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source: trunk/src/Scantable.h@ 2812

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Last change on this file since 2812 was 2811, checked in by WataruKawasaki, 12 years ago

New Development: No

JIRA Issue: No

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: parameter of tool functions

Test Programs:

Put in Release Notes: No

Module(s): sd.scantable

Description: add a new parameter 'retfitres' to sd.scantable.apply_bltable() and sd.scantable.sub_baseline().

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File size: 32.5 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	#include <coordinates/Coordinates/SpectralCoordinate.h>
31	#include <measures/TableMeasures/ScalarMeasColumn.h>
32	#include <scimath/Mathematics/FFTServer.h>
33	#include <tables/Tables/ArrayColumn.h>
34	#include <tables/Tables/ScalarColumn.h>
35	#include <tables/Tables/Table.h>
36
37	#include "MathUtils.h"
38	#include "STBaselineEnum.h"
39	#include "STFit.h"
40	#include "STFitEntry.h"
41	#include "STFocus.h"
42	#include "STFrequencies.h"
43	#include "STHeader.h"
44	#include "STHistory.h"
45	#include "STMolecules.h"
46	#include "STPol.h"
47	#include "STSelector.h"
48	#include "STTcal.h"
49	#include "STWeather.h"
50
51	namespace asap {
52
53	class Fitter;
54	class STLineFinder;
55	class STBaselineTable;
56
57	/**
58	* This class contains and wraps a casa::Table, which is used to store
59	* all the information. This can be either a MemoryTable or a
60	* disk based Table.
61	* It provides access functions to the underlying table
62	* It contains n subtables:
63	* @li weather
64	* @li frequencies
65	* @li molecules
66	* @li tcal
67	* @li focus
68	* @li fits
69	*
70	* @brief The main ASAP data container
71	* @author Malte Marquarding
72	* @date
73	* @version
74	*/
75	class Scantable
76	{
77
78	friend class STMath;
79
80	public:
81	/**
82	* Default constructor
83	*/
84	explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
85
86	/**
87	* Create a Scantable object from an existing table on disk
88	* @param[in] name the name of the existing Scantable
89	*/
90	explicit Scantable(const std::string& name,
91	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	std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
320	int getCycle(int whichrow) const { return cycleCol_(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
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
345	void setTsys(const std::vector<float>& newvals, int whichrow);
346
347	float getElevation(int whichrow) const
348	{ return elCol_(whichrow); }
349	float getAzimuth(int whichrow) const
350	{ return azCol_(whichrow); }
351	float getParAngle(int whichrow) const
352	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
353	int getTcalId(int whichrow) const
354	{ return mtcalidCol_(whichrow); }
355
356	std::string getSourceName(int whichrow) const
357	{ return srcnCol_(whichrow); }
358
359	std::vector<bool> getMask(int whichrow) const;
360	std::vector<float> getSpectrum(int whichrow,
361	const std::string& poltype = "" ) const;
362
363	void setSpectrum(const std::vector<float>& spec, int whichrow);
364
365	std::string getPolarizationLabel(int index, const std::string& ptype) const
366	{ return STPol::getPolLabel(index, ptype ); }
367
368	/**
369	* Write the Scantable to disk
370	* @param filename the output file name
371	*/
372	void makePersistent(const std::string& filename);
373
374	std::vector<std::string> getHistory() const
375	{ return historyTable_.getHistory(); };
376
377	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
378
379	void appendToHistoryTable(const STHistory& otherhist)
380	{ historyTable_.append(otherhist); }
381
382	std::string headerSummary();
383	void summary(const std::string& filename="");
384	std::string oldheaderSummary();
385	// std::string summary();
386	void oldsummary(const std::string& filename="");
387
388	//std::string getTime(int whichrow=-1, bool showdate=true) const;
389	std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
390	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
391
392	// returns unit, conversion frame, doppler, base-frame
393
394	/**
395	* Get the frequency set up
396	* This is forwarded to the STFrequencies subtable
397	* @return unit, frame, doppler
398	*/
399	std::vector<std::string> getCoordInfo() const
400	{ return freqTable_.getInfo(); };
401
402	void setCoordInfo(std::vector<string> theinfo)
403	{ return freqTable_.setInfo(theinfo); };
404
405
406	std::vector<double> getAbcissa(int whichrow) const;
407
408	std::vector<float> getWeather(int whichrow) const;
409
410	std::string getAbcissaLabel(int whichrow) const;
411	std::vector<double> getRestFrequencies() const
412	{ return moleculeTable_.getRestFrequencies(); }
413	std::vector<double> getRestFrequency(int id) const
414	{ return moleculeTable_.getRestFrequency(id); }
415
416	/**
417	void setRestFrequencies(double rf, const std::string& name = "",
418	const std::string& = "Hz");
419	**/
420	// Modified by Takeshi Nakazato 05/09/2008
421	/***
422	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
423	const std::string& = "Hz");
424	***/
425	void setRestFrequencies(vector<double> rf,
426	const vector<std::string>& name = vector<std::string>(1,""),
427	const std::string& = "Hz");
428
429	//void setRestFrequencies(const std::string& name);
430	void setRestFrequencies(const vector<std::string>& name);
431
432	void shift(int npix);
433
434	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
435
436	void convertDirection(const std::string& newframe);
437
438	STFrequencies& frequencies() { return freqTable_; }
439	const STFrequencies& frequencies() const { return freqTable_; }
440	STWeather& weather() { return weatherTable_; }
441	const STWeather& weather() const { return weatherTable_; }
442	STFocus& focus() { return focusTable_; }
443	const STFocus& focus() const { return focusTable_; }
444	STTcal& tcal() { return tcalTable_; }
445	const STTcal& tcal() const { return tcalTable_; }
446	STMolecules& molecules() { return moleculeTable_; }
447	const STMolecules& molecules() const { return moleculeTable_; }
448	STHistory& history() { return historyTable_; }
449	const STHistory& history() const { return historyTable_; }
450	STFit& fit() { return fitTable_; }
451	const STFit& fit() const { return fitTable_; }
452
453	std::vector<std::string> columnNames() const;
454
455	void addFit(const STFitEntry& fit, int row);
456	STFitEntry getFit(int row) const
457	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
458
459	//Added by TT
460	/**
461	* Get the antenna name
462	* @return antenna name string
463	*/
464	casa::String getAntennaName() const;
465
466	/**
467	* For GBT MS data only. check a scan list
468	* against the information found in GBT_GO table for
469	* scan number orders to get correct pairs.
470	* @param[in] scan list
471	* @return status
472	*/
473	int checkScanInfo(const std::vector<int>& scanlist) const;
474
475	/**
476	* Get the direction as a vector, for a specific row
477	* @param[in] whichrow the row numbyyer
478	* @return the direction in a vector
479	*/
480	std::vector<double> getDirectionVector(int whichrow) const;
481
482	/**
483	* Set a flag indicating whether the data was parallactified
484	* @param[in] flag true or false
485	*/
486	void parallactify(bool flag)
487	{ focusTable_.setParallactify(flag); }
488
489	/**
490	* Reshape spectrum
491	* @param[in] nmin, nmax minimum and maximum channel
492	* @param[in] irow row number
493	*
494	* 30/07/2008 Takeshi Nakazato
495	**/
496	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
497	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
498
499	/**
500	* Change channel number under fixed bandwidth
501	* @param[in] nchan, dnu new channel number and spectral resolution
502	* @param[in] irow row number
503	*
504	* 27/08/2008 Takeshi Nakazato
505	**/
506	void regridChannel( int nchan, double dnu ) ;
507	void regridChannel( int nchan, double dnu, int irow ) ;
508	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
509	void regridSpecChannel( double dnu, int nchan=-1 ) ;
510
511	bool getFlagtraFast(casa::uInt whichrow);
512
513	std::vector<std::string> applyBaselineTable(const std::string& bltable,
514	const bool returnfitresult,
515	const std::string& outbltable,
516	const bool outbltableexists,
517	const bool overwrite);
518	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList,
519	const bool returnfitresult,
520	const std::string& outbltable,
521	const bool outbltableexists,
522	const bool overwrite);
523	void polyBaseline(const std::vector<bool>& mask,
524	int order,
525	float thresClip,
526	int nIterClip,
527	bool getResidual=true,
528	const std::string& progressInfo="true,1000",
529	const bool outLogger=false,
530	const std::string& blfile="",
531	const std::string& bltable="");
532	void autoPolyBaseline(const std::vector<bool>& mask,
533	int order,
534	float thresClip,
535	int nIterClip,
536	const std::vector<int>& edge,
537	float threshold=3.0,
538	int chanAvgLimit=1,
539	bool getResidual=true,
540	const std::string& progressInfo="true,1000",
541	const bool outLogger=false,
542	const std::string& blfile="",
543	const std::string& bltable="");
544	void chebyshevBaseline(const std::vector<bool>& mask,
545	int order,
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	const std::string& bltable="");
553	void autoChebyshevBaseline(const std::vector<bool>& mask,
554	int order,
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	const std::string& bltable="");
565	void cubicSplineBaseline(const std::vector<bool>& mask,
566	int nPiece,
567	float thresClip,
568	int nIterClip,
569	bool getResidual=true,
570	const std::string& progressInfo="true,1000",
571	const bool outLogger=false,
572	const std::string& blfile="",
573	const std::string& bltable="");
574	void autoCubicSplineBaseline(const std::vector<bool>& mask,
575	int nPiece,
576	float thresClip,
577	int nIterClip,
578	const std::vector<int>& edge,
579	float threshold=3.0,
580	int chanAvgLimit=1,
581	bool getResidual=true,
582	const std::string& progressInfo="true,1000",
583	const bool outLogger=false,
584	const std::string& blfile="",
585	const std::string& bltable="");
586	void sinusoidBaseline(const std::vector<bool>& mask,
587	const std::string& fftInfo,
588	const std::vector<int>& addNWaves,
589	const std::vector<int>& rejectNWaves,
590	float thresClip,
591	int nIterClip,
592	bool getResidual=true,
593	const std::string& progressInfo="true,1000",
594	const bool outLogger=false,
595	const std::string& blfile="",
596	const std::string& bltable="");
597	void autoSinusoidBaseline(const std::vector<bool>& mask,
598	const std::string& fftInfo,
599	const std::vector<int>& addNWaves,
600	const std::vector<int>& rejectNWaves,
601	float thresClip,
602	int nIterClip,
603	const std::vector<int>& edge,
604	float threshold=3.0,
605	int chanAvgLimit=1,
606	bool getResidual=true,
607	const std::string& progressInfo="true,1000",
608	const bool outLogger=false,
609	const std::string& blfile="",
610	const std::string& bltable="");
611	std::vector<float> execFFT(const int whichrow,
612	const std::vector<bool>& inMask,
613	bool getRealImag=false,
614	bool getAmplitudeOnly=false);
615	float getRms(const std::vector<bool>& mask, int whichrow);
616	std::string formatBaselineParams(const std::vector<float>& params,
617	const std::vector<bool>& fixed,
618	float rms,
619	int nClipped,
620	const std::string& masklist,
621	int whichrow,
622	bool verbose=false,
623	bool csvformat=false,
624	int start=-1,
625	int count=-1,
626	bool resetparamid=false) const;
627	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
628	const std::vector<float>& params,
629	const std::vector<bool>& fixed,
630	float rms,
631	int nClipped,
632	const std::string& masklist,
633	int whichrow,
634	bool verbose=false,
635	bool csvformat=false) const;
636	std::vector<uint> getMoleculeIdColumnData() const;
637	void setMoleculeIdColumnData(const std::vector<uint>& molids);
638	double calculateModelSelectionCriteria(const std::string& valname,
639	const std::string& blfunc,
640	int order,
641	const std::vector<bool>& inMask,
642	int whichrow,
643	bool useLineFinder,
644	const std::vector<int>& edge,
645	float threshold,
646	int chanAvgLimit);
647	static std::vector<bool> getMaskFromMaskList(const int nchan,
648	const std::vector<int>& masklist);
649	static casa::Vector<casa::uInt> getMaskListFromMask(
650	const std::vector<bool>& mask);
651	static std::vector<int> splitToIntList(const std::string& str,
652	const char delim);
653	static std::vector<string> splitToStringList(const std::string& str,
654	const char delim);
655
656	void dropXPol();
657
658	private:
659
660	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
661
662	/**
663	* Turns a time value into a formatted string
664	* @param x
665	* @return
666	*/
667	std::string formatSec(casa::Double x) const;
668
669	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
670	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
671
672	/**
673	* Turns a casa::MDirection into a nicely formatted string
674	* @param md an casa::MDirection
675	* @return
676	*/
677	std::string formatDirection(const casa::MDirection& md) const;
678
679	/**
680	* Create a unique file name for the paged (temporary) table
681	* @return just the name
682	*/
683	static casa::String generateName();
684
685	/**
686	* attach to cached columns
687	*/
688	void attach();
689
690	/**
691	* Set up the main casa::Table
692	*/
693	void setupMainTable();
694
695	void attachSubtables();
696	void copySubtables(const Scantable& other);
697
698	/**
699	* Convert an "old" asap1 style row index into a new index
700	* @param[in] therow
701	* @return and index into @table_
702	*/
703	int rowToScanIndex(int therow);
704
705	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
706
707	static const casa::uInt version_ = 4;
708
709	STSelector selector_;
710
711	casa::Table::TableType type_;
712
713	// the actual data
714	casa::Table table_;
715	casa::Table originalTable_;
716
717	STTcal tcalTable_;
718	STFrequencies freqTable_;
719	STWeather weatherTable_;
720	STFocus focusTable_;
721	STMolecules moleculeTable_;
722	STHistory historyTable_;
723	STFit fitTable_;
724
725	// Cached Columns to avoid reconstructing them for each row get/put
726	casa::ScalarColumn<casa::Double> integrCol_;
727	casa::MDirection::ScalarColumn dirCol_;
728	casa::MEpoch::ScalarColumn timeCol_;
729	casa::ScalarColumn<casa::Float> azCol_;
730	casa::ScalarColumn<casa::Float> elCol_;
731	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
732	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
733	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
734	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
735	casa::ArrayColumn<casa::uChar> flagsCol_;
736
737	// id in frequencies table
738	casa::ScalarColumn<casa::uInt> mfreqidCol_;
739	// id in tcal table
740	casa::ScalarColumn<casa::uInt> mtcalidCol_;
741
742	casa::ArrayColumn<casa::String> histitemCol_;
743	casa::ScalarColumn<casa::Int> mfitidCol_;
744	casa::ScalarColumn<casa::uInt> mweatheridCol_;
745
746	casa::ScalarColumn<casa::uInt> mfocusidCol_;
747
748	casa::ScalarColumn<casa::uInt> mmolidCol_;
749
750	static std::map<std::string, STPol::STPolFactory *> factories_;
751	void initFactories();
752
753	/**
754	* Add an auxiliary column to the main table and attach it to a
755	* cached column. Use for adding new columns that the original asap2
756	* tables do not have.
757	* @param[in] col reference to the cached column to be attached
758	* @param[in] colName column name in asap table
759	* @param[in] defValue default value to fill in the column
760	*
761	* 25/10/2009 Wataru Kawasaki
762	*/
763	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
764	const casa::String&,
765	const T2&);
766	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
767	const casa::String&,
768	const casa::Array<T2>&);
769
770	double getNormalPolynomial(int n, double x);
771	double getChebyshevPolynomial(int n, double x);
772	std::vector<std::vector<double> > getPolynomialModel(int order,
773	int nchan,
774	double (Scantable::*pfunc)(int, double));
775	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
776	double (Scantable::*pfunc)(int, double),
777	std::vector<int>& nChanNos);
778	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
779	const std::vector<bool>& mask,
780	int order,
781	std::vector<float>& params,
782	float& rms,
783	std::vector<bool>& finalMask,
784	float clipth,
785	int clipn);
786	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
787	const std::vector<bool>& mask,
788	int order,
789	std::vector<float>& params,
790	float& rms,
791	std::vector<bool>& finalMask,
792	int& nClipped,
793	float thresClip=3.0,
794	int nIterClip=0,
795	bool getResidual=true);
796	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
797	const std::vector<bool>& mask,
798	int order,
799	std::vector<float>& params,
800	float& rms,
801	std::vector<bool>& finalMask,
802	float clipth,
803	int clipn);
804	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
805	const std::vector<bool>& mask,
806	int order,
807	std::vector<float>& params,
808	float& rms,
809	std::vector<bool>& finalMask,
810	int& nClipped,
811	float thresClip=3.0,
812	int nIterClip=0,
813	bool getResidual=true);
814	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
815	const std::vector<bool>& mask,
816	const std::vector<std::vector<double> >& model,
817	std::vector<float>& params,
818	float& rms,
819	std::vector<bool>& finalMask,
820	int& nClipped,
821	float thresClip=3.0,
822	int nIterClip=0,
823	bool getResidual=true);
824	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
825	const std::vector<bool>& mask,
826	std::vector<int>& idxEdge,
827	std::vector<float>& params,
828	float& rms,
829	std::vector<bool>& finalMask,
830	float clipth,
831	int clipn);
832	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
833	const std::vector<bool>& mask,
834	int nPiece,
835	std::vector<int>& idxEdge,
836	std::vector<float>& params,
837	float& rms,
838	std::vector<bool>& finalMask,
839	float clipth,
840	int clipn);
841	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
842	const std::vector<bool>& mask,
843	int nPiece,
844	bool useGivenPieceBoundary,
845	std::vector<int>& idxEdge,
846	std::vector<float>& params,
847	float& rms,
848	std::vector<bool>& finalMask,
849	int& nClipped,
850	float thresClip=3.0,
851	int nIterClip=0,
852	bool getResidual=true);
853	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
854	const std::vector<bool>& mask,
855	const std::vector<std::vector<double> >& model,
856	int nPiece,
857	bool useGivenPieceBoundary,
858	std::vector<int>& idxEdge,
859	std::vector<float>& params,
860	float& rms,
861	std::vector<bool>& finalMask,
862	int& nClipped,
863	float thresClip=3.0,
864	int nIterClip=0,
865	bool getResidual=true);
866	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
867	const std::vector<bool>& mask,
868	const std::vector<int>& waveNumbers,
869	std::vector<float>& params,
870	float& rms,
871	std::vector<bool>& finalMask,
872	float clipth,
873	int clipn);
874	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
875	const std::vector<bool>& mask,
876	const std::vector<int>& waveNumbers,
877	std::vector<float>& params,
878	float& rms,
879	std::vector<bool>& finalMask,
880	int& nClipped,
881	float thresClip=3.0,
882	int nIterClip=0,
883	bool getResidual=true);
884	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
885	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
886	std::vector<int>& nChanNos);
887	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
888	const std::vector<int>& rejectNWaves);
889	std::vector<int> selectWaveNumbers(const int whichrow,
890	const std::vector<bool>& chanMask,
891	//const std::string& fftInfo,
892	const bool applyFFT,
893	const std::string& fftMethod,
894	const std::string& fftThresh,
895	const std::vector<int>& addNWaves,
896	const std::vector<int>& rejectNWaves);
897	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
898	void parseFFTInfo(const std::string& fftInfo,
899	bool& applyFFT,
900	std::string& fftMethod,
901	std::string& fftThresh);
902	void parseFFTThresholdInfo(const std::string& fftThresh,
903	std::string& fftThAttr,
904	float& fftThSigma,
905	int& fftThTop);
906	void doSelectWaveNumbers(const int whichrow,
907	const std::vector<bool>& chanMask,
908	const std::string& fftMethod,
909	const float fftThSigma,
910	const int fftThTop,
911	const std::string& fftThAttr,
912	std::vector<int>& nWaves);
913	void addAuxWaveNumbers(const int whichrow,
914	const std::vector<int>& addNWaves,
915	const std::vector<int>& rejectNWaves,
916	std::vector<int>& nWaves);
917	void setWaveNumberListUptoNyquistFreq(const int whichrow,
918	std::vector<int>& nWaves);
919	void initialiseBaselining(const std::string& blfile,
920	std::ofstream& ofs,
921	const bool outLogger,
922	bool& outTextFile,
923	bool& csvFormat,
924	casa::String& coordInfo,
925	bool& hasSameNchan,
926	const std::string& progressInfo,
927	bool& showProgress,
928	int& minNRow,
929	casa::Vector<casa::Double>& timeSecCol);
930	void finaliseBaselining(const bool outBaselineTable,
931	STBaselineTable* pbt,
932	const string& bltable,
933	const bool outTextFile,
934	std::ofstream& ofs);
935	void initLineFinder(const std::vector<int>& edge,
936	const float threshold,
937	const int chanAvgLimit,
938	STLineFinder& lineFinder);
939	bool hasSameNchanOverIFs();
940	std::string getMaskRangeList(const std::vector<bool>& mask,
941	int whichrow,
942	const casa::String& coordInfo,
943	bool hasSameNchan,
944	bool verbose=false);
945	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
946	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
947	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
948	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
949	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
950	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);
951	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);
952	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
953	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
954
955	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
956
957	double doCalculateModelSelectionCriteria(const std::string& valname,
958	const std::vector<float>& spec,
959	const std::vector<bool>& mask,
960	const std::string& blfunc,
961	int order);
962	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
963	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
964	void parseBlInfo(const std::string& blInfo, int& whichrow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF);
965	std::vector<float> doApplyBaselineTable(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms);
966	std::vector<float> doSubtractBaseline(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms, std::vector<bool>& finalmask, float clipth, int clipn, bool uself, int irow, float lfth, std::vector<int>& lfedge, int lfavg);
967
968	};
969	} // namespace
970
971	#endif

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