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source: trunk/src/Scantable.h @ 2321

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Last change on this file since 2321 was 2321, checked in by Malte Marquarding, 13 years ago
Ticket #249: scantbable schema was changed. This required an update to scantable version 4. I have added a class STUpgrade to handle all schema upgrades. This is handled transparently in the scantable constructor
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 24.0 KB

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1	//
2	// C++ Interface: 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	#ifndef ASAPSCANTABLE_H
13	#define ASAPSCANTABLE_H
14
15	// STL
16	#include <fstream>
17	#include <iostream>
18	#include <sstream>
19	#include <string>
20	#include <vector>
21	// AIPS++
22	#include <casa/aips.h>
23	#include <casa/Arrays/MaskedArray.h>
24	#include <casa/Arrays/Vector.h>
25	#include <casa/BasicSL/String.h>
26	#include <casa/Containers/Record.h>
27	#include <casa/Exceptions/Error.h>
28	#include <casa/Quanta/Quantum.h>
29	#include <casa/Utilities/CountedPtr.h>
30
31	#include <coordinates/Coordinates/SpectralCoordinate.h>
32
33	#include <measures/TableMeasures/ScalarMeasColumn.h>
34
35	#include <scimath/Mathematics/FFTServer.h>
36
37	#include <tables/Tables/ArrayColumn.h>
38	#include <tables/Tables/ScalarColumn.h>
39	#include <tables/Tables/Table.h>
40
41	#include "Logger.h"
42	#include "MathUtils.h"
43	#include "STFit.h"
44	#include "STFitEntry.h"
45	#include "STFitter.h"
46	#include "STFocus.h"
47	#include "STFrequencies.h"
48	#include "STHeader.h"
49	#include "STHistory.h"
50	#include "STMolecules.h"
51	#include "STPol.h"
52	#include "STSelector.h"
53	#include "STTcal.h"
54	#include "STWeather.h"
55
56	namespace asap {
57
58	/**
59	* This class contains and wraps a casa::Table, which is used to store
60	* all the information. This can be either a MemoryTable or a
61	* disk based Table.
62	* It provides access functions to the underlying table
63	* It contains n subtables:
64	* @li weather
65	* @li frequencies
66	* @li molecules
67	* @li tcal
68	* @li focus
69	* @li fits
70	*
71	* @brief The main ASAP data container
72	* @author Malte Marquarding
73	* @date
74	* @version
75	*/
76	class Scantable : private Logger
77	{
78
79	friend class STMath;
80
81	public:
82	/**
83	* Default constructor
84	*/
85	explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
86
87	/**
88	* Create a Scantable object from an existing table on disk
89	* @param[in] name the name of the existing Scantable
90	*/
91	explicit Scantable(const std::string& name,
92	casa::Table::TableType ttype = casa::Table::Memory);
93
94	/// @fixme this is only sensible for MemoryTables....
95	Scantable(const Scantable& other, bool clear=true);
96
97	/**
98	* Destructor
99	*/
100	virtual ~Scantable();
101
102	/**
103	* get a const reference to the underlying casa::Table
104	* @return const \ref casa::Table reference
105	*/
106	const casa::Table& table() const;
107
108	/**
109	* get a reference to the underlying casa::Table with the Selection
110	* object applied if set
111	* @return casa::Table reference
112	*/
113	casa::Table& table();
114
115
116	/**
117	* Get a handle to the selection object
118	* @return constant STSelector reference
119	*/
120	const STSelector& getSelection() const { return selector_; }
121
122	/**
123	* Set the data to be a subset as defined by the STSelector
124	* @param selection a STSelector object
125	*/
126	void setSelection(const STSelector& selection);
127
128	/**
129	* unset the selection of the data
130	*/
131	void unsetSelection();
132	/**
133	* set the header
134	* @param[in] sth an STHeader object
135	*/
136	void setHeader( const STHeader& sth );
137
138	/**
139	* get the header information
140	* @return an STHeader object
141	*/
142	STHeader getHeader( ) const;
143
144	/**
145	* Checks if the "other" Scantable is conformant with this,
146	* i.e. if header values are the same.
147	* @param[in] other another Scantable
148	* @return true or false
149	*/
150	bool conformant( const Scantable& other);
151
152	/**
153	*
154	* @param stype The type of the source, 0 = on, 1 = off
155	*/
156	void setSourceType(int stype);
157
158
159	/**
160	* The number of scans in the table
161	* @return number of scans in the table
162	*/
163	int nscan() const;
164
165	casa::MEpoch::Types getTimeReference() const;
166
167
168	casa::MEpoch getEpoch(int whichrow) const;
169
170	/**
171	* Get global antenna position
172	* @return casa::MPosition
173	*/
174	casa::MPosition getAntennaPosition() const;
175
176	/**
177	* the @ref casa::MDirection for a specific row
178	* @param[in] whichrow the row number
179	* return casa::MDirection
180	*/
181	casa::MDirection getDirection( int whichrow ) const;
182
183	/**
184	* get the direction type as a string, e.g. "J2000"
185	* @param[in] whichrow the row number
186	* return the direction string
187	*/
188	std::string getDirectionString( int whichrow ) const;
189
190	/**
191	* set the direction type as a string, e.g. "J2000"
192	* @param[in] refstr the direction type
193	*/
194	void setDirectionRefString(const std::string& refstr="");
195
196	/**
197	* get the direction reference string
198	* @return a string describing the direction reference
199	*/
200	std::string getDirectionRefString() const;
201
202	/**
203	* Return the Flux unit of the data, e.g. "Jy" or "K"
204	* @return string
205	*/
206	std::string getFluxUnit() const;
207
208	/**
209	* Set the Flux unit of the data
210	* @param unit a string representing the unit, e.g "Jy" or "K"
211	*/
212	void setFluxUnit( const std::string& unit );
213
214	/**
215	* Set the Stokes type of the data
216	* @param feedtype a string representing the type, e.g "circular" or "linear"
217	*/
218	void setFeedType( const std::string& feedtype );
219
220	/**
221	*
222	* @param instrument a string representing an insturment. see xxx
223	*/
224	void setInstrument( const std::string& instrument );
225
226	/**
227	* (Re)calculate the azimuth and elevationnfor all rows
228	*/
229	void calculateAZEL();
230
231	/**
232	* "hard" flag the data, this flags everything selected in setSelection()
233	* param[in] msk a boolean mask of length nchan describing the points to
234	* to be flagged
235	*/
236	//void flag( const std::vector<bool>& msk = std::vector<bool>());
237	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
238
239	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
240
241	/**
242	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
243	* param[in] rows list of row numbers to be flagged
244	*/
245	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
246
247	/**
248	* Get flagRow info at the specified row. If true, the whole data
249	* at the row should be flagged.
250	*/
251	bool getFlagRow(int whichrow) const
252	{ return (flagrowCol_(whichrow) > 0); }
253
254	/**
255	* Flag the data outside a specified range (in a channel-based manner).
256	* (CAS-1807 Wataru Kawasaki)
257	*/
258	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
259
260	/**
261	* Return a list of booleans with the size of nchan for a specified row, to get info
262	* about which channel is clipped.
263	*/
264	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
265	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
266	casa::Vector<casa::uChar> flgs);
267
268	/**
269	* Return a list of row numbers with respect to the original table.
270	* @return a list of unsigned ints
271	*/
272	std::vector<unsigned int> rownumbers() const;
273
274
275	/**
276	* Get the number of beams in the data or a specific scan
277	* @param scanno the scan number to get the number of beams for.
278	* If scanno<0 the number is retrieved from the header.
279	* @return an integer number
280	*/
281	int nbeam(int scanno=-1) const;
282	/**
283	* Get the number of IFs in the data or a specific scan
284	* @param scanno the scan number to get the number of IFs for.
285	* If scanno<0 the number is retrieved from the header.
286	* @return an integer number
287	*/
288	int nif(int scanno=-1) const;
289	/**
290	* Get the number of polarizations in the data or a specific scan
291	* @param scanno the scan number to get the number of polarizations for.
292	* If scanno<0 the number is retrieved from the header.
293	* @return an integer number
294	*/
295	int npol(int scanno=-1) const;
296
297	std::string getPolType() const;
298
299
300	/**
301	* Get the number of integartion cycles
302	* @param scanno the scan number to get the number of rows for.
303	* If scanno<0 the number is retrieved from the header.
304	* @return the number of rows (for the specified scanno)
305	*/
306	int nrow(int scanno=-1) const;
307
308	int getBeam(int whichrow) const;
309	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
310
311	int getIF(int whichrow) const;
312	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
313
314	int getPol(int whichrow) const;
315	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
316
317	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
318	int getScan(int whichrow) const { return scanCol_(whichrow); }
319
320	//TT addition
321	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
322
323	/**
324	* Get the number of channels in the data or a specific IF. This currently
325	* varies only with IF number
326	* @param ifno the IF number to get the number of channels for.
327	* If ifno<0 the number is retrieved from the header.
328	* @return an integer number
329	*/
330	int nchan(int ifno=-1) const;
331	int getChannels(int whichrow) const;
332
333	int ncycle(int scanno=-1) const;
334	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
335
336	double getInterval(int whichrow) const
337	{ return integrCol_(whichrow); }
338
339	float getTsys(int whichrow) const
340	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
341	std::vector<float> getTsysSpectrum(int whichrow) const ;
342	float getElevation(int whichrow) const
343	{ return elCol_(whichrow); }
344	float getAzimuth(int whichrow) const
345	{ return azCol_(whichrow); }
346	float getParAngle(int whichrow) const
347	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
348	int getTcalId(int whichrow) const
349	{ return mtcalidCol_(whichrow); }
350
351	std::string getSourceName(int whichrow) const
352	{ return srcnCol_(whichrow); }
353
354	std::vector<bool> getMask(int whichrow) const;
355	std::vector<float> getSpectrum(int whichrow,
356	const std::string& poltype = "" ) const;
357
358	void setSpectrum(const std::vector<float>& spec, int whichrow);
359
360	std::string getPolarizationLabel(int index, const std::string& ptype) const
361	{ return STPol::getPolLabel(index, ptype ); }
362
363	/**
364	* Write the Scantable to disk
365	* @param filename the output file name
366	*/
367	void makePersistent(const std::string& filename);
368
369	std::vector<std::string> getHistory() const
370	{ return historyTable_.getHistory(); };
371
372	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
373
374	void appendToHistoryTable(const STHistory& otherhist)
375	{ historyTable_.append(otherhist); }
376
377	std::string headerSummary();
378	void summary(const std::string& filename="");
379	std::string oldheaderSummary();
380	// std::string summary();
381	void oldsummary(const std::string& filename="");
382
383	//std::string getTime(int whichrow=-1, bool showdate=true) const;
384	std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
385	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
386
387	// returns unit, conversion frame, doppler, base-frame
388
389	/**
390	* Get the frequency set up
391	* This is forwarded to the STFrequencies subtable
392	* @return unit, frame, doppler
393	*/
394	std::vector<std::string> getCoordInfo() const
395	{ return freqTable_.getInfo(); };
396
397	void setCoordInfo(std::vector<string> theinfo)
398	{ return freqTable_.setInfo(theinfo); };
399
400
401	std::vector<double> getAbcissa(int whichrow) const;
402
403	std::vector<float> getWeather(int whichrow) const;
404
405	std::string getAbcissaLabel(int whichrow) const;
406	std::vector<double> getRestFrequencies() const
407	{ return moleculeTable_.getRestFrequencies(); }
408	std::vector<double> getRestFrequency(int id) const
409	{ return moleculeTable_.getRestFrequency(id); }
410
411	/**
412	void setRestFrequencies(double rf, const std::string& name = "",
413	const std::string& = "Hz");
414	**/
415	// Modified by Takeshi Nakazato 05/09/2008
416	/***
417	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
418	const std::string& = "Hz");
419	***/
420	void setRestFrequencies(vector<double> rf,
421	const vector<std::string>& name = vector<std::string>(1,""),
422	const std::string& = "Hz");
423
424	//void setRestFrequencies(const std::string& name);
425	void setRestFrequencies(const vector<std::string>& name);
426
427	void shift(int npix);
428
429	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
430
431	void convertDirection(const std::string& newframe);
432
433	STFrequencies& frequencies() { return freqTable_; }
434	const STFrequencies& frequencies() const { return freqTable_; }
435	STWeather& weather() { return weatherTable_; }
436	const STWeather& weather() const { return weatherTable_; }
437	STFocus& focus() { return focusTable_; }
438	const STFocus& focus() const { return focusTable_; }
439	STTcal& tcal() { return tcalTable_; }
440	const STTcal& tcal() const { return tcalTable_; }
441	STMolecules& molecules() { return moleculeTable_; }
442	const STMolecules& molecules() const { return moleculeTable_; }
443	STHistory& history() { return historyTable_; }
444	const STHistory& history() const { return historyTable_; }
445	STFit& fit() { return fitTable_; }
446	const STFit& fit() const { return fitTable_; }
447
448	std::vector<std::string> columnNames() const;
449
450	void addFit(const STFitEntry& fit, int row);
451	STFitEntry getFit(int row) const
452	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
453
454	//Added by TT
455	/**
456	* Get the antenna name
457	* @return antenna name string
458	*/
459	casa::String getAntennaName() const;
460
461	/**
462	* For GBT MS data only. check a scan list
463	* against the information found in GBT_GO table for
464	* scan number orders to get correct pairs.
465	* @param[in] scan list
466	* @return status
467	*/
468	int checkScanInfo(const std::vector<int>& scanlist) const;
469
470	/**
471	* Get the direction as a vector, for a specific row
472	* @param[in] whichrow the row numbyyer
473	* @return the direction in a vector
474	*/
475	std::vector<double> getDirectionVector(int whichrow) const;
476
477	/**
478	* Set a flag indicating whether the data was parallactified
479	* @param[in] flag true or false
480	*/
481	void parallactify(bool flag)
482	{ focus().setParallactify(flag); }
483
484	/**
485	* Reshape spectrum
486	* @param[in] nmin, nmax minimum and maximum channel
487	* @param[in] irow row number
488	*
489	* 30/07/2008 Takeshi Nakazato
490	**/
491	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
492	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
493
494	/**
495	* Change channel number under fixed bandwidth
496	* @param[in] nchan, dnu new channel number and spectral resolution
497	* @param[in] irow row number
498	*
499	* 27/08/2008 Takeshi Nakazato
500	**/
501	void regridChannel( int nchan, double dnu ) ;
502	void regridChannel( int nchan, double dnu, int irow ) ;
503
504	bool getFlagtraFast(casa::uInt whichrow);
505
506	void polyBaseline(const std::vector<bool>& mask,
507	int order,
508	bool getResidual=true,
509	const std::string& progressInfo="true,1000",
510	const bool outLogger=false,
511	const std::string& blfile="");
512	void autoPolyBaseline(const std::vector<bool>& mask,
513	int order,
514	const std::vector<int>& edge,
515	float threshold=3.0,
516	int chanAvgLimit=1,
517	bool getResidual=true,
518	const std::string& progressInfo="true,1000",
519	const bool outLogger=false,
520	const std::string& blfile="");
521	void cubicSplineBaseline(const std::vector<bool>& mask,
522	int nPiece,
523	float thresClip,
524	int nIterClip,
525	bool getResidual=true,
526	const std::string& progressInfo="true,1000",
527	const bool outLogger=false,
528	const std::string& blfile="");
529	void autoCubicSplineBaseline(const std::vector<bool>& mask,
530	int nPiece,
531	float thresClip,
532	int nIterClip,
533	const std::vector<int>& edge,
534	float threshold=3.0,
535	int chanAvgLimit=1,
536	bool getResidual=true,
537	const std::string& progressInfo="true,1000",
538	const bool outLogger=false,
539	const std::string& blfile="");
540	void sinusoidBaseline(const std::vector<bool>& mask,
541	const bool applyFFT,
542	const std::string& fftMethod,
543	const std::string& fftThresh,
544	const std::vector<int>& addNWaves,
545	const std::vector<int>& rejectNWaves,
546	float thresClip,
547	int nIterClip,
548	bool getResidual=true,
549	const std::string& progressInfo="true,1000",
550	const bool outLogger=false,
551	const std::string& blfile="");
552	void autoSinusoidBaseline(const std::vector<bool>& mask,
553	const bool applyFFT,
554	const std::string& fftMethod,
555	const std::string& fftThresh,
556	const std::vector<int>& addNWaves,
557	const std::vector<int>& rejectNWaves,
558	float thresClip,
559	int nIterClip,
560	const std::vector<int>& edge,
561	float threshold=3.0,
562	int chanAvgLimit=1,
563	bool getResidual=true,
564	const std::string& progressInfo="true,1000",
565	const bool outLogger=false,
566	const std::string& blfile="");
567	std::vector<float> execFFT(const int whichrow,
568	const std::vector<bool>& inMask,
569	bool getRealImag=false,
570	bool getAmplitudeOnly=false);
571	float getRms(const std::vector<bool>& mask, int whichrow);
572	std::string formatBaselineParams(const std::vector<float>& params,
573	const std::vector<bool>& fixed,
574	float rms,
575	int nClipped,
576	const std::string& masklist,
577	int whichrow,
578	bool verbose=false,
579	int start=-1,
580	int count=-1,
581	bool resetparamid=false) const;
582	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
583	const std::vector<float>& params,
584	const std::vector<bool>& fixed,
585	float rms,
586	int nClipped,
587	const std::string& masklist,
588	int whichrow,
589	bool verbose=false) const;
590
591
592	private:
593
594	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
595
596	/**
597	* Turns a time value into a formatted string
598	* @param x
599	* @return
600	*/
601	std::string formatSec(casa::Double x) const;
602
603	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
604	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
605
606	/**
607	* Turns a casa::MDirection into a nicely formatted string
608	* @param md an casa::MDirection
609	* @return
610	*/
611	std::string formatDirection(const casa::MDirection& md) const;
612
613	/**
614	* Create a unique file name for the paged (temporary) table
615	* @return just the name
616	*/
617	static casa::String generateName();
618
619	/**
620	* attach to cached columns
621	*/
622	void attach();
623
624	/**
625	* Set up the main casa::Table
626	*/
627	void setupMainTable();
628
629	void attachSubtables();
630	void copySubtables(const Scantable& other);
631
632	/**
633	* Convert an "old" asap1 style row index into a new index
634	* @param[in] therow
635	* @return and index into @table_
636	*/
637	int rowToScanIndex(int therow);
638
639	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
640
641	static const casa::uInt version_ = 4;
642
643	STSelector selector_;
644
645	casa::Table::TableType type_;
646
647	// the actual data
648	casa::Table table_;
649	casa::Table originalTable_;
650
651	STTcal tcalTable_;
652	STFrequencies freqTable_;
653	STWeather weatherTable_;
654	STFocus focusTable_;
655	STMolecules moleculeTable_;
656	STHistory historyTable_;
657	STFit fitTable_;
658
659	// Cached Columns to avoid reconstructing them for each row get/put
660	casa::ScalarColumn<casa::Double> integrCol_;
661	casa::MDirection::ScalarColumn dirCol_;
662	casa::MEpoch::ScalarColumn timeCol_;
663	casa::ScalarColumn<casa::Float> azCol_;
664	casa::ScalarColumn<casa::Float> elCol_;
665	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
666	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
667	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
668	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
669	casa::ArrayColumn<casa::uChar> flagsCol_;
670
671	// id in frequencies table
672	casa::ScalarColumn<casa::uInt> mfreqidCol_;
673	// id in tcal table
674	casa::ScalarColumn<casa::uInt> mtcalidCol_;
675
676	casa::ArrayColumn<casa::String> histitemCol_;
677	casa::ScalarColumn<casa::Int> mfitidCol_;
678	casa::ScalarColumn<casa::uInt> mweatheridCol_;
679
680	casa::ScalarColumn<casa::uInt> mfocusidCol_;
681
682	casa::ScalarColumn<casa::uInt> mmolidCol_;
683
684	static std::map<std::string, STPol::STPolFactory *> factories_;
685	void initFactories();
686
687	/**
688	* Add an auxiliary column to the main table and attach it to a
689	* cached column. Use for adding new columns that the original asap2
690	* tables do not have.
691	* @param[in] col reference to the cached column to be attached
692	* @param[in] colName column name in asap table
693	* @param[in] defValue default value to fill in the column
694	*
695	* 25/10/2009 Wataru Kawasaki
696	*/
697	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
698	const casa::String&,
699	const T2&);
700	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
701	const casa::String&,
702	const casa::Array<T2>&);
703
704	void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
705	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
706	const std::vector<bool>& mask,
707	int nPiece,
708	std::vector<int>& idxEdge,
709	std::vector<float>& params,
710	int& nClipped,
711	float thresClip=3.0,
712	int nIterClip=1,
713	bool getResidual=true);
714	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
715	const std::vector<bool>& mask,
716	const std::vector<int>& waveNumbers,
717	std::vector<float>& params,
718	int& nClipped,
719	float thresClip=3.0,
720	int nIterClip=1,
721	bool getResidual=true);
722	void selectWaveNumbers(const int whichrow,
723	const std::vector<bool>& chanMask,
724	const bool applyFFT,
725	const std::string& fftMethod,
726	const std::string& fftThresh,
727	const std::vector<int>& addNWaves,
728	const std::vector<int>& rejectNWaves,
729	std::vector<int>& nWaves);
730	void parseThresholdExpression(const std::string& fftThresh,
731	std::string& fftThAttr,
732	float& fftThSigma,
733	int& fftThTop);
734	void doSelectWaveNumbers(const int whichrow,
735	const std::vector<bool>& chanMask,
736	const std::string& fftMethod,
737	const float fftThSigma,
738	const int fftThTop,
739	const std::string& fftThAttr,
740	std::vector<int>& nWaves);
741	void addAuxWaveNumbers(const std::vector<int>& addNWaves,
742	const std::vector<int>& rejectNWaves,
743	std::vector<int>& nWaves);
744	bool hasSameNchanOverIFs();
745	std::string getMaskRangeList(const std::vector<bool>& mask,
746	int whichrow,
747	const casa::String& coordInfo,
748	bool hasSameNchan,
749	bool verbose=false);
750	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
751	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const;
752	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose) const;
753	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
754	//std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
755	void outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, Fitter& fitter);
756	void outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped);
757	void outputFittingResult(bool outLogger, bool outTextFile, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped);
758	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
759	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
760
761	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
762
763
764	};
765
766	} // namespace
767
768	#endif

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