source: trunk/src/Scantable.cpp@ 2768

Last change on this file since 2768 was 2767, checked in by WataruKawasaki, 12 years ago

New Development: Yes

JIRA Issue: Yes CAS-4794

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: No

Module(s): sd

Description: functions to apply/write STBaselineTable in which baseline parameters stored.


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File size: 168.0 KB
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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#include <sys/time.h>
14
15#include <atnf/PKSIO/SrcType.h>
16
17#include <casa/aips.h>
18#include <casa/iomanip.h>
19#include <casa/iostream.h>
20#include <casa/OS/File.h>
21#include <casa/OS/Path.h>
22#include <casa/Logging/LogIO.h>
23#include <casa/Arrays/Array.h>
24#include <casa/Arrays/ArrayAccessor.h>
25#include <casa/Arrays/ArrayLogical.h>
26#include <casa/Arrays/ArrayMath.h>
27#include <casa/Arrays/MaskArrMath.h>
28#include <casa/Arrays/Slice.h>
29#include <casa/Arrays/Vector.h>
30#include <casa/Arrays/VectorSTLIterator.h>
31#include <casa/BasicMath/Math.h>
32#include <casa/BasicSL/Constants.h>
33#include <casa/Containers/RecordField.h>
34#include <casa/Logging/LogIO.h>
35#include <casa/Quanta/MVAngle.h>
36#include <casa/Quanta/MVTime.h>
37#include <casa/Utilities/GenSort.h>
38
39#include <coordinates/Coordinates/CoordinateUtil.h>
40
41// needed to avoid error in .tcc
42#include <measures/Measures/MCDirection.h>
43//
44#include <measures/Measures/MDirection.h>
45#include <measures/Measures/MEpoch.h>
46#include <measures/Measures/MFrequency.h>
47#include <measures/Measures/MeasRef.h>
48#include <measures/Measures/MeasTable.h>
49#include <measures/TableMeasures/ScalarMeasColumn.h>
50#include <measures/TableMeasures/TableMeasDesc.h>
51#include <measures/TableMeasures/TableMeasRefDesc.h>
52#include <measures/TableMeasures/TableMeasValueDesc.h>
53
54#include <tables/Tables/ArrColDesc.h>
55#include <tables/Tables/ExprNode.h>
56#include <tables/Tables/ScaColDesc.h>
57#include <tables/Tables/SetupNewTab.h>
58#include <tables/Tables/TableCopy.h>
59#include <tables/Tables/TableDesc.h>
60#include <tables/Tables/TableIter.h>
61#include <tables/Tables/TableParse.h>
62#include <tables/Tables/TableRecord.h>
63#include <tables/Tables/TableRow.h>
64#include <tables/Tables/TableVector.h>
65
66#include "MathUtils.h"
67#include "STAttr.h"
68#include "STBaselineTable.h"
69#include "STLineFinder.h"
70#include "STPolCircular.h"
71#include "STPolLinear.h"
72#include "STPolStokes.h"
73#include "STUpgrade.h"
74#include "STFitter.h"
75#include "Scantable.h"
76
77#define debug 1
78
79using namespace casa;
80
81namespace asap {
82
83std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
84
85void Scantable::initFactories() {
86 if ( factories_.empty() ) {
87 Scantable::factories_["linear"] = &STPolLinear::myFactory;
88 Scantable::factories_["circular"] = &STPolCircular::myFactory;
89 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
90 }
91}
92
93Scantable::Scantable(Table::TableType ttype) :
94 type_(ttype)
95{
96 initFactories();
97 setupMainTable();
98 freqTable_ = STFrequencies(*this);
99 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
100 weatherTable_ = STWeather(*this);
101 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
102 focusTable_ = STFocus(*this);
103 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
104 tcalTable_ = STTcal(*this);
105 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
106 moleculeTable_ = STMolecules(*this);
107 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
108 historyTable_ = STHistory(*this);
109 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
110 fitTable_ = STFit(*this);
111 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
112 table_.tableInfo().setType( "Scantable" ) ;
113 originalTable_ = table_;
114 attach();
115}
116
117Scantable::Scantable(const std::string& name, Table::TableType ttype) :
118 type_(ttype)
119{
120 initFactories();
121
122 Table tab(name, Table::Update);
123 uInt version = tab.keywordSet().asuInt("VERSION");
124 if (version != version_) {
125 STUpgrade upgrader(version_);
126 LogIO os( LogOrigin( "Scantable" ) ) ;
127 os << LogIO::WARN
128 << name << " data format version " << version
129 << " is deprecated" << endl
130 << "Running upgrade."<< endl
131 << LogIO::POST ;
132 std::string outname = upgrader.upgrade(name);
133 if ( outname != name ) {
134 os << LogIO::WARN
135 << "Data will be loaded from " << outname << " instead of "
136 << name << LogIO::POST ;
137 tab = Table(outname, Table::Update ) ;
138 }
139 }
140 if ( type_ == Table::Memory ) {
141 table_ = tab.copyToMemoryTable(generateName());
142 } else {
143 table_ = tab;
144 }
145 table_.tableInfo().setType( "Scantable" ) ;
146
147 attachSubtables();
148 originalTable_ = table_;
149 attach();
150}
151/*
152Scantable::Scantable(const std::string& name, Table::TableType ttype) :
153 type_(ttype)
154{
155 initFactories();
156 Table tab(name, Table::Update);
157 uInt version = tab.keywordSet().asuInt("VERSION");
158 if (version != version_) {
159 throw(AipsError("Unsupported version of ASAP file."));
160 }
161 if ( type_ == Table::Memory ) {
162 table_ = tab.copyToMemoryTable(generateName());
163 } else {
164 table_ = tab;
165 }
166
167 attachSubtables();
168 originalTable_ = table_;
169 attach();
170}
171*/
172
173Scantable::Scantable( const Scantable& other, bool clear )
174{
175 // with or without data
176 String newname = String(generateName());
177 type_ = other.table_.tableType();
178 if ( other.table_.tableType() == Table::Memory ) {
179 if ( clear ) {
180 table_ = TableCopy::makeEmptyMemoryTable(newname,
181 other.table_, True);
182 } else
183 table_ = other.table_.copyToMemoryTable(newname);
184 } else {
185 other.table_.deepCopy(newname, Table::New, False,
186 other.table_.endianFormat(),
187 Bool(clear));
188 table_ = Table(newname, Table::Update);
189 table_.markForDelete();
190 }
191 table_.tableInfo().setType( "Scantable" ) ;
192 /// @todo reindex SCANNO, recompute nbeam, nif, npol
193 if ( clear ) copySubtables(other);
194 attachSubtables();
195 originalTable_ = table_;
196 attach();
197}
198
199void Scantable::copySubtables(const Scantable& other) {
200 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
201 TableCopy::copyRows(t, other.freqTable_.table());
202 t = table_.rwKeywordSet().asTable("FOCUS");
203 TableCopy::copyRows(t, other.focusTable_.table());
204 t = table_.rwKeywordSet().asTable("WEATHER");
205 TableCopy::copyRows(t, other.weatherTable_.table());
206 t = table_.rwKeywordSet().asTable("TCAL");
207 TableCopy::copyRows(t, other.tcalTable_.table());
208 t = table_.rwKeywordSet().asTable("MOLECULES");
209 TableCopy::copyRows(t, other.moleculeTable_.table());
210 t = table_.rwKeywordSet().asTable("HISTORY");
211 TableCopy::copyRows(t, other.historyTable_.table());
212 t = table_.rwKeywordSet().asTable("FIT");
213 TableCopy::copyRows(t, other.fitTable_.table());
214}
215
216void Scantable::attachSubtables()
217{
218 freqTable_ = STFrequencies(table_);
219 focusTable_ = STFocus(table_);
220 weatherTable_ = STWeather(table_);
221 tcalTable_ = STTcal(table_);
222 moleculeTable_ = STMolecules(table_);
223 historyTable_ = STHistory(table_);
224 fitTable_ = STFit(table_);
225}
226
227Scantable::~Scantable()
228{
229}
230
231void Scantable::setupMainTable()
232{
233 TableDesc td("", "1", TableDesc::Scratch);
234 td.comment() = "An ASAP Scantable";
235 td.rwKeywordSet().define("VERSION", uInt(version_));
236
237 // n Cycles
238 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
239 // new index every nBeam x nIF x nPol
240 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
241
242 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
243 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
244 // linear, circular, stokes
245 td.rwKeywordSet().define("POLTYPE", String("linear"));
246 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
247
248 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
249 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
250
251 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
252 refbeamnoColumn.setDefault(Int(-1));
253 td.addColumn(refbeamnoColumn);
254
255 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
256 flagrowColumn.setDefault(uInt(0));
257 td.addColumn(flagrowColumn);
258
259 td.addColumn(ScalarColumnDesc<Double>("TIME"));
260 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
261 TableMeasValueDesc measVal(td, "TIME");
262 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
263 mepochCol.write(td);
264
265 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
266
267 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
268 // Type of source (on=0, off=1, other=-1)
269 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
270 stypeColumn.setDefault(Int(-1));
271 td.addColumn(stypeColumn);
272 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
273
274 //The actual Data Vectors
275 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
276 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
277 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
278
279 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
280 IPosition(1,2),
281 ColumnDesc::Direct));
282 TableMeasRefDesc mdirRef(MDirection::J2000); // default
283 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
284 // the TableMeasDesc gives the column a type
285 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
286 // a uder set table type e.g. GALCTIC, B1950 ...
287 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
288 // writing create the measure column
289 mdirCol.write(td);
290 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
291 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
292 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
293
294 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
295 ScalarColumnDesc<Int> fitColumn("FIT_ID");
296 fitColumn.setDefault(Int(-1));
297 td.addColumn(fitColumn);
298
299 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
300 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
301
302 // columns which just get dragged along, as they aren't used in asap
303 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
304 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
305 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
306 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
307
308 td.rwKeywordSet().define("OBSMODE", String(""));
309
310 // Now create Table SetUp from the description.
311 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
312 table_ = Table(aNewTab, type_, 0);
313 originalTable_ = table_;
314}
315
316void Scantable::attach()
317{
318 timeCol_.attach(table_, "TIME");
319 srcnCol_.attach(table_, "SRCNAME");
320 srctCol_.attach(table_, "SRCTYPE");
321 specCol_.attach(table_, "SPECTRA");
322 flagsCol_.attach(table_, "FLAGTRA");
323 tsysCol_.attach(table_, "TSYS");
324 cycleCol_.attach(table_,"CYCLENO");
325 scanCol_.attach(table_, "SCANNO");
326 beamCol_.attach(table_, "BEAMNO");
327 ifCol_.attach(table_, "IFNO");
328 polCol_.attach(table_, "POLNO");
329 integrCol_.attach(table_, "INTERVAL");
330 azCol_.attach(table_, "AZIMUTH");
331 elCol_.attach(table_, "ELEVATION");
332 dirCol_.attach(table_, "DIRECTION");
333 fldnCol_.attach(table_, "FIELDNAME");
334 rbeamCol_.attach(table_, "REFBEAMNO");
335
336 mweatheridCol_.attach(table_,"WEATHER_ID");
337 mfitidCol_.attach(table_,"FIT_ID");
338 mfreqidCol_.attach(table_, "FREQ_ID");
339 mtcalidCol_.attach(table_, "TCAL_ID");
340 mfocusidCol_.attach(table_, "FOCUS_ID");
341 mmolidCol_.attach(table_, "MOLECULE_ID");
342
343 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
344 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
345
346}
347
348template<class T, class T2>
349void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
350 const String& colName,
351 const T2& defValue)
352{
353 try {
354 col.attach(table_, colName);
355 } catch (TableError& err) {
356 String errMesg = err.getMesg();
357 if (errMesg == "Table column " + colName + " is unknown") {
358 table_.addColumn(ScalarColumnDesc<T>(colName));
359 col.attach(table_, colName);
360 col.fillColumn(static_cast<T>(defValue));
361 } else {
362 throw;
363 }
364 } catch (...) {
365 throw;
366 }
367}
368
369template<class T, class T2>
370void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
371 const String& colName,
372 const Array<T2>& defValue)
373{
374 try {
375 col.attach(table_, colName);
376 } catch (TableError& err) {
377 String errMesg = err.getMesg();
378 if (errMesg == "Table column " + colName + " is unknown") {
379 table_.addColumn(ArrayColumnDesc<T>(colName));
380 col.attach(table_, colName);
381
382 int size = 0;
383 ArrayIterator<T2>& it = defValue.begin();
384 while (it != defValue.end()) {
385 ++size;
386 ++it;
387 }
388 IPosition ip(1, size);
389 Array<T>& arr(ip);
390 for (int i = 0; i < size; ++i)
391 arr[i] = static_cast<T>(defValue[i]);
392
393 col.fillColumn(arr);
394 } else {
395 throw;
396 }
397 } catch (...) {
398 throw;
399 }
400}
401
402void Scantable::setHeader(const STHeader& sdh)
403{
404 table_.rwKeywordSet().define("nIF", sdh.nif);
405 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
406 table_.rwKeywordSet().define("nPol", sdh.npol);
407 table_.rwKeywordSet().define("nChan", sdh.nchan);
408 table_.rwKeywordSet().define("Observer", sdh.observer);
409 table_.rwKeywordSet().define("Project", sdh.project);
410 table_.rwKeywordSet().define("Obstype", sdh.obstype);
411 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
412 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
413 table_.rwKeywordSet().define("Equinox", sdh.equinox);
414 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
415 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
416 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
417 table_.rwKeywordSet().define("UTC", sdh.utc);
418 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
419 table_.rwKeywordSet().define("Epoch", sdh.epoch);
420 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
421}
422
423STHeader Scantable::getHeader() const
424{
425 STHeader sdh;
426 table_.keywordSet().get("nBeam",sdh.nbeam);
427 table_.keywordSet().get("nIF",sdh.nif);
428 table_.keywordSet().get("nPol",sdh.npol);
429 table_.keywordSet().get("nChan",sdh.nchan);
430 table_.keywordSet().get("Observer", sdh.observer);
431 table_.keywordSet().get("Project", sdh.project);
432 table_.keywordSet().get("Obstype", sdh.obstype);
433 table_.keywordSet().get("AntennaName", sdh.antennaname);
434 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
435 table_.keywordSet().get("Equinox", sdh.equinox);
436 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
437 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
438 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
439 table_.keywordSet().get("UTC", sdh.utc);
440 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
441 table_.keywordSet().get("Epoch", sdh.epoch);
442 table_.keywordSet().get("POLTYPE", sdh.poltype);
443 return sdh;
444}
445
446void Scantable::setSourceType( int stype )
447{
448 if ( stype < 0 || stype > 1 )
449 throw(AipsError("Illegal sourcetype."));
450 TableVector<Int> tabvec(table_, "SRCTYPE");
451 tabvec = Int(stype);
452}
453
454bool Scantable::conformant( const Scantable& other )
455{
456 return this->getHeader().conformant(other.getHeader());
457}
458
459
460
461std::string Scantable::formatSec(Double x) const
462{
463 Double xcop = x;
464 MVTime mvt(xcop/24./3600.); // make days
465
466 if (x < 59.95)
467 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
468 else if (x < 3599.95)
469 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
470 else {
471 ostringstream oss;
472 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
473 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
474 return String(oss);
475 }
476};
477
478std::string Scantable::formatDirection(const MDirection& md) const
479{
480 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
481 Int prec = 7;
482
483 String ref = md.getRefString();
484 MVAngle mvLon(t[0]);
485 String sLon = mvLon.string(MVAngle::TIME,prec);
486 uInt tp = md.getRef().getType();
487 if (tp == MDirection::GALACTIC ||
488 tp == MDirection::SUPERGAL ) {
489 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
490 }
491 MVAngle mvLat(t[1]);
492 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
493 return ref + String(" ") + sLon + String(" ") + sLat;
494}
495
496
497std::string Scantable::getFluxUnit() const
498{
499 return table_.keywordSet().asString("FluxUnit");
500}
501
502void Scantable::setFluxUnit(const std::string& unit)
503{
504 String tmp(unit);
505 Unit tU(tmp);
506 if (tU==Unit("K") || tU==Unit("Jy")) {
507 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
508 } else {
509 throw AipsError("Illegal unit - must be compatible with Jy or K");
510 }
511}
512
513void Scantable::setInstrument(const std::string& name)
514{
515 bool throwIt = true;
516 // create an Instrument to see if this is valid
517 STAttr::convertInstrument(name, throwIt);
518 String nameU(name);
519 nameU.upcase();
520 table_.rwKeywordSet().define(String("AntennaName"), nameU);
521}
522
523void Scantable::setFeedType(const std::string& feedtype)
524{
525 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
526 std::string msg = "Illegal feed type "+ feedtype;
527 throw(casa::AipsError(msg));
528 }
529 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
530}
531
532MPosition Scantable::getAntennaPosition() const
533{
534 Vector<Double> antpos;
535 table_.keywordSet().get("AntennaPosition", antpos);
536 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
537 return MPosition(mvpos);
538}
539
540void Scantable::makePersistent(const std::string& filename)
541{
542 String inname(filename);
543 Path path(inname);
544 /// @todo reindex SCANNO, recompute nbeam, nif, npol
545 inname = path.expandedName();
546 // 2011/03/04 TN
547 // We can comment out this workaround since the essential bug is
548 // fixed in casacore (r20889 in google code).
549 table_.deepCopy(inname, Table::New);
550// // WORKAROUND !!! for Table bug
551// // Remove when fixed in casacore
552// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
553// Table tab = table_.copyToMemoryTable(generateName());
554// tab.deepCopy(inname, Table::New);
555// tab.markForDelete();
556//
557// } else {
558// table_.deepCopy(inname, Table::New);
559// }
560}
561
562int Scantable::nbeam( int scanno ) const
563{
564 if ( scanno < 0 ) {
565 Int n;
566 table_.keywordSet().get("nBeam",n);
567 return int(n);
568 } else {
569 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
570 Table t = table_(table_.col("SCANNO") == scanno);
571 ROTableRow row(t);
572 const TableRecord& rec = row.get(0);
573 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
574 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
575 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
576 ROTableVector<uInt> v(subt, "BEAMNO");
577 return int(v.nelements());
578 }
579 return 0;
580}
581
582int Scantable::nif( int scanno ) const
583{
584 if ( scanno < 0 ) {
585 Int n;
586 table_.keywordSet().get("nIF",n);
587 return int(n);
588 } else {
589 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
590 Table t = table_(table_.col("SCANNO") == scanno);
591 ROTableRow row(t);
592 const TableRecord& rec = row.get(0);
593 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
594 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
595 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
596 if ( subt.nrow() == 0 ) return 0;
597 ROTableVector<uInt> v(subt, "IFNO");
598 return int(v.nelements());
599 }
600 return 0;
601}
602
603int Scantable::npol( int scanno ) const
604{
605 if ( scanno < 0 ) {
606 Int n;
607 table_.keywordSet().get("nPol",n);
608 return n;
609 } else {
610 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
611 Table t = table_(table_.col("SCANNO") == scanno);
612 ROTableRow row(t);
613 const TableRecord& rec = row.get(0);
614 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
615 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
616 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
617 if ( subt.nrow() == 0 ) return 0;
618 ROTableVector<uInt> v(subt, "POLNO");
619 return int(v.nelements());
620 }
621 return 0;
622}
623
624int Scantable::ncycle( int scanno ) const
625{
626 if ( scanno < 0 ) {
627 Block<String> cols(2);
628 cols[0] = "SCANNO";
629 cols[1] = "CYCLENO";
630 TableIterator it(table_, cols);
631 int n = 0;
632 while ( !it.pastEnd() ) {
633 ++n;
634 ++it;
635 }
636 return n;
637 } else {
638 Table t = table_(table_.col("SCANNO") == scanno);
639 ROTableRow row(t);
640 const TableRecord& rec = row.get(0);
641 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
642 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
643 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
644 if ( subt.nrow() == 0 ) return 0;
645 return int(subt.nrow());
646 }
647 return 0;
648}
649
650
651int Scantable::nrow( int scanno ) const
652{
653 return int(table_.nrow());
654}
655
656int Scantable::nchan( int ifno ) const
657{
658 if ( ifno < 0 ) {
659 Int n;
660 table_.keywordSet().get("nChan",n);
661 return int(n);
662 } else {
663 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
664 // vary with these
665 Table t = table_(table_.col("IFNO") == ifno, 1);
666 if ( t.nrow() == 0 ) return 0;
667 ROArrayColumn<Float> v(t, "SPECTRA");
668 return v.shape(0)(0);
669 }
670 return 0;
671}
672
673int Scantable::nscan() const {
674 Vector<uInt> scannos(scanCol_.getColumn());
675 uInt nout = genSort( scannos, Sort::Ascending,
676 Sort::QuickSort|Sort::NoDuplicates );
677 return int(nout);
678}
679
680int Scantable::getChannels(int whichrow) const
681{
682 return specCol_.shape(whichrow)(0);
683}
684
685int Scantable::getBeam(int whichrow) const
686{
687 return beamCol_(whichrow);
688}
689
690std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
691{
692 Vector<uInt> nos(col.getColumn());
693 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
694 nos.resize(n, True);
695 std::vector<uint> stlout;
696 nos.tovector(stlout);
697 return stlout;
698}
699
700int Scantable::getIF(int whichrow) const
701{
702 return ifCol_(whichrow);
703}
704
705int Scantable::getPol(int whichrow) const
706{
707 return polCol_(whichrow);
708}
709
710std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
711{
712 return formatTime(me, showdate, 0);
713}
714
715std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
716{
717 MVTime mvt(me.getValue());
718 if (showdate)
719 //mvt.setFormat(MVTime::YMD);
720 mvt.setFormat(MVTime::YMD, prec);
721 else
722 //mvt.setFormat(MVTime::TIME);
723 mvt.setFormat(MVTime::TIME, prec);
724 ostringstream oss;
725 oss << mvt;
726 return String(oss);
727}
728
729void Scantable::calculateAZEL()
730{
731 LogIO os( LogOrigin( "Scantable", "calculateAZEL()", WHERE ) ) ;
732 MPosition mp = getAntennaPosition();
733 MEpoch::ROScalarColumn timeCol(table_, "TIME");
734 ostringstream oss;
735 oss << mp;
736 os << "Computed azimuth/elevation using " << endl
737 << String(oss) << endl;
738 for (Int i=0; i<nrow(); ++i) {
739 MEpoch me = timeCol(i);
740 MDirection md = getDirection(i);
741 os << " Time: " << formatTime(me,False)
742 << " Direction: " << formatDirection(md)
743 << endl << " => ";
744 MeasFrame frame(mp, me);
745 Vector<Double> azel =
746 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
747 frame)
748 )().getAngle("rad").getValue();
749 azCol_.put(i,Float(azel[0]));
750 elCol_.put(i,Float(azel[1]));
751 os << "azel: " << azel[0]/C::pi*180.0 << " "
752 << azel[1]/C::pi*180.0 << " (deg)" << LogIO::POST;
753 }
754}
755
756void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
757{
758 for (uInt i=0; i<table_.nrow(); ++i) {
759 Vector<uChar> flgs = flagsCol_(i);
760 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
761 flagsCol_.put(i, flgs);
762 }
763}
764
765std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
766{
767 Vector<uChar> flags;
768 flagsCol_.get(uInt(whichrow), flags);
769 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
770 Vector<Bool> bflag(flags.shape());
771 convertArray(bflag, flags);
772 //bflag = !bflag;
773
774 std::vector<bool> mask;
775 bflag.tovector(mask);
776 return mask;
777}
778
779void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
780 Vector<uChar> flgs)
781{
782 Vector<Float> spcs = specCol_(whichrow);
783 uInt nchannel = spcs.nelements();
784 if (spcs.nelements() != nchannel) {
785 throw(AipsError("Data has incorrect number of channels"));
786 }
787 uChar userflag = 1 << 7;
788 if (unflag) {
789 userflag = 0 << 7;
790 }
791 if (clipoutside) {
792 for (uInt j = 0; j < nchannel; ++j) {
793 Float spc = spcs(j);
794 if ((spc >= uthres) || (spc <= dthres)) {
795 flgs(j) = userflag;
796 }
797 }
798 } else {
799 for (uInt j = 0; j < nchannel; ++j) {
800 Float spc = spcs(j);
801 if ((spc < uthres) && (spc > dthres)) {
802 flgs(j) = userflag;
803 }
804 }
805 }
806}
807
808
809void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
810 std::vector<bool>::const_iterator it;
811 uInt ntrue = 0;
812 if (whichrow >= int(table_.nrow()) ) {
813 throw(AipsError("Invalid row number"));
814 }
815 for (it = msk.begin(); it != msk.end(); ++it) {
816 if ( *it ) {
817 ntrue++;
818 }
819 }
820 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
821 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
822 throw(AipsError("Trying to flag whole scantable."));
823 uChar userflag = 1 << 7;
824 if ( unflag ) {
825 userflag = 0 << 7;
826 }
827 if (whichrow > -1 ) {
828 applyChanFlag(uInt(whichrow), msk, userflag);
829 } else {
830 for ( uInt i=0; i<table_.nrow(); ++i) {
831 applyChanFlag(i, msk, userflag);
832 }
833 }
834}
835
836void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
837{
838 if (whichrow >= table_.nrow() ) {
839 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
840 }
841 Vector<uChar> flgs = flagsCol_(whichrow);
842 if ( msk.size() == 0 ) {
843 flgs = flagval;
844 flagsCol_.put(whichrow, flgs);
845 return;
846 }
847 if ( int(msk.size()) != nchan( getIF(whichrow) ) ) {
848 throw(AipsError("Mask has incorrect number of channels."));
849 }
850 if ( flgs.nelements() != msk.size() ) {
851 throw(AipsError("Mask has incorrect number of channels."
852 " Probably varying with IF. Please flag per IF"));
853 }
854 std::vector<bool>::const_iterator it;
855 uInt j = 0;
856 for (it = msk.begin(); it != msk.end(); ++it) {
857 if ( *it ) {
858 flgs(j) = flagval;
859 }
860 ++j;
861 }
862 flagsCol_.put(whichrow, flgs);
863}
864
865void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
866{
867 if (selector_.empty() && (rows.size() == table_.nrow()) && !unflag)
868 throw(AipsError("Trying to flag whole scantable."));
869
870 uInt rowflag = (unflag ? 0 : 1);
871 std::vector<uInt>::const_iterator it;
872 for (it = rows.begin(); it != rows.end(); ++it)
873 flagrowCol_.put(*it, rowflag);
874}
875
876std::vector<bool> Scantable::getMask(int whichrow) const
877{
878 Vector<uChar> flags;
879 flagsCol_.get(uInt(whichrow), flags);
880 Vector<Bool> bflag(flags.shape());
881 convertArray(bflag, flags);
882 bflag = !bflag;
883 std::vector<bool> mask;
884 bflag.tovector(mask);
885 return mask;
886}
887
888std::vector<float> Scantable::getSpectrum( int whichrow,
889 const std::string& poltype ) const
890{
891 LogIO os( LogOrigin( "Scantable", "getSpectrum()", WHERE ) ) ;
892
893 String ptype = poltype;
894 if (poltype == "" ) ptype = getPolType();
895 if ( whichrow < 0 || whichrow >= nrow() )
896 throw(AipsError("Illegal row number."));
897 std::vector<float> out;
898 Vector<Float> arr;
899 uInt requestedpol = polCol_(whichrow);
900 String basetype = getPolType();
901 if ( ptype == basetype ) {
902 specCol_.get(whichrow, arr);
903 } else {
904 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
905 basetype));
906 uInt row = uInt(whichrow);
907 stpol->setSpectra(getPolMatrix(row));
908 Float fang,fhand;
909 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
910 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
911 stpol->setPhaseCorrections(fang, fhand);
912 arr = stpol->getSpectrum(requestedpol, ptype);
913 }
914 if ( arr.nelements() == 0 )
915
916 os << "Not enough polarisations present to do the conversion."
917 << LogIO::POST;
918 arr.tovector(out);
919 return out;
920}
921
922void Scantable::setSpectrum( const std::vector<float>& spec,
923 int whichrow )
924{
925 Vector<Float> spectrum(spec);
926 Vector<Float> arr;
927 specCol_.get(whichrow, arr);
928 if ( spectrum.nelements() != arr.nelements() )
929 throw AipsError("The spectrum has incorrect number of channels.");
930 specCol_.put(whichrow, spectrum);
931}
932
933
934String Scantable::generateName()
935{
936 return (File::newUniqueName("./","temp")).baseName();
937}
938
939const casa::Table& Scantable::table( ) const
940{
941 return table_;
942}
943
944casa::Table& Scantable::table( )
945{
946 return table_;
947}
948
949std::string Scantable::getPolType() const
950{
951 return table_.keywordSet().asString("POLTYPE");
952}
953
954void Scantable::unsetSelection()
955{
956 table_ = originalTable_;
957 attach();
958 selector_.reset();
959}
960
961void Scantable::setSelection( const STSelector& selection )
962{
963 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
964 if ( tab.nrow() == 0 ) {
965 throw(AipsError("Selection contains no data. Not applying it."));
966 }
967 table_ = tab;
968 attach();
969// tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
970// vector<uint> selectedIFs = getIFNos() ;
971// Int newnIF = selectedIFs.size() ;
972// tab.rwKeywordSet().define("nIF",newnIF) ;
973// if ( newnIF != 0 ) {
974// Int newnChan = 0 ;
975// for ( Int i = 0 ; i < newnIF ; i++ ) {
976// Int nChan = nchan( selectedIFs[i] ) ;
977// if ( newnChan > nChan )
978// newnChan = nChan ;
979// }
980// tab.rwKeywordSet().define("nChan",newnChan) ;
981// }
982// tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
983 selector_ = selection;
984}
985
986
987std::string Scantable::headerSummary()
988{
989 // Format header info
990// STHeader sdh;
991// sdh = getHeader();
992// sdh.print();
993 ostringstream oss;
994 oss.flags(std::ios_base::left);
995 String tmp;
996 // Project
997 table_.keywordSet().get("Project", tmp);
998 oss << setw(15) << "Project:" << tmp << endl;
999 // Observation date
1000 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1001 // Observer
1002 oss << setw(15) << "Observer:"
1003 << table_.keywordSet().asString("Observer") << endl;
1004 // Antenna Name
1005 table_.keywordSet().get("AntennaName", tmp);
1006 oss << setw(15) << "Antenna Name:" << tmp << endl;
1007 // Obs type
1008 table_.keywordSet().get("Obstype", tmp);
1009 // Records (nrow)
1010 oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl;
1011 oss << setw(15) << "Obs. Type:" << tmp << endl;
1012 // Beams, IFs, Polarizations, and Channels
1013 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1014 << setw(15) << "IFs:" << setw(4) << nif() << endl
1015 << setw(15) << "Polarisations:" << setw(4) << npol()
1016 << "(" << getPolType() << ")" << endl
1017 << setw(15) << "Channels:" << nchan() << endl;
1018 // Flux unit
1019 table_.keywordSet().get("FluxUnit", tmp);
1020 oss << setw(15) << "Flux Unit:" << tmp << endl;
1021 // Abscissa Unit
1022 oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl;
1023 // Selection
1024 oss << selector_.print() << endl;
1025
1026 return String(oss);
1027}
1028
1029void Scantable::summary( const std::string& filename )
1030{
1031 ostringstream oss;
1032 ofstream ofs;
1033 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1034
1035 if (filename != "")
1036 ofs.open( filename.c_str(), ios::out );
1037
1038 oss << endl;
1039 oss << asap::SEPERATOR << endl;
1040 oss << " Scan Table Summary" << endl;
1041 oss << asap::SEPERATOR << endl;
1042
1043 // Format header info
1044 oss << headerSummary();
1045 oss << endl;
1046
1047 if (table_.nrow() <= 0){
1048 oss << asap::SEPERATOR << endl;
1049 oss << "The MAIN table is empty: there are no data!!!" << endl;
1050 oss << asap::SEPERATOR << endl;
1051
1052 ols << String(oss) << LogIO::POST;
1053 if (ofs) {
1054 ofs << String(oss) << flush;
1055 ofs.close();
1056 }
1057 return;
1058 }
1059
1060
1061
1062 // main table
1063 String dirtype = "Position ("
1064 + getDirectionRefString()
1065 + ")";
1066 oss.flags(std::ios_base::left);
1067 oss << setw(5) << "Scan"
1068 << setw(15) << "Source"
1069 << setw(35) << "Time range"
1070 << setw(2) << "" << setw(7) << "Int[s]"
1071 << setw(7) << "Record"
1072 << setw(8) << "SrcType"
1073 << setw(8) << "FreqIDs"
1074 << setw(7) << "MolIDs" << endl;
1075 oss << setw(7)<< "" << setw(6) << "Beam"
1076 << setw(23) << dirtype << endl;
1077
1078 oss << asap::SEPERATOR << endl;
1079
1080 // Flush summary and clear up the string
1081 ols << String(oss) << LogIO::POST;
1082 if (ofs) ofs << String(oss) << flush;
1083 oss.str("");
1084 oss.clear();
1085
1086
1087 // Get Freq_ID map
1088 ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID");
1089 Int nfid = ftabIds.nrow();
1090 if (nfid <= 0){
1091 oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl;
1092 oss << asap::SEPERATOR << endl;
1093
1094 ols << String(oss) << LogIO::POST;
1095 if (ofs) {
1096 ofs << String(oss) << flush;
1097 ofs.close();
1098 }
1099 return;
1100 }
1101 // Storages of overall IFNO, POLNO, and nchan per FREQ_ID
1102 // the orders are identical to ID in FREQ subtable
1103 Block< Vector<uInt> > ifNos(nfid), polNos(nfid);
1104 Vector<Int> fIdchans(nfid,-1);
1105 map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair
1106 for (Int i=0; i < nfid; i++){
1107 // fidMap[freqId] returns row number in FREQ subtable
1108 fidMap.insert(pair<uInt, Int>(ftabIds(i),i));
1109 ifNos[i] = Vector<uInt>();
1110 polNos[i] = Vector<uInt>();
1111 }
1112
1113 TableIterator iter(table_, "SCANNO");
1114
1115 // Vars for keeping track of time, freqids, molIds in a SCANNO
1116 Vector<uInt> freqids;
1117 Vector<uInt> molids;
1118 Vector<uInt> beamids(1,0);
1119 Vector<MDirection> beamDirs;
1120 Vector<Int> stypeids(1,0);
1121 Vector<String> stypestrs;
1122 Int nfreq(1);
1123 Int nmol(1);
1124 uInt nbeam(1);
1125 uInt nstype(1);
1126
1127 Double btime(0.0), etime(0.0);
1128 Double meanIntTim(0.0);
1129
1130 uInt currFreqId(0), ftabRow(0);
1131 Int iflen(0), pollen(0);
1132
1133 while (!iter.pastEnd()) {
1134 Table subt = iter.table();
1135 uInt snrow = subt.nrow();
1136 ROTableRow row(subt);
1137 const TableRecord& rec = row.get(0);
1138
1139 // relevant columns
1140 ROScalarColumn<Double> mjdCol(subt,"TIME");
1141 ROScalarColumn<Double> intervalCol(subt,"INTERVAL");
1142 MDirection::ROScalarColumn dirCol(subt,"DIRECTION");
1143
1144 ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID");
1145 ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID");
1146 ROScalarColumn<uInt> beamCol(subt,"BEAMNO");
1147 ROScalarColumn<Int> stypeCol(subt,"SRCTYPE");
1148
1149 ROScalarColumn<uInt> ifNoCol(subt,"IFNO");
1150 ROScalarColumn<uInt> polNoCol(subt,"POLNO");
1151
1152
1153 // Times
1154 meanIntTim = sum(intervalCol.getColumn()) / (double) snrow;
1155 minMax(btime, etime, mjdCol.getColumn());
1156 etime += meanIntTim/C::day;
1157
1158 // MOLECULE_ID and FREQ_ID
1159 molids = getNumbers(molIdCol);
1160 molids.shape(nmol);
1161
1162 freqids = getNumbers(freqIdCol);
1163 freqids.shape(nfreq);
1164
1165 // Add first beamid, and srcNames
1166 beamids.resize(1,False);
1167 beamDirs.resize(1,False);
1168 beamids(0)=beamCol(0);
1169 beamDirs(0)=dirCol(0);
1170 nbeam = 1;
1171
1172 stypeids.resize(1,False);
1173 stypeids(0)=stypeCol(0);
1174 nstype = 1;
1175
1176 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1177 currFreqId=freqIdCol(0);
1178 ftabRow = fidMap[currFreqId];
1179 // Assumes an identical number of channels per FREQ_ID
1180 if (fIdchans(ftabRow) < 0 ) {
1181 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1182 fIdchans(ftabRow)=(*spec).shape()(0);
1183 }
1184 // Should keep ifNos and polNos form the previous SCANNO
1185 if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) {
1186 ifNos[ftabRow].shape(iflen);
1187 iflen++;
1188 ifNos[ftabRow].resize(iflen,True);
1189 ifNos[ftabRow](iflen-1) = ifNoCol(0);
1190 }
1191 if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) {
1192 polNos[ftabRow].shape(pollen);
1193 pollen++;
1194 polNos[ftabRow].resize(pollen,True);
1195 polNos[ftabRow](pollen-1) = polNoCol(0);
1196 }
1197
1198 for (uInt i=1; i < snrow; i++){
1199 // Need to list BEAMNO and DIRECTION in the same order
1200 if ( !anyEQ(beamids,beamCol(i)) ) {
1201 nbeam++;
1202 beamids.resize(nbeam,True);
1203 beamids(nbeam-1)=beamCol(i);
1204 beamDirs.resize(nbeam,True);
1205 beamDirs(nbeam-1)=dirCol(i);
1206 }
1207
1208 // SRCTYPE is Int (getNumber takes only uInt)
1209 if ( !anyEQ(stypeids,stypeCol(i)) ) {
1210 nstype++;
1211 stypeids.resize(nstype,True);
1212 stypeids(nstype-1)=stypeCol(i);
1213 }
1214
1215 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1216 currFreqId=freqIdCol(i);
1217 ftabRow = fidMap[currFreqId];
1218 if (fIdchans(ftabRow) < 0 ) {
1219 const TableRecord& rec = row.get(i);
1220 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1221 fIdchans(ftabRow) = (*spec).shape()(0);
1222 }
1223 if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) {
1224 ifNos[ftabRow].shape(iflen);
1225 iflen++;
1226 ifNos[ftabRow].resize(iflen,True);
1227 ifNos[ftabRow](iflen-1) = ifNoCol(i);
1228 }
1229 if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) {
1230 polNos[ftabRow].shape(pollen);
1231 pollen++;
1232 polNos[ftabRow].resize(pollen,True);
1233 polNos[ftabRow](pollen-1) = polNoCol(i);
1234 }
1235 } // end of row iteration
1236
1237 stypestrs.resize(nstype,False);
1238 for (uInt j=0; j < nstype; j++)
1239 stypestrs(j) = SrcType::getName(stypeids(j));
1240
1241 // Format Scan summary
1242 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1243 << std::left << setw(1) << ""
1244 << setw(15) << rec.asString("SRCNAME")
1245 << setw(21) << MVTime(btime).string(MVTime::YMD,7)
1246 << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7)
1247 << setw(3) << "" << setw(6) << meanIntTim << setw(1) << ""
1248 << std::right << setw(5) << snrow << setw(2) << ""
1249 << std::left << stypestrs << setw(1) << ""
1250 << freqids << setw(1) << ""
1251 << molids << endl;
1252 // Format Beam summary
1253 for (uInt j=0; j < nbeam; j++) {
1254 oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << ""
1255 << formatDirection(beamDirs(j)) << endl;
1256 }
1257 // Flush summary every scan and clear up the string
1258 ols << String(oss) << LogIO::POST;
1259 if (ofs) ofs << String(oss) << flush;
1260 oss.str("");
1261 oss.clear();
1262
1263 ++iter;
1264 } // end of scan iteration
1265 oss << asap::SEPERATOR << endl;
1266
1267 // List FRECUENCIES Table (using STFrequencies.print may be slow)
1268 oss << "FREQUENCIES: " << nfreq << endl;
1269 oss << std::right << setw(5) << "ID" << setw(2) << ""
1270 << std::left << setw(5) << "IFNO" << setw(2) << ""
1271 << setw(8) << "Frame"
1272 << setw(16) << "RefVal"
1273 << setw(7) << "RefPix"
1274 << setw(15) << "Increment"
1275 << setw(9) << "Channels"
1276 << setw(6) << "POLNOs" << endl;
1277 Int tmplen;
1278 for (Int i=0; i < nfid; i++){
1279 // List row=i of FREQUENCIES subtable
1280 ifNos[i].shape(tmplen);
1281 if (tmplen >= 1) {
1282 oss << std::right << setw(5) << ftabIds(i) << setw(2) << ""
1283 << setw(3) << ifNos[i](0) << setw(1) << ""
1284 << std::left << setw(46) << frequencies().print(ftabIds(i))
1285 << setw(2) << ""
1286 << std::right << setw(8) << fIdchans[i] << setw(2) << ""
1287 << std::left << polNos[i];
1288 if (tmplen > 1) {
1289 oss << " (" << tmplen << " chains)";
1290 }
1291 oss << endl;
1292 }
1293
1294 }
1295 oss << asap::SEPERATOR << endl;
1296
1297 // List MOLECULES Table (currently lists all rows)
1298 oss << "MOLECULES: " << endl;
1299 if (molecules().nrow() <= 0) {
1300 oss << " MOLECULES subtable is empty: there are no data" << endl;
1301 } else {
1302 ROTableRow row(molecules().table());
1303 oss << std::right << setw(5) << "ID"
1304 << std::left << setw(3) << ""
1305 << setw(18) << "RestFreq"
1306 << setw(15) << "Name" << endl;
1307 for (Int i=0; i < molecules().nrow(); i++){
1308 const TableRecord& rec=row.get(i);
1309 oss << std::right << setw(5) << rec.asuInt("ID")
1310 << std::left << setw(3) << ""
1311 << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << ""
1312 << rec.asArrayString("NAME") << endl;
1313 }
1314 }
1315 oss << asap::SEPERATOR << endl;
1316 ols << String(oss) << LogIO::POST;
1317 if (ofs) {
1318 ofs << String(oss) << flush;
1319 ofs.close();
1320 }
1321 // return String(oss);
1322}
1323
1324
1325std::string Scantable::oldheaderSummary()
1326{
1327 // Format header info
1328// STHeader sdh;
1329// sdh = getHeader();
1330// sdh.print();
1331 ostringstream oss;
1332 oss.flags(std::ios_base::left);
1333 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1334 << setw(15) << "IFs:" << setw(4) << nif() << endl
1335 << setw(15) << "Polarisations:" << setw(4) << npol()
1336 << "(" << getPolType() << ")" << endl
1337 << setw(15) << "Channels:" << nchan() << endl;
1338 String tmp;
1339 oss << setw(15) << "Observer:"
1340 << table_.keywordSet().asString("Observer") << endl;
1341 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1342 table_.keywordSet().get("Project", tmp);
1343 oss << setw(15) << "Project:" << tmp << endl;
1344 table_.keywordSet().get("Obstype", tmp);
1345 oss << setw(15) << "Obs. Type:" << tmp << endl;
1346 table_.keywordSet().get("AntennaName", tmp);
1347 oss << setw(15) << "Antenna Name:" << tmp << endl;
1348 table_.keywordSet().get("FluxUnit", tmp);
1349 oss << setw(15) << "Flux Unit:" << tmp << endl;
1350 int nid = moleculeTable_.nrow();
1351 Bool firstline = True;
1352 oss << setw(15) << "Rest Freqs:";
1353 for (int i=0; i<nid; i++) {
1354 Table t = table_(table_.col("MOLECULE_ID") == i, 1);
1355 if (t.nrow() > 0) {
1356 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
1357 if (vec.nelements() > 0) {
1358 if (firstline) {
1359 oss << setprecision(10) << vec << " [Hz]" << endl;
1360 firstline=False;
1361 }
1362 else{
1363 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1364 }
1365 } else {
1366 oss << "none" << endl;
1367 }
1368 }
1369 }
1370
1371 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
1372 oss << selector_.print() << endl;
1373 return String(oss);
1374}
1375
1376 //std::string Scantable::summary( const std::string& filename )
1377void Scantable::oldsummary( const std::string& filename )
1378{
1379 ostringstream oss;
1380 ofstream ofs;
1381 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1382
1383 if (filename != "")
1384 ofs.open( filename.c_str(), ios::out );
1385
1386 oss << endl;
1387 oss << asap::SEPERATOR << endl;
1388 oss << " Scan Table Summary" << endl;
1389 oss << asap::SEPERATOR << endl;
1390
1391 // Format header info
1392 oss << oldheaderSummary();
1393 oss << endl;
1394
1395 // main table
1396 String dirtype = "Position ("
1397 + getDirectionRefString()
1398 + ")";
1399 oss.flags(std::ios_base::left);
1400 oss << setw(5) << "Scan" << setw(15) << "Source"
1401 << setw(10) << "Time" << setw(18) << "Integration"
1402 << setw(15) << "Source Type" << endl;
1403 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
1404 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
1405 << setw(8) << "Frame" << setw(16)
1406 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1407 << setw(7) << "Channels"
1408 << endl;
1409 oss << asap::SEPERATOR << endl;
1410
1411 // Flush summary and clear up the string
1412 ols << String(oss) << LogIO::POST;
1413 if (ofs) ofs << String(oss) << flush;
1414 oss.str("");
1415 oss.clear();
1416
1417 TableIterator iter(table_, "SCANNO");
1418 while (!iter.pastEnd()) {
1419 Table subt = iter.table();
1420 ROTableRow row(subt);
1421 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1422 const TableRecord& rec = row.get(0);
1423 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1424 << std::left << setw(1) << ""
1425 << setw(15) << rec.asString("SRCNAME")
1426 << setw(10) << formatTime(timeCol(0), false);
1427 // count the cycles in the scan
1428 TableIterator cyciter(subt, "CYCLENO");
1429 int nint = 0;
1430 while (!cyciter.pastEnd()) {
1431 ++nint;
1432 ++cyciter;
1433 }
1434 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
1435 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1436 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
1437
1438 TableIterator biter(subt, "BEAMNO");
1439 while (!biter.pastEnd()) {
1440 Table bsubt = biter.table();
1441 ROTableRow brow(bsubt);
1442 const TableRecord& brec = brow.get(0);
1443 uInt row0 = bsubt.rowNumbers(table_)[0];
1444 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
1445 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
1446 TableIterator iiter(bsubt, "IFNO");
1447 while (!iiter.pastEnd()) {
1448 Table isubt = iiter.table();
1449 ROTableRow irow(isubt);
1450 const TableRecord& irec = irow.get(0);
1451 oss << setw(9) << "";
1452 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
1453 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1454 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
1455 << endl;
1456
1457 ++iiter;
1458 }
1459 ++biter;
1460 }
1461 // Flush summary every scan and clear up the string
1462 ols << String(oss) << LogIO::POST;
1463 if (ofs) ofs << String(oss) << flush;
1464 oss.str("");
1465 oss.clear();
1466
1467 ++iter;
1468 }
1469 oss << asap::SEPERATOR << endl;
1470 ols << String(oss) << LogIO::POST;
1471 if (ofs) {
1472 ofs << String(oss) << flush;
1473 ofs.close();
1474 }
1475 // return String(oss);
1476}
1477
1478// std::string Scantable::getTime(int whichrow, bool showdate) const
1479// {
1480// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1481// MEpoch me;
1482// if (whichrow > -1) {
1483// me = timeCol(uInt(whichrow));
1484// } else {
1485// Double tm;
1486// table_.keywordSet().get("UTC",tm);
1487// me = MEpoch(MVEpoch(tm));
1488// }
1489// return formatTime(me, showdate);
1490// }
1491
1492std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
1493{
1494 MEpoch me;
1495 me = getEpoch(whichrow);
1496 return formatTime(me, showdate, prec);
1497}
1498
1499MEpoch Scantable::getEpoch(int whichrow) const
1500{
1501 if (whichrow > -1) {
1502 return timeCol_(uInt(whichrow));
1503 } else {
1504 Double tm;
1505 table_.keywordSet().get("UTC",tm);
1506 return MEpoch(MVEpoch(tm));
1507 }
1508}
1509
1510std::string Scantable::getDirectionString(int whichrow) const
1511{
1512 return formatDirection(getDirection(uInt(whichrow)));
1513}
1514
1515
1516SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1517 const MPosition& mp = getAntennaPosition();
1518 const MDirection& md = getDirection(whichrow);
1519 const MEpoch& me = timeCol_(whichrow);
1520 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1521 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1522 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
1523 mfreqidCol_(whichrow));
1524}
1525
1526std::vector< double > Scantable::getAbcissa( int whichrow ) const
1527{
1528 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
1529 std::vector<double> stlout;
1530 int nchan = specCol_(whichrow).nelements();
1531 String us = freqTable_.getUnitString();
1532 if ( us == "" || us == "pixel" || us == "channel" ) {
1533 for (int i=0; i<nchan; ++i) {
1534 stlout.push_back(double(i));
1535 }
1536 return stlout;
1537 }
1538 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
1539 Vector<Double> pixel(nchan);
1540 Vector<Double> world;
1541 indgen(pixel);
1542 if ( Unit(us) == Unit("Hz") ) {
1543 for ( int i=0; i < nchan; ++i) {
1544 Double world;
1545 spc.toWorld(world, pixel[i]);
1546 stlout.push_back(double(world));
1547 }
1548 } else if ( Unit(us) == Unit("km/s") ) {
1549 Vector<Double> world;
1550 spc.pixelToVelocity(world, pixel);
1551 world.tovector(stlout);
1552 }
1553 return stlout;
1554}
1555void Scantable::setDirectionRefString( const std::string & refstr )
1556{
1557 MDirection::Types mdt;
1558 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1559 throw(AipsError("Illegal Direction frame."));
1560 }
1561 if ( refstr == "" ) {
1562 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1563 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1564 } else {
1565 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1566 }
1567}
1568
1569std::string Scantable::getDirectionRefString( ) const
1570{
1571 return table_.keywordSet().asString("DIRECTIONREF");
1572}
1573
1574MDirection Scantable::getDirection(int whichrow ) const
1575{
1576 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1577 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1578 if ( usertype != type ) {
1579 MDirection::Types mdt;
1580 if (!MDirection::getType(mdt, usertype)) {
1581 throw(AipsError("Illegal Direction frame."));
1582 }
1583 return dirCol_.convert(uInt(whichrow), mdt);
1584 } else {
1585 return dirCol_(uInt(whichrow));
1586 }
1587}
1588
1589std::string Scantable::getAbcissaLabel( int whichrow ) const
1590{
1591 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
1592 const MPosition& mp = getAntennaPosition();
1593 const MDirection& md = getDirection(whichrow);
1594 const MEpoch& me = timeCol_(whichrow);
1595 //const Double& rf = mmolidCol_(whichrow);
1596 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1597 SpectralCoordinate spc =
1598 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
1599
1600 String s = "Channel";
1601 Unit u = Unit(freqTable_.getUnitString());
1602 if (u == Unit("km/s")) {
1603 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
1604 } else if (u == Unit("Hz")) {
1605 Vector<String> wau(1);wau = u.getName();
1606 spc.setWorldAxisUnits(wau);
1607 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
1608 }
1609 return s;
1610
1611}
1612
1613/**
1614void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
1615 const std::string& unit )
1616**/
1617void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1618 const std::string& unit )
1619
1620{
1621 ///@todo lookup in line table to fill in name and formattedname
1622 Unit u(unit);
1623 //Quantum<Double> urf(rf, u);
1624 Quantum<Vector<Double> >urf(rf, u);
1625 Vector<String> formattedname(0);
1626 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1627
1628 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1629 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
1630 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1631 tabvec = id;
1632}
1633
1634/**
1635void asap::Scantable::setRestFrequencies( const std::string& name )
1636{
1637 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1638 ///@todo implement
1639}
1640**/
1641
1642void Scantable::setRestFrequencies( const vector<std::string>& name )
1643{
1644 (void) name; // suppress unused warning
1645 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1646 ///@todo implement
1647}
1648
1649std::vector< unsigned int > Scantable::rownumbers( ) const
1650{
1651 std::vector<unsigned int> stlout;
1652 Vector<uInt> vec = table_.rowNumbers();
1653 vec.tovector(stlout);
1654 return stlout;
1655}
1656
1657
1658Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
1659{
1660 ROTableRow row(table_);
1661 const TableRecord& rec = row.get(whichrow);
1662 Table t =
1663 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1664 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1665 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1666 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1667 ROArrayColumn<Float> speccol(t, "SPECTRA");
1668 return speccol.getColumn();
1669}
1670
1671std::vector< std::string > Scantable::columnNames( ) const
1672{
1673 Vector<String> vec = table_.tableDesc().columnNames();
1674 return mathutil::tovectorstring(vec);
1675}
1676
1677MEpoch::Types Scantable::getTimeReference( ) const
1678{
1679 return MEpoch::castType(timeCol_.getMeasRef().getType());
1680}
1681
1682void Scantable::addFit( const STFitEntry& fit, int row )
1683{
1684 //cout << mfitidCol_(uInt(row)) << endl;
1685 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1686 os << mfitidCol_(uInt(row)) << LogIO::POST ;
1687 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1688 mfitidCol_.put(uInt(row), id);
1689}
1690
1691void Scantable::shift(int npix)
1692{
1693 Vector<uInt> fids(mfreqidCol_.getColumn());
1694 genSort( fids, Sort::Ascending,
1695 Sort::QuickSort|Sort::NoDuplicates );
1696 for (uInt i=0; i<fids.nelements(); ++i) {
1697 frequencies().shiftRefPix(npix, fids[i]);
1698 }
1699}
1700
1701String Scantable::getAntennaName() const
1702{
1703 String out;
1704 table_.keywordSet().get("AntennaName", out);
1705 String::size_type pos1 = out.find("@") ;
1706 String::size_type pos2 = out.find("//") ;
1707 if ( pos2 != String::npos )
1708 out = out.substr(pos2+2,pos1-pos2-2) ;
1709 else if ( pos1 != String::npos )
1710 out = out.substr(0,pos1) ;
1711 return out;
1712}
1713
1714int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
1715{
1716 String tbpath;
1717 int ret = 0;
1718 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1719 table_.keywordSet().get("GBT_GO", tbpath);
1720 Table t(tbpath,Table::Old);
1721 // check each scan if other scan of the pair exist
1722 int nscan = scanlist.size();
1723 for (int i = 0; i < nscan; i++) {
1724 Table subt = t( t.col("SCAN") == scanlist[i]+1 );
1725 if (subt.nrow()==0) {
1726 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1727 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1728 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
1729 ret = 1;
1730 break;
1731 }
1732 ROTableRow row(subt);
1733 const TableRecord& rec = row.get(0);
1734 int scan1seqn = rec.asuInt("PROCSEQN");
1735 int laston1 = rec.asuInt("LASTON");
1736 if ( rec.asuInt("PROCSIZE")==2 ) {
1737 if ( i < nscan-1 ) {
1738 Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
1739 if ( subt2.nrow() == 0) {
1740 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1741
1742 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1743 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
1744 ret = 1;
1745 break;
1746 }
1747 ROTableRow row2(subt2);
1748 const TableRecord& rec2 = row2.get(0);
1749 int scan2seqn = rec2.asuInt("PROCSEQN");
1750 int laston2 = rec2.asuInt("LASTON");
1751 if (scan1seqn == 1 && scan2seqn == 2) {
1752 if (laston1 == laston2) {
1753 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1754 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1755 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1756 i +=1;
1757 }
1758 else {
1759 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1760 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1761 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1762 }
1763 }
1764 else if (scan1seqn==2 && scan2seqn == 1) {
1765 if (laston1 == laston2) {
1766 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1767 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1768 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
1769 ret = 1;
1770 break;
1771 }
1772 }
1773 else {
1774 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1775 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1776 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
1777 ret = 1;
1778 break;
1779 }
1780 }
1781 }
1782 else {
1783 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1784 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1785 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
1786 }
1787 //if ( i >= nscan ) break;
1788 }
1789 }
1790 else {
1791 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1792 //cerr<<"No reference to GBT_GO table."<<endl;
1793 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
1794 ret = 1;
1795 }
1796 return ret;
1797}
1798
1799std::vector<double> Scantable::getDirectionVector(int whichrow) const
1800{
1801 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1802 std::vector<double> dir;
1803 Dir.tovector(dir);
1804 return dir;
1805}
1806
1807void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1808 throw( casa::AipsError )
1809{
1810 // assumed that all rows have same nChan
1811 Vector<Float> arr = specCol_( 0 ) ;
1812 int nChan = arr.nelements() ;
1813
1814 // if nmin < 0 or nmax < 0, nothing to do
1815 if ( nmin < 0 ) {
1816 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1817 }
1818 if ( nmax < 0 ) {
1819 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1820 }
1821
1822 // if nmin > nmax, exchange values
1823 if ( nmin > nmax ) {
1824 int tmp = nmax ;
1825 nmax = nmin ;
1826 nmin = tmp ;
1827 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1828 os << "Swap values. Applied range is ["
1829 << nmin << ", " << nmax << "]" << LogIO::POST ;
1830 }
1831
1832 // if nmin exceeds nChan, nothing to do
1833 if ( nmin >= nChan ) {
1834 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1835 }
1836
1837 // if nmax exceeds nChan, reset nmax to nChan
1838 if ( nmax >= nChan-1 ) {
1839 if ( nmin == 0 ) {
1840 // nothing to do
1841 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1842 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1843 return ;
1844 }
1845 else {
1846 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1847 os << "Specified maximum exceeds nChan. Applied range is ["
1848 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1849 nmax = nChan - 1 ;
1850 }
1851 }
1852
1853 // reshape specCol_ and flagCol_
1854 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1855 reshapeSpectrum( nmin, nmax, irow ) ;
1856 }
1857
1858 // update FREQUENCIES subtable
1859 Double refpix ;
1860 Double refval ;
1861 Double increment ;
1862 int freqnrow = freqTable_.table().nrow() ;
1863 Vector<uInt> oldId( freqnrow ) ;
1864 Vector<uInt> newId( freqnrow ) ;
1865 for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
1866 freqTable_.getEntry( refpix, refval, increment, irow ) ;
1867 /***
1868 * need to shift refpix to nmin
1869 * note that channel nmin in old index will be channel 0 in new one
1870 ***/
1871 refval = refval - ( refpix - nmin ) * increment ;
1872 refpix = 0 ;
1873 freqTable_.setEntry( refpix, refval, increment, irow ) ;
1874 }
1875
1876 // update nchan
1877 int newsize = nmax - nmin + 1 ;
1878 table_.rwKeywordSet().define( "nChan", newsize ) ;
1879
1880 // update bandwidth
1881 // assumed all spectra in the scantable have same bandwidth
1882 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1883
1884 return ;
1885}
1886
1887void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1888{
1889 // reshape specCol_ and flagCol_
1890 Vector<Float> oldspec = specCol_( irow ) ;
1891 Vector<uChar> oldflag = flagsCol_( irow ) ;
1892 Vector<Float> oldtsys = tsysCol_( irow ) ;
1893 uInt newsize = nmax - nmin + 1 ;
1894 Slice slice( nmin, newsize, 1 ) ;
1895 specCol_.put( irow, oldspec( slice ) ) ;
1896 flagsCol_.put( irow, oldflag( slice ) ) ;
1897 if ( oldspec.size() == oldtsys.size() )
1898 tsysCol_.put( irow, oldtsys( slice ) ) ;
1899
1900 return ;
1901}
1902
1903void asap::Scantable::regridSpecChannel( double dnu, int nChan )
1904{
1905 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1906 os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ;
1907 int freqnrow = freqTable_.table().nrow() ;
1908 Vector<bool> firstTime( freqnrow, true ) ;
1909 double oldincr, factor;
1910 uInt currId;
1911 Double refpix ;
1912 Double refval ;
1913 Double increment ;
1914 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1915 currId = mfreqidCol_(irow);
1916 vector<double> abcissa = getAbcissa( irow ) ;
1917 if (nChan < 0) {
1918 int oldsize = abcissa.size() ;
1919 double bw = (abcissa[oldsize-1]-abcissa[0]) + \
1920 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ;
1921 nChan = int( ceil( abs(bw/dnu) ) ) ;
1922 }
1923 // actual regridding
1924 regridChannel( nChan, dnu, irow ) ;
1925
1926 // update FREQUENCIES subtable
1927 if (firstTime[currId]) {
1928 oldincr = abcissa[1]-abcissa[0] ;
1929 factor = dnu/oldincr ;
1930 firstTime[currId] = false ;
1931 freqTable_.getEntry( refpix, refval, increment, currId ) ;
1932
1933 //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ;
1934 if (factor > 0 ) {
1935 refpix = (refpix + 0.5)/factor - 0.5;
1936 } else {
1937 refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5;
1938 }
1939 freqTable_.setEntry( refpix, refval, increment*factor, currId ) ;
1940 //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ;
1941 //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ;
1942 }
1943 }
1944}
1945
1946void asap::Scantable::regridChannel( int nChan, double dnu )
1947{
1948 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1949 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
1950 // assumed that all rows have same nChan
1951 Vector<Float> arr = specCol_( 0 ) ;
1952 int oldsize = arr.nelements() ;
1953
1954 // if oldsize == nChan, nothing to do
1955 if ( oldsize == nChan ) {
1956 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
1957 return ;
1958 }
1959
1960 // if oldChan < nChan, unphysical operation
1961 if ( oldsize < nChan ) {
1962 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
1963 return ;
1964 }
1965
1966 // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary)
1967 vector<string> coordinfo = getCoordInfo() ;
1968 string oldinfo = coordinfo[0] ;
1969 coordinfo[0] = "Hz" ;
1970 setCoordInfo( coordinfo ) ;
1971 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1972 regridChannel( nChan, dnu, irow ) ;
1973 }
1974 coordinfo[0] = oldinfo ;
1975 setCoordInfo( coordinfo ) ;
1976
1977
1978 // NOTE: this method does not update metadata such as
1979 // FREQUENCIES subtable, nChan, Bandwidth, etc.
1980
1981 return ;
1982}
1983
1984void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
1985{
1986 // logging
1987 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
1988 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
1989
1990 Vector<Float> oldspec = specCol_( irow ) ;
1991 Vector<uChar> oldflag = flagsCol_( irow ) ;
1992 Vector<Float> oldtsys = tsysCol_( irow ) ;
1993 Vector<Float> newspec( nChan, 0 ) ;
1994 Vector<uChar> newflag( nChan, true ) ;
1995 Vector<Float> newtsys ;
1996 bool regridTsys = false ;
1997 if (oldtsys.size() == oldspec.size()) {
1998 regridTsys = true ;
1999 newtsys.resize(nChan,false) ;
2000 newtsys = 0 ;
2001 }
2002
2003 // regrid
2004 vector<double> abcissa = getAbcissa( irow ) ;
2005 int oldsize = abcissa.size() ;
2006 double olddnu = abcissa[1] - abcissa[0] ;
2007 //int ichan = 0 ;
2008 double wsum = 0.0 ;
2009 Vector<double> zi( nChan+1 ) ;
2010 Vector<double> yi( oldsize + 1 ) ;
2011 yi[0] = abcissa[0] - 0.5 * olddnu ;
2012 for ( int ii = 1 ; ii < oldsize ; ii++ )
2013 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2014 yi[oldsize] = abcissa[oldsize-1] \
2015 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
2016 //zi[0] = abcissa[0] - 0.5 * olddnu ;
2017 zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ;
2018 for ( int ii = 1 ; ii < nChan ; ii++ )
2019 zi[ii] = zi[0] + dnu * ii ;
2020 zi[nChan] = zi[nChan-1] + dnu ;
2021 // Access zi and yi in ascending order
2022 int izs = ((dnu > 0) ? 0 : nChan ) ;
2023 int ize = ((dnu > 0) ? nChan : 0 ) ;
2024 int izincr = ((dnu > 0) ? 1 : -1 ) ;
2025 int ichan = ((olddnu > 0) ? 0 : oldsize ) ;
2026 int iye = ((olddnu > 0) ? oldsize : 0 ) ;
2027 int iyincr = ((olddnu > 0) ? 1 : -1 ) ;
2028 //for ( int ii = izs ; ii != ize ; ii+=izincr ){
2029 int ii = izs ;
2030 while (ii != ize) {
2031 // always zl < zr
2032 double zl = zi[ii] ;
2033 double zr = zi[ii+izincr] ;
2034 // Need to access smaller index for the new spec, flag, and tsys.
2035 // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc.
2036 int i = min(ii, ii+izincr) ;
2037 //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) {
2038 int jj = ichan ;
2039 while (jj != iye) {
2040 // always yl < yr
2041 double yl = yi[jj] ;
2042 double yr = yi[jj+iyincr] ;
2043 // Need to access smaller index for the original spec, flag, and tsys.
2044 // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc.
2045 int j = min(jj, jj+iyincr) ;
2046 if ( yr <= zl ) {
2047 jj += iyincr ;
2048 continue ;
2049 }
2050 else if ( yl <= zl ) {
2051 if ( yr < zr ) {
2052 if (!oldflag[j]) {
2053 newspec[i] += oldspec[j] * ( yr - zl ) ;
2054 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ;
2055 wsum += ( yr - zl ) ;
2056 }
2057 newflag[i] = newflag[i] && oldflag[j] ;
2058 }
2059 else {
2060 if (!oldflag[j]) {
2061 newspec[i] += oldspec[j] * abs(dnu) ;
2062 if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ;
2063 wsum += abs(dnu) ;
2064 }
2065 newflag[i] = newflag[i] && oldflag[j] ;
2066 ichan = jj ;
2067 break ;
2068 }
2069 }
2070 else if ( yl < zr ) {
2071 if ( yr <= zr ) {
2072 if (!oldflag[j]) {
2073 newspec[i] += oldspec[j] * ( yr - yl ) ;
2074 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ;
2075 wsum += ( yr - yl ) ;
2076 }
2077 newflag[i] = newflag[i] && oldflag[j] ;
2078 }
2079 else {
2080 if (!oldflag[j]) {
2081 newspec[i] += oldspec[j] * ( zr - yl ) ;
2082 if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ;
2083 wsum += ( zr - yl ) ;
2084 }
2085 newflag[i] = newflag[i] && oldflag[j] ;
2086 ichan = jj ;
2087 break ;
2088 }
2089 }
2090 else {
2091 ichan = jj - iyincr ;
2092 break ;
2093 }
2094 jj += iyincr ;
2095 }
2096 if ( wsum != 0.0 ) {
2097 newspec[i] /= wsum ;
2098 if (regridTsys) newtsys[i] /= wsum ;
2099 }
2100 wsum = 0.0 ;
2101 ii += izincr ;
2102 }
2103// if ( dnu > 0.0 ) {
2104// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2105// double zl = zi[ii] ;
2106// double zr = zi[ii+1] ;
2107// for ( int j = ichan ; j < oldsize ; j++ ) {
2108// double yl = yi[j] ;
2109// double yr = yi[j+1] ;
2110// if ( yl <= zl ) {
2111// if ( yr <= zl ) {
2112// continue ;
2113// }
2114// else if ( yr <= zr ) {
2115// if (!oldflag[j]) {
2116// newspec[ii] += oldspec[j] * ( yr - zl ) ;
2117// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ;
2118// wsum += ( yr - zl ) ;
2119// }
2120// newflag[ii] = newflag[ii] && oldflag[j] ;
2121// }
2122// else {
2123// if (!oldflag[j]) {
2124// newspec[ii] += oldspec[j] * dnu ;
2125// if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ;
2126// wsum += dnu ;
2127// }
2128// newflag[ii] = newflag[ii] && oldflag[j] ;
2129// ichan = j ;
2130// break ;
2131// }
2132// }
2133// else if ( yl < zr ) {
2134// if ( yr <= zr ) {
2135// if (!oldflag[j]) {
2136// newspec[ii] += oldspec[j] * ( yr - yl ) ;
2137// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ;
2138// wsum += ( yr - yl ) ;
2139// }
2140// newflag[ii] = newflag[ii] && oldflag[j] ;
2141// }
2142// else {
2143// if (!oldflag[j]) {
2144// newspec[ii] += oldspec[j] * ( zr - yl ) ;
2145// if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ;
2146// wsum += ( zr - yl ) ;
2147// }
2148// newflag[ii] = newflag[ii] && oldflag[j] ;
2149// ichan = j ;
2150// break ;
2151// }
2152// }
2153// else {
2154// ichan = j - 1 ;
2155// break ;
2156// }
2157// }
2158// if ( wsum != 0.0 ) {
2159// newspec[ii] /= wsum ;
2160// if (regridTsys) newtsys[ii] /= wsum ;
2161// }
2162// wsum = 0.0 ;
2163// }
2164// }
2165// else if ( dnu < 0.0 ) {
2166// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2167// double zl = zi[ii] ;
2168// double zr = zi[ii+1] ;
2169// for ( int j = ichan ; j < oldsize ; j++ ) {
2170// double yl = yi[j] ;
2171// double yr = yi[j+1] ;
2172// if ( yl >= zl ) {
2173// if ( yr >= zl ) {
2174// continue ;
2175// }
2176// else if ( yr >= zr ) {
2177// if (!oldflag[j]) {
2178// newspec[ii] += oldspec[j] * abs( yr - zl ) ;
2179// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ;
2180// wsum += abs( yr - zl ) ;
2181// }
2182// newflag[ii] = newflag[ii] && oldflag[j] ;
2183// }
2184// else {
2185// if (!oldflag[j]) {
2186// newspec[ii] += oldspec[j] * abs( dnu ) ;
2187// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ;
2188// wsum += abs( dnu ) ;
2189// }
2190// newflag[ii] = newflag[ii] && oldflag[j] ;
2191// ichan = j ;
2192// break ;
2193// }
2194// }
2195// else if ( yl > zr ) {
2196// if ( yr >= zr ) {
2197// if (!oldflag[j]) {
2198// newspec[ii] += oldspec[j] * abs( yr - yl ) ;
2199// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ;
2200// wsum += abs( yr - yl ) ;
2201// }
2202// newflag[ii] = newflag[ii] && oldflag[j] ;
2203// }
2204// else {
2205// if (!oldflag[j]) {
2206// newspec[ii] += oldspec[j] * abs( zr - yl ) ;
2207// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ;
2208// wsum += abs( zr - yl ) ;
2209// }
2210// newflag[ii] = newflag[ii] && oldflag[j] ;
2211// ichan = j ;
2212// break ;
2213// }
2214// }
2215// else {
2216// ichan = j - 1 ;
2217// break ;
2218// }
2219// }
2220// if ( wsum != 0.0 ) {
2221// newspec[ii] /= wsum ;
2222// if (regridTsys) newtsys[ii] /= wsum ;
2223// }
2224// wsum = 0.0 ;
2225// }
2226// }
2227// // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
2228// // pile += dnu ;
2229// // wedge = olddnu * ( refChan + 1 ) ;
2230// // while ( wedge < pile ) {
2231// // newspec[0] += olddnu * oldspec[refChan] ;
2232// // newflag[0] = newflag[0] || oldflag[refChan] ;
2233// // //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
2234// // refChan++ ;
2235// // wedge += olddnu ;
2236// // wsum += olddnu ;
2237// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2238// // }
2239// // frac = ( wedge - pile ) / olddnu ;
2240// // wsum += ( 1.0 - frac ) * olddnu ;
2241// // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2242// // newflag[0] = newflag[0] || oldflag[refChan] ;
2243// // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
2244// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2245// // newspec[0] /= wsum ;
2246// // //ofs << "newspec[0] = " << newspec[0] << endl ;
2247// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2248
2249// // /***
2250// // * ichan = 1 - nChan-2
2251// // ***/
2252// // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
2253// // pile += dnu ;
2254// // newspec[ichan] += frac * olddnu * oldspec[refChan] ;
2255// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2256// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
2257// // refChan++ ;
2258// // wedge += olddnu ;
2259// // wsum = frac * olddnu ;
2260// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2261// // while ( wedge < pile ) {
2262// // newspec[ichan] += olddnu * oldspec[refChan] ;
2263// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2264// // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
2265// // refChan++ ;
2266// // wedge += olddnu ;
2267// // wsum += olddnu ;
2268// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2269// // }
2270// // frac = ( wedge - pile ) / olddnu ;
2271// // wsum += ( 1.0 - frac ) * olddnu ;
2272// // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2273// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2274// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
2275// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2276// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2277// // newspec[ichan] /= wsum ;
2278// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
2279// // }
2280
2281// // /***
2282// // * ichan = nChan-1
2283// // ***/
2284// // // NOTE: Assumed that all spectra have the same bandwidth
2285// // pile += dnu ;
2286// // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
2287// // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
2288// // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2289// // refChan++ ;
2290// // wedge += olddnu ;
2291// // wsum = frac * olddnu ;
2292// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2293// // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
2294// // newspec[nChan-1] += olddnu * oldspec[jchan] ;
2295// // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
2296// // wsum += olddnu ;
2297// // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2298// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2299// // }
2300// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2301// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2302// // newspec[nChan-1] /= wsum ;
2303// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
2304
2305// // // ofs.close() ;
2306
2307 specCol_.put( irow, newspec ) ;
2308 flagsCol_.put( irow, newflag ) ;
2309 if (regridTsys) tsysCol_.put( irow, newtsys );
2310
2311 return ;
2312}
2313
2314void Scantable::regridChannel( int nChan, double dnu, double fmin, int irow )
2315{
2316 Vector<Float> oldspec = specCol_( irow ) ;
2317 Vector<uChar> oldflag = flagsCol_( irow ) ;
2318 Vector<Float> oldtsys = tsysCol_( irow ) ;
2319 Vector<Float> newspec( nChan, 0 ) ;
2320 Vector<uChar> newflag( nChan, true ) ;
2321 Vector<Float> newtsys ;
2322 bool regridTsys = false ;
2323 if (oldtsys.size() == oldspec.size()) {
2324 regridTsys = true ;
2325 newtsys.resize(nChan,false) ;
2326 newtsys = 0 ;
2327 }
2328
2329 // regrid
2330 vector<double> abcissa = getAbcissa( irow ) ;
2331 int oldsize = abcissa.size() ;
2332 double olddnu = abcissa[1] - abcissa[0] ;
2333 //int ichan = 0 ;
2334 double wsum = 0.0 ;
2335 Vector<double> zi( nChan+1 ) ;
2336 Vector<double> yi( oldsize + 1 ) ;
2337 Block<uInt> count( nChan, 0 ) ;
2338 yi[0] = abcissa[0] - 0.5 * olddnu ;
2339 for ( int ii = 1 ; ii < oldsize ; ii++ )
2340 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2341 yi[oldsize] = abcissa[oldsize-1] \
2342 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
2343// cout << "olddnu=" << olddnu << ", dnu=" << dnu << " (diff=" << olddnu-dnu << ")" << endl ;
2344// cout << "yi[0]=" << yi[0] << ", fmin=" << fmin << " (diff=" << yi[0]-fmin << ")" << endl ;
2345// cout << "oldsize=" << oldsize << ", nChan=" << nChan << endl ;
2346
2347 // do not regrid if input parameters are almost same as current
2348 // spectral setup
2349 double dnuDiff = abs( ( dnu - olddnu ) / olddnu ) ;
2350 double oldfmin = min( yi[0], yi[oldsize] ) ;
2351 double fminDiff = abs( ( fmin - oldfmin ) / oldfmin ) ;
2352 double nChanDiff = nChan - oldsize ;
2353 double eps = 1.0e-8 ;
2354 if ( nChanDiff == 0 && dnuDiff < eps && fminDiff < eps )
2355 return ;
2356
2357 //zi[0] = abcissa[0] - 0.5 * olddnu ;
2358 //zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ;
2359 if ( dnu > 0 )
2360 zi[0] = fmin - 0.5 * dnu ;
2361 else
2362 zi[0] = fmin + nChan * abs(dnu) ;
2363 for ( int ii = 1 ; ii < nChan ; ii++ )
2364 zi[ii] = zi[0] + dnu * ii ;
2365 zi[nChan] = zi[nChan-1] + dnu ;
2366 // Access zi and yi in ascending order
2367 int izs = ((dnu > 0) ? 0 : nChan ) ;
2368 int ize = ((dnu > 0) ? nChan : 0 ) ;
2369 int izincr = ((dnu > 0) ? 1 : -1 ) ;
2370 int ichan = ((olddnu > 0) ? 0 : oldsize ) ;
2371 int iye = ((olddnu > 0) ? oldsize : 0 ) ;
2372 int iyincr = ((olddnu > 0) ? 1 : -1 ) ;
2373 //for ( int ii = izs ; ii != ize ; ii+=izincr ){
2374 int ii = izs ;
2375 while (ii != ize) {
2376 // always zl < zr
2377 double zl = zi[ii] ;
2378 double zr = zi[ii+izincr] ;
2379 // Need to access smaller index for the new spec, flag, and tsys.
2380 // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc.
2381 int i = min(ii, ii+izincr) ;
2382 //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) {
2383 int jj = ichan ;
2384 while (jj != iye) {
2385 // always yl < yr
2386 double yl = yi[jj] ;
2387 double yr = yi[jj+iyincr] ;
2388 // Need to access smaller index for the original spec, flag, and tsys.
2389 // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc.
2390 int j = min(jj, jj+iyincr) ;
2391 if ( yr <= zl ) {
2392 jj += iyincr ;
2393 continue ;
2394 }
2395 else if ( yl <= zl ) {
2396 if ( yr < zr ) {
2397 if (!oldflag[j]) {
2398 newspec[i] += oldspec[j] * ( yr - zl ) ;
2399 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ;
2400 wsum += ( yr - zl ) ;
2401 count[i]++ ;
2402 }
2403 newflag[i] = newflag[i] && oldflag[j] ;
2404 }
2405 else {
2406 if (!oldflag[j]) {
2407 newspec[i] += oldspec[j] * abs(dnu) ;
2408 if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ;
2409 wsum += abs(dnu) ;
2410 count[i]++ ;
2411 }
2412 newflag[i] = newflag[i] && oldflag[j] ;
2413 ichan = jj ;
2414 break ;
2415 }
2416 }
2417 else if ( yl < zr ) {
2418 if ( yr <= zr ) {
2419 if (!oldflag[j]) {
2420 newspec[i] += oldspec[j] * ( yr - yl ) ;
2421 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ;
2422 wsum += ( yr - yl ) ;
2423 count[i]++ ;
2424 }
2425 newflag[i] = newflag[i] && oldflag[j] ;
2426 }
2427 else {
2428 if (!oldflag[j]) {
2429 newspec[i] += oldspec[j] * ( zr - yl ) ;
2430 if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ;
2431 wsum += ( zr - yl ) ;
2432 count[i]++ ;
2433 }
2434 newflag[i] = newflag[i] && oldflag[j] ;
2435 ichan = jj ;
2436 break ;
2437 }
2438 }
2439 else {
2440 //ichan = jj - iyincr ;
2441 break ;
2442 }
2443 jj += iyincr ;
2444 }
2445 if ( wsum != 0.0 ) {
2446 newspec[i] /= wsum ;
2447 if (regridTsys) newtsys[i] /= wsum ;
2448 }
2449 wsum = 0.0 ;
2450 ii += izincr ;
2451 }
2452
2453 // flag out channels without data
2454 // this is tentative since there is no specific definition
2455 // on bit flag...
2456 uChar noData = 1 << 7 ;
2457 for ( Int i = 0 ; i < nChan ; i++ ) {
2458 if ( count[i] == 0 )
2459 newflag[i] = noData ;
2460 }
2461
2462 specCol_.put( irow, newspec ) ;
2463 flagsCol_.put( irow, newflag ) ;
2464 if (regridTsys) tsysCol_.put( irow, newtsys );
2465
2466 return ;
2467}
2468
2469std::vector<float> Scantable::getWeather(int whichrow) const
2470{
2471 std::vector<float> out(5);
2472 //Float temperature, pressure, humidity, windspeed, windaz;
2473 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
2474 mweatheridCol_(uInt(whichrow)));
2475
2476
2477 return out;
2478}
2479
2480bool Scantable::getFlagtraFast(uInt whichrow)
2481{
2482 uChar flag;
2483 Vector<uChar> flags;
2484 flagsCol_.get(whichrow, flags);
2485 flag = flags[0];
2486 for (uInt i = 1; i < flags.size(); ++i) {
2487 flag &= flags[i];
2488 }
2489 return ((flag >> 7) == 1);
2490}
2491
2492std::vector<std::string> Scantable::applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite)
2493{
2494 STBaselineTable* btin = new STBaselineTable(bltable);
2495
2496 Vector<Bool> applyCol = btin->getApply();
2497 int nRowBl = applyCol.size();
2498 if (nRowBl != nrow()) {
2499 throw(AipsError("Scantable and bltable have different number of rows."));
2500 }
2501
2502 std::vector<std::string> res;
2503 res.clear();
2504
2505 bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite));
2506 bool bltableidentical = (bltable == outbltable);
2507 STBaselineTable* btout = new STBaselineTable(*this);
2508 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
2509 Vector<Double> timeSecCol = tcol->getColumn();
2510
2511 for (int whichrow = 0; whichrow < nRowBl; ++whichrow) {
2512 if (applyCol[whichrow]) {
2513 std::vector<float> spec = getSpectrum(whichrow);
2514
2515 //--channel mask-- maybe the following choices should be available
2516 std::vector<bool> mask = btin->getMask(whichrow); //use mask_bltable only (default)
2517 //std::vector<bool> mask = getMask(whichrow); // or mask_scantable only
2518 //std::vector<bool> mask = getCompositeChanMask(whichrow, btin->getMask(whichrow)); // or mask_scantable && mask_bltable
2519
2520 STBaselineFunc::FuncName ftype = btin->getFunctionName(whichrow);
2521 std::vector<int> fpar = btin->getFuncParam(whichrow);
2522 std::vector<float> params;
2523 float rms;
2524 std::vector<float> resfit = doApplyBaselineTable(spec, mask, ftype, fpar, params, rms);
2525
2526 setSpectrum(resfit, whichrow);
2527
2528 res.push_back(packFittingResults(whichrow, params, rms));
2529
2530 if (outBaselineTable) {
2531 Vector<Int> fparam(fpar.size());
2532 for (uInt j = 0; j < fparam.size(); ++j) {
2533 fparam[j] = (Int)fpar[j];
2534 }
2535 std::vector<int> maskList0;
2536 maskList0.clear();
2537 for (uInt j = 0; j < mask.size(); ++j) {
2538 if (mask[j]) {
2539 if ((j == 0)||(j == mask.size()-1)) {
2540 maskList0.push_back(j);
2541 } else {
2542 if ((mask[j])&&(!mask[j-1])) {
2543 maskList0.push_back(j);
2544 }
2545 if ((mask[j])&&(!mask[j+1])) {
2546 maskList0.push_back(j);
2547 }
2548 }
2549 }
2550 }
2551 Vector<uInt> maskList(maskList0.size());
2552 for (uInt j = 0; j < maskList0.size(); ++j) {
2553 maskList[j] = (uInt)maskList0[j];
2554 }
2555
2556 if (outbltableexists) {
2557 if (overwrite) {
2558 if (bltableidentical) {
2559 btin->setresult(uInt(whichrow), Vector<Float>(params), Float(rms));
2560 } else {
2561 btout->setresult(uInt(whichrow), Vector<Float>(params), Float(rms));
2562 }
2563 }
2564 } else {
2565 btout->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)),
2566 uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
2567 uInt(0), timeSecCol[whichrow], Bool(true), ftype, fparam,
2568 Vector<Float>(), maskList, Vector<Float>(params),
2569 Float(rms), uInt(spec.size()), Float(3.0), uInt(0),
2570 Float(0.0), uInt(0), Vector<uInt>());
2571 }
2572 }
2573 }
2574 }
2575
2576 if (outBaselineTable) {
2577 if (bltableidentical) {
2578 btin->save(outbltable);
2579 } else {
2580 btout->save(outbltable);
2581 }
2582 }
2583 delete btin;
2584 delete btout;
2585
2586 return res;
2587}
2588
2589std::vector<std::string> Scantable::subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite)
2590{
2591 int nRowBl = blInfoList.size();
2592 int nRowSt = nrow();
2593
2594 std::vector<std::string> res;
2595 res.clear();
2596
2597 bool outBaselineTable = ((outbltable != "") && (!outbltableexists || overwrite));
2598 if ((outbltable != "") && outbltableexists && !overwrite) {
2599 throw(AipsError("Cannot overwrite bltable. Set overwrite=True."));
2600 }
2601
2602 STBaselineTable* bt = new STBaselineTable(*this);
2603 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
2604 Vector<Double> timeSecCol = tcol->getColumn();
2605
2606 if (outBaselineTable && !outbltableexists) {
2607 for (int i = 0; i < nRowSt; ++i) {
2608 bt->appendbasedata(getScan(i), getCycle(i), getBeam(i), getIF(i), getPol(i),
2609 0, timeSecCol[i]);
2610 bt->setApply(i, false);
2611 }
2612 }
2613
2614 for (int i = 0; i < nRowBl; ++i) {
2615 int irow;
2616 STBaselineFunc::FuncName ftype;
2617 std::vector<bool> mask;
2618 std::vector<int> fpar;
2619 float clipth;
2620 int clipn;
2621 bool uself;
2622 float lfth;
2623 std::vector<int> lfedge;
2624 int lfavg;
2625 parseBlInfo(blInfoList[i], irow, ftype, fpar, mask, clipth, clipn, uself, lfth, lfedge, lfavg);
2626
2627 if (irow < nRowSt) {
2628 std::vector<float> spec = getSpectrum(irow);
2629 std::vector<float> params;
2630 float rms;
2631 std::vector<bool> finalmask;
2632
2633 std::vector<float> resfit = doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, clipth, clipn, uself, irow, lfth, lfedge, lfavg);
2634 setSpectrum(resfit, irow);
2635 res.push_back(packFittingResults(irow, params, rms));
2636
2637 if (outBaselineTable) {
2638 Vector<Int> fparam(fpar.size());
2639 for (uInt j = 0; j < fparam.size(); ++j) {
2640 fparam[j] = (Int)fpar[j];
2641 }
2642 std::vector<int> maskList0;
2643 maskList0.clear();
2644 for (uInt j = 0; j < finalmask.size(); ++j) {
2645 if (finalmask[j]) {
2646 if ((j == 0)||(j == finalmask.size()-1)) {
2647 maskList0.push_back(j);
2648 } else {
2649 if ((finalmask[j])&&(!finalmask[j-1])) {
2650 maskList0.push_back(j);
2651 }
2652 if ((finalmask[j])&&(!finalmask[j+1])) {
2653 maskList0.push_back(j);
2654 }
2655 }
2656 }
2657 }
2658 Vector<uInt> maskList(maskList0.size());
2659 for (uInt j = 0; j < maskList0.size(); ++j) {
2660 maskList[j] = (uInt)maskList0[j];
2661 }
2662
2663 bt->setdata(uInt(irow),
2664 uInt(getScan(irow)), uInt(getCycle(irow)),
2665 uInt(getBeam(irow)), uInt(getIF(irow)), uInt(getPol(irow)),
2666 uInt(0), timeSecCol[irow], Bool(true), ftype, fparam,
2667 Vector<Float>(), maskList, Vector<Float>(params),
2668 Float(rms), uInt(spec.size()), Float(clipth), uInt(clipn),
2669 Float(0.0), uInt(0), Vector<uInt>());
2670 }
2671
2672 }
2673 }
2674
2675 if (outBaselineTable) {
2676 bt->save(outbltable);
2677 }
2678 delete bt;
2679
2680 return res;
2681}
2682
2683std::vector<float> Scantable::doApplyBaselineTable(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms)
2684{
2685 std::vector<bool> finalmask;
2686 std::vector<int> lfedge;
2687 return doSubtractBaseline(spec, mask, ftype, fpar, params, rms, finalmask, 0.0, 0, false, 0, 0.0, lfedge, 0);
2688}
2689
2690 std::vector<float> Scantable::doSubtractBaseline(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms, std::vector<bool>& finalmask, float clipth, int clipn, bool uself, int irow, float lfth, std::vector<int>& lfedge, int lfavg)
2691{
2692 //---replace mask with (mask AND mask_linefinder).
2693 if (uself) {
2694 STLineFinder lineFinder = STLineFinder();
2695 lineFinder.setOptions(lfth, 3, lfavg);
2696
2697 int minEdgeSize = getIFNos().size()*2;
2698 int edgeSize = lfedge.size();
2699 std::vector<int> currentEdge;
2700 currentEdge.clear();
2701 if (edgeSize >= 2) {
2702 int idx = 0;
2703 if (edgeSize > 2) {
2704 if (edgeSize < minEdgeSize) {
2705 throw(AipsError("Length of edge element info is less than that of IFs"));
2706 }
2707 idx = 2 * getIF(irow);
2708 }
2709 currentEdge.push_back(lfedge[idx]);
2710 currentEdge.push_back(lfedge[idx+1]);
2711 } else {
2712 throw(AipsError("Wrong length of edge element"));
2713 }
2714 lineFinder.setData(spec);
2715 lineFinder.findLines(getCompositeChanMask(irow, mask), currentEdge, irow);
2716
2717 std::vector<bool> lfcompmask = lineFinder.getMask();
2718 mask.clear();
2719 mask.resize(lfcompmask.size());
2720 for (uInt i = 0; i < mask.size(); ++i) {
2721 mask[i] = lfcompmask[i];
2722 }
2723 }
2724 //---
2725
2726 std::vector<float> res;
2727 if (ftype == STBaselineFunc::Polynomial) {
2728 res = doPolynomialFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn);
2729 } else if (ftype == STBaselineFunc::Chebyshev) {
2730 res = doChebyshevFitting(spec, mask, fpar[0], params, rms, finalmask, clipth, clipn);
2731 } else if (ftype == STBaselineFunc::CSpline) {
2732 if (fpar.size() > 1) { // reading from baseline table in which pieceEdges are already calculated and stored.
2733 res = doCubicSplineFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn);
2734 } else { // usual cspline fitting by giving nPiece only. fpar will be replaced with pieceEdges.
2735 res = doCubicSplineFitting(spec, mask, fpar[0], fpar, params, rms, finalmask, clipth, clipn);
2736 }
2737 } else if (ftype == STBaselineFunc::Sinusoid) {
2738 res = doSinusoidFitting(spec, mask, fpar, params, rms, finalmask, clipth, clipn);
2739 }
2740
2741 return res;
2742}
2743
2744std::string Scantable::packFittingResults(const int irow, const std::vector<float>& params, const float rms)
2745{
2746 // returned value: "irow:params[0],params[1],..,params[n-1]:rms"
2747 ostringstream os;
2748 os << irow << ':';
2749 for (uInt i = 0; i < params.size(); ++i) {
2750 if (i > 0) {
2751 os << ',';
2752 }
2753 os << params[i];
2754 }
2755 os << ':' << rms;
2756
2757 return os.str();
2758}
2759
2760void Scantable::parseBlInfo(const std::string& blInfo, int& irow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF)
2761{
2762 // The baseline info to be parsed must be column-delimited string like
2763 // "0:chebyshev:5:3,5,169,174,485,487" where the elements are
2764 // row number, funcType, funcOrder, maskList, clipThreshold, clipNIter,
2765 // useLineFinder, lfThreshold, lfEdge and lfChanAvgLimit.
2766
2767 std::vector<string> res = splitToStringList(blInfo, ':');
2768 if (res.size() < 4) {
2769 throw(AipsError("baseline info has bad format")) ;
2770 }
2771
2772 string ftype0, fpar0, masklist0, uself0, edge0;
2773 std::vector<int> masklist;
2774
2775 stringstream ss;
2776 ss << res[0];
2777 ss >> irow;
2778 ss.clear(); ss.str("");
2779
2780 ss << res[1];
2781 ss >> ftype0;
2782 if (ftype0 == "poly") {
2783 ftype = STBaselineFunc::Polynomial;
2784 } else if (ftype0 == "cspline") {
2785 ftype = STBaselineFunc::CSpline;
2786 } else if (ftype0 == "sinusoid") {
2787 ftype = STBaselineFunc::Sinusoid;
2788 } else if (ftype0 == "chebyshev") {
2789 ftype = STBaselineFunc::Chebyshev;
2790 } else {
2791 throw(AipsError("invalid function type."));
2792 }
2793 ss.clear(); ss.str("");
2794
2795 ss << res[2];
2796 ss >> fpar0;
2797 fpar = splitToIntList(fpar0, ',');
2798 ss.clear(); ss.str("");
2799
2800 ss << res[3];
2801 ss >> masklist0;
2802 mask = getMaskFromMaskList(nchan(getIF(irow)), splitToIntList(masklist0, ','));
2803
2804 ss << res[4];
2805 ss >> thresClip;
2806 ss.clear(); ss.str("");
2807
2808 ss << res[5];
2809 ss >> nIterClip;
2810 ss.clear(); ss.str("");
2811
2812 ss << res[6];
2813 ss >> uself0;
2814 if (uself0 == "true") {
2815 useLineFinder = true;
2816 } else {
2817 useLineFinder = false;
2818 }
2819 ss.clear(); ss.str("");
2820
2821 if (useLineFinder) {
2822 ss << res[7];
2823 ss >> thresLF;
2824 ss.clear(); ss.str("");
2825
2826 ss << res[8];
2827 ss >> edge0;
2828 edgeLF = splitToIntList(edge0, ',');
2829 ss.clear(); ss.str("");
2830
2831 ss << res[9];
2832 ss >> avgLF;
2833 ss.clear(); ss.str("");
2834 }
2835
2836}
2837
2838std::vector<int> Scantable::splitToIntList(const std::string& s, const char delim)
2839{
2840 istringstream iss(s);
2841 string tmp;
2842 int tmpi;
2843 std::vector<int> res;
2844 stringstream ss;
2845 while (getline(iss, tmp, delim)) {
2846 ss << tmp;
2847 ss >> tmpi;
2848 res.push_back(tmpi);
2849 ss.clear(); ss.str("");
2850 }
2851
2852 return res;
2853}
2854
2855std::vector<string> Scantable::splitToStringList(const std::string& s, const char delim)
2856{
2857 istringstream iss(s);
2858 std::string tmp;
2859 std::vector<string> res;
2860 while (getline(iss, tmp, delim)) {
2861 res.push_back(tmp);
2862 }
2863
2864 return res;
2865}
2866
2867std::vector<bool> Scantable::getMaskFromMaskList(const int nchan, const std::vector<int>& masklist)
2868{
2869 if (masklist.size() % 2 != 0) {
2870 throw(AipsError("masklist must have even number of elements."));
2871 }
2872
2873 std::vector<bool> res(nchan);
2874
2875 for (int i = 0; i < nchan; ++i) {
2876 res[i] = false;
2877 }
2878 for (uInt j = 0; j < masklist.size(); j += 2) {
2879 for (int i = masklist[j]; i <= masklist[j+1]; ++i) {
2880 res[i] = true;
2881 }
2882 }
2883
2884 return res;
2885}
2886
2887void Scantable::polyBaseline(const std::vector<bool>& mask, int order, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile, const std::string& bltable)
2888{
2889 /****
2890 double TimeStart = mathutil::gettimeofday_sec();
2891 ****/
2892
2893 try {
2894 ofstream ofs;
2895 String coordInfo = "";
2896 bool hasSameNchan = true;
2897 bool outTextFile = false;
2898 bool csvFormat = false;
2899
2900 if (blfile != "") {
2901 csvFormat = (blfile.substr(0, 1) == "T");
2902 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
2903 if (ofs) outTextFile = true;
2904 }
2905
2906 if (outLogger || outTextFile) {
2907 coordInfo = getCoordInfo()[0];
2908 if (coordInfo == "") coordInfo = "channel";
2909 hasSameNchan = hasSameNchanOverIFs();
2910 }
2911
2912 bool showProgress;
2913 int minNRow;
2914 parseProgressInfo(progressInfo, showProgress, minNRow);
2915
2916 int nRow = nrow();
2917 std::vector<bool> chanMask;
2918 std::vector<bool> finalChanMask;
2919 float rms;
2920
2921 //---
2922 bool outBaselintTable = (bltable != "");
2923 STBaselineTable* bt = new STBaselineTable(*this);
2924 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
2925 Vector<Double> timeSecCol = tcol->getColumn();
2926 //---
2927
2928 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2929 std::vector<float> sp = getSpectrum(whichrow);
2930 chanMask = getCompositeChanMask(whichrow, mask);
2931 std::vector<float> params(order+1);
2932 int nClipped = 0;
2933 std::vector<float> res = doPolynomialFitting(sp, chanMask, order, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
2934
2935 //---
2936 if (outBaselintTable) {
2937 Vector<Int> fparam(1);
2938 fparam[0] = order;
2939 std::vector<int> finalMaskList0;
2940 finalMaskList0.clear();
2941 for (uInt i = 0; i < finalChanMask.size(); ++i) {
2942 if (finalChanMask[i]) {
2943 if ((i == 0)||(i == finalChanMask.size()-1)) {
2944 finalMaskList0.push_back(i);
2945 } else {
2946 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
2947 finalMaskList0.push_back(i);
2948 }
2949 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
2950 finalMaskList0.push_back(i);
2951 }
2952 }
2953 }
2954 }
2955 Vector<uInt> finalMaskList(finalMaskList0.size());
2956 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
2957 finalMaskList[i] = (uInt)finalMaskList0[i];
2958 }
2959
2960 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
2961 uInt(0),
2962 timeSecCol[whichrow],
2963 Bool(true),
2964 STBaselineFunc::Polynomial,
2965 fparam,
2966 Vector<Float>(),
2967 finalMaskList,
2968 Vector<Float>(params),
2969 Float(rms),
2970 uInt(sp.size()),
2971 Float(thresClip),
2972 uInt(nIterClip),
2973 Float(0.0),
2974 uInt(0),
2975 Vector<uInt>());
2976 } else {
2977 setSpectrum(res, whichrow);
2978 }
2979 //---
2980
2981 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "chebyshevBaseline()", params, nClipped);
2982 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2983 }
2984
2985 //---
2986 if (outBaselintTable) {
2987 bt->save(bltable);
2988 }
2989 //---
2990 delete bt;
2991
2992 if (outTextFile) ofs.close();
2993
2994 } catch (...) {
2995 throw;
2996 }
2997
2998 /****
2999 double TimeEnd = mathutil::gettimeofday_sec();
3000 double elapse1 = TimeEnd - TimeStart;
3001 std::cout << "poly-new : " << elapse1 << " (sec.)" << endl;
3002 ****/
3003}
3004
3005void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, 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, const std::string& bltable)
3006{
3007 try {
3008 ofstream ofs;
3009 String coordInfo = "";
3010 bool hasSameNchan = true;
3011 bool outTextFile = false;
3012 bool csvFormat = false;
3013
3014 if (blfile != "") {
3015 csvFormat = (blfile.substr(0, 1) == "T");
3016 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3017 if (ofs) outTextFile = true;
3018 }
3019
3020 if (outLogger || outTextFile) {
3021 coordInfo = getCoordInfo()[0];
3022 if (coordInfo == "") coordInfo = "channel";
3023 hasSameNchan = hasSameNchanOverIFs();
3024 }
3025
3026 bool showProgress;
3027 int minNRow;
3028 parseProgressInfo(progressInfo, showProgress, minNRow);
3029
3030 int minEdgeSize = getIFNos().size()*2;
3031 STLineFinder lineFinder = STLineFinder();
3032 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3033
3034 int nRow = nrow();
3035 std::vector<bool> chanMask;
3036 std::vector<bool> finalChanMask;
3037 float rms;
3038
3039 //---
3040 bool outBaselintTable = (bltable != "");
3041 STBaselineTable* bt = new STBaselineTable(*this);
3042 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
3043 Vector<Double> timeSecCol = tcol->getColumn();
3044 //---
3045
3046 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3047 std::vector<float> sp = getSpectrum(whichrow);
3048 //-- composote given channel mask and flagtra --------
3049 int edgeSize = edge.size();
3050 std::vector<int> currentEdge;
3051 currentEdge.clear();
3052 if (edgeSize >= 2) {
3053 int idx = 0;
3054 if (edgeSize > 2) {
3055 if (edgeSize < minEdgeSize) {
3056 throw(AipsError("Length of edge element info is less than that of IFs"));
3057 }
3058 idx = 2 * getIF(whichrow);
3059 }
3060 currentEdge.push_back(edge[idx]);
3061 currentEdge.push_back(edge[idx+1]);
3062 } else {
3063 throw(AipsError("Wrong length of edge element"));
3064 }
3065 lineFinder.setData(sp);
3066 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
3067 chanMask = lineFinder.getMask();
3068 //-- composote given channel mask and flagtra END --------
3069
3070 std::vector<float> params(order+1);
3071 int nClipped = 0;
3072 std::vector<float> res = doPolynomialFitting(sp, chanMask, order, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
3073
3074 if (outBaselintTable) {
3075 Vector<Int> fparam(1);
3076 fparam[0] = order;
3077 std::vector<int> finalMaskList0;
3078 finalMaskList0.clear();
3079 for (uInt i = 0; i < finalChanMask.size(); ++i) {
3080 if (finalChanMask[i]) {
3081 if ((i == 0)||(i == finalChanMask.size()-1)) {
3082 finalMaskList0.push_back(i);
3083 } else {
3084 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
3085 finalMaskList0.push_back(i);
3086 }
3087 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
3088 finalMaskList0.push_back(i);
3089 }
3090 }
3091 }
3092 }
3093 Vector<uInt> finalMaskList(finalMaskList0.size());
3094 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
3095 finalMaskList[i] = (uInt)finalMaskList0[i];
3096 }
3097
3098 Vector<uInt> cEdge(currentEdge.size());
3099 for (uInt i = 0; i < currentEdge.size(); ++i) {
3100 cEdge[i] = currentEdge[i];
3101 }
3102
3103 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
3104 uInt(0),
3105 timeSecCol[whichrow],
3106 Bool(true),
3107 STBaselineFunc::Polynomial,
3108 fparam,
3109 Vector<Float>(),
3110 finalMaskList,
3111 Vector<Float>(params),
3112 Float(rms),
3113 uInt(sp.size()),
3114 Float(thresClip),
3115 uInt(nIterClip),
3116 Float(threshold),
3117 uInt(chanAvgLimit),
3118 cEdge);
3119 } else {
3120 setSpectrum(res, whichrow);
3121 }
3122
3123 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()", params, nClipped);
3124 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3125 }
3126
3127 //---
3128 if (outBaselintTable) {
3129 bt->save(bltable);
3130 }
3131 //---
3132 delete bt;
3133
3134 if (outTextFile) ofs.close();
3135
3136 } catch (...) {
3137 throw;
3138 }
3139}
3140
3141void Scantable::chebyshevBaseline(const std::vector<bool>& mask, int order, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile, const std::string& bltable)
3142{
3143 //
3144 double TimeStart = mathutil::gettimeofday_sec();
3145 //
3146
3147 try {
3148 ofstream ofs;
3149 String coordInfo = "";
3150 bool hasSameNchan = true;
3151 bool outTextFile = false;
3152 bool csvFormat = false;
3153
3154 if (blfile != "") {
3155 csvFormat = (blfile.substr(0, 1) == "T");
3156 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3157 if (ofs) outTextFile = true;
3158 }
3159
3160 if (outLogger || outTextFile) {
3161 coordInfo = getCoordInfo()[0];
3162 if (coordInfo == "") coordInfo = "channel";
3163 hasSameNchan = hasSameNchanOverIFs();
3164 }
3165
3166 bool showProgress;
3167 int minNRow;
3168 parseProgressInfo(progressInfo, showProgress, minNRow);
3169
3170 int nRow = nrow();
3171 std::vector<bool> chanMask;
3172 std::vector<bool> finalChanMask;
3173 float rms;
3174
3175 //---
3176 bool outBaselintTable = (bltable != "");
3177 STBaselineTable* bt = new STBaselineTable(*this);
3178 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
3179 Vector<Double> timeSecCol = tcol->getColumn();
3180 //---
3181
3182 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3183 std::vector<float> sp = getSpectrum(whichrow);
3184 chanMask = getCompositeChanMask(whichrow, mask);
3185 std::vector<float> params(order+1);
3186 int nClipped = 0;
3187 std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
3188
3189 //---
3190 if (outBaselintTable) {
3191 Vector<Int> fparam(1);
3192 fparam[0] = order;
3193 std::vector<int> finalMaskList0;
3194 finalMaskList0.clear();
3195 for (uInt i = 0; i < finalChanMask.size(); ++i) {
3196 if (finalChanMask[i]) {
3197 if ((i == 0)||(i == finalChanMask.size()-1)) {
3198 finalMaskList0.push_back(i);
3199 } else {
3200 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
3201 finalMaskList0.push_back(i);
3202 }
3203 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
3204 finalMaskList0.push_back(i);
3205 }
3206 }
3207 }
3208 }
3209 Vector<uInt> finalMaskList(finalMaskList0.size());
3210 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
3211 finalMaskList[i] = (uInt)finalMaskList0[i];
3212 }
3213
3214 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
3215 uInt(0),
3216 timeSecCol[whichrow],
3217 Bool(true),
3218 STBaselineFunc::Chebyshev,
3219 fparam,
3220 Vector<Float>(),
3221 finalMaskList,
3222 Vector<Float>(params),
3223 Float(rms),
3224 uInt(sp.size()),
3225 Float(thresClip),
3226 uInt(nIterClip),
3227 Float(0.0),
3228 uInt(0),
3229 Vector<uInt>());
3230 } else {
3231 setSpectrum(res, whichrow);
3232 }
3233 //---
3234
3235 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "chebyshevBaseline()", params, nClipped);
3236 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3237 }
3238
3239 //---
3240 if (outBaselintTable) {
3241 bt->save(bltable);
3242 }
3243 //---
3244 delete bt;
3245
3246 if (outTextFile) ofs.close();
3247
3248 } catch (...) {
3249 throw;
3250 }
3251
3252 double TimeEnd = mathutil::gettimeofday_sec();
3253 double elapse1 = TimeEnd - TimeStart;
3254 std::cout << "cheby : " << elapse1 << " (sec.)" << endl;
3255}
3256
3257void Scantable::autoChebyshevBaseline(const std::vector<bool>& mask, int order, 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, const std::string& bltable)
3258{
3259 try {
3260 ofstream ofs;
3261 String coordInfo = "";
3262 bool hasSameNchan = true;
3263 bool outTextFile = false;
3264 bool csvFormat = false;
3265
3266 if (blfile != "") {
3267 csvFormat = (blfile.substr(0, 1) == "T");
3268 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3269 if (ofs) outTextFile = true;
3270 }
3271
3272 if (outLogger || outTextFile) {
3273 coordInfo = getCoordInfo()[0];
3274 if (coordInfo == "") coordInfo = "channel";
3275 hasSameNchan = hasSameNchanOverIFs();
3276 }
3277
3278 bool showProgress;
3279 int minNRow;
3280 parseProgressInfo(progressInfo, showProgress, minNRow);
3281
3282 int minEdgeSize = getIFNos().size()*2;
3283 STLineFinder lineFinder = STLineFinder();
3284 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3285
3286 int nRow = nrow();
3287 std::vector<bool> chanMask;
3288 std::vector<bool> finalChanMask;
3289 float rms;
3290
3291 //---
3292 bool outBaselintTable = (bltable != "");
3293 STBaselineTable* bt = new STBaselineTable(*this);
3294 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
3295 Vector<Double> timeSecCol = tcol->getColumn();
3296 //---
3297
3298 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3299 std::vector<float> sp = getSpectrum(whichrow);
3300 //-- composote given channel mask and flagtra --------
3301 int edgeSize = edge.size();
3302 std::vector<int> currentEdge;
3303 currentEdge.clear();
3304 if (edgeSize >= 2) {
3305 int idx = 0;
3306 if (edgeSize > 2) {
3307 if (edgeSize < minEdgeSize) {
3308 throw(AipsError("Length of edge element info is less than that of IFs"));
3309 }
3310 idx = 2 * getIF(whichrow);
3311 }
3312 currentEdge.push_back(edge[idx]);
3313 currentEdge.push_back(edge[idx+1]);
3314 } else {
3315 throw(AipsError("Wrong length of edge element"));
3316 }
3317 lineFinder.setData(sp);
3318 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
3319 chanMask = lineFinder.getMask();
3320 //-- composote given channel mask and flagtra END --------
3321
3322 std::vector<float> params(order+1);
3323 int nClipped = 0;
3324 std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
3325
3326 if (outBaselintTable) {
3327 Vector<Int> fparam(1);
3328 fparam[0] = order;
3329 std::vector<int> finalMaskList0;
3330 finalMaskList0.clear();
3331 for (uInt i = 0; i < finalChanMask.size(); ++i) {
3332 if (finalChanMask[i]) {
3333 if ((i == 0)||(i == finalChanMask.size()-1)) {
3334 finalMaskList0.push_back(i);
3335 } else {
3336 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
3337 finalMaskList0.push_back(i);
3338 }
3339 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
3340 finalMaskList0.push_back(i);
3341 }
3342 }
3343 }
3344 }
3345 Vector<uInt> finalMaskList(finalMaskList0.size());
3346 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
3347 finalMaskList[i] = (uInt)finalMaskList0[i];
3348 }
3349
3350 Vector<uInt> cEdge(currentEdge.size());
3351 for (uInt i = 0; i < currentEdge.size(); ++i) {
3352 cEdge[i] = currentEdge[i];
3353 }
3354
3355 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
3356 uInt(0),
3357 timeSecCol[whichrow],
3358 Bool(true),
3359 STBaselineFunc::Chebyshev,
3360 fparam,
3361 Vector<Float>(),
3362 finalMaskList,
3363 Vector<Float>(params),
3364 Float(rms),
3365 uInt(sp.size()),
3366 Float(thresClip),
3367 uInt(nIterClip),
3368 Float(threshold),
3369 uInt(chanAvgLimit),
3370 cEdge);
3371 } else {
3372 setSpectrum(res, whichrow);
3373 }
3374
3375 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()", params, nClipped);
3376 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3377 }
3378
3379 //---
3380 if (outBaselintTable) {
3381 bt->save(bltable);
3382 }
3383 //---
3384 delete bt;
3385
3386 if (outTextFile) ofs.close();
3387
3388 } catch (...) {
3389 throw;
3390 }
3391}
3392
3393double Scantable::calculateModelSelectionCriteria(const std::string& valname, const std::string& blfunc, int order, const std::vector<bool>& inMask, int whichrow, bool useLineFinder, const std::vector<int>& edge, float threshold, int chanAvgLimit)
3394{
3395 std::vector<float> sp = getSpectrum(whichrow);
3396 std::vector<bool> chanMask;
3397 chanMask.clear();
3398
3399 if (useLineFinder) {
3400 int minEdgeSize = getIFNos().size()*2;
3401
3402 int edgeSize = edge.size();
3403 std::vector<int> currentEdge;
3404 currentEdge.clear();
3405 if (edgeSize >= 2) {
3406 int idx = 0;
3407 if (edgeSize > 2) {
3408 if (edgeSize < minEdgeSize) {
3409 throw(AipsError("Length of edge element info is less than that of IFs"));
3410 }
3411 idx = 2 * getIF(whichrow);
3412 }
3413 currentEdge.push_back(edge[idx]);
3414 currentEdge.push_back(edge[idx+1]);
3415 } else {
3416 throw(AipsError("Wrong length of edge element"));
3417 }
3418
3419 STLineFinder lineFinder = STLineFinder();
3420 lineFinder.setData(sp);
3421 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3422 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
3423 chanMask = lineFinder.getMask();
3424
3425 } else {
3426
3427 chanMask = getCompositeChanMask(whichrow, inMask);
3428 }
3429
3430 return doCalculateModelSelectionCriteria(valname, sp, chanMask, blfunc, order);
3431}
3432
3433double Scantable::doCalculateModelSelectionCriteria(const std::string& valname, const std::vector<float>& spec, const std::vector<bool>& mask, const std::string& blfunc, int order)
3434{
3435 int nparam;
3436 std::vector<float> params;
3437 std::vector<bool> finalChanMask;
3438 float rms;
3439 int nClipped = 0;
3440 std::vector<float> res;
3441 if (blfunc == "poly") {
3442 nparam = order + 1;
3443 res = doPolynomialFitting(spec, mask, order, params, rms, finalChanMask, nClipped);
3444 } else if (blfunc == "chebyshev") {
3445 nparam = order + 1;
3446 res = doChebyshevFitting(spec, mask, order, params, rms, finalChanMask, nClipped);
3447 } else if (blfunc == "cspline") {
3448 std::vector<int> pieceEdges;//(order+1); //order = npiece
3449 nparam = order + 3;
3450 //params.resize(4*order);
3451 res = doCubicSplineFitting(spec, mask, order, false, pieceEdges, params, rms, finalChanMask, nClipped);
3452 } else if (blfunc == "sinusoid") {
3453 std::vector<int> nWaves;
3454 nWaves.clear();
3455 for (int i = 0; i <= order; ++i) {
3456 nWaves.push_back(i);
3457 }
3458 nparam = 2*order + 1; // order = nwave
3459 res = doSinusoidFitting(spec, mask, nWaves, params, rms, finalChanMask, nClipped);
3460 } else {
3461 throw(AipsError("blfunc must be poly, chebyshev, cspline or sinusoid."));
3462 }
3463
3464 double msq = 0.0;
3465 int nusedchan = 0;
3466 int nChan = res.size();
3467 for (int i = 0; i < nChan; ++i) {
3468 if (mask[i]) {
3469 msq += (double)res[i]*(double)res[i];
3470 nusedchan++;
3471 }
3472 }
3473 if (nusedchan == 0) {
3474 throw(AipsError("all channels masked."));
3475 }
3476 msq /= (double)nusedchan;
3477
3478 nparam++; //add 1 for sigma of Gaussian distribution
3479 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
3480
3481 if (valname.find("aic") == 0) {
3482 // Original Akaike Information Criterion (AIC)
3483 double aic = nusedchan * (log(2.0 * PI * msq) + 1.0) + 2.0 * nparam;
3484
3485 // Corrected AIC by Sugiura(1978) (AICc)
3486 if (valname == "aicc") {
3487 if (nusedchan - nparam - 1 <= 0) {
3488 throw(AipsError("channel size is too small to calculate AICc."));
3489 }
3490 aic += 2.0*nparam*(nparam + 1)/(double)(nusedchan - nparam - 1);
3491 }
3492
3493 return aic;
3494
3495 } else if (valname == "bic") {
3496 // Bayesian Information Criterion (BIC)
3497 double bic = nusedchan * log(msq) + nparam * log((double)nusedchan);
3498 return bic;
3499
3500 } else if (valname == "gcv") {
3501 // Generalised Cross Validation
3502 double x = 1.0 - (double)nparam / (double)nusedchan;
3503 double gcv = msq / (x * x);
3504 return gcv;
3505
3506 } else {
3507 throw(AipsError("valname must be aic, aicc, bic or gcv."));
3508 }
3509}
3510
3511double Scantable::getNormalPolynomial(int n, double x) {
3512 if (n == 0) {
3513 return 1.0;
3514 } else if (n > 0) {
3515 double res = 1.0;
3516 for (int i = 0; i < n; ++i) {
3517 res *= x;
3518 }
3519 return res;
3520 } else {
3521 if (x == 0.0) {
3522 throw(AipsError("infinity result: x=0 given for negative power."));
3523 } else {
3524 return pow(x, (double)n);
3525 }
3526 }
3527}
3528
3529double Scantable::getChebyshevPolynomial(int n, double x) {
3530 if ((x < -1.0)||(x > 1.0)) {
3531 throw(AipsError("out of definition range (-1 <= x <= 1)."));
3532 } else if (x == 1.0) {
3533 return 1.0;
3534 } else if (x == 0.0) {
3535 double res;
3536 if (n%2 == 0) {
3537 if (n%4 == 0) {
3538 res = 1.0;
3539 } else {
3540 res = -1.0;
3541 }
3542 } else {
3543 res = 0.0;
3544 }
3545 return res;
3546 } else if (x == -1.0) {
3547 double res = (n%2 == 0 ? 1.0 : -1.0);
3548 return res;
3549 } else if (n < 0) {
3550 throw(AipsError("the order must be zero or positive."));
3551 } else if (n == 0) {
3552 return 1.0;
3553 } else if (n == 1) {
3554 return x;
3555 } else {
3556 double res = 0.0;
3557 for (int m = 0; m <= n/2; ++m) {
3558 double c = 1.0;
3559 if (m > 0) {
3560 for (int i = 1; i <= m; ++i) {
3561 c *= (double)(n-2*m+i)/(double)i;
3562 }
3563 }
3564 res += (m%2 == 0 ? 1.0 : -1.0)*(double)n/(double)(n-m)*pow(2.0*x, (double)(n-2*m))/2.0*c;
3565 }
3566 return res;
3567 }
3568}
3569
3570std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data, const std::vector<bool>& mask, int order, std::vector<float>& params, float& rms, std::vector<bool>& finalmask, float clipth, int clipn)
3571{
3572 int nClipped = 0;
3573 return doPolynomialFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn);
3574}
3575
3576std::vector<float> Scantable::doPolynomialFitting(const std::vector<float>& data, const std::vector<bool>& mask, int order, std::vector<float>& params, float& rms, std::vector<bool>& finalMask, int& nClipped, float thresClip, int nIterClip, bool getResidual)
3577{
3578 return doLeastSquareFitting(data, mask, &Scantable::getNormalPolynomial, order, params, rms, finalMask, nClipped, thresClip, nIterClip, getResidual);
3579}
3580
3581std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, const std::vector<bool>& mask, int order, std::vector<float>& params, float& rms, std::vector<bool>& finalmask, float clipth, int clipn)
3582{
3583 int nClipped = 0;
3584 return doChebyshevFitting(data, mask, order, params, rms, finalmask, nClipped, clipth, clipn);
3585}
3586
3587std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, const std::vector<bool>& mask, int order, std::vector<float>& params, float& rms, std::vector<bool>& finalMask, int& nClipped, float thresClip, int nIterClip, bool getResidual)
3588{
3589 return doLeastSquareFitting(data, mask, &Scantable::getChebyshevPolynomial, order, params, rms, finalMask, nClipped, thresClip, nIterClip, getResidual);
3590}
3591
3592std::vector<float> Scantable::doLeastSquareFitting(const std::vector<float>& data, const std::vector<bool>& mask, double (Scantable::*pfunc)(int, double), int order, std::vector<float>& params, float& rms, std::vector<bool>& finalMask, int& nClipped, float thresClip, int nIterClip, bool getResidual)
3593{
3594 if (data.size() != mask.size()) {
3595 throw(AipsError("data and mask sizes are not identical"));
3596 }
3597 if (order < 0) {
3598 throw(AipsError("maximum order of polynomial must not be negative."));
3599 }
3600
3601 int nChan = data.size();
3602
3603 finalMask.clear();
3604 finalMask.resize(nChan);
3605
3606 std::vector<int> maskArray;
3607 std::vector<int> x;
3608 for (int i = 0; i < nChan; ++i) {
3609 maskArray.push_back(mask[i] ? 1 : 0);
3610 if (mask[i]) {
3611 x.push_back(i);
3612 }
3613 finalMask[i] = mask[i];
3614 }
3615
3616 int initNData = x.size();
3617
3618 int nData = initNData;
3619 int nDOF = order + 1; //number of parameters to solve.
3620
3621 // xArray : contains elemental values for computing the least-square matrix.
3622 // xArray.size() is nDOF and xArray[*].size() is nChan.
3623 // Each xArray element are as follows:
3624 //
3625 // (for normal polynomials)
3626 // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
3627 // xArray[1] = {0.0, 1.0, 2.0, ..., (nChan-1)}
3628 // xArray[n-1] = ...,
3629 // xArray[n] = {0.0^n, 1.0^n, 2.0^n, ..., (nChan-1)^n}
3630 // where (0 <= n <= order)
3631 //
3632 // (for Chebyshev polynomials)
3633 // xArray[0] = {T0(-1), T0(2/(nChan-1)-1), T0(4/(nChan-1)-1), ..., T0(1)},
3634 // xArray[n-1] = ...,
3635 // xArray[n] = {Tn(-1), Tn(2/(nChan-1)-1), Tn(4/(nChan-1)-1), ..., Tn(1)}
3636 // where (0 <= n <= order),
3637 std::vector<std::vector<double> > xArray;
3638 double xFactor, xShift;
3639 if (pfunc == &Scantable::getChebyshevPolynomial) {
3640 xFactor = 2.0/(double)(nChan - 1);
3641 xShift = -1.0;
3642 } else {
3643 xFactor = 1.0;
3644 xShift = 0.0;
3645 }
3646 for (int i = 0; i < nDOF; ++i) {
3647 std::vector<double> xs;
3648 xs.clear();
3649 for (int j = 0; j < nChan; ++j) {
3650 xs.push_back((this->*pfunc)(i, xFactor*(double)j + xShift));
3651 }
3652 xArray.push_back(xs);
3653 }
3654
3655 std::vector<double> z1, r1, residual;
3656 for (int i = 0; i < nChan; ++i) {
3657 z1.push_back((double)data[i]);
3658 r1.push_back(0.0);
3659 residual.push_back(0.0);
3660 }
3661
3662 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3663 // xMatrix : horizontal concatenation of
3664 // the least-sq. matrix (left) and an
3665 // identity matrix (right).
3666 // the right part is used to calculate the inverse matrix of the left part.
3667 double xMatrix[nDOF][2*nDOF];
3668 double zMatrix[nDOF];
3669 for (int i = 0; i < nDOF; ++i) {
3670 for (int j = 0; j < 2*nDOF; ++j) {
3671 xMatrix[i][j] = 0.0;
3672 }
3673 xMatrix[i][nDOF+i] = 1.0;
3674 zMatrix[i] = 0.0;
3675 }
3676
3677 int nUseData = 0;
3678 for (int k = 0; k < nChan; ++k) {
3679 if (maskArray[k] == 0) continue;
3680
3681 for (int i = 0; i < nDOF; ++i) {
3682 for (int j = i; j < nDOF; ++j) {
3683 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
3684 }
3685 zMatrix[i] += z1[k] * xArray[i][k];
3686 }
3687
3688 nUseData++;
3689 }
3690
3691 if (nUseData < 1) {
3692 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
3693 }
3694
3695 for (int i = 0; i < nDOF; ++i) {
3696 for (int j = 0; j < i; ++j) {
3697 xMatrix[i][j] = xMatrix[j][i];
3698 }
3699 }
3700
3701 std::vector<double> invDiag;
3702 for (int i = 0; i < nDOF; ++i) {
3703 invDiag.push_back(1.0/xMatrix[i][i]);
3704 for (int j = 0; j < nDOF; ++j) {
3705 xMatrix[i][j] *= invDiag[i];
3706 }
3707 }
3708
3709 for (int k = 0; k < nDOF; ++k) {
3710 for (int i = 0; i < nDOF; ++i) {
3711 if (i != k) {
3712 double factor1 = xMatrix[k][k];
3713 double factor2 = xMatrix[i][k];
3714 for (int j = k; j < 2*nDOF; ++j) {
3715 xMatrix[i][j] *= factor1;
3716 xMatrix[i][j] -= xMatrix[k][j]*factor2;
3717 xMatrix[i][j] /= factor1;
3718 }
3719 }
3720 }
3721 double xDiag = xMatrix[k][k];
3722 for (int j = k; j < 2*nDOF; ++j) {
3723 xMatrix[k][j] /= xDiag;
3724 }
3725 }
3726
3727 for (int i = 0; i < nDOF; ++i) {
3728 for (int j = 0; j < nDOF; ++j) {
3729 xMatrix[i][nDOF+j] *= invDiag[j];
3730 }
3731 }
3732 //compute a vector y which consists of the coefficients of Chebyshev polynomials.
3733 std::vector<double> y;
3734 params.clear();
3735 for (int i = 0; i < nDOF; ++i) {
3736 y.push_back(0.0);
3737 for (int j = 0; j < nDOF; ++j) {
3738 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3739 }
3740 params.push_back(y[i]);
3741 }
3742
3743 for (int i = 0; i < nChan; ++i) {
3744 r1[i] = y[0];
3745 for (int j = 1; j < nDOF; ++j) {
3746 r1[i] += y[j]*xArray[j][i];
3747 }
3748 residual[i] = z1[i] - r1[i];
3749 }
3750
3751 double stdDev = 0.0;
3752 for (int i = 0; i < nChan; ++i) {
3753 stdDev += residual[i]*residual[i]*(double)maskArray[i];
3754 }
3755 stdDev = sqrt(stdDev/(double)nData);
3756 rms = (float)stdDev;
3757
3758 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3759 break;
3760 } else {
3761
3762 double thres = stdDev * thresClip;
3763 int newNData = 0;
3764 for (int i = 0; i < nChan; ++i) {
3765 if (abs(residual[i]) >= thres) {
3766 maskArray[i] = 0;
3767 finalMask[i] = false;
3768 }
3769 if (maskArray[i] > 0) {
3770 newNData++;
3771 }
3772 }
3773 if (newNData == nData) {
3774 break; //no more flag to add. iteration stops.
3775 } else {
3776 nData = newNData;
3777 }
3778
3779 }
3780 }
3781
3782 nClipped = initNData - nData;
3783
3784 std::vector<float> result;
3785 result.clear();
3786 if (getResidual) {
3787 for (int i = 0; i < nChan; ++i) {
3788 result.push_back((float)residual[i]);
3789 }
3790 } else {
3791 for (int i = 0; i < nChan; ++i) {
3792 result.push_back((float)r1[i]);
3793 }
3794 }
3795
3796 return result;
3797}
3798
3799void 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, const std::string& bltable)
3800{
3801 try {
3802 ofstream ofs;
3803 String coordInfo = "";
3804 bool hasSameNchan = true;
3805 bool outTextFile = false;
3806 bool csvFormat = false;
3807
3808 if (blfile != "") {
3809 csvFormat = (blfile.substr(0, 1) == "T");
3810 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3811 if (ofs) outTextFile = true;
3812 }
3813
3814 if (outLogger || outTextFile) {
3815 coordInfo = getCoordInfo()[0];
3816 if (coordInfo == "") coordInfo = "channel";
3817 hasSameNchan = hasSameNchanOverIFs();
3818 }
3819
3820 bool showProgress;
3821 int minNRow;
3822 parseProgressInfo(progressInfo, showProgress, minNRow);
3823
3824 int nRow = nrow();
3825 std::vector<bool> chanMask;
3826 std::vector<bool> finalChanMask;
3827 float rms;
3828
3829 //---
3830 bool outBaselintTable = (bltable != "");
3831 STBaselineTable* bt = new STBaselineTable(*this);
3832 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
3833 Vector<Double> timeSecCol = tcol->getColumn();
3834 //---
3835
3836
3837 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3838 std::vector<float> sp = getSpectrum(whichrow);
3839 chanMask = getCompositeChanMask(whichrow, mask);
3840 std::vector<int> pieceEdges;//(nPiece+1);
3841 std::vector<float> params;//(nPiece*4);
3842 int nClipped = 0;
3843 std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, false, pieceEdges, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
3844
3845 //---
3846 if (outBaselintTable) {
3847 Vector<Int> fparam(nPiece);
3848 for (uInt i = 0; i < fparam.size(); ++i) {
3849 fparam[i] = pieceEdges[i];
3850 }
3851 std::vector<int> finalMaskList0;
3852 finalMaskList0.clear();
3853 for (uInt i = 0; i < finalChanMask.size(); ++i) {
3854 if (finalChanMask[i]) {
3855 if ((i == 0)||(i == finalChanMask.size()-1)) {
3856 finalMaskList0.push_back(i);
3857 } else {
3858 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
3859 finalMaskList0.push_back(i);
3860 }
3861 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
3862 finalMaskList0.push_back(i);
3863 }
3864 }
3865 }
3866 }
3867 Vector<uInt> finalMaskList(finalMaskList0.size());
3868 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
3869 finalMaskList[i] = (uInt)finalMaskList0[i];
3870 }
3871
3872 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
3873 uInt(0),
3874 timeSecCol[whichrow],
3875 Bool(true),
3876 STBaselineFunc::CSpline,
3877 fparam,
3878 Vector<Float>(),
3879 finalMaskList,
3880 Vector<Float>(params),
3881 Float(rms),
3882 uInt(sp.size()),
3883 Float(thresClip),
3884 uInt(nIterClip),
3885 Float(0.0),
3886 uInt(0),
3887 Vector<uInt>());
3888 } else {
3889 setSpectrum(res, whichrow);
3890 }
3891 //---
3892
3893 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
3894 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3895 }
3896
3897 //---
3898 if (outBaselintTable) {
3899 bt->save(bltable);
3900 }
3901 //---
3902 delete bt;
3903
3904 if (outTextFile) ofs.close();
3905
3906 } catch (...) {
3907 throw;
3908 }
3909}
3910
3911void 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, const std::string& bltable)
3912{
3913 try {
3914 ofstream ofs;
3915 String coordInfo = "";
3916 bool hasSameNchan = true;
3917 bool outTextFile = false;
3918 bool csvFormat = false;
3919
3920 if (blfile != "") {
3921 csvFormat = (blfile.substr(0, 1) == "T");
3922 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3923 if (ofs) outTextFile = true;
3924 }
3925
3926 if (outLogger || outTextFile) {
3927 coordInfo = getCoordInfo()[0];
3928 if (coordInfo == "") coordInfo = "channel";
3929 hasSameNchan = hasSameNchanOverIFs();
3930 }
3931
3932 bool showProgress;
3933 int minNRow;
3934 parseProgressInfo(progressInfo, showProgress, minNRow);
3935
3936 int minEdgeSize = getIFNos().size()*2;
3937 STLineFinder lineFinder = STLineFinder();
3938 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3939
3940 int nRow = nrow();
3941 std::vector<bool> chanMask;
3942 std::vector<bool> finalChanMask;
3943 float rms;
3944
3945 //---
3946 bool outBaselintTable = (bltable != "");
3947 STBaselineTable* bt = new STBaselineTable(*this);
3948 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
3949 Vector<Double> timeSecCol = tcol->getColumn();
3950 //---
3951
3952 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3953 std::vector<float> sp = getSpectrum(whichrow);
3954 //-- composote given channel mask and flagtra --------
3955 int edgeSize = edge.size();
3956 std::vector<int> currentEdge;
3957 currentEdge.clear();
3958 if (edgeSize >= 2) {
3959 int idx = 0;
3960 if (edgeSize > 2) {
3961 if (edgeSize < minEdgeSize) {
3962 throw(AipsError("Length of edge element info is less than that of IFs"));
3963 }
3964 idx = 2 * getIF(whichrow);
3965 }
3966 currentEdge.push_back(edge[idx]);
3967 currentEdge.push_back(edge[idx+1]);
3968 } else {
3969 throw(AipsError("Wrong length of edge element"));
3970 }
3971 lineFinder.setData(sp);
3972 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
3973 chanMask = lineFinder.getMask();
3974 //-- composote given channel mask and flagtra END --------
3975
3976 std::vector<int> pieceEdges;//(nPiece+1);
3977 std::vector<float> params;//(nPiece*4);
3978 int nClipped = 0;
3979 std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, false, pieceEdges, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
3980
3981 if (outBaselintTable) {
3982 Vector<Int> fparam(nPiece);
3983 for (uInt i = 0; i < fparam.size(); ++i) {
3984 fparam[i] = pieceEdges[i];
3985 }
3986 std::vector<int> finalMaskList0;
3987 finalMaskList0.clear();
3988 for (uInt i = 0; i < finalChanMask.size(); ++i) {
3989 if (finalChanMask[i]) {
3990 if ((i == 0)||(i == finalChanMask.size()-1)) {
3991 finalMaskList0.push_back(i);
3992 } else {
3993 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
3994 finalMaskList0.push_back(i);
3995 }
3996 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
3997 finalMaskList0.push_back(i);
3998 }
3999 }
4000 }
4001 }
4002 Vector<uInt> finalMaskList(finalMaskList0.size());
4003 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
4004 finalMaskList[i] = (uInt)finalMaskList0[i];
4005 }
4006
4007 Vector<uInt> cEdge(currentEdge.size());
4008 for (uInt i = 0; i < currentEdge.size(); ++i) {
4009 cEdge[i] = currentEdge[i];
4010 }
4011
4012 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
4013 uInt(0),
4014 timeSecCol[whichrow],
4015 Bool(true),
4016 STBaselineFunc::CSpline,
4017 fparam,
4018 Vector<Float>(),
4019 finalMaskList,
4020 Vector<Float>(params),
4021 Float(rms),
4022 uInt(sp.size()),
4023 Float(thresClip),
4024 uInt(nIterClip),
4025 Float(threshold),
4026 uInt(chanAvgLimit),
4027 cEdge);
4028 } else {
4029 setSpectrum(res, whichrow);
4030 }
4031
4032 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
4033 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
4034 }
4035
4036 //---
4037 if (outBaselintTable) {
4038 bt->save(bltable);
4039 }
4040 //---
4041 delete bt;
4042
4043 if (outTextFile) ofs.close();
4044
4045 } catch (...) {
4046 throw;
4047 }
4048}
4049
4050std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, std::vector<int>& idxEdge, std::vector<float>& params, float& rms, std::vector<bool>& finalmask, float clipth, int clipn)
4051{
4052 int nClipped = 0;
4053 return doCubicSplineFitting(data, mask, idxEdge.size()-1, true, idxEdge, params, rms, finalmask, nClipped, clipth, clipn);
4054}
4055
4056std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, float& rms, std::vector<bool>& finalmask, float clipth, int clipn)
4057{
4058 int nClipped = 0;
4059 return doCubicSplineFitting(data, mask, nPiece, false, idxEdge, params, rms, finalmask, nClipped, clipth, clipn);
4060}
4061
4062std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, bool useGivenPieceBoundary, std::vector<int>& idxEdge, std::vector<float>& params, float& rms, std::vector<bool>& finalMask, int& nClipped, float thresClip, int nIterClip, bool getResidual)
4063{
4064 if (data.size() != mask.size()) {
4065 throw(AipsError("data and mask sizes are not identical"));
4066 }
4067 if (nPiece < 1) {
4068 throw(AipsError("number of the sections must be one or more"));
4069 }
4070
4071 int nChan = data.size();
4072
4073 finalMask.clear();
4074 finalMask.resize(nChan);
4075
4076 std::vector<int> maskArray(nChan);
4077 std::vector<int> x(nChan);
4078 int j = 0;
4079 for (int i = 0; i < nChan; ++i) {
4080 maskArray[i] = mask[i] ? 1 : 0;
4081 if (mask[i]) {
4082 x[j] = i;
4083 j++;
4084 }
4085 finalMask[i] = mask[i];
4086 }
4087 int initNData = j;
4088
4089 if (initNData < nPiece) {
4090 throw(AipsError("too few non-flagged channels"));
4091 }
4092
4093 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
4094 std::vector<double> invEdge(nPiece-1);
4095
4096 if (useGivenPieceBoundary) {
4097 if ((int)idxEdge.size() != nPiece+1) {
4098 throw(AipsError("pieceEdge.size() must be equal to nPiece+1."));
4099 }
4100 } else {
4101 idxEdge.clear();
4102 idxEdge.resize(nPiece+1);
4103 idxEdge[0] = x[0];
4104 }
4105 for (int i = 1; i < nPiece; ++i) {
4106 int valX = x[nElement*i];
4107 if (!useGivenPieceBoundary) {
4108 idxEdge[i] = valX;
4109 }
4110 invEdge[i-1] = 1.0/(double)valX;
4111 }
4112 if (!useGivenPieceBoundary) {
4113 idxEdge[nPiece] = x[initNData-1]+1;
4114 }
4115
4116 params.clear();
4117 params.resize(nPiece*4);
4118
4119 int nData = initNData;
4120 int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
4121
4122 std::vector<double> x1(nChan), x2(nChan), x3(nChan);
4123 std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan);
4124 std::vector<double> r1(nChan), residual(nChan);
4125 for (int i = 0; i < nChan; ++i) {
4126 double di = (double)i;
4127 double dD = (double)data[i];
4128 x1[i] = di;
4129 x2[i] = di*di;
4130 x3[i] = di*di*di;
4131 z1[i] = dD;
4132 x1z1[i] = dD*di;
4133 x2z1[i] = dD*di*di;
4134 x3z1[i] = dD*di*di*di;
4135 r1[i] = 0.0;
4136 residual[i] = 0.0;
4137 }
4138
4139 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
4140 // xMatrix : horizontal concatenation of
4141 // the least-sq. matrix (left) and an
4142 // identity matrix (right).
4143 // the right part is used to calculate the inverse matrix of the left part.
4144
4145 double xMatrix[nDOF][2*nDOF];
4146 double zMatrix[nDOF];
4147 for (int i = 0; i < nDOF; ++i) {
4148 for (int j = 0; j < 2*nDOF; ++j) {
4149 xMatrix[i][j] = 0.0;
4150 }
4151 xMatrix[i][nDOF+i] = 1.0;
4152 zMatrix[i] = 0.0;
4153 }
4154
4155 for (int n = 0; n < nPiece; ++n) {
4156 int nUseDataInPiece = 0;
4157 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
4158
4159 if (maskArray[i] == 0) continue;
4160
4161 xMatrix[0][0] += 1.0;
4162 xMatrix[0][1] += x1[i];
4163 xMatrix[0][2] += x2[i];
4164 xMatrix[0][3] += x3[i];
4165 xMatrix[1][1] += x2[i];
4166 xMatrix[1][2] += x3[i];
4167 xMatrix[1][3] += x2[i]*x2[i];
4168 xMatrix[2][2] += x2[i]*x2[i];
4169 xMatrix[2][3] += x3[i]*x2[i];
4170 xMatrix[3][3] += x3[i]*x3[i];
4171 zMatrix[0] += z1[i];
4172 zMatrix[1] += x1z1[i];
4173 zMatrix[2] += x2z1[i];
4174 zMatrix[3] += x3z1[i];
4175
4176 for (int j = 0; j < n; ++j) {
4177 double q = 1.0 - x1[i]*invEdge[j];
4178 q = q*q*q;
4179 xMatrix[0][j+4] += q;
4180 xMatrix[1][j+4] += q*x1[i];
4181 xMatrix[2][j+4] += q*x2[i];
4182 xMatrix[3][j+4] += q*x3[i];
4183 for (int k = 0; k < j; ++k) {
4184 double r = 1.0 - x1[i]*invEdge[k];
4185 r = r*r*r;
4186 xMatrix[k+4][j+4] += r*q;
4187 }
4188 xMatrix[j+4][j+4] += q*q;
4189 zMatrix[j+4] += q*z1[i];
4190 }
4191
4192 nUseDataInPiece++;
4193 }
4194
4195 if (nUseDataInPiece < 1) {
4196 std::vector<string> suffixOfPieceNumber(4);
4197 suffixOfPieceNumber[0] = "th";
4198 suffixOfPieceNumber[1] = "st";
4199 suffixOfPieceNumber[2] = "nd";
4200 suffixOfPieceNumber[3] = "rd";
4201 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
4202 ostringstream oss;
4203 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
4204 oss << " piece of the spectrum. can't execute fitting anymore.";
4205 throw(AipsError(String(oss)));
4206 }
4207 }
4208
4209 for (int i = 0; i < nDOF; ++i) {
4210 for (int j = 0; j < i; ++j) {
4211 xMatrix[i][j] = xMatrix[j][i];
4212 }
4213 }
4214
4215 std::vector<double> invDiag(nDOF);
4216 for (int i = 0; i < nDOF; ++i) {
4217 invDiag[i] = 1.0/xMatrix[i][i];
4218 for (int j = 0; j < nDOF; ++j) {
4219 xMatrix[i][j] *= invDiag[i];
4220 }
4221 }
4222
4223 for (int k = 0; k < nDOF; ++k) {
4224 for (int i = 0; i < nDOF; ++i) {
4225 if (i != k) {
4226 double factor1 = xMatrix[k][k];
4227 double factor2 = xMatrix[i][k];
4228 for (int j = k; j < 2*nDOF; ++j) {
4229 xMatrix[i][j] *= factor1;
4230 xMatrix[i][j] -= xMatrix[k][j]*factor2;
4231 xMatrix[i][j] /= factor1;
4232 }
4233 }
4234 }
4235 double xDiag = xMatrix[k][k];
4236 for (int j = k; j < 2*nDOF; ++j) {
4237 xMatrix[k][j] /= xDiag;
4238 }
4239 }
4240
4241 for (int i = 0; i < nDOF; ++i) {
4242 for (int j = 0; j < nDOF; ++j) {
4243 xMatrix[i][nDOF+j] *= invDiag[j];
4244 }
4245 }
4246
4247 //compute a vector y which consists of the coefficients of the best-fit spline curves
4248 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
4249 //cubic terms for the other pieces (in case nPiece>1).
4250 std::vector<double> y(nDOF);
4251 for (int i = 0; i < nDOF; ++i) {
4252 y[i] = 0.0;
4253 for (int j = 0; j < nDOF; ++j) {
4254 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
4255 }
4256 }
4257
4258 double a0 = y[0];
4259 double a1 = y[1];
4260 double a2 = y[2];
4261 double a3 = y[3];
4262
4263 int j = 0;
4264 for (int n = 0; n < nPiece; ++n) {
4265 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
4266 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
4267 }
4268 params[j] = a0;
4269 params[j+1] = a1;
4270 params[j+2] = a2;
4271 params[j+3] = a3;
4272 j += 4;
4273
4274 if (n == nPiece-1) break;
4275
4276 double d = y[4+n];
4277 double iE = invEdge[n];
4278 a0 += d;
4279 a1 -= 3.0*d*iE;
4280 a2 += 3.0*d*iE*iE;
4281 a3 -= d*iE*iE*iE;
4282 }
4283
4284 //subtract constant value for masked regions at the edge of spectrum
4285 if (idxEdge[0] > 0) {
4286 int n = idxEdge[0];
4287 for (int i = 0; i < idxEdge[0]; ++i) {
4288 //--cubic extrapolate--
4289 //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i];
4290 //--linear extrapolate--
4291 //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n];
4292 //--constant--
4293 r1[i] = r1[n];
4294 }
4295 }
4296
4297 if (idxEdge[nPiece] < nChan) {
4298 int n = idxEdge[nPiece]-1;
4299 for (int i = idxEdge[nPiece]; i < nChan; ++i) {
4300 //--cubic extrapolate--
4301 //int m = 4*(nPiece-1);
4302 //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i];
4303 //--linear extrapolate--
4304 //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n];
4305 //--constant--
4306 r1[i] = r1[n];
4307 }
4308 }
4309
4310 for (int i = 0; i < nChan; ++i) {
4311 residual[i] = z1[i] - r1[i];
4312 }
4313
4314 double stdDev = 0.0;
4315 for (int i = 0; i < nChan; ++i) {
4316 stdDev += residual[i]*residual[i]*(double)maskArray[i];
4317 }
4318 stdDev = sqrt(stdDev/(double)nData);
4319 rms = (float)stdDev;
4320
4321 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
4322 break;
4323 } else {
4324
4325 double thres = stdDev * thresClip;
4326 int newNData = 0;
4327 for (int i = 0; i < nChan; ++i) {
4328 if (abs(residual[i]) >= thres) {
4329 maskArray[i] = 0;
4330 finalMask[i] = false;
4331 }
4332 if (maskArray[i] > 0) {
4333 newNData++;
4334 }
4335 }
4336 if (newNData == nData) {
4337 break; //no more flag to add. iteration stops.
4338 } else {
4339 nData = newNData;
4340 }
4341
4342 }
4343 }
4344
4345 nClipped = initNData - nData;
4346
4347 std::vector<float> result(nChan);
4348 if (getResidual) {
4349 for (int i = 0; i < nChan; ++i) {
4350 result[i] = (float)residual[i];
4351 }
4352 } else {
4353 for (int i = 0; i < nChan; ++i) {
4354 result[i] = (float)r1[i];
4355 }
4356 }
4357
4358 return result;
4359}
4360
4361void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const std::string& fftInfo, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
4362//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)
4363{
4364 bool applyFFT;
4365 std::string fftMethod;
4366 std::string fftThresh;
4367
4368 nWaves.clear();
4369
4370 parseFFTInfo(fftInfo, applyFFT, fftMethod, fftThresh);
4371 if (applyFFT) {
4372 string fftThAttr;
4373 float fftThSigma;
4374 int fftThTop;
4375 parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
4376 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
4377 }
4378
4379 addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves);
4380}
4381
4382void Scantable::parseFFTInfo(const std::string& fftInfo, bool& applyFFT, std::string& fftMethod, std::string& fftThresh)
4383{
4384 istringstream iss(fftInfo);
4385 std::string tmp;
4386 std::vector<string> res;
4387 while (getline(iss, tmp, ',')) {
4388 res.push_back(tmp);
4389 }
4390 if (res.size() < 3) {
4391 throw(AipsError("wrong value in 'fftinfo' parameter")) ;
4392 }
4393 applyFFT = (res[0] == "true");
4394 fftMethod = res[1];
4395 fftThresh = res[2];
4396}
4397
4398void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
4399{
4400 uInt idxSigma = fftThresh.find("sigma");
4401 uInt idxTop = fftThresh.find("top");
4402
4403 if (idxSigma == fftThresh.size() - 5) {
4404 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
4405 is >> fftThSigma;
4406 fftThAttr = "sigma";
4407 } else if (idxTop == 0) {
4408 std::istringstream is(fftThresh.substr(3));
4409 is >> fftThTop;
4410 fftThAttr = "top";
4411 } else {
4412 bool isNumber = true;
4413 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
4414 char ch = (fftThresh.substr(i, 1).c_str())[0];
4415 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
4416 isNumber = false;
4417 break;
4418 }
4419 }
4420 if (isNumber) {
4421 std::istringstream is(fftThresh);
4422 is >> fftThSigma;
4423 fftThAttr = "sigma";
4424 } else {
4425 throw(AipsError("fftthresh has a wrong value"));
4426 }
4427 }
4428}
4429
4430void 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)
4431{
4432 std::vector<float> fspec;
4433 if (fftMethod == "fft") {
4434 fspec = execFFT(whichrow, chanMask, false, true);
4435 //} else if (fftMethod == "lsp") {
4436 // fspec = lombScarglePeriodogram(whichrow);
4437 }
4438
4439 if (fftThAttr == "sigma") {
4440 float mean = 0.0;
4441 float mean2 = 0.0;
4442 for (uInt i = 0; i < fspec.size(); ++i) {
4443 mean += fspec[i];
4444 mean2 += fspec[i]*fspec[i];
4445 }
4446 mean /= float(fspec.size());
4447 mean2 /= float(fspec.size());
4448 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
4449
4450 for (uInt i = 0; i < fspec.size(); ++i) {
4451 if (fspec[i] >= thres) {
4452 nWaves.push_back(i);
4453 }
4454 }
4455
4456 } else if (fftThAttr == "top") {
4457 for (int i = 0; i < fftThTop; ++i) {
4458 float max = 0.0;
4459 int maxIdx = 0;
4460 for (uInt j = 0; j < fspec.size(); ++j) {
4461 if (fspec[j] > max) {
4462 max = fspec[j];
4463 maxIdx = j;
4464 }
4465 }
4466 nWaves.push_back(maxIdx);
4467 fspec[maxIdx] = 0.0;
4468 }
4469
4470 }
4471
4472 if (nWaves.size() > 1) {
4473 sort(nWaves.begin(), nWaves.end());
4474 }
4475}
4476
4477void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
4478{
4479 std::vector<int> tempAddNWaves, tempRejectNWaves;
4480 tempAddNWaves.clear();
4481 tempRejectNWaves.clear();
4482
4483 for (uInt i = 0; i < addNWaves.size(); ++i) {
4484 tempAddNWaves.push_back(addNWaves[i]);
4485 }
4486 if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) {
4487 setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves);
4488 }
4489
4490 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
4491 tempRejectNWaves.push_back(rejectNWaves[i]);
4492 }
4493 if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) {
4494 setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves);
4495 }
4496
4497 for (uInt i = 0; i < tempAddNWaves.size(); ++i) {
4498 bool found = false;
4499 for (uInt j = 0; j < nWaves.size(); ++j) {
4500 if (nWaves[j] == tempAddNWaves[i]) {
4501 found = true;
4502 break;
4503 }
4504 }
4505 if (!found) nWaves.push_back(tempAddNWaves[i]);
4506 }
4507
4508 for (uInt i = 0; i < tempRejectNWaves.size(); ++i) {
4509 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
4510 if (*j == tempRejectNWaves[i]) {
4511 j = nWaves.erase(j);
4512 } else {
4513 ++j;
4514 }
4515 }
4516 }
4517
4518 if (nWaves.size() > 1) {
4519 sort(nWaves.begin(), nWaves.end());
4520 unique(nWaves.begin(), nWaves.end());
4521 }
4522}
4523
4524void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves)
4525{
4526 int val = nWaves[0];
4527 int nyquistFreq = nchan(getIF(whichrow))/2+1;
4528 nWaves.clear();
4529 if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759
4530 nWaves.push_back(0);
4531 }
4532 while (val <= nyquistFreq) {
4533 nWaves.push_back(val);
4534 val++;
4535 }
4536}
4537
4538void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo, 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, const std::string& bltable)
4539{
4540 try {
4541 ofstream ofs;
4542 String coordInfo = "";
4543 bool hasSameNchan = true;
4544 bool outTextFile = false;
4545 bool csvFormat = false;
4546
4547 if (blfile != "") {
4548 csvFormat = (blfile.substr(0, 1) == "T");
4549 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
4550 if (ofs) outTextFile = true;
4551 }
4552
4553 if (outLogger || outTextFile) {
4554 coordInfo = getCoordInfo()[0];
4555 if (coordInfo == "") coordInfo = "channel";
4556 hasSameNchan = hasSameNchanOverIFs();
4557 }
4558
4559 bool showProgress;
4560 int minNRow;
4561 parseProgressInfo(progressInfo, showProgress, minNRow);
4562
4563 int nRow = nrow();
4564 std::vector<bool> chanMask;
4565 std::vector<int> nWaves;
4566 std::vector<bool> finalChanMask;
4567 float rms;
4568
4569 //---
4570 bool outBaselintTable = (bltable != "");
4571 STBaselineTable* bt = new STBaselineTable(*this);
4572 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
4573 Vector<Double> timeSecCol = tcol->getColumn();
4574 //---
4575
4576 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
4577 std::vector<float> sp = getSpectrum(whichrow);
4578 chanMask = getCompositeChanMask(whichrow, mask);
4579 selectWaveNumbers(whichrow, chanMask, fftInfo, addNWaves, rejectNWaves, nWaves);
4580
4581 std::vector<float> params;
4582 int nClipped = 0;
4583 std::vector<float> res = doSinusoidFitting(sp, chanMask, nWaves, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
4584
4585 //---
4586 if (outBaselintTable) {
4587 uInt nparam = nWaves.size();
4588 Vector<Int> fparam(nparam);
4589 for (uInt i = 0; i < nparam; ++i) {
4590 fparam[i] = nWaves[i];
4591 }
4592 std::vector<int> finalMaskList0;
4593 finalMaskList0.clear();
4594 for (uInt i = 0; i < finalChanMask.size(); ++i) {
4595 if (finalChanMask[i]) {
4596 if ((i == 0)||(i == finalChanMask.size()-1)) {
4597 finalMaskList0.push_back(i);
4598 } else {
4599 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
4600 finalMaskList0.push_back(i);
4601 }
4602 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
4603 finalMaskList0.push_back(i);
4604 }
4605 }
4606 }
4607 }
4608 Vector<uInt> finalMaskList(finalMaskList0.size());
4609 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
4610 finalMaskList[i] = (uInt)finalMaskList0[i];
4611 }
4612
4613 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
4614 uInt(0),
4615 timeSecCol[whichrow],
4616 Bool(true),
4617 STBaselineFunc::Sinusoid,
4618 fparam,
4619 Vector<Float>(),
4620 finalMaskList,
4621 Vector<Float>(params),
4622 Float(rms),
4623 uInt(sp.size()),
4624 Float(thresClip),
4625 uInt(nIterClip),
4626 Float(0.0),
4627 uInt(0),
4628 Vector<uInt>());
4629 } else {
4630 setSpectrum(res, whichrow);
4631 }
4632 //---
4633
4634 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
4635 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
4636 }
4637
4638 //---
4639 if (outBaselintTable) {
4640 bt->save(bltable);
4641 }
4642 //---
4643 delete bt;
4644
4645 if (outTextFile) ofs.close();
4646
4647 } catch (...) {
4648 throw;
4649 }
4650}
4651
4652void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const std::string& fftInfo, 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, const std::string& bltable)
4653//void 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, const std::string& bltable)
4654{
4655 try {
4656 ofstream ofs;
4657 String coordInfo = "";
4658 bool hasSameNchan = true;
4659 bool outTextFile = false;
4660 bool csvFormat = false;
4661
4662 if (blfile != "") {
4663 csvFormat = (blfile.substr(0, 1) == "T");
4664 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
4665 if (ofs) outTextFile = true;
4666 }
4667
4668 if (outLogger || outTextFile) {
4669 coordInfo = getCoordInfo()[0];
4670 if (coordInfo == "") coordInfo = "channel";
4671 hasSameNchan = hasSameNchanOverIFs();
4672 }
4673
4674 bool showProgress;
4675 int minNRow;
4676 parseProgressInfo(progressInfo, showProgress, minNRow);
4677
4678 int minEdgeSize = getIFNos().size()*2;
4679 STLineFinder lineFinder = STLineFinder();
4680 lineFinder.setOptions(threshold, 3, chanAvgLimit);
4681
4682 int nRow = nrow();
4683 std::vector<bool> chanMask;
4684 std::vector<int> nWaves;
4685 std::vector<bool> finalChanMask;
4686 float rms;
4687
4688 //---
4689 bool outBaselintTable = (bltable != "");
4690 STBaselineTable* bt = new STBaselineTable(*this);
4691 ROScalarColumn<Double> *tcol = new ROScalarColumn<Double>(table_, "TIME");
4692 Vector<Double> timeSecCol = tcol->getColumn();
4693 //---
4694
4695 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
4696 std::vector<float> sp = getSpectrum(whichrow);
4697 //-- composote given channel mask and flagtra --------
4698 int edgeSize = edge.size();
4699 std::vector<int> currentEdge;
4700 currentEdge.clear();
4701 if (edgeSize >= 2) {
4702 int idx = 0;
4703 if (edgeSize > 2) {
4704 if (edgeSize < minEdgeSize) {
4705 throw(AipsError("Length of edge element info is less than that of IFs"));
4706 }
4707 idx = 2 * getIF(whichrow);
4708 }
4709 currentEdge.push_back(edge[idx]);
4710 currentEdge.push_back(edge[idx+1]);
4711 } else {
4712 throw(AipsError("Wrong length of edge element"));
4713 }
4714 lineFinder.setData(sp);
4715 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
4716 chanMask = lineFinder.getMask();
4717 //-- composote given channel mask and flagtra END --------
4718 selectWaveNumbers(whichrow, chanMask, fftInfo, addNWaves, rejectNWaves, nWaves);
4719
4720 std::vector<float> params;
4721 int nClipped = 0;
4722 std::vector<float> res = doSinusoidFitting(sp, chanMask, nWaves, params, rms, finalChanMask, nClipped, thresClip, nIterClip, getResidual);
4723
4724 //---
4725 if (outBaselintTable) {
4726 uInt nparam = nWaves.size();
4727 Vector<Int> fparam(nparam);
4728 for (uInt i = 0; i < nparam; ++i) {
4729 fparam[i] = nWaves[i];
4730 }
4731 std::vector<int> finalMaskList0;
4732 finalMaskList0.clear();
4733 for (uInt i = 0; i < finalChanMask.size(); ++i) {
4734 if (finalChanMask[i]) {
4735 if ((i == 0)||(i == finalChanMask.size()-1)) {
4736 finalMaskList0.push_back(i);
4737 } else {
4738 if ((finalChanMask[i])&&(!finalChanMask[i-1])) {
4739 finalMaskList0.push_back(i);
4740 }
4741 if ((finalChanMask[i])&&(!finalChanMask[i+1])) {
4742 finalMaskList0.push_back(i);
4743 }
4744 }
4745 }
4746 }
4747 Vector<uInt> finalMaskList(finalMaskList0.size());
4748 for (uInt i = 0; i < finalMaskList0.size(); ++i) {
4749 finalMaskList[i] = (uInt)finalMaskList0[i];
4750 }
4751
4752 Vector<uInt> cEdge(currentEdge.size());
4753 for (uInt i = 0; i < currentEdge.size(); ++i) {
4754 cEdge[i] = currentEdge[i];
4755 }
4756
4757 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
4758 uInt(0),
4759 timeSecCol[whichrow],
4760 Bool(true),
4761 STBaselineFunc::Sinusoid,
4762 fparam,
4763 Vector<Float>(),
4764 finalMaskList,
4765 Vector<Float>(params),
4766 Float(rms),
4767 uInt(sp.size()),
4768 Float(thresClip),
4769 uInt(nIterClip),
4770 Float(threshold),
4771 uInt(chanAvgLimit),
4772 cEdge);
4773 } else {
4774 setSpectrum(res, whichrow);
4775 }
4776 //---
4777
4778 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
4779 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
4780 }
4781
4782 //---
4783 if (outBaselintTable) {
4784 bt->save(bltable);
4785 }
4786 //---
4787 delete bt;
4788
4789 if (outTextFile) ofs.close();
4790
4791 } catch (...) {
4792 throw;
4793 }
4794}
4795
4796std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, float& rms, std::vector<bool>& finalmask, float clipth, int clipn)
4797{
4798 int nClipped = 0;
4799 return doSinusoidFitting(data, mask, waveNumbers, params, rms, finalmask, nClipped, clipth, clipn);
4800}
4801
4802std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, float& rms, std::vector<bool>& finalMask, int& nClipped, float thresClip, int nIterClip, bool getResidual)
4803{
4804 if (data.size() != mask.size()) {
4805 throw(AipsError("data and mask sizes are not identical"));
4806 }
4807 if (data.size() < 2) {
4808 throw(AipsError("data size is too short"));
4809 }
4810 if (waveNumbers.size() == 0) {
4811 throw(AipsError("no wave numbers given"));
4812 }
4813 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
4814 nWaves.reserve(waveNumbers.size());
4815 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
4816 sort(nWaves.begin(), nWaves.end());
4817 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
4818 nWaves.erase(end_it, nWaves.end());
4819
4820 int minNWaves = nWaves[0];
4821 if (minNWaves < 0) {
4822 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
4823 }
4824 bool hasConstantTerm = (minNWaves == 0);
4825
4826 int nChan = data.size();
4827
4828 finalMask.clear();
4829 finalMask.resize(nChan);
4830
4831 std::vector<int> maskArray;
4832 std::vector<int> x;
4833 for (int i = 0; i < nChan; ++i) {
4834 maskArray.push_back(mask[i] ? 1 : 0);
4835 if (mask[i]) {
4836 x.push_back(i);
4837 }
4838 finalMask[i] = mask[i];
4839 }
4840
4841 int initNData = x.size();
4842
4843 int nData = initNData;
4844 int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
4845
4846 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
4847 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)
4848
4849 // xArray : contains elemental values for computing the least-square matrix.
4850 // xArray.size() is nDOF and xArray[*].size() is nChan.
4851 // Each xArray element are as follows:
4852 // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
4853 // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
4854 // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
4855 // where (1 <= n <= nMaxWavesInSW),
4856 // or,
4857 // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
4858 // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
4859 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
4860 std::vector<std::vector<double> > xArray;
4861 if (hasConstantTerm) {
4862 std::vector<double> xu;
4863 for (int j = 0; j < nChan; ++j) {
4864 xu.push_back(1.0);
4865 }
4866 xArray.push_back(xu);
4867 }
4868 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
4869 double xFactor = baseXFactor*(double)nWaves[i];
4870 std::vector<double> xs, xc;
4871 xs.clear();
4872 xc.clear();
4873 for (int j = 0; j < nChan; ++j) {
4874 xs.push_back(sin(xFactor*(double)j));
4875 xc.push_back(cos(xFactor*(double)j));
4876 }
4877 xArray.push_back(xs);
4878 xArray.push_back(xc);
4879 }
4880
4881 std::vector<double> z1, r1, residual;
4882 for (int i = 0; i < nChan; ++i) {
4883 z1.push_back((double)data[i]);
4884 r1.push_back(0.0);
4885 residual.push_back(0.0);
4886 }
4887
4888 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
4889 // xMatrix : horizontal concatenation of
4890 // the least-sq. matrix (left) and an
4891 // identity matrix (right).
4892 // the right part is used to calculate the inverse matrix of the left part.
4893 double xMatrix[nDOF][2*nDOF];
4894 double zMatrix[nDOF];
4895 for (int i = 0; i < nDOF; ++i) {
4896 for (int j = 0; j < 2*nDOF; ++j) {
4897 xMatrix[i][j] = 0.0;
4898 }
4899 xMatrix[i][nDOF+i] = 1.0;
4900 zMatrix[i] = 0.0;
4901 }
4902
4903 int nUseData = 0;
4904 for (int k = 0; k < nChan; ++k) {
4905 if (maskArray[k] == 0) continue;
4906
4907 for (int i = 0; i < nDOF; ++i) {
4908 for (int j = i; j < nDOF; ++j) {
4909 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
4910 }
4911 zMatrix[i] += z1[k] * xArray[i][k];
4912 }
4913
4914 nUseData++;
4915 }
4916
4917 if (nUseData < 1) {
4918 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
4919 }
4920
4921 for (int i = 0; i < nDOF; ++i) {
4922 for (int j = 0; j < i; ++j) {
4923 xMatrix[i][j] = xMatrix[j][i];
4924 }
4925 }
4926
4927 std::vector<double> invDiag;
4928 for (int i = 0; i < nDOF; ++i) {
4929 invDiag.push_back(1.0/xMatrix[i][i]);
4930 for (int j = 0; j < nDOF; ++j) {
4931 xMatrix[i][j] *= invDiag[i];
4932 }
4933 }
4934
4935 for (int k = 0; k < nDOF; ++k) {
4936 for (int i = 0; i < nDOF; ++i) {
4937 if (i != k) {
4938 double factor1 = xMatrix[k][k];
4939 double factor2 = xMatrix[i][k];
4940 for (int j = k; j < 2*nDOF; ++j) {
4941 xMatrix[i][j] *= factor1;
4942 xMatrix[i][j] -= xMatrix[k][j]*factor2;
4943 xMatrix[i][j] /= factor1;
4944 }
4945 }
4946 }
4947 double xDiag = xMatrix[k][k];
4948 for (int j = k; j < 2*nDOF; ++j) {
4949 xMatrix[k][j] /= xDiag;
4950 }
4951 }
4952
4953 for (int i = 0; i < nDOF; ++i) {
4954 for (int j = 0; j < nDOF; ++j) {
4955 xMatrix[i][nDOF+j] *= invDiag[j];
4956 }
4957 }
4958 //compute a vector y which consists of the coefficients of the sinusoids forming the
4959 //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
4960 //and cosine functions, respectively.
4961 std::vector<double> y;
4962 params.clear();
4963 for (int i = 0; i < nDOF; ++i) {
4964 y.push_back(0.0);
4965 for (int j = 0; j < nDOF; ++j) {
4966 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
4967 }
4968 params.push_back(y[i]);
4969 }
4970
4971 for (int i = 0; i < nChan; ++i) {
4972 r1[i] = y[0];
4973 for (int j = 1; j < nDOF; ++j) {
4974 r1[i] += y[j]*xArray[j][i];
4975 }
4976 residual[i] = z1[i] - r1[i];
4977 }
4978
4979 double stdDev = 0.0;
4980 for (int i = 0; i < nChan; ++i) {
4981 stdDev += residual[i]*residual[i]*(double)maskArray[i];
4982 }
4983 stdDev = sqrt(stdDev/(double)nData);
4984 rms = (float)stdDev;
4985
4986 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
4987 break;
4988 } else {
4989
4990 double thres = stdDev * thresClip;
4991 int newNData = 0;
4992 for (int i = 0; i < nChan; ++i) {
4993 if (abs(residual[i]) >= thres) {
4994 maskArray[i] = 0;
4995 finalMask[i] = false;
4996 }
4997 if (maskArray[i] > 0) {
4998 newNData++;
4999 }
5000 }
5001 if (newNData == nData) {
5002 break; //no more flag to add. iteration stops.
5003 } else {
5004 nData = newNData;
5005 }
5006
5007 }
5008 }
5009
5010 nClipped = initNData - nData;
5011
5012 std::vector<float> result;
5013 if (getResidual) {
5014 for (int i = 0; i < nChan; ++i) {
5015 result.push_back((float)residual[i]);
5016 }
5017 } else {
5018 for (int i = 0; i < nChan; ++i) {
5019 result.push_back((float)r1[i]);
5020 }
5021 }
5022
5023 return result;
5024}
5025
5026void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
5027{
5028 std::vector<double> dAbcissa = getAbcissa(whichrow);
5029 std::vector<float> abcissa;
5030 for (uInt i = 0; i < dAbcissa.size(); ++i) {
5031 abcissa.push_back((float)dAbcissa[i]);
5032 }
5033 std::vector<float> spec = getSpectrum(whichrow);
5034
5035 fitter.setData(abcissa, spec, mask);
5036 fitter.lfit();
5037}
5038
5039std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
5040{
5041 /****
5042 double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd;
5043 double elapse1 = 0.0;
5044 double elapse2 = 0.0;
5045
5046 ms1TimeStart = mathutil::gettimeofday_sec();
5047 ****/
5048
5049 std::vector<bool> mask = getMask(whichrow);
5050
5051 /****
5052 ms1TimeEnd = mathutil::gettimeofday_sec();
5053 elapse1 = ms1TimeEnd - ms1TimeStart;
5054 std::cout << "ms1 : " << elapse1 << " (sec.)" << endl;
5055 ms2TimeStart = mathutil::gettimeofday_sec();
5056 ****/
5057
5058 uInt maskSize = mask.size();
5059 if (inMask.size() != 0) {
5060 if (maskSize != inMask.size()) {
5061 throw(AipsError("mask sizes are not the same."));
5062 }
5063 for (uInt i = 0; i < maskSize; ++i) {
5064 mask[i] = mask[i] && inMask[i];
5065 }
5066 }
5067
5068 /****
5069 ms2TimeEnd = mathutil::gettimeofday_sec();
5070 elapse2 = ms2TimeEnd - ms2TimeStart;
5071 std::cout << "ms2 : " << elapse2 << " (sec.)" << endl;
5072 ****/
5073
5074 return mask;
5075}
5076
5077/*
5078std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
5079{
5080 int edgeSize = edge.size();
5081 std::vector<int> currentEdge;
5082 if (edgeSize >= 2) {
5083 int idx = 0;
5084 if (edgeSize > 2) {
5085 if (edgeSize < minEdgeSize) {
5086 throw(AipsError("Length of edge element info is less than that of IFs"));
5087 }
5088 idx = 2 * getIF(whichrow);
5089 }
5090 currentEdge.push_back(edge[idx]);
5091 currentEdge.push_back(edge[idx+1]);
5092 } else {
5093 throw(AipsError("Wrong length of edge element"));
5094 }
5095
5096 lineFinder.setData(getSpectrum(whichrow));
5097 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
5098
5099 return lineFinder.getMask();
5100}
5101*/
5102
5103/* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
5104void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter)
5105{
5106 if (outLogger || outTextFile) {
5107 std::vector<float> params = fitter.getParameters();
5108 std::vector<bool> fixed = fitter.getFixedParameters();
5109 float rms = getRms(chanMask, whichrow);
5110 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
5111
5112 if (outLogger) {
5113 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
5114 ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false, csvFormat) << LogIO::POST ;
5115 }
5116 if (outTextFile) {
5117 ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true, csvFormat) << flush;
5118 }
5119 }
5120}
5121
5122/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
5123void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, 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)
5124{
5125 if (outLogger || outTextFile) {
5126 /****
5127 double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd;
5128 double elapse1 = 0.0;
5129 double elapse2 = 0.0;
5130
5131 ms1TimeStart = mathutil::gettimeofday_sec();
5132 ****/
5133
5134 float rms = getRms(chanMask, whichrow);
5135
5136 /****
5137 ms1TimeEnd = mathutil::gettimeofday_sec();
5138 elapse1 = ms1TimeEnd - ms1TimeStart;
5139 std::cout << "ot1 : " << elapse1 << " (sec.)" << endl;
5140 ms2TimeStart = mathutil::gettimeofday_sec();
5141 ****/
5142
5143 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
5144 std::vector<bool> fixed;
5145 fixed.clear();
5146
5147 if (outLogger) {
5148 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
5149 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ;
5150 }
5151 if (outTextFile) {
5152 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush;
5153 }
5154
5155 /****
5156 ms2TimeEnd = mathutil::gettimeofday_sec();
5157 elapse2 = ms2TimeEnd - ms2TimeStart;
5158 std::cout << "ot2 : " << elapse2 << " (sec.)" << endl;
5159 ****/
5160
5161 }
5162}
5163
5164/* for chebyshev/sinusoid. will be merged once chebyshev/sinusoid is available in fitter (2011/3/10 WK) */
5165void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, 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)
5166{
5167 if (outLogger || outTextFile) {
5168 float rms = getRms(chanMask, whichrow);
5169 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
5170 std::vector<bool> fixed;
5171 fixed.clear();
5172
5173 if (outLogger) {
5174 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
5175 ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ;
5176 }
5177 if (outTextFile) {
5178 ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush;
5179 }
5180 }
5181}
5182
5183void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
5184{
5185 int idxDelimiter = progressInfo.find(",");
5186 if (idxDelimiter < 0) {
5187 throw(AipsError("wrong value in 'showprogress' parameter")) ;
5188 }
5189 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
5190 std::istringstream is(progressInfo.substr(idxDelimiter+1));
5191 is >> minNRow;
5192}
5193
5194void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
5195{
5196 if (showProgress && (nTotal >= nTotalThreshold)) {
5197 int nInterval = int(floor(double(nTotal)/100.0));
5198 if (nInterval == 0) nInterval++;
5199
5200 if (nProcessed % nInterval == 0) {
5201 printf("\r"); //go to the head of line
5202 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
5203 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
5204 printf("\x1b[39m\x1b[0m"); //set default attributes
5205 fflush(NULL);
5206 }
5207
5208 if (nProcessed == nTotal - 1) {
5209 printf("\r\x1b[K"); //clear
5210 fflush(NULL);
5211 }
5212
5213 }
5214}
5215
5216std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
5217{
5218 std::vector<bool> mask = getMask(whichrow);
5219
5220 if (inMask.size() > 0) {
5221 uInt maskSize = mask.size();
5222 if (maskSize != inMask.size()) {
5223 throw(AipsError("mask sizes are not the same."));
5224 }
5225 for (uInt i = 0; i < maskSize; ++i) {
5226 mask[i] = mask[i] && inMask[i];
5227 }
5228 }
5229
5230 Vector<Float> spec = getSpectrum(whichrow);
5231 mathutil::doZeroOrderInterpolation(spec, mask);
5232
5233 FFTServer<Float,Complex> ffts;
5234 Vector<Complex> fftres;
5235 ffts.fft0(fftres, spec);
5236
5237 std::vector<float> res;
5238 float norm = float(2.0/double(spec.size()));
5239
5240 if (getRealImag) {
5241 for (uInt i = 0; i < fftres.size(); ++i) {
5242 res.push_back(real(fftres[i])*norm);
5243 res.push_back(imag(fftres[i])*norm);
5244 }
5245 } else {
5246 for (uInt i = 0; i < fftres.size(); ++i) {
5247 res.push_back(abs(fftres[i])*norm);
5248 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
5249 }
5250 }
5251
5252 return res;
5253}
5254
5255
5256float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
5257{
5258 /****
5259 double ms1TimeStart, ms1TimeEnd;
5260 double elapse1 = 0.0;
5261 ms1TimeStart = mathutil::gettimeofday_sec();
5262 ****/
5263
5264 Vector<Float> spec;
5265 specCol_.get(whichrow, spec);
5266
5267 /****
5268 ms1TimeEnd = mathutil::gettimeofday_sec();
5269 elapse1 = ms1TimeEnd - ms1TimeStart;
5270 std::cout << "rm1 : " << elapse1 << " (sec.)" << endl;
5271 ****/
5272
5273 return (float)doGetRms(mask, spec);
5274}
5275
5276double Scantable::doGetRms(const std::vector<bool>& mask, const Vector<Float>& spec)
5277{
5278 double mean = 0.0;
5279 double smean = 0.0;
5280 int n = 0;
5281 for (uInt i = 0; i < spec.nelements(); ++i) {
5282 if (mask[i]) {
5283 double val = (double)spec[i];
5284 mean += val;
5285 smean += val*val;
5286 n++;
5287 }
5288 }
5289
5290 mean /= (double)n;
5291 smean /= (double)n;
5292
5293 return sqrt(smean - mean*mean);
5294}
5295
5296std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const
5297{
5298 if (verbose) {
5299 ostringstream oss;
5300
5301 if (csvformat) {
5302 oss << getScan(whichrow) << ",";
5303 oss << getBeam(whichrow) << ",";
5304 oss << getIF(whichrow) << ",";
5305 oss << getPol(whichrow) << ",";
5306 oss << getCycle(whichrow) << ",";
5307 String commaReplacedMasklist = masklist;
5308 string::size_type pos = 0;
5309 while (pos = commaReplacedMasklist.find(","), pos != string::npos) {
5310 commaReplacedMasklist.replace(pos, 1, ";");
5311 pos++;
5312 }
5313 oss << commaReplacedMasklist << ",";
5314 } else {
5315 oss << " Scan[" << getScan(whichrow) << "]";
5316 oss << " Beam[" << getBeam(whichrow) << "]";
5317 oss << " IF[" << getIF(whichrow) << "]";
5318 oss << " Pol[" << getPol(whichrow) << "]";
5319 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
5320 oss << "Fitter range = " << masklist << endl;
5321 oss << "Baseline parameters" << endl;
5322 }
5323 oss << flush;
5324
5325 return String(oss);
5326 }
5327
5328 return "";
5329}
5330
5331std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const
5332{
5333 if (verbose) {
5334 ostringstream oss;
5335
5336 if (csvformat) {
5337 oss << rms << ",";
5338 if (nClipped >= 0) {
5339 oss << nClipped;
5340 }
5341 } else {
5342 oss << "Results of baseline fit" << endl;
5343 oss << " rms = " << setprecision(6) << rms << endl;
5344 if (nClipped >= 0) {
5345 oss << " Number of clipped channels = " << nClipped << endl;
5346 }
5347 for (int i = 0; i < 60; ++i) {
5348 oss << "-";
5349 }
5350 }
5351 oss << endl;
5352 oss << flush;
5353
5354 return String(oss);
5355 }
5356
5357 return "";
5358}
5359
5360std::string Scantable::formatBaselineParams(const std::vector<float>& params,
5361 const std::vector<bool>& fixed,
5362 float rms,
5363 int nClipped,
5364 const std::string& masklist,
5365 int whichrow,
5366 bool verbose,
5367 bool csvformat,
5368 int start, int count,
5369 bool resetparamid) const
5370{
5371 int nParam = (int)(params.size());
5372
5373 if (nParam < 1) {
5374 return(" Not fitted");
5375 } else {
5376
5377 ostringstream oss;
5378 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
5379
5380 if (start < 0) start = 0;
5381 if (count < 0) count = nParam;
5382 int end = start + count;
5383 if (end > nParam) end = nParam;
5384 int paramidoffset = (resetparamid) ? (-start) : 0;
5385
5386 for (int i = start; i < end; ++i) {
5387 if (i > start) {
5388 oss << ",";
5389 }
5390 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
5391 if (csvformat) {
5392 oss << params[i] << sFix;
5393 } else {
5394 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
5395 }
5396 }
5397
5398 if (csvformat) {
5399 oss << ",";
5400 } else {
5401 oss << endl;
5402 }
5403 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
5404
5405 return String(oss);
5406 }
5407
5408}
5409
5410std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose, bool csvformat) const
5411{
5412 int nOutParam = (int)(params.size());
5413 int nPiece = (int)(ranges.size()) - 1;
5414
5415 if (nOutParam < 1) {
5416 return(" Not fitted");
5417 } else if (nPiece < 0) {
5418 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat);
5419 } else if (nPiece < 1) {
5420 return(" Bad count of the piece edge info");
5421 } else if (nOutParam % nPiece != 0) {
5422 return(" Bad count of the output baseline parameters");
5423 } else {
5424
5425 int nParam = nOutParam / nPiece;
5426
5427 ostringstream oss;
5428 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
5429
5430 if (csvformat) {
5431 for (int i = 0; i < nPiece; ++i) {
5432 oss << ranges[i] << "," << (ranges[i+1]-1) << ",";
5433 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
5434 }
5435 } else {
5436 stringstream ss;
5437 ss << ranges[nPiece] << flush;
5438 int wRange = ss.str().size() * 2 + 5;
5439
5440 for (int i = 0; i < nPiece; ++i) {
5441 ss.str("");
5442 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
5443 oss << left << setw(wRange) << ss.str();
5444 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
5445 //oss << endl;
5446 }
5447 }
5448
5449 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
5450
5451 return String(oss);
5452 }
5453
5454}
5455
5456bool Scantable::hasSameNchanOverIFs()
5457{
5458 int nIF = nif(-1);
5459 int nCh;
5460 int totalPositiveNChan = 0;
5461 int nPositiveNChan = 0;
5462
5463 for (int i = 0; i < nIF; ++i) {
5464 nCh = nchan(i);
5465 if (nCh > 0) {
5466 totalPositiveNChan += nCh;
5467 nPositiveNChan++;
5468 }
5469 }
5470
5471 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
5472}
5473
5474std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
5475{
5476 if (mask.size() <= 0) {
5477 throw(AipsError("The mask elements should be > 0"));
5478 }
5479 int IF = getIF(whichrow);
5480 if (mask.size() != (uInt)nchan(IF)) {
5481 throw(AipsError("Number of channels in scantable != number of mask elements"));
5482 }
5483
5484 if (verbose) {
5485 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
5486 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
5487 if (!hasSameNchan) {
5488 logOs << endl << "This mask is only valid for IF=" << IF;
5489 }
5490 logOs << LogIO::POST;
5491 }
5492
5493 std::vector<double> abcissa = getAbcissa(whichrow);
5494 std::vector<int> edge = getMaskEdgeIndices(mask);
5495
5496 ostringstream oss;
5497 oss.setf(ios::fixed);
5498 oss << setprecision(1) << "[";
5499 for (uInt i = 0; i < edge.size(); i+=2) {
5500 if (i > 0) oss << ",";
5501 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
5502 }
5503 oss << "]" << flush;
5504
5505 return String(oss);
5506}
5507
5508std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
5509{
5510 if (mask.size() <= 0) {
5511 throw(AipsError("The mask elements should be > 0"));
5512 }
5513
5514 std::vector<int> out, startIndices, endIndices;
5515 int maskSize = mask.size();
5516
5517 startIndices.clear();
5518 endIndices.clear();
5519
5520 if (mask[0]) {
5521 startIndices.push_back(0);
5522 }
5523 for (int i = 1; i < maskSize; ++i) {
5524 if ((!mask[i-1]) && mask[i]) {
5525 startIndices.push_back(i);
5526 } else if (mask[i-1] && (!mask[i])) {
5527 endIndices.push_back(i-1);
5528 }
5529 }
5530 if (mask[maskSize-1]) {
5531 endIndices.push_back(maskSize-1);
5532 }
5533
5534 if (startIndices.size() != endIndices.size()) {
5535 throw(AipsError("Inconsistent Mask Size: bad data?"));
5536 }
5537 for (uInt i = 0; i < startIndices.size(); ++i) {
5538 if (startIndices[i] > endIndices[i]) {
5539 throw(AipsError("Mask start index > mask end index"));
5540 }
5541 }
5542
5543 out.clear();
5544 for (uInt i = 0; i < startIndices.size(); ++i) {
5545 out.push_back(startIndices[i]);
5546 out.push_back(endIndices[i]);
5547 }
5548
5549 return out;
5550}
5551
5552vector<float> Scantable::getTsysSpectrum( int whichrow ) const
5553{
5554 Vector<Float> tsys( tsysCol_(whichrow) ) ;
5555 vector<float> stlTsys ;
5556 tsys.tovector( stlTsys ) ;
5557 return stlTsys ;
5558}
5559
5560vector<uint> Scantable::getMoleculeIdColumnData() const
5561{
5562 Vector<uInt> molIds(mmolidCol_.getColumn());
5563 vector<uint> res;
5564 molIds.tovector(res);
5565 return res;
5566}
5567
5568void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids)
5569{
5570 Vector<uInt> molIds(molids);
5571 Vector<uInt> arr(mmolidCol_.getColumn());
5572 if ( molIds.nelements() != arr.nelements() )
5573 throw AipsError("The input data size must be the number of rows.");
5574 mmolidCol_.putColumn(molIds);
5575}
5576
5577
5578}
5579//namespace asap
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