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source: trunk/src/Scantable.h @ 2666

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Last change on this file since 2666 was 2666, checked in by Malte Marquarding, 12 years ago
Ticket #173: added setting of constraints on the fitter.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 25.5 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
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	class Fitter;
59
60	/**
61	* This class contains and wraps a casa::Table, which is used to store
62	* all the information. This can be either a MemoryTable or a
63	* disk based Table.
64	* It provides access functions to the underlying table
65	* It contains n subtables:
66	* @li weather
67	* @li frequencies
68	* @li molecules
69	* @li tcal
70	* @li focus
71	* @li fits
72	*
73	* @brief The main ASAP data container
74	* @author Malte Marquarding
75	* @date
76	* @version
77	*/
78	class Scantable
79	{
80
81	friend class STMath;
82
83	public:
84	/**
85	* Default constructor
86	*/
87	explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
88
89	/**
90	* Create a Scantable object from an existing table on disk
91	* @param[in] name the name of the existing Scantable
92	*/
93	explicit Scantable(const std::string& name,
94	casa::Table::TableType ttype = casa::Table::Memory);
95
96	/// @fixme this is only sensible for MemoryTables....
97	Scantable(const Scantable& other, bool clear=true);
98
99	/**
100	* Destructor
101	*/
102	virtual ~Scantable();
103
104	/**
105	* get a const reference to the underlying casa::Table
106	* @return const \ref casa::Table reference
107	*/
108	const casa::Table& table() const;
109
110	/**
111	* get a reference to the underlying casa::Table with the Selection
112	* object applied if set
113	* @return casa::Table reference
114	*/
115	casa::Table& table();
116
117
118	/**
119	* Get a handle to the selection object
120	* @return constant STSelector reference
121	*/
122	const STSelector& getSelection() const { return selector_; }
123
124	/**
125	* Set the data to be a subset as defined by the STSelector
126	* @param selection a STSelector object
127	*/
128	void setSelection(const STSelector& selection);
129
130	/**
131	* unset the selection of the data
132	*/
133	void unsetSelection();
134	/**
135	* set the header
136	* @param[in] sth an STHeader object
137	*/
138	void setHeader( const STHeader& sth );
139
140	/**
141	* get the header information
142	* @return an STHeader object
143	*/
144	STHeader getHeader( ) const;
145
146	/**
147	* Checks if the "other" Scantable is conformant with this,
148	* i.e. if header values are the same.
149	* @param[in] other another Scantable
150	* @return true or false
151	*/
152	bool conformant( const Scantable& other);
153
154	/**
155	*
156	* @param stype The type of the source, 0 = on, 1 = off
157	*/
158	void setSourceType(int stype);
159
160
161	/**
162	* The number of scans in the table
163	* @return number of scans in the table
164	*/
165	int nscan() const;
166
167	casa::MEpoch::Types getTimeReference() const;
168
169
170	casa::MEpoch getEpoch(int whichrow) const;
171
172	/**
173	* Get global antenna position
174	* @return casa::MPosition
175	*/
176	casa::MPosition getAntennaPosition() const;
177
178	/**
179	* the @ref casa::MDirection for a specific row
180	* @param[in] whichrow the row number
181	* return casa::MDirection
182	*/
183	casa::MDirection getDirection( int whichrow ) const;
184
185	/**
186	* get the direction type as a string, e.g. "J2000"
187	* @param[in] whichrow the row number
188	* return the direction string
189	*/
190	std::string getDirectionString( int whichrow ) const;
191
192	/**
193	* set the direction type as a string, e.g. "J2000"
194	* @param[in] refstr the direction type
195	*/
196	void setDirectionRefString(const std::string& refstr="");
197
198	/**
199	* get the direction reference string
200	* @return a string describing the direction reference
201	*/
202	std::string getDirectionRefString() const;
203
204	/**
205	* Return the Flux unit of the data, e.g. "Jy" or "K"
206	* @return string
207	*/
208	std::string getFluxUnit() const;
209
210	/**
211	* Set the Flux unit of the data
212	* @param unit a string representing the unit, e.g "Jy" or "K"
213	*/
214	void setFluxUnit( const std::string& unit );
215
216	/**
217	* Set the Stokes type of the data
218	* @param feedtype a string representing the type, e.g "circular" or "linear"
219	*/
220	void setFeedType( const std::string& feedtype );
221
222	/**
223	*
224	* @param instrument a string representing an insturment. see xxx
225	*/
226	void setInstrument( const std::string& instrument );
227
228	/**
229	* (Re)calculate the azimuth and elevationnfor all rows
230	*/
231	void calculateAZEL();
232
233	/**
234	* "hard" flag the data, this flags everything selected in setSelection()
235	* param[in] msk a boolean mask of length nchan describing the points to
236	* to be flagged
237	*/
238	//void flag( const std::vector<bool>& msk = std::vector<bool>());
239	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
240
241	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
242
243	/**
244	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
245	* param[in] rows list of row numbers to be flagged
246	*/
247	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
248
249	/**
250	* Get flagRow info at the specified row. If true, the whole data
251	* at the row should be flagged.
252	*/
253	bool getFlagRow(int whichrow) const
254	{ return (flagrowCol_(whichrow) > 0); }
255
256	/**
257	* Flag the data outside a specified range (in a channel-based manner).
258	* (CAS-1807 Wataru Kawasaki)
259	*/
260	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
261
262	/**
263	* Return a list of booleans with the size of nchan for a specified row, to get info
264	* about which channel is clipped.
265	*/
266	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
267	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
268	casa::Vector<casa::uChar> flgs);
269
270	/**
271	* Return a list of row numbers with respect to the original table.
272	* @return a list of unsigned ints
273	*/
274	std::vector<unsigned int> rownumbers() const;
275
276
277	/**
278	* Get the number of beams in the data or a specific scan
279	* @param scanno the scan number to get the number of beams for.
280	* If scanno<0 the number is retrieved from the header.
281	* @return an integer number
282	*/
283	int nbeam(int scanno=-1) const;
284	/**
285	* Get the number of IFs in the data or a specific scan
286	* @param scanno the scan number to get the number of IFs for.
287	* If scanno<0 the number is retrieved from the header.
288	* @return an integer number
289	*/
290	int nif(int scanno=-1) const;
291	/**
292	* Get the number of polarizations in the data or a specific scan
293	* @param scanno the scan number to get the number of polarizations for.
294	* If scanno<0 the number is retrieved from the header.
295	* @return an integer number
296	*/
297	int npol(int scanno=-1) const;
298
299	std::string getPolType() const;
300
301
302	/**
303	* Get the number of integartion cycles
304	* @param scanno the scan number to get the number of rows for.
305	* If scanno<0 the number is retrieved from the header.
306	* @return the number of rows (for the specified scanno)
307	*/
308	int nrow(int scanno=-1) const;
309
310	int getBeam(int whichrow) const;
311	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
312
313	int getIF(int whichrow) const;
314	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
315
316	int getPol(int whichrow) const;
317	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
318
319	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
320	int getScan(int whichrow) const { return scanCol_(whichrow); }
321
322	//TT addition
323	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
324
325	/**
326	* Get the number of channels in the data or a specific IF. This currently
327	* varies only with IF number
328	* @param ifno the IF number to get the number of channels for.
329	* If ifno<0 the number is retrieved from the header.
330	* @return an integer number
331	*/
332	int nchan(int ifno=-1) const;
333	int getChannels(int whichrow) const;
334
335	int ncycle(int scanno=-1) const;
336	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
337
338	double getInterval(int whichrow) const
339	{ return integrCol_(whichrow); }
340
341	float getTsys(int whichrow) const
342	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
343	std::vector<float> getTsysSpectrum(int whichrow) const ;
344	float getElevation(int whichrow) const
345	{ return elCol_(whichrow); }
346	float getAzimuth(int whichrow) const
347	{ return azCol_(whichrow); }
348	float getParAngle(int whichrow) const
349	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
350	int getTcalId(int whichrow) const
351	{ return mtcalidCol_(whichrow); }
352
353	std::string getSourceName(int whichrow) const
354	{ return srcnCol_(whichrow); }
355
356	std::vector<bool> getMask(int whichrow) const;
357	std::vector<float> getSpectrum(int whichrow,
358	const std::string& poltype = "" ) const;
359
360	void setSpectrum(const std::vector<float>& spec, int whichrow);
361
362	std::string getPolarizationLabel(int index, const std::string& ptype) const
363	{ return STPol::getPolLabel(index, ptype ); }
364
365	/**
366	* Write the Scantable to disk
367	* @param filename the output file name
368	*/
369	void makePersistent(const std::string& filename);
370
371	std::vector<std::string> getHistory() const
372	{ return historyTable_.getHistory(); };
373
374	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
375
376	void appendToHistoryTable(const STHistory& otherhist)
377	{ historyTable_.append(otherhist); }
378
379	std::string headerSummary();
380	void summary(const std::string& filename="");
381	std::string oldheaderSummary();
382	// std::string summary();
383	void oldsummary(const std::string& filename="");
384
385	//std::string getTime(int whichrow=-1, bool showdate=true) const;
386	std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
387	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
388
389	// returns unit, conversion frame, doppler, base-frame
390
391	/**
392	* Get the frequency set up
393	* This is forwarded to the STFrequencies subtable
394	* @return unit, frame, doppler
395	*/
396	std::vector<std::string> getCoordInfo() const
397	{ return freqTable_.getInfo(); };
398
399	void setCoordInfo(std::vector<string> theinfo)
400	{ return freqTable_.setInfo(theinfo); };
401
402
403	std::vector<double> getAbcissa(int whichrow) const;
404
405	std::vector<float> getWeather(int whichrow) const;
406
407	std::string getAbcissaLabel(int whichrow) const;
408	std::vector<double> getRestFrequencies() const
409	{ return moleculeTable_.getRestFrequencies(); }
410	std::vector<double> getRestFrequency(int id) const
411	{ return moleculeTable_.getRestFrequency(id); }
412
413	/**
414	void setRestFrequencies(double rf, const std::string& name = "",
415	const std::string& = "Hz");
416	**/
417	// Modified by Takeshi Nakazato 05/09/2008
418	/***
419	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
420	const std::string& = "Hz");
421	***/
422	void setRestFrequencies(vector<double> rf,
423	const vector<std::string>& name = vector<std::string>(1,""),
424	const std::string& = "Hz");
425
426	//void setRestFrequencies(const std::string& name);
427	void setRestFrequencies(const vector<std::string>& name);
428
429	void shift(int npix);
430
431	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
432
433	void convertDirection(const std::string& newframe);
434
435	STFrequencies& frequencies() { return freqTable_; }
436	const STFrequencies& frequencies() const { return freqTable_; }
437	STWeather& weather() { return weatherTable_; }
438	const STWeather& weather() const { return weatherTable_; }
439	STFocus& focus() { return focusTable_; }
440	const STFocus& focus() const { return focusTable_; }
441	STTcal& tcal() { return tcalTable_; }
442	const STTcal& tcal() const { return tcalTable_; }
443	STMolecules& molecules() { return moleculeTable_; }
444	const STMolecules& molecules() const { return moleculeTable_; }
445	STHistory& history() { return historyTable_; }
446	const STHistory& history() const { return historyTable_; }
447	STFit& fit() { return fitTable_; }
448	const STFit& fit() const { return fitTable_; }
449
450	std::vector<std::string> columnNames() const;
451
452	void addFit(const STFitEntry& fit, int row);
453	STFitEntry getFit(int row) const
454	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
455
456	//Added by TT
457	/**
458	* Get the antenna name
459	* @return antenna name string
460	*/
461	casa::String getAntennaName() const;
462
463	/**
464	* For GBT MS data only. check a scan list
465	* against the information found in GBT_GO table for
466	* scan number orders to get correct pairs.
467	* @param[in] scan list
468	* @return status
469	*/
470	int checkScanInfo(const std::vector<int>& scanlist) const;
471
472	/**
473	* Get the direction as a vector, for a specific row
474	* @param[in] whichrow the row numbyyer
475	* @return the direction in a vector
476	*/
477	std::vector<double> getDirectionVector(int whichrow) const;
478
479	/**
480	* Set a flag indicating whether the data was parallactified
481	* @param[in] flag true or false
482	*/
483	void parallactify(bool flag)
484	{ focusTable_.setParallactify(flag); }
485
486	/**
487	* Reshape spectrum
488	* @param[in] nmin, nmax minimum and maximum channel
489	* @param[in] irow row number
490	*
491	* 30/07/2008 Takeshi Nakazato
492	**/
493	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
494	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
495
496	/**
497	* Change channel number under fixed bandwidth
498	* @param[in] nchan, dnu new channel number and spectral resolution
499	* @param[in] irow row number
500	*
501	* 27/08/2008 Takeshi Nakazato
502	**/
503	void regridChannel( int nchan, double dnu ) ;
504	void regridChannel( int nchan, double dnu, int irow ) ;
505	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
506
507	void regridSpecChannel( double dnu, int nchan=-1 ) ;
508
509	bool getFlagtraFast(casa::uInt whichrow);
510
511	void polyBaseline(const std::vector<bool>& mask,
512	int order,
513	bool getResidual=true,
514	const std::string& progressInfo="true,1000",
515	const bool outLogger=false,
516	const std::string& blfile="");
517	void autoPolyBaseline(const std::vector<bool>& mask,
518	int order,
519	const std::vector<int>& edge,
520	float threshold=3.0,
521	int chanAvgLimit=1,
522	bool getResidual=true,
523	const std::string& progressInfo="true,1000",
524	const bool outLogger=false,
525	const std::string& blfile="");
526	void chebyshevBaseline(const std::vector<bool>& mask,
527	int order,
528	float thresClip,
529	int nIterClip,
530	bool getResidual=true,
531	const std::string& progressInfo="true,1000",
532	const bool outLogger=false,
533	const std::string& blfile="");
534	void autoChebyshevBaseline(const std::vector<bool>& mask,
535	int order,
536	float thresClip,
537	int nIterClip,
538	const std::vector<int>& edge,
539	float threshold=3.0,
540	int chanAvgLimit=1,
541	bool getResidual=true,
542	const std::string& progressInfo="true,1000",
543	const bool outLogger=false,
544	const std::string& blfile="");
545	void cubicSplineBaseline(const std::vector<bool>& mask,
546	int nPiece,
547	float thresClip,
548	int nIterClip,
549	bool getResidual=true,
550	const std::string& progressInfo="true,1000",
551	const bool outLogger=false,
552	const std::string& blfile="");
553	void autoCubicSplineBaseline(const std::vector<bool>& mask,
554	int nPiece,
555	float thresClip,
556	int nIterClip,
557	const std::vector<int>& edge,
558	float threshold=3.0,
559	int chanAvgLimit=1,
560	bool getResidual=true,
561	const std::string& progressInfo="true,1000",
562	const bool outLogger=false,
563	const std::string& blfile="");
564	void sinusoidBaseline(const std::vector<bool>& mask,
565	const bool applyFFT,
566	const std::string& fftMethod,
567	const std::string& fftThresh,
568	const std::vector<int>& addNWaves,
569	const std::vector<int>& rejectNWaves,
570	float thresClip,
571	int nIterClip,
572	bool getResidual=true,
573	const std::string& progressInfo="true,1000",
574	const bool outLogger=false,
575	const std::string& blfile="");
576	void autoSinusoidBaseline(const std::vector<bool>& mask,
577	const bool applyFFT,
578	const std::string& fftMethod,
579	const std::string& fftThresh,
580	const std::vector<int>& addNWaves,
581	const std::vector<int>& rejectNWaves,
582	float thresClip,
583	int nIterClip,
584	const std::vector<int>& edge,
585	float threshold=3.0,
586	int chanAvgLimit=1,
587	bool getResidual=true,
588	const std::string& progressInfo="true,1000",
589	const bool outLogger=false,
590	const std::string& blfile="");
591	std::vector<float> execFFT(const int whichrow,
592	const std::vector<bool>& inMask,
593	bool getRealImag=false,
594	bool getAmplitudeOnly=false);
595	float getRms(const std::vector<bool>& mask, int whichrow);
596	std::string formatBaselineParams(const std::vector<float>& params,
597	const std::vector<bool>& fixed,
598	float rms,
599	int nClipped,
600	const std::string& masklist,
601	int whichrow,
602	bool verbose=false,
603	bool csvformat=false,
604	int start=-1,
605	int count=-1,
606	bool resetparamid=false) const;
607	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
608	const std::vector<float>& params,
609	const std::vector<bool>& fixed,
610	float rms,
611	int nClipped,
612	const std::string& masklist,
613	int whichrow,
614	bool verbose=false,
615	bool csvformat=false) const;
616	std::vector<uint> getMoleculeIdColumnData() const;
617	void setMoleculeIdColumnData(const std::vector<uint>& molids);
618
619
620	private:
621
622	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
623
624	/**
625	* Turns a time value into a formatted string
626	* @param x
627	* @return
628	*/
629	std::string formatSec(casa::Double x) const;
630
631	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
632	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
633
634	/**
635	* Turns a casa::MDirection into a nicely formatted string
636	* @param md an casa::MDirection
637	* @return
638	*/
639	std::string formatDirection(const casa::MDirection& md) const;
640
641	/**
642	* Create a unique file name for the paged (temporary) table
643	* @return just the name
644	*/
645	static casa::String generateName();
646
647	/**
648	* attach to cached columns
649	*/
650	void attach();
651
652	/**
653	* Set up the main casa::Table
654	*/
655	void setupMainTable();
656
657	void attachSubtables();
658	void copySubtables(const Scantable& other);
659
660	/**
661	* Convert an "old" asap1 style row index into a new index
662	* @param[in] therow
663	* @return and index into @table_
664	*/
665	int rowToScanIndex(int therow);
666
667	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
668
669	static const casa::uInt version_ = 4;
670
671	STSelector selector_;
672
673	casa::Table::TableType type_;
674
675	// the actual data
676	casa::Table table_;
677	casa::Table originalTable_;
678
679	STTcal tcalTable_;
680	STFrequencies freqTable_;
681	STWeather weatherTable_;
682	STFocus focusTable_;
683	STMolecules moleculeTable_;
684	STHistory historyTable_;
685	STFit fitTable_;
686
687	// Cached Columns to avoid reconstructing them for each row get/put
688	casa::ScalarColumn<casa::Double> integrCol_;
689	casa::MDirection::ScalarColumn dirCol_;
690	casa::MEpoch::ScalarColumn timeCol_;
691	casa::ScalarColumn<casa::Float> azCol_;
692	casa::ScalarColumn<casa::Float> elCol_;
693	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
694	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
695	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
696	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
697	casa::ArrayColumn<casa::uChar> flagsCol_;
698
699	// id in frequencies table
700	casa::ScalarColumn<casa::uInt> mfreqidCol_;
701	// id in tcal table
702	casa::ScalarColumn<casa::uInt> mtcalidCol_;
703
704	casa::ArrayColumn<casa::String> histitemCol_;
705	casa::ScalarColumn<casa::Int> mfitidCol_;
706	casa::ScalarColumn<casa::uInt> mweatheridCol_;
707
708	casa::ScalarColumn<casa::uInt> mfocusidCol_;
709
710	casa::ScalarColumn<casa::uInt> mmolidCol_;
711
712	static std::map<std::string, STPol::STPolFactory *> factories_;
713	void initFactories();
714
715	/**
716	* Add an auxiliary column to the main table and attach it to a
717	* cached column. Use for adding new columns that the original asap2
718	* tables do not have.
719	* @param[in] col reference to the cached column to be attached
720	* @param[in] colName column name in asap table
721	* @param[in] defValue default value to fill in the column
722	*
723	* 25/10/2009 Wataru Kawasaki
724	*/
725	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
726	const casa::String&,
727	const T2&);
728	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
729	const casa::String&,
730	const casa::Array<T2>&);
731
732	void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
733	double getChebyshevPolynomial(int n, double x);
734	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
735	const std::vector<bool>& mask,
736	int order,
737	std::vector<float>& params,
738	int& nClipped,
739	float thresClip=3.0,
740	int nIterClip=1,
741	bool getResidual=true);
742	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
743	const std::vector<bool>& mask,
744	int nPiece,
745	std::vector<int>& idxEdge,
746	std::vector<float>& params,
747	int& nClipped,
748	float thresClip=3.0,
749	int nIterClip=1,
750	bool getResidual=true);
751	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
752	const std::vector<bool>& mask,
753	const std::vector<int>& waveNumbers,
754	std::vector<float>& params,
755	int& nClipped,
756	float thresClip=3.0,
757	int nIterClip=1,
758	bool getResidual=true);
759	void selectWaveNumbers(const int whichrow,
760	const std::vector<bool>& chanMask,
761	const bool applyFFT,
762	const std::string& fftMethod,
763	const std::string& fftThresh,
764	const std::vector<int>& addNWaves,
765	const std::vector<int>& rejectNWaves,
766	std::vector<int>& nWaves);
767	void parseThresholdExpression(const std::string& fftThresh,
768	std::string& fftThAttr,
769	float& fftThSigma,
770	int& fftThTop);
771	void doSelectWaveNumbers(const int whichrow,
772	const std::vector<bool>& chanMask,
773	const std::string& fftMethod,
774	const float fftThSigma,
775	const int fftThTop,
776	const std::string& fftThAttr,
777	std::vector<int>& nWaves);
778	void addAuxWaveNumbers(const int whichrow,
779	const std::vector<int>& addNWaves,
780	const std::vector<int>& rejectNWaves,
781	std::vector<int>& nWaves);
782	void setWaveNumberListUptoNyquistFreq(const int whichrow,
783	std::vector<int>& nWaves);
784	bool hasSameNchanOverIFs();
785	std::string getMaskRangeList(const std::vector<bool>& mask,
786	int whichrow,
787	const casa::String& coordInfo,
788	bool hasSameNchan,
789	bool verbose=false);
790	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
791	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
792	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
793	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
794	//std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
795	void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casa::String& funcName, Fitter& fitter);
796	void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, 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);
797	void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, 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);
798	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
799	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
800
801	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
802
803	};
804
805	} // namespace
806
807	#endif

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