source: trunk/src/Scantable.cpp@ 2760

Last change on this file since 2760 was 2740, checked in by WataruKawasaki, 12 years ago

New Development: No

JIRA Issue: Yes CAS-4794

Ready for Test: No

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: No

Module(s): sd

Description:


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 142.3 KB
Line 
1//
2// C++ Implementation: Scantable
3//
4// Description:
5//
6//
7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005
8//
9// Copyright: See COPYING file that comes with this distribution
10//
11//
12#include <map>
13#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
2492void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2493{
2494 try {
2495 ofstream ofs;
2496 String coordInfo = "";
2497 bool hasSameNchan = true;
2498 bool outTextFile = false;
2499 bool csvFormat = false;
2500
2501 if (blfile != "") {
2502 csvFormat = (blfile.substr(0, 1) == "T");
2503 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
2504 if (ofs) outTextFile = true;
2505 }
2506
2507 if (outLogger || outTextFile) {
2508 coordInfo = getCoordInfo()[0];
2509 if (coordInfo == "") coordInfo = "channel";
2510 hasSameNchan = hasSameNchanOverIFs();
2511 }
2512
2513 Fitter fitter = Fitter();
2514 fitter.setExpression("poly", order);
2515 //fitter.setIterClipping(thresClip, nIterClip);
2516
2517 int nRow = nrow();
2518 std::vector<bool> chanMask;
2519 bool showProgress;
2520 int minNRow;
2521 parseProgressInfo(progressInfo, showProgress, minNRow);
2522
2523 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2524 chanMask = getCompositeChanMask(whichrow, mask);
2525 fitBaseline(chanMask, whichrow, fitter);
2526 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2527 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
2528 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2529 }
2530
2531 if (outTextFile) ofs.close();
2532
2533 } catch (...) {
2534 throw;
2535 }
2536}
2537
2538void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2539{
2540 try {
2541 ofstream ofs;
2542 String coordInfo = "";
2543 bool hasSameNchan = true;
2544 bool outTextFile = false;
2545 bool csvFormat = false;
2546
2547 if (blfile != "") {
2548 csvFormat = (blfile.substr(0, 1) == "T");
2549 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
2550 if (ofs) outTextFile = true;
2551 }
2552
2553 if (outLogger || outTextFile) {
2554 coordInfo = getCoordInfo()[0];
2555 if (coordInfo == "") coordInfo = "channel";
2556 hasSameNchan = hasSameNchanOverIFs();
2557 }
2558
2559 Fitter fitter = Fitter();
2560 fitter.setExpression("poly", order);
2561 //fitter.setIterClipping(thresClip, nIterClip);
2562
2563 int nRow = nrow();
2564 std::vector<bool> chanMask;
2565 int minEdgeSize = getIFNos().size()*2;
2566 STLineFinder lineFinder = STLineFinder();
2567 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2568
2569 bool showProgress;
2570 int minNRow;
2571 parseProgressInfo(progressInfo, showProgress, minNRow);
2572
2573 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2574
2575 //-------------------------------------------------------
2576 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2577 //-------------------------------------------------------
2578 int edgeSize = edge.size();
2579 std::vector<int> currentEdge;
2580 if (edgeSize >= 2) {
2581 int idx = 0;
2582 if (edgeSize > 2) {
2583 if (edgeSize < minEdgeSize) {
2584 throw(AipsError("Length of edge element info is less than that of IFs"));
2585 }
2586 idx = 2 * getIF(whichrow);
2587 }
2588 currentEdge.push_back(edge[idx]);
2589 currentEdge.push_back(edge[idx+1]);
2590 } else {
2591 throw(AipsError("Wrong length of edge element"));
2592 }
2593 lineFinder.setData(getSpectrum(whichrow));
2594 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2595 chanMask = lineFinder.getMask();
2596 //-------------------------------------------------------
2597
2598 fitBaseline(chanMask, whichrow, fitter);
2599 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2600
2601 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
2602 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2603 }
2604
2605 if (outTextFile) ofs.close();
2606
2607 } catch (...) {
2608 throw;
2609 }
2610}
2611
2612void 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)
2613{
2614 try {
2615 ofstream ofs;
2616 String coordInfo = "";
2617 bool hasSameNchan = true;
2618 bool outTextFile = false;
2619 bool csvFormat = false;
2620
2621 if (blfile != "") {
2622 csvFormat = (blfile.substr(0, 1) == "T");
2623 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
2624 if (ofs) outTextFile = true;
2625 }
2626
2627 if (outLogger || outTextFile) {
2628 coordInfo = getCoordInfo()[0];
2629 if (coordInfo == "") coordInfo = "channel";
2630 hasSameNchan = hasSameNchanOverIFs();
2631 }
2632
2633 bool showProgress;
2634 int minNRow;
2635 parseProgressInfo(progressInfo, showProgress, minNRow);
2636
2637 int nRow = nrow();
2638 std::vector<bool> chanMask;
2639 std::vector<bool> finalChanMask;
2640 float rms;
2641
2642 //---
2643 bool outBaselineParamTable = false;
2644 STBaselineTable* bt = new STBaselineTable(*this);
2645 //---
2646
2647 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2648 std::vector<float> sp = getSpectrum(whichrow);
2649 chanMask = getCompositeChanMask(whichrow, mask);
2650 std::vector<float> params(order+1);
2651 int nClipped = 0;
2652 std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, finalChanMask, rms, nClipped, thresClip, nIterClip, getResidual);
2653
2654 //---
2655 if (outBaselineParamTable) {
2656 bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)),
2657 uInt(0),
2658 Double(0.0), // <-- Double(getTime(whichrow, false)),
2659 uInt(nchan(whichrow)),
2660 STBaselineFunc::Chebyshev,
2661 Vector<uInt>(1), // ==> MUST BE Vector<uInt> containing 'order'.
2662 Vector<Float>(), // ==> for ffpar. ** dummy **
2663 uInt(nIterClip),
2664 Float(thresClip),
2665 Vector<uInt>(5), // <-- Vector<uInt>(finalChanMask),
2666 Vector<Float>(params),
2667 Float(rms));
2668 } else {
2669 setSpectrum(res, whichrow);
2670 }
2671 //---
2672
2673 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "chebyshevBaseline()", params, nClipped);
2674 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2675 }
2676
2677 //---
2678 if (outBaselineParamTable) {
2679 bt->save("chebyparamtable");
2680 }
2681 //---
2682 delete bt;
2683
2684 if (outTextFile) ofs.close();
2685
2686 } catch (...) {
2687 throw;
2688 }
2689}
2690
2691double 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)
2692{
2693 if (useLineFinder) {
2694 int minEdgeSize = getIFNos().size()*2;
2695
2696
2697 int edgeSize = edge.size();
2698 std::vector<int> currentEdge;
2699 if (edgeSize >= 2) {
2700 int idx = 0;
2701 if (edgeSize > 2) {
2702 if (edgeSize < minEdgeSize) {
2703 throw(AipsError("Length of edge element info is less than that of IFs"));
2704 }
2705 idx = 2 * getIF(whichrow);
2706 }
2707 currentEdge.push_back(edge[idx]);
2708 currentEdge.push_back(edge[idx+1]);
2709 } else {
2710 throw(AipsError("Wrong length of edge element"));
2711 }
2712
2713 STLineFinder lineFinder = STLineFinder();
2714 std::vector<float> sp = getSpectrum(whichrow);
2715 lineFinder.setData(sp);
2716 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2717 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
2718 std::vector<bool> chanMask = lineFinder.getMask();
2719
2720 return doCalculateModelSelectionCriteria(valname, sp, chanMask, blfunc, order);
2721
2722 } else {
2723 return doCalculateModelSelectionCriteria(valname, getSpectrum(whichrow), getCompositeChanMask(whichrow, inMask), blfunc, order);
2724 }
2725
2726}
2727
2728double Scantable::doCalculateModelSelectionCriteria(const std::string& valname, const std::vector<float>& spec, const std::vector<bool>& mask, const std::string& blfunc, int order)
2729{
2730 int nparam;
2731 std::vector<float> params;
2732 std::vector<bool> finalChanMask;
2733 float rms;
2734 int nClipped = 0;
2735 float thresClip = 0.0;
2736 int nIterClip = 0;
2737 std::vector<float> res;
2738 if (blfunc == "chebyshev") {
2739 nparam = order + 1;
2740 res = doChebyshevFitting(spec, mask, order, params, finalChanMask, rms, nClipped, thresClip, nIterClip, true);
2741 } else if (blfunc == "sinusoid") {
2742 std::vector<int> nWaves;
2743 nWaves.clear();
2744 for (int i = 0; i <= order; ++i) {
2745 nWaves.push_back(i);
2746 }
2747 nparam = 2*order + 1; // order = nwave
2748 res = doSinusoidFitting(spec, mask, nWaves, params, nClipped, thresClip, nIterClip, true);
2749 } else if (blfunc == "cspline") {
2750 std::vector<int> pieceEdges(order+1); //order = npiece
2751 nparam = order + 3;
2752 params.resize(4*order);
2753 res = doCubicSplineFitting(spec, mask, order, pieceEdges, params, nClipped, thresClip, nIterClip, true);
2754 } else {
2755 throw(AipsError("blfunc must be chebyshev, cspline or sinusoid."));
2756 }
2757
2758 double msq = 0.0;
2759 int nusedchan = 0;
2760 int nChan = res.size();
2761 for (int i = 0; i < nChan; ++i) {
2762 if (mask[i]) {
2763 msq += (double)res[i]*(double)res[i];
2764 nusedchan++;
2765 }
2766 }
2767 if (nusedchan == 0) {
2768 throw(AipsError("all channels masked."));
2769 }
2770 msq /= (double)nusedchan;
2771
2772 nparam++; //add 1 for sigma of Gaussian distribution
2773 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
2774
2775 if (valname.find("aic") == 0) {
2776 // Original Akaike Information Criterion (AIC)
2777 double aic = nusedchan * (log(2.0 * PI * msq) + 1.0) + 2.0 * nparam;
2778
2779 // Corrected AIC by Sugiura(1978)
2780 if (valname == "aicc") {
2781 if (nusedchan - nparam - 1 <= 0) {
2782 throw(AipsError("channel size is too small to calculate AICc."));
2783 }
2784 aic += 2.0*nparam*(nparam + 1)/(double)(nusedchan - nparam - 1);
2785 }
2786
2787 return aic;
2788
2789 } else if (valname == "bic") {
2790 // Bayesian Information Criterion (BIC)
2791 double bic = nusedchan * log(msq) + nparam * log((double)nusedchan);
2792 return bic;
2793
2794 } else if (valname == "gcv") {
2795 // Generalised Cross Validation
2796 double x = 1.0 - (double)nparam / (double)nusedchan;
2797 double gcv = msq / (x * x);
2798 return gcv;
2799
2800 } else {
2801 throw(AipsError("valname must be aic, aicc, bic or gcv."));
2802 }
2803}
2804
2805void 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)
2806{
2807 try {
2808 ofstream ofs;
2809 String coordInfo = "";
2810 bool hasSameNchan = true;
2811 bool outTextFile = false;
2812 bool csvFormat = false;
2813
2814 if (blfile != "") {
2815 csvFormat = (blfile.substr(0, 1) == "T");
2816 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
2817 if (ofs) outTextFile = true;
2818 }
2819
2820 if (outLogger || outTextFile) {
2821 coordInfo = getCoordInfo()[0];
2822 if (coordInfo == "") coordInfo = "channel";
2823 hasSameNchan = hasSameNchanOverIFs();
2824 }
2825
2826 int nRow = nrow();
2827 std::vector<bool> chanMask;
2828 int minEdgeSize = getIFNos().size()*2;
2829 STLineFinder lineFinder = STLineFinder();
2830 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2831
2832 bool showProgress;
2833 int minNRow;
2834 parseProgressInfo(progressInfo, showProgress, minNRow);
2835
2836 std::vector<bool> finalChanMask;
2837 float rms;
2838
2839 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2840 std::vector<float> sp = getSpectrum(whichrow);
2841
2842 //-------------------------------------------------------
2843 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2844 //-------------------------------------------------------
2845 int edgeSize = edge.size();
2846 std::vector<int> currentEdge;
2847 if (edgeSize >= 2) {
2848 int idx = 0;
2849 if (edgeSize > 2) {
2850 if (edgeSize < minEdgeSize) {
2851 throw(AipsError("Length of edge element info is less than that of IFs"));
2852 }
2853 idx = 2 * getIF(whichrow);
2854 }
2855 currentEdge.push_back(edge[idx]);
2856 currentEdge.push_back(edge[idx+1]);
2857 } else {
2858 throw(AipsError("Wrong length of edge element"));
2859 }
2860 //lineFinder.setData(getSpectrum(whichrow));
2861 lineFinder.setData(sp);
2862 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2863 chanMask = lineFinder.getMask();
2864 //-------------------------------------------------------
2865
2866
2867 //fitBaseline(chanMask, whichrow, fitter);
2868 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2869 std::vector<float> params(order+1);
2870 int nClipped = 0;
2871 std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, finalChanMask, rms, nClipped, thresClip, nIterClip, getResidual);
2872 setSpectrum(res, whichrow);
2873
2874 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()", params, nClipped);
2875 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2876 }
2877
2878 if (outTextFile) ofs.close();
2879
2880 } catch (...) {
2881 throw;
2882 }
2883}
2884
2885 /*
2886double Scantable::getChebyshevPolynomial(int n, double x) {
2887 if ((x < -1.0)||(x > 1.0)) {
2888 throw(AipsError("out of definition range (-1 <= x <= 1)."));
2889 } else if (n < 0) {
2890 throw(AipsError("the order must be zero or positive."));
2891 } else if (n == 0) {
2892 return 1.0;
2893 } else if (n == 1) {
2894 return x;
2895 } else {
2896 return 2.0*x*getChebyshevPolynomial(n-1, x) - getChebyshevPolynomial(n-2, x);
2897 }
2898}
2899 */
2900double Scantable::getChebyshevPolynomial(int n, double x) {
2901 if ((x < -1.0)||(x > 1.0)) {
2902 throw(AipsError("out of definition range (-1 <= x <= 1)."));
2903 } else if (x == 1.0) {
2904 return 1.0;
2905 } else if (x == 0.0) {
2906 double res;
2907 if (n%2 == 0) {
2908 if (n%4 == 0) {
2909 res = 1.0;
2910 } else {
2911 res = -1.0;
2912 }
2913 } else {
2914 res = 0.0;
2915 }
2916 return res;
2917 } else if (x == -1.0) {
2918 double res = (n%2 == 0 ? 1.0 : -1.0);
2919 return res;
2920 } else if (n < 0) {
2921 throw(AipsError("the order must be zero or positive."));
2922 } else if (n == 0) {
2923 return 1.0;
2924 } else if (n == 1) {
2925 return x;
2926 } else {
2927 double res = 0.0;
2928 for (int m = 0; m <= n/2; ++m) {
2929 double c = 1.0;
2930 if (m > 0) {
2931 for (int i = 1; i <= m; ++i) {
2932 c *= (double)(n-2*m+i)/(double)i;
2933 }
2934 }
2935 res += (m%2 == 0 ? 1.0 : -1.0)*(double)n/(double)(n-m)*pow(2.0*x, (double)(n-2*m))/2.0*c;
2936 }
2937 return res;
2938 }
2939}
2940
2941std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, const std::vector<bool>& mask, int order, std::vector<float>& params, std::vector<bool>& finalMask, float& rms, int& nClipped, float thresClip, int nIterClip, bool getResidual)
2942{
2943 if (data.size() != mask.size()) {
2944 throw(AipsError("data and mask sizes are not identical"));
2945 }
2946 if (order < 0) {
2947 throw(AipsError("maximum order of Chebyshev polynomial must not be negative."));
2948 }
2949
2950 int nChan = data.size();
2951
2952 finalMask.clear();
2953 finalMask.resize(nChan);
2954
2955 std::vector<int> maskArray;
2956 std::vector<int> x;
2957 for (int i = 0; i < nChan; ++i) {
2958 maskArray.push_back(mask[i] ? 1 : 0);
2959 if (mask[i]) {
2960 x.push_back(i);
2961 }
2962 finalMask[i] = mask[i];
2963 }
2964
2965 int initNData = x.size();
2966
2967 int nData = initNData;
2968 int nDOF = order + 1; //number of parameters to solve.
2969
2970 // xArray : contains elemental values for computing the least-square matrix.
2971 // xArray.size() is nDOF and xArray[*].size() is nChan.
2972 // Each xArray element are as follows:
2973 // xArray[0] = {T0(-1), T0(2/(nChan-1)-1), T0(4/(nChan-1)-1), ..., T0(1)},
2974 // xArray[n-1] = ...,
2975 // xArray[n] = {Tn(-1), Tn(2/(nChan-1)-1), Tn(4/(nChan-1)-1), ..., Tn(1)}
2976 // where (0 <= n <= order),
2977 std::vector<std::vector<double> > xArray;
2978 for (int i = 0; i < nDOF; ++i) {
2979 double xFactor = 2.0/(double)(nChan - 1);
2980 std::vector<double> xs;
2981 xs.clear();
2982 for (int j = 0; j < nChan; ++j) {
2983 xs.push_back(getChebyshevPolynomial(i, xFactor*(double)j-1.0));
2984 }
2985 xArray.push_back(xs);
2986 }
2987
2988 std::vector<double> z1, r1, residual;
2989 for (int i = 0; i < nChan; ++i) {
2990 z1.push_back((double)data[i]);
2991 r1.push_back(0.0);
2992 residual.push_back(0.0);
2993 }
2994
2995 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
2996 // xMatrix : horizontal concatenation of
2997 // the least-sq. matrix (left) and an
2998 // identity matrix (right).
2999 // the right part is used to calculate the inverse matrix of the left part.
3000 double xMatrix[nDOF][2*nDOF];
3001 double zMatrix[nDOF];
3002 for (int i = 0; i < nDOF; ++i) {
3003 for (int j = 0; j < 2*nDOF; ++j) {
3004 xMatrix[i][j] = 0.0;
3005 }
3006 xMatrix[i][nDOF+i] = 1.0;
3007 zMatrix[i] = 0.0;
3008 }
3009
3010 int nUseData = 0;
3011 for (int k = 0; k < nChan; ++k) {
3012 if (maskArray[k] == 0) continue;
3013
3014 for (int i = 0; i < nDOF; ++i) {
3015 for (int j = i; j < nDOF; ++j) {
3016 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
3017 }
3018 zMatrix[i] += z1[k] * xArray[i][k];
3019 }
3020
3021 nUseData++;
3022 }
3023
3024 if (nUseData < 1) {
3025 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
3026 }
3027
3028 for (int i = 0; i < nDOF; ++i) {
3029 for (int j = 0; j < i; ++j) {
3030 xMatrix[i][j] = xMatrix[j][i];
3031 }
3032 }
3033
3034 std::vector<double> invDiag;
3035 for (int i = 0; i < nDOF; ++i) {
3036 invDiag.push_back(1.0/xMatrix[i][i]);
3037 for (int j = 0; j < nDOF; ++j) {
3038 xMatrix[i][j] *= invDiag[i];
3039 }
3040 }
3041
3042 for (int k = 0; k < nDOF; ++k) {
3043 for (int i = 0; i < nDOF; ++i) {
3044 if (i != k) {
3045 double factor1 = xMatrix[k][k];
3046 double factor2 = xMatrix[i][k];
3047 for (int j = k; j < 2*nDOF; ++j) {
3048 xMatrix[i][j] *= factor1;
3049 xMatrix[i][j] -= xMatrix[k][j]*factor2;
3050 xMatrix[i][j] /= factor1;
3051 }
3052 }
3053 }
3054 double xDiag = xMatrix[k][k];
3055 for (int j = k; j < 2*nDOF; ++j) {
3056 xMatrix[k][j] /= xDiag;
3057 }
3058 }
3059
3060 for (int i = 0; i < nDOF; ++i) {
3061 for (int j = 0; j < nDOF; ++j) {
3062 xMatrix[i][nDOF+j] *= invDiag[j];
3063 }
3064 }
3065 //compute a vector y which consists of the coefficients of the sinusoids forming the
3066 //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
3067 //and cosine functions, respectively.
3068 std::vector<double> y;
3069 params.clear();
3070 for (int i = 0; i < nDOF; ++i) {
3071 y.push_back(0.0);
3072 for (int j = 0; j < nDOF; ++j) {
3073 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3074 }
3075 params.push_back(y[i]);
3076 }
3077
3078 for (int i = 0; i < nChan; ++i) {
3079 r1[i] = y[0];
3080 for (int j = 1; j < nDOF; ++j) {
3081 r1[i] += y[j]*xArray[j][i];
3082 }
3083 residual[i] = z1[i] - r1[i];
3084 }
3085
3086 double stdDev = 0.0;
3087 for (int i = 0; i < nChan; ++i) {
3088 stdDev += residual[i]*residual[i]*(double)maskArray[i];
3089 }
3090 stdDev = sqrt(stdDev/(double)nData);
3091 rms = (float)stdDev;
3092
3093 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3094 break;
3095 } else {
3096
3097 double thres = stdDev * thresClip;
3098 int newNData = 0;
3099 for (int i = 0; i < nChan; ++i) {
3100 if (abs(residual[i]) >= thres) {
3101 maskArray[i] = 0;
3102 finalMask[i] = false;
3103 }
3104 if (maskArray[i] > 0) {
3105 newNData++;
3106 }
3107 }
3108 if (newNData == nData) {
3109 break; //no more flag to add. iteration stops.
3110 } else {
3111 nData = newNData;
3112 }
3113
3114 }
3115 }
3116
3117 nClipped = initNData - nData;
3118
3119 std::vector<float> result;
3120 if (getResidual) {
3121 for (int i = 0; i < nChan; ++i) {
3122 result.push_back((float)residual[i]);
3123 }
3124 } else {
3125 for (int i = 0; i < nChan; ++i) {
3126 result.push_back((float)r1[i]);
3127 }
3128 }
3129
3130 return result;
3131}
3132
3133void 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)
3134{
3135 /*************
3136 double totTimeStart, totTimeEnd, blTimeStart, blTimeEnd, ioTimeStart, ioTimeEnd, msTimeStart, msTimeEnd, seTimeStart, seTimeEnd, otTimeStart, otTimeEnd, prTimeStart, prTimeEnd;
3137 double elapseMs = 0.0;
3138 double elapseSe = 0.0;
3139 double elapseOt = 0.0;
3140 double elapsePr = 0.0;
3141 double elapseBl = 0.0;
3142 double elapseIo = 0.0;
3143 totTimeStart = mathutil::gettimeofday_sec();
3144 *************/
3145
3146 try {
3147 ofstream ofs;
3148 String coordInfo = "";
3149 bool hasSameNchan = true;
3150 bool outTextFile = false;
3151 bool csvFormat = false;
3152
3153 if (blfile != "") {
3154 csvFormat = (blfile.substr(0, 1) == "T");
3155 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3156 if (ofs) outTextFile = true;
3157 }
3158
3159 if (outLogger || outTextFile) {
3160 coordInfo = getCoordInfo()[0];
3161 if (coordInfo == "") coordInfo = "channel";
3162 hasSameNchan = hasSameNchanOverIFs();
3163 }
3164
3165 //Fitter fitter = Fitter();
3166 //fitter.setExpression("cspline", nPiece);
3167 //fitter.setIterClipping(thresClip, nIterClip);
3168
3169 bool showProgress;
3170 int minNRow;
3171 parseProgressInfo(progressInfo, showProgress, minNRow);
3172
3173 int nRow = nrow();
3174 std::vector<bool> chanMask;
3175
3176 //--------------------------------
3177 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3178 /******************
3179 ioTimeStart = mathutil::gettimeofday_sec();
3180 **/
3181 std::vector<float> sp = getSpectrum(whichrow);
3182 /**
3183 ioTimeEnd = mathutil::gettimeofday_sec();
3184 elapseIo += (double)(ioTimeEnd - ioTimeStart);
3185 msTimeStart = mathutil::gettimeofday_sec();
3186 ******************/
3187
3188 chanMask = getCompositeChanMask(whichrow, mask);
3189
3190 /**
3191 msTimeEnd = mathutil::gettimeofday_sec();
3192 elapseMs += (double)(msTimeEnd - msTimeStart);
3193 blTimeStart = mathutil::gettimeofday_sec();
3194 **/
3195
3196 //fitBaseline(chanMask, whichrow, fitter);
3197 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
3198 std::vector<int> pieceEdges(nPiece+1);
3199 std::vector<float> params(nPiece*4);
3200 int nClipped = 0;
3201 std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
3202
3203 /**
3204 blTimeEnd = mathutil::gettimeofday_sec();
3205 elapseBl += (double)(blTimeEnd - blTimeStart);
3206 seTimeStart = mathutil::gettimeofday_sec();
3207 **/
3208
3209
3210 setSpectrum(res, whichrow);
3211 //
3212
3213 /**
3214 seTimeEnd = mathutil::gettimeofday_sec();
3215 elapseSe += (double)(seTimeEnd - seTimeStart);
3216 otTimeStart = mathutil::gettimeofday_sec();
3217 **/
3218
3219 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
3220
3221 /**
3222 otTimeEnd = mathutil::gettimeofday_sec();
3223 elapseOt += (double)(otTimeEnd - otTimeStart);
3224 prTimeStart = mathutil::gettimeofday_sec();
3225 **/
3226
3227 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3228
3229 /******************
3230 prTimeEnd = mathutil::gettimeofday_sec();
3231 elapsePr += (double)(prTimeEnd - prTimeStart);
3232 ******************/
3233 }
3234 //--------------------------------
3235
3236 if (outTextFile) ofs.close();
3237
3238 } catch (...) {
3239 throw;
3240 }
3241 /***************
3242 totTimeEnd = mathutil::gettimeofday_sec();
3243 std::cout << "io : " << elapseIo << " (sec.)" << endl;
3244 std::cout << "ms : " << elapseMs << " (sec.)" << endl;
3245 std::cout << "bl : " << elapseBl << " (sec.)" << endl;
3246 std::cout << "se : " << elapseSe << " (sec.)" << endl;
3247 std::cout << "ot : " << elapseOt << " (sec.)" << endl;
3248 std::cout << "pr : " << elapsePr << " (sec.)" << endl;
3249 std::cout << "total : " << (double)(totTimeEnd - totTimeStart) << " (sec.)" << endl;
3250 ***************/
3251}
3252
3253void 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)
3254{
3255 try {
3256 ofstream ofs;
3257 String coordInfo = "";
3258 bool hasSameNchan = true;
3259 bool outTextFile = false;
3260 bool csvFormat = false;
3261
3262 if (blfile != "") {
3263 csvFormat = (blfile.substr(0, 1) == "T");
3264 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3265 if (ofs) outTextFile = true;
3266 }
3267
3268 if (outLogger || outTextFile) {
3269 coordInfo = getCoordInfo()[0];
3270 if (coordInfo == "") coordInfo = "channel";
3271 hasSameNchan = hasSameNchanOverIFs();
3272 }
3273
3274 //Fitter fitter = Fitter();
3275 //fitter.setExpression("cspline", nPiece);
3276 //fitter.setIterClipping(thresClip, nIterClip);
3277
3278 int nRow = nrow();
3279 std::vector<bool> chanMask;
3280 int minEdgeSize = getIFNos().size()*2;
3281 STLineFinder lineFinder = STLineFinder();
3282 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3283
3284 bool showProgress;
3285 int minNRow;
3286 parseProgressInfo(progressInfo, showProgress, minNRow);
3287
3288 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3289 std::vector<float> sp = getSpectrum(whichrow);
3290
3291 //-------------------------------------------------------
3292 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
3293 //-------------------------------------------------------
3294 int edgeSize = edge.size();
3295 std::vector<int> currentEdge;
3296 if (edgeSize >= 2) {
3297 int idx = 0;
3298 if (edgeSize > 2) {
3299 if (edgeSize < minEdgeSize) {
3300 throw(AipsError("Length of edge element info is less than that of IFs"));
3301 }
3302 idx = 2 * getIF(whichrow);
3303 }
3304 currentEdge.push_back(edge[idx]);
3305 currentEdge.push_back(edge[idx+1]);
3306 } else {
3307 throw(AipsError("Wrong length of edge element"));
3308 }
3309 //lineFinder.setData(getSpectrum(whichrow));
3310 lineFinder.setData(sp);
3311 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
3312 chanMask = lineFinder.getMask();
3313 //-------------------------------------------------------
3314
3315
3316 //fitBaseline(chanMask, whichrow, fitter);
3317 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
3318 std::vector<int> pieceEdges(nPiece+1);
3319 std::vector<float> params(nPiece*4);
3320 int nClipped = 0;
3321 std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
3322 setSpectrum(res, whichrow);
3323 //
3324
3325 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
3326 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3327 }
3328
3329 if (outTextFile) ofs.close();
3330
3331 } catch (...) {
3332 throw;
3333 }
3334}
3335
3336std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
3337{
3338 if (data.size() != mask.size()) {
3339 throw(AipsError("data and mask sizes are not identical"));
3340 }
3341 if (nPiece < 1) {
3342 throw(AipsError("number of the sections must be one or more"));
3343 }
3344
3345 int nChan = data.size();
3346 std::vector<int> maskArray(nChan);
3347 std::vector<int> x(nChan);
3348 int j = 0;
3349 for (int i = 0; i < nChan; ++i) {
3350 maskArray[i] = mask[i] ? 1 : 0;
3351 if (mask[i]) {
3352 x[j] = i;
3353 j++;
3354 }
3355 }
3356 int initNData = j;
3357
3358 if (initNData < nPiece) {
3359 throw(AipsError("too few non-flagged channels"));
3360 }
3361
3362 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
3363 std::vector<double> invEdge(nPiece-1);
3364 idxEdge[0] = x[0];
3365 for (int i = 1; i < nPiece; ++i) {
3366 int valX = x[nElement*i];
3367 idxEdge[i] = valX;
3368 invEdge[i-1] = 1.0/(double)valX;
3369 }
3370 idxEdge[nPiece] = x[initNData-1]+1;
3371
3372 int nData = initNData;
3373 int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
3374
3375 std::vector<double> x1(nChan), x2(nChan), x3(nChan);
3376 std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan);
3377 std::vector<double> r1(nChan), residual(nChan);
3378 for (int i = 0; i < nChan; ++i) {
3379 double di = (double)i;
3380 double dD = (double)data[i];
3381 x1[i] = di;
3382 x2[i] = di*di;
3383 x3[i] = di*di*di;
3384 z1[i] = dD;
3385 x1z1[i] = dD*di;
3386 x2z1[i] = dD*di*di;
3387 x3z1[i] = dD*di*di*di;
3388 r1[i] = 0.0;
3389 residual[i] = 0.0;
3390 }
3391
3392 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3393 // xMatrix : horizontal concatenation of
3394 // the least-sq. matrix (left) and an
3395 // identity matrix (right).
3396 // the right part is used to calculate the inverse matrix of the left part.
3397 double xMatrix[nDOF][2*nDOF];
3398 double zMatrix[nDOF];
3399 for (int i = 0; i < nDOF; ++i) {
3400 for (int j = 0; j < 2*nDOF; ++j) {
3401 xMatrix[i][j] = 0.0;
3402 }
3403 xMatrix[i][nDOF+i] = 1.0;
3404 zMatrix[i] = 0.0;
3405 }
3406
3407 for (int n = 0; n < nPiece; ++n) {
3408 int nUseDataInPiece = 0;
3409 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
3410
3411 if (maskArray[i] == 0) continue;
3412
3413 xMatrix[0][0] += 1.0;
3414 xMatrix[0][1] += x1[i];
3415 xMatrix[0][2] += x2[i];
3416 xMatrix[0][3] += x3[i];
3417 xMatrix[1][1] += x2[i];
3418 xMatrix[1][2] += x3[i];
3419 xMatrix[1][3] += x2[i]*x2[i];
3420 xMatrix[2][2] += x2[i]*x2[i];
3421 xMatrix[2][3] += x3[i]*x2[i];
3422 xMatrix[3][3] += x3[i]*x3[i];
3423 zMatrix[0] += z1[i];
3424 zMatrix[1] += x1z1[i];
3425 zMatrix[2] += x2z1[i];
3426 zMatrix[3] += x3z1[i];
3427
3428 for (int j = 0; j < n; ++j) {
3429 double q = 1.0 - x1[i]*invEdge[j];
3430 q = q*q*q;
3431 xMatrix[0][j+4] += q;
3432 xMatrix[1][j+4] += q*x1[i];
3433 xMatrix[2][j+4] += q*x2[i];
3434 xMatrix[3][j+4] += q*x3[i];
3435 for (int k = 0; k < j; ++k) {
3436 double r = 1.0 - x1[i]*invEdge[k];
3437 r = r*r*r;
3438 xMatrix[k+4][j+4] += r*q;
3439 }
3440 xMatrix[j+4][j+4] += q*q;
3441 zMatrix[j+4] += q*z1[i];
3442 }
3443
3444 nUseDataInPiece++;
3445 }
3446
3447 if (nUseDataInPiece < 1) {
3448 std::vector<string> suffixOfPieceNumber(4);
3449 suffixOfPieceNumber[0] = "th";
3450 suffixOfPieceNumber[1] = "st";
3451 suffixOfPieceNumber[2] = "nd";
3452 suffixOfPieceNumber[3] = "rd";
3453 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
3454 ostringstream oss;
3455 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
3456 oss << " piece of the spectrum. can't execute fitting anymore.";
3457 throw(AipsError(String(oss)));
3458 }
3459 }
3460
3461 for (int i = 0; i < nDOF; ++i) {
3462 for (int j = 0; j < i; ++j) {
3463 xMatrix[i][j] = xMatrix[j][i];
3464 }
3465 }
3466
3467 std::vector<double> invDiag(nDOF);
3468 for (int i = 0; i < nDOF; ++i) {
3469 invDiag[i] = 1.0/xMatrix[i][i];
3470 for (int j = 0; j < nDOF; ++j) {
3471 xMatrix[i][j] *= invDiag[i];
3472 }
3473 }
3474
3475 for (int k = 0; k < nDOF; ++k) {
3476 for (int i = 0; i < nDOF; ++i) {
3477 if (i != k) {
3478 double factor1 = xMatrix[k][k];
3479 double factor2 = xMatrix[i][k];
3480 for (int j = k; j < 2*nDOF; ++j) {
3481 xMatrix[i][j] *= factor1;
3482 xMatrix[i][j] -= xMatrix[k][j]*factor2;
3483 xMatrix[i][j] /= factor1;
3484 }
3485 }
3486 }
3487 double xDiag = xMatrix[k][k];
3488 for (int j = k; j < 2*nDOF; ++j) {
3489 xMatrix[k][j] /= xDiag;
3490 }
3491 }
3492
3493 for (int i = 0; i < nDOF; ++i) {
3494 for (int j = 0; j < nDOF; ++j) {
3495 xMatrix[i][nDOF+j] *= invDiag[j];
3496 }
3497 }
3498 //compute a vector y which consists of the coefficients of the best-fit spline curves
3499 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
3500 //cubic terms for the other pieces (in case nPiece>1).
3501 std::vector<double> y(nDOF);
3502 for (int i = 0; i < nDOF; ++i) {
3503 y[i] = 0.0;
3504 for (int j = 0; j < nDOF; ++j) {
3505 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3506 }
3507 }
3508
3509 double a0 = y[0];
3510 double a1 = y[1];
3511 double a2 = y[2];
3512 double a3 = y[3];
3513
3514 int j = 0;
3515 for (int n = 0; n < nPiece; ++n) {
3516 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
3517 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
3518 }
3519 params[j] = a0;
3520 params[j+1] = a1;
3521 params[j+2] = a2;
3522 params[j+3] = a3;
3523 j += 4;
3524
3525 if (n == nPiece-1) break;
3526
3527 double d = y[4+n];
3528 double iE = invEdge[n];
3529 a0 += d;
3530 a1 -= 3.0*d*iE;
3531 a2 += 3.0*d*iE*iE;
3532 a3 -= d*iE*iE*iE;
3533 }
3534
3535 //subtract constant value for masked regions at the edge of spectrum
3536 if (idxEdge[0] > 0) {
3537 int n = idxEdge[0];
3538 for (int i = 0; i < idxEdge[0]; ++i) {
3539 //--cubic extrapolate--
3540 //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i];
3541 //--linear extrapolate--
3542 //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n];
3543 //--constant--
3544 r1[i] = r1[n];
3545 }
3546 }
3547 if (idxEdge[nPiece] < nChan) {
3548 int n = idxEdge[nPiece]-1;
3549 for (int i = idxEdge[nPiece]; i < nChan; ++i) {
3550 //--cubic extrapolate--
3551 //int m = 4*(nPiece-1);
3552 //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i];
3553 //--linear extrapolate--
3554 //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n];
3555 //--constant--
3556 r1[i] = r1[n];
3557 }
3558 }
3559
3560 for (int i = 0; i < nChan; ++i) {
3561 residual[i] = z1[i] - r1[i];
3562 }
3563
3564 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3565 break;
3566 } else {
3567 double stdDev = 0.0;
3568 for (int i = 0; i < nChan; ++i) {
3569 stdDev += residual[i]*residual[i]*(double)maskArray[i];
3570 }
3571 stdDev = sqrt(stdDev/(double)nData);
3572
3573 double thres = stdDev * thresClip;
3574 int newNData = 0;
3575 for (int i = 0; i < nChan; ++i) {
3576 if (abs(residual[i]) >= thres) {
3577 maskArray[i] = 0;
3578 }
3579 if (maskArray[i] > 0) {
3580 newNData++;
3581 }
3582 }
3583 if (newNData == nData) {
3584 break; //no more flag to add. iteration stops.
3585 } else {
3586 nData = newNData;
3587 }
3588 }
3589 }
3590
3591 nClipped = initNData - nData;
3592
3593 std::vector<float> result(nChan);
3594 if (getResidual) {
3595 for (int i = 0; i < nChan; ++i) {
3596 result[i] = (float)residual[i];
3597 }
3598 } else {
3599 for (int i = 0; i < nChan; ++i) {
3600 result[i] = (float)r1[i];
3601 }
3602 }
3603
3604 return result;
3605}
3606
3607void 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)
3608{
3609 nWaves.clear();
3610
3611 if (applyFFT) {
3612 string fftThAttr;
3613 float fftThSigma;
3614 int fftThTop;
3615 parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
3616 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
3617 }
3618
3619 addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves);
3620}
3621
3622void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
3623{
3624 uInt idxSigma = fftThresh.find("sigma");
3625 uInt idxTop = fftThresh.find("top");
3626
3627 if (idxSigma == fftThresh.size() - 5) {
3628 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
3629 is >> fftThSigma;
3630 fftThAttr = "sigma";
3631 } else if (idxTop == 0) {
3632 std::istringstream is(fftThresh.substr(3));
3633 is >> fftThTop;
3634 fftThAttr = "top";
3635 } else {
3636 bool isNumber = true;
3637 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
3638 char ch = (fftThresh.substr(i, 1).c_str())[0];
3639 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
3640 isNumber = false;
3641 break;
3642 }
3643 }
3644 if (isNumber) {
3645 std::istringstream is(fftThresh);
3646 is >> fftThSigma;
3647 fftThAttr = "sigma";
3648 } else {
3649 throw(AipsError("fftthresh has a wrong value"));
3650 }
3651 }
3652}
3653
3654void 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)
3655{
3656 std::vector<float> fspec;
3657 if (fftMethod == "fft") {
3658 fspec = execFFT(whichrow, chanMask, false, true);
3659 //} else if (fftMethod == "lsp") {
3660 // fspec = lombScarglePeriodogram(whichrow);
3661 }
3662
3663 if (fftThAttr == "sigma") {
3664 float mean = 0.0;
3665 float mean2 = 0.0;
3666 for (uInt i = 0; i < fspec.size(); ++i) {
3667 mean += fspec[i];
3668 mean2 += fspec[i]*fspec[i];
3669 }
3670 mean /= float(fspec.size());
3671 mean2 /= float(fspec.size());
3672 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
3673
3674 for (uInt i = 0; i < fspec.size(); ++i) {
3675 if (fspec[i] >= thres) {
3676 nWaves.push_back(i);
3677 }
3678 }
3679
3680 } else if (fftThAttr == "top") {
3681 for (int i = 0; i < fftThTop; ++i) {
3682 float max = 0.0;
3683 int maxIdx = 0;
3684 for (uInt j = 0; j < fspec.size(); ++j) {
3685 if (fspec[j] > max) {
3686 max = fspec[j];
3687 maxIdx = j;
3688 }
3689 }
3690 nWaves.push_back(maxIdx);
3691 fspec[maxIdx] = 0.0;
3692 }
3693
3694 }
3695
3696 if (nWaves.size() > 1) {
3697 sort(nWaves.begin(), nWaves.end());
3698 }
3699}
3700
3701void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
3702{
3703 std::vector<int> tempAddNWaves, tempRejectNWaves;
3704 for (uInt i = 0; i < addNWaves.size(); ++i) {
3705 tempAddNWaves.push_back(addNWaves[i]);
3706 }
3707 if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) {
3708 setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves);
3709 }
3710
3711 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
3712 tempRejectNWaves.push_back(rejectNWaves[i]);
3713 }
3714 if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) {
3715 setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves);
3716 }
3717
3718 for (uInt i = 0; i < tempAddNWaves.size(); ++i) {
3719 bool found = false;
3720 for (uInt j = 0; j < nWaves.size(); ++j) {
3721 if (nWaves[j] == tempAddNWaves[i]) {
3722 found = true;
3723 break;
3724 }
3725 }
3726 if (!found) nWaves.push_back(tempAddNWaves[i]);
3727 }
3728
3729 for (uInt i = 0; i < tempRejectNWaves.size(); ++i) {
3730 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
3731 if (*j == tempRejectNWaves[i]) {
3732 j = nWaves.erase(j);
3733 } else {
3734 ++j;
3735 }
3736 }
3737 }
3738
3739 if (nWaves.size() > 1) {
3740 sort(nWaves.begin(), nWaves.end());
3741 unique(nWaves.begin(), nWaves.end());
3742 }
3743}
3744
3745void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves)
3746{
3747 if ((nWaves.size() == 2)&&(nWaves[1] == -999)) {
3748 int val = nWaves[0];
3749 int nyquistFreq = nchan(getIF(whichrow))/2+1;
3750 nWaves.clear();
3751 if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759
3752 nWaves.push_back(0);
3753 }
3754 while (val <= nyquistFreq) {
3755 nWaves.push_back(val);
3756 val++;
3757 }
3758 }
3759}
3760
3761void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
3762{
3763 try {
3764 ofstream ofs;
3765 String coordInfo = "";
3766 bool hasSameNchan = true;
3767 bool outTextFile = false;
3768 bool csvFormat = false;
3769
3770 if (blfile != "") {
3771 csvFormat = (blfile.substr(0, 1) == "T");
3772 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3773 if (ofs) outTextFile = true;
3774 }
3775
3776 if (outLogger || outTextFile) {
3777 coordInfo = getCoordInfo()[0];
3778 if (coordInfo == "") coordInfo = "channel";
3779 hasSameNchan = hasSameNchanOverIFs();
3780 }
3781
3782 //Fitter fitter = Fitter();
3783 //fitter.setExpression("sinusoid", nWaves);
3784 //fitter.setIterClipping(thresClip, nIterClip);
3785
3786 int nRow = nrow();
3787 std::vector<bool> chanMask;
3788 std::vector<int> nWaves;
3789
3790 bool showProgress;
3791 int minNRow;
3792 parseProgressInfo(progressInfo, showProgress, minNRow);
3793
3794 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3795 chanMask = getCompositeChanMask(whichrow, mask);
3796 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
3797
3798 //FOR DEBUGGING------------
3799 /*
3800 if (whichrow < 0) {// == nRow -1) {
3801 cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow);
3802 if (applyFFT) {
3803 cout << "[ ";
3804 for (uInt j = 0; j < nWaves.size(); ++j) {
3805 cout << nWaves[j] << ", ";
3806 }
3807 cout << " ] " << endl;
3808 }
3809 cout << flush;
3810 }
3811 */
3812 //-------------------------
3813
3814 //fitBaseline(chanMask, whichrow, fitter);
3815 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
3816 std::vector<float> params;
3817 int nClipped = 0;
3818 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
3819 setSpectrum(res, whichrow);
3820 //
3821
3822 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
3823 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3824 }
3825
3826 if (outTextFile) ofs.close();
3827
3828 } catch (...) {
3829 throw;
3830 }
3831}
3832
3833void 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)
3834{
3835 try {
3836 ofstream ofs;
3837 String coordInfo = "";
3838 bool hasSameNchan = true;
3839 bool outTextFile = false;
3840 bool csvFormat = false;
3841
3842 if (blfile != "") {
3843 csvFormat = (blfile.substr(0, 1) == "T");
3844 ofs.open(blfile.substr(1).c_str(), ios::out | ios::app);
3845 if (ofs) outTextFile = true;
3846 }
3847
3848 if (outLogger || outTextFile) {
3849 coordInfo = getCoordInfo()[0];
3850 if (coordInfo == "") coordInfo = "channel";
3851 hasSameNchan = hasSameNchanOverIFs();
3852 }
3853
3854 //Fitter fitter = Fitter();
3855 //fitter.setExpression("sinusoid", nWaves);
3856 //fitter.setIterClipping(thresClip, nIterClip);
3857
3858 int nRow = nrow();
3859 std::vector<bool> chanMask;
3860 std::vector<int> nWaves;
3861
3862 int minEdgeSize = getIFNos().size()*2;
3863 STLineFinder lineFinder = STLineFinder();
3864 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3865
3866 bool showProgress;
3867 int minNRow;
3868 parseProgressInfo(progressInfo, showProgress, minNRow);
3869
3870 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3871
3872 //-------------------------------------------------------
3873 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
3874 //-------------------------------------------------------
3875 int edgeSize = edge.size();
3876 std::vector<int> currentEdge;
3877 if (edgeSize >= 2) {
3878 int idx = 0;
3879 if (edgeSize > 2) {
3880 if (edgeSize < minEdgeSize) {
3881 throw(AipsError("Length of edge element info is less than that of IFs"));
3882 }
3883 idx = 2 * getIF(whichrow);
3884 }
3885 currentEdge.push_back(edge[idx]);
3886 currentEdge.push_back(edge[idx+1]);
3887 } else {
3888 throw(AipsError("Wrong length of edge element"));
3889 }
3890 lineFinder.setData(getSpectrum(whichrow));
3891 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
3892 chanMask = lineFinder.getMask();
3893 //-------------------------------------------------------
3894
3895 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
3896
3897 //fitBaseline(chanMask, whichrow, fitter);
3898 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
3899 std::vector<float> params;
3900 int nClipped = 0;
3901 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
3902 setSpectrum(res, whichrow);
3903 //
3904
3905 outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
3906 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3907 }
3908
3909 if (outTextFile) ofs.close();
3910
3911 } catch (...) {
3912 throw;
3913 }
3914}
3915
3916std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual)
3917{
3918 if (data.size() != mask.size()) {
3919 throw(AipsError("data and mask sizes are not identical"));
3920 }
3921 if (data.size() < 2) {
3922 throw(AipsError("data size is too short"));
3923 }
3924 if (waveNumbers.size() == 0) {
3925 throw(AipsError("no wave numbers given"));
3926 }
3927 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
3928 nWaves.reserve(waveNumbers.size());
3929 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
3930 sort(nWaves.begin(), nWaves.end());
3931 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
3932 nWaves.erase(end_it, nWaves.end());
3933
3934 int minNWaves = nWaves[0];
3935 if (minNWaves < 0) {
3936 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
3937 }
3938 bool hasConstantTerm = (minNWaves == 0);
3939
3940 int nChan = data.size();
3941 std::vector<int> maskArray;
3942 std::vector<int> x;
3943 for (int i = 0; i < nChan; ++i) {
3944 maskArray.push_back(mask[i] ? 1 : 0);
3945 if (mask[i]) {
3946 x.push_back(i);
3947 }
3948 }
3949
3950 int initNData = x.size();
3951
3952 int nData = initNData;
3953 int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
3954
3955 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
3956 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)
3957
3958 // xArray : contains elemental values for computing the least-square matrix.
3959 // xArray.size() is nDOF and xArray[*].size() is nChan.
3960 // Each xArray element are as follows:
3961 // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
3962 // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
3963 // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
3964 // where (1 <= n <= nMaxWavesInSW),
3965 // or,
3966 // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
3967 // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
3968 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
3969 std::vector<std::vector<double> > xArray;
3970 if (hasConstantTerm) {
3971 std::vector<double> xu;
3972 for (int j = 0; j < nChan; ++j) {
3973 xu.push_back(1.0);
3974 }
3975 xArray.push_back(xu);
3976 }
3977 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
3978 double xFactor = baseXFactor*(double)nWaves[i];
3979 std::vector<double> xs, xc;
3980 xs.clear();
3981 xc.clear();
3982 for (int j = 0; j < nChan; ++j) {
3983 xs.push_back(sin(xFactor*(double)j));
3984 xc.push_back(cos(xFactor*(double)j));
3985 }
3986 xArray.push_back(xs);
3987 xArray.push_back(xc);
3988 }
3989
3990 std::vector<double> z1, r1, residual;
3991 for (int i = 0; i < nChan; ++i) {
3992 z1.push_back((double)data[i]);
3993 r1.push_back(0.0);
3994 residual.push_back(0.0);
3995 }
3996
3997 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3998 // xMatrix : horizontal concatenation of
3999 // the least-sq. matrix (left) and an
4000 // identity matrix (right).
4001 // the right part is used to calculate the inverse matrix of the left part.
4002 double xMatrix[nDOF][2*nDOF];
4003 double zMatrix[nDOF];
4004 for (int i = 0; i < nDOF; ++i) {
4005 for (int j = 0; j < 2*nDOF; ++j) {
4006 xMatrix[i][j] = 0.0;
4007 }
4008 xMatrix[i][nDOF+i] = 1.0;
4009 zMatrix[i] = 0.0;
4010 }
4011
4012 int nUseData = 0;
4013 for (int k = 0; k < nChan; ++k) {
4014 if (maskArray[k] == 0) continue;
4015
4016 for (int i = 0; i < nDOF; ++i) {
4017 for (int j = i; j < nDOF; ++j) {
4018 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
4019 }
4020 zMatrix[i] += z1[k] * xArray[i][k];
4021 }
4022
4023 nUseData++;
4024 }
4025
4026 if (nUseData < 1) {
4027 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
4028 }
4029
4030 for (int i = 0; i < nDOF; ++i) {
4031 for (int j = 0; j < i; ++j) {
4032 xMatrix[i][j] = xMatrix[j][i];
4033 }
4034 }
4035
4036 std::vector<double> invDiag;
4037 for (int i = 0; i < nDOF; ++i) {
4038 invDiag.push_back(1.0/xMatrix[i][i]);
4039 for (int j = 0; j < nDOF; ++j) {
4040 xMatrix[i][j] *= invDiag[i];
4041 }
4042 }
4043
4044 for (int k = 0; k < nDOF; ++k) {
4045 for (int i = 0; i < nDOF; ++i) {
4046 if (i != k) {
4047 double factor1 = xMatrix[k][k];
4048 double factor2 = xMatrix[i][k];
4049 for (int j = k; j < 2*nDOF; ++j) {
4050 xMatrix[i][j] *= factor1;
4051 xMatrix[i][j] -= xMatrix[k][j]*factor2;
4052 xMatrix[i][j] /= factor1;
4053 }
4054 }
4055 }
4056 double xDiag = xMatrix[k][k];
4057 for (int j = k; j < 2*nDOF; ++j) {
4058 xMatrix[k][j] /= xDiag;
4059 }
4060 }
4061
4062 for (int i = 0; i < nDOF; ++i) {
4063 for (int j = 0; j < nDOF; ++j) {
4064 xMatrix[i][nDOF+j] *= invDiag[j];
4065 }
4066 }
4067 //compute a vector y which consists of the coefficients of the sinusoids forming the
4068 //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
4069 //and cosine functions, respectively.
4070 std::vector<double> y;
4071 params.clear();
4072 for (int i = 0; i < nDOF; ++i) {
4073 y.push_back(0.0);
4074 for (int j = 0; j < nDOF; ++j) {
4075 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
4076 }
4077 params.push_back(y[i]);
4078 }
4079
4080 for (int i = 0; i < nChan; ++i) {
4081 r1[i] = y[0];
4082 for (int j = 1; j < nDOF; ++j) {
4083 r1[i] += y[j]*xArray[j][i];
4084 }
4085 residual[i] = z1[i] - r1[i];
4086 }
4087
4088 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
4089 break;
4090 } else {
4091 double stdDev = 0.0;
4092 for (int i = 0; i < nChan; ++i) {
4093 stdDev += residual[i]*residual[i]*(double)maskArray[i];
4094 }
4095 stdDev = sqrt(stdDev/(double)nData);
4096
4097 double thres = stdDev * thresClip;
4098 int newNData = 0;
4099 for (int i = 0; i < nChan; ++i) {
4100 if (abs(residual[i]) >= thres) {
4101 maskArray[i] = 0;
4102 }
4103 if (maskArray[i] > 0) {
4104 newNData++;
4105 }
4106 }
4107 if (newNData == nData) {
4108 break; //no more flag to add. iteration stops.
4109 } else {
4110 nData = newNData;
4111 }
4112 }
4113 }
4114
4115 nClipped = initNData - nData;
4116
4117 std::vector<float> result;
4118 if (getResidual) {
4119 for (int i = 0; i < nChan; ++i) {
4120 result.push_back((float)residual[i]);
4121 }
4122 } else {
4123 for (int i = 0; i < nChan; ++i) {
4124 result.push_back((float)r1[i]);
4125 }
4126 }
4127
4128 return result;
4129}
4130
4131void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
4132{
4133 std::vector<double> dAbcissa = getAbcissa(whichrow);
4134 std::vector<float> abcissa;
4135 for (uInt i = 0; i < dAbcissa.size(); ++i) {
4136 abcissa.push_back((float)dAbcissa[i]);
4137 }
4138 std::vector<float> spec = getSpectrum(whichrow);
4139
4140 fitter.setData(abcissa, spec, mask);
4141 fitter.lfit();
4142}
4143
4144std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
4145{
4146 /****
4147 double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd;
4148 double elapse1 = 0.0;
4149 double elapse2 = 0.0;
4150
4151 ms1TimeStart = mathutil::gettimeofday_sec();
4152 ****/
4153
4154 std::vector<bool> mask = getMask(whichrow);
4155
4156 /****
4157 ms1TimeEnd = mathutil::gettimeofday_sec();
4158 elapse1 = ms1TimeEnd - ms1TimeStart;
4159 std::cout << "ms1 : " << elapse1 << " (sec.)" << endl;
4160 ms2TimeStart = mathutil::gettimeofday_sec();
4161 ****/
4162
4163 uInt maskSize = mask.size();
4164 if (inMask.size() != 0) {
4165 if (maskSize != inMask.size()) {
4166 throw(AipsError("mask sizes are not the same."));
4167 }
4168 for (uInt i = 0; i < maskSize; ++i) {
4169 mask[i] = mask[i] && inMask[i];
4170 }
4171 }
4172
4173 /****
4174 ms2TimeEnd = mathutil::gettimeofday_sec();
4175 elapse2 = ms2TimeEnd - ms2TimeStart;
4176 std::cout << "ms2 : " << elapse2 << " (sec.)" << endl;
4177 ****/
4178
4179 return mask;
4180}
4181
4182/*
4183std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
4184{
4185 int edgeSize = edge.size();
4186 std::vector<int> currentEdge;
4187 if (edgeSize >= 2) {
4188 int idx = 0;
4189 if (edgeSize > 2) {
4190 if (edgeSize < minEdgeSize) {
4191 throw(AipsError("Length of edge element info is less than that of IFs"));
4192 }
4193 idx = 2 * getIF(whichrow);
4194 }
4195 currentEdge.push_back(edge[idx]);
4196 currentEdge.push_back(edge[idx+1]);
4197 } else {
4198 throw(AipsError("Wrong length of edge element"));
4199 }
4200
4201 lineFinder.setData(getSpectrum(whichrow));
4202 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
4203
4204 return lineFinder.getMask();
4205}
4206*/
4207
4208/* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
4209void 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)
4210{
4211 if (outLogger || outTextFile) {
4212 std::vector<float> params = fitter.getParameters();
4213 std::vector<bool> fixed = fitter.getFixedParameters();
4214 float rms = getRms(chanMask, whichrow);
4215 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
4216
4217 if (outLogger) {
4218 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
4219 ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false, csvFormat) << LogIO::POST ;
4220 }
4221 if (outTextFile) {
4222 ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true, csvFormat) << flush;
4223 }
4224 }
4225}
4226
4227/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
4228void 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)
4229{
4230 if (outLogger || outTextFile) {
4231 /****
4232 double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd;
4233 double elapse1 = 0.0;
4234 double elapse2 = 0.0;
4235
4236 ms1TimeStart = mathutil::gettimeofday_sec();
4237 ****/
4238
4239 float rms = getRms(chanMask, whichrow);
4240
4241 /****
4242 ms1TimeEnd = mathutil::gettimeofday_sec();
4243 elapse1 = ms1TimeEnd - ms1TimeStart;
4244 std::cout << "ot1 : " << elapse1 << " (sec.)" << endl;
4245 ms2TimeStart = mathutil::gettimeofday_sec();
4246 ****/
4247
4248 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
4249 std::vector<bool> fixed;
4250 fixed.clear();
4251
4252 if (outLogger) {
4253 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
4254 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ;
4255 }
4256 if (outTextFile) {
4257 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush;
4258 }
4259
4260 /****
4261 ms2TimeEnd = mathutil::gettimeofday_sec();
4262 elapse2 = ms2TimeEnd - ms2TimeStart;
4263 std::cout << "ot2 : " << elapse2 << " (sec.)" << endl;
4264 ****/
4265
4266 }
4267}
4268
4269/* for chebyshev/sinusoid. will be merged once chebyshev/sinusoid is available in fitter (2011/3/10 WK) */
4270void 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)
4271{
4272 if (outLogger || outTextFile) {
4273 float rms = getRms(chanMask, whichrow);
4274 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
4275 std::vector<bool> fixed;
4276 fixed.clear();
4277
4278 if (outLogger) {
4279 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
4280 ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ;
4281 }
4282 if (outTextFile) {
4283 ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush;
4284 }
4285 }
4286}
4287
4288void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
4289{
4290 int idxDelimiter = progressInfo.find(",");
4291 if (idxDelimiter < 0) {
4292 throw(AipsError("wrong value in 'showprogress' parameter")) ;
4293 }
4294 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
4295 std::istringstream is(progressInfo.substr(idxDelimiter+1));
4296 is >> minNRow;
4297}
4298
4299void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
4300{
4301 if (showProgress && (nTotal >= nTotalThreshold)) {
4302 int nInterval = int(floor(double(nTotal)/100.0));
4303 if (nInterval == 0) nInterval++;
4304
4305 if (nProcessed % nInterval == 0) {
4306 printf("\r"); //go to the head of line
4307 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
4308 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
4309 printf("\x1b[39m\x1b[0m"); //set default attributes
4310 fflush(NULL);
4311 }
4312
4313 if (nProcessed == nTotal - 1) {
4314 printf("\r\x1b[K"); //clear
4315 fflush(NULL);
4316 }
4317
4318 }
4319}
4320
4321std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
4322{
4323 std::vector<bool> mask = getMask(whichrow);
4324
4325 if (inMask.size() > 0) {
4326 uInt maskSize = mask.size();
4327 if (maskSize != inMask.size()) {
4328 throw(AipsError("mask sizes are not the same."));
4329 }
4330 for (uInt i = 0; i < maskSize; ++i) {
4331 mask[i] = mask[i] && inMask[i];
4332 }
4333 }
4334
4335 Vector<Float> spec = getSpectrum(whichrow);
4336 mathutil::doZeroOrderInterpolation(spec, mask);
4337
4338 FFTServer<Float,Complex> ffts;
4339 Vector<Complex> fftres;
4340 ffts.fft0(fftres, spec);
4341
4342 std::vector<float> res;
4343 float norm = float(2.0/double(spec.size()));
4344
4345 if (getRealImag) {
4346 for (uInt i = 0; i < fftres.size(); ++i) {
4347 res.push_back(real(fftres[i])*norm);
4348 res.push_back(imag(fftres[i])*norm);
4349 }
4350 } else {
4351 for (uInt i = 0; i < fftres.size(); ++i) {
4352 res.push_back(abs(fftres[i])*norm);
4353 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
4354 }
4355 }
4356
4357 return res;
4358}
4359
4360
4361float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
4362{
4363 /****
4364 double ms1TimeStart, ms1TimeEnd;
4365 double elapse1 = 0.0;
4366 ms1TimeStart = mathutil::gettimeofday_sec();
4367 ****/
4368
4369 Vector<Float> spec;
4370 specCol_.get(whichrow, spec);
4371
4372 /****
4373 ms1TimeEnd = mathutil::gettimeofday_sec();
4374 elapse1 = ms1TimeEnd - ms1TimeStart;
4375 std::cout << "rm1 : " << elapse1 << " (sec.)" << endl;
4376 ****/
4377
4378 return (float)doGetRms(mask, spec);
4379}
4380
4381double Scantable::doGetRms(const std::vector<bool>& mask, const Vector<Float>& spec)
4382{
4383 double mean = 0.0;
4384 double smean = 0.0;
4385 int n = 0;
4386 for (uInt i = 0; i < spec.nelements(); ++i) {
4387 if (mask[i]) {
4388 double val = (double)spec[i];
4389 mean += val;
4390 smean += val*val;
4391 n++;
4392 }
4393 }
4394
4395 mean /= (double)n;
4396 smean /= (double)n;
4397
4398 return sqrt(smean - mean*mean);
4399}
4400
4401std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const
4402{
4403 if (verbose) {
4404 ostringstream oss;
4405
4406 if (csvformat) {
4407 oss << getScan(whichrow) << ",";
4408 oss << getBeam(whichrow) << ",";
4409 oss << getIF(whichrow) << ",";
4410 oss << getPol(whichrow) << ",";
4411 oss << getCycle(whichrow) << ",";
4412 String commaReplacedMasklist = masklist;
4413 string::size_type pos = 0;
4414 while (pos = commaReplacedMasklist.find(","), pos != string::npos) {
4415 commaReplacedMasklist.replace(pos, 1, ";");
4416 pos++;
4417 }
4418 oss << commaReplacedMasklist << ",";
4419 } else {
4420 oss << " Scan[" << getScan(whichrow) << "]";
4421 oss << " Beam[" << getBeam(whichrow) << "]";
4422 oss << " IF[" << getIF(whichrow) << "]";
4423 oss << " Pol[" << getPol(whichrow) << "]";
4424 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
4425 oss << "Fitter range = " << masklist << endl;
4426 oss << "Baseline parameters" << endl;
4427 }
4428 oss << flush;
4429
4430 return String(oss);
4431 }
4432
4433 return "";
4434}
4435
4436std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const
4437{
4438 if (verbose) {
4439 ostringstream oss;
4440
4441 if (csvformat) {
4442 oss << rms << ",";
4443 if (nClipped >= 0) {
4444 oss << nClipped;
4445 }
4446 } else {
4447 oss << "Results of baseline fit" << endl;
4448 oss << " rms = " << setprecision(6) << rms << endl;
4449 if (nClipped >= 0) {
4450 oss << " Number of clipped channels = " << nClipped << endl;
4451 }
4452 for (int i = 0; i < 60; ++i) {
4453 oss << "-";
4454 }
4455 }
4456 oss << endl;
4457 oss << flush;
4458
4459 return String(oss);
4460 }
4461
4462 return "";
4463}
4464
4465std::string Scantable::formatBaselineParams(const std::vector<float>& params,
4466 const std::vector<bool>& fixed,
4467 float rms,
4468 int nClipped,
4469 const std::string& masklist,
4470 int whichrow,
4471 bool verbose,
4472 bool csvformat,
4473 int start, int count,
4474 bool resetparamid) const
4475{
4476 int nParam = (int)(params.size());
4477
4478 if (nParam < 1) {
4479 return(" Not fitted");
4480 } else {
4481
4482 ostringstream oss;
4483 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
4484
4485 if (start < 0) start = 0;
4486 if (count < 0) count = nParam;
4487 int end = start + count;
4488 if (end > nParam) end = nParam;
4489 int paramidoffset = (resetparamid) ? (-start) : 0;
4490
4491 for (int i = start; i < end; ++i) {
4492 if (i > start) {
4493 oss << ",";
4494 }
4495 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
4496 if (csvformat) {
4497 oss << params[i] << sFix;
4498 } else {
4499 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
4500 }
4501 }
4502
4503 if (csvformat) {
4504 oss << ",";
4505 } else {
4506 oss << endl;
4507 }
4508 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
4509
4510 return String(oss);
4511 }
4512
4513}
4514
4515std::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
4516{
4517 int nOutParam = (int)(params.size());
4518 int nPiece = (int)(ranges.size()) - 1;
4519
4520 if (nOutParam < 1) {
4521 return(" Not fitted");
4522 } else if (nPiece < 0) {
4523 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat);
4524 } else if (nPiece < 1) {
4525 return(" Bad count of the piece edge info");
4526 } else if (nOutParam % nPiece != 0) {
4527 return(" Bad count of the output baseline parameters");
4528 } else {
4529
4530 int nParam = nOutParam / nPiece;
4531
4532 ostringstream oss;
4533 oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat);
4534
4535 if (csvformat) {
4536 for (int i = 0; i < nPiece; ++i) {
4537 oss << ranges[i] << "," << (ranges[i+1]-1) << ",";
4538 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
4539 }
4540 } else {
4541 stringstream ss;
4542 ss << ranges[nPiece] << flush;
4543 int wRange = ss.str().size() * 2 + 5;
4544
4545 for (int i = 0; i < nPiece; ++i) {
4546 ss.str("");
4547 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
4548 oss << left << setw(wRange) << ss.str();
4549 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true);
4550 //oss << endl;
4551 }
4552 }
4553
4554 oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat);
4555
4556 return String(oss);
4557 }
4558
4559}
4560
4561bool Scantable::hasSameNchanOverIFs()
4562{
4563 int nIF = nif(-1);
4564 int nCh;
4565 int totalPositiveNChan = 0;
4566 int nPositiveNChan = 0;
4567
4568 for (int i = 0; i < nIF; ++i) {
4569 nCh = nchan(i);
4570 if (nCh > 0) {
4571 totalPositiveNChan += nCh;
4572 nPositiveNChan++;
4573 }
4574 }
4575
4576 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
4577}
4578
4579std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
4580{
4581 if (mask.size() <= 0) {
4582 throw(AipsError("The mask elements should be > 0"));
4583 }
4584 int IF = getIF(whichrow);
4585 if (mask.size() != (uInt)nchan(IF)) {
4586 throw(AipsError("Number of channels in scantable != number of mask elements"));
4587 }
4588
4589 if (verbose) {
4590 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
4591 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
4592 if (!hasSameNchan) {
4593 logOs << endl << "This mask is only valid for IF=" << IF;
4594 }
4595 logOs << LogIO::POST;
4596 }
4597
4598 std::vector<double> abcissa = getAbcissa(whichrow);
4599 std::vector<int> edge = getMaskEdgeIndices(mask);
4600
4601 ostringstream oss;
4602 oss.setf(ios::fixed);
4603 oss << setprecision(1) << "[";
4604 for (uInt i = 0; i < edge.size(); i+=2) {
4605 if (i > 0) oss << ",";
4606 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
4607 }
4608 oss << "]" << flush;
4609
4610 return String(oss);
4611}
4612
4613std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
4614{
4615 if (mask.size() <= 0) {
4616 throw(AipsError("The mask elements should be > 0"));
4617 }
4618
4619 std::vector<int> out, startIndices, endIndices;
4620 int maskSize = mask.size();
4621
4622 startIndices.clear();
4623 endIndices.clear();
4624
4625 if (mask[0]) {
4626 startIndices.push_back(0);
4627 }
4628 for (int i = 1; i < maskSize; ++i) {
4629 if ((!mask[i-1]) && mask[i]) {
4630 startIndices.push_back(i);
4631 } else if (mask[i-1] && (!mask[i])) {
4632 endIndices.push_back(i-1);
4633 }
4634 }
4635 if (mask[maskSize-1]) {
4636 endIndices.push_back(maskSize-1);
4637 }
4638
4639 if (startIndices.size() != endIndices.size()) {
4640 throw(AipsError("Inconsistent Mask Size: bad data?"));
4641 }
4642 for (uInt i = 0; i < startIndices.size(); ++i) {
4643 if (startIndices[i] > endIndices[i]) {
4644 throw(AipsError("Mask start index > mask end index"));
4645 }
4646 }
4647
4648 out.clear();
4649 for (uInt i = 0; i < startIndices.size(); ++i) {
4650 out.push_back(startIndices[i]);
4651 out.push_back(endIndices[i]);
4652 }
4653
4654 return out;
4655}
4656
4657vector<float> Scantable::getTsysSpectrum( int whichrow ) const
4658{
4659 Vector<Float> tsys( tsysCol_(whichrow) ) ;
4660 vector<float> stlTsys ;
4661 tsys.tovector( stlTsys ) ;
4662 return stlTsys ;
4663}
4664
4665vector<uint> Scantable::getMoleculeIdColumnData() const
4666{
4667 Vector<uInt> molIds(mmolidCol_.getColumn());
4668 vector<uint> res;
4669 molIds.tovector(res);
4670 return res;
4671}
4672
4673void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids)
4674{
4675 Vector<uInt> molIds(molids);
4676 Vector<uInt> arr(mmolidCol_.getColumn());
4677 if ( molIds.nelements() != arr.nelements() )
4678 throw AipsError("The input data size must be the number of rows.");
4679 mmolidCol_.putColumn(molIds);
4680}
4681
4682
4683}
4684//namespace asap
Note: See TracBrowser for help on using the repository browser.