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source: branches/mergetest/src/STMath.h @ 1779

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Last change on this file since 1779 was 1779, checked in by Kana Sugimoto, 14 years ago

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JIRA Issue: No (test merging alma branch)

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[805]	1	//
	2	// C++ Interface: STMath
	3	//
	4	// Description:
	5	//
	6	//
	7	// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2006
	8	//
	9	// Copyright: See COPYING file that comes with this distribution
	10	//
	11	//
	12	#ifndef ASAPSTMATH_H
	13	#define ASAPSTMATH_H
[2]	14
[38]	15	#include <string>
[805]	16	#include <map>
	17
[130]	18	#include <casa/aips.h>
[81]	19	#include <casa/Utilities/CountedPtr.h>
[805]	20	#include <casa/BasicSL/String.h>
	21	#include <casa/Arrays/Vector.h>
	22	#include <scimath/Mathematics/InterpolateArray1D.h>
[294]	23
[805]	24	#include "Scantable.h"
[834]	25	#include "STDefs.h"
[896]	26	#include "STPol.h"
[894]	27	#include "Logger.h"
[2]	28
[83]	29	namespace asap {
[2]	30
[805]	31	/**
[1106]	32	* Mathmatical operations on Scantable objects
	33	* @author Malte Marquarding
[805]	34	*/
[890]	35	class STMath : private Logger {
[716]	36	public:
[1106]	37	// typedef for long method name
[805]	38	typedef casa::InterpolateArray1D<casa::Double,
	39	casa::Float>::InterpolationMethod imethod;
[299]	40
[1106]	41	// typedef for std::map
[805]	42	typedef std::map<std::string, imethod> imap;
[177]	43
[1106]	44	/**
	45	* whether to operate on the given Scantable or return a new one
	46	* @param insitu the toggle for this behaviour
	47	*/
[1353]	48	explicit STMath(bool insitu=true);
[221]	49
[995]	50	virtual ~STMath();
[227]	51
[805]	52	/**
[1295]	53	* get the currnt @attr inistu_ state
[805]	54	*/
	55	bool insitu() const { return insitu_;};
[1143]	56
[1106]	57	/**
	58	* set the currnt @attr inistu state
	59	* @param b the new state
	60	*/
[805]	61	void setInsitu(bool b) { insitu_ = b; };
[262]	62
[1106]	63
[1140]	64	/**
	65	* average a vector of Scantables
	66	* @param in the vector of Scantables to average
[1295]	67	* @param mask an optional mask to apply on specific weights
[1140]	68	* @param weight weighting scheme
	69	* @param avmode the mode ov averaging. Per "SCAN" or "ALL".
	70	* @return a casa::CountedPtr<Scantable> which either holds a new Scantable
	71	* or returns the imput pointer.
	72	*/
[805]	73	casa::CountedPtr<Scantable>
	74	average( const std::vector<casa::CountedPtr<Scantable> >& in,
[858]	75	const std::vector<bool>& mask = std::vector<bool>(),
	76	const std::string& weight = "NONE",
[977]	77	const std::string& avmode = "SCAN");
[1066]	78
[1140]	79	/**
	80	* median average a vector of Scantables. See also STMath::average
	81	* @param in the Scantable to average
	82	* @param mode the averaging mode. Currently only "MEDIAN"
	83	* @param avmode the mode ov averaging. Per "SCAN" or "ALL".
	84	* @return a casa::CountedPtr<Scantable> which either holds a new Scantable
	85	* or returns the imput pointer.
	86	*/
[1069]	87	casa::CountedPtr<Scantable>
	88	averageChannel( const casa::CountedPtr<Scantable> & in,
[1078]	89	const std::string& mode = "MEDIAN",
	90	const std::string& avmode = "SCAN");
[1069]	91
[1140]	92	/**
[1145]	93	* Average polarisations together. really only useful if only linears are
	94	* available.
[1140]	95	* @param in the input Scantable
	96	* @param mask an optional mask if weight allows one
	97	* @param weight weighting scheme
[1143]	98	* @return
[1140]	99	*/
[940]	100	casa::CountedPtr< Scantable >
	101	averagePolarisations( const casa::CountedPtr< Scantable > & in,
[1140]	102	const std::vector<bool>& mask,
	103	const std::string& weight );
[234]	104
[1145]	105	/**
	106	* Average beams together.
	107	* @param in the input Scantable
	108	* @param mask an optional mask if weight allows one
	109	* @param weight weighting scheme
	110	* @return
	111	*/
	112	casa::CountedPtr< Scantable >
	113	averageBeams( const casa::CountedPtr< Scantable > & in,
	114	const std::vector<bool>& mask,
	115	const std::string& weight );
	116
[805]	117	casa::CountedPtr<Scantable>
	118	unaryOperate( const casa::CountedPtr<Scantable>& in, float val,
	119	const std::string& mode, bool tsys=false );
[169]	120
[1779]	121	// array operation
[1308]	122	casa::CountedPtr<Scantable>
[1779]	123	arrayOperate( const casa::CountedPtr<Scantable>& in,
	124	const std::vector<float> val,
	125	const std::string& mode,
	126	const std::string& opmode="channel",
	127	bool tsys=false );
	128
	129	// channel operation
	130	casa::CountedPtr<Scantable>
	131	arrayOperateChannel( const casa::CountedPtr<Scantable>& in,
	132	const std::vector<float> val,
	133	const std::string& mode, bool tsys=false );
	134
	135	// row operation
	136	casa::CountedPtr<Scantable>
	137	arrayOperateRow( const casa::CountedPtr<Scantable>& in,
	138	const std::vector<float> val,
	139	const std::string& mode, bool tsys=false );
	140
	141	// 2d array operation
	142	casa::CountedPtr<Scantable>
	143	array2dOperate( const casa::CountedPtr<Scantable>& in,
	144	const std::vector< std::vector<float> > val,
	145	const std::string& mode, bool tsys=false );
	146
	147	casa::CountedPtr<Scantable>
[1570]	148	binaryOperate( const casa::CountedPtr<Scantable>& left,
	149	const casa::CountedPtr<Scantable>& right,
[1308]	150	const std::string& mode);
	151
[1066]	152	casa::CountedPtr<Scantable> autoQuotient(const casa::CountedPtr<Scantable>& in,
	153	const std::string& mode = "NEAREST",
	154	bool preserve = true);
	155
	156	casa::CountedPtr<Scantable> quotient( const casa::CountedPtr<Scantable>& on,
	157	const casa::CountedPtr<Scantable>& off,
[805]	158	bool preserve = true );
[169]	159
[1391]	160	/**
	161	* Calibrate total power scans (translated from GBTIDL)
[1779]	162	* @param calon uncalibrated Scantable with CAL noise signal
[1391]	163	* @param caloff uncalibrated Scantable with no CAL signal
	164	* @param tcal optional scalar Tcal, CAL temperature (K)
[1779]	165	* @return casa::CountedPtr<Scantable> which holds a calibrated Scantable
[1391]	166	* (spectrum - average of the two CAL on and off spectra;
	167	* tsys - mean Tsys = <caloff>*Tcal/<calon-caloff> + Tcal/2)
[1779]	168	*/
[1391]	169	casa::CountedPtr<Scantable> dototalpower( const casa::CountedPtr<Scantable>& calon,
	170	const casa::CountedPtr<Scantable>& caloff,
	171	casa::Float tcal=1.0 );
	172
	173	/**
	174	* Combine signal and reference scans (translated from GBTIDL)
	175	* @param sig Scantable which contains signal scans
	176	* @param ref Scantable which contains reference scans
	177	* @param smoothref optional Boxcar smooth width of the reference scans
	178	* default: no smoothing (=1)
[1779]	179	* @param tsysv optional scalar Tsys value at the zenith, required to
	180	* set tau, as well
[1391]	181	* @param tau optional scalar Tau value
	182	* @return casa::CountedPtr<Scantable> which holds combined scans
	183	* (spectrum = (sig-ref)/ref * Tsys )
	184	*/
	185	casa::CountedPtr<Scantable> dosigref( const casa::CountedPtr<Scantable>& sig,
	186	const casa::CountedPtr<Scantable>& ref,
	187	int smoothref=1,
	188	casa::Float tsysv=0.0,
	189	casa::Float tau=0.0 );
	190
[1779]	191	/**
[1391]	192	* Calibrate GBT Nod scan pairs (translated from GBTIDL)
	193	* @param s Scantable which contains Nod scans
	194	* @param scans Vector of scan numbers
	195	* @param smoothref optional Boxcar smooth width of the reference scans
	196	* @param tsysv optional scalar Tsys value at the zenith, required to
	197	* set tau, as well
[1779]	198	* @param tau optional scalar Tau value
[1391]	199	* @param tcal optional scalar Tcal, CAL temperature (K)
	200	* @return casa::CountedPtr<Scantable> which holds calibrated scans
	201	*/
	202	casa::CountedPtr<Scantable> donod( const casa::CountedPtr<Scantable>& s,
	203	const std::vector<int>& scans,
	204	int smoothref=1,
	205	casa::Float tsysv=0.0,
	206	casa::Float tau=0.0,
	207	casa::Float tcal=0.0 );
	208
	209	/**
	210	* Calibrate frequency switched scans (translated from GBTIDL)
	211	* @param s Scantable which contains frequency switched scans
	212	* @param scans Vector of scan numbers
	213	* @param smoothref optional Boxcar smooth width of the reference scans
	214	* @param tsysv optional scalar Tsys value at the zenith, required to
	215	* set tau, as well
	216	* @param tau optional scalar Tau value
	217	* @param tcal optional scalar Tcal, CAL temperature (K)
	218	* @return casa::CountedPtr<Scantable> which holds calibrated scans
	219	*/
	220	casa::CountedPtr<Scantable> dofs( const casa::CountedPtr<Scantable>& s,
	221	const std::vector<int>& scans,
	222	int smoothref=1,
	223	casa::Float tsysv=0.0,
	224	casa::Float tau=0.0,
	225	casa::Float tcal=0.0 );
	226
[1779]	227	/**
	228	* Calibrate data with Chopper-Wheel like calibration method
	229	* which adopts position switching by antenna motion,
	230	* wobbler (nutator) switching and On-The-Fly observation.
	231	*
	232	* The method is applicable to APEX, and other telescopes other than GBT.
	233	*
	234	* @param a Scantable which contains ON and OFF scans
	235	* @param a string that indicates calibration mode
	236	* @param a string that indicates antenna name
	237	**/
	238	casa::CountedPtr<Scantable> cwcal( const casa::CountedPtr<Scantable>& s,
	239	const casa::String calmode,
	240	const casa::String antname );
[1391]	241
[1779]	242	/**
	243	* Calibrate frequency switched scans with Chopper-Wheel like
	244	* calibration method.
	245	*
	246	* The method is applicable to APEX, and other telescopes other than GBT.
	247	*
	248	* @param a Scantable which contains ON and OFF scans
	249	* @param a string that indicates antenna name
	250	**/
	251	casa::CountedPtr<Scantable> cwcalfs( const casa::CountedPtr<Scantable>& s,
	252	const casa::String antname );
	253
	254
	255	/**
	256	* Folding frequency-switch data
	257	* @param sig
	258	* @param ref
	259	* @param choffset
	260	**/
	261	casa::CountedPtr<Scantable> dofold( const casa::CountedPtr<Scantable> &sig,
	262	const casa::CountedPtr<Scantable> &ref,
	263	casa::Double choffset,
	264	casa::Double choffset = 0.0 );
	265
	266	/**
	267	* ALMA calibration
	268	**/
	269	casa::CountedPtr<Scantable> almacal( const casa::CountedPtr<Scantable>& s,
	270	const casa::String calmode ) ;
	271	casa::CountedPtr<Scantable> almacalfs( const casa::CountedPtr<Scantable>& s ) ;
	272
[805]	273	casa::CountedPtr<Scantable>
	274	freqSwitch( const casa::CountedPtr<Scantable>& in );
[716]	275
[805]	276	std::vector<float> statistic(const casa::CountedPtr<Scantable>& in,
	277	const std::vector<bool>& mask,
	278	const std::string& which);
[457]	279
[1779]	280	std::vector< int > minMaxChan(const casa::CountedPtr<Scantable>& in,
	281	const std::vector<bool>& mask,
	282	const std::string& which);
	283
[805]	284	casa::CountedPtr<Scantable> bin( const casa::CountedPtr<Scantable>& in,
	285	int width=5);
	286	casa::CountedPtr<Scantable>
	287	resample(const casa::CountedPtr<Scantable>& in,
	288	const std::string& method, float width);
[457]	289
[805]	290	casa::CountedPtr<Scantable>
	291	smooth(const casa::CountedPtr<Scantable>& in, const std::string& kernel,
[1570]	292	float width, int order=2);
[169]	293
[805]	294	casa::CountedPtr<Scantable>
	295	gainElevation(const casa::CountedPtr<Scantable>& in,
[867]	296	const std::vector<float>& coeff,
[805]	297	const std::string& fileName,
[995]	298	const std::string& method);
[805]	299	casa::CountedPtr<Scantable>
	300	convertFlux(const casa::CountedPtr<Scantable>& in, float d,
	301	float etaap, float jyperk);
[152]	302
[805]	303	casa::CountedPtr<Scantable> opacity(const casa::CountedPtr<Scantable>& in,
[1689]	304	const std::vector<float>& tau);
[144]	305
[841]	306	casa::CountedPtr<Scantable>
	307	merge(const std::vector<casa::CountedPtr<Scantable> >& in);
	308
[896]	309	casa::CountedPtr<Scantable>
	310	invertPhase( const casa::CountedPtr<Scantable>& in);
[912]	311
[896]	312	casa::CountedPtr<Scantable>
	313	rotateXYPhase( const casa::CountedPtr<Scantable>& in, float phase);
[912]	314
[896]	315	casa::CountedPtr<Scantable>
	316	rotateLinPolPhase( const casa::CountedPtr<Scantable>& in, float phase);
	317
	318	casa::CountedPtr<Scantable>
	319	swapPolarisations(const casa::CountedPtr<Scantable>& in);
	320
[917]	321	casa::CountedPtr<Scantable>
	322	frequencyAlign( const casa::CountedPtr<Scantable>& in,
[927]	323	const std::string& refTime = "",
	324	const std::string& method = "cubic" );
[917]	325
[992]	326	casa::CountedPtr<Scantable>
	327	convertPolarisation( const casa::CountedPtr<Scantable>& in,
	328	const std::string& newtype);
[1143]	329
[1140]	330	casa::CountedPtr<Scantable>
[1143]	331	mxExtract( const casa::CountedPtr<Scantable>& in,
	332	const std::string& srctype = "on");
[992]	333
[1192]	334	/**
	335	* "hard" flag the data, this flags everything selected in setSelection()
	336	* @param frequency the frequency to remove
	337	* @param width the number of lags to flag left to the side of the frequency
	338	*/
	339	casa::CountedPtr<Scantable>
[1570]	340	lagFlag( const casa::CountedPtr<Scantable>& in, double start,
	341	double end, const std::string& mode="frequency");
[1192]	342
[1779]	343	// test for average spectra with different channel/resolution
	344	casa::CountedPtr<Scantable>
	345	new_average( const std::vector<casa::CountedPtr<Scantable> >& in,
	346	const bool& compel,
	347	const std::vector<bool>& mask = std::vector<bool>(),
	348	const std::string& weight = "NONE",
	349	const std::string& avmode = "SCAN" )
	350	throw (casa::AipsError) ;
	351
[805]	352	private:
[896]	353	casa::CountedPtr<Scantable> applyToPol( const casa::CountedPtr<Scantable>& in,
	354	STPol::polOperation fptr,
	355	casa::Float phase);
	356
[805]	357	static imethod stringToIMethod(const std::string& in);
	358	static WeightType stringToWeight(const std::string& in);
[146]	359
[805]	360	void scaleByVector(casa::Table& in,
	361	const casa::Vector<casa::Float>& factor,
	362	bool dotsys);
[152]	363
[805]	364	void scaleFromAsciiTable(casa::Table& in, const std::string& filename,
	365	const std::string& method,
	366	const casa::Vector<casa::Float>& xout,
	367	bool dotsys);
[162]	368
[805]	369	void scaleFromTable(casa::Table& in, const casa::Table& table,
	370	const std::string& method,
	371	const casa::Vector<casa::Float>& xout, bool dotsys);
[227]	372
[805]	373	void convertBrightnessUnits(casa::CountedPtr<Scantable>& in,
	374	bool tokelvin, float cfac);
[227]	375
[1570]	376	casa::CountedPtr< Scantable >
[1374]	377	smoothOther( const casa::CountedPtr< Scantable >& in,
	378	const std::string& kernel,
[1570]	379	float width, int order=2 );
[1374]	380
[805]	381	casa::CountedPtr< Scantable >
	382	getScantable(const casa::CountedPtr< Scantable >& in, bool droprows);
[230]	383
[805]	384	casa::MaskedArray<casa::Float>
	385	maskedArray( const casa::Vector<casa::Float>& s,
	386	const casa::Vector<casa::uChar>& f );
[1779]	387	casa::MaskedArray<casa::Double>
	388	maskedArray( const casa::Vector<casa::Double>& s,
	389	const casa::Vector<casa::uChar>& f );
[805]	390	casa::Vector<casa::uChar>
	391	flagsFromMA(const casa::MaskedArray<casa::Float>& ma);
[230]	392
[1779]	393	vector<float> getSpectrumFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode = "before" ) ;
	394	vector<float> getTcalFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ;
	395	vector<float> getTsysFromTime( string reftime, casa::CountedPtr<Scantable>& s, string mode="before" ) ;
	396	vector<int> getRowIdFromTime( string reftime, casa::CountedPtr<Scantable>& s ) ;
	397
	398	// Chopper-Wheel type calibration
	399	vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on,
	400	casa::CountedPtr<Scantable>& off,
	401	casa::CountedPtr<Scantable>& sky,
	402	casa::CountedPtr<Scantable>& hot,
	403	casa::CountedPtr<Scantable>& cold,
	404	int index,
	405	string antname ) ;
	406	// Tsys * (ON-OFF)/OFF
	407	vector<float> getCalibratedSpectra( casa::CountedPtr<Scantable>& on,
	408	casa::CountedPtr<Scantable>& off,
	409	int index ) ;
	410	vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig,
	411	casa::CountedPtr<Scantable>& ref,
	412	casa::CountedPtr<Scantable>& sky,
	413	casa::CountedPtr<Scantable>& hot,
	414	casa::CountedPtr<Scantable>& cold,
	415	int index ) ;
	416	vector<float> getFSCalibratedSpectra( casa::CountedPtr<Scantable>& sig,
	417	casa::CountedPtr<Scantable>& ref,
	418	vector< casa::CountedPtr<Scantable> >& sky,
	419	vector< casa::CountedPtr<Scantable> >& hot,
	420	vector< casa::CountedPtr<Scantable> >& cold,
	421	int index ) ;
	422	double getMJD( string strtime ) ;
	423
[805]	424	bool insitu_;
	425	};
[234]	426
[805]	427	}
[165]	428	#endif

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