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source: trunk/src/Scantable.h @ 3090

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Last change on this file since 3090 was 3090, checked in by Kana Sugimoto, 8 years ago

New Development: No

JIRA Issue: No

Ready for Test: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

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Description: yet another modification to get rid of clang build warnings.

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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	#include <map>
22	// AIPS++
23	#include <casa/aips.h>
24	#include <casa/Arrays/MaskedArray.h>
25	#include <casa/Arrays/Vector.h>
26	#include <casa/BasicSL/String.h>
27	#include <casa/Containers/Record.h>
28	#include <casa/Exceptions/Error.h>
29	#include <casa/Quanta/Quantum.h>
30	#include <casa/Utilities/CountedPtr.h>
31	#include <coordinates/Coordinates/SpectralCoordinate.h>
32	#include <measures/TableMeasures/ScalarMeasColumn.h>
33	#include <scimath/Mathematics/FFTServer.h>
34	#include <tables/Tables/ArrayColumn.h>
35	#include <tables/Tables/ScalarColumn.h>
36	#include <tables/Tables/Table.h>
37
38	#include "MathUtils.h"
39	#include "STBaselineEnum.h"
40	#include "STFit.h"
41	#include "STFitEntry.h"
42	#include "STFocus.h"
43	#include "STFrequencies.h"
44	#include "STHeader.h"
45	#include "STHistory.h"
46	#include "STMolecules.h"
47	#include "STPol.h"
48	#include "STSelector.h"
49	#include "STTcal.h"
50	#include "STWeather.h"
51
52	namespace asap {
53
54	class Fitter;
55	struct STLineFinder;
56	class STBaselineTable;
57
58	/**
59	* This class contains and wraps a casa::Table, which is used to store
60	* all the information. This can be either a MemoryTable or a
61	* disk based Table.
62	* It provides access functions to the underlying table
63	* It contains n subtables:
64	* @li weather
65	* @li frequencies
66	* @li molecules
67	* @li tcal
68	* @li focus
69	* @li fits
70	*
71	* @brief The main ASAP data container
72	* @author Malte Marquarding
73	* @date
74	* @version
75	*/
76	class Scantable
77	{
78
79	friend class STMath;
80
81	public:
82	/**
83	* Default constructor
84	*/
85	explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
86
87	/**
88	* Create a Scantable object from an existing table on disk
89	* @param[in] name the name of the existing Scantable
90	*/
91	explicit Scantable(const std::string& name,
92	casa::Table::TableType ttype = casa::Table::Memory);
93
94	/// @fixme this is only sensible for MemoryTables....
95	Scantable(const Scantable& other, bool clear=true);
96
97	/**
98	* Destructor
99	*/
100	virtual ~Scantable();
101
102	/**
103	* get a const reference to the underlying casa::Table
104	* @return const \ref casa::Table reference
105	*/
106	const casa::Table& table() const;
107
108	/**
109	* get a reference to the underlying casa::Table with the Selection
110	* object applied if set
111	* @return casa::Table reference
112	*/
113	casa::Table& table();
114
115
116	/**
117	* Get a handle to the selection object
118	* @return constant STSelector reference
119	*/
120	const STSelector& getSelection() const { return selector_; }
121
122	/**
123	* Set the data to be a subset as defined by the STSelector
124	* @param selection a STSelector object
125	*/
126	void setSelection(const STSelector& selection);
127
128	/**
129	* unset the selection of the data
130	*/
131	void unsetSelection();
132	/**
133	* set the header
134	* @param[in] sth an STHeader object
135	*/
136	void setHeader( const STHeader& sth );
137
138	/**
139	* get the header information
140	* @return an STHeader object
141	*/
142	STHeader getHeader( ) const;
143
144	/**
145	* Checks if the "other" Scantable is conformant with this,
146	* i.e. if header values are the same.
147	* @param[in] other another Scantable
148	* @return true or false
149	*/
150	bool conformant( const Scantable& other);
151
152	/**
153	*
154	* @param stype The type of the source, 0 = on, 1 = off
155	*/
156	void setSourceType(int stype);
157
158	/**
159	*
160	* @param stype The name of the source
161	*/
162	void setSourceName(const std::string& name);
163
164
165	/**
166	* The number of scans in the table
167	* @return number of scans in the table
168	*/
169	int nscan() const;
170
171	casa::MEpoch::Types getTimeReference() const;
172
173
174	casa::MEpoch getEpoch(int whichrow) const;
175
176	/**
177	* Get global antenna position
178	* @return casa::MPosition
179	*/
180	casa::MPosition getAntennaPosition() const;
181
182	/**
183	* the @ref casa::MDirection for a specific row
184	* @param[in] whichrow the row number
185	* return casa::MDirection
186	*/
187	casa::MDirection getDirection( int whichrow ) const;
188
189	/**
190	* get the direction type as a string, e.g. "J2000"
191	* @param[in] whichrow the row number
192	* return the direction string
193	*/
194	std::string getDirectionString( int whichrow ) const;
195
196	/**
197	* set the direction type as a string, e.g. "J2000"
198	* @param[in] refstr the direction type
199	*/
200	void setDirectionRefString(const std::string& refstr="");
201
202	/**
203	* get the direction reference string
204	* @return a string describing the direction reference
205	*/
206	std::string getDirectionRefString() const;
207
208	/**
209	* Return the Flux unit of the data, e.g. "Jy" or "K"
210	* @return string
211	*/
212	std::string getFluxUnit() const;
213
214	/**
215	* Set the Flux unit of the data
216	* @param unit a string representing the unit, e.g "Jy" or "K"
217	*/
218	void setFluxUnit( const std::string& unit );
219
220	/**
221	* Set the Stokes type of the data
222	* @param feedtype a string representing the type, e.g "circular" or "linear"
223	*/
224	void setFeedType( const std::string& feedtype );
225
226	/**
227	*
228	* @param instrument a string representing an insturment. see xxx
229	*/
230	void setInstrument( const std::string& instrument );
231
232	/**
233	* (Re)calculate the azimuth and elevationnfor all rows
234	*/
235	void calculateAZEL();
236
237	/**
238	* "hard" flag the data, this flags everything selected in setSelection()
239	* param[in] msk a boolean mask of length nchan describing the points to
240	* to be flagged
241	*/
242	//void flag( const std::vector<bool>& msk = std::vector<bool>());
243	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
244
245	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
246
247	/**
248	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
249	* param[in] rows list of row numbers to be flagged
250	*/
251	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
252
253	/**
254	* Get flagRow info at the specified row. If true, the whole data
255	* at the row should be flagged.
256	*/
257	bool getFlagRow(int whichrow) const
258	{ return (flagrowCol_(whichrow) > 0); }
259
260	/**
261	* Flag the data outside a specified range (in a channel-based manner).
262	* (CAS-1807 Wataru Kawasaki)
263	*/
264	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
265
266	/**
267	* Return a list of booleans with the size of nchan for a specified row, to get info
268	* about which channel is clipped.
269	*/
270	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
271	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
272	casa::Vector<casa::uChar> flgs);
273
274	/**
275	* Return a list of row numbers with respect to the original table.
276	* @return a list of unsigned ints
277	*/
278	std::vector<unsigned int> rownumbers() const;
279
280
281	/**
282	* Get the number of beams in the data or a specific scan
283	* @param scanno the scan number to get the number of beams for.
284	* If scanno<0 the number is retrieved from the header.
285	* @return an integer number
286	*/
287	int nbeam(int scanno=-1) const;
288	/**
289	* Get the number of IFs in the data or a specific scan
290	* @param scanno the scan number to get the number of IFs for.
291	* If scanno<0 the number is retrieved from the header.
292	* @return an integer number
293	*/
294	int nif(int scanno=-1) const;
295	/**
296	* Get the number of polarizations in the data or a specific scan
297	* @param scanno the scan number to get the number of polarizations for.
298	* If scanno<0 the number is retrieved from the header.
299	* @return an integer number
300	*/
301	int npol(int scanno=-1) const;
302
303	std::string getPolType() const;
304
305
306	/**
307	* Get the number of integartion cycles
308	* @param scanno the scan number to get the number of rows for.
309	* If scanno<0 the number is retrieved from the header.
310	* @return the number of rows (for the specified scanno)
311	*/
312	int nrow(int scanno=-1) const;
313
314	int getBeam(int whichrow) const;
315	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
316
317	int getIF(int whichrow) const;
318	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
319
320	int getPol(int whichrow) const;
321	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
322
323	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
324	int getScan(int whichrow) const { return scanCol_(whichrow); }
325
326	std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
327	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
328
329	//TT addition
330	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
331
332	/**
333	* Get the number of channels in the data or a specific IF. This currently
334	* varies only with IF number
335	* @param ifno the IF number to get the number of channels for.
336	* If ifno<0 the number is retrieved from the header.
337	* @return an integer number
338	*/
339	int nchan(int ifno=-1) const;
340	int getChannels(int whichrow) const;
341
342	int ncycle(int scanno=-1) const;
343
344
345	double getInterval(int whichrow) const
346	{ return integrCol_(whichrow); }
347
348	float getTsys(int whichrow) const
349	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
350	std::vector<float> getTsysSpectrum(int whichrow) const ;
351
352	void setTsys(const std::vector<float>& newvals, int whichrow);
353
354	float getElevation(int whichrow) const
355	{ return elCol_(whichrow); }
356	float getAzimuth(int whichrow) const
357	{ return azCol_(whichrow); }
358	float getParAngle(int whichrow) const
359	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
360	int getTcalId(int whichrow) const
361	{ return mtcalidCol_(whichrow); }
362
363	std::string getSourceName(int whichrow) const
364	{ return srcnCol_(whichrow); }
365
366	std::vector<bool> getMask(int whichrow) const;
367	std::vector<float> getSpectrum(int whichrow,
368	const std::string& poltype = "" ) const;
369
370	void setSpectrum(const std::vector<float>& spec, int whichrow);
371
372	std::string getPolarizationLabel(int index, const std::string& ptype) const
373	{ return STPol::getPolLabel(index, ptype ); }
374
375	/**
376	* Write the Scantable to disk
377	* @param filename the output file name
378	*/
379	void makePersistent(const std::string& filename);
380
381	std::vector<std::string> getHistory(int nrow=-1, int start=0) const
382	{ return historyTable_.getHistory(nrow, start); }
383
384	uint historyLength()
385	{ return historyTable_.nrow(); }
386
387	void dropHistory() { historyTable_.drop(); }
388
389	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
390
391	void appendToHistoryTable(const STHistory& otherhist)
392	{ historyTable_.append(otherhist); }
393
394	std::string headerSummary();
395	void summary(const std::string& filename="");
396	std::string oldheaderSummary();
397	// std::string summary();
398	void oldsummary(const std::string& filename="");
399
400	//std::string getTime(int whichrow=-1, bool showdate=true) const;
401	std::string getTime(int whichrow=-1, bool showdate=true,
402	casa::uInt prec=0) const;
403	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
404
405	// returns unit, conversion frame, doppler, base-frame
406
407	/**
408	* Get the frequency set up
409	* This is forwarded to the STFrequencies subtable
410	* @return unit, frame, doppler
411	*/
412	std::vector<std::string> getCoordInfo() const
413	{ return freqTable_.getInfo(); };
414
415	void setCoordInfo(std::vector<string> theinfo)
416	{ return freqTable_.setInfo(theinfo); };
417
418
419	std::vector<double> getAbcissa(int whichrow) const;
420
421	std::vector<float> getWeather(int whichrow) const;
422
423	std::string getAbcissaLabel(int whichrow) const;
424	std::vector<double> getRestFrequencies() const
425	{ return moleculeTable_.getRestFrequencies(); }
426	std::vector<double> getRestFrequency(int id) const
427	{ return moleculeTable_.getRestFrequency(id); }
428
429	/**
430	void setRestFrequencies(double rf, const std::string& name = "",
431	const std::string& = "Hz");
432	**/
433	// Modified by Takeshi Nakazato 05/09/2008
434	/***
435	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
436	const std::string& = "Hz");
437	***/
438	void setRestFrequencies(vector<double> rf,
439	const vector<std::string>& name = vector<std::string>(1,""),
440	const std::string& = "Hz");
441
442	//void setRestFrequencies(const std::string& name);
443	void setRestFrequencies(const vector<std::string>& name);
444
445	void shift(int npix);
446
447	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
448
449	void convertDirection(const std::string& newframe);
450
451	STFrequencies& frequencies() { return freqTable_; }
452	const STFrequencies& frequencies() const { return freqTable_; }
453	STWeather& weather() { return weatherTable_; }
454	const STWeather& weather() const { return weatherTable_; }
455	STFocus& focus() { return focusTable_; }
456	const STFocus& focus() const { return focusTable_; }
457	STTcal& tcal() { return tcalTable_; }
458	const STTcal& tcal() const { return tcalTable_; }
459	STMolecules& molecules() { return moleculeTable_; }
460	const STMolecules& molecules() const { return moleculeTable_; }
461	STHistory& history() { return historyTable_; }
462	const STHistory& history() const { return historyTable_; }
463	STFit& fit() { return fitTable_; }
464	const STFit& fit() const { return fitTable_; }
465
466	std::vector<std::string> columnNames() const;
467
468	void addFit(const STFitEntry& fit, int row);
469	STFitEntry getFit(int row) const
470	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
471
472	//Added by TT
473	/**
474	* Get the antenna name
475	* @return antenna name string
476	*/
477	casa::String getAntennaName() const;
478
479	/**
480	* For GBT MS data only. check a scan list
481	* against the information found in GBT_GO table for
482	* scan number orders to get correct pairs.
483	* @param[in] scan list
484	* @return status
485	*/
486	int checkScanInfo(const std::vector<int>& scanlist) const;
487
488	/**
489	* Get the direction as a vector, for a specific row
490	* @param[in] whichrow the row numbyyer
491	* @return the direction in a vector
492	*/
493	std::vector<double> getDirectionVector(int whichrow) const;
494
495	/**
496	* Set a flag indicating whether the data was parallactified
497	* @param[in] flag true or false
498	*/
499	void parallactify(bool flag)
500	{ focusTable_.setParallactify(flag); }
501
502	/**
503	* Reshape spectrum
504	* @param[in] nmin, nmax minimum and maximum channel
505	* @param[in] irow row number
506	*
507	* 30/07/2008 Takeshi Nakazato
508	**/
509	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
510	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
511
512	/**
513	* Change channel number under fixed bandwidth
514	* @param[in] nchan, dnu new channel number and spectral resolution
515	* @param[in] irow row number
516	*
517	* 27/08/2008 Takeshi Nakazato
518	**/
519	void regridChannel( int nchan, double dnu ) ;
520	void regridChannel( int nchan, double dnu, int irow ) ;
521	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
522	void regridSpecChannel( double dnu, int nchan=-1 ) ;
523
524	bool isAllChannelsFlagged(casa::uInt whichrow);
525
526	std::vector<std::string> applyBaselineTable(const std::string& bltable,
527	const bool returnfitresult,
528	const std::string& outbltable,
529	const bool outbltableexists,
530	const bool overwrite);
531	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList,
532	const bool returnfitresult,
533	const std::string& outbltable,
534	const bool outbltableexists,
535	const bool overwrite);
536	void polyBaseline(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 autoPolyBaseline(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 chebyshevBaseline(const std::vector<bool>& mask,
558	int order,
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 autoChebyshevBaseline(const std::vector<bool>& mask,
567	int order,
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 cubicSplineBaseline(const std::vector<bool>& mask,
579	int nPiece,
580	float thresClip,
581	int nIterClip,
582	bool getResidual=true,
583	const std::string& progressInfo="true,1000",
584	const bool outLogger=false,
585	const std::string& blfile="",
586	const std::string& bltable="");
587	void autoCubicSplineBaseline(const std::vector<bool>& mask,
588	int nPiece,
589	float thresClip,
590	int nIterClip,
591	const std::vector<int>& edge,
592	float threshold=3.0,
593	int chanAvgLimit=1,
594	bool getResidual=true,
595	const std::string& progressInfo="true,1000",
596	const bool outLogger=false,
597	const std::string& blfile="",
598	const std::string& bltable="");
599	void sinusoidBaseline(const std::vector<bool>& mask,
600	const std::string& fftInfo,
601	const std::vector<int>& addNWaves,
602	const std::vector<int>& rejectNWaves,
603	float thresClip,
604	int nIterClip,
605	bool getResidual=true,
606	const std::string& progressInfo="true,1000",
607	const bool outLogger=false,
608	const std::string& blfile="",
609	const std::string& bltable="");
610	void autoSinusoidBaseline(const std::vector<bool>& mask,
611	const std::string& fftInfo,
612	const std::vector<int>& addNWaves,
613	const std::vector<int>& rejectNWaves,
614	float thresClip,
615	int nIterClip,
616	const std::vector<int>& edge,
617	float threshold=3.0,
618	int chanAvgLimit=1,
619	bool getResidual=true,
620	const std::string& progressInfo="true,1000",
621	const bool outLogger=false,
622	const std::string& blfile="",
623	const std::string& bltable="");
624	std::vector<float> execFFT(const int whichrow,
625	const std::vector<bool>& inMask,
626	bool getRealImag=false,
627	bool getAmplitudeOnly=false);
628	float getRms(const std::vector<bool>& mask, int whichrow);
629	std::string formatBaselineParams(const std::vector<float>& params,
630	const std::vector<bool>& fixed,
631	float rms,
632	int nClipped,
633	const std::string& masklist,
634	int whichrow,
635	bool verbose=false,
636	bool csvformat=false,
637	int start=-1,
638	int count=-1,
639	bool resetparamid=false) const;
640	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
641	const std::vector<float>& params,
642	const std::vector<bool>& fixed,
643	float rms,
644	int nClipped,
645	const std::string& masklist,
646	int whichrow,
647	bool verbose=false,
648	bool csvformat=false) const;
649	std::vector<uint> getMoleculeIdColumnData() const;
650	void setMoleculeIdColumnData(const std::vector<uint>& molids);
651
652	/**
653	* Get row idx of root table
654	**/
655	std::vector<uint> getRootTableRowNumbers() const;
656
657	double calculateModelSelectionCriteria(const std::string& valname,
658	const std::string& blfunc,
659	int order,
660	const std::vector<bool>& inMask,
661	int whichrow,
662	bool useLineFinder,
663	const std::vector<int>& edge,
664	float threshold,
665	int chanAvgLimit);
666	static std::vector<bool> getMaskFromMaskList(const int nchan,
667	const std::vector<int>& masklist);
668	static casa::Vector<casa::uInt> getMaskListFromMask(
669	const std::vector<bool>& mask);
670	static std::vector<int> splitToIntList(const std::string& str,
671	const char delim);
672	static std::vector<string> splitToStringList(const std::string& str,
673	const char delim);
674
675	void dropXPol();
676
677	private:
678
679	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
680
681	/**
682	* Turns a time value into a formatted string
683	* @param x
684	* @return
685	*/
686	std::string formatSec(casa::Double x) const;
687
688	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
689	std::string formatTime(const casa::MEpoch& me, bool showdate,
690	casa::uInt prec)const;
691
692	/**
693	* Turns a casa::MDirection into a nicely formatted string
694	* @param md an casa::MDirection
695	* @param prec output precision of direction
696	* @return
697	*/
698	std::string formatDirection(const casa::MDirection& md, casa::Int prec=7) const;
699
700	/**
701	* Create a unique file name for the paged (temporary) table
702	* @return just the name
703	*/
704	static casa::String generateName();
705
706	/**
707	* attach to cached columns
708	*/
709	void attach();
710
711	/**
712	* Set up the main casa::Table
713	*/
714	void setupMainTable();
715
716	void attachSubtables();
717	void copySubtables(const Scantable& other);
718
719	/**
720	* Convert an "old" asap1 style row index into a new index
721	* @param[in] therow
722	* @return and index into @table_
723	*/
724	int rowToScanIndex(int therow);
725
726	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
727
728	/**
729	* Returns a number of elements with "true" in a bool vector.
730	* @param[in] mask (boolean vector)
731	* @return the numerb of elements in true
732	*/
733	std::size_t nValidMask(const std::vector<bool>& mask);
734
735	static const casa::uInt version_ = 4;
736
737	STSelector selector_;
738
739	casa::Table::TableType type_;
740
741	// the actual data
742	casa::Table table_;
743	casa::Table originalTable_;
744
745	STTcal tcalTable_;
746	STFrequencies freqTable_;
747	STWeather weatherTable_;
748	STFocus focusTable_;
749	STMolecules moleculeTable_;
750	STHistory historyTable_;
751	STFit fitTable_;
752
753	// Cached Columns to avoid reconstructing them for each row get/put
754	casa::ScalarColumn<casa::Double> integrCol_;
755	casa::MDirection::ScalarColumn dirCol_;
756	casa::MEpoch::ScalarColumn timeCol_;
757	casa::ScalarColumn<casa::Float> azCol_;
758	casa::ScalarColumn<casa::Float> elCol_;
759	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
760	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
761	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
762	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
763	casa::ArrayColumn<casa::uChar> flagsCol_;
764
765	// id in frequencies table
766	casa::ScalarColumn<casa::uInt> mfreqidCol_;
767	// id in tcal table
768	casa::ScalarColumn<casa::uInt> mtcalidCol_;
769
770	casa::ArrayColumn<casa::String> histitemCol_;
771	casa::ScalarColumn<casa::Int> mfitidCol_;
772	casa::ScalarColumn<casa::uInt> mweatheridCol_;
773
774	casa::ScalarColumn<casa::uInt> mfocusidCol_;
775
776	casa::ScalarColumn<casa::uInt> mmolidCol_;
777
778	static std::map<std::string, STPol::STPolFactory *> factories_;
779	void initFactories();
780
781	/**
782	* Add an auxiliary column to the main table and attach it to a
783	* cached column. Use for adding new columns that the original asap2
784	* tables do not have.
785	* @param[in] col reference to the cached column to be attached
786	* @param[in] colName column name in asap table
787	* @param[in] defValue default value to fill in the column
788	*
789	* 25/10/2009 Wataru Kawasaki
790	*/
791	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
792	const casa::String&,
793	const T2&);
794	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
795	const casa::String&,
796	const casa::Array<T2>&);
797
798	double getNormalPolynomial(int n, double x);
799	double getChebyshevPolynomial(int n, double x);
800	std::vector<std::vector<double> > getPolynomialModel(int order,
801	int nchan,
802	double (Scantable::*pfunc)(int, double));
803	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
804	double (Scantable::*pfunc)(int, double),
805	std::vector<int>& nChanNos);
806	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
807	const std::vector<bool>& mask,
808	int order,
809	std::vector<float>& params,
810	float& rms,
811	std::vector<bool>& finalMask,
812	float clipth,
813	int clipn);
814	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
815	const std::vector<bool>& mask,
816	int order,
817	std::vector<float>& params,
818	float& rms,
819	std::vector<bool>& finalMask,
820	int& nClipped,
821	float thresClip=3.0,
822	int nIterClip=0,
823	bool getResidual=true);
824	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
825	const std::vector<bool>& mask,
826	int order,
827	std::vector<float>& params,
828	float& rms,
829	std::vector<bool>& finalMask,
830	float clipth,
831	int clipn);
832	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
833	const std::vector<bool>& mask,
834	int order,
835	std::vector<float>& params,
836	float& rms,
837	std::vector<bool>& finalMask,
838	int& nClipped,
839	float thresClip=3.0,
840	int nIterClip=0,
841	bool getResidual=true);
842	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
843	const std::vector<bool>& mask,
844	const std::vector<std::vector<double> >& model,
845	std::vector<float>& params,
846	float& rms,
847	std::vector<bool>& finalMask,
848	int& nClipped,
849	float thresClip=3.0,
850	int nIterClip=0,
851	bool getResidual=true);
852	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
853	const std::vector<bool>& mask,
854	std::vector<int>& idxEdge,
855	std::vector<float>& params,
856	float& rms,
857	std::vector<bool>& finalMask,
858	float clipth,
859	int clipn);
860	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
861	const std::vector<bool>& mask,
862	int nPiece,
863	std::vector<int>& idxEdge,
864	std::vector<float>& params,
865	float& rms,
866	std::vector<bool>& finalMask,
867	float clipth,
868	int clipn);
869	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
870	const std::vector<bool>& mask,
871	int nPiece,
872	bool useGivenPieceBoundary,
873	std::vector<int>& idxEdge,
874	std::vector<float>& params,
875	float& rms,
876	std::vector<bool>& finalMask,
877	int& nClipped,
878	float thresClip=3.0,
879	int nIterClip=0,
880	bool getResidual=true);
881	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
882	const std::vector<bool>& mask,
883	const std::vector<std::vector<double> >& model,
884	int nPiece,
885	bool useGivenPieceBoundary,
886	std::vector<int>& idxEdge,
887	std::vector<float>& params,
888	float& rms,
889	std::vector<bool>& finalMask,
890	int& nClipped,
891	float thresClip=3.0,
892	int nIterClip=0,
893	bool getResidual=true);
894	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
895	const std::vector<bool>& mask,
896	const std::vector<int>& waveNumbers,
897	std::vector<float>& params,
898	float& rms,
899	std::vector<bool>& finalMask,
900	float clipth,
901	int clipn);
902	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
903	const std::vector<bool>& mask,
904	const std::vector<int>& waveNumbers,
905	std::vector<float>& params,
906	float& rms,
907	std::vector<bool>& finalMask,
908	int& nClipped,
909	float thresClip=3.0,
910	int nIterClip=0,
911	bool getResidual=true);
912	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
913	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
914	std::vector<int>& nChanNos);
915	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
916	const std::vector<int>& rejectNWaves);
917	std::vector<int> selectWaveNumbers(const int whichrow,
918	const std::vector<bool>& chanMask,
919	//const std::string& fftInfo,
920	const bool applyFFT,
921	const std::string& fftMethod,
922	const std::string& fftThresh,
923	const std::vector<int>& addNWaves,
924	const std::vector<int>& rejectNWaves);
925	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
926	void parseFFTInfo(const std::string& fftInfo,
927	bool& applyFFT,
928	std::string& fftMethod,
929	std::string& fftThresh);
930	void parseFFTThresholdInfo(const std::string& fftThresh,
931	std::string& fftThAttr,
932	float& fftThSigma,
933	int& fftThTop);
934	void doSelectWaveNumbers(const int whichrow,
935	const std::vector<bool>& chanMask,
936	const std::string& fftMethod,
937	const float fftThSigma,
938	const int fftThTop,
939	const std::string& fftThAttr,
940	std::vector<int>& nWaves);
941	void addAuxWaveNumbers(const int whichrow,
942	const std::vector<int>& addNWaves,
943	const std::vector<int>& rejectNWaves,
944	std::vector<int>& nWaves);
945	void setWaveNumberListUptoNyquistFreq(const int whichrow,
946	std::vector<int>& nWaves);
947	void initialiseBaselining(const std::string& blfile,
948	std::ofstream& ofs,
949	const bool outLogger,
950	bool& outTextFile,
951	bool& csvFormat,
952	casa::String& coordInfo,
953	bool& hasSameNchan,
954	const std::string& progressInfo,
955	bool& showProgress,
956	int& minNRow,
957	casa::Vector<casa::Double>& timeSecCol);
958	void finaliseBaselining(const bool outBaselineTable,
959	STBaselineTable* pbt,
960	const string& bltable,
961	const bool outTextFile,
962	std::ofstream& ofs);
963	void initLineFinder(const std::vector<int>& edge,
964	const float threshold,
965	const int chanAvgLimit,
966	STLineFinder& lineFinder);
967	bool hasSameNchanOverIFs();
968	std::string getMaskRangeList(const std::vector<bool>& mask,
969	int whichrow,
970	const casa::String& coordInfo,
971	bool hasSameNchan,
972	bool verbose=false);
973	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
974	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
975	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
976	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
977	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
978	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);
979	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);
980	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
981	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
982
983	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
984
985	double doCalculateModelSelectionCriteria(const std::string& valname,
986	const std::vector<float>& spec,
987	const std::vector<bool>& mask,
988	const std::string& blfunc,
989	int order);
990	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
991	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
992	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);
993	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, int irow);
994	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);
995
996	// storage of cubic spline model for various number of channels
997	map<size_t, vector< vector<double> > > cubicSplineModelPool_;
998
999	};
1000	} // namespace
1001
1002	#endif

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