source: trunk/src/Scantable.cpp@ 2804

Last change on this file since 2804 was 2791, checked in by Malte Marquarding, 12 years ago

Ticket #289: added anility to set Tsys, both for scalar and vector values

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1//
2// C++ Implementation: Scantable
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005-2013
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12#include <map>
13#include <sys/time.h>
14
15#include <atnf/PKSIO/SrcType.h>
16
17#include <casa/aips.h>
18#include <casa/iomanip.h>
19#include <casa/iostream.h>
20#include <casa/OS/File.h>
21#include <casa/OS/Path.h>
22#include <casa/Logging/LogIO.h>
23#include <casa/Arrays/Array.h>
24#include <casa/Arrays/ArrayAccessor.h>
25#include <casa/Arrays/ArrayLogical.h>
26#include <casa/Arrays/ArrayMath.h>
27#include <casa/Arrays/MaskArrMath.h>
28#include <casa/Arrays/Slice.h>
29#include <casa/Arrays/Vector.h>
30#include <casa/Arrays/VectorSTLIterator.h>
31#include <casa/BasicMath/Math.h>
32#include <casa/BasicSL/Constants.h>
33#include <casa/Containers/RecordField.h>
34#include <casa/Logging/LogIO.h>
35#include <casa/Quanta/MVAngle.h>
36#include <casa/Quanta/MVTime.h>
37#include <casa/Utilities/GenSort.h>
38
39#include <coordinates/Coordinates/CoordinateUtil.h>
40
41// needed to avoid error in .tcc
42#include <measures/Measures/MCDirection.h>
43//
44#include <measures/Measures/MDirection.h>
45#include <measures/Measures/MEpoch.h>
46#include <measures/Measures/MFrequency.h>
47#include <measures/Measures/MeasRef.h>
48#include <measures/Measures/MeasTable.h>
49#include <measures/TableMeasures/ScalarMeasColumn.h>
50#include <measures/TableMeasures/TableMeasDesc.h>
51#include <measures/TableMeasures/TableMeasRefDesc.h>
52#include <measures/TableMeasures/TableMeasValueDesc.h>
53
54#include <tables/Tables/ArrColDesc.h>
55#include <tables/Tables/ExprNode.h>
56#include <tables/Tables/ScaColDesc.h>
57#include <tables/Tables/SetupNewTab.h>
58#include <tables/Tables/TableCopy.h>
59#include <tables/Tables/TableDesc.h>
60#include <tables/Tables/TableIter.h>
61#include <tables/Tables/TableParse.h>
62#include <tables/Tables/TableRecord.h>
63#include <tables/Tables/TableRow.h>
64#include <tables/Tables/TableVector.h>
65
66#include "MathUtils.h"
67#include "STAttr.h"
68#include "STBaselineTable.h"
69#include "STLineFinder.h"
70#include "STPolCircular.h"
71#include "STPolLinear.h"
72#include "STPolStokes.h"
73#include "STUpgrade.h"
74#include "STFitter.h"
75#include "Scantable.h"
76
77#define debug 1
78
79using namespace casa;
80
81namespace asap {
82
83std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
84
85void Scantable::initFactories() {
86 if ( factories_.empty() ) {
87 Scantable::factories_["linear"] = &STPolLinear::myFactory;
88 Scantable::factories_["circular"] = &STPolCircular::myFactory;
89 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
90 }
91}
92
93Scantable::Scantable(Table::TableType ttype) :
94 type_(ttype)
95{
96 initFactories();
97 setupMainTable();
98 freqTable_ = STFrequencies(*this);
99 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
100 weatherTable_ = STWeather(*this);
101 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
102 focusTable_ = STFocus(*this);
103 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
104 tcalTable_ = STTcal(*this);
105 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
106 moleculeTable_ = STMolecules(*this);
107 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
108 historyTable_ = STHistory(*this);
109 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
110 fitTable_ = STFit(*this);
111 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
112 table_.tableInfo().setType( "Scantable" ) ;
113 originalTable_ = table_;
114 attach();
115}
116
117Scantable::Scantable(const std::string& name, Table::TableType ttype) :
118 type_(ttype)
119{
120 initFactories();
121
122 Table tab(name, Table::Update);
123 uInt version = tab.keywordSet().asuInt("VERSION");
124 if (version != version_) {
125 STUpgrade upgrader(version_);
126 LogIO os( LogOrigin( "Scantable" ) ) ;
127 os << LogIO::WARN
128 << name << " data format version " << version
129 << " is deprecated" << endl
130 << "Running upgrade."<< endl
131 << LogIO::POST ;
132 std::string outname = upgrader.upgrade(name);
133 if ( outname != name ) {
134 os << LogIO::WARN
135 << "Data will be loaded from " << outname << " instead of "
136 << name << LogIO::POST ;
137 tab = Table(outname, Table::Update ) ;
138 }
139 }
140 if ( type_ == Table::Memory ) {
141 table_ = tab.copyToMemoryTable(generateName());
142 } else {
143 table_ = tab;
144 }
145 table_.tableInfo().setType( "Scantable" ) ;
146
147 attachSubtables();
148 originalTable_ = table_;
149 attach();
150}
151/*
152Scantable::Scantable(const std::string& name, Table::TableType ttype) :
153 type_(ttype)
154{
155 initFactories();
156 Table tab(name, Table::Update);
157 uInt version = tab.keywordSet().asuInt("VERSION");
158 if (version != version_) {
159 throw(AipsError("Unsupported version of ASAP file."));
160 }
161 if ( type_ == Table::Memory ) {
162 table_ = tab.copyToMemoryTable(generateName());
163 } else {
164 table_ = tab;
165 }
166
167 attachSubtables();
168 originalTable_ = table_;
169 attach();
170}
171*/
172
173Scantable::Scantable( const Scantable& other, bool clear )
174{
175 // with or without data
176 String newname = String(generateName());
177 type_ = other.table_.tableType();
178 if ( other.table_.tableType() == Table::Memory ) {
179 if ( clear ) {
180 table_ = TableCopy::makeEmptyMemoryTable(newname,
181 other.table_, True);
182 } else
183 table_ = other.table_.copyToMemoryTable(newname);
184 } else {
185 other.table_.deepCopy(newname, Table::New, False,
186 other.table_.endianFormat(),
187 Bool(clear));
188 table_ = Table(newname, Table::Update);
189 table_.markForDelete();
190 }
191 table_.tableInfo().setType( "Scantable" ) ;
192 /// @todo reindex SCANNO, recompute nbeam, nif, npol
193 if ( clear ) copySubtables(other);
194 attachSubtables();
195 originalTable_ = table_;
196 attach();
197}
198
199void Scantable::copySubtables(const Scantable& other) {
200 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
201 TableCopy::copyRows(t, other.freqTable_.table());
202 t = table_.rwKeywordSet().asTable("FOCUS");
203 TableCopy::copyRows(t, other.focusTable_.table());
204 t = table_.rwKeywordSet().asTable("WEATHER");
205 TableCopy::copyRows(t, other.weatherTable_.table());
206 t = table_.rwKeywordSet().asTable("TCAL");
207 TableCopy::copyRows(t, other.tcalTable_.table());
208 t = table_.rwKeywordSet().asTable("MOLECULES");
209 TableCopy::copyRows(t, other.moleculeTable_.table());
210 t = table_.rwKeywordSet().asTable("HISTORY");
211 TableCopy::copyRows(t, other.historyTable_.table());
212 t = table_.rwKeywordSet().asTable("FIT");
213 TableCopy::copyRows(t, other.fitTable_.table());
214}
215
216void Scantable::attachSubtables()
217{
218 freqTable_ = STFrequencies(table_);
219 focusTable_ = STFocus(table_);
220 weatherTable_ = STWeather(table_);
221 tcalTable_ = STTcal(table_);
222 moleculeTable_ = STMolecules(table_);
223 historyTable_ = STHistory(table_);
224 fitTable_ = STFit(table_);
225}
226
227Scantable::~Scantable()
228{
229}
230
231void Scantable::setupMainTable()
232{
233 TableDesc td("", "1", TableDesc::Scratch);
234 td.comment() = "An ASAP Scantable";
235 td.rwKeywordSet().define("VERSION", uInt(version_));
236
237 // n Cycles
238 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
239 // new index every nBeam x nIF x nPol
240 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
241
242 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
243 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
244 // linear, circular, stokes
245 td.rwKeywordSet().define("POLTYPE", String("linear"));
246 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
247
248 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
249 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
250
251 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
252 refbeamnoColumn.setDefault(Int(-1));
253 td.addColumn(refbeamnoColumn);
254
255 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
256 flagrowColumn.setDefault(uInt(0));
257 td.addColumn(flagrowColumn);
258
259 td.addColumn(ScalarColumnDesc<Double>("TIME"));
260 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
261 TableMeasValueDesc measVal(td, "TIME");
262 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
263 mepochCol.write(td);
264
265 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
266
267 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
268 // Type of source (on=0, off=1, other=-1)
269 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
270 stypeColumn.setDefault(Int(-1));
271 td.addColumn(stypeColumn);
272 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
273
274 //The actual Data Vectors
275 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
276 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
277 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
278
279 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
280 IPosition(1,2),
281 ColumnDesc::Direct));
282 TableMeasRefDesc mdirRef(MDirection::J2000); // default
283 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
284 // the TableMeasDesc gives the column a type
285 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
286 // a uder set table type e.g. GALCTIC, B1950 ...
287 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
288 // writing create the measure column
289 mdirCol.write(td);
290 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
291 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
292 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
293
294 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
295 ScalarColumnDesc<Int> fitColumn("FIT_ID");
296 fitColumn.setDefault(Int(-1));
297 td.addColumn(fitColumn);
298
299 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
300 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
301
302 // columns which just get dragged along, as they aren't used in asap
303 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
304 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
305 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
306 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
307
308 td.rwKeywordSet().define("OBSMODE", String(""));
309
310 // Now create Table SetUp from the description.
311 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
312 table_ = Table(aNewTab, type_, 0);
313 originalTable_ = table_;
314}
315
316void Scantable::attach()
317{
318 timeCol_.attach(table_, "TIME");
319 srcnCol_.attach(table_, "SRCNAME");
320 srctCol_.attach(table_, "SRCTYPE");
321 specCol_.attach(table_, "SPECTRA");
322 flagsCol_.attach(table_, "FLAGTRA");
323 tsysCol_.attach(table_, "TSYS");
324 cycleCol_.attach(table_,"CYCLENO");
325 scanCol_.attach(table_, "SCANNO");
326 beamCol_.attach(table_, "BEAMNO");
327 ifCol_.attach(table_, "IFNO");
328 polCol_.attach(table_, "POLNO");
329 integrCol_.attach(table_, "INTERVAL");
330 azCol_.attach(table_, "AZIMUTH");
331 elCol_.attach(table_, "ELEVATION");
332 dirCol_.attach(table_, "DIRECTION");
333 fldnCol_.attach(table_, "FIELDNAME");
334 rbeamCol_.attach(table_, "REFBEAMNO");
335
336 mweatheridCol_.attach(table_,"WEATHER_ID");
337 mfitidCol_.attach(table_,"FIT_ID");
338 mfreqidCol_.attach(table_, "FREQ_ID");
339 mtcalidCol_.attach(table_, "TCAL_ID");
340 mfocusidCol_.attach(table_, "FOCUS_ID");
341 mmolidCol_.attach(table_, "MOLECULE_ID");
342
343 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
344 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
345
346}
347
348template<class T, class T2>
349void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
350 const String& colName,
351 const T2& defValue)
352{
353 try {
354 col.attach(table_, colName);
355 } catch (TableError& err) {
356 String errMesg = err.getMesg();
357 if (errMesg == "Table column " + colName + " is unknown") {
358 table_.addColumn(ScalarColumnDesc<T>(colName));
359 col.attach(table_, colName);
360 col.fillColumn(static_cast<T>(defValue));
361 } else {
362 throw;
363 }
364 } catch (...) {
365 throw;
366 }
367}
368
369template<class T, class T2>
370void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
371 const String& colName,
372 const Array<T2>& defValue)
373{
374 try {
375 col.attach(table_, colName);
376 } catch (TableError& err) {
377 String errMesg = err.getMesg();
378 if (errMesg == "Table column " + colName + " is unknown") {
379 table_.addColumn(ArrayColumnDesc<T>(colName));
380 col.attach(table_, colName);
381
382 int size = 0;
383 ArrayIterator<T2>& it = defValue.begin();
384 while (it != defValue.end()) {
385 ++size;
386 ++it;
387 }
388 IPosition ip(1, size);
389 Array<T>& arr(ip);
390 for (int i = 0; i < size; ++i)
391 arr[i] = static_cast<T>(defValue[i]);
392
393 col.fillColumn(arr);
394 } else {
395 throw;
396 }
397 } catch (...) {
398 throw;
399 }
400}
401
402void Scantable::setHeader(const STHeader& sdh)
403{
404 table_.rwKeywordSet().define("nIF", sdh.nif);
405 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
406 table_.rwKeywordSet().define("nPol", sdh.npol);
407 table_.rwKeywordSet().define("nChan", sdh.nchan);
408 table_.rwKeywordSet().define("Observer", sdh.observer);
409 table_.rwKeywordSet().define("Project", sdh.project);
410 table_.rwKeywordSet().define("Obstype", sdh.obstype);
411 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
412 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
413 table_.rwKeywordSet().define("Equinox", sdh.equinox);
414 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
415 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
416 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
417 table_.rwKeywordSet().define("UTC", sdh.utc);
418 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
419 table_.rwKeywordSet().define("Epoch", sdh.epoch);
420 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
421}
422
423STHeader Scantable::getHeader() const
424{
425 STHeader sdh;
426 table_.keywordSet().get("nBeam",sdh.nbeam);
427 table_.keywordSet().get("nIF",sdh.nif);
428 table_.keywordSet().get("nPol",sdh.npol);
429 table_.keywordSet().get("nChan",sdh.nchan);
430 table_.keywordSet().get("Observer", sdh.observer);
431 table_.keywordSet().get("Project", sdh.project);
432 table_.keywordSet().get("Obstype", sdh.obstype);
433 table_.keywordSet().get("AntennaName", sdh.antennaname);
434 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
435 table_.keywordSet().get("Equinox", sdh.equinox);
436 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
437 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
438 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
439 table_.keywordSet().get("UTC", sdh.utc);
440 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
441 table_.keywordSet().get("Epoch", sdh.epoch);
442 table_.keywordSet().get("POLTYPE", sdh.poltype);
443 return sdh;
444}
445
446void Scantable::setSourceType( int stype )
447{
448 if ( stype < 0 || stype > 1 )
449 throw(AipsError("Illegal sourcetype."));
450 TableVector<Int> tabvec(table_, "SRCTYPE");
451 tabvec = Int(stype);
452}
453
454bool Scantable::conformant( const Scantable& other )
455{
456 return this->getHeader().conformant(other.getHeader());
457}
458
459
460
461std::string Scantable::formatSec(Double x) const
462{
463 Double xcop = x;
464 MVTime mvt(xcop/24./3600.); // make days
465
466 if (x < 59.95)
467 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
468 else if (x < 3599.95)
469 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
470 else {
471 ostringstream oss;
472 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
473 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
474 return String(oss);
475 }
476};
477
478std::string Scantable::formatDirection(const MDirection& md) const
479{
480 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
481 Int prec = 7;
482
483 String ref = md.getRefString();
484 MVAngle mvLon(t[0]);
485 String sLon = mvLon.string(MVAngle::TIME,prec);
486 uInt tp = md.getRef().getType();
487 if (tp == MDirection::GALACTIC ||
488 tp == MDirection::SUPERGAL ) {
489 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
490 }
491 MVAngle mvLat(t[1]);
492 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
493 return ref + String(" ") + sLon + String(" ") + sLat;
494}
495
496
497std::string Scantable::getFluxUnit() const
498{
499 return table_.keywordSet().asString("FluxUnit");
500}
501
502void Scantable::setFluxUnit(const std::string& unit)
503{
504 String tmp(unit);
505 Unit tU(tmp);
506 if (tU==Unit("K") || tU==Unit("Jy")) {
507 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
508 } else {
509 throw AipsError("Illegal unit - must be compatible with Jy or K");
510 }
511}
512
513void Scantable::setInstrument(const std::string& name)
514{
515 bool throwIt = true;
516 // create an Instrument to see if this is valid
517 STAttr::convertInstrument(name, throwIt);
518 String nameU(name);
519 nameU.upcase();
520 table_.rwKeywordSet().define(String("AntennaName"), nameU);
521}
522
523void Scantable::setFeedType(const std::string& feedtype)
524{
525 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
526 std::string msg = "Illegal feed type "+ feedtype;
527 throw(casa::AipsError(msg));
528 }
529 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
530}
531
532MPosition Scantable::getAntennaPosition() const
533{
534 Vector<Double> antpos;
535 table_.keywordSet().get("AntennaPosition", antpos);
536 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
537 return MPosition(mvpos);
538}
539
540void Scantable::makePersistent(const std::string& filename)
541{
542 String inname(filename);
543 Path path(inname);
544 /// @todo reindex SCANNO, recompute nbeam, nif, npol
545 inname = path.expandedName();
546 // 2011/03/04 TN
547 // We can comment out this workaround since the essential bug is
548 // fixed in casacore (r20889 in google code).
549 table_.deepCopy(inname, Table::New);
550// // WORKAROUND !!! for Table bug
551// // Remove when fixed in casacore
552// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
553// Table tab = table_.copyToMemoryTable(generateName());
554// tab.deepCopy(inname, Table::New);
555// tab.markForDelete();
556//
557// } else {
558// table_.deepCopy(inname, Table::New);
559// }
560}
561
562int Scantable::nbeam( int scanno ) const
563{
564 if ( scanno < 0 ) {
565 Int n;
566 table_.keywordSet().get("nBeam",n);
567 return int(n);
568 } else {
569 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
570 Table t = table_(table_.col("SCANNO") == scanno);
571 ROTableRow row(t);
572 const TableRecord& rec = row.get(0);
573 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
574 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
575 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
576 ROTableVector<uInt> v(subt, "BEAMNO");
577 return int(v.nelements());
578 }
579 return 0;
580}
581
582int Scantable::nif( int scanno ) const
583{
584 if ( scanno < 0 ) {
585 Int n;
586 table_.keywordSet().get("nIF",n);
587 return int(n);
588 } else {
589 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
590 Table t = table_(table_.col("SCANNO") == scanno);
591 ROTableRow row(t);
592 const TableRecord& rec = row.get(0);
593 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
594 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
595 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
596 if ( subt.nrow() == 0 ) return 0;
597 ROTableVector<uInt> v(subt, "IFNO");
598 return int(v.nelements());
599 }
600 return 0;
601}
602
603int Scantable::npol( int scanno ) const
604{
605 if ( scanno < 0 ) {
606 Int n;
607 table_.keywordSet().get("nPol",n);
608 return n;
609 } else {
610 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
611 Table t = table_(table_.col("SCANNO") == scanno);
612 ROTableRow row(t);
613 const TableRecord& rec = row.get(0);
614 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
615 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
616 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
617 if ( subt.nrow() == 0 ) return 0;
618 ROTableVector<uInt> v(subt, "POLNO");
619 return int(v.nelements());
620 }
621 return 0;
622}
623
624int Scantable::ncycle( int scanno ) const
625{
626 if ( scanno < 0 ) {
627 Block<String> cols(2);
628 cols[0] = "SCANNO";
629 cols[1] = "CYCLENO";
630 TableIterator it(table_, cols);
631 int n = 0;
632 while ( !it.pastEnd() ) {
633 ++n;
634 ++it;
635 }
636 return n;
637 } else {
638 Table t = table_(table_.col("SCANNO") == scanno);
639 ROTableRow row(t);
640 const TableRecord& rec = row.get(0);
641 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
642 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
643 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
644 if ( subt.nrow() == 0 ) return 0;
645 return int(subt.nrow());
646 }
647 return 0;
648}
649
650
651int Scantable::nrow( int scanno ) const
652{
653 return int(table_.nrow());
654}
655
656int Scantable::nchan( int ifno ) const
657{
658 if ( ifno < 0 ) {
659 Int n;
660 table_.keywordSet().get("nChan",n);
661 return int(n);
662 } else {
663 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
664 // vary with these
665 Table t = table_(table_.col("IFNO") == ifno, 1);
666 if ( t.nrow() == 0 ) return 0;
667 ROArrayColumn<Float> v(t, "SPECTRA");
668 return v.shape(0)(0);
669 }
670 return 0;
671}
672
673int Scantable::nscan() const {
674 Vector<uInt> scannos(scanCol_.getColumn());
675 uInt nout = genSort( scannos, Sort::Ascending,
676 Sort::QuickSort|Sort::NoDuplicates );
677 return int(nout);
678}
679
680int Scantable::getChannels(int whichrow) const
681{
682 return specCol_.shape(whichrow)(0);
683}
684
685int Scantable::getBeam(int whichrow) const
686{
687 return beamCol_(whichrow);
688}
689
690std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
691{
692 Vector<uInt> nos(col.getColumn());
693 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
694 nos.resize(n, True);
695 std::vector<uint> stlout;
696 nos.tovector(stlout);
697 return stlout;
698}
699
700int Scantable::getIF(int whichrow) const
701{
702 return ifCol_(whichrow);
703}
704
705int Scantable::getPol(int whichrow) const
706{
707 return polCol_(whichrow);
708}
709
710std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
711{
712 return formatTime(me, showdate, 0);
713}
714
715std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
716{
717 MVTime mvt(me.getValue());
718 if (showdate)
719 //mvt.setFormat(MVTime::YMD);
720 mvt.setFormat(MVTime::YMD, prec);
721 else
722 //mvt.setFormat(MVTime::TIME);
723 mvt.setFormat(MVTime::TIME, prec);
724 ostringstream oss;
725 oss << mvt;
726 return String(oss);
727}
728
729void Scantable::calculateAZEL()
730{
731 LogIO os( LogOrigin( "Scantable", "calculateAZEL()", WHERE ) ) ;
732 MPosition mp = getAntennaPosition();
733 MEpoch::ROScalarColumn timeCol(table_, "TIME");
734 ostringstream oss;
735 oss << mp;
736 os << "Computed azimuth/elevation using " << endl
737 << String(oss) << endl;
738 for (Int i=0; i<nrow(); ++i) {
739 MEpoch me = timeCol(i);
740 MDirection md = getDirection(i);
741 os << " Time: " << formatTime(me,False)
742 << " Direction: " << formatDirection(md)
743 << endl << " => ";
744 MeasFrame frame(mp, me);
745 Vector<Double> azel =
746 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
747 frame)
748 )().getAngle("rad").getValue();
749 azCol_.put(i,Float(azel[0]));
750 elCol_.put(i,Float(azel[1]));
751 os << "azel: " << azel[0]/C::pi*180.0 << " "
752 << azel[1]/C::pi*180.0 << " (deg)" << LogIO::POST;
753 }
754}
755
756void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
757{
758 for (uInt i=0; i<table_.nrow(); ++i) {
759 Vector<uChar> flgs = flagsCol_(i);
760 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
761 flagsCol_.put(i, flgs);
762 }
763}
764
765std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
766{
767 Vector<uChar> flags;
768 flagsCol_.get(uInt(whichrow), flags);
769 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
770 Vector<Bool> bflag(flags.shape());
771 convertArray(bflag, flags);
772 //bflag = !bflag;
773
774 std::vector<bool> mask;
775 bflag.tovector(mask);
776 return mask;
777}
778
779void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
780 Vector<uChar> flgs)
781{
782 Vector<Float> spcs = specCol_(whichrow);
783 uInt nchannel = spcs.nelements();
784 if (spcs.nelements() != nchannel) {
785 throw(AipsError("Data has incorrect number of channels"));
786 }
787 uChar userflag = 1 << 7;
788 if (unflag) {
789 userflag = 0 << 7;
790 }
791 if (clipoutside) {
792 for (uInt j = 0; j < nchannel; ++j) {
793 Float spc = spcs(j);
794 if ((spc >= uthres) || (spc <= dthres)) {
795 flgs(j) = userflag;
796 }
797 }
798 } else {
799 for (uInt j = 0; j < nchannel; ++j) {
800 Float spc = spcs(j);
801 if ((spc < uthres) && (spc > dthres)) {
802 flgs(j) = userflag;
803 }
804 }
805 }
806}
807
808
809void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
810 std::vector<bool>::const_iterator it;
811 uInt ntrue = 0;
812 if (whichrow >= int(table_.nrow()) ) {
813 throw(AipsError("Invalid row number"));
814 }
815 for (it = msk.begin(); it != msk.end(); ++it) {
816 if ( *it ) {
817 ntrue++;
818 }
819 }
820 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
821 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
822 throw(AipsError("Trying to flag whole scantable."));
823 uChar userflag = 1 << 7;
824 if ( unflag ) {
825 userflag = 0 << 7;
826 }
827 if (whichrow > -1 ) {
828 applyChanFlag(uInt(whichrow), msk, userflag);
829 } else {
830 for ( uInt i=0; i<table_.nrow(); ++i) {
831 applyChanFlag(i, msk, userflag);
832 }
833 }
834}
835
836void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
837{
838 if (whichrow >= table_.nrow() ) {
839 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
840 }
841 Vector<uChar> flgs = flagsCol_(whichrow);
842 if ( msk.size() == 0 ) {
843 flgs = flagval;
844 flagsCol_.put(whichrow, flgs);
845 return;
846 }
847 if ( int(msk.size()) != nchan( getIF(whichrow) ) ) {
848 throw(AipsError("Mask has incorrect number of channels."));
849 }
850 if ( flgs.nelements() != msk.size() ) {
851 throw(AipsError("Mask has incorrect number of channels."
852 " Probably varying with IF. Please flag per IF"));
853 }
854 std::vector<bool>::const_iterator it;
855 uInt j = 0;
856 for (it = msk.begin(); it != msk.end(); ++it) {
857 if ( *it ) {
858 flgs(j) = flagval;
859 }
860 ++j;
861 }
862 flagsCol_.put(whichrow, flgs);
863}
864
865void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
866{
867 if (selector_.empty() && (rows.size() == table_.nrow()) && !unflag)
868 throw(AipsError("Trying to flag whole scantable."));
869
870 uInt rowflag = (unflag ? 0 : 1);
871 std::vector<uInt>::const_iterator it;
872 for (it = rows.begin(); it != rows.end(); ++it)
873 flagrowCol_.put(*it, rowflag);
874}
875
876std::vector<bool> Scantable::getMask(int whichrow) const
877{
878 Vector<uChar> flags;
879 flagsCol_.get(uInt(whichrow), flags);
880 Vector<Bool> bflag(flags.shape());
881 convertArray(bflag, flags);
882 bflag = !bflag;
883 std::vector<bool> mask;
884 bflag.tovector(mask);
885 return mask;
886}
887
888std::vector<float> Scantable::getSpectrum( int whichrow,
889 const std::string& poltype ) const
890{
891 LogIO os( LogOrigin( "Scantable", "getSpectrum()", WHERE ) ) ;
892
893 String ptype = poltype;
894 if (poltype == "" ) ptype = getPolType();
895 if ( whichrow < 0 || whichrow >= nrow() )
896 throw(AipsError("Illegal row number."));
897 std::vector<float> out;
898 Vector<Float> arr;
899 uInt requestedpol = polCol_(whichrow);
900 String basetype = getPolType();
901 if ( ptype == basetype ) {
902 specCol_.get(whichrow, arr);
903 } else {
904 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
905 basetype));
906 uInt row = uInt(whichrow);
907 stpol->setSpectra(getPolMatrix(row));
908 Float fang,fhand;
909 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
910 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
911 stpol->setPhaseCorrections(fang, fhand);
912 arr = stpol->getSpectrum(requestedpol, ptype);
913 }
914 if ( arr.nelements() == 0 )
915
916 os << "Not enough polarisations present to do the conversion."
917 << LogIO::POST;
918 arr.tovector(out);
919 return out;
920}
921
922void Scantable::setSpectrum( const std::vector<float>& spec,
923 int whichrow )
924{
925 Vector<Float> spectrum(spec);
926 Vector<Float> arr;
927 specCol_.get(whichrow, arr);
928 if ( spectrum.nelements() != arr.nelements() )
929 throw AipsError("The spectrum has incorrect number of channels.");
930 specCol_.put(whichrow, spectrum);
931}
932
933
934String Scantable::generateName()
935{
936 return (File::newUniqueName("./","temp")).baseName();
937}
938
939const casa::Table& Scantable::table( ) const
940{
941 return table_;
942}
943
944casa::Table& Scantable::table( )
945{
946 return table_;
947}
948
949std::string Scantable::getPolType() const
950{
951 return table_.keywordSet().asString("POLTYPE");
952}
953
954void Scantable::unsetSelection()
955{
956 table_ = originalTable_;
957 attach();
958 selector_.reset();
959}
960
961void Scantable::setSelection( const STSelector& selection )
962{
963 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
964 if ( tab.nrow() == 0 ) {
965 throw(AipsError("Selection contains no data. Not applying it."));
966 }
967 table_ = tab;
968 attach();
969// tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
970// vector<uint> selectedIFs = getIFNos() ;
971// Int newnIF = selectedIFs.size() ;
972// tab.rwKeywordSet().define("nIF",newnIF) ;
973// if ( newnIF != 0 ) {
974// Int newnChan = 0 ;
975// for ( Int i = 0 ; i < newnIF ; i++ ) {
976// Int nChan = nchan( selectedIFs[i] ) ;
977// if ( newnChan > nChan )
978// newnChan = nChan ;
979// }
980// tab.rwKeywordSet().define("nChan",newnChan) ;
981// }
982// tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
983 selector_ = selection;
984}
985
986
987std::string Scantable::headerSummary()
988{
989 // Format header info
990// STHeader sdh;
991// sdh = getHeader();
992// sdh.print();
993 ostringstream oss;
994 oss.flags(std::ios_base::left);
995 String tmp;
996 // Project
997 table_.keywordSet().get("Project", tmp);
998 oss << setw(15) << "Project:" << tmp << endl;
999 // Observation date
1000 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1001 // Observer
1002 oss << setw(15) << "Observer:"
1003 << table_.keywordSet().asString("Observer") << endl;
1004 // Antenna Name
1005 table_.keywordSet().get("AntennaName", tmp);
1006 oss << setw(15) << "Antenna Name:" << tmp << endl;
1007 // Obs type
1008 table_.keywordSet().get("Obstype", tmp);
1009 // Records (nrow)
1010 oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl;
1011 oss << setw(15) << "Obs. Type:" << tmp << endl;
1012 // Beams, IFs, Polarizations, and Channels
1013 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1014 << setw(15) << "IFs:" << setw(4) << nif() << endl
1015 << setw(15) << "Polarisations:" << setw(4) << npol()
1016 << "(" << getPolType() << ")" << endl
1017 << setw(15) << "Channels:" << nchan() << endl;
1018 // Flux unit
1019 table_.keywordSet().get("FluxUnit", tmp);
1020 oss << setw(15) << "Flux Unit:" << tmp << endl;
1021 // Abscissa Unit
1022 oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl;
1023 // Selection
1024 oss << selector_.print() << endl;
1025
1026 return String(oss);
1027}
1028
1029void Scantable::summary( const std::string& filename )
1030{
1031 ostringstream oss;
1032 ofstream ofs;
1033 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1034
1035 if (filename != "")
1036 ofs.open( filename.c_str(), ios::out );
1037
1038 oss << endl;
1039 oss << asap::SEPERATOR << endl;
1040 oss << " Scan Table Summary" << endl;
1041 oss << asap::SEPERATOR << endl;
1042
1043 // Format header info
1044 oss << headerSummary();
1045 oss << endl;
1046
1047 if (table_.nrow() <= 0){
1048 oss << asap::SEPERATOR << endl;
1049 oss << "The MAIN table is empty: there are no data!!!" << endl;
1050 oss << asap::SEPERATOR << endl;
1051
1052 ols << String(oss) << LogIO::POST;
1053 if (ofs) {
1054 ofs << String(oss) << flush;
1055 ofs.close();
1056 }
1057 return;
1058 }
1059
1060
1061
1062 // main table
1063 String dirtype = "Position ("
1064 + getDirectionRefString()
1065 + ")";
1066 oss.flags(std::ios_base::left);
1067 oss << setw(5) << "Scan"
1068 << setw(15) << "Source"
1069 << setw(35) << "Time range"
1070 << setw(2) << "" << setw(7) << "Int[s]"
1071 << setw(7) << "Record"
1072 << setw(8) << "SrcType"
1073 << setw(8) << "FreqIDs"
1074 << setw(7) << "MolIDs" << endl;
1075 oss << setw(7)<< "" << setw(6) << "Beam"
1076 << setw(23) << dirtype << endl;
1077
1078 oss << asap::SEPERATOR << endl;
1079
1080 // Flush summary and clear up the string
1081 ols << String(oss) << LogIO::POST;
1082 if (ofs) ofs << String(oss) << flush;
1083 oss.str("");
1084 oss.clear();
1085
1086
1087 // Get Freq_ID map
1088 ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID");
1089 Int nfid = ftabIds.nrow();
1090 if (nfid <= 0){
1091 oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl;
1092 oss << asap::SEPERATOR << endl;
1093
1094 ols << String(oss) << LogIO::POST;
1095 if (ofs) {
1096 ofs << String(oss) << flush;
1097 ofs.close();
1098 }
1099 return;
1100 }
1101 // Storages of overall IFNO, POLNO, and nchan per FREQ_ID
1102 // the orders are identical to ID in FREQ subtable
1103 Block< Vector<uInt> > ifNos(nfid), polNos(nfid);
1104 Vector<Int> fIdchans(nfid,-1);
1105 map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair
1106 for (Int i=0; i < nfid; i++){
1107 // fidMap[freqId] returns row number in FREQ subtable
1108 fidMap.insert(pair<uInt, Int>(ftabIds(i),i));
1109 ifNos[i] = Vector<uInt>();
1110 polNos[i] = Vector<uInt>();
1111 }
1112
1113 TableIterator iter(table_, "SCANNO");
1114
1115 // Vars for keeping track of time, freqids, molIds in a SCANNO
1116 Vector<uInt> freqids;
1117 Vector<uInt> molids;
1118 Vector<uInt> beamids(1,0);
1119 Vector<MDirection> beamDirs;
1120 Vector<Int> stypeids(1,0);
1121 Vector<String> stypestrs;
1122 Int nfreq(1);
1123 Int nmol(1);
1124 uInt nbeam(1);
1125 uInt nstype(1);
1126
1127 Double btime(0.0), etime(0.0);
1128 Double meanIntTim(0.0);
1129
1130 uInt currFreqId(0), ftabRow(0);
1131 Int iflen(0), pollen(0);
1132
1133 while (!iter.pastEnd()) {
1134 Table subt = iter.table();
1135 uInt snrow = subt.nrow();
1136 ROTableRow row(subt);
1137 const TableRecord& rec = row.get(0);
1138
1139 // relevant columns
1140 ROScalarColumn<Double> mjdCol(subt,"TIME");
1141 ROScalarColumn<Double> intervalCol(subt,"INTERVAL");
1142 MDirection::ROScalarColumn dirCol(subt,"DIRECTION");
1143
1144 ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID");
1145 ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID");
1146 ROScalarColumn<uInt> beamCol(subt,"BEAMNO");
1147 ROScalarColumn<Int> stypeCol(subt,"SRCTYPE");
1148
1149 ROScalarColumn<uInt> ifNoCol(subt,"IFNO");
1150 ROScalarColumn<uInt> polNoCol(subt,"POLNO");
1151
1152
1153 // Times
1154 meanIntTim = sum(intervalCol.getColumn()) / (double) snrow;
1155 minMax(btime, etime, mjdCol.getColumn());
1156 etime += meanIntTim/C::day;
1157
1158 // MOLECULE_ID and FREQ_ID
1159 molids = getNumbers(molIdCol);
1160 molids.shape(nmol);
1161
1162 freqids = getNumbers(freqIdCol);
1163 freqids.shape(nfreq);
1164
1165 // Add first beamid, and srcNames
1166 beamids.resize(1,False);
1167 beamDirs.resize(1,False);
1168 beamids(0)=beamCol(0);
1169 beamDirs(0)=dirCol(0);
1170 nbeam = 1;
1171
1172 stypeids.resize(1,False);
1173 stypeids(0)=stypeCol(0);
1174 nstype = 1;
1175
1176 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1177 currFreqId=freqIdCol(0);
1178 ftabRow = fidMap[currFreqId];
1179 // Assumes an identical number of channels per FREQ_ID
1180 if (fIdchans(ftabRow) < 0 ) {
1181 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1182 fIdchans(ftabRow)=(*spec).shape()(0);
1183 }
1184 // Should keep ifNos and polNos form the previous SCANNO
1185 if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) {
1186 ifNos[ftabRow].shape(iflen);
1187 iflen++;
1188 ifNos[ftabRow].resize(iflen,True);
1189 ifNos[ftabRow](iflen-1) = ifNoCol(0);
1190 }
1191 if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) {
1192 polNos[ftabRow].shape(pollen);
1193 pollen++;
1194 polNos[ftabRow].resize(pollen,True);
1195 polNos[ftabRow](pollen-1) = polNoCol(0);
1196 }
1197
1198 for (uInt i=1; i < snrow; i++){
1199 // Need to list BEAMNO and DIRECTION in the same order
1200 if ( !anyEQ(beamids,beamCol(i)) ) {
1201 nbeam++;
1202 beamids.resize(nbeam,True);
1203 beamids(nbeam-1)=beamCol(i);
1204 beamDirs.resize(nbeam,True);
1205 beamDirs(nbeam-1)=dirCol(i);
1206 }
1207
1208 // SRCTYPE is Int (getNumber takes only uInt)
1209 if ( !anyEQ(stypeids,stypeCol(i)) ) {
1210 nstype++;
1211 stypeids.resize(nstype,True);
1212 stypeids(nstype-1)=stypeCol(i);
1213 }
1214
1215 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1216 currFreqId=freqIdCol(i);
1217 ftabRow = fidMap[currFreqId];
1218 if (fIdchans(ftabRow) < 0 ) {
1219 const TableRecord& rec = row.get(i);
1220 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1221 fIdchans(ftabRow) = (*spec).shape()(0);
1222 }
1223 if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) {
1224 ifNos[ftabRow].shape(iflen);
1225 iflen++;
1226 ifNos[ftabRow].resize(iflen,True);
1227 ifNos[ftabRow](iflen-1) = ifNoCol(i);
1228 }
1229 if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) {
1230 polNos[ftabRow].shape(pollen);
1231 pollen++;
1232 polNos[ftabRow].resize(pollen,True);
1233 polNos[ftabRow](pollen-1) = polNoCol(i);
1234 }
1235 } // end of row iteration
1236
1237 stypestrs.resize(nstype,False);
1238 for (uInt j=0; j < nstype; j++)
1239 stypestrs(j) = SrcType::getName(stypeids(j));
1240
1241 // Format Scan summary
1242 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1243 << std::left << setw(1) << ""
1244 << setw(15) << rec.asString("SRCNAME")
1245 << setw(21) << MVTime(btime).string(MVTime::YMD,7)
1246 << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7)
1247 << setw(3) << "" << setw(6) << meanIntTim << setw(1) << ""
1248 << std::right << setw(5) << snrow << setw(2) << ""
1249 << std::left << stypestrs << setw(1) << ""
1250 << freqids << setw(1) << ""
1251 << molids << endl;
1252 // Format Beam summary
1253 for (uInt j=0; j < nbeam; j++) {
1254 oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << ""
1255 << formatDirection(beamDirs(j)) << endl;
1256 }
1257 // Flush summary every scan and clear up the string
1258 ols << String(oss) << LogIO::POST;
1259 if (ofs) ofs << String(oss) << flush;
1260 oss.str("");
1261 oss.clear();
1262
1263 ++iter;
1264 } // end of scan iteration
1265 oss << asap::SEPERATOR << endl;
1266
1267 // List FRECUENCIES Table (using STFrequencies.print may be slow)
1268 oss << "FREQUENCIES: " << nfreq << endl;
1269 oss << std::right << setw(5) << "ID" << setw(2) << ""
1270 << std::left << setw(5) << "IFNO" << setw(2) << ""
1271 << setw(8) << "Frame"
1272 << setw(16) << "RefVal"
1273 << setw(7) << "RefPix"
1274 << setw(15) << "Increment"
1275 << setw(9) << "Channels"
1276 << setw(6) << "POLNOs" << endl;
1277 Int tmplen;
1278 for (Int i=0; i < nfid; i++){
1279 // List row=i of FREQUENCIES subtable
1280 ifNos[i].shape(tmplen);
1281 if (tmplen >= 1) {
1282 oss << std::right << setw(5) << ftabIds(i) << setw(2) << ""
1283 << setw(3) << ifNos[i](0) << setw(1) << ""
1284 << std::left << setw(46) << frequencies().print(ftabIds(i))
1285 << setw(2) << ""
1286 << std::right << setw(8) << fIdchans[i] << setw(2) << ""
1287 << std::left << polNos[i];
1288 if (tmplen > 1) {
1289 oss << " (" << tmplen << " chains)";
1290 }
1291 oss << endl;
1292 }
1293
1294 }
1295 oss << asap::SEPERATOR << endl;
1296
1297 // List MOLECULES Table (currently lists all rows)
1298 oss << "MOLECULES: " << endl;
1299 if (molecules().nrow() <= 0) {
1300 oss << " MOLECULES subtable is empty: there are no data" << endl;
1301 } else {
1302 ROTableRow row(molecules().table());
1303 oss << std::right << setw(5) << "ID"
1304 << std::left << setw(3) << ""
1305 << setw(18) << "RestFreq"
1306 << setw(15) << "Name" << endl;
1307 for (Int i=0; i < molecules().nrow(); i++){
1308 const TableRecord& rec=row.get(i);
1309 oss << std::right << setw(5) << rec.asuInt("ID")
1310 << std::left << setw(3) << ""
1311 << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << ""
1312 << rec.asArrayString("NAME") << endl;
1313 }
1314 }
1315 oss << asap::SEPERATOR << endl;
1316 ols << String(oss) << LogIO::POST;
1317 if (ofs) {
1318 ofs << String(oss) << flush;
1319 ofs.close();
1320 }
1321 // return String(oss);
1322}
1323
1324
1325std::string Scantable::oldheaderSummary()
1326{
1327 // Format header info
1328// STHeader sdh;
1329// sdh = getHeader();
1330// sdh.print();
1331 ostringstream oss;
1332 oss.flags(std::ios_base::left);
1333 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1334 << setw(15) << "IFs:" << setw(4) << nif() << endl
1335 << setw(15) << "Polarisations:" << setw(4) << npol()
1336 << "(" << getPolType() << ")" << endl
1337 << setw(15) << "Channels:" << nchan() << endl;
1338 String tmp;
1339 oss << setw(15) << "Observer:"
1340 << table_.keywordSet().asString("Observer") << endl;
1341 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1342 table_.keywordSet().get("Project", tmp);
1343 oss << setw(15) << "Project:" << tmp << endl;
1344 table_.keywordSet().get("Obstype", tmp);
1345 oss << setw(15) << "Obs. Type:" << tmp << endl;
1346 table_.keywordSet().get("AntennaName", tmp);
1347 oss << setw(15) << "Antenna Name:" << tmp << endl;
1348 table_.keywordSet().get("FluxUnit", tmp);
1349 oss << setw(15) << "Flux Unit:" << tmp << endl;
1350 int nid = moleculeTable_.nrow();
1351 Bool firstline = True;
1352 oss << setw(15) << "Rest Freqs:";
1353 for (int i=0; i<nid; i++) {
1354 Table t = table_(table_.col("MOLECULE_ID") == i, 1);
1355 if (t.nrow() > 0) {
1356 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
1357 if (vec.nelements() > 0) {
1358 if (firstline) {
1359 oss << setprecision(10) << vec << " [Hz]" << endl;
1360 firstline=False;
1361 }
1362 else{
1363 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1364 }
1365 } else {
1366 oss << "none" << endl;
1367 }
1368 }
1369 }
1370
1371 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
1372 oss << selector_.print() << endl;
1373 return String(oss);
1374}
1375
1376 //std::string Scantable::summary( const std::string& filename )
1377void Scantable::oldsummary( const std::string& filename )
1378{
1379 ostringstream oss;
1380 ofstream ofs;
1381 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1382
1383 if (filename != "")
1384 ofs.open( filename.c_str(), ios::out );
1385
1386 oss << endl;
1387 oss << asap::SEPERATOR << endl;
1388 oss << " Scan Table Summary" << endl;
1389 oss << asap::SEPERATOR << endl;
1390
1391 // Format header info
1392 oss << oldheaderSummary();
1393 oss << endl;
1394
1395 // main table
1396 String dirtype = "Position ("
1397 + getDirectionRefString()
1398 + ")";
1399 oss.flags(std::ios_base::left);
1400 oss << setw(5) << "Scan" << setw(15) << "Source"
1401 << setw(10) << "Time" << setw(18) << "Integration"
1402 << setw(15) << "Source Type" << endl;
1403 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
1404 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
1405 << setw(8) << "Frame" << setw(16)
1406 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1407 << setw(7) << "Channels"
1408 << endl;
1409 oss << asap::SEPERATOR << endl;
1410
1411 // Flush summary and clear up the string
1412 ols << String(oss) << LogIO::POST;
1413 if (ofs) ofs << String(oss) << flush;
1414 oss.str("");
1415 oss.clear();
1416
1417 TableIterator iter(table_, "SCANNO");
1418 while (!iter.pastEnd()) {
1419 Table subt = iter.table();
1420 ROTableRow row(subt);
1421 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1422 const TableRecord& rec = row.get(0);
1423 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1424 << std::left << setw(1) << ""
1425 << setw(15) << rec.asString("SRCNAME")
1426 << setw(10) << formatTime(timeCol(0), false);
1427 // count the cycles in the scan
1428 TableIterator cyciter(subt, "CYCLENO");
1429 int nint = 0;
1430 while (!cyciter.pastEnd()) {
1431 ++nint;
1432 ++cyciter;
1433 }
1434 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
1435 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1436 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
1437
1438 TableIterator biter(subt, "BEAMNO");
1439 while (!biter.pastEnd()) {
1440 Table bsubt = biter.table();
1441 ROTableRow brow(bsubt);
1442 const TableRecord& brec = brow.get(0);
1443 uInt row0 = bsubt.rowNumbers(table_)[0];
1444 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
1445 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
1446 TableIterator iiter(bsubt, "IFNO");
1447 while (!iiter.pastEnd()) {
1448 Table isubt = iiter.table();
1449 ROTableRow irow(isubt);
1450 const TableRecord& irec = irow.get(0);
1451 oss << setw(9) << "";
1452 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
1453 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1454 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
1455 << endl;
1456
1457 ++iiter;
1458 }
1459 ++biter;
1460 }
1461 // Flush summary every scan and clear up the string
1462 ols << String(oss) << LogIO::POST;
1463 if (ofs) ofs << String(oss) << flush;
1464 oss.str("");
1465 oss.clear();
1466
1467 ++iter;
1468 }
1469 oss << asap::SEPERATOR << endl;
1470 ols << String(oss) << LogIO::POST;
1471 if (ofs) {
1472 ofs << String(oss) << flush;
1473 ofs.close();
1474 }
1475 // return String(oss);
1476}
1477
1478// std::string Scantable::getTime(int whichrow, bool showdate) const
1479// {
1480// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1481// MEpoch me;
1482// if (whichrow > -1) {
1483// me = timeCol(uInt(whichrow));
1484// } else {
1485// Double tm;
1486// table_.keywordSet().get("UTC",tm);
1487// me = MEpoch(MVEpoch(tm));
1488// }
1489// return formatTime(me, showdate);
1490// }
1491
1492std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
1493{
1494 MEpoch me;
1495 me = getEpoch(whichrow);
1496 return formatTime(me, showdate, prec);
1497}
1498
1499MEpoch Scantable::getEpoch(int whichrow) const
1500{
1501 if (whichrow > -1) {
1502 return timeCol_(uInt(whichrow));
1503 } else {
1504 Double tm;
1505 table_.keywordSet().get("UTC",tm);
1506 return MEpoch(MVEpoch(tm));
1507 }
1508}
1509
1510std::string Scantable::getDirectionString(int whichrow) const
1511{
1512 return formatDirection(getDirection(uInt(whichrow)));
1513}
1514
1515
1516SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1517 const MPosition& mp = getAntennaPosition();
1518 const MDirection& md = getDirection(whichrow);
1519 const MEpoch& me = timeCol_(whichrow);
1520 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1521 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1522 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
1523 mfreqidCol_(whichrow));
1524}
1525
1526std::vector< double > Scantable::getAbcissa( int whichrow ) const
1527{
1528 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
1529 std::vector<double> stlout;
1530 int nchan = specCol_(whichrow).nelements();
1531 String us = freqTable_.getUnitString();
1532 if ( us == "" || us == "pixel" || us == "channel" ) {
1533 for (int i=0; i<nchan; ++i) {
1534 stlout.push_back(double(i));
1535 }
1536 return stlout;
1537 }
1538 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
1539 Vector<Double> pixel(nchan);
1540 Vector<Double> world;
1541 indgen(pixel);
1542 if ( Unit(us) == Unit("Hz") ) {
1543 for ( int i=0; i < nchan; ++i) {
1544 Double world;
1545 spc.toWorld(world, pixel[i]);
1546 stlout.push_back(double(world));
1547 }
1548 } else if ( Unit(us) == Unit("km/s") ) {
1549 Vector<Double> world;
1550 spc.pixelToVelocity(world, pixel);
1551 world.tovector(stlout);
1552 }
1553 return stlout;
1554}
1555void Scantable::setDirectionRefString( const std::string & refstr )
1556{
1557 MDirection::Types mdt;
1558 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1559 throw(AipsError("Illegal Direction frame."));
1560 }
1561 if ( refstr == "" ) {
1562 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1563 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1564 } else {
1565 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1566 }
1567}
1568
1569std::string Scantable::getDirectionRefString( ) const
1570{
1571 return table_.keywordSet().asString("DIRECTIONREF");
1572}
1573
1574MDirection Scantable::getDirection(int whichrow ) const
1575{
1576 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1577 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1578 if ( usertype != type ) {
1579 MDirection::Types mdt;
1580 if (!MDirection::getType(mdt, usertype)) {
1581 throw(AipsError("Illegal Direction frame."));
1582 }
1583 return dirCol_.convert(uInt(whichrow), mdt);
1584 } else {
1585 return dirCol_(uInt(whichrow));
1586 }
1587}
1588
1589std::string Scantable::getAbcissaLabel( int whichrow ) const
1590{
1591 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
1592 const MPosition& mp = getAntennaPosition();
1593 const MDirection& md = getDirection(whichrow);
1594 const MEpoch& me = timeCol_(whichrow);
1595 //const Double& rf = mmolidCol_(whichrow);
1596 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1597 SpectralCoordinate spc =
1598 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
1599
1600 String s = "Channel";
1601 Unit u = Unit(freqTable_.getUnitString());
1602 if (u == Unit("km/s")) {
1603 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
1604 } else if (u == Unit("Hz")) {
1605 Vector<String> wau(1);wau = u.getName();
1606 spc.setWorldAxisUnits(wau);
1607 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
1608 }
1609 return s;
1610
1611}
1612
1613/**
1614void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
1615 const std::string& unit )
1616**/
1617void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1618 const std::string& unit )
1619
1620{
1621 ///@todo lookup in line table to fill in name and formattedname
1622 Unit u(unit);
1623 //Quantum<Double> urf(rf, u);
1624 Quantum<Vector<Double> >urf(rf, u);
1625 Vector<String> formattedname(0);
1626 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1627
1628 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1629 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
1630 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1631 tabvec = id;
1632}
1633
1634/**
1635void asap::Scantable::setRestFrequencies( const std::string& name )
1636{
1637 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1638 ///@todo implement
1639}
1640**/
1641
1642void Scantable::setRestFrequencies( const vector<std::string>& name )
1643{
1644 (void) name; // suppress unused warning
1645 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1646 ///@todo implement
1647}
1648
1649std::vector< unsigned int > Scantable::rownumbers( ) const
1650{
1651 std::vector<unsigned int> stlout;
1652 Vector<uInt> vec = table_.rowNumbers();
1653 vec.tovector(stlout);
1654 return stlout;
1655}
1656
1657
1658Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
1659{
1660 ROTableRow row(table_);
1661 const TableRecord& rec = row.get(whichrow);
1662 Table t =
1663 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1664 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1665 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1666 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1667 ROArrayColumn<Float> speccol(t, "SPECTRA");
1668 return speccol.getColumn();
1669}
1670
1671std::vector< std::string > Scantable::columnNames( ) const
1672{
1673 Vector<String> vec = table_.tableDesc().columnNames();
1674 return mathutil::tovectorstring(vec);
1675}
1676
1677MEpoch::Types Scantable::getTimeReference( ) const
1678{
1679 return MEpoch::castType(timeCol_.getMeasRef().getType());
1680}
1681
1682void Scantable::addFit( const STFitEntry& fit, int row )
1683{
1684 //cout << mfitidCol_(uInt(row)) << endl;
1685 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1686 os << mfitidCol_(uInt(row)) << LogIO::POST ;
1687 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1688 mfitidCol_.put(uInt(row), id);
1689}
1690
1691void Scantable::shift(int npix)
1692{
1693 Vector<uInt> fids(mfreqidCol_.getColumn());
1694 genSort( fids, Sort::Ascending,
1695 Sort::QuickSort|Sort::NoDuplicates );
1696 for (uInt i=0; i<fids.nelements(); ++i) {
1697 frequencies().shiftRefPix(npix, fids[i]);
1698 }
1699}
1700
1701String Scantable::getAntennaName() const
1702{
1703 String out;
1704 table_.keywordSet().get("AntennaName", out);
1705 String::size_type pos1 = out.find("@") ;
1706 String::size_type pos2 = out.find("//") ;
1707 if ( pos2 != String::npos )
1708 out = out.substr(pos2+2,pos1-pos2-2) ;
1709 else if ( pos1 != String::npos )
1710 out = out.substr(0,pos1) ;
1711 return out;
1712}
1713
1714int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
1715{
1716 String tbpath;
1717 int ret = 0;
1718 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1719 table_.keywordSet().get("GBT_GO", tbpath);
1720 Table t(tbpath,Table::Old);
1721 // check each scan if other scan of the pair exist
1722 int nscan = scanlist.size();
1723 for (int i = 0; i < nscan; i++) {
1724 Table subt = t( t.col("SCAN") == scanlist[i]+1 );
1725 if (subt.nrow()==0) {
1726 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1727 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1728 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
1729 ret = 1;
1730 break;
1731 }
1732 ROTableRow row(subt);
1733 const TableRecord& rec = row.get(0);
1734 int scan1seqn = rec.asuInt("PROCSEQN");
1735 int laston1 = rec.asuInt("LASTON");
1736 if ( rec.asuInt("PROCSIZE")==2 ) {
1737 if ( i < nscan-1 ) {
1738 Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
1739 if ( subt2.nrow() == 0) {
1740 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1741
1742 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1743 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
1744 ret = 1;
1745 break;
1746 }
1747 ROTableRow row2(subt2);
1748 const TableRecord& rec2 = row2.get(0);
1749 int scan2seqn = rec2.asuInt("PROCSEQN");
1750 int laston2 = rec2.asuInt("LASTON");
1751 if (scan1seqn == 1 && scan2seqn == 2) {
1752 if (laston1 == laston2) {
1753 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1754 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1755 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1756 i +=1;
1757 }
1758 else {
1759 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1760 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1761 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1762 }
1763 }
1764 else if (scan1seqn==2 && scan2seqn == 1) {
1765 if (laston1 == laston2) {
1766 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1767 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1768 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
1769 ret = 1;
1770 break;
1771 }
1772 }
1773 else {
1774 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1775 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1776 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
1777 ret = 1;
1778 break;
1779 }
1780 }
1781 }
1782 else {
1783 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1784 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1785 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
1786 }
1787 //if ( i >= nscan ) break;
1788 }
1789 }
1790 else {
1791 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1792 //cerr<<"No reference to GBT_GO table."<<endl;
1793 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
1794 ret = 1;
1795 }
1796 return ret;
1797}
1798
1799std::vector<double> Scantable::getDirectionVector(int whichrow) const
1800{
1801 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1802 std::vector<double> dir;
1803 Dir.tovector(dir);
1804 return dir;
1805}
1806
1807void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1808 throw( casa::AipsError )
1809{
1810 // assumed that all rows have same nChan
1811 Vector<Float> arr = specCol_( 0 ) ;
1812 int nChan = arr.nelements() ;
1813
1814 // if nmin < 0 or nmax < 0, nothing to do
1815 if ( nmin < 0 ) {
1816 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1817 }
1818 if ( nmax < 0 ) {
1819 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1820 }
1821
1822 // if nmin > nmax, exchange values
1823 if ( nmin > nmax ) {
1824 int tmp = nmax ;
1825 nmax = nmin ;
1826 nmin = tmp ;
1827 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1828 os << "Swap values. Applied range is ["
1829 << nmin << ", " << nmax << "]" << LogIO::POST ;
1830 }
1831
1832 // if nmin exceeds nChan, nothing to do
1833 if ( nmin >= nChan ) {
1834 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1835 }
1836
1837 // if nmax exceeds nChan, reset nmax to nChan
1838 if ( nmax >= nChan-1 ) {
1839 if ( nmin == 0 ) {
1840 // nothing to do
1841 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1842 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1843 return ;
1844 }
1845 else {
1846 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1847 os << "Specified maximum exceeds nChan. Applied range is ["
1848 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1849 nmax = nChan - 1 ;
1850 }
1851 }
1852
1853 // reshape specCol_ and flagCol_
1854 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1855 reshapeSpectrum( nmin, nmax, irow ) ;
1856 }
1857
1858 // update FREQUENCIES subtable
1859 Double refpix ;
1860 Double refval ;
1861 Double increment ;
1862 int freqnrow = freqTable_.table().nrow() ;
1863 Vector<uInt> oldId( freqnrow ) ;
1864 Vector<uInt> newId( freqnrow ) ;
1865 for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
1866 freqTable_.getEntry( refpix, refval, increment, irow ) ;
1867 /***
1868 * need to shift refpix to nmin
1869 * note that channel nmin in old index will be channel 0 in new one
1870 ***/
1871 refval = refval - ( refpix - nmin ) * increment ;
1872 refpix = 0 ;
1873 freqTable_.setEntry( refpix, refval, increment, irow ) ;
1874 }
1875
1876 // update nchan
1877 int newsize = nmax - nmin + 1 ;
1878 table_.rwKeywordSet().define( "nChan", newsize ) ;
1879
1880 // update bandwidth
1881 // assumed all spectra in the scantable have same bandwidth
1882 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1883
1884 return ;
1885}
1886
1887void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1888{
1889 // reshape specCol_ and flagCol_
1890 Vector<Float> oldspec = specCol_( irow ) ;
1891 Vector<uChar> oldflag = flagsCol_( irow ) ;
1892 Vector<Float> oldtsys = tsysCol_( irow ) ;
1893 uInt newsize = nmax - nmin + 1 ;
1894 Slice slice( nmin, newsize, 1 ) ;
1895 specCol_.put( irow, oldspec( slice ) ) ;
1896 flagsCol_.put( irow, oldflag( slice ) ) ;
1897 if ( oldspec.size() == oldtsys.size() )
1898 tsysCol_.put( irow, oldtsys( slice ) ) ;
1899
1900 return ;
1901}
1902
1903void asap::Scantable::regridSpecChannel( double dnu, int nChan )
1904{
1905 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1906 os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ;
1907 int freqnrow = freqTable_.table().nrow() ;
1908 Vector<bool> firstTime( freqnrow, true ) ;
1909 double oldincr, factor;
1910 uInt currId;
1911 Double refpix ;
1912 Double refval ;
1913 Double increment ;
1914 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1915 currId = mfreqidCol_(irow);
1916 vector<double> abcissa = getAbcissa( irow ) ;
1917 if (nChan < 0) {
1918 int oldsize = abcissa.size() ;
1919 double bw = (abcissa[oldsize-1]-abcissa[0]) + \
1920 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ;
1921 nChan = int( ceil( abs(bw/dnu) ) ) ;
1922 }
1923 // actual regridding
1924 regridChannel( nChan, dnu, irow ) ;
1925
1926 // update FREQUENCIES subtable
1927 if (firstTime[currId]) {
1928 oldincr = abcissa[1]-abcissa[0] ;
1929 factor = dnu/oldincr ;
1930 firstTime[currId] = false ;
1931 freqTable_.getEntry( refpix, refval, increment, currId ) ;
1932
1933 //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ;
1934 if (factor > 0 ) {
1935 refpix = (refpix + 0.5)/factor - 0.5;
1936 } else {
1937 refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5;
1938 }
1939 freqTable_.setEntry( refpix, refval, increment*factor, currId ) ;
1940 //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ;
1941 //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ;
1942 }
1943 }
1944}
1945
1946void asap::Scantable::regridChannel( int nChan, double dnu )
1947{
1948 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1949 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
1950 // assumed that all rows have same nChan
1951 Vector<Float> arr = specCol_( 0 ) ;
1952 int oldsize = arr.nelements() ;
1953
1954 // if oldsize == nChan, nothing to do
1955 if ( oldsize == nChan ) {
1956 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
1957 return ;
1958 }
1959
1960 // if oldChan < nChan, unphysical operation
1961 if ( oldsize < nChan ) {
1962 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
1963 return ;
1964 }
1965
1966 // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary)
1967 vector<string> coordinfo = getCoordInfo() ;
1968 string oldinfo = coordinfo[0] ;
1969 coordinfo[0] = "Hz" ;
1970 setCoordInfo( coordinfo ) ;
1971 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1972 regridChannel( nChan, dnu, irow ) ;
1973 }
1974 coordinfo[0] = oldinfo ;
1975 setCoordInfo( coordinfo ) ;
1976
1977
1978 // NOTE: this method does not update metadata such as
1979 // FREQUENCIES subtable, nChan, Bandwidth, etc.
1980
1981 return ;
1982}
1983
1984void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
1985{
1986 // logging
1987 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
1988 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
1989
1990 Vector<Float> oldspec = specCol_( irow ) ;
1991 Vector<uChar> oldflag = flagsCol_( irow ) ;
1992 Vector<Float> oldtsys = tsysCol_( irow ) ;
1993 Vector<Float> newspec( nChan, 0 ) ;
1994 Vector<uChar> newflag( nChan, true ) ;
1995 Vector<Float> newtsys ;
1996 bool regridTsys = false ;
1997 if (oldtsys.size() == oldspec.size()) {
1998 regridTsys = true ;
1999 newtsys.resize(nChan,false) ;
2000 newtsys = 0 ;
2001 }
2002
2003 // regrid
2004 vector<double> abcissa = getAbcissa( irow ) ;
2005 int oldsize = abcissa.size() ;
2006 double olddnu = abcissa[1] - abcissa[0] ;
2007 //int ichan = 0 ;
2008 double wsum = 0.0 ;
2009 Vector<double> zi( nChan+1 ) ;
2010 Vector<double> yi( oldsize + 1 ) ;
2011 yi[0] = abcissa[0] - 0.5 * olddnu ;
2012 for ( int ii = 1 ; ii < oldsize ; ii++ )
2013 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2014 yi[oldsize] = abcissa[oldsize-1] \
2015 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
2016 //zi[0] = abcissa[0] - 0.5 * olddnu ;
2017 zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ;
2018 for ( int ii = 1 ; ii < nChan ; ii++ )
2019 zi[ii] = zi[0] + dnu * ii ;
2020 zi[nChan] = zi[nChan-1] + dnu ;
2021 // Access zi and yi in ascending order
2022 int izs = ((dnu > 0) ? 0 : nChan ) ;
2023 int ize = ((dnu > 0) ? nChan : 0 ) ;
2024 int izincr = ((dnu > 0) ? 1 : -1 ) ;
2025 int ichan = ((olddnu > 0) ? 0 : oldsize ) ;
2026 int iye = ((olddnu > 0) ? oldsize : 0 ) ;
2027 int iyincr = ((olddnu > 0) ? 1 : -1 ) ;
2028 //for ( int ii = izs ; ii != ize ; ii+=izincr ){
2029 int ii = izs ;
2030 while (ii != ize) {
2031 // always zl < zr
2032 double zl = zi[ii] ;
2033 double zr = zi[ii+izincr] ;
2034 // Need to access smaller index for the new spec, flag, and tsys.
2035 // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc.
2036 int i = min(ii, ii+izincr) ;
2037 //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) {
2038 int jj = ichan ;
2039 while (jj != iye) {
2040 // always yl < yr
2041 double yl = yi[jj] ;
2042 double yr = yi[jj+iyincr] ;
2043 // Need to access smaller index for the original spec, flag, and tsys.
2044 // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc.
2045 int j = min(jj, jj+iyincr) ;
2046 if ( yr <= zl ) {
2047 jj += iyincr ;
2048 continue ;
2049 }
2050 else if ( yl <= zl ) {
2051 if ( yr < zr ) {
2052 if (!oldflag[j]) {
2053 newspec[i] += oldspec[j] * ( yr - zl ) ;
2054 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ;
2055 wsum += ( yr - zl ) ;
2056 }
2057 newflag[i] = newflag[i] && oldflag[j] ;
2058 }
2059 else {
2060 if (!oldflag[j]) {
2061 newspec[i] += oldspec[j] * abs(dnu) ;
2062 if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ;
2063 wsum += abs(dnu) ;
2064 }
2065 newflag[i] = newflag[i] && oldflag[j] ;
2066 ichan = jj ;
2067 break ;
2068 }
2069 }
2070 else if ( yl < zr ) {
2071 if ( yr <= zr ) {
2072 if (!oldflag[j]) {
2073 newspec[i] += oldspec[j] * ( yr - yl ) ;
2074 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ;
2075 wsum += ( yr - yl ) ;
2076 }
2077 newflag[i] = newflag[i] && oldflag[j] ;
2078 }
2079 else {
2080 if (!oldflag[j]) {
2081 newspec[i] += oldspec[j] * ( zr - yl ) ;
2082 if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ;
2083 wsum += ( zr - yl ) ;
2084 }
2085 newflag[i] = newflag[i] && oldflag[j] ;
2086 ichan = jj ;
2087 break ;
2088 }
2089 }
2090 else {
2091 ichan = jj - iyincr ;
2092 break ;
2093 }
2094 jj += iyincr ;
2095 }
2096 if ( wsum != 0.0 ) {
2097 newspec[i] /= wsum ;
2098 if (regridTsys) newtsys[i] /= wsum ;
2099 }
2100 wsum = 0.0 ;
2101 ii += izincr ;
2102 }
2103// if ( dnu > 0.0 ) {
2104// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2105// double zl = zi[ii] ;
2106// double zr = zi[ii+1] ;
2107// for ( int j = ichan ; j < oldsize ; j++ ) {
2108// double yl = yi[j] ;
2109// double yr = yi[j+1] ;
2110// if ( yl <= zl ) {
2111// if ( yr <= zl ) {
2112// continue ;
2113// }
2114// else if ( yr <= zr ) {
2115// if (!oldflag[j]) {
2116// newspec[ii] += oldspec[j] * ( yr - zl ) ;
2117// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ;
2118// wsum += ( yr - zl ) ;
2119// }
2120// newflag[ii] = newflag[ii] && oldflag[j] ;
2121// }
2122// else {
2123// if (!oldflag[j]) {
2124// newspec[ii] += oldspec[j] * dnu ;
2125// if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ;
2126// wsum += dnu ;
2127// }
2128// newflag[ii] = newflag[ii] && oldflag[j] ;
2129// ichan = j ;
2130// break ;
2131// }
2132// }
2133// else if ( yl < zr ) {
2134// if ( yr <= zr ) {
2135// if (!oldflag[j]) {
2136// newspec[ii] += oldspec[j] * ( yr - yl ) ;
2137// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ;
2138// wsum += ( yr - yl ) ;
2139// }
2140// newflag[ii] = newflag[ii] && oldflag[j] ;
2141// }
2142// else {
2143// if (!oldflag[j]) {
2144// newspec[ii] += oldspec[j] * ( zr - yl ) ;
2145// if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ;
2146// wsum += ( zr - yl ) ;
2147// }
2148// newflag[ii] = newflag[ii] && oldflag[j] ;
2149// ichan = j ;
2150// break ;
2151// }
2152// }
2153// else {
2154// ichan = j - 1 ;
2155// break ;
2156// }
2157// }
2158// if ( wsum != 0.0 ) {
2159// newspec[ii] /= wsum ;
2160// if (regridTsys) newtsys[ii] /= wsum ;
2161// }
2162// wsum = 0.0 ;
2163// }
2164// }
2165// else if ( dnu < 0.0 ) {
2166// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2167// double zl = zi[ii] ;
2168// double zr = zi[ii+1] ;
2169// for ( int j = ichan ; j < oldsize ; j++ ) {
2170// double yl = yi[j] ;
2171// double yr = yi[j+1] ;
2172// if ( yl >= zl ) {
2173// if ( yr >= zl ) {
2174// continue ;
2175// }
2176// else if ( yr >= zr ) {
2177// if (!oldflag[j]) {
2178// newspec[ii] += oldspec[j] * abs( yr - zl ) ;
2179// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ;
2180// wsum += abs( yr - zl ) ;
2181// }
2182// newflag[ii] = newflag[ii] && oldflag[j] ;
2183// }
2184// else {
2185// if (!oldflag[j]) {
2186// newspec[ii] += oldspec[j] * abs( dnu ) ;
2187// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ;
2188// wsum += abs( dnu ) ;
2189// }
2190// newflag[ii] = newflag[ii] && oldflag[j] ;
2191// ichan = j ;
2192// break ;
2193// }
2194// }
2195// else if ( yl > zr ) {
2196// if ( yr >= zr ) {
2197// if (!oldflag[j]) {
2198// newspec[ii] += oldspec[j] * abs( yr - yl ) ;
2199// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ;
2200// wsum += abs( yr - yl ) ;
2201// }
2202// newflag[ii] = newflag[ii] && oldflag[j] ;
2203// }
2204// else {
2205// if (!oldflag[j]) {
2206// newspec[ii] += oldspec[j] * abs( zr - yl ) ;
2207// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ;
2208// wsum += abs( zr - yl ) ;
2209// }
2210// newflag[ii] = newflag[ii] && oldflag[j] ;
2211// ichan = j ;
2212// break ;
2213// }
2214// }
2215// else {
2216// ichan = j - 1 ;
2217// break ;
2218// }
2219// }
2220// if ( wsum != 0.0 ) {
2221// newspec[ii] /= wsum ;
2222// if (regridTsys) newtsys[ii] /= wsum ;
2223// }
2224// wsum = 0.0 ;
2225// }
2226// }
2227// // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
2228// // pile += dnu ;
2229// // wedge = olddnu * ( refChan + 1 ) ;
2230// // while ( wedge < pile ) {
2231// // newspec[0] += olddnu * oldspec[refChan] ;
2232// // newflag[0] = newflag[0] || oldflag[refChan] ;
2233// // //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
2234// // refChan++ ;
2235// // wedge += olddnu ;
2236// // wsum += olddnu ;
2237// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2238// // }
2239// // frac = ( wedge - pile ) / olddnu ;
2240// // wsum += ( 1.0 - frac ) * olddnu ;
2241// // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2242// // newflag[0] = newflag[0] || oldflag[refChan] ;
2243// // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
2244// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2245// // newspec[0] /= wsum ;
2246// // //ofs << "newspec[0] = " << newspec[0] << endl ;
2247// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2248
2249// // /***
2250// // * ichan = 1 - nChan-2
2251// // ***/
2252// // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
2253// // pile += dnu ;
2254// // newspec[ichan] += frac * olddnu * oldspec[refChan] ;
2255// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2256// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
2257// // refChan++ ;
2258// // wedge += olddnu ;
2259// // wsum = frac * olddnu ;
2260// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2261// // while ( wedge < pile ) {
2262// // newspec[ichan] += olddnu * oldspec[refChan] ;
2263// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2264// // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
2265// // refChan++ ;
2266// // wedge += olddnu ;
2267// // wsum += olddnu ;
2268// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2269// // }
2270// // frac = ( wedge - pile ) / olddnu ;
2271// // wsum += ( 1.0 - frac ) * olddnu ;
2272// // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2273// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2274// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
2275// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2276// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2277// // newspec[ichan] /= wsum ;
2278// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
2279// // }
2280
2281// // /***
2282// // * ichan = nChan-1
2283// // ***/
2284// // // NOTE: Assumed that all spectra have the same bandwidth
2285// // pile += dnu ;
2286// // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
2287// // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
2288// // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2289// // refChan++ ;
2290// // wedge += olddnu ;
2291// // wsum = frac * olddnu ;
2292// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2293// // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
2294// // newspec[nChan-1] += olddnu * oldspec[jchan] ;
2295// // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
2296// // wsum += olddnu ;
2297// // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2298// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2299// // }
2300// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2301// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2302// // newspec[nChan-1] /= wsum ;
2303// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
2304
2305// // // ofs.close() ;
2306
2307 specCol_.put( irow, newspec ) ;
2308 flagsCol_.put( irow, newflag ) ;
2309 if (regridTsys) tsysCol_.put( irow, newtsys );
2310
2311 return ;
2312}
2313
2314void Scantable::regridChannel( int nChan, double dnu, double fmin, int irow )
2315{
2316 Vector<Float> oldspec = specCol_( irow ) ;
2317 Vector<uChar> oldflag = flagsCol_( irow ) ;
2318 Vector<Float> oldtsys = tsysCol_( irow ) ;
2319 Vector<Float> newspec( nChan, 0 ) ;
2320 Vector<uChar> newflag( nChan, true ) ;
2321 Vector<Float> newtsys ;
2322 bool regridTsys = false ;
2323 if (oldtsys.size() == oldspec.size()) {
2324 regridTsys = true ;
2325 newtsys.resize(nChan,false) ;
2326 newtsys = 0 ;
2327 }
2328
2329 // regrid
2330 vector<double> abcissa = getAbcissa( irow ) ;
2331 int oldsize = abcissa.size() ;
2332 double olddnu = abcissa[1] - abcissa[0] ;
2333 //int ichan = 0 ;
2334 double wsum = 0.0 ;
2335 Vector<double> zi( nChan+1 ) ;
2336 Vector<double> yi( oldsize + 1 ) ;
2337 Block<uInt> count( nChan, 0 ) ;
2338 yi[0] = abcissa[0] - 0.5 * olddnu ;
2339 for ( int ii = 1 ; ii < oldsize ; ii++ )
2340 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2341 yi[oldsize] = abcissa[oldsize-1] \
2342 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
2343// cout << "olddnu=" << olddnu << ", dnu=" << dnu << " (diff=" << olddnu-dnu << ")" << endl ;
2344// cout << "yi[0]=" << yi[0] << ", fmin=" << fmin << " (diff=" << yi[0]-fmin << ")" << endl ;
2345// cout << "oldsize=" << oldsize << ", nChan=" << nChan << endl ;
2346
2347 // do not regrid if input parameters are almost same as current
2348 // spectral setup
2349 double dnuDiff = abs( ( dnu - olddnu ) / olddnu ) ;
2350 double oldfmin = min( yi[0], yi[oldsize] ) ;
2351 double fminDiff = abs( ( fmin - oldfmin ) / oldfmin ) ;
2352 double nChanDiff = nChan - oldsize ;
2353 double eps = 1.0e-8 ;
2354 if ( nChanDiff == 0 && dnuDiff < eps && fminDiff < eps )
2355 return ;
2356
2357 //zi[0] = abcissa[0] - 0.5 * olddnu ;
2358 //zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ;
2359 if ( dnu > 0 )
2360 zi[0] = fmin - 0.5 * dnu ;
2361 else
2362 zi[0] = fmin + nChan * abs(dnu) ;
2363 for ( int ii = 1 ; ii < nChan ; ii++ )
2364 zi[ii] = zi[0] + dnu * ii ;
2365 zi[nChan] = zi[nChan-1] + dnu ;
2366 // Access zi and yi in ascending order
2367 int izs = ((dnu > 0) ? 0 : nChan ) ;
2368 int ize = ((dnu > 0) ? nChan : 0 ) ;
2369 int izincr = ((dnu > 0) ? 1 : -1 ) ;
2370 int ichan = ((olddnu > 0) ? 0 : oldsize ) ;
2371 int iye = ((olddnu > 0) ? oldsize : 0 ) ;
2372 int iyincr = ((olddnu > 0) ? 1 : -1 ) ;
2373 //for ( int ii = izs ; ii != ize ; ii+=izincr ){
2374 int ii = izs ;
2375 while (ii != ize) {
2376 // always zl < zr
2377 double zl = zi[ii] ;
2378 double zr = zi[ii+izincr] ;
2379 // Need to access smaller index for the new spec, flag, and tsys.
2380 // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc.
2381 int i = min(ii, ii+izincr) ;
2382 //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) {
2383 int jj = ichan ;
2384 while (jj != iye) {
2385 // always yl < yr
2386 double yl = yi[jj] ;
2387 double yr = yi[jj+iyincr] ;
2388 // Need to access smaller index for the original spec, flag, and tsys.
2389 // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc.
2390 int j = min(jj, jj+iyincr) ;
2391 if ( yr <= zl ) {
2392 jj += iyincr ;
2393 continue ;
2394 }
2395 else if ( yl <= zl ) {
2396 if ( yr < zr ) {
2397 if (!oldflag[j]) {
2398 newspec[i] += oldspec[j] * ( yr - zl ) ;
2399 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ;
2400 wsum += ( yr - zl ) ;
2401 count[i]++ ;
2402 }
2403 newflag[i] = newflag[i] && oldflag[j] ;
2404 }
2405 else {
2406 if (!oldflag[j]) {
2407 newspec[i] += oldspec[j] * abs(dnu) ;
2408 if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ;
2409 wsum += abs(dnu) ;
2410 count[i]++ ;
2411 }
2412 newflag[i] = newflag[i] && oldflag[j] ;
2413 ichan = jj ;
2414 break ;
2415 }
2416 }
2417 else if ( yl < zr ) {
2418 if ( yr <= zr ) {
2419 if (!oldflag[j]) {
2420 newspec[i] += oldspec[j] * ( yr - yl ) ;
2421 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ;
2422 wsum += ( yr - yl ) ;
2423 count[i]++ ;
2424 }
2425 newflag[i] = newflag[i] && oldflag[j] ;
2426 }
2427 else {
2428 if (!oldflag[j]) {
2429 newspec[i] += oldspec[j] * ( zr - yl ) ;
2430 if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ;
2431 wsum += ( zr - yl ) ;
2432 count[i]++ ;
2433 }
2434 newflag[i] = newflag[i] && oldflag[j] ;
2435 ichan = jj ;
2436 break ;
2437 }
2438 }
2439 else {
2440 //ichan = jj - iyincr ;
2441 break ;
2442 }
2443 jj += iyincr ;
2444 }
2445 if ( wsum != 0.0 ) {
2446 newspec[i] /= wsum ;
2447 if (regridTsys) newtsys[i] /= wsum ;
2448 }
2449 wsum = 0.0 ;
2450 ii += izincr ;
2451 }
2452
2453 // flag out channels without data
2454 // this is tentative since there is no specific definition
2455 // on bit flag...
2456 uChar noData = 1 << 7 ;
2457 for ( Int i = 0 ; i < nChan ; i++ ) {
2458 if ( count[i] == 0 )
2459 newflag[i] = noData ;
2460 }
2461
2462 specCol_.put( irow, newspec ) ;
2463 flagsCol_.put( irow, newflag ) ;
2464 if (regridTsys) tsysCol_.put( irow, newtsys );
2465
2466 return ;
2467}
2468
2469std::vector<float> Scantable::getWeather(int whichrow) const
2470{
2471 std::vector<float> out(5);
2472 //Float temperature, pressure, humidity, windspeed, windaz;
2473 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
2474 mweatheridCol_(uInt(whichrow)));
2475
2476
2477 return out;
2478}
2479
2480bool Scantable::getFlagtraFast(uInt whichrow)
2481{
2482 uChar flag;
2483 Vector<uChar> flags;
2484 flagsCol_.get(whichrow, flags);
2485 flag = flags[0];
2486 for (uInt i = 1; i < flags.size(); ++i) {
2487 flag &= flags[i];
2488 }
2489 return ((flag >> 7) == 1);
2490}
2491
2492std::vector<std::string> Scantable::applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite)
2493{
2494 STBaselineTable btin = STBaselineTable(bltable);
2495
2496 Vector<Bool> applyCol = btin.getApply();
2497 int nRowBl = applyCol.size();
2498 if (nRowBl != nrow()) {
2499 throw(AipsError("Scantable and bltable have different number of rows."));
2500 }
2501
2502 std::vector<std::string> res;
2503 res.clear();
2504
2505 bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite));
2506 bool bltableidentical = (bltable == outbltable);
2507 STBaselineTable btout = STBaselineTable(*this);
2508 ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME");
2509 Vector<Double> timeSecCol = tcol.getColumn();
2510
2511 for (int whichrow = 0; whichrow < nRowBl; ++whichrow) {
2512 if (applyCol[whichrow]) {
2513 std::vector<float> spec = getSpectrum(whichrow);
2514
2515 std::vector<bool> mask = btin.getMask(whichrow); //use mask_bltable only
2516
2517 STBaselineFunc::FuncName ftype = btin.getFunctionName(whichrow);
2518 std::vector<int> fpar = btin.getFuncParam(whichrow);
2519 std::vector<float> params;
2520 float rms;
2521 std::vector<float> resfit = doApplyBaselineTable(spec, mask, ftype, fpar, params, rms);
2522
2523 setSpectrum(resfit, whichrow);
2524
2525 res.push_back(packFittingResults(whichrow, params, rms));
2526
2527 if (outBaselineTable) {
2528 if (outbltableexists) {
2529 if (overwrite) {
2530 if (bltableidentical) {
2531 btin.setresult(uInt(whichrow), Vector<Float>(params), Float(rms));
2532 } else {
2533 btout.setresult(uInt(whichrow), Vector<Float>(params), Float(rms));
2534 }
2535 }
2536 } else {
2537 btout.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
2538 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
2539 true, ftype, fpar, std::vector<float>(),
2540 getMaskListFromMask(mask), params, rms, spec.size(),
2541 3.0, 0, 0.0, 0, std::vector<int>());
2542 }
2543 }
2544 }
2545 }
2546
2547 if (outBaselineTable) {
2548 if (bltableidentical) {
2549 btin.save(outbltable);
2550 } else {
2551 btout.save(outbltable);
2552 }
2553 }
2554
2555 return res;
2556}
2557
2558std::vector<std::string> Scantable::subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite)
2559{
2560 int nRowBl = blInfoList.size();
2561 int nRowSt = nrow();
2562
2563 std::vector<std::string> res;
2564 res.clear();
2565
2566 bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite));
2567 if ((outbltable != "") && outbltableexists && !overwrite) {
2568 throw(AipsError("Cannot overwrite bltable. Set overwrite=True."));
2569 }
2570
2571 STBaselineTable bt = STBaselineTable(*this);
2572 ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME");
2573 Vector<Double> timeSecCol = tcol.getColumn();
2574
2575 if (outBaselineTable && !outbltableexists) {
2576 for (int i = 0; i < nRowSt; ++i) {
2577 bt.appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i),
2578 0, timeSecCol[i]);
2579 bt.setApply(i, false);
2580 }
2581 }
2582
2583 for (int i = 0; i < nRowBl; ++i) {
2584 int irow;
2585 STBaselineFunc::FuncName ftype;
2586 std::vector<bool> mask;
2587 std::vector<int> fpar;
2588 float clipth;
2589 int clipn;
2590 bool uself;
2591 float lfth;
2592 std::vector<int> lfedge;
2593 int lfavg;
2594 parseBlInfo(blInfoList[i], irow, ftype, fpar, mask, clipth, clipn, uself, lfth, lfedge, lfavg);
2595
2596 if (irow < nRowSt) {
2597 std::vector<float> spec = getSpectrum(irow);
2598 std::vector<float> params;
2599 float rms;
2600 std::vector<bool> finalmask;
2601
2602 std::vector<float> resfit = doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, clipth, clipn, uself, irow, lfth, lfedge, lfavg);
2603 setSpectrum(resfit, irow);
2604 res.push_back(packFittingResults(irow, params, rms));
2605
2606 if (outBaselineTable) {
2607 Vector<Int> fparam(fpar.size());
2608 for (uInt j = 0; j < fparam.size(); ++j) {
2609 fparam[j] = (Int)fpar[j];
2610 }
2611
2612 bt.setdata(uInt(irow),
2613 uInt(getScan(irow)), uInt(getCycle(irow)),
2614 uInt(getBeam(irow)), uInt(getIF(irow)), uInt(getPol(irow)),
2615 uInt(0), timeSecCol[irow], Bool(true), ftype, fparam,
2616 Vector<Float>(), getMaskListFromMask(finalmask), Vector<Float>(params),
2617 Float(rms), uInt(spec.size()), Float(clipth), uInt(clipn),
2618 Float(0.0), uInt(0), Vector<uInt>());
2619 }
2620
2621 }
2622 }
2623
2624 if (outBaselineTable) {
2625 bt.save(outbltable);
2626 }
2627
2628 return res;
2629}
2630
2631std::vector<float> Scantable::doApplyBaselineTable(std::vector<float>& spec,
2632 std::vector<bool>& mask,
2633 const STBaselineFunc::FuncName ftype,
2634 std::vector<int>& fpar,
2635 std::vector<float>& params,
2636 float&rms)
2637{
2638 std::vector<bool> finalmask;
2639 std::vector<int> lfedge;
2640 return doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, 0.0, 0, false, 0, 0.0, lfedge, 0);
2641}
2642
2643std::vector<float> Scantable::doSubtractBaseline(std::vector<float>& spec,
2644 std::vector<bool>& mask,
2645 const STBaselineFunc::FuncName ftype,
2646 std::vector<int>& fpar,
2647 std::vector<float>& params,
2648 float&rms,
2649 std::vector<bool>& finalmask,
2650 float clipth,
2651 int clipn,
2652 bool uself,
2653 int irow,
2654 float lfth,
2655 std::vector<int>& lfedge,
2656 int lfavg)
2657{
2658 if (uself) {
2659 STLineFinder lineFinder = STLineFinder();
2660 initLineFinder(lfedge, lfth, lfavg, lineFinder);
2661 std::vector<int> currentEdge;
2662 mask = getCompositeChanMask(irow, mask, lfedge, currentEdge, lineFinder);
2663 }
2664
2665 std::vector<float> res;
2666 if (ftype == STBaselineFunc::Polynomial) {
2667 res = doPolynomialFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn);
2668 } else if (ftype == STBaselineFunc::Chebyshev) {
2669 res = doChebyshevFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn);
2670 } else if (ftype == STBaselineFunc::CSpline) {
2671 if (fpar.size() > 1) { // reading from baseline table in which pieceEdges are already calculated and stored.
2672 res = doCubicSplineFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn);
2673 } else { // usual cspline fitting by giving nPiece only. fpar will be replaced with pieceEdges.
2674 res = doCubicSplineFitting(spec, mask, fpar[0], fpar, params, rms, finalmask, clipth, clipn);
2675 }
2676 } else if (ftype == STBaselineFunc::Sinusoid) {
2677 res = doSinusoidFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn);
2678 }
2679
2680 return res;
2681}
2682
2683std::string Scantable::packFittingResults(const int irow, const std::vector<float>& params, const float rms)
2684{
2685 // returned value: "irow:params[0],params[1],..,params[n-1]:rms"
2686 ostringstream os;
2687 os << irow << ':';
2688 for (uInt i = 0; i < params.size(); ++i) {
2689 if (i > 0) {
2690 os << ',';
2691 }
2692 os << params[i];
2693 }
2694 os << ':' << rms;
2695
2696 return os.str();
2697}
2698
2699void Scantable::parseBlInfo(const std::string& blInfo, int& irow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF)
2700{
2701 // The baseline info to be parsed must be column-delimited string like
2702 // "0:chebyshev:5:3,5,169,174,485,487" where the elements are
2703 // row number, funcType, funcOrder, maskList, clipThreshold, clipNIter,
2704 // useLineFinder, lfThreshold, lfEdge and lfChanAvgLimit.
2705
2706 std::vector<string> res = splitToStringList(blInfo, ':');
2707 if (res.size() < 4) {
2708 throw(AipsError("baseline info has bad format")) ;
2709 }
2710
2711 string ftype0, fpar0, masklist0, uself0, edge0;
2712 std::vector<int> masklist;
2713
2714 stringstream ss;
2715 ss << res[0];
2716 ss >> irow;
2717 ss.clear(); ss.str("");
2718
2719 ss << res[1];
2720 ss >> ftype0;
2721 if (ftype0 == "poly") {
2722 ftype = STBaselineFunc::Polynomial;
2723 } else if (ftype0 == "cspline") {
2724 ftype = STBaselineFunc::CSpline;
2725 } else if (ftype0 == "sinusoid") {
2726 ftype = STBaselineFunc::Sinusoid;
2727 } else if (ftype0 == "chebyshev") {
2728 ftype = STBaselineFunc::Chebyshev;
2729 } else {
2730 throw(AipsError("invalid function type."));
2731 }
2732 ss.clear(); ss.str("");
2733
2734 ss << res[2];
2735 ss >> fpar0;
2736 fpar = splitToIntList(fpar0, ',');
2737 ss.clear(); ss.str("");
2738
2739 ss << res[3];
2740 ss >> masklist0;
2741 mask = getMaskFromMaskList(nchan(getIF(irow)), splitToIntList(masklist0, ','));
2742
2743 ss << res[4];
2744 ss >> thresClip;
2745 ss.clear(); ss.str("");
2746
2747 ss << res[5];
2748 ss >> nIterClip;
2749 ss.clear(); ss.str("");
2750
2751 ss << res[6];
2752 ss >> uself0;
2753 if (uself0 == "true") {
2754 useLineFinder = true;
2755 } else {
2756 useLineFinder = false;
2757 }
2758 ss.clear(); ss.str("");
2759
2760 if (useLineFinder) {
2761 ss << res[7];
2762 ss >> thresLF;
2763 ss.clear(); ss.str("");
2764
2765 ss << res[8];
2766 ss >> edge0;
2767 edgeLF = splitToIntList(edge0, ',');
2768 ss.clear(); ss.str("");
2769
2770 ss << res[9];
2771 ss >> avgLF;
2772 ss.clear(); ss.str("");
2773 }
2774
2775}
2776
2777std::vector<int> Scantable::splitToIntList(const std::string& s, const char delim)
2778{
2779 istringstream iss(s);
2780 string tmp;
2781 int tmpi;
2782 std::vector<int> res;
2783 stringstream ss;
2784 while (getline(iss, tmp, delim)) {
2785 ss << tmp;
2786 ss >> tmpi;
2787 res.push_back(tmpi);
2788 ss.clear(); ss.str("");
2789 }
2790
2791 return res;
2792}
2793
2794std::vector<string> Scantable::splitToStringList(const std::string& s, const char delim)
2795{
2796 istringstream iss(s);
2797 std::string tmp;
2798 std::vector<string> res;
2799 while (getline(iss, tmp, delim)) {
2800 res.push_back(tmp);
2801 }
2802
2803 return res;
2804}
2805
2806std::vector<bool> Scantable::getMaskFromMaskList(const int nchan, const std::vector<int>& masklist)
2807{
2808 if (masklist.size() % 2 != 0) {
2809 throw(AipsError("masklist must have even number of elements."));
2810 }
2811
2812 std::vector<bool> res(nchan);
2813
2814 for (int i = 0; i < nchan; ++i) {
2815 res[i] = false;
2816 }
2817 for (uInt j = 0; j < masklist.size(); j += 2) {
2818 for (int i = masklist[j]; i <= masklist[j+1]; ++i) {
2819 res[i] = true;
2820 }
2821 }
2822
2823 return res;
2824}
2825
2826Vector<uInt> Scantable::getMaskListFromMask(const std::vector<bool>& mask)
2827{
2828 std::vector<int> masklist;
2829 masklist.clear();
2830
2831 for (uInt i = 0; i < mask.size(); ++i) {
2832 if (mask[i]) {
2833 if ((i == 0)||(i == mask.size()-1)) {
2834 masklist.push_back(i);
2835 } else {
2836 if ((mask[i])&&(!mask[i-1])) {
2837 masklist.push_back(i);
2838 }
2839 if ((mask[i])&&(!mask[i+1])) {
2840 masklist.push_back(i);
2841 }
2842 }
2843 }
2844 }
2845
2846 Vector<uInt> res(masklist.size());
2847 for (uInt i = 0; i < masklist.size(); ++i) {
2848 res[i] = (uInt)masklist[i];
2849 }
2850
2851 return res;
2852}
2853
2854void Scantable::initialiseBaselining(const std::string& blfile,
2855 ofstream& ofs,
2856 const bool outLogger,
2857 bool& outTextFile,
2858 bool& csvFormat,
2859 String& coordInfo,
2860 bool& hasSameNchan,
2861 const std::string& progressInfo,
2862 bool& showProgress,
2863 int& minNRow,
2864 Vector<Double>& timeSecCol)
2865{
2866 csvFormat = false;
2867 outTextFile = false;
2868
2869 if (blfile != "") {
2870 csvFormat = (blfile.substr(0, 1) == "T");
2871 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
2872 if (ofs) outTextFile = true;
2873 }
2874
2875 coordInfo = "";
2876 hasSameNchan = true;
2877
2878 if (outLogger || outTextFile) {
2879 coordInfo = getCoordInfo()[0];
2880 if (coordInfo == "") coordInfo = "channel";
2881 hasSameNchan = hasSameNchanOverIFs();
2882 }
2883
2884 parseProgressInfo(progressInfo, showProgress, minNRow);
2885
2886 ROScalarColumn<Double> tcol = ROScalarColumn<Double>(table_, "TIME");
2887 timeSecCol = tcol.getColumn();
2888}
2889
2890void Scantable::finaliseBaselining(const bool outBaselineTable,
2891 STBaselineTable* pbt,
2892 const string& bltable,
2893 const bool outTextFile,
2894 ofstream& ofs)
2895{
2896 if (outBaselineTable) {
2897 pbt->save(bltable);
2898 }
2899
2900 if (outTextFile) ofs.close();
2901}
2902
2903void Scantable::initLineFinder(const std::vector<int>& edge,
2904 const float threshold,
2905 const int chanAvgLimit,
2906 STLineFinder& lineFinder)
2907{
2908 if ((edge.size() > 2) && (edge.size() < getIFNos().size()*2)) {
2909 throw(AipsError("Length of edge element info is less than that of IFs"));
2910 }
2911
2912 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2913}
2914
2915void Scantable::polyBaseline(const std::vector<bool>& mask, int order,
2916 float thresClip, int nIterClip,
2917 bool getResidual,
2918 const std::string& progressInfo,
2919 const bool outLogger, const std::string& blfile,
2920 const std::string& bltable)
2921{
2922 /****
2923 double TimeStart = mathutil::gettimeofday_sec();
2924 ****/
2925
2926 try {
2927 ofstream ofs;
2928 String coordInfo;
2929 bool hasSameNchan, outTextFile, csvFormat, showProgress;
2930 int minNRow;
2931 int nRow = nrow();
2932 std::vector<bool> chanMask, finalChanMask;
2933 float rms;
2934 bool outBaselineTable = (bltable != "");
2935 STBaselineTable bt = STBaselineTable(*this);
2936 Vector<Double> timeSecCol;
2937
2938 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
2939 coordInfo, hasSameNchan,
2940 progressInfo, showProgress, minNRow,
2941 timeSecCol);
2942
2943 std::vector<int> nChanNos;
2944 std::vector<std::vector<std::vector<double> > > modelReservoir;
2945 modelReservoir = getPolynomialModelReservoir(order,
2946 &Scantable::getNormalPolynomial,
2947 nChanNos);
2948
2949 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2950 std::vector<float> sp = getSpectrum(whichrow);
2951 chanMask = getCompositeChanMask(whichrow, mask);
2952
2953 std::vector<float> params;
2954 int nClipped = 0;
2955 std::vector<float> res = doLeastSquareFitting(sp, chanMask,
2956 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
2957 params, rms, finalChanMask,
2958 nClipped, thresClip, nIterClip, getResidual);
2959
2960 if (outBaselineTable) {
2961 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
2962 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
2963 true, STBaselineFunc::Polynomial, order, std::vector<float>(),
2964 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
2965 thresClip, nIterClip, 0.0, 0, std::vector<int>());
2966 } else {
2967 setSpectrum(res, whichrow);
2968 }
2969
2970 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
2971 coordInfo, hasSameNchan, ofs, "polyBaseline()",
2972 params, nClipped);
2973 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2974 }
2975
2976 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
2977
2978 } catch (...) {
2979 throw;
2980 }
2981
2982 /****
2983 double TimeEnd = mathutil::gettimeofday_sec();
2984 double elapse1 = TimeEnd - TimeStart;
2985 std::cout << "poly-new : " << elapse1 << " (sec.)" << endl;
2986 ****/
2987}
2988
2989void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order,
2990 float thresClip, int nIterClip,
2991 const std::vector<int>& edge,
2992 float threshold, int chanAvgLimit,
2993 bool getResidual,
2994 const std::string& progressInfo,
2995 const bool outLogger, const std::string& blfile,
2996 const std::string& bltable)
2997{
2998 try {
2999 ofstream ofs;
3000 String coordInfo;
3001 bool hasSameNchan, outTextFile, csvFormat, showProgress;
3002 int minNRow;
3003 int nRow = nrow();
3004 std::vector<bool> chanMask, finalChanMask;
3005 float rms;
3006 bool outBaselineTable = (bltable != "");
3007 STBaselineTable bt = STBaselineTable(*this);
3008 Vector<Double> timeSecCol;
3009 STLineFinder lineFinder = STLineFinder();
3010
3011 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3012 coordInfo, hasSameNchan,
3013 progressInfo, showProgress, minNRow,
3014 timeSecCol);
3015
3016 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
3017
3018 std::vector<int> nChanNos;
3019 std::vector<std::vector<std::vector<double> > > modelReservoir;
3020 modelReservoir = getPolynomialModelReservoir(order,
3021 &Scantable::getNormalPolynomial,
3022 nChanNos);
3023
3024 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3025 std::vector<float> sp = getSpectrum(whichrow);
3026 std::vector<int> currentEdge;
3027 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
3028
3029 std::vector<float> params;
3030 int nClipped = 0;
3031 std::vector<float> res = doLeastSquareFitting(sp, chanMask,
3032 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3033 params, rms, finalChanMask,
3034 nClipped, thresClip, nIterClip, getResidual);
3035
3036 if (outBaselineTable) {
3037 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3038 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3039 true, STBaselineFunc::Polynomial, order, std::vector<float>(),
3040 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3041 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
3042 } else {
3043 setSpectrum(res, whichrow);
3044 }
3045
3046 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3047 coordInfo, hasSameNchan, ofs, "autoPolyBaseline()",
3048 params, nClipped);
3049 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3050 }
3051
3052 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
3053
3054 } catch (...) {
3055 throw;
3056 }
3057}
3058
3059void Scantable::chebyshevBaseline(const std::vector<bool>& mask, int order,
3060 float thresClip, int nIterClip,
3061 bool getResidual,
3062 const std::string& progressInfo,
3063 const bool outLogger, const std::string& blfile,
3064 const std::string& bltable)
3065{
3066 /*
3067 double TimeStart = mathutil::gettimeofday_sec();
3068 */
3069
3070 try {
3071 ofstream ofs;
3072 String coordInfo;
3073 bool hasSameNchan, outTextFile, csvFormat, showProgress;
3074 int minNRow;
3075 int nRow = nrow();
3076 std::vector<bool> chanMask, finalChanMask;
3077 float rms;
3078 bool outBaselineTable = (bltable != "");
3079 STBaselineTable bt = STBaselineTable(*this);
3080 Vector<Double> timeSecCol;
3081
3082 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3083 coordInfo, hasSameNchan,
3084 progressInfo, showProgress, minNRow,
3085 timeSecCol);
3086
3087 std::vector<int> nChanNos;
3088 std::vector<std::vector<std::vector<double> > > modelReservoir;
3089 modelReservoir = getPolynomialModelReservoir(order,
3090 &Scantable::getChebyshevPolynomial,
3091 nChanNos);
3092
3093 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3094 std::vector<float> sp = getSpectrum(whichrow);
3095 chanMask = getCompositeChanMask(whichrow, mask);
3096
3097 std::vector<float> params;
3098 int nClipped = 0;
3099 std::vector<float> res = doLeastSquareFitting(sp, chanMask,
3100 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3101 params, rms, finalChanMask,
3102 nClipped, thresClip, nIterClip, getResidual);
3103
3104 if (outBaselineTable) {
3105 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3106 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3107 true, STBaselineFunc::Chebyshev, order, std::vector<float>(),
3108 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3109 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3110 } else {
3111 setSpectrum(res, whichrow);
3112 }
3113
3114 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3115 coordInfo, hasSameNchan, ofs, "chebyshevBaseline()",
3116 params, nClipped);
3117 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3118 }
3119
3120 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
3121
3122 } catch (...) {
3123 throw;
3124 }
3125
3126 /*
3127 double TimeEnd = mathutil::gettimeofday_sec();
3128 double elapse1 = TimeEnd - TimeStart;
3129 std::cout << "cheby : " << elapse1 << " (sec.)" << endl;
3130 */
3131}
3132
3133void Scantable::autoChebyshevBaseline(const std::vector<bool>& mask, int order,
3134 float thresClip, int nIterClip,
3135 const std::vector<int>& edge,
3136 float threshold, int chanAvgLimit,
3137 bool getResidual,
3138 const std::string& progressInfo,
3139 const bool outLogger, const std::string& blfile,
3140 const std::string& bltable)
3141{
3142 try {
3143 ofstream ofs;
3144 String coordInfo;
3145 bool hasSameNchan, outTextFile, csvFormat, showProgress;
3146 int minNRow;
3147 int nRow = nrow();
3148 std::vector<bool> chanMask, finalChanMask;
3149 float rms;
3150 bool outBaselineTable = (bltable != "");
3151 STBaselineTable bt = STBaselineTable(*this);
3152 Vector<Double> timeSecCol;
3153 STLineFinder lineFinder = STLineFinder();
3154
3155 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3156 coordInfo, hasSameNchan,
3157 progressInfo, showProgress, minNRow,
3158 timeSecCol);
3159
3160 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
3161
3162 std::vector<int> nChanNos;
3163 std::vector<std::vector<std::vector<double> > > modelReservoir;
3164 modelReservoir = getPolynomialModelReservoir(order,
3165 &Scantable::getChebyshevPolynomial,
3166 nChanNos);
3167
3168 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3169 std::vector<float> sp = getSpectrum(whichrow);
3170 std::vector<int> currentEdge;
3171 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
3172
3173 std::vector<float> params;
3174 int nClipped = 0;
3175 std::vector<float> res = doLeastSquareFitting(sp, chanMask,
3176 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3177 params, rms, finalChanMask,
3178 nClipped, thresClip, nIterClip, getResidual);
3179
3180 if (outBaselineTable) {
3181 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3182 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3183 true, STBaselineFunc::Chebyshev, order, std::vector<float>(),
3184 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3185 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
3186 } else {
3187 setSpectrum(res, whichrow);
3188 }
3189
3190 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3191 coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()",
3192 params, nClipped);
3193 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3194 }
3195
3196 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
3197
3198 } catch (...) {
3199 throw;
3200 }
3201}
3202
3203double Scantable::calculateModelSelectionCriteria(const std::string& valname,
3204 const std::string& blfunc,
3205 int order,
3206 const std::vector<bool>& inMask,
3207 int whichrow,
3208 bool useLineFinder,
3209 const std::vector<int>& edge,
3210 float threshold,
3211 int chanAvgLimit)
3212{
3213 std::vector<float> sp = getSpectrum(whichrow);
3214 std::vector<bool> chanMask;
3215 chanMask.clear();
3216
3217 if (useLineFinder) {
3218 STLineFinder lineFinder = STLineFinder();
3219 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
3220 std::vector<int> currentEdge;
3221 chanMask = getCompositeChanMask(whichrow, inMask, edge, currentEdge, lineFinder);
3222 } else {
3223 chanMask = getCompositeChanMask(whichrow, inMask);
3224 }
3225
3226 return doCalculateModelSelectionCriteria(valname, sp, chanMask, blfunc, order);
3227}
3228
3229double Scantable::doCalculateModelSelectionCriteria(const std::string& valname, const std::vector<float>& spec, const std::vector<bool>& mask, const std::string& blfunc, int order)
3230{
3231 int nparam;
3232 std::vector<float> params;
3233 std::vector<bool> finalChanMask;
3234 float rms;
3235 int nClipped = 0;
3236 std::vector<float> res;
3237 if (blfunc == "poly") {
3238 nparam = order + 1;
3239 res = doPolynomialFitting(spec, mask, order, params, rms, finalChanMask, nClipped);
3240 } else if (blfunc == "chebyshev") {
3241 nparam = order + 1;
3242 res = doChebyshevFitting(spec, mask, order, params, rms, finalChanMask, nClipped);
3243 } else if (blfunc == "cspline") {
3244 std::vector<int> pieceEdges;//(order+1); //order = npiece
3245 nparam = order + 3;
3246 res = doCubicSplineFitting(spec, mask, order, false, pieceEdges, params, rms, finalChanMask, nClipped);
3247 } else if (blfunc == "sinusoid") {
3248 std::vector<int> nWaves;
3249 nWaves.clear();
3250 for (int i = 0; i <= order; ++i) {
3251 nWaves.push_back(i);
3252 }
3253 nparam = 2*order + 1; // order = nwave
3254 res = doSinusoidFitting(spec, mask, nWaves, params, rms, finalChanMask, nClipped);
3255 } else {
3256 throw(AipsError("blfunc must be poly, chebyshev, cspline or sinusoid."));
3257 }
3258
3259 double msq = 0.0;
3260 int nusedchan = 0;
3261 int nChan = res.size();
3262 for (int i = 0; i < nChan; ++i) {
3263 if (mask[i]) {
3264 msq += (double)res[i]*(double)res[i];
3265 nusedchan++;
3266 }
3267 }
3268 if (nusedchan == 0) {
3269 throw(AipsError("all channels masked."));
3270 }
3271 msq /= (double)nusedchan;
3272
3273 nparam++; //add 1 for sigma of Gaussian distribution
3274 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
3275
3276 if (valname.find("aic") == 0) {
3277 // Original Akaike Information Criterion (AIC)
3278 double aic = nusedchan * (log(2.0 * PI * msq) + 1.0) + 2.0 * nparam;
3279
3280 // Corrected AIC by Sugiura(1978) (AICc)
3281 if (valname == "aicc") {
3282 if (nusedchan - nparam - 1 <= 0) {
3283 throw(AipsError("channel size is too small to calculate AICc."));
3284 }
3285 aic += 2.0*nparam*(nparam + 1)/(double)(nusedchan - nparam - 1);
3286 }
3287
3288 return aic;
3289
3290 } else if (valname == "bic") {
3291 // Bayesian Information Criterion (BIC)
3292 double bic = nusedchan * log(msq) + nparam * log((double)nusedchan);
3293 return bic;
3294
3295 } else if (valname == "gcv") {
3296 // Generalised Cross Validation
3297 double x = 1.0 - (double)nparam / (double)nusedchan;
3298 double gcv = msq / (x * x);
3299 return gcv;
3300
3301 } else {
3302 throw(AipsError("valname must be aic, aicc, bic or gcv."));
3303 }
3304}
3305
3306double Scantable::getNormalPolynomial(int n, double x) {
3307 if (n == 0) {
3308 return 1.0;
3309 } else if (n > 0) {
3310 double res = 1.0;
3311 for (int i = 0; i < n; ++i) {
3312 res *= x;
3313 }
3314 return res;
3315 } else {
3316 if (x == 0.0) {
3317 throw(AipsError("infinity result: x=0 given for negative power."));
3318 } else {
3319 return pow(x, (double)n);
3320 }
3321 }
3322}
3323
3324double Scantable::getChebyshevPolynomial(int n, double x) {
3325 if ((x < -1.0)||(x > 1.0)) {
3326 throw(AipsError("out of definition range (-1 <= x <= 1)."));
3327 } else if (x == 1.0) {
3328 return 1.0;
3329 } else if (x == 0.0) {
3330 double res;
3331 if (n%2 == 0) {
3332 if (n%4 == 0) {
3333 res = 1.0;
3334 } else {
3335 res = -1.0;
3336 }
3337 } else {
3338 res = 0.0;
3339 }
3340 return res;
3341 } else if (x == -1.0) {
3342 double res = (n%2 == 0 ? 1.0 : -1.0);
3343 return res;
3344 } else if (n < 0) {
3345 throw(AipsError("the order must be zero or positive."));
3346 } else if (n == 0) {
3347 return 1.0;
3348 } else if (n == 1) {
3349 return x;
3350 } else {
3351 double res = 0.0;
3352 for (int m = 0; m <= n/2; ++m) {
3353 double c = 1.0;
3354 if (m > 0) {
3355 for (int i = 1; i <= m; ++i) {
3356 c *= (double)(n-2*m+i)/(double)i;
3357 }
3358 }
3359 res += (m%2 == 0 ? 1.0 : -1.0)*(double)n/(double)(n-m)*pow(2.0*x, (double)(n-2*m))/2.0*c;
3360 }
3361 return res;
3362 }
3363}
3364
3365std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data,
3366 const std::vector<bool>& mask,
3367 int order,
3368 std::vector<float>& params,
3369 float& rms,
3370 std::vector<bool>& finalmask,
3371 float clipth,
3372 int clipn)
3373{
3374 int nClipped = 0;
3375 return doPolynomialFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn);
3376}
3377
3378std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data,
3379 const std::vector<bool>& mask,
3380 int order,
3381 std::vector<float>& params,
3382 float& rms,
3383 std::vector<bool>& finalMask,
3384 int& nClipped,
3385 float thresClip,
3386 int nIterClip,
3387 bool getResidual)
3388{
3389 return doLeastSquareFitting(data, mask,
3390 getPolynomialModel(order, data.size(), &Scantable::getNormalPolynomial),
3391 params, rms, finalMask,
3392 nClipped, thresClip, nIterClip,
3393 getResidual);
3394}
3395
3396std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data,
3397 const std::vector<bool>& mask,
3398 int order,
3399 std::vector<float>& params,
3400 float& rms,
3401 std::vector<bool>& finalmask,
3402 float clipth,
3403 int clipn)
3404{
3405 int nClipped = 0;
3406 return doChebyshevFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn);
3407}
3408
3409std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data,
3410 const std::vector<bool>& mask,
3411 int order,
3412 std::vector<float>& params,
3413 float& rms,
3414 std::vector<bool>& finalMask,
3415 int& nClipped,
3416 float thresClip,
3417 int nIterClip,
3418 bool getResidual)
3419{
3420 return doLeastSquareFitting(data, mask,
3421 getPolynomialModel(order, data.size(), &Scantable::getChebyshevPolynomial),
3422 params, rms, finalMask,
3423 nClipped, thresClip, nIterClip,
3424 getResidual);
3425}
3426
3427std::vector<std::vector<double> > Scantable::getPolynomialModel(int order, int nchan, double (Scantable::*pfunc)(int, double))
3428{
3429 // model : contains model values for computing the least-square matrix.
3430 // model.size() is nmodel and model[*].size() is nchan.
3431 // Each model element are as follows:
3432 //
3433 // (for normal polynomials)
3434 // model[0] = {1.0, 1.0, 1.0, ..., 1.0},
3435 // model[1] = {0.0, 1.0, 2.0, ..., (nchan-1)}
3436 // model[n-1] = ...,
3437 // model[n] = {0.0^n, 1.0^n, 2.0^n, ..., (nchan-1)^n}
3438 // where (0 <= n <= order)
3439 //
3440 // (for Chebyshev polynomials)
3441 // model[0] = {T0(-1), T0(2/(nchan-1)-1), T0(4/(nchan-1)-1), ..., T0(1)},
3442 // model[n-1] = ...,
3443 // model[n] = {Tn(-1), Tn(2/(nchan-1)-1), Tn(4/(nchan-1)-1), ..., Tn(1)}
3444 // where (0 <= n <= order),
3445
3446 int nmodel = order + 1;
3447 std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan));
3448
3449 double stretch, shift;
3450 if (pfunc == &Scantable::getChebyshevPolynomial) {
3451 stretch = 2.0/(double)(nchan - 1);
3452 shift = -1.0;
3453 } else {
3454 stretch = 1.0;
3455 shift = 0.0;
3456 }
3457
3458 for (int i = 0; i < nmodel; ++i) {
3459 for (int j = 0; j < nchan; ++j) {
3460 model[i][j] = (this->*pfunc)(i, stretch*(double)j + shift);
3461 }
3462 }
3463
3464 return model;
3465}
3466
3467std::vector<std::vector<std::vector<double> > > Scantable::getPolynomialModelReservoir(int order,
3468 double (Scantable::*pfunc)(int, double),
3469 std::vector<int>& nChanNos)
3470{
3471 std::vector<std::vector<std::vector<double> > > res;
3472 res.clear();
3473 nChanNos.clear();
3474
3475 std::vector<uint> ifNos = getIFNos();
3476 for (uint i = 0; i < ifNos.size(); ++i) {
3477 int currNchan = nchan(ifNos[i]);
3478 bool hasDifferentNchan = (i == 0);
3479 for (uint j = 0; j < i; ++j) {
3480 if (currNchan != nchan(ifNos[j])) {
3481 hasDifferentNchan = true;
3482 break;
3483 }
3484 }
3485 if (hasDifferentNchan) {
3486 res.push_back(getPolynomialModel(order, currNchan, pfunc));
3487 nChanNos.push_back(currNchan);
3488 }
3489 }
3490
3491 return res;
3492}
3493
3494std::vector<float> Scantable::doLeastSquareFitting(const std::vector<float>& data,
3495 const std::vector<bool>& mask,
3496 const std::vector<std::vector<double> >& model,
3497 std::vector<float>& params,
3498 float& rms,
3499 std::vector<bool>& finalMask,
3500 int& nClipped,
3501 float thresClip,
3502 int nIterClip,
3503 bool getResidual)
3504{
3505 int nDOF = model.size();
3506 int nChan = data.size();
3507
3508 if (nDOF == 0) {
3509 throw(AipsError("no model data given"));
3510 }
3511 if (nChan < 2) {
3512 throw(AipsError("data size is too few"));
3513 }
3514 if (nChan != (int)mask.size()) {
3515 throw(AipsError("data and mask sizes are not identical"));
3516 }
3517 for (int i = 0; i < nDOF; ++i) {
3518 if (nChan != (int)model[i].size()) {
3519 throw(AipsError("data and model sizes are not identical"));
3520 }
3521 }
3522
3523 params.clear();
3524 params.resize(nDOF);
3525
3526 finalMask.clear();
3527 finalMask.resize(nChan);
3528
3529 std::vector<int> maskArray(nChan);
3530 int j = 0;
3531 for (int i = 0; i < nChan; ++i) {
3532 maskArray[i] = mask[i] ? 1 : 0;
3533 if (mask[i]) {
3534 j++;
3535 }
3536 finalMask[i] = mask[i];
3537 }
3538
3539 int initNData = j;
3540 int nData = initNData;
3541
3542 std::vector<double> z1(nChan), r1(nChan), residual(nChan);
3543 for (int i = 0; i < nChan; ++i) {
3544 z1[i] = (double)data[i];
3545 r1[i] = 0.0;
3546 residual[i] = 0.0;
3547 }
3548
3549 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3550 // xMatrix : horizontal concatenation of
3551 // the least-sq. matrix (left) and an
3552 // identity matrix (right).
3553 // the right part is used to calculate the inverse matrix of the left part.
3554 double xMatrix[nDOF][2*nDOF];
3555 double zMatrix[nDOF];
3556 for (int i = 0; i < nDOF; ++i) {
3557 for (int j = 0; j < 2*nDOF; ++j) {
3558 xMatrix[i][j] = 0.0;
3559 }
3560 xMatrix[i][nDOF+i] = 1.0;
3561 zMatrix[i] = 0.0;
3562 }
3563
3564 int nUseData = 0;
3565 for (int k = 0; k < nChan; ++k) {
3566 if (maskArray[k] == 0) continue;
3567
3568 for (int i = 0; i < nDOF; ++i) {
3569 for (int j = i; j < nDOF; ++j) {
3570 xMatrix[i][j] += model[i][k] * model[j][k];
3571 }
3572 zMatrix[i] += z1[k] * model[i][k];
3573 }
3574
3575 nUseData++;
3576 }
3577
3578 if (nUseData < 1) {
3579 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
3580 }
3581
3582 for (int i = 0; i < nDOF; ++i) {
3583 for (int j = 0; j < i; ++j) {
3584 xMatrix[i][j] = xMatrix[j][i];
3585 }
3586 }
3587
3588 std::vector<double> invDiag(nDOF);
3589 for (int i = 0; i < nDOF; ++i) {
3590 invDiag[i] = 1.0 / xMatrix[i][i];
3591 for (int j = 0; j < nDOF; ++j) {
3592 xMatrix[i][j] *= invDiag[i];
3593 }
3594 }
3595
3596 for (int k = 0; k < nDOF; ++k) {
3597 for (int i = 0; i < nDOF; ++i) {
3598 if (i != k) {
3599 double factor1 = xMatrix[k][k];
3600 double invfactor1 = 1.0 / factor1;
3601 double factor2 = xMatrix[i][k];
3602 for (int j = k; j < 2*nDOF; ++j) {
3603 xMatrix[i][j] *= factor1;
3604 xMatrix[i][j] -= xMatrix[k][j]*factor2;
3605 xMatrix[i][j] *= invfactor1;
3606 }
3607 }
3608 }
3609 double invXDiag = 1.0 / xMatrix[k][k];
3610 for (int j = k; j < 2*nDOF; ++j) {
3611 xMatrix[k][j] *= invXDiag;
3612 }
3613 }
3614
3615 for (int i = 0; i < nDOF; ++i) {
3616 for (int j = 0; j < nDOF; ++j) {
3617 xMatrix[i][nDOF+j] *= invDiag[j];
3618 }
3619 }
3620 //compute a vector y in which coefficients of the best-fit
3621 //model functions are stored.
3622 //in case of polynomials, y consists of (a0,a1,a2,...)
3623 //where ai is the coefficient of the term x^i.
3624 //in case of sinusoids, y consists of (a0,s1,c1,s2,c2,...)
3625 //where a0 is constant term and s* and c* are of sine
3626 //and cosine functions, respectively.
3627 std::vector<double> y(nDOF);
3628 for (int i = 0; i < nDOF; ++i) {
3629 y[i] = 0.0;
3630 for (int j = 0; j < nDOF; ++j) {
3631 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3632 }
3633 params[i] = (float)y[i];
3634 }
3635
3636 for (int i = 0; i < nChan; ++i) {
3637 r1[i] = y[0];
3638 for (int j = 1; j < nDOF; ++j) {
3639 r1[i] += y[j]*model[j][i];
3640 }
3641 residual[i] = z1[i] - r1[i];
3642 }
3643
3644 double stdDev = 0.0;
3645 for (int i = 0; i < nChan; ++i) {
3646 stdDev += residual[i]*residual[i]*(double)maskArray[i];
3647 }
3648 stdDev = sqrt(stdDev/(double)nData);
3649 rms = (float)stdDev;
3650
3651 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3652 break;
3653 } else {
3654
3655 double thres = stdDev * thresClip;
3656 int newNData = 0;
3657 for (int i = 0; i < nChan; ++i) {
3658 if (abs(residual[i]) >= thres) {
3659 maskArray[i] = 0;
3660 finalMask[i] = false;
3661 }
3662 if (maskArray[i] > 0) {
3663 newNData++;
3664 }
3665 }
3666 if (newNData == nData) {
3667 break; //no more flag to add. iteration stops.
3668 } else {
3669 nData = newNData;
3670 }
3671
3672 }
3673 }
3674
3675 nClipped = initNData - nData;
3676
3677 std::vector<float> result(nChan);
3678 if (getResidual) {
3679 for (int i = 0; i < nChan; ++i) {
3680 result[i] = (float)residual[i];
3681 }
3682 } else {
3683 for (int i = 0; i < nChan; ++i) {
3684 result[i] = (float)r1[i];
3685 }
3686 }
3687
3688 return result;
3689}
3690
3691void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece,
3692 float thresClip, int nIterClip,
3693 bool getResidual,
3694 const std::string& progressInfo,
3695 const bool outLogger, const std::string& blfile,
3696 const std::string& bltable)
3697{
3698 /****
3699 double TimeStart = mathutil::gettimeofday_sec();
3700 ****/
3701
3702 try {
3703 ofstream ofs;
3704 String coordInfo;
3705 bool hasSameNchan, outTextFile, csvFormat, showProgress;
3706 int minNRow;
3707 int nRow = nrow();
3708 std::vector<bool> chanMask, finalChanMask;
3709 float rms;
3710 bool outBaselineTable = (bltable != "");
3711 STBaselineTable bt = STBaselineTable(*this);
3712 Vector<Double> timeSecCol;
3713
3714 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3715 coordInfo, hasSameNchan,
3716 progressInfo, showProgress, minNRow,
3717 timeSecCol);
3718
3719 std::vector<int> nChanNos;
3720 std::vector<std::vector<std::vector<double> > > modelReservoir;
3721 modelReservoir = getPolynomialModelReservoir(3,
3722 &Scantable::getNormalPolynomial,
3723 nChanNos);
3724
3725 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3726 std::vector<float> sp = getSpectrum(whichrow);
3727 chanMask = getCompositeChanMask(whichrow, mask);
3728
3729 std::vector<int> pieceEdges;
3730 std::vector<float> params;
3731 int nClipped = 0;
3732 std::vector<float> res = doCubicSplineLeastSquareFitting(sp, chanMask,
3733 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3734 nPiece, false, pieceEdges, params, rms, finalChanMask,
3735 nClipped, thresClip, nIterClip, getResidual);
3736
3737 if (outBaselineTable) {
3738 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3739 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3740 true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(),
3741 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3742 thresClip, nIterClip, 0.0, 0, std::vector<int>());
3743 } else {
3744 setSpectrum(res, whichrow);
3745 }
3746
3747 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3748 coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()",
3749 pieceEdges, params, nClipped);
3750 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3751 }
3752
3753 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
3754
3755 } catch (...) {
3756 throw;
3757 }
3758
3759 /****
3760 double TimeEnd = mathutil::gettimeofday_sec();
3761 double elapse1 = TimeEnd - TimeStart;
3762 std::cout << "cspline-new : " << elapse1 << " (sec.)" << endl;
3763 ****/
3764}
3765
3766void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece,
3767 float thresClip, int nIterClip,
3768 const std::vector<int>& edge,
3769 float threshold, int chanAvgLimit,
3770 bool getResidual,
3771 const std::string& progressInfo,
3772 const bool outLogger, const std::string& blfile,
3773 const std::string& bltable)
3774{
3775 try {
3776 ofstream ofs;
3777 String coordInfo;
3778 bool hasSameNchan, outTextFile, csvFormat, showProgress;
3779 int minNRow;
3780 int nRow = nrow();
3781 std::vector<bool> chanMask, finalChanMask;
3782 float rms;
3783 bool outBaselineTable = (bltable != "");
3784 STBaselineTable bt = STBaselineTable(*this);
3785 Vector<Double> timeSecCol;
3786 STLineFinder lineFinder = STLineFinder();
3787
3788 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
3789 coordInfo, hasSameNchan,
3790 progressInfo, showProgress, minNRow,
3791 timeSecCol);
3792
3793 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
3794
3795 std::vector<int> nChanNos;
3796 std::vector<std::vector<std::vector<double> > > modelReservoir;
3797 modelReservoir = getPolynomialModelReservoir(3,
3798 &Scantable::getNormalPolynomial,
3799 nChanNos);
3800
3801 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3802 std::vector<float> sp = getSpectrum(whichrow);
3803 std::vector<int> currentEdge;
3804 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
3805
3806 std::vector<int> pieceEdges;
3807 std::vector<float> params;
3808 int nClipped = 0;
3809 std::vector<float> res = doCubicSplineLeastSquareFitting(sp, chanMask,
3810 modelReservoir[getIdxOfNchan(sp.size(), nChanNos)],
3811 nPiece, false, pieceEdges, params, rms, finalChanMask,
3812 nClipped, thresClip, nIterClip, getResidual);
3813
3814 if (outBaselineTable) {
3815 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
3816 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
3817 true, STBaselineFunc::CSpline, pieceEdges, std::vector<float>(),
3818 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
3819 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
3820 } else {
3821 setSpectrum(res, whichrow);
3822 }
3823
3824 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
3825 coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()",
3826 pieceEdges, params, nClipped);
3827 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3828 }
3829
3830 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
3831
3832 } catch (...) {
3833 throw;
3834 }
3835}
3836
3837std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data,
3838 const std::vector<bool>& mask,
3839 std::vector<int>& idxEdge,
3840 std::vector<float>& params,
3841 float& rms,
3842 std::vector<bool>& finalmask,
3843 float clipth,
3844 int clipn)
3845{
3846 int nClipped = 0;
3847 return doCubicSplineFitting(data, mask, idxEdge.size()-1, true, idxEdge, params, rms, finalmask, nClipped, clipth, clipn);
3848}
3849
3850std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data,
3851 const std::vector<bool>& mask,
3852 int nPiece,
3853 std::vector<int>& idxEdge,
3854 std::vector<float>& params,
3855 float& rms,
3856 std::vector<bool>& finalmask,
3857 float clipth,
3858 int clipn)
3859{
3860 int nClipped = 0;
3861 return doCubicSplineFitting(data, mask, nPiece, false, idxEdge, params, rms, finalmask, nClipped, clipth, clipn);
3862}
3863
3864std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data,
3865 const std::vector<bool>& mask,
3866 int nPiece,
3867 bool useGivenPieceBoundary,
3868 std::vector<int>& idxEdge,
3869 std::vector<float>& params,
3870 float& rms,
3871 std::vector<bool>& finalMask,
3872 int& nClipped,
3873 float thresClip,
3874 int nIterClip,
3875 bool getResidual)
3876{
3877 return doCubicSplineLeastSquareFitting(data, mask,
3878 getPolynomialModel(3, data.size(), &Scantable::getNormalPolynomial),
3879 nPiece, useGivenPieceBoundary, idxEdge,
3880 params, rms, finalMask,
3881 nClipped, thresClip, nIterClip,
3882 getResidual);
3883}
3884
3885std::vector<float> Scantable::doCubicSplineLeastSquareFitting(const std::vector<float>& data,
3886 const std::vector<bool>& mask,
3887 const std::vector<std::vector<double> >& model,
3888 int nPiece,
3889 bool useGivenPieceBoundary,
3890 std::vector<int>& idxEdge,
3891 std::vector<float>& params,
3892 float& rms,
3893 std::vector<bool>& finalMask,
3894 int& nClipped,
3895 float thresClip,
3896 int nIterClip,
3897 bool getResidual)
3898{
3899 int nDOF = nPiece + 3; //number of independent parameters to solve, namely, 4+(nPiece-1).
3900 int nModel = model.size();
3901 int nChan = data.size();
3902
3903 if (nModel != 4) {
3904 throw(AipsError("model size must be 4."));
3905 }
3906 if (nPiece < 1) {
3907 throw(AipsError("number of the sections must be one or more"));
3908 }
3909 if (nChan < 2*nPiece) {
3910 throw(AipsError("data size is too few"));
3911 }
3912 if (nChan != (int)mask.size()) {
3913 throw(AipsError("data and mask sizes are not identical"));
3914 }
3915 for (int i = 0; i < nModel; ++i) {
3916 if (nChan != (int)model[i].size()) {
3917 throw(AipsError("data and model sizes are not identical"));
3918 }
3919 }
3920
3921 params.clear();
3922 params.resize(nPiece*nModel);
3923
3924 finalMask.clear();
3925 finalMask.resize(nChan);
3926
3927 std::vector<int> maskArray(nChan);
3928 std::vector<int> x(nChan);
3929 int j = 0;
3930 for (int i = 0; i < nChan; ++i) {
3931 maskArray[i] = mask[i] ? 1 : 0;
3932 if (mask[i]) {
3933 x[j] = i;
3934 j++;
3935 }
3936 finalMask[i] = mask[i];
3937 }
3938
3939 int initNData = j;
3940 int nData = initNData;
3941
3942 if (initNData < nPiece) {
3943 throw(AipsError("too few non-flagged channels"));
3944 }
3945
3946 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
3947 std::vector<double> invEdge(nPiece-1);
3948
3949 if (useGivenPieceBoundary) {
3950 if ((int)idxEdge.size() != nPiece+1) {
3951 throw(AipsError("pieceEdge.size() must be equal to nPiece+1."));
3952 }
3953 } else {
3954 idxEdge.clear();
3955 idxEdge.resize(nPiece+1);
3956 idxEdge[0] = x[0];
3957 }
3958 for (int i = 1; i < nPiece; ++i) {
3959 int valX = x[nElement*i];
3960 if (!useGivenPieceBoundary) {
3961 idxEdge[i] = valX;
3962 }
3963 invEdge[i-1] = 1.0/(double)valX;
3964 }
3965 if (!useGivenPieceBoundary) {
3966 idxEdge[nPiece] = x[initNData-1]+1;
3967 }
3968
3969 std::vector<double> z1(nChan), r1(nChan), residual(nChan);
3970 for (int i = 0; i < nChan; ++i) {
3971 z1[i] = (double)data[i];
3972 r1[i] = 0.0;
3973 residual[i] = 0.0;
3974 }
3975
3976 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3977 // xMatrix : horizontal concatenation of
3978 // the least-sq. matrix (left) and an
3979 // identity matrix (right).
3980 // the right part is used to calculate the inverse matrix of the left part.
3981
3982 double xMatrix[nDOF][2*nDOF];
3983 double zMatrix[nDOF];
3984 for (int i = 0; i < nDOF; ++i) {
3985 for (int j = 0; j < 2*nDOF; ++j) {
3986 xMatrix[i][j] = 0.0;
3987 }
3988 xMatrix[i][nDOF+i] = 1.0;
3989 zMatrix[i] = 0.0;
3990 }
3991
3992 for (int n = 0; n < nPiece; ++n) {
3993 int nUseDataInPiece = 0;
3994 for (int k = idxEdge[n]; k < idxEdge[n+1]; ++k) {
3995
3996 if (maskArray[k] == 0) continue;
3997
3998 for (int i = 0; i < nModel; ++i) {
3999 for (int j = i; j < nModel; ++j) {
4000 xMatrix[i][j] += model[i][k] * model[j][k];
4001 }
4002 zMatrix[i] += z1[k] * model[i][k];
4003 }
4004
4005 for (int i = 0; i < n; ++i) {
4006 double q = 1.0 - model[1][k]*invEdge[i];
4007 q = q*q*q;
4008 for (int j = 0; j < nModel; ++j) {
4009 xMatrix[j][i+nModel] += q * model[j][k];
4010 }
4011 for (int j = 0; j < i; ++j) {
4012 double r = 1.0 - model[1][k]*invEdge[j];
4013 r = r*r*r;
4014 xMatrix[j+nModel][i+nModel] += r*q;
4015 }
4016 xMatrix[i+nModel][i+nModel] += q*q;
4017 zMatrix[i+nModel] += q*z1[k];
4018 }
4019
4020 nUseDataInPiece++;
4021 }
4022
4023 if (nUseDataInPiece < 1) {
4024 std::vector<string> suffixOfPieceNumber(4);
4025 suffixOfPieceNumber[0] = "th";
4026 suffixOfPieceNumber[1] = "st";
4027 suffixOfPieceNumber[2] = "nd";
4028 suffixOfPieceNumber[3] = "rd";
4029 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
4030 ostringstream oss;
4031 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
4032 oss << " piece of the spectrum. can't execute fitting anymore.";
4033 throw(AipsError(String(oss)));
4034 }
4035 }
4036
4037 for (int i = 0; i < nDOF; ++i) {
4038 for (int j = 0; j < i; ++j) {
4039 xMatrix[i][j] = xMatrix[j][i];
4040 }
4041 }
4042
4043 std::vector<double> invDiag(nDOF);
4044 for (int i = 0; i < nDOF; ++i) {
4045 invDiag[i] = 1.0 / xMatrix[i][i];
4046 for (int j = 0; j < nDOF; ++j) {
4047 xMatrix[i][j] *= invDiag[i];
4048 }
4049 }
4050
4051 for (int k = 0; k < nDOF; ++k) {
4052 for (int i = 0; i < nDOF; ++i) {
4053 if (i != k) {
4054 double factor1 = xMatrix[k][k];
4055 double invfactor1 = 1.0 / factor1;
4056 double factor2 = xMatrix[i][k];
4057 for (int j = k; j < 2*nDOF; ++j) {
4058 xMatrix[i][j] *= factor1;
4059 xMatrix[i][j] -= xMatrix[k][j]*factor2;
4060 xMatrix[i][j] *= invfactor1;
4061 }
4062 }
4063 }
4064 double invXDiag = 1.0 / xMatrix[k][k];
4065 for (int j = k; j < 2*nDOF; ++j) {
4066 xMatrix[k][j] *= invXDiag;
4067 }
4068 }
4069
4070 for (int i = 0; i < nDOF; ++i) {
4071 for (int j = 0; j < nDOF; ++j) {
4072 xMatrix[i][nDOF+j] *= invDiag[j];
4073 }
4074 }
4075
4076 //compute a vector y which consists of the coefficients of the best-fit spline curves
4077 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
4078 //cubic terms for the other pieces (in case nPiece>1).
4079 std::vector<double> y(nDOF);
4080 for (int i = 0; i < nDOF; ++i) {
4081 y[i] = 0.0;
4082 for (int j = 0; j < nDOF; ++j) {
4083 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
4084 }
4085 }
4086
4087 std::vector<double> a(nModel);
4088 for (int i = 0; i < nModel; ++i) {
4089 a[i] = y[i];
4090 }
4091
4092 int j = 0;
4093 for (int n = 0; n < nPiece; ++n) {
4094 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
4095 r1[i] = 0.0;
4096 for (int j = 0; j < nModel; ++j) {
4097 r1[i] += a[j] * model[j][i];
4098 }
4099 }
4100 for (int i = 0; i < nModel; ++i) {
4101 params[j+i] = a[i];
4102 }
4103 j += nModel;
4104
4105 if (n == nPiece-1) break;
4106
4107 double d = y[n+nModel];
4108 double iE = invEdge[n];
4109 a[0] += d;
4110 a[1] -= 3.0 * d * iE;
4111 a[2] += 3.0 * d * iE * iE;
4112 a[3] -= d * iE * iE * iE;
4113 }
4114
4115 //subtract constant value for masked regions at the edge of spectrum
4116 if (idxEdge[0] > 0) {
4117 int n = idxEdge[0];
4118 for (int i = 0; i < idxEdge[0]; ++i) {
4119 //--cubic extrapolate--
4120 //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i];
4121 //--linear extrapolate--
4122 //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n];
4123 //--constant--
4124 r1[i] = r1[n];
4125 }
4126 }
4127
4128 if (idxEdge[nPiece] < nChan) {
4129 int n = idxEdge[nPiece]-1;
4130 for (int i = idxEdge[nPiece]; i < nChan; ++i) {
4131 //--cubic extrapolate--
4132 //int m = 4*(nPiece-1);
4133 //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i];
4134 //--linear extrapolate--
4135 //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n];
4136 //--constant--
4137 r1[i] = r1[n];
4138 }
4139 }
4140
4141 for (int i = 0; i < nChan; ++i) {
4142 residual[i] = z1[i] - r1[i];
4143 }
4144
4145 double stdDev = 0.0;
4146 for (int i = 0; i < nChan; ++i) {
4147 stdDev += residual[i]*residual[i]*(double)maskArray[i];
4148 }
4149 stdDev = sqrt(stdDev/(double)nData);
4150 rms = (float)stdDev;
4151
4152 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
4153 break;
4154 } else {
4155
4156 double thres = stdDev * thresClip;
4157 int newNData = 0;
4158 for (int i = 0; i < nChan; ++i) {
4159 if (abs(residual[i]) >= thres) {
4160 maskArray[i] = 0;
4161 finalMask[i] = false;
4162 }
4163 if (maskArray[i] > 0) {
4164 newNData++;
4165 }
4166 }
4167 if (newNData == nData) {
4168 break; //no more flag to add. iteration stops.
4169 } else {
4170 nData = newNData;
4171 }
4172
4173 }
4174 }
4175
4176 nClipped = initNData - nData;
4177
4178 std::vector<float> result(nChan);
4179 if (getResidual) {
4180 for (int i = 0; i < nChan; ++i) {
4181 result[i] = (float)residual[i];
4182 }
4183 } else {
4184 for (int i = 0; i < nChan; ++i) {
4185 result[i] = (float)r1[i];
4186 }
4187 }
4188
4189 return result;
4190}
4191
4192std::vector<int> Scantable::selectWaveNumbers(const std::vector<int>& addNWaves,
4193 const std::vector<int>& rejectNWaves)
4194{
4195 std::vector<bool> chanMask;
4196 std::string fftMethod;
4197 std::string fftThresh;
4198
4199 return selectWaveNumbers(0, chanMask, false, fftMethod, fftThresh, addNWaves, rejectNWaves);
4200}
4201
4202std::vector<int> Scantable::selectWaveNumbers(const int whichrow,
4203 const std::vector<bool>& chanMask,
4204 const bool applyFFT,
4205 const std::string& fftMethod,
4206 const std::string& fftThresh,
4207 const std::vector<int>& addNWaves,
4208 const std::vector<int>& rejectNWaves)
4209{
4210 std::vector<int> nWaves;
4211 nWaves.clear();
4212
4213 if (applyFFT) {
4214 string fftThAttr;
4215 float fftThSigma;
4216 int fftThTop;
4217 parseFFTThresholdInfo(fftThresh, fftThAttr, fftThSigma, fftThTop);
4218 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
4219 }
4220
4221 addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves);
4222
4223 return nWaves;
4224}
4225
4226int Scantable::getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos)
4227{
4228 int idx = -1;
4229 for (uint i = 0; i < nChanNos.size(); ++i) {
4230 if (nChan == nChanNos[i]) {
4231 idx = i;
4232 break;
4233 }
4234 }
4235
4236 if (idx < 0) {
4237 throw(AipsError("nChan not found in nChhanNos."));
4238 }
4239
4240 return idx;
4241}
4242
4243void Scantable::parseFFTInfo(const std::string& fftInfo, bool& applyFFT, std::string& fftMethod, std::string& fftThresh)
4244{
4245 istringstream iss(fftInfo);
4246 std::string tmp;
4247 std::vector<string> res;
4248 while (getline(iss, tmp, ',')) {
4249 res.push_back(tmp);
4250 }
4251 if (res.size() < 3) {
4252 throw(AipsError("wrong value in 'fftinfo' parameter")) ;
4253 }
4254 applyFFT = (res[0] == "true");
4255 fftMethod = res[1];
4256 fftThresh = res[2];
4257}
4258
4259void Scantable::parseFFTThresholdInfo(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
4260{
4261 uInt idxSigma = fftThresh.find("sigma");
4262 uInt idxTop = fftThresh.find("top");
4263
4264 if (idxSigma == fftThresh.size() - 5) {
4265 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
4266 is >> fftThSigma;
4267 fftThAttr = "sigma";
4268 } else if (idxTop == 0) {
4269 std::istringstream is(fftThresh.substr(3));
4270 is >> fftThTop;
4271 fftThAttr = "top";
4272 } else {
4273 bool isNumber = true;
4274 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
4275 char ch = (fftThresh.substr(i, 1).c_str())[0];
4276 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
4277 isNumber = false;
4278 break;
4279 }
4280 }
4281 if (isNumber) {
4282 std::istringstream is(fftThresh);
4283 is >> fftThSigma;
4284 fftThAttr = "sigma";
4285 } else {
4286 throw(AipsError("fftthresh has a wrong value"));
4287 }
4288 }
4289}
4290
4291void Scantable::doSelectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const std::string& fftMethod, const float fftThSigma, const int fftThTop, const std::string& fftThAttr, std::vector<int>& nWaves)
4292{
4293 std::vector<float> fspec;
4294 if (fftMethod == "fft") {
4295 fspec = execFFT(whichrow, chanMask, false, true);
4296 //} else if (fftMethod == "lsp") {
4297 // fspec = lombScarglePeriodogram(whichrow);
4298 }
4299
4300 if (fftThAttr == "sigma") {
4301 float mean = 0.0;
4302 float mean2 = 0.0;
4303 for (uInt i = 0; i < fspec.size(); ++i) {
4304 mean += fspec[i];
4305 mean2 += fspec[i]*fspec[i];
4306 }
4307 mean /= float(fspec.size());
4308 mean2 /= float(fspec.size());
4309 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
4310
4311 for (uInt i = 0; i < fspec.size(); ++i) {
4312 if (fspec[i] >= thres) {
4313 nWaves.push_back(i);
4314 }
4315 }
4316
4317 } else if (fftThAttr == "top") {
4318 for (int i = 0; i < fftThTop; ++i) {
4319 float max = 0.0;
4320 int maxIdx = 0;
4321 for (uInt j = 0; j < fspec.size(); ++j) {
4322 if (fspec[j] > max) {
4323 max = fspec[j];
4324 maxIdx = j;
4325 }
4326 }
4327 nWaves.push_back(maxIdx);
4328 fspec[maxIdx] = 0.0;
4329 }
4330
4331 }
4332
4333 if (nWaves.size() > 1) {
4334 sort(nWaves.begin(), nWaves.end());
4335 }
4336}
4337
4338void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
4339{
4340 std::vector<int> tempAddNWaves, tempRejectNWaves;
4341 tempAddNWaves.clear();
4342 tempRejectNWaves.clear();
4343
4344 for (uInt i = 0; i < addNWaves.size(); ++i) {
4345 tempAddNWaves.push_back(addNWaves[i]);
4346 }
4347 if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) {
4348 setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves);
4349 }
4350
4351 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
4352 tempRejectNWaves.push_back(rejectNWaves[i]);
4353 }
4354 if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) {
4355 setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves);
4356 }
4357
4358 for (uInt i = 0; i < tempAddNWaves.size(); ++i) {
4359 bool found = false;
4360 for (uInt j = 0; j < nWaves.size(); ++j) {
4361 if (nWaves[j] == tempAddNWaves[i]) {
4362 found = true;
4363 break;
4364 }
4365 }
4366 if (!found) nWaves.push_back(tempAddNWaves[i]);
4367 }
4368
4369 for (uInt i = 0; i < tempRejectNWaves.size(); ++i) {
4370 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
4371 if (*j == tempRejectNWaves[i]) {
4372 j = nWaves.erase(j);
4373 } else {
4374 ++j;
4375 }
4376 }
4377 }
4378
4379 if (nWaves.size() > 1) {
4380 sort(nWaves.begin(), nWaves.end());
4381 unique(nWaves.begin(), nWaves.end());
4382 }
4383}
4384
4385void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves)
4386{
4387 int val = nWaves[0];
4388 int nyquistFreq = nchan(getIF(whichrow))/2+1;
4389 nWaves.clear();
4390 if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759
4391 nWaves.push_back(0);
4392 }
4393 while (val <= nyquistFreq) {
4394 nWaves.push_back(val);
4395 val++;
4396 }
4397}
4398
4399void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo,
4400 const std::vector<int>& addNWaves,
4401 const std::vector<int>& rejectNWaves,
4402 float thresClip, int nIterClip,
4403 bool getResidual,
4404 const std::string& progressInfo,
4405 const bool outLogger, const std::string& blfile,
4406 const std::string& bltable)
4407{
4408 /****
4409 double TimeStart = mathutil::gettimeofday_sec();
4410 ****/
4411
4412 try {
4413 ofstream ofs;
4414 String coordInfo;
4415 bool hasSameNchan, outTextFile, csvFormat, showProgress;
4416 int minNRow;
4417 int nRow = nrow();
4418 std::vector<bool> chanMask, finalChanMask;
4419 float rms;
4420 bool outBaselineTable = (bltable != "");
4421 STBaselineTable bt = STBaselineTable(*this);
4422 Vector<Double> timeSecCol;
4423
4424 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
4425 coordInfo, hasSameNchan,
4426 progressInfo, showProgress, minNRow,
4427 timeSecCol);
4428
4429 bool applyFFT;
4430 std::string fftMethod, fftThresh;
4431 parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh);
4432
4433 std::vector<int> nWaves;
4434 std::vector<int> nChanNos;
4435 std::vector<std::vector<std::vector<double> > > modelReservoir;
4436 if (!applyFFT) {
4437 nWaves = selectWaveNumbers(addNWaves, rejectNWaves);
4438 modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos);
4439 }
4440
4441 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
4442 std::vector<float> sp = getSpectrum(whichrow);
4443 chanMask = getCompositeChanMask(whichrow, mask);
4444 std::vector<std::vector<double> > model;
4445 if (applyFFT) {
4446 nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh,
4447 addNWaves, rejectNWaves);
4448 model = getSinusoidModel(nWaves, sp.size());
4449 } else {
4450 model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)];
4451 }
4452
4453 std::vector<float> params;
4454 int nClipped = 0;
4455 std::vector<float> res = doLeastSquareFitting(sp, chanMask, model,
4456 params, rms, finalChanMask,
4457 nClipped, thresClip, nIterClip, getResidual);
4458
4459 if (outBaselineTable) {
4460 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4461 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4462 true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(),
4463 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
4464 thresClip, nIterClip, 0.0, 0, std::vector<int>());
4465 } else {
4466 setSpectrum(res, whichrow);
4467 }
4468
4469 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
4470 coordInfo, hasSameNchan, ofs, "sinusoidBaseline()",
4471 params, nClipped);
4472 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
4473 }
4474
4475 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
4476
4477 } catch (...) {
4478 throw;
4479 }
4480
4481 /****
4482 double TimeEnd = mathutil::gettimeofday_sec();
4483 double elapse1 = TimeEnd - TimeStart;
4484 std::cout << "sinusoid-old : " << elapse1 << " (sec.)" << endl;
4485 ****/
4486}
4487
4488void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo,
4489 const std::vector<int>& addNWaves,
4490 const std::vector<int>& rejectNWaves,
4491 float thresClip, int nIterClip,
4492 const std::vector<int>& edge,
4493 float threshold, int chanAvgLimit,
4494 bool getResidual,
4495 const std::string& progressInfo,
4496 const bool outLogger, const std::string& blfile,
4497 const std::string& bltable)
4498{
4499 try {
4500 ofstream ofs;
4501 String coordInfo;
4502 bool hasSameNchan, outTextFile, csvFormat, showProgress;
4503 int minNRow;
4504 int nRow = nrow();
4505 std::vector<bool> chanMask, finalChanMask;
4506 float rms;
4507 bool outBaselineTable = (bltable != "");
4508 STBaselineTable bt = STBaselineTable(*this);
4509 Vector<Double> timeSecCol;
4510 STLineFinder lineFinder = STLineFinder();
4511
4512 initialiseBaselining(blfile, ofs, outLogger, outTextFile, csvFormat,
4513 coordInfo, hasSameNchan,
4514 progressInfo, showProgress, minNRow,
4515 timeSecCol);
4516
4517 initLineFinder(edge, threshold, chanAvgLimit, lineFinder);
4518
4519 bool applyFFT;
4520 string fftMethod, fftThresh;
4521 parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh);
4522
4523 std::vector<int> nWaves;
4524 std::vector<int> nChanNos;
4525 std::vector<std::vector<std::vector<double> > > modelReservoir;
4526 if (!applyFFT) {
4527 nWaves = selectWaveNumbers(addNWaves, rejectNWaves);
4528 modelReservoir = getSinusoidModelReservoir(nWaves, nChanNos);
4529 }
4530
4531 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
4532 std::vector<float> sp = getSpectrum(whichrow);
4533 std::vector<int> currentEdge;
4534 chanMask = getCompositeChanMask(whichrow, mask, edge, currentEdge, lineFinder);
4535 std::vector<std::vector<double> > model;
4536 if (applyFFT) {
4537 nWaves = selectWaveNumbers(whichrow, chanMask, true, fftMethod, fftThresh,
4538 addNWaves, rejectNWaves);
4539 model = getSinusoidModel(nWaves, sp.size());
4540 } else {
4541 model = modelReservoir[getIdxOfNchan(sp.size(), nChanNos)];
4542 }
4543
4544 std::vector<float> params;
4545 int nClipped = 0;
4546 std::vector<float> res = doLeastSquareFitting(sp, chanMask, model,
4547 params, rms, finalChanMask,
4548 nClipped, thresClip, nIterClip, getResidual);
4549
4550 if (outBaselineTable) {
4551 bt.appenddata(getScan(whichrow), getCycle(whichrow), getBeam(whichrow),
4552 getIF(whichrow), getPol(whichrow), 0, timeSecCol[whichrow],
4553 true, STBaselineFunc::Sinusoid, nWaves, std::vector<float>(),
4554 getMaskListFromMask(finalChanMask), params, rms, sp.size(),
4555 thresClip, nIterClip, threshold, chanAvgLimit, currentEdge);
4556 } else {
4557 setSpectrum(res, whichrow);
4558 }
4559
4560 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow,
4561 coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()",
4562 params, nClipped);
4563 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
4564 }
4565
4566 finaliseBaselining(outBaselineTable, &bt, bltable, outTextFile, ofs);
4567
4568 } catch (...) {
4569 throw;
4570 }
4571}
4572
4573std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data,
4574 const std::vector<bool>& mask,
4575 const std::vector<int>& waveNumbers,
4576 std::vector<float>& params,
4577 float& rms,
4578 std::vector<bool>& finalmask,
4579 float clipth,
4580 int clipn)
4581{
4582 int nClipped = 0;
4583 return doSinusoidFitting(data, mask, waveNumbers, params, rms, finalmask, nClipped, clipth, clipn);
4584}
4585
4586std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data,
4587 const std::vector<bool>& mask,
4588 const std::vector<int>& waveNumbers,
4589 std::vector<float>& params,
4590 float& rms,
4591 std::vector<bool>& finalMask,
4592 int& nClipped,
4593 float thresClip,
4594 int nIterClip,
4595 bool getResidual)
4596{
4597 return doLeastSquareFitting(data, mask,
4598 getSinusoidModel(waveNumbers, data.size()),
4599 params, rms, finalMask,
4600 nClipped, thresClip, nIterClip,
4601 getResidual);
4602}
4603
4604std::vector<std::vector<std::vector<double> > > Scantable::getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
4605 std::vector<int>& nChanNos)
4606{
4607 std::vector<std::vector<std::vector<double> > > res;
4608 res.clear();
4609 nChanNos.clear();
4610
4611 std::vector<uint> ifNos = getIFNos();
4612 for (uint i = 0; i < ifNos.size(); ++i) {
4613 int currNchan = nchan(ifNos[i]);
4614 bool hasDifferentNchan = (i == 0);
4615 for (uint j = 0; j < i; ++j) {
4616 if (currNchan != nchan(ifNos[j])) {
4617 hasDifferentNchan = true;
4618 break;
4619 }
4620 }
4621 if (hasDifferentNchan) {
4622 res.push_back(getSinusoidModel(waveNumbers, currNchan));
4623 nChanNos.push_back(currNchan);
4624 }
4625 }
4626
4627 return res;
4628}
4629
4630std::vector<std::vector<double> > Scantable::getSinusoidModel(const std::vector<int>& waveNumbers, int nchan)
4631{
4632 // model : contains elemental values for computing the least-square matrix.
4633 // model.size() is nmodel and model[*].size() is nchan.
4634 // Each model element are as follows:
4635 // model[0] = {1.0, 1.0, 1.0, ..., 1.0},
4636 // model[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nchan])},
4637 // model[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nchan])},
4638 // where (1 <= n <= nMaxWavesInSW),
4639 // or,
4640 // model[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nchan])},
4641 // model[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nchan])},
4642 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
4643
4644 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
4645 nWaves.reserve(waveNumbers.size());
4646 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
4647 sort(nWaves.begin(), nWaves.end());
4648 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
4649 nWaves.erase(end_it, nWaves.end());
4650
4651 int minNWaves = nWaves[0];
4652 if (minNWaves < 0) {
4653 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
4654 }
4655 bool hasConstantTerm = (minNWaves == 0);
4656 int nmodel = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
4657
4658 std::vector<std::vector<double> > model(nmodel, std::vector<double>(nchan));
4659
4660 if (hasConstantTerm) {
4661 for (int j = 0; j < nchan; ++j) {
4662 model[0][j] = 1.0;
4663 }
4664 }
4665
4666 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
4667 double stretch0 = 2.0*PI/(double)(nchan-1);
4668
4669 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
4670 int sidx = hasConstantTerm ? 2*i-1 : 2*i;
4671 int cidx = sidx + 1;
4672 double stretch = stretch0*(double)nWaves[i];
4673
4674 for (int j = 0; j < nchan; ++j) {
4675 model[sidx][j] = sin(stretch*(double)j);
4676 model[cidx][j] = cos(stretch*(double)j);
4677 }
4678 }
4679
4680 return model;
4681}
4682
4683std::vector<bool> Scantable::getCompositeChanMask(int whichrow,
4684 const std::vector<bool>& inMask)
4685{
4686 std::vector<bool> mask = getMask(whichrow);
4687 uInt maskSize = mask.size();
4688 if (inMask.size() != 0) {
4689 if (maskSize != inMask.size()) {
4690 throw(AipsError("mask sizes are not the same."));
4691 }
4692 for (uInt i = 0; i < maskSize; ++i) {
4693 mask[i] = mask[i] && inMask[i];
4694 }
4695 }
4696
4697 return mask;
4698}
4699
4700std::vector<bool> Scantable::getCompositeChanMask(int whichrow,
4701 const std::vector<bool>& inMask,
4702 const std::vector<int>& edge,
4703 std::vector<int>& currEdge,
4704 STLineFinder& lineFinder)
4705{
4706 std::vector<uint> ifNos = getIFNos();
4707 if ((edge.size() > 2) && (edge.size() < ifNos.size()*2)) {
4708 throw(AipsError("Length of edge element info is less than that of IFs"));
4709 }
4710
4711 uint idx = 0;
4712 if (edge.size() > 2) {
4713 int ifVal = getIF(whichrow);
4714 bool foundIF = false;
4715 for (uint i = 0; i < ifNos.size(); ++i) {
4716 if (ifVal == (int)ifNos[i]) {
4717 idx = 2*i;
4718 foundIF = true;
4719 break;
4720 }
4721 }
4722 if (!foundIF) {
4723 throw(AipsError("bad IF number"));
4724 }
4725 }
4726
4727 currEdge.clear();
4728 currEdge.resize(2);
4729 currEdge[0] = edge[idx];
4730 currEdge[1] = edge[idx+1];
4731
4732 lineFinder.setData(getSpectrum(whichrow));
4733 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currEdge, whichrow);
4734
4735 return lineFinder.getMask();
4736}
4737
4738/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
4739void Scantable::outputFittingResult(bool outLogger,
4740 bool outTextFile,
4741 bool csvFormat,
4742 const std::vector<bool>& chanMask,
4743 int whichrow,
4744 const casa::String& coordInfo,
4745 bool hasSameNchan,
4746 ofstream& ofs,
4747 const casa::String& funcName,
4748 const std::vector<int>& edge,
4749 const std::vector<float>& params,
4750 const int nClipped)
4751{
4752 if (outLogger || outTextFile) {
4753 float rms = getRms(chanMask, whichrow);
4754 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
4755 std::vector<bool> fixed;
4756 fixed.clear();
4757
4758 if (outLogger) {
4759 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
4760 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped,
4761 masklist, whichrow, false, csvFormat) << LogIO::POST ;
4762 }
4763 if (outTextFile) {
4764 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped,
4765 masklist, whichrow, true, csvFormat) << flush;
4766 }
4767 }
4768}
4769
4770/* for poly/chebyshev/sinusoid. */
4771void Scantable::outputFittingResult(bool outLogger,
4772 bool outTextFile,
4773 bool csvFormat,
4774 const std::vector<bool>& chanMask,
4775 int whichrow,
4776 const casa::String& coordInfo,
4777 bool hasSameNchan,
4778 ofstream& ofs,
4779 const casa::String& funcName,
4780 const std::vector<float>& params,
4781 const int nClipped)
4782{
4783 if (outLogger || outTextFile) {
4784 float rms = getRms(chanMask, whichrow);
4785 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
4786 std::vector<bool> fixed;
4787 fixed.clear();
4788
4789 if (outLogger) {
4790 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
4791 ols << formatBaselineParams(params, fixed, rms, nClipped,
4792 masklist, whichrow, false, csvFormat) << LogIO::POST ;
4793 }
4794 if (outTextFile) {
4795 ofs << formatBaselineParams(params, fixed, rms, nClipped,
4796 masklist, whichrow, true, csvFormat) << flush;
4797 }
4798 }
4799}
4800
4801void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
4802{
4803 int idxDelimiter = progressInfo.find(",");
4804 if (idxDelimiter < 0) {
4805 throw(AipsError("wrong value in 'showprogress' parameter")) ;
4806 }
4807 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
4808 std::istringstream is(progressInfo.substr(idxDelimiter+1));
4809 is >> minNRow;
4810}
4811
4812void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
4813{
4814 if (showProgress && (nTotal >= nTotalThreshold)) {
4815 int nInterval = int(floor(double(nTotal)/100.0));
4816 if (nInterval == 0) nInterval++;
4817
4818 if (nProcessed % nInterval == 0) {
4819 printf("\r"); //go to the head of line
4820 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
4821 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
4822 printf("\x1b[39m\x1b[0m"); //set default attributes
4823 fflush(NULL);
4824 }
4825
4826 if (nProcessed == nTotal - 1) {
4827 printf("\r\x1b[K"); //clear
4828 fflush(NULL);
4829 }
4830
4831 }
4832}
4833
4834std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
4835{
4836 std::vector<bool> mask = getMask(whichrow);
4837
4838 if (inMask.size() > 0) {
4839 uInt maskSize = mask.size();
4840 if (maskSize != inMask.size()) {
4841 throw(AipsError("mask sizes are not the same."));
4842 }
4843 for (uInt i = 0; i < maskSize; ++i) {
4844 mask[i] = mask[i] && inMask[i];
4845 }
4846 }
4847
4848 Vector<Float> spec = getSpectrum(whichrow);
4849 mathutil::doZeroOrderInterpolation(spec, mask);
4850
4851 FFTServer<Float,Complex> ffts;
4852 Vector<Complex> fftres;
4853 ffts.fft0(fftres, spec);
4854
4855 std::vector<float> res;
4856 float norm = float(2.0/double(spec.size()));
4857
4858 if (getRealImag) {
4859 for (uInt i = 0; i < fftres.size(); ++i) {
4860 res.push_back(real(fftres[i])*norm);
4861 res.push_back(imag(fftres[i])*norm);
4862 }
4863 } else {
4864 for (uInt i = 0; i < fftres.size(); ++i) {
4865 res.push_back(abs(fftres[i])*norm);
4866 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
4867 }
4868 }
4869
4870 return res;
4871}
4872
4873
4874float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
4875{
4876 /****
4877 double ms1TimeStart, ms1TimeEnd;
4878 double elapse1 = 0.0;
4879 ms1TimeStart = mathutil::gettimeofday_sec();
4880 ****/
4881
4882 Vector<Float> spec;
4883 specCol_.get(whichrow, spec);
4884
4885 /****
4886 ms1TimeEnd = mathutil::gettimeofday_sec();
4887 elapse1 = ms1TimeEnd - ms1TimeStart;
4888 std::cout << "rm1 : " << elapse1 << " (sec.)" << endl;
4889 ****/
4890
4891 return (float)doGetRms(mask, spec);
4892}
4893
4894double Scantable::doGetRms(const std::vector<bool>& mask, const Vector<Float>& spec)
4895{
4896 double mean = 0.0;
4897 double smean = 0.0;
4898 int n = 0;
4899 for (uInt i = 0; i < spec.nelements(); ++i) {
4900 if (mask[i]) {
4901 double val = (double)spec[i];
4902 mean += val;
4903 smean += val*val;
4904 n++;
4905 }
4906 }
4907
4908 mean /= (double)n;
4909 smean /= (double)n;
4910
4911 return sqrt(smean - mean*mean);
4912}
4913
4914std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const
4915{
4916 if (verbose) {
4917 ostringstream oss;
4918
4919 if (csvformat) {
4920 oss << getScan(whichrow) << ",";
4921 oss << getBeam(whichrow) << ",";
4922 oss << getIF(whichrow) << ",";
4923 oss << getPol(whichrow) << ",";
4924 oss << getCycle(whichrow) << ",";
4925 String commaReplacedMasklist = masklist;
4926 string::size_type pos = 0;
4927 while (pos = commaReplacedMasklist.find(","), pos != string::npos) {
4928 commaReplacedMasklist.replace(pos, 1, ";");
4929 pos++;
4930 }
4931 oss << commaReplacedMasklist << ",";
4932 } else {
4933 oss << " Scan[" << getScan(whichrow) << "]";
4934 oss << " Beam[" << getBeam(whichrow) << "]";
4935 oss << " IF[" << getIF(whichrow) << "]";
4936 oss << " Pol[" << getPol(whichrow) << "]";
4937 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
4938 oss << "Fitter range = " << masklist << endl;
4939 oss << "Baseline parameters" << endl;
4940 }
4941 oss << flush;
4942
4943 return String(oss);
4944 }
4945
4946 return "";
4947}
4948
4949std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const
4950{
4951 if (verbose) {
4952 ostringstream oss;
4953
4954 if (csvformat) {
4955 oss << rms << ",";
4956 if (nClipped >= 0) {
4957 oss << nClipped;
4958 }
4959 } else {
4960 oss << "Results of baseline fit" << endl;
4961 oss << " rms = " << setprecision(6) << rms << endl;
4962 if (nClipped >= 0) {
4963 oss << " Number of clipped channels = " << nClipped << endl;
4964 }
4965 for (int i = 0; i < 60; ++i) {
4966 oss << "-";
4967 }
4968 }
4969 oss << endl;
4970 oss << flush;
4971
4972 return String(oss);
4973 }
4974
4975 return "";
4976}
4977
4978std::string Scantable::formatBaselineParams(const std::vector<float>& params,
4979 const std::vector<bool>& fixed,
4980 float rms,
4981 int nClipped,
4982 const std::string& masklist,
4983 int whichrow,
4984 bool verbose,
4985 bool csvformat,
4986 int start, int count,
4987 bool resetparamid) const
4988{
4989 int nParam = (int)(params.size());
4990
4991 if (nParam < 1) {
4992 return(" Not fitted");
4993 } else {
4994
4995 ostringstream oss;
4996 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
4997
4998 if (start < 0) start = 0;
4999 if (count < 0) count = nParam;
5000 int end = start + count;
5001 if (end > nParam) end = nParam;
5002 int paramidoffset = (resetparamid) ? (-start) : 0;
5003
5004 for (int i = start; i < end; ++i) {
5005 if (i > start) {
5006 oss << ",";
5007 }
5008 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
5009 if (csvformat) {
5010 oss << params[i] << sFix;
5011 } else {
5012 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
5013 }
5014 }
5015
5016 if (csvformat) {
5017 oss << ",";
5018 } else {
5019 oss << endl;
5020 }
5021 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
5022
5023 return String(oss);
5024 }
5025
5026}
5027
5028std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose, bool csvformat) const
5029{
5030 int nOutParam = (int)(params.size());
5031 int nPiece = (int)(ranges.size()) - 1;
5032
5033 if (nOutParam < 1) {
5034 return(" Not fitted");
5035 } else if (nPiece < 0) {
5036 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat);
5037 } else if (nPiece < 1) {
5038 return(" Bad count of the piece edge info");
5039 } else if (nOutParam % nPiece != 0) {
5040 return(" Bad count of the output baseline parameters");
5041 } else {
5042
5043 int nParam = nOutParam / nPiece;
5044
5045 ostringstream oss;
5046 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
5047
5048 if (csvformat) {
5049 for (int i = 0; i < nPiece; ++i) {
5050 oss << ranges[i] << "," << (ranges[i+1]-1) << ",";
5051 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
5052 }
5053 } else {
5054 stringstream ss;
5055 ss << ranges[nPiece] << flush;
5056 int wRange = ss.str().size() * 2 + 5;
5057
5058 for (int i = 0; i < nPiece; ++i) {
5059 ss.str("");
5060 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
5061 oss << left << setw(wRange) << ss.str();
5062 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
5063 //oss << endl;
5064 }
5065 }
5066
5067 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
5068
5069 return String(oss);
5070 }
5071
5072}
5073
5074bool Scantable::hasSameNchanOverIFs()
5075{
5076 int nIF = nif(-1);
5077 int nCh;
5078 int totalPositiveNChan = 0;
5079 int nPositiveNChan = 0;
5080
5081 for (int i = 0; i < nIF; ++i) {
5082 nCh = nchan(i);
5083 if (nCh > 0) {
5084 totalPositiveNChan += nCh;
5085 nPositiveNChan++;
5086 }
5087 }
5088
5089 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
5090}
5091
5092std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
5093{
5094 if (mask.size() <= 0) {
5095 throw(AipsError("The mask elements should be > 0"));
5096 }
5097 int IF = getIF(whichrow);
5098 if (mask.size() != (uInt)nchan(IF)) {
5099 throw(AipsError("Number of channels in scantable != number of mask elements"));
5100 }
5101
5102 if (verbose) {
5103 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
5104 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
5105 if (!hasSameNchan) {
5106 logOs << endl << "This mask is only valid for IF=" << IF;
5107 }
5108 logOs << LogIO::POST;
5109 }
5110
5111 std::vector<double> abcissa = getAbcissa(whichrow);
5112 std::vector<int> edge = getMaskEdgeIndices(mask);
5113
5114 ostringstream oss;
5115 oss.setf(ios::fixed);
5116 oss << setprecision(1) << "[";
5117 for (uInt i = 0; i < edge.size(); i+=2) {
5118 if (i > 0) oss << ",";
5119 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
5120 }
5121 oss << "]" << flush;
5122
5123 return String(oss);
5124}
5125
5126std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
5127{
5128 if (mask.size() <= 0) {
5129 throw(AipsError("The mask elements should be > 0"));
5130 }
5131
5132 std::vector<int> out, startIndices, endIndices;
5133 int maskSize = mask.size();
5134
5135 startIndices.clear();
5136 endIndices.clear();
5137
5138 if (mask[0]) {
5139 startIndices.push_back(0);
5140 }
5141 for (int i = 1; i < maskSize; ++i) {
5142 if ((!mask[i-1]) && mask[i]) {
5143 startIndices.push_back(i);
5144 } else if (mask[i-1] && (!mask[i])) {
5145 endIndices.push_back(i-1);
5146 }
5147 }
5148 if (mask[maskSize-1]) {
5149 endIndices.push_back(maskSize-1);
5150 }
5151
5152 if (startIndices.size() != endIndices.size()) {
5153 throw(AipsError("Inconsistent Mask Size: bad data?"));
5154 }
5155 for (uInt i = 0; i < startIndices.size(); ++i) {
5156 if (startIndices[i] > endIndices[i]) {
5157 throw(AipsError("Mask start index > mask end index"));
5158 }
5159 }
5160
5161 out.clear();
5162 for (uInt i = 0; i < startIndices.size(); ++i) {
5163 out.push_back(startIndices[i]);
5164 out.push_back(endIndices[i]);
5165 }
5166
5167 return out;
5168}
5169
5170void Scantable::setTsys(const std::vector<float>& newvals, int whichrow) {
5171 Vector<Float> tsys(newvals);
5172 if (whichrow > -1) {
5173 if (tsysCol_.shape(whichrow) != tsys.shape())
5174 throw(AipsError("Given Tsys values are not of the same shape"));
5175 tsysCol_.put(whichrow, tsys);
5176 } else {
5177 tsysCol_.fillColumn(tsys);
5178 }
5179}
5180
5181vector<float> Scantable::getTsysSpectrum( int whichrow ) const
5182{
5183 Vector<Float> tsys( tsysCol_(whichrow) ) ;
5184 vector<float> stlTsys ;
5185 tsys.tovector( stlTsys ) ;
5186 return stlTsys ;
5187}
5188
5189vector<uint> Scantable::getMoleculeIdColumnData() const
5190{
5191 Vector<uInt> molIds(mmolidCol_.getColumn());
5192 vector<uint> res;
5193 molIds.tovector(res);
5194 return res;
5195}
5196
5197void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids)
5198{
5199 Vector<uInt> molIds(molids);
5200 Vector<uInt> arr(mmolidCol_.getColumn());
5201 if ( molIds.nelements() != arr.nelements() )
5202 throw AipsError("The input data size must be the number of rows.");
5203 mmolidCol_.putColumn(molIds);
5204}
5205
5206
5207void Scantable::dropXPol()
5208{
5209 if (npol() <= 2) {
5210 return;
5211 }
5212 if (!selector_.empty()) {
5213 throw AipsError("Can only operate with empty selection");
5214 }
5215 std::string taql = "SELECT FROM $1 WHERE POLNO IN [0,1]";
5216 Table tab = tableCommand(taql, table_);
5217 table_ = tab;
5218 table_.rwKeywordSet().define("nPol", Int(2));
5219 originalTable_ = table_;
5220 attach();
5221}
5222
5223}
5224//namespace asap
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