source: trunk/src/Scantable.cpp@ 2592

Last change on this file since 2592 was 2591, checked in by WataruKawasaki, 12 years ago

New Development: Yes

JIRA Issue: Yes CSV-1869

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: No

Module(s): asap

Description: added a scantable function to get/set moleculesID columns data.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 121.7 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/Arrays/Array.h>
23#include <casa/Arrays/ArrayAccessor.h>
24#include <casa/Arrays/ArrayLogical.h>
25#include <casa/Arrays/ArrayMath.h>
26#include <casa/Arrays/MaskArrMath.h>
27#include <casa/Arrays/Slice.h>
28#include <casa/Arrays/Vector.h>
29#include <casa/Arrays/VectorSTLIterator.h>
30#include <casa/BasicMath/Math.h>
31#include <casa/BasicSL/Constants.h>
32#include <casa/Containers/RecordField.h>
33#include <casa/Logging/LogIO.h>
34#include <casa/Quanta/MVAngle.h>
35#include <casa/Quanta/MVTime.h>
36#include <casa/Utilities/GenSort.h>
37
38#include <coordinates/Coordinates/CoordinateUtil.h>
39
40// needed to avoid error in .tcc
41#include <measures/Measures/MCDirection.h>
42//
43#include <measures/Measures/MDirection.h>
44#include <measures/Measures/MEpoch.h>
45#include <measures/Measures/MFrequency.h>
46#include <measures/Measures/MeasRef.h>
47#include <measures/Measures/MeasTable.h>
48#include <measures/TableMeasures/ScalarMeasColumn.h>
49#include <measures/TableMeasures/TableMeasDesc.h>
50#include <measures/TableMeasures/TableMeasRefDesc.h>
51#include <measures/TableMeasures/TableMeasValueDesc.h>
52
53#include <tables/Tables/ArrColDesc.h>
54#include <tables/Tables/ExprNode.h>
55#include <tables/Tables/ScaColDesc.h>
56#include <tables/Tables/SetupNewTab.h>
57#include <tables/Tables/TableCopy.h>
58#include <tables/Tables/TableDesc.h>
59#include <tables/Tables/TableIter.h>
60#include <tables/Tables/TableParse.h>
61#include <tables/Tables/TableRecord.h>
62#include <tables/Tables/TableRow.h>
63#include <tables/Tables/TableVector.h>
64
65#include "MathUtils.h"
66#include "STAttr.h"
67#include "STLineFinder.h"
68#include "STPolCircular.h"
69#include "STPolLinear.h"
70#include "STPolStokes.h"
71#include "STUpgrade.h"
72#include "Scantable.h"
73
74#define debug 1
75
76using namespace casa;
77
78namespace asap {
79
80std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
81
82void Scantable::initFactories() {
83 if ( factories_.empty() ) {
84 Scantable::factories_["linear"] = &STPolLinear::myFactory;
85 Scantable::factories_["circular"] = &STPolCircular::myFactory;
86 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
87 }
88}
89
90Scantable::Scantable(Table::TableType ttype) :
91 type_(ttype)
92{
93 initFactories();
94 setupMainTable();
95 freqTable_ = STFrequencies(*this);
96 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
97 weatherTable_ = STWeather(*this);
98 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
99 focusTable_ = STFocus(*this);
100 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
101 tcalTable_ = STTcal(*this);
102 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
103 moleculeTable_ = STMolecules(*this);
104 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
105 historyTable_ = STHistory(*this);
106 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
107 fitTable_ = STFit(*this);
108 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
109 table_.tableInfo().setType( "Scantable" ) ;
110 originalTable_ = table_;
111 attach();
112}
113
114Scantable::Scantable(const std::string& name, Table::TableType ttype) :
115 type_(ttype)
116{
117 initFactories();
118
119 Table tab(name, Table::Update);
120 uInt version = tab.keywordSet().asuInt("VERSION");
121 if (version != version_) {
122 STUpgrade upgrader(version_);
123 LogIO os( LogOrigin( "Scantable" ) ) ;
124 os << LogIO::WARN
125 << name << " data format version " << version
126 << " is deprecated" << endl
127 << "Running upgrade."<< endl
128 << LogIO::POST ;
129 std::string outname = upgrader.upgrade(name);
130 if ( outname != name ) {
131 os << LogIO::WARN
132 << "Data will be loaded from " << outname << " instead of "
133 << name << LogIO::POST ;
134 tab = Table(outname, Table::Update ) ;
135 }
136 }
137 if ( type_ == Table::Memory ) {
138 table_ = tab.copyToMemoryTable(generateName());
139 } else {
140 table_ = tab;
141 }
142 table_.tableInfo().setType( "Scantable" ) ;
143
144 attachSubtables();
145 originalTable_ = table_;
146 attach();
147}
148/*
149Scantable::Scantable(const std::string& name, Table::TableType ttype) :
150 type_(ttype)
151{
152 initFactories();
153 Table tab(name, Table::Update);
154 uInt version = tab.keywordSet().asuInt("VERSION");
155 if (version != version_) {
156 throw(AipsError("Unsupported version of ASAP file."));
157 }
158 if ( type_ == Table::Memory ) {
159 table_ = tab.copyToMemoryTable(generateName());
160 } else {
161 table_ = tab;
162 }
163
164 attachSubtables();
165 originalTable_ = table_;
166 attach();
167}
168*/
169
170Scantable::Scantable( const Scantable& other, bool clear ):
171 Logger()
172{
173 // with or without data
174 String newname = String(generateName());
175 type_ = other.table_.tableType();
176 if ( other.table_.tableType() == Table::Memory ) {
177 if ( clear ) {
178 table_ = TableCopy::makeEmptyMemoryTable(newname,
179 other.table_, True);
180 } else
181 table_ = other.table_.copyToMemoryTable(newname);
182 } else {
183 other.table_.deepCopy(newname, Table::New, False,
184 other.table_.endianFormat(),
185 Bool(clear));
186 table_ = Table(newname, Table::Update);
187 table_.markForDelete();
188 }
189 table_.tableInfo().setType( "Scantable" ) ;
190 /// @todo reindex SCANNO, recompute nbeam, nif, npol
191 if ( clear ) copySubtables(other);
192 attachSubtables();
193 originalTable_ = table_;
194 attach();
195}
196
197void Scantable::copySubtables(const Scantable& other) {
198 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
199 TableCopy::copyRows(t, other.freqTable_.table());
200 t = table_.rwKeywordSet().asTable("FOCUS");
201 TableCopy::copyRows(t, other.focusTable_.table());
202 t = table_.rwKeywordSet().asTable("WEATHER");
203 TableCopy::copyRows(t, other.weatherTable_.table());
204 t = table_.rwKeywordSet().asTable("TCAL");
205 TableCopy::copyRows(t, other.tcalTable_.table());
206 t = table_.rwKeywordSet().asTable("MOLECULES");
207 TableCopy::copyRows(t, other.moleculeTable_.table());
208 t = table_.rwKeywordSet().asTable("HISTORY");
209 TableCopy::copyRows(t, other.historyTable_.table());
210 t = table_.rwKeywordSet().asTable("FIT");
211 TableCopy::copyRows(t, other.fitTable_.table());
212}
213
214void Scantable::attachSubtables()
215{
216 freqTable_ = STFrequencies(table_);
217 focusTable_ = STFocus(table_);
218 weatherTable_ = STWeather(table_);
219 tcalTable_ = STTcal(table_);
220 moleculeTable_ = STMolecules(table_);
221 historyTable_ = STHistory(table_);
222 fitTable_ = STFit(table_);
223}
224
225Scantable::~Scantable()
226{
227}
228
229void Scantable::setupMainTable()
230{
231 TableDesc td("", "1", TableDesc::Scratch);
232 td.comment() = "An ASAP Scantable";
233 td.rwKeywordSet().define("VERSION", uInt(version_));
234
235 // n Cycles
236 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
237 // new index every nBeam x nIF x nPol
238 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
239
240 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
241 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
242 // linear, circular, stokes
243 td.rwKeywordSet().define("POLTYPE", String("linear"));
244 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
245
246 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
247 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
248
249 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
250 refbeamnoColumn.setDefault(Int(-1));
251 td.addColumn(refbeamnoColumn);
252
253 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
254 flagrowColumn.setDefault(uInt(0));
255 td.addColumn(flagrowColumn);
256
257 td.addColumn(ScalarColumnDesc<Double>("TIME"));
258 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
259 TableMeasValueDesc measVal(td, "TIME");
260 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
261 mepochCol.write(td);
262
263 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
264
265 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
266 // Type of source (on=0, off=1, other=-1)
267 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
268 stypeColumn.setDefault(Int(-1));
269 td.addColumn(stypeColumn);
270 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
271
272 //The actual Data Vectors
273 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
274 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
275 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
276
277 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
278 IPosition(1,2),
279 ColumnDesc::Direct));
280 TableMeasRefDesc mdirRef(MDirection::J2000); // default
281 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
282 // the TableMeasDesc gives the column a type
283 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
284 // a uder set table type e.g. GALCTIC, B1950 ...
285 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
286 // writing create the measure column
287 mdirCol.write(td);
288 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
289 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
290 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
291
292 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
293 ScalarColumnDesc<Int> fitColumn("FIT_ID");
294 fitColumn.setDefault(Int(-1));
295 td.addColumn(fitColumn);
296
297 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
298 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
299
300 // columns which just get dragged along, as they aren't used in asap
301 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
302 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
303 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
304 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
305
306 td.rwKeywordSet().define("OBSMODE", String(""));
307
308 // Now create Table SetUp from the description.
309 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
310 table_ = Table(aNewTab, type_, 0);
311 originalTable_ = table_;
312}
313
314void Scantable::attach()
315{
316 timeCol_.attach(table_, "TIME");
317 srcnCol_.attach(table_, "SRCNAME");
318 srctCol_.attach(table_, "SRCTYPE");
319 specCol_.attach(table_, "SPECTRA");
320 flagsCol_.attach(table_, "FLAGTRA");
321 tsysCol_.attach(table_, "TSYS");
322 cycleCol_.attach(table_,"CYCLENO");
323 scanCol_.attach(table_, "SCANNO");
324 beamCol_.attach(table_, "BEAMNO");
325 ifCol_.attach(table_, "IFNO");
326 polCol_.attach(table_, "POLNO");
327 integrCol_.attach(table_, "INTERVAL");
328 azCol_.attach(table_, "AZIMUTH");
329 elCol_.attach(table_, "ELEVATION");
330 dirCol_.attach(table_, "DIRECTION");
331 fldnCol_.attach(table_, "FIELDNAME");
332 rbeamCol_.attach(table_, "REFBEAMNO");
333
334 mweatheridCol_.attach(table_,"WEATHER_ID");
335 mfitidCol_.attach(table_,"FIT_ID");
336 mfreqidCol_.attach(table_, "FREQ_ID");
337 mtcalidCol_.attach(table_, "TCAL_ID");
338 mfocusidCol_.attach(table_, "FOCUS_ID");
339 mmolidCol_.attach(table_, "MOLECULE_ID");
340
341 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
342 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
343
344}
345
346template<class T, class T2>
347void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
348 const String& colName,
349 const T2& defValue)
350{
351 try {
352 col.attach(table_, colName);
353 } catch (TableError& err) {
354 String errMesg = err.getMesg();
355 if (errMesg == "Table column " + colName + " is unknown") {
356 table_.addColumn(ScalarColumnDesc<T>(colName));
357 col.attach(table_, colName);
358 col.fillColumn(static_cast<T>(defValue));
359 } else {
360 throw;
361 }
362 } catch (...) {
363 throw;
364 }
365}
366
367template<class T, class T2>
368void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
369 const String& colName,
370 const Array<T2>& defValue)
371{
372 try {
373 col.attach(table_, colName);
374 } catch (TableError& err) {
375 String errMesg = err.getMesg();
376 if (errMesg == "Table column " + colName + " is unknown") {
377 table_.addColumn(ArrayColumnDesc<T>(colName));
378 col.attach(table_, colName);
379
380 int size = 0;
381 ArrayIterator<T2>& it = defValue.begin();
382 while (it != defValue.end()) {
383 ++size;
384 ++it;
385 }
386 IPosition ip(1, size);
387 Array<T>& arr(ip);
388 for (int i = 0; i < size; ++i)
389 arr[i] = static_cast<T>(defValue[i]);
390
391 col.fillColumn(arr);
392 } else {
393 throw;
394 }
395 } catch (...) {
396 throw;
397 }
398}
399
400void Scantable::setHeader(const STHeader& sdh)
401{
402 table_.rwKeywordSet().define("nIF", sdh.nif);
403 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
404 table_.rwKeywordSet().define("nPol", sdh.npol);
405 table_.rwKeywordSet().define("nChan", sdh.nchan);
406 table_.rwKeywordSet().define("Observer", sdh.observer);
407 table_.rwKeywordSet().define("Project", sdh.project);
408 table_.rwKeywordSet().define("Obstype", sdh.obstype);
409 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
410 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
411 table_.rwKeywordSet().define("Equinox", sdh.equinox);
412 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
413 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
414 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
415 table_.rwKeywordSet().define("UTC", sdh.utc);
416 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
417 table_.rwKeywordSet().define("Epoch", sdh.epoch);
418 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
419}
420
421STHeader Scantable::getHeader() const
422{
423 STHeader sdh;
424 table_.keywordSet().get("nBeam",sdh.nbeam);
425 table_.keywordSet().get("nIF",sdh.nif);
426 table_.keywordSet().get("nPol",sdh.npol);
427 table_.keywordSet().get("nChan",sdh.nchan);
428 table_.keywordSet().get("Observer", sdh.observer);
429 table_.keywordSet().get("Project", sdh.project);
430 table_.keywordSet().get("Obstype", sdh.obstype);
431 table_.keywordSet().get("AntennaName", sdh.antennaname);
432 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
433 table_.keywordSet().get("Equinox", sdh.equinox);
434 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
435 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
436 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
437 table_.keywordSet().get("UTC", sdh.utc);
438 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
439 table_.keywordSet().get("Epoch", sdh.epoch);
440 table_.keywordSet().get("POLTYPE", sdh.poltype);
441 return sdh;
442}
443
444void Scantable::setSourceType( int stype )
445{
446 if ( stype < 0 || stype > 1 )
447 throw(AipsError("Illegal sourcetype."));
448 TableVector<Int> tabvec(table_, "SRCTYPE");
449 tabvec = Int(stype);
450}
451
452bool Scantable::conformant( const Scantable& other )
453{
454 return this->getHeader().conformant(other.getHeader());
455}
456
457
458
459std::string Scantable::formatSec(Double x) const
460{
461 Double xcop = x;
462 MVTime mvt(xcop/24./3600.); // make days
463
464 if (x < 59.95)
465 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
466 else if (x < 3599.95)
467 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
468 else {
469 ostringstream oss;
470 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
471 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
472 return String(oss);
473 }
474};
475
476std::string Scantable::formatDirection(const MDirection& md) const
477{
478 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
479 Int prec = 7;
480
481 String ref = md.getRefString();
482 MVAngle mvLon(t[0]);
483 String sLon = mvLon.string(MVAngle::TIME,prec);
484 uInt tp = md.getRef().getType();
485 if (tp == MDirection::GALACTIC ||
486 tp == MDirection::SUPERGAL ) {
487 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
488 }
489 MVAngle mvLat(t[1]);
490 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
491 return ref + String(" ") + sLon + String(" ") + sLat;
492}
493
494
495std::string Scantable::getFluxUnit() const
496{
497 return table_.keywordSet().asString("FluxUnit");
498}
499
500void Scantable::setFluxUnit(const std::string& unit)
501{
502 String tmp(unit);
503 Unit tU(tmp);
504 if (tU==Unit("K") || tU==Unit("Jy")) {
505 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
506 } else {
507 throw AipsError("Illegal unit - must be compatible with Jy or K");
508 }
509}
510
511void Scantable::setInstrument(const std::string& name)
512{
513 bool throwIt = true;
514 // create an Instrument to see if this is valid
515 STAttr::convertInstrument(name, throwIt);
516 String nameU(name);
517 nameU.upcase();
518 table_.rwKeywordSet().define(String("AntennaName"), nameU);
519}
520
521void Scantable::setFeedType(const std::string& feedtype)
522{
523 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
524 std::string msg = "Illegal feed type "+ feedtype;
525 throw(casa::AipsError(msg));
526 }
527 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
528}
529
530MPosition Scantable::getAntennaPosition() const
531{
532 Vector<Double> antpos;
533 table_.keywordSet().get("AntennaPosition", antpos);
534 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
535 return MPosition(mvpos);
536}
537
538void Scantable::makePersistent(const std::string& filename)
539{
540 String inname(filename);
541 Path path(inname);
542 /// @todo reindex SCANNO, recompute nbeam, nif, npol
543 inname = path.expandedName();
544 // 2011/03/04 TN
545 // We can comment out this workaround since the essential bug is
546 // fixed in casacore (r20889 in google code).
547 table_.deepCopy(inname, Table::New);
548// // WORKAROUND !!! for Table bug
549// // Remove when fixed in casacore
550// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
551// Table tab = table_.copyToMemoryTable(generateName());
552// tab.deepCopy(inname, Table::New);
553// tab.markForDelete();
554//
555// } else {
556// table_.deepCopy(inname, Table::New);
557// }
558}
559
560int Scantable::nbeam( int scanno ) const
561{
562 if ( scanno < 0 ) {
563 Int n;
564 table_.keywordSet().get("nBeam",n);
565 return int(n);
566 } else {
567 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
568 Table t = table_(table_.col("SCANNO") == scanno);
569 ROTableRow row(t);
570 const TableRecord& rec = row.get(0);
571 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
572 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
573 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
574 ROTableVector<uInt> v(subt, "BEAMNO");
575 return int(v.nelements());
576 }
577 return 0;
578}
579
580int Scantable::nif( int scanno ) const
581{
582 if ( scanno < 0 ) {
583 Int n;
584 table_.keywordSet().get("nIF",n);
585 return int(n);
586 } else {
587 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
588 Table t = table_(table_.col("SCANNO") == scanno);
589 ROTableRow row(t);
590 const TableRecord& rec = row.get(0);
591 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
592 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
593 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
594 if ( subt.nrow() == 0 ) return 0;
595 ROTableVector<uInt> v(subt, "IFNO");
596 return int(v.nelements());
597 }
598 return 0;
599}
600
601int Scantable::npol( int scanno ) const
602{
603 if ( scanno < 0 ) {
604 Int n;
605 table_.keywordSet().get("nPol",n);
606 return n;
607 } else {
608 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
609 Table t = table_(table_.col("SCANNO") == scanno);
610 ROTableRow row(t);
611 const TableRecord& rec = row.get(0);
612 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
613 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
614 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
615 if ( subt.nrow() == 0 ) return 0;
616 ROTableVector<uInt> v(subt, "POLNO");
617 return int(v.nelements());
618 }
619 return 0;
620}
621
622int Scantable::ncycle( int scanno ) const
623{
624 if ( scanno < 0 ) {
625 Block<String> cols(2);
626 cols[0] = "SCANNO";
627 cols[1] = "CYCLENO";
628 TableIterator it(table_, cols);
629 int n = 0;
630 while ( !it.pastEnd() ) {
631 ++n;
632 ++it;
633 }
634 return n;
635 } else {
636 Table t = table_(table_.col("SCANNO") == scanno);
637 ROTableRow row(t);
638 const TableRecord& rec = row.get(0);
639 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
640 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
641 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
642 if ( subt.nrow() == 0 ) return 0;
643 return int(subt.nrow());
644 }
645 return 0;
646}
647
648
649int Scantable::nrow( int scanno ) const
650{
651 return int(table_.nrow());
652}
653
654int Scantable::nchan( int ifno ) const
655{
656 if ( ifno < 0 ) {
657 Int n;
658 table_.keywordSet().get("nChan",n);
659 return int(n);
660 } else {
661 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
662 // vary with these
663 Table t = table_(table_.col("IFNO") == ifno, 1);
664 if ( t.nrow() == 0 ) return 0;
665 ROArrayColumn<Float> v(t, "SPECTRA");
666 return v.shape(0)(0);
667 }
668 return 0;
669}
670
671int Scantable::nscan() const {
672 Vector<uInt> scannos(scanCol_.getColumn());
673 uInt nout = genSort( scannos, Sort::Ascending,
674 Sort::QuickSort|Sort::NoDuplicates );
675 return int(nout);
676}
677
678int Scantable::getChannels(int whichrow) const
679{
680 return specCol_.shape(whichrow)(0);
681}
682
683int Scantable::getBeam(int whichrow) const
684{
685 return beamCol_(whichrow);
686}
687
688std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
689{
690 Vector<uInt> nos(col.getColumn());
691 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
692 nos.resize(n, True);
693 std::vector<uint> stlout;
694 nos.tovector(stlout);
695 return stlout;
696}
697
698int Scantable::getIF(int whichrow) const
699{
700 return ifCol_(whichrow);
701}
702
703int Scantable::getPol(int whichrow) const
704{
705 return polCol_(whichrow);
706}
707
708std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
709{
710 return formatTime(me, showdate, 0);
711}
712
713std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
714{
715 MVTime mvt(me.getValue());
716 if (showdate)
717 //mvt.setFormat(MVTime::YMD);
718 mvt.setFormat(MVTime::YMD, prec);
719 else
720 //mvt.setFormat(MVTime::TIME);
721 mvt.setFormat(MVTime::TIME, prec);
722 ostringstream oss;
723 oss << mvt;
724 return String(oss);
725}
726
727void Scantable::calculateAZEL()
728{
729 MPosition mp = getAntennaPosition();
730 MEpoch::ROScalarColumn timeCol(table_, "TIME");
731 ostringstream oss;
732 oss << "Computed azimuth/elevation using " << endl
733 << mp << endl;
734 for (Int i=0; i<nrow(); ++i) {
735 MEpoch me = timeCol(i);
736 MDirection md = getDirection(i);
737 oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md)
738 << endl << " => ";
739 MeasFrame frame(mp, me);
740 Vector<Double> azel =
741 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
742 frame)
743 )().getAngle("rad").getValue();
744 azCol_.put(i,Float(azel[0]));
745 elCol_.put(i,Float(azel[1]));
746 oss << "azel: " << azel[0]/C::pi*180.0 << " "
747 << azel[1]/C::pi*180.0 << " (deg)" << endl;
748 }
749 pushLog(String(oss));
750}
751
752void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
753{
754 for (uInt i=0; i<table_.nrow(); ++i) {
755 Vector<uChar> flgs = flagsCol_(i);
756 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
757 flagsCol_.put(i, flgs);
758 }
759}
760
761std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
762{
763 Vector<uChar> flags;
764 flagsCol_.get(uInt(whichrow), flags);
765 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
766 Vector<Bool> bflag(flags.shape());
767 convertArray(bflag, flags);
768 //bflag = !bflag;
769
770 std::vector<bool> mask;
771 bflag.tovector(mask);
772 return mask;
773}
774
775void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
776 Vector<uChar> flgs)
777{
778 Vector<Float> spcs = specCol_(whichrow);
779 uInt nchannel = spcs.nelements();
780 if (spcs.nelements() != nchannel) {
781 throw(AipsError("Data has incorrect number of channels"));
782 }
783 uChar userflag = 1 << 7;
784 if (unflag) {
785 userflag = 0 << 7;
786 }
787 if (clipoutside) {
788 for (uInt j = 0; j < nchannel; ++j) {
789 Float spc = spcs(j);
790 if ((spc >= uthres) || (spc <= dthres)) {
791 flgs(j) = userflag;
792 }
793 }
794 } else {
795 for (uInt j = 0; j < nchannel; ++j) {
796 Float spc = spcs(j);
797 if ((spc < uthres) && (spc > dthres)) {
798 flgs(j) = userflag;
799 }
800 }
801 }
802}
803
804
805void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
806 std::vector<bool>::const_iterator it;
807 uInt ntrue = 0;
808 if (whichrow >= int(table_.nrow()) ) {
809 throw(AipsError("Invalid row number"));
810 }
811 for (it = msk.begin(); it != msk.end(); ++it) {
812 if ( *it ) {
813 ntrue++;
814 }
815 }
816 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
817 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
818 throw(AipsError("Trying to flag whole scantable."));
819 uChar userflag = 1 << 7;
820 if ( unflag ) {
821 userflag = 0 << 7;
822 }
823 if (whichrow > -1 ) {
824 applyChanFlag(uInt(whichrow), msk, userflag);
825 } else {
826 for ( uInt i=0; i<table_.nrow(); ++i) {
827 applyChanFlag(i, msk, userflag);
828 }
829 }
830}
831
832void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
833{
834 if (whichrow >= table_.nrow() ) {
835 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
836 }
837 Vector<uChar> flgs = flagsCol_(whichrow);
838 if ( msk.size() == 0 ) {
839 flgs = flagval;
840 flagsCol_.put(whichrow, flgs);
841 return;
842 }
843 if ( int(msk.size()) != nchan( getIF(whichrow) ) ) {
844 throw(AipsError("Mask has incorrect number of channels."));
845 }
846 if ( flgs.nelements() != msk.size() ) {
847 throw(AipsError("Mask has incorrect number of channels."
848 " Probably varying with IF. Please flag per IF"));
849 }
850 std::vector<bool>::const_iterator it;
851 uInt j = 0;
852 for (it = msk.begin(); it != msk.end(); ++it) {
853 if ( *it ) {
854 flgs(j) = flagval;
855 }
856 ++j;
857 }
858 flagsCol_.put(whichrow, flgs);
859}
860
861void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
862{
863 if ( selector_.empty() && (rows.size() == table_.nrow()) )
864 throw(AipsError("Trying to flag whole scantable."));
865
866 uInt rowflag = (unflag ? 0 : 1);
867 std::vector<uInt>::const_iterator it;
868 for (it = rows.begin(); it != rows.end(); ++it)
869 flagrowCol_.put(*it, rowflag);
870}
871
872std::vector<bool> Scantable::getMask(int whichrow) const
873{
874 Vector<uChar> flags;
875 flagsCol_.get(uInt(whichrow), flags);
876 Vector<Bool> bflag(flags.shape());
877 convertArray(bflag, flags);
878 bflag = !bflag;
879 std::vector<bool> mask;
880 bflag.tovector(mask);
881 return mask;
882}
883
884std::vector<float> Scantable::getSpectrum( int whichrow,
885 const std::string& poltype ) const
886{
887 String ptype = poltype;
888 if (poltype == "" ) ptype = getPolType();
889 if ( whichrow < 0 || whichrow >= nrow() )
890 throw(AipsError("Illegal row number."));
891 std::vector<float> out;
892 Vector<Float> arr;
893 uInt requestedpol = polCol_(whichrow);
894 String basetype = getPolType();
895 if ( ptype == basetype ) {
896 specCol_.get(whichrow, arr);
897 } else {
898 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
899 basetype));
900 uInt row = uInt(whichrow);
901 stpol->setSpectra(getPolMatrix(row));
902 Float fang,fhand;
903 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
904 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
905 stpol->setPhaseCorrections(fang, fhand);
906 arr = stpol->getSpectrum(requestedpol, ptype);
907 }
908 if ( arr.nelements() == 0 )
909 pushLog("Not enough polarisations present to do the conversion.");
910 arr.tovector(out);
911 return out;
912}
913
914void Scantable::setSpectrum( const std::vector<float>& spec,
915 int whichrow )
916{
917 Vector<Float> spectrum(spec);
918 Vector<Float> arr;
919 specCol_.get(whichrow, arr);
920 if ( spectrum.nelements() != arr.nelements() )
921 throw AipsError("The spectrum has incorrect number of channels.");
922 specCol_.put(whichrow, spectrum);
923}
924
925
926String Scantable::generateName()
927{
928 return (File::newUniqueName("./","temp")).baseName();
929}
930
931const casa::Table& Scantable::table( ) const
932{
933 return table_;
934}
935
936casa::Table& Scantable::table( )
937{
938 return table_;
939}
940
941std::string Scantable::getPolType() const
942{
943 return table_.keywordSet().asString("POLTYPE");
944}
945
946void Scantable::unsetSelection()
947{
948 table_ = originalTable_;
949 attach();
950 selector_.reset();
951}
952
953void Scantable::setSelection( const STSelector& selection )
954{
955 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
956 if ( tab.nrow() == 0 ) {
957 throw(AipsError("Selection contains no data. Not applying it."));
958 }
959 table_ = tab;
960 attach();
961// tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
962// vector<uint> selectedIFs = getIFNos() ;
963// Int newnIF = selectedIFs.size() ;
964// tab.rwKeywordSet().define("nIF",newnIF) ;
965// if ( newnIF != 0 ) {
966// Int newnChan = 0 ;
967// for ( Int i = 0 ; i < newnIF ; i++ ) {
968// Int nChan = nchan( selectedIFs[i] ) ;
969// if ( newnChan > nChan )
970// newnChan = nChan ;
971// }
972// tab.rwKeywordSet().define("nChan",newnChan) ;
973// }
974// tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
975 selector_ = selection;
976}
977
978
979std::string Scantable::headerSummary()
980{
981 // Format header info
982// STHeader sdh;
983// sdh = getHeader();
984// sdh.print();
985 ostringstream oss;
986 oss.flags(std::ios_base::left);
987 String tmp;
988 // Project
989 table_.keywordSet().get("Project", tmp);
990 oss << setw(15) << "Project:" << tmp << endl;
991 // Observation date
992 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
993 // Observer
994 oss << setw(15) << "Observer:"
995 << table_.keywordSet().asString("Observer") << endl;
996 // Antenna Name
997 table_.keywordSet().get("AntennaName", tmp);
998 oss << setw(15) << "Antenna Name:" << tmp << endl;
999 // Obs type
1000 table_.keywordSet().get("Obstype", tmp);
1001 // Records (nrow)
1002 oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl;
1003 oss << setw(15) << "Obs. Type:" << tmp << endl;
1004 // Beams, IFs, Polarizations, and Channels
1005 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1006 << setw(15) << "IFs:" << setw(4) << nif() << endl
1007 << setw(15) << "Polarisations:" << setw(4) << npol()
1008 << "(" << getPolType() << ")" << endl
1009 << setw(15) << "Channels:" << nchan() << endl;
1010 // Flux unit
1011 table_.keywordSet().get("FluxUnit", tmp);
1012 oss << setw(15) << "Flux Unit:" << tmp << endl;
1013 // Abscissa Unit
1014 oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl;
1015 // Selection
1016 oss << selector_.print() << endl;
1017
1018 return String(oss);
1019}
1020
1021void Scantable::summary( const std::string& filename )
1022{
1023 ostringstream oss;
1024 ofstream ofs;
1025 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1026
1027 if (filename != "")
1028 ofs.open( filename.c_str(), ios::out );
1029
1030 oss << endl;
1031 oss << asap::SEPERATOR << endl;
1032 oss << " Scan Table Summary" << endl;
1033 oss << asap::SEPERATOR << endl;
1034
1035 // Format header info
1036 oss << headerSummary();
1037 oss << endl;
1038
1039 if (table_.nrow() <= 0){
1040 oss << asap::SEPERATOR << endl;
1041 oss << "The MAIN table is empty: there are no data!!!" << endl;
1042 oss << asap::SEPERATOR << endl;
1043
1044 ols << String(oss) << LogIO::POST;
1045 if (ofs) {
1046 ofs << String(oss) << flush;
1047 ofs.close();
1048 }
1049 return;
1050 }
1051
1052
1053
1054 // main table
1055 String dirtype = "Position ("
1056 + getDirectionRefString()
1057 + ")";
1058 oss.flags(std::ios_base::left);
1059 oss << setw(5) << "Scan"
1060 << setw(15) << "Source"
1061 << setw(35) << "Time range"
1062 << setw(2) << "" << setw(7) << "Int[s]"
1063 << setw(7) << "Record"
1064 << setw(8) << "SrcType"
1065 << setw(8) << "FreqIDs"
1066 << setw(7) << "MolIDs" << endl;
1067 oss << setw(7)<< "" << setw(6) << "Beam"
1068 << setw(23) << dirtype << endl;
1069
1070 oss << asap::SEPERATOR << endl;
1071
1072 // Flush summary and clear up the string
1073 ols << String(oss) << LogIO::POST;
1074 if (ofs) ofs << String(oss) << flush;
1075 oss.str("");
1076 oss.clear();
1077
1078
1079 // Get Freq_ID map
1080 ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID");
1081 Int nfid = ftabIds.nrow();
1082 if (nfid <= 0){
1083 oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl;
1084 oss << asap::SEPERATOR << endl;
1085
1086 ols << String(oss) << LogIO::POST;
1087 if (ofs) {
1088 ofs << String(oss) << flush;
1089 ofs.close();
1090 }
1091 return;
1092 }
1093 // Storages of overall IFNO, POLNO, and nchan per FREQ_ID
1094 // the orders are identical to ID in FREQ subtable
1095 Block< Vector<uInt> > ifNos(nfid), polNos(nfid);
1096 Vector<Int> fIdchans(nfid,-1);
1097 map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair
1098 for (Int i=0; i < nfid; i++){
1099 // fidMap[freqId] returns row number in FREQ subtable
1100 fidMap.insert(pair<uInt, Int>(ftabIds(i),i));
1101 ifNos[i] = Vector<uInt>();
1102 polNos[i] = Vector<uInt>();
1103 }
1104
1105 TableIterator iter(table_, "SCANNO");
1106
1107 // Vars for keeping track of time, freqids, molIds in a SCANNO
1108 Vector<uInt> freqids;
1109 Vector<uInt> molids;
1110 Vector<uInt> beamids(1,0);
1111 Vector<MDirection> beamDirs;
1112 Vector<Int> stypeids(1,0);
1113 Vector<String> stypestrs;
1114 Int nfreq(1);
1115 Int nmol(1);
1116 uInt nbeam(1);
1117 uInt nstype(1);
1118
1119 Double btime(0.0), etime(0.0);
1120 Double meanIntTim(0.0);
1121
1122 uInt currFreqId(0), ftabRow(0);
1123 Int iflen(0), pollen(0);
1124
1125 while (!iter.pastEnd()) {
1126 Table subt = iter.table();
1127 uInt snrow = subt.nrow();
1128 ROTableRow row(subt);
1129 const TableRecord& rec = row.get(0);
1130
1131 // relevant columns
1132 ROScalarColumn<Double> mjdCol(subt,"TIME");
1133 ROScalarColumn<Double> intervalCol(subt,"INTERVAL");
1134 MDirection::ROScalarColumn dirCol(subt,"DIRECTION");
1135
1136 ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID");
1137 ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID");
1138 ROScalarColumn<uInt> beamCol(subt,"BEAMNO");
1139 ROScalarColumn<Int> stypeCol(subt,"SRCTYPE");
1140
1141 ROScalarColumn<uInt> ifNoCol(subt,"IFNO");
1142 ROScalarColumn<uInt> polNoCol(subt,"POLNO");
1143
1144
1145 // Times
1146 meanIntTim = sum(intervalCol.getColumn()) / (double) snrow;
1147 minMax(btime, etime, mjdCol.getColumn());
1148 etime += meanIntTim/C::day;
1149
1150 // MOLECULE_ID and FREQ_ID
1151 molids = getNumbers(molIdCol);
1152 molids.shape(nmol);
1153
1154 freqids = getNumbers(freqIdCol);
1155 freqids.shape(nfreq);
1156
1157 // Add first beamid, and srcNames
1158 beamids.resize(1,False);
1159 beamDirs.resize(1,False);
1160 beamids(0)=beamCol(0);
1161 beamDirs(0)=dirCol(0);
1162 nbeam = 1;
1163
1164 stypeids.resize(1,False);
1165 stypeids(0)=stypeCol(0);
1166 nstype = 1;
1167
1168 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1169 currFreqId=freqIdCol(0);
1170 ftabRow = fidMap[currFreqId];
1171 // Assumes an identical number of channels per FREQ_ID
1172 if (fIdchans(ftabRow) < 0 ) {
1173 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1174 fIdchans(ftabRow)=(*spec).shape()(0);
1175 }
1176 // Should keep ifNos and polNos form the previous SCANNO
1177 if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) {
1178 ifNos[ftabRow].shape(iflen);
1179 iflen++;
1180 ifNos[ftabRow].resize(iflen,True);
1181 ifNos[ftabRow](iflen-1) = ifNoCol(0);
1182 }
1183 if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) {
1184 polNos[ftabRow].shape(pollen);
1185 pollen++;
1186 polNos[ftabRow].resize(pollen,True);
1187 polNos[ftabRow](pollen-1) = polNoCol(0);
1188 }
1189
1190 for (uInt i=1; i < snrow; i++){
1191 // Need to list BEAMNO and DIRECTION in the same order
1192 if ( !anyEQ(beamids,beamCol(i)) ) {
1193 nbeam++;
1194 beamids.resize(nbeam,True);
1195 beamids(nbeam-1)=beamCol(i);
1196 beamDirs.resize(nbeam,True);
1197 beamDirs(nbeam-1)=dirCol(i);
1198 }
1199
1200 // SRCTYPE is Int (getNumber takes only uInt)
1201 if ( !anyEQ(stypeids,stypeCol(i)) ) {
1202 nstype++;
1203 stypeids.resize(nstype,True);
1204 stypeids(nstype-1)=stypeCol(i);
1205 }
1206
1207 // Global listings of nchan/IFNO/POLNO per FREQ_ID
1208 currFreqId=freqIdCol(i);
1209 ftabRow = fidMap[currFreqId];
1210 if (fIdchans(ftabRow) < 0 ) {
1211 const TableRecord& rec = row.get(i);
1212 RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA");
1213 fIdchans(ftabRow) = (*spec).shape()(0);
1214 }
1215 if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) {
1216 ifNos[ftabRow].shape(iflen);
1217 iflen++;
1218 ifNos[ftabRow].resize(iflen,True);
1219 ifNos[ftabRow](iflen-1) = ifNoCol(i);
1220 }
1221 if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) {
1222 polNos[ftabRow].shape(pollen);
1223 pollen++;
1224 polNos[ftabRow].resize(pollen,True);
1225 polNos[ftabRow](pollen-1) = polNoCol(i);
1226 }
1227 } // end of row iteration
1228
1229 stypestrs.resize(nstype,False);
1230 for (uInt j=0; j < nstype; j++)
1231 stypestrs(j) = SrcType::getName(stypeids(j));
1232
1233 // Format Scan summary
1234 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1235 << std::left << setw(1) << ""
1236 << setw(15) << rec.asString("SRCNAME")
1237 << setw(21) << MVTime(btime).string(MVTime::YMD,7)
1238 << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7)
1239 << setw(3) << "" << setw(6) << meanIntTim << setw(1) << ""
1240 << std::right << setw(5) << snrow << setw(2) << ""
1241 << std::left << stypestrs << setw(1) << ""
1242 << freqids << setw(1) << ""
1243 << molids << endl;
1244 // Format Beam summary
1245 for (uInt j=0; j < nbeam; j++) {
1246 oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << ""
1247 << formatDirection(beamDirs(j)) << endl;
1248 }
1249 // Flush summary every scan and clear up the string
1250 ols << String(oss) << LogIO::POST;
1251 if (ofs) ofs << String(oss) << flush;
1252 oss.str("");
1253 oss.clear();
1254
1255 ++iter;
1256 } // end of scan iteration
1257 oss << asap::SEPERATOR << endl;
1258
1259 // List FRECUENCIES Table (using STFrequencies.print may be slow)
1260 oss << "FREQUENCIES: " << nfreq << endl;
1261 oss << std::right << setw(5) << "ID" << setw(2) << ""
1262 << std::left << setw(5) << "IFNO" << setw(2) << ""
1263 << setw(8) << "Frame"
1264 << setw(16) << "RefVal"
1265 << setw(7) << "RefPix"
1266 << setw(15) << "Increment"
1267 << setw(9) << "Channels"
1268 << setw(6) << "POLNOs" << endl;
1269 Int tmplen;
1270 for (Int i=0; i < nfid; i++){
1271 // List row=i of FREQUENCIES subtable
1272 ifNos[i].shape(tmplen);
1273 if (tmplen >= 1) {
1274 oss << std::right << setw(5) << ftabIds(i) << setw(2) << ""
1275 << setw(3) << ifNos[i](0) << setw(1) << ""
1276 << std::left << setw(46) << frequencies().print(ftabIds(i))
1277 << setw(2) << ""
1278 << std::right << setw(8) << fIdchans[i] << setw(2) << ""
1279 << std::left << polNos[i];
1280 if (tmplen > 1) {
1281 oss << " (" << tmplen << " chains)";
1282 }
1283 oss << endl;
1284 }
1285
1286 }
1287 oss << asap::SEPERATOR << endl;
1288
1289 // List MOLECULES Table (currently lists all rows)
1290 oss << "MOLECULES: " << endl;
1291 if (molecules().nrow() <= 0) {
1292 oss << " MOLECULES subtable is empty: there are no data" << endl;
1293 } else {
1294 ROTableRow row(molecules().table());
1295 oss << std::right << setw(5) << "ID"
1296 << std::left << setw(3) << ""
1297 << setw(18) << "RestFreq"
1298 << setw(15) << "Name" << endl;
1299 for (Int i=0; i < molecules().nrow(); i++){
1300 const TableRecord& rec=row.get(i);
1301 oss << std::right << setw(5) << rec.asuInt("ID")
1302 << std::left << setw(3) << ""
1303 << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << ""
1304 << rec.asArrayString("NAME") << endl;
1305 }
1306 }
1307 oss << asap::SEPERATOR << endl;
1308 ols << String(oss) << LogIO::POST;
1309 if (ofs) {
1310 ofs << String(oss) << flush;
1311 ofs.close();
1312 }
1313 // return String(oss);
1314}
1315
1316
1317std::string Scantable::oldheaderSummary()
1318{
1319 // Format header info
1320// STHeader sdh;
1321// sdh = getHeader();
1322// sdh.print();
1323 ostringstream oss;
1324 oss.flags(std::ios_base::left);
1325 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
1326 << setw(15) << "IFs:" << setw(4) << nif() << endl
1327 << setw(15) << "Polarisations:" << setw(4) << npol()
1328 << "(" << getPolType() << ")" << endl
1329 << setw(15) << "Channels:" << nchan() << endl;
1330 String tmp;
1331 oss << setw(15) << "Observer:"
1332 << table_.keywordSet().asString("Observer") << endl;
1333 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
1334 table_.keywordSet().get("Project", tmp);
1335 oss << setw(15) << "Project:" << tmp << endl;
1336 table_.keywordSet().get("Obstype", tmp);
1337 oss << setw(15) << "Obs. Type:" << tmp << endl;
1338 table_.keywordSet().get("AntennaName", tmp);
1339 oss << setw(15) << "Antenna Name:" << tmp << endl;
1340 table_.keywordSet().get("FluxUnit", tmp);
1341 oss << setw(15) << "Flux Unit:" << tmp << endl;
1342 int nid = moleculeTable_.nrow();
1343 Bool firstline = True;
1344 oss << setw(15) << "Rest Freqs:";
1345 for (int i=0; i<nid; i++) {
1346 Table t = table_(table_.col("MOLECULE_ID") == i, 1);
1347 if (t.nrow() > 0) {
1348 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
1349 if (vec.nelements() > 0) {
1350 if (firstline) {
1351 oss << setprecision(10) << vec << " [Hz]" << endl;
1352 firstline=False;
1353 }
1354 else{
1355 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1356 }
1357 } else {
1358 oss << "none" << endl;
1359 }
1360 }
1361 }
1362
1363 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
1364 oss << selector_.print() << endl;
1365 return String(oss);
1366}
1367
1368 //std::string Scantable::summary( const std::string& filename )
1369void Scantable::oldsummary( const std::string& filename )
1370{
1371 ostringstream oss;
1372 ofstream ofs;
1373 LogIO ols(LogOrigin("Scantable", "summary", WHERE));
1374
1375 if (filename != "")
1376 ofs.open( filename.c_str(), ios::out );
1377
1378 oss << endl;
1379 oss << asap::SEPERATOR << endl;
1380 oss << " Scan Table Summary" << endl;
1381 oss << asap::SEPERATOR << endl;
1382
1383 // Format header info
1384 oss << oldheaderSummary();
1385 oss << endl;
1386
1387 // main table
1388 String dirtype = "Position ("
1389 + getDirectionRefString()
1390 + ")";
1391 oss.flags(std::ios_base::left);
1392 oss << setw(5) << "Scan" << setw(15) << "Source"
1393 << setw(10) << "Time" << setw(18) << "Integration"
1394 << setw(15) << "Source Type" << endl;
1395 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
1396 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
1397 << setw(8) << "Frame" << setw(16)
1398 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1399 << setw(7) << "Channels"
1400 << endl;
1401 oss << asap::SEPERATOR << endl;
1402
1403 // Flush summary and clear up the string
1404 ols << String(oss) << LogIO::POST;
1405 if (ofs) ofs << String(oss) << flush;
1406 oss.str("");
1407 oss.clear();
1408
1409 TableIterator iter(table_, "SCANNO");
1410 while (!iter.pastEnd()) {
1411 Table subt = iter.table();
1412 ROTableRow row(subt);
1413 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1414 const TableRecord& rec = row.get(0);
1415 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1416 << std::left << setw(1) << ""
1417 << setw(15) << rec.asString("SRCNAME")
1418 << setw(10) << formatTime(timeCol(0), false);
1419 // count the cycles in the scan
1420 TableIterator cyciter(subt, "CYCLENO");
1421 int nint = 0;
1422 while (!cyciter.pastEnd()) {
1423 ++nint;
1424 ++cyciter;
1425 }
1426 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
1427 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1428 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
1429
1430 TableIterator biter(subt, "BEAMNO");
1431 while (!biter.pastEnd()) {
1432 Table bsubt = biter.table();
1433 ROTableRow brow(bsubt);
1434 const TableRecord& brec = brow.get(0);
1435 uInt row0 = bsubt.rowNumbers(table_)[0];
1436 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
1437 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
1438 TableIterator iiter(bsubt, "IFNO");
1439 while (!iiter.pastEnd()) {
1440 Table isubt = iiter.table();
1441 ROTableRow irow(isubt);
1442 const TableRecord& irec = irow.get(0);
1443 oss << setw(9) << "";
1444 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
1445 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1446 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
1447 << endl;
1448
1449 ++iiter;
1450 }
1451 ++biter;
1452 }
1453 // Flush summary every scan and clear up the string
1454 ols << String(oss) << LogIO::POST;
1455 if (ofs) ofs << String(oss) << flush;
1456 oss.str("");
1457 oss.clear();
1458
1459 ++iter;
1460 }
1461 oss << asap::SEPERATOR << endl;
1462 ols << String(oss) << LogIO::POST;
1463 if (ofs) {
1464 ofs << String(oss) << flush;
1465 ofs.close();
1466 }
1467 // return String(oss);
1468}
1469
1470// std::string Scantable::getTime(int whichrow, bool showdate) const
1471// {
1472// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1473// MEpoch me;
1474// if (whichrow > -1) {
1475// me = timeCol(uInt(whichrow));
1476// } else {
1477// Double tm;
1478// table_.keywordSet().get("UTC",tm);
1479// me = MEpoch(MVEpoch(tm));
1480// }
1481// return formatTime(me, showdate);
1482// }
1483
1484std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
1485{
1486 MEpoch me;
1487 me = getEpoch(whichrow);
1488 return formatTime(me, showdate, prec);
1489}
1490
1491MEpoch Scantable::getEpoch(int whichrow) const
1492{
1493 if (whichrow > -1) {
1494 return timeCol_(uInt(whichrow));
1495 } else {
1496 Double tm;
1497 table_.keywordSet().get("UTC",tm);
1498 return MEpoch(MVEpoch(tm));
1499 }
1500}
1501
1502std::string Scantable::getDirectionString(int whichrow) const
1503{
1504 return formatDirection(getDirection(uInt(whichrow)));
1505}
1506
1507
1508SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1509 const MPosition& mp = getAntennaPosition();
1510 const MDirection& md = getDirection(whichrow);
1511 const MEpoch& me = timeCol_(whichrow);
1512 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1513 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1514 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
1515 mfreqidCol_(whichrow));
1516}
1517
1518std::vector< double > Scantable::getAbcissa( int whichrow ) const
1519{
1520 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
1521 std::vector<double> stlout;
1522 int nchan = specCol_(whichrow).nelements();
1523 String us = freqTable_.getUnitString();
1524 if ( us == "" || us == "pixel" || us == "channel" ) {
1525 for (int i=0; i<nchan; ++i) {
1526 stlout.push_back(double(i));
1527 }
1528 return stlout;
1529 }
1530 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
1531 Vector<Double> pixel(nchan);
1532 Vector<Double> world;
1533 indgen(pixel);
1534 if ( Unit(us) == Unit("Hz") ) {
1535 for ( int i=0; i < nchan; ++i) {
1536 Double world;
1537 spc.toWorld(world, pixel[i]);
1538 stlout.push_back(double(world));
1539 }
1540 } else if ( Unit(us) == Unit("km/s") ) {
1541 Vector<Double> world;
1542 spc.pixelToVelocity(world, pixel);
1543 world.tovector(stlout);
1544 }
1545 return stlout;
1546}
1547void Scantable::setDirectionRefString( const std::string & refstr )
1548{
1549 MDirection::Types mdt;
1550 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1551 throw(AipsError("Illegal Direction frame."));
1552 }
1553 if ( refstr == "" ) {
1554 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1555 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1556 } else {
1557 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1558 }
1559}
1560
1561std::string Scantable::getDirectionRefString( ) const
1562{
1563 return table_.keywordSet().asString("DIRECTIONREF");
1564}
1565
1566MDirection Scantable::getDirection(int whichrow ) const
1567{
1568 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1569 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1570 if ( usertype != type ) {
1571 MDirection::Types mdt;
1572 if (!MDirection::getType(mdt, usertype)) {
1573 throw(AipsError("Illegal Direction frame."));
1574 }
1575 return dirCol_.convert(uInt(whichrow), mdt);
1576 } else {
1577 return dirCol_(uInt(whichrow));
1578 }
1579}
1580
1581std::string Scantable::getAbcissaLabel( int whichrow ) const
1582{
1583 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
1584 const MPosition& mp = getAntennaPosition();
1585 const MDirection& md = getDirection(whichrow);
1586 const MEpoch& me = timeCol_(whichrow);
1587 //const Double& rf = mmolidCol_(whichrow);
1588 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1589 SpectralCoordinate spc =
1590 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
1591
1592 String s = "Channel";
1593 Unit u = Unit(freqTable_.getUnitString());
1594 if (u == Unit("km/s")) {
1595 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
1596 } else if (u == Unit("Hz")) {
1597 Vector<String> wau(1);wau = u.getName();
1598 spc.setWorldAxisUnits(wau);
1599 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
1600 }
1601 return s;
1602
1603}
1604
1605/**
1606void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
1607 const std::string& unit )
1608**/
1609void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1610 const std::string& unit )
1611
1612{
1613 ///@todo lookup in line table to fill in name and formattedname
1614 Unit u(unit);
1615 //Quantum<Double> urf(rf, u);
1616 Quantum<Vector<Double> >urf(rf, u);
1617 Vector<String> formattedname(0);
1618 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1619
1620 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1621 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
1622 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1623 tabvec = id;
1624}
1625
1626/**
1627void asap::Scantable::setRestFrequencies( const std::string& name )
1628{
1629 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1630 ///@todo implement
1631}
1632**/
1633
1634void Scantable::setRestFrequencies( const vector<std::string>& name )
1635{
1636 (void) name; // suppress unused warning
1637 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1638 ///@todo implement
1639}
1640
1641std::vector< unsigned int > Scantable::rownumbers( ) const
1642{
1643 std::vector<unsigned int> stlout;
1644 Vector<uInt> vec = table_.rowNumbers();
1645 vec.tovector(stlout);
1646 return stlout;
1647}
1648
1649
1650Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
1651{
1652 ROTableRow row(table_);
1653 const TableRecord& rec = row.get(whichrow);
1654 Table t =
1655 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1656 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1657 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1658 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1659 ROArrayColumn<Float> speccol(t, "SPECTRA");
1660 return speccol.getColumn();
1661}
1662
1663std::vector< std::string > Scantable::columnNames( ) const
1664{
1665 Vector<String> vec = table_.tableDesc().columnNames();
1666 return mathutil::tovectorstring(vec);
1667}
1668
1669MEpoch::Types Scantable::getTimeReference( ) const
1670{
1671 return MEpoch::castType(timeCol_.getMeasRef().getType());
1672}
1673
1674void Scantable::addFit( const STFitEntry& fit, int row )
1675{
1676 //cout << mfitidCol_(uInt(row)) << endl;
1677 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1678 os << mfitidCol_(uInt(row)) << LogIO::POST ;
1679 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1680 mfitidCol_.put(uInt(row), id);
1681}
1682
1683void Scantable::shift(int npix)
1684{
1685 Vector<uInt> fids(mfreqidCol_.getColumn());
1686 genSort( fids, Sort::Ascending,
1687 Sort::QuickSort|Sort::NoDuplicates );
1688 for (uInt i=0; i<fids.nelements(); ++i) {
1689 frequencies().shiftRefPix(npix, fids[i]);
1690 }
1691}
1692
1693String Scantable::getAntennaName() const
1694{
1695 String out;
1696 table_.keywordSet().get("AntennaName", out);
1697 String::size_type pos1 = out.find("@") ;
1698 String::size_type pos2 = out.find("//") ;
1699 if ( pos2 != String::npos )
1700 out = out.substr(pos2+2,pos1-pos2-2) ;
1701 else if ( pos1 != String::npos )
1702 out = out.substr(0,pos1) ;
1703 return out;
1704}
1705
1706int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
1707{
1708 String tbpath;
1709 int ret = 0;
1710 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1711 table_.keywordSet().get("GBT_GO", tbpath);
1712 Table t(tbpath,Table::Old);
1713 // check each scan if other scan of the pair exist
1714 int nscan = scanlist.size();
1715 for (int i = 0; i < nscan; i++) {
1716 Table subt = t( t.col("SCAN") == scanlist[i]+1 );
1717 if (subt.nrow()==0) {
1718 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1719 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1720 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
1721 ret = 1;
1722 break;
1723 }
1724 ROTableRow row(subt);
1725 const TableRecord& rec = row.get(0);
1726 int scan1seqn = rec.asuInt("PROCSEQN");
1727 int laston1 = rec.asuInt("LASTON");
1728 if ( rec.asuInt("PROCSIZE")==2 ) {
1729 if ( i < nscan-1 ) {
1730 Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
1731 if ( subt2.nrow() == 0) {
1732 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1733
1734 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1735 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
1736 ret = 1;
1737 break;
1738 }
1739 ROTableRow row2(subt2);
1740 const TableRecord& rec2 = row2.get(0);
1741 int scan2seqn = rec2.asuInt("PROCSEQN");
1742 int laston2 = rec2.asuInt("LASTON");
1743 if (scan1seqn == 1 && scan2seqn == 2) {
1744 if (laston1 == laston2) {
1745 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1746 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1747 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1748 i +=1;
1749 }
1750 else {
1751 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1752 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1753 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1754 }
1755 }
1756 else if (scan1seqn==2 && scan2seqn == 1) {
1757 if (laston1 == laston2) {
1758 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1759 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1760 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
1761 ret = 1;
1762 break;
1763 }
1764 }
1765 else {
1766 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1767 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1768 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
1769 ret = 1;
1770 break;
1771 }
1772 }
1773 }
1774 else {
1775 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1776 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1777 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
1778 }
1779 //if ( i >= nscan ) break;
1780 }
1781 }
1782 else {
1783 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1784 //cerr<<"No reference to GBT_GO table."<<endl;
1785 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
1786 ret = 1;
1787 }
1788 return ret;
1789}
1790
1791std::vector<double> Scantable::getDirectionVector(int whichrow) const
1792{
1793 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1794 std::vector<double> dir;
1795 Dir.tovector(dir);
1796 return dir;
1797}
1798
1799void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1800 throw( casa::AipsError )
1801{
1802 // assumed that all rows have same nChan
1803 Vector<Float> arr = specCol_( 0 ) ;
1804 int nChan = arr.nelements() ;
1805
1806 // if nmin < 0 or nmax < 0, nothing to do
1807 if ( nmin < 0 ) {
1808 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1809 }
1810 if ( nmax < 0 ) {
1811 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1812 }
1813
1814 // if nmin > nmax, exchange values
1815 if ( nmin > nmax ) {
1816 int tmp = nmax ;
1817 nmax = nmin ;
1818 nmin = tmp ;
1819 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1820 os << "Swap values. Applied range is ["
1821 << nmin << ", " << nmax << "]" << LogIO::POST ;
1822 }
1823
1824 // if nmin exceeds nChan, nothing to do
1825 if ( nmin >= nChan ) {
1826 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1827 }
1828
1829 // if nmax exceeds nChan, reset nmax to nChan
1830 if ( nmax >= nChan ) {
1831 if ( nmin == 0 ) {
1832 // nothing to do
1833 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1834 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1835 return ;
1836 }
1837 else {
1838 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1839 os << "Specified maximum exceeds nChan. Applied range is ["
1840 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1841 nmax = nChan - 1 ;
1842 }
1843 }
1844
1845 // reshape specCol_ and flagCol_
1846 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1847 reshapeSpectrum( nmin, nmax, irow ) ;
1848 }
1849
1850 // update FREQUENCIES subtable
1851 Double refpix ;
1852 Double refval ;
1853 Double increment ;
1854 int freqnrow = freqTable_.table().nrow() ;
1855 Vector<uInt> oldId( freqnrow ) ;
1856 Vector<uInt> newId( freqnrow ) ;
1857 for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
1858 freqTable_.getEntry( refpix, refval, increment, irow ) ;
1859 /***
1860 * need to shift refpix to nmin
1861 * note that channel nmin in old index will be channel 0 in new one
1862 ***/
1863 refval = refval - ( refpix - nmin ) * increment ;
1864 refpix = 0 ;
1865 freqTable_.setEntry( refpix, refval, increment, irow ) ;
1866 }
1867
1868 // update nchan
1869 int newsize = nmax - nmin + 1 ;
1870 table_.rwKeywordSet().define( "nChan", newsize ) ;
1871
1872 // update bandwidth
1873 // assumed all spectra in the scantable have same bandwidth
1874 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1875
1876 return ;
1877}
1878
1879void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1880{
1881 // reshape specCol_ and flagCol_
1882 Vector<Float> oldspec = specCol_( irow ) ;
1883 Vector<uChar> oldflag = flagsCol_( irow ) ;
1884 Vector<Float> oldtsys = tsysCol_( irow ) ;
1885 uInt newsize = nmax - nmin + 1 ;
1886 Slice slice( nmin, newsize, 1 ) ;
1887 specCol_.put( irow, oldspec( slice ) ) ;
1888 flagsCol_.put( irow, oldflag( slice ) ) ;
1889 if ( oldspec.size() == oldtsys.size() )
1890 tsysCol_.put( irow, oldtsys( slice ) ) ;
1891
1892 return ;
1893}
1894
1895void asap::Scantable::regridSpecChannel( double dnu, int nChan )
1896{
1897 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1898 os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ;
1899 int freqnrow = freqTable_.table().nrow() ;
1900 Vector<bool> firstTime( freqnrow, true ) ;
1901 double oldincr, factor;
1902 uInt currId;
1903 Double refpix ;
1904 Double refval ;
1905 Double increment ;
1906 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1907 currId = mfreqidCol_(irow);
1908 vector<double> abcissa = getAbcissa( irow ) ;
1909 if (nChan < 0) {
1910 int oldsize = abcissa.size() ;
1911 double bw = (abcissa[oldsize-1]-abcissa[0]) + \
1912 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ;
1913 nChan = int( ceil( abs(bw/dnu) ) ) ;
1914 }
1915 // actual regridding
1916 regridChannel( nChan, dnu, irow ) ;
1917
1918 // update FREQUENCIES subtable
1919 if (firstTime[currId]) {
1920 oldincr = abcissa[1]-abcissa[0] ;
1921 factor = dnu/oldincr ;
1922 firstTime[currId] = false ;
1923 freqTable_.getEntry( refpix, refval, increment, currId ) ;
1924
1925 //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ;
1926 if (factor > 0 ) {
1927 refpix = (refpix + 0.5)/factor - 0.5;
1928 } else {
1929 refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5;
1930 }
1931 freqTable_.setEntry( refpix, refval, increment*factor, currId ) ;
1932 //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ;
1933 //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ;
1934 }
1935 }
1936}
1937
1938void asap::Scantable::regridChannel( int nChan, double dnu )
1939{
1940 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1941 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
1942 // assumed that all rows have same nChan
1943 Vector<Float> arr = specCol_( 0 ) ;
1944 int oldsize = arr.nelements() ;
1945
1946 // if oldsize == nChan, nothing to do
1947 if ( oldsize == nChan ) {
1948 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
1949 return ;
1950 }
1951
1952 // if oldChan < nChan, unphysical operation
1953 if ( oldsize < nChan ) {
1954 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
1955 return ;
1956 }
1957
1958 // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary)
1959 vector<string> coordinfo = getCoordInfo() ;
1960 string oldinfo = coordinfo[0] ;
1961 coordinfo[0] = "Hz" ;
1962 setCoordInfo( coordinfo ) ;
1963 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1964 regridChannel( nChan, dnu, irow ) ;
1965 }
1966 coordinfo[0] = oldinfo ;
1967 setCoordInfo( coordinfo ) ;
1968
1969
1970 // NOTE: this method does not update metadata such as
1971 // FREQUENCIES subtable, nChan, Bandwidth, etc.
1972
1973 return ;
1974}
1975
1976void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
1977{
1978 // logging
1979 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
1980 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
1981
1982 Vector<Float> oldspec = specCol_( irow ) ;
1983 Vector<uChar> oldflag = flagsCol_( irow ) ;
1984 Vector<Float> oldtsys = tsysCol_( irow ) ;
1985 Vector<Float> newspec( nChan, 0 ) ;
1986 Vector<uChar> newflag( nChan, true ) ;
1987 Vector<Float> newtsys ;
1988 bool regridTsys = false ;
1989 if (oldtsys.size() == oldspec.size()) {
1990 regridTsys = true ;
1991 newtsys.resize(nChan,false) ;
1992 newtsys = 0 ;
1993 }
1994
1995 // regrid
1996 vector<double> abcissa = getAbcissa( irow ) ;
1997 int oldsize = abcissa.size() ;
1998 double olddnu = abcissa[1] - abcissa[0] ;
1999 //int ichan = 0 ;
2000 double wsum = 0.0 ;
2001 Vector<double> zi( nChan+1 ) ;
2002 Vector<double> yi( oldsize + 1 ) ;
2003 yi[0] = abcissa[0] - 0.5 * olddnu ;
2004 for ( int ii = 1 ; ii < oldsize ; ii++ )
2005 yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ;
2006 yi[oldsize] = abcissa[oldsize-1] \
2007 + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ;
2008 //zi[0] = abcissa[0] - 0.5 * olddnu ;
2009 zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ;
2010 for ( int ii = 1 ; ii < nChan ; ii++ )
2011 zi[ii] = zi[0] + dnu * ii ;
2012 zi[nChan] = zi[nChan-1] + dnu ;
2013 // Access zi and yi in ascending order
2014 int izs = ((dnu > 0) ? 0 : nChan ) ;
2015 int ize = ((dnu > 0) ? nChan : 0 ) ;
2016 int izincr = ((dnu > 0) ? 1 : -1 ) ;
2017 int ichan = ((olddnu > 0) ? 0 : oldsize ) ;
2018 int iye = ((olddnu > 0) ? oldsize : 0 ) ;
2019 int iyincr = ((olddnu > 0) ? 1 : -1 ) ;
2020 //for ( int ii = izs ; ii != ize ; ii+=izincr ){
2021 int ii = izs ;
2022 while (ii != ize) {
2023 // always zl < zr
2024 double zl = zi[ii] ;
2025 double zr = zi[ii+izincr] ;
2026 // Need to access smaller index for the new spec, flag, and tsys.
2027 // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc.
2028 int i = min(ii, ii+izincr) ;
2029 //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) {
2030 int jj = ichan ;
2031 while (jj != iye) {
2032 // always yl < yr
2033 double yl = yi[jj] ;
2034 double yr = yi[jj+iyincr] ;
2035 // Need to access smaller index for the original spec, flag, and tsys.
2036 // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc.
2037 int j = min(jj, jj+iyincr) ;
2038 if ( yr <= zl ) {
2039 jj += iyincr ;
2040 continue ;
2041 }
2042 else if ( yl <= zl ) {
2043 if ( yr < zr ) {
2044 if (!oldflag[j]) {
2045 newspec[i] += oldspec[j] * ( yr - zl ) ;
2046 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ;
2047 wsum += ( yr - zl ) ;
2048 }
2049 newflag[i] = newflag[i] && oldflag[j] ;
2050 }
2051 else {
2052 if (!oldflag[j]) {
2053 newspec[i] += oldspec[j] * abs(dnu) ;
2054 if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ;
2055 wsum += abs(dnu) ;
2056 }
2057 newflag[i] = newflag[i] && oldflag[j] ;
2058 ichan = jj ;
2059 break ;
2060 }
2061 }
2062 else if ( yl < zr ) {
2063 if ( yr <= zr ) {
2064 if (!oldflag[j]) {
2065 newspec[i] += oldspec[j] * ( yr - yl ) ;
2066 if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ;
2067 wsum += ( yr - yl ) ;
2068 }
2069 newflag[i] = newflag[i] && oldflag[j] ;
2070 }
2071 else {
2072 if (!oldflag[j]) {
2073 newspec[i] += oldspec[j] * ( zr - yl ) ;
2074 if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ;
2075 wsum += ( zr - yl ) ;
2076 }
2077 newflag[i] = newflag[i] && oldflag[j] ;
2078 ichan = jj ;
2079 break ;
2080 }
2081 }
2082 else {
2083 ichan = jj - iyincr ;
2084 break ;
2085 }
2086 jj += iyincr ;
2087 }
2088 if ( wsum != 0.0 ) {
2089 newspec[i] /= wsum ;
2090 if (regridTsys) newtsys[i] /= wsum ;
2091 }
2092 wsum = 0.0 ;
2093 ii += izincr ;
2094 }
2095// if ( dnu > 0.0 ) {
2096// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2097// double zl = zi[ii] ;
2098// double zr = zi[ii+1] ;
2099// for ( int j = ichan ; j < oldsize ; j++ ) {
2100// double yl = yi[j] ;
2101// double yr = yi[j+1] ;
2102// if ( yl <= zl ) {
2103// if ( yr <= zl ) {
2104// continue ;
2105// }
2106// else if ( yr <= zr ) {
2107// if (!oldflag[j]) {
2108// newspec[ii] += oldspec[j] * ( yr - zl ) ;
2109// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ;
2110// wsum += ( yr - zl ) ;
2111// }
2112// newflag[ii] = newflag[ii] && oldflag[j] ;
2113// }
2114// else {
2115// if (!oldflag[j]) {
2116// newspec[ii] += oldspec[j] * dnu ;
2117// if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ;
2118// wsum += dnu ;
2119// }
2120// newflag[ii] = newflag[ii] && oldflag[j] ;
2121// ichan = j ;
2122// break ;
2123// }
2124// }
2125// else if ( yl < zr ) {
2126// if ( yr <= zr ) {
2127// if (!oldflag[j]) {
2128// newspec[ii] += oldspec[j] * ( yr - yl ) ;
2129// if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ;
2130// wsum += ( yr - yl ) ;
2131// }
2132// newflag[ii] = newflag[ii] && oldflag[j] ;
2133// }
2134// else {
2135// if (!oldflag[j]) {
2136// newspec[ii] += oldspec[j] * ( zr - yl ) ;
2137// if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ;
2138// wsum += ( zr - yl ) ;
2139// }
2140// newflag[ii] = newflag[ii] && oldflag[j] ;
2141// ichan = j ;
2142// break ;
2143// }
2144// }
2145// else {
2146// ichan = j - 1 ;
2147// break ;
2148// }
2149// }
2150// if ( wsum != 0.0 ) {
2151// newspec[ii] /= wsum ;
2152// if (regridTsys) newtsys[ii] /= wsum ;
2153// }
2154// wsum = 0.0 ;
2155// }
2156// }
2157// else if ( dnu < 0.0 ) {
2158// for ( int ii = 0 ; ii < nChan ; ii++ ) {
2159// double zl = zi[ii] ;
2160// double zr = zi[ii+1] ;
2161// for ( int j = ichan ; j < oldsize ; j++ ) {
2162// double yl = yi[j] ;
2163// double yr = yi[j+1] ;
2164// if ( yl >= zl ) {
2165// if ( yr >= zl ) {
2166// continue ;
2167// }
2168// else if ( yr >= zr ) {
2169// if (!oldflag[j]) {
2170// newspec[ii] += oldspec[j] * abs( yr - zl ) ;
2171// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ;
2172// wsum += abs( yr - zl ) ;
2173// }
2174// newflag[ii] = newflag[ii] && oldflag[j] ;
2175// }
2176// else {
2177// if (!oldflag[j]) {
2178// newspec[ii] += oldspec[j] * abs( dnu ) ;
2179// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ;
2180// wsum += abs( dnu ) ;
2181// }
2182// newflag[ii] = newflag[ii] && oldflag[j] ;
2183// ichan = j ;
2184// break ;
2185// }
2186// }
2187// else if ( yl > zr ) {
2188// if ( yr >= zr ) {
2189// if (!oldflag[j]) {
2190// newspec[ii] += oldspec[j] * abs( yr - yl ) ;
2191// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ;
2192// wsum += abs( yr - yl ) ;
2193// }
2194// newflag[ii] = newflag[ii] && oldflag[j] ;
2195// }
2196// else {
2197// if (!oldflag[j]) {
2198// newspec[ii] += oldspec[j] * abs( zr - yl ) ;
2199// if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ;
2200// wsum += abs( zr - yl ) ;
2201// }
2202// newflag[ii] = newflag[ii] && oldflag[j] ;
2203// ichan = j ;
2204// break ;
2205// }
2206// }
2207// else {
2208// ichan = j - 1 ;
2209// break ;
2210// }
2211// }
2212// if ( wsum != 0.0 ) {
2213// newspec[ii] /= wsum ;
2214// if (regridTsys) newtsys[ii] /= wsum ;
2215// }
2216// wsum = 0.0 ;
2217// }
2218// }
2219// // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
2220// // pile += dnu ;
2221// // wedge = olddnu * ( refChan + 1 ) ;
2222// // while ( wedge < pile ) {
2223// // newspec[0] += olddnu * oldspec[refChan] ;
2224// // newflag[0] = newflag[0] || oldflag[refChan] ;
2225// // //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
2226// // refChan++ ;
2227// // wedge += olddnu ;
2228// // wsum += olddnu ;
2229// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2230// // }
2231// // frac = ( wedge - pile ) / olddnu ;
2232// // wsum += ( 1.0 - frac ) * olddnu ;
2233// // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2234// // newflag[0] = newflag[0] || oldflag[refChan] ;
2235// // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
2236// // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
2237// // newspec[0] /= wsum ;
2238// // //ofs << "newspec[0] = " << newspec[0] << endl ;
2239// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2240
2241// // /***
2242// // * ichan = 1 - nChan-2
2243// // ***/
2244// // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
2245// // pile += dnu ;
2246// // newspec[ichan] += frac * olddnu * oldspec[refChan] ;
2247// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2248// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
2249// // refChan++ ;
2250// // wedge += olddnu ;
2251// // wsum = frac * olddnu ;
2252// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2253// // while ( wedge < pile ) {
2254// // newspec[ichan] += olddnu * oldspec[refChan] ;
2255// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2256// // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
2257// // refChan++ ;
2258// // wedge += olddnu ;
2259// // wsum += olddnu ;
2260// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2261// // }
2262// // frac = ( wedge - pile ) / olddnu ;
2263// // wsum += ( 1.0 - frac ) * olddnu ;
2264// // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
2265// // newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
2266// // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
2267// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2268// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
2269// // newspec[ichan] /= wsum ;
2270// // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
2271// // }
2272
2273// // /***
2274// // * ichan = nChan-1
2275// // ***/
2276// // // NOTE: Assumed that all spectra have the same bandwidth
2277// // pile += dnu ;
2278// // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
2279// // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
2280// // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2281// // refChan++ ;
2282// // wedge += olddnu ;
2283// // wsum = frac * olddnu ;
2284// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2285// // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
2286// // newspec[nChan-1] += olddnu * oldspec[jchan] ;
2287// // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
2288// // wsum += olddnu ;
2289// // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
2290// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2291// // }
2292// // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
2293// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
2294// // newspec[nChan-1] /= wsum ;
2295// // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
2296
2297// // // ofs.close() ;
2298
2299 specCol_.put( irow, newspec ) ;
2300 flagsCol_.put( irow, newflag ) ;
2301 if (regridTsys) tsysCol_.put( irow, newtsys );
2302
2303 return ;
2304}
2305
2306std::vector<float> Scantable::getWeather(int whichrow) const
2307{
2308 std::vector<float> out(5);
2309 //Float temperature, pressure, humidity, windspeed, windaz;
2310 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
2311 mweatheridCol_(uInt(whichrow)));
2312
2313
2314 return out;
2315}
2316
2317bool Scantable::getFlagtraFast(uInt whichrow)
2318{
2319 uChar flag;
2320 Vector<uChar> flags;
2321 flagsCol_.get(whichrow, flags);
2322 flag = flags[0];
2323 for (uInt i = 1; i < flags.size(); ++i) {
2324 flag &= flags[i];
2325 }
2326 return ((flag >> 7) == 1);
2327}
2328
2329void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile)
2330{
2331 try {
2332 ofstream ofs;
2333 String coordInfo = "";
2334 bool hasSameNchan = true;
2335 bool outTextFile = false;
2336
2337 if (blfile != "") {
2338 ofs.open(blfile.c_str(), ios::out | ios::app);
2339 if (ofs) outTextFile = true;
2340 }
2341
2342 if (outLogger || outTextFile) {
2343 coordInfo = getCoordInfo()[0];
2344 if (coordInfo == "") coordInfo = "channel";
2345 hasSameNchan = hasSameNchanOverIFs();
2346 }
2347
2348 Fitter fitter = Fitter();
2349 fitter.setExpression("poly", order);
2350 //fitter.setIterClipping(thresClip, nIterClip);
2351
2352 int nRow = nrow();
2353 std::vector<bool> chanMask;
2354 bool showProgress;
2355 int minNRow;
2356 parseProgressInfo(progressInfo, showProgress, minNRow);
2357
2358 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2359 chanMask = getCompositeChanMask(whichrow, mask);
2360 fitBaseline(chanMask, whichrow, fitter);
2361 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2362 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
2363 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2364 }
2365
2366 if (outTextFile) ofs.close();
2367
2368 } catch (...) {
2369 throw;
2370 }
2371}
2372
2373void 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)
2374{
2375 try {
2376 ofstream ofs;
2377 String coordInfo = "";
2378 bool hasSameNchan = true;
2379 bool outTextFile = false;
2380
2381 if (blfile != "") {
2382 ofs.open(blfile.c_str(), ios::out | ios::app);
2383 if (ofs) outTextFile = true;
2384 }
2385
2386 if (outLogger || outTextFile) {
2387 coordInfo = getCoordInfo()[0];
2388 if (coordInfo == "") coordInfo = "channel";
2389 hasSameNchan = hasSameNchanOverIFs();
2390 }
2391
2392 Fitter fitter = Fitter();
2393 fitter.setExpression("poly", order);
2394 //fitter.setIterClipping(thresClip, nIterClip);
2395
2396 int nRow = nrow();
2397 std::vector<bool> chanMask;
2398 int minEdgeSize = getIFNos().size()*2;
2399 STLineFinder lineFinder = STLineFinder();
2400 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2401
2402 bool showProgress;
2403 int minNRow;
2404 parseProgressInfo(progressInfo, showProgress, minNRow);
2405
2406 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2407
2408 //-------------------------------------------------------
2409 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2410 //-------------------------------------------------------
2411 int edgeSize = edge.size();
2412 std::vector<int> currentEdge;
2413 if (edgeSize >= 2) {
2414 int idx = 0;
2415 if (edgeSize > 2) {
2416 if (edgeSize < minEdgeSize) {
2417 throw(AipsError("Length of edge element info is less than that of IFs"));
2418 }
2419 idx = 2 * getIF(whichrow);
2420 }
2421 currentEdge.push_back(edge[idx]);
2422 currentEdge.push_back(edge[idx+1]);
2423 } else {
2424 throw(AipsError("Wrong length of edge element"));
2425 }
2426 lineFinder.setData(getSpectrum(whichrow));
2427 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2428 chanMask = lineFinder.getMask();
2429 //-------------------------------------------------------
2430
2431 fitBaseline(chanMask, whichrow, fitter);
2432 setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2433
2434 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
2435 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2436 }
2437
2438 if (outTextFile) ofs.close();
2439
2440 } catch (...) {
2441 throw;
2442 }
2443}
2444
2445void 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)
2446{
2447 /*************/
2448 //clock_t totTimeStart, totTimeEnd, blTimeStart, blTimeEnd, ioTimeStart, ioTimeEnd;
2449 double totTimeStart, totTimeEnd, blTimeStart, blTimeEnd, ioTimeStart, ioTimeEnd, msTimeStart, msTimeEnd, seTimeStart, seTimeEnd, otTimeStart, otTimeEnd, prTimeStart, prTimeEnd;
2450 double elapseMs = 0.0;
2451 double elapseSe = 0.0;
2452 double elapseOt = 0.0;
2453 double elapsePr = 0.0;
2454 double elapseBl = 0.0;
2455 double elapseIo = 0.0;
2456 //totTimeStart = clock();
2457 totTimeStart = mathutil::gettimeofday_sec();
2458 /*************/
2459
2460 try {
2461 ofstream ofs;
2462 String coordInfo = "";
2463 bool hasSameNchan = true;
2464 bool outTextFile = false;
2465
2466 if (blfile != "") {
2467 ofs.open(blfile.c_str(), ios::out | ios::app);
2468 if (ofs) outTextFile = true;
2469 }
2470
2471 if (outLogger || outTextFile) {
2472 coordInfo = getCoordInfo()[0];
2473 if (coordInfo == "") coordInfo = "channel";
2474 hasSameNchan = hasSameNchanOverIFs();
2475 }
2476
2477 //Fitter fitter = Fitter();
2478 //fitter.setExpression("cspline", nPiece);
2479 //fitter.setIterClipping(thresClip, nIterClip);
2480
2481 bool showProgress;
2482 int minNRow;
2483 parseProgressInfo(progressInfo, showProgress, minNRow);
2484
2485 int nRow = nrow();
2486 std::vector<bool> chanMask;
2487
2488 //--------------------------------
2489 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2490 /******************/
2491 //ioTimeStart = clock();
2492 ioTimeStart = mathutil::gettimeofday_sec();
2493 /**/
2494 std::vector<float> sp = getSpectrum(whichrow);
2495 /**/
2496 //ioTimeEnd = clock();
2497 ioTimeEnd = mathutil::gettimeofday_sec();
2498 elapseIo += (double)(ioTimeEnd - ioTimeStart);
2499
2500 //blTimeStart = clock();
2501 msTimeStart = mathutil::gettimeofday_sec();
2502 /******************/
2503
2504 chanMask = getCompositeChanMask(whichrow, mask);
2505
2506 /**/
2507 msTimeEnd = mathutil::gettimeofday_sec();
2508 elapseMs += (double)(msTimeEnd - msTimeStart);
2509 blTimeStart = mathutil::gettimeofday_sec();
2510 /**/
2511
2512 //fitBaseline(chanMask, whichrow, fitter);
2513 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2514 std::vector<int> pieceEdges(nPiece+1);
2515 std::vector<float> params(nPiece*4);
2516 int nClipped = 0;
2517 std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2518
2519 /**/
2520 blTimeEnd = mathutil::gettimeofday_sec();
2521 elapseBl += (double)(blTimeEnd - blTimeStart);
2522 seTimeStart = mathutil::gettimeofday_sec();
2523 /**/
2524
2525
2526 setSpectrum(res, whichrow);
2527 //
2528
2529 /**/
2530 seTimeEnd = mathutil::gettimeofday_sec();
2531 elapseSe += (double)(seTimeEnd - seTimeStart);
2532 otTimeStart = mathutil::gettimeofday_sec();
2533 /**/
2534
2535 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped);
2536
2537 /**/
2538 otTimeEnd = mathutil::gettimeofday_sec();
2539 elapseOt += (double)(otTimeEnd - otTimeStart);
2540 prTimeStart = mathutil::gettimeofday_sec();
2541 /**/
2542
2543 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2544
2545 /******************/
2546 //blTimeEnd = clock();
2547 prTimeEnd = mathutil::gettimeofday_sec();
2548 elapsePr += (double)(prTimeEnd - prTimeStart);
2549 /******************/
2550 }
2551 //--------------------------------
2552
2553 if (outTextFile) ofs.close();
2554
2555 } catch (...) {
2556 throw;
2557 }
2558 /***************/
2559 //totTimeEnd = clock();
2560 totTimeEnd = mathutil::gettimeofday_sec();
2561 //std::cout << "io : " << elapseIo/CLOCKS_PER_SEC << " (sec.)" << endl;
2562 //std::cout << "bl : " << elapseBl/CLOCKS_PER_SEC << " (sec.)" << endl;
2563 //std::cout << "total : " << (double)(totTimeEnd - totTimeStart)/CLOCKS_PER_SEC << " (sec.)" << endl;
2564 std::cout << "io : " << elapseIo << " (sec.)" << endl;
2565 std::cout << "ms : " << elapseMs << " (sec.)" << endl;
2566 std::cout << "bl : " << elapseBl << " (sec.)" << endl;
2567 std::cout << "se : " << elapseSe << " (sec.)" << endl;
2568 std::cout << "ot : " << elapseOt << " (sec.)" << endl;
2569 std::cout << "pr : " << elapsePr << " (sec.)" << endl;
2570 std::cout << "total : " << (double)(totTimeEnd - totTimeStart) << " (sec.)" << endl;
2571 /***************/
2572}
2573
2574void 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)
2575{
2576 /*************
2577 clock_t totTimeStart, totTimeEnd, blTimeStart, blTimeEnd, ioTimeStart, ioTimeEnd;
2578 double elapseBl = 0.0;
2579 double elapseIo = 0.0;
2580 totTimeStart = clock();
2581 *************/
2582
2583 try {
2584 ofstream ofs;
2585 String coordInfo = "";
2586 bool hasSameNchan = true;
2587 bool outTextFile = false;
2588
2589 if (blfile != "") {
2590 ofs.open(blfile.c_str(), ios::out | ios::app);
2591 if (ofs) outTextFile = true;
2592 }
2593
2594 if (outLogger || outTextFile) {
2595 coordInfo = getCoordInfo()[0];
2596 if (coordInfo == "") coordInfo = "channel";
2597 hasSameNchan = hasSameNchanOverIFs();
2598 }
2599
2600 //Fitter fitter = Fitter();
2601 //fitter.setExpression("cspline", nPiece);
2602 //fitter.setIterClipping(thresClip, nIterClip);
2603
2604 int nRow = nrow();
2605 std::vector<bool> chanMask;
2606 int minEdgeSize = getIFNos().size()*2;
2607 STLineFinder lineFinder = STLineFinder();
2608 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2609
2610 bool showProgress;
2611 int minNRow;
2612 parseProgressInfo(progressInfo, showProgress, minNRow);
2613
2614 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2615 /******************
2616 ioTimeStart = clock();
2617 */
2618 std::vector<float> sp = getSpectrum(whichrow);
2619 /*
2620 ioTimeEnd = clock();
2621 elapseIo += (double)(ioTimeEnd - ioTimeStart);
2622
2623 blTimeStart = clock();
2624 ******************/
2625
2626 //-------------------------------------------------------
2627 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2628 //-------------------------------------------------------
2629 int edgeSize = edge.size();
2630 std::vector<int> currentEdge;
2631 if (edgeSize >= 2) {
2632 int idx = 0;
2633 if (edgeSize > 2) {
2634 if (edgeSize < minEdgeSize) {
2635 throw(AipsError("Length of edge element info is less than that of IFs"));
2636 }
2637 idx = 2 * getIF(whichrow);
2638 }
2639 currentEdge.push_back(edge[idx]);
2640 currentEdge.push_back(edge[idx+1]);
2641 } else {
2642 throw(AipsError("Wrong length of edge element"));
2643 }
2644 lineFinder.setData(getSpectrum(whichrow));
2645 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2646 chanMask = lineFinder.getMask();
2647 //-------------------------------------------------------
2648
2649
2650 //fitBaseline(chanMask, whichrow, fitter);
2651 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
2652 std::vector<int> pieceEdges(nPiece+1);
2653 std::vector<float> params(nPiece*4);
2654 int nClipped = 0;
2655 std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual);
2656 setSpectrum(res, whichrow);
2657 //
2658
2659 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped);
2660 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
2661
2662 /******************
2663 blTimeEnd = clock();
2664 elapseBl += (double)(blTimeEnd - blTimeStart);
2665 ******************/
2666
2667 }
2668
2669 if (outTextFile) ofs.close();
2670
2671 } catch (...) {
2672 throw;
2673 }
2674
2675 /***************
2676 totTimeEnd = clock();
2677 std::cout << "io : " << elapseIo/CLOCKS_PER_SEC << " (sec.)" << endl;
2678 std::cout << "bl : " << elapseBl/CLOCKS_PER_SEC << " (sec.)" << endl;
2679 std::cout << "total : " << (double)(totTimeEnd - totTimeStart)/CLOCKS_PER_SEC << " (sec.)" << endl;
2680 ***************/
2681}
2682
2683std::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)
2684{
2685 if (data.size() != mask.size()) {
2686 throw(AipsError("data and mask sizes are not identical"));
2687 }
2688 if (nPiece < 1) {
2689 throw(AipsError("number of the sections must be one or more"));
2690 }
2691
2692 int nChan = data.size();
2693 std::vector<int> maskArray(nChan);
2694 std::vector<int> x(nChan);
2695 int j = 0;
2696 for (int i = 0; i < nChan; ++i) {
2697 maskArray[i] = mask[i] ? 1 : 0;
2698 if (mask[i]) {
2699 x[j] = i;
2700 j++;
2701 }
2702 }
2703 int initNData = j;
2704
2705 if (initNData < nPiece) {
2706 throw(AipsError("too few non-flagged channels"));
2707 }
2708
2709 int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5));
2710 std::vector<double> invEdge(nPiece-1);
2711 idxEdge[0] = x[0];
2712 for (int i = 1; i < nPiece; ++i) {
2713 int valX = x[nElement*i];
2714 idxEdge[i] = valX;
2715 invEdge[i-1] = 1.0/(double)valX;
2716 }
2717 idxEdge[nPiece] = x[initNData-1]+1;
2718
2719 int nData = initNData;
2720 int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
2721
2722 std::vector<double> x1(nChan), x2(nChan), x3(nChan);
2723 std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan);
2724 std::vector<double> r1(nChan), residual(nChan);
2725 for (int i = 0; i < nChan; ++i) {
2726 double di = (double)i;
2727 double dD = (double)data[i];
2728 x1[i] = di;
2729 x2[i] = di*di;
2730 x3[i] = di*di*di;
2731 z1[i] = dD;
2732 x1z1[i] = dD*di;
2733 x2z1[i] = dD*di*di;
2734 x3z1[i] = dD*di*di*di;
2735 r1[i] = 0.0;
2736 residual[i] = 0.0;
2737 }
2738
2739 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
2740 // xMatrix : horizontal concatenation of
2741 // the least-sq. matrix (left) and an
2742 // identity matrix (right).
2743 // the right part is used to calculate the inverse matrix of the left part.
2744 double xMatrix[nDOF][2*nDOF];
2745 double zMatrix[nDOF];
2746 for (int i = 0; i < nDOF; ++i) {
2747 for (int j = 0; j < 2*nDOF; ++j) {
2748 xMatrix[i][j] = 0.0;
2749 }
2750 xMatrix[i][nDOF+i] = 1.0;
2751 zMatrix[i] = 0.0;
2752 }
2753
2754 for (int n = 0; n < nPiece; ++n) {
2755 int nUseDataInPiece = 0;
2756 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2757
2758 if (maskArray[i] == 0) continue;
2759
2760 xMatrix[0][0] += 1.0;
2761 xMatrix[0][1] += x1[i];
2762 xMatrix[0][2] += x2[i];
2763 xMatrix[0][3] += x3[i];
2764 xMatrix[1][1] += x2[i];
2765 xMatrix[1][2] += x3[i];
2766 xMatrix[1][3] += x2[i]*x2[i];
2767 xMatrix[2][2] += x2[i]*x2[i];
2768 xMatrix[2][3] += x3[i]*x2[i];
2769 xMatrix[3][3] += x3[i]*x3[i];
2770 zMatrix[0] += z1[i];
2771 zMatrix[1] += x1z1[i];
2772 zMatrix[2] += x2z1[i];
2773 zMatrix[3] += x3z1[i];
2774
2775 for (int j = 0; j < n; ++j) {
2776 double q = 1.0 - x1[i]*invEdge[j];
2777 q = q*q*q;
2778 xMatrix[0][j+4] += q;
2779 xMatrix[1][j+4] += q*x1[i];
2780 xMatrix[2][j+4] += q*x2[i];
2781 xMatrix[3][j+4] += q*x3[i];
2782 for (int k = 0; k < j; ++k) {
2783 double r = 1.0 - x1[i]*invEdge[k];
2784 r = r*r*r;
2785 xMatrix[k+4][j+4] += r*q;
2786 }
2787 xMatrix[j+4][j+4] += q*q;
2788 zMatrix[j+4] += q*z1[i];
2789 }
2790
2791 nUseDataInPiece++;
2792 }
2793
2794 if (nUseDataInPiece < 1) {
2795 std::vector<string> suffixOfPieceNumber(4);
2796 suffixOfPieceNumber[0] = "th";
2797 suffixOfPieceNumber[1] = "st";
2798 suffixOfPieceNumber[2] = "nd";
2799 suffixOfPieceNumber[3] = "rd";
2800 int idxNoDataPiece = (n % 10 <= 3) ? n : 0;
2801 ostringstream oss;
2802 oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece];
2803 oss << " piece of the spectrum. can't execute fitting anymore.";
2804 throw(AipsError(String(oss)));
2805 }
2806 }
2807
2808 for (int i = 0; i < nDOF; ++i) {
2809 for (int j = 0; j < i; ++j) {
2810 xMatrix[i][j] = xMatrix[j][i];
2811 }
2812 }
2813
2814 std::vector<double> invDiag(nDOF);
2815 for (int i = 0; i < nDOF; ++i) {
2816 invDiag[i] = 1.0/xMatrix[i][i];
2817 for (int j = 0; j < nDOF; ++j) {
2818 xMatrix[i][j] *= invDiag[i];
2819 }
2820 }
2821
2822 for (int k = 0; k < nDOF; ++k) {
2823 for (int i = 0; i < nDOF; ++i) {
2824 if (i != k) {
2825 double factor1 = xMatrix[k][k];
2826 double factor2 = xMatrix[i][k];
2827 for (int j = k; j < 2*nDOF; ++j) {
2828 xMatrix[i][j] *= factor1;
2829 xMatrix[i][j] -= xMatrix[k][j]*factor2;
2830 xMatrix[i][j] /= factor1;
2831 }
2832 }
2833 }
2834 double xDiag = xMatrix[k][k];
2835 for (int j = k; j < 2*nDOF; ++j) {
2836 xMatrix[k][j] /= xDiag;
2837 }
2838 }
2839
2840 for (int i = 0; i < nDOF; ++i) {
2841 for (int j = 0; j < nDOF; ++j) {
2842 xMatrix[i][nDOF+j] *= invDiag[j];
2843 }
2844 }
2845 //compute a vector y which consists of the coefficients of the best-fit spline curves
2846 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
2847 //cubic terms for the other pieces (in case nPiece>1).
2848 std::vector<double> y(nDOF);
2849 for (int i = 0; i < nDOF; ++i) {
2850 y[i] = 0.0;
2851 for (int j = 0; j < nDOF; ++j) {
2852 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
2853 }
2854 }
2855
2856 double a0 = y[0];
2857 double a1 = y[1];
2858 double a2 = y[2];
2859 double a3 = y[3];
2860
2861 int j = 0;
2862 for (int n = 0; n < nPiece; ++n) {
2863 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2864 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
2865 }
2866 params[j] = a0;
2867 params[j+1] = a1;
2868 params[j+2] = a2;
2869 params[j+3] = a3;
2870 j += 4;
2871
2872 if (n == nPiece-1) break;
2873
2874 double d = y[4+n];
2875 double iE = invEdge[n];
2876 a0 += d;
2877 a1 -= 3.0*d*iE;
2878 a2 += 3.0*d*iE*iE;
2879 a3 -= d*iE*iE*iE;
2880 }
2881
2882 //subtract constant value for masked regions at the edge of spectrum
2883 if (idxEdge[0] > 0) {
2884 int n = idxEdge[0];
2885 for (int i = 0; i < idxEdge[0]; ++i) {
2886 //--cubic extrapolate--
2887 //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i];
2888 //--linear extrapolate--
2889 //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n];
2890 //--constant--
2891 r1[i] = r1[n];
2892 }
2893 }
2894 if (idxEdge[nPiece] < nChan) {
2895 int n = idxEdge[nPiece]-1;
2896 for (int i = idxEdge[nPiece]; i < nChan; ++i) {
2897 //--cubic extrapolate--
2898 //int m = 4*(nPiece-1);
2899 //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i];
2900 //--linear extrapolate--
2901 //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n];
2902 //--constant--
2903 r1[i] = r1[n];
2904 }
2905 }
2906
2907 for (int i = 0; i < nChan; ++i) {
2908 residual[i] = z1[i] - r1[i];
2909 }
2910
2911 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
2912 break;
2913 } else {
2914 double stdDev = 0.0;
2915 for (int i = 0; i < nChan; ++i) {
2916 stdDev += residual[i]*residual[i]*(double)maskArray[i];
2917 }
2918 stdDev = sqrt(stdDev/(double)nData);
2919
2920 double thres = stdDev * thresClip;
2921 int newNData = 0;
2922 for (int i = 0; i < nChan; ++i) {
2923 if (abs(residual[i]) >= thres) {
2924 maskArray[i] = 0;
2925 }
2926 if (maskArray[i] > 0) {
2927 newNData++;
2928 }
2929 }
2930 if (newNData == nData) {
2931 break; //no more flag to add. iteration stops.
2932 } else {
2933 nData = newNData;
2934 }
2935 }
2936 }
2937
2938 nClipped = initNData - nData;
2939
2940 std::vector<float> result(nChan);
2941 if (getResidual) {
2942 for (int i = 0; i < nChan; ++i) {
2943 result[i] = (float)residual[i];
2944 }
2945 } else {
2946 for (int i = 0; i < nChan; ++i) {
2947 result[i] = (float)r1[i];
2948 }
2949 }
2950
2951 return result;
2952}
2953
2954void 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)
2955{
2956 nWaves.clear();
2957
2958 if (applyFFT) {
2959 string fftThAttr;
2960 float fftThSigma;
2961 int fftThTop;
2962 parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop);
2963 doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves);
2964 }
2965
2966 addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves);
2967}
2968
2969void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop)
2970{
2971 uInt idxSigma = fftThresh.find("sigma");
2972 uInt idxTop = fftThresh.find("top");
2973
2974 if (idxSigma == fftThresh.size() - 5) {
2975 std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5));
2976 is >> fftThSigma;
2977 fftThAttr = "sigma";
2978 } else if (idxTop == 0) {
2979 std::istringstream is(fftThresh.substr(3));
2980 is >> fftThTop;
2981 fftThAttr = "top";
2982 } else {
2983 bool isNumber = true;
2984 for (uInt i = 0; i < fftThresh.size()-1; ++i) {
2985 char ch = (fftThresh.substr(i, 1).c_str())[0];
2986 if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) {
2987 isNumber = false;
2988 break;
2989 }
2990 }
2991 if (isNumber) {
2992 std::istringstream is(fftThresh);
2993 is >> fftThSigma;
2994 fftThAttr = "sigma";
2995 } else {
2996 throw(AipsError("fftthresh has a wrong value"));
2997 }
2998 }
2999}
3000
3001void 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)
3002{
3003 std::vector<float> fspec;
3004 if (fftMethod == "fft") {
3005 fspec = execFFT(whichrow, chanMask, false, true);
3006 //} else if (fftMethod == "lsp") {
3007 // fspec = lombScarglePeriodogram(whichrow);
3008 }
3009
3010 if (fftThAttr == "sigma") {
3011 float mean = 0.0;
3012 float mean2 = 0.0;
3013 for (uInt i = 0; i < fspec.size(); ++i) {
3014 mean += fspec[i];
3015 mean2 += fspec[i]*fspec[i];
3016 }
3017 mean /= float(fspec.size());
3018 mean2 /= float(fspec.size());
3019 float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean));
3020
3021 for (uInt i = 0; i < fspec.size(); ++i) {
3022 if (fspec[i] >= thres) {
3023 nWaves.push_back(i);
3024 }
3025 }
3026
3027 } else if (fftThAttr == "top") {
3028 for (int i = 0; i < fftThTop; ++i) {
3029 float max = 0.0;
3030 int maxIdx = 0;
3031 for (uInt j = 0; j < fspec.size(); ++j) {
3032 if (fspec[j] > max) {
3033 max = fspec[j];
3034 maxIdx = j;
3035 }
3036 }
3037 nWaves.push_back(maxIdx);
3038 fspec[maxIdx] = 0.0;
3039 }
3040
3041 }
3042
3043 if (nWaves.size() > 1) {
3044 sort(nWaves.begin(), nWaves.end());
3045 }
3046}
3047
3048void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves)
3049{
3050 std::vector<int> tempAddNWaves, tempRejectNWaves;
3051 for (uInt i = 0; i < addNWaves.size(); ++i) {
3052 tempAddNWaves.push_back(addNWaves[i]);
3053 }
3054 if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) {
3055 setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves);
3056 }
3057
3058 for (uInt i = 0; i < rejectNWaves.size(); ++i) {
3059 tempRejectNWaves.push_back(rejectNWaves[i]);
3060 }
3061 if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) {
3062 setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves);
3063 }
3064
3065 for (uInt i = 0; i < tempAddNWaves.size(); ++i) {
3066 bool found = false;
3067 for (uInt j = 0; j < nWaves.size(); ++j) {
3068 if (nWaves[j] == tempAddNWaves[i]) {
3069 found = true;
3070 break;
3071 }
3072 }
3073 if (!found) nWaves.push_back(tempAddNWaves[i]);
3074 }
3075
3076 for (uInt i = 0; i < tempRejectNWaves.size(); ++i) {
3077 for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) {
3078 if (*j == tempRejectNWaves[i]) {
3079 j = nWaves.erase(j);
3080 } else {
3081 ++j;
3082 }
3083 }
3084 }
3085
3086 if (nWaves.size() > 1) {
3087 sort(nWaves.begin(), nWaves.end());
3088 unique(nWaves.begin(), nWaves.end());
3089 }
3090}
3091
3092void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves)
3093{
3094 if ((nWaves.size() == 2)&&(nWaves[1] == -999)) {
3095 int val = nWaves[0];
3096 int nyquistFreq = nchan(getIF(whichrow))/2+1;
3097 nWaves.clear();
3098 if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759
3099 nWaves.push_back(0);
3100 }
3101 while (val <= nyquistFreq) {
3102 nWaves.push_back(val);
3103 val++;
3104 }
3105 }
3106}
3107
3108void 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)
3109{
3110 try {
3111 ofstream ofs;
3112 String coordInfo = "";
3113 bool hasSameNchan = true;
3114 bool outTextFile = false;
3115
3116 if (blfile != "") {
3117 ofs.open(blfile.c_str(), ios::out | ios::app);
3118 if (ofs) outTextFile = true;
3119 }
3120
3121 if (outLogger || outTextFile) {
3122 coordInfo = getCoordInfo()[0];
3123 if (coordInfo == "") coordInfo = "channel";
3124 hasSameNchan = hasSameNchanOverIFs();
3125 }
3126
3127 //Fitter fitter = Fitter();
3128 //fitter.setExpression("sinusoid", nWaves);
3129 //fitter.setIterClipping(thresClip, nIterClip);
3130
3131 int nRow = nrow();
3132 std::vector<bool> chanMask;
3133 std::vector<int> nWaves;
3134
3135 bool showProgress;
3136 int minNRow;
3137 parseProgressInfo(progressInfo, showProgress, minNRow);
3138
3139 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3140 chanMask = getCompositeChanMask(whichrow, mask);
3141 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
3142
3143 //FOR DEBUGGING------------
3144 /*
3145 if (whichrow < 0) {// == nRow -1) {
3146 cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow);
3147 if (applyFFT) {
3148 cout << "[ ";
3149 for (uInt j = 0; j < nWaves.size(); ++j) {
3150 cout << nWaves[j] << ", ";
3151 }
3152 cout << " ] " << endl;
3153 }
3154 cout << flush;
3155 }
3156 */
3157 //-------------------------
3158
3159 //fitBaseline(chanMask, whichrow, fitter);
3160 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
3161 std::vector<float> params;
3162 int nClipped = 0;
3163 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
3164 setSpectrum(res, whichrow);
3165 //
3166
3167 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped);
3168 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3169 }
3170
3171 if (outTextFile) ofs.close();
3172
3173 } catch (...) {
3174 throw;
3175 }
3176}
3177
3178void 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)
3179{
3180 try {
3181 ofstream ofs;
3182 String coordInfo = "";
3183 bool hasSameNchan = true;
3184 bool outTextFile = false;
3185
3186 if (blfile != "") {
3187 ofs.open(blfile.c_str(), ios::out | ios::app);
3188 if (ofs) outTextFile = true;
3189 }
3190
3191 if (outLogger || outTextFile) {
3192 coordInfo = getCoordInfo()[0];
3193 if (coordInfo == "") coordInfo = "channel";
3194 hasSameNchan = hasSameNchanOverIFs();
3195 }
3196
3197 //Fitter fitter = Fitter();
3198 //fitter.setExpression("sinusoid", nWaves);
3199 //fitter.setIterClipping(thresClip, nIterClip);
3200
3201 int nRow = nrow();
3202 std::vector<bool> chanMask;
3203 std::vector<int> nWaves;
3204
3205 int minEdgeSize = getIFNos().size()*2;
3206 STLineFinder lineFinder = STLineFinder();
3207 lineFinder.setOptions(threshold, 3, chanAvgLimit);
3208
3209 bool showProgress;
3210 int minNRow;
3211 parseProgressInfo(progressInfo, showProgress, minNRow);
3212
3213 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
3214
3215 //-------------------------------------------------------
3216 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
3217 //-------------------------------------------------------
3218 int edgeSize = edge.size();
3219 std::vector<int> currentEdge;
3220 if (edgeSize >= 2) {
3221 int idx = 0;
3222 if (edgeSize > 2) {
3223 if (edgeSize < minEdgeSize) {
3224 throw(AipsError("Length of edge element info is less than that of IFs"));
3225 }
3226 idx = 2 * getIF(whichrow);
3227 }
3228 currentEdge.push_back(edge[idx]);
3229 currentEdge.push_back(edge[idx+1]);
3230 } else {
3231 throw(AipsError("Wrong length of edge element"));
3232 }
3233 lineFinder.setData(getSpectrum(whichrow));
3234 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
3235 chanMask = lineFinder.getMask();
3236 //-------------------------------------------------------
3237
3238 selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves);
3239
3240 //fitBaseline(chanMask, whichrow, fitter);
3241 //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow);
3242 std::vector<float> params;
3243 int nClipped = 0;
3244 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual);
3245 setSpectrum(res, whichrow);
3246 //
3247
3248 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped);
3249 showProgressOnTerminal(whichrow, nRow, showProgress, minNRow);
3250 }
3251
3252 if (outTextFile) ofs.close();
3253
3254 } catch (...) {
3255 throw;
3256 }
3257}
3258
3259std::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)
3260{
3261 if (data.size() != mask.size()) {
3262 throw(AipsError("data and mask sizes are not identical"));
3263 }
3264 if (data.size() < 2) {
3265 throw(AipsError("data size is too short"));
3266 }
3267 if (waveNumbers.size() == 0) {
3268 throw(AipsError("no wave numbers given"));
3269 }
3270 std::vector<int> nWaves; // sorted and uniqued array of wave numbers
3271 nWaves.reserve(waveNumbers.size());
3272 copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves));
3273 sort(nWaves.begin(), nWaves.end());
3274 std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end());
3275 nWaves.erase(end_it, nWaves.end());
3276
3277 int minNWaves = nWaves[0];
3278 if (minNWaves < 0) {
3279 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
3280 }
3281 bool hasConstantTerm = (minNWaves == 0);
3282
3283 int nChan = data.size();
3284 std::vector<int> maskArray;
3285 std::vector<int> x;
3286 for (int i = 0; i < nChan; ++i) {
3287 maskArray.push_back(mask[i] ? 1 : 0);
3288 if (mask[i]) {
3289 x.push_back(i);
3290 }
3291 }
3292
3293 int initNData = x.size();
3294
3295 int nData = initNData;
3296 int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve.
3297
3298 const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...)
3299 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)
3300
3301 // xArray : contains elemental values for computing the least-square matrix.
3302 // xArray.size() is nDOF and xArray[*].size() is nChan.
3303 // Each xArray element are as follows:
3304 // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0},
3305 // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])},
3306 // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])},
3307 // where (1 <= n <= nMaxWavesInSW),
3308 // or,
3309 // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])},
3310 // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])},
3311 // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()).
3312 std::vector<std::vector<double> > xArray;
3313 if (hasConstantTerm) {
3314 std::vector<double> xu;
3315 for (int j = 0; j < nChan; ++j) {
3316 xu.push_back(1.0);
3317 }
3318 xArray.push_back(xu);
3319 }
3320 for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) {
3321 double xFactor = baseXFactor*(double)nWaves[i];
3322 std::vector<double> xs, xc;
3323 xs.clear();
3324 xc.clear();
3325 for (int j = 0; j < nChan; ++j) {
3326 xs.push_back(sin(xFactor*(double)j));
3327 xc.push_back(cos(xFactor*(double)j));
3328 }
3329 xArray.push_back(xs);
3330 xArray.push_back(xc);
3331 }
3332
3333 std::vector<double> z1, r1, residual;
3334 for (int i = 0; i < nChan; ++i) {
3335 z1.push_back((double)data[i]);
3336 r1.push_back(0.0);
3337 residual.push_back(0.0);
3338 }
3339
3340 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
3341 // xMatrix : horizontal concatenation of
3342 // the least-sq. matrix (left) and an
3343 // identity matrix (right).
3344 // the right part is used to calculate the inverse matrix of the left part.
3345 double xMatrix[nDOF][2*nDOF];
3346 double zMatrix[nDOF];
3347 for (int i = 0; i < nDOF; ++i) {
3348 for (int j = 0; j < 2*nDOF; ++j) {
3349 xMatrix[i][j] = 0.0;
3350 }
3351 xMatrix[i][nDOF+i] = 1.0;
3352 zMatrix[i] = 0.0;
3353 }
3354
3355 int nUseData = 0;
3356 for (int k = 0; k < nChan; ++k) {
3357 if (maskArray[k] == 0) continue;
3358
3359 for (int i = 0; i < nDOF; ++i) {
3360 for (int j = i; j < nDOF; ++j) {
3361 xMatrix[i][j] += xArray[i][k] * xArray[j][k];
3362 }
3363 zMatrix[i] += z1[k] * xArray[i][k];
3364 }
3365
3366 nUseData++;
3367 }
3368
3369 if (nUseData < 1) {
3370 throw(AipsError("all channels clipped or masked. can't execute fitting anymore."));
3371 }
3372
3373 for (int i = 0; i < nDOF; ++i) {
3374 for (int j = 0; j < i; ++j) {
3375 xMatrix[i][j] = xMatrix[j][i];
3376 }
3377 }
3378
3379 std::vector<double> invDiag;
3380 for (int i = 0; i < nDOF; ++i) {
3381 invDiag.push_back(1.0/xMatrix[i][i]);
3382 for (int j = 0; j < nDOF; ++j) {
3383 xMatrix[i][j] *= invDiag[i];
3384 }
3385 }
3386
3387 for (int k = 0; k < nDOF; ++k) {
3388 for (int i = 0; i < nDOF; ++i) {
3389 if (i != k) {
3390 double factor1 = xMatrix[k][k];
3391 double factor2 = xMatrix[i][k];
3392 for (int j = k; j < 2*nDOF; ++j) {
3393 xMatrix[i][j] *= factor1;
3394 xMatrix[i][j] -= xMatrix[k][j]*factor2;
3395 xMatrix[i][j] /= factor1;
3396 }
3397 }
3398 }
3399 double xDiag = xMatrix[k][k];
3400 for (int j = k; j < 2*nDOF; ++j) {
3401 xMatrix[k][j] /= xDiag;
3402 }
3403 }
3404
3405 for (int i = 0; i < nDOF; ++i) {
3406 for (int j = 0; j < nDOF; ++j) {
3407 xMatrix[i][nDOF+j] *= invDiag[j];
3408 }
3409 }
3410 //compute a vector y which consists of the coefficients of the sinusoids forming the
3411 //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine
3412 //and cosine functions, respectively.
3413 std::vector<double> y;
3414 params.clear();
3415 for (int i = 0; i < nDOF; ++i) {
3416 y.push_back(0.0);
3417 for (int j = 0; j < nDOF; ++j) {
3418 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
3419 }
3420 params.push_back(y[i]);
3421 }
3422
3423 for (int i = 0; i < nChan; ++i) {
3424 r1[i] = y[0];
3425 for (int j = 1; j < nDOF; ++j) {
3426 r1[i] += y[j]*xArray[j][i];
3427 }
3428 residual[i] = z1[i] - r1[i];
3429 }
3430
3431 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
3432 break;
3433 } else {
3434 double stdDev = 0.0;
3435 for (int i = 0; i < nChan; ++i) {
3436 stdDev += residual[i]*residual[i]*(double)maskArray[i];
3437 }
3438 stdDev = sqrt(stdDev/(double)nData);
3439
3440 double thres = stdDev * thresClip;
3441 int newNData = 0;
3442 for (int i = 0; i < nChan; ++i) {
3443 if (abs(residual[i]) >= thres) {
3444 maskArray[i] = 0;
3445 }
3446 if (maskArray[i] > 0) {
3447 newNData++;
3448 }
3449 }
3450 if (newNData == nData) {
3451 break; //no more flag to add. iteration stops.
3452 } else {
3453 nData = newNData;
3454 }
3455 }
3456 }
3457
3458 nClipped = initNData - nData;
3459
3460 std::vector<float> result;
3461 if (getResidual) {
3462 for (int i = 0; i < nChan; ++i) {
3463 result.push_back((float)residual[i]);
3464 }
3465 } else {
3466 for (int i = 0; i < nChan; ++i) {
3467 result.push_back((float)r1[i]);
3468 }
3469 }
3470
3471 return result;
3472}
3473
3474void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
3475{
3476 std::vector<double> dAbcissa = getAbcissa(whichrow);
3477 std::vector<float> abcissa;
3478 for (uInt i = 0; i < dAbcissa.size(); ++i) {
3479 abcissa.push_back((float)dAbcissa[i]);
3480 }
3481 std::vector<float> spec = getSpectrum(whichrow);
3482
3483 fitter.setData(abcissa, spec, mask);
3484 fitter.lfit();
3485}
3486
3487std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
3488{
3489 /****
3490 double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd;
3491 double elapse1 = 0.0;
3492 double elapse2 = 0.0;
3493
3494 ms1TimeStart = mathutil::gettimeofday_sec();
3495 ****/
3496
3497 std::vector<bool> mask = getMask(whichrow);
3498
3499 /****
3500 ms1TimeEnd = mathutil::gettimeofday_sec();
3501 elapse1 = ms1TimeEnd - ms1TimeStart;
3502 std::cout << "ms1 : " << elapse1 << " (sec.)" << endl;
3503 ms2TimeStart = mathutil::gettimeofday_sec();
3504 ****/
3505
3506 uInt maskSize = mask.size();
3507 if (inMask.size() != 0) {
3508 if (maskSize != inMask.size()) {
3509 throw(AipsError("mask sizes are not the same."));
3510 }
3511 for (uInt i = 0; i < maskSize; ++i) {
3512 mask[i] = mask[i] && inMask[i];
3513 }
3514 }
3515
3516 /****
3517 ms2TimeEnd = mathutil::gettimeofday_sec();
3518 elapse2 = ms2TimeEnd - ms2TimeStart;
3519 std::cout << "ms2 : " << elapse2 << " (sec.)" << endl;
3520 ****/
3521
3522 return mask;
3523}
3524
3525/*
3526std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
3527{
3528 int edgeSize = edge.size();
3529 std::vector<int> currentEdge;
3530 if (edgeSize >= 2) {
3531 int idx = 0;
3532 if (edgeSize > 2) {
3533 if (edgeSize < minEdgeSize) {
3534 throw(AipsError("Length of edge element info is less than that of IFs"));
3535 }
3536 idx = 2 * getIF(whichrow);
3537 }
3538 currentEdge.push_back(edge[idx]);
3539 currentEdge.push_back(edge[idx+1]);
3540 } else {
3541 throw(AipsError("Wrong length of edge element"));
3542 }
3543
3544 lineFinder.setData(getSpectrum(whichrow));
3545 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
3546
3547 return lineFinder.getMask();
3548}
3549*/
3550
3551/* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
3552void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter)
3553{
3554 if (outLogger || outTextFile) {
3555 std::vector<float> params = fitter.getParameters();
3556 std::vector<bool> fixed = fitter.getFixedParameters();
3557 float rms = getRms(chanMask, whichrow);
3558 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3559
3560 if (outLogger) {
3561 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3562 ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false) << LogIO::POST ;
3563 }
3564 if (outTextFile) {
3565 ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true) << flush;
3566 }
3567 }
3568}
3569
3570/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
3571void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped)
3572{
3573 if (outLogger || outTextFile) {
3574 /****
3575 double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd;
3576 double elapse1 = 0.0;
3577 double elapse2 = 0.0;
3578
3579 ms1TimeStart = mathutil::gettimeofday_sec();
3580 ****/
3581
3582 float rms = getRms(chanMask, whichrow);
3583
3584 /****
3585 ms1TimeEnd = mathutil::gettimeofday_sec();
3586 elapse1 = ms1TimeEnd - ms1TimeStart;
3587 std::cout << "ot1 : " << elapse1 << " (sec.)" << endl;
3588 ms2TimeStart = mathutil::gettimeofday_sec();
3589 ****/
3590
3591 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3592 std::vector<bool> fixed;
3593 fixed.clear();
3594
3595 if (outLogger) {
3596 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3597 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
3598 }
3599 if (outTextFile) {
3600 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true);// << flush;
3601 }
3602
3603 /****
3604 ms2TimeEnd = mathutil::gettimeofday_sec();
3605 elapse2 = ms2TimeEnd - ms2TimeStart;
3606 std::cout << "ot2 : " << elapse2 << " (sec.)" << endl;
3607 ****/
3608
3609 }
3610}
3611
3612/* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */
3613void Scantable::outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped)
3614{
3615 if (outLogger || outTextFile) {
3616 float rms = getRms(chanMask, whichrow);
3617 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
3618 std::vector<bool> fixed;
3619 fixed.clear();
3620
3621 if (outLogger) {
3622 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
3623 ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false) << LogIO::POST ;
3624 }
3625 if (outTextFile) {
3626 ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true) << flush;
3627 }
3628 }
3629}
3630
3631void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow)
3632{
3633 int idxDelimiter = progressInfo.find(",");
3634 if (idxDelimiter < 0) {
3635 throw(AipsError("wrong value in 'showprogress' parameter")) ;
3636 }
3637 showProgress = (progressInfo.substr(0, idxDelimiter) == "true");
3638 std::istringstream is(progressInfo.substr(idxDelimiter+1));
3639 is >> minNRow;
3640}
3641
3642void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold)
3643{
3644 if (showProgress && (nTotal >= nTotalThreshold)) {
3645 int nInterval = int(floor(double(nTotal)/100.0));
3646 if (nInterval == 0) nInterval++;
3647
3648 if (nProcessed % nInterval == 0) {
3649 printf("\r"); //go to the head of line
3650 printf("\x1b[31m\x1b[1m"); //set red color, highlighted
3651 printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) );
3652 printf("\x1b[39m\x1b[0m"); //set default attributes
3653 fflush(NULL);
3654 }
3655
3656 if (nProcessed == nTotal - 1) {
3657 printf("\r\x1b[K"); //clear
3658 fflush(NULL);
3659 }
3660
3661 }
3662}
3663
3664std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly)
3665{
3666 std::vector<bool> mask = getMask(whichrow);
3667
3668 if (inMask.size() > 0) {
3669 uInt maskSize = mask.size();
3670 if (maskSize != inMask.size()) {
3671 throw(AipsError("mask sizes are not the same."));
3672 }
3673 for (uInt i = 0; i < maskSize; ++i) {
3674 mask[i] = mask[i] && inMask[i];
3675 }
3676 }
3677
3678 Vector<Float> spec = getSpectrum(whichrow);
3679 mathutil::doZeroOrderInterpolation(spec, mask);
3680
3681 FFTServer<Float,Complex> ffts;
3682 Vector<Complex> fftres;
3683 ffts.fft0(fftres, spec);
3684
3685 std::vector<float> res;
3686 float norm = float(2.0/double(spec.size()));
3687
3688 if (getRealImag) {
3689 for (uInt i = 0; i < fftres.size(); ++i) {
3690 res.push_back(real(fftres[i])*norm);
3691 res.push_back(imag(fftres[i])*norm);
3692 }
3693 } else {
3694 for (uInt i = 0; i < fftres.size(); ++i) {
3695 res.push_back(abs(fftres[i])*norm);
3696 if (!getAmplitudeOnly) res.push_back(arg(fftres[i]));
3697 }
3698 }
3699
3700 return res;
3701}
3702
3703
3704float Scantable::getRms(const std::vector<bool>& mask, int whichrow)
3705{
3706 /****
3707 double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd;
3708 double elapse1 = 0.0;
3709 double elapse2 = 0.0;
3710
3711 ms1TimeStart = mathutil::gettimeofday_sec();
3712 ****/
3713
3714 Vector<Float> spec;
3715
3716 specCol_.get(whichrow, spec);
3717
3718 /****
3719 ms1TimeEnd = mathutil::gettimeofday_sec();
3720 elapse1 = ms1TimeEnd - ms1TimeStart;
3721 std::cout << "rm1 : " << elapse1 << " (sec.)" << endl;
3722 ms2TimeStart = mathutil::gettimeofday_sec();
3723 ****/
3724
3725 float mean = 0.0;
3726 float smean = 0.0;
3727 int n = 0;
3728 for (uInt i = 0; i < spec.nelements(); ++i) {
3729 if (mask[i]) {
3730 mean += spec[i];
3731 smean += spec[i]*spec[i];
3732 n++;
3733 }
3734 }
3735
3736 mean /= (float)n;
3737 smean /= (float)n;
3738
3739 /****
3740 ms2TimeEnd = mathutil::gettimeofday_sec();
3741 elapse2 = ms2TimeEnd - ms2TimeStart;
3742 std::cout << "rm2 : " << elapse2 << " (sec.)" << endl;
3743 ****/
3744
3745 return sqrt(smean - mean*mean);
3746}
3747
3748
3749std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const
3750{
3751 ostringstream oss;
3752
3753 if (verbose) {
3754 oss << " Scan[" << getScan(whichrow) << "]";
3755 oss << " Beam[" << getBeam(whichrow) << "]";
3756 oss << " IF[" << getIF(whichrow) << "]";
3757 oss << " Pol[" << getPol(whichrow) << "]";
3758 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
3759 oss << "Fitter range = " << masklist << endl;
3760 oss << "Baseline parameters" << endl;
3761 oss << flush;
3762 }
3763
3764 return String(oss);
3765}
3766
3767std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const
3768{
3769 ostringstream oss;
3770
3771 if (verbose) {
3772 oss << "Results of baseline fit" << endl;
3773 oss << " rms = " << setprecision(6) << rms << endl;
3774 if (nClipped >= 0) {
3775 oss << " Number of clipped channels = " << nClipped << endl;
3776 }
3777 for (int i = 0; i < 60; ++i) {
3778 oss << "-";
3779 }
3780 oss << endl;
3781 oss << flush;
3782 }
3783
3784 return String(oss);
3785}
3786
3787std::string Scantable::formatBaselineParams(const std::vector<float>& params,
3788 const std::vector<bool>& fixed,
3789 float rms,
3790 int nClipped,
3791 const std::string& masklist,
3792 int whichrow,
3793 bool verbose,
3794 int start, int count,
3795 bool resetparamid) const
3796{
3797 int nParam = (int)(params.size());
3798
3799 if (nParam < 1) {
3800 return(" Not fitted");
3801 } else {
3802
3803 ostringstream oss;
3804 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3805
3806 if (start < 0) start = 0;
3807 if (count < 0) count = nParam;
3808 int end = start + count;
3809 if (end > nParam) end = nParam;
3810 int paramidoffset = (resetparamid) ? (-start) : 0;
3811
3812 for (int i = start; i < end; ++i) {
3813 if (i > start) {
3814 oss << ",";
3815 }
3816 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
3817 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
3818 }
3819
3820 oss << endl;
3821 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
3822
3823 return String(oss);
3824 }
3825
3826}
3827
3828 std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose) const
3829{
3830 int nOutParam = (int)(params.size());
3831 int nPiece = (int)(ranges.size()) - 1;
3832
3833 if (nOutParam < 1) {
3834 return(" Not fitted");
3835 } else if (nPiece < 0) {
3836 return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose);
3837 } else if (nPiece < 1) {
3838 return(" Bad count of the piece edge info");
3839 } else if (nOutParam % nPiece != 0) {
3840 return(" Bad count of the output baseline parameters");
3841 } else {
3842
3843 int nParam = nOutParam / nPiece;
3844
3845 ostringstream oss;
3846 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
3847
3848 stringstream ss;
3849 ss << ranges[nPiece] << flush;
3850 int wRange = ss.str().size() * 2 + 5;
3851
3852 for (int i = 0; i < nPiece; ++i) {
3853 ss.str("");
3854 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
3855 oss << left << setw(wRange) << ss.str();
3856 oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, i*nParam, nParam, true);
3857 }
3858
3859 oss << formatBaselineParamsFooter(rms, nClipped, verbose);
3860
3861 return String(oss);
3862 }
3863
3864}
3865
3866bool Scantable::hasSameNchanOverIFs()
3867{
3868 int nIF = nif(-1);
3869 int nCh;
3870 int totalPositiveNChan = 0;
3871 int nPositiveNChan = 0;
3872
3873 for (int i = 0; i < nIF; ++i) {
3874 nCh = nchan(i);
3875 if (nCh > 0) {
3876 totalPositiveNChan += nCh;
3877 nPositiveNChan++;
3878 }
3879 }
3880
3881 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
3882}
3883
3884std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
3885{
3886 if (mask.size() <= 0) {
3887 throw(AipsError("The mask elements should be > 0"));
3888 }
3889 int IF = getIF(whichrow);
3890 if (mask.size() != (uInt)nchan(IF)) {
3891 throw(AipsError("Number of channels in scantable != number of mask elements"));
3892 }
3893
3894 if (verbose) {
3895 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
3896 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
3897 if (!hasSameNchan) {
3898 logOs << endl << "This mask is only valid for IF=" << IF;
3899 }
3900 logOs << LogIO::POST;
3901 }
3902
3903 std::vector<double> abcissa = getAbcissa(whichrow);
3904 std::vector<int> edge = getMaskEdgeIndices(mask);
3905
3906 ostringstream oss;
3907 oss.setf(ios::fixed);
3908 oss << setprecision(1) << "[";
3909 for (uInt i = 0; i < edge.size(); i+=2) {
3910 if (i > 0) oss << ",";
3911 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
3912 }
3913 oss << "]" << flush;
3914
3915 return String(oss);
3916}
3917
3918std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
3919{
3920 if (mask.size() <= 0) {
3921 throw(AipsError("The mask elements should be > 0"));
3922 }
3923
3924 std::vector<int> out, startIndices, endIndices;
3925 int maskSize = mask.size();
3926
3927 startIndices.clear();
3928 endIndices.clear();
3929
3930 if (mask[0]) {
3931 startIndices.push_back(0);
3932 }
3933 for (int i = 1; i < maskSize; ++i) {
3934 if ((!mask[i-1]) && mask[i]) {
3935 startIndices.push_back(i);
3936 } else if (mask[i-1] && (!mask[i])) {
3937 endIndices.push_back(i-1);
3938 }
3939 }
3940 if (mask[maskSize-1]) {
3941 endIndices.push_back(maskSize-1);
3942 }
3943
3944 if (startIndices.size() != endIndices.size()) {
3945 throw(AipsError("Inconsistent Mask Size: bad data?"));
3946 }
3947 for (uInt i = 0; i < startIndices.size(); ++i) {
3948 if (startIndices[i] > endIndices[i]) {
3949 throw(AipsError("Mask start index > mask end index"));
3950 }
3951 }
3952
3953 out.clear();
3954 for (uInt i = 0; i < startIndices.size(); ++i) {
3955 out.push_back(startIndices[i]);
3956 out.push_back(endIndices[i]);
3957 }
3958
3959 return out;
3960}
3961
3962vector<float> Scantable::getTsysSpectrum( int whichrow ) const
3963{
3964 Vector<Float> tsys( tsysCol_(whichrow) ) ;
3965 vector<float> stlTsys ;
3966 tsys.tovector( stlTsys ) ;
3967 return stlTsys ;
3968}
3969
3970vector<uint> Scantable::getMoleculeIdColumnData() const
3971{
3972 Vector<uInt> molIds(mmolidCol_.getColumn());
3973 vector<uint> res;
3974 molIds.tovector(res);
3975 return res;
3976}
3977
3978void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids)
3979{
3980 Vector<uInt> molIds(molids);
3981 Vector<uInt> arr(mmolidCol_.getColumn());
3982 if ( molIds.nelements() != arr.nelements() )
3983 throw AipsError("The input data size must be the number of rows.");
3984 mmolidCol_.putColumn(molIds);
3985}
3986
3987
3988}
3989//namespace asap
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