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source: trunk/src/Scantable.h@ 2771

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Last change on this file since 2771 was 2767, checked in by WataruKawasaki, 12 years ago

New Development: Yes

JIRA Issue: Yes CAS-4794

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: No

Module(s): sd

Description: functions to apply/write STBaselineTable in which baseline parameters stored.

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File size: 30.5 KB

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[824]	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
[2]	14
	15	// STL
[2186]	16	#include <fstream>
	17	#include <iostream>
	18	#include <sstream>
[2]	19	#include <string>
	20	#include <vector>
	21	// AIPS++
[455]	22	#include <casa/aips.h>
[322]	23	#include <casa/Arrays/MaskedArray.h>
[2186]	24	#include <casa/Arrays/Vector.h>
[80]	25	#include <casa/BasicSL/String.h>
[2186]	26	#include <casa/Containers/Record.h>
	27	#include <casa/Exceptions/Error.h>
	28	#include <casa/Quanta/Quantum.h>
[824]	29	#include <casa/Utilities/CountedPtr.h>
[2186]	30	#include <coordinates/Coordinates/SpectralCoordinate.h>
[824]	31	#include <measures/TableMeasures/ScalarMeasColumn.h>
[2186]	32	#include <scimath/Mathematics/FFTServer.h>
	33	#include <tables/Tables/ArrayColumn.h>
	34	#include <tables/Tables/ScalarColumn.h>
	35	#include <tables/Tables/Table.h>
[1819]	36
[2186]	37	#include "MathUtils.h"
[2767]	38	#include "STBaselineEnum.h"
[2186]	39	#include "STFit.h"
	40	#include "STFitEntry.h"
[2666]	41	//#include "STFitter.h"
[2186]	42	#include "STFocus.h"
	43	#include "STFrequencies.h"
[901]	44	#include "STHeader.h"
[2186]	45	#include "STHistory.h"
[824]	46	#include "STMolecules.h"
[2186]	47	#include "STPol.h"
[824]	48	#include "STSelector.h"
[2186]	49	#include "STTcal.h"
	50	#include "STWeather.h"
[2]	51
[824]	52	namespace asap {
[2]	53
[2666]	54	class Fitter;
	55
[824]	56	/**
	57	* This class contains and wraps a casa::Table, which is used to store
	58	* all the information. This can be either a MemoryTable or a
	59	* disk based Table.
	60	* It provides access functions to the underlying table
	61	* It contains n subtables:
	62	* @li weather
	63	* @li frequencies
	64	* @li molecules
	65	* @li tcal
	66	* @li focus
	67	* @li fits
	68	*
	69	* @brief The main ASAP data container
	70	* @author Malte Marquarding
	71	* @date
	72	* @version
	73	*/
[2658]	74	class Scantable
[824]	75	{
[902]	76
	77	friend class STMath;
	78
[2]	79	public:
[824]	80	/**
	81	* Default constructor
	82	*/
[1350]	83	explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
[19]	84
[824]	85	/**
[2321]	86	* Create a Scantable object from an existing table on disk
[824]	87	* @param[in] name the name of the existing Scantable
	88	*/
[2321]	89	explicit Scantable(const std::string& name,
	90	casa::Table::TableType ttype = casa::Table::Memory);
[2]	91
[824]	92	/// @fixme this is only sensible for MemoryTables....
	93	Scantable(const Scantable& other, bool clear=true);
[161]	94
[824]	95	/**
	96	* Destructor
	97	*/
	98	virtual ~Scantable();
[745]	99
[824]	100	/**
	101	* get a const reference to the underlying casa::Table
[1104]	102	* @return const \ref casa::Table reference
[824]	103	*/
	104	const casa::Table& table() const;
[19]	105
[824]	106	/**
	107	* get a reference to the underlying casa::Table with the Selection
	108	* object applied if set
	109	* @return casa::Table reference
	110	*/
	111	casa::Table& table();
[21]	112
[845]	113
	114	/**
	115	* Get a handle to the selection object
	116	* @return constant STSelector reference
	117	*/
	118	const STSelector& getSelection() const { return selector_; }
	119
	120	/**
	121	* Set the data to be a subset as defined by the STSelector
	122	* @param selection a STSelector object
	123	*/
[824]	124	void setSelection(const STSelector& selection);
[845]	125
	126	/**
	127	* unset the selection of the data
	128	*/
[824]	129	void unsetSelection();
	130	/**
	131	* set the header
[1295]	132	* @param[in] sth an STHeader object
[824]	133	*/
[901]	134	void setHeader( const STHeader& sth );
[386]	135
[824]	136	/**
	137	* get the header information
[901]	138	* @return an STHeader object
[824]	139	*/
[901]	140	STHeader getHeader( ) const;
[1068]	141
[824]	142	/**
	143	* Checks if the "other" Scantable is conformant with this,
	144	* i.e. if header values are the same.
	145	* @param[in] other another Scantable
	146	* @return true or false
	147	*/
	148	bool conformant( const Scantable& other);
[430]	149
[824]	150	/**
[1068]	151	*
	152	* @param stype The type of the source, 0 = on, 1 = off
	153	*/
	154	void setSourceType(int stype);
	155
	156
	157	/**
[1104]	158	* The number of scans in the table
[824]	159	* @return number of scans in the table
	160	*/
[845]	161	int nscan() const;
[490]	162
[915]	163	casa::MEpoch::Types getTimeReference() const;
[21]	164
[1411]	165
	166	casa::MEpoch getEpoch(int whichrow) const;
	167
[824]	168	/**
	169	* Get global antenna position
[845]	170	* @return casa::MPosition
[824]	171	*/
	172	casa::MPosition getAntennaPosition() const;
[490]	173
[1441]	174	/**
	175	* the @ref casa::MDirection for a specific row
	176	* @param[in] whichrow the row number
	177	* return casa::MDirection
	178	*/
[987]	179	casa::MDirection getDirection( int whichrow ) const;
[1598]	180
[1441]	181	/**
	182	* get the direction type as a string, e.g. "J2000"
	183	* @param[in] whichrow the row number
	184	* return the direction string
	185	*/
[1068]	186	std::string getDirectionString( int whichrow ) const;
	187
[1441]	188	/**
	189	* set the direction type as a string, e.g. "J2000"
	190	* @param[in] refstr the direction type
	191	*/
[987]	192	void setDirectionRefString(const std::string& refstr="");
[1441]	193
[1104]	194	/**
	195	* get the direction reference string
	196	* @return a string describing the direction reference
	197	*/
[1598]	198	std::string getDirectionRefString() const;
[987]	199
[824]	200	/**
[845]	201	* Return the Flux unit of the data, e.g. "Jy" or "K"
	202	* @return string
[824]	203	*/
	204	std::string getFluxUnit() const;
[472]	205
[824]	206	/**
[845]	207	* Set the Flux unit of the data
	208	* @param unit a string representing the unit, e.g "Jy" or "K"
[824]	209	*/
	210	void setFluxUnit( const std::string& unit );
[472]	211
[824]	212	/**
[1189]	213	* Set the Stokes type of the data
[1295]	214	* @param feedtype a string representing the type, e.g "circular" or "linear"
[1189]	215	*/
	216	void setFeedType( const std::string& feedtype );
	217
	218	/**
[824]	219	*
[845]	220	* @param instrument a string representing an insturment. see xxx
[824]	221	*/
	222	void setInstrument( const std::string& instrument );
[2]	223
[845]	224	/**
	225	* (Re)calculate the azimuth and elevationnfor all rows
	226	*/
[824]	227	void calculateAZEL();
[745]	228
[824]	229	/**
[845]	230	* "hard" flag the data, this flags everything selected in setSelection()
[1104]	231	* param[in] msk a boolean mask of length nchan describing the points to
	232	* to be flagged
[824]	233	*/
[1430]	234	//void flag( const std::vector<bool>& msk = std::vector<bool>());
[1994]	235	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
[455]	236
[1994]	237	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
	238
[852]	239	/**
[1819]	240	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
	241	* param[in] rows list of row numbers to be flagged
	242	*/
	243	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
	244
	245	/**
	246	* Get flagRow info at the specified row. If true, the whole data
	247	* at the row should be flagged.
	248	*/
	249	bool getFlagRow(int whichrow) const
	250	{ return (flagrowCol_(whichrow) > 0); }
	251
	252	/**
	253	* Flag the data outside a specified range (in a channel-based manner).
	254	* (CAS-1807 Wataru Kawasaki)
	255	*/
	256	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
	257
	258	/**
	259	* Return a list of booleans with the size of nchan for a specified row, to get info
	260	* about which channel is clipped.
	261	*/
	262	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
	263	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
	264	casa::Vector<casa::uChar> flgs);
	265
	266	/**
[852]	267	* Return a list of row numbers with respect to the original table.
[902]	268	* @return a list of unsigned ints
[852]	269	*/
	270	std::vector<unsigned int> rownumbers() const;
[845]	271
[852]	272
[845]	273	/**
	274	* Get the number of beams in the data or a specific scan
	275	* @param scanno the scan number to get the number of beams for.
	276	* If scanno<0 the number is retrieved from the header.
	277	* @return an integer number
	278	*/
[824]	279	int nbeam(int scanno=-1) const;
[845]	280	/**
	281	* Get the number of IFs in the data or a specific scan
	282	* @param scanno the scan number to get the number of IFs for.
	283	* If scanno<0 the number is retrieved from the header.
	284	* @return an integer number
	285	*/
[824]	286	int nif(int scanno=-1) const;
[845]	287	/**
	288	* Get the number of polarizations in the data or a specific scan
	289	* @param scanno the scan number to get the number of polarizations for.
	290	* If scanno<0 the number is retrieved from the header.
	291	* @return an integer number
	292	*/
[824]	293	int npol(int scanno=-1) const;
[794]	294
[896]	295	std::string getPolType() const;
	296
[845]	297
	298	/**
	299	* Get the number of integartion cycles
	300	* @param scanno the scan number to get the number of rows for.
	301	* If scanno<0 the number is retrieved from the header.
[1104]	302	* @return the number of rows (for the specified scanno)
[845]	303	*/
[824]	304	int nrow(int scanno=-1) const;
[794]	305
[1111]	306	int getBeam(int whichrow) const;
[1694]	307	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
[50]	308
[847]	309	int getIF(int whichrow) const;
[1694]	310	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
[1111]	311
[847]	312	int getPol(int whichrow) const;
[1694]	313	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
[1111]	314
[1694]	315	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
[865]	316	int getScan(int whichrow) const { return scanCol_(whichrow); }
[1111]	317
[2667]	318	std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
	319	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
	320
[1819]	321	//TT addition
	322	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
	323
[1111]	324	/**
	325	* Get the number of channels in the data or a specific IF. This currently
	326	* varies only with IF number
	327	* @param ifno the IF number to get the number of channels for.
	328	* If ifno<0 the number is retrieved from the header.
	329	* @return an integer number
	330	*/
	331	int nchan(int ifno=-1) const;
[923]	332	int getChannels(int whichrow) const;
[206]	333
[1111]	334	int ncycle(int scanno=-1) const;
	335
[2667]	336
[847]	337	double getInterval(int whichrow) const
	338	{ return integrCol_(whichrow); }
[845]	339
[865]	340	float getTsys(int whichrow) const
	341	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
[2161]	342	std::vector<float> getTsysSpectrum(int whichrow) const ;
[847]	343	float getElevation(int whichrow) const
	344	{ return elCol_(whichrow); }
	345	float getAzimuth(int whichrow) const
	346	{ return azCol_(whichrow); }
[865]	347	float getParAngle(int whichrow) const
[1819]	348	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
	349	int getTcalId(int whichrow) const
	350	{ return mtcalidCol_(whichrow); }
[386]	351
[865]	352	std::string getSourceName(int whichrow) const
	353	{ return srcnCol_(whichrow); }
	354
[847]	355	std::vector<bool> getMask(int whichrow) const;
[896]	356	std::vector<float> getSpectrum(int whichrow,
[905]	357	const std::string& poltype = "" ) const;
[847]	358
[884]	359	void setSpectrum(const std::vector<float>& spec, int whichrow);
	360
[902]	361	std::string getPolarizationLabel(int index, const std::string& ptype) const
	362	{ return STPol::getPolLabel(index, ptype ); }
[401]	363
[845]	364	/**
	365	* Write the Scantable to disk
	366	* @param filename the output file name
	367	*/
[824]	368	void makePersistent(const std::string& filename);
[745]	369
[860]	370	std::vector<std::string> getHistory() const
	371	{ return historyTable_.getHistory(); };
[483]	372
[860]	373	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
[488]	374
[860]	375	void appendToHistoryTable(const STHistory& otherhist)
	376	{ historyTable_.append(otherhist); }
	377
[2163]	378	std::string headerSummary();
[2290]	379	void summary(const std::string& filename="");
	380	std::string oldheaderSummary();
[2286]	381	// std::string summary();
[2290]	382	void oldsummary(const std::string& filename="");
	383
[1947]	384	//std::string getTime(int whichrow=-1, bool showdate=true) const;
	385	std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
[1350]	386	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
[19]	387
[847]	388	// returns unit, conversion frame, doppler, base-frame
[18]	389
[847]	390	/**
	391	* Get the frequency set up
	392	* This is forwarded to the STFrequencies subtable
	393	* @return unit, frame, doppler
	394	*/
	395	std::vector<std::string> getCoordInfo() const
	396	{ return freqTable_.getInfo(); };
	397
	398	void setCoordInfo(std::vector<string> theinfo)
	399	{ return freqTable_.setInfo(theinfo); };
	400
[865]	401
	402	std::vector<double> getAbcissa(int whichrow) const;
	403
[1730]	404	std::vector<float> getWeather(int whichrow) const;
	405
[847]	406	std::string getAbcissaLabel(int whichrow) const;
	407	std::vector<double> getRestFrequencies() const
	408	{ return moleculeTable_.getRestFrequencies(); }
[1819]	409	std::vector<double> getRestFrequency(int id) const
	410	{ return moleculeTable_.getRestFrequency(id); }
[847]	411
[1819]	412	/**
[1170]	413	void setRestFrequencies(double rf, const std::string& name = "",
	414	const std::string& = "Hz");
[1819]	415	**/
	416	// Modified by Takeshi Nakazato 05/09/2008
	417	/***
	418	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
	419	const std::string& = "Hz");
	420	***/
	421	void setRestFrequencies(vector<double> rf,
	422	const vector<std::string>& name = vector<std::string>(1,""),
	423	const std::string& = "Hz");
[847]	424
[1819]	425	//void setRestFrequencies(const std::string& name);
	426	void setRestFrequencies(const vector<std::string>& name);
	427
[1360]	428	void shift(int npix);
	429
[1598]	430	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
	431
[987]	432	void convertDirection(const std::string& newframe);
	433
[824]	434	STFrequencies& frequencies() { return freqTable_; }
[1375]	435	const STFrequencies& frequencies() const { return freqTable_; }
[824]	436	STWeather& weather() { return weatherTable_; }
[1375]	437	const STWeather& weather() const { return weatherTable_; }
[824]	438	STFocus& focus() { return focusTable_; }
[1375]	439	const STFocus& focus() const { return focusTable_; }
[824]	440	STTcal& tcal() { return tcalTable_; }
[1375]	441	const STTcal& tcal() const { return tcalTable_; }
[824]	442	STMolecules& molecules() { return moleculeTable_; }
[1375]	443	const STMolecules& molecules() const { return moleculeTable_; }
[860]	444	STHistory& history() { return historyTable_; }
[1375]	445	const STHistory& history() const { return historyTable_; }
[972]	446	STFit& fit() { return fitTable_; }
[1375]	447	const STFit& fit() const { return fitTable_; }
[2]	448
[902]	449	std::vector<std::string> columnNames() const;
[896]	450
[972]	451	void addFit(const STFitEntry& fit, int row);
	452	STFitEntry getFit(int row) const
	453	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
	454
[1391]	455	//Added by TT
	456	/**
	457	* Get the antenna name
	458	* @return antenna name string
	459	*/
[1819]	460	casa::String getAntennaName() const;
[1391]	461
	462	/**
	463	* For GBT MS data only. check a scan list
	464	* against the information found in GBT_GO table for
	465	* scan number orders to get correct pairs.
	466	* @param[in] scan list
	467	* @return status
	468	*/
	469	int checkScanInfo(const std::vector<int>& scanlist) const;
	470
	471	/**
	472	* Get the direction as a vector, for a specific row
	473	* @param[in] whichrow the row numbyyer
	474	* @return the direction in a vector
	475	*/
	476	std::vector<double> getDirectionVector(int whichrow) const;
	477
[1586]	478	/**
	479	* Set a flag indicating whether the data was parallactified
	480	* @param[in] flag true or false
	481	*/
[1598]	482	void parallactify(bool flag)
[2357]	483	{ focusTable_.setParallactify(flag); }
[1727]	484
[1819]	485	/**
	486	* Reshape spectrum
	487	* @param[in] nmin, nmax minimum and maximum channel
	488	* @param[in] irow row number
	489	*
	490	* 30/07/2008 Takeshi Nakazato
	491	**/
	492	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
	493	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
	494
	495	/**
	496	* Change channel number under fixed bandwidth
	497	* @param[in] nchan, dnu new channel number and spectral resolution
	498	* @param[in] irow row number
	499	*
	500	* 27/08/2008 Takeshi Nakazato
	501	**/
	502	void regridChannel( int nchan, double dnu ) ;
	503	void regridChannel( int nchan, double dnu, int irow ) ;
[2595]	504	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
[2435]	505	void regridSpecChannel( double dnu, int nchan=-1 ) ;
	506
[2047]	507	bool getFlagtraFast(casa::uInt whichrow);
[1819]	508
[2767]	509	std::vector<std::string> applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
	510	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
	511	void polyBaseline(const std::vector<bool>& mask,
	512	int order,
	513	float thresClip,
	514	int nIterClip,
[2094]	515	bool getResidual=true,
[2189]	516	const std::string& progressInfo="true,1000",
[2767]	517	const bool outLogger=false,
	518	const std::string& blfile="",
	519	const std::string& bltable="");
[2012]	520	void autoPolyBaseline(const std::vector<bool>& mask,
[2767]	521	int order,
	522	float thresClip,
	523	int nIterClip,
	524	const std::vector<int>& edge,
	525	float threshold=3.0,
	526	int chanAvgLimit=1,
	527	bool getResidual=true,
	528	const std::string& progressInfo="true,1000",
	529	const bool outLogger=false,
	530	const std::string& blfile="",
	531	const std::string& bltable="");
[2645]	532	void chebyshevBaseline(const std::vector<bool>& mask,
	533	int order,
	534	float thresClip,
	535	int nIterClip,
	536	bool getResidual=true,
	537	const std::string& progressInfo="true,1000",
	538	const bool outLogger=false,
[2767]	539	const std::string& blfile="",
	540	const std::string& bltable="");
[2645]	541	void autoChebyshevBaseline(const std::vector<bool>& mask,
	542	int order,
	543	float thresClip,
	544	int nIterClip,
	545	const std::vector<int>& edge,
	546	float threshold=3.0,
	547	int chanAvgLimit=1,
	548	bool getResidual=true,
	549	const std::string& progressInfo="true,1000",
	550	const bool outLogger=false,
[2767]	551	const std::string& blfile="",
	552	const std::string& bltable="");
[2012]	553	void cubicSplineBaseline(const std::vector<bool>& mask,
	554	int nPiece,
	555	float thresClip,
	556	int nIterClip,
[2094]	557	bool getResidual=true,
[2189]	558	const std::string& progressInfo="true,1000",
	559	const bool outLogger=false,
[2767]	560	const std::string& blfile="",
	561	const std::string& bltable="");
[2012]	562	void autoCubicSplineBaseline(const std::vector<bool>& mask,
	563	int nPiece,
	564	float thresClip,
	565	int nIterClip,
	566	const std::vector<int>& edge,
	567	float threshold=3.0,
	568	int chanAvgLimit=1,
[2094]	569	bool getResidual=true,
[2189]	570	const std::string& progressInfo="true,1000",
	571	const bool outLogger=false,
[2767]	572	const std::string& blfile="",
	573	const std::string& bltable="");
[2047]	574	void sinusoidBaseline(const std::vector<bool>& mask,
[2767]	575	const std::string& fftInfo,
[2186]	576	const std::vector<int>& addNWaves,
	577	const std::vector<int>& rejectNWaves,
[2047]	578	float thresClip,
	579	int nIterClip,
[2081]	580	bool getResidual=true,
[2189]	581	const std::string& progressInfo="true,1000",
	582	const bool outLogger=false,
[2767]	583	const std::string& blfile="",
	584	const std::string& bltable="");
[2047]	585	void autoSinusoidBaseline(const std::vector<bool>& mask,
[2767]	586	const std::string& fftInfo,
[2186]	587	const std::vector<int>& addNWaves,
	588	const std::vector<int>& rejectNWaves,
[2047]	589	float thresClip,
	590	int nIterClip,
	591	const std::vector<int>& edge,
	592	float threshold=3.0,
	593	int chanAvgLimit=1,
[2081]	594	bool getResidual=true,
[2189]	595	const std::string& progressInfo="true,1000",
	596	const bool outLogger=false,
[2767]	597	const std::string& blfile="",
	598	const std::string& bltable="");
[2186]	599	std::vector<float> execFFT(const int whichrow,
	600	const std::vector<bool>& inMask,
	601	bool getRealImag=false,
	602	bool getAmplitudeOnly=false);
[2012]	603	float getRms(const std::vector<bool>& mask, int whichrow);
	604	std::string formatBaselineParams(const std::vector<float>& params,
	605	const std::vector<bool>& fixed,
	606	float rms,
[2193]	607	int nClipped,
[2012]	608	const std::string& masklist,
	609	int whichrow,
[2064]	610	bool verbose=false,
[2641]	611	bool csvformat=false,
[2064]	612	int start=-1,
	613	int count=-1,
	614	bool resetparamid=false) const;
[2012]	615	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
	616	const std::vector<float>& params,
	617	const std::vector<bool>& fixed,
	618	float rms,
[2193]	619	int nClipped,
[2012]	620	const std::string& masklist,
	621	int whichrow,
[2641]	622	bool verbose=false,
	623	bool csvformat=false) const;
[2591]	624	std::vector<uint> getMoleculeIdColumnData() const;
	625	void setMoleculeIdColumnData(const std::vector<uint>& molids);
[2713]	626	double calculateModelSelectionCriteria(const std::string& valname,
	627	const std::string& blfunc,
	628	int order,
	629	const std::vector<bool>& inMask,
	630	int whichrow,
	631	bool useLineFinder,
	632	const std::vector<int>& edge,
	633	float threshold,
	634	int chanAvgLimit);
[2767]	635	static std::vector<bool> getMaskFromMaskList(const int nchan,
	636	const std::vector<int>& masklist);
	637	static std::vector<int> splitToIntList(const std::string& str, const char delim);
	638	static std::vector<string> splitToStringList(const std::string& str, const char delim);
[1907]	639
[2012]	640
[2767]	641
[824]	642	private:
[896]	643
	644	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
	645
[824]	646	/**
[2005]	647	* Turns a time value into a formatted string
[824]	648	* @param x
	649	* @return
	650	*/
	651	std::string formatSec(casa::Double x) const;
[18]	652
[824]	653	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[1947]	654	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
[22]	655
[824]	656	/**
	657	* Turns a casa::MDirection into a nicely formatted string
	658	* @param md an casa::MDirection
	659	* @return
	660	*/
	661	std::string formatDirection(const casa::MDirection& md) const;
[19]	662
[824]	663	/**
	664	* Create a unique file name for the paged (temporary) table
	665	* @return just the name
	666	*/
	667	static casa::String generateName();
[286]	668
[824]	669	/**
	670	* attach to cached columns
	671	*/
	672	void attach();
[50]	673
[824]	674	/**
	675	* Set up the main casa::Table
	676	*/
	677	void setupMainTable();
[88]	678
[859]	679	void attachSubtables();
[865]	680	void copySubtables(const Scantable& other);
	681
[824]	682	/**
	683	* Convert an "old" asap1 style row index into a new index
	684	* @param[in] therow
	685	* @return and index into @table_
	686	*/
	687	int rowToScanIndex(int therow);
[212]	688
[1694]	689	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]	690
[2321]	691	static const casa::uInt version_ = 4;
[286]	692
[824]	693	STSelector selector_;
[236]	694
[824]	695	casa::Table::TableType type_;
[465]	696
[824]	697	// the actual data
	698	casa::Table table_;
	699	casa::Table originalTable_;
[745]	700
[824]	701	STTcal tcalTable_;
	702	STFrequencies freqTable_;
	703	STWeather weatherTable_;
	704	STFocus focusTable_;
	705	STMolecules moleculeTable_;
[860]	706	STHistory historyTable_;
[960]	707	STFit fitTable_;
[860]	708
[824]	709	// Cached Columns to avoid reconstructing them for each row get/put
[847]	710	casa::ScalarColumn<casa::Double> integrCol_;
[824]	711	casa::MDirection::ScalarColumn dirCol_;
[847]	712	casa::MEpoch::ScalarColumn timeCol_;
[923]	713	casa::ScalarColumn<casa::Float> azCol_;
	714	casa::ScalarColumn<casa::Float> elCol_;
[824]	715	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]	716	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]	717	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]	718	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]	719	casa::ArrayColumn<casa::uChar> flagsCol_;
[430]	720
[824]	721	// id in frequencies table
	722	casa::ScalarColumn<casa::uInt> mfreqidCol_;
	723	// id in tcal table
	724	casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]	725
[824]	726	casa::ArrayColumn<casa::String> histitemCol_;
[972]	727	casa::ScalarColumn<casa::Int> mfitidCol_;
[824]	728	casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]	729
[824]	730	casa::ScalarColumn<casa::uInt> mfocusidCol_;
	731
	732	casa::ScalarColumn<casa::uInt> mmolidCol_;
	733
[896]	734	static std::map<std::string, STPol::STPolFactory *> factories_;
	735	void initFactories();
	736
[1819]	737	/**
	738	* Add an auxiliary column to the main table and attach it to a
	739	* cached column. Use for adding new columns that the original asap2
	740	* tables do not have.
	741	* @param[in] col reference to the cached column to be attached
	742	* @param[in] colName column name in asap table
	743	* @param[in] defValue default value to fill in the column
	744	*
	745	* 25/10/2009 Wataru Kawasaki
	746	*/
	747	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
	748	const casa::String&,
	749	const T2&);
	750	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
	751	const casa::String&,
	752	const casa::Array<T2>&);
[1907]	753
[2012]	754	void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
[2767]	755	double getNormalPolynomial(int n, double x);
[2645]	756	double getChebyshevPolynomial(int n, double x);
[2767]	757	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	758	const std::vector<bool>& mask,
	759	int order,
	760	std::vector<float>& params,
	761	float& rms,
	762	std::vector<bool>& finalMask,
	763	float clipth,
	764	int clipn);
	765	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	766	const std::vector<bool>& mask,
	767	int order,
	768	std::vector<float>& params,
	769	float& rms,
	770	std::vector<bool>& finalMask,
	771	int& nClipped,
	772	float thresClip=3.0,
	773	int nIterClip=0,
	774	bool getResidual=true);
[2645]	775	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
[2767]	776	const std::vector<bool>& mask,
	777	int order,
	778	std::vector<float>& params,
	779	float& rms,
	780	std::vector<bool>& finalMask,
	781	float clipth,
	782	int clipn);
	783	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
	784	const std::vector<bool>& mask,
	785	int order,
	786	std::vector<float>& params,
	787	float& rms,
	788	std::vector<bool>& finalMask,
	789	int& nClipped,
	790	float thresClip=3.0,
	791	int nIterClip=0,
	792	bool getResidual=true);
	793	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
	794	const std::vector<bool>& mask,
	795	double (Scantable::*pfunc)(int, double),
	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> doCubicSplineFitting(const std::vector<float>& data,
[2645]	805	const std::vector<bool>& mask,
[2767]	806	std::vector<int>& idxEdge,
[2645]	807	std::vector<float>& params,
[2767]	808	float& rms,
[2737]	809	std::vector<bool>& finalMask,
[2767]	810	float clipth,
	811	int clipn);
	812	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	813	const std::vector<bool>& mask,
	814	int nPiece,
	815	std::vector<int>& idxEdge,
	816	std::vector<float>& params,
[2737]	817	float& rms,
[2767]	818	std::vector<bool>& finalMask,
	819	float clipth,
	820	int clipn);
[2012]	821	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	822	const std::vector<bool>& mask,
[2081]	823	int nPiece,
[2767]	824	bool useGivenPieceBoundary,
[2064]	825	std::vector<int>& idxEdge,
[2012]	826	std::vector<float>& params,
[2767]	827	float& rms,
	828	std::vector<bool>& finalMask,
[2193]	829	int& nClipped,
[2012]	830	float thresClip=3.0,
[2767]	831	int nIterClip=0,
[2094]	832	bool getResidual=true);
[2047]	833	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	834	const std::vector<bool>& mask,
[2081]	835	const std::vector<int>& waveNumbers,
[2047]	836	std::vector<float>& params,
[2767]	837	float& rms,
	838	std::vector<bool>& finalMask,
	839	float clipth,
	840	int clipn);
	841	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	842	const std::vector<bool>& mask,
	843	const std::vector<int>& waveNumbers,
	844	std::vector<float>& params,
	845	float& rms,
	846	std::vector<bool>& finalMask,
[2193]	847	int& nClipped,
[2047]	848	float thresClip=3.0,
[2767]	849	int nIterClip=0,
[2094]	850	bool getResidual=true);
[2186]	851	void selectWaveNumbers(const int whichrow,
	852	const std::vector<bool>& chanMask,
[2767]	853	const std::string& fftInfo,
	854	//const bool applyFFT,
	855	//const std::string& fftMethod,
	856	//const std::string& fftThresh,
[2186]	857	const std::vector<int>& addNWaves,
	858	const std::vector<int>& rejectNWaves,
	859	std::vector<int>& nWaves);
[2767]	860	void parseFFTInfo(const std::string& fftInfo,
	861	bool& applyFFT,
	862	std::string& fftMethod,
	863	std::string& fftThresh);
[2186]	864	void parseThresholdExpression(const std::string& fftThresh,
	865	std::string& fftThAttr,
	866	float& fftThSigma,
	867	int& fftThTop);
	868	void doSelectWaveNumbers(const int whichrow,
	869	const std::vector<bool>& chanMask,
	870	const std::string& fftMethod,
	871	const float fftThSigma,
	872	const int fftThTop,
	873	const std::string& fftThAttr,
	874	std::vector<int>& nWaves);
[2411]	875	void addAuxWaveNumbers(const int whichrow,
	876	const std::vector<int>& addNWaves,
[2186]	877	const std::vector<int>& rejectNWaves,
	878	std::vector<int>& nWaves);
[2411]	879	void setWaveNumberListUptoNyquistFreq(const int whichrow,
	880	std::vector<int>& nWaves);
[2012]	881	bool hasSameNchanOverIFs();
	882	std::string getMaskRangeList(const std::vector<bool>& mask,
	883	int whichrow,
	884	const casa::String& coordInfo,
[2047]	885	bool hasSameNchan,
	886	bool verbose=false);
	887	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2641]	888	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
	889	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
[2012]	890	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
	891	//std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
[2641]	892	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, Fitter& fitter);
	893	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);
	894	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);
[2189]	895	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
	896	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]	897
	898	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
	899
[2713]	900	double doCalculateModelSelectionCriteria(const std::string& valname,
	901	const std::vector<float>& spec,
	902	const std::vector<bool>& mask,
	903	const std::string& blfunc,
	904	int order);
[2737]	905	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
[2767]	906	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
	907	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);
	908	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);
	909	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);
[2713]	910
[2]	911	};
[824]	912	} // namespace
	913
[2]	914	#endif

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