source: branches/casa-prerelease/pre-asap/src/Scantable.cpp@ 2342

Last change on this file since 2342 was 2290, checked in by Kana Sugimoto, 13 years ago

New Development: Yes

JIRA Issue: Yes (CAS-3219/ASAP-247)

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs: sdlist unit test (reference data to be updated)

Put in Release Notes: Yes

Module(s): scantable.summary, sdlist

Description:

Output format of scantable summary changed.
Less use of TableIterator for speed up scantable.summary/sdlist now lists a scantable
with 348,000 records (NRO 45m w/ 25beams x 13,920scans) in ~30sec (was ~7 min previously).


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 109.3 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 "Scantable.h"
71
72using namespace casa;
73
74namespace asap {
75
76std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
77
78void Scantable::initFactories() {
79 if ( factories_.empty() ) {
80 Scantable::factories_["linear"] = &STPolLinear::myFactory;
81 Scantable::factories_["circular"] = &STPolCircular::myFactory;
82 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
83 }
84}
85
86Scantable::Scantable(Table::TableType ttype) :
87 type_(ttype)
88{
89 initFactories();
90 setupMainTable();
91 freqTable_ = STFrequencies(*this);
92 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
93 weatherTable_ = STWeather(*this);
94 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
95 focusTable_ = STFocus(*this);
96 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
97 tcalTable_ = STTcal(*this);
98 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
99 moleculeTable_ = STMolecules(*this);
100 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
101 historyTable_ = STHistory(*this);
102 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
103 fitTable_ = STFit(*this);
104 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
105 table_.tableInfo().setType( "Scantable" ) ;
106 originalTable_ = table_;
107 attach();
108}
109
110Scantable::Scantable(const std::string& name, Table::TableType ttype) :
111 type_(ttype)
112{
113 initFactories();
114
115 Table tab(name, Table::Update);
116 uInt version = tab.keywordSet().asuInt("VERSION");
117 if (version != version_) {
118 if ( version == 2 && version_ == 3 ) {
119 // run asap2to3 command
120 LogIO os( LogOrigin( "Scantable" ) ) ;
121 string command="asap2to3" ;
122 string exec=command+" in="+name ;
123 string outname=name ;
124 if ( name.at(name.length()-1) == '/' )
125 outname = outname.substr( 0, name.length()-1 ) ;
126 outname += ".asap3" ;
127 os << LogIO::WARN
128 << name << " is incompatible data format (Scantable v2)." << endl
129 << "Running " << command << " to create " << outname << ", " << endl
130 << "which is identical to " << name << " but compatible " << endl
131 << "data format with current software version (Scantable v3)."
132 << LogIO::POST ;
133 int ret = system( string("which "+command+" > /dev/null 2>&1").c_str() ) ;
134 if ( ret != 0 )
135 throw(AipsError(command+" is not installed")) ;
136 os << LogIO::WARN
137 << "Data will be loaded from " << outname << " instead of "
138 << name << LogIO::POST ;
139 int tmp = system( exec.c_str() ) ;
140 (void) tmp;
141 tab = Table(outname, Table::Update ) ;
142 //os << "tab.tableName()=" << tab.tableName() << LogIO::POST ;
143 }
144 else {
145 throw(AipsError("Unsupported version of ASAP file."));
146 }
147 }
148 if ( type_ == Table::Memory ) {
149 table_ = tab.copyToMemoryTable(generateName());
150 } else {
151 table_ = tab;
152 }
153 table_.tableInfo().setType( "Scantable" ) ;
154
155 attachSubtables();
156 originalTable_ = table_;
157 attach();
158}
159/*
160Scantable::Scantable(const std::string& name, Table::TableType ttype) :
161 type_(ttype)
162{
163 initFactories();
164 Table tab(name, Table::Update);
165 uInt version = tab.keywordSet().asuInt("VERSION");
166 if (version != version_) {
167 throw(AipsError("Unsupported version of ASAP file."));
168 }
169 if ( type_ == Table::Memory ) {
170 table_ = tab.copyToMemoryTable(generateName());
171 } else {
172 table_ = tab;
173 }
174
175 attachSubtables();
176 originalTable_ = table_;
177 attach();
178}
179*/
180
181Scantable::Scantable( const Scantable& other, bool clear ):
182 Logger()
183{
184 // with or without data
185 String newname = String(generateName());
186 type_ = other.table_.tableType();
187 if ( other.table_.tableType() == Table::Memory ) {
188 if ( clear ) {
189 table_ = TableCopy::makeEmptyMemoryTable(newname,
190 other.table_, True);
191 } else
192 table_ = other.table_.copyToMemoryTable(newname);
193 } else {
194 other.table_.deepCopy(newname, Table::New, False,
195 other.table_.endianFormat(),
196 Bool(clear));
197 table_ = Table(newname, Table::Update);
198 table_.markForDelete();
199 }
200 table_.tableInfo().setType( "Scantable" ) ;
201 /// @todo reindex SCANNO, recompute nbeam, nif, npol
202 if ( clear ) copySubtables(other);
203 attachSubtables();
204 originalTable_ = table_;
205 attach();
206}
207
208void Scantable::copySubtables(const Scantable& other) {
209 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
210 TableCopy::copyRows(t, other.freqTable_.table());
211 t = table_.rwKeywordSet().asTable("FOCUS");
212 TableCopy::copyRows(t, other.focusTable_.table());
213 t = table_.rwKeywordSet().asTable("WEATHER");
214 TableCopy::copyRows(t, other.weatherTable_.table());
215 t = table_.rwKeywordSet().asTable("TCAL");
216 TableCopy::copyRows(t, other.tcalTable_.table());
217 t = table_.rwKeywordSet().asTable("MOLECULES");
218 TableCopy::copyRows(t, other.moleculeTable_.table());
219 t = table_.rwKeywordSet().asTable("HISTORY");
220 TableCopy::copyRows(t, other.historyTable_.table());
221 t = table_.rwKeywordSet().asTable("FIT");
222 TableCopy::copyRows(t, other.fitTable_.table());
223}
224
225void Scantable::attachSubtables()
226{
227 freqTable_ = STFrequencies(table_);
228 focusTable_ = STFocus(table_);
229 weatherTable_ = STWeather(table_);
230 tcalTable_ = STTcal(table_);
231 moleculeTable_ = STMolecules(table_);
232 historyTable_ = STHistory(table_);
233 fitTable_ = STFit(table_);
234}
235
236Scantable::~Scantable()
237{
238 //cout << "~Scantable() " << this << endl;
239}
240
241void Scantable::setupMainTable()
242{
243 TableDesc td("", "1", TableDesc::Scratch);
244 td.comment() = "An ASAP Scantable";
245 td.rwKeywordSet().define("VERSION", uInt(version_));
246
247 // n Cycles
248 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
249 // new index every nBeam x nIF x nPol
250 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
251
252 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
253 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
254 // linear, circular, stokes
255 td.rwKeywordSet().define("POLTYPE", String("linear"));
256 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
257
258 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
259 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
260
261 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
262 refbeamnoColumn.setDefault(Int(-1));
263 td.addColumn(refbeamnoColumn);
264
265 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
266 flagrowColumn.setDefault(uInt(0));
267 td.addColumn(flagrowColumn);
268
269 td.addColumn(ScalarColumnDesc<Double>("TIME"));
270 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
271 TableMeasValueDesc measVal(td, "TIME");
272 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
273 mepochCol.write(td);
274
275 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
276
277 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
278 // Type of source (on=0, off=1, other=-1)
279 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
280 stypeColumn.setDefault(Int(-1));
281 td.addColumn(stypeColumn);
282 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
283
284 //The actual Data Vectors
285 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
286 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
287 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
288
289 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
290 IPosition(1,2),
291 ColumnDesc::Direct));
292 TableMeasRefDesc mdirRef(MDirection::J2000); // default
293 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
294 // the TableMeasDesc gives the column a type
295 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
296 // a uder set table type e.g. GALCTIC, B1950 ...
297 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
298 // writing create the measure column
299 mdirCol.write(td);
300 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
301 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
302 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
303
304 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
305 ScalarColumnDesc<Int> fitColumn("FIT_ID");
306 fitColumn.setDefault(Int(-1));
307 td.addColumn(fitColumn);
308
309 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
310 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
311
312 // columns which just get dragged along, as they aren't used in asap
313 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
314 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
315 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
316 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
317
318 td.rwKeywordSet().define("OBSMODE", String(""));
319
320 // Now create Table SetUp from the description.
321 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
322 table_ = Table(aNewTab, type_, 0);
323 originalTable_ = table_;
324}
325
326void Scantable::attach()
327{
328 timeCol_.attach(table_, "TIME");
329 srcnCol_.attach(table_, "SRCNAME");
330 srctCol_.attach(table_, "SRCTYPE");
331 specCol_.attach(table_, "SPECTRA");
332 flagsCol_.attach(table_, "FLAGTRA");
333 tsysCol_.attach(table_, "TSYS");
334 cycleCol_.attach(table_,"CYCLENO");
335 scanCol_.attach(table_, "SCANNO");
336 beamCol_.attach(table_, "BEAMNO");
337 ifCol_.attach(table_, "IFNO");
338 polCol_.attach(table_, "POLNO");
339 integrCol_.attach(table_, "INTERVAL");
340 azCol_.attach(table_, "AZIMUTH");
341 elCol_.attach(table_, "ELEVATION");
342 dirCol_.attach(table_, "DIRECTION");
343 fldnCol_.attach(table_, "FIELDNAME");
344 rbeamCol_.attach(table_, "REFBEAMNO");
345
346 mweatheridCol_.attach(table_,"WEATHER_ID");
347 mfitidCol_.attach(table_,"FIT_ID");
348 mfreqidCol_.attach(table_, "FREQ_ID");
349 mtcalidCol_.attach(table_, "TCAL_ID");
350 mfocusidCol_.attach(table_, "FOCUS_ID");
351 mmolidCol_.attach(table_, "MOLECULE_ID");
352
353 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
354 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
355
356}
357
358template<class T, class T2>
359void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
360 const String& colName,
361 const T2& defValue)
362{
363 try {
364 col.attach(table_, colName);
365 } catch (TableError& err) {
366 String errMesg = err.getMesg();
367 if (errMesg == "Table column " + colName + " is unknown") {
368 table_.addColumn(ScalarColumnDesc<T>(colName));
369 col.attach(table_, colName);
370 col.fillColumn(static_cast<T>(defValue));
371 } else {
372 throw;
373 }
374 } catch (...) {
375 throw;
376 }
377}
378
379template<class T, class T2>
380void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
381 const String& colName,
382 const Array<T2>& defValue)
383{
384 try {
385 col.attach(table_, colName);
386 } catch (TableError& err) {
387 String errMesg = err.getMesg();
388 if (errMesg == "Table column " + colName + " is unknown") {
389 table_.addColumn(ArrayColumnDesc<T>(colName));
390 col.attach(table_, colName);
391
392 int size = 0;
393 ArrayIterator<T2>& it = defValue.begin();
394 while (it != defValue.end()) {
395 ++size;
396 ++it;
397 }
398 IPosition ip(1, size);
399 Array<T>& arr(ip);
400 for (int i = 0; i < size; ++i)
401 arr[i] = static_cast<T>(defValue[i]);
402
403 col.fillColumn(arr);
404 } else {
405 throw;
406 }
407 } catch (...) {
408 throw;
409 }
410}
411
412void Scantable::setHeader(const STHeader& sdh)
413{
414 table_.rwKeywordSet().define("nIF", sdh.nif);
415 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
416 table_.rwKeywordSet().define("nPol", sdh.npol);
417 table_.rwKeywordSet().define("nChan", sdh.nchan);
418 table_.rwKeywordSet().define("Observer", sdh.observer);
419 table_.rwKeywordSet().define("Project", sdh.project);
420 table_.rwKeywordSet().define("Obstype", sdh.obstype);
421 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
422 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
423 table_.rwKeywordSet().define("Equinox", sdh.equinox);
424 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
425 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
426 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
427 table_.rwKeywordSet().define("UTC", sdh.utc);
428 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
429 table_.rwKeywordSet().define("Epoch", sdh.epoch);
430 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
431}
432
433STHeader Scantable::getHeader() const
434{
435 STHeader sdh;
436 table_.keywordSet().get("nBeam",sdh.nbeam);
437 table_.keywordSet().get("nIF",sdh.nif);
438 table_.keywordSet().get("nPol",sdh.npol);
439 table_.keywordSet().get("nChan",sdh.nchan);
440 table_.keywordSet().get("Observer", sdh.observer);
441 table_.keywordSet().get("Project", sdh.project);
442 table_.keywordSet().get("Obstype", sdh.obstype);
443 table_.keywordSet().get("AntennaName", sdh.antennaname);
444 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
445 table_.keywordSet().get("Equinox", sdh.equinox);
446 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
447 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
448 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
449 table_.keywordSet().get("UTC", sdh.utc);
450 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
451 table_.keywordSet().get("Epoch", sdh.epoch);
452 table_.keywordSet().get("POLTYPE", sdh.poltype);
453 return sdh;
454}
455
456void Scantable::setSourceType( int stype )
457{
458 if ( stype < 0 || stype > 1 )
459 throw(AipsError("Illegal sourcetype."));
460 TableVector<Int> tabvec(table_, "SRCTYPE");
461 tabvec = Int(stype);
462}
463
464bool Scantable::conformant( const Scantable& other )
465{
466 return this->getHeader().conformant(other.getHeader());
467}
468
469
470
471std::string Scantable::formatSec(Double x) const
472{
473 Double xcop = x;
474 MVTime mvt(xcop/24./3600.); // make days
475
476 if (x < 59.95)
477 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
478 else if (x < 3599.95)
479 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
480 else {
481 ostringstream oss;
482 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
483 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
484 return String(oss);
485 }
486};
487
488std::string Scantable::formatDirection(const MDirection& md) const
489{
490 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
491 Int prec = 7;
492
493 MVAngle mvLon(t[0]);
494 String sLon = mvLon.string(MVAngle::TIME,prec);
495 uInt tp = md.getRef().getType();
496 if (tp == MDirection::GALACTIC ||
497 tp == MDirection::SUPERGAL ) {
498 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
499 }
500 MVAngle mvLat(t[1]);
501 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
502 return sLon + String(" ") + sLat;
503}
504
505
506std::string Scantable::getFluxUnit() const
507{
508 return table_.keywordSet().asString("FluxUnit");
509}
510
511void Scantable::setFluxUnit(const std::string& unit)
512{
513 String tmp(unit);
514 Unit tU(tmp);
515 if (tU==Unit("K") || tU==Unit("Jy")) {
516 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
517 } else {
518 throw AipsError("Illegal unit - must be compatible with Jy or K");
519 }
520}
521
522void Scantable::setInstrument(const std::string& name)
523{
524 bool throwIt = true;
525 // create an Instrument to see if this is valid
526 STAttr::convertInstrument(name, throwIt);
527 String nameU(name);
528 nameU.upcase();
529 table_.rwKeywordSet().define(String("AntennaName"), nameU);
530}
531
532void Scantable::setFeedType(const std::string& feedtype)
533{
534 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
535 std::string msg = "Illegal feed type "+ feedtype;
536 throw(casa::AipsError(msg));
537 }
538 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
539}
540
541MPosition Scantable::getAntennaPosition() const
542{
543 Vector<Double> antpos;
544 table_.keywordSet().get("AntennaPosition", antpos);
545 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
546 return MPosition(mvpos);
547}
548
549void Scantable::makePersistent(const std::string& filename)
550{
551 String inname(filename);
552 Path path(inname);
553 /// @todo reindex SCANNO, recompute nbeam, nif, npol
554 inname = path.expandedName();
555 // 2011/03/04 TN
556 // We can comment out this workaround since the essential bug is
557 // fixed in casacore (r20889 in google code).
558 table_.deepCopy(inname, Table::New);
559// // WORKAROUND !!! for Table bug
560// // Remove when fixed in casacore
561// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
562// Table tab = table_.copyToMemoryTable(generateName());
563// tab.deepCopy(inname, Table::New);
564// tab.markForDelete();
565//
566// } else {
567// table_.deepCopy(inname, Table::New);
568// }
569}
570
571int Scantable::nbeam( int scanno ) const
572{
573 if ( scanno < 0 ) {
574 Int n;
575 table_.keywordSet().get("nBeam",n);
576 return int(n);
577 } else {
578 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
579 Table t = table_(table_.col("SCANNO") == scanno);
580 ROTableRow row(t);
581 const TableRecord& rec = row.get(0);
582 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
583 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
584 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
585 ROTableVector<uInt> v(subt, "BEAMNO");
586 return int(v.nelements());
587 }
588 return 0;
589}
590
591int Scantable::nif( int scanno ) const
592{
593 if ( scanno < 0 ) {
594 Int n;
595 table_.keywordSet().get("nIF",n);
596 return int(n);
597 } else {
598 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
599 Table t = table_(table_.col("SCANNO") == scanno);
600 ROTableRow row(t);
601 const TableRecord& rec = row.get(0);
602 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
603 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
604 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
605 if ( subt.nrow() == 0 ) return 0;
606 ROTableVector<uInt> v(subt, "IFNO");
607 return int(v.nelements());
608 }
609 return 0;
610}
611
612int Scantable::npol( int scanno ) const
613{
614 if ( scanno < 0 ) {
615 Int n;
616 table_.keywordSet().get("nPol",n);
617 return n;
618 } else {
619 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
620 Table t = table_(table_.col("SCANNO") == scanno);
621 ROTableRow row(t);
622 const TableRecord& rec = row.get(0);
623 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
624 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
625 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
626 if ( subt.nrow() == 0 ) return 0;
627 ROTableVector<uInt> v(subt, "POLNO");
628 return int(v.nelements());
629 }
630 return 0;
631}
632
633int Scantable::ncycle( int scanno ) const
634{
635 if ( scanno < 0 ) {
636 Block<String> cols(2);
637 cols[0] = "SCANNO";
638 cols[1] = "CYCLENO";
639 TableIterator it(table_, cols);
640 int n = 0;
641 while ( !it.pastEnd() ) {
642 ++n;
643 ++it;
644 }
645 return n;
646 } else {
647 Table t = table_(table_.col("SCANNO") == scanno);
648 ROTableRow row(t);
649 const TableRecord& rec = row.get(0);
650 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
651 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
652 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
653 if ( subt.nrow() == 0 ) return 0;
654 return int(subt.nrow());
655 }
656 return 0;
657}
658
659
660int Scantable::nrow( int scanno ) const
661{
662 return int(table_.nrow());
663}
664
665int Scantable::nchan( int ifno ) const
666{
667 if ( ifno < 0 ) {
668 Int n;
669 table_.keywordSet().get("nChan",n);
670 return int(n);
671 } else {
672 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
673 // vary with these
674 Table t = table_(table_.col("IFNO") == ifno, 1);
675 if ( t.nrow() == 0 ) return 0;
676 ROArrayColumn<Float> v(t, "SPECTRA");
677 return v.shape(0)(0);
678 }
679 return 0;
680}
681
682int Scantable::nscan() const {
683 Vector<uInt> scannos(scanCol_.getColumn());
684 uInt nout = genSort( scannos, Sort::Ascending,
685 Sort::QuickSort|Sort::NoDuplicates );
686 return int(nout);
687}
688
689int Scantable::getChannels(int whichrow) const
690{
691 return specCol_.shape(whichrow)(0);
692}
693
694int Scantable::getBeam(int whichrow) const
695{
696 return beamCol_(whichrow);
697}
698
699std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
700{
701 Vector<uInt> nos(col.getColumn());
702 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
703 nos.resize(n, True);
704 std::vector<uint> stlout;
705 nos.tovector(stlout);
706 return stlout;
707}
708
709int Scantable::getIF(int whichrow) const
710{
711 return ifCol_(whichrow);
712}
713
714int Scantable::getPol(int whichrow) const
715{
716 return polCol_(whichrow);
717}
718
719std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
720{
721 return formatTime(me, showdate, 0);
722}
723
724std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
725{
726 MVTime mvt(me.getValue());
727 if (showdate)
728 //mvt.setFormat(MVTime::YMD);
729 mvt.setFormat(MVTime::YMD, prec);
730 else
731 //mvt.setFormat(MVTime::TIME);
732 mvt.setFormat(MVTime::TIME, prec);
733 ostringstream oss;
734 oss << mvt;
735 return String(oss);
736}
737
738void Scantable::calculateAZEL()
739{
740 MPosition mp = getAntennaPosition();
741 MEpoch::ROScalarColumn timeCol(table_, "TIME");
742 ostringstream oss;
743 oss << "Computed azimuth/elevation using " << endl
744 << mp << endl;
745 for (Int i=0; i<nrow(); ++i) {
746 MEpoch me = timeCol(i);
747 MDirection md = getDirection(i);
748 oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md)
749 << endl << " => ";
750 MeasFrame frame(mp, me);
751 Vector<Double> azel =
752 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
753 frame)
754 )().getAngle("rad").getValue();
755 azCol_.put(i,Float(azel[0]));
756 elCol_.put(i,Float(azel[1]));
757 oss << "azel: " << azel[0]/C::pi*180.0 << " "
758 << azel[1]/C::pi*180.0 << " (deg)" << endl;
759 }
760 pushLog(String(oss));
761}
762
763void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
764{
765 for (uInt i=0; i<table_.nrow(); ++i) {
766 Vector<uChar> flgs = flagsCol_(i);
767 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
768 flagsCol_.put(i, flgs);
769 }
770}
771
772std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
773{
774 Vector<uChar> flags;
775 flagsCol_.get(uInt(whichrow), flags);
776 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
777 Vector<Bool> bflag(flags.shape());
778 convertArray(bflag, flags);
779 //bflag = !bflag;
780
781 std::vector<bool> mask;
782 bflag.tovector(mask);
783 return mask;
784}
785
786void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
787 Vector<uChar> flgs)
788{
789 Vector<Float> spcs = specCol_(whichrow);
790 uInt nchannel = nchan();
791 if (spcs.nelements() != nchannel) {
792 throw(AipsError("Data has incorrect number of channels"));
793 }
794 uChar userflag = 1 << 7;
795 if (unflag) {
796 userflag = 0 << 7;
797 }
798 if (clipoutside) {
799 for (uInt j = 0; j < nchannel; ++j) {
800 Float spc = spcs(j);
801 if ((spc >= uthres) || (spc <= dthres)) {
802 flgs(j) = userflag;
803 }
804 }
805 } else {
806 for (uInt j = 0; j < nchannel; ++j) {
807 Float spc = spcs(j);
808 if ((spc < uthres) && (spc > dthres)) {
809 flgs(j) = userflag;
810 }
811 }
812 }
813}
814
815
816void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
817 std::vector<bool>::const_iterator it;
818 uInt ntrue = 0;
819 if (whichrow >= int(table_.nrow()) ) {
820 throw(AipsError("Invalid row number"));
821 }
822 for (it = msk.begin(); it != msk.end(); ++it) {
823 if ( *it ) {
824 ntrue++;
825 }
826 }
827 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
828 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
829 throw(AipsError("Trying to flag whole scantable."));
830 uChar userflag = 1 << 7;
831 if ( unflag ) {
832 userflag = 0 << 7;
833 }
834 if (whichrow > -1 ) {
835 applyChanFlag(uInt(whichrow), msk, userflag);
836 } else {
837 for ( uInt i=0; i<table_.nrow(); ++i) {
838 applyChanFlag(i, msk, userflag);
839 }
840 }
841}
842
843void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
844{
845 if (whichrow >= table_.nrow() ) {
846 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
847 }
848 Vector<uChar> flgs = flagsCol_(whichrow);
849 if ( msk.size() == 0 ) {
850 flgs = flagval;
851 flagsCol_.put(whichrow, flgs);
852 return;
853 }
854 if ( int(msk.size()) != nchan() ) {
855 throw(AipsError("Mask has incorrect number of channels."));
856 }
857 if ( flgs.nelements() != msk.size() ) {
858 throw(AipsError("Mask has incorrect number of channels."
859 " Probably varying with IF. Please flag per IF"));
860 }
861 std::vector<bool>::const_iterator it;
862 uInt j = 0;
863 for (it = msk.begin(); it != msk.end(); ++it) {
864 if ( *it ) {
865 flgs(j) = flagval;
866 }
867 ++j;
868 }
869 flagsCol_.put(whichrow, flgs);
870}
871
872void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
873{
874 if ( selector_.empty() && (rows.size() == table_.nrow()) )
875 throw(AipsError("Trying to flag whole scantable."));
876
877 uInt rowflag = (unflag ? 0 : 1);
878 std::vector<uInt>::const_iterator it;
879 for (it = rows.begin(); it != rows.end(); ++it)
880 flagrowCol_.put(*it, rowflag);
881}
882
883std::vector<bool> Scantable::getMask(int whichrow) const
884{
885 Vector<uChar> flags;
886 flagsCol_.get(uInt(whichrow), flags);
887 Vector<Bool> bflag(flags.shape());
888 convertArray(bflag, flags);
889 bflag = !bflag;
890 std::vector<bool> mask;
891 bflag.tovector(mask);
892 return mask;
893}
894
895std::vector<float> Scantable::getSpectrum( int whichrow,
896 const std::string& poltype ) const
897{
898 String ptype = poltype;
899 if (poltype == "" ) ptype = getPolType();
900 if ( whichrow < 0 || whichrow >= nrow() )
901 throw(AipsError("Illegal row number."));
902 std::vector<float> out;
903 Vector<Float> arr;
904 uInt requestedpol = polCol_(whichrow);
905 String basetype = getPolType();
906 if ( ptype == basetype ) {
907 specCol_.get(whichrow, arr);
908 } else {
909 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
910 basetype));
911 uInt row = uInt(whichrow);
912 stpol->setSpectra(getPolMatrix(row));
913 Float fang,fhand;
914 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
915 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
916 stpol->setPhaseCorrections(fang, fhand);
917 arr = stpol->getSpectrum(requestedpol, ptype);
918 }
919 if ( arr.nelements() == 0 )
920 pushLog("Not enough polarisations present to do the conversion.");
921 arr.tovector(out);
922 return out;
923}
924
925void Scantable::setSpectrum( const std::vector<float>& spec,
926 int whichrow )
927{
928 Vector<Float> spectrum(spec);
929 Vector<Float> arr;
930 specCol_.get(whichrow, arr);
931 if ( spectrum.nelements() != arr.nelements() )
932 throw AipsError("The spectrum has incorrect number of channels.");
933 specCol_.put(whichrow, spectrum);
934}
935
936
937String Scantable::generateName()
938{
939 return (File::newUniqueName("./","temp")).baseName();
940}
941
942const casa::Table& Scantable::table( ) const
943{
944 return table_;
945}
946
947casa::Table& Scantable::table( )
948{
949 return table_;
950}
951
952std::string Scantable::getPolType() const
953{
954 return table_.keywordSet().asString("POLTYPE");
955}
956
957void Scantable::unsetSelection()
958{
959 table_ = originalTable_;
960 attach();
961 selector_.reset();
962}
963
964void Scantable::setSelection( const STSelector& selection )
965{
966 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
967 if ( tab.nrow() == 0 ) {
968 throw(AipsError("Selection contains no data. Not applying it."));
969 }
970 table_ = tab;
971 attach();
972// tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
973// vector<uint> selectedIFs = getIFNos() ;
974// Int newnIF = selectedIFs.size() ;
975// tab.rwKeywordSet().define("nIF",newnIF) ;
976// if ( newnIF != 0 ) {
977// Int newnChan = 0 ;
978// for ( Int i = 0 ; i < newnIF ; i++ ) {
979// Int nChan = nchan( selectedIFs[i] ) ;
980// if ( newnChan > nChan )
981// newnChan = nChan ;
982// }
983// tab.rwKeywordSet().define("nChan",newnChan) ;
984// }
985// tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
986 selector_ = selection;
987}
988
989
990std::string Scantable::headerSummary()
991{
992 // Format header info
993// STHeader sdh;
994// sdh = getHeader();
995// sdh.print();
996 ostringstream oss;
997 oss.flags(std::ios_base::left);
998 String tmp;
999 // Project
1000 table_.keywordSet().get("Project", tmp);
1001 oss << setw(15) << "Project:" << tmp << endl;
1002 // Observation date
1003 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1004 // Observer
1005 oss << setw(15) << "Observer:"
1006 << table_.keywordSet().asString("Observer") << endl;
1007 // Antenna Name
1008 table_.keywordSet().get("AntennaName", tmp);
1009 oss << setw(15) << "Antenna Name:" << tmp << endl;
1010 // Obs type
1011 table_.keywordSet().get("Obstype", tmp);
1012 // Records (nrow)
1013 oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl;
1014 oss << setw(15) << "Obs. Type:" << tmp << endl;
1015 // Beams, IFs, Polarizations, and Channels
1016 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1017 << setw(15) << "IFs:" << setw(4) << nif() << endl
1018 << setw(15) << "Polarisations:" << setw(4) << npol()
1019 << "(" << getPolType() << ")" << endl
1020 << setw(15) << "Channels:" << nchan() << endl;
1021 // Flux unit
1022 table_.keywordSet().get("FluxUnit", tmp);
1023 oss << setw(15) << "Flux Unit:" << tmp << endl;
1024 // Abscissa Unit
1025 oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl;
1026 // Selection
1027 oss << selector_.print() << endl;
1028
1029 return String(oss);
1030}
1031
1032void Scantable::summary( const std::string& filename )
1033{
1034 ostringstream oss;
1035 ofstream ofs;
1036 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1037
1038 if (filename != "")
1039 ofs.open( filename.c_str(), ios::out );
1040
1041 oss << endl;
1042 oss << asap::SEPERATOR << endl;
1043 oss << " Scan Table Summary" << endl;
1044 oss << asap::SEPERATOR << endl;
1045
1046 // Format header info
1047 oss << headerSummary();
1048 oss << endl;
1049
1050 if (table_.nrow() <= 0){
1051 oss << asap::SEPERATOR << endl;
1052 oss << "The MAIN table is empty: there are no data!!!" << endl;
1053 oss << asap::SEPERATOR << endl;
1054
1055 ols << String(oss) << LogIO::POST;
1056 if (ofs) {
1057 ofs << String(oss) << flush;
1058 ofs.close();
1059 }
1060 return;
1061 }
1062
1063
1064
1065 // main table
1066 String dirtype = "Position ("
1067 + getDirectionRefString()
1068 + ")";
1069 oss.flags(std::ios_base::left);
1070 oss << setw(5) << "Scan"
1071 << setw(15) << "Source"
1072 << setw(35) << "Time range"
1073 << setw(2) << "" << setw(7) << "Int[s]"
1074 << setw(7) << "Record"
1075 << setw(8) << "SrcType"
1076 << setw(8) << "FreqIDs"
1077 << setw(7) << "MolIDs" << endl;
1078 oss << setw(7)<< "" << setw(6) << "Beam"
1079 << setw(23) << dirtype << endl;
1080
1081 oss << asap::SEPERATOR << endl;
1082
1083 // Flush summary and clear up the string
1084 ols << String(oss) << LogIO::POST;
1085 if (ofs) ofs << String(oss) << flush;
1086 oss.str("");
1087 oss.clear();
1088
1089
1090 // Get Freq_ID map
1091 ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID");
1092 Int nfid = ftabIds.nrow();
1093 if (nfid <= 0){
1094 oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl;
1095 oss << asap::SEPERATOR << endl;
1096
1097 ols << String(oss) << LogIO::POST;
1098 if (ofs) {
1099 ofs << String(oss) << flush;
1100 ofs.close();
1101 }
1102 return;
1103 }
1104 // Storages of overall IFNO, POLNO, and nchan per FREQ_ID
1105 // the orders are identical to ID in FREQ subtable
1106 Block< Vector<uInt> > ifNos(nfid), polNos(nfid);
1107 Vector<Int> fIdchans(nfid,-1);
1108 map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair
1109 for (Int i=0; i < nfid; i++){
1110 // fidMap[freqId] returns row number in FREQ subtable
1111 fidMap.insert(pair<uInt, Int>(ftabIds(i),i));
1112 ifNos[i] = Vector<uInt>();
1113 polNos[i] = Vector<uInt>();
1114 }
1115
1116 TableIterator iter(table_, "SCANNO");
1117
1118 // Vars for keeping track of time, freqids, molIds in a SCANNO
1119 Vector<uInt> freqids;
1120 Vector<uInt> molids;
1121 Vector<uInt> beamids(1,0);
1122 Vector<MDirection> beamDirs;
1123 Vector<Int> stypeids(1,0);
1124 Vector<String> stypestrs;
1125 Int nfreq(1);
1126 Int nmol(1);
1127 uInt nbeam(1);
1128 uInt nstype(1);
1129
1130 Double btime(0.0), etime(0.0);
1131 Double meanIntTim(0.0);
1132
1133 uInt currFreqId(0), ftabRow(0);
1134 Int iflen(0), pollen(0);
1135
1136 while (!iter.pastEnd()) {
1137 Table subt = iter.table();
1138 uInt snrow = subt.nrow();
1139 ROTableRow row(subt);
1140 const TableRecord& rec = row.get(0);
1141
1142 // relevant columns
1143 ROScalarColumn<Double> mjdCol(subt,"TIME");
1144 ROScalarColumn<Double> intervalCol(subt,"INTERVAL");
1145 MDirection::ROScalarColumn dirCol(subt,"DIRECTION");
1146
1147 ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID");
1148 ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID");
1149 ROScalarColumn<uInt> beamCol(subt,"BEAMNO");
1150 ROScalarColumn<Int> stypeCol(subt,"SRCTYPE");
1151
1152 ROScalarColumn<uInt> ifNoCol(subt,"IFNO");
1153 ROScalarColumn<uInt> polNoCol(subt,"POLNO");
1154
1155
1156 // Times
1157 meanIntTim = sum(intervalCol.getColumn()) / (double) snrow;
1158 minMax(btime, etime, mjdCol.getColumn());
1159 etime += meanIntTim/C::day;
1160
1161 // MOLECULE_ID and FREQ_ID
1162 molids = getNumbers(molIdCol);
1163 molids.shape(nmol);
1164
1165 freqids = getNumbers(freqIdCol);
1166 freqids.shape(nfreq);
1167
1168 // Add first beamid, and srcNames
1169 beamids.resize(1,False);
1170 beamDirs.resize(1,False);
1171 beamids(0)=beamCol(0);
1172 beamDirs(0)=dirCol(0);
1173 nbeam = 1;
1174
1175 stypeids.resize(1,False);
1176 stypeids(0)=stypeCol(0);
1177 nstype = 1;
1178
1179 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1180 currFreqId=freqIdCol(0);
1181 ftabRow = fidMap[currFreqId];
1182 // Assumes an identical number of channels per FREQ_ID
1183 if (fIdchans(ftabRow) < 0 ) {
1184 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1185 fIdchans(ftabRow)=(*spec).shape()(0);
1186 }
1187 // Should keep ifNos and polNos form the previous SCANNO
1188 if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) {
1189 ifNos[ftabRow].shape(iflen);
1190 iflen++;
1191 ifNos[ftabRow].resize(iflen,True);
1192 ifNos[ftabRow](iflen-1) = ifNoCol(0);
1193 }
1194 if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) {
1195 polNos[ftabRow].shape(pollen);
1196 pollen++;
1197 polNos[ftabRow].resize(pollen,True);
1198 polNos[ftabRow](pollen-1) = polNoCol(0);
1199 }
1200
1201 for (uInt i=1; i < snrow; i++){
1202 // Need to list BEAMNO and DIRECTION in the same order
1203 if ( !anyEQ(beamids,beamCol(i)) ) {
1204 nbeam++;
1205 beamids.resize(nbeam,True);
1206 beamids(nbeam-1)=beamCol(i);
1207 beamDirs.resize(nbeam,True);
1208 beamDirs(nbeam-1)=dirCol(i);
1209 }
1210
1211 // SRCTYPE is Int (getNumber takes only uInt)
1212 if ( !anyEQ(stypeids,stypeCol(i)) ) {
1213 nstype++;
1214 stypeids.resize(nstype,True);
1215 stypeids(nstype-1)=stypeCol(i);
1216 }
1217
1218 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1219 currFreqId=freqIdCol(i);
1220 ftabRow = fidMap[currFreqId];
1221 if (fIdchans(ftabRow) < 0 ) {
1222 const TableRecord& rec = row.get(i);
1223 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1224 fIdchans(ftabRow) = (*spec).shape()(0);
1225 }
1226 if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) {
1227 ifNos[ftabRow].shape(iflen);
1228 iflen++;
1229 ifNos[ftabRow].resize(iflen,True);
1230 ifNos[ftabRow](iflen-1) = ifNoCol(i);
1231 }
1232 if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) {
1233 polNos[ftabRow].shape(pollen);
1234 pollen++;
1235 polNos[ftabRow].resize(pollen,True);
1236 polNos[ftabRow](pollen-1) = polNoCol(i);
1237 }
1238 } // end of row iteration
1239
1240 stypestrs.resize(nstype,False);
1241 for (uInt j=0; j < nstype; j++)
1242 stypestrs(j) = SrcType::getName(stypeids(j));
1243
1244 // Format Scan summary
1245 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1246 << std::left << setw(1) << ""
1247 << setw(15) << rec.asString("SRCNAME")
1248 << setw(21) << MVTime(btime).string(MVTime::YMD,7)
1249 << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7)
1250 << setw(3) << "" << setw(6) << meanIntTim << setw(1) << ""
1251 << std::right << setw(5) << snrow << setw(2) << ""
1252 << std::left << stypestrs << setw(1) << ""
1253 << freqids << setw(1) << ""
1254 << molids << endl;
1255 // Format Beam summary
1256 for (uInt j=0; j < nbeam; j++) {
1257 oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << ""
1258 << formatDirection(beamDirs(j)) << endl;
1259 }
1260 // Flush summary every scan and clear up the string
1261 ols << String(oss) << LogIO::POST;
1262 if (ofs) ofs << String(oss) << flush;
1263 oss.str("");
1264 oss.clear();
1265
1266 ++iter;
1267 } // end of scan iteration
1268 oss << asap::SEPERATOR << endl;
1269
1270 // List FRECUENCIES Table (using STFrequencies.print may be slow)
1271 oss << "FREQUENCIES: " << nfreq << endl;
1272 oss << std::right << setw(5) << "ID" << setw(2) << ""
1273 << std::left << setw(5) << "IFNO" << setw(2) << ""
1274 << setw(8) << "Frame"
1275 << setw(16) << "RefVal"
1276 << setw(7) << "RefPix"
1277 << setw(15) << "Increment"
1278 << setw(9) << "Channels"
1279 << setw(6) << "POLNOs" << endl;
1280 Int tmplen;
1281 for (Int i=0; i < nfid; i++){
1282 // List row=i of FREQUENCIES subtable
1283 ifNos[i].shape(tmplen);
1284 if (tmplen == 1) {
1285 oss << std::right << setw(5) << ftabIds(i) << setw(2) << ""
1286 << setw(3) << ifNos[i](0) << setw(1) << ""
1287 << std::left << setw(46) << frequencies().print(ftabIds(i))
1288 << setw(2) << ""
1289 << std::right << setw(8) << fIdchans[i] << setw(2) << ""
1290 << std::left << polNos[i] << endl;
1291 } else if (tmplen > 0 ) {
1292 // You shouldn't come here
1293 oss << std::left
1294 << "Multiple IFNOs in FREQ_ID = " << ftabIds(i)
1295 << " !!!" << endl;
1296 }
1297 }
1298 oss << asap::SEPERATOR << endl;
1299
1300 // List MOLECULES Table (currently lists all rows)
1301 oss << "MOLECULES: " << endl;
1302 if (molecules().nrow() <= 0) {
1303 oss << " MOLECULES subtable is empty: there are no data" << endl;
1304 } else {
1305 ROTableRow row(molecules().table());
1306 oss << std::right << setw(5) << "ID"
1307 << std::left << setw(3) << ""
1308 << setw(18) << "RestFreq"
1309 << setw(15) << "Name" << endl;
1310 for (Int i=0; i < molecules().nrow(); i++){
1311 const TableRecord& rec=row.get(i);
1312 oss << std::right << setw(5) << rec.asuInt("ID")
1313 << std::left << setw(3) << ""
1314 << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << ""
1315 << rec.asArrayString("NAME") << endl;
1316 }
1317 }
1318 oss << asap::SEPERATOR << endl;
1319 ols << String(oss) << LogIO::POST;
1320 if (ofs) {
1321 ofs << String(oss) << flush;
1322 ofs.close();
1323 }
1324 // return String(oss);
1325}
1326
1327
1328std::string Scantable::oldheaderSummary()
1329{
1330 // Format header info
1331// STHeader sdh;
1332// sdh = getHeader();
1333// sdh.print();
1334 ostringstream oss;
1335 oss.flags(std::ios_base::left);
1336 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1337 << setw(15) << "IFs:" << setw(4) << nif() << endl
1338 << setw(15) << "Polarisations:" << setw(4) << npol()
1339 << "(" << getPolType() << ")" << endl
1340 << setw(15) << "Channels:" << nchan() << endl;
1341 String tmp;
1342 oss << setw(15) << "Observer:"
1343 << table_.keywordSet().asString("Observer") << endl;
1344 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1345 table_.keywordSet().get("Project", tmp);
1346 oss << setw(15) << "Project:" << tmp << endl;
1347 table_.keywordSet().get("Obstype", tmp);
1348 oss << setw(15) << "Obs. Type:" << tmp << endl;
1349 table_.keywordSet().get("AntennaName", tmp);
1350 oss << setw(15) << "Antenna Name:" << tmp << endl;
1351 table_.keywordSet().get("FluxUnit", tmp);
1352 oss << setw(15) << "Flux Unit:" << tmp << endl;
1353 int nid = moleculeTable_.nrow();
1354 Bool firstline = True;
1355 oss << setw(15) << "Rest Freqs:";
1356 for (int i=0; i<nid; i++) {
1357 Table t = table_(table_.col("MOLECULE_ID") == i, 1);
1358 if (t.nrow() > 0) {
1359 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
1360 if (vec.nelements() > 0) {
1361 if (firstline) {
1362 oss << setprecision(10) << vec << " [Hz]" << endl;
1363 firstline=False;
1364 }
1365 else{
1366 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1367 }
1368 } else {
1369 oss << "none" << endl;
1370 }
1371 }
1372 }
1373
1374 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
1375 oss << selector_.print() << endl;
1376 return String(oss);
1377}
1378
1379 //std::string Scantable::summary( const std::string& filename )
1380void Scantable::oldsummary( const std::string& filename )
1381{
1382 ostringstream oss;
1383 ofstream ofs;
1384 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1385
1386 if (filename != "")
1387 ofs.open( filename.c_str(), ios::out );
1388
1389 oss << endl;
1390 oss << asap::SEPERATOR << endl;
1391 oss << " Scan Table Summary" << endl;
1392 oss << asap::SEPERATOR << endl;
1393
1394 // Format header info
1395 oss << oldheaderSummary();
1396 oss << endl;
1397
1398 // main table
1399 String dirtype = "Position ("
1400 + getDirectionRefString()
1401 + ")";
1402 oss.flags(std::ios_base::left);
1403 oss << setw(5) << "Scan" << setw(15) << "Source"
1404 << setw(10) << "Time" << setw(18) << "Integration"
1405 << setw(15) << "Source Type" << endl;
1406 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
1407 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
1408 << setw(8) << "Frame" << setw(16)
1409 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1410 << setw(7) << "Channels"
1411 << endl;
1412 oss << asap::SEPERATOR << endl;
1413
1414 // Flush summary and clear up the string
1415 ols << String(oss) << LogIO::POST;
1416 if (ofs) ofs << String(oss) << flush;
1417 oss.str("");
1418 oss.clear();
1419
1420 TableIterator iter(table_, "SCANNO");
1421 while (!iter.pastEnd()) {
1422 Table subt = iter.table();
1423 ROTableRow row(subt);
1424 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1425 const TableRecord& rec = row.get(0);
1426 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1427 << std::left << setw(1) << ""
1428 << setw(15) << rec.asString("SRCNAME")
1429 << setw(10) << formatTime(timeCol(0), false);
1430 // count the cycles in the scan
1431 TableIterator cyciter(subt, "CYCLENO");
1432 int nint = 0;
1433 while (!cyciter.pastEnd()) {
1434 ++nint;
1435 ++cyciter;
1436 }
1437 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
1438 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1439 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
1440
1441 TableIterator biter(subt, "BEAMNO");
1442 while (!biter.pastEnd()) {
1443 Table bsubt = biter.table();
1444 ROTableRow brow(bsubt);
1445 const TableRecord& brec = brow.get(0);
1446 uInt row0 = bsubt.rowNumbers(table_)[0];
1447 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
1448 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
1449 TableIterator iiter(bsubt, "IFNO");
1450 while (!iiter.pastEnd()) {
1451 Table isubt = iiter.table();
1452 ROTableRow irow(isubt);
1453 const TableRecord& irec = irow.get(0);
1454 oss << setw(9) << "";
1455 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
1456 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1457 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
1458 << endl;
1459
1460 ++iiter;
1461 }
1462 ++biter;
1463 }
1464 // Flush summary every scan and clear up the string
1465 ols << String(oss) << LogIO::POST;
1466 if (ofs) ofs << String(oss) << flush;
1467 oss.str("");
1468 oss.clear();
1469
1470 ++iter;
1471 }
1472 oss << asap::SEPERATOR << endl;
1473 ols << String(oss) << LogIO::POST;
1474 if (ofs) {
1475 ofs << String(oss) << flush;
1476 ofs.close();
1477 }
1478 // return String(oss);
1479}
1480
1481// std::string Scantable::getTime(int whichrow, bool showdate) const
1482// {
1483// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1484// MEpoch me;
1485// if (whichrow > -1) {
1486// me = timeCol(uInt(whichrow));
1487// } else {
1488// Double tm;
1489// table_.keywordSet().get("UTC",tm);
1490// me = MEpoch(MVEpoch(tm));
1491// }
1492// return formatTime(me, showdate);
1493// }
1494
1495std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
1496{
1497 MEpoch me;
1498 me = getEpoch(whichrow);
1499 return formatTime(me, showdate, prec);
1500}
1501
1502MEpoch Scantable::getEpoch(int whichrow) const
1503{
1504 if (whichrow > -1) {
1505 return timeCol_(uInt(whichrow));
1506 } else {
1507 Double tm;
1508 table_.keywordSet().get("UTC",tm);
1509 return MEpoch(MVEpoch(tm));
1510 }
1511}
1512
1513std::string Scantable::getDirectionString(int whichrow) const
1514{
1515 return formatDirection(getDirection(uInt(whichrow)));
1516}
1517
1518
1519SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1520 const MPosition& mp = getAntennaPosition();
1521 const MDirection& md = getDirection(whichrow);
1522 const MEpoch& me = timeCol_(whichrow);
1523 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1524 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1525 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
1526 mfreqidCol_(whichrow));
1527}
1528
1529std::vector< double > Scantable::getAbcissa( int whichrow ) const
1530{
1531 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
1532 std::vector<double> stlout;
1533 int nchan = specCol_(whichrow).nelements();
1534 String us = freqTable_.getUnitString();
1535 if ( us == "" || us == "pixel" || us == "channel" ) {
1536 for (int i=0; i<nchan; ++i) {
1537 stlout.push_back(double(i));
1538 }
1539 return stlout;
1540 }
1541 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
1542 Vector<Double> pixel(nchan);
1543 Vector<Double> world;
1544 indgen(pixel);
1545 if ( Unit(us) == Unit("Hz") ) {
1546 for ( int i=0; i < nchan; ++i) {
1547 Double world;
1548 spc.toWorld(world, pixel[i]);
1549 stlout.push_back(double(world));
1550 }
1551 } else if ( Unit(us) == Unit("km/s") ) {
1552 Vector<Double> world;
1553 spc.pixelToVelocity(world, pixel);
1554 world.tovector(stlout);
1555 }
1556 return stlout;
1557}
1558void Scantable::setDirectionRefString( const std::string & refstr )
1559{
1560 MDirection::Types mdt;
1561 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1562 throw(AipsError("Illegal Direction frame."));
1563 }
1564 if ( refstr == "" ) {
1565 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1566 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1567 } else {
1568 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1569 }
1570}
1571
1572std::string Scantable::getDirectionRefString( ) const
1573{
1574 return table_.keywordSet().asString("DIRECTIONREF");
1575}
1576
1577MDirection Scantable::getDirection(int whichrow ) const
1578{
1579 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1580 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1581 if ( usertype != type ) {
1582 MDirection::Types mdt;
1583 if (!MDirection::getType(mdt, usertype)) {
1584 throw(AipsError("Illegal Direction frame."));
1585 }
1586 return dirCol_.convert(uInt(whichrow), mdt);
1587 } else {
1588 return dirCol_(uInt(whichrow));
1589 }
1590}
1591
1592std::string Scantable::getAbcissaLabel( int whichrow ) const
1593{
1594 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
1595 const MPosition& mp = getAntennaPosition();
1596 const MDirection& md = getDirection(whichrow);
1597 const MEpoch& me = timeCol_(whichrow);
1598 //const Double& rf = mmolidCol_(whichrow);
1599 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1600 SpectralCoordinate spc =
1601 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
1602
1603 String s = "Channel";
1604 Unit u = Unit(freqTable_.getUnitString());
1605 if (u == Unit("km/s")) {
1606 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
1607 } else if (u == Unit("Hz")) {
1608 Vector<String> wau(1);wau = u.getName();
1609 spc.setWorldAxisUnits(wau);
1610 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
1611 }
1612 return s;
1613
1614}
1615
1616/**
1617void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
1618 const std::string& unit )
1619**/
1620void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1621 const std::string& unit )
1622
1623{
1624 ///@todo lookup in line table to fill in name and formattedname
1625 Unit u(unit);
1626 //Quantum<Double> urf(rf, u);
1627 Quantum<Vector<Double> >urf(rf, u);
1628 Vector<String> formattedname(0);
1629 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1630
1631 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1632 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
1633 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1634 tabvec = id;
1635}
1636
1637/**
1638void asap::Scantable::setRestFrequencies( const std::string& name )
1639{
1640 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1641 ///@todo implement
1642}
1643**/
1644
1645void Scantable::setRestFrequencies( const vector<std::string>& name )
1646{
1647 (void) name; // suppress unused warning
1648 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1649 ///@todo implement
1650}
1651
1652std::vector< unsigned int > Scantable::rownumbers( ) const
1653{
1654 std::vector<unsigned int> stlout;
1655 Vector<uInt> vec = table_.rowNumbers();
1656 vec.tovector(stlout);
1657 return stlout;
1658}
1659
1660
1661Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
1662{
1663 ROTableRow row(table_);
1664 const TableRecord& rec = row.get(whichrow);
1665 Table t =
1666 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1667 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1668 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1669 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1670 ROArrayColumn<Float> speccol(t, "SPECTRA");
1671 return speccol.getColumn();
1672}
1673
1674std::vector< std::string > Scantable::columnNames( ) const
1675{
1676 Vector<String> vec = table_.tableDesc().columnNames();
1677 return mathutil::tovectorstring(vec);
1678}
1679
1680MEpoch::Types Scantable::getTimeReference( ) const
1681{
1682 return MEpoch::castType(timeCol_.getMeasRef().getType());
1683}
1684
1685void Scantable::addFit( const STFitEntry& fit, int row )
1686{
1687 //cout << mfitidCol_(uInt(row)) << endl;
1688 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1689 os << mfitidCol_(uInt(row)) << LogIO::POST ;
1690 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1691 mfitidCol_.put(uInt(row), id);
1692}
1693
1694void Scantable::shift(int npix)
1695{
1696 Vector<uInt> fids(mfreqidCol_.getColumn());
1697 genSort( fids, Sort::Ascending,
1698 Sort::QuickSort|Sort::NoDuplicates );
1699 for (uInt i=0; i<fids.nelements(); ++i) {
1700 frequencies().shiftRefPix(npix, fids[i]);
1701 }
1702}
1703
1704String Scantable::getAntennaName() const
1705{
1706 String out;
1707 table_.keywordSet().get("AntennaName", out);
1708 String::size_type pos1 = out.find("@") ;
1709 String::size_type pos2 = out.find("//") ;
1710 if ( pos2 != String::npos )
1711 out = out.substr(pos2+2,pos1-pos2-2) ;
1712 else if ( pos1 != String::npos )
1713 out = out.substr(0,pos1) ;
1714 return out;
1715}
1716
1717int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
1718{
1719 String tbpath;
1720 int ret = 0;
1721 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1722 table_.keywordSet().get("GBT_GO", tbpath);
1723 Table t(tbpath,Table::Old);
1724 // check each scan if other scan of the pair exist
1725 int nscan = scanlist.size();
1726 for (int i = 0; i < nscan; i++) {
1727 Table subt = t( t.col("SCAN") == scanlist[i]+1 );
1728 if (subt.nrow()==0) {
1729 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1730 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1731 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
1732 ret = 1;
1733 break;
1734 }
1735 ROTableRow row(subt);
1736 const TableRecord& rec = row.get(0);
1737 int scan1seqn = rec.asuInt("PROCSEQN");
1738 int laston1 = rec.asuInt("LASTON");
1739 if ( rec.asuInt("PROCSIZE")==2 ) {
1740 if ( i < nscan-1 ) {
1741 Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
1742 if ( subt2.nrow() == 0) {
1743 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1744
1745 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1746 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
1747 ret = 1;
1748 break;
1749 }
1750 ROTableRow row2(subt2);
1751 const TableRecord& rec2 = row2.get(0);
1752 int scan2seqn = rec2.asuInt("PROCSEQN");
1753 int laston2 = rec2.asuInt("LASTON");
1754 if (scan1seqn == 1 && scan2seqn == 2) {
1755 if (laston1 == laston2) {
1756 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1757 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1758 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1759 i +=1;
1760 }
1761 else {
1762 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1763 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1764 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1765 }
1766 }
1767 else if (scan1seqn==2 && scan2seqn == 1) {
1768 if (laston1 == laston2) {
1769 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1770 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1771 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
1772 ret = 1;
1773 break;
1774 }
1775 }
1776 else {
1777 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1778 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1779 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
1780 ret = 1;
1781 break;
1782 }
1783 }
1784 }
1785 else {
1786 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1787 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1788 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
1789 }
1790 //if ( i >= nscan ) break;
1791 }
1792 }
1793 else {
1794 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1795 //cerr<<"No reference to GBT_GO table."<<endl;
1796 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
1797 ret = 1;
1798 }
1799 return ret;
1800}
1801
1802std::vector<double> Scantable::getDirectionVector(int whichrow) const
1803{
1804 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1805 std::vector<double> dir;
1806 Dir.tovector(dir);
1807 return dir;
1808}
1809
1810void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1811 throw( casa::AipsError )
1812{
1813 // assumed that all rows have same nChan
1814 Vector<Float> arr = specCol_( 0 ) ;
1815 int nChan = arr.nelements() ;
1816
1817 // if nmin < 0 or nmax < 0, nothing to do
1818 if ( nmin < 0 ) {
1819 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1820 }
1821 if ( nmax < 0 ) {
1822 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1823 }
1824
1825 // if nmin > nmax, exchange values
1826 if ( nmin > nmax ) {
1827 int tmp = nmax ;
1828 nmax = nmin ;
1829 nmin = tmp ;
1830 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1831 os << "Swap values. Applied range is ["
1832 << nmin << ", " << nmax << "]" << LogIO::POST ;
1833 }
1834
1835 // if nmin exceeds nChan, nothing to do
1836 if ( nmin >= nChan ) {
1837 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1838 }
1839
1840 // if nmax exceeds nChan, reset nmax to nChan
1841 if ( nmax >= nChan ) {
1842 if ( nmin == 0 ) {
1843 // nothing to do
1844 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1845 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1846 return ;
1847 }
1848 else {
1849 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1850 os << "Specified maximum exceeds nChan. Applied range is ["
1851 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1852 nmax = nChan - 1 ;
1853 }
1854 }
1855
1856 // reshape specCol_ and flagCol_
1857 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1858 reshapeSpectrum( nmin, nmax, irow ) ;
1859 }
1860
1861 // update FREQUENCIES subtable
1862 Double refpix ;
1863 Double refval ;
1864 Double increment ;
1865 int freqnrow = freqTable_.table().nrow() ;
1866 Vector<uInt> oldId( freqnrow ) ;
1867 Vector<uInt> newId( freqnrow ) ;
1868 for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
1869 freqTable_.getEntry( refpix, refval, increment, irow ) ;
1870 /***
1871 * need to shift refpix to nmin
1872 * note that channel nmin in old index will be channel 0 in new one
1873 ***/
1874 refval = refval - ( refpix - nmin ) * increment ;
1875 refpix = 0 ;
1876 freqTable_.setEntry( refpix, refval, increment, irow ) ;
1877 }
1878
1879 // update nchan
1880 int newsize = nmax - nmin + 1 ;
1881 table_.rwKeywordSet().define( "nChan", newsize ) ;
1882
1883 // update bandwidth
1884 // assumed all spectra in the scantable have same bandwidth
1885 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1886
1887 return ;
1888}
1889
1890void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1891{
1892 // reshape specCol_ and flagCol_
1893 Vector<Float> oldspec = specCol_( irow ) ;
1894 Vector<uChar> oldflag = flagsCol_( irow ) ;
1895 uInt newsize = nmax - nmin + 1 ;
1896 specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ;
1897 flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ;
1898
1899 return ;
1900}
1901
1902void asap::Scantable::regridChannel( int nChan, double dnu )
1903{
1904 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1905 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
1906 // assumed that all rows have same nChan
1907 Vector<Float> arr = specCol_( 0 ) ;
1908 int oldsize = arr.nelements() ;
1909
1910 // if oldsize == nChan, nothing to do
1911 if ( oldsize == nChan ) {
1912 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
1913 return ;
1914 }
1915
1916 // if oldChan < nChan, unphysical operation
1917 if ( oldsize < nChan ) {
1918 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
1919 return ;
1920 }
1921
1922 // change channel number for specCol_ and flagCol_
1923 Vector<Float> newspec( nChan, 0 ) ;
1924 Vector<uChar> newflag( nChan, false ) ;
1925 vector<string> coordinfo = getCoordInfo() ;
1926 string oldinfo = coordinfo[0] ;
1927 coordinfo[0] = "Hz" ;
1928 setCoordInfo( coordinfo ) ;
1929 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1930 regridChannel( nChan, dnu, irow ) ;
1931 }
1932 coordinfo[0] = oldinfo ;
1933 setCoordInfo( coordinfo ) ;
1934
1935
1936 // NOTE: this method does not update metadata such as
1937 // FREQUENCIES subtable, nChan, Bandwidth, etc.
1938
1939 return ;
1940}
1941
1942void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
1943{
1944 // logging
1945 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
1946 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
1947
1948 Vector<Float> oldspec = specCol_( irow ) ;
1949 Vector<uChar> oldflag = flagsCol_( irow ) ;
1950 Vector<Float> newspec( nChan, 0 ) ;
1951 Vector<uChar> newflag( nChan, false ) ;
1952
1953 // regrid
1954 vector<double> abcissa = getAbcissa( irow ) ;
1955 int oldsize = abcissa.size() ;
1956 double olddnu = abcissa[1] - abcissa[0] ;
1957 //int refChan = 0 ;
1958 //double frac = 0.0 ;
1959 //double wedge = 0.0 ;
1960 //double pile = 0.0 ;
1961 int ichan = 0 ;
1962 double wsum = 0.0 ;
1963 Vector<Float> zi( nChan+1 ) ;
1964 Vector<Float> yi( oldsize + 1 ) ;
1965 zi[0] = abcissa[0] - 0.5 * olddnu ;
1966 zi[1] = zi[1] + dnu ;
1967 for ( int ii = 2 ; ii < nChan ; ii++ )
1968 zi[ii] = zi[0] + dnu * ii ;
1969 zi[nChan] = zi[nChan-1] + dnu ;
1970 yi[0] = abcissa[0] - 0.5 * olddnu ;
1971 yi[1] = abcissa[1] + 0.5 * olddnu ;
1972 for ( int ii = 2 ; ii < oldsize ; ii++ )
1973 yi[ii] = abcissa[ii-1] + olddnu ;
1974 yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ;
1975 if ( dnu > 0.0 ) {
1976 for ( int ii = 0 ; ii < nChan ; ii++ ) {
1977 double zl = zi[ii] ;
1978 double zr = zi[ii+1] ;
1979 for ( int j = ichan ; j < oldsize ; j++ ) {
1980 double yl = yi[j] ;
1981 double yr = yi[j+1] ;
1982 if ( yl <= zl ) {
1983 if ( yr <= zl ) {
1984 continue ;
1985 }
1986 else if ( yr <= zr ) {
1987 newspec[ii] += oldspec[j] * ( yr - zl ) ;
1988 newflag[ii] = newflag[ii] || oldflag[j] ;
1989 wsum += ( yr - zl ) ;
1990 }
1991 else {
1992 newspec[ii] += oldspec[j] * dnu ;
1993 newflag[ii] = newflag[ii] || oldflag[j] ;
1994 wsum += dnu ;
1995 ichan = j ;
1996 break ;
1997 }
1998 }
1999 else if ( yl < zr ) {
2000 if ( yr <= zr ) {
2001 newspec[ii] += oldspec[j] * ( yr - yl ) ;
2002 newflag[ii] = newflag[ii] || oldflag[j] ;
2003 wsum += ( yr - yl ) ;
2004 }
2005 else {
2006 newspec[ii] += oldspec[j] * ( zr - yl ) ;
2007 newflag[ii] = newflag[ii] || oldflag[j] ;
2008 wsum += ( zr - yl ) ;
2009 ichan = j ;
2010 break ;
2011 }
2012 }
2013 else {
2014 ichan = j - 1 ;
2015 break ;
2016 }
2017 }
2018 if ( wsum != 0.0 )
2019 newspec[ii] /= wsum ;
2020 wsum = 0.0 ;
2021 }
2022 }
2023 else if ( dnu < 0.0 ) {
2024 for ( int ii = 0 ; ii < nChan ; ii++ ) {
2025 double zl = zi[ii] ;
2026 double zr = zi[ii+1] ;
2027 for ( int j = ichan ; j < oldsize ; j++ ) {
2028 double yl = yi[j] ;
2029 double yr = yi[j+1] ;
2030 if ( yl >= zl ) {
2031 if ( yr >= zl ) {
2032 continue ;
2033 }
2034 else if ( yr >= zr ) {
2035 newspec[ii] += oldspec[j] * abs( yr - zl ) ;
2036 newflag[ii] = newflag[ii] || oldflag[j] ;
2037 wsum += abs( yr - zl ) ;
2038 }
2039 else {
2040 newspec[ii] += oldspec[j] * abs( dnu ) ;
2041 newflag[ii] = newflag[ii] || oldflag[j] ;
2042 wsum += abs( dnu ) ;
2043 ichan = j ;
2044 break ;
2045 }
2046 }
2047 else if ( yl > zr ) {
2048 if ( yr >= zr ) {
2049 newspec[ii] += oldspec[j] * abs( yr - yl ) ;
2050 newflag[ii] = newflag[ii] || oldflag[j] ;
2051 wsum += abs( yr - yl ) ;
2052 }
2053 else {
2054 newspec[ii] += oldspec[j] * abs( zr - yl ) ;
2055 newflag[ii] = newflag[ii] || oldflag[j] ;
2056 wsum += abs( zr - yl ) ;
2057 ichan = j ;
2058 break ;
2059 }
2060 }
2061 else {
2062 ichan = j - 1 ;
2063 break ;
2064 }
2065 }
2066 if ( wsum != 0.0 )
2067 newspec[ii] /= wsum ;
2068 wsum = 0.0 ;
2069 }
2070 }
2071// * ichan = 0
2072// ***/
2073// //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
2074// pile += dnu ;
2075// wedge = olddnu * ( refChan + 1 ) ;
2076// while ( wedge < pile ) {
2077// newspec[0] += olddnu * oldspec[refChan] ;
2078// newflag[0] = newflag[0] || oldflag[refChan] ;
2079// //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
2080// refChan++ ;
2081// wedge += olddnu ;
2082// wsum += olddnu ;
2083// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2084// }
2085// frac = ( wedge - pile ) / olddnu ;
2086// wsum += ( 1.0 - frac ) * olddnu ;
2087// newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2088// newflag[0] = newflag[0] || oldflag[refChan] ;
2089// //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
2090// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2091// newspec[0] /= wsum ;
2092// //ofs << "newspec[0] = " << newspec[0] << endl ;
2093// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2094
2095// /***
2096// * ichan = 1 - nChan-2
2097// ***/
2098// for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
2099// pile += dnu ;
2100// newspec[ichan] += frac * olddnu * oldspec[refChan] ;
2101// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2102// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
2103// refChan++ ;
2104// wedge += olddnu ;
2105// wsum = frac * olddnu ;
2106// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2107// while ( wedge < pile ) {
2108// newspec[ichan] += olddnu * oldspec[refChan] ;
2109// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2110// //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
2111// refChan++ ;
2112// wedge += olddnu ;
2113// wsum += olddnu ;
2114// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2115// }
2116// frac = ( wedge - pile ) / olddnu ;
2117// wsum += ( 1.0 - frac ) * olddnu ;
2118// newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2119// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2120// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
2121// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2122// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2123// newspec[ichan] /= wsum ;
2124// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
2125// }
2126
2127// /***
2128// * ichan = nChan-1
2129// ***/
2130// // NOTE: Assumed that all spectra have the same bandwidth
2131// pile += dnu ;
2132// newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
2133// newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
2134// //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2135// refChan++ ;
2136// wedge += olddnu ;
2137// wsum = frac * olddnu ;
2138// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2139// for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
2140// newspec[nChan-1] += olddnu * oldspec[jchan] ;
2141// newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
2142// wsum += olddnu ;
2143// //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2144// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2145// }
2146// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2147// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2148// newspec[nChan-1] /= wsum ;
2149// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
2150
2151// // ofs.close() ;
2152
2153 specCol_.put( irow, newspec ) ;
2154 flagsCol_.put( irow, newflag ) ;
2155
2156 return ;
2157}
2158
2159std::vector<float> Scantable::getWeather(int whichrow) const
2160{
2161 std::vector<float> out(5);
2162 //Float temperature, pressure, humidity, windspeed, windaz;
2163 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
2164 mweatheridCol_(uInt(whichrow)));
2165
2166
2167 return out;
2168}
2169
2170bool Scantable::getFlagtraFast(uInt whichrow)
2171{
2172 uChar flag;
2173 Vector<uChar> flags;
2174 flagsCol_.get(whichrow, flags);
2175 flag = flags[0];
2176 for (uInt i = 1; i < flags.size(); ++i) {
2177 flag &= flags[i];
2178 }
2179 return ((flag >> 7) == 1);
2180}
2181
2182void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2183{
2184 try {
2185 ofstream ofs;
2186 String coordInfo = "";
2187 bool hasSameNchan = true;
2188 bool outTextFile = false;
2189
2190 if (blfile != "") {
2191 ofs.open(blfile.c_str(), ios::out | ios::app);
2192 if (ofs) outTextFile = true;
2193 }
2194
2195 if (outLogger || outTextFile) {
2196 coordInfo = getCoordInfo()[0];
2197 if (coordInfo == "") coordInfo = "channel";
2198 hasSameNchan = hasSameNchanOverIFs();
2199 }
2200
2201 Fitter fitter = Fitter();
2202 fitter.setExpression("poly", order);
2203 //fitter.setIterClipping(thresClip, nIterClip);
2204
2205 int nRow = nrow();
2206 std::vector<bool> chanMask;
2207 bool showProgress;
2208 int minNRow;
2209 parseProgressInfo(progressInfo, showProgress, minNRow);
2210
2211 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2212 chanMask = getCompositeChanMask(whichrow, mask);
2213 fitBaseline(chanMask, whichrow, fitter);
2214 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2215 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
2216 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2217 }
2218
2219 if (outTextFile) ofs.close();
2220
2221 } catch (...) {
2222 throw;
2223 }
2224}
2225
2226void 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)
2227{
2228 try {
2229 ofstream ofs;
2230 String coordInfo = "";
2231 bool hasSameNchan = true;
2232 bool outTextFile = false;
2233
2234 if (blfile != "") {
2235 ofs.open(blfile.c_str(), ios::out | ios::app);
2236 if (ofs) outTextFile = true;
2237 }
2238
2239 if (outLogger || outTextFile) {
2240 coordInfo = getCoordInfo()[0];
2241 if (coordInfo == "") coordInfo = "channel";
2242 hasSameNchan = hasSameNchanOverIFs();
2243 }
2244
2245 Fitter fitter = Fitter();
2246 fitter.setExpression("poly", order);
2247 //fitter.setIterClipping(thresClip, nIterClip);
2248
2249 int nRow = nrow();
2250 std::vector<bool> chanMask;
2251 int minEdgeSize = getIFNos().size()*2;
2252 STLineFinder lineFinder = STLineFinder();
2253 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2254
2255 bool showProgress;
2256 int minNRow;
2257 parseProgressInfo(progressInfo, showProgress, minNRow);
2258
2259 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2260
2261 //-------------------------------------------------------
2262 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2263 //-------------------------------------------------------
2264 int edgeSize = edge.size();
2265 std::vector<int> currentEdge;
2266 if (edgeSize >= 2) {
2267 int idx = 0;
2268 if (edgeSize > 2) {
2269 if (edgeSize < minEdgeSize) {
2270 throw(AipsError("Length of edge element info is less than that of IFs"));
2271 }
2272 idx = 2 * getIF(whichrow);
2273 }
2274 currentEdge.push_back(edge[idx]);
2275 currentEdge.push_back(edge[idx+1]);
2276 } else {
2277 throw(AipsError("Wrong length of edge element"));
2278 }
2279 lineFinder.setData(getSpectrum(whichrow));
2280 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2281 chanMask = lineFinder.getMask();
2282 //-------------------------------------------------------
2283
2284 fitBaseline(chanMask, whichrow, fitter);
2285 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2286
2287 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
2288 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2289 }
2290
2291 if (outTextFile) ofs.close();
2292
2293 } catch (...) {
2294 throw;
2295 }
2296}
2297
2298void 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)
2299{
2300 try {
2301 ofstream ofs;
2302 String coordInfo = "";
2303 bool hasSameNchan = true;
2304 bool outTextFile = false;
2305
2306 if (blfile != "") {
2307 ofs.open(blfile.c_str(), ios::out | ios::app);
2308 if (ofs) outTextFile = true;
2309 }
2310
2311 if (outLogger || outTextFile) {
2312 coordInfo = getCoordInfo()[0];
2313 if (coordInfo == "") coordInfo = "channel";
2314 hasSameNchan = hasSameNchanOverIFs();
2315 }
2316
2317 //Fitter fitter = Fitter();
2318 //fitter.setExpression("cspline", nPiece);
2319 //fitter.setIterClipping(thresClip, nIterClip);
2320
2321 int nRow = nrow();
2322 std::vector<bool> chanMask;
2323 bool showProgress;
2324 int minNRow;
2325 parseProgressInfo(progressInfo, showProgress, minNRow);
2326
2327 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2328 chanMask = getCompositeChanMask(whichrow, mask);
2329 //fitBaseline(chanMask, whichrow, fitter);
2330 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2331 std::vector<int> pieceEdges;
2332 std::vector<float> params;
2333 int nClipped = 0;
2334 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2335 setSpectrum(res, whichrow);
2336 //
2337
2338 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
2339 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2340 }
2341
2342 if (outTextFile) ofs.close();
2343
2344 } catch (...) {
2345 throw;
2346 }
2347}
2348
2349void 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)
2350{
2351 try {
2352 ofstream ofs;
2353 String coordInfo = "";
2354 bool hasSameNchan = true;
2355 bool outTextFile = false;
2356
2357 if (blfile != "") {
2358 ofs.open(blfile.c_str(), ios::out | ios::app);
2359 if (ofs) outTextFile = true;
2360 }
2361
2362 if (outLogger || outTextFile) {
2363 coordInfo = getCoordInfo()[0];
2364 if (coordInfo == "") coordInfo = "channel";
2365 hasSameNchan = hasSameNchanOverIFs();
2366 }
2367
2368 //Fitter fitter = Fitter();
2369 //fitter.setExpression("cspline", nPiece);
2370 //fitter.setIterClipping(thresClip, nIterClip);
2371
2372 int nRow = nrow();
2373 std::vector<bool> chanMask;
2374 int minEdgeSize = getIFNos().size()*2;
2375 STLineFinder lineFinder = STLineFinder();
2376 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2377
2378 bool showProgress;
2379 int minNRow;
2380 parseProgressInfo(progressInfo, showProgress, minNRow);
2381
2382 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2383
2384 //-------------------------------------------------------
2385 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2386 //-------------------------------------------------------
2387 int edgeSize = edge.size();
2388 std::vector<int> currentEdge;
2389 if (edgeSize >= 2) {
2390 int idx = 0;
2391 if (edgeSize > 2) {
2392 if (edgeSize < minEdgeSize) {
2393 throw(AipsError("Length of edge element info is less than that of IFs"));
2394 }
2395 idx = 2 * getIF(whichrow);
2396 }
2397 currentEdge.push_back(edge[idx]);
2398 currentEdge.push_back(edge[idx+1]);
2399 } else {
2400 throw(AipsError("Wrong length of edge element"));
2401 }
2402 lineFinder.setData(getSpectrum(whichrow));
2403 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2404 chanMask = lineFinder.getMask();
2405 //-------------------------------------------------------
2406
2407
2408 //fitBaseline(chanMask, whichrow, fitter);
2409 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2410 std::vector<int> pieceEdges;
2411 std::vector<float> params;
2412 int nClipped = 0;
2413 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2414 setSpectrum(res, whichrow);
2415 //
2416
2417 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
2418 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2419 }
2420
2421 if (outTextFile) ofs.close();
2422
2423 } catch (...) {
2424 throw;
2425 }
2426}
2427
2428std::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)
2429{
2430 if (data.size() != mask.size()) {
2431 throw(AipsError("data and mask sizes are not identical"));
2432 }
2433 if (nPiece < 1) {
2434 throw(AipsError("number of the sections must be one or more"));
2435 }
2436
2437 int nChan = data.size();
2438 std::vector<int> maskArray;
2439 std::vector<int> x;
2440 for (int i = 0; i < nChan; ++i) {
2441 maskArray.push_back(mask[i] ? 1 : 0);
2442 if (mask[i]) {
2443 x.push_back(i);
2444 }
2445 }
2446
2447 int initNData = x.size();
2448 if (initNData < nPiece) {
2449 throw(AipsError("too few non-flagged channels"));
2450 }
2451
2452 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
2453 std::vector<double> invEdge;
2454 idxEdge.clear();
2455 idxEdge.push_back(x[0]);
2456 for (int i = 1; i < nPiece; ++i) {
2457 int valX = x[nElement*i];
2458 idxEdge.push_back(valX);
2459 invEdge.push_back(1.0/(double)valX);
2460 }
2461 idxEdge.push_back(x[x.size()-1]+1);
2462
2463 int nData = initNData;
2464 int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
2465
2466 std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1, residual;
2467 for (int i = 0; i < nChan; ++i) {
2468 double di = (double)i;
2469 double dD = (double)data[i];
2470 x1.push_back(di);
2471 x2.push_back(di*di);
2472 x3.push_back(di*di*di);
2473 z1.push_back(dD);
2474 x1z1.push_back(dD*di);
2475 x2z1.push_back(dD*di*di);
2476 x3z1.push_back(dD*di*di*di);
2477 r1.push_back(0.0);
2478 residual.push_back(0.0);
2479 }
2480
2481 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
2482 // xMatrix : horizontal concatenation of
2483 // the least-sq. matrix (left) and an
2484 // identity matrix (right).
2485 // the right part is used to calculate the inverse matrix of the left part.
2486 double xMatrix[nDOF][2*nDOF];
2487 double zMatrix[nDOF];
2488 for (int i = 0; i < nDOF; ++i) {
2489 for (int j = 0; j < 2*nDOF; ++j) {
2490 xMatrix[i][j] = 0.0;
2491 }
2492 xMatrix[i][nDOF+i] = 1.0;
2493 zMatrix[i] = 0.0;
2494 }
2495
2496 for (int n = 0; n < nPiece; ++n) {
2497 int nUseDataInPiece = 0;
2498 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2499
2500 if (maskArray[i] == 0) continue;
2501
2502 xMatrix[0][0] += 1.0;
2503 xMatrix[0][1] += x1[i];
2504 xMatrix[0][2] += x2[i];
2505 xMatrix[0][3] += x3[i];
2506 xMatrix[1][1] += x2[i];
2507 xMatrix[1][2] += x3[i];
2508 xMatrix[1][3] += x2[i]*x2[i];
2509 xMatrix[2][2] += x2[i]*x2[i];
2510 xMatrix[2][3] += x3[i]*x2[i];
2511 xMatrix[3][3] += x3[i]*x3[i];
2512 zMatrix[0] += z1[i];
2513 zMatrix[1] += x1z1[i];
2514 zMatrix[2] += x2z1[i];
2515 zMatrix[3] += x3z1[i];
2516
2517 for (int j = 0; j < n; ++j) {
2518 double q = 1.0 - x1[i]*invEdge[j];
2519 q = q*q*q;
2520 xMatrix[0][j+4] += q;
2521 xMatrix[1][j+4] += q*x1[i];
2522 xMatrix[2][j+4] += q*x2[i];
2523 xMatrix[3][j+4] += q*x3[i];
2524 for (int k = 0; k < j; ++k) {
2525 double r = 1.0 - x1[i]*invEdge[k];
2526 r = r*r*r;
2527 xMatrix[k+4][j+4] += r*q;
2528 }
2529 xMatrix[j+4][j+4] += q*q;
2530 zMatrix[j+4] += q*z1[i];
2531 }
2532
2533 nUseDataInPiece++;
2534 }
2535
2536 if (nUseDataInPiece < 1) {
2537 std::vector<string> suffixOfPieceNumber(4);
2538 suffixOfPieceNumber[0] = "th";
2539 suffixOfPieceNumber[1] = "st";
2540 suffixOfPieceNumber[2] = "nd";
2541 suffixOfPieceNumber[3] = "rd";
2542 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
2543 ostringstream oss;
2544 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
2545 oss << " piece of the spectrum. can't execute fitting anymore.";
2546 throw(AipsError(String(oss)));
2547 }
2548 }
2549
2550 for (int i = 0; i < nDOF; ++i) {
2551 for (int j = 0; j < i; ++j) {
2552 xMatrix[i][j] = xMatrix[j][i];
2553 }
2554 }
2555
2556 std::vector<double> invDiag;
2557 for (int i = 0; i < nDOF; ++i) {
2558 invDiag.push_back(1.0/xMatrix[i][i]);
2559 for (int j = 0; j < nDOF; ++j) {
2560 xMatrix[i][j] *= invDiag[i];
2561 }
2562 }
2563
2564 for (int k = 0; k < nDOF; ++k) {
2565 for (int i = 0; i < nDOF; ++i) {
2566 if (i != k) {
2567 double factor1 = xMatrix[k][k];
2568 double factor2 = xMatrix[i][k];
2569 for (int j = k; j < 2*nDOF; ++j) {
2570 xMatrix[i][j] *= factor1;
2571 xMatrix[i][j] -= xMatrix[k][j]*factor2;
2572 xMatrix[i][j] /= factor1;
2573 }
2574 }
2575 }
2576 double xDiag = xMatrix[k][k];
2577 for (int j = k; j < 2*nDOF; ++j) {
2578 xMatrix[k][j] /= xDiag;
2579 }
2580 }
2581
2582 for (int i = 0; i < nDOF; ++i) {
2583 for (int j = 0; j < nDOF; ++j) {
2584 xMatrix[i][nDOF+j] *= invDiag[j];
2585 }
2586 }
2587 //compute a vector y which consists of the coefficients of the best-fit spline curves
2588 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
2589 //cubic terms for the other pieces (in case nPiece>1).
2590 std::vector<double> y;
2591 y.clear();
2592 for (int i = 0; i < nDOF; ++i) {
2593 y.push_back(0.0);
2594 for (int j = 0; j < nDOF; ++j) {
2595 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
2596 }
2597 }
2598
2599 double a0 = y[0];
2600 double a1 = y[1];
2601 double a2 = y[2];
2602 double a3 = y[3];
2603 params.clear();
2604
2605 for (int n = 0; n < nPiece; ++n) {
2606 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2607 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
2608 residual[i] = z1[i] - r1[i];
2609 }
2610 params.push_back(a0);
2611 params.push_back(a1);
2612 params.push_back(a2);
2613 params.push_back(a3);
2614
2615 if (n == nPiece-1) break;
2616
2617 double d = y[4+n];
2618 double iE = invEdge[n];
2619 a0 += d;
2620 a1 -= 3.0*d*iE;
2621 a2 += 3.0*d*iE*iE;
2622 a3 -= d*iE*iE*iE;
2623 }
2624
2625 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
2626 break;
2627 } else {
2628 double stdDev = 0.0;
2629 for (int i = 0; i < nChan; ++i) {
2630 stdDev += residual[i]*residual[i]*(double)maskArray[i];
2631 }
2632 stdDev = sqrt(stdDev/(double)nData);
2633
2634 double thres = stdDev * thresClip;
2635 int newNData = 0;
2636 for (int i = 0; i < nChan; ++i) {
2637 if (abs(residual[i]) >= thres) {
2638 maskArray[i] = 0;
2639 }
2640 if (maskArray[i] > 0) {
2641 newNData++;
2642 }
2643 }
2644 if (newNData == nData) {
2645 break; //no more flag to add. iteration stops.
2646 } else {
2647 nData = newNData;
2648 }
2649 }
2650 }
2651
2652 nClipped = initNData - nData;
2653
2654 std::vector<float> result;
2655 if (getResidual) {
2656 for (int i = 0; i < nChan; ++i) {
2657 result.push_back((float)residual[i]);
2658 }
2659 } else {
2660 for (int i = 0; i < nChan; ++i) {
2661 result.push_back((float)r1[i]);
2662 }
2663 }
2664
2665 return result;
2666}
2667
2668 void 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)
2669{
2670 nWaves.clear();
2671
2672 if (applyFFT) {
2673 string fftThAttr;
2674 float fftThSigma;
2675 int fftThTop;
2676 parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
2677 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
2678 }
2679
2680 addAuxWaveNumbers(addNWaves, rejectNWaves, nWaves);
2681}
2682
2683void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
2684{
2685 uInt idxSigma = fftThresh.find("sigma");
2686 uInt idxTop = fftThresh.find("top");
2687
2688 if (idxSigma == fftThresh.size() - 5) {
2689 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
2690 is >> fftThSigma;
2691 fftThAttr = "sigma";
2692 } else if (idxTop == 0) {
2693 std::istringstream is(fftThresh.substr(3));
2694 is >> fftThTop;
2695 fftThAttr = "top";
2696 } else {
2697 bool isNumber = true;
2698 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
2699 char ch = (fftThresh.substr(i, 1).c_str())[0];
2700 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
2701 isNumber = false;
2702 break;
2703 }
2704 }
2705 if (isNumber) {
2706 std::istringstream is(fftThresh);
2707 is >> fftThSigma;
2708 fftThAttr = "sigma";
2709 } else {
2710 throw(AipsError("fftthresh has a wrong value"));
2711 }
2712 }
2713}
2714
2715void 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)
2716{
2717 std::vector<float> fspec;
2718 if (fftMethod == "fft") {
2719 fspec = execFFT(whichrow, chanMask, false, true);
2720 //} else if (fftMethod == "lsp") {
2721 // fspec = lombScarglePeriodogram(whichrow);
2722 }
2723
2724 if (fftThAttr == "sigma") {
2725 float mean = 0.0;
2726 float mean2 = 0.0;
2727 for (uInt i = 0; i < fspec.size(); ++i) {
2728 mean += fspec[i];
2729 mean2 += fspec[i]*fspec[i];
2730 }
2731 mean /= float(fspec.size());
2732 mean2 /= float(fspec.size());
2733 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
2734
2735 for (uInt i = 0; i < fspec.size(); ++i) {
2736 if (fspec[i] >= thres) {
2737 nWaves.push_back(i);
2738 }
2739 }
2740
2741 } else if (fftThAttr == "top") {
2742 for (int i = 0; i < fftThTop; ++i) {
2743 float max = 0.0;
2744 int maxIdx = 0;
2745 for (uInt j = 0; j < fspec.size(); ++j) {
2746 if (fspec[j] > max) {
2747 max = fspec[j];
2748 maxIdx = j;
2749 }
2750 }
2751 nWaves.push_back(maxIdx);
2752 fspec[maxIdx] = 0.0;
2753 }
2754
2755 }
2756
2757 if (nWaves.size() > 1) {
2758 sort(nWaves.begin(), nWaves.end());
2759 }
2760}
2761
2762void Scantable::addAuxWaveNumbers(const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
2763{
2764 for (uInt i = 0; i < addNWaves.size(); ++i) {
2765 bool found = false;
2766 for (uInt j = 0; j < nWaves.size(); ++j) {
2767 if (nWaves[j] == addNWaves[i]) {
2768 found = true;
2769 break;
2770 }
2771 }
2772 if (!found) nWaves.push_back(addNWaves[i]);
2773 }
2774
2775 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
2776 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
2777 if (*j == rejectNWaves[i]) {
2778 j = nWaves.erase(j);
2779 } else {
2780 ++j;
2781 }
2782 }
2783 }
2784
2785 if (nWaves.size() > 1) {
2786 sort(nWaves.begin(), nWaves.end());
2787 unique(nWaves.begin(), nWaves.end());
2788 }
2789}
2790
2791void 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)
2792{
2793 try {
2794 ofstream ofs;
2795 String coordInfo = "";
2796 bool hasSameNchan = true;
2797 bool outTextFile = false;
2798
2799 if (blfile != "") {
2800 ofs.open(blfile.c_str(), ios::out | ios::app);
2801 if (ofs) outTextFile = true;
2802 }
2803
2804 if (outLogger || outTextFile) {
2805 coordInfo = getCoordInfo()[0];
2806 if (coordInfo == "") coordInfo = "channel";
2807 hasSameNchan = hasSameNchanOverIFs();
2808 }
2809
2810 //Fitter fitter = Fitter();
2811 //fitter.setExpression("sinusoid", nWaves);
2812 //fitter.setIterClipping(thresClip, nIterClip);
2813
2814 int nRow = nrow();
2815 std::vector<bool> chanMask;
2816 std::vector<int> nWaves;
2817
2818 bool showProgress;
2819 int minNRow;
2820 parseProgressInfo(progressInfo, showProgress, minNRow);
2821
2822 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2823 chanMask = getCompositeChanMask(whichrow, mask);
2824 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
2825
2826 //FOR DEBUGGING------------
2827 if (whichrow < 0) {// == nRow -1) {
2828 cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow);
2829 if (applyFFT) {
2830 cout << "[ ";
2831 for (uInt j = 0; j < nWaves.size(); ++j) {
2832 cout << nWaves[j] << ", ";
2833 }
2834 cout << " ] " << endl;
2835 }
2836 cout << flush;
2837 }
2838 //-------------------------
2839
2840 //fitBaseline(chanMask, whichrow, fitter);
2841 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2842 std::vector<float> params;
2843 int nClipped = 0;
2844 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
2845 setSpectrum(res, whichrow);
2846 //
2847
2848 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
2849 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2850 }
2851
2852 if (outTextFile) ofs.close();
2853
2854 } catch (...) {
2855 throw;
2856 }
2857}
2858
2859void 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)
2860{
2861 try {
2862 ofstream ofs;
2863 String coordInfo = "";
2864 bool hasSameNchan = true;
2865 bool outTextFile = false;
2866
2867 if (blfile != "") {
2868 ofs.open(blfile.c_str(), ios::out | ios::app);
2869 if (ofs) outTextFile = true;
2870 }
2871
2872 if (outLogger || outTextFile) {
2873 coordInfo = getCoordInfo()[0];
2874 if (coordInfo == "") coordInfo = "channel";
2875 hasSameNchan = hasSameNchanOverIFs();
2876 }
2877
2878 //Fitter fitter = Fitter();
2879 //fitter.setExpression("sinusoid", nWaves);
2880 //fitter.setIterClipping(thresClip, nIterClip);
2881
2882 int nRow = nrow();
2883 std::vector<bool> chanMask;
2884 std::vector<int> nWaves;
2885
2886 int minEdgeSize = getIFNos().size()*2;
2887 STLineFinder lineFinder = STLineFinder();
2888 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2889
2890 bool showProgress;
2891 int minNRow;
2892 parseProgressInfo(progressInfo, showProgress, minNRow);
2893
2894 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2895
2896 //-------------------------------------------------------
2897 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2898 //-------------------------------------------------------
2899 int edgeSize = edge.size();
2900 std::vector<int> currentEdge;
2901 if (edgeSize >= 2) {
2902 int idx = 0;
2903 if (edgeSize > 2) {
2904 if (edgeSize < minEdgeSize) {
2905 throw(AipsError("Length of edge element info is less than that of IFs"));
2906 }
2907 idx = 2 * getIF(whichrow);
2908 }
2909 currentEdge.push_back(edge[idx]);
2910 currentEdge.push_back(edge[idx+1]);
2911 } else {
2912 throw(AipsError("Wrong length of edge element"));
2913 }
2914 lineFinder.setData(getSpectrum(whichrow));
2915 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2916 chanMask = lineFinder.getMask();
2917 //-------------------------------------------------------
2918
2919 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
2920
2921 //fitBaseline(chanMask, whichrow, fitter);
2922 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2923 std::vector<float> params;
2924 int nClipped = 0;
2925 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
2926 setSpectrum(res, whichrow);
2927 //
2928
2929 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
2930 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2931 }
2932
2933 if (outTextFile) ofs.close();
2934
2935 } catch (...) {
2936 throw;
2937 }
2938}
2939
2940std::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)
2941{
2942 if (data.size() != mask.size()) {
2943 throw(AipsError("data and mask sizes are not identical"));
2944 }
2945 if (data.size() < 2) {
2946 throw(AipsError("data size is too short"));
2947 }
2948 if (waveNumbers.size() == 0) {
2949 throw(AipsError("no wave numbers given"));
2950 }
2951 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
2952 nWaves.reserve(waveNumbers.size());
2953 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
2954 sort(nWaves.begin(), nWaves.end());
2955 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
2956 nWaves.erase(end_it, nWaves.end());
2957
2958 int minNWaves = nWaves[0];
2959 if (minNWaves < 0) {
2960 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
2961 }
2962 bool hasConstantTerm = (minNWaves == 0);
2963
2964 int nChan = data.size();
2965 std::vector<int> maskArray;
2966 std::vector<int> x;
2967 for (int i = 0; i < nChan; ++i) {
2968 maskArray.push_back(mask[i] ? 1 : 0);
2969 if (mask[i]) {
2970 x.push_back(i);
2971 }
2972 }
2973
2974 int initNData = x.size();
2975
2976 int nData = initNData;
2977 int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
2978
2979 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
2980 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)
2981
2982 // xArray : contains elemental values for computing the least-square matrix.
2983 // xArray.size() is nDOF and xArray[*].size() is nChan.
2984 // Each xArray element are as follows:
2985 // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
2986 // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
2987 // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
2988 // where (1 <= n <= nMaxWavesInSW),
2989 // or,
2990 // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
2991 // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
2992 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
2993 std::vector<std::vector<double> > xArray;
2994 if (hasConstantTerm) {
2995 std::vector<double> xu;
2996 for (int j = 0; j < nChan; ++j) {
2997 xu.push_back(1.0);
2998 }
2999 xArray.push_back(xu);
3000 }
3001 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
3002 double xFactor = baseXFactor*(double)nWaves[i];
3003 std::vector<double> xs, xc;
3004 xs.clear();
3005 xc.clear();
3006 for (int j = 0; j < nChan; ++j) {
3007 xs.push_back(sin(xFactor*(double)j));
3008 xc.push_back(cos(xFactor*(double)j));
3009 }
3010 xArray.push_back(xs);
3011 xArray.push_back(xc);
3012 }
3013
3014 std::vector<double> z1, r1, residual;
3015 for (int i = 0; i < nChan; ++i) {
3016 z1.push_back((double)data[i]);
3017 r1.push_back(0.0);
3018 residual.push_back(0.0);
3019 }
3020
3021 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3022 // xMatrix : horizontal concatenation of
3023 // the least-sq. matrix (left) and an
3024 // identity matrix (right).
3025 // the right part is used to calculate the inverse matrix of the left part.
3026 double xMatrix[nDOF][2*nDOF];
3027 double zMatrix[nDOF];
3028 for (int i = 0; i < nDOF; ++i) {
3029 for (int j = 0; j < 2*nDOF; ++j) {
3030 xMatrix[i][j] = 0.0;
3031 }
3032 xMatrix[i][nDOF+i] = 1.0;
3033 zMatrix[i] = 0.0;
3034 }
3035
3036 int nUseData = 0;
3037 for (int k = 0; k < nChan; ++k) {
3038 if (maskArray[k] == 0) continue;
3039
3040 for (int i = 0; i < nDOF; ++i) {
3041 for (int j = i; j < nDOF; ++j) {
3042 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
3043 }
3044 zMatrix[i] += z1[k] * xArray[i][k];
3045 }
3046
3047 nUseData++;
3048 }
3049
3050 if (nUseData < 1) {
3051 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
3052 }
3053
3054 for (int i = 0; i < nDOF; ++i) {
3055 for (int j = 0; j < i; ++j) {
3056 xMatrix[i][j] = xMatrix[j][i];
3057 }
3058 }
3059
3060 std::vector<double> invDiag;
3061 for (int i = 0; i < nDOF; ++i) {
3062 invDiag.push_back(1.0/xMatrix[i][i]);
3063 for (int j = 0; j < nDOF; ++j) {
3064 xMatrix[i][j] *= invDiag[i];
3065 }
3066 }
3067
3068 for (int k = 0; k < nDOF; ++k) {
3069 for (int i = 0; i < nDOF; ++i) {
3070 if (i != k) {
3071 double factor1 = xMatrix[k][k];
3072 double factor2 = xMatrix[i][k];
3073 for (int j = k; j < 2*nDOF; ++j) {
3074 xMatrix[i][j] *= factor1;
3075 xMatrix[i][j] -= xMatrix[k][j]*factor2;
3076 xMatrix[i][j] /= factor1;
3077 }
3078 }
3079 }
3080 double xDiag = xMatrix[k][k];
3081 for (int j = k; j < 2*nDOF; ++j) {
3082 xMatrix[k][j] /= xDiag;
3083 }
3084 }
3085
3086 for (int i = 0; i < nDOF; ++i) {
3087 for (int j = 0; j < nDOF; ++j) {
3088 xMatrix[i][nDOF+j] *= invDiag[j];
3089 }
3090 }
3091 //compute a vector y which consists of the coefficients of the sinusoids forming the
3092 //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
3093 //and cosine functions, respectively.
3094 std::vector<double> y;
3095 params.clear();
3096 for (int i = 0; i < nDOF; ++i) {
3097 y.push_back(0.0);
3098 for (int j = 0; j < nDOF; ++j) {
3099 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3100 }
3101 params.push_back(y[i]);
3102 }
3103
3104 for (int i = 0; i < nChan; ++i) {
3105 r1[i] = y[0];
3106 for (int j = 1; j < nDOF; ++j) {
3107 r1[i] += y[j]*xArray[j][i];
3108 }
3109 residual[i] = z1[i] - r1[i];
3110 }
3111
3112 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3113 break;
3114 } else {
3115 double stdDev = 0.0;
3116 for (int i = 0; i < nChan; ++i) {
3117 stdDev += residual[i]*residual[i]*(double)maskArray[i];
3118 }
3119 stdDev = sqrt(stdDev/(double)nData);
3120
3121 double thres = stdDev * thresClip;
3122 int newNData = 0;
3123 for (int i = 0; i < nChan; ++i) {
3124 if (abs(residual[i]) >= thres) {
3125 maskArray[i] = 0;
3126 }
3127 if (maskArray[i] > 0) {
3128 newNData++;
3129 }
3130 }
3131 if (newNData == nData) {
3132 break; //no more flag to add. iteration stops.
3133 } else {
3134 nData = newNData;
3135 }
3136 }
3137 }
3138
3139 nClipped = initNData - nData;
3140
3141 std::vector<float> result;
3142 if (getResidual) {
3143 for (int i = 0; i < nChan; ++i) {
3144 result.push_back((float)residual[i]);
3145 }
3146 } else {
3147 for (int i = 0; i < nChan; ++i) {
3148 result.push_back((float)r1[i]);
3149 }
3150 }
3151
3152 return result;
3153}
3154
3155void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
3156{
3157 std::vector<double> dAbcissa = getAbcissa(whichrow);
3158 std::vector<float> abcissa;
3159 for (uInt i = 0; i < dAbcissa.size(); ++i) {
3160 abcissa.push_back((float)dAbcissa[i]);
3161 }
3162 std::vector<float> spec = getSpectrum(whichrow);
3163
3164 fitter.setData(abcissa, spec, mask);
3165 fitter.lfit();
3166}
3167
3168std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
3169{
3170 std::vector<bool> mask = getMask(whichrow);
3171 uInt maskSize = mask.size();
3172 if (maskSize != inMask.size()) {
3173 throw(AipsError("mask sizes are not the same."));
3174 }
3175 for (uInt i = 0; i < maskSize; ++i) {
3176 mask[i] = mask[i] && inMask[i];
3177 }
3178
3179 return mask;
3180}
3181
3182/*
3183std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
3184{
3185 int edgeSize = edge.size();
3186 std::vector<int> currentEdge;
3187 if (edgeSize >= 2) {
3188 int idx = 0;
3189 if (edgeSize > 2) {
3190 if (edgeSize < minEdgeSize) {
3191 throw(AipsError("Length of edge element info is less than that of IFs"));
3192 }
3193 idx = 2 * getIF(whichrow);
3194 }
3195 currentEdge.push_back(edge[idx]);
3196 currentEdge.push_back(edge[idx+1]);
3197 } else {
3198 throw(AipsError("Wrong length of edge element"));
3199 }
3200
3201 lineFinder.setData(getSpectrum(whichrow));
3202 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
3203
3204 return lineFinder.getMask();
3205}
3206*/
3207
3208/* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
3209void 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)
3210{
3211 if (outLogger || outTextFile) {
3212 std::vector<float> params = fitter.getParameters();
3213 std::vector<bool> fixed = fitter.getFixedParameters();
3214 float rms = getRms(chanMask, whichrow);
3215 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3216
3217 if (outLogger) {
3218 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3219 ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ;
3220 }
3221 if (outTextFile) {
3222 ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush;
3223 }
3224 }
3225}
3226
3227/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
3228void 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)
3229{
3230 if (outLogger || outTextFile) {
3231 float rms = getRms(chanMask, whichrow);
3232 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3233 std::vector<bool> fixed;
3234 fixed.clear();
3235
3236 if (outLogger) {
3237 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3238 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
3239 }
3240 if (outTextFile) {
3241 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
3242 }
3243 }
3244}
3245
3246/* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */
3247void 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)
3248{
3249 if (outLogger || outTextFile) {
3250 float rms = getRms(chanMask, whichrow);
3251 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3252 std::vector<bool> fixed;
3253 fixed.clear();
3254
3255 if (outLogger) {
3256 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3257 ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
3258 }
3259 if (outTextFile) {
3260 ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
3261 }
3262 }
3263}
3264
3265void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
3266{
3267 int idxDelimiter = progressInfo.find(",");
3268 if (idxDelimiter < 0) {
3269 throw(AipsError("wrong value in 'showprogress' parameter")) ;
3270 }
3271 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
3272 std::istringstream is(progressInfo.substr(idxDelimiter+1));
3273 is >> minNRow;
3274}
3275
3276void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
3277{
3278 if (showProgress && (nTotal >= nTotalThreshold)) {
3279 int nInterval = int(floor(double(nTotal)/100.0));
3280 if (nInterval == 0) nInterval++;
3281
3282 if (nProcessed % nInterval == 0) {
3283 printf("\r"); //go to the head of line
3284 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
3285 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
3286 printf("\x1b[39m\x1b[0m"); //set default attributes
3287 fflush(NULL);
3288 }
3289
3290 if (nProcessed == nTotal - 1) {
3291 printf("\r\x1b[K"); //clear
3292 fflush(NULL);
3293 }
3294
3295 }
3296}
3297
3298std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
3299{
3300 std::vector<bool> mask = getMask(whichrow);
3301
3302 if (inMask.size() > 0) {
3303 uInt maskSize = mask.size();
3304 if (maskSize != inMask.size()) {
3305 throw(AipsError("mask sizes are not the same."));
3306 }
3307 for (uInt i = 0; i < maskSize; ++i) {
3308 mask[i] = mask[i] && inMask[i];
3309 }
3310 }
3311
3312 Vector<Float> spec = getSpectrum(whichrow);
3313 mathutil::doZeroOrderInterpolation(spec, mask);
3314
3315 FFTServer<Float,Complex> ffts;
3316 Vector<Complex> fftres;
3317 ffts.fft0(fftres, spec);
3318
3319 std::vector<float> res;
3320 float norm = float(2.0/double(spec.size()));
3321
3322 if (getRealImag) {
3323 for (uInt i = 0; i < fftres.size(); ++i) {
3324 res.push_back(real(fftres[i])*norm);
3325 res.push_back(imag(fftres[i])*norm);
3326 }
3327 } else {
3328 for (uInt i = 0; i < fftres.size(); ++i) {
3329 res.push_back(abs(fftres[i])*norm);
3330 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
3331 }
3332 }
3333
3334 return res;
3335}
3336
3337
3338float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
3339{
3340 Vector<Float> spec;
3341 specCol_.get(whichrow, spec);
3342
3343 float mean = 0.0;
3344 float smean = 0.0;
3345 int n = 0;
3346 for (uInt i = 0; i < spec.nelements(); ++i) {
3347 if (mask[i]) {
3348 mean += spec[i];
3349 smean += spec[i]*spec[i];
3350 n++;
3351 }
3352 }
3353
3354 mean /= (float)n;
3355 smean /= (float)n;
3356
3357 return sqrt(smean - mean*mean);
3358}
3359
3360
3361std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const
3362{
3363 ostringstream oss;
3364
3365 if (verbose) {
3366 oss << " Scan[" << getScan(whichrow) << "]";
3367 oss << " Beam[" << getBeam(whichrow) << "]";
3368 oss << " IF[" << getIF(whichrow) << "]";
3369 oss << " Pol[" << getPol(whichrow) << "]";
3370 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
3371 oss << "Fitter range = " << masklist << endl;
3372 oss << "Baseline parameters" << endl;
3373 oss << flush;
3374 }
3375
3376 return String(oss);
3377}
3378
3379std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const
3380{
3381 ostringstream oss;
3382
3383 if (verbose) {
3384 oss << "Results of baseline fit" << endl;
3385 oss << " rms = " << setprecision(6) << rms << endl;
3386 if (nClipped >= 0) {
3387 oss << " Number of clipped channels = " << nClipped << endl;
3388 }
3389 for (int i = 0; i < 60; ++i) {
3390 oss << "-";
3391 }
3392 oss << endl;
3393 oss << flush;
3394 }
3395
3396 return String(oss);
3397}
3398
3399std::string Scantable::formatBaselineParams(const std::vector<float>& params,
3400 const std::vector<bool>& fixed,
3401 float rms,
3402 int nClipped,
3403 const std::string& masklist,
3404 int whichrow,
3405 bool verbose,
3406 int start, int count,
3407 bool resetparamid) const
3408{
3409 int nParam = (int)(params.size());
3410
3411 if (nParam < 1) {
3412 return(" Not fitted");
3413 } else {
3414
3415 ostringstream oss;
3416 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3417
3418 if (start < 0) start = 0;
3419 if (count < 0) count = nParam;
3420 int end = start + count;
3421 if (end > nParam) end = nParam;
3422 int paramidoffset = (resetparamid) ? (-start) : 0;
3423
3424 for (int i = start; i < end; ++i) {
3425 if (i > start) {
3426 oss << ",";
3427 }
3428 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
3429 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
3430 }
3431
3432 oss << endl;
3433 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
3434
3435 return String(oss);
3436 }
3437
3438}
3439
3440 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
3441{
3442 int nOutParam = (int)(params.size());
3443 int nPiece = (int)(ranges.size()) - 1;
3444
3445 if (nOutParam < 1) {
3446 return(" Not fitted");
3447 } else if (nPiece < 0) {
3448 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose);
3449 } else if (nPiece < 1) {
3450 return(" Bad count of the piece edge info");
3451 } else if (nOutParam % nPiece != 0) {
3452 return(" Bad count of the output baseline parameters");
3453 } else {
3454
3455 int nParam = nOutParam / nPiece;
3456
3457 ostringstream oss;
3458 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3459
3460 stringstream ss;
3461 ss << ranges[nPiece] << flush;
3462 int wRange = ss.str().size() * 2 + 5;
3463
3464 for (int i = 0; i < nPiece; ++i) {
3465 ss.str("");
3466 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
3467 oss << left << setw(wRange) << ss.str();
3468 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true);
3469 }
3470
3471 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
3472
3473 return String(oss);
3474 }
3475
3476}
3477
3478bool Scantable::hasSameNchanOverIFs()
3479{
3480 int nIF = nif(-1);
3481 int nCh;
3482 int totalPositiveNChan = 0;
3483 int nPositiveNChan = 0;
3484
3485 for (int i = 0; i < nIF; ++i) {
3486 nCh = nchan(i);
3487 if (nCh > 0) {
3488 totalPositiveNChan += nCh;
3489 nPositiveNChan++;
3490 }
3491 }
3492
3493 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
3494}
3495
3496std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
3497{
3498 if (mask.size() < 2) {
3499 throw(AipsError("The mask elements should be > 1"));
3500 }
3501 int IF = getIF(whichrow);
3502 if (mask.size() != (uInt)nchan(IF)) {
3503 throw(AipsError("Number of channels in scantable != number of mask elements"));
3504 }
3505
3506 if (verbose) {
3507 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
3508 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
3509 if (!hasSameNchan) {
3510 logOs << endl << "This mask is only valid for IF=" << IF;
3511 }
3512 logOs << LogIO::POST;
3513 }
3514
3515 std::vector<double> abcissa = getAbcissa(whichrow);
3516 std::vector<int> edge = getMaskEdgeIndices(mask);
3517
3518 ostringstream oss;
3519 oss.setf(ios::fixed);
3520 oss << setprecision(1) << "[";
3521 for (uInt i = 0; i < edge.size(); i+=2) {
3522 if (i > 0) oss << ",";
3523 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
3524 }
3525 oss << "]" << flush;
3526
3527 return String(oss);
3528}
3529
3530std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
3531{
3532 if (mask.size() < 2) {
3533 throw(AipsError("The mask elements should be > 1"));
3534 }
3535
3536 std::vector<int> out, startIndices, endIndices;
3537 int maskSize = mask.size();
3538
3539 startIndices.clear();
3540 endIndices.clear();
3541
3542 if (mask[0]) {
3543 startIndices.push_back(0);
3544 }
3545 for (int i = 1; i < maskSize; ++i) {
3546 if ((!mask[i-1]) && mask[i]) {
3547 startIndices.push_back(i);
3548 } else if (mask[i-1] && (!mask[i])) {
3549 endIndices.push_back(i-1);
3550 }
3551 }
3552 if (mask[maskSize-1]) {
3553 endIndices.push_back(maskSize-1);
3554 }
3555
3556 if (startIndices.size() != endIndices.size()) {
3557 throw(AipsError("Inconsistent Mask Size: bad data?"));
3558 }
3559 for (uInt i = 0; i < startIndices.size(); ++i) {
3560 if (startIndices[i] > endIndices[i]) {
3561 throw(AipsError("Mask start index > mask end index"));
3562 }
3563 }
3564
3565 out.clear();
3566 for (uInt i = 0; i < startIndices.size(); ++i) {
3567 out.push_back(startIndices[i]);
3568 out.push_back(endIndices[i]);
3569 }
3570
3571 return out;
3572}
3573
3574vector<float> Scantable::getTsysSpectrum( int whichrow ) const
3575{
3576 Vector<Float> tsys( tsysCol_(whichrow) ) ;
3577 vector<float> stlTsys ;
3578 tsys.tovector( stlTsys ) ;
3579 return stlTsys ;
3580}
3581
3582
3583}
3584//namespace asap
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