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source: trunk/src/Scantable.h@ 2744

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Last change on this file since 2744 was 2737, checked in by WataruKawasaki, 12 years ago

New Development: No

JIRA Issue: Yes CAS-4794

Ready for Test: No

Interface Changes: No

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Put in Release Notes: No

Module(s): sd

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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>
	30
[2186]	31	#include <coordinates/Coordinates/SpectralCoordinate.h>
[322]	32
[824]	33	#include <measures/TableMeasures/ScalarMeasColumn.h>
	34
[2186]	35	#include <scimath/Mathematics/FFTServer.h>
[1598]	36
[2186]	37	#include <tables/Tables/ArrayColumn.h>
	38	#include <tables/Tables/ScalarColumn.h>
	39	#include <tables/Tables/Table.h>
[1819]	40
[2658]	41
[2186]	42	#include "MathUtils.h"
	43	#include "STFit.h"
	44	#include "STFitEntry.h"
[2666]	45	//#include "STFitter.h"
[2186]	46	#include "STFocus.h"
	47	#include "STFrequencies.h"
[901]	48	#include "STHeader.h"
[2186]	49	#include "STHistory.h"
[824]	50	#include "STMolecules.h"
[2186]	51	#include "STPol.h"
[824]	52	#include "STSelector.h"
[2186]	53	#include "STTcal.h"
	54	#include "STWeather.h"
[2]	55
[824]	56	namespace asap {
[2]	57
[2666]	58	class Fitter;
	59
[824]	60	/**
	61	* This class contains and wraps a casa::Table, which is used to store
	62	* all the information. This can be either a MemoryTable or a
	63	* disk based Table.
	64	* It provides access functions to the underlying table
	65	* It contains n subtables:
	66	* @li weather
	67	* @li frequencies
	68	* @li molecules
	69	* @li tcal
	70	* @li focus
	71	* @li fits
	72	*
	73	* @brief The main ASAP data container
	74	* @author Malte Marquarding
	75	* @date
	76	* @version
	77	*/
[2658]	78	class Scantable
[824]	79	{
[902]	80
	81	friend class STMath;
	82
[2]	83	public:
[824]	84	/**
	85	* Default constructor
	86	*/
[1350]	87	explicit Scantable(casa::Table::TableType ttype = casa::Table::Memory);
[19]	88
[824]	89	/**
[2321]	90	* Create a Scantable object from an existing table on disk
[824]	91	* @param[in] name the name of the existing Scantable
	92	*/
[2321]	93	explicit Scantable(const std::string& name,
	94	casa::Table::TableType ttype = casa::Table::Memory);
[2]	95
[824]	96	/// @fixme this is only sensible for MemoryTables....
	97	Scantable(const Scantable& other, bool clear=true);
[161]	98
[824]	99	/**
	100	* Destructor
	101	*/
	102	virtual ~Scantable();
[745]	103
[824]	104	/**
	105	* get a const reference to the underlying casa::Table
[1104]	106	* @return const \ref casa::Table reference
[824]	107	*/
	108	const casa::Table& table() const;
[19]	109
[824]	110	/**
	111	* get a reference to the underlying casa::Table with the Selection
	112	* object applied if set
	113	* @return casa::Table reference
	114	*/
	115	casa::Table& table();
[21]	116
[845]	117
	118	/**
	119	* Get a handle to the selection object
	120	* @return constant STSelector reference
	121	*/
	122	const STSelector& getSelection() const { return selector_; }
	123
	124	/**
	125	* Set the data to be a subset as defined by the STSelector
	126	* @param selection a STSelector object
	127	*/
[824]	128	void setSelection(const STSelector& selection);
[845]	129
	130	/**
	131	* unset the selection of the data
	132	*/
[824]	133	void unsetSelection();
	134	/**
	135	* set the header
[1295]	136	* @param[in] sth an STHeader object
[824]	137	*/
[901]	138	void setHeader( const STHeader& sth );
[386]	139
[824]	140	/**
	141	* get the header information
[901]	142	* @return an STHeader object
[824]	143	*/
[901]	144	STHeader getHeader( ) const;
[1068]	145
[824]	146	/**
	147	* Checks if the "other" Scantable is conformant with this,
	148	* i.e. if header values are the same.
	149	* @param[in] other another Scantable
	150	* @return true or false
	151	*/
	152	bool conformant( const Scantable& other);
[430]	153
[824]	154	/**
[1068]	155	*
	156	* @param stype The type of the source, 0 = on, 1 = off
	157	*/
	158	void setSourceType(int stype);
	159
	160
	161	/**
[1104]	162	* The number of scans in the table
[824]	163	* @return number of scans in the table
	164	*/
[845]	165	int nscan() const;
[490]	166
[915]	167	casa::MEpoch::Types getTimeReference() const;
[21]	168
[1411]	169
	170	casa::MEpoch getEpoch(int whichrow) const;
	171
[824]	172	/**
	173	* Get global antenna position
[845]	174	* @return casa::MPosition
[824]	175	*/
	176	casa::MPosition getAntennaPosition() const;
[490]	177
[1441]	178	/**
	179	* the @ref casa::MDirection for a specific row
	180	* @param[in] whichrow the row number
	181	* return casa::MDirection
	182	*/
[987]	183	casa::MDirection getDirection( int whichrow ) const;
[1598]	184
[1441]	185	/**
	186	* get the direction type as a string, e.g. "J2000"
	187	* @param[in] whichrow the row number
	188	* return the direction string
	189	*/
[1068]	190	std::string getDirectionString( int whichrow ) const;
	191
[1441]	192	/**
	193	* set the direction type as a string, e.g. "J2000"
	194	* @param[in] refstr the direction type
	195	*/
[987]	196	void setDirectionRefString(const std::string& refstr="");
[1441]	197
[1104]	198	/**
	199	* get the direction reference string
	200	* @return a string describing the direction reference
	201	*/
[1598]	202	std::string getDirectionRefString() const;
[987]	203
[824]	204	/**
[845]	205	* Return the Flux unit of the data, e.g. "Jy" or "K"
	206	* @return string
[824]	207	*/
	208	std::string getFluxUnit() const;
[472]	209
[824]	210	/**
[845]	211	* Set the Flux unit of the data
	212	* @param unit a string representing the unit, e.g "Jy" or "K"
[824]	213	*/
	214	void setFluxUnit( const std::string& unit );
[472]	215
[824]	216	/**
[1189]	217	* Set the Stokes type of the data
[1295]	218	* @param feedtype a string representing the type, e.g "circular" or "linear"
[1189]	219	*/
	220	void setFeedType( const std::string& feedtype );
	221
	222	/**
[824]	223	*
[845]	224	* @param instrument a string representing an insturment. see xxx
[824]	225	*/
	226	void setInstrument( const std::string& instrument );
[2]	227
[845]	228	/**
	229	* (Re)calculate the azimuth and elevationnfor all rows
	230	*/
[824]	231	void calculateAZEL();
[745]	232
[824]	233	/**
[845]	234	* "hard" flag the data, this flags everything selected in setSelection()
[1104]	235	* param[in] msk a boolean mask of length nchan describing the points to
	236	* to be flagged
[824]	237	*/
[1430]	238	//void flag( const std::vector<bool>& msk = std::vector<bool>());
[1994]	239	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
[455]	240
[1994]	241	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
	242
[852]	243	/**
[1819]	244	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
	245	* param[in] rows list of row numbers to be flagged
	246	*/
	247	void flagRow( const std::vector<casa::uInt>& rows = std::vector<casa::uInt>(), bool unflag=false);
	248
	249	/**
	250	* Get flagRow info at the specified row. If true, the whole data
	251	* at the row should be flagged.
	252	*/
	253	bool getFlagRow(int whichrow) const
	254	{ return (flagrowCol_(whichrow) > 0); }
	255
	256	/**
	257	* Flag the data outside a specified range (in a channel-based manner).
	258	* (CAS-1807 Wataru Kawasaki)
	259	*/
	260	void clip(const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
	261
	262	/**
	263	* Return a list of booleans with the size of nchan for a specified row, to get info
	264	* about which channel is clipped.
	265	*/
	266	std::vector<bool> getClipMask(int whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag);
	267	void srchChannelsToClip(casa::uInt whichrow, const casa::Float uthres, const casa::Float dthres, bool clipoutside, bool unflag,
	268	casa::Vector<casa::uChar> flgs);
	269
	270	/**
[852]	271	* Return a list of row numbers with respect to the original table.
[902]	272	* @return a list of unsigned ints
[852]	273	*/
	274	std::vector<unsigned int> rownumbers() const;
[845]	275
[852]	276
[845]	277	/**
	278	* Get the number of beams in the data or a specific scan
	279	* @param scanno the scan number to get the number of beams for.
	280	* If scanno<0 the number is retrieved from the header.
	281	* @return an integer number
	282	*/
[824]	283	int nbeam(int scanno=-1) const;
[845]	284	/**
	285	* Get the number of IFs in the data or a specific scan
	286	* @param scanno the scan number to get the number of IFs for.
	287	* If scanno<0 the number is retrieved from the header.
	288	* @return an integer number
	289	*/
[824]	290	int nif(int scanno=-1) const;
[845]	291	/**
	292	* Get the number of polarizations in the data or a specific scan
	293	* @param scanno the scan number to get the number of polarizations for.
	294	* If scanno<0 the number is retrieved from the header.
	295	* @return an integer number
	296	*/
[824]	297	int npol(int scanno=-1) const;
[794]	298
[896]	299	std::string getPolType() const;
	300
[845]	301
	302	/**
	303	* Get the number of integartion cycles
	304	* @param scanno the scan number to get the number of rows for.
	305	* If scanno<0 the number is retrieved from the header.
[1104]	306	* @return the number of rows (for the specified scanno)
[845]	307	*/
[824]	308	int nrow(int scanno=-1) const;
[794]	309
[1111]	310	int getBeam(int whichrow) const;
[1694]	311	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
[50]	312
[847]	313	int getIF(int whichrow) const;
[1694]	314	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
[1111]	315
[847]	316	int getPol(int whichrow) const;
[1694]	317	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
[1111]	318
[1694]	319	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
[865]	320	int getScan(int whichrow) const { return scanCol_(whichrow); }
[1111]	321
[2667]	322	std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
	323	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
	324
[1819]	325	//TT addition
	326	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
	327
[1111]	328	/**
	329	* Get the number of channels in the data or a specific IF. This currently
	330	* varies only with IF number
	331	* @param ifno the IF number to get the number of channels for.
	332	* If ifno<0 the number is retrieved from the header.
	333	* @return an integer number
	334	*/
	335	int nchan(int ifno=-1) const;
[923]	336	int getChannels(int whichrow) const;
[206]	337
[1111]	338	int ncycle(int scanno=-1) const;
	339
[2667]	340
[847]	341	double getInterval(int whichrow) const
	342	{ return integrCol_(whichrow); }
[845]	343
[865]	344	float getTsys(int whichrow) const
	345	{ return casa::Vector<casa::Float>(tsysCol_(whichrow))(0); }
[2161]	346	std::vector<float> getTsysSpectrum(int whichrow) const ;
[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 ) ;
[1819]	509
[2435]	510	void regridSpecChannel( double dnu, int nchan=-1 ) ;
	511
[2047]	512	bool getFlagtraFast(casa::uInt whichrow);
[1819]	513
[2012]	514	void polyBaseline(const std::vector<bool>& mask,
	515	int order,
[2094]	516	bool getResidual=true,
[2189]	517	const std::string& progressInfo="true,1000",
	518	const bool outLogger=false,
[2012]	519	const std::string& blfile="");
	520	void autoPolyBaseline(const std::vector<bool>& mask,
	521	int order,
	522	const std::vector<int>& edge,
	523	float threshold=3.0,
	524	int chanAvgLimit=1,
[2094]	525	bool getResidual=true,
[2189]	526	const std::string& progressInfo="true,1000",
	527	const bool outLogger=false,
[2012]	528	const std::string& blfile="");
[2645]	529	void chebyshevBaseline(const std::vector<bool>& mask,
	530	int order,
	531	float thresClip,
	532	int nIterClip,
	533	bool getResidual=true,
	534	const std::string& progressInfo="true,1000",
	535	const bool outLogger=false,
	536	const std::string& blfile="");
	537	void autoChebyshevBaseline(const std::vector<bool>& mask,
	538	int order,
	539	float thresClip,
	540	int nIterClip,
	541	const std::vector<int>& edge,
	542	float threshold=3.0,
	543	int chanAvgLimit=1,
	544	bool getResidual=true,
	545	const std::string& progressInfo="true,1000",
	546	const bool outLogger=false,
	547	const std::string& blfile="");
[2012]	548	void cubicSplineBaseline(const std::vector<bool>& mask,
	549	int nPiece,
	550	float thresClip,
	551	int nIterClip,
[2094]	552	bool getResidual=true,
[2189]	553	const std::string& progressInfo="true,1000",
	554	const bool outLogger=false,
[2012]	555	const std::string& blfile="");
	556	void autoCubicSplineBaseline(const std::vector<bool>& mask,
	557	int nPiece,
	558	float thresClip,
	559	int nIterClip,
	560	const std::vector<int>& edge,
	561	float threshold=3.0,
	562	int chanAvgLimit=1,
[2094]	563	bool getResidual=true,
[2189]	564	const std::string& progressInfo="true,1000",
	565	const bool outLogger=false,
[2012]	566	const std::string& blfile="");
[2047]	567	void sinusoidBaseline(const std::vector<bool>& mask,
[2186]	568	const bool applyFFT,
	569	const std::string& fftMethod,
	570	const std::string& fftThresh,
	571	const std::vector<int>& addNWaves,
	572	const std::vector<int>& rejectNWaves,
[2047]	573	float thresClip,
	574	int nIterClip,
[2081]	575	bool getResidual=true,
[2189]	576	const std::string& progressInfo="true,1000",
	577	const bool outLogger=false,
[2047]	578	const std::string& blfile="");
	579	void autoSinusoidBaseline(const std::vector<bool>& mask,
[2186]	580	const bool applyFFT,
	581	const std::string& fftMethod,
	582	const std::string& fftThresh,
	583	const std::vector<int>& addNWaves,
	584	const std::vector<int>& rejectNWaves,
[2047]	585	float thresClip,
	586	int nIterClip,
	587	const std::vector<int>& edge,
	588	float threshold=3.0,
	589	int chanAvgLimit=1,
[2081]	590	bool getResidual=true,
[2189]	591	const std::string& progressInfo="true,1000",
	592	const bool outLogger=false,
[2047]	593	const std::string& blfile="");
[2186]	594	std::vector<float> execFFT(const int whichrow,
	595	const std::vector<bool>& inMask,
	596	bool getRealImag=false,
	597	bool getAmplitudeOnly=false);
[2012]	598	float getRms(const std::vector<bool>& mask, int whichrow);
	599	std::string formatBaselineParams(const std::vector<float>& params,
	600	const std::vector<bool>& fixed,
	601	float rms,
[2193]	602	int nClipped,
[2012]	603	const std::string& masklist,
	604	int whichrow,
[2064]	605	bool verbose=false,
[2641]	606	bool csvformat=false,
[2064]	607	int start=-1,
	608	int count=-1,
	609	bool resetparamid=false) const;
[2012]	610	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
	611	const std::vector<float>& params,
	612	const std::vector<bool>& fixed,
	613	float rms,
[2193]	614	int nClipped,
[2012]	615	const std::string& masklist,
	616	int whichrow,
[2641]	617	bool verbose=false,
	618	bool csvformat=false) const;
[2591]	619	std::vector<uint> getMoleculeIdColumnData() const;
	620	void setMoleculeIdColumnData(const std::vector<uint>& molids);
[2713]	621	double calculateModelSelectionCriteria(const std::string& valname,
	622	const std::string& blfunc,
	623	int order,
	624	const std::vector<bool>& inMask,
	625	int whichrow,
	626	bool useLineFinder,
	627	const std::vector<int>& edge,
	628	float threshold,
	629	int chanAvgLimit);
[1907]	630
[2012]	631
[824]	632	private:
[896]	633
	634	casa::Matrix<casa::Float> getPolMatrix( casa::uInt whichrow ) const;
	635
[824]	636	/**
[2005]	637	* Turns a time value into a formatted string
[824]	638	* @param x
	639	* @return
	640	*/
	641	std::string formatSec(casa::Double x) const;
[18]	642
[824]	643	std::string formatTime(const casa::MEpoch& me, bool showdate)const;
[1947]	644	std::string formatTime(const casa::MEpoch& me, bool showdate, casa::uInt prec)const;
[22]	645
[824]	646	/**
	647	* Turns a casa::MDirection into a nicely formatted string
	648	* @param md an casa::MDirection
	649	* @return
	650	*/
	651	std::string formatDirection(const casa::MDirection& md) const;
[19]	652
[824]	653	/**
	654	* Create a unique file name for the paged (temporary) table
	655	* @return just the name
	656	*/
	657	static casa::String generateName();
[286]	658
[824]	659	/**
	660	* attach to cached columns
	661	*/
	662	void attach();
[50]	663
[824]	664	/**
	665	* Set up the main casa::Table
	666	*/
	667	void setupMainTable();
[88]	668
[859]	669	void attachSubtables();
[865]	670	void copySubtables(const Scantable& other);
	671
[824]	672	/**
	673	* Convert an "old" asap1 style row index into a new index
	674	* @param[in] therow
	675	* @return and index into @table_
	676	*/
	677	int rowToScanIndex(int therow);
[212]	678
[1694]	679	std::vector<uint> getNumbers(const casa::ScalarColumn<casa::uInt>& col) const;
[1111]	680
[2321]	681	static const casa::uInt version_ = 4;
[286]	682
[824]	683	STSelector selector_;
[236]	684
[824]	685	casa::Table::TableType type_;
[465]	686
[824]	687	// the actual data
	688	casa::Table table_;
	689	casa::Table originalTable_;
[745]	690
[824]	691	STTcal tcalTable_;
	692	STFrequencies freqTable_;
	693	STWeather weatherTable_;
	694	STFocus focusTable_;
	695	STMolecules moleculeTable_;
[860]	696	STHistory historyTable_;
[960]	697	STFit fitTable_;
[860]	698
[824]	699	// Cached Columns to avoid reconstructing them for each row get/put
[847]	700	casa::ScalarColumn<casa::Double> integrCol_;
[824]	701	casa::MDirection::ScalarColumn dirCol_;
[847]	702	casa::MEpoch::ScalarColumn timeCol_;
[923]	703	casa::ScalarColumn<casa::Float> azCol_;
	704	casa::ScalarColumn<casa::Float> elCol_;
[824]	705	casa::ScalarColumn<casa::String> srcnCol_, fldnCol_;
[1819]	706	casa::ScalarColumn<casa::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
[1068]	707	casa::ScalarColumn<casa::Int> rbeamCol_, srctCol_;
[865]	708	casa::ArrayColumn<casa::Float> specCol_, tsysCol_;
[824]	709	casa::ArrayColumn<casa::uChar> flagsCol_;
[430]	710
[824]	711	// id in frequencies table
	712	casa::ScalarColumn<casa::uInt> mfreqidCol_;
	713	// id in tcal table
	714	casa::ScalarColumn<casa::uInt> mtcalidCol_;
[430]	715
[824]	716	casa::ArrayColumn<casa::String> histitemCol_;
[972]	717	casa::ScalarColumn<casa::Int> mfitidCol_;
[824]	718	casa::ScalarColumn<casa::uInt> mweatheridCol_;
[322]	719
[824]	720	casa::ScalarColumn<casa::uInt> mfocusidCol_;
	721
	722	casa::ScalarColumn<casa::uInt> mmolidCol_;
	723
[896]	724	static std::map<std::string, STPol::STPolFactory *> factories_;
	725	void initFactories();
	726
[1819]	727	/**
	728	* Add an auxiliary column to the main table and attach it to a
	729	* cached column. Use for adding new columns that the original asap2
	730	* tables do not have.
	731	* @param[in] col reference to the cached column to be attached
	732	* @param[in] colName column name in asap table
	733	* @param[in] defValue default value to fill in the column
	734	*
	735	* 25/10/2009 Wataru Kawasaki
	736	*/
	737	template<class T, class T2> void attachAuxColumnDef(casa::ScalarColumn<T>&,
	738	const casa::String&,
	739	const T2&);
	740	template<class T, class T2> void attachAuxColumnDef(casa::ArrayColumn<T>&,
	741	const casa::String&,
	742	const casa::Array<T2>&);
[1907]	743
[2012]	744	void fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter);
[2645]	745	double getChebyshevPolynomial(int n, double x);
	746	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
	747	const std::vector<bool>& mask,
	748	int order,
	749	std::vector<float>& params,
[2737]	750	std::vector<bool>& finalMask,
	751	float& rms,
[2645]	752	int& nClipped,
	753	float thresClip=3.0,
	754	int nIterClip=1,
	755	bool getResidual=true);
[2012]	756	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	757	const std::vector<bool>& mask,
[2081]	758	int nPiece,
[2064]	759	std::vector<int>& idxEdge,
[2012]	760	std::vector<float>& params,
[2193]	761	int& nClipped,
[2012]	762	float thresClip=3.0,
[2058]	763	int nIterClip=1,
[2094]	764	bool getResidual=true);
[2047]	765	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	766	const std::vector<bool>& mask,
[2081]	767	const std::vector<int>& waveNumbers,
[2047]	768	std::vector<float>& params,
[2193]	769	int& nClipped,
[2047]	770	float thresClip=3.0,
[2058]	771	int nIterClip=1,
[2094]	772	bool getResidual=true);
[2186]	773	void selectWaveNumbers(const int whichrow,
	774	const std::vector<bool>& chanMask,
	775	const bool applyFFT,
	776	const std::string& fftMethod,
	777	const std::string& fftThresh,
	778	const std::vector<int>& addNWaves,
	779	const std::vector<int>& rejectNWaves,
	780	std::vector<int>& nWaves);
	781	void parseThresholdExpression(const std::string& fftThresh,
	782	std::string& fftThAttr,
	783	float& fftThSigma,
	784	int& fftThTop);
	785	void doSelectWaveNumbers(const int whichrow,
	786	const std::vector<bool>& chanMask,
	787	const std::string& fftMethod,
	788	const float fftThSigma,
	789	const int fftThTop,
	790	const std::string& fftThAttr,
	791	std::vector<int>& nWaves);
[2411]	792	void addAuxWaveNumbers(const int whichrow,
	793	const std::vector<int>& addNWaves,
[2186]	794	const std::vector<int>& rejectNWaves,
	795	std::vector<int>& nWaves);
[2411]	796	void setWaveNumberListUptoNyquistFreq(const int whichrow,
	797	std::vector<int>& nWaves);
[2012]	798	bool hasSameNchanOverIFs();
	799	std::string getMaskRangeList(const std::vector<bool>& mask,
	800	int whichrow,
	801	const casa::String& coordInfo,
[2047]	802	bool hasSameNchan,
	803	bool verbose=false);
	804	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2641]	805	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
	806	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
[2012]	807	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
	808	//std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder);
[2641]	809	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);
	810	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);
	811	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]	812	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
	813	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]	814
	815	void applyChanFlag( casa::uInt whichrow, const std::vector<bool>& msk, casa::uChar flagval);
	816
[2713]	817	double doCalculateModelSelectionCriteria(const std::string& valname,
	818	const std::vector<float>& spec,
	819	const std::vector<bool>& mask,
	820	const std::string& blfunc,
	821	int order);
[2737]	822	double doGetRms(const std::vector<bool>& mask, const casa::Vector<casa::Float>& spec);
[2713]	823
[2]	824	};
	825
[824]	826	} // namespace
	827
[2]	828	#endif

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