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source: trunk/src/Scantable.h@ 2828

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Last change on this file since 2828 was 2820, checked in by Malte Marquarding, 11 years ago
Issue #293: added scantbale.drop_history and added extra parameters to scantable.history to allow selection of rows
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
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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(int nrow=-1, int start=0) const
381	{ return historyTable_.getHistory(nrow, start); }
382
383	uint historyLength()
384	{ return historyTable_.nrow(); }
385
386	void dropHistory() { historyTable_.drop(); }
387
388	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
389
390	void appendToHistoryTable(const STHistory& otherhist)
391	{ historyTable_.append(otherhist); }
392
393	std::string headerSummary();
394	void summary(const std::string& filename="");
395	std::string oldheaderSummary();
396	// std::string summary();
397	void oldsummary(const std::string& filename="");
398
399	//std::string getTime(int whichrow=-1, bool showdate=true) const;
400	std::string getTime(int whichrow=-1, bool showdate=true,
401	casa::uInt prec=0) const;
402	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
403
404	// returns unit, conversion frame, doppler, base-frame
405
406	/**
407	* Get the frequency set up
408	* This is forwarded to the STFrequencies subtable
409	* @return unit, frame, doppler
410	*/
411	std::vector<std::string> getCoordInfo() const
412	{ return freqTable_.getInfo(); };
413
414	void setCoordInfo(std::vector<string> theinfo)
415	{ return freqTable_.setInfo(theinfo); };
416
417
418	std::vector<double> getAbcissa(int whichrow) const;
419
420	std::vector<float> getWeather(int whichrow) const;
421
422	std::string getAbcissaLabel(int whichrow) const;
423	std::vector<double> getRestFrequencies() const
424	{ return moleculeTable_.getRestFrequencies(); }
425	std::vector<double> getRestFrequency(int id) const
426	{ return moleculeTable_.getRestFrequency(id); }
427
428	/**
429	void setRestFrequencies(double rf, const std::string& name = "",
430	const std::string& = "Hz");
431	**/
432	// Modified by Takeshi Nakazato 05/09/2008
433	/***
434	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
435	const std::string& = "Hz");
436	***/
437	void setRestFrequencies(vector<double> rf,
438	const vector<std::string>& name = vector<std::string>(1,""),
439	const std::string& = "Hz");
440
441	//void setRestFrequencies(const std::string& name);
442	void setRestFrequencies(const vector<std::string>& name);
443
444	void shift(int npix);
445
446	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
447
448	void convertDirection(const std::string& newframe);
449
450	STFrequencies& frequencies() { return freqTable_; }
451	const STFrequencies& frequencies() const { return freqTable_; }
452	STWeather& weather() { return weatherTable_; }
453	const STWeather& weather() const { return weatherTable_; }
454	STFocus& focus() { return focusTable_; }
455	const STFocus& focus() const { return focusTable_; }
456	STTcal& tcal() { return tcalTable_; }
457	const STTcal& tcal() const { return tcalTable_; }
458	STMolecules& molecules() { return moleculeTable_; }
459	const STMolecules& molecules() const { return moleculeTable_; }
460	STHistory& history() { return historyTable_; }
461	const STHistory& history() const { return historyTable_; }
462	STFit& fit() { return fitTable_; }
463	const STFit& fit() const { return fitTable_; }
464
465	std::vector<std::string> columnNames() const;
466
467	void addFit(const STFitEntry& fit, int row);
468	STFitEntry getFit(int row) const
469	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
470
471	//Added by TT
472	/**
473	* Get the antenna name
474	* @return antenna name string
475	*/
476	casa::String getAntennaName() const;
477
478	/**
479	* For GBT MS data only. check a scan list
480	* against the information found in GBT_GO table for
481	* scan number orders to get correct pairs.
482	* @param[in] scan list
483	* @return status
484	*/
485	int checkScanInfo(const std::vector<int>& scanlist) const;
486
487	/**
488	* Get the direction as a vector, for a specific row
489	* @param[in] whichrow the row numbyyer
490	* @return the direction in a vector
491	*/
492	std::vector<double> getDirectionVector(int whichrow) const;
493
494	/**
495	* Set a flag indicating whether the data was parallactified
496	* @param[in] flag true or false
497	*/
498	void parallactify(bool flag)
499	{ focusTable_.setParallactify(flag); }
500
501	/**
502	* Reshape spectrum
503	* @param[in] nmin, nmax minimum and maximum channel
504	* @param[in] irow row number
505	*
506	* 30/07/2008 Takeshi Nakazato
507	**/
508	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
509	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
510
511	/**
512	* Change channel number under fixed bandwidth
513	* @param[in] nchan, dnu new channel number and spectral resolution
514	* @param[in] irow row number
515	*
516	* 27/08/2008 Takeshi Nakazato
517	**/
518	void regridChannel( int nchan, double dnu ) ;
519	void regridChannel( int nchan, double dnu, int irow ) ;
520	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
521	void regridSpecChannel( double dnu, int nchan=-1 ) ;
522
523	bool getFlagtraFast(casa::uInt whichrow);
524
525	std::vector<std::string> applyBaselineTable(const std::string& bltable,
526	const bool returnfitresult,
527	const std::string& outbltable,
528	const bool outbltableexists,
529	const bool overwrite);
530	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList,
531	const bool returnfitresult,
532	const std::string& outbltable,
533	const bool outbltableexists,
534	const bool overwrite);
535	void polyBaseline(const std::vector<bool>& mask,
536	int order,
537	float thresClip,
538	int nIterClip,
539	bool getResidual=true,
540	const std::string& progressInfo="true,1000",
541	const bool outLogger=false,
542	const std::string& blfile="",
543	const std::string& bltable="");
544	void autoPolyBaseline(const std::vector<bool>& mask,
545	int order,
546	float thresClip,
547	int nIterClip,
548	const std::vector<int>& edge,
549	float threshold=3.0,
550	int chanAvgLimit=1,
551	bool getResidual=true,
552	const std::string& progressInfo="true,1000",
553	const bool outLogger=false,
554	const std::string& blfile="",
555	const std::string& bltable="");
556	void chebyshevBaseline(const std::vector<bool>& mask,
557	int order,
558	float thresClip,
559	int nIterClip,
560	bool getResidual=true,
561	const std::string& progressInfo="true,1000",
562	const bool outLogger=false,
563	const std::string& blfile="",
564	const std::string& bltable="");
565	void autoChebyshevBaseline(const std::vector<bool>& mask,
566	int order,
567	float thresClip,
568	int nIterClip,
569	const std::vector<int>& edge,
570	float threshold=3.0,
571	int chanAvgLimit=1,
572	bool getResidual=true,
573	const std::string& progressInfo="true,1000",
574	const bool outLogger=false,
575	const std::string& blfile="",
576	const std::string& bltable="");
577	void cubicSplineBaseline(const std::vector<bool>& mask,
578	int nPiece,
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 autoCubicSplineBaseline(const std::vector<bool>& mask,
587	int nPiece,
588	float thresClip,
589	int nIterClip,
590	const std::vector<int>& edge,
591	float threshold=3.0,
592	int chanAvgLimit=1,
593	bool getResidual=true,
594	const std::string& progressInfo="true,1000",
595	const bool outLogger=false,
596	const std::string& blfile="",
597	const std::string& bltable="");
598	void sinusoidBaseline(const std::vector<bool>& mask,
599	const std::string& fftInfo,
600	const std::vector<int>& addNWaves,
601	const std::vector<int>& rejectNWaves,
602	float thresClip,
603	int nIterClip,
604	bool getResidual=true,
605	const std::string& progressInfo="true,1000",
606	const bool outLogger=false,
607	const std::string& blfile="",
608	const std::string& bltable="");
609	void autoSinusoidBaseline(const std::vector<bool>& mask,
610	const std::string& fftInfo,
611	const std::vector<int>& addNWaves,
612	const std::vector<int>& rejectNWaves,
613	float thresClip,
614	int nIterClip,
615	const std::vector<int>& edge,
616	float threshold=3.0,
617	int chanAvgLimit=1,
618	bool getResidual=true,
619	const std::string& progressInfo="true,1000",
620	const bool outLogger=false,
621	const std::string& blfile="",
622	const std::string& bltable="");
623	std::vector<float> execFFT(const int whichrow,
624	const std::vector<bool>& inMask,
625	bool getRealImag=false,
626	bool getAmplitudeOnly=false);
627	float getRms(const std::vector<bool>& mask, int whichrow);
628	std::string formatBaselineParams(const std::vector<float>& params,
629	const std::vector<bool>& fixed,
630	float rms,
631	int nClipped,
632	const std::string& masklist,
633	int whichrow,
634	bool verbose=false,
635	bool csvformat=false,
636	int start=-1,
637	int count=-1,
638	bool resetparamid=false) const;
639	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
640	const std::vector<float>& params,
641	const std::vector<bool>& fixed,
642	float rms,
643	int nClipped,
644	const std::string& masklist,
645	int whichrow,
646	bool verbose=false,
647	bool csvformat=false) const;
648	std::vector<uint> getMoleculeIdColumnData() const;
649	void setMoleculeIdColumnData(const std::vector<uint>& molids);
650	double calculateModelSelectionCriteria(const std::string& valname,
651	const std::string& blfunc,
652	int order,
653	const std::vector<bool>& inMask,
654	int whichrow,
655	bool useLineFinder,
656	const std::vector<int>& edge,
657	float threshold,
658	int chanAvgLimit);
659	static std::vector<bool> getMaskFromMaskList(const int nchan,
660	const std::vector<int>& masklist);
661	static casa::Vector<casa::uInt> getMaskListFromMask(
662	const std::vector<bool>& mask);
663	static std::vector<int> splitToIntList(const std::string& str,
664	const char delim);
665	static std::vector<string> splitToStringList(const std::string& str,
666	const char delim);
667
668	void dropXPol();
669
670	private:
671
672	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
673
674	/**
675	* Turns a time value into a formatted string
676	* @param x
677	* @return
678	*/
679	std::string formatSec(casa::Double x) const;
680
681	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
682	std::string formatTime(const casa::MEpoch& me, bool showdate,
683	casa::uInt prec)const;
684
685	/**
686	* Turns a casa::MDirection into a nicely formatted string
687	* @param md an casa::MDirection
688	* @return
689	*/
690	std::string formatDirection(const casa::MDirection& md) const;
691
692	/**
693	* Create a unique file name for the paged (temporary) table
694	* @return just the name
695	*/
696	static casa::String generateName();
697
698	/**
699	* attach to cached columns
700	*/
701	void attach();
702
703	/**
704	* Set up the main casa::Table
705	*/
706	void setupMainTable();
707
708	void attachSubtables();
709	void copySubtables(const Scantable& other);
710
711	/**
712	* Convert an "old" asap1 style row index into a new index
713	* @param[in] therow
714	* @return and index into @table_
715	*/
716	int rowToScanIndex(int therow);
717
718	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
719
720	static const casa::uInt version_ = 4;
721
722	STSelector selector_;
723
724	casa::Table::TableType type_;
725
726	// the actual data
727	casa::Table table_;
728	casa::Table originalTable_;
729
730	STTcal tcalTable_;
731	STFrequencies freqTable_;
732	STWeather weatherTable_;
733	STFocus focusTable_;
734	STMolecules moleculeTable_;
735	STHistory historyTable_;
736	STFit fitTable_;
737
738	// Cached Columns to avoid reconstructing them for each row get/put
739	casa::ScalarColumn<casa::Double> integrCol_;
740	casa::MDirection::ScalarColumn dirCol_;
741	casa::MEpoch::ScalarColumn timeCol_;
742	casa::ScalarColumn<casa::Float> azCol_;
743	casa::ScalarColumn<casa::Float> elCol_;
744	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
745	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
746	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
747	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
748	casa::ArrayColumn<casa::uChar> flagsCol_;
749
750	// id in frequencies table
751	casa::ScalarColumn<casa::uInt> mfreqidCol_;
752	// id in tcal table
753	casa::ScalarColumn<casa::uInt> mtcalidCol_;
754
755	casa::ArrayColumn<casa::String> histitemCol_;
756	casa::ScalarColumn<casa::Int> mfitidCol_;
757	casa::ScalarColumn<casa::uInt> mweatheridCol_;
758
759	casa::ScalarColumn<casa::uInt> mfocusidCol_;
760
761	casa::ScalarColumn<casa::uInt> mmolidCol_;
762
763	static std::map<std::string, STPol::STPolFactory *> factories_;
764	void initFactories();
765
766	/**
767	* Add an auxiliary column to the main table and attach it to a
768	* cached column. Use for adding new columns that the original asap2
769	* tables do not have.
770	* @param[in] col reference to the cached column to be attached
771	* @param[in] colName column name in asap table
772	* @param[in] defValue default value to fill in the column
773	*
774	* 25/10/2009 Wataru Kawasaki
775	*/
776	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
777	const casa::String&,
778	const T2&);
779	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
780	const casa::String&,
781	const casa::Array<T2>&);
782
783	double getNormalPolynomial(int n, double x);
784	double getChebyshevPolynomial(int n, double x);
785	std::vector<std::vector<double> > getPolynomialModel(int order,
786	int nchan,
787	double (Scantable::*pfunc)(int, double));
788	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
789	double (Scantable::*pfunc)(int, double),
790	std::vector<int>& nChanNos);
791	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
792	const std::vector<bool>& mask,
793	int order,
794	std::vector<float>& params,
795	float& rms,
796	std::vector<bool>& finalMask,
797	float clipth,
798	int clipn);
799	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
800	const std::vector<bool>& mask,
801	int order,
802	std::vector<float>& params,
803	float& rms,
804	std::vector<bool>& finalMask,
805	int& nClipped,
806	float thresClip=3.0,
807	int nIterClip=0,
808	bool getResidual=true);
809	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
810	const std::vector<bool>& mask,
811	int order,
812	std::vector<float>& params,
813	float& rms,
814	std::vector<bool>& finalMask,
815	float clipth,
816	int clipn);
817	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
818	const std::vector<bool>& mask,
819	int order,
820	std::vector<float>& params,
821	float& rms,
822	std::vector<bool>& finalMask,
823	int& nClipped,
824	float thresClip=3.0,
825	int nIterClip=0,
826	bool getResidual=true);
827	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
828	const std::vector<bool>& mask,
829	const std::vector<std::vector<double> >& model,
830	std::vector<float>& params,
831	float& rms,
832	std::vector<bool>& finalMask,
833	int& nClipped,
834	float thresClip=3.0,
835	int nIterClip=0,
836	bool getResidual=true);
837	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
838	const std::vector<bool>& mask,
839	std::vector<int>& idxEdge,
840	std::vector<float>& params,
841	float& rms,
842	std::vector<bool>& finalMask,
843	float clipth,
844	int clipn);
845	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
846	const std::vector<bool>& mask,
847	int nPiece,
848	std::vector<int>& idxEdge,
849	std::vector<float>& params,
850	float& rms,
851	std::vector<bool>& finalMask,
852	float clipth,
853	int clipn);
854	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
855	const std::vector<bool>& mask,
856	int nPiece,
857	bool useGivenPieceBoundary,
858	std::vector<int>& idxEdge,
859	std::vector<float>& params,
860	float& rms,
861	std::vector<bool>& finalMask,
862	int& nClipped,
863	float thresClip=3.0,
864	int nIterClip=0,
865	bool getResidual=true);
866	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
867	const std::vector<bool>& mask,
868	const std::vector<std::vector<double> >& model,
869	int nPiece,
870	bool useGivenPieceBoundary,
871	std::vector<int>& idxEdge,
872	std::vector<float>& params,
873	float& rms,
874	std::vector<bool>& finalMask,
875	int& nClipped,
876	float thresClip=3.0,
877	int nIterClip=0,
878	bool getResidual=true);
879	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
880	const std::vector<bool>& mask,
881	const std::vector<int>& waveNumbers,
882	std::vector<float>& params,
883	float& rms,
884	std::vector<bool>& finalMask,
885	float clipth,
886	int clipn);
887	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
888	const std::vector<bool>& mask,
889	const std::vector<int>& waveNumbers,
890	std::vector<float>& params,
891	float& rms,
892	std::vector<bool>& finalMask,
893	int& nClipped,
894	float thresClip=3.0,
895	int nIterClip=0,
896	bool getResidual=true);
897	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
898	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
899	std::vector<int>& nChanNos);
900	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
901	const std::vector<int>& rejectNWaves);
902	std::vector<int> selectWaveNumbers(const int whichrow,
903	const std::vector<bool>& chanMask,
904	//const std::string& fftInfo,
905	const bool applyFFT,
906	const std::string& fftMethod,
907	const std::string& fftThresh,
908	const std::vector<int>& addNWaves,
909	const std::vector<int>& rejectNWaves);
910	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
911	void parseFFTInfo(const std::string& fftInfo,
912	bool& applyFFT,
913	std::string& fftMethod,
914	std::string& fftThresh);
915	void parseFFTThresholdInfo(const std::string& fftThresh,
916	std::string& fftThAttr,
917	float& fftThSigma,
918	int& fftThTop);
919	void doSelectWaveNumbers(const int whichrow,
920	const std::vector<bool>& chanMask,
921	const std::string& fftMethod,
922	const float fftThSigma,
923	const int fftThTop,
924	const std::string& fftThAttr,
925	std::vector<int>& nWaves);
926	void addAuxWaveNumbers(const int whichrow,
927	const std::vector<int>& addNWaves,
928	const std::vector<int>& rejectNWaves,
929	std::vector<int>& nWaves);
930	void setWaveNumberListUptoNyquistFreq(const int whichrow,
931	std::vector<int>& nWaves);
932	void initialiseBaselining(const std::string& blfile,
933	std::ofstream& ofs,
934	const bool outLogger,
935	bool& outTextFile,
936	bool& csvFormat,
937	casa::String& coordInfo,
938	bool& hasSameNchan,
939	const std::string& progressInfo,
940	bool& showProgress,
941	int& minNRow,
942	casa::Vector<casa::Double>& timeSecCol);
943	void finaliseBaselining(const bool outBaselineTable,
944	STBaselineTable* pbt,
945	const string& bltable,
946	const bool outTextFile,
947	std::ofstream& ofs);
948	void initLineFinder(const std::vector<int>& edge,
949	const float threshold,
950	const int chanAvgLimit,
951	STLineFinder& lineFinder);
952	bool hasSameNchanOverIFs();
953	std::string getMaskRangeList(const std::vector<bool>& mask,
954	int whichrow,
955	const casa::String& coordInfo,
956	bool hasSameNchan,
957	bool verbose=false);
958	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
959	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
960	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
961	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
962	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
963	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);
964	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);
965	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
966	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
967
968	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
969
970	double doCalculateModelSelectionCriteria(const std::string& valname,
971	const std::vector<float>& spec,
972	const std::vector<bool>& mask,
973	const std::string& blfunc,
974	int order);
975	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
976	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
977	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);
978	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);
979	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);
980
981	};
982	} // namespace
983
984	#endif

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