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source: trunk/python/asapfitter.py@ 1824

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Last change on this file since 1824 was 1819, checked in by Kana Sugimoto, 14 years ago

New Development: No

JIRA Issue: No (merge alma branch to trunk)

Ready for Test: Yes

Interface Changes: No

Test Programs: regressions may work

Module(s): all single dish modules

Description:

Merged all changes in alma (r1386:1818) and newfiller (r1774:1818) branch.

Property svn:eol-style set to native
Property svn:keywords set to Author Date Id Revision

File size: 26.1 KB

Rev	Line
[113]	1	import _asap
[259]	2	from asap import rcParams
[1819]	3	from asap import print_log, print_log_dec
[1295]	4	from asap import _n_bools
[1536]	5	from asap import mask_and
[1819]	6	from asap import asaplog
[113]	7
	8	class fitter:
	9	"""
	10	The fitting class for ASAP.
	11	"""
[723]	12
[113]	13	def __init__(self):
	14	"""
	15	Create a fitter object. No state is set.
	16	"""
	17	self.fitter = _asap.fitter()
	18	self.x = None
	19	self.y = None
	20	self.mask = None
	21	self.fitfunc = None
[515]	22	self.fitfuncs = None
[113]	23	self.fitted = False
	24	self.data = None
[515]	25	self.components = 0
	26	self._fittedrow = 0
[113]	27	self._p = None
[515]	28	self._selection = None
[1391]	29	self.uselinear = False
[113]	30
	31	def set_data(self, xdat, ydat, mask=None):
	32	"""
[158]	33	Set the absissa and ordinate for the fit. Also set the mask
[113]	34	indicationg valid points.
	35	This can be used for data vectors retrieved from a scantable.
	36	For scantable fitting use 'fitter.set_scan(scan, mask)'.
	37	Parameters:
[158]	38	xdat: the abcissa values
[113]	39	ydat: the ordinate values
	40	mask: an optional mask
[723]	41
[113]	42	"""
	43	self.fitted = False
	44	self.x = xdat
	45	self.y = ydat
	46	if mask == None:
[1295]	47	self.mask = _n_bools(len(xdat), True)
[113]	48	else:
	49	self.mask = mask
	50	return
	51
	52	def set_scan(self, thescan=None, mask=None):
	53	"""
	54	Set the 'data' (a scantable) of the fitter.
	55	Parameters:
	56	thescan: a scantable
[1420]	57	mask: a msk retrieved from the scantable
[113]	58	"""
	59	if not thescan:
[723]	60	msg = "Please give a correct scan"
	61	if rcParams['verbose']:
[1819]	62	#print msg
	63	asaplog.push(msg)
	64	print_log('ERROR')
[723]	65	return
	66	else:
	67	raise TypeError(msg)
[113]	68	self.fitted = False
	69	self.data = thescan
[1075]	70	self.mask = None
[113]	71	if mask is None:
[1295]	72	self.mask = _n_bools(self.data.nchan(), True)
[113]	73	else:
	74	self.mask = mask
	75	return
	76
	77	def set_function(self, **kwargs):
	78	"""
	79	Set the function to be fit.
	80	Parameters:
[1589]	81	poly: use a polynomial of the order given with nonlinear least squares fit
[1391]	82	lpoly: use polynomial of the order given with linear least squares fit
[113]	83	gauss: fit the number of gaussian specified
[1819]	84	lorentz: fit the number of lorentzian specified
[113]	85	Example:
[1391]	86	fitter.set_function(poly=3) # will fit a 3rd order polynomial via nonlinear method
	87	fitter.set_function(lpoly=3) # will fit a 3rd order polynomial via linear method
[1819]	88	fitter.set_function(gauss=2) # will fit two gaussians
	89	fitter.set_function(lorentz=2) # will fit two lorentzians
[113]	90	"""
[723]	91	#default poly order 0
[515]	92	n=0
[113]	93	if kwargs.has_key('poly'):
	94	self.fitfunc = 'poly'
	95	n = kwargs.get('poly')
[515]	96	self.components = [n]
[1589]	97	self.uselinear = False
[1391]	98	elif kwargs.has_key('lpoly'):
	99	self.fitfunc = 'poly'
	100	n = kwargs.get('lpoly')
	101	self.components = [n]
	102	self.uselinear = True
[113]	103	elif kwargs.has_key('gauss'):
	104	n = kwargs.get('gauss')
	105	self.fitfunc = 'gauss'
[515]	106	self.fitfuncs = [ 'gauss' for i in range(n) ]
	107	self.components = [ 3 for i in range(n) ]
[1589]	108	self.uselinear = False
[1819]	109	elif kwargs.has_key('lorentz'):
	110	n = kwargs.get('lorentz')
	111	self.fitfunc = 'lorentz'
	112	self.fitfuncs = [ 'lorentz' for i in range(n) ]
	113	self.components = [ 3 for i in range(n) ]
	114	self.uselinear = False
[515]	115	else:
[723]	116	msg = "Invalid function type."
	117	if rcParams['verbose']:
[1819]	118	#print msg
	119	asaplog.push(msg)
	120	print_log('ERROR')
[723]	121	return
	122	else:
	123	raise TypeError(msg)
	124
[113]	125	self.fitter.setexpression(self.fitfunc,n)
[1232]	126	self.fitted = False
[113]	127	return
[723]	128
[1589]	129	@print_log_dec
[1075]	130	def fit(self, row=0, estimate=False):
[113]	131	"""
	132	Execute the actual fitting process. All the state has to be set.
	133	Parameters:
[1075]	134	row: specify the row in the scantable
	135	estimate: auto-compute an initial parameter set (default False)
	136	This can be used to compute estimates even if fit was
	137	called before.
[113]	138	Example:
[515]	139	s = scantable('myscan.asap')
	140	s.set_cursor(thepol=1) # select second pol
[113]	141	f = fitter()
	142	f.set_scan(s)
	143	f.set_function(poly=0)
[723]	144	f.fit(row=0) # fit first row
[113]	145	"""
	146	if ((self.x is None or self.y is None) and self.data is None) \
	147	or self.fitfunc is None:
[723]	148	msg = "Fitter not yet initialised. Please set data & fit function"
	149	if rcParams['verbose']:
[1819]	150	#print msg
	151	asaplog.push(msg)
	152	print_log('ERROR')
[723]	153	return
	154	else:
	155	raise RuntimeError(msg)
	156
[113]	157	else:
	158	if self.data is not None:
[515]	159	self.x = self.data._getabcissa(row)
	160	self.y = self.data._getspectrum(row)
[1536]	161	self.mask = mask_and(self.mask, self.data._getmask(row))
[723]	162	asaplog.push("Fitting:")
[943]	163	i = row
[1536]	164	out = "Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (self.data.getscan(i),
	165	self.data.getbeam(i),
	166	self.data.getif(i),
[1589]	167	self.data.getpol(i),
[1536]	168	self.data.getcycle(i))
[1075]	169	asaplog.push(out,False)
[515]	170	self.fitter.setdata(self.x, self.y, self.mask)
[1819]	171	if self.fitfunc == 'gauss' or self.fitfunc == 'lorentz':
[113]	172	ps = self.fitter.getparameters()
[1075]	173	if len(ps) == 0 or estimate:
[113]	174	self.fitter.estimate()
[626]	175	try:
[1232]	176	fxdpar = list(self.fitter.getfixedparameters())
	177	if len(fxdpar) and fxdpar.count(0) == 0:
	178	raise RuntimeError,"No point fitting, if all parameters are fixed."
[1391]	179	if self.uselinear:
	180	converged = self.fitter.lfit()
	181	else:
	182	converged = self.fitter.fit()
[1075]	183	if not converged:
	184	raise RuntimeError,"Fit didn't converge."
[626]	185	except RuntimeError, msg:
[723]	186	if rcParams['verbose']:
[1819]	187	#print msg
	188	print_log()
	189	asaplog.push(str(msg))
	190	print_log('ERROR')
[723]	191	else:
	192	raise
[515]	193	self._fittedrow = row
[113]	194	self.fitted = True
[1819]	195	print_log()
[113]	196	return
	197
[1232]	198	def store_fit(self, filename=None):
[526]	199	"""
[1232]	200	Save the fit parameters.
	201	Parameters:
	202	filename: if specified save as an ASCII file, if None (default)
	203	store it in the scnatable
[526]	204	"""
[515]	205	if self.fitted and self.data is not None:
	206	pars = list(self.fitter.getparameters())
	207	fixed = list(self.fitter.getfixedparameters())
[975]	208	from asap.asapfit import asapfit
	209	fit = asapfit()
	210	fit.setparameters(pars)
	211	fit.setfixedparameters(fixed)
	212	fit.setfunctions(self.fitfuncs)
	213	fit.setcomponents(self.components)
	214	fit.setframeinfo(self.data._getcoordinfo())
[1232]	215	if filename is not None:
	216	import os
	217	filename = os.path.expandvars(os.path.expanduser(filename))
	218	if os.path.exists(filename):
	219	raise IOError("File '%s' exists." % filename)
	220	fit.save(filename)
	221	else:
	222	self.data._addfit(fit,self._fittedrow)
[515]	223
[1589]	224	@print_log_dec
[1017]	225	def set_parameters(self,args,*kwargs):
[526]	226	"""
	227	Set the parameters to be fitted.
	228	Parameters:
	229	params: a vector of parameters
	230	fixed: a vector of which parameters are to be held fixed
	231	(default is none)
	232	component: in case of multiple gaussians, the index of the
	233	component
[1017]	234	"""
	235	component = None
	236	fixed = None
	237	params = None
[1031]	238
[1017]	239	if len(args) and isinstance(args[0],dict):
	240	kwargs = args[0]
	241	if kwargs.has_key("fixed"): fixed = kwargs["fixed"]
	242	if kwargs.has_key("params"): params = kwargs["params"]
	243	if len(args) == 2 and isinstance(args[1], int):
	244	component = args[1]
[515]	245	if self.fitfunc is None:
[723]	246	msg = "Please specify a fitting function first."
	247	if rcParams['verbose']:
[1819]	248	#print msg
	249	asaplog.push(msg)
	250	print_log('ERROR')
[723]	251	return
	252	else:
	253	raise RuntimeError(msg)
[1819]	254	if (self.fitfunc == "gauss" or self.fitfunc == 'lorentz') and component is not None:
[1017]	255	if not self.fitted and sum(self.fitter.getparameters()) == 0:
[1295]	256	pars = _n_bools(len(self.components)*3, False)
	257	fxd = _n_bools(len(pars), False)
[515]	258	else:
[723]	259	pars = list(self.fitter.getparameters())
[515]	260	fxd = list(self.fitter.getfixedparameters())
	261	i = 3*component
	262	pars[i:i+3] = params
	263	fxd[i:i+3] = fixed
	264	params = pars
[723]	265	fixed = fxd
[113]	266	self.fitter.setparameters(params)
	267	if fixed is not None:
	268	self.fitter.setfixedparameters(fixed)
[1819]	269	print_log()
[113]	270	return
[515]	271
[1217]	272	def set_gauss_parameters(self, peak, centre, fwhm,
[1409]	273	peakfixed=0, centrefixed=0,
[1217]	274	fwhmfixed=0,
[515]	275	component=0):
[113]	276	"""
[515]	277	Set the Parameters of a 'Gaussian' component, set with set_function.
	278	Parameters:
[1232]	279	peak, centre, fwhm: The gaussian parameters
[515]	280	peakfixed,
[1409]	281	centrefixed,
[1217]	282	fwhmfixed: Optional parameters to indicate if
[515]	283	the paramters should be held fixed during
	284	the fitting process. The default is to keep
	285	all parameters flexible.
[526]	286	component: The number of the component (Default is the
	287	component 0)
[515]	288	"""
	289	if self.fitfunc != "gauss":
[723]	290	msg = "Function only operates on Gaussian components."
	291	if rcParams['verbose']:
[1819]	292	#print msg
	293	asaplog.push(msg)
	294	print_log('ERROR')
[723]	295	return
	296	else:
	297	raise ValueError(msg)
[515]	298	if 0 <= component < len(self.components):
[1217]	299	d = {'params':[peak, centre, fwhm],
[1409]	300	'fixed':[peakfixed, centrefixed, fwhmfixed]}
[1017]	301	self.set_parameters(d, component)
[515]	302	else:
[723]	303	msg = "Please select a valid component."
	304	if rcParams['verbose']:
[1819]	305	#print msg
	306	asaplog.push(msg)
	307	print_log('ERROR')
[723]	308	return
	309	else:
	310	raise ValueError(msg)
	311
[1819]	312	def set_lorentz_parameters(self, peak, centre, fwhm,
	313	peakfixed=0, centrefixed=0,
	314	fwhmfixed=0,
	315	component=0):
	316	"""
	317	Set the Parameters of a 'Lorentzian' component, set with set_function.
	318	Parameters:
	319	peak, centre, fwhm: The gaussian parameters
	320	peakfixed,
	321	centrefixed,
	322	fwhmfixed: Optional parameters to indicate if
	323	the paramters should be held fixed during
	324	the fitting process. The default is to keep
	325	all parameters flexible.
	326	component: The number of the component (Default is the
	327	component 0)
	328	"""
	329	if self.fitfunc != "lorentz":
	330	msg = "Function only operates on Lorentzian components."
	331	if rcParams['verbose']:
	332	#print msg
	333	asaplog.push(msg)
	334	print_log('ERROR')
	335	return
	336	else:
	337	raise ValueError(msg)
	338	if 0 <= component < len(self.components):
	339	d = {'params':[peak, centre, fwhm],
	340	'fixed':[peakfixed, centrefixed, fwhmfixed]}
	341	self.set_parameters(d, component)
	342	else:
	343	msg = "Please select a valid component."
	344	if rcParams['verbose']:
	345	#print msg
	346	asaplog.push(msg)
	347	print_log('ERROR')
	348	return
	349	else:
	350	raise ValueError(msg)
	351
[975]	352	def get_area(self, component=None):
	353	"""
[1819]	354	Return the area under the fitted gaussian/lorentzian component.
[975]	355	Parameters:
[1819]	356	component: the gaussian/lorentzian component selection,
[975]	357	default (None) is the sum of all components
	358	Note:
[1819]	359	This will only work for gaussian/lorentzian fits.
[975]	360	"""
	361	if not self.fitted: return
[1819]	362	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[975]	363	pars = list(self.fitter.getparameters())
	364	from math import log,pi,sqrt
[1819]	365	if self.fitfunc == "gauss":
	366	fac = sqrt(pi/log(16.0))
	367	elif self.fitfunc == "lorentz":
	368	fac = pi/2.0
[975]	369	areas = []
	370	for i in range(len(self.components)):
	371	j = i*3
	372	cpars = pars[j:j+3]
	373	areas.append(fac * cpars[0] * cpars[2])
	374	else:
	375	return None
	376	if component is not None:
	377	return areas[component]
	378	else:
	379	return sum(areas)
	380
[1075]	381	def get_errors(self, component=None):
[515]	382	"""
[1075]	383	Return the errors in the parameters.
	384	Parameters:
	385	component: get the errors for the specified component
	386	only, default is all components
	387	"""
	388	if not self.fitted:
	389	msg = "Not yet fitted."
	390	if rcParams['verbose']:
[1819]	391	#print msg
	392	asaplog.push(msg)
	393	print_log('ERROR')
[1075]	394	return
	395	else:
	396	raise RuntimeError(msg)
	397	errs = list(self.fitter.geterrors())
	398	cerrs = errs
	399	if component is not None:
[1819]	400	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[1075]	401	i = 3*component
	402	if i < len(errs):
	403	cerrs = errs[i:i+3]
	404	return cerrs
	405
	406	def get_parameters(self, component=None, errors=False):
	407	"""
[113]	408	Return the fit paramters.
[526]	409	Parameters:
	410	component: get the parameters for the specified component
	411	only, default is all components
[113]	412	"""
	413	if not self.fitted:
[723]	414	msg = "Not yet fitted."
	415	if rcParams['verbose']:
[1819]	416	#print msg
	417	asaplog.push(msg)
	418	print_log('ERROR')
[723]	419	return
	420	else:
	421	raise RuntimeError(msg)
[113]	422	pars = list(self.fitter.getparameters())
	423	fixed = list(self.fitter.getfixedparameters())
[1075]	424	errs = list(self.fitter.geterrors())
[1039]	425	area = []
[723]	426	if component is not None:
[1819]	427	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[515]	428	i = 3*component
	429	cpars = pars[i:i+3]
	430	cfixed = fixed[i:i+3]
[1075]	431	cerrs = errs[i:i+3]
[1039]	432	a = self.get_area(component)
	433	area = [a for i in range(3)]
[515]	434	else:
	435	cpars = pars
[723]	436	cfixed = fixed
[1075]	437	cerrs = errs
[515]	438	else:
	439	cpars = pars
	440	cfixed = fixed
[1075]	441	cerrs = errs
[1819]	442	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[1039]	443	for c in range(len(self.components)):
	444	a = self.get_area(c)
	445	area += [a for i in range(3)]
[1088]	446	fpars = self._format_pars(cpars, cfixed, errors and cerrs, area)
[723]	447	if rcParams['verbose']:
[1819]	448	#print fpars
	449	asaplog.push(fpars)
	450	print_log()
[1075]	451	return {'params':cpars, 'fixed':cfixed, 'formatted': fpars,
	452	'errors':cerrs}
[723]	453
[1075]	454	def _format_pars(self, pars, fixed, errors, area):
[113]	455	out = ''
	456	if self.fitfunc == 'poly':
	457	c = 0
[515]	458	for i in range(len(pars)):
	459	fix = ""
[1232]	460	if len(fixed) and fixed[i]: fix = "(fixed)"
[1088]	461	if errors :
	462	out += ' p%d%s= %3.6f (%1.6f),' % (c,fix,pars[i], errors[i])
	463	else:
	464	out += ' p%d%s= %3.6f,' % (c,fix,pars[i])
[113]	465	c+=1
[515]	466	out = out[:-1] # remove trailing ','
[1819]	467	elif self.fitfunc == 'gauss' or self.fitfunc == 'lorentz':
[113]	468	i = 0
	469	c = 0
[515]	470	aunit = ''
	471	ounit = ''
[113]	472	if self.data:
[515]	473	aunit = self.data.get_unit()
	474	ounit = self.data.get_fluxunit()
[113]	475	while i < len(pars):
[1039]	476	if len(area):
	477	out += ' %2d: peak = %3.3f %s , centre = %3.3f %s, FWHM = %3.3f %s\n area = %3.3f %s %s\n' % (c,pars[i],ounit,pars[i+1],aunit,pars[i+2],aunit, area[i],ounit,aunit)
[1017]	478	else:
	479	out += ' %2d: peak = %3.3f %s , centre = %3.3f %s, FWHM = %3.3f %s\n' % (c,pars[i],ounit,pars[i+1],aunit,pars[i+2],aunit,ounit,aunit)
[113]	480	c+=1
	481	i+=3
	482	return out
[723]	483
[113]	484	def get_estimate(self):
	485	"""
[515]	486	Return the parameter estimates (for non-linear functions).
[113]	487	"""
	488	pars = self.fitter.getestimate()
[943]	489	fixed = self.fitter.getfixedparameters()
[723]	490	if rcParams['verbose']:
[1819]	491	#print self._format_pars(pars,fixed,None)
	492	asaplog.push(self._format_pars(pars,fixed,None))
	493	print_log()
[113]	494	return pars
	495
	496	def get_residual(self):
	497	"""
	498	Return the residual of the fit.
	499	"""
	500	if not self.fitted:
[723]	501	msg = "Not yet fitted."
	502	if rcParams['verbose']:
[1819]	503	#print msg
	504	asaplog.push(msg)
	505	print_log('ERROR')
[723]	506	return
	507	else:
	508	raise RuntimeError(msg)
[113]	509	return self.fitter.getresidual()
	510
	511	def get_chi2(self):
	512	"""
	513	Return chi^2.
	514	"""
	515	if not self.fitted:
[723]	516	msg = "Not yet fitted."
	517	if rcParams['verbose']:
[1819]	518	#print msg
	519	asaplog.push(msg)
	520	print_log('ERROR')
[723]	521	return
	522	else:
	523	raise RuntimeError(msg)
[113]	524	ch2 = self.fitter.getchi2()
[723]	525	if rcParams['verbose']:
[1819]	526	#print 'Chi^2 = %3.3f' % (ch2)
	527	asaplog.push( 'Chi^2 = %3.3f' % (ch2) )
	528	print_log()
[723]	529	return ch2
[113]	530
	531	def get_fit(self):
	532	"""
	533	Return the fitted ordinate values.
	534	"""
	535	if not self.fitted:
[723]	536	msg = "Not yet fitted."
	537	if rcParams['verbose']:
[1819]	538	#print msg
	539	asaplog.push(msg)
	540	print_log('ERROR')
[723]	541	return
	542	else:
	543	raise RuntimeError(msg)
[113]	544	return self.fitter.getfit()
	545
[1589]	546	@print_log_dec
[113]	547	def commit(self):
	548	"""
[526]	549	Return a new scan where the fits have been commited (subtracted)
[113]	550	"""
	551	if not self.fitted:
[723]	552	msg = "Not yet fitted."
	553	if rcParams['verbose']:
[1819]	554	#print msg
	555	asaplog.push(msg)
	556	print_log('ERROR')
[723]	557	return
	558	else:
	559	raise RuntimeError(msg)
[975]	560	from asap import scantable
	561	if not isinstance(self.data, scantable):
[723]	562	msg = "Not a scantable"
	563	if rcParams['verbose']:
[1819]	564	#print msg
	565	asaplog.push(msg)
	566	print_log('ERROR')
[723]	567	return
	568	else:
	569	raise TypeError(msg)
[113]	570	scan = self.data.copy()
[259]	571	scan._setspectrum(self.fitter.getresidual())
[1819]	572	print_log()
[1092]	573	return scan
[113]	574
[1589]	575	@print_log_dec
[1689]	576	def plot(self, residual=False, components=None, plotparms=False,
	577	filename=None):
[113]	578	"""
	579	Plot the last fit.
	580	Parameters:
	581	residual: an optional parameter indicating if the residual
	582	should be plotted (default 'False')
[526]	583	components: a list of components to plot, e.g [0,1],
	584	-1 plots the total fit. Default is to only
	585	plot the total fit.
	586	plotparms: Inidicates if the parameter values should be present
	587	on the plot
[113]	588	"""
	589	if not self.fitted:
	590	return
[723]	591	if not self._p or self._p.is_dead:
	592	if rcParams['plotter.gui']:
	593	from asap.asaplotgui import asaplotgui as asaplot
	594	else:
	595	from asap.asaplot import asaplot
	596	self._p = asaplot()
	597	self._p.hold()
[113]	598	self._p.clear()
[515]	599	self._p.set_panels()
[652]	600	self._p.palette(0)
[113]	601	tlab = 'Spectrum'
[723]	602	xlab = 'Abcissa'
[1017]	603	ylab = 'Ordinate'
[1739]	604	from numpy import ma,logical_not,logical_and,array
[1273]	605	m = self.mask
[113]	606	if self.data:
[515]	607	tlab = self.data._getsourcename(self._fittedrow)
	608	xlab = self.data._getabcissalabel(self._fittedrow)
[1273]	609	m = logical_and(self.mask,
[1306]	610	array(self.data._getmask(self._fittedrow),
	611	copy=False))
[1589]	612
[626]	613	ylab = self.data._get_ordinate_label()
[515]	614
[1075]	615	colours = ["#777777","#dddddd","red","orange","purple","green","magenta", "cyan"]
[1819]	616	nomask=True
	617	for i in range(len(m)):
	618	nomask = nomask and m[i]
	619	label0='Masked Region'
	620	label1='Spectrum'
	621	if ( nomask ):
	622	label0=label1
	623	else:
	624	y = ma.masked_array( self.y, mask = m )
	625	self._p.palette(1,colours)
	626	self._p.set_line( label = label1 )
	627	self._p.plot( self.x, y )
[652]	628	self._p.palette(0,colours)
[1819]	629	self._p.set_line(label=label0)
[1273]	630	y = ma.masked_array(self.y,mask=logical_not(m))
[1088]	631	self._p.plot(self.x, y)
[113]	632	if residual:
[1819]	633	self._p.palette(7)
[515]	634	self._p.set_line(label='Residual')
[1116]	635	y = ma.masked_array(self.get_residual(),
[1273]	636	mask=logical_not(m))
[1088]	637	self._p.plot(self.x, y)
[652]	638	self._p.palette(2)
[515]	639	if components is not None:
	640	cs = components
	641	if isinstance(components,int): cs = [components]
[526]	642	if plotparms:
[1031]	643	self._p.text(0.15,0.15,str(self.get_parameters()['formatted']),size=8)
[515]	644	n = len(self.components)
[652]	645	self._p.palette(3)
[515]	646	for c in cs:
	647	if 0 <= c < n:
	648	lab = self.fitfuncs[c]+str(c)
	649	self._p.set_line(label=lab)
[1116]	650	y = ma.masked_array(self.fitter.evaluate(c),
[1273]	651	mask=logical_not(m))
[1088]	652
	653	self._p.plot(self.x, y)
[515]	654	elif c == -1:
[652]	655	self._p.palette(2)
[515]	656	self._p.set_line(label="Total Fit")
[1116]	657	y = ma.masked_array(self.fitter.getfit(),
[1273]	658	mask=logical_not(m))
[1088]	659	self._p.plot(self.x, y)
[515]	660	else:
[652]	661	self._p.palette(2)
[515]	662	self._p.set_line(label='Fit')
[1116]	663	y = ma.masked_array(self.fitter.getfit(),
[1273]	664	mask=logical_not(m))
[1088]	665	self._p.plot(self.x, y)
[723]	666	xlim=[min(self.x),max(self.x)]
	667	self._p.axes.set_xlim(xlim)
[113]	668	self._p.set_axes('xlabel',xlab)
	669	self._p.set_axes('ylabel',ylab)
	670	self._p.set_axes('title',tlab)
	671	self._p.release()
[723]	672	if (not rcParams['plotter.gui']):
	673	self._p.save(filename)
[1819]	674	print_log()
[113]	675
[1589]	676	@print_log_dec
[1061]	677	def auto_fit(self, insitu=None, plot=False):
[113]	678	"""
[515]	679	Return a scan where the function is applied to all rows for
	680	all Beams/IFs/Pols.
[723]	681
[113]	682	"""
	683	from asap import scantable
[515]	684	if not isinstance(self.data, scantable) :
[723]	685	msg = "Data is not a scantable"
	686	if rcParams['verbose']:
[1819]	687	#print msg
	688	asaplog.push(msg)
	689	print_log('ERROR')
[723]	690	return
	691	else:
	692	raise TypeError(msg)
[259]	693	if insitu is None: insitu = rcParams['insitu']
	694	if not insitu:
	695	scan = self.data.copy()
	696	else:
	697	scan = self.data
[880]	698	rows = xrange(scan.nrow())
[1819]	699	# Save parameters of baseline fits as a class attribute.
	700	# NOTICE: This does not reflect changes in scantable!
	701	if len(rows) > 0: self.blpars=[]
[876]	702	asaplog.push("Fitting:")
	703	for r in rows:
[1536]	704	out = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (scan.getscan(r),
	705	scan.getbeam(r),
	706	scan.getif(r),
[1589]	707	scan.getpol(r),
[1536]	708	scan.getcycle(r))
[880]	709	asaplog.push(out, False)
[876]	710	self.x = scan._getabcissa(r)
	711	self.y = scan._getspectrum(r)
[1536]	712	self.mask = mask_and(self.mask, scan._getmask(r))
[876]	713	self.data = None
	714	self.fit()
	715	x = self.get_parameters()
[1819]	716	fpar = self.get_parameters()
[1061]	717	if plot:
	718	self.plot(residual=True)
	719	x = raw_input("Accept fit ([y]/n): ")
	720	if x.upper() == 'N':
[1819]	721	self.blpars.append(None)
[1061]	722	continue
[880]	723	scan._setspectrum(self.fitter.getresidual(), r)
[1819]	724	self.blpars.append(fpar)
[1061]	725	if plot:
	726	self._p.unmap()
	727	self._p = None
[1819]	728	print_log()
[876]	729	return scan

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