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source: trunk/src/Scantable.h@ 2796

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Last change on this file since 2796 was 2791, checked in by Malte Marquarding, 12 years ago
Ticket #289: added anility to set Tsys, both for scalar and vector values
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 32.3 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"
	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 ;
[2791]	344
	345	void setTsys(const std::vector<float>& newvals, int whichrow);
	346
[847]	347	float getElevation(int whichrow) const
	348	{ return elCol_(whichrow); }
	349	float getAzimuth(int whichrow) const
	350	{ return azCol_(whichrow); }
[865]	351	float getParAngle(int whichrow) const
[1819]	352	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
	353	int getTcalId(int whichrow) const
	354	{ return mtcalidCol_(whichrow); }
[386]	355
[865]	356	std::string getSourceName(int whichrow) const
	357	{ return srcnCol_(whichrow); }
	358
[847]	359	std::vector<bool> getMask(int whichrow) const;
[896]	360	std::vector<float> getSpectrum(int whichrow,
[905]	361	const std::string& poltype = "" ) const;
[847]	362
[884]	363	void setSpectrum(const std::vector<float>& spec, int whichrow);
	364
[902]	365	std::string getPolarizationLabel(int index, const std::string& ptype) const
	366	{ return STPol::getPolLabel(index, ptype ); }
[401]	367
[845]	368	/**
	369	* Write the Scantable to disk
	370	* @param filename the output file name
	371	*/
[824]	372	void makePersistent(const std::string& filename);
[745]	373
[860]	374	std::vector<std::string> getHistory() const
	375	{ return historyTable_.getHistory(); };
[483]	376
[860]	377	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
[488]	378
[860]	379	void appendToHistoryTable(const STHistory& otherhist)
	380	{ historyTable_.append(otherhist); }
	381
[2163]	382	std::string headerSummary();
[2290]	383	void summary(const std::string& filename="");
	384	std::string oldheaderSummary();
[2286]	385	// std::string summary();
[2290]	386	void oldsummary(const std::string& filename="");
	387
[1947]	388	//std::string getTime(int whichrow=-1, bool showdate=true) const;
	389	std::string getTime(int whichrow=-1, bool showdate=true, casa::uInt prec=0) const;
[1350]	390	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
[19]	391
[847]	392	// returns unit, conversion frame, doppler, base-frame
[18]	393
[847]	394	/**
	395	* Get the frequency set up
	396	* This is forwarded to the STFrequencies subtable
	397	* @return unit, frame, doppler
	398	*/
	399	std::vector<std::string> getCoordInfo() const
	400	{ return freqTable_.getInfo(); };
	401
	402	void setCoordInfo(std::vector<string> theinfo)
	403	{ return freqTable_.setInfo(theinfo); };
	404
[865]	405
	406	std::vector<double> getAbcissa(int whichrow) const;
	407
[1730]	408	std::vector<float> getWeather(int whichrow) const;
	409
[847]	410	std::string getAbcissaLabel(int whichrow) const;
	411	std::vector<double> getRestFrequencies() const
	412	{ return moleculeTable_.getRestFrequencies(); }
[1819]	413	std::vector<double> getRestFrequency(int id) const
	414	{ return moleculeTable_.getRestFrequency(id); }
[847]	415
[1819]	416	/**
[1170]	417	void setRestFrequencies(double rf, const std::string& name = "",
	418	const std::string& = "Hz");
[1819]	419	**/
	420	// Modified by Takeshi Nakazato 05/09/2008
	421	/***
	422	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
	423	const std::string& = "Hz");
	424	***/
	425	void setRestFrequencies(vector<double> rf,
	426	const vector<std::string>& name = vector<std::string>(1,""),
	427	const std::string& = "Hz");
[847]	428
[1819]	429	//void setRestFrequencies(const std::string& name);
	430	void setRestFrequencies(const vector<std::string>& name);
	431
[1360]	432	void shift(int npix);
	433
[1598]	434	casa::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
	435
[987]	436	void convertDirection(const std::string& newframe);
	437
[824]	438	STFrequencies& frequencies() { return freqTable_; }
[1375]	439	const STFrequencies& frequencies() const { return freqTable_; }
[824]	440	STWeather& weather() { return weatherTable_; }
[1375]	441	const STWeather& weather() const { return weatherTable_; }
[824]	442	STFocus& focus() { return focusTable_; }
[1375]	443	const STFocus& focus() const { return focusTable_; }
[824]	444	STTcal& tcal() { return tcalTable_; }
[1375]	445	const STTcal& tcal() const { return tcalTable_; }
[824]	446	STMolecules& molecules() { return moleculeTable_; }
[1375]	447	const STMolecules& molecules() const { return moleculeTable_; }
[860]	448	STHistory& history() { return historyTable_; }
[1375]	449	const STHistory& history() const { return historyTable_; }
[972]	450	STFit& fit() { return fitTable_; }
[1375]	451	const STFit& fit() const { return fitTable_; }
[2]	452
[902]	453	std::vector<std::string> columnNames() const;
[896]	454
[972]	455	void addFit(const STFitEntry& fit, int row);
	456	STFitEntry getFit(int row) const
	457	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
	458
[1391]	459	//Added by TT
	460	/**
	461	* Get the antenna name
	462	* @return antenna name string
	463	*/
[1819]	464	casa::String getAntennaName() const;
[1391]	465
	466	/**
	467	* For GBT MS data only. check a scan list
	468	* against the information found in GBT_GO table for
	469	* scan number orders to get correct pairs.
	470	* @param[in] scan list
	471	* @return status
	472	*/
	473	int checkScanInfo(const std::vector<int>& scanlist) const;
	474
	475	/**
	476	* Get the direction as a vector, for a specific row
	477	* @param[in] whichrow the row numbyyer
	478	* @return the direction in a vector
	479	*/
	480	std::vector<double> getDirectionVector(int whichrow) const;
	481
[1586]	482	/**
	483	* Set a flag indicating whether the data was parallactified
	484	* @param[in] flag true or false
	485	*/
[1598]	486	void parallactify(bool flag)
[2357]	487	{ focusTable_.setParallactify(flag); }
[1727]	488
[1819]	489	/**
	490	* Reshape spectrum
	491	* @param[in] nmin, nmax minimum and maximum channel
	492	* @param[in] irow row number
	493	*
	494	* 30/07/2008 Takeshi Nakazato
	495	**/
	496	void reshapeSpectrum( int nmin, int nmax ) throw( casa::AipsError );
	497	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
	498
	499	/**
	500	* Change channel number under fixed bandwidth
	501	* @param[in] nchan, dnu new channel number and spectral resolution
	502	* @param[in] irow row number
	503	*
	504	* 27/08/2008 Takeshi Nakazato
	505	**/
	506	void regridChannel( int nchan, double dnu ) ;
	507	void regridChannel( int nchan, double dnu, int irow ) ;
[2595]	508	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
[2435]	509	void regridSpecChannel( double dnu, int nchan=-1 ) ;
	510
[2047]	511	bool getFlagtraFast(casa::uInt whichrow);
[1819]	512
[2767]	513	std::vector<std::string> applyBaselineTable(const std::string& bltable, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
	514	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList, const std::string& outbltable, const bool outbltableexists, const bool overwrite);
	515	void polyBaseline(const std::vector<bool>& mask,
	516	int order,
	517	float thresClip,
	518	int nIterClip,
[2094]	519	bool getResidual=true,
[2189]	520	const std::string& progressInfo="true,1000",
[2767]	521	const bool outLogger=false,
	522	const std::string& blfile="",
	523	const std::string& bltable="");
[2012]	524	void autoPolyBaseline(const std::vector<bool>& mask,
[2767]	525	int order,
	526	float thresClip,
	527	int nIterClip,
	528	const std::vector<int>& edge,
	529	float threshold=3.0,
	530	int chanAvgLimit=1,
	531	bool getResidual=true,
	532	const std::string& progressInfo="true,1000",
	533	const bool outLogger=false,
	534	const std::string& blfile="",
	535	const std::string& bltable="");
[2645]	536	void chebyshevBaseline(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,
[2767]	543	const std::string& blfile="",
	544	const std::string& bltable="");
[2645]	545	void autoChebyshevBaseline(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,
[2767]	555	const std::string& blfile="",
	556	const std::string& bltable="");
[2012]	557	void cubicSplineBaseline(const std::vector<bool>& mask,
	558	int nPiece,
	559	float thresClip,
	560	int nIterClip,
[2094]	561	bool getResidual=true,
[2189]	562	const std::string& progressInfo="true,1000",
	563	const bool outLogger=false,
[2767]	564	const std::string& blfile="",
	565	const std::string& bltable="");
[2012]	566	void autoCubicSplineBaseline(const std::vector<bool>& mask,
	567	int nPiece,
	568	float thresClip,
	569	int nIterClip,
	570	const std::vector<int>& edge,
	571	float threshold=3.0,
	572	int chanAvgLimit=1,
[2094]	573	bool getResidual=true,
[2189]	574	const std::string& progressInfo="true,1000",
	575	const bool outLogger=false,
[2767]	576	const std::string& blfile="",
	577	const std::string& bltable="");
[2047]	578	void sinusoidBaseline(const std::vector<bool>& mask,
[2767]	579	const std::string& fftInfo,
[2186]	580	const std::vector<int>& addNWaves,
	581	const std::vector<int>& rejectNWaves,
[2047]	582	float thresClip,
	583	int nIterClip,
[2081]	584	bool getResidual=true,
[2189]	585	const std::string& progressInfo="true,1000",
	586	const bool outLogger=false,
[2767]	587	const std::string& blfile="",
	588	const std::string& bltable="");
[2047]	589	void autoSinusoidBaseline(const std::vector<bool>& mask,
[2767]	590	const std::string& fftInfo,
[2186]	591	const std::vector<int>& addNWaves,
	592	const std::vector<int>& rejectNWaves,
[2047]	593	float thresClip,
	594	int nIterClip,
	595	const std::vector<int>& edge,
	596	float threshold=3.0,
	597	int chanAvgLimit=1,
[2081]	598	bool getResidual=true,
[2189]	599	const std::string& progressInfo="true,1000",
	600	const bool outLogger=false,
[2767]	601	const std::string& blfile="",
	602	const std::string& bltable="");
[2186]	603	std::vector<float> execFFT(const int whichrow,
	604	const std::vector<bool>& inMask,
	605	bool getRealImag=false,
	606	bool getAmplitudeOnly=false);
[2012]	607	float getRms(const std::vector<bool>& mask, int whichrow);
	608	std::string formatBaselineParams(const std::vector<float>& params,
	609	const std::vector<bool>& fixed,
	610	float rms,
[2193]	611	int nClipped,
[2012]	612	const std::string& masklist,
	613	int whichrow,
[2064]	614	bool verbose=false,
[2641]	615	bool csvformat=false,
[2064]	616	int start=-1,
	617	int count=-1,
	618	bool resetparamid=false) const;
[2012]	619	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
	620	const std::vector<float>& params,
	621	const std::vector<bool>& fixed,
	622	float rms,
[2193]	623	int nClipped,
[2012]	624	const std::string& masklist,
	625	int whichrow,
[2641]	626	bool verbose=false,
	627	bool csvformat=false) const;
[2591]	628	std::vector<uint> getMoleculeIdColumnData() const;
	629	void setMoleculeIdColumnData(const std::vector<uint>& molids);
[2713]	630	double calculateModelSelectionCriteria(const std::string& valname,
	631	const std::string& blfunc,
	632	int order,
	633	const std::vector<bool>& inMask,
	634	int whichrow,
	635	bool useLineFinder,
	636	const std::vector<int>& edge,
	637	float threshold,
	638	int chanAvgLimit);
[2767]	639	static std::vector<bool> getMaskFromMaskList(const int nchan,
[2789]	640	const std::vector<int>& masklist);
	641	static casa::Vector<casa::uInt> getMaskListFromMask(
	642	const std::vector<bool>& mask);
	643	static std::vector<int> splitToIntList(const std::string& str,
	644	const char delim);
	645	static std::vector<string> splitToStringList(const std::string& str,
	646	const char delim);
[1907]	647
[2789]	648	void dropXPol();
[2012]	649
[824]	650	private:
[896]	651
	652	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
	653
[824]	654	/**
[2005]	655	* Turns a time value into a formatted string
[824]	656	* @param x
	657	* @return
	658	*/
	659	std::string formatSec(casa::Double x) const;
[18]	660
[824]	661	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[1947]	662	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
[22]	663
[824]	664	/**
	665	* Turns a casa::MDirection into a nicely formatted string
	666	* @param md an casa::MDirection
	667	* @return
	668	*/
	669	std::string formatDirection(const casa::MDirection& md) const;
[19]	670
[824]	671	/**
	672	* Create a unique file name for the paged (temporary) table
	673	* @return just the name
	674	*/
	675	static casa::String generateName();
[286]	676
[824]	677	/**
	678	* attach to cached columns
	679	*/
	680	void attach();
[50]	681
[824]	682	/**
	683	* Set up the main casa::Table
	684	*/
	685	void setupMainTable();
[88]	686
[859]	687	void attachSubtables();
[865]	688	void copySubtables(const Scantable& other);
	689
[824]	690	/**
	691	* Convert an "old" asap1 style row index into a new index
	692	* @param[in] therow
	693	* @return and index into @table_
	694	*/
	695	int rowToScanIndex(int therow);
[212]	696
[1694]	697	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]	698
[2321]	699	static const casa::uInt version_ = 4;
[286]	700
[824]	701	STSelector selector_;
[236]	702
[824]	703	casa::Table::TableType type_;
[465]	704
[824]	705	// the actual data
	706	casa::Table table_;
	707	casa::Table originalTable_;
[745]	708
[824]	709	STTcal tcalTable_;
	710	STFrequencies freqTable_;
	711	STWeather weatherTable_;
	712	STFocus focusTable_;
	713	STMolecules moleculeTable_;
[860]	714	STHistory historyTable_;
[960]	715	STFit fitTable_;
[860]	716
[824]	717	// Cached Columns to avoid reconstructing them for each row get/put
[847]	718	casa::ScalarColumn<casa::Double> integrCol_;
[824]	719	casa::MDirection::ScalarColumn dirCol_;
[847]	720	casa::MEpoch::ScalarColumn timeCol_;
[923]	721	casa::ScalarColumn<casa::Float> azCol_;
	722	casa::ScalarColumn<casa::Float> elCol_;
[824]	723	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]	724	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]	725	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]	726	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]	727	casa::ArrayColumn<casa::uChar> flagsCol_;
[430]	728
[824]	729	// id in frequencies table
	730	casa::ScalarColumn<casa::uInt> mfreqidCol_;
	731	// id in tcal table
	732	casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]	733
[824]	734	casa::ArrayColumn<casa::String> histitemCol_;
[972]	735	casa::ScalarColumn<casa::Int> mfitidCol_;
[824]	736	casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]	737
[824]	738	casa::ScalarColumn<casa::uInt> mfocusidCol_;
	739
	740	casa::ScalarColumn<casa::uInt> mmolidCol_;
	741
[896]	742	static std::map<std::string, STPol::STPolFactory *> factories_;
	743	void initFactories();
	744
[1819]	745	/**
	746	* Add an auxiliary column to the main table and attach it to a
	747	* cached column. Use for adding new columns that the original asap2
	748	* tables do not have.
	749	* @param[in] col reference to the cached column to be attached
	750	* @param[in] colName column name in asap table
	751	* @param[in] defValue default value to fill in the column
	752	*
	753	* 25/10/2009 Wataru Kawasaki
	754	*/
	755	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
	756	const casa::String&,
	757	const T2&);
	758	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
	759	const casa::String&,
	760	const casa::Array<T2>&);
[1907]	761
[2767]	762	double getNormalPolynomial(int n, double x);
[2645]	763	double getChebyshevPolynomial(int n, double x);
[2773]	764	std::vector<std::vector<double> > getPolynomialModel(int order,
	765	int nchan,
	766	double (Scantable::*pfunc)(int, double));
	767	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
	768	double (Scantable::*pfunc)(int, double),
	769	std::vector<int>& nChanNos);
[2767]	770	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	771	const std::vector<bool>& mask,
	772	int order,
	773	std::vector<float>& params,
	774	float& rms,
	775	std::vector<bool>& finalMask,
	776	float clipth,
	777	int clipn);
	778	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	779	const std::vector<bool>& mask,
	780	int order,
	781	std::vector<float>& params,
	782	float& rms,
	783	std::vector<bool>& finalMask,
	784	int& nClipped,
	785	float thresClip=3.0,
	786	int nIterClip=0,
	787	bool getResidual=true);
[2645]	788	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
[2767]	789	const std::vector<bool>& mask,
	790	int order,
	791	std::vector<float>& params,
	792	float& rms,
	793	std::vector<bool>& finalMask,
	794	float clipth,
	795	int clipn);
	796	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
	797	const std::vector<bool>& mask,
	798	int order,
	799	std::vector<float>& params,
	800	float& rms,
	801	std::vector<bool>& finalMask,
	802	int& nClipped,
	803	float thresClip=3.0,
	804	int nIterClip=0,
	805	bool getResidual=true);
	806	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
	807	const std::vector<bool>& mask,
[2773]	808	const std::vector<std::vector<double> >& model,
[2767]	809	std::vector<float>& params,
	810	float& rms,
	811	std::vector<bool>& finalMask,
	812	int& nClipped,
	813	float thresClip=3.0,
	814	int nIterClip=0,
	815	bool getResidual=true);
	816	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
[2645]	817	const std::vector<bool>& mask,
[2767]	818	std::vector<int>& idxEdge,
[2645]	819	std::vector<float>& params,
[2767]	820	float& rms,
[2737]	821	std::vector<bool>& finalMask,
[2767]	822	float clipth,
	823	int clipn);
	824	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	825	const std::vector<bool>& mask,
	826	int nPiece,
	827	std::vector<int>& idxEdge,
	828	std::vector<float>& params,
[2737]	829	float& rms,
[2767]	830	std::vector<bool>& finalMask,
	831	float clipth,
	832	int clipn);
[2012]	833	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	834	const std::vector<bool>& mask,
[2081]	835	int nPiece,
[2767]	836	bool useGivenPieceBoundary,
[2064]	837	std::vector<int>& idxEdge,
[2012]	838	std::vector<float>& params,
[2767]	839	float& rms,
	840	std::vector<bool>& finalMask,
[2193]	841	int& nClipped,
[2012]	842	float thresClip=3.0,
[2767]	843	int nIterClip=0,
[2094]	844	bool getResidual=true);
[2773]	845	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
	846	const std::vector<bool>& mask,
	847	const std::vector<std::vector<double> >& model,
	848	int nPiece,
	849	bool useGivenPieceBoundary,
	850	std::vector<int>& idxEdge,
	851	std::vector<float>& params,
	852	float& rms,
	853	std::vector<bool>& finalMask,
	854	int& nClipped,
	855	float thresClip=3.0,
	856	int nIterClip=0,
	857	bool getResidual=true);
[2047]	858	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	859	const std::vector<bool>& mask,
[2081]	860	const std::vector<int>& waveNumbers,
[2047]	861	std::vector<float>& params,
[2767]	862	float& rms,
	863	std::vector<bool>& finalMask,
	864	float clipth,
	865	int clipn);
	866	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	867	const std::vector<bool>& mask,
	868	const std::vector<int>& waveNumbers,
	869	std::vector<float>& params,
	870	float& rms,
	871	std::vector<bool>& finalMask,
[2193]	872	int& nClipped,
[2047]	873	float thresClip=3.0,
[2767]	874	int nIterClip=0,
[2094]	875	bool getResidual=true);
[2773]	876	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
	877	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
	878	std::vector<int>& nChanNos);
	879	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
	880	const std::vector<int>& rejectNWaves);
	881	std::vector<int> selectWaveNumbers(const int whichrow,
	882	const std::vector<bool>& chanMask,
	883	//const std::string& fftInfo,
	884	const bool applyFFT,
	885	const std::string& fftMethod,
	886	const std::string& fftThresh,
	887	const std::vector<int>& addNWaves,
	888	const std::vector<int>& rejectNWaves);
	889	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
[2767]	890	void parseFFTInfo(const std::string& fftInfo,
	891	bool& applyFFT,
	892	std::string& fftMethod,
	893	std::string& fftThresh);
[2773]	894	void parseFFTThresholdInfo(const std::string& fftThresh,
	895	std::string& fftThAttr,
	896	float& fftThSigma,
	897	int& fftThTop);
[2186]	898	void doSelectWaveNumbers(const int whichrow,
	899	const std::vector<bool>& chanMask,
	900	const std::string& fftMethod,
	901	const float fftThSigma,
	902	const int fftThTop,
	903	const std::string& fftThAttr,
	904	std::vector<int>& nWaves);
[2411]	905	void addAuxWaveNumbers(const int whichrow,
	906	const std::vector<int>& addNWaves,
[2186]	907	const std::vector<int>& rejectNWaves,
	908	std::vector<int>& nWaves);
[2411]	909	void setWaveNumberListUptoNyquistFreq(const int whichrow,
	910	std::vector<int>& nWaves);
[2773]	911	void initialiseBaselining(const std::string& blfile,
	912	std::ofstream& ofs,
	913	const bool outLogger,
	914	bool& outTextFile,
	915	bool& csvFormat,
	916	casa::String& coordInfo,
	917	bool& hasSameNchan,
	918	const std::string& progressInfo,
	919	bool& showProgress,
	920	int& minNRow,
	921	casa::Vector<casa::Double>& timeSecCol);
	922	void finaliseBaselining(const bool outBaselineTable,
	923	STBaselineTable* pbt,
	924	const string& bltable,
	925	const bool outTextFile,
	926	std::ofstream& ofs);
	927	void initLineFinder(const std::vector<int>& edge,
	928	const float threshold,
	929	const int chanAvgLimit,
	930	STLineFinder& lineFinder);
[2012]	931	bool hasSameNchanOverIFs();
	932	std::string getMaskRangeList(const std::vector<bool>& mask,
	933	int whichrow,
	934	const casa::String& coordInfo,
[2047]	935	bool hasSameNchan,
	936	bool verbose=false);
	937	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2641]	938	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
	939	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
[2012]	940	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
[2773]	941	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
[2641]	942	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);
	943	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]	944	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
	945	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]	946
	947	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
	948
[2713]	949	double doCalculateModelSelectionCriteria(const std::string& valname,
	950	const std::vector<float>& spec,
	951	const std::vector<bool>& mask,
	952	const std::string& blfunc,
	953	int order);
[2737]	954	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
[2767]	955	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
	956	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);
	957	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);
	958	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]	959
[2]	960	};
[824]	961	} // namespace
	962
[2]	963	#endif

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