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source: trunk/src/Scantable.h@ 2782

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Last change on this file since 2782 was 2773, checked in by WataruKawasaki, 12 years ago

New Development: No

JIRA Issue: No

Ready for Test: Yes

Interface Changes: No

What Interface Changed:

Test Programs:

Put in Release Notes: Yes

Module(s): sd

Description: optimisation/refactoring the baselining functions for scantable.

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File size: 32.2 KB

Rev	Line
[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"
	41	#include "STFocus.h"
	42	#include "STFrequencies.h"
[901]	43	#include "STHeader.h"
[2186]	44	#include "STHistory.h"
[824]	45	#include "STMolecules.h"
[2186]	46	#include "STPol.h"
[824]	47	#include "STSelector.h"
[2186]	48	#include "STTcal.h"
	49	#include "STWeather.h"
[2]	50
[824]	51	namespace asap {
[2]	52
[2666]	53	class Fitter;
[2773]	54	class STLineFinder;
	55	class STBaselineTable;
[2666]	56
[824]	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	*/
[2658]	75	class Scantable
[824]	76	{
[902]	77
	78	friend class STMath;
	79
[2]	80	public:
[824]	81	/**
	82	* Default constructor
	83	*/
[1350]	84	explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
[19]	85
[824]	86	/**
[2321]	87	* Create a Scantable object from an existing table on disk
[824]	88	* @param[in] name the name of the existing Scantable
	89	*/
[2321]	90	explicit Scantable(const std::string& name,
	91	casa::Table::TableType ttype = casa::Table::Memory);
[2]	92
[824]	93	/// @fixme this is only sensible for MemoryTables....
	94	Scantable(const Scantable& other, bool clear=true);
[161]	95
[824]	96	/**
	97	* Destructor
	98	*/
	99	virtual ~Scantable();
[745]	100
[824]	101	/**
	102	* get a const reference to the underlying casa::Table
[1104]	103	* @return const \ref casa::Table reference
[824]	104	*/
	105	const casa::Table& table() const;
[19]	106
[824]	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();
[21]	113
[845]	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	*/
[824]	125	void setSelection(const STSelector& selection);
[845]	126
	127	/**
	128	* unset the selection of the data
	129	*/
[824]	130	void unsetSelection();
	131	/**
	132	* set the header
[1295]	133	* @param[in] sth an STHeader object
[824]	134	*/
[901]	135	void setHeader( const STHeader& sth );
[386]	136
[824]	137	/**
	138	* get the header information
[901]	139	* @return an STHeader object
[824]	140	*/
[901]	141	STHeader getHeader( ) const;
[1068]	142
[824]	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);
[430]	150
[824]	151	/**
[1068]	152	*
	153	* @param stype The type of the source, 0 = on, 1 = off
	154	*/
	155	void setSourceType(int stype);
	156
	157
	158	/**
[1104]	159	* The number of scans in the table
[824]	160	* @return number of scans in the table
	161	*/
[845]	162	int nscan() const;
[490]	163
[915]	164	casa::MEpoch::Types getTimeReference() const;
[21]	165
[1411]	166
	167	casa::MEpoch getEpoch(int whichrow) const;
	168
[824]	169	/**
	170	* Get global antenna position
[845]	171	* @return casa::MPosition
[824]	172	*/
	173	casa::MPosition getAntennaPosition() const;
[490]	174
[1441]	175	/**
	176	* the @ref casa::MDirection for a specific row
	177	* @param[in] whichrow the row number
	178	* return casa::MDirection
	179	*/
[987]	180	casa::MDirection getDirection( int whichrow ) const;
[1598]	181
[1441]	182	/**
	183	* get the direction type as a string, e.g. "J2000"
	184	* @param[in] whichrow the row number
	185	* return the direction string
	186	*/
[1068]	187	std::string getDirectionString( int whichrow ) const;
	188
[1441]	189	/**
	190	* set the direction type as a string, e.g. "J2000"
	191	* @param[in] refstr the direction type
	192	*/
[987]	193	void setDirectionRefString(const std::string& refstr="");
[1441]	194
[1104]	195	/**
	196	* get the direction reference string
	197	* @return a string describing the direction reference
	198	*/
[1598]	199	std::string getDirectionRefString() const;
[987]	200
[824]	201	/**
[845]	202	* Return the Flux unit of the data, e.g. "Jy" or "K"
	203	* @return string
[824]	204	*/
	205	std::string getFluxUnit() const;
[472]	206
[824]	207	/**
[845]	208	* Set the Flux unit of the data
	209	* @param unit a string representing the unit, e.g "Jy" or "K"
[824]	210	*/
	211	void setFluxUnit( const std::string& unit );
[472]	212
[824]	213	/**
[1189]	214	* Set the Stokes type of the data
[1295]	215	* @param feedtype a string representing the type, e.g "circular" or "linear"
[1189]	216	*/
	217	void setFeedType( const std::string& feedtype );
	218
	219	/**
[824]	220	*
[845]	221	* @param instrument a string representing an insturment. see xxx
[824]	222	*/
	223	void setInstrument( const std::string& instrument );
[2]	224
[845]	225	/**
	226	* (Re)calculate the azimuth and elevationnfor all rows
	227	*/
[824]	228	void calculateAZEL();
[745]	229
[824]	230	/**
[845]	231	* "hard" flag the data, this flags everything selected in setSelection()
[1104]	232	* param[in] msk a boolean mask of length nchan describing the points to
	233	* to be flagged
[824]	234	*/
[1430]	235	//void flag( const std::vector<bool>& msk = std::vector<bool>());
[1994]	236	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
[455]	237
[1994]	238	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
	239
[852]	240	/**
[1819]	241	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
	242	* param[in] rows list of row numbers to be flagged
	243	*/
	244	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
	245
	246	/**
	247	* Get flagRow info at the specified row. If true, the whole data
	248	* at the row should be flagged.
	249	*/
	250	bool getFlagRow(int whichrow) const
	251	{ return (flagrowCol_(whichrow) > 0); }
	252
	253	/**
	254	* Flag the data outside a specified range (in a channel-based manner).
	255	* (CAS-1807 Wataru Kawasaki)
	256	*/
	257	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
	258
	259	/**
	260	* Return a list of booleans with the size of nchan for a specified row, to get info
	261	* about which channel is clipped.
	262	*/
	263	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
	264	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
	265	casa::Vector<casa::uChar> flgs);
	266
	267	/**
[852]	268	* Return a list of row numbers with respect to the original table.
[902]	269	* @return a list of unsigned ints
[852]	270	*/
	271	std::vector<unsigned int> rownumbers() const;
[845]	272
[852]	273
[845]	274	/**
	275	* Get the number of beams in the data or a specific scan
	276	* @param scanno the scan number to get the number of beams for.
	277	* If scanno<0 the number is retrieved from the header.
	278	* @return an integer number
	279	*/
[824]	280	int nbeam(int scanno=-1) const;
[845]	281	/**
	282	* Get the number of IFs in the data or a specific scan
	283	* @param scanno the scan number to get the number of IFs for.
	284	* If scanno<0 the number is retrieved from the header.
	285	* @return an integer number
	286	*/
[824]	287	int nif(int scanno=-1) const;
[845]	288	/**
	289	* Get the number of polarizations in the data or a specific scan
	290	* @param scanno the scan number to get the number of polarizations for.
	291	* If scanno<0 the number is retrieved from the header.
	292	* @return an integer number
	293	*/
[824]	294	int npol(int scanno=-1) const;
[794]	295
[896]	296	std::string getPolType() const;
	297
[845]	298
	299	/**
	300	* Get the number of integartion cycles
	301	* @param scanno the scan number to get the number of rows for.
	302	* If scanno<0 the number is retrieved from the header.
[1104]	303	* @return the number of rows (for the specified scanno)
[845]	304	*/
[824]	305	int nrow(int scanno=-1) const;
[794]	306
[1111]	307	int getBeam(int whichrow) const;
[1694]	308	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
[50]	309
[847]	310	int getIF(int whichrow) const;
[1694]	311	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
[1111]	312
[847]	313	int getPol(int whichrow) const;
[1694]	314	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
[1111]	315
[1694]	316	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
[865]	317	int getScan(int whichrow) const { return scanCol_(whichrow); }
[1111]	318
[2667]	319	std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
	320	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
	321
[1819]	322	//TT addition
	323	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
	324
[1111]	325	/**
	326	* Get the number of channels in the data or a specific IF. This currently
	327	* varies only with IF number
	328	* @param ifno the IF number to get the number of channels for.
	329	* If ifno<0 the number is retrieved from the header.
	330	* @return an integer number
	331	*/
	332	int nchan(int ifno=-1) const;
[923]	333	int getChannels(int whichrow) const;
[206]	334
[1111]	335	int ncycle(int scanno=-1) const;
	336
[2667]	337
[847]	338	double getInterval(int whichrow) const
	339	{ return integrCol_(whichrow); }
[845]	340
[865]	341	float getTsys(int whichrow) const
	342	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
[2161]	343	std::vector<float> getTsysSpectrum(int whichrow) const ;
[847]	344	float getElevation(int whichrow) const
	345	{ return elCol_(whichrow); }
	346	float getAzimuth(int whichrow) const
	347	{ return azCol_(whichrow); }
[865]	348	float getParAngle(int whichrow) const
[1819]	349	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
	350	int getTcalId(int whichrow) const
	351	{ return mtcalidCol_(whichrow); }
[386]	352
[865]	353	std::string getSourceName(int whichrow) const
	354	{ return srcnCol_(whichrow); }
	355
[847]	356	std::vector<bool> getMask(int whichrow) const;
[896]	357	std::vector<float> getSpectrum(int whichrow,
[905]	358	const std::string& poltype = "" ) const;
[847]	359
[884]	360	void setSpectrum(const std::vector<float>& spec, int whichrow);
	361
[902]	362	std::string getPolarizationLabel(int index, const std::string& ptype) const
	363	{ return STPol::getPolLabel(index, ptype ); }
[401]	364
[845]	365	/**
	366	* Write the Scantable to disk
	367	* @param filename the output file name
	368	*/
[824]	369	void makePersistent(const std::string& filename);
[745]	370
[860]	371	std::vector<std::string> getHistory() const
	372	{ return historyTable_.getHistory(); };
[483]	373
[860]	374	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
[488]	375
[860]	376	void appendToHistoryTable(const STHistory& otherhist)
	377	{ historyTable_.append(otherhist); }
	378
[2163]	379	std::string headerSummary();
[2290]	380	void summary(const std::string& filename="");
	381	std::string oldheaderSummary();
[2286]	382	// std::string summary();
[2290]	383	void oldsummary(const std::string& filename="");
	384
[1947]	385	//std::string getTime(int whichrow=-1, bool showdate=true) const;
	386	std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
[1350]	387	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
[19]	388
[847]	389	// returns unit, conversion frame, doppler, base-frame
[18]	390
[847]	391	/**
	392	* Get the frequency set up
	393	* This is forwarded to the STFrequencies subtable
	394	* @return unit, frame, doppler
	395	*/
	396	std::vector<std::string> getCoordInfo() const
	397	{ return freqTable_.getInfo(); };
	398
	399	void setCoordInfo(std::vector<string> theinfo)
	400	{ return freqTable_.setInfo(theinfo); };
	401
[865]	402
	403	std::vector<double> getAbcissa(int whichrow) const;
	404
[1730]	405	std::vector<float> getWeather(int whichrow) const;
	406
[847]	407	std::string getAbcissaLabel(int whichrow) const;
	408	std::vector<double> getRestFrequencies() const
	409	{ return moleculeTable_.getRestFrequencies(); }
[1819]	410	std::vector<double> getRestFrequency(int id) const
	411	{ return moleculeTable_.getRestFrequency(id); }
[847]	412
[1819]	413	/**
[1170]	414	void setRestFrequencies(double rf, const std::string& name = "",
	415	const std::string& = "Hz");
[1819]	416	**/
	417	// Modified by Takeshi Nakazato 05/09/2008
	418	/***
	419	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
	420	const std::string& = "Hz");
	421	***/
	422	void setRestFrequencies(vector<double> rf,
	423	const vector<std::string>& name = vector<std::string>(1,""),
	424	const std::string& = "Hz");
[847]	425
[1819]	426	//void setRestFrequencies(const std::string& name);
	427	void setRestFrequencies(const vector<std::string>& name);
	428
[1360]	429	void shift(int npix);
	430
[1598]	431	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
	432
[987]	433	void convertDirection(const std::string& newframe);
	434
[824]	435	STFrequencies& frequencies() { return freqTable_; }
[1375]	436	const STFrequencies& frequencies() const { return freqTable_; }
[824]	437	STWeather& weather() { return weatherTable_; }
[1375]	438	const STWeather& weather() const { return weatherTable_; }
[824]	439	STFocus& focus() { return focusTable_; }
[1375]	440	const STFocus& focus() const { return focusTable_; }
[824]	441	STTcal& tcal() { return tcalTable_; }
[1375]	442	const STTcal& tcal() const { return tcalTable_; }
[824]	443	STMolecules& molecules() { return moleculeTable_; }
[1375]	444	const STMolecules& molecules() const { return moleculeTable_; }
[860]	445	STHistory& history() { return historyTable_; }
[1375]	446	const STHistory& history() const { return historyTable_; }
[972]	447	STFit& fit() { return fitTable_; }
[1375]	448	const STFit& fit() const { return fitTable_; }
[2]	449
[902]	450	std::vector<std::string> columnNames() const;
[896]	451
[972]	452	void addFit(const STFitEntry& fit, int row);
	453	STFitEntry getFit(int row) const
	454	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
	455
[1391]	456	//Added by TT
	457	/**
	458	* Get the antenna name
	459	* @return antenna name string
	460	*/
[1819]	461	casa::String getAntennaName() const;
[1391]	462
	463	/**
	464	* For GBT MS data only. check a scan list
	465	* against the information found in GBT_GO table for
	466	* scan number orders to get correct pairs.
	467	* @param[in] scan list
	468	* @return status
	469	*/
	470	int checkScanInfo(const std::vector<int>& scanlist) const;
	471
	472	/**
	473	* Get the direction as a vector, for a specific row
	474	* @param[in] whichrow the row numbyyer
	475	* @return the direction in a vector
	476	*/
	477	std::vector<double> getDirectionVector(int whichrow) const;
	478
[1586]	479	/**
	480	* Set a flag indicating whether the data was parallactified
	481	* @param[in] flag true or false
	482	*/
[1598]	483	void parallactify(bool flag)
[2357]	484	{ focusTable_.setParallactify(flag); }
[1727]	485
[1819]	486	/**
	487	* Reshape spectrum
	488	* @param[in] nmin, nmax minimum and maximum channel
	489	* @param[in] irow row number
	490	*
	491	* 30/07/2008 Takeshi Nakazato
	492	**/
	493	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
	494	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
	495
	496	/**
	497	* Change channel number under fixed bandwidth
	498	* @param[in] nchan, dnu new channel number and spectral resolution
	499	* @param[in] irow row number
	500	*
	501	* 27/08/2008 Takeshi Nakazato
	502	**/
	503	void regridChannel( int nchan, double dnu ) ;
	504	void regridChannel( int nchan, double dnu, int irow ) ;
[2595]	505	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
[2435]	506	void regridSpecChannel( double dnu, int nchan=-1 ) ;
	507
[2047]	508	bool getFlagtraFast(casa::uInt whichrow);
[1819]	509
[2767]	510	std::vector<std::string> applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
	511	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
	512	void polyBaseline(const std::vector<bool>& mask,
	513	int order,
	514	float thresClip,
	515	int nIterClip,
[2094]	516	bool getResidual=true,
[2189]	517	const std::string& progressInfo="true,1000",
[2767]	518	const bool outLogger=false,
	519	const std::string& blfile="",
	520	const std::string& bltable="");
[2012]	521	void autoPolyBaseline(const std::vector<bool>& mask,
[2767]	522	int order,
	523	float thresClip,
	524	int nIterClip,
	525	const std::vector<int>& edge,
	526	float threshold=3.0,
	527	int chanAvgLimit=1,
	528	bool getResidual=true,
	529	const std::string& progressInfo="true,1000",
	530	const bool outLogger=false,
	531	const std::string& blfile="",
	532	const std::string& bltable="");
[2645]	533	void chebyshevBaseline(const std::vector<bool>& mask,
	534	int order,
	535	float thresClip,
	536	int nIterClip,
	537	bool getResidual=true,
	538	const std::string& progressInfo="true,1000",
	539	const bool outLogger=false,
[2767]	540	const std::string& blfile="",
	541	const std::string& bltable="");
[2645]	542	void autoChebyshevBaseline(const std::vector<bool>& mask,
	543	int order,
	544	float thresClip,
	545	int nIterClip,
	546	const std::vector<int>& edge,
	547	float threshold=3.0,
	548	int chanAvgLimit=1,
	549	bool getResidual=true,
	550	const std::string& progressInfo="true,1000",
	551	const bool outLogger=false,
[2767]	552	const std::string& blfile="",
	553	const std::string& bltable="");
[2012]	554	void cubicSplineBaseline(const std::vector<bool>& mask,
	555	int nPiece,
	556	float thresClip,
	557	int nIterClip,
[2094]	558	bool getResidual=true,
[2189]	559	const std::string& progressInfo="true,1000",
	560	const bool outLogger=false,
[2767]	561	const std::string& blfile="",
	562	const std::string& bltable="");
[2012]	563	void autoCubicSplineBaseline(const std::vector<bool>& mask,
	564	int nPiece,
	565	float thresClip,
	566	int nIterClip,
	567	const std::vector<int>& edge,
	568	float threshold=3.0,
	569	int chanAvgLimit=1,
[2094]	570	bool getResidual=true,
[2189]	571	const std::string& progressInfo="true,1000",
	572	const bool outLogger=false,
[2767]	573	const std::string& blfile="",
	574	const std::string& bltable="");
[2047]	575	void sinusoidBaseline(const std::vector<bool>& mask,
[2767]	576	const std::string& fftInfo,
[2186]	577	const std::vector<int>& addNWaves,
	578	const std::vector<int>& rejectNWaves,
[2047]	579	float thresClip,
	580	int nIterClip,
[2081]	581	bool getResidual=true,
[2189]	582	const std::string& progressInfo="true,1000",
	583	const bool outLogger=false,
[2767]	584	const std::string& blfile="",
	585	const std::string& bltable="");
[2047]	586	void autoSinusoidBaseline(const std::vector<bool>& mask,
[2767]	587	const std::string& fftInfo,
[2186]	588	const std::vector<int>& addNWaves,
	589	const std::vector<int>& rejectNWaves,
[2047]	590	float thresClip,
	591	int nIterClip,
	592	const std::vector<int>& edge,
	593	float threshold=3.0,
	594	int chanAvgLimit=1,
[2081]	595	bool getResidual=true,
[2189]	596	const std::string& progressInfo="true,1000",
	597	const bool outLogger=false,
[2767]	598	const std::string& blfile="",
	599	const std::string& bltable="");
[2186]	600	std::vector<float> execFFT(const int whichrow,
	601	const std::vector<bool>& inMask,
	602	bool getRealImag=false,
	603	bool getAmplitudeOnly=false);
[2012]	604	float getRms(const std::vector<bool>& mask, int whichrow);
	605	std::string formatBaselineParams(const std::vector<float>& params,
	606	const std::vector<bool>& fixed,
	607	float rms,
[2193]	608	int nClipped,
[2012]	609	const std::string& masklist,
	610	int whichrow,
[2064]	611	bool verbose=false,
[2641]	612	bool csvformat=false,
[2064]	613	int start=-1,
	614	int count=-1,
	615	bool resetparamid=false) const;
[2012]	616	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
	617	const std::vector<float>& params,
	618	const std::vector<bool>& fixed,
	619	float rms,
[2193]	620	int nClipped,
[2012]	621	const std::string& masklist,
	622	int whichrow,
[2641]	623	bool verbose=false,
	624	bool csvformat=false) const;
[2591]	625	std::vector<uint> getMoleculeIdColumnData() const;
	626	void setMoleculeIdColumnData(const std::vector<uint>& molids);
[2713]	627	double calculateModelSelectionCriteria(const std::string& valname,
	628	const std::string& blfunc,
	629	int order,
	630	const std::vector<bool>& inMask,
	631	int whichrow,
	632	bool useLineFinder,
	633	const std::vector<int>& edge,
	634	float threshold,
	635	int chanAvgLimit);
[2767]	636	static std::vector<bool> getMaskFromMaskList(const int nchan,
	637	const std::vector<int>& masklist);
[2773]	638	static casa::Vector<casa::uInt> getMaskListFromMask(const std::vector<bool>& mask);
[2767]	639	static std::vector<int> splitToIntList(const std::string& str, const char delim);
	640	static std::vector<string> splitToStringList(const std::string& str, const char delim);
[1907]	641
[2012]	642
[2767]	643
[824]	644	private:
[896]	645
	646	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
	647
[824]	648	/**
[2005]	649	* Turns a time value into a formatted string
[824]	650	* @param x
	651	* @return
	652	*/
	653	std::string formatSec(casa::Double x) const;
[18]	654
[824]	655	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[1947]	656	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
[22]	657
[824]	658	/**
	659	* Turns a casa::MDirection into a nicely formatted string
	660	* @param md an casa::MDirection
	661	* @return
	662	*/
	663	std::string formatDirection(const casa::MDirection& md) const;
[19]	664
[824]	665	/**
	666	* Create a unique file name for the paged (temporary) table
	667	* @return just the name
	668	*/
	669	static casa::String generateName();
[286]	670
[824]	671	/**
	672	* attach to cached columns
	673	*/
	674	void attach();
[50]	675
[824]	676	/**
	677	* Set up the main casa::Table
	678	*/
	679	void setupMainTable();
[88]	680
[859]	681	void attachSubtables();
[865]	682	void copySubtables(const Scantable& other);
	683
[824]	684	/**
	685	* Convert an "old" asap1 style row index into a new index
	686	* @param[in] therow
	687	* @return and index into @table_
	688	*/
	689	int rowToScanIndex(int therow);
[212]	690
[1694]	691	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]	692
[2321]	693	static const casa::uInt version_ = 4;
[286]	694
[824]	695	STSelector selector_;
[236]	696
[824]	697	casa::Table::TableType type_;
[465]	698
[824]	699	// the actual data
	700	casa::Table table_;
	701	casa::Table originalTable_;
[745]	702
[824]	703	STTcal tcalTable_;
	704	STFrequencies freqTable_;
	705	STWeather weatherTable_;
	706	STFocus focusTable_;
	707	STMolecules moleculeTable_;
[860]	708	STHistory historyTable_;
[960]	709	STFit fitTable_;
[860]	710
[824]	711	// Cached Columns to avoid reconstructing them for each row get/put
[847]	712	casa::ScalarColumn<casa::Double> integrCol_;
[824]	713	casa::MDirection::ScalarColumn dirCol_;
[847]	714	casa::MEpoch::ScalarColumn timeCol_;
[923]	715	casa::ScalarColumn<casa::Float> azCol_;
	716	casa::ScalarColumn<casa::Float> elCol_;
[824]	717	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]	718	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]	719	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]	720	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]	721	casa::ArrayColumn<casa::uChar> flagsCol_;
[430]	722
[824]	723	// id in frequencies table
	724	casa::ScalarColumn<casa::uInt> mfreqidCol_;
	725	// id in tcal table
	726	casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]	727
[824]	728	casa::ArrayColumn<casa::String> histitemCol_;
[972]	729	casa::ScalarColumn<casa::Int> mfitidCol_;
[824]	730	casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]	731
[824]	732	casa::ScalarColumn<casa::uInt> mfocusidCol_;
	733
	734	casa::ScalarColumn<casa::uInt> mmolidCol_;
	735
[896]	736	static std::map<std::string, STPol::STPolFactory *> factories_;
	737	void initFactories();
	738
[1819]	739	/**
	740	* Add an auxiliary column to the main table and attach it to a
	741	* cached column. Use for adding new columns that the original asap2
	742	* tables do not have.
	743	* @param[in] col reference to the cached column to be attached
	744	* @param[in] colName column name in asap table
	745	* @param[in] defValue default value to fill in the column
	746	*
	747	* 25/10/2009 Wataru Kawasaki
	748	*/
	749	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
	750	const casa::String&,
	751	const T2&);
	752	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
	753	const casa::String&,
	754	const casa::Array<T2>&);
[1907]	755
[2767]	756	double getNormalPolynomial(int n, double x);
[2645]	757	double getChebyshevPolynomial(int n, double x);
[2773]	758	std::vector<std::vector<double> > getPolynomialModel(int order,
	759	int nchan,
	760	double (Scantable::*pfunc)(int, double));
	761	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
	762	double (Scantable::*pfunc)(int, double),
	763	std::vector<int>& nChanNos);
[2767]	764	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	765	const std::vector<bool>& mask,
	766	int order,
	767	std::vector<float>& params,
	768	float& rms,
	769	std::vector<bool>& finalMask,
	770	float clipth,
	771	int clipn);
	772	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	773	const std::vector<bool>& mask,
	774	int order,
	775	std::vector<float>& params,
	776	float& rms,
	777	std::vector<bool>& finalMask,
	778	int& nClipped,
	779	float thresClip=3.0,
	780	int nIterClip=0,
	781	bool getResidual=true);
[2645]	782	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
[2767]	783	const std::vector<bool>& mask,
	784	int order,
	785	std::vector<float>& params,
	786	float& rms,
	787	std::vector<bool>& finalMask,
	788	float clipth,
	789	int clipn);
	790	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
	791	const std::vector<bool>& mask,
	792	int order,
	793	std::vector<float>& params,
	794	float& rms,
	795	std::vector<bool>& finalMask,
	796	int& nClipped,
	797	float thresClip=3.0,
	798	int nIterClip=0,
	799	bool getResidual=true);
	800	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
	801	const std::vector<bool>& mask,
[2773]	802	const std::vector<std::vector<double> >& model,
[2767]	803	std::vector<float>& params,
	804	float& rms,
	805	std::vector<bool>& finalMask,
	806	int& nClipped,
	807	float thresClip=3.0,
	808	int nIterClip=0,
	809	bool getResidual=true);
	810	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
[2645]	811	const std::vector<bool>& mask,
[2767]	812	std::vector<int>& idxEdge,
[2645]	813	std::vector<float>& params,
[2767]	814	float& rms,
[2737]	815	std::vector<bool>& finalMask,
[2767]	816	float clipth,
	817	int clipn);
	818	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	819	const std::vector<bool>& mask,
	820	int nPiece,
	821	std::vector<int>& idxEdge,
	822	std::vector<float>& params,
[2737]	823	float& rms,
[2767]	824	std::vector<bool>& finalMask,
	825	float clipth,
	826	int clipn);
[2012]	827	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	828	const std::vector<bool>& mask,
[2081]	829	int nPiece,
[2767]	830	bool useGivenPieceBoundary,
[2064]	831	std::vector<int>& idxEdge,
[2012]	832	std::vector<float>& params,
[2767]	833	float& rms,
	834	std::vector<bool>& finalMask,
[2193]	835	int& nClipped,
[2012]	836	float thresClip=3.0,
[2767]	837	int nIterClip=0,
[2094]	838	bool getResidual=true);
[2773]	839	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
	840	const std::vector<bool>& mask,
	841	const std::vector<std::vector<double> >& model,
	842	int nPiece,
	843	bool useGivenPieceBoundary,
	844	std::vector<int>& idxEdge,
	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);
[2047]	852	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	853	const std::vector<bool>& mask,
[2081]	854	const std::vector<int>& waveNumbers,
[2047]	855	std::vector<float>& params,
[2767]	856	float& rms,
	857	std::vector<bool>& finalMask,
	858	float clipth,
	859	int clipn);
	860	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	861	const std::vector<bool>& mask,
	862	const std::vector<int>& waveNumbers,
	863	std::vector<float>& params,
	864	float& rms,
	865	std::vector<bool>& finalMask,
[2193]	866	int& nClipped,
[2047]	867	float thresClip=3.0,
[2767]	868	int nIterClip=0,
[2094]	869	bool getResidual=true);
[2773]	870	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
	871	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
	872	std::vector<int>& nChanNos);
	873	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
	874	const std::vector<int>& rejectNWaves);
	875	std::vector<int> selectWaveNumbers(const int whichrow,
	876	const std::vector<bool>& chanMask,
	877	//const std::string& fftInfo,
	878	const bool applyFFT,
	879	const std::string& fftMethod,
	880	const std::string& fftThresh,
	881	const std::vector<int>& addNWaves,
	882	const std::vector<int>& rejectNWaves);
	883	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
[2767]	884	void parseFFTInfo(const std::string& fftInfo,
	885	bool& applyFFT,
	886	std::string& fftMethod,
	887	std::string& fftThresh);
[2773]	888	void parseFFTThresholdInfo(const std::string& fftThresh,
	889	std::string& fftThAttr,
	890	float& fftThSigma,
	891	int& fftThTop);
[2186]	892	void doSelectWaveNumbers(const int whichrow,
	893	const std::vector<bool>& chanMask,
	894	const std::string& fftMethod,
	895	const float fftThSigma,
	896	const int fftThTop,
	897	const std::string& fftThAttr,
	898	std::vector<int>& nWaves);
[2411]	899	void addAuxWaveNumbers(const int whichrow,
	900	const std::vector<int>& addNWaves,
[2186]	901	const std::vector<int>& rejectNWaves,
	902	std::vector<int>& nWaves);
[2411]	903	void setWaveNumberListUptoNyquistFreq(const int whichrow,
	904	std::vector<int>& nWaves);
[2773]	905	void initialiseBaselining(const std::string& blfile,
	906	std::ofstream& ofs,
	907	const bool outLogger,
	908	bool& outTextFile,
	909	bool& csvFormat,
	910	casa::String& coordInfo,
	911	bool& hasSameNchan,
	912	const std::string& progressInfo,
	913	bool& showProgress,
	914	int& minNRow,
	915	casa::Vector<casa::Double>& timeSecCol);
	916	void finaliseBaselining(const bool outBaselineTable,
	917	STBaselineTable* pbt,
	918	const string& bltable,
	919	const bool outTextFile,
	920	std::ofstream& ofs);
	921	void initLineFinder(const std::vector<int>& edge,
	922	const float threshold,
	923	const int chanAvgLimit,
	924	STLineFinder& lineFinder);
[2012]	925	bool hasSameNchanOverIFs();
	926	std::string getMaskRangeList(const std::vector<bool>& mask,
	927	int whichrow,
	928	const casa::String& coordInfo,
[2047]	929	bool hasSameNchan,
	930	bool verbose=false);
	931	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2641]	932	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
	933	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
[2012]	934	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
[2773]	935	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
[2641]	936	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);
	937	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]	938	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
	939	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]	940
	941	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
	942
[2713]	943	double doCalculateModelSelectionCriteria(const std::string& valname,
	944	const std::vector<float>& spec,
	945	const std::vector<bool>& mask,
	946	const std::string& blfunc,
	947	int order);
[2737]	948	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
[2767]	949	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
	950	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);
	951	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);
	952	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]	953
[2]	954	};
[824]	955	} // namespace
	956
[2]	957	#endif

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