1103 STMath::invertPhase( const CountedPtr < Scantable >& in )
1104{
1105 return applyToPol(in, &STPol::invertPhase, Float(0.0));
1106}
1107
1108CountedPtr< Scantable >
1109 STMath::rotateXYPhase( const CountedPtr < Scantable >& in, float phase )
1110{
1111 return applyToPol(in, &STPol::rotatePhase, Float(phase));
1112}
1113
1114CountedPtr< Scantable >
1115 STMath::rotateLinPolPhase( const CountedPtr < Scantable >& in, float phase )
1116{
1117 return applyToPol(in, &STPol::rotateLinPolPhase, Float(phase));
1118}
1119
1120CountedPtr< Scantable > STMath::applyToPol( const CountedPtr<Scantable>& in,
1121 STPol::polOperation fptr,
1122 Float phase )
1123{
1124 CountedPtr< Scantable > out = getScantable(in, false);
1125 Table& tout = out->table();
1126 Block<String> cols(4);
1127 cols[0] = String("SCANNO");
1128 cols[1] = String("BEAMNO");
1129 cols[2] = String("IFNO");
1130 cols[3] = String("CYCLENO");
1131 TableIterator iter(tout, cols);
1132 STPol* stpol = STPol::getPolClass(out->factories_, out->getPolType() );
1133 while (!iter.pastEnd()) {
1134 Table t = iter.table();
1135 ArrayColumn<Float> speccol(t, "SPECTRA");
1136 ScalarColumn<uInt> focidcol(t, "FOCUS_ID");
1137 ScalarColumn<Float> parancol(t, "PARANGLE");
1138 Matrix<Float> pols = speccol.getColumn();
1139 try {
1140 stpol->setSpectra(pols);
1141 Float fang,fhand,parang;
1142 fang = in->focusTable_.getTotalFeedAngle(focidcol(0));
1143 fhand = in->focusTable_.getFeedHand(focidcol(0));
1144 parang = parancol(0);
1145 /// @todo re-enable this
1146 // disable total feed angle to support paralactifying Caswell style
1147 stpol->setPhaseCorrections(parang, -parang, fhand);
1148 (stpol->*fptr)(phase);
1149 speccol.putColumn(stpol->getSpectra());
1150 Matrix<Float> tmp = stpol->getSpectra();
1151 } catch (AipsError& e) {
1152 delete stpol;stpol=0;
1153 throw(e);
1154 }
1155 ++iter;
1156 }
1157 delete stpol;stpol=0;
1158 return out;
1159}
1160
1161CountedPtr< Scantable >
1162 STMath::swapPolarisations( const CountedPtr< Scantable > & in )
1163{
1164 CountedPtr< Scantable > out = getScantable(in, false);
1165 Table& tout = out->table();
1166 Table t0 = tout(tout.col("POLNO") == 0);
1167 Table t1 = tout(tout.col("POLNO") == 1);
1168 if ( t0.nrow() != t1.nrow() )
1169 throw(AipsError("Inconsistent number of polarisations"));
1170 ArrayColumn<Float> speccol0(t0, "SPECTRA");
1171 ArrayColumn<uChar> flagcol0(t0, "FLAGTRA");
1172 ArrayColumn<Float> speccol1(t1, "SPECTRA");
1173 ArrayColumn<uChar> flagcol1(t1, "FLAGTRA");
1174 Matrix<Float> s0 = speccol0.getColumn();
1175 Matrix<uChar> f0 = flagcol0.getColumn();
1176 speccol0.putColumn(speccol1.getColumn());
1177 flagcol0.putColumn(flagcol1.getColumn());
1178 speccol1.putColumn(s0);
1179 flagcol1.putColumn(f0);
1180 return out;
1181}
1182
1183CountedPtr< Scantable >
1184 STMath::averagePolarisations( const CountedPtr< Scantable > & in,
1185 const std::vector<bool>& mask,
1186 const std::string& weight )
1187{
1188 if (in->npol() < 2 )
1189 throw(AipsError("averagePolarisations can only be applied to two or more"
1190 "polarisations"));
1191 bool insitu = insitu_;
1192 setInsitu(false);
1193 CountedPtr< Scantable > pols = getScantable(in, true);
1194 setInsitu(insitu);
1195 Table& tout = pols->table();
1196 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
1197 Table tab = tableCommand(taql, in->table());
1198 if (tab.nrow() == 0 )
1199 throw(AipsError("Could not find any rows with POLNO==0 and POLNO==1"));
1200 TableCopy::copyRows(tout, tab);
1201 TableVector<uInt> vec(tout, "POLNO");
1202 vec = 0;
1203 pols->table_.rwKeywordSet().define("nPol", Int(1));
1204 pols->table_.rwKeywordSet().define("POLTYPE", String("stokes"));
1205 std::vector<CountedPtr<Scantable> > vpols;
1206 vpols.push_back(pols);
1207 CountedPtr< Scantable > out = average(vpols, mask, weight, "SCAN");
1208 return out;
1209}
1210
1211CountedPtr< Scantable >
1212 STMath::averageBeams( const CountedPtr< Scantable > & in,
1213 const std::vector<bool>& mask,
1214 const std::string& weight )
1215{
1216 bool insitu = insitu_;
1217 setInsitu(false);
1218 CountedPtr< Scantable > beams = getScantable(in, false);
1219 setInsitu(insitu);
1220 Table& tout = beams->table();
1221 // give all rows the same BEAMNO
1222 TableVector<uInt> vec(tout, "BEAMNO");
1223 vec = 0;
1224 beams->table_.rwKeywordSet().define("nBeam", Int(1));
1225 std::vector<CountedPtr<Scantable> > vbeams;
1226 vbeams.push_back(beams);
1227 CountedPtr< Scantable > out = average(vbeams, mask, weight, "SCAN");
1228 return out;
1229}
1230
1231
1232CountedPtr< Scantable >
1233 asap::STMath::frequencyAlign( const CountedPtr< Scantable > & in,
1234 const std::string & refTime,
1235 const std::string & method)
1236{
1237 // clone as this is not working insitu
1238 bool insitu = insitu_;
1239 setInsitu(false);
1240 CountedPtr< Scantable > out = getScantable(in, false);
1241 setInsitu(insitu);
1242 Table& tout = out->table();
1243 // Get reference Epoch to time of first row or given String
1244 Unit DAY(String("d"));
1245 MEpoch::Ref epochRef(in->getTimeReference());
1246 MEpoch refEpoch;
1247 if (refTime.length()>0) {
1248 Quantum<Double> qt;
1249 if (MVTime::read(qt,refTime)) {
1250 MVEpoch mv(qt);
1251 refEpoch = MEpoch(mv, epochRef);
1252 } else {
1253 throw(AipsError("Invalid format for Epoch string"));
1254 }
1255 } else {
1256 refEpoch = in->timeCol_(0);
1257 }
1258 MPosition refPos = in->getAntennaPosition();
1259
1260 InterpolateArray1D<Double,Float>::InterpolationMethod interp = stringToIMethod(method);
1261 // test if user frame is different to base frame
1262 if ( in->frequencies().getFrameString(true)
1263 == in->frequencies().getFrameString(false) ) {
1264 throw(AipsError("Can't convert as no output frame has been set"
1265 " (use set_freqframe) or it is aligned already."));
1266 }
1267 MFrequency::Types system = in->frequencies().getFrame();
1268 MVTime mvt(refEpoch.getValue());
1269 String epochout = mvt.string(MVTime::YMD) + String(" (") + refEpoch.getRefString() + String(")");
1270 ostringstream oss;
1271 oss << "Aligned at reference Epoch " << epochout
1272 << " in frame " << MFrequency::showType(system);
1273 pushLog(String(oss));
1274 // set up the iterator
1275 Block<String> cols(4);
1276 // select by constant direction
1277 cols[0] = String("SRCNAME");
1278 cols[1] = String("BEAMNO");
1279 // select by IF ( no of channels varies over this )
1280 cols[2] = String("IFNO");
1281 // select by restfrequency
1282 cols[3] = String("MOLECULE_ID");
1283 TableIterator iter(tout, cols);
1284 while ( !iter.pastEnd() ) {
1285 Table t = iter.table();
1286 MDirection::ROScalarColumn dirCol(t, "DIRECTION");
1287 TableIterator fiter(t, "FREQ_ID");
1288 // determine nchan from the first row. This should work as
1289 // we are iterating over BEAMNO and IFNO // we should have constant direction
1290
1291 ROArrayColumn<Float> sCol(t, "SPECTRA");
1292 MDirection direction = dirCol(0);
1293 uInt nchan = sCol(0).nelements();
1294 while ( !fiter.pastEnd() ) {
1295 Table ftab = fiter.table();
1296 ScalarColumn<uInt> freqidCol(ftab, "FREQ_ID");
1297 // get the SpectralCoordinate for the freqid, which we are iterating over
1298 SpectralCoordinate sC = in->frequencies().getSpectralCoordinate(freqidCol(0));
1299 FrequencyAligner<Float> fa( sC, nchan, refEpoch,
1300 direction, refPos, system );
1301 // realign the SpectralCoordinate and put into the output Scantable
1302 Vector<String> units(1);
1303 units = String("Hz");
1304 Bool linear=True;
1305 SpectralCoordinate sc2 = fa.alignedSpectralCoordinate(linear);
1306 sc2.setWorldAxisUnits(units);
1307 uInt id = out->frequencies().addEntry(sc2.referencePixel()[0],
1308 sc2.referenceValue()[0],
1309 sc2.increment()[0]);
1310 TableVector<uInt> tvec(ftab, "FREQ_ID");
1311 tvec = id;
1312 // create the "global" abcissa for alignment with same FREQ_ID
1313 Vector<Double> abc(nchan);
1314 Double w;
1315 for (uInt i=0; i<nchan; i++) {
1316 sC.toWorld(w,Double(i));
1317 abc[i] = w;
1318 }
1319 // cache abcissa for same time stamps, so iterate over those
1320 TableIterator timeiter(ftab, "TIME");
1321 while ( !timeiter.pastEnd() ) {
1322 Table tab = timeiter.table();
1323 ArrayColumn<Float> specCol(tab, "SPECTRA");
1324 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1325 MEpoch::ROScalarColumn timeCol(tab, "TIME");
1326 // use align abcissa cache after the first row
1327 bool first = true;
1328 // these rows should be just be POLNO
1329 for (int i=0; i<int(tab.nrow()); ++i) {
1330 // input values
1331 Vector<uChar> flag = flagCol(i);
1332 Vector<Bool> mask(flag.shape());
1333 Vector<Float> specOut, spec;
1334 spec = specCol(i);
1335 Vector<Bool> maskOut;Vector<uChar> flagOut;
1336 convertArray(mask, flag);
1337 // alignment
1338 Bool ok = fa.align(specOut, maskOut, abc, spec,
1339 mask, timeCol(i), !first,
1340 interp, False);
1341 // back into scantable
1342 flagOut.resize(maskOut.nelements());
1343 convertArray(flagOut, maskOut);
1344 flagCol.put(i, flagOut);
1345 specCol.put(i, specOut);
1346 // start abcissa caching
1347 first = false;
1348 }
1349 // next timestamp
1350 ++timeiter;
1351 }
1352 // next FREQ_ID
1353 ++fiter;
1354 }
1355 // next aligner
1356 ++iter;
1357 }
1358 // set this afterwards to ensure we are doing insitu correctly.
1359 out->frequencies().setFrame(system, true);
1360 return out;
1361}
1362
1363CountedPtr<Scantable>
1364 asap::STMath::convertPolarisation( const CountedPtr<Scantable>& in,
1365 const std::string & newtype )
1366{
1367 if (in->npol() != 2 && in->npol() != 4)
1368 throw(AipsError("Can only convert two or four polarisations."));
1369 if ( in->getPolType() == newtype )
1370 throw(AipsError("No need to convert."));
1371 if ( ! in->selector_.empty() )
1372 throw(AipsError("Can only convert whole scantable. Unset the selection."));
1373 bool insitu = insitu_;
1374 setInsitu(false);
1375 CountedPtr< Scantable > out = getScantable(in, true);
1376 setInsitu(insitu);
1377 Table& tout = out->table();
1378 tout.rwKeywordSet().define("POLTYPE", String(newtype));
1379
1380 Block<String> cols(4);
1381 cols[0] = "SCANNO";
1382 cols[1] = "CYCLENO";
1383 cols[2] = "BEAMNO";
1384 cols[3] = "IFNO";
1385 TableIterator it(in->originalTable_, cols);
1386 String basetype = in->getPolType();
1387 STPol* stpol = STPol::getPolClass(in->factories_, basetype);
1388 try {
1389 while ( !it.pastEnd() ) {
1390 Table tab = it.table();
1391 uInt row = tab.rowNumbers()[0];
1392 stpol->setSpectra(in->getPolMatrix(row));
1393 Float fang,fhand,parang;
1394 fang = in->focusTable_.getTotalFeedAngle(in->mfocusidCol_(row));
1395 fhand = in->focusTable_.getFeedHand(in->mfocusidCol_(row));
1396 parang = in->paraCol_(row);
1397 /// @todo re-enable this
1398 // disable total feed angle to support paralactifying Caswell style
1399 stpol->setPhaseCorrections(parang, -parang, fhand);
1400 Int npolout = 0;
1401 for (uInt i=0; i<tab.nrow(); ++i) {
1402 Vector<Float> outvec = stpol->getSpectrum(i, newtype);
1403 if ( outvec.nelements() > 0 ) {
1404 tout.addRow();
1405 TableCopy::copyRows(tout, tab, tout.nrow()-1, 0, 1);
1406 ArrayColumn<Float> sCol(tout,"SPECTRA");
1407 ScalarColumn<uInt> pCol(tout,"POLNO");
1408 sCol.put(tout.nrow()-1 ,outvec);
1409 pCol.put(tout.nrow()-1 ,uInt(npolout));
1410 npolout++;
1411 }
1412 }
1413 tout.rwKeywordSet().define("nPol", npolout);
1414 ++it;
1415 }
1416 } catch (AipsError& e) {
1417 delete stpol;
1418 throw(e);
1419 }
1420 delete stpol;
1421 return out;
1422}
1423
1424CountedPtr< Scantable >
1425 asap::STMath::mxExtract( const CountedPtr< Scantable > & in,
1426 const std::string & scantype )
1427{
1428 bool insitu = insitu_;
1429 setInsitu(false);
1430 CountedPtr< Scantable > out = getScantable(in, true);
1431 setInsitu(insitu);
1432 Table& tout = out->table();
1433 std::string taql = "SELECT FROM $1 WHERE BEAMNO != REFBEAMNO";
1434 if (scantype == "on") {
1435 taql = "SELECT FROM $1 WHERE BEAMNO == REFBEAMNO";
1436 }
1437 Table tab = tableCommand(taql, in->table());
1438 TableCopy::copyRows(tout, tab);
1439 if (scantype == "on") {
1440 // re-index SCANNO to 0
1441 TableVector<uInt> vec(tout, "SCANNO");
1442 vec = 0;
1443 }
1444 return out;
1445}
1446
1447CountedPtr< Scantable >
1448 asap::STMath::lagFlag( const CountedPtr< Scantable > & in,
1449 double frequency, double width )
1450{
1451 CountedPtr< Scantable > out = getScantable(in, false);
1452 Table& tout = out->table();
1453 TableIterator iter(tout, "FREQ_ID");
1454 FFTServer<Float,Complex> ffts;
1455 while ( !iter.pastEnd() ) {
1456 Table tab = iter.table();
1457 Double rp,rv,inc;
1458 ROTableRow row(tab);
1459 const TableRecord& rec = row.get(0);
1460 uInt freqid = rec.asuInt("FREQ_ID");
1461 out->frequencies().getEntry(rp, rv, inc, freqid);
1462 ArrayColumn<Float> specCol(tab, "SPECTRA");
1463 ArrayColumn<uChar> flagCol(tab, "FLAGTRA");
1464 for (int i=0; i<int(tab.nrow()); ++i) {
1465 Vector<Float> spec = specCol(i);
1466 Vector<uChar> flag = flagCol(i);
1467 Int lag0 = Int(spec.nelements()*abs(inc)/(frequency+width)+0.5);
1468 Int lag1 = Int(spec.nelements()*abs(inc)/(frequency-width)+0.5);
1469 for (int k=0; k < flag.nelements(); ++k ) {
1470 if (flag[k] > 0) {
1471 spec[k] = 0.0;
1472 }
1473 }
1474 Vector<Complex> lags;
1475 ffts.fft0(lags, spec);
1476 Int start = max(0, lag0);
1477 Int end = min(Int(lags.nelements()-1), lag1);
1478 if (start == end) {
1479 lags[start] = Complex(0.0);
1480 } else {
1481 for (int j=start; j <=end ;++j) {
1482 lags[j] = Complex(0.0);
1483 }
1484 }
1485 ffts.fft0(spec, lags);
1486 specCol.put(i, spec);
1487 }
1488 ++iter;
1489 }
1490 return out;
1491}
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