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source: trunk/src/Scantable.h@ 2782

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Last change on this file since 2782 was 2773, checked in by WataruKawasaki, 12 years ago

New Development: No

JIRA Issue: No

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: Yes

Module(s): sd

Description: optimisation/refactoring the baselining functions for scantable.

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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	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	void regridSpecChannel( double dnu, int nchan=-1 ) ;
507
508	bool getFlagtraFast(casa::uInt whichrow);
509
510	std::vector<std::string> applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
511	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
512	void polyBaseline(const std::vector<bool>& mask,
513	int order,
514	float thresClip,
515	int nIterClip,
516	bool getResidual=true,
517	const std::string& progressInfo="true,1000",
518	const bool outLogger=false,
519	const std::string& blfile="",
520	const std::string& bltable="");
521	void autoPolyBaseline(const std::vector<bool>& mask,
522	int order,
523	float thresClip,
524	int nIterClip,
525	const std::vector<int>& edge,
526	float threshold=3.0,
527	int chanAvgLimit=1,
528	bool getResidual=true,
529	const std::string& progressInfo="true,1000",
530	const bool outLogger=false,
531	const std::string& blfile="",
532	const std::string& bltable="");
533	void chebyshevBaseline(const std::vector<bool>& mask,
534	int order,
535	float thresClip,
536	int nIterClip,
537	bool getResidual=true,
538	const std::string& progressInfo="true,1000",
539	const bool outLogger=false,
540	const std::string& blfile="",
541	const std::string& bltable="");
542	void autoChebyshevBaseline(const std::vector<bool>& mask,
543	int order,
544	float thresClip,
545	int nIterClip,
546	const std::vector<int>& edge,
547	float threshold=3.0,
548	int chanAvgLimit=1,
549	bool getResidual=true,
550	const std::string& progressInfo="true,1000",
551	const bool outLogger=false,
552	const std::string& blfile="",
553	const std::string& bltable="");
554	void cubicSplineBaseline(const std::vector<bool>& mask,
555	int nPiece,
556	float thresClip,
557	int nIterClip,
558	bool getResidual=true,
559	const std::string& progressInfo="true,1000",
560	const bool outLogger=false,
561	const std::string& blfile="",
562	const std::string& bltable="");
563	void autoCubicSplineBaseline(const std::vector<bool>& mask,
564	int nPiece,
565	float thresClip,
566	int nIterClip,
567	const std::vector<int>& edge,
568	float threshold=3.0,
569	int chanAvgLimit=1,
570	bool getResidual=true,
571	const std::string& progressInfo="true,1000",
572	const bool outLogger=false,
573	const std::string& blfile="",
574	const std::string& bltable="");
575	void sinusoidBaseline(const std::vector<bool>& mask,
576	const std::string& fftInfo,
577	const std::vector<int>& addNWaves,
578	const std::vector<int>& rejectNWaves,
579	float thresClip,
580	int nIterClip,
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 autoSinusoidBaseline(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	const std::vector<int>& edge,
593	float threshold=3.0,
594	int chanAvgLimit=1,
595	bool getResidual=true,
596	const std::string& progressInfo="true,1000",
597	const bool outLogger=false,
598	const std::string& blfile="",
599	const std::string& bltable="");
600	std::vector<float> execFFT(const int whichrow,
601	const std::vector<bool>& inMask,
602	bool getRealImag=false,
603	bool getAmplitudeOnly=false);
604	float getRms(const std::vector<bool>& mask, int whichrow);
605	std::string formatBaselineParams(const std::vector<float>& params,
606	const std::vector<bool>& fixed,
607	float rms,
608	int nClipped,
609	const std::string& masklist,
610	int whichrow,
611	bool verbose=false,
612	bool csvformat=false,
613	int start=-1,
614	int count=-1,
615	bool resetparamid=false) const;
616	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
617	const std::vector<float>& params,
618	const std::vector<bool>& fixed,
619	float rms,
620	int nClipped,
621	const std::string& masklist,
622	int whichrow,
623	bool verbose=false,
624	bool csvformat=false) const;
625	std::vector<uint> getMoleculeIdColumnData() const;
626	void setMoleculeIdColumnData(const std::vector<uint>& molids);
627	double calculateModelSelectionCriteria(const std::string& valname,
628	const std::string& blfunc,
629	int order,
630	const std::vector<bool>& inMask,
631	int whichrow,
632	bool useLineFinder,
633	const std::vector<int>& edge,
634	float threshold,
635	int chanAvgLimit);
636	static std::vector<bool> getMaskFromMaskList(const int nchan,
637	const std::vector<int>& masklist);
638	static casa::Vector<casa::uInt> getMaskListFromMask(const std::vector<bool>& mask);
639	static std::vector<int> splitToIntList(const std::string& str, const char delim);
640	static std::vector<string> splitToStringList(const std::string& str, const char delim);
641
642
643
644	private:
645
646	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
647
648	/**
649	* Turns a time value into a formatted string
650	* @param x
651	* @return
652	*/
653	std::string formatSec(casa::Double x) const;
654
655	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
656	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
657
658	/**
659	* Turns a casa::MDirection into a nicely formatted string
660	* @param md an casa::MDirection
661	* @return
662	*/
663	std::string formatDirection(const casa::MDirection& md) const;
664
665	/**
666	* Create a unique file name for the paged (temporary) table
667	* @return just the name
668	*/
669	static casa::String generateName();
670
671	/**
672	* attach to cached columns
673	*/
674	void attach();
675
676	/**
677	* Set up the main casa::Table
678	*/
679	void setupMainTable();
680
681	void attachSubtables();
682	void copySubtables(const Scantable& other);
683
684	/**
685	* Convert an "old" asap1 style row index into a new index
686	* @param[in] therow
687	* @return and index into @table_
688	*/
689	int rowToScanIndex(int therow);
690
691	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
692
693	static const casa::uInt version_ = 4;
694
695	STSelector selector_;
696
697	casa::Table::TableType type_;
698
699	// the actual data
700	casa::Table table_;
701	casa::Table originalTable_;
702
703	STTcal tcalTable_;
704	STFrequencies freqTable_;
705	STWeather weatherTable_;
706	STFocus focusTable_;
707	STMolecules moleculeTable_;
708	STHistory historyTable_;
709	STFit fitTable_;
710
711	// Cached Columns to avoid reconstructing them for each row get/put
712	casa::ScalarColumn<casa::Double> integrCol_;
713	casa::MDirection::ScalarColumn dirCol_;
714	casa::MEpoch::ScalarColumn timeCol_;
715	casa::ScalarColumn<casa::Float> azCol_;
716	casa::ScalarColumn<casa::Float> elCol_;
717	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
718	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
719	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
720	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
721	casa::ArrayColumn<casa::uChar> flagsCol_;
722
723	// id in frequencies table
724	casa::ScalarColumn<casa::uInt> mfreqidCol_;
725	// id in tcal table
726	casa::ScalarColumn<casa::uInt> mtcalidCol_;
727
728	casa::ArrayColumn<casa::String> histitemCol_;
729	casa::ScalarColumn<casa::Int> mfitidCol_;
730	casa::ScalarColumn<casa::uInt> mweatheridCol_;
731
732	casa::ScalarColumn<casa::uInt> mfocusidCol_;
733
734	casa::ScalarColumn<casa::uInt> mmolidCol_;
735
736	static std::map<std::string, STPol::STPolFactory *> factories_;
737	void initFactories();
738
739	/**
740	* Add an auxiliary column to the main table and attach it to a
741	* cached column. Use for adding new columns that the original asap2
742	* tables do not have.
743	* @param[in] col reference to the cached column to be attached
744	* @param[in] colName column name in asap table
745	* @param[in] defValue default value to fill in the column
746	*
747	* 25/10/2009 Wataru Kawasaki
748	*/
749	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
750	const casa::String&,
751	const T2&);
752	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
753	const casa::String&,
754	const casa::Array<T2>&);
755
756	double getNormalPolynomial(int n, double x);
757	double getChebyshevPolynomial(int n, double x);
758	std::vector<std::vector<double> > getPolynomialModel(int order,
759	int nchan,
760	double (Scantable::*pfunc)(int, double));
761	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
762	double (Scantable::*pfunc)(int, double),
763	std::vector<int>& nChanNos);
764	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
765	const std::vector<bool>& mask,
766	int order,
767	std::vector<float>& params,
768	float& rms,
769	std::vector<bool>& finalMask,
770	float clipth,
771	int clipn);
772	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
773	const std::vector<bool>& mask,
774	int order,
775	std::vector<float>& params,
776	float& rms,
777	std::vector<bool>& finalMask,
778	int& nClipped,
779	float thresClip=3.0,
780	int nIterClip=0,
781	bool getResidual=true);
782	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
783	const std::vector<bool>& mask,
784	int order,
785	std::vector<float>& params,
786	float& rms,
787	std::vector<bool>& finalMask,
788	float clipth,
789	int clipn);
790	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
791	const std::vector<bool>& mask,
792	int order,
793	std::vector<float>& params,
794	float& rms,
795	std::vector<bool>& finalMask,
796	int& nClipped,
797	float thresClip=3.0,
798	int nIterClip=0,
799	bool getResidual=true);
800	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
801	const std::vector<bool>& mask,
802	const std::vector<std::vector<double> >& model,
803	std::vector<float>& params,
804	float& rms,
805	std::vector<bool>& finalMask,
806	int& nClipped,
807	float thresClip=3.0,
808	int nIterClip=0,
809	bool getResidual=true);
810	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
811	const std::vector<bool>& mask,
812	std::vector<int>& idxEdge,
813	std::vector<float>& params,
814	float& rms,
815	std::vector<bool>& finalMask,
816	float clipth,
817	int clipn);
818	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
819	const std::vector<bool>& mask,
820	int nPiece,
821	std::vector<int>& idxEdge,
822	std::vector<float>& params,
823	float& rms,
824	std::vector<bool>& finalMask,
825	float clipth,
826	int clipn);
827	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
828	const std::vector<bool>& mask,
829	int nPiece,
830	bool useGivenPieceBoundary,
831	std::vector<int>& idxEdge,
832	std::vector<float>& params,
833	float& rms,
834	std::vector<bool>& finalMask,
835	int& nClipped,
836	float thresClip=3.0,
837	int nIterClip=0,
838	bool getResidual=true);
839	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
840	const std::vector<bool>& mask,
841	const std::vector<std::vector<double> >& model,
842	int nPiece,
843	bool useGivenPieceBoundary,
844	std::vector<int>& idxEdge,
845	std::vector<float>& params,
846	float& rms,
847	std::vector<bool>& finalMask,
848	int& nClipped,
849	float thresClip=3.0,
850	int nIterClip=0,
851	bool getResidual=true);
852	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
853	const std::vector<bool>& mask,
854	const std::vector<int>& waveNumbers,
855	std::vector<float>& params,
856	float& rms,
857	std::vector<bool>& finalMask,
858	float clipth,
859	int clipn);
860	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
861	const std::vector<bool>& mask,
862	const std::vector<int>& waveNumbers,
863	std::vector<float>& params,
864	float& rms,
865	std::vector<bool>& finalMask,
866	int& nClipped,
867	float thresClip=3.0,
868	int nIterClip=0,
869	bool getResidual=true);
870	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
871	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
872	std::vector<int>& nChanNos);
873	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
874	const std::vector<int>& rejectNWaves);
875	std::vector<int> selectWaveNumbers(const int whichrow,
876	const std::vector<bool>& chanMask,
877	//const std::string& fftInfo,
878	const bool applyFFT,
879	const std::string& fftMethod,
880	const std::string& fftThresh,
881	const std::vector<int>& addNWaves,
882	const std::vector<int>& rejectNWaves);
883	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
884	void parseFFTInfo(const std::string& fftInfo,
885	bool& applyFFT,
886	std::string& fftMethod,
887	std::string& fftThresh);
888	void parseFFTThresholdInfo(const std::string& fftThresh,
889	std::string& fftThAttr,
890	float& fftThSigma,
891	int& fftThTop);
892	void doSelectWaveNumbers(const int whichrow,
893	const std::vector<bool>& chanMask,
894	const std::string& fftMethod,
895	const float fftThSigma,
896	const int fftThTop,
897	const std::string& fftThAttr,
898	std::vector<int>& nWaves);
899	void addAuxWaveNumbers(const int whichrow,
900	const std::vector<int>& addNWaves,
901	const std::vector<int>& rejectNWaves,
902	std::vector<int>& nWaves);
903	void setWaveNumberListUptoNyquistFreq(const int whichrow,
904	std::vector<int>& nWaves);
905	void initialiseBaselining(const std::string& blfile,
906	std::ofstream& ofs,
907	const bool outLogger,
908	bool& outTextFile,
909	bool& csvFormat,
910	casa::String& coordInfo,
911	bool& hasSameNchan,
912	const std::string& progressInfo,
913	bool& showProgress,
914	int& minNRow,
915	casa::Vector<casa::Double>& timeSecCol);
916	void finaliseBaselining(const bool outBaselineTable,
917	STBaselineTable* pbt,
918	const string& bltable,
919	const bool outTextFile,
920	std::ofstream& ofs);
921	void initLineFinder(const std::vector<int>& edge,
922	const float threshold,
923	const int chanAvgLimit,
924	STLineFinder& lineFinder);
925	bool hasSameNchanOverIFs();
926	std::string getMaskRangeList(const std::vector<bool>& mask,
927	int whichrow,
928	const casa::String& coordInfo,
929	bool hasSameNchan,
930	bool verbose=false);
931	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
932	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
933	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
934	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
935	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
936	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);
937	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);
938	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
939	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
940
941	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
942
943	double doCalculateModelSelectionCriteria(const std::string& valname,
944	const std::vector<float>& spec,
945	const std::vector<bool>& mask,
946	const std::string& blfunc,
947	int order);
948	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
949	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
950	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);
951	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);
952	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);
953
954	};
955	} // namespace
956
957	#endif

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