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source: trunk/src/Scantable.h @ 2818

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Last change on this file since 2818 was 2818, checked in by Malte Marquarding, 11 years ago
Issue #291: added scantable.set_sourcename to overwrite sourcename to allow freq_align to work. Exposed 'SOURCE' averaging to python api. Added some logging to freq_align refering to the sources it aligns to
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 32.6 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	* @param stype The name of the source
160	*/
161	void setSourceName(const std::string& name);
162
163
164	/**
165	* The number of scans in the table
166	* @return number of scans in the table
167	*/
168	int nscan() const;
169
170	casa::MEpoch::Types getTimeReference() const;
171
172
173	casa::MEpoch getEpoch(int whichrow) const;
174
175	/**
176	* Get global antenna position
177	* @return casa::MPosition
178	*/
179	casa::MPosition getAntennaPosition() const;
180
181	/**
182	* the @ref casa::MDirection for a specific row
183	* @param[in] whichrow the row number
184	* return casa::MDirection
185	*/
186	casa::MDirection getDirection( int whichrow ) const;
187
188	/**
189	* get the direction type as a string, e.g. "J2000"
190	* @param[in] whichrow the row number
191	* return the direction string
192	*/
193	std::string getDirectionString( int whichrow ) const;
194
195	/**
196	* set the direction type as a string, e.g. "J2000"
197	* @param[in] refstr the direction type
198	*/
199	void setDirectionRefString(const std::string& refstr="");
200
201	/**
202	* get the direction reference string
203	* @return a string describing the direction reference
204	*/
205	std::string getDirectionRefString() const;
206
207	/**
208	* Return the Flux unit of the data, e.g. "Jy" or "K"
209	* @return string
210	*/
211	std::string getFluxUnit() const;
212
213	/**
214	* Set the Flux unit of the data
215	* @param unit a string representing the unit, e.g "Jy" or "K"
216	*/
217	void setFluxUnit( const std::string& unit );
218
219	/**
220	* Set the Stokes type of the data
221	* @param feedtype a string representing the type, e.g "circular" or "linear"
222	*/
223	void setFeedType( const std::string& feedtype );
224
225	/**
226	*
227	* @param instrument a string representing an insturment. see xxx
228	*/
229	void setInstrument( const std::string& instrument );
230
231	/**
232	* (Re)calculate the azimuth and elevationnfor all rows
233	*/
234	void calculateAZEL();
235
236	/**
237	* "hard" flag the data, this flags everything selected in setSelection()
238	* param[in] msk a boolean mask of length nchan describing the points to
239	* to be flagged
240	*/
241	//void flag( const std::vector<bool>& msk = std::vector<bool>());
242	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
243
244	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
245
246	/**
247	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
248	* param[in] rows list of row numbers to be flagged
249	*/
250	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
251
252	/**
253	* Get flagRow info at the specified row. If true, the whole data
254	* at the row should be flagged.
255	*/
256	bool getFlagRow(int whichrow) const
257	{ return (flagrowCol_(whichrow) > 0); }
258
259	/**
260	* Flag the data outside a specified range (in a channel-based manner).
261	* (CAS-1807 Wataru Kawasaki)
262	*/
263	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
264
265	/**
266	* Return a list of booleans with the size of nchan for a specified row, to get info
267	* about which channel is clipped.
268	*/
269	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
270	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
271	casa::Vector<casa::uChar> flgs);
272
273	/**
274	* Return a list of row numbers with respect to the original table.
275	* @return a list of unsigned ints
276	*/
277	std::vector<unsigned int> rownumbers() const;
278
279
280	/**
281	* Get the number of beams in the data or a specific scan
282	* @param scanno the scan number to get the number of beams for.
283	* If scanno<0 the number is retrieved from the header.
284	* @return an integer number
285	*/
286	int nbeam(int scanno=-1) const;
287	/**
288	* Get the number of IFs in the data or a specific scan
289	* @param scanno the scan number to get the number of IFs for.
290	* If scanno<0 the number is retrieved from the header.
291	* @return an integer number
292	*/
293	int nif(int scanno=-1) const;
294	/**
295	* Get the number of polarizations in the data or a specific scan
296	* @param scanno the scan number to get the number of polarizations for.
297	* If scanno<0 the number is retrieved from the header.
298	* @return an integer number
299	*/
300	int npol(int scanno=-1) const;
301
302	std::string getPolType() const;
303
304
305	/**
306	* Get the number of integartion cycles
307	* @param scanno the scan number to get the number of rows for.
308	* If scanno<0 the number is retrieved from the header.
309	* @return the number of rows (for the specified scanno)
310	*/
311	int nrow(int scanno=-1) const;
312
313	int getBeam(int whichrow) const;
314	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
315
316	int getIF(int whichrow) const;
317	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
318
319	int getPol(int whichrow) const;
320	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
321
322	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
323	int getScan(int whichrow) const { return scanCol_(whichrow); }
324
325	std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
326	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
327
328	//TT addition
329	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
330
331	/**
332	* Get the number of channels in the data or a specific IF. This currently
333	* varies only with IF number
334	* @param ifno the IF number to get the number of channels for.
335	* If ifno<0 the number is retrieved from the header.
336	* @return an integer number
337	*/
338	int nchan(int ifno=-1) const;
339	int getChannels(int whichrow) const;
340
341	int ncycle(int scanno=-1) const;
342
343
344	double getInterval(int whichrow) const
345	{ return integrCol_(whichrow); }
346
347	float getTsys(int whichrow) const
348	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
349	std::vector<float> getTsysSpectrum(int whichrow) const ;
350
351	void setTsys(const std::vector<float>& newvals, int whichrow);
352
353	float getElevation(int whichrow) const
354	{ return elCol_(whichrow); }
355	float getAzimuth(int whichrow) const
356	{ return azCol_(whichrow); }
357	float getParAngle(int whichrow) const
358	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
359	int getTcalId(int whichrow) const
360	{ return mtcalidCol_(whichrow); }
361
362	std::string getSourceName(int whichrow) const
363	{ return srcnCol_(whichrow); }
364
365	std::vector<bool> getMask(int whichrow) const;
366	std::vector<float> getSpectrum(int whichrow,
367	const std::string& poltype = "" ) const;
368
369	void setSpectrum(const std::vector<float>& spec, int whichrow);
370
371	std::string getPolarizationLabel(int index, const std::string& ptype) const
372	{ return STPol::getPolLabel(index, ptype ); }
373
374	/**
375	* Write the Scantable to disk
376	* @param filename the output file name
377	*/
378	void makePersistent(const std::string& filename);
379
380	std::vector<std::string> getHistory() const
381	{ return historyTable_.getHistory(); };
382
383	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
384
385	void appendToHistoryTable(const STHistory& otherhist)
386	{ historyTable_.append(otherhist); }
387
388	std::string headerSummary();
389	void summary(const std::string& filename="");
390	std::string oldheaderSummary();
391	// std::string summary();
392	void oldsummary(const std::string& filename="");
393
394	//std::string getTime(int whichrow=-1, bool showdate=true) const;
395	std::string getTime(int whichrow=-1, bool showdate=true,
396	casa::uInt prec=0) const;
397	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
398
399	// returns unit, conversion frame, doppler, base-frame
400
401	/**
402	* Get the frequency set up
403	* This is forwarded to the STFrequencies subtable
404	* @return unit, frame, doppler
405	*/
406	std::vector<std::string> getCoordInfo() const
407	{ return freqTable_.getInfo(); };
408
409	void setCoordInfo(std::vector<string> theinfo)
410	{ return freqTable_.setInfo(theinfo); };
411
412
413	std::vector<double> getAbcissa(int whichrow) const;
414
415	std::vector<float> getWeather(int whichrow) const;
416
417	std::string getAbcissaLabel(int whichrow) const;
418	std::vector<double> getRestFrequencies() const
419	{ return moleculeTable_.getRestFrequencies(); }
420	std::vector<double> getRestFrequency(int id) const
421	{ return moleculeTable_.getRestFrequency(id); }
422
423	/**
424	void setRestFrequencies(double rf, const std::string& name = "",
425	const std::string& = "Hz");
426	**/
427	// Modified by Takeshi Nakazato 05/09/2008
428	/***
429	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
430	const std::string& = "Hz");
431	***/
432	void setRestFrequencies(vector<double> rf,
433	const vector<std::string>& name = vector<std::string>(1,""),
434	const std::string& = "Hz");
435
436	//void setRestFrequencies(const std::string& name);
437	void setRestFrequencies(const vector<std::string>& name);
438
439	void shift(int npix);
440
441	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
442
443	void convertDirection(const std::string& newframe);
444
445	STFrequencies& frequencies() { return freqTable_; }
446	const STFrequencies& frequencies() const { return freqTable_; }
447	STWeather& weather() { return weatherTable_; }
448	const STWeather& weather() const { return weatherTable_; }
449	STFocus& focus() { return focusTable_; }
450	const STFocus& focus() const { return focusTable_; }
451	STTcal& tcal() { return tcalTable_; }
452	const STTcal& tcal() const { return tcalTable_; }
453	STMolecules& molecules() { return moleculeTable_; }
454	const STMolecules& molecules() const { return moleculeTable_; }
455	STHistory& history() { return historyTable_; }
456	const STHistory& history() const { return historyTable_; }
457	STFit& fit() { return fitTable_; }
458	const STFit& fit() const { return fitTable_; }
459
460	std::vector<std::string> columnNames() const;
461
462	void addFit(const STFitEntry& fit, int row);
463	STFitEntry getFit(int row) const
464	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
465
466	//Added by TT
467	/**
468	* Get the antenna name
469	* @return antenna name string
470	*/
471	casa::String getAntennaName() const;
472
473	/**
474	* For GBT MS data only. check a scan list
475	* against the information found in GBT_GO table for
476	* scan number orders to get correct pairs.
477	* @param[in] scan list
478	* @return status
479	*/
480	int checkScanInfo(const std::vector<int>& scanlist) const;
481
482	/**
483	* Get the direction as a vector, for a specific row
484	* @param[in] whichrow the row numbyyer
485	* @return the direction in a vector
486	*/
487	std::vector<double> getDirectionVector(int whichrow) const;
488
489	/**
490	* Set a flag indicating whether the data was parallactified
491	* @param[in] flag true or false
492	*/
493	void parallactify(bool flag)
494	{ focusTable_.setParallactify(flag); }
495
496	/**
497	* Reshape spectrum
498	* @param[in] nmin, nmax minimum and maximum channel
499	* @param[in] irow row number
500	*
501	* 30/07/2008 Takeshi Nakazato
502	**/
503	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
504	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
505
506	/**
507	* Change channel number under fixed bandwidth
508	* @param[in] nchan, dnu new channel number and spectral resolution
509	* @param[in] irow row number
510	*
511	* 27/08/2008 Takeshi Nakazato
512	**/
513	void regridChannel( int nchan, double dnu ) ;
514	void regridChannel( int nchan, double dnu, int irow ) ;
515	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
516	void regridSpecChannel( double dnu, int nchan=-1 ) ;
517
518	bool getFlagtraFast(casa::uInt whichrow);
519
520	std::vector<std::string> applyBaselineTable(const std::string& bltable,
521	const bool returnfitresult,
522	const std::string& outbltable,
523	const bool outbltableexists,
524	const bool overwrite);
525	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList,
526	const bool returnfitresult,
527	const std::string& outbltable,
528	const bool outbltableexists,
529	const bool overwrite);
530	void polyBaseline(const std::vector<bool>& mask,
531	int order,
532	float thresClip,
533	int nIterClip,
534	bool getResidual=true,
535	const std::string& progressInfo="true,1000",
536	const bool outLogger=false,
537	const std::string& blfile="",
538	const std::string& bltable="");
539	void autoPolyBaseline(const std::vector<bool>& mask,
540	int order,
541	float thresClip,
542	int nIterClip,
543	const std::vector<int>& edge,
544	float threshold=3.0,
545	int chanAvgLimit=1,
546	bool getResidual=true,
547	const std::string& progressInfo="true,1000",
548	const bool outLogger=false,
549	const std::string& blfile="",
550	const std::string& bltable="");
551	void chebyshevBaseline(const std::vector<bool>& mask,
552	int order,
553	float thresClip,
554	int nIterClip,
555	bool getResidual=true,
556	const std::string& progressInfo="true,1000",
557	const bool outLogger=false,
558	const std::string& blfile="",
559	const std::string& bltable="");
560	void autoChebyshevBaseline(const std::vector<bool>& mask,
561	int order,
562	float thresClip,
563	int nIterClip,
564	const std::vector<int>& edge,
565	float threshold=3.0,
566	int chanAvgLimit=1,
567	bool getResidual=true,
568	const std::string& progressInfo="true,1000",
569	const bool outLogger=false,
570	const std::string& blfile="",
571	const std::string& bltable="");
572	void cubicSplineBaseline(const std::vector<bool>& mask,
573	int nPiece,
574	float thresClip,
575	int nIterClip,
576	bool getResidual=true,
577	const std::string& progressInfo="true,1000",
578	const bool outLogger=false,
579	const std::string& blfile="",
580	const std::string& bltable="");
581	void autoCubicSplineBaseline(const std::vector<bool>& mask,
582	int nPiece,
583	float thresClip,
584	int nIterClip,
585	const std::vector<int>& edge,
586	float threshold=3.0,
587	int chanAvgLimit=1,
588	bool getResidual=true,
589	const std::string& progressInfo="true,1000",
590	const bool outLogger=false,
591	const std::string& blfile="",
592	const std::string& bltable="");
593	void sinusoidBaseline(const std::vector<bool>& mask,
594	const std::string& fftInfo,
595	const std::vector<int>& addNWaves,
596	const std::vector<int>& rejectNWaves,
597	float thresClip,
598	int nIterClip,
599	bool getResidual=true,
600	const std::string& progressInfo="true,1000",
601	const bool outLogger=false,
602	const std::string& blfile="",
603	const std::string& bltable="");
604	void autoSinusoidBaseline(const std::vector<bool>& mask,
605	const std::string& fftInfo,
606	const std::vector<int>& addNWaves,
607	const std::vector<int>& rejectNWaves,
608	float thresClip,
609	int nIterClip,
610	const std::vector<int>& edge,
611	float threshold=3.0,
612	int chanAvgLimit=1,
613	bool getResidual=true,
614	const std::string& progressInfo="true,1000",
615	const bool outLogger=false,
616	const std::string& blfile="",
617	const std::string& bltable="");
618	std::vector<float> execFFT(const int whichrow,
619	const std::vector<bool>& inMask,
620	bool getRealImag=false,
621	bool getAmplitudeOnly=false);
622	float getRms(const std::vector<bool>& mask, int whichrow);
623	std::string formatBaselineParams(const std::vector<float>& params,
624	const std::vector<bool>& fixed,
625	float rms,
626	int nClipped,
627	const std::string& masklist,
628	int whichrow,
629	bool verbose=false,
630	bool csvformat=false,
631	int start=-1,
632	int count=-1,
633	bool resetparamid=false) const;
634	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
635	const std::vector<float>& params,
636	const std::vector<bool>& fixed,
637	float rms,
638	int nClipped,
639	const std::string& masklist,
640	int whichrow,
641	bool verbose=false,
642	bool csvformat=false) const;
643	std::vector<uint> getMoleculeIdColumnData() const;
644	void setMoleculeIdColumnData(const std::vector<uint>& molids);
645	double calculateModelSelectionCriteria(const std::string& valname,
646	const std::string& blfunc,
647	int order,
648	const std::vector<bool>& inMask,
649	int whichrow,
650	bool useLineFinder,
651	const std::vector<int>& edge,
652	float threshold,
653	int chanAvgLimit);
654	static std::vector<bool> getMaskFromMaskList(const int nchan,
655	const std::vector<int>& masklist);
656	static casa::Vector<casa::uInt> getMaskListFromMask(
657	const std::vector<bool>& mask);
658	static std::vector<int> splitToIntList(const std::string& str,
659	const char delim);
660	static std::vector<string> splitToStringList(const std::string& str,
661	const char delim);
662
663	void dropXPol();
664
665	private:
666
667	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
668
669	/**
670	* Turns a time value into a formatted string
671	* @param x
672	* @return
673	*/
674	std::string formatSec(casa::Double x) const;
675
676	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
677	std::string formatTime(const casa::MEpoch& me, bool showdate,
678	casa::uInt prec)const;
679
680	/**
681	* Turns a casa::MDirection into a nicely formatted string
682	* @param md an casa::MDirection
683	* @return
684	*/
685	std::string formatDirection(const casa::MDirection& md) const;
686
687	/**
688	* Create a unique file name for the paged (temporary) table
689	* @return just the name
690	*/
691	static casa::String generateName();
692
693	/**
694	* attach to cached columns
695	*/
696	void attach();
697
698	/**
699	* Set up the main casa::Table
700	*/
701	void setupMainTable();
702
703	void attachSubtables();
704	void copySubtables(const Scantable& other);
705
706	/**
707	* Convert an "old" asap1 style row index into a new index
708	* @param[in] therow
709	* @return and index into @table_
710	*/
711	int rowToScanIndex(int therow);
712
713	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
714
715	static const casa::uInt version_ = 4;
716
717	STSelector selector_;
718
719	casa::Table::TableType type_;
720
721	// the actual data
722	casa::Table table_;
723	casa::Table originalTable_;
724
725	STTcal tcalTable_;
726	STFrequencies freqTable_;
727	STWeather weatherTable_;
728	STFocus focusTable_;
729	STMolecules moleculeTable_;
730	STHistory historyTable_;
731	STFit fitTable_;
732
733	// Cached Columns to avoid reconstructing them for each row get/put
734	casa::ScalarColumn<casa::Double> integrCol_;
735	casa::MDirection::ScalarColumn dirCol_;
736	casa::MEpoch::ScalarColumn timeCol_;
737	casa::ScalarColumn<casa::Float> azCol_;
738	casa::ScalarColumn<casa::Float> elCol_;
739	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
740	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
741	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
742	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
743	casa::ArrayColumn<casa::uChar> flagsCol_;
744
745	// id in frequencies table
746	casa::ScalarColumn<casa::uInt> mfreqidCol_;
747	// id in tcal table
748	casa::ScalarColumn<casa::uInt> mtcalidCol_;
749
750	casa::ArrayColumn<casa::String> histitemCol_;
751	casa::ScalarColumn<casa::Int> mfitidCol_;
752	casa::ScalarColumn<casa::uInt> mweatheridCol_;
753
754	casa::ScalarColumn<casa::uInt> mfocusidCol_;
755
756	casa::ScalarColumn<casa::uInt> mmolidCol_;
757
758	static std::map<std::string, STPol::STPolFactory *> factories_;
759	void initFactories();
760
761	/**
762	* Add an auxiliary column to the main table and attach it to a
763	* cached column. Use for adding new columns that the original asap2
764	* tables do not have.
765	* @param[in] col reference to the cached column to be attached
766	* @param[in] colName column name in asap table
767	* @param[in] defValue default value to fill in the column
768	*
769	* 25/10/2009 Wataru Kawasaki
770	*/
771	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
772	const casa::String&,
773	const T2&);
774	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
775	const casa::String&,
776	const casa::Array<T2>&);
777
778	double getNormalPolynomial(int n, double x);
779	double getChebyshevPolynomial(int n, double x);
780	std::vector<std::vector<double> > getPolynomialModel(int order,
781	int nchan,
782	double (Scantable::*pfunc)(int, double));
783	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
784	double (Scantable::*pfunc)(int, double),
785	std::vector<int>& nChanNos);
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	float clipth,
793	int clipn);
794	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
795	const std::vector<bool>& mask,
796	int order,
797	std::vector<float>& params,
798	float& rms,
799	std::vector<bool>& finalMask,
800	int& nClipped,
801	float thresClip=3.0,
802	int nIterClip=0,
803	bool getResidual=true);
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	float clipth,
811	int clipn);
812	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
813	const std::vector<bool>& mask,
814	int order,
815	std::vector<float>& params,
816	float& rms,
817	std::vector<bool>& finalMask,
818	int& nClipped,
819	float thresClip=3.0,
820	int nIterClip=0,
821	bool getResidual=true);
822	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
823	const std::vector<bool>& mask,
824	const std::vector<std::vector<double> >& model,
825	std::vector<float>& params,
826	float& rms,
827	std::vector<bool>& finalMask,
828	int& nClipped,
829	float thresClip=3.0,
830	int nIterClip=0,
831	bool getResidual=true);
832	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
833	const std::vector<bool>& mask,
834	std::vector<int>& idxEdge,
835	std::vector<float>& params,
836	float& rms,
837	std::vector<bool>& finalMask,
838	float clipth,
839	int clipn);
840	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
841	const std::vector<bool>& mask,
842	int nPiece,
843	std::vector<int>& idxEdge,
844	std::vector<float>& params,
845	float& rms,
846	std::vector<bool>& finalMask,
847	float clipth,
848	int clipn);
849	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
850	const std::vector<bool>& mask,
851	int nPiece,
852	bool useGivenPieceBoundary,
853	std::vector<int>& idxEdge,
854	std::vector<float>& params,
855	float& rms,
856	std::vector<bool>& finalMask,
857	int& nClipped,
858	float thresClip=3.0,
859	int nIterClip=0,
860	bool getResidual=true);
861	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
862	const std::vector<bool>& mask,
863	const std::vector<std::vector<double> >& model,
864	int nPiece,
865	bool useGivenPieceBoundary,
866	std::vector<int>& idxEdge,
867	std::vector<float>& params,
868	float& rms,
869	std::vector<bool>& finalMask,
870	int& nClipped,
871	float thresClip=3.0,
872	int nIterClip=0,
873	bool getResidual=true);
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	float clipth,
881	int clipn);
882	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
883	const std::vector<bool>& mask,
884	const std::vector<int>& waveNumbers,
885	std::vector<float>& params,
886	float& rms,
887	std::vector<bool>& finalMask,
888	int& nClipped,
889	float thresClip=3.0,
890	int nIterClip=0,
891	bool getResidual=true);
892	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
893	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
894	std::vector<int>& nChanNos);
895	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
896	const std::vector<int>& rejectNWaves);
897	std::vector<int> selectWaveNumbers(const int whichrow,
898	const std::vector<bool>& chanMask,
899	//const std::string& fftInfo,
900	const bool applyFFT,
901	const std::string& fftMethod,
902	const std::string& fftThresh,
903	const std::vector<int>& addNWaves,
904	const std::vector<int>& rejectNWaves);
905	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
906	void parseFFTInfo(const std::string& fftInfo,
907	bool& applyFFT,
908	std::string& fftMethod,
909	std::string& fftThresh);
910	void parseFFTThresholdInfo(const std::string& fftThresh,
911	std::string& fftThAttr,
912	float& fftThSigma,
913	int& fftThTop);
914	void doSelectWaveNumbers(const int whichrow,
915	const std::vector<bool>& chanMask,
916	const std::string& fftMethod,
917	const float fftThSigma,
918	const int fftThTop,
919	const std::string& fftThAttr,
920	std::vector<int>& nWaves);
921	void addAuxWaveNumbers(const int whichrow,
922	const std::vector<int>& addNWaves,
923	const std::vector<int>& rejectNWaves,
924	std::vector<int>& nWaves);
925	void setWaveNumberListUptoNyquistFreq(const int whichrow,
926	std::vector<int>& nWaves);
927	void initialiseBaselining(const std::string& blfile,
928	std::ofstream& ofs,
929	const bool outLogger,
930	bool& outTextFile,
931	bool& csvFormat,
932	casa::String& coordInfo,
933	bool& hasSameNchan,
934	const std::string& progressInfo,
935	bool& showProgress,
936	int& minNRow,
937	casa::Vector<casa::Double>& timeSecCol);
938	void finaliseBaselining(const bool outBaselineTable,
939	STBaselineTable* pbt,
940	const string& bltable,
941	const bool outTextFile,
942	std::ofstream& ofs);
943	void initLineFinder(const std::vector<int>& edge,
944	const float threshold,
945	const int chanAvgLimit,
946	STLineFinder& lineFinder);
947	bool hasSameNchanOverIFs();
948	std::string getMaskRangeList(const std::vector<bool>& mask,
949	int whichrow,
950	const casa::String& coordInfo,
951	bool hasSameNchan,
952	bool verbose=false);
953	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
954	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
955	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
956	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
957	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
958	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);
959	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);
960	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
961	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
962
963	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
964
965	double doCalculateModelSelectionCriteria(const std::string& valname,
966	const std::vector<float>& spec,
967	const std::vector<bool>& mask,
968	const std::string& blfunc,
969	int order);
970	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
971	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
972	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);
973	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);
974	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);
975
976	};
977	} // namespace
978
979	#endif

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