source: trunk/src/Scantable.cpp@ 2080

Last change on this file since 2080 was 2080, checked in by Takeshi Nakazato, 14 years ago

New Development: No

JIRA Issue: No

Ready for Test: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

Put in Release Notes: Yes/No

Module(s): Module Names change impacts.

Description: Describe your changes here...

Update nBeam, nIF, nPol, and nChan table keywords when any selection
is applied.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 86.5 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 <fstream>
14
15#include <casa/aips.h>
16#include <casa/iostream.h>
17#include <casa/iomanip.h>
18#include <casa/OS/Path.h>
19#include <casa/OS/File.h>
20#include <casa/Arrays/Array.h>
21#include <casa/Arrays/ArrayMath.h>
22#include <casa/Arrays/MaskArrMath.h>
23#include <casa/Arrays/ArrayLogical.h>
24#include <casa/Arrays/ArrayAccessor.h>
25#include <casa/Arrays/Vector.h>
26#include <casa/Arrays/VectorSTLIterator.h>
27#include <casa/Arrays/Slice.h>
28#include <casa/BasicMath/Math.h>
29#include <casa/BasicSL/Constants.h>
30#include <casa/Quanta/MVAngle.h>
31#include <casa/Containers/RecordField.h>
32#include <casa/Utilities/GenSort.h>
33#include <casa/Logging/LogIO.h>
34
35#include <tables/Tables/TableParse.h>
36#include <tables/Tables/TableDesc.h>
37#include <tables/Tables/TableCopy.h>
38#include <tables/Tables/SetupNewTab.h>
39#include <tables/Tables/ScaColDesc.h>
40#include <tables/Tables/ArrColDesc.h>
41#include <tables/Tables/TableRow.h>
42#include <tables/Tables/TableVector.h>
43#include <tables/Tables/TableIter.h>
44
45#include <tables/Tables/ExprNode.h>
46#include <tables/Tables/TableRecord.h>
47#include <casa/Quanta/MVTime.h>
48#include <casa/Quanta/MVAngle.h>
49#include <measures/Measures/MeasRef.h>
50#include <measures/Measures/MeasTable.h>
51// needed to avoid error in .tcc
52#include <measures/Measures/MCDirection.h>
53//
54#include <measures/Measures/MDirection.h>
55#include <measures/Measures/MFrequency.h>
56#include <measures/Measures/MEpoch.h>
57#include <measures/TableMeasures/TableMeasRefDesc.h>
58#include <measures/TableMeasures/TableMeasValueDesc.h>
59#include <measures/TableMeasures/TableMeasDesc.h>
60#include <measures/TableMeasures/ScalarMeasColumn.h>
61#include <coordinates/Coordinates/CoordinateUtil.h>
62
63#include <atnf/PKSIO/SrcType.h>
64#include "Scantable.h"
65#include "STPolLinear.h"
66#include "STPolCircular.h"
67#include "STPolStokes.h"
68#include "STAttr.h"
69#include "STLineFinder.h"
70#include "MathUtils.h"
71
72using namespace casa;
73
74namespace asap {
75
76std::map<std::string, STPol::STPolFactory *> Scantable::factories_;
77
78void Scantable::initFactories() {
79 if ( factories_.empty() ) {
80 Scantable::factories_["linear"] = &STPolLinear::myFactory;
81 Scantable::factories_["circular"] = &STPolCircular::myFactory;
82 Scantable::factories_["stokes"] = &STPolStokes::myFactory;
83 }
84}
85
86Scantable::Scantable(Table::TableType ttype) :
87 type_(ttype)
88{
89 initFactories();
90 setupMainTable();
91 freqTable_ = STFrequencies(*this);
92 table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
93 weatherTable_ = STWeather(*this);
94 table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
95 focusTable_ = STFocus(*this);
96 table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
97 tcalTable_ = STTcal(*this);
98 table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
99 moleculeTable_ = STMolecules(*this);
100 table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
101 historyTable_ = STHistory(*this);
102 table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table());
103 fitTable_ = STFit(*this);
104 table_.rwKeywordSet().defineTable("FIT", fitTable_.table());
105 table_.tableInfo().setType( "Scantable" ) ;
106 originalTable_ = table_;
107 attach();
108}
109
110Scantable::Scantable(const std::string& name, Table::TableType ttype) :
111 type_(ttype)
112{
113 initFactories();
114
115 Table tab(name, Table::Update);
116 uInt version = tab.keywordSet().asuInt("VERSION");
117 if (version != version_) {
118 throw(AipsError("Unsupported version of ASAP file."));
119 }
120 if ( type_ == Table::Memory ) {
121 table_ = tab.copyToMemoryTable(generateName());
122 } else {
123 table_ = tab;
124 }
125 table_.tableInfo().setType( "Scantable" ) ;
126
127 attachSubtables();
128 originalTable_ = table_;
129 attach();
130}
131/*
132Scantable::Scantable(const std::string& name, Table::TableType ttype) :
133 type_(ttype)
134{
135 initFactories();
136 Table tab(name, Table::Update);
137 uInt version = tab.keywordSet().asuInt("VERSION");
138 if (version != version_) {
139 throw(AipsError("Unsupported version of ASAP file."));
140 }
141 if ( type_ == Table::Memory ) {
142 table_ = tab.copyToMemoryTable(generateName());
143 } else {
144 table_ = tab;
145 }
146
147 attachSubtables();
148 originalTable_ = table_;
149 attach();
150}
151*/
152
153Scantable::Scantable( const Scantable& other, bool clear )
154{
155 // with or without data
156 String newname = String(generateName());
157 type_ = other.table_.tableType();
158 if ( other.table_.tableType() == Table::Memory ) {
159 if ( clear ) {
160 table_ = TableCopy::makeEmptyMemoryTable(newname,
161 other.table_, True);
162 } else
163 table_ = other.table_.copyToMemoryTable(newname);
164 } else {
165 other.table_.deepCopy(newname, Table::New, False,
166 other.table_.endianFormat(),
167 Bool(clear));
168 table_ = Table(newname, Table::Update);
169 table_.markForDelete();
170 }
171 table_.tableInfo().setType( "Scantable" ) ;
172 /// @todo reindex SCANNO, recompute nbeam, nif, npol
173 if ( clear ) copySubtables(other);
174 attachSubtables();
175 originalTable_ = table_;
176 attach();
177}
178
179void Scantable::copySubtables(const Scantable& other) {
180 Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
181 TableCopy::copyRows(t, other.freqTable_.table());
182 t = table_.rwKeywordSet().asTable("FOCUS");
183 TableCopy::copyRows(t, other.focusTable_.table());
184 t = table_.rwKeywordSet().asTable("WEATHER");
185 TableCopy::copyRows(t, other.weatherTable_.table());
186 t = table_.rwKeywordSet().asTable("TCAL");
187 TableCopy::copyRows(t, other.tcalTable_.table());
188 t = table_.rwKeywordSet().asTable("MOLECULES");
189 TableCopy::copyRows(t, other.moleculeTable_.table());
190 t = table_.rwKeywordSet().asTable("HISTORY");
191 TableCopy::copyRows(t, other.historyTable_.table());
192 t = table_.rwKeywordSet().asTable("FIT");
193 TableCopy::copyRows(t, other.fitTable_.table());
194}
195
196void Scantable::attachSubtables()
197{
198 freqTable_ = STFrequencies(table_);
199 focusTable_ = STFocus(table_);
200 weatherTable_ = STWeather(table_);
201 tcalTable_ = STTcal(table_);
202 moleculeTable_ = STMolecules(table_);
203 historyTable_ = STHistory(table_);
204 fitTable_ = STFit(table_);
205}
206
207Scantable::~Scantable()
208{
209 //cout << "~Scantable() " << this << endl;
210}
211
212void Scantable::setupMainTable()
213{
214 TableDesc td("", "1", TableDesc::Scratch);
215 td.comment() = "An ASAP Scantable";
216 td.rwKeywordSet().define("VERSION", uInt(version_));
217
218 // n Cycles
219 td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
220 // new index every nBeam x nIF x nPol
221 td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
222
223 td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
224 td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
225 // linear, circular, stokes
226 td.rwKeywordSet().define("POLTYPE", String("linear"));
227 td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
228
229 td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
230 td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
231
232 ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO");
233 refbeamnoColumn.setDefault(Int(-1));
234 td.addColumn(refbeamnoColumn);
235
236 ScalarColumnDesc<uInt> flagrowColumn("FLAGROW");
237 flagrowColumn.setDefault(uInt(0));
238 td.addColumn(flagrowColumn);
239
240 td.addColumn(ScalarColumnDesc<Double>("TIME"));
241 TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
242 TableMeasValueDesc measVal(td, "TIME");
243 TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
244 mepochCol.write(td);
245
246 td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
247
248 td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
249 // Type of source (on=0, off=1, other=-1)
250 ScalarColumnDesc<Int> stypeColumn("SRCTYPE");
251 stypeColumn.setDefault(Int(-1));
252 td.addColumn(stypeColumn);
253 td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
254
255 //The actual Data Vectors
256 td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
257 td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
258 td.addColumn(ArrayColumnDesc<Float>("TSYS"));
259
260 td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
261 IPosition(1,2),
262 ColumnDesc::Direct));
263 TableMeasRefDesc mdirRef(MDirection::J2000); // default
264 TableMeasValueDesc tmvdMDir(td, "DIRECTION");
265 // the TableMeasDesc gives the column a type
266 TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
267 // a uder set table type e.g. GALCTIC, B1950 ...
268 td.rwKeywordSet().define("DIRECTIONREF", String("J2000"));
269 // writing create the measure column
270 mdirCol.write(td);
271 td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
272 td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
273 td.addColumn(ScalarColumnDesc<Float>("OPACITY"));
274
275 td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
276 ScalarColumnDesc<Int> fitColumn("FIT_ID");
277 fitColumn.setDefault(Int(-1));
278 td.addColumn(fitColumn);
279
280 td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
281 td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
282
283 // columns which just get dragged along, as they aren't used in asap
284 td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY"));
285 td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION"));
286 td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION"));
287 td.addColumn(ArrayColumnDesc<Double>("SCANRATE"));
288
289 td.rwKeywordSet().define("OBSMODE", String(""));
290
291 // Now create Table SetUp from the description.
292 SetupNewTable aNewTab(generateName(), td, Table::Scratch);
293 table_ = Table(aNewTab, type_, 0);
294 originalTable_ = table_;
295}
296
297void Scantable::attach()
298{
299 timeCol_.attach(table_, "TIME");
300 srcnCol_.attach(table_, "SRCNAME");
301 srctCol_.attach(table_, "SRCTYPE");
302 specCol_.attach(table_, "SPECTRA");
303 flagsCol_.attach(table_, "FLAGTRA");
304 tsysCol_.attach(table_, "TSYS");
305 cycleCol_.attach(table_,"CYCLENO");
306 scanCol_.attach(table_, "SCANNO");
307 beamCol_.attach(table_, "BEAMNO");
308 ifCol_.attach(table_, "IFNO");
309 polCol_.attach(table_, "POLNO");
310 integrCol_.attach(table_, "INTERVAL");
311 azCol_.attach(table_, "AZIMUTH");
312 elCol_.attach(table_, "ELEVATION");
313 dirCol_.attach(table_, "DIRECTION");
314 fldnCol_.attach(table_, "FIELDNAME");
315 rbeamCol_.attach(table_, "REFBEAMNO");
316
317 mweatheridCol_.attach(table_,"WEATHER_ID");
318 mfitidCol_.attach(table_,"FIT_ID");
319 mfreqidCol_.attach(table_, "FREQ_ID");
320 mtcalidCol_.attach(table_, "TCAL_ID");
321 mfocusidCol_.attach(table_, "FOCUS_ID");
322 mmolidCol_.attach(table_, "MOLECULE_ID");
323
324 //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki)
325 attachAuxColumnDef(flagrowCol_, "FLAGROW", 0);
326
327}
328
329template<class T, class T2>
330void Scantable::attachAuxColumnDef(ScalarColumn<T>& col,
331 const String& colName,
332 const T2& defValue)
333{
334 try {
335 col.attach(table_, colName);
336 } catch (TableError& err) {
337 String errMesg = err.getMesg();
338 if (errMesg == "Table column " + colName + " is unknown") {
339 table_.addColumn(ScalarColumnDesc<T>(colName));
340 col.attach(table_, colName);
341 col.fillColumn(static_cast<T>(defValue));
342 } else {
343 throw;
344 }
345 } catch (...) {
346 throw;
347 }
348}
349
350template<class T, class T2>
351void Scantable::attachAuxColumnDef(ArrayColumn<T>& col,
352 const String& colName,
353 const Array<T2>& defValue)
354{
355 try {
356 col.attach(table_, colName);
357 } catch (TableError& err) {
358 String errMesg = err.getMesg();
359 if (errMesg == "Table column " + colName + " is unknown") {
360 table_.addColumn(ArrayColumnDesc<T>(colName));
361 col.attach(table_, colName);
362
363 int size = 0;
364 ArrayIterator<T2>& it = defValue.begin();
365 while (it != defValue.end()) {
366 ++size;
367 ++it;
368 }
369 IPosition ip(1, size);
370 Array<T>& arr(ip);
371 for (int i = 0; i < size; ++i)
372 arr[i] = static_cast<T>(defValue[i]);
373
374 col.fillColumn(arr);
375 } else {
376 throw;
377 }
378 } catch (...) {
379 throw;
380 }
381}
382
383void Scantable::setHeader(const STHeader& sdh)
384{
385 table_.rwKeywordSet().define("nIF", sdh.nif);
386 table_.rwKeywordSet().define("nBeam", sdh.nbeam);
387 table_.rwKeywordSet().define("nPol", sdh.npol);
388 table_.rwKeywordSet().define("nChan", sdh.nchan);
389 table_.rwKeywordSet().define("Observer", sdh.observer);
390 table_.rwKeywordSet().define("Project", sdh.project);
391 table_.rwKeywordSet().define("Obstype", sdh.obstype);
392 table_.rwKeywordSet().define("AntennaName", sdh.antennaname);
393 table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition);
394 table_.rwKeywordSet().define("Equinox", sdh.equinox);
395 table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref);
396 table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq);
397 table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth);
398 table_.rwKeywordSet().define("UTC", sdh.utc);
399 table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
400 table_.rwKeywordSet().define("Epoch", sdh.epoch);
401 table_.rwKeywordSet().define("POLTYPE", sdh.poltype);
402}
403
404STHeader Scantable::getHeader() const
405{
406 STHeader sdh;
407 table_.keywordSet().get("nBeam",sdh.nbeam);
408 table_.keywordSet().get("nIF",sdh.nif);
409 table_.keywordSet().get("nPol",sdh.npol);
410 table_.keywordSet().get("nChan",sdh.nchan);
411 table_.keywordSet().get("Observer", sdh.observer);
412 table_.keywordSet().get("Project", sdh.project);
413 table_.keywordSet().get("Obstype", sdh.obstype);
414 table_.keywordSet().get("AntennaName", sdh.antennaname);
415 table_.keywordSet().get("AntennaPosition", sdh.antennaposition);
416 table_.keywordSet().get("Equinox", sdh.equinox);
417 table_.keywordSet().get("FreqRefFrame", sdh.freqref);
418 table_.keywordSet().get("FreqRefVal", sdh.reffreq);
419 table_.keywordSet().get("Bandwidth", sdh.bandwidth);
420 table_.keywordSet().get("UTC", sdh.utc);
421 table_.keywordSet().get("FluxUnit", sdh.fluxunit);
422 table_.keywordSet().get("Epoch", sdh.epoch);
423 table_.keywordSet().get("POLTYPE", sdh.poltype);
424 return sdh;
425}
426
427void Scantable::setSourceType( int stype )
428{
429 if ( stype < 0 || stype > 1 )
430 throw(AipsError("Illegal sourcetype."));
431 TableVector<Int> tabvec(table_, "SRCTYPE");
432 tabvec = Int(stype);
433}
434
435bool Scantable::conformant( const Scantable& other )
436{
437 return this->getHeader().conformant(other.getHeader());
438}
439
440
441
442std::string Scantable::formatSec(Double x) const
443{
444 Double xcop = x;
445 MVTime mvt(xcop/24./3600.); // make days
446
447 if (x < 59.95)
448 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s";
449 else if (x < 3599.95)
450 return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" ";
451 else {
452 ostringstream oss;
453 oss << setw(2) << std::right << setprecision(1) << mvt.hour();
454 oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " ";
455 return String(oss);
456 }
457};
458
459std::string Scantable::formatDirection(const MDirection& md) const
460{
461 Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
462 Int prec = 7;
463
464 MVAngle mvLon(t[0]);
465 String sLon = mvLon.string(MVAngle::TIME,prec);
466 uInt tp = md.getRef().getType();
467 if (tp == MDirection::GALACTIC ||
468 tp == MDirection::SUPERGAL ) {
469 sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec);
470 }
471 MVAngle mvLat(t[1]);
472 String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec);
473 return sLon + String(" ") + sLat;
474}
475
476
477std::string Scantable::getFluxUnit() const
478{
479 return table_.keywordSet().asString("FluxUnit");
480}
481
482void Scantable::setFluxUnit(const std::string& unit)
483{
484 String tmp(unit);
485 Unit tU(tmp);
486 if (tU==Unit("K") || tU==Unit("Jy")) {
487 table_.rwKeywordSet().define(String("FluxUnit"), tmp);
488 } else {
489 throw AipsError("Illegal unit - must be compatible with Jy or K");
490 }
491}
492
493void Scantable::setInstrument(const std::string& name)
494{
495 bool throwIt = true;
496 // create an Instrument to see if this is valid
497 STAttr::convertInstrument(name, throwIt);
498 String nameU(name);
499 nameU.upcase();
500 table_.rwKeywordSet().define(String("AntennaName"), nameU);
501}
502
503void Scantable::setFeedType(const std::string& feedtype)
504{
505 if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) {
506 std::string msg = "Illegal feed type "+ feedtype;
507 throw(casa::AipsError(msg));
508 }
509 table_.rwKeywordSet().define(String("POLTYPE"), feedtype);
510}
511
512MPosition Scantable::getAntennaPosition() const
513{
514 Vector<Double> antpos;
515 table_.keywordSet().get("AntennaPosition", antpos);
516 MVPosition mvpos(antpos(0),antpos(1),antpos(2));
517 return MPosition(mvpos);
518}
519
520void Scantable::makePersistent(const std::string& filename)
521{
522 String inname(filename);
523 Path path(inname);
524 /// @todo reindex SCANNO, recompute nbeam, nif, npol
525 inname = path.expandedName();
526 // 2011/03/04 TN
527 // We can comment out this workaround since the essential bug is
528 // fixed in casacore (r20889 in google code).
529 table_.deepCopy(inname, Table::New);
530// // WORKAROUND !!! for Table bug
531// // Remove when fixed in casacore
532// if ( table_.tableType() == Table::Memory && !selector_.empty() ) {
533// Table tab = table_.copyToMemoryTable(generateName());
534// tab.deepCopy(inname, Table::New);
535// tab.markForDelete();
536//
537// } else {
538// table_.deepCopy(inname, Table::New);
539// }
540}
541
542int Scantable::nbeam( int scanno ) const
543{
544 if ( scanno < 0 ) {
545 Int n;
546 table_.keywordSet().get("nBeam",n);
547 return int(n);
548 } else {
549 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
550 Table t = table_(table_.col("SCANNO") == scanno);
551 ROTableRow row(t);
552 const TableRecord& rec = row.get(0);
553 Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO"))
554 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
555 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
556 ROTableVector<uInt> v(subt, "BEAMNO");
557 return int(v.nelements());
558 }
559 return 0;
560}
561
562int Scantable::nif( int scanno ) const
563{
564 if ( scanno < 0 ) {
565 Int n;
566 table_.keywordSet().get("nIF",n);
567 return int(n);
568 } else {
569 // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
570 Table t = table_(table_.col("SCANNO") == scanno);
571 ROTableRow row(t);
572 const TableRecord& rec = row.get(0);
573 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
574 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
575 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
576 if ( subt.nrow() == 0 ) return 0;
577 ROTableVector<uInt> v(subt, "IFNO");
578 return int(v.nelements());
579 }
580 return 0;
581}
582
583int Scantable::npol( int scanno ) const
584{
585 if ( scanno < 0 ) {
586 Int n;
587 table_.keywordSet().get("nPol",n);
588 return n;
589 } else {
590 // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
591 Table t = table_(table_.col("SCANNO") == scanno);
592 ROTableRow row(t);
593 const TableRecord& rec = row.get(0);
594 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
595 && t.col("IFNO") == Int(rec.asuInt("IFNO"))
596 && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
597 if ( subt.nrow() == 0 ) return 0;
598 ROTableVector<uInt> v(subt, "POLNO");
599 return int(v.nelements());
600 }
601 return 0;
602}
603
604int Scantable::ncycle( int scanno ) const
605{
606 if ( scanno < 0 ) {
607 Block<String> cols(2);
608 cols[0] = "SCANNO";
609 cols[1] = "CYCLENO";
610 TableIterator it(table_, cols);
611 int n = 0;
612 while ( !it.pastEnd() ) {
613 ++n;
614 ++it;
615 }
616 return n;
617 } else {
618 Table t = table_(table_.col("SCANNO") == scanno);
619 ROTableRow row(t);
620 const TableRecord& rec = row.get(0);
621 Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
622 && t.col("POLNO") == Int(rec.asuInt("POLNO"))
623 && t.col("IFNO") == Int(rec.asuInt("IFNO")) );
624 if ( subt.nrow() == 0 ) return 0;
625 return int(subt.nrow());
626 }
627 return 0;
628}
629
630
631int Scantable::nrow( int scanno ) const
632{
633 return int(table_.nrow());
634}
635
636int Scantable::nchan( int ifno ) const
637{
638 if ( ifno < 0 ) {
639 Int n;
640 table_.keywordSet().get("nChan",n);
641 return int(n);
642 } else {
643 // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't
644 // vary with these
645 Table t = table_(table_.col("IFNO") == ifno);
646 if ( t.nrow() == 0 ) return 0;
647 ROArrayColumn<Float> v(t, "SPECTRA");
648 return v.shape(0)(0);
649 }
650 return 0;
651}
652
653int Scantable::nscan() const {
654 Vector<uInt> scannos(scanCol_.getColumn());
655 uInt nout = genSort( scannos, Sort::Ascending,
656 Sort::QuickSort|Sort::NoDuplicates );
657 return int(nout);
658}
659
660int Scantable::getChannels(int whichrow) const
661{
662 return specCol_.shape(whichrow)(0);
663}
664
665int Scantable::getBeam(int whichrow) const
666{
667 return beamCol_(whichrow);
668}
669
670std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const
671{
672 Vector<uInt> nos(col.getColumn());
673 uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates );
674 nos.resize(n, True);
675 std::vector<uint> stlout;
676 nos.tovector(stlout);
677 return stlout;
678}
679
680int Scantable::getIF(int whichrow) const
681{
682 return ifCol_(whichrow);
683}
684
685int Scantable::getPol(int whichrow) const
686{
687 return polCol_(whichrow);
688}
689
690std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
691{
692 return formatTime(me, showdate, 0);
693}
694
695std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const
696{
697 MVTime mvt(me.getValue());
698 if (showdate)
699 //mvt.setFormat(MVTime::YMD);
700 mvt.setFormat(MVTime::YMD, prec);
701 else
702 //mvt.setFormat(MVTime::TIME);
703 mvt.setFormat(MVTime::TIME, prec);
704 ostringstream oss;
705 oss << mvt;
706 return String(oss);
707}
708
709void Scantable::calculateAZEL()
710{
711 MPosition mp = getAntennaPosition();
712 MEpoch::ROScalarColumn timeCol(table_, "TIME");
713 ostringstream oss;
714 oss << "Computed azimuth/elevation using " << endl
715 << mp << endl;
716 for (Int i=0; i<nrow(); ++i) {
717 MEpoch me = timeCol(i);
718 MDirection md = getDirection(i);
719 oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md)
720 << endl << " => ";
721 MeasFrame frame(mp, me);
722 Vector<Double> azel =
723 MDirection::Convert(md, MDirection::Ref(MDirection::AZEL,
724 frame)
725 )().getAngle("rad").getValue();
726 azCol_.put(i,Float(azel[0]));
727 elCol_.put(i,Float(azel[1]));
728 oss << "azel: " << azel[0]/C::pi*180.0 << " "
729 << azel[1]/C::pi*180.0 << " (deg)" << endl;
730 }
731 pushLog(String(oss));
732}
733
734void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag)
735{
736 for (uInt i=0; i<table_.nrow(); ++i) {
737 Vector<uChar> flgs = flagsCol_(i);
738 srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs);
739 flagsCol_.put(i, flgs);
740 }
741}
742
743std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag)
744{
745 Vector<uChar> flags;
746 flagsCol_.get(uInt(whichrow), flags);
747 srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags);
748 Vector<Bool> bflag(flags.shape());
749 convertArray(bflag, flags);
750 //bflag = !bflag;
751
752 std::vector<bool> mask;
753 bflag.tovector(mask);
754 return mask;
755}
756
757void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag,
758 Vector<uChar> flgs)
759{
760 Vector<Float> spcs = specCol_(whichrow);
761 uInt nchannel = nchan();
762 if (spcs.nelements() != nchannel) {
763 throw(AipsError("Data has incorrect number of channels"));
764 }
765 uChar userflag = 1 << 7;
766 if (unflag) {
767 userflag = 0 << 7;
768 }
769 if (clipoutside) {
770 for (uInt j = 0; j < nchannel; ++j) {
771 Float spc = spcs(j);
772 if ((spc >= uthres) || (spc <= dthres)) {
773 flgs(j) = userflag;
774 }
775 }
776 } else {
777 for (uInt j = 0; j < nchannel; ++j) {
778 Float spc = spcs(j);
779 if ((spc < uthres) && (spc > dthres)) {
780 flgs(j) = userflag;
781 }
782 }
783 }
784}
785
786
787void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) {
788 std::vector<bool>::const_iterator it;
789 uInt ntrue = 0;
790 if (whichrow >= int(table_.nrow()) ) {
791 throw(AipsError("Invalid row number"));
792 }
793 for (it = msk.begin(); it != msk.end(); ++it) {
794 if ( *it ) {
795 ntrue++;
796 }
797 }
798 //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
799 if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) )
800 throw(AipsError("Trying to flag whole scantable."));
801 uChar userflag = 1 << 7;
802 if ( unflag ) {
803 userflag = 0 << 7;
804 }
805 if (whichrow > -1 ) {
806 applyChanFlag(uInt(whichrow), msk, userflag);
807 } else {
808 for ( uInt i=0; i<table_.nrow(); ++i) {
809 applyChanFlag(i, msk, userflag);
810 }
811 }
812}
813
814void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval )
815{
816 if (whichrow >= table_.nrow() ) {
817 throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) );
818 }
819 Vector<uChar> flgs = flagsCol_(whichrow);
820 if ( msk.size() == 0 ) {
821 flgs = flagval;
822 flagsCol_.put(whichrow, flgs);
823 return;
824 }
825 if ( int(msk.size()) != nchan() ) {
826 throw(AipsError("Mask has incorrect number of channels."));
827 }
828 if ( flgs.nelements() != msk.size() ) {
829 throw(AipsError("Mask has incorrect number of channels."
830 " Probably varying with IF. Please flag per IF"));
831 }
832 std::vector<bool>::const_iterator it;
833 uInt j = 0;
834 for (it = msk.begin(); it != msk.end(); ++it) {
835 if ( *it ) {
836 flgs(j) = flagval;
837 }
838 ++j;
839 }
840 flagsCol_.put(whichrow, flgs);
841}
842
843void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag)
844{
845 if ( selector_.empty() && (rows.size() == table_.nrow()) )
846 throw(AipsError("Trying to flag whole scantable."));
847
848 uInt rowflag = (unflag ? 0 : 1);
849 std::vector<uInt>::const_iterator it;
850 for (it = rows.begin(); it != rows.end(); ++it)
851 flagrowCol_.put(*it, rowflag);
852}
853
854std::vector<bool> Scantable::getMask(int whichrow) const
855{
856 Vector<uChar> flags;
857 flagsCol_.get(uInt(whichrow), flags);
858 Vector<Bool> bflag(flags.shape());
859 convertArray(bflag, flags);
860 bflag = !bflag;
861 std::vector<bool> mask;
862 bflag.tovector(mask);
863 return mask;
864}
865
866std::vector<float> Scantable::getSpectrum( int whichrow,
867 const std::string& poltype ) const
868{
869 String ptype = poltype;
870 if (poltype == "" ) ptype = getPolType();
871 if ( whichrow < 0 || whichrow >= nrow() )
872 throw(AipsError("Illegal row number."));
873 std::vector<float> out;
874 Vector<Float> arr;
875 uInt requestedpol = polCol_(whichrow);
876 String basetype = getPolType();
877 if ( ptype == basetype ) {
878 specCol_.get(whichrow, arr);
879 } else {
880 CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_,
881 basetype));
882 uInt row = uInt(whichrow);
883 stpol->setSpectra(getPolMatrix(row));
884 Float fang,fhand;
885 fang = focusTable_.getTotalAngle(mfocusidCol_(row));
886 fhand = focusTable_.getFeedHand(mfocusidCol_(row));
887 stpol->setPhaseCorrections(fang, fhand);
888 arr = stpol->getSpectrum(requestedpol, ptype);
889 }
890 if ( arr.nelements() == 0 )
891 pushLog("Not enough polarisations present to do the conversion.");
892 arr.tovector(out);
893 return out;
894}
895
896void Scantable::setSpectrum( const std::vector<float>& spec,
897 int whichrow )
898{
899 Vector<Float> spectrum(spec);
900 Vector<Float> arr;
901 specCol_.get(whichrow, arr);
902 if ( spectrum.nelements() != arr.nelements() )
903 throw AipsError("The spectrum has incorrect number of channels.");
904 specCol_.put(whichrow, spectrum);
905}
906
907
908String Scantable::generateName()
909{
910 return (File::newUniqueName("./","temp")).baseName();
911}
912
913const casa::Table& Scantable::table( ) const
914{
915 return table_;
916}
917
918casa::Table& Scantable::table( )
919{
920 return table_;
921}
922
923std::string Scantable::getPolType() const
924{
925 return table_.keywordSet().asString("POLTYPE");
926}
927
928void Scantable::unsetSelection()
929{
930 table_ = originalTable_;
931 attach();
932 selector_.reset();
933}
934
935void Scantable::setSelection( const STSelector& selection )
936{
937 Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
938 if ( tab.nrow() == 0 ) {
939 throw(AipsError("Selection contains no data. Not applying it."));
940 }
941 table_ = tab;
942 attach();
943 tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ;
944 vector<uint> selectedIFs = getIFNos() ;
945 Int newnIF = selectedIFs.size() ;
946 tab.rwKeywordSet().define("nIF",newnIF) ;
947 if ( newnIF != 0 ) {
948 Int newnChan = 0 ;
949 for ( Int i = 0 ; i < newnIF ; i++ ) {
950 Int nChan = nchan( selectedIFs[i] ) ;
951 if ( newnChan > nChan )
952 newnChan = nChan ;
953 }
954 tab.rwKeywordSet().define("nChan",newnChan) ;
955 }
956 tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ;
957 selector_ = selection;
958}
959
960std::string Scantable::summary( bool verbose )
961{
962 // Format header info
963 ostringstream oss;
964 oss << endl;
965 oss << asap::SEPERATOR << endl;
966 oss << " Scan Table Summary" << endl;
967 oss << asap::SEPERATOR << endl;
968 oss.flags(std::ios_base::left);
969 oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
970 << setw(15) << "IFs:" << setw(4) << nif() << endl
971 << setw(15) << "Polarisations:" << setw(4) << npol()
972 << "(" << getPolType() << ")" << endl
973 << setw(15) << "Channels:" << nchan() << endl;
974 String tmp;
975 oss << setw(15) << "Observer:"
976 << table_.keywordSet().asString("Observer") << endl;
977 oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
978 table_.keywordSet().get("Project", tmp);
979 oss << setw(15) << "Project:" << tmp << endl;
980 table_.keywordSet().get("Obstype", tmp);
981 oss << setw(15) << "Obs. Type:" << tmp << endl;
982 table_.keywordSet().get("AntennaName", tmp);
983 oss << setw(15) << "Antenna Name:" << tmp << endl;
984 table_.keywordSet().get("FluxUnit", tmp);
985 oss << setw(15) << "Flux Unit:" << tmp << endl;
986 //Vector<Double> vec(moleculeTable_.getRestFrequencies());
987 int nid = moleculeTable_.nrow();
988 Bool firstline = True;
989 oss << setw(15) << "Rest Freqs:";
990 for (int i=0; i<nid; i++) {
991 Table t = table_(table_.col("MOLECULE_ID") == i);
992 if (t.nrow() > 0) {
993 Vector<Double> vec(moleculeTable_.getRestFrequency(i));
994 if (vec.nelements() > 0) {
995 if (firstline) {
996 oss << setprecision(10) << vec << " [Hz]" << endl;
997 firstline=False;
998 }
999 else{
1000 oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl;
1001 }
1002 } else {
1003 oss << "none" << endl;
1004 }
1005 }
1006 }
1007
1008 oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl;
1009 oss << selector_.print() << endl;
1010 oss << endl;
1011 // main table
1012 String dirtype = "Position ("
1013 + getDirectionRefString()
1014 + ")";
1015 oss << setw(5) << "Scan" << setw(15) << "Source"
1016 << setw(10) << "Time" << setw(18) << "Integration"
1017 << setw(15) << "Source Type" << endl;
1018 oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl;
1019 oss << setw(10) << "" << setw(3) << "IF" << setw(3) << ""
1020 << setw(8) << "Frame" << setw(16)
1021 << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment"
1022 << setw(7) << "Channels"
1023 << endl;
1024 oss << asap::SEPERATOR << endl;
1025 TableIterator iter(table_, "SCANNO");
1026 while (!iter.pastEnd()) {
1027 Table subt = iter.table();
1028 ROTableRow row(subt);
1029 MEpoch::ROScalarColumn timeCol(subt,"TIME");
1030 const TableRecord& rec = row.get(0);
1031 oss << setw(4) << std::right << rec.asuInt("SCANNO")
1032 << std::left << setw(1) << ""
1033 << setw(15) << rec.asString("SRCNAME")
1034 << setw(10) << formatTime(timeCol(0), false);
1035 // count the cycles in the scan
1036 TableIterator cyciter(subt, "CYCLENO");
1037 int nint = 0;
1038 while (!cyciter.pastEnd()) {
1039 ++nint;
1040 ++cyciter;
1041 }
1042 oss << setw(3) << std::right << nint << setw(3) << " x " << std::left
1043 << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << ""
1044 << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl;
1045
1046 TableIterator biter(subt, "BEAMNO");
1047 while (!biter.pastEnd()) {
1048 Table bsubt = biter.table();
1049 ROTableRow brow(bsubt);
1050 const TableRecord& brec = brow.get(0);
1051 uInt row0 = bsubt.rowNumbers(table_)[0];
1052 oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left;
1053 oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl;
1054 TableIterator iiter(bsubt, "IFNO");
1055 while (!iiter.pastEnd()) {
1056 Table isubt = iiter.table();
1057 ROTableRow irow(isubt);
1058 const TableRecord& irec = irow.get(0);
1059 oss << setw(9) << "";
1060 oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left
1061 << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID"))
1062 << setw(3) << "" << nchan(irec.asuInt("IFNO"))
1063 << endl;
1064
1065 ++iiter;
1066 }
1067 ++biter;
1068 }
1069 ++iter;
1070 }
1071 /// @todo implement verbose mode
1072 return String(oss);
1073}
1074
1075// std::string Scantable::getTime(int whichrow, bool showdate) const
1076// {
1077// MEpoch::ROScalarColumn timeCol(table_, "TIME");
1078// MEpoch me;
1079// if (whichrow > -1) {
1080// me = timeCol(uInt(whichrow));
1081// } else {
1082// Double tm;
1083// table_.keywordSet().get("UTC",tm);
1084// me = MEpoch(MVEpoch(tm));
1085// }
1086// return formatTime(me, showdate);
1087// }
1088
1089std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const
1090{
1091 MEpoch me;
1092 me = getEpoch(whichrow);
1093 return formatTime(me, showdate, prec);
1094}
1095
1096MEpoch Scantable::getEpoch(int whichrow) const
1097{
1098 if (whichrow > -1) {
1099 return timeCol_(uInt(whichrow));
1100 } else {
1101 Double tm;
1102 table_.keywordSet().get("UTC",tm);
1103 return MEpoch(MVEpoch(tm));
1104 }
1105}
1106
1107std::string Scantable::getDirectionString(int whichrow) const
1108{
1109 return formatDirection(getDirection(uInt(whichrow)));
1110}
1111
1112
1113SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const {
1114 const MPosition& mp = getAntennaPosition();
1115 const MDirection& md = getDirection(whichrow);
1116 const MEpoch& me = timeCol_(whichrow);
1117 //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1118 Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1119 return freqTable_.getSpectralCoordinate(md, mp, me, rf,
1120 mfreqidCol_(whichrow));
1121}
1122
1123std::vector< double > Scantable::getAbcissa( int whichrow ) const
1124{
1125 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number"));
1126 std::vector<double> stlout;
1127 int nchan = specCol_(whichrow).nelements();
1128 String us = freqTable_.getUnitString();
1129 if ( us == "" || us == "pixel" || us == "channel" ) {
1130 for (int i=0; i<nchan; ++i) {
1131 stlout.push_back(double(i));
1132 }
1133 return stlout;
1134 }
1135 SpectralCoordinate spc = getSpectralCoordinate(whichrow);
1136 Vector<Double> pixel(nchan);
1137 Vector<Double> world;
1138 indgen(pixel);
1139 if ( Unit(us) == Unit("Hz") ) {
1140 for ( int i=0; i < nchan; ++i) {
1141 Double world;
1142 spc.toWorld(world, pixel[i]);
1143 stlout.push_back(double(world));
1144 }
1145 } else if ( Unit(us) == Unit("km/s") ) {
1146 Vector<Double> world;
1147 spc.pixelToVelocity(world, pixel);
1148 world.tovector(stlout);
1149 }
1150 return stlout;
1151}
1152void Scantable::setDirectionRefString( const std::string & refstr )
1153{
1154 MDirection::Types mdt;
1155 if (refstr != "" && !MDirection::getType(mdt, refstr)) {
1156 throw(AipsError("Illegal Direction frame."));
1157 }
1158 if ( refstr == "" ) {
1159 String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType());
1160 table_.rwKeywordSet().define("DIRECTIONREF", defaultstr);
1161 } else {
1162 table_.rwKeywordSet().define("DIRECTIONREF", String(refstr));
1163 }
1164}
1165
1166std::string Scantable::getDirectionRefString( ) const
1167{
1168 return table_.keywordSet().asString("DIRECTIONREF");
1169}
1170
1171MDirection Scantable::getDirection(int whichrow ) const
1172{
1173 String usertype = table_.keywordSet().asString("DIRECTIONREF");
1174 String type = MDirection::showType(dirCol_.getMeasRef().getType());
1175 if ( usertype != type ) {
1176 MDirection::Types mdt;
1177 if (!MDirection::getType(mdt, usertype)) {
1178 throw(AipsError("Illegal Direction frame."));
1179 }
1180 return dirCol_.convert(uInt(whichrow), mdt);
1181 } else {
1182 return dirCol_(uInt(whichrow));
1183 }
1184}
1185
1186std::string Scantable::getAbcissaLabel( int whichrow ) const
1187{
1188 if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number"));
1189 const MPosition& mp = getAntennaPosition();
1190 const MDirection& md = getDirection(whichrow);
1191 const MEpoch& me = timeCol_(whichrow);
1192 //const Double& rf = mmolidCol_(whichrow);
1193 const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow));
1194 SpectralCoordinate spc =
1195 freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow));
1196
1197 String s = "Channel";
1198 Unit u = Unit(freqTable_.getUnitString());
1199 if (u == Unit("km/s")) {
1200 s = CoordinateUtil::axisLabel(spc, 0, True,True, True);
1201 } else if (u == Unit("Hz")) {
1202 Vector<String> wau(1);wau = u.getName();
1203 spc.setWorldAxisUnits(wau);
1204 s = CoordinateUtil::axisLabel(spc, 0, True, True, False);
1205 }
1206 return s;
1207
1208}
1209
1210/**
1211void asap::Scantable::setRestFrequencies( double rf, const std::string& name,
1212 const std::string& unit )
1213**/
1214void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name,
1215 const std::string& unit )
1216
1217{
1218 ///@todo lookup in line table to fill in name and formattedname
1219 Unit u(unit);
1220 //Quantum<Double> urf(rf, u);
1221 Quantum<Vector<Double> >urf(rf, u);
1222 Vector<String> formattedname(0);
1223 //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl;
1224
1225 //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, "");
1226 uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname);
1227 TableVector<uInt> tabvec(table_, "MOLECULE_ID");
1228 tabvec = id;
1229}
1230
1231/**
1232void asap::Scantable::setRestFrequencies( const std::string& name )
1233{
1234 throw(AipsError("setRestFrequencies( const std::string& name ) NYI"));
1235 ///@todo implement
1236}
1237**/
1238
1239void Scantable::setRestFrequencies( const vector<std::string>& name )
1240{
1241 throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI"));
1242 ///@todo implement
1243}
1244
1245std::vector< unsigned int > Scantable::rownumbers( ) const
1246{
1247 std::vector<unsigned int> stlout;
1248 Vector<uInt> vec = table_.rowNumbers();
1249 vec.tovector(stlout);
1250 return stlout;
1251}
1252
1253
1254Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const
1255{
1256 ROTableRow row(table_);
1257 const TableRecord& rec = row.get(whichrow);
1258 Table t =
1259 originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO"))
1260 && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO"))
1261 && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO"))
1262 && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) );
1263 ROArrayColumn<Float> speccol(t, "SPECTRA");
1264 return speccol.getColumn();
1265}
1266
1267std::vector< std::string > Scantable::columnNames( ) const
1268{
1269 Vector<String> vec = table_.tableDesc().columnNames();
1270 return mathutil::tovectorstring(vec);
1271}
1272
1273MEpoch::Types Scantable::getTimeReference( ) const
1274{
1275 return MEpoch::castType(timeCol_.getMeasRef().getType());
1276}
1277
1278void Scantable::addFit( const STFitEntry& fit, int row )
1279{
1280 //cout << mfitidCol_(uInt(row)) << endl;
1281 LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ;
1282 os << mfitidCol_(uInt(row)) << LogIO::POST ;
1283 uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row)));
1284 mfitidCol_.put(uInt(row), id);
1285}
1286
1287void Scantable::shift(int npix)
1288{
1289 Vector<uInt> fids(mfreqidCol_.getColumn());
1290 genSort( fids, Sort::Ascending,
1291 Sort::QuickSort|Sort::NoDuplicates );
1292 for (uInt i=0; i<fids.nelements(); ++i) {
1293 frequencies().shiftRefPix(npix, fids[i]);
1294 }
1295}
1296
1297String Scantable::getAntennaName() const
1298{
1299 String out;
1300 table_.keywordSet().get("AntennaName", out);
1301 String::size_type pos1 = out.find("@") ;
1302 String::size_type pos2 = out.find("//") ;
1303 if ( pos2 != String::npos )
1304 out = out.substr(pos2+2,pos1-pos2-2) ;
1305 else if ( pos1 != String::npos )
1306 out = out.substr(0,pos1) ;
1307 return out;
1308}
1309
1310int Scantable::checkScanInfo(const std::vector<int>& scanlist) const
1311{
1312 String tbpath;
1313 int ret = 0;
1314 if ( table_.keywordSet().isDefined("GBT_GO") ) {
1315 table_.keywordSet().get("GBT_GO", tbpath);
1316 Table t(tbpath,Table::Old);
1317 // check each scan if other scan of the pair exist
1318 int nscan = scanlist.size();
1319 for (int i = 0; i < nscan; i++) {
1320 Table subt = t( t.col("SCAN") == scanlist[i]+1 );
1321 if (subt.nrow()==0) {
1322 //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl;
1323 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1324 os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST;
1325 ret = 1;
1326 break;
1327 }
1328 ROTableRow row(subt);
1329 const TableRecord& rec = row.get(0);
1330 int scan1seqn = rec.asuInt("PROCSEQN");
1331 int laston1 = rec.asuInt("LASTON");
1332 if ( rec.asuInt("PROCSIZE")==2 ) {
1333 if ( i < nscan-1 ) {
1334 Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 );
1335 if ( subt2.nrow() == 0) {
1336 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1337
1338 //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl;
1339 os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST;
1340 ret = 1;
1341 break;
1342 }
1343 ROTableRow row2(subt2);
1344 const TableRecord& rec2 = row2.get(0);
1345 int scan2seqn = rec2.asuInt("PROCSEQN");
1346 int laston2 = rec2.asuInt("LASTON");
1347 if (scan1seqn == 1 && scan2seqn == 2) {
1348 if (laston1 == laston2) {
1349 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1350 //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1351 os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1352 i +=1;
1353 }
1354 else {
1355 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1356 //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl;
1357 os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST;
1358 }
1359 }
1360 else if (scan1seqn==2 && scan2seqn == 1) {
1361 if (laston1 == laston2) {
1362 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1363 //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl;
1364 os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST;
1365 ret = 1;
1366 break;
1367 }
1368 }
1369 else {
1370 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1371 //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl;
1372 os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST;
1373 ret = 1;
1374 break;
1375 }
1376 }
1377 }
1378 else {
1379 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1380 //cerr<<"The scan does not appear to be standard obsevation."<<endl;
1381 os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST;
1382 }
1383 //if ( i >= nscan ) break;
1384 }
1385 }
1386 else {
1387 LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ;
1388 //cerr<<"No reference to GBT_GO table."<<endl;
1389 os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST;
1390 ret = 1;
1391 }
1392 return ret;
1393}
1394
1395std::vector<double> Scantable::getDirectionVector(int whichrow) const
1396{
1397 Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue();
1398 std::vector<double> dir;
1399 Dir.tovector(dir);
1400 return dir;
1401}
1402
1403void asap::Scantable::reshapeSpectrum( int nmin, int nmax )
1404 throw( casa::AipsError )
1405{
1406 // assumed that all rows have same nChan
1407 Vector<Float> arr = specCol_( 0 ) ;
1408 int nChan = arr.nelements() ;
1409
1410 // if nmin < 0 or nmax < 0, nothing to do
1411 if ( nmin < 0 ) {
1412 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1413 }
1414 if ( nmax < 0 ) {
1415 throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ;
1416 }
1417
1418 // if nmin > nmax, exchange values
1419 if ( nmin > nmax ) {
1420 int tmp = nmax ;
1421 nmax = nmin ;
1422 nmin = tmp ;
1423 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1424 os << "Swap values. Applied range is ["
1425 << nmin << ", " << nmax << "]" << LogIO::POST ;
1426 }
1427
1428 // if nmin exceeds nChan, nothing to do
1429 if ( nmin >= nChan ) {
1430 throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ;
1431 }
1432
1433 // if nmax exceeds nChan, reset nmax to nChan
1434 if ( nmax >= nChan ) {
1435 if ( nmin == 0 ) {
1436 // nothing to do
1437 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1438 os << "Whole range is selected. Nothing to do." << LogIO::POST ;
1439 return ;
1440 }
1441 else {
1442 LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ;
1443 os << "Specified maximum exceeds nChan. Applied range is ["
1444 << nmin << ", " << nChan-1 << "]." << LogIO::POST ;
1445 nmax = nChan - 1 ;
1446 }
1447 }
1448
1449 // reshape specCol_ and flagCol_
1450 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1451 reshapeSpectrum( nmin, nmax, irow ) ;
1452 }
1453
1454 // update FREQUENCIES subtable
1455 Double refpix ;
1456 Double refval ;
1457 Double increment ;
1458 int freqnrow = freqTable_.table().nrow() ;
1459 Vector<uInt> oldId( freqnrow ) ;
1460 Vector<uInt> newId( freqnrow ) ;
1461 for ( int irow = 0 ; irow < freqnrow ; irow++ ) {
1462 freqTable_.getEntry( refpix, refval, increment, irow ) ;
1463 /***
1464 * need to shift refpix to nmin
1465 * note that channel nmin in old index will be channel 0 in new one
1466 ***/
1467 refval = refval - ( refpix - nmin ) * increment ;
1468 refpix = 0 ;
1469 freqTable_.setEntry( refpix, refval, increment, irow ) ;
1470 }
1471
1472 // update nchan
1473 int newsize = nmax - nmin + 1 ;
1474 table_.rwKeywordSet().define( "nChan", newsize ) ;
1475
1476 // update bandwidth
1477 // assumed all spectra in the scantable have same bandwidth
1478 table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ;
1479
1480 return ;
1481}
1482
1483void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow )
1484{
1485 // reshape specCol_ and flagCol_
1486 Vector<Float> oldspec = specCol_( irow ) ;
1487 Vector<uChar> oldflag = flagsCol_( irow ) ;
1488 uInt newsize = nmax - nmin + 1 ;
1489 specCol_.put( irow, oldspec( Slice( nmin, newsize, 1 ) ) ) ;
1490 flagsCol_.put( irow, oldflag( Slice( nmin, newsize, 1 ) ) ) ;
1491
1492 return ;
1493}
1494
1495void asap::Scantable::regridChannel( int nChan, double dnu )
1496{
1497 LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ;
1498 os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ;
1499 // assumed that all rows have same nChan
1500 Vector<Float> arr = specCol_( 0 ) ;
1501 int oldsize = arr.nelements() ;
1502
1503 // if oldsize == nChan, nothing to do
1504 if ( oldsize == nChan ) {
1505 os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ;
1506 return ;
1507 }
1508
1509 // if oldChan < nChan, unphysical operation
1510 if ( oldsize < nChan ) {
1511 os << "Unphysical operation. Nothing to do." << LogIO::POST ;
1512 return ;
1513 }
1514
1515 // change channel number for specCol_ and flagCol_
1516 Vector<Float> newspec( nChan, 0 ) ;
1517 Vector<uChar> newflag( nChan, false ) ;
1518 vector<string> coordinfo = getCoordInfo() ;
1519 string oldinfo = coordinfo[0] ;
1520 coordinfo[0] = "Hz" ;
1521 setCoordInfo( coordinfo ) ;
1522 for ( int irow = 0 ; irow < nrow() ; irow++ ) {
1523 regridChannel( nChan, dnu, irow ) ;
1524 }
1525 coordinfo[0] = oldinfo ;
1526 setCoordInfo( coordinfo ) ;
1527
1528
1529 // NOTE: this method does not update metadata such as
1530 // FREQUENCIES subtable, nChan, Bandwidth, etc.
1531
1532 return ;
1533}
1534
1535void asap::Scantable::regridChannel( int nChan, double dnu, int irow )
1536{
1537 // logging
1538 //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ;
1539 //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ;
1540
1541 Vector<Float> oldspec = specCol_( irow ) ;
1542 Vector<uChar> oldflag = flagsCol_( irow ) ;
1543 Vector<Float> newspec( nChan, 0 ) ;
1544 Vector<uChar> newflag( nChan, false ) ;
1545
1546 // regrid
1547 vector<double> abcissa = getAbcissa( irow ) ;
1548 int oldsize = abcissa.size() ;
1549 double olddnu = abcissa[1] - abcissa[0] ;
1550 //int refChan = 0 ;
1551 //double frac = 0.0 ;
1552 //double wedge = 0.0 ;
1553 //double pile = 0.0 ;
1554 int ichan = 0 ;
1555 double wsum = 0.0 ;
1556 Vector<Float> z( nChan ) ;
1557 z[0] = abcissa[0] - 0.5 * olddnu + 0.5 * dnu ;
1558 for ( int ii = 1 ; ii < nChan ; ii++ )
1559 z[ii] = z[ii-1] + dnu ;
1560 Vector<Float> zi( nChan+1 ) ;
1561 Vector<Float> yi( oldsize + 1 ) ;
1562 zi[0] = z[0] - 0.5 * dnu ;
1563 zi[1] = z[0] + 0.5 * dnu ;
1564 for ( int ii = 2 ; ii < nChan ; ii++ )
1565 zi[ii] = zi[ii-1] + dnu ;
1566 zi[nChan] = z[nChan-1] + 0.5 * dnu ;
1567 yi[0] = abcissa[0] - 0.5 * olddnu ;
1568 yi[1] = abcissa[1] + 0.5 * olddnu ;
1569 for ( int ii = 2 ; ii < oldsize ; ii++ )
1570 yi[ii] = abcissa[ii-1] + olddnu ;
1571 yi[oldsize] = abcissa[oldsize-1] + 0.5 * olddnu ;
1572 if ( dnu > 0.0 ) {
1573 for ( int ii = 0 ; ii < nChan ; ii++ ) {
1574 double zl = zi[ii] ;
1575 double zr = zi[ii+1] ;
1576 for ( int j = ichan ; j < oldsize ; j++ ) {
1577 double yl = yi[j] ;
1578 double yr = yi[j+1] ;
1579 if ( yl <= zl ) {
1580 if ( yr <= zl ) {
1581 continue ;
1582 }
1583 else if ( yr <= zr ) {
1584 newspec[ii] += oldspec[j] * ( yr - zl ) ;
1585 newflag[ii] = newflag[ii] || oldflag[j] ;
1586 wsum += ( yr - zl ) ;
1587 }
1588 else {
1589 newspec[ii] += oldspec[j] * dnu ;
1590 newflag[ii] = newflag[ii] || oldflag[j] ;
1591 wsum += dnu ;
1592 ichan = j ;
1593 break ;
1594 }
1595 }
1596 else if ( yl < zr ) {
1597 if ( yr <= zr ) {
1598 newspec[ii] += oldspec[j] * ( yr - yl ) ;
1599 newflag[ii] = newflag[ii] || oldflag[j] ;
1600 wsum += ( yr - yl ) ;
1601 }
1602 else {
1603 newspec[ii] += oldspec[j] * ( zr - yl ) ;
1604 newflag[ii] = newflag[ii] || oldflag[j] ;
1605 wsum += ( zr - yl ) ;
1606 ichan = j ;
1607 break ;
1608 }
1609 }
1610 else {
1611 ichan = j - 1 ;
1612 break ;
1613 }
1614 }
1615 newspec[ii] /= wsum ;
1616 wsum = 0.0 ;
1617 }
1618 }
1619 else if ( dnu < 0.0 ) {
1620 for ( int ii = 0 ; ii < nChan ; ii++ ) {
1621 double zl = zi[ii] ;
1622 double zr = zi[ii+1] ;
1623 for ( int j = ichan ; j < oldsize ; j++ ) {
1624 double yl = yi[j] ;
1625 double yr = yi[j+1] ;
1626 if ( yl >= zl ) {
1627 if ( yr >= zl ) {
1628 continue ;
1629 }
1630 else if ( yr >= zr ) {
1631 newspec[ii] += oldspec[j] * abs( yr - zl ) ;
1632 newflag[ii] = newflag[ii] || oldflag[j] ;
1633 wsum += abs( yr - zl ) ;
1634 }
1635 else {
1636 newspec[ii] += oldspec[j] * abs( dnu ) ;
1637 newflag[ii] = newflag[ii] || oldflag[j] ;
1638 wsum += abs( dnu ) ;
1639 ichan = j ;
1640 break ;
1641 }
1642 }
1643 else if ( yl > zr ) {
1644 if ( yr >= zr ) {
1645 newspec[ii] += oldspec[j] * abs( yr - yl ) ;
1646 newflag[ii] = newflag[ii] || oldflag[j] ;
1647 wsum += abs( yr - yl ) ;
1648 }
1649 else {
1650 newspec[ii] += oldspec[j] * abs( zr - yl ) ;
1651 newflag[ii] = newflag[ii] || oldflag[j] ;
1652 wsum += abs( zr - yl ) ;
1653 ichan = j ;
1654 break ;
1655 }
1656 }
1657 else {
1658 ichan = j - 1 ;
1659 break ;
1660 }
1661 }
1662 newspec[ii] /= wsum ;
1663 wsum = 0.0 ;
1664 }
1665 }
1666// * ichan = 0
1667// ***/
1668// //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ;
1669// pile += dnu ;
1670// wedge = olddnu * ( refChan + 1 ) ;
1671// while ( wedge < pile ) {
1672// newspec[0] += olddnu * oldspec[refChan] ;
1673// newflag[0] = newflag[0] || oldflag[refChan] ;
1674// //ofs << "channel " << refChan << " is included in new channel 0" << endl ;
1675// refChan++ ;
1676// wedge += olddnu ;
1677// wsum += olddnu ;
1678// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
1679// }
1680// frac = ( wedge - pile ) / olddnu ;
1681// wsum += ( 1.0 - frac ) * olddnu ;
1682// newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
1683// newflag[0] = newflag[0] || oldflag[refChan] ;
1684// //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ;
1685// //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ;
1686// newspec[0] /= wsum ;
1687// //ofs << "newspec[0] = " << newspec[0] << endl ;
1688// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
1689
1690// /***
1691// * ichan = 1 - nChan-2
1692// ***/
1693// for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) {
1694// pile += dnu ;
1695// newspec[ichan] += frac * olddnu * oldspec[refChan] ;
1696// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
1697// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ;
1698// refChan++ ;
1699// wedge += olddnu ;
1700// wsum = frac * olddnu ;
1701// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
1702// while ( wedge < pile ) {
1703// newspec[ichan] += olddnu * oldspec[refChan] ;
1704// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
1705// //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ;
1706// refChan++ ;
1707// wedge += olddnu ;
1708// wsum += olddnu ;
1709// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
1710// }
1711// frac = ( wedge - pile ) / olddnu ;
1712// wsum += ( 1.0 - frac ) * olddnu ;
1713// newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ;
1714// newflag[ichan] = newflag[ichan] || oldflag[refChan] ;
1715// //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ;
1716// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
1717// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ;
1718// newspec[ichan] /= wsum ;
1719// //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ;
1720// }
1721
1722// /***
1723// * ichan = nChan-1
1724// ***/
1725// // NOTE: Assumed that all spectra have the same bandwidth
1726// pile += dnu ;
1727// newspec[nChan-1] += frac * olddnu * oldspec[refChan] ;
1728// newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ;
1729// //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
1730// refChan++ ;
1731// wedge += olddnu ;
1732// wsum = frac * olddnu ;
1733// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
1734// for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) {
1735// newspec[nChan-1] += olddnu * oldspec[jchan] ;
1736// newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ;
1737// wsum += olddnu ;
1738// //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ;
1739// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
1740// }
1741// //ofs << "wedge = " << wedge << ", pile = " << pile << endl ;
1742// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ;
1743// newspec[nChan-1] /= wsum ;
1744// //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ;
1745
1746// // ofs.close() ;
1747
1748 specCol_.put( irow, newspec ) ;
1749 flagsCol_.put( irow, newflag ) ;
1750
1751 return ;
1752}
1753
1754std::vector<float> Scantable::getWeather(int whichrow) const
1755{
1756 std::vector<float> out(5);
1757 //Float temperature, pressure, humidity, windspeed, windaz;
1758 weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4],
1759 mweatheridCol_(uInt(whichrow)));
1760
1761
1762 return out;
1763}
1764
1765bool Scantable::getFlagtraFast(uInt whichrow)
1766{
1767 uChar flag;
1768 Vector<uChar> flags;
1769 flagsCol_.get(whichrow, flags);
1770 flag = flags[0];
1771 for (uInt i = 1; i < flags.size(); ++i) {
1772 flag &= flags[i];
1773 }
1774 return ((flag >> 7) == 1);
1775}
1776
1777void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool outLogger, const std::string& blfile)
1778{
1779 ofstream ofs;
1780 String coordInfo;
1781 bool hasSameNchan = true;
1782 bool outTextFile = false;
1783
1784 if (blfile != "") {
1785 ofs.open(blfile.c_str(), ios::out | ios::app);
1786 if (ofs) outTextFile = true;
1787 }
1788
1789 if (outLogger || outTextFile) {
1790 coordInfo = getCoordInfo()[0];
1791 if (coordInfo == "") coordInfo = "channel";
1792 hasSameNchan = hasSameNchanOverIFs();
1793 }
1794
1795 Fitter fitter = Fitter();
1796 fitter.setExpression("poly", order);
1797
1798 int nRow = nrow();
1799 std::vector<bool> chanMask;
1800
1801 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
1802 chanMask = getCompositeChanMask(whichrow, mask);
1803 fitBaseline(chanMask, whichrow, fitter);
1804 setSpectrum(fitter.getResidual(), whichrow);
1805 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter);
1806 }
1807
1808 if (outTextFile) ofs.close();
1809}
1810
1811void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile)
1812{
1813 ofstream ofs;
1814 String coordInfo;
1815 bool hasSameNchan = true;
1816 bool outTextFile = false;
1817
1818 if (blfile != "") {
1819 ofs.open(blfile.c_str(), ios::out | ios::app);
1820 if (ofs) outTextFile = true;
1821 }
1822
1823 if (outLogger || outTextFile) {
1824 coordInfo = getCoordInfo()[0];
1825 if (coordInfo == "") coordInfo = "channel";
1826 hasSameNchan = hasSameNchanOverIFs();
1827 }
1828
1829 Fitter fitter = Fitter();
1830 fitter.setExpression("poly", order);
1831
1832 int nRow = nrow();
1833 std::vector<bool> chanMask;
1834 int minEdgeSize = getIFNos().size()*2;
1835 STLineFinder lineFinder = STLineFinder();
1836 lineFinder.setOptions(threshold, 3, chanAvgLimit);
1837
1838 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
1839
1840 //-------------------------------------------------------
1841 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
1842 //-------------------------------------------------------
1843 int edgeSize = edge.size();
1844 std::vector<int> currentEdge;
1845 if (edgeSize >= 2) {
1846 int idx = 0;
1847 if (edgeSize > 2) {
1848 if (edgeSize < minEdgeSize) {
1849 throw(AipsError("Length of edge element info is less than that of IFs"));
1850 }
1851 idx = 2 * getIF(whichrow);
1852 }
1853 currentEdge.push_back(edge[idx]);
1854 currentEdge.push_back(edge[idx+1]);
1855 } else {
1856 throw(AipsError("Wrong length of edge element"));
1857 }
1858 lineFinder.setData(getSpectrum(whichrow));
1859 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
1860 chanMask = lineFinder.getMask();
1861 //-------------------------------------------------------
1862
1863 fitBaseline(chanMask, whichrow, fitter);
1864 setSpectrum(fitter.getResidual(), whichrow);
1865
1866 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter);
1867 }
1868
1869 if (outTextFile) ofs.close();
1870}
1871
1872void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool outLogger, const std::string& blfile) {
1873 ofstream ofs;
1874 String coordInfo;
1875 bool hasSameNchan = true;
1876 bool outTextFile = false;
1877
1878 if (blfile != "") {
1879 ofs.open(blfile.c_str(), ios::out | ios::app);
1880 if (ofs) outTextFile = true;
1881 }
1882
1883 if (outLogger || outTextFile) {
1884 coordInfo = getCoordInfo()[0];
1885 if (coordInfo == "") coordInfo = "channel";
1886 hasSameNchan = hasSameNchanOverIFs();
1887 }
1888
1889 //Fitter fitter = Fitter();
1890 //fitter.setExpression("cspline", nPiece);
1891
1892 int nRow = nrow();
1893 std::vector<bool> chanMask;
1894
1895 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
1896 chanMask = getCompositeChanMask(whichrow, mask);
1897 //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip);
1898 //setSpectrum(fitter.getResidual(), whichrow);
1899 std::vector<int> pieceRanges;
1900 std::vector<float> params;
1901 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, pieceRanges, params, nPiece, thresClip, nIterClip, true);
1902 setSpectrum(res, whichrow);
1903 //
1904
1905 std::vector<bool> fixed;
1906 fixed.clear();
1907 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceRanges, params, fixed);
1908 }
1909
1910 if (outTextFile) ofs.close();
1911}
1912
1913void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile)
1914{
1915 ofstream ofs;
1916 String coordInfo;
1917 bool hasSameNchan = true;
1918 bool outTextFile = false;
1919
1920 if (blfile != "") {
1921 ofs.open(blfile.c_str(), ios::out | ios::app);
1922 if (ofs) outTextFile = true;
1923 }
1924
1925 if (outLogger || outTextFile) {
1926 coordInfo = getCoordInfo()[0];
1927 if (coordInfo == "") coordInfo = "channel";
1928 hasSameNchan = hasSameNchanOverIFs();
1929 }
1930
1931 //Fitter fitter = Fitter();
1932 //fitter.setExpression("cspline", nPiece);
1933
1934 int nRow = nrow();
1935 std::vector<bool> chanMask;
1936 int minEdgeSize = getIFNos().size()*2;
1937 STLineFinder lineFinder = STLineFinder();
1938 lineFinder.setOptions(threshold, 3, chanAvgLimit);
1939
1940 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
1941
1942 //-------------------------------------------------------
1943 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
1944 //-------------------------------------------------------
1945 int edgeSize = edge.size();
1946 std::vector<int> currentEdge;
1947 if (edgeSize >= 2) {
1948 int idx = 0;
1949 if (edgeSize > 2) {
1950 if (edgeSize < minEdgeSize) {
1951 throw(AipsError("Length of edge element info is less than that of IFs"));
1952 }
1953 idx = 2 * getIF(whichrow);
1954 }
1955 currentEdge.push_back(edge[idx]);
1956 currentEdge.push_back(edge[idx+1]);
1957 } else {
1958 throw(AipsError("Wrong length of edge element"));
1959 }
1960 lineFinder.setData(getSpectrum(whichrow));
1961 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
1962 chanMask = lineFinder.getMask();
1963 //-------------------------------------------------------
1964
1965
1966 //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip);
1967 //setSpectrum(fitter.getResidual(), whichrow);
1968 std::vector<int> pieceRanges;
1969 std::vector<float> params;
1970 std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, pieceRanges, params, nPiece, thresClip, nIterClip, true);
1971 setSpectrum(res, whichrow);
1972 //
1973
1974 std::vector<bool> fixed;
1975 fixed.clear();
1976 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceRanges, params, fixed);
1977 }
1978
1979 if (outTextFile) ofs.close();
1980}
1981
1982std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, std::vector<int>& idxEdge, std::vector<float>& params, int nPiece, float thresClip, int nIterClip, bool getResidual) {
1983 if (nPiece < 1) {
1984 throw(AipsError("wrong number of the sections for fitting"));
1985 }
1986 if (data.size() != mask.size()) {
1987 throw(AipsError("data and mask have different size"));
1988 }
1989
1990 int nChan = data.size();
1991 std::vector<int> maskArray;
1992 std::vector<int> x;
1993 for (int i = 0; i < nChan; ++i) {
1994 maskArray.push_back(mask[i] ? 1 : 0);
1995 if (mask[i]) {
1996 x.push_back(i);
1997 }
1998 }
1999
2000 int nData = x.size();
2001 int nElement = (int)(floor(floor((double)(nData/nPiece))+0.5));
2002 std::vector<double> invEdge;
2003
2004 idxEdge.clear();
2005 idxEdge.push_back(x[0]);
2006
2007 for (int i = 1; i < nPiece; ++i) {
2008 int valX = x[nElement*i];
2009 idxEdge.push_back(valX);
2010 invEdge.push_back(1.0/(double)valX);
2011 }
2012
2013 idxEdge.push_back(x[x.size()-1]+1);
2014
2015 std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1;
2016 for (int i = 0; i < nChan; ++i) {
2017 double di = (double)i;
2018 double dD = (double)data[i];
2019 x1.push_back(di);
2020 x2.push_back(di*di);
2021 x3.push_back(di*di*di);
2022 z1.push_back(dD);
2023 x1z1.push_back(dD*di);
2024 x2z1.push_back(dD*di*di);
2025 x3z1.push_back(dD*di*di*di);
2026 r1.push_back(0.0);
2027 }
2028
2029 int currentNData = nData;
2030 int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1).
2031
2032 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
2033 // xMatrix : horizontal concatenation of
2034 // the least-sq. matrix (left) and an
2035 // identity matrix (right).
2036 // the right part is used to calculate the inverse matrix of the left part.
2037 double xMatrix[nDOF][2*nDOF];
2038 double zMatrix[nDOF];
2039 for (int i = 0; i < nDOF; ++i) {
2040 for (int j = 0; j < 2*nDOF; ++j) {
2041 xMatrix[i][j] = 0.0;
2042 }
2043 xMatrix[i][nDOF+i] = 1.0;
2044 zMatrix[i] = 0.0;
2045 }
2046
2047 for (int n = 0; n < nPiece; ++n) {
2048 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2049
2050 if (maskArray[i] == 0) continue;
2051
2052 xMatrix[0][0] += 1.0;
2053 xMatrix[0][1] += x1[i];
2054 xMatrix[0][2] += x2[i];
2055 xMatrix[0][3] += x3[i];
2056 xMatrix[1][1] += x2[i];
2057 xMatrix[1][2] += x3[i];
2058 xMatrix[1][3] += x2[i]*x2[i];
2059 xMatrix[2][2] += x2[i]*x2[i];
2060 xMatrix[2][3] += x3[i]*x2[i];
2061 xMatrix[3][3] += x3[i]*x3[i];
2062 zMatrix[0] += z1[i];
2063 zMatrix[1] += x1z1[i];
2064 zMatrix[2] += x2z1[i];
2065 zMatrix[3] += x3z1[i];
2066
2067 for (int j = 0; j < n; ++j) {
2068 double q = 1.0 - x1[i]*invEdge[j];
2069 q = q*q*q;
2070 xMatrix[0][j+4] += q;
2071 xMatrix[1][j+4] += q*x1[i];
2072 xMatrix[2][j+4] += q*x2[i];
2073 xMatrix[3][j+4] += q*x3[i];
2074 for (int k = 0; k < j; ++k) {
2075 double r = 1.0 - x1[i]*invEdge[k];
2076 r = r*r*r;
2077 xMatrix[k+4][j+4] += r*q;
2078 }
2079 xMatrix[j+4][j+4] += q*q;
2080 zMatrix[j+4] += q*z1[i];
2081 }
2082
2083 }
2084 }
2085
2086 for (int i = 0; i < nDOF; ++i) {
2087 for (int j = 0; j < i; ++j) {
2088 xMatrix[i][j] = xMatrix[j][i];
2089 }
2090 }
2091
2092 std::vector<double> invDiag;
2093 for (int i = 0; i < nDOF; ++i) {
2094 invDiag.push_back(1.0/xMatrix[i][i]);
2095 for (int j = 0; j < nDOF; ++j) {
2096 xMatrix[i][j] *= invDiag[i];
2097 }
2098 }
2099
2100 for (int k = 0; k < nDOF; ++k) {
2101 for (int i = 0; i < nDOF; ++i) {
2102 if (i != k) {
2103 double factor1 = xMatrix[k][k];
2104 double factor2 = xMatrix[i][k];
2105 for (int j = k; j < 2*nDOF; ++j) {
2106 xMatrix[i][j] *= factor1;
2107 xMatrix[i][j] -= xMatrix[k][j]*factor2;
2108 xMatrix[i][j] /= factor1;
2109 }
2110 }
2111 }
2112 double xDiag = xMatrix[k][k];
2113 for (int j = k; j < 2*nDOF; ++j) {
2114 xMatrix[k][j] /= xDiag;
2115 }
2116 }
2117
2118 for (int i = 0; i < nDOF; ++i) {
2119 for (int j = 0; j < nDOF; ++j) {
2120 xMatrix[i][nDOF+j] *= invDiag[j];
2121 }
2122 }
2123 //compute a vector y which consists of the coefficients of the best-fit spline curves
2124 //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of
2125 //cubic terms for the other pieces (in case nPiece>1).
2126 std::vector<double> y;
2127 y.clear();
2128 for (int i = 0; i < nDOF; ++i) {
2129 y.push_back(0.0);
2130 for (int j = 0; j < nDOF; ++j) {
2131 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
2132 }
2133 }
2134
2135 double a0 = y[0];
2136 double a1 = y[1];
2137 double a2 = y[2];
2138 double a3 = y[3];
2139 params.clear();
2140
2141 for (int n = 0; n < nPiece; ++n) {
2142 for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) {
2143 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
2144 }
2145 params.push_back(a0);
2146 params.push_back(a1);
2147 params.push_back(a2);
2148 params.push_back(a3);
2149
2150 if (n == nPiece-1) break;
2151
2152 double d = y[4+n];
2153 double iE = invEdge[n];
2154 a0 += d;
2155 a1 -= 3.0*d*iE;
2156 a2 += 3.0*d*iE*iE;
2157 a3 -= d*iE*iE*iE;
2158 }
2159
2160 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
2161 break;
2162 } else {
2163 std::vector<double> rz;
2164 double stdDev = 0.0;
2165 for (int i = 0; i < nChan; ++i) {
2166 double val = abs(r1[i] - z1[i]);
2167 rz.push_back(val);
2168 stdDev += val*val*(double)maskArray[i];
2169 }
2170 stdDev = sqrt(stdDev/(double)nData);
2171
2172 double thres = stdDev * thresClip;
2173 int newNData = 0;
2174 for (int i = 0; i < nChan; ++i) {
2175 if (rz[i] >= thres) {
2176 maskArray[i] = 0;
2177 }
2178 if (maskArray[i] > 0) {
2179 newNData++;
2180 }
2181 }
2182 if (newNData == currentNData) {
2183 break; //no more flag to add. iteration stops.
2184 } else {
2185 currentNData = newNData;
2186 }
2187 }
2188 }
2189
2190 std::vector<float> result;
2191 if (getResidual) {
2192 for (int i = 0; i < nChan; ++i) {
2193 result.push_back((float)(z1[i] - r1[i]));
2194 }
2195 } else {
2196 for (int i = 0; i < nChan; ++i) {
2197 result.push_back((float)r1[i]);
2198 }
2199 }
2200
2201 return result;
2202}
2203
2204void Scantable::sinusoidBaseline(const std::vector<bool>& mask, int nMinWavesInSW, int nMaxWavesInSW, float thresClip, int nIterClip, bool outLogger, const std::string& blfile) {
2205 ofstream ofs;
2206 String coordInfo;
2207 bool hasSameNchan = true;
2208 bool outTextFile = false;
2209
2210 if (blfile != "") {
2211 ofs.open(blfile.c_str(), ios::out | ios::app);
2212 if (ofs) outTextFile = true;
2213 }
2214
2215 if (outLogger || outTextFile) {
2216 coordInfo = getCoordInfo()[0];
2217 if (coordInfo == "") coordInfo = "channel";
2218 hasSameNchan = hasSameNchanOverIFs();
2219 }
2220
2221 //Fitter fitter = Fitter();
2222 //fitter.setExpression("sinusoid", nMaxWavesInSW);
2223
2224 int nRow = nrow();
2225 std::vector<bool> chanMask;
2226
2227 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2228 chanMask = getCompositeChanMask(whichrow, mask);
2229 //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip);
2230 //setSpectrum(fitter.getResidual(), whichrow);
2231 std::vector<int> pieceRanges;
2232 std::vector<float> params;
2233 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nMinWavesInSW, nMaxWavesInSW, params, thresClip, nIterClip, true);
2234 setSpectrum(res, whichrow);
2235 //
2236
2237 std::vector<bool> fixed;
2238 fixed.clear();
2239 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", pieceRanges, params, fixed);
2240 }
2241
2242 if (outTextFile) ofs.close();
2243}
2244
2245void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, int nMinWavesInSW, int nMaxWavesInSW, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool outLogger, const std::string& blfile)
2246{
2247 ofstream ofs;
2248 String coordInfo;
2249 bool hasSameNchan = true;
2250 bool outTextFile = false;
2251
2252 if (blfile != "") {
2253 ofs.open(blfile.c_str(), ios::out | ios::app);
2254 if (ofs) outTextFile = true;
2255 }
2256
2257 if (outLogger || outTextFile) {
2258 coordInfo = getCoordInfo()[0];
2259 if (coordInfo == "") coordInfo = "channel";
2260 hasSameNchan = hasSameNchanOverIFs();
2261 }
2262
2263 //Fitter fitter = Fitter();
2264 //fitter.setExpression("sinusoid", nMaxWavesInSW);
2265
2266 int nRow = nrow();
2267 std::vector<bool> chanMask;
2268 int minEdgeSize = getIFNos().size()*2;
2269 STLineFinder lineFinder = STLineFinder();
2270 lineFinder.setOptions(threshold, 3, chanAvgLimit);
2271
2272 for (int whichrow = 0; whichrow < nRow; ++whichrow) {
2273
2274 //-------------------------------------------------------
2275 //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder);
2276 //-------------------------------------------------------
2277 int edgeSize = edge.size();
2278 std::vector<int> currentEdge;
2279 if (edgeSize >= 2) {
2280 int idx = 0;
2281 if (edgeSize > 2) {
2282 if (edgeSize < minEdgeSize) {
2283 throw(AipsError("Length of edge element info is less than that of IFs"));
2284 }
2285 idx = 2 * getIF(whichrow);
2286 }
2287 currentEdge.push_back(edge[idx]);
2288 currentEdge.push_back(edge[idx+1]);
2289 } else {
2290 throw(AipsError("Wrong length of edge element"));
2291 }
2292 lineFinder.setData(getSpectrum(whichrow));
2293 lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow);
2294 chanMask = lineFinder.getMask();
2295 //-------------------------------------------------------
2296
2297
2298 //fitBaseline(chanMask, whichrow, fitter, thresClip, nIterClip);
2299 //setSpectrum(fitter.getResidual(), whichrow);
2300 std::vector<int> pieceRanges;
2301 std::vector<float> params;
2302 std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nMinWavesInSW, nMaxWavesInSW, params, thresClip, nIterClip, true);
2303 setSpectrum(res, whichrow);
2304 //
2305
2306 std::vector<bool> fixed;
2307 fixed.clear();
2308 outputFittingResult(outLogger, outTextFile, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", pieceRanges, params, fixed);
2309 }
2310
2311 if (outTextFile) ofs.close();
2312}
2313
2314std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nMinWavesInSW, int nMaxWavesInSW, std::vector<float>& params, float thresClip, int nIterClip, bool getResidual) {
2315 if (data.size() != mask.size()) {
2316 throw(AipsError("data and mask have different size"));
2317 }
2318 if ((nMinWavesInSW < 0) || (nMaxWavesInSW < 0)) {
2319 throw(AipsError("wave number must be positive or zero (i.e. constant)"));
2320 } else {
2321 if (nMaxWavesInSW < nMinWavesInSW) {
2322 int temp = nMaxWavesInSW;
2323 nMaxWavesInSW = nMinWavesInSW;
2324 nMinWavesInSW = temp;
2325 }
2326 }
2327
2328 int nChan = data.size();
2329 std::vector<int> maskArray;
2330 std::vector<int> x;
2331 for (int i = 0; i < nChan; ++i) {
2332 maskArray.push_back(mask[i] ? 1 : 0);
2333 if (mask[i]) {
2334 x.push_back(i);
2335 }
2336 }
2337
2338 int nData = x.size();
2339
2340 std::vector<double> x1, x2, x3, z1, x1z1, x2z1, x3z1, r1;
2341 for (int i = 0; i < nChan; ++i) {
2342 double di = (double)i;
2343 double dD = (double)data[i];
2344 x1.push_back(di);
2345 x2.push_back(di*di);
2346 x3.push_back(di*di*di);
2347 z1.push_back(dD);
2348 x1z1.push_back(di*dD);
2349 x2z1.push_back(di*di*dD);
2350 x3z1.push_back(di*di*di*dD);
2351 r1.push_back(0.0);
2352 }
2353
2354 int currentNData = nData;
2355 int nDOF = nMaxWavesInSW + 1; //number of parameters to solve.
2356
2357 for (int nClip = 0; nClip < nIterClip+1; ++nClip) {
2358 //xMatrix : horizontal concatenation of the least-sq. matrix (left) and an
2359 //identity matrix (right).
2360 //the right part is used to calculate the inverse matrix of the left part.
2361 double xMatrix[nDOF][2*nDOF];
2362 double zMatrix[nDOF];
2363 for (int i = 0; i < nDOF; ++i) {
2364 for (int j = 0; j < 2*nDOF; ++j) {
2365 xMatrix[i][j] = 0.0;
2366 }
2367 xMatrix[i][nDOF+i] = 1.0;
2368 zMatrix[i] = 0.0;
2369 }
2370
2371 for (int i = 0; i < currentNData; ++i) {
2372 if (maskArray[i] == 0) continue;
2373 xMatrix[0][0] += 1.0;
2374 xMatrix[0][1] += x1[i];
2375 xMatrix[0][2] += x2[i];
2376 xMatrix[0][3] += x3[i];
2377 xMatrix[1][1] += x2[i];
2378 xMatrix[1][2] += x3[i];
2379 xMatrix[1][3] += x2[i]*x2[i];
2380 xMatrix[2][2] += x2[i]*x2[i];
2381 xMatrix[2][3] += x3[i]*x2[i];
2382 xMatrix[3][3] += x3[i]*x3[i];
2383 zMatrix[0] += z1[i];
2384 zMatrix[1] += x1z1[i];
2385 zMatrix[2] += x2z1[i];
2386 zMatrix[3] += x3z1[i];
2387 }
2388
2389 for (int i = 0; i < nDOF; ++i) {
2390 for (int j = 0; j < i; ++j) {
2391 xMatrix[i][j] = xMatrix[j][i];
2392 }
2393 }
2394
2395 std::vector<double> invDiag;
2396 for (int i = 0; i < nDOF; ++i) {
2397 invDiag.push_back(1.0/xMatrix[i][i]);
2398 for (int j = 0; j < nDOF; ++j) {
2399 xMatrix[i][j] *= invDiag[i];
2400 }
2401 }
2402
2403 for (int k = 0; k < nDOF; ++k) {
2404 for (int i = 0; i < nDOF; ++i) {
2405 if (i != k) {
2406 double factor1 = xMatrix[k][k];
2407 double factor2 = xMatrix[i][k];
2408 for (int j = k; j < 2*nDOF; ++j) {
2409 xMatrix[i][j] *= factor1;
2410 xMatrix[i][j] -= xMatrix[k][j]*factor2;
2411 xMatrix[i][j] /= factor1;
2412 }
2413 }
2414 }
2415 double xDiag = xMatrix[k][k];
2416 for (int j = k; j < 2*nDOF; ++j) {
2417 xMatrix[k][j] /= xDiag;
2418 }
2419 }
2420
2421 for (int i = 0; i < nDOF; ++i) {
2422 for (int j = 0; j < nDOF; ++j) {
2423 xMatrix[i][nDOF+j] *= invDiag[j];
2424 }
2425 }
2426 //compute a vector y which consists of the coefficients of the sinusoids forming the
2427 //best-fit curves (a0,b0,a1,b1,...), namely, a* and b* are of sine and cosine functions,
2428 //respectively.
2429 std::vector<double> y;
2430 for (int i = 0; i < nDOF; ++i) {
2431 y.push_back(0.0);
2432 for (int j = 0; j < nDOF; ++j) {
2433 y[i] += xMatrix[i][nDOF+j]*zMatrix[j];
2434 }
2435 }
2436
2437 double a0 = y[0];
2438 double a1 = y[1];
2439 double a2 = y[2];
2440 double a3 = y[3];
2441 params.clear();
2442
2443 for (int i = 0; i < nChan; ++i) {
2444 r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i];
2445 }
2446 params.push_back(a0);
2447 params.push_back(a1);
2448 params.push_back(a2);
2449 params.push_back(a3);
2450
2451
2452 if ((nClip == nIterClip) || (thresClip <= 0.0)) {
2453 break;
2454 } else {
2455 std::vector<double> rz;
2456 double stdDev = 0.0;
2457 for (int i = 0; i < nChan; ++i) {
2458 double val = abs(r1[i] - z1[i]);
2459 rz.push_back(val);
2460 stdDev += val*val*(double)maskArray[i];
2461 }
2462 stdDev = sqrt(stdDev/(double)nData);
2463
2464 double thres = stdDev * thresClip;
2465 int newNData = 0;
2466 for (int i = 0; i < nChan; ++i) {
2467 if (rz[i] >= thres) {
2468 maskArray[i] = 0;
2469 }
2470 if (maskArray[i] > 0) {
2471 newNData++;
2472 }
2473 }
2474 if (newNData == currentNData) {
2475 break; //no additional flag. finish iteration.
2476 } else {
2477 currentNData = newNData;
2478 }
2479 }
2480 }
2481
2482 std::vector<float> result;
2483 if (getResidual) {
2484 for (int i = 0; i < nChan; ++i) {
2485 result.push_back((float)(z1[i] - r1[i]));
2486 }
2487 } else {
2488 for (int i = 0; i < nChan; ++i) {
2489 result.push_back((float)r1[i]);
2490 }
2491 }
2492
2493 return result;
2494}
2495
2496void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter)
2497{
2498 std::vector<double> abcsd = getAbcissa(whichrow);
2499 std::vector<float> abcs;
2500 for (uInt i = 0; i < abcsd.size(); ++i) {
2501 abcs.push_back((float)abcsd[i]);
2502 }
2503 std::vector<float> spec = getSpectrum(whichrow);
2504
2505 fitter.setData(abcs, spec, mask);
2506 fitter.lfit();
2507}
2508
2509std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask)
2510{
2511 std::vector<bool> chanMask = getMask(whichrow);
2512 uInt chanMaskSize = chanMask.size();
2513 if (chanMaskSize != inMask.size()) {
2514 throw(AipsError("different mask sizes"));
2515 }
2516 for (uInt i = 0; i < chanMaskSize; ++i) {
2517 chanMask[i] = chanMask[i] && inMask[i];
2518 }
2519
2520 return chanMask;
2521}
2522
2523/*
2524std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder)
2525{
2526 int edgeSize = edge.size();
2527 std::vector<int> currentEdge;
2528 if (edgeSize >= 2) {
2529 int idx = 0;
2530 if (edgeSize > 2) {
2531 if (edgeSize < minEdgeSize) {
2532 throw(AipsError("Length of edge element info is less than that of IFs"));
2533 }
2534 idx = 2 * getIF(whichrow);
2535 }
2536 currentEdge.push_back(edge[idx]);
2537 currentEdge.push_back(edge[idx+1]);
2538 } else {
2539 throw(AipsError("Wrong length of edge element"));
2540 }
2541
2542 lineFinder.setData(getSpectrum(whichrow));
2543 lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow);
2544
2545 return lineFinder.getMask();
2546}
2547*/
2548
2549/* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */
2550void 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) {
2551 if (outLogger || outTextFile) {
2552 std::vector<float> params = fitter.getParameters();
2553 std::vector<bool> fixed = fitter.getFixedParameters();
2554 float rms = getRms(chanMask, whichrow);
2555 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
2556
2557 if (outLogger) {
2558 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
2559 ols << formatBaselineParams(params, fixed, rms, masklist, whichrow, false) << LogIO::POST ;
2560 }
2561 if (outTextFile) {
2562 ofs << formatBaselineParams(params, fixed, rms, masklist, whichrow, true) << flush;
2563 }
2564 }
2565}
2566
2567/* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */
2568void 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 std::vector<bool>& fixed) {
2569 if (outLogger || outTextFile) {
2570 float rms = getRms(chanMask, whichrow);
2571 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
2572
2573 if (outLogger) {
2574 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
2575 ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, masklist, whichrow, false) << LogIO::POST ;
2576 }
2577 if (outTextFile) {
2578 ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, masklist, whichrow, true) << flush;
2579 }
2580 }
2581}
2582
2583/* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */
2584void 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 std::vector<bool>& fixed) {
2585 if (outLogger || outTextFile) {
2586 float rms = getRms(chanMask, whichrow);
2587 String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan);
2588
2589 if (outLogger) {
2590 LogIO ols(LogOrigin("Scantable", funcName, WHERE));
2591 ols << formatBaselineParams(params, fixed, rms, masklist, whichrow, false) << LogIO::POST ;
2592 }
2593 if (outTextFile) {
2594 ofs << formatBaselineParams(params, fixed, rms, masklist, whichrow, true) << flush;
2595 }
2596 }
2597}
2598
2599float Scantable::getRms(const std::vector<bool>& mask, int whichrow) {
2600 Vector<Float> spec;
2601 specCol_.get(whichrow, spec);
2602
2603 float mean = 0.0;
2604 float smean = 0.0;
2605 int n = 0;
2606 for (uInt i = 0; i < spec.nelements(); ++i) {
2607 if (mask[i]) {
2608 mean += spec[i];
2609 smean += spec[i]*spec[i];
2610 n++;
2611 }
2612 }
2613
2614 mean /= (float)n;
2615 smean /= (float)n;
2616
2617 return sqrt(smean - mean*mean);
2618}
2619
2620
2621std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const
2622{
2623 ostringstream oss;
2624
2625 if (verbose) {
2626 for (int i = 0; i < 60; ++i) {
2627 oss << "-";
2628 }
2629 oss << endl;
2630 oss << " Scan[" << getScan(whichrow) << "]";
2631 oss << " Beam[" << getBeam(whichrow) << "]";
2632 oss << " IF[" << getIF(whichrow) << "]";
2633 oss << " Pol[" << getPol(whichrow) << "]";
2634 oss << " Cycle[" << getCycle(whichrow) << "]: " << endl;
2635 oss << "Fitter range = " << masklist << endl;
2636 oss << "Baseline parameters" << endl;
2637 oss << flush;
2638 }
2639
2640 return String(oss);
2641}
2642
2643std::string Scantable::formatBaselineParamsFooter(float rms, bool verbose) const
2644{
2645 ostringstream oss;
2646
2647 if (verbose) {
2648 oss << "Results of baseline fit" << endl;
2649 oss << " rms = " << setprecision(6) << rms << endl;
2650 }
2651
2652 return String(oss);
2653}
2654
2655 std::string Scantable::formatBaselineParams(const std::vector<float>& params, const std::vector<bool>& fixed, float rms, const std::string& masklist, int whichrow, bool verbose, int start, int count, bool resetparamid) const
2656{
2657 int nParam = (int)(params.size());
2658
2659 if (nParam < 1) {
2660 return(" Not fitted");
2661 } else {
2662
2663 ostringstream oss;
2664 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
2665
2666 if (start < 0) start = 0;
2667 if (count < 0) count = nParam;
2668 int end = start + count;
2669 if (end > nParam) end = nParam;
2670 int paramidoffset = (resetparamid) ? (-start) : 0;
2671
2672 for (int i = start; i < end; ++i) {
2673 if (i > start) {
2674 oss << ",";
2675 }
2676 std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : "";
2677 oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i];
2678 }
2679
2680 oss << endl;
2681 oss << formatBaselineParamsFooter(rms, verbose);
2682
2683 return String(oss);
2684 }
2685
2686}
2687
2688std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, const std::string& masklist, int whichrow, bool verbose) const
2689{
2690 int nOutParam = (int)(params.size());
2691 int nPiece = (int)(ranges.size()) - 1;
2692
2693 if (nOutParam < 1) {
2694 return(" Not fitted");
2695 } else if (nPiece < 0) {
2696 return formatBaselineParams(params, fixed, rms, masklist, whichrow, verbose);
2697 } else if (nPiece < 1) {
2698 return(" Bad count of the piece edge info");
2699 } else if (nOutParam % nPiece != 0) {
2700 return(" Bad count of the output baseline parameters");
2701 } else {
2702
2703 int nParam = nOutParam / nPiece;
2704
2705 ostringstream oss;
2706 oss << formatBaselineParamsHeader(whichrow, masklist, verbose);
2707
2708 stringstream ss;
2709 ss << ranges[nPiece] << flush;
2710 int wRange = ss.str().size() * 2 + 5;
2711
2712 for (int i = 0; i < nPiece; ++i) {
2713 ss.str("");
2714 ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]";
2715 oss << left << setw(wRange) << ss.str();
2716 oss << formatBaselineParams(params, fixed, rms, masklist, whichrow, false, i*nParam, nParam, true);
2717 }
2718
2719 oss << formatBaselineParamsFooter(rms, verbose);
2720
2721 return String(oss);
2722 }
2723
2724}
2725
2726bool Scantable::hasSameNchanOverIFs()
2727{
2728 int nIF = nif(-1);
2729 int nCh;
2730 int totalPositiveNChan = 0;
2731 int nPositiveNChan = 0;
2732
2733 for (int i = 0; i < nIF; ++i) {
2734 nCh = nchan(i);
2735 if (nCh > 0) {
2736 totalPositiveNChan += nCh;
2737 nPositiveNChan++;
2738 }
2739 }
2740
2741 return (totalPositiveNChan == (nPositiveNChan * nchan(0)));
2742}
2743
2744std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose)
2745{
2746 if (mask.size() < 2) {
2747 throw(AipsError("The mask elements should be > 1"));
2748 }
2749 int IF = getIF(whichrow);
2750 if (mask.size() != (uInt)nchan(IF)) {
2751 throw(AipsError("Number of channels in scantable != number of mask elements"));
2752 }
2753
2754 if (verbose) {
2755 LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE));
2756 logOs << LogIO::WARN << "The current mask window unit is " << coordInfo;
2757 if (!hasSameNchan) {
2758 logOs << endl << "This mask is only valid for IF=" << IF;
2759 }
2760 logOs << LogIO::POST;
2761 }
2762
2763 std::vector<double> abcissa = getAbcissa(whichrow);
2764 std::vector<int> edge = getMaskEdgeIndices(mask);
2765
2766 ostringstream oss;
2767 oss.setf(ios::fixed);
2768 oss << setprecision(1) << "[";
2769 for (uInt i = 0; i < edge.size(); i+=2) {
2770 if (i > 0) oss << ",";
2771 oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]";
2772 }
2773 oss << "]" << flush;
2774
2775 return String(oss);
2776}
2777
2778std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask)
2779{
2780 if (mask.size() < 2) {
2781 throw(AipsError("The mask elements should be > 1"));
2782 }
2783
2784 std::vector<int> out, startIndices, endIndices;
2785 int maskSize = mask.size();
2786
2787 startIndices.clear();
2788 endIndices.clear();
2789
2790 if (mask[0]) {
2791 startIndices.push_back(0);
2792 }
2793 for (int i = 1; i < maskSize; ++i) {
2794 if ((!mask[i-1]) && mask[i]) {
2795 startIndices.push_back(i);
2796 } else if (mask[i-1] && (!mask[i])) {
2797 endIndices.push_back(i-1);
2798 }
2799 }
2800 if (mask[maskSize-1]) {
2801 endIndices.push_back(maskSize-1);
2802 }
2803
2804 if (startIndices.size() != endIndices.size()) {
2805 throw(AipsError("Inconsistent Mask Size: bad data?"));
2806 }
2807 for (uInt i = 0; i < startIndices.size(); ++i) {
2808 if (startIndices[i] > endIndices[i]) {
2809 throw(AipsError("Mask start index > mask end index"));
2810 }
2811 }
2812
2813 out.clear();
2814 for (uInt i = 0; i < startIndices.size(); ++i) {
2815 out.push_back(startIndices[i]);
2816 out.push_back(endIndices[i]);
2817 }
2818
2819 return out;
2820}
2821
2822
2823/*
2824STFitEntry Scantable::polyBaseline(const std::vector<bool>& mask, int order, int rowno)
2825{
2826 Fitter fitter = Fitter();
2827 fitter.setExpression("poly", order);
2828
2829 std::vector<bool> fmask = getMask(rowno);
2830 if (fmask.size() != mask.size()) {
2831 throw(AipsError("different mask sizes"));
2832 }
2833 for (int i = 0; i < fmask.size(); ++i) {
2834 fmask[i] = fmask[i] && mask[i];
2835 }
2836
2837 fitBaseline(fmask, rowno, fitter);
2838 setSpectrum(fitter.getResidual(), rowno);
2839 return fitter.getFitEntry();
2840}
2841*/
2842
2843}
2844//namespace asap
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