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source: trunk/src/Scantable.h@ 2190

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Last change on this file since 2190 was 2189, checked in by WataruKawasaki, 13 years ago

New Development: No

JIRA Issue: Yes CAS-3149

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: scantable.*_baseline() parameter

Test Programs:

Put in Release Notes: No

Module(s):

Description: Added two parameters 'showprogress' and 'minnrow' to scantable.*_baseline() to enable to show progress status during time-consuming processes.

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Property svn:keywords set to Author Date Id Revision

File size: 23.7 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 form an existing table on disk
89	* @param[in] name the name of the existing Scantable
90	*/
91	explicit Scantable(const std::string& name, casa::Table::TableType ttype = casa::Table::Memory);
92
93	/// @fixme this is only sensible for MemoryTables....
94	Scantable(const Scantable& other, bool clear=true);
95
96	/**
97	* Destructor
98	*/
99	virtual ~Scantable();
100
101	/**
102	* get a const reference to the underlying casa::Table
103	* @return const \ref casa::Table reference
104	*/
105	const casa::Table& table() const;
106
107	/**
108	* get a reference to the underlying casa::Table with the Selection
109	* object applied if set
110	* @return casa::Table reference
111	*/
112	casa::Table& table();
113
114
115	/**
116	* Get a handle to the selection object
117	* @return constant STSelector reference
118	*/
119	const STSelector& getSelection() const { return selector_; }
120
121	/**
122	* Set the data to be a subset as defined by the STSelector
123	* @param selection a STSelector object
124	*/
125	void setSelection(const STSelector& selection);
126
127	/**
128	* unset the selection of the data
129	*/
130	void unsetSelection();
131	/**
132	* set the header
133	* @param[in] sth an STHeader object
134	*/
135	void setHeader( const STHeader& sth );
136
137	/**
138	* get the header information
139	* @return an STHeader object
140	*/
141	STHeader getHeader( ) const;
142
143	/**
144	* Checks if the "other" Scantable is conformant with this,
145	* i.e. if header values are the same.
146	* @param[in] other another Scantable
147	* @return true or false
148	*/
149	bool conformant( const Scantable& other);
150
151	/**
152	*
153	* @param stype The type of the source, 0 = on, 1 = off
154	*/
155	void setSourceType(int stype);
156
157
158	/**
159	* The number of scans in the table
160	* @return number of scans in the table
161	*/
162	int nscan() const;
163
164	casa::MEpoch::Types getTimeReference() const;
165
166
167	casa::MEpoch getEpoch(int whichrow) const;
168
169	/**
170	* Get global antenna position
171	* @return casa::MPosition
172	*/
173	casa::MPosition getAntennaPosition() const;
174
175	/**
176	* the @ref casa::MDirection for a specific row
177	* @param[in] whichrow the row number
178	* return casa::MDirection
179	*/
180	casa::MDirection getDirection( int whichrow ) const;
181
182	/**
183	* get the direction type as a string, e.g. "J2000"
184	* @param[in] whichrow the row number
185	* return the direction string
186	*/
187	std::string getDirectionString( int whichrow ) const;
188
189	/**
190	* set the direction type as a string, e.g. "J2000"
191	* @param[in] refstr the direction type
192	*/
193	void setDirectionRefString(const std::string& refstr="");
194
195	/**
196	* get the direction reference string
197	* @return a string describing the direction reference
198	*/
199	std::string getDirectionRefString() const;
200
201	/**
202	* Return the Flux unit of the data, e.g. "Jy" or "K"
203	* @return string
204	*/
205	std::string getFluxUnit() const;
206
207	/**
208	* Set the Flux unit of the data
209	* @param unit a string representing the unit, e.g "Jy" or "K"
210	*/
211	void setFluxUnit( const std::string& unit );
212
213	/**
214	* Set the Stokes type of the data
215	* @param feedtype a string representing the type, e.g "circular" or "linear"
216	*/
217	void setFeedType( const std::string& feedtype );
218
219	/**
220	*
221	* @param instrument a string representing an insturment. see xxx
222	*/
223	void setInstrument( const std::string& instrument );
224
225	/**
226	* (Re)calculate the azimuth and elevationnfor all rows
227	*/
228	void calculateAZEL();
229
230	/**
231	* "hard" flag the data, this flags everything selected in setSelection()
232	* param[in] msk a boolean mask of length nchan describing the points to
233	* to be flagged
234	*/
235	//void flag( const std::vector<bool>& msk = std::vector<bool>());
236	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
237
238	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
239
240	/**
241	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
242	* param[in] rows list of row numbers to be flagged
243	*/
244	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
245
246	/**
247	* Get flagRow info at the specified row. If true, the whole data
248	* at the row should be flagged.
249	*/
250	bool getFlagRow(int whichrow) const
251	{ return (flagrowCol_(whichrow) > 0); }
252
253	/**
254	* Flag the data outside a specified range (in a channel-based manner).
255	* (CAS-1807 Wataru Kawasaki)
256	*/
257	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
258
259	/**
260	* Return a list of booleans with the size of nchan for a specified row, to get info
261	* about which channel is clipped.
262	*/
263	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
264	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
265	casa::Vector<casa::uChar> flgs);
266
267	/**
268	* Return a list of row numbers with respect to the original table.
269	* @return a list of unsigned ints
270	*/
271	std::vector<unsigned int> rownumbers() const;
272
273
274	/**
275	* Get the number of beams in the data or a specific scan
276	* @param scanno the scan number to get the number of beams for.
277	* If scanno<0 the number is retrieved from the header.
278	* @return an integer number
279	*/
280	int nbeam(int scanno=-1) const;
281	/**
282	* Get the number of IFs in the data or a specific scan
283	* @param scanno the scan number to get the number of IFs for.
284	* If scanno<0 the number is retrieved from the header.
285	* @return an integer number
286	*/
287	int nif(int scanno=-1) const;
288	/**
289	* Get the number of polarizations in the data or a specific scan
290	* @param scanno the scan number to get the number of polarizations for.
291	* If scanno<0 the number is retrieved from the header.
292	* @return an integer number
293	*/
294	int npol(int scanno=-1) const;
295
296	std::string getPolType() const;
297
298
299	/**
300	* Get the number of integartion cycles
301	* @param scanno the scan number to get the number of rows for.
302	* If scanno<0 the number is retrieved from the header.
303	* @return the number of rows (for the specified scanno)
304	*/
305	int nrow(int scanno=-1) const;
306
307	int getBeam(int whichrow) const;
308	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
309
310	int getIF(int whichrow) const;
311	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
312
313	int getPol(int whichrow) const;
314	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
315
316	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
317	int getScan(int whichrow) const { return scanCol_(whichrow); }
318
319	//TT addition
320	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
321
322	/**
323	* Get the number of channels in the data or a specific IF. This currently
324	* varies only with IF number
325	* @param ifno the IF number to get the number of channels for.
326	* If ifno<0 the number is retrieved from the header.
327	* @return an integer number
328	*/
329	int nchan(int ifno=-1) const;
330	int getChannels(int whichrow) const;
331
332	int ncycle(int scanno=-1) const;
333	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
334
335	double getInterval(int whichrow) const
336	{ return integrCol_(whichrow); }
337
338	float getTsys(int whichrow) const
339	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
340	std::vector<float> getTsysSpectrum(int whichrow) const ;
341	float getElevation(int whichrow) const
342	{ return elCol_(whichrow); }
343	float getAzimuth(int whichrow) const
344	{ return azCol_(whichrow); }
345	float getParAngle(int whichrow) const
346	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
347	int getTcalId(int whichrow) const
348	{ return mtcalidCol_(whichrow); }
349
350	std::string getSourceName(int whichrow) const
351	{ return srcnCol_(whichrow); }
352
353	std::vector<bool> getMask(int whichrow) const;
354	std::vector<float> getSpectrum(int whichrow,
355	const std::string& poltype = "" ) const;
356
357	void setSpectrum(const std::vector<float>& spec, int whichrow);
358
359	std::string getPolarizationLabel(int index, const std::string& ptype) const
360	{ return STPol::getPolLabel(index, ptype ); }
361
362	/**
363	* Write the Scantable to disk
364	* @param filename the output file name
365	*/
366	void makePersistent(const std::string& filename);
367
368	std::vector<std::string> getHistory() const
369	{ return historyTable_.getHistory(); };
370
371	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
372
373	void appendToHistoryTable(const STHistory& otherhist)
374	{ historyTable_.append(otherhist); }
375
376	std::string headerSummary();
377	std::string summary();
378	//std::string getTime(int whichrow=-1, bool showdate=true) const;
379	std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
380	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
381
382	// returns unit, conversion frame, doppler, base-frame
383
384	/**
385	* Get the frequency set up
386	* This is forwarded to the STFrequencies subtable
387	* @return unit, frame, doppler
388	*/
389	std::vector<std::string> getCoordInfo() const
390	{ return freqTable_.getInfo(); };
391
392	void setCoordInfo(std::vector<string> theinfo)
393	{ return freqTable_.setInfo(theinfo); };
394
395
396	std::vector<double> getAbcissa(int whichrow) const;
397
398	std::vector<float> getWeather(int whichrow) const;
399
400	std::string getAbcissaLabel(int whichrow) const;
401	std::vector<double> getRestFrequencies() const
402	{ return moleculeTable_.getRestFrequencies(); }
403	std::vector<double> getRestFrequency(int id) const
404	{ return moleculeTable_.getRestFrequency(id); }
405
406	/**
407	void setRestFrequencies(double rf, const std::string& name = "",
408	const std::string& = "Hz");
409	**/
410	// Modified by Takeshi Nakazato 05/09/2008
411	/***
412	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
413	const std::string& = "Hz");
414	***/
415	void setRestFrequencies(vector<double> rf,
416	const vector<std::string>& name = vector<std::string>(1,""),
417	const std::string& = "Hz");
418
419	//void setRestFrequencies(const std::string& name);
420	void setRestFrequencies(const vector<std::string>& name);
421
422	void shift(int npix);
423
424	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
425
426	void convertDirection(const std::string& newframe);
427
428	STFrequencies& frequencies() { return freqTable_; }
429	const STFrequencies& frequencies() const { return freqTable_; }
430	STWeather& weather() { return weatherTable_; }
431	const STWeather& weather() const { return weatherTable_; }
432	STFocus& focus() { return focusTable_; }
433	const STFocus& focus() const { return focusTable_; }
434	STTcal& tcal() { return tcalTable_; }
435	const STTcal& tcal() const { return tcalTable_; }
436	STMolecules& molecules() { return moleculeTable_; }
437	const STMolecules& molecules() const { return moleculeTable_; }
438	STHistory& history() { return historyTable_; }
439	const STHistory& history() const { return historyTable_; }
440	STFit& fit() { return fitTable_; }
441	const STFit& fit() const { return fitTable_; }
442
443	std::vector<std::string> columnNames() const;
444
445	void addFit(const STFitEntry& fit, int row);
446	STFitEntry getFit(int row) const
447	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
448
449	//Added by TT
450	/**
451	* Get the antenna name
452	* @return antenna name string
453	*/
454	casa::String getAntennaName() const;
455
456	/**
457	* For GBT MS data only. check a scan list
458	* against the information found in GBT_GO table for
459	* scan number orders to get correct pairs.
460	* @param[in] scan list
461	* @return status
462	*/
463	int checkScanInfo(const std::vector<int>& scanlist) const;
464
465	/**
466	* Get the direction as a vector, for a specific row
467	* @param[in] whichrow the row numbyyer
468	* @return the direction in a vector
469	*/
470	std::vector<double> getDirectionVector(int whichrow) const;
471
472	/**
473	* Set a flag indicating whether the data was parallactified
474	* @param[in] flag true or false
475	*/
476	void parallactify(bool flag)
477	{ focus().setParallactify(flag); }
478
479	/**
480	* Reshape spectrum
481	* @param[in] nmin, nmax minimum and maximum channel
482	* @param[in] irow row number
483	*
484	* 30/07/2008 Takeshi Nakazato
485	**/
486	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
487	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
488
489	/**
490	* Change channel number under fixed bandwidth
491	* @param[in] nchan, dnu new channel number and spectral resolution
492	* @param[in] irow row number
493	*
494	* 27/08/2008 Takeshi Nakazato
495	**/
496	void regridChannel( int nchan, double dnu ) ;
497	void regridChannel( int nchan, double dnu, int irow ) ;
498
499	bool getFlagtraFast(casa::uInt whichrow);
500
501	void polyBaseline(const std::vector<bool>& mask,
502	int order,
503	bool getResidual=true,
504	const std::string& progressInfo="true,1000",
505	const bool outLogger=false,
506	const std::string& blfile="");
507	void autoPolyBaseline(const std::vector<bool>& mask,
508	int order,
509	const std::vector<int>& edge,
510	float threshold=3.0,
511	int chanAvgLimit=1,
512	bool getResidual=true,
513	const std::string& progressInfo="true,1000",
514	const bool outLogger=false,
515	const std::string& blfile="");
516	void cubicSplineBaseline(const std::vector<bool>& mask,
517	int nPiece,
518	float thresClip,
519	int nIterClip,
520	bool getResidual=true,
521	const std::string& progressInfo="true,1000",
522	const bool outLogger=false,
523	const std::string& blfile="");
524	void autoCubicSplineBaseline(const std::vector<bool>& mask,
525	int nPiece,
526	float thresClip,
527	int nIterClip,
528	const std::vector<int>& edge,
529	float threshold=3.0,
530	int chanAvgLimit=1,
531	bool getResidual=true,
532	const std::string& progressInfo="true,1000",
533	const bool outLogger=false,
534	const std::string& blfile="");
535	void sinusoidBaseline(const std::vector<bool>& mask,
536	const bool applyFFT,
537	const std::string& fftMethod,
538	const std::string& fftThresh,
539	const std::vector<int>& addNWaves,
540	const std::vector<int>& rejectNWaves,
541	float thresClip,
542	int nIterClip,
543	bool getResidual=true,
544	const std::string& progressInfo="true,1000",
545	const bool outLogger=false,
546	const std::string& blfile="");
547	void autoSinusoidBaseline(const std::vector<bool>& mask,
548	const bool applyFFT,
549	const std::string& fftMethod,
550	const std::string& fftThresh,
551	const std::vector<int>& addNWaves,
552	const std::vector<int>& rejectNWaves,
553	float thresClip,
554	int nIterClip,
555	const std::vector<int>& edge,
556	float threshold=3.0,
557	int chanAvgLimit=1,
558	bool getResidual=true,
559	const std::string& progressInfo="true,1000",
560	const bool outLogger=false,
561	const std::string& blfile="");
562	std::vector<float> execFFT(const int whichrow,
563	const std::vector<bool>& inMask,
564	bool getRealImag=false,
565	bool getAmplitudeOnly=false);
566	float getRms(const std::vector<bool>& mask, int whichrow);
567	std::string formatBaselineParams(const std::vector<float>& params,
568	const std::vector<bool>& fixed,
569	float rms,
570	const std::string& masklist,
571	int whichrow,
572	bool verbose=false,
573	int start=-1,
574	int count=-1,
575	bool resetparamid=false) const;
576	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
577	const std::vector<float>& params,
578	const std::vector<bool>& fixed,
579	float rms,
580	const std::string& masklist,
581	int whichrow,
582	bool verbose=false) const;
583
584
585	private:
586
587	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
588
589	/**
590	* Turns a time value into a formatted string
591	* @param x
592	* @return
593	*/
594	std::string formatSec(casa::Double x) const;
595
596	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
597	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
598
599	/**
600	* Turns a casa::MDirection into a nicely formatted string
601	* @param md an casa::MDirection
602	* @return
603	*/
604	std::string formatDirection(const casa::MDirection& md) const;
605
606	/**
607	* Create a unique file name for the paged (temporary) table
608	* @return just the name
609	*/
610	static casa::String generateName();
611
612	/**
613	* attach to cached columns
614	*/
615	void attach();
616
617	/**
618	* Set up the main casa::Table
619	*/
620	void setupMainTable();
621
622	void attachSubtables();
623	void copySubtables(const Scantable& other);
624
625	/**
626	* Convert an "old" asap1 style row index into a new index
627	* @param[in] therow
628	* @return and index into @table_
629	*/
630	int rowToScanIndex(int therow);
631
632	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
633
634	static const casa::uInt version_ = 3;
635
636	STSelector selector_;
637
638	casa::Table::TableType type_;
639
640	// the actual data
641	casa::Table table_;
642	casa::Table originalTable_;
643
644	STTcal tcalTable_;
645	STFrequencies freqTable_;
646	STWeather weatherTable_;
647	STFocus focusTable_;
648	STMolecules moleculeTable_;
649	STHistory historyTable_;
650	STFit fitTable_;
651
652	// Cached Columns to avoid reconstructing them for each row get/put
653	casa::ScalarColumn<casa::Double> integrCol_;
654	casa::MDirection::ScalarColumn dirCol_;
655	casa::MEpoch::ScalarColumn timeCol_;
656	casa::ScalarColumn<casa::Float> azCol_;
657	casa::ScalarColumn<casa::Float> elCol_;
658	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
659	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
660	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
661	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
662	casa::ArrayColumn<casa::uChar> flagsCol_;
663
664	// id in frequencies table
665	casa::ScalarColumn<casa::uInt> mfreqidCol_;
666	// id in tcal table
667	casa::ScalarColumn<casa::uInt> mtcalidCol_;
668
669	casa::ArrayColumn<casa::String> histitemCol_;
670	casa::ScalarColumn<casa::Int> mfitidCol_;
671	casa::ScalarColumn<casa::uInt> mweatheridCol_;
672
673	casa::ScalarColumn<casa::uInt> mfocusidCol_;
674
675	casa::ScalarColumn<casa::uInt> mmolidCol_;
676
677	static std::map<std::string, STPol::STPolFactory *> factories_;
678	void initFactories();
679
680	/**
681	* Add an auxiliary column to the main table and attach it to a
682	* cached column. Use for adding new columns that the original asap2
683	* tables do not have.
684	* @param[in] col reference to the cached column to be attached
685	* @param[in] colName column name in asap table
686	* @param[in] defValue default value to fill in the column
687	*
688	* 25/10/2009 Wataru Kawasaki
689	*/
690	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
691	const casa::String&,
692	const T2&);
693	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
694	const casa::String&,
695	const casa::Array<T2>&);
696
697	void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
698	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
699	const std::vector<bool>& mask,
700	int nPiece,
701	std::vector<int>& idxEdge,
702	std::vector<float>& params,
703	float thresClip=3.0,
704	int nIterClip=1,
705	bool getResidual=true);
706	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
707	const std::vector<bool>& mask,
708	const std::vector<int>& waveNumbers,
709	std::vector<float>& params,
710	float thresClip=3.0,
711	int nIterClip=1,
712	bool getResidual=true);
713	void selectWaveNumbers(const int whichrow,
714	const std::vector<bool>& chanMask,
715	const bool applyFFT,
716	const std::string& fftMethod,
717	const std::string& fftThresh,
718	const std::vector<int>& addNWaves,
719	const std::vector<int>& rejectNWaves,
720	std::vector<int>& nWaves);
721	void parseThresholdExpression(const std::string& fftThresh,
722	std::string& fftThAttr,
723	float& fftThSigma,
724	int& fftThTop);
725	void doSelectWaveNumbers(const int whichrow,
726	const std::vector<bool>& chanMask,
727	const std::string& fftMethod,
728	const float fftThSigma,
729	const int fftThTop,
730	const std::string& fftThAttr,
731	std::vector<int>& nWaves);
732	void addAuxWaveNumbers(const std::vector<int>& addNWaves,
733	const std::vector<int>& rejectNWaves,
734	std::vector<int>& nWaves);
735	bool hasSameNchanOverIFs();
736	std::string getMaskRangeList(const std::vector<bool>& mask,
737	int whichrow,
738	const casa::String& coordInfo,
739	bool hasSameNchan,
740	bool verbose=false);
741	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
742	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose) const;
743	std::string formatBaselineParamsFooter(float rms, bool verbose) const;
744	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
745	//std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
746	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);
747	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);
748	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);
749	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
750	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
751
752	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
753
754
755	};
756
757	} // namespace
758
759	#endif

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