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source: trunk/src/Scantable.h @ 2791

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Last change on this file since 2791 was 2791, checked in by Malte Marquarding, 11 years ago
Ticket #289: added anility to set Tsys, both for scalar and vector values
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 32.3 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, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
514	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
515	void polyBaseline(const std::vector<bool>& mask,
516	int order,
517	float thresClip,
518	int nIterClip,
519	bool getResidual=true,
520	const std::string& progressInfo="true,1000",
521	const bool outLogger=false,
522	const std::string& blfile="",
523	const std::string& bltable="");
524	void autoPolyBaseline(const std::vector<bool>& mask,
525	int order,
526	float thresClip,
527	int nIterClip,
528	const std::vector<int>& edge,
529	float threshold=3.0,
530	int chanAvgLimit=1,
531	bool getResidual=true,
532	const std::string& progressInfo="true,1000",
533	const bool outLogger=false,
534	const std::string& blfile="",
535	const std::string& bltable="");
536	void chebyshevBaseline(const std::vector<bool>& mask,
537	int order,
538	float thresClip,
539	int nIterClip,
540	bool getResidual=true,
541	const std::string& progressInfo="true,1000",
542	const bool outLogger=false,
543	const std::string& blfile="",
544	const std::string& bltable="");
545	void autoChebyshevBaseline(const std::vector<bool>& mask,
546	int order,
547	float thresClip,
548	int nIterClip,
549	const std::vector<int>& edge,
550	float threshold=3.0,
551	int chanAvgLimit=1,
552	bool getResidual=true,
553	const std::string& progressInfo="true,1000",
554	const bool outLogger=false,
555	const std::string& blfile="",
556	const std::string& bltable="");
557	void cubicSplineBaseline(const std::vector<bool>& mask,
558	int nPiece,
559	float thresClip,
560	int nIterClip,
561	bool getResidual=true,
562	const std::string& progressInfo="true,1000",
563	const bool outLogger=false,
564	const std::string& blfile="",
565	const std::string& bltable="");
566	void autoCubicSplineBaseline(const std::vector<bool>& mask,
567	int nPiece,
568	float thresClip,
569	int nIterClip,
570	const std::vector<int>& edge,
571	float threshold=3.0,
572	int chanAvgLimit=1,
573	bool getResidual=true,
574	const std::string& progressInfo="true,1000",
575	const bool outLogger=false,
576	const std::string& blfile="",
577	const std::string& bltable="");
578	void sinusoidBaseline(const std::vector<bool>& mask,
579	const std::string& fftInfo,
580	const std::vector<int>& addNWaves,
581	const std::vector<int>& rejectNWaves,
582	float thresClip,
583	int nIterClip,
584	bool getResidual=true,
585	const std::string& progressInfo="true,1000",
586	const bool outLogger=false,
587	const std::string& blfile="",
588	const std::string& bltable="");
589	void autoSinusoidBaseline(const std::vector<bool>& mask,
590	const std::string& fftInfo,
591	const std::vector<int>& addNWaves,
592	const std::vector<int>& rejectNWaves,
593	float thresClip,
594	int nIterClip,
595	const std::vector<int>& edge,
596	float threshold=3.0,
597	int chanAvgLimit=1,
598	bool getResidual=true,
599	const std::string& progressInfo="true,1000",
600	const bool outLogger=false,
601	const std::string& blfile="",
602	const std::string& bltable="");
603	std::vector<float> execFFT(const int whichrow,
604	const std::vector<bool>& inMask,
605	bool getRealImag=false,
606	bool getAmplitudeOnly=false);
607	float getRms(const std::vector<bool>& mask, int whichrow);
608	std::string formatBaselineParams(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,
616	int start=-1,
617	int count=-1,
618	bool resetparamid=false) const;
619	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
620	const std::vector<float>& params,
621	const std::vector<bool>& fixed,
622	float rms,
623	int nClipped,
624	const std::string& masklist,
625	int whichrow,
626	bool verbose=false,
627	bool csvformat=false) const;
628	std::vector<uint> getMoleculeIdColumnData() const;
629	void setMoleculeIdColumnData(const std::vector<uint>& molids);
630	double calculateModelSelectionCriteria(const std::string& valname,
631	const std::string& blfunc,
632	int order,
633	const std::vector<bool>& inMask,
634	int whichrow,
635	bool useLineFinder,
636	const std::vector<int>& edge,
637	float threshold,
638	int chanAvgLimit);
639	static std::vector<bool> getMaskFromMaskList(const int nchan,
640	const std::vector<int>& masklist);
641	static casa::Vector<casa::uInt> getMaskListFromMask(
642	const std::vector<bool>& mask);
643	static std::vector<int> splitToIntList(const std::string& str,
644	const char delim);
645	static std::vector<string> splitToStringList(const std::string& str,
646	const char delim);
647
648	void dropXPol();
649
650	private:
651
652	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
653
654	/**
655	* Turns a time value into a formatted string
656	* @param x
657	* @return
658	*/
659	std::string formatSec(casa::Double x) const;
660
661	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
662	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
663
664	/**
665	* Turns a casa::MDirection into a nicely formatted string
666	* @param md an casa::MDirection
667	* @return
668	*/
669	std::string formatDirection(const casa::MDirection& md) const;
670
671	/**
672	* Create a unique file name for the paged (temporary) table
673	* @return just the name
674	*/
675	static casa::String generateName();
676
677	/**
678	* attach to cached columns
679	*/
680	void attach();
681
682	/**
683	* Set up the main casa::Table
684	*/
685	void setupMainTable();
686
687	void attachSubtables();
688	void copySubtables(const Scantable& other);
689
690	/**
691	* Convert an "old" asap1 style row index into a new index
692	* @param[in] therow
693	* @return and index into @table_
694	*/
695	int rowToScanIndex(int therow);
696
697	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
698
699	static const casa::uInt version_ = 4;
700
701	STSelector selector_;
702
703	casa::Table::TableType type_;
704
705	// the actual data
706	casa::Table table_;
707	casa::Table originalTable_;
708
709	STTcal tcalTable_;
710	STFrequencies freqTable_;
711	STWeather weatherTable_;
712	STFocus focusTable_;
713	STMolecules moleculeTable_;
714	STHistory historyTable_;
715	STFit fitTable_;
716
717	// Cached Columns to avoid reconstructing them for each row get/put
718	casa::ScalarColumn<casa::Double> integrCol_;
719	casa::MDirection::ScalarColumn dirCol_;
720	casa::MEpoch::ScalarColumn timeCol_;
721	casa::ScalarColumn<casa::Float> azCol_;
722	casa::ScalarColumn<casa::Float> elCol_;
723	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
724	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
725	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
726	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
727	casa::ArrayColumn<casa::uChar> flagsCol_;
728
729	// id in frequencies table
730	casa::ScalarColumn<casa::uInt> mfreqidCol_;
731	// id in tcal table
732	casa::ScalarColumn<casa::uInt> mtcalidCol_;
733
734	casa::ArrayColumn<casa::String> histitemCol_;
735	casa::ScalarColumn<casa::Int> mfitidCol_;
736	casa::ScalarColumn<casa::uInt> mweatheridCol_;
737
738	casa::ScalarColumn<casa::uInt> mfocusidCol_;
739
740	casa::ScalarColumn<casa::uInt> mmolidCol_;
741
742	static std::map<std::string, STPol::STPolFactory *> factories_;
743	void initFactories();
744
745	/**
746	* Add an auxiliary column to the main table and attach it to a
747	* cached column. Use for adding new columns that the original asap2
748	* tables do not have.
749	* @param[in] col reference to the cached column to be attached
750	* @param[in] colName column name in asap table
751	* @param[in] defValue default value to fill in the column
752	*
753	* 25/10/2009 Wataru Kawasaki
754	*/
755	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
756	const casa::String&,
757	const T2&);
758	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
759	const casa::String&,
760	const casa::Array<T2>&);
761
762	double getNormalPolynomial(int n, double x);
763	double getChebyshevPolynomial(int n, double x);
764	std::vector<std::vector<double> > getPolynomialModel(int order,
765	int nchan,
766	double (Scantable::*pfunc)(int, double));
767	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
768	double (Scantable::*pfunc)(int, double),
769	std::vector<int>& nChanNos);
770	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
771	const std::vector<bool>& mask,
772	int order,
773	std::vector<float>& params,
774	float& rms,
775	std::vector<bool>& finalMask,
776	float clipth,
777	int clipn);
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	int& nClipped,
785	float thresClip=3.0,
786	int nIterClip=0,
787	bool getResidual=true);
788	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
789	const std::vector<bool>& mask,
790	int order,
791	std::vector<float>& params,
792	float& rms,
793	std::vector<bool>& finalMask,
794	float clipth,
795	int clipn);
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	int& nClipped,
803	float thresClip=3.0,
804	int nIterClip=0,
805	bool getResidual=true);
806	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
807	const std::vector<bool>& mask,
808	const std::vector<std::vector<double> >& model,
809	std::vector<float>& params,
810	float& rms,
811	std::vector<bool>& finalMask,
812	int& nClipped,
813	float thresClip=3.0,
814	int nIterClip=0,
815	bool getResidual=true);
816	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
817	const std::vector<bool>& mask,
818	std::vector<int>& idxEdge,
819	std::vector<float>& params,
820	float& rms,
821	std::vector<bool>& finalMask,
822	float clipth,
823	int clipn);
824	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
825	const std::vector<bool>& mask,
826	int nPiece,
827	std::vector<int>& idxEdge,
828	std::vector<float>& params,
829	float& rms,
830	std::vector<bool>& finalMask,
831	float clipth,
832	int clipn);
833	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
834	const std::vector<bool>& mask,
835	int nPiece,
836	bool useGivenPieceBoundary,
837	std::vector<int>& idxEdge,
838	std::vector<float>& params,
839	float& rms,
840	std::vector<bool>& finalMask,
841	int& nClipped,
842	float thresClip=3.0,
843	int nIterClip=0,
844	bool getResidual=true);
845	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
846	const std::vector<bool>& mask,
847	const std::vector<std::vector<double> >& model,
848	int nPiece,
849	bool useGivenPieceBoundary,
850	std::vector<int>& idxEdge,
851	std::vector<float>& params,
852	float& rms,
853	std::vector<bool>& finalMask,
854	int& nClipped,
855	float thresClip=3.0,
856	int nIterClip=0,
857	bool getResidual=true);
858	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
859	const std::vector<bool>& mask,
860	const std::vector<int>& waveNumbers,
861	std::vector<float>& params,
862	float& rms,
863	std::vector<bool>& finalMask,
864	float clipth,
865	int clipn);
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	int& nClipped,
873	float thresClip=3.0,
874	int nIterClip=0,
875	bool getResidual=true);
876	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
877	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
878	std::vector<int>& nChanNos);
879	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
880	const std::vector<int>& rejectNWaves);
881	std::vector<int> selectWaveNumbers(const int whichrow,
882	const std::vector<bool>& chanMask,
883	//const std::string& fftInfo,
884	const bool applyFFT,
885	const std::string& fftMethod,
886	const std::string& fftThresh,
887	const std::vector<int>& addNWaves,
888	const std::vector<int>& rejectNWaves);
889	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
890	void parseFFTInfo(const std::string& fftInfo,
891	bool& applyFFT,
892	std::string& fftMethod,
893	std::string& fftThresh);
894	void parseFFTThresholdInfo(const std::string& fftThresh,
895	std::string& fftThAttr,
896	float& fftThSigma,
897	int& fftThTop);
898	void doSelectWaveNumbers(const int whichrow,
899	const std::vector<bool>& chanMask,
900	const std::string& fftMethod,
901	const float fftThSigma,
902	const int fftThTop,
903	const std::string& fftThAttr,
904	std::vector<int>& nWaves);
905	void addAuxWaveNumbers(const int whichrow,
906	const std::vector<int>& addNWaves,
907	const std::vector<int>& rejectNWaves,
908	std::vector<int>& nWaves);
909	void setWaveNumberListUptoNyquistFreq(const int whichrow,
910	std::vector<int>& nWaves);
911	void initialiseBaselining(const std::string& blfile,
912	std::ofstream& ofs,
913	const bool outLogger,
914	bool& outTextFile,
915	bool& csvFormat,
916	casa::String& coordInfo,
917	bool& hasSameNchan,
918	const std::string& progressInfo,
919	bool& showProgress,
920	int& minNRow,
921	casa::Vector<casa::Double>& timeSecCol);
922	void finaliseBaselining(const bool outBaselineTable,
923	STBaselineTable* pbt,
924	const string& bltable,
925	const bool outTextFile,
926	std::ofstream& ofs);
927	void initLineFinder(const std::vector<int>& edge,
928	const float threshold,
929	const int chanAvgLimit,
930	STLineFinder& lineFinder);
931	bool hasSameNchanOverIFs();
932	std::string getMaskRangeList(const std::vector<bool>& mask,
933	int whichrow,
934	const casa::String& coordInfo,
935	bool hasSameNchan,
936	bool verbose=false);
937	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
938	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
939	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
940	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
941	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
942	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);
943	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);
944	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
945	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
946
947	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
948
949	double doCalculateModelSelectionCriteria(const std::string& valname,
950	const std::vector<float>& spec,
951	const std::vector<bool>& mask,
952	const std::string& blfunc,
953	int order);
954	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
955	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
956	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);
957	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);
958	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);
959
960	};
961	} // namespace
962
963	#endif

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