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Scantable.h @ 3106

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Last change on this file since 3106 was 3106, checked in by Takeshi Nakazato, 8 years ago

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Description: Describe your changes here...

Check-in asap modifications from Jim regarding casacore namespace conversion.

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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>
[3043]	21	#include <map>
[2]	22	// AIPS++
[455]	23	#include <casa/aips.h>
[322]	24	#include <casa/Arrays/MaskedArray.h>
[2186]	25	#include <casa/Arrays/Vector.h>
[80]	26	#include <casa/BasicSL/String.h>
[2186]	27	#include <casa/Containers/Record.h>
	28	#include <casa/Exceptions/Error.h>
	29	#include <casa/Quanta/Quantum.h>
[824]	30	#include <casa/Utilities/CountedPtr.h>
[2186]	31	#include <coordinates/Coordinates/SpectralCoordinate.h>
[824]	32	#include <measures/TableMeasures/ScalarMeasColumn.h>
[2186]	33	#include <scimath/Mathematics/FFTServer.h>
	34	#include <tables/Tables/ArrayColumn.h>
	35	#include <tables/Tables/ScalarColumn.h>
	36	#include <tables/Tables/Table.h>
[1819]	37
[2186]	38	#include "MathUtils.h"
[2767]	39	#include "STBaselineEnum.h"
[2186]	40	#include "STFit.h"
	41	#include "STFitEntry.h"
	42	#include "STFocus.h"
	43	#include "STFrequencies.h"
[901]	44	#include "STHeader.h"
[2186]	45	#include "STHistory.h"
[824]	46	#include "STMolecules.h"
[2186]	47	#include "STPol.h"
[824]	48	#include "STSelector.h"
[2186]	49	#include "STTcal.h"
	50	#include "STWeather.h"
[2]	51
[824]	52	namespace asap {
[2]	53
[2666]	54	class Fitter;
[3090]	55	struct STLineFinder;
[2773]	56	class STBaselineTable;
[2666]	57
[824]	58	/**
[3106]	59	* This class contains and wraps a casacore::Table, which is used to store
[824]	60	* all the information. This can be either a MemoryTable or a
	61	* disk based Table.
	62	* It provides access functions to the underlying table
	63	* It contains n subtables:
	64	* @li weather
	65	* @li frequencies
	66	* @li molecules
	67	* @li tcal
	68	* @li focus
	69	* @li fits
	70	*
	71	* @brief The main ASAP data container
	72	* @author Malte Marquarding
	73	* @date
	74	* @version
	75	*/
[2658]	76	class Scantable
[824]	77	{
[902]	78
	79	friend class STMath;
	80
[2]	81	public:
[824]	82	/**
	83	* Default constructor
	84	*/
[3106]	85	explicit Scantable(casacore::Table::TableType ttype = casacore::Table::Memory);
[19]	86
[824]	87	/**
[2321]	88	* Create a Scantable object from an existing table on disk
[824]	89	* @param[in] name the name of the existing Scantable
	90	*/
[2321]	91	explicit Scantable(const std::string& name,
[3106]	92	casacore::Table::TableType ttype = casacore::Table::Memory);
[2]	93
[824]	94	/// @fixme this is only sensible for MemoryTables....
	95	Scantable(const Scantable& other, bool clear=true);
[161]	96
[824]	97	/**
	98	* Destructor
	99	*/
	100	virtual ~Scantable();
[745]	101
[824]	102	/**
[3106]	103	* get a const reference to the underlying casacore::Table
	104	* @return const \ref casacore::Table reference
[824]	105	*/
[3106]	106	const casacore::Table& table() const;
[19]	107
[824]	108	/**
[3106]	109	* get a reference to the underlying casacore::Table with the Selection
[824]	110	* object applied if set
[3106]	111	* @return casacore::Table reference
[824]	112	*/
[3106]	113	casacore::Table& table();
[21]	114
[845]	115
	116	/**
	117	* Get a handle to the selection object
	118	* @return constant STSelector reference
	119	*/
	120	const STSelector& getSelection() const { return selector_; }
	121
	122	/**
	123	* Set the data to be a subset as defined by the STSelector
	124	* @param selection a STSelector object
	125	*/
[824]	126	void setSelection(const STSelector& selection);
[845]	127
	128	/**
	129	* unset the selection of the data
	130	*/
[824]	131	void unsetSelection();
	132	/**
	133	* set the header
[1295]	134	* @param[in] sth an STHeader object
[824]	135	*/
[901]	136	void setHeader( const STHeader& sth );
[386]	137
[824]	138	/**
	139	* get the header information
[901]	140	* @return an STHeader object
[824]	141	*/
[901]	142	STHeader getHeader( ) const;
[1068]	143
[824]	144	/**
	145	* Checks if the "other" Scantable is conformant with this,
	146	* i.e. if header values are the same.
	147	* @param[in] other another Scantable
	148	* @return true or false
	149	*/
	150	bool conformant( const Scantable& other);
[430]	151
[824]	152	/**
[1068]	153	*
	154	* @param stype The type of the source, 0 = on, 1 = off
	155	*/
	156	void setSourceType(int stype);
	157
[2818]	158	/**
	159	*
	160	* @param stype The name of the source
	161	*/
	162	void setSourceName(const std::string& name);
[1068]	163
[2818]	164
[1068]	165	/**
[1104]	166	* The number of scans in the table
[824]	167	* @return number of scans in the table
	168	*/
[845]	169	int nscan() const;
[490]	170
[3106]	171	casacore::MEpoch::Types getTimeReference() const;
[21]	172
[1411]	173
[3106]	174	casacore::MEpoch getEpoch(int whichrow) const;
[1411]	175
[824]	176	/**
	177	* Get global antenna position
[3106]	178	* @return casacore::MPosition
[824]	179	*/
[3106]	180	casacore::MPosition getAntennaPosition() const;
[490]	181
[1441]	182	/**
[3106]	183	* the @ref casacore::MDirection for a specific row
[1441]	184	* @param[in] whichrow the row number
[3106]	185	* return casacore::MDirection
[1441]	186	*/
[3106]	187	casacore::MDirection getDirection( int whichrow ) const;
[1598]	188
[1441]	189	/**
	190	* get the direction type as a string, e.g. "J2000"
	191	* @param[in] whichrow the row number
	192	* return the direction string
	193	*/
[1068]	194	std::string getDirectionString( int whichrow ) const;
	195
[1441]	196	/**
	197	* set the direction type as a string, e.g. "J2000"
	198	* @param[in] refstr the direction type
	199	*/
[987]	200	void setDirectionRefString(const std::string& refstr="");
[1441]	201
[1104]	202	/**
	203	* get the direction reference string
	204	* @return a string describing the direction reference
	205	*/
[1598]	206	std::string getDirectionRefString() const;
[987]	207
[824]	208	/**
[845]	209	* Return the Flux unit of the data, e.g. "Jy" or "K"
	210	* @return string
[824]	211	*/
	212	std::string getFluxUnit() const;
[472]	213
[824]	214	/**
[845]	215	* Set the Flux unit of the data
	216	* @param unit a string representing the unit, e.g "Jy" or "K"
[824]	217	*/
	218	void setFluxUnit( const std::string& unit );
[472]	219
[824]	220	/**
[1189]	221	* Set the Stokes type of the data
[1295]	222	* @param feedtype a string representing the type, e.g "circular" or "linear"
[1189]	223	*/
	224	void setFeedType( const std::string& feedtype );
	225
	226	/**
[824]	227	*
[845]	228	* @param instrument a string representing an insturment. see xxx
[824]	229	*/
	230	void setInstrument( const std::string& instrument );
[2]	231
[845]	232	/**
	233	* (Re)calculate the azimuth and elevationnfor all rows
	234	*/
[824]	235	void calculateAZEL();
[745]	236
[824]	237	/**
[845]	238	* "hard" flag the data, this flags everything selected in setSelection()
[1104]	239	* param[in] msk a boolean mask of length nchan describing the points to
	240	* to be flagged
[824]	241	*/
[1430]	242	//void flag( const std::vector<bool>& msk = std::vector<bool>());
[1994]	243	//void flag( const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
[455]	244
[1994]	245	void flag( int whichrow = -1, const std::vector<bool>& msk = std::vector<bool>(), bool unflag=false);
	246
[852]	247	/**
[1819]	248	* Flag the data in a row-based manner. (CAS-1433 Wataru Kawasaki)
	249	* param[in] rows list of row numbers to be flagged
	250	*/
[3106]	251	void flagRow( const std::vector<casacore::uInt>& rows = std::vector<casacore::uInt>(), bool unflag=false);
[1819]	252
	253	/**
	254	* Get flagRow info at the specified row. If true, the whole data
	255	* at the row should be flagged.
	256	*/
	257	bool getFlagRow(int whichrow) const
	258	{ return (flagrowCol_(whichrow) > 0); }
	259
	260	/**
	261	* Flag the data outside a specified range (in a channel-based manner).
	262	* (CAS-1807 Wataru Kawasaki)
	263	*/
[3106]	264	void clip(const casacore::Float uthres, const casacore::Float dthres, bool clipoutside, bool unflag);
[1819]	265
	266	/**
	267	* Return a list of booleans with the size of nchan for a specified row, to get info
	268	* about which channel is clipped.
	269	*/
[3106]	270	std::vector<bool> getClipMask(int whichrow, const casacore::Float uthres, const casacore::Float dthres, bool clipoutside, bool unflag);
	271	void srchChannelsToClip(casacore::uInt whichrow, const casacore::Float uthres, const casacore::Float dthres, bool clipoutside, bool unflag,
	272	casacore::Vector<casacore::uChar> flgs);
[1819]	273
	274	/**
[852]	275	* Return a list of row numbers with respect to the original table.
[902]	276	* @return a list of unsigned ints
[852]	277	*/
	278	std::vector<unsigned int> rownumbers() const;
[845]	279
[852]	280
[845]	281	/**
	282	* Get the number of beams in the data or a specific scan
	283	* @param scanno the scan number to get the number of beams for.
	284	* If scanno<0 the number is retrieved from the header.
	285	* @return an integer number
	286	*/
[824]	287	int nbeam(int scanno=-1) const;
[845]	288	/**
	289	* Get the number of IFs in the data or a specific scan
	290	* @param scanno the scan number to get the number of IFs for.
	291	* If scanno<0 the number is retrieved from the header.
	292	* @return an integer number
	293	*/
[824]	294	int nif(int scanno=-1) const;
[845]	295	/**
	296	* Get the number of polarizations in the data or a specific scan
	297	* @param scanno the scan number to get the number of polarizations for.
	298	* If scanno<0 the number is retrieved from the header.
	299	* @return an integer number
	300	*/
[824]	301	int npol(int scanno=-1) const;
[794]	302
[896]	303	std::string getPolType() const;
	304
[845]	305
	306	/**
	307	* Get the number of integartion cycles
	308	* @param scanno the scan number to get the number of rows for.
	309	* If scanno<0 the number is retrieved from the header.
[1104]	310	* @return the number of rows (for the specified scanno)
[845]	311	*/
[824]	312	int nrow(int scanno=-1) const;
[794]	313
[1111]	314	int getBeam(int whichrow) const;
[1694]	315	std::vector<uint> getBeamNos() const { return getNumbers(beamCol_); }
[50]	316
[847]	317	int getIF(int whichrow) const;
[1694]	318	std::vector<uint> getIFNos() const { return getNumbers(ifCol_); }
[1111]	319
[847]	320	int getPol(int whichrow) const;
[1694]	321	std::vector<uint> getPolNos() const { return getNumbers(polCol_); }
[1111]	322
[1694]	323	std::vector<uint> getScanNos() const { return getNumbers(scanCol_); }
[865]	324	int getScan(int whichrow) const { return scanCol_(whichrow); }
[1111]	325
[2667]	326	std::vector<uint> getCycleNos() const { return getNumbers(cycleCol_); }
	327	int getCycle(int whichrow) const { return cycleCol_(whichrow); }
	328
[1819]	329	//TT addition
	330	std::vector<uint> getMolNos() {return getNumbers(mmolidCol_); }
	331
[1111]	332	/**
	333	* Get the number of channels in the data or a specific IF. This currently
	334	* varies only with IF number
	335	* @param ifno the IF number to get the number of channels for.
	336	* If ifno<0 the number is retrieved from the header.
	337	* @return an integer number
	338	*/
	339	int nchan(int ifno=-1) const;
[923]	340	int getChannels(int whichrow) const;
[206]	341
[1111]	342	int ncycle(int scanno=-1) const;
	343
[2667]	344
[847]	345	double getInterval(int whichrow) const
	346	{ return integrCol_(whichrow); }
[845]	347
[865]	348	float getTsys(int whichrow) const
[3106]	349	{ return casacore::Vector<casacore::Float>(tsysCol_(whichrow))(0); }
[2161]	350	std::vector<float> getTsysSpectrum(int whichrow) const ;
[2791]	351
	352	void setTsys(const std::vector<float>& newvals, int whichrow);
	353
[847]	354	float getElevation(int whichrow) const
	355	{ return elCol_(whichrow); }
	356	float getAzimuth(int whichrow) const
	357	{ return azCol_(whichrow); }
[865]	358	float getParAngle(int whichrow) const
[1819]	359	{ return focus().getParAngle(mfocusidCol_(whichrow)); }
	360	int getTcalId(int whichrow) const
	361	{ return mtcalidCol_(whichrow); }
[386]	362
[865]	363	std::string getSourceName(int whichrow) const
	364	{ return srcnCol_(whichrow); }
	365
[847]	366	std::vector<bool> getMask(int whichrow) const;
[896]	367	std::vector<float> getSpectrum(int whichrow,
[905]	368	const std::string& poltype = "" ) const;
[847]	369
[884]	370	void setSpectrum(const std::vector<float>& spec, int whichrow);
	371
[902]	372	std::string getPolarizationLabel(int index, const std::string& ptype) const
	373	{ return STPol::getPolLabel(index, ptype ); }
[401]	374
[845]	375	/**
	376	* Write the Scantable to disk
	377	* @param filename the output file name
	378	*/
[824]	379	void makePersistent(const std::string& filename);
[745]	380
[2820]	381	std::vector<std::string> getHistory(int nrow=-1, int start=0) const
	382	{ return historyTable_.getHistory(nrow, start); }
[483]	383
[2820]	384	uint historyLength()
	385	{ return historyTable_.nrow(); }
	386
	387	void dropHistory() { historyTable_.drop(); }
	388
[860]	389	void addHistory(const std::string& hist) { historyTable_.addEntry(hist); }
[488]	390
[860]	391	void appendToHistoryTable(const STHistory& otherhist)
	392	{ historyTable_.append(otherhist); }
	393
[2163]	394	std::string headerSummary();
[2290]	395	void summary(const std::string& filename="");
	396	std::string oldheaderSummary();
[2286]	397	// std::string summary();
[2290]	398	void oldsummary(const std::string& filename="");
	399
[1947]	400	//std::string getTime(int whichrow=-1, bool showdate=true) const;
[2818]	401	std::string getTime(int whichrow=-1, bool showdate=true,
[3106]	402	casacore::uInt prec=0) const;
[1350]	403	double getIntTime(int whichrow) const { return integrCol_(whichrow); }
[19]	404
[847]	405	// returns unit, conversion frame, doppler, base-frame
[18]	406
[847]	407	/**
	408	* Get the frequency set up
	409	* This is forwarded to the STFrequencies subtable
	410	* @return unit, frame, doppler
	411	*/
	412	std::vector<std::string> getCoordInfo() const
	413	{ return freqTable_.getInfo(); };
	414
	415	void setCoordInfo(std::vector<string> theinfo)
	416	{ return freqTable_.setInfo(theinfo); };
	417
[865]	418
	419	std::vector<double> getAbcissa(int whichrow) const;
	420
[1730]	421	std::vector<float> getWeather(int whichrow) const;
	422
[847]	423	std::string getAbcissaLabel(int whichrow) const;
	424	std::vector<double> getRestFrequencies() const
	425	{ return moleculeTable_.getRestFrequencies(); }
[1819]	426	std::vector<double> getRestFrequency(int id) const
	427	{ return moleculeTable_.getRestFrequency(id); }
[847]	428
[1819]	429	/**
[1170]	430	void setRestFrequencies(double rf, const std::string& name = "",
	431	const std::string& = "Hz");
[1819]	432	**/
	433	// Modified by Takeshi Nakazato 05/09/2008
	434	/***
	435	void setRestFrequencies(vector<double> rf, const vector<std::string>& name = "",
	436	const std::string& = "Hz");
	437	***/
	438	void setRestFrequencies(vector<double> rf,
	439	const vector<std::string>& name = vector<std::string>(1,""),
	440	const std::string& = "Hz");
[847]	441
[1819]	442	//void setRestFrequencies(const std::string& name);
	443	void setRestFrequencies(const vector<std::string>& name);
	444
[1360]	445	void shift(int npix);
	446
[3106]	447	casacore::SpectralCoordinate getSpectralCoordinate(int whichrow) const;
[1598]	448
[987]	449	void convertDirection(const std::string& newframe);
	450
[824]	451	STFrequencies& frequencies() { return freqTable_; }
[1375]	452	const STFrequencies& frequencies() const { return freqTable_; }
[824]	453	STWeather& weather() { return weatherTable_; }
[1375]	454	const STWeather& weather() const { return weatherTable_; }
[824]	455	STFocus& focus() { return focusTable_; }
[1375]	456	const STFocus& focus() const { return focusTable_; }
[824]	457	STTcal& tcal() { return tcalTable_; }
[1375]	458	const STTcal& tcal() const { return tcalTable_; }
[824]	459	STMolecules& molecules() { return moleculeTable_; }
[1375]	460	const STMolecules& molecules() const { return moleculeTable_; }
[860]	461	STHistory& history() { return historyTable_; }
[1375]	462	const STHistory& history() const { return historyTable_; }
[972]	463	STFit& fit() { return fitTable_; }
[1375]	464	const STFit& fit() const { return fitTable_; }
[2]	465
[902]	466	std::vector<std::string> columnNames() const;
[896]	467
[972]	468	void addFit(const STFitEntry& fit, int row);
	469	STFitEntry getFit(int row) const
	470	{ STFitEntry fe; fitTable_.getEntry(fe, mfitidCol_(row)); return fe; }
	471
[1391]	472	//Added by TT
	473	/**
	474	* Get the antenna name
	475	* @return antenna name string
	476	*/
[3106]	477	casacore::String getAntennaName() const;
[1391]	478
	479	/**
	480	* For GBT MS data only. check a scan list
	481	* against the information found in GBT_GO table for
	482	* scan number orders to get correct pairs.
	483	* @param[in] scan list
	484	* @return status
	485	*/
	486	int checkScanInfo(const std::vector<int>& scanlist) const;
	487
	488	/**
	489	* Get the direction as a vector, for a specific row
	490	* @param[in] whichrow the row numbyyer
	491	* @return the direction in a vector
	492	*/
	493	std::vector<double> getDirectionVector(int whichrow) const;
	494
[1586]	495	/**
	496	* Set a flag indicating whether the data was parallactified
	497	* @param[in] flag true or false
	498	*/
[1598]	499	void parallactify(bool flag)
[2357]	500	{ focusTable_.setParallactify(flag); }
[1727]	501
[1819]	502	/**
	503	* Reshape spectrum
	504	* @param[in] nmin, nmax minimum and maximum channel
	505	* @param[in] irow row number
	506	*
	507	* 30/07/2008 Takeshi Nakazato
	508	**/
[3106]	509	void reshapeSpectrum( int nmin, int nmax ) throw( casacore::AipsError );
[1819]	510	void reshapeSpectrum( int nmin, int nmax, int irow ) ;
	511
	512	/**
	513	* Change channel number under fixed bandwidth
	514	* @param[in] nchan, dnu new channel number and spectral resolution
	515	* @param[in] irow row number
	516	*
	517	* 27/08/2008 Takeshi Nakazato
	518	**/
	519	void regridChannel( int nchan, double dnu ) ;
	520	void regridChannel( int nchan, double dnu, int irow ) ;
[2595]	521	void regridChannel( int nchan, double dnu, double fmin, int irow ) ;
[2435]	522	void regridSpecChannel( double dnu, int nchan=-1 ) ;
	523
[3106]	524	bool isAllChannelsFlagged(casacore::uInt whichrow);
[1819]	525
[2811]	526	std::vector<std::string> applyBaselineTable(const std::string& bltable,
	527	const bool returnfitresult,
	528	const std::string& outbltable,
	529	const bool outbltableexists,
	530	const bool overwrite);
	531	std::vector<std::string> subBaseline(const std::vector<std::string>& blInfoList,
	532	const bool returnfitresult,
	533	const std::string& outbltable,
	534	const bool outbltableexists,
	535	const bool overwrite);
[2767]	536	void polyBaseline(const std::vector<bool>& mask,
	537	int order,
	538	float thresClip,
	539	int nIterClip,
[2094]	540	bool getResidual=true,
[2189]	541	const std::string& progressInfo="true,1000",
[2767]	542	const bool outLogger=false,
	543	const std::string& blfile="",
	544	const std::string& bltable="");
[2012]	545	void autoPolyBaseline(const std::vector<bool>& mask,
[2767]	546	int order,
	547	float thresClip,
	548	int nIterClip,
	549	const std::vector<int>& edge,
	550	float threshold=3.0,
	551	int chanAvgLimit=1,
	552	bool getResidual=true,
	553	const std::string& progressInfo="true,1000",
	554	const bool outLogger=false,
	555	const std::string& blfile="",
	556	const std::string& bltable="");
[2645]	557	void chebyshevBaseline(const std::vector<bool>& mask,
	558	int order,
	559	float thresClip,
	560	int nIterClip,
	561	bool getResidual=true,
	562	const std::string& progressInfo="true,1000",
	563	const bool outLogger=false,
[2767]	564	const std::string& blfile="",
	565	const std::string& bltable="");
[2645]	566	void autoChebyshevBaseline(const std::vector<bool>& mask,
	567	int order,
	568	float thresClip,
	569	int nIterClip,
	570	const std::vector<int>& edge,
	571	float threshold=3.0,
	572	int chanAvgLimit=1,
	573	bool getResidual=true,
	574	const std::string& progressInfo="true,1000",
	575	const bool outLogger=false,
[2767]	576	const std::string& blfile="",
	577	const std::string& bltable="");
[2012]	578	void cubicSplineBaseline(const std::vector<bool>& mask,
	579	int nPiece,
	580	float thresClip,
	581	int nIterClip,
[2094]	582	bool getResidual=true,
[2189]	583	const std::string& progressInfo="true,1000",
	584	const bool outLogger=false,
[2767]	585	const std::string& blfile="",
	586	const std::string& bltable="");
[2012]	587	void autoCubicSplineBaseline(const std::vector<bool>& mask,
	588	int nPiece,
	589	float thresClip,
	590	int nIterClip,
	591	const std::vector<int>& edge,
	592	float threshold=3.0,
	593	int chanAvgLimit=1,
[2094]	594	bool getResidual=true,
[2189]	595	const std::string& progressInfo="true,1000",
	596	const bool outLogger=false,
[2767]	597	const std::string& blfile="",
	598	const std::string& bltable="");
[2047]	599	void sinusoidBaseline(const std::vector<bool>& mask,
[2767]	600	const std::string& fftInfo,
[2186]	601	const std::vector<int>& addNWaves,
	602	const std::vector<int>& rejectNWaves,
[2047]	603	float thresClip,
	604	int nIterClip,
[2081]	605	bool getResidual=true,
[2189]	606	const std::string& progressInfo="true,1000",
	607	const bool outLogger=false,
[2767]	608	const std::string& blfile="",
	609	const std::string& bltable="");
[2047]	610	void autoSinusoidBaseline(const std::vector<bool>& mask,
[2767]	611	const std::string& fftInfo,
[2186]	612	const std::vector<int>& addNWaves,
	613	const std::vector<int>& rejectNWaves,
[2047]	614	float thresClip,
	615	int nIterClip,
	616	const std::vector<int>& edge,
	617	float threshold=3.0,
	618	int chanAvgLimit=1,
[2081]	619	bool getResidual=true,
[2189]	620	const std::string& progressInfo="true,1000",
	621	const bool outLogger=false,
[2767]	622	const std::string& blfile="",
	623	const std::string& bltable="");
[2186]	624	std::vector<float> execFFT(const int whichrow,
	625	const std::vector<bool>& inMask,
	626	bool getRealImag=false,
	627	bool getAmplitudeOnly=false);
[2012]	628	float getRms(const std::vector<bool>& mask, int whichrow);
	629	std::string formatBaselineParams(const std::vector<float>& params,
	630	const std::vector<bool>& fixed,
	631	float rms,
[2193]	632	int nClipped,
[2012]	633	const std::string& masklist,
	634	int whichrow,
[2064]	635	bool verbose=false,
[2641]	636	bool csvformat=false,
[2064]	637	int start=-1,
	638	int count=-1,
	639	bool resetparamid=false) const;
[2012]	640	std::string formatPiecewiseBaselineParams(const std::vector<int>& ranges,
	641	const std::vector<float>& params,
	642	const std::vector<bool>& fixed,
	643	float rms,
[2193]	644	int nClipped,
[2012]	645	const std::string& masklist,
	646	int whichrow,
[2641]	647	bool verbose=false,
	648	bool csvformat=false) const;
[2591]	649	std::vector<uint> getMoleculeIdColumnData() const;
	650	void setMoleculeIdColumnData(const std::vector<uint>& molids);
[2888]	651
	652	/**
	653	* Get row idx of root table
	654	**/
	655	std::vector<uint> getRootTableRowNumbers() const;
	656
[2713]	657	double calculateModelSelectionCriteria(const std::string& valname,
	658	const std::string& blfunc,
	659	int order,
	660	const std::vector<bool>& inMask,
	661	int whichrow,
	662	bool useLineFinder,
	663	const std::vector<int>& edge,
	664	float threshold,
	665	int chanAvgLimit);
[2767]	666	static std::vector<bool> getMaskFromMaskList(const int nchan,
[2789]	667	const std::vector<int>& masklist);
[3106]	668	static casacore::Vector<casacore::uInt> getMaskListFromMask(
[2789]	669	const std::vector<bool>& mask);
	670	static std::vector<int> splitToIntList(const std::string& str,
	671	const char delim);
	672	static std::vector<string> splitToStringList(const std::string& str,
	673	const char delim);
[1907]	674
[2789]	675	void dropXPol();
[2012]	676
[824]	677	private:
[896]	678
[3106]	679	casacore::Matrix<casacore::Float> getPolMatrix( casacore::uInt whichrow ) const;
[896]	680
[824]	681	/**
[2005]	682	* Turns a time value into a formatted string
[824]	683	* @param x
	684	* @return
	685	*/
[3106]	686	std::string formatSec(casacore::Double x) const;
[18]	687
[3106]	688	std::string formatTime(const casacore::MEpoch& me, bool showdate)const;
	689	std::string formatTime(const casacore::MEpoch& me, bool showdate,
	690	casacore::uInt prec)const;
[22]	691
[824]	692	/**
[3106]	693	* Turns a casacore::MDirection into a nicely formatted string
	694	* @param md an casacore::MDirection
[2969]	695	* @param prec output precision of direction
[824]	696	* @return
	697	*/
[3106]	698	std::string formatDirection(const casacore::MDirection& md, casacore::Int prec=7) const;
[19]	699
[824]	700	/**
	701	* Create a unique file name for the paged (temporary) table
	702	* @return just the name
	703	*/
[3106]	704	static casacore::String generateName();
[286]	705
[824]	706	/**
	707	* attach to cached columns
	708	*/
	709	void attach();
[50]	710
[824]	711	/**
[3106]	712	* Set up the main casacore::Table
[824]	713	*/
	714	void setupMainTable();
[88]	715
[859]	716	void attachSubtables();
[865]	717	void copySubtables(const Scantable& other);
	718
[824]	719	/**
	720	* Convert an "old" asap1 style row index into a new index
	721	* @param[in] therow
	722	* @return and index into @table_
	723	*/
	724	int rowToScanIndex(int therow);
[212]	725
[3106]	726	std::vector<uint> getNumbers(const casacore::ScalarColumn<casacore::uInt>& col) const;
[1111]	727
[3023]	728	/**
	729	* Returns a number of elements with "true" in a bool vector.
	730	* @param[in] mask (boolean vector)
	731	* @return the numerb of elements in true
	732	*/
	733	std::size_t nValidMask(const std::vector<bool>& mask);
	734
[3106]	735	static const casacore::uInt version_ = 4;
[286]	736
[824]	737	STSelector selector_;
[236]	738
[3106]	739	casacore::Table::TableType type_;
[465]	740
[824]	741	// the actual data
[3106]	742	casacore::Table table_;
	743	casacore::Table originalTable_;
[745]	744
[824]	745	STTcal tcalTable_;
	746	STFrequencies freqTable_;
	747	STWeather weatherTable_;
	748	STFocus focusTable_;
	749	STMolecules moleculeTable_;
[860]	750	STHistory historyTable_;
[960]	751	STFit fitTable_;
[860]	752
[824]	753	// Cached Columns to avoid reconstructing them for each row get/put
[3106]	754	casacore::ScalarColumn<casacore::Double> integrCol_;
	755	casacore::MDirection::ScalarColumn dirCol_;
	756	casacore::MEpoch::ScalarColumn timeCol_;
	757	casacore::ScalarColumn<casacore::Float> azCol_;
	758	casacore::ScalarColumn<casacore::Float> elCol_;
	759	casacore::ScalarColumn<casacore::String> srcnCol_, fldnCol_;
	760	casacore::ScalarColumn<casacore::uInt> scanCol_, beamCol_, ifCol_, polCol_, cycleCol_, flagrowCol_;
	761	casacore::ScalarColumn<casacore::Int> rbeamCol_, srctCol_;
	762	casacore::ArrayColumn<casacore::Float> specCol_, tsysCol_;
	763	casacore::ArrayColumn<casacore::uChar> flagsCol_;
[430]	764
[824]	765	// id in frequencies table
[3106]	766	casacore::ScalarColumn<casacore::uInt> mfreqidCol_;
[824]	767	// id in tcal table
[3106]	768	casacore::ScalarColumn<casacore::uInt> mtcalidCol_;
[430]	769
[3106]	770	casacore::ArrayColumn<casacore::String> histitemCol_;
	771	casacore::ScalarColumn<casacore::Int> mfitidCol_;
	772	casacore::ScalarColumn<casacore::uInt> mweatheridCol_;
[322]	773
[3106]	774	casacore::ScalarColumn<casacore::uInt> mfocusidCol_;
[824]	775
[3106]	776	casacore::ScalarColumn<casacore::uInt> mmolidCol_;
[824]	777
[896]	778	static std::map<std::string, STPol::STPolFactory *> factories_;
	779	void initFactories();
	780
[1819]	781	/**
	782	* Add an auxiliary column to the main table and attach it to a
	783	* cached column. Use for adding new columns that the original asap2
	784	* tables do not have.
	785	* @param[in] col reference to the cached column to be attached
	786	* @param[in] colName column name in asap table
	787	* @param[in] defValue default value to fill in the column
	788	*
	789	* 25/10/2009 Wataru Kawasaki
	790	*/
[3106]	791	template<class T, class T2> void attachAuxColumnDef(casacore::ScalarColumn<T>&,
	792	const casacore::String&,
[1819]	793	const T2&);
[3106]	794	template<class T, class T2> void attachAuxColumnDef(casacore::ArrayColumn<T>&,
	795	const casacore::String&,
	796	const casacore::Array<T2>&);
[1907]	797
[2767]	798	double getNormalPolynomial(int n, double x);
[2645]	799	double getChebyshevPolynomial(int n, double x);
[2773]	800	std::vector<std::vector<double> > getPolynomialModel(int order,
	801	int nchan,
	802	double (Scantable::*pfunc)(int, double));
	803	std::vector<std::vector<std::vector<double> > > getPolynomialModelReservoir(int order,
	804	double (Scantable::*pfunc)(int, double),
	805	std::vector<int>& nChanNos);
[2767]	806	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	807	const std::vector<bool>& mask,
	808	int order,
	809	std::vector<float>& params,
	810	float& rms,
	811	std::vector<bool>& finalMask,
	812	float clipth,
	813	int clipn);
	814	std::vector<float> doPolynomialFitting(const std::vector<float>& data,
	815	const std::vector<bool>& mask,
	816	int order,
	817	std::vector<float>& params,
	818	float& rms,
	819	std::vector<bool>& finalMask,
	820	int& nClipped,
	821	float thresClip=3.0,
	822	int nIterClip=0,
	823	bool getResidual=true);
[2645]	824	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
[2767]	825	const std::vector<bool>& mask,
	826	int order,
	827	std::vector<float>& params,
	828	float& rms,
	829	std::vector<bool>& finalMask,
	830	float clipth,
	831	int clipn);
	832	std::vector<float> doChebyshevFitting(const std::vector<float>& data,
	833	const std::vector<bool>& mask,
	834	int order,
	835	std::vector<float>& params,
	836	float& rms,
	837	std::vector<bool>& finalMask,
	838	int& nClipped,
	839	float thresClip=3.0,
	840	int nIterClip=0,
	841	bool getResidual=true);
	842	std::vector<float> doLeastSquareFitting(const std::vector<float>& data,
	843	const std::vector<bool>& mask,
[2773]	844	const std::vector<std::vector<double> >& model,
[2767]	845	std::vector<float>& params,
	846	float& rms,
	847	std::vector<bool>& finalMask,
	848	int& nClipped,
	849	float thresClip=3.0,
	850	int nIterClip=0,
	851	bool getResidual=true);
	852	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
[2645]	853	const std::vector<bool>& mask,
[2767]	854	std::vector<int>& idxEdge,
[2645]	855	std::vector<float>& params,
[2767]	856	float& rms,
[2737]	857	std::vector<bool>& finalMask,
[2767]	858	float clipth,
	859	int clipn);
	860	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	861	const std::vector<bool>& mask,
	862	int nPiece,
	863	std::vector<int>& idxEdge,
	864	std::vector<float>& params,
[2737]	865	float& rms,
[2767]	866	std::vector<bool>& finalMask,
	867	float clipth,
	868	int clipn);
[2012]	869	std::vector<float> doCubicSplineFitting(const std::vector<float>& data,
	870	const std::vector<bool>& mask,
[2081]	871	int nPiece,
[2767]	872	bool useGivenPieceBoundary,
[2064]	873	std::vector<int>& idxEdge,
[2012]	874	std::vector<float>& params,
[2767]	875	float& rms,
	876	std::vector<bool>& finalMask,
[2193]	877	int& nClipped,
[2012]	878	float thresClip=3.0,
[2767]	879	int nIterClip=0,
[2094]	880	bool getResidual=true);
[2773]	881	std::vector<float> doCubicSplineLeastSquareFitting(const std::vector<float>& data,
	882	const std::vector<bool>& mask,
	883	const std::vector<std::vector<double> >& model,
	884	int nPiece,
	885	bool useGivenPieceBoundary,
	886	std::vector<int>& idxEdge,
	887	std::vector<float>& params,
	888	float& rms,
	889	std::vector<bool>& finalMask,
	890	int& nClipped,
	891	float thresClip=3.0,
	892	int nIterClip=0,
	893	bool getResidual=true);
[2047]	894	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	895	const std::vector<bool>& mask,
[2081]	896	const std::vector<int>& waveNumbers,
[2047]	897	std::vector<float>& params,
[2767]	898	float& rms,
	899	std::vector<bool>& finalMask,
	900	float clipth,
	901	int clipn);
	902	std::vector<float> doSinusoidFitting(const std::vector<float>& data,
	903	const std::vector<bool>& mask,
	904	const std::vector<int>& waveNumbers,
	905	std::vector<float>& params,
	906	float& rms,
	907	std::vector<bool>& finalMask,
[2193]	908	int& nClipped,
[2047]	909	float thresClip=3.0,
[2767]	910	int nIterClip=0,
[2094]	911	bool getResidual=true);
[2773]	912	std::vector<std::vector<double> > getSinusoidModel(const std::vector<int>& waveNumbers, int nchan);
	913	std::vector<std::vector<std::vector<double> > > getSinusoidModelReservoir(const std::vector<int>& waveNumbers,
	914	std::vector<int>& nChanNos);
	915	std::vector<int> selectWaveNumbers(const std::vector<int>& addNWaves,
	916	const std::vector<int>& rejectNWaves);
	917	std::vector<int> selectWaveNumbers(const int whichrow,
	918	const std::vector<bool>& chanMask,
	919	//const std::string& fftInfo,
	920	const bool applyFFT,
	921	const std::string& fftMethod,
	922	const std::string& fftThresh,
	923	const std::vector<int>& addNWaves,
	924	const std::vector<int>& rejectNWaves);
	925	int getIdxOfNchan(const int nChan, const std::vector<int>& nChanNos);
[2767]	926	void parseFFTInfo(const std::string& fftInfo,
	927	bool& applyFFT,
	928	std::string& fftMethod,
	929	std::string& fftThresh);
[2773]	930	void parseFFTThresholdInfo(const std::string& fftThresh,
	931	std::string& fftThAttr,
	932	float& fftThSigma,
	933	int& fftThTop);
[2186]	934	void doSelectWaveNumbers(const int whichrow,
	935	const std::vector<bool>& chanMask,
	936	const std::string& fftMethod,
	937	const float fftThSigma,
	938	const int fftThTop,
	939	const std::string& fftThAttr,
	940	std::vector<int>& nWaves);
[2411]	941	void addAuxWaveNumbers(const int whichrow,
	942	const std::vector<int>& addNWaves,
[2186]	943	const std::vector<int>& rejectNWaves,
	944	std::vector<int>& nWaves);
[2411]	945	void setWaveNumberListUptoNyquistFreq(const int whichrow,
	946	std::vector<int>& nWaves);
[2773]	947	void initialiseBaselining(const std::string& blfile,
	948	std::ofstream& ofs,
	949	const bool outLogger,
	950	bool& outTextFile,
	951	bool& csvFormat,
[3106]	952	casacore::String& coordInfo,
[2773]	953	bool& hasSameNchan,
	954	const std::string& progressInfo,
	955	bool& showProgress,
	956	int& minNRow,
[3106]	957	casacore::Vector<casacore::Double>& timeSecCol);
[2773]	958	void finaliseBaselining(const bool outBaselineTable,
	959	STBaselineTable* pbt,
	960	const string& bltable,
	961	const bool outTextFile,
	962	std::ofstream& ofs);
	963	void initLineFinder(const std::vector<int>& edge,
	964	const float threshold,
	965	const int chanAvgLimit,
	966	STLineFinder& lineFinder);
[2012]	967	bool hasSameNchanOverIFs();
	968	std::string getMaskRangeList(const std::vector<bool>& mask,
	969	int whichrow,
[3106]	970	const casacore::String& coordInfo,
[2047]	971	bool hasSameNchan,
	972	bool verbose=false);
	973	std::vector<int> getMaskEdgeIndices(const std::vector<bool>& mask);
[2641]	974	std::string formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const;
	975	std::string formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const;
[2012]	976	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask);
[2773]	977	std::vector<bool> getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, std::vector<int>& currEdge, STLineFinder& lineFinder);
[3106]	978	void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casacore::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casacore::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped);
	979	void outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casacore::String& coordInfo, bool hasSameNchan, std::ofstream& ofs, const casacore::String& funcName, const std::vector<float>& params, const int nClipped);
[2189]	980	void parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow);
	981	void showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress=true, const int nTotalThreshold=1000);
[1994]	982
[3106]	983	void applyChanFlag( casacore::uInt whichrow, const std::vector<bool>& msk, casacore::uChar flagval);
[1994]	984
[2713]	985	double doCalculateModelSelectionCriteria(const std::string& valname,
	986	const std::vector<float>& spec,
	987	const std::vector<bool>& mask,
	988	const std::string& blfunc,
	989	int order);
[3106]	990	double doGetRms(const std::vector<bool>& mask, const casacore::Vector<casacore::Float>& spec);
[2767]	991	std::string packFittingResults(const int irow, const std::vector<float>& params, const float rms);
	992	void parseBlInfo(const std::string& blInfo, int& whichrow, STBaselineFunc::FuncName& ftype, std::vector<int>& fpar, std::vector<bool>& mask, float& thresClip, int& nIterClip, bool& useLineFinder, float& thresLF, std::vector<int>& edgeLF, int& avgLF);
[3048]	993	std::vector<float> doApplyBaselineTable(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms, int irow);
[2767]	994	std::vector<float> doSubtractBaseline(std::vector<float>& spec, std::vector<bool>& mask, const STBaselineFunc::FuncName ftype, std::vector<int>& fpar, std::vector<float>& params, float&rms, std::vector<bool>& finalmask, float clipth, int clipn, bool uself, int irow, float lfth, std::vector<int>& lfedge, int lfavg);
[2713]	995
[3043]	996	// storage of cubic spline model for various number of channels
	997	map<size_t, vector< vector<double> > > cubicSplineModelPool_;
	998
[2]	999	};
[824]	1000	} // namespace
	1001
[2]	1002	#endif

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