source: trunk/src/STMath.cpp@ 1250

Last change on this file since 1250 was 1232, checked in by mar637, 18 years ago

Merge from Release2.1.0b tag

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