source: trunk/src/Scantable.cpp@ 2438

Last change on this file since 2438 was 2437, checked in by Kana Sugimoto, 13 years ago

New Development: No

JIRA Issue: Yes

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs: unit test of sdsmooth

Put in Release Notes: No

Module(s):

Description:

Changed the equation to calculate regridded spectral coordinate in
scantable.regrid_channel() so that it would have the same values as
the result of scantable.bin().
scantable.bin() now rebins Tsys arrays if necessary.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 113.2 KB
Line 
1//
2// C++ Implementation: Scantable
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12#include <map>
13
14#include <atnf/PKSIO/SrcType.h>
15
16#include <casa/aips.h>
17#include <casa/iomanip.h>
18#include <casa/iostream.h>
19#include <casa/OS/File.h>
20#include <casa/OS/Path.h>
21#include <casa/Arrays/Array.h>
22#include <casa/Arrays/ArrayAccessor.h>
23#include <casa/Arrays/ArrayLogical.h>
24#include <casa/Arrays/ArrayMath.h>
25#include <casa/Arrays/MaskArrMath.h>
26#include <casa/Arrays/Slice.h>
27#include <casa/Arrays/Vector.h>
28#include <casa/Arrays/VectorSTLIterator.h>
29#include <casa/BasicMath/Math.h>
30#include <casa/BasicSL/Constants.h>
31#include <casa/Containers/RecordField.h>
32#include <casa/Logging/LogIO.h>
33#include <casa/Quanta/MVAngle.h>
34#include <casa/Quanta/MVTime.h>
35#include <casa/Utilities/GenSort.h>
36
37#include <coordinates/Coordinates/CoordinateUtil.h>
38
39// needed to avoid error in .tcc
40#include <measures/Measures/MCDirection.h>
41//
42#include <measures/Measures/MDirection.h>
43#include <measures/Measures/MEpoch.h>
44#include <measures/Measures/MFrequency.h>
45#include <measures/Measures/MeasRef.h>
46#include <measures/Measures/MeasTable.h>
47#include <measures/TableMeasures/ScalarMeasColumn.h>
48#include <measures/TableMeasures/TableMeasDesc.h>
49#include <measures/TableMeasures/TableMeasRefDesc.h>
50#include <measures/TableMeasures/TableMeasValueDesc.h>
51
52#include <tables/Tables/ArrColDesc.h>
53#include <tables/Tables/ExprNode.h>
54#include <tables/Tables/ScaColDesc.h>
55#include <tables/Tables/SetupNewTab.h>
56#include <tables/Tables/TableCopy.h>
57#include <tables/Tables/TableDesc.h>
58#include <tables/Tables/TableIter.h>
59#include <tables/Tables/TableParse.h>
60#include <tables/Tables/TableRecord.h>
61#include <tables/Tables/TableRow.h>
62#include <tables/Tables/TableVector.h>
63
64#include "MathUtils.h"
65#include "STAttr.h"
66#include "STLineFinder.h"
67#include "STPolCircular.h"
68#include "STPolLinear.h"
69#include "STPolStokes.h"
70#include "STUpgrade.h"
71#include "Scantable.h"
72
73using namespace casa;
74
75namespace asap {
76
77std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
78
79void Scantable::initFactories() {
80 if ( factories_.empty() ) {
81 Scantable::factories_["linear"] = &STPolLinear::myFactory;
82 Scantable::factories_["circular"] = &STPolCircular::myFactory;
83 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
84 }
85}
86
87Scantable::Scantable(Table::TableType ttype) :
88 type_(ttype)
89{
90 initFactories();
91 setupMainTable();
92 freqTable_ = STFrequencies(*this);
93 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
94 weatherTable_ = STWeather(*this);
95 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
96 focusTable_ = STFocus(*this);
97 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
98 tcalTable_ = STTcal(*this);
99 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
100 moleculeTable_ = STMolecules(*this);
101 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
102 historyTable_ = STHistory(*this);
103 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
104 fitTable_ = STFit(*this);
105 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
106 table_.tableInfo().setType( "Scantable" ) ;
107 originalTable_ = table_;
108 attach();
109}
110
111Scantable::Scantable(const std::string& name, Table::TableType ttype) :
112 type_(ttype)
113{
114 initFactories();
115
116 Table tab(name, Table::Update);
117 uInt version = tab.keywordSet().asuInt("VERSION");
118 if (version != version_) {
119 STUpgrade upgrader(version_);
120 LogIO os( LogOrigin( "Scantable" ) ) ;
121 os << LogIO::WARN
122 << name << " data format version " << version
123 << " is deprecated" << endl
124 << "Running upgrade."<< endl
125 << LogIO::POST ;
126 std::string outname = upgrader.upgrade(name);
127 if ( outname != name ) {
128 os << LogIO::WARN
129 << "Data will be loaded from " << outname << " instead of "
130 << name << LogIO::POST ;
131 tab = Table(outname, Table::Update ) ;
132 }
133 }
134 if ( type_ == Table::Memory ) {
135 table_ = tab.copyToMemoryTable(generateName());
136 } else {
137 table_ = tab;
138 }
139 table_.tableInfo().setType( "Scantable" ) ;
140
141 attachSubtables();
142 originalTable_ = table_;
143 attach();
144}
145/*
146Scantable::Scantable(const std::string& name, Table::TableType ttype) :
147 type_(ttype)
148{
149 initFactories();
150 Table tab(name, Table::Update);
151 uInt version = tab.keywordSet().asuInt("VERSION");
152 if (version != version_) {
153 throw(AipsError("Unsupported version of ASAP file."));
154 }
155 if ( type_ == Table::Memory ) {
156 table_ = tab.copyToMemoryTable(generateName());
157 } else {
158 table_ = tab;
159 }
160
161 attachSubtables();
162 originalTable_ = table_;
163 attach();
164}
165*/
166
167Scantable::Scantable( const Scantable& other, bool clear ):
168 Logger()
169{
170 // with or without data
171 String newname = String(generateName());
172 type_ = other.table_.tableType();
173 if ( other.table_.tableType() == Table::Memory ) {
174 if ( clear ) {
175 table_ = TableCopy::makeEmptyMemoryTable(newname,
176 other.table_, True);
177 } else
178 table_ = other.table_.copyToMemoryTable(newname);
179 } else {
180 other.table_.deepCopy(newname, Table::New, False,
181 other.table_.endianFormat(),
182 Bool(clear));
183 table_ = Table(newname, Table::Update);
184 table_.markForDelete();
185 }
186 table_.tableInfo().setType( "Scantable" ) ;
187 /// @todo reindex SCANNO, recompute nbeam, nif, npol
188 if ( clear ) copySubtables(other);
189 attachSubtables();
190 originalTable_ = table_;
191 attach();
192}
193
194void Scantable::copySubtables(const Scantable& other) {
195 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
196 TableCopy::copyRows(t, other.freqTable_.table());
197 t = table_.rwKeywordSet().asTable("FOCUS");
198 TableCopy::copyRows(t, other.focusTable_.table());
199 t = table_.rwKeywordSet().asTable("WEATHER");
200 TableCopy::copyRows(t, other.weatherTable_.table());
201 t = table_.rwKeywordSet().asTable("TCAL");
202 TableCopy::copyRows(t, other.tcalTable_.table());
203 t = table_.rwKeywordSet().asTable("MOLECULES");
204 TableCopy::copyRows(t, other.moleculeTable_.table());
205 t = table_.rwKeywordSet().asTable("HISTORY");
206 TableCopy::copyRows(t, other.historyTable_.table());
207 t = table_.rwKeywordSet().asTable("FIT");
208 TableCopy::copyRows(t, other.fitTable_.table());
209}
210
211void Scantable::attachSubtables()
212{
213 freqTable_ = STFrequencies(table_);
214 focusTable_ = STFocus(table_);
215 weatherTable_ = STWeather(table_);
216 tcalTable_ = STTcal(table_);
217 moleculeTable_ = STMolecules(table_);
218 historyTable_ = STHistory(table_);
219 fitTable_ = STFit(table_);
220}
221
222Scantable::~Scantable()
223{
224}
225
226void Scantable::setupMainTable()
227{
228 TableDesc td("", "1", TableDesc::Scratch);
229 td.comment() = "An ASAP Scantable";
230 td.rwKeywordSet().define("VERSION", uInt(version_));
231
232 // n Cycles
233 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
234 // new index every nBeam x nIF x nPol
235 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
236
237 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
238 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
239 // linear, circular, stokes
240 td.rwKeywordSet().define("POLTYPE", String("linear"));
241 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
242
243 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
244 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
245
246 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
247 refbeamnoColumn.setDefault(Int(-1));
248 td.addColumn(refbeamnoColumn);
249
250 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
251 flagrowColumn.setDefault(uInt(0));
252 td.addColumn(flagrowColumn);
253
254 td.addColumn(ScalarColumnDesc<Double>("TIME"));
255 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
256 TableMeasValueDesc measVal(td, "TIME");
257 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
258 mepochCol.write(td);
259
260 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
261
262 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
263 // Type of source (on=0, off=1, other=-1)
264 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
265 stypeColumn.setDefault(Int(-1));
266 td.addColumn(stypeColumn);
267 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
268
269 //The actual Data Vectors
270 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
271 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
272 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
273
274 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
275 IPosition(1,2),
276 ColumnDesc::Direct));
277 TableMeasRefDesc mdirRef(MDirection::J2000); // default
278 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
279 // the TableMeasDesc gives the column a type
280 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
281 // a uder set table type e.g. GALCTIC, B1950 ...
282 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
283 // writing create the measure column
284 mdirCol.write(td);
285 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
286 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
287 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
288
289 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
290 ScalarColumnDesc<Int> fitColumn("FIT_ID");
291 fitColumn.setDefault(Int(-1));
292 td.addColumn(fitColumn);
293
294 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
295 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
296
297 // columns which just get dragged along, as they aren't used in asap
298 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
299 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
300 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
301 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
302
303 td.rwKeywordSet().define("OBSMODE", String(""));
304
305 // Now create Table SetUp from the description.
306 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
307 table_ = Table(aNewTab, type_, 0);
308 originalTable_ = table_;
309}
310
311void Scantable::attach()
312{
313 timeCol_.attach(table_, "TIME");
314 srcnCol_.attach(table_, "SRCNAME");
315 srctCol_.attach(table_, "SRCTYPE");
316 specCol_.attach(table_, "SPECTRA");
317 flagsCol_.attach(table_, "FLAGTRA");
318 tsysCol_.attach(table_, "TSYS");
319 cycleCol_.attach(table_,"CYCLENO");
320 scanCol_.attach(table_, "SCANNO");
321 beamCol_.attach(table_, "BEAMNO");
322 ifCol_.attach(table_, "IFNO");
323 polCol_.attach(table_, "POLNO");
324 integrCol_.attach(table_, "INTERVAL");
325 azCol_.attach(table_, "AZIMUTH");
326 elCol_.attach(table_, "ELEVATION");
327 dirCol_.attach(table_, "DIRECTION");
328 fldnCol_.attach(table_, "FIELDNAME");
329 rbeamCol_.attach(table_, "REFBEAMNO");
330
331 mweatheridCol_.attach(table_,"WEATHER_ID");
332 mfitidCol_.attach(table_,"FIT_ID");
333 mfreqidCol_.attach(table_, "FREQ_ID");
334 mtcalidCol_.attach(table_, "TCAL_ID");
335 mfocusidCol_.attach(table_, "FOCUS_ID");
336 mmolidCol_.attach(table_, "MOLECULE_ID");
337
338 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
339 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
340
341}
342
343template<class T, class T2>
344void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
345 const String& colName,
346 const T2& defValue)
347{
348 try {
349 col.attach(table_, colName);
350 } catch (TableError& err) {
351 String errMesg = err.getMesg();
352 if (errMesg == "Table column " + colName + " is unknown") {
353 table_.addColumn(ScalarColumnDesc<T>(colName));
354 col.attach(table_, colName);
355 col.fillColumn(static_cast<T>(defValue));
356 } else {
357 throw;
358 }
359 } catch (...) {
360 throw;
361 }
362}
363
364template<class T, class T2>
365void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
366 const String& colName,
367 const Array<T2>& defValue)
368{
369 try {
370 col.attach(table_, colName);
371 } catch (TableError& err) {
372 String errMesg = err.getMesg();
373 if (errMesg == "Table column " + colName + " is unknown") {
374 table_.addColumn(ArrayColumnDesc<T>(colName));
375 col.attach(table_, colName);
376
377 int size = 0;
378 ArrayIterator<T2>& it = defValue.begin();
379 while (it != defValue.end()) {
380 ++size;
381 ++it;
382 }
383 IPosition ip(1, size);
384 Array<T>& arr(ip);
385 for (int i = 0; i < size; ++i)
386 arr[i] = static_cast<T>(defValue[i]);
387
388 col.fillColumn(arr);
389 } else {
390 throw;
391 }
392 } catch (...) {
393 throw;
394 }
395}
396
397void Scantable::setHeader(const STHeader& sdh)
398{
399 table_.rwKeywordSet().define("nIF", sdh.nif);
400 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
401 table_.rwKeywordSet().define("nPol", sdh.npol);
402 table_.rwKeywordSet().define("nChan", sdh.nchan);
403 table_.rwKeywordSet().define("Observer", sdh.observer);
404 table_.rwKeywordSet().define("Project", sdh.project);
405 table_.rwKeywordSet().define("Obstype", sdh.obstype);
406 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
407 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
408 table_.rwKeywordSet().define("Equinox", sdh.equinox);
409 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
410 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
411 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
412 table_.rwKeywordSet().define("UTC", sdh.utc);
413 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
414 table_.rwKeywordSet().define("Epoch", sdh.epoch);
415 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
416}
417
418STHeader Scantable::getHeader() const
419{
420 STHeader sdh;
421 table_.keywordSet().get("nBeam",sdh.nbeam);
422 table_.keywordSet().get("nIF",sdh.nif);
423 table_.keywordSet().get("nPol",sdh.npol);
424 table_.keywordSet().get("nChan",sdh.nchan);
425 table_.keywordSet().get("Observer", sdh.observer);
426 table_.keywordSet().get("Project", sdh.project);
427 table_.keywordSet().get("Obstype", sdh.obstype);
428 table_.keywordSet().get("AntennaName", sdh.antennaname);
429 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
430 table_.keywordSet().get("Equinox", sdh.equinox);
431 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
432 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
433 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
434 table_.keywordSet().get("UTC", sdh.utc);
435 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
436 table_.keywordSet().get("Epoch", sdh.epoch);
437 table_.keywordSet().get("POLTYPE", sdh.poltype);
438 return sdh;
439}
440
441void Scantable::setSourceType( int stype )
442{
443 if ( stype < 0 || stype > 1 )
444 throw(AipsError("Illegal sourcetype."));
445 TableVector<Int> tabvec(table_, "SRCTYPE");
446 tabvec = Int(stype);
447}
448
449bool Scantable::conformant( const Scantable& other )
450{
451 return this->getHeader().conformant(other.getHeader());
452}
453
454
455
456std::string Scantable::formatSec(Double x) const
457{
458 Double xcop = x;
459 MVTime mvt(xcop/24./3600.); // make days
460
461 if (x < 59.95)
462 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
463 else if (x < 3599.95)
464 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
465 else {
466 ostringstream oss;
467 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
468 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
469 return String(oss);
470 }
471};
472
473std::string Scantable::formatDirection(const MDirection& md) const
474{
475 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
476 Int prec = 7;
477
478 MVAngle mvLon(t[0]);
479 String sLon = mvLon.string(MVAngle::TIME,prec);
480 uInt tp = md.getRef().getType();
481 if (tp == MDirection::GALACTIC ||
482 tp == MDirection::SUPERGAL ) {
483 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
484 }
485 MVAngle mvLat(t[1]);
486 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
487 return sLon + String(" ") + sLat;
488}
489
490
491std::string Scantable::getFluxUnit() const
492{
493 return table_.keywordSet().asString("FluxUnit");
494}
495
496void Scantable::setFluxUnit(const std::string& unit)
497{
498 String tmp(unit);
499 Unit tU(tmp);
500 if (tU==Unit("K") || tU==Unit("Jy")) {
501 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
502 } else {
503 throw AipsError("Illegal unit - must be compatible with Jy or K");
504 }
505}
506
507void Scantable::setInstrument(const std::string& name)
508{
509 bool throwIt = true;
510 // create an Instrument to see if this is valid
511 STAttr::convertInstrument(name, throwIt);
512 String nameU(name);
513 nameU.upcase();
514 table_.rwKeywordSet().define(String("AntennaName"), nameU);
515}
516
517void Scantable::setFeedType(const std::string& feedtype)
518{
519 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
520 std::string msg = "Illegal feed type "+ feedtype;
521 throw(casa::AipsError(msg));
522 }
523 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
524}
525
526MPosition Scantable::getAntennaPosition() const
527{
528 Vector<Double> antpos;
529 table_.keywordSet().get("AntennaPosition", antpos);
530 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
531 return MPosition(mvpos);
532}
533
534void Scantable::makePersistent(const std::string& filename)
535{
536 String inname(filename);
537 Path path(inname);
538 /// @todo reindex SCANNO, recompute nbeam, nif, npol
539 inname = path.expandedName();
540 // 2011/03/04 TN
541 // We can comment out this workaround since the essential bug is
542 // fixed in casacore (r20889 in google code).
543 table_.deepCopy(inname, Table::New);
544// // WORKAROUND !!! for Table bug
545// // Remove when fixed in casacore
546// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
547// Table tab = table_.copyToMemoryTable(generateName());
548// tab.deepCopy(inname, Table::New);
549// tab.markForDelete();
550//
551// } else {
552// table_.deepCopy(inname, Table::New);
553// }
554}
555
556int Scantable::nbeam( int scanno ) const
557{
558 if ( scanno < 0 ) {
559 Int n;
560 table_.keywordSet().get("nBeam",n);
561 return int(n);
562 } else {
563 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
564 Table t = table_(table_.col("SCANNO") == scanno);
565 ROTableRow row(t);
566 const TableRecord& rec = row.get(0);
567 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
568 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
569 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
570 ROTableVector<uInt> v(subt, "BEAMNO");
571 return int(v.nelements());
572 }
573 return 0;
574}
575
576int Scantable::nif( int scanno ) const
577{
578 if ( scanno < 0 ) {
579 Int n;
580 table_.keywordSet().get("nIF",n);
581 return int(n);
582 } else {
583 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
584 Table t = table_(table_.col("SCANNO") == scanno);
585 ROTableRow row(t);
586 const TableRecord& rec = row.get(0);
587 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
588 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
589 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
590 if ( subt.nrow() == 0 ) return 0;
591 ROTableVector<uInt> v(subt, "IFNO");
592 return int(v.nelements());
593 }
594 return 0;
595}
596
597int Scantable::npol( int scanno ) const
598{
599 if ( scanno < 0 ) {
600 Int n;
601 table_.keywordSet().get("nPol",n);
602 return n;
603 } else {
604 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
605 Table t = table_(table_.col("SCANNO") == scanno);
606 ROTableRow row(t);
607 const TableRecord& rec = row.get(0);
608 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
609 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
610 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
611 if ( subt.nrow() == 0 ) return 0;
612 ROTableVector<uInt> v(subt, "POLNO");
613 return int(v.nelements());
614 }
615 return 0;
616}
617
618int Scantable::ncycle( int scanno ) const
619{
620 if ( scanno < 0 ) {
621 Block<String> cols(2);
622 cols[0] = "SCANNO";
623 cols[1] = "CYCLENO";
624 TableIterator it(table_, cols);
625 int n = 0;
626 while ( !it.pastEnd() ) {
627 ++n;
628 ++it;
629 }
630 return n;
631 } else {
632 Table t = table_(table_.col("SCANNO") == scanno);
633 ROTableRow row(t);
634 const TableRecord& rec = row.get(0);
635 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
636 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
637 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
638 if ( subt.nrow() == 0 ) return 0;
639 return int(subt.nrow());
640 }
641 return 0;
642}
643
644
645int Scantable::nrow( int scanno ) const
646{
647 return int(table_.nrow());
648}
649
650int Scantable::nchan( int ifno ) const
651{
652 if ( ifno < 0 ) {
653 Int n;
654 table_.keywordSet().get("nChan",n);
655 return int(n);
656 } else {
657 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
658 // vary with these
659 Table t = table_(table_.col("IFNO") == ifno, 1);
660 if ( t.nrow() == 0 ) return 0;
661 ROArrayColumn<Float> v(t, "SPECTRA");
662 return v.shape(0)(0);
663 }
664 return 0;
665}
666
667int Scantable::nscan() const {
668 Vector<uInt> scannos(scanCol_.getColumn());
669 uInt nout = genSort( scannos, Sort::Ascending,
670 Sort::QuickSort|Sort::NoDuplicates );
671 return int(nout);
672}
673
674int Scantable::getChannels(int whichrow) const
675{
676 return specCol_.shape(whichrow)(0);
677}
678
679int Scantable::getBeam(int whichrow) const
680{
681 return beamCol_(whichrow);
682}
683
684std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
685{
686 Vector<uInt> nos(col.getColumn());
687 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
688 nos.resize(n, True);
689 std::vector<uint> stlout;
690 nos.tovector(stlout);
691 return stlout;
692}
693
694int Scantable::getIF(int whichrow) const
695{
696 return ifCol_(whichrow);
697}
698
699int Scantable::getPol(int whichrow) const
700{
701 return polCol_(whichrow);
702}
703
704std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
705{
706 return formatTime(me, showdate, 0);
707}
708
709std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
710{
711 MVTime mvt(me.getValue());
712 if (showdate)
713 //mvt.setFormat(MVTime::YMD);
714 mvt.setFormat(MVTime::YMD, prec);
715 else
716 //mvt.setFormat(MVTime::TIME);
717 mvt.setFormat(MVTime::TIME, prec);
718 ostringstream oss;
719 oss << mvt;
720 return String(oss);
721}
722
723void Scantable::calculateAZEL()
724{
725 MPosition mp = getAntennaPosition();
726 MEpoch::ROScalarColumn timeCol(table_, "TIME");
727 ostringstream oss;
728 oss << "Computed azimuth/elevation using " << endl
729 << mp << endl;
730 for (Int i=0; i<nrow(); ++i) {
731 MEpoch me = timeCol(i);
732 MDirection md = getDirection(i);
733 oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md)
734 << endl << " => ";
735 MeasFrame frame(mp, me);
736 Vector<Double> azel =
737 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
738 frame)
739 )().getAngle("rad").getValue();
740 azCol_.put(i,Float(azel[0]));
741 elCol_.put(i,Float(azel[1]));
742 oss << "azel: " << azel[0]/C::pi*180.0 << " "
743 << azel[1]/C::pi*180.0 << " (deg)" << endl;
744 }
745 pushLog(String(oss));
746}
747
748void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
749{
750 for (uInt i=0; i<table_.nrow(); ++i) {
751 Vector<uChar> flgs = flagsCol_(i);
752 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
753 flagsCol_.put(i, flgs);
754 }
755}
756
757std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
758{
759 Vector<uChar> flags;
760 flagsCol_.get(uInt(whichrow), flags);
761 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
762 Vector<Bool> bflag(flags.shape());
763 convertArray(bflag, flags);
764 //bflag = !bflag;
765
766 std::vector<bool> mask;
767 bflag.tovector(mask);
768 return mask;
769}
770
771void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
772 Vector<uChar> flgs)
773{
774 Vector<Float> spcs = specCol_(whichrow);
775 uInt nchannel = spcs.nelements();
776 if (spcs.nelements() != nchannel) {
777 throw(AipsError("Data has incorrect number of channels"));
778 }
779 uChar userflag = 1 << 7;
780 if (unflag) {
781 userflag = 0 << 7;
782 }
783 if (clipoutside) {
784 for (uInt j = 0; j < nchannel; ++j) {
785 Float spc = spcs(j);
786 if ((spc >= uthres) || (spc <= dthres)) {
787 flgs(j) = userflag;
788 }
789 }
790 } else {
791 for (uInt j = 0; j < nchannel; ++j) {
792 Float spc = spcs(j);
793 if ((spc < uthres) && (spc > dthres)) {
794 flgs(j) = userflag;
795 }
796 }
797 }
798}
799
800
801void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
802 std::vector<bool>::const_iterator it;
803 uInt ntrue = 0;
804 if (whichrow >= int(table_.nrow()) ) {
805 throw(AipsError("Invalid row number"));
806 }
807 for (it = msk.begin(); it != msk.end(); ++it) {
808 if ( *it ) {
809 ntrue++;
810 }
811 }
812 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
813 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
814 throw(AipsError("Trying to flag whole scantable."));
815 uChar userflag = 1 << 7;
816 if ( unflag ) {
817 userflag = 0 << 7;
818 }
819 if (whichrow > -1 ) {
820 applyChanFlag(uInt(whichrow), msk, userflag);
821 } else {
822 for ( uInt i=0; i<table_.nrow(); ++i) {
823 applyChanFlag(i, msk, userflag);
824 }
825 }
826}
827
828void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
829{
830 if (whichrow >= table_.nrow() ) {
831 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
832 }
833 Vector<uChar> flgs = flagsCol_(whichrow);
834 if ( msk.size() == 0 ) {
835 flgs = flagval;
836 flagsCol_.put(whichrow, flgs);
837 return;
838 }
839 if ( int(msk.size()) != nchan( getIF(whichrow) ) ) {
840 throw(AipsError("Mask has incorrect number of channels."));
841 }
842 if ( flgs.nelements() != msk.size() ) {
843 throw(AipsError("Mask has incorrect number of channels."
844 " Probably varying with IF. Please flag per IF"));
845 }
846 std::vector<bool>::const_iterator it;
847 uInt j = 0;
848 for (it = msk.begin(); it != msk.end(); ++it) {
849 if ( *it ) {
850 flgs(j) = flagval;
851 }
852 ++j;
853 }
854 flagsCol_.put(whichrow, flgs);
855}
856
857void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
858{
859 if ( selector_.empty() && (rows.size() == table_.nrow()) )
860 throw(AipsError("Trying to flag whole scantable."));
861
862 uInt rowflag = (unflag ? 0 : 1);
863 std::vector<uInt>::const_iterator it;
864 for (it = rows.begin(); it != rows.end(); ++it)
865 flagrowCol_.put(*it, rowflag);
866}
867
868std::vector<bool> Scantable::getMask(int whichrow) const
869{
870 Vector<uChar> flags;
871 flagsCol_.get(uInt(whichrow), flags);
872 Vector<Bool> bflag(flags.shape());
873 convertArray(bflag, flags);
874 bflag = !bflag;
875 std::vector<bool> mask;
876 bflag.tovector(mask);
877 return mask;
878}
879
880std::vector<float> Scantable::getSpectrum( int whichrow,
881 const std::string& poltype ) const
882{
883 String ptype = poltype;
884 if (poltype == "" ) ptype = getPolType();
885 if ( whichrow < 0 || whichrow >= nrow() )
886 throw(AipsError("Illegal row number."));
887 std::vector<float> out;
888 Vector<Float> arr;
889 uInt requestedpol = polCol_(whichrow);
890 String basetype = getPolType();
891 if ( ptype == basetype ) {
892 specCol_.get(whichrow, arr);
893 } else {
894 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
895 basetype));
896 uInt row = uInt(whichrow);
897 stpol->setSpectra(getPolMatrix(row));
898 Float fang,fhand;
899 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
900 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
901 stpol->setPhaseCorrections(fang, fhand);
902 arr = stpol->getSpectrum(requestedpol, ptype);
903 }
904 if ( arr.nelements() == 0 )
905 pushLog("Not enough polarisations present to do the conversion.");
906 arr.tovector(out);
907 return out;
908}
909
910void Scantable::setSpectrum( const std::vector<float>& spec,
911 int whichrow )
912{
913 Vector<Float> spectrum(spec);
914 Vector<Float> arr;
915 specCol_.get(whichrow, arr);
916 if ( spectrum.nelements() != arr.nelements() )
917 throw AipsError("The spectrum has incorrect number of channels.");
918 specCol_.put(whichrow, spectrum);
919}
920
921
922String Scantable::generateName()
923{
924 return (File::newUniqueName("./","temp")).baseName();
925}
926
927const casa::Table& Scantable::table( ) const
928{
929 return table_;
930}
931
932casa::Table& Scantable::table( )
933{
934 return table_;
935}
936
937std::string Scantable::getPolType() const
938{
939 return table_.keywordSet().asString("POLTYPE");
940}
941
942void Scantable::unsetSelection()
943{
944 table_ = originalTable_;
945 attach();
946 selector_.reset();
947}
948
949void Scantable::setSelection( const STSelector& selection )
950{
951 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
952 if ( tab.nrow() == 0 ) {
953 throw(AipsError("Selection contains no data. Not applying it."));
954 }
955 table_ = tab;
956 attach();
957// tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
958// vector<uint> selectedIFs = getIFNos() ;
959// Int newnIF = selectedIFs.size() ;
960// tab.rwKeywordSet().define("nIF",newnIF) ;
961// if ( newnIF != 0 ) {
962// Int newnChan = 0 ;
963// for ( Int i = 0 ; i < newnIF ; i++ ) {
964// Int nChan = nchan( selectedIFs[i] ) ;
965// if ( newnChan > nChan )
966// newnChan = nChan ;
967// }
968// tab.rwKeywordSet().define("nChan",newnChan) ;
969// }
970// tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
971 selector_ = selection;
972}
973
974
975std::string Scantable::headerSummary()
976{
977 // Format header info
978// STHeader sdh;
979// sdh = getHeader();
980// sdh.print();
981 ostringstream oss;
982 oss.flags(std::ios_base::left);
983 String tmp;
984 // Project
985 table_.keywordSet().get("Project", tmp);
986 oss << setw(15) << "Project:" << tmp << endl;
987 // Observation date
988 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
989 // Observer
990 oss << setw(15) << "Observer:"
991 << table_.keywordSet().asString("Observer") << endl;
992 // Antenna Name
993 table_.keywordSet().get("AntennaName", tmp);
994 oss << setw(15) << "Antenna Name:" << tmp << endl;
995 // Obs type
996 table_.keywordSet().get("Obstype", tmp);
997 // Records (nrow)
998 oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl;
999 oss << setw(15) << "Obs. Type:" << tmp << endl;
1000 // Beams, IFs, Polarizations, and Channels
1001 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1002 << setw(15) << "IFs:" << setw(4) << nif() << endl
1003 << setw(15) << "Polarisations:" << setw(4) << npol()
1004 << "(" << getPolType() << ")" << endl
1005 << setw(15) << "Channels:" << nchan() << endl;
1006 // Flux unit
1007 table_.keywordSet().get("FluxUnit", tmp);
1008 oss << setw(15) << "Flux Unit:" << tmp << endl;
1009 // Abscissa Unit
1010 oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl;
1011 // Selection
1012 oss << selector_.print() << endl;
1013
1014 return String(oss);
1015}
1016
1017void Scantable::summary( const std::string& filename )
1018{
1019 ostringstream oss;
1020 ofstream ofs;
1021 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1022
1023 if (filename != "")
1024 ofs.open( filename.c_str(), ios::out );
1025
1026 oss << endl;
1027 oss << asap::SEPERATOR << endl;
1028 oss << " Scan Table Summary" << endl;
1029 oss << asap::SEPERATOR << endl;
1030
1031 // Format header info
1032 oss << headerSummary();
1033 oss << endl;
1034
1035 if (table_.nrow() <= 0){
1036 oss << asap::SEPERATOR << endl;
1037 oss << "The MAIN table is empty: there are no data!!!" << endl;
1038 oss << asap::SEPERATOR << endl;
1039
1040 ols << String(oss) << LogIO::POST;
1041 if (ofs) {
1042 ofs << String(oss) << flush;
1043 ofs.close();
1044 }
1045 return;
1046 }
1047
1048
1049
1050 // main table
1051 String dirtype = "Position ("
1052 + getDirectionRefString()
1053 + ")";
1054 oss.flags(std::ios_base::left);
1055 oss << setw(5) << "Scan"
1056 << setw(15) << "Source"
1057 << setw(35) << "Time range"
1058 << setw(2) << "" << setw(7) << "Int[s]"
1059 << setw(7) << "Record"
1060 << setw(8) << "SrcType"
1061 << setw(8) << "FreqIDs"
1062 << setw(7) << "MolIDs" << endl;
1063 oss << setw(7)<< "" << setw(6) << "Beam"
1064 << setw(23) << dirtype << endl;
1065
1066 oss << asap::SEPERATOR << endl;
1067
1068 // Flush summary and clear up the string
1069 ols << String(oss) << LogIO::POST;
1070 if (ofs) ofs << String(oss) << flush;
1071 oss.str("");
1072 oss.clear();
1073
1074
1075 // Get Freq_ID map
1076 ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID");
1077 Int nfid = ftabIds.nrow();
1078 if (nfid <= 0){
1079 oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl;
1080 oss << asap::SEPERATOR << endl;
1081
1082 ols << String(oss) << LogIO::POST;
1083 if (ofs) {
1084 ofs << String(oss) << flush;
1085 ofs.close();
1086 }
1087 return;
1088 }
1089 // Storages of overall IFNO, POLNO, and nchan per FREQ_ID
1090 // the orders are identical to ID in FREQ subtable
1091 Block< Vector<uInt> > ifNos(nfid), polNos(nfid);
1092 Vector<Int> fIdchans(nfid,-1);
1093 map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair
1094 for (Int i=0; i < nfid; i++){
1095 // fidMap[freqId] returns row number in FREQ subtable
1096 fidMap.insert(pair<uInt, Int>(ftabIds(i),i));
1097 ifNos[i] = Vector<uInt>();
1098 polNos[i] = Vector<uInt>();
1099 }
1100
1101 TableIterator iter(table_, "SCANNO");
1102
1103 // Vars for keeping track of time, freqids, molIds in a SCANNO
1104 Vector<uInt> freqids;
1105 Vector<uInt> molids;
1106 Vector<uInt> beamids(1,0);
1107 Vector<MDirection> beamDirs;
1108 Vector<Int> stypeids(1,0);
1109 Vector<String> stypestrs;
1110 Int nfreq(1);
1111 Int nmol(1);
1112 uInt nbeam(1);
1113 uInt nstype(1);
1114
1115 Double btime(0.0), etime(0.0);
1116 Double meanIntTim(0.0);
1117
1118 uInt currFreqId(0), ftabRow(0);
1119 Int iflen(0), pollen(0);
1120
1121 while (!iter.pastEnd()) {
1122 Table subt = iter.table();
1123 uInt snrow = subt.nrow();
1124 ROTableRow row(subt);
1125 const TableRecord& rec = row.get(0);
1126
1127 // relevant columns
1128 ROScalarColumn<Double> mjdCol(subt,"TIME");
1129 ROScalarColumn<Double> intervalCol(subt,"INTERVAL");
1130 MDirection::ROScalarColumn dirCol(subt,"DIRECTION");
1131
1132 ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID");
1133 ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID");
1134 ROScalarColumn<uInt> beamCol(subt,"BEAMNO");
1135 ROScalarColumn<Int> stypeCol(subt,"SRCTYPE");
1136
1137 ROScalarColumn<uInt> ifNoCol(subt,"IFNO");
1138 ROScalarColumn<uInt> polNoCol(subt,"POLNO");
1139
1140
1141 // Times
1142 meanIntTim = sum(intervalCol.getColumn()) / (double) snrow;
1143 minMax(btime, etime, mjdCol.getColumn());
1144 etime += meanIntTim/C::day;
1145
1146 // MOLECULE_ID and FREQ_ID
1147 molids = getNumbers(molIdCol);
1148 molids.shape(nmol);
1149
1150 freqids = getNumbers(freqIdCol);
1151 freqids.shape(nfreq);
1152
1153 // Add first beamid, and srcNames
1154 beamids.resize(1,False);
1155 beamDirs.resize(1,False);
1156 beamids(0)=beamCol(0);
1157 beamDirs(0)=dirCol(0);
1158 nbeam = 1;
1159
1160 stypeids.resize(1,False);
1161 stypeids(0)=stypeCol(0);
1162 nstype = 1;
1163
1164 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1165 currFreqId=freqIdCol(0);
1166 ftabRow = fidMap[currFreqId];
1167 // Assumes an identical number of channels per FREQ_ID
1168 if (fIdchans(ftabRow) < 0 ) {
1169 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1170 fIdchans(ftabRow)=(*spec).shape()(0);
1171 }
1172 // Should keep ifNos and polNos form the previous SCANNO
1173 if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) {
1174 ifNos[ftabRow].shape(iflen);
1175 iflen++;
1176 ifNos[ftabRow].resize(iflen,True);
1177 ifNos[ftabRow](iflen-1) = ifNoCol(0);
1178 }
1179 if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) {
1180 polNos[ftabRow].shape(pollen);
1181 pollen++;
1182 polNos[ftabRow].resize(pollen,True);
1183 polNos[ftabRow](pollen-1) = polNoCol(0);
1184 }
1185
1186 for (uInt i=1; i < snrow; i++){
1187 // Need to list BEAMNO and DIRECTION in the same order
1188 if ( !anyEQ(beamids,beamCol(i)) ) {
1189 nbeam++;
1190 beamids.resize(nbeam,True);
1191 beamids(nbeam-1)=beamCol(i);
1192 beamDirs.resize(nbeam,True);
1193 beamDirs(nbeam-1)=dirCol(i);
1194 }
1195
1196 // SRCTYPE is Int (getNumber takes only uInt)
1197 if ( !anyEQ(stypeids,stypeCol(i)) ) {
1198 nstype++;
1199 stypeids.resize(nstype,True);
1200 stypeids(nstype-1)=stypeCol(i);
1201 }
1202
1203 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1204 currFreqId=freqIdCol(i);
1205 ftabRow = fidMap[currFreqId];
1206 if (fIdchans(ftabRow) < 0 ) {
1207 const TableRecord& rec = row.get(i);
1208 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1209 fIdchans(ftabRow) = (*spec).shape()(0);
1210 }
1211 if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) {
1212 ifNos[ftabRow].shape(iflen);
1213 iflen++;
1214 ifNos[ftabRow].resize(iflen,True);
1215 ifNos[ftabRow](iflen-1) = ifNoCol(i);
1216 }
1217 if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) {
1218 polNos[ftabRow].shape(pollen);
1219 pollen++;
1220 polNos[ftabRow].resize(pollen,True);
1221 polNos[ftabRow](pollen-1) = polNoCol(i);
1222 }
1223 } // end of row iteration
1224
1225 stypestrs.resize(nstype,False);
1226 for (uInt j=0; j < nstype; j++)
1227 stypestrs(j) = SrcType::getName(stypeids(j));
1228
1229 // Format Scan summary
1230 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1231 << std::left << setw(1) << ""
1232 << setw(15) << rec.asString("SRCNAME")
1233 << setw(21) << MVTime(btime).string(MVTime::YMD,7)
1234 << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7)
1235 << setw(3) << "" << setw(6) << meanIntTim << setw(1) << ""
1236 << std::right << setw(5) << snrow << setw(2) << ""
1237 << std::left << stypestrs << setw(1) << ""
1238 << freqids << setw(1) << ""
1239 << molids << endl;
1240 // Format Beam summary
1241 for (uInt j=0; j < nbeam; j++) {
1242 oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << ""
1243 << formatDirection(beamDirs(j)) << endl;
1244 }
1245 // Flush summary every scan and clear up the string
1246 ols << String(oss) << LogIO::POST;
1247 if (ofs) ofs << String(oss) << flush;
1248 oss.str("");
1249 oss.clear();
1250
1251 ++iter;
1252 } // end of scan iteration
1253 oss << asap::SEPERATOR << endl;
1254
1255 // List FRECUENCIES Table (using STFrequencies.print may be slow)
1256 oss << "FREQUENCIES: " << nfreq << endl;
1257 oss << std::right << setw(5) << "ID" << setw(2) << ""
1258 << std::left << setw(5) << "IFNO" << setw(2) << ""
1259 << setw(8) << "Frame"
1260 << setw(16) << "RefVal"
1261 << setw(7) << "RefPix"
1262 << setw(15) << "Increment"
1263 << setw(9) << "Channels"
1264 << setw(6) << "POLNOs" << endl;
1265 Int tmplen;
1266 for (Int i=0; i < nfid; i++){
1267 // List row=i of FREQUENCIES subtable
1268 ifNos[i].shape(tmplen);
1269 if (tmplen == 1) {
1270 oss << std::right << setw(5) << ftabIds(i) << setw(2) << ""
1271 << setw(3) << ifNos[i](0) << setw(1) << ""
1272 << std::left << setw(46) << frequencies().print(ftabIds(i))
1273 << setw(2) << ""
1274 << std::right << setw(8) << fIdchans[i] << setw(2) << ""
1275 << std::left << polNos[i] << endl;
1276 } else if (tmplen > 0 ) {
1277 // You shouldn't come here
1278 oss << std::left
1279 << "Multiple IFNOs in FREQ_ID = " << ftabIds(i)
1280 << " !!!" << endl;
1281 }
1282 }
1283 oss << asap::SEPERATOR << endl;
1284
1285 // List MOLECULES Table (currently lists all rows)
1286 oss << "MOLECULES: " << endl;
1287 if (molecules().nrow() <= 0) {
1288 oss << " MOLECULES subtable is empty: there are no data" << endl;
1289 } else {
1290 ROTableRow row(molecules().table());
1291 oss << std::right << setw(5) << "ID"
1292 << std::left << setw(3) << ""
1293 << setw(18) << "RestFreq"
1294 << setw(15) << "Name" << endl;
1295 for (Int i=0; i < molecules().nrow(); i++){
1296 const TableRecord& rec=row.get(i);
1297 oss << std::right << setw(5) << rec.asuInt("ID")
1298 << std::left << setw(3) << ""
1299 << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << ""
1300 << rec.asArrayString("NAME") << endl;
1301 }
1302 }
1303 oss << asap::SEPERATOR << endl;
1304 ols << String(oss) << LogIO::POST;
1305 if (ofs) {
1306 ofs << String(oss) << flush;
1307 ofs.close();
1308 }
1309 // return String(oss);
1310}
1311
1312
1313std::string Scantable::oldheaderSummary()
1314{
1315 // Format header info
1316// STHeader sdh;
1317// sdh = getHeader();
1318// sdh.print();
1319 ostringstream oss;
1320 oss.flags(std::ios_base::left);
1321 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1322 << setw(15) << "IFs:" << setw(4) << nif() << endl
1323 << setw(15) << "Polarisations:" << setw(4) << npol()
1324 << "(" << getPolType() << ")" << endl
1325 << setw(15) << "Channels:" << nchan() << endl;
1326 String tmp;
1327 oss << setw(15) << "Observer:"
1328 << table_.keywordSet().asString("Observer") << endl;
1329 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1330 table_.keywordSet().get("Project", tmp);
1331 oss << setw(15) << "Project:" << tmp << endl;
1332 table_.keywordSet().get("Obstype", tmp);
1333 oss << setw(15) << "Obs. Type:" << tmp << endl;
1334 table_.keywordSet().get("AntennaName", tmp);
1335 oss << setw(15) << "Antenna Name:" << tmp << endl;
1336 table_.keywordSet().get("FluxUnit", tmp);
1337 oss << setw(15) << "Flux Unit:" << tmp << endl;
1338 int nid = moleculeTable_.nrow();
1339 Bool firstline = True;
1340 oss << setw(15) << "Rest Freqs:";
1341 for (int i=0; i<nid; i++) {
1342 Table t = table_(table_.col("MOLECULE_ID") == i, 1);
1343 if (t.nrow() > 0) {
1344 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
1345 if (vec.nelements() > 0) {
1346 if (firstline) {
1347 oss << setprecision(10) << vec << " [Hz]" << endl;
1348 firstline=False;
1349 }
1350 else{
1351 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1352 }
1353 } else {
1354 oss << "none" << endl;
1355 }
1356 }
1357 }
1358
1359 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
1360 oss << selector_.print() << endl;
1361 return String(oss);
1362}
1363
1364 //std::string Scantable::summary( const std::string& filename )
1365void Scantable::oldsummary( const std::string& filename )
1366{
1367 ostringstream oss;
1368 ofstream ofs;
1369 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1370
1371 if (filename != "")
1372 ofs.open( filename.c_str(), ios::out );
1373
1374 oss << endl;
1375 oss << asap::SEPERATOR << endl;
1376 oss << " Scan Table Summary" << endl;
1377 oss << asap::SEPERATOR << endl;
1378
1379 // Format header info
1380 oss << oldheaderSummary();
1381 oss << endl;
1382
1383 // main table
1384 String dirtype = "Position ("
1385 + getDirectionRefString()
1386 + ")";
1387 oss.flags(std::ios_base::left);
1388 oss << setw(5) << "Scan" << setw(15) << "Source"
1389 << setw(10) << "Time" << setw(18) << "Integration"
1390 << setw(15) << "Source Type" << endl;
1391 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
1392 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
1393 << setw(8) << "Frame" << setw(16)
1394 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1395 << setw(7) << "Channels"
1396 << endl;
1397 oss << asap::SEPERATOR << endl;
1398
1399 // Flush summary and clear up the string
1400 ols << String(oss) << LogIO::POST;
1401 if (ofs) ofs << String(oss) << flush;
1402 oss.str("");
1403 oss.clear();
1404
1405 TableIterator iter(table_, "SCANNO");
1406 while (!iter.pastEnd()) {
1407 Table subt = iter.table();
1408 ROTableRow row(subt);
1409 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1410 const TableRecord& rec = row.get(0);
1411 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1412 << std::left << setw(1) << ""
1413 << setw(15) << rec.asString("SRCNAME")
1414 << setw(10) << formatTime(timeCol(0), false);
1415 // count the cycles in the scan
1416 TableIterator cyciter(subt, "CYCLENO");
1417 int nint = 0;
1418 while (!cyciter.pastEnd()) {
1419 ++nint;
1420 ++cyciter;
1421 }
1422 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
1423 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1424 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
1425
1426 TableIterator biter(subt, "BEAMNO");
1427 while (!biter.pastEnd()) {
1428 Table bsubt = biter.table();
1429 ROTableRow brow(bsubt);
1430 const TableRecord& brec = brow.get(0);
1431 uInt row0 = bsubt.rowNumbers(table_)[0];
1432 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
1433 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
1434 TableIterator iiter(bsubt, "IFNO");
1435 while (!iiter.pastEnd()) {
1436 Table isubt = iiter.table();
1437 ROTableRow irow(isubt);
1438 const TableRecord& irec = irow.get(0);
1439 oss << setw(9) << "";
1440 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
1441 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1442 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
1443 << endl;
1444
1445 ++iiter;
1446 }
1447 ++biter;
1448 }
1449 // Flush summary every scan and clear up the string
1450 ols << String(oss) << LogIO::POST;
1451 if (ofs) ofs << String(oss) << flush;
1452 oss.str("");
1453 oss.clear();
1454
1455 ++iter;
1456 }
1457 oss << asap::SEPERATOR << endl;
1458 ols << String(oss) << LogIO::POST;
1459 if (ofs) {
1460 ofs << String(oss) << flush;
1461 ofs.close();
1462 }
1463 // return String(oss);
1464}
1465
1466// std::string Scantable::getTime(int whichrow, bool showdate) const
1467// {
1468// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1469// MEpoch me;
1470// if (whichrow > -1) {
1471// me = timeCol(uInt(whichrow));
1472// } else {
1473// Double tm;
1474// table_.keywordSet().get("UTC",tm);
1475// me = MEpoch(MVEpoch(tm));
1476// }
1477// return formatTime(me, showdate);
1478// }
1479
1480std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
1481{
1482 MEpoch me;
1483 me = getEpoch(whichrow);
1484 return formatTime(me, showdate, prec);
1485}
1486
1487MEpoch Scantable::getEpoch(int whichrow) const
1488{
1489 if (whichrow > -1) {
1490 return timeCol_(uInt(whichrow));
1491 } else {
1492 Double tm;
1493 table_.keywordSet().get("UTC",tm);
1494 return MEpoch(MVEpoch(tm));
1495 }
1496}
1497
1498std::string Scantable::getDirectionString(int whichrow) const
1499{
1500 return formatDirection(getDirection(uInt(whichrow)));
1501}
1502
1503
1504SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1505 const MPosition& mp = getAntennaPosition();
1506 const MDirection& md = getDirection(whichrow);
1507 const MEpoch& me = timeCol_(whichrow);
1508 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1509 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1510 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
1511 mfreqidCol_(whichrow));
1512}
1513
1514std::vector< double > Scantable::getAbcissa( int whichrow ) const
1515{
1516 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
1517 std::vector<double> stlout;
1518 int nchan = specCol_(whichrow).nelements();
1519 String us = freqTable_.getUnitString();
1520 if ( us == "" || us == "pixel" || us == "channel" ) {
1521 for (int i=0; i<nchan; ++i) {
1522 stlout.push_back(double(i));
1523 }
1524 return stlout;
1525 }
1526 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
1527 Vector<Double> pixel(nchan);
1528 Vector<Double> world;
1529 indgen(pixel);
1530 if ( Unit(us) == Unit("Hz") ) {
1531 for ( int i=0; i < nchan; ++i) {
1532 Double world;
1533 spc.toWorld(world, pixel[i]);
1534 stlout.push_back(double(world));
1535 }
1536 } else if ( Unit(us) == Unit("km/s") ) {
1537 Vector<Double> world;
1538 spc.pixelToVelocity(world, pixel);
1539 world.tovector(stlout);
1540 }
1541 return stlout;
1542}
1543void Scantable::setDirectionRefString( const std::string & refstr )
1544{
1545 MDirection::Types mdt;
1546 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1547 throw(AipsError("Illegal Direction frame."));
1548 }
1549 if ( refstr == "" ) {
1550 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1551 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1552 } else {
1553 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1554 }
1555}
1556
1557std::string Scantable::getDirectionRefString( ) const
1558{
1559 return table_.keywordSet().asString("DIRECTIONREF");
1560}
1561
1562MDirection Scantable::getDirection(int whichrow ) const
1563{
1564 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1565 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1566 if ( usertype != type ) {
1567 MDirection::Types mdt;
1568 if (!MDirection::getType(mdt, usertype)) {
1569 throw(AipsError("Illegal Direction frame."));
1570 }
1571 return dirCol_.convert(uInt(whichrow), mdt);
1572 } else {
1573 return dirCol_(uInt(whichrow));
1574 }
1575}
1576
1577std::string Scantable::getAbcissaLabel( int whichrow ) const
1578{
1579 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
1580 const MPosition& mp = getAntennaPosition();
1581 const MDirection& md = getDirection(whichrow);
1582 const MEpoch& me = timeCol_(whichrow);
1583 //const Double& rf = mmolidCol_(whichrow);
1584 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1585 SpectralCoordinate spc =
1586 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
1587
1588 String s = "Channel";
1589 Unit u = Unit(freqTable_.getUnitString());
1590 if (u == Unit("km/s")) {
1591 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
1592 } else if (u == Unit("Hz")) {
1593 Vector<String> wau(1);wau = u.getName();
1594 spc.setWorldAxisUnits(wau);
1595 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
1596 }
1597 return s;
1598
1599}
1600
1601/**
1602void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
1603 const std::string& unit )
1604**/
1605void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1606 const std::string& unit )
1607
1608{
1609 ///@todo lookup in line table to fill in name and formattedname
1610 Unit u(unit);
1611 //Quantum<Double> urf(rf, u);
1612 Quantum<Vector<Double> >urf(rf, u);
1613 Vector<String> formattedname(0);
1614 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1615
1616 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1617 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
1618 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1619 tabvec = id;
1620}
1621
1622/**
1623void asap::Scantable::setRestFrequencies( const std::string& name )
1624{
1625 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1626 ///@todo implement
1627}
1628**/
1629
1630void Scantable::setRestFrequencies( const vector<std::string>& name )
1631{
1632 (void) name; // suppress unused warning
1633 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1634 ///@todo implement
1635}
1636
1637std::vector< unsigned int > Scantable::rownumbers( ) const
1638{
1639 std::vector<unsigned int> stlout;
1640 Vector<uInt> vec = table_.rowNumbers();
1641 vec.tovector(stlout);
1642 return stlout;
1643}
1644
1645
1646Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
1647{
1648 ROTableRow row(table_);
1649 const TableRecord& rec = row.get(whichrow);
1650 Table t =
1651 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1652 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1653 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1654 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1655 ROArrayColumn<Float> speccol(t, "SPECTRA");
1656 return speccol.getColumn();
1657}
1658
1659std::vector< std::string > Scantable::columnNames( ) const
1660{
1661 Vector<String> vec = table_.tableDesc().columnNames();
1662 return mathutil::tovectorstring(vec);
1663}
1664
1665MEpoch::Types Scantable::getTimeReference( ) const
1666{
1667 return MEpoch::castType(timeCol_.getMeasRef().getType());
1668}
1669
1670void Scantable::addFit( const STFitEntry& fit, int row )
1671{
1672 //cout << mfitidCol_(uInt(row)) << endl;
1673 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1674 os << mfitidCol_(uInt(row)) << LogIO::POST ;
1675 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1676 mfitidCol_.put(uInt(row), id);
1677}
1678
1679void Scantable::shift(int npix)
1680{
1681 Vector<uInt> fids(mfreqidCol_.getColumn());
1682 genSort( fids, Sort::Ascending,
1683 Sort::QuickSort|Sort::NoDuplicates );
1684 for (uInt i=0; i<fids.nelements(); ++i) {
1685 frequencies().shiftRefPix(npix, fids[i]);
1686 }
1687}
1688
1689String Scantable::getAntennaName() const
1690{
1691 String out;
1692 table_.keywordSet().get("AntennaName", out);
1693 String::size_type pos1 = out.find("@") ;
1694 String::size_type pos2 = out.find("//") ;
1695 if ( pos2 != String::npos )
1696 out = out.substr(pos2+2,pos1-pos2-2) ;
1697 else if ( pos1 != String::npos )
1698 out = out.substr(0,pos1) ;
1699 return out;
1700}
1701
1702int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
1703{
1704 String tbpath;
1705 int ret = 0;
1706 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1707 table_.keywordSet().get("GBT_GO", tbpath);
1708 Table t(tbpath,Table::Old);
1709 // check each scan if other scan of the pair exist
1710 int nscan = scanlist.size();
1711 for (int i = 0; i < nscan; i++) {
1712 Table subt = t( t.col("SCAN") == scanlist[i]+1 );
1713 if (subt.nrow()==0) {
1714 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1715 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1716 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
1717 ret = 1;
1718 break;
1719 }
1720 ROTableRow row(subt);
1721 const TableRecord& rec = row.get(0);
1722 int scan1seqn = rec.asuInt("PROCSEQN");
1723 int laston1 = rec.asuInt("LASTON");
1724 if ( rec.asuInt("PROCSIZE")==2 ) {
1725 if ( i < nscan-1 ) {
1726 Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
1727 if ( subt2.nrow() == 0) {
1728 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1729
1730 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1731 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
1732 ret = 1;
1733 break;
1734 }
1735 ROTableRow row2(subt2);
1736 const TableRecord& rec2 = row2.get(0);
1737 int scan2seqn = rec2.asuInt("PROCSEQN");
1738 int laston2 = rec2.asuInt("LASTON");
1739 if (scan1seqn == 1 && scan2seqn == 2) {
1740 if (laston1 == laston2) {
1741 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1742 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1743 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1744 i +=1;
1745 }
1746 else {
1747 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1748 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1749 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1750 }
1751 }
1752 else if (scan1seqn==2 && scan2seqn == 1) {
1753 if (laston1 == laston2) {
1754 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1755 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1756 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
1757 ret = 1;
1758 break;
1759 }
1760 }
1761 else {
1762 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1763 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1764 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
1765 ret = 1;
1766 break;
1767 }
1768 }
1769 }
1770 else {
1771 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1772 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1773 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
1774 }
1775 //if ( i >= nscan ) break;
1776 }
1777 }
1778 else {
1779 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1780 //cerr<<"No reference to GBT_GO table."<<endl;
1781 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
1782 ret = 1;
1783 }
1784 return ret;
1785}
1786
1787std::vector<double> Scantable::getDirectionVector(int whichrow) const
1788{
1789 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1790 std::vector<double> dir;
1791 Dir.tovector(dir);
1792 return dir;
1793}
1794
1795void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1796 throw( casa::AipsError )
1797{
1798 // assumed that all rows have same nChan
1799 Vector<Float> arr = specCol_( 0 ) ;
1800 int nChan = arr.nelements() ;
1801
1802 // if nmin < 0 or nmax < 0, nothing to do
1803 if ( nmin < 0 ) {
1804 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1805 }
1806 if ( nmax < 0 ) {
1807 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1808 }
1809
1810 // if nmin > nmax, exchange values
1811 if ( nmin > nmax ) {
1812 int tmp = nmax ;
1813 nmax = nmin ;
1814 nmin = tmp ;
1815 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1816 os << "Swap values. Applied range is ["
1817 << nmin << ", " << nmax << "]" << LogIO::POST ;
1818 }
1819
1820 // if nmin exceeds nChan, nothing to do
1821 if ( nmin >= nChan ) {
1822 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1823 }
1824
1825 // if nmax exceeds nChan, reset nmax to nChan
1826 if ( nmax >= nChan ) {
1827 if ( nmin == 0 ) {
1828 // nothing to do
1829 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1830 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1831 return ;
1832 }
1833 else {
1834 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1835 os << "Specified maximum exceeds nChan. Applied range is ["
1836 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1837 nmax = nChan - 1 ;
1838 }
1839 }
1840
1841 // reshape specCol_ and flagCol_
1842 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1843 reshapeSpectrum( nmin, nmax, irow ) ;
1844 }
1845
1846 // update FREQUENCIES subtable
1847 Double refpix ;
1848 Double refval ;
1849 Double increment ;
1850 int freqnrow = freqTable_.table().nrow() ;
1851 Vector<uInt> oldId( freqnrow ) ;
1852 Vector<uInt> newId( freqnrow ) ;
1853 for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
1854 freqTable_.getEntry( refpix, refval, increment, irow ) ;
1855 /***
1856 * need to shift refpix to nmin
1857 * note that channel nmin in old index will be channel 0 in new one
1858 ***/
1859 refval = refval - ( refpix - nmin ) * increment ;
1860 refpix = 0 ;
1861 freqTable_.setEntry( refpix, refval, increment, irow ) ;
1862 }
1863
1864 // update nchan
1865 int newsize = nmax - nmin + 1 ;
1866 table_.rwKeywordSet().define( "nChan", newsize ) ;
1867
1868 // update bandwidth
1869 // assumed all spectra in the scantable have same bandwidth
1870 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1871
1872 return ;
1873}
1874
1875void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1876{
1877 // reshape specCol_ and flagCol_
1878 Vector<Float> oldspec = specCol_( irow ) ;
1879 Vector<uChar> oldflag = flagsCol_( irow ) ;
1880 uInt newsize = nmax - nmin + 1 ;
1881 specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ;
1882 flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ;
1883
1884 return ;
1885}
1886
1887void asap::Scantable::regridSpecChannel( double dnu, int nChan )
1888{
1889 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1890 os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ;
1891 int freqnrow = freqTable_.table().nrow() ;
1892 Vector<bool> firstTime( freqnrow, true ) ;
1893 double oldincr, factor;
1894 uInt currId;
1895 Double refpix ;
1896 Double refval ;
1897 Double increment ;
1898 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1899 currId = mfreqidCol_(irow);
1900 vector<double> abcissa = getAbcissa( irow ) ;
1901 if (nChan < 0) {
1902 int oldsize = abcissa.size() ;
1903 double bw = (abcissa[oldsize-1]-abcissa[0]) + \
1904 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ;
1905 nChan = int( ceil( abs(bw/dnu) ) ) ;
1906 }
1907 // actual regridding
1908 regridChannel( nChan, dnu, irow ) ;
1909
1910 // update FREQUENCIES subtable
1911 if (firstTime[currId]) {
1912 oldincr = abcissa[1]-abcissa[0] ;
1913 factor = dnu/oldincr ;
1914 firstTime[currId] = false ;
1915 freqTable_.getEntry( refpix, refval, increment, currId ) ;
1916 /***
1917 * need to shift refpix to 0
1918 ***/
1919 //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ;
1920 refpix = (refpix + 0.5)/factor - 0.5;
1921 freqTable_.setEntry( refpix, refval, increment*factor, currId ) ;
1922 os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ;
1923 os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ;
1924 }
1925 }
1926}
1927
1928void asap::Scantable::regridChannel( int nChan, double dnu )
1929{
1930 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1931 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
1932 // assumed that all rows have same nChan
1933 Vector<Float> arr = specCol_( 0 ) ;
1934 int oldsize = arr.nelements() ;
1935
1936 // if oldsize == nChan, nothing to do
1937 if ( oldsize == nChan ) {
1938 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
1939 return ;
1940 }
1941
1942 // if oldChan < nChan, unphysical operation
1943 if ( oldsize < nChan ) {
1944 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
1945 return ;
1946 }
1947
1948 // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary)
1949 vector<string> coordinfo = getCoordInfo() ;
1950 string oldinfo = coordinfo[0] ;
1951 coordinfo[0] = "Hz" ;
1952 setCoordInfo( coordinfo ) ;
1953 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1954 regridChannel( nChan, dnu, irow ) ;
1955 }
1956 coordinfo[0] = oldinfo ;
1957 setCoordInfo( coordinfo ) ;
1958
1959
1960 // NOTE: this method does not update metadata such as
1961 // FREQUENCIES subtable, nChan, Bandwidth, etc.
1962
1963 return ;
1964}
1965
1966void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
1967{
1968 // logging
1969 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
1970 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
1971
1972 Vector<Float> oldspec = specCol_( irow ) ;
1973 Vector<uChar> oldflag = flagsCol_( irow ) ;
1974 Vector<Float> oldtsys = tsysCol_( irow ) ;
1975 Vector<Float> newspec( nChan, 0 ) ;
1976 Vector<uChar> newflag( nChan, true ) ;
1977 Vector<Float> newtsys ;
1978 bool regridTsys = false ;
1979 if (oldtsys.size() == oldspec.size()) {
1980 regridTsys = true ;
1981 newtsys.resize(nChan,false) ;
1982 newtsys = 0 ;
1983 }
1984
1985 // regrid
1986 vector<double> abcissa = getAbcissa( irow ) ;
1987 int oldsize = abcissa.size() ;
1988 double olddnu = abcissa[1] - abcissa[0] ;
1989 int ichan = 0 ;
1990 double wsum = 0.0 ;
1991 Vector<double> zi( nChan+1 ) ;
1992 Vector<double> yi( oldsize + 1 ) ;
1993 zi[0] = abcissa[0] - 0.5 * olddnu ;
1994 for ( int ii = 1 ; ii < nChan ; ii++ )
1995 zi[ii] = zi[0] + dnu * ii ;
1996 zi[nChan] = zi[nChan-1] + dnu ;
1997 yi[0] = abcissa[0] - 0.5 * olddnu ;
1998 for ( int ii = 1 ; ii < oldsize ; ii++ )
1999 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2000 yi[oldsize] = abcissa[oldsize-1] \
2001 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
2002 if ( dnu > 0.0 ) {
2003 for ( int ii = 0 ; ii < nChan ; ii++ ) {
2004 double zl = zi[ii] ;
2005 double zr = zi[ii+1] ;
2006 for ( int j = ichan ; j < oldsize ; j++ ) {
2007 double yl = yi[j] ;
2008 double yr = yi[j+1] ;
2009 if ( yl <= zl ) {
2010 if ( yr <= zl ) {
2011 continue ;
2012 }
2013 else if ( yr <= zr ) {
2014 if (!oldflag[j]) {
2015 newspec[ii] += oldspec[j] * ( yr - zl ) ;
2016 if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ;
2017 wsum += ( yr - zl ) ;
2018 }
2019 newflag[ii] = newflag[ii] && oldflag[j] ;
2020 }
2021 else {
2022 if (!oldflag[j]) {
2023 newspec[ii] += oldspec[j] * dnu ;
2024 if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ;
2025 wsum += dnu ;
2026 }
2027 newflag[ii] = newflag[ii] && oldflag[j] ;
2028 ichan = j ;
2029 break ;
2030 }
2031 }
2032 else if ( yl < zr ) {
2033 if ( yr <= zr ) {
2034 if (!oldflag[j]) {
2035 newspec[ii] += oldspec[j] * ( yr - yl ) ;
2036 if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ;
2037 wsum += ( yr - yl ) ;
2038 }
2039 newflag[ii] = newflag[ii] && oldflag[j] ;
2040 }
2041 else {
2042 if (!oldflag[j]) {
2043 newspec[ii] += oldspec[j] * ( zr - yl ) ;
2044 if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ;
2045 wsum += ( zr - yl ) ;
2046 }
2047 newflag[ii] = newflag[ii] && oldflag[j] ;
2048 ichan = j ;
2049 break ;
2050 }
2051 }
2052 else {
2053 ichan = j - 1 ;
2054 break ;
2055 }
2056 }
2057 if ( wsum != 0.0 ) {
2058 newspec[ii] /= wsum ;
2059 if (regridTsys) newtsys[ii] /= wsum ;
2060 }
2061 wsum = 0.0 ;
2062 }
2063 }
2064 else if ( dnu < 0.0 ) {
2065 for ( int ii = 0 ; ii < nChan ; ii++ ) {
2066 double zl = zi[ii] ;
2067 double zr = zi[ii+1] ;
2068 for ( int j = ichan ; j < oldsize ; j++ ) {
2069 double yl = yi[j] ;
2070 double yr = yi[j+1] ;
2071 if ( yl >= zl ) {
2072 if ( yr >= zl ) {
2073 continue ;
2074 }
2075 else if ( yr >= zr ) {
2076 if (!oldflag[j]) {
2077 newspec[ii] += oldspec[j] * abs( yr - zl ) ;
2078 if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ;
2079 wsum += abs( yr - zl ) ;
2080 }
2081 newflag[ii] = newflag[ii] && oldflag[j] ;
2082 }
2083 else {
2084 if (!oldflag[j]) {
2085 newspec[ii] += oldspec[j] * abs( dnu ) ;
2086 if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ;
2087 wsum += abs( dnu ) ;
2088 }
2089 newflag[ii] = newflag[ii] && oldflag[j] ;
2090 ichan = j ;
2091 break ;
2092 }
2093 }
2094 else if ( yl > zr ) {
2095 if ( yr >= zr ) {
2096 if (!oldflag[j]) {
2097 newspec[ii] += oldspec[j] * abs( yr - yl ) ;
2098 if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ;
2099 wsum += abs( yr - yl ) ;
2100 }
2101 newflag[ii] = newflag[ii] && oldflag[j] ;
2102 }
2103 else {
2104 if (!oldflag[j]) {
2105 newspec[ii] += oldspec[j] * abs( zr - yl ) ;
2106 if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ;
2107 wsum += abs( zr - yl ) ;
2108 }
2109 newflag[ii] = newflag[ii] && oldflag[j] ;
2110 ichan = j ;
2111 break ;
2112 }
2113 }
2114 else {
2115 ichan = j - 1 ;
2116 break ;
2117 }
2118 }
2119 if ( wsum != 0.0 ) {
2120 newspec[ii] /= wsum ;
2121 if (regridTsys) newtsys[ii] /= wsum ;
2122 }
2123 wsum = 0.0 ;
2124 }
2125 }
2126// //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
2127// pile += dnu ;
2128// wedge = olddnu * ( refChan + 1 ) ;
2129// while ( wedge < pile ) {
2130// newspec[0] += olddnu * oldspec[refChan] ;
2131// newflag[0] = newflag[0] || oldflag[refChan] ;
2132// //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
2133// refChan++ ;
2134// wedge += olddnu ;
2135// wsum += olddnu ;
2136// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2137// }
2138// frac = ( wedge - pile ) / olddnu ;
2139// wsum += ( 1.0 - frac ) * olddnu ;
2140// newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2141// newflag[0] = newflag[0] || oldflag[refChan] ;
2142// //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
2143// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2144// newspec[0] /= wsum ;
2145// //ofs << "newspec[0] = " << newspec[0] << endl ;
2146// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2147
2148// /***
2149// * ichan = 1 - nChan-2
2150// ***/
2151// for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
2152// pile += dnu ;
2153// newspec[ichan] += frac * olddnu * oldspec[refChan] ;
2154// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2155// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
2156// refChan++ ;
2157// wedge += olddnu ;
2158// wsum = frac * olddnu ;
2159// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2160// while ( wedge < pile ) {
2161// newspec[ichan] += olddnu * oldspec[refChan] ;
2162// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2163// //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
2164// refChan++ ;
2165// wedge += olddnu ;
2166// wsum += olddnu ;
2167// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2168// }
2169// frac = ( wedge - pile ) / olddnu ;
2170// wsum += ( 1.0 - frac ) * olddnu ;
2171// newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2172// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2173// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
2174// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2175// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2176// newspec[ichan] /= wsum ;
2177// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
2178// }
2179
2180// /***
2181// * ichan = nChan-1
2182// ***/
2183// // NOTE: Assumed that all spectra have the same bandwidth
2184// pile += dnu ;
2185// newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
2186// newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
2187// //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2188// refChan++ ;
2189// wedge += olddnu ;
2190// wsum = frac * olddnu ;
2191// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2192// for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
2193// newspec[nChan-1] += olddnu * oldspec[jchan] ;
2194// newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
2195// wsum += olddnu ;
2196// //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2197// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2198// }
2199// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2200// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2201// newspec[nChan-1] /= wsum ;
2202// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
2203
2204// // ofs.close() ;
2205
2206 specCol_.put( irow, newspec ) ;
2207 flagsCol_.put( irow, newflag ) ;
2208 if (regridTsys) tsysCol_.put( irow, newtsys );
2209
2210 return ;
2211}
2212
2213std::vector<float> Scantable::getWeather(int whichrow) const
2214{
2215 std::vector<float> out(5);
2216 //Float temperature, pressure, humidity, windspeed, windaz;
2217 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
2218 mweatheridCol_(uInt(whichrow)));
2219
2220
2221 return out;
2222}
2223
2224bool Scantable::getFlagtraFast(uInt whichrow)
2225{
2226 uChar flag;
2227 Vector<uChar> flags;
2228 flagsCol_.get(whichrow, flags);
2229 flag = flags[0];
2230 for (uInt i = 1; i < flags.size(); ++i) {
2231 flag &= flags[i];
2232 }
2233 return ((flag >> 7) == 1);
2234}
2235
2236void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2237{
2238 try {
2239 ofstream ofs;
2240 String coordInfo = "";
2241 bool hasSameNchan = true;
2242 bool outTextFile = false;
2243
2244 if (blfile != "") {
2245 ofs.open(blfile.c_str(), ios::out | ios::app);
2246 if (ofs) outTextFile = true;
2247 }
2248
2249 if (outLogger || outTextFile) {
2250 coordInfo = getCoordInfo()[0];
2251 if (coordInfo == "") coordInfo = "channel";
2252 hasSameNchan = hasSameNchanOverIFs();
2253 }
2254
2255 Fitter fitter = Fitter();
2256 fitter.setExpression("poly", order);
2257 //fitter.setIterClipping(thresClip, nIterClip);
2258
2259 int nRow = nrow();
2260 std::vector<bool> chanMask;
2261 bool showProgress;
2262 int minNRow;
2263 parseProgressInfo(progressInfo, showProgress, minNRow);
2264
2265 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2266 chanMask = getCompositeChanMask(whichrow, mask);
2267 fitBaseline(chanMask, whichrow, fitter);
2268 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2269 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
2270 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2271 }
2272
2273 if (outTextFile) ofs.close();
2274
2275 } catch (...) {
2276 throw;
2277 }
2278}
2279
2280void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2281{
2282 try {
2283 ofstream ofs;
2284 String coordInfo = "";
2285 bool hasSameNchan = true;
2286 bool outTextFile = false;
2287
2288 if (blfile != "") {
2289 ofs.open(blfile.c_str(), ios::out | ios::app);
2290 if (ofs) outTextFile = true;
2291 }
2292
2293 if (outLogger || outTextFile) {
2294 coordInfo = getCoordInfo()[0];
2295 if (coordInfo == "") coordInfo = "channel";
2296 hasSameNchan = hasSameNchanOverIFs();
2297 }
2298
2299 Fitter fitter = Fitter();
2300 fitter.setExpression("poly", order);
2301 //fitter.setIterClipping(thresClip, nIterClip);
2302
2303 int nRow = nrow();
2304 std::vector<bool> chanMask;
2305 int minEdgeSize = getIFNos().size()*2;
2306 STLineFinder lineFinder = STLineFinder();
2307 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2308
2309 bool showProgress;
2310 int minNRow;
2311 parseProgressInfo(progressInfo, showProgress, minNRow);
2312
2313 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2314
2315 //-------------------------------------------------------
2316 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2317 //-------------------------------------------------------
2318 int edgeSize = edge.size();
2319 std::vector<int> currentEdge;
2320 if (edgeSize >= 2) {
2321 int idx = 0;
2322 if (edgeSize > 2) {
2323 if (edgeSize < minEdgeSize) {
2324 throw(AipsError("Length of edge element info is less than that of IFs"));
2325 }
2326 idx = 2 * getIF(whichrow);
2327 }
2328 currentEdge.push_back(edge[idx]);
2329 currentEdge.push_back(edge[idx+1]);
2330 } else {
2331 throw(AipsError("Wrong length of edge element"));
2332 }
2333 lineFinder.setData(getSpectrum(whichrow));
2334 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2335 chanMask = lineFinder.getMask();
2336 //-------------------------------------------------------
2337
2338 fitBaseline(chanMask, whichrow, fitter);
2339 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2340
2341 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
2342 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2343 }
2344
2345 if (outTextFile) ofs.close();
2346
2347 } catch (...) {
2348 throw;
2349 }
2350}
2351
2352void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2353{
2354 try {
2355 ofstream ofs;
2356 String coordInfo = "";
2357 bool hasSameNchan = true;
2358 bool outTextFile = false;
2359
2360 if (blfile != "") {
2361 ofs.open(blfile.c_str(), ios::out | ios::app);
2362 if (ofs) outTextFile = true;
2363 }
2364
2365 if (outLogger || outTextFile) {
2366 coordInfo = getCoordInfo()[0];
2367 if (coordInfo == "") coordInfo = "channel";
2368 hasSameNchan = hasSameNchanOverIFs();
2369 }
2370
2371 //Fitter fitter = Fitter();
2372 //fitter.setExpression("cspline", nPiece);
2373 //fitter.setIterClipping(thresClip, nIterClip);
2374
2375 bool showProgress;
2376 int minNRow;
2377 parseProgressInfo(progressInfo, showProgress, minNRow);
2378
2379 int nRow = nrow();
2380 std::vector<bool> chanMask;
2381
2382 //--------------------------------
2383 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2384 chanMask = getCompositeChanMask(whichrow, mask);
2385 //fitBaseline(chanMask, whichrow, fitter);
2386 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2387 std::vector<int> pieceEdges(nPiece+1);
2388 std::vector<float> params(nPiece*4);
2389 int nClipped = 0;
2390 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2391 setSpectrum(res, whichrow);
2392 //
2393
2394 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
2395 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2396 }
2397 //--------------------------------
2398
2399 if (outTextFile) ofs.close();
2400
2401 } catch (...) {
2402 throw;
2403 }
2404}
2405
2406void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2407{
2408 try {
2409 ofstream ofs;
2410 String coordInfo = "";
2411 bool hasSameNchan = true;
2412 bool outTextFile = false;
2413
2414 if (blfile != "") {
2415 ofs.open(blfile.c_str(), ios::out | ios::app);
2416 if (ofs) outTextFile = true;
2417 }
2418
2419 if (outLogger || outTextFile) {
2420 coordInfo = getCoordInfo()[0];
2421 if (coordInfo == "") coordInfo = "channel";
2422 hasSameNchan = hasSameNchanOverIFs();
2423 }
2424
2425 //Fitter fitter = Fitter();
2426 //fitter.setExpression("cspline", nPiece);
2427 //fitter.setIterClipping(thresClip, nIterClip);
2428
2429 int nRow = nrow();
2430 std::vector<bool> chanMask;
2431 int minEdgeSize = getIFNos().size()*2;
2432 STLineFinder lineFinder = STLineFinder();
2433 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2434
2435 bool showProgress;
2436 int minNRow;
2437 parseProgressInfo(progressInfo, showProgress, minNRow);
2438
2439 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2440
2441 //-------------------------------------------------------
2442 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2443 //-------------------------------------------------------
2444 int edgeSize = edge.size();
2445 std::vector<int> currentEdge;
2446 if (edgeSize >= 2) {
2447 int idx = 0;
2448 if (edgeSize > 2) {
2449 if (edgeSize < minEdgeSize) {
2450 throw(AipsError("Length of edge element info is less than that of IFs"));
2451 }
2452 idx = 2 * getIF(whichrow);
2453 }
2454 currentEdge.push_back(edge[idx]);
2455 currentEdge.push_back(edge[idx+1]);
2456 } else {
2457 throw(AipsError("Wrong length of edge element"));
2458 }
2459 lineFinder.setData(getSpectrum(whichrow));
2460 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2461 chanMask = lineFinder.getMask();
2462 //-------------------------------------------------------
2463
2464
2465 //fitBaseline(chanMask, whichrow, fitter);
2466 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2467 std::vector<int> pieceEdges(nPiece+1);
2468 std::vector<float> params(nPiece*4);
2469 int nClipped = 0;
2470 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2471 setSpectrum(res, whichrow);
2472 //
2473
2474 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
2475 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2476 }
2477
2478 if (outTextFile) ofs.close();
2479
2480 } catch (...) {
2481 throw;
2482 }
2483}
2484
2485std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
2486{
2487 if (data.size() != mask.size()) {
2488 throw(AipsError("data and mask sizes are not identical"));
2489 }
2490 if (nPiece < 1) {
2491 throw(AipsError("number of the sections must be one or more"));
2492 }
2493
2494 int nChan = data.size();
2495 std::vector<int> maskArray(nChan);
2496 std::vector<int> x(nChan);
2497 int j = 0;
2498 for (int i = 0; i < nChan; ++i) {
2499 maskArray[i] = mask[i] ? 1 : 0;
2500 if (mask[i]) {
2501 x[j] = i;
2502 j++;
2503 }
2504 }
2505 int initNData = j;
2506
2507 if (initNData < nPiece) {
2508 throw(AipsError("too few non-flagged channels"));
2509 }
2510
2511 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
2512 std::vector<double> invEdge(nPiece-1);
2513 idxEdge[0] = x[0];
2514 for (int i = 1; i < nPiece; ++i) {
2515 int valX = x[nElement*i];
2516 idxEdge[i] = valX;
2517 invEdge[i-1] = 1.0/(double)valX;
2518 }
2519 idxEdge[nPiece] = x[initNData-1]+1;
2520
2521 int nData = initNData;
2522 int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
2523
2524 std::vector<double> x1(nChan), x2(nChan), x3(nChan);
2525 std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan);
2526 std::vector<double> r1(nChan), residual(nChan);
2527 for (int i = 0; i < nChan; ++i) {
2528 double di = (double)i;
2529 double dD = (double)data[i];
2530 x1[i] = di;
2531 x2[i] = di*di;
2532 x3[i] = di*di*di;
2533 z1[i] = dD;
2534 x1z1[i] = dD*di;
2535 x2z1[i] = dD*di*di;
2536 x3z1[i] = dD*di*di*di;
2537 r1[i] = 0.0;
2538 residual[i] = 0.0;
2539 }
2540
2541 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
2542 // xMatrix : horizontal concatenation of
2543 // the least-sq. matrix (left) and an
2544 // identity matrix (right).
2545 // the right part is used to calculate the inverse matrix of the left part.
2546 double xMatrix[nDOF][2*nDOF];
2547 double zMatrix[nDOF];
2548 for (int i = 0; i < nDOF; ++i) {
2549 for (int j = 0; j < 2*nDOF; ++j) {
2550 xMatrix[i][j] = 0.0;
2551 }
2552 xMatrix[i][nDOF+i] = 1.0;
2553 zMatrix[i] = 0.0;
2554 }
2555
2556 for (int n = 0; n < nPiece; ++n) {
2557 int nUseDataInPiece = 0;
2558 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2559
2560 if (maskArray[i] == 0) continue;
2561
2562 xMatrix[0][0] += 1.0;
2563 xMatrix[0][1] += x1[i];
2564 xMatrix[0][2] += x2[i];
2565 xMatrix[0][3] += x3[i];
2566 xMatrix[1][1] += x2[i];
2567 xMatrix[1][2] += x3[i];
2568 xMatrix[1][3] += x2[i]*x2[i];
2569 xMatrix[2][2] += x2[i]*x2[i];
2570 xMatrix[2][3] += x3[i]*x2[i];
2571 xMatrix[3][3] += x3[i]*x3[i];
2572 zMatrix[0] += z1[i];
2573 zMatrix[1] += x1z1[i];
2574 zMatrix[2] += x2z1[i];
2575 zMatrix[3] += x3z1[i];
2576
2577 for (int j = 0; j < n; ++j) {
2578 double q = 1.0 - x1[i]*invEdge[j];
2579 q = q*q*q;
2580 xMatrix[0][j+4] += q;
2581 xMatrix[1][j+4] += q*x1[i];
2582 xMatrix[2][j+4] += q*x2[i];
2583 xMatrix[3][j+4] += q*x3[i];
2584 for (int k = 0; k < j; ++k) {
2585 double r = 1.0 - x1[i]*invEdge[k];
2586 r = r*r*r;
2587 xMatrix[k+4][j+4] += r*q;
2588 }
2589 xMatrix[j+4][j+4] += q*q;
2590 zMatrix[j+4] += q*z1[i];
2591 }
2592
2593 nUseDataInPiece++;
2594 }
2595
2596 if (nUseDataInPiece < 1) {
2597 std::vector<string> suffixOfPieceNumber(4);
2598 suffixOfPieceNumber[0] = "th";
2599 suffixOfPieceNumber[1] = "st";
2600 suffixOfPieceNumber[2] = "nd";
2601 suffixOfPieceNumber[3] = "rd";
2602 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
2603 ostringstream oss;
2604 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
2605 oss << " piece of the spectrum. can't execute fitting anymore.";
2606 throw(AipsError(String(oss)));
2607 }
2608 }
2609
2610 for (int i = 0; i < nDOF; ++i) {
2611 for (int j = 0; j < i; ++j) {
2612 xMatrix[i][j] = xMatrix[j][i];
2613 }
2614 }
2615
2616 std::vector<double> invDiag(nDOF);
2617 for (int i = 0; i < nDOF; ++i) {
2618 invDiag[i] = 1.0/xMatrix[i][i];
2619 for (int j = 0; j < nDOF; ++j) {
2620 xMatrix[i][j] *= invDiag[i];
2621 }
2622 }
2623
2624 for (int k = 0; k < nDOF; ++k) {
2625 for (int i = 0; i < nDOF; ++i) {
2626 if (i != k) {
2627 double factor1 = xMatrix[k][k];
2628 double factor2 = xMatrix[i][k];
2629 for (int j = k; j < 2*nDOF; ++j) {
2630 xMatrix[i][j] *= factor1;
2631 xMatrix[i][j] -= xMatrix[k][j]*factor2;
2632 xMatrix[i][j] /= factor1;
2633 }
2634 }
2635 }
2636 double xDiag = xMatrix[k][k];
2637 for (int j = k; j < 2*nDOF; ++j) {
2638 xMatrix[k][j] /= xDiag;
2639 }
2640 }
2641
2642 for (int i = 0; i < nDOF; ++i) {
2643 for (int j = 0; j < nDOF; ++j) {
2644 xMatrix[i][nDOF+j] *= invDiag[j];
2645 }
2646 }
2647 //compute a vector y which consists of the coefficients of the best-fit spline curves
2648 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
2649 //cubic terms for the other pieces (in case nPiece>1).
2650 std::vector<double> y(nDOF);
2651 for (int i = 0; i < nDOF; ++i) {
2652 y[i] = 0.0;
2653 for (int j = 0; j < nDOF; ++j) {
2654 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
2655 }
2656 }
2657
2658 double a0 = y[0];
2659 double a1 = y[1];
2660 double a2 = y[2];
2661 double a3 = y[3];
2662
2663 int j = 0;
2664 for (int n = 0; n < nPiece; ++n) {
2665 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2666 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
2667 }
2668 params[j] = a0;
2669 params[j+1] = a1;
2670 params[j+2] = a2;
2671 params[j+3] = a3;
2672 j += 4;
2673
2674 if (n == nPiece-1) break;
2675
2676 double d = y[4+n];
2677 double iE = invEdge[n];
2678 a0 += d;
2679 a1 -= 3.0*d*iE;
2680 a2 += 3.0*d*iE*iE;
2681 a3 -= d*iE*iE*iE;
2682 }
2683
2684 //subtract constant value for masked regions at the edge of spectrum
2685 if (idxEdge[0] > 0) {
2686 int n = idxEdge[0];
2687 for (int i = 0; i < idxEdge[0]; ++i) {
2688 //--cubic extrapolate--
2689 //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i];
2690 //--linear extrapolate--
2691 //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n];
2692 //--constant--
2693 r1[i] = r1[n];
2694 }
2695 }
2696 if (idxEdge[nPiece] < nChan) {
2697 int n = idxEdge[nPiece]-1;
2698 for (int i = idxEdge[nPiece]; i < nChan; ++i) {
2699 //--cubic extrapolate--
2700 //int m = 4*(nPiece-1);
2701 //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i];
2702 //--linear extrapolate--
2703 //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n];
2704 //--constant--
2705 r1[i] = r1[n];
2706 }
2707 }
2708
2709 for (int i = 0; i < nChan; ++i) {
2710 residual[i] = z1[i] - r1[i];
2711 }
2712
2713 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
2714 break;
2715 } else {
2716 double stdDev = 0.0;
2717 for (int i = 0; i < nChan; ++i) {
2718 stdDev += residual[i]*residual[i]*(double)maskArray[i];
2719 }
2720 stdDev = sqrt(stdDev/(double)nData);
2721
2722 double thres = stdDev * thresClip;
2723 int newNData = 0;
2724 for (int i = 0; i < nChan; ++i) {
2725 if (abs(residual[i]) >= thres) {
2726 maskArray[i] = 0;
2727 }
2728 if (maskArray[i] > 0) {
2729 newNData++;
2730 }
2731 }
2732 if (newNData == nData) {
2733 break; //no more flag to add. iteration stops.
2734 } else {
2735 nData = newNData;
2736 }
2737 }
2738 }
2739
2740 nClipped = initNData - nData;
2741
2742 std::vector<float> result(nChan);
2743 if (getResidual) {
2744 for (int i = 0; i < nChan; ++i) {
2745 result[i] = (float)residual[i];
2746 }
2747 } else {
2748 for (int i = 0; i < nChan; ++i) {
2749 result[i] = (float)r1[i];
2750 }
2751 }
2752
2753 return result;
2754}
2755
2756void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
2757{
2758 nWaves.clear();
2759
2760 if (applyFFT) {
2761 string fftThAttr;
2762 float fftThSigma;
2763 int fftThTop;
2764 parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
2765 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
2766 }
2767
2768 addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves);
2769}
2770
2771void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
2772{
2773 uInt idxSigma = fftThresh.find("sigma");
2774 uInt idxTop = fftThresh.find("top");
2775
2776 if (idxSigma == fftThresh.size() - 5) {
2777 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
2778 is >> fftThSigma;
2779 fftThAttr = "sigma";
2780 } else if (idxTop == 0) {
2781 std::istringstream is(fftThresh.substr(3));
2782 is >> fftThTop;
2783 fftThAttr = "top";
2784 } else {
2785 bool isNumber = true;
2786 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
2787 char ch = (fftThresh.substr(i, 1).c_str())[0];
2788 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
2789 isNumber = false;
2790 break;
2791 }
2792 }
2793 if (isNumber) {
2794 std::istringstream is(fftThresh);
2795 is >> fftThSigma;
2796 fftThAttr = "sigma";
2797 } else {
2798 throw(AipsError("fftthresh has a wrong value"));
2799 }
2800 }
2801}
2802
2803void 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)
2804{
2805 std::vector<float> fspec;
2806 if (fftMethod == "fft") {
2807 fspec = execFFT(whichrow, chanMask, false, true);
2808 //} else if (fftMethod == "lsp") {
2809 // fspec = lombScarglePeriodogram(whichrow);
2810 }
2811
2812 if (fftThAttr == "sigma") {
2813 float mean = 0.0;
2814 float mean2 = 0.0;
2815 for (uInt i = 0; i < fspec.size(); ++i) {
2816 mean += fspec[i];
2817 mean2 += fspec[i]*fspec[i];
2818 }
2819 mean /= float(fspec.size());
2820 mean2 /= float(fspec.size());
2821 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
2822
2823 for (uInt i = 0; i < fspec.size(); ++i) {
2824 if (fspec[i] >= thres) {
2825 nWaves.push_back(i);
2826 }
2827 }
2828
2829 } else if (fftThAttr == "top") {
2830 for (int i = 0; i < fftThTop; ++i) {
2831 float max = 0.0;
2832 int maxIdx = 0;
2833 for (uInt j = 0; j < fspec.size(); ++j) {
2834 if (fspec[j] > max) {
2835 max = fspec[j];
2836 maxIdx = j;
2837 }
2838 }
2839 nWaves.push_back(maxIdx);
2840 fspec[maxIdx] = 0.0;
2841 }
2842
2843 }
2844
2845 if (nWaves.size() > 1) {
2846 sort(nWaves.begin(), nWaves.end());
2847 }
2848}
2849
2850void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
2851{
2852 std::vector<int> tempAddNWaves, tempRejectNWaves;
2853 for (uInt i = 0; i < addNWaves.size(); ++i) {
2854 tempAddNWaves.push_back(addNWaves[i]);
2855 }
2856 if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) {
2857 setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves);
2858 }
2859
2860 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
2861 tempRejectNWaves.push_back(rejectNWaves[i]);
2862 }
2863 if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) {
2864 setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves);
2865 }
2866
2867 for (uInt i = 0; i < tempAddNWaves.size(); ++i) {
2868 bool found = false;
2869 for (uInt j = 0; j < nWaves.size(); ++j) {
2870 if (nWaves[j] == tempAddNWaves[i]) {
2871 found = true;
2872 break;
2873 }
2874 }
2875 if (!found) nWaves.push_back(tempAddNWaves[i]);
2876 }
2877
2878 for (uInt i = 0; i < tempRejectNWaves.size(); ++i) {
2879 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
2880 if (*j == tempRejectNWaves[i]) {
2881 j = nWaves.erase(j);
2882 } else {
2883 ++j;
2884 }
2885 }
2886 }
2887
2888 if (nWaves.size() > 1) {
2889 sort(nWaves.begin(), nWaves.end());
2890 unique(nWaves.begin(), nWaves.end());
2891 }
2892}
2893
2894void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves)
2895{
2896 if ((nWaves.size() == 2)&&(nWaves[1] == -999)) {
2897 int val = nWaves[0];
2898 int nyquistFreq = nchan(getIF(whichrow))/2+1;
2899 nWaves.clear();
2900 if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759
2901 nWaves.push_back(0);
2902 }
2903 while (val <= nyquistFreq) {
2904 nWaves.push_back(val);
2905 val++;
2906 }
2907 }
2908}
2909
2910void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2911{
2912 try {
2913 ofstream ofs;
2914 String coordInfo = "";
2915 bool hasSameNchan = true;
2916 bool outTextFile = false;
2917
2918 if (blfile != "") {
2919 ofs.open(blfile.c_str(), ios::out | ios::app);
2920 if (ofs) outTextFile = true;
2921 }
2922
2923 if (outLogger || outTextFile) {
2924 coordInfo = getCoordInfo()[0];
2925 if (coordInfo == "") coordInfo = "channel";
2926 hasSameNchan = hasSameNchanOverIFs();
2927 }
2928
2929 //Fitter fitter = Fitter();
2930 //fitter.setExpression("sinusoid", nWaves);
2931 //fitter.setIterClipping(thresClip, nIterClip);
2932
2933 int nRow = nrow();
2934 std::vector<bool> chanMask;
2935 std::vector<int> nWaves;
2936
2937 bool showProgress;
2938 int minNRow;
2939 parseProgressInfo(progressInfo, showProgress, minNRow);
2940
2941 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2942 chanMask = getCompositeChanMask(whichrow, mask);
2943 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
2944
2945 //FOR DEBUGGING------------
2946 /*
2947 if (whichrow < 0) {// == nRow -1) {
2948 cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow);
2949 if (applyFFT) {
2950 cout << "[ ";
2951 for (uInt j = 0; j < nWaves.size(); ++j) {
2952 cout << nWaves[j] << ", ";
2953 }
2954 cout << " ] " << endl;
2955 }
2956 cout << flush;
2957 }
2958 */
2959 //-------------------------
2960
2961 //fitBaseline(chanMask, whichrow, fitter);
2962 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2963 std::vector<float> params;
2964 int nClipped = 0;
2965 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
2966 setSpectrum(res, whichrow);
2967 //
2968
2969 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
2970 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2971 }
2972
2973 if (outTextFile) ofs.close();
2974
2975 } catch (...) {
2976 throw;
2977 }
2978}
2979
2980void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2981{
2982 try {
2983 ofstream ofs;
2984 String coordInfo = "";
2985 bool hasSameNchan = true;
2986 bool outTextFile = false;
2987
2988 if (blfile != "") {
2989 ofs.open(blfile.c_str(), ios::out | ios::app);
2990 if (ofs) outTextFile = true;
2991 }
2992
2993 if (outLogger || outTextFile) {
2994 coordInfo = getCoordInfo()[0];
2995 if (coordInfo == "") coordInfo = "channel";
2996 hasSameNchan = hasSameNchanOverIFs();
2997 }
2998
2999 //Fitter fitter = Fitter();
3000 //fitter.setExpression("sinusoid", nWaves);
3001 //fitter.setIterClipping(thresClip, nIterClip);
3002
3003 int nRow = nrow();
3004 std::vector<bool> chanMask;
3005 std::vector<int> nWaves;
3006
3007 int minEdgeSize = getIFNos().size()*2;
3008 STLineFinder lineFinder = STLineFinder();
3009 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3010
3011 bool showProgress;
3012 int minNRow;
3013 parseProgressInfo(progressInfo, showProgress, minNRow);
3014
3015 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3016
3017 //-------------------------------------------------------
3018 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
3019 //-------------------------------------------------------
3020 int edgeSize = edge.size();
3021 std::vector<int> currentEdge;
3022 if (edgeSize >= 2) {
3023 int idx = 0;
3024 if (edgeSize > 2) {
3025 if (edgeSize < minEdgeSize) {
3026 throw(AipsError("Length of edge element info is less than that of IFs"));
3027 }
3028 idx = 2 * getIF(whichrow);
3029 }
3030 currentEdge.push_back(edge[idx]);
3031 currentEdge.push_back(edge[idx+1]);
3032 } else {
3033 throw(AipsError("Wrong length of edge element"));
3034 }
3035 lineFinder.setData(getSpectrum(whichrow));
3036 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
3037 chanMask = lineFinder.getMask();
3038 //-------------------------------------------------------
3039
3040 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
3041
3042 //fitBaseline(chanMask, whichrow, fitter);
3043 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
3044 std::vector<float> params;
3045 int nClipped = 0;
3046 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
3047 setSpectrum(res, whichrow);
3048 //
3049
3050 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
3051 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3052 }
3053
3054 if (outTextFile) ofs.close();
3055
3056 } catch (...) {
3057 throw;
3058 }
3059}
3060
3061std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
3062{
3063 if (data.size() != mask.size()) {
3064 throw(AipsError("data and mask sizes are not identical"));
3065 }
3066 if (data.size() < 2) {
3067 throw(AipsError("data size is too short"));
3068 }
3069 if (waveNumbers.size() == 0) {
3070 throw(AipsError("no wave numbers given"));
3071 }
3072 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
3073 nWaves.reserve(waveNumbers.size());
3074 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
3075 sort(nWaves.begin(), nWaves.end());
3076 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
3077 nWaves.erase(end_it, nWaves.end());
3078
3079 int minNWaves = nWaves[0];
3080 if (minNWaves < 0) {
3081 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
3082 }
3083 bool hasConstantTerm = (minNWaves == 0);
3084
3085 int nChan = data.size();
3086 std::vector<int> maskArray;
3087 std::vector<int> x;
3088 for (int i = 0; i < nChan; ++i) {
3089 maskArray.push_back(mask[i] ? 1 : 0);
3090 if (mask[i]) {
3091 x.push_back(i);
3092 }
3093 }
3094
3095 int initNData = x.size();
3096
3097 int nData = initNData;
3098 int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
3099
3100 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
3101 double baseXFactor = 2.0*PI/(double)(nChan-1); //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK)
3102
3103 // xArray : contains elemental values for computing the least-square matrix.
3104 // xArray.size() is nDOF and xArray[*].size() is nChan.
3105 // Each xArray element are as follows:
3106 // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
3107 // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
3108 // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
3109 // where (1 <= n <= nMaxWavesInSW),
3110 // or,
3111 // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
3112 // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
3113 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
3114 std::vector<std::vector<double> > xArray;
3115 if (hasConstantTerm) {
3116 std::vector<double> xu;
3117 for (int j = 0; j < nChan; ++j) {
3118 xu.push_back(1.0);
3119 }
3120 xArray.push_back(xu);
3121 }
3122 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
3123 double xFactor = baseXFactor*(double)nWaves[i];
3124 std::vector<double> xs, xc;
3125 xs.clear();
3126 xc.clear();
3127 for (int j = 0; j < nChan; ++j) {
3128 xs.push_back(sin(xFactor*(double)j));
3129 xc.push_back(cos(xFactor*(double)j));
3130 }
3131 xArray.push_back(xs);
3132 xArray.push_back(xc);
3133 }
3134
3135 std::vector<double> z1, r1, residual;
3136 for (int i = 0; i < nChan; ++i) {
3137 z1.push_back((double)data[i]);
3138 r1.push_back(0.0);
3139 residual.push_back(0.0);
3140 }
3141
3142 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3143 // xMatrix : horizontal concatenation of
3144 // the least-sq. matrix (left) and an
3145 // identity matrix (right).
3146 // the right part is used to calculate the inverse matrix of the left part.
3147 double xMatrix[nDOF][2*nDOF];
3148 double zMatrix[nDOF];
3149 for (int i = 0; i < nDOF; ++i) {
3150 for (int j = 0; j < 2*nDOF; ++j) {
3151 xMatrix[i][j] = 0.0;
3152 }
3153 xMatrix[i][nDOF+i] = 1.0;
3154 zMatrix[i] = 0.0;
3155 }
3156
3157 int nUseData = 0;
3158 for (int k = 0; k < nChan; ++k) {
3159 if (maskArray[k] == 0) continue;
3160
3161 for (int i = 0; i < nDOF; ++i) {
3162 for (int j = i; j < nDOF; ++j) {
3163 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
3164 }
3165 zMatrix[i] += z1[k] * xArray[i][k];
3166 }
3167
3168 nUseData++;
3169 }
3170
3171 if (nUseData < 1) {
3172 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
3173 }
3174
3175 for (int i = 0; i < nDOF; ++i) {
3176 for (int j = 0; j < i; ++j) {
3177 xMatrix[i][j] = xMatrix[j][i];
3178 }
3179 }
3180
3181 std::vector<double> invDiag;
3182 for (int i = 0; i < nDOF; ++i) {
3183 invDiag.push_back(1.0/xMatrix[i][i]);
3184 for (int j = 0; j < nDOF; ++j) {
3185 xMatrix[i][j] *= invDiag[i];
3186 }
3187 }
3188
3189 for (int k = 0; k < nDOF; ++k) {
3190 for (int i = 0; i < nDOF; ++i) {
3191 if (i != k) {
3192 double factor1 = xMatrix[k][k];
3193 double factor2 = xMatrix[i][k];
3194 for (int j = k; j < 2*nDOF; ++j) {
3195 xMatrix[i][j] *= factor1;
3196 xMatrix[i][j] -= xMatrix[k][j]*factor2;
3197 xMatrix[i][j] /= factor1;
3198 }
3199 }
3200 }
3201 double xDiag = xMatrix[k][k];
3202 for (int j = k; j < 2*nDOF; ++j) {
3203 xMatrix[k][j] /= xDiag;
3204 }
3205 }
3206
3207 for (int i = 0; i < nDOF; ++i) {
3208 for (int j = 0; j < nDOF; ++j) {
3209 xMatrix[i][nDOF+j] *= invDiag[j];
3210 }
3211 }
3212 //compute a vector y which consists of the coefficients of the sinusoids forming the
3213 //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
3214 //and cosine functions, respectively.
3215 std::vector<double> y;
3216 params.clear();
3217 for (int i = 0; i < nDOF; ++i) {
3218 y.push_back(0.0);
3219 for (int j = 0; j < nDOF; ++j) {
3220 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3221 }
3222 params.push_back(y[i]);
3223 }
3224
3225 for (int i = 0; i < nChan; ++i) {
3226 r1[i] = y[0];
3227 for (int j = 1; j < nDOF; ++j) {
3228 r1[i] += y[j]*xArray[j][i];
3229 }
3230 residual[i] = z1[i] - r1[i];
3231 }
3232
3233 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3234 break;
3235 } else {
3236 double stdDev = 0.0;
3237 for (int i = 0; i < nChan; ++i) {
3238 stdDev += residual[i]*residual[i]*(double)maskArray[i];
3239 }
3240 stdDev = sqrt(stdDev/(double)nData);
3241
3242 double thres = stdDev * thresClip;
3243 int newNData = 0;
3244 for (int i = 0; i < nChan; ++i) {
3245 if (abs(residual[i]) >= thres) {
3246 maskArray[i] = 0;
3247 }
3248 if (maskArray[i] > 0) {
3249 newNData++;
3250 }
3251 }
3252 if (newNData == nData) {
3253 break; //no more flag to add. iteration stops.
3254 } else {
3255 nData = newNData;
3256 }
3257 }
3258 }
3259
3260 nClipped = initNData - nData;
3261
3262 std::vector<float> result;
3263 if (getResidual) {
3264 for (int i = 0; i < nChan; ++i) {
3265 result.push_back((float)residual[i]);
3266 }
3267 } else {
3268 for (int i = 0; i < nChan; ++i) {
3269 result.push_back((float)r1[i]);
3270 }
3271 }
3272
3273 return result;
3274}
3275
3276void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
3277{
3278 std::vector<double> dAbcissa = getAbcissa(whichrow);
3279 std::vector<float> abcissa;
3280 for (uInt i = 0; i < dAbcissa.size(); ++i) {
3281 abcissa.push_back((float)dAbcissa[i]);
3282 }
3283 std::vector<float> spec = getSpectrum(whichrow);
3284
3285 fitter.setData(abcissa, spec, mask);
3286 fitter.lfit();
3287}
3288
3289std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
3290{
3291 std::vector<bool> mask = getMask(whichrow);
3292 uInt maskSize = mask.size();
3293 if (inMask.size() != 0) {
3294 if (maskSize != inMask.size()) {
3295 throw(AipsError("mask sizes are not the same."));
3296 }
3297 for (uInt i = 0; i < maskSize; ++i) {
3298 mask[i] = mask[i] && inMask[i];
3299 }
3300 }
3301
3302 return mask;
3303}
3304
3305/*
3306std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
3307{
3308 int edgeSize = edge.size();
3309 std::vector<int> currentEdge;
3310 if (edgeSize >= 2) {
3311 int idx = 0;
3312 if (edgeSize > 2) {
3313 if (edgeSize < minEdgeSize) {
3314 throw(AipsError("Length of edge element info is less than that of IFs"));
3315 }
3316 idx = 2 * getIF(whichrow);
3317 }
3318 currentEdge.push_back(edge[idx]);
3319 currentEdge.push_back(edge[idx+1]);
3320 } else {
3321 throw(AipsError("Wrong length of edge element"));
3322 }
3323
3324 lineFinder.setData(getSpectrum(whichrow));
3325 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
3326
3327 return lineFinder.getMask();
3328}
3329*/
3330
3331/* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
3332void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter)
3333{
3334 if (outLogger || outTextFile) {
3335 std::vector<float> params = fitter.getParameters();
3336 std::vector<bool> fixed = fitter.getFixedParameters();
3337 float rms = getRms(chanMask, whichrow);
3338 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3339
3340 if (outLogger) {
3341 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3342 ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ;
3343 }
3344 if (outTextFile) {
3345 ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush;
3346 }
3347 }
3348}
3349
3350/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
3351void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped)
3352{
3353 if (outLogger || outTextFile) {
3354 float rms = getRms(chanMask, whichrow);
3355 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3356 std::vector<bool> fixed;
3357 fixed.clear();
3358
3359 if (outLogger) {
3360 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3361 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
3362 }
3363 if (outTextFile) {
3364 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
3365 }
3366 }
3367}
3368
3369/* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */
3370void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped)
3371{
3372 if (outLogger || outTextFile) {
3373 float rms = getRms(chanMask, whichrow);
3374 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3375 std::vector<bool> fixed;
3376 fixed.clear();
3377
3378 if (outLogger) {
3379 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3380 ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
3381 }
3382 if (outTextFile) {
3383 ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
3384 }
3385 }
3386}
3387
3388void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
3389{
3390 int idxDelimiter = progressInfo.find(",");
3391 if (idxDelimiter < 0) {
3392 throw(AipsError("wrong value in 'showprogress' parameter")) ;
3393 }
3394 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
3395 std::istringstream is(progressInfo.substr(idxDelimiter+1));
3396 is >> minNRow;
3397}
3398
3399void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
3400{
3401 if (showProgress && (nTotal >= nTotalThreshold)) {
3402 int nInterval = int(floor(double(nTotal)/100.0));
3403 if (nInterval == 0) nInterval++;
3404
3405 if (nProcessed % nInterval == 0) {
3406 printf("\r"); //go to the head of line
3407 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
3408 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
3409 printf("\x1b[39m\x1b[0m"); //set default attributes
3410 fflush(NULL);
3411 }
3412
3413 if (nProcessed == nTotal - 1) {
3414 printf("\r\x1b[K"); //clear
3415 fflush(NULL);
3416 }
3417
3418 }
3419}
3420
3421std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
3422{
3423 std::vector<bool> mask = getMask(whichrow);
3424
3425 if (inMask.size() > 0) {
3426 uInt maskSize = mask.size();
3427 if (maskSize != inMask.size()) {
3428 throw(AipsError("mask sizes are not the same."));
3429 }
3430 for (uInt i = 0; i < maskSize; ++i) {
3431 mask[i] = mask[i] && inMask[i];
3432 }
3433 }
3434
3435 Vector<Float> spec = getSpectrum(whichrow);
3436 mathutil::doZeroOrderInterpolation(spec, mask);
3437
3438 FFTServer<Float,Complex> ffts;
3439 Vector<Complex> fftres;
3440 ffts.fft0(fftres, spec);
3441
3442 std::vector<float> res;
3443 float norm = float(2.0/double(spec.size()));
3444
3445 if (getRealImag) {
3446 for (uInt i = 0; i < fftres.size(); ++i) {
3447 res.push_back(real(fftres[i])*norm);
3448 res.push_back(imag(fftres[i])*norm);
3449 }
3450 } else {
3451 for (uInt i = 0; i < fftres.size(); ++i) {
3452 res.push_back(abs(fftres[i])*norm);
3453 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
3454 }
3455 }
3456
3457 return res;
3458}
3459
3460
3461float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
3462{
3463 Vector<Float> spec;
3464 specCol_.get(whichrow, spec);
3465
3466 float mean = 0.0;
3467 float smean = 0.0;
3468 int n = 0;
3469 for (uInt i = 0; i < spec.nelements(); ++i) {
3470 if (mask[i]) {
3471 mean += spec[i];
3472 smean += spec[i]*spec[i];
3473 n++;
3474 }
3475 }
3476
3477 mean /= (float)n;
3478 smean /= (float)n;
3479
3480 return sqrt(smean - mean*mean);
3481}
3482
3483
3484std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const
3485{
3486 ostringstream oss;
3487
3488 if (verbose) {
3489 oss << " Scan[" << getScan(whichrow) << "]";
3490 oss << " Beam[" << getBeam(whichrow) << "]";
3491 oss << " IF[" << getIF(whichrow) << "]";
3492 oss << " Pol[" << getPol(whichrow) << "]";
3493 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
3494 oss << "Fitter range = " << masklist << endl;
3495 oss << "Baseline parameters" << endl;
3496 oss << flush;
3497 }
3498
3499 return String(oss);
3500}
3501
3502std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const
3503{
3504 ostringstream oss;
3505
3506 if (verbose) {
3507 oss << "Results of baseline fit" << endl;
3508 oss << " rms = " << setprecision(6) << rms << endl;
3509 if (nClipped >= 0) {
3510 oss << " Number of clipped channels = " << nClipped << endl;
3511 }
3512 for (int i = 0; i < 60; ++i) {
3513 oss << "-";
3514 }
3515 oss << endl;
3516 oss << flush;
3517 }
3518
3519 return String(oss);
3520}
3521
3522std::string Scantable::formatBaselineParams(const std::vector<float>& params,
3523 const std::vector<bool>& fixed,
3524 float rms,
3525 int nClipped,
3526 const std::string& masklist,
3527 int whichrow,
3528 bool verbose,
3529 int start, int count,
3530 bool resetparamid) const
3531{
3532 int nParam = (int)(params.size());
3533
3534 if (nParam < 1) {
3535 return(" Not fitted");
3536 } else {
3537
3538 ostringstream oss;
3539 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3540
3541 if (start < 0) start = 0;
3542 if (count < 0) count = nParam;
3543 int end = start + count;
3544 if (end > nParam) end = nParam;
3545 int paramidoffset = (resetparamid) ? (-start) : 0;
3546
3547 for (int i = start; i < end; ++i) {
3548 if (i > start) {
3549 oss << ",";
3550 }
3551 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
3552 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
3553 }
3554
3555 oss << endl;
3556 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
3557
3558 return String(oss);
3559 }
3560
3561}
3562
3563 std::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) const
3564{
3565 int nOutParam = (int)(params.size());
3566 int nPiece = (int)(ranges.size()) - 1;
3567
3568 if (nOutParam < 1) {
3569 return(" Not fitted");
3570 } else if (nPiece < 0) {
3571 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose);
3572 } else if (nPiece < 1) {
3573 return(" Bad count of the piece edge info");
3574 } else if (nOutParam % nPiece != 0) {
3575 return(" Bad count of the output baseline parameters");
3576 } else {
3577
3578 int nParam = nOutParam / nPiece;
3579
3580 ostringstream oss;
3581 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3582
3583 stringstream ss;
3584 ss << ranges[nPiece] << flush;
3585 int wRange = ss.str().size() * 2 + 5;
3586
3587 for (int i = 0; i < nPiece; ++i) {
3588 ss.str("");
3589 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
3590 oss << left << setw(wRange) << ss.str();
3591 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true);
3592 }
3593
3594 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
3595
3596 return String(oss);
3597 }
3598
3599}
3600
3601bool Scantable::hasSameNchanOverIFs()
3602{
3603 int nIF = nif(-1);
3604 int nCh;
3605 int totalPositiveNChan = 0;
3606 int nPositiveNChan = 0;
3607
3608 for (int i = 0; i < nIF; ++i) {
3609 nCh = nchan(i);
3610 if (nCh > 0) {
3611 totalPositiveNChan += nCh;
3612 nPositiveNChan++;
3613 }
3614 }
3615
3616 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
3617}
3618
3619std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
3620{
3621 if (mask.size() <= 0) {
3622 throw(AipsError("The mask elements should be > 0"));
3623 }
3624 int IF = getIF(whichrow);
3625 if (mask.size() != (uInt)nchan(IF)) {
3626 throw(AipsError("Number of channels in scantable != number of mask elements"));
3627 }
3628
3629 if (verbose) {
3630 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
3631 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
3632 if (!hasSameNchan) {
3633 logOs << endl << "This mask is only valid for IF=" << IF;
3634 }
3635 logOs << LogIO::POST;
3636 }
3637
3638 std::vector<double> abcissa = getAbcissa(whichrow);
3639 std::vector<int> edge = getMaskEdgeIndices(mask);
3640
3641 ostringstream oss;
3642 oss.setf(ios::fixed);
3643 oss << setprecision(1) << "[";
3644 for (uInt i = 0; i < edge.size(); i+=2) {
3645 if (i > 0) oss << ",";
3646 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
3647 }
3648 oss << "]" << flush;
3649
3650 return String(oss);
3651}
3652
3653std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
3654{
3655 if (mask.size() <= 0) {
3656 throw(AipsError("The mask elements should be > 0"));
3657 }
3658
3659 std::vector<int> out, startIndices, endIndices;
3660 int maskSize = mask.size();
3661
3662 startIndices.clear();
3663 endIndices.clear();
3664
3665 if (mask[0]) {
3666 startIndices.push_back(0);
3667 }
3668 for (int i = 1; i < maskSize; ++i) {
3669 if ((!mask[i-1]) && mask[i]) {
3670 startIndices.push_back(i);
3671 } else if (mask[i-1] && (!mask[i])) {
3672 endIndices.push_back(i-1);
3673 }
3674 }
3675 if (mask[maskSize-1]) {
3676 endIndices.push_back(maskSize-1);
3677 }
3678
3679 if (startIndices.size() != endIndices.size()) {
3680 throw(AipsError("Inconsistent Mask Size: bad data?"));
3681 }
3682 for (uInt i = 0; i < startIndices.size(); ++i) {
3683 if (startIndices[i] > endIndices[i]) {
3684 throw(AipsError("Mask start index > mask end index"));
3685 }
3686 }
3687
3688 out.clear();
3689 for (uInt i = 0; i < startIndices.size(); ++i) {
3690 out.push_back(startIndices[i]);
3691 out.push_back(endIndices[i]);
3692 }
3693
3694 return out;
3695}
3696
3697vector<float> Scantable::getTsysSpectrum( int whichrow ) const
3698{
3699 Vector<Float> tsys( tsysCol_(whichrow) ) ;
3700 vector<float> stlTsys ;
3701 tsys.tovector( stlTsys ) ;
3702 return stlTsys ;
3703}
3704
3705
3706}
3707//namespace asap
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