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source: trunk/python/asapfitter.py@ 1840

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Last change on this file since 1840 was 1826, checked in by Malte Marquarding, 14 years ago
Tidy up of imports (now imported from asap.). Also fixed some whitespace/tab issues
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
[1826]	2	from asap.parameters import rcParams
	3	from asap.logging import asaplog, print_log, print_log_dec
	4	from asap.utils import _n_bools, mask_and
[113]	5
[1826]	6
[113]	7	class fitter:
	8	"""
	9	The fitting class for ASAP.
	10	"""
[723]	11
[113]	12	def __init__(self):
	13	"""
	14	Create a fitter object. No state is set.
	15	"""
	16	self.fitter = _asap.fitter()
	17	self.x = None
	18	self.y = None
	19	self.mask = None
	20	self.fitfunc = None
[515]	21	self.fitfuncs = None
[113]	22	self.fitted = False
	23	self.data = None
[515]	24	self.components = 0
	25	self._fittedrow = 0
[113]	26	self._p = None
[515]	27	self._selection = None
[1391]	28	self.uselinear = False
[113]	29
	30	def set_data(self, xdat, ydat, mask=None):
	31	"""
[158]	32	Set the absissa and ordinate for the fit. Also set the mask
[113]	33	indicationg valid points.
	34	This can be used for data vectors retrieved from a scantable.
	35	For scantable fitting use 'fitter.set_scan(scan, mask)'.
	36	Parameters:
[158]	37	xdat: the abcissa values
[113]	38	ydat: the ordinate values
	39	mask: an optional mask
[723]	40
[113]	41	"""
	42	self.fitted = False
	43	self.x = xdat
	44	self.y = ydat
	45	if mask == None:
[1295]	46	self.mask = _n_bools(len(xdat), True)
[113]	47	else:
	48	self.mask = mask
	49	return
	50
	51	def set_scan(self, thescan=None, mask=None):
	52	"""
	53	Set the 'data' (a scantable) of the fitter.
	54	Parameters:
	55	thescan: a scantable
[1420]	56	mask: a msk retrieved from the scantable
[113]	57	"""
	58	if not thescan:
[723]	59	msg = "Please give a correct scan"
	60	if rcParams['verbose']:
[1819]	61	#print msg
	62	asaplog.push(msg)
	63	print_log('ERROR')
[723]	64	return
	65	else:
	66	raise TypeError(msg)
[113]	67	self.fitted = False
	68	self.data = thescan
[1075]	69	self.mask = None
[113]	70	if mask is None:
[1295]	71	self.mask = _n_bools(self.data.nchan(), True)
[113]	72	else:
	73	self.mask = mask
	74	return
	75
	76	def set_function(self, **kwargs):
	77	"""
	78	Set the function to be fit.
	79	Parameters:
[1589]	80	poly: use a polynomial of the order given with nonlinear least squares fit
[1391]	81	lpoly: use polynomial of the order given with linear least squares fit
[113]	82	gauss: fit the number of gaussian specified
[1819]	83	lorentz: fit the number of lorentzian specified
[113]	84	Example:
[1391]	85	fitter.set_function(poly=3) # will fit a 3rd order polynomial via nonlinear method
	86	fitter.set_function(lpoly=3) # will fit a 3rd order polynomial via linear method
[1819]	87	fitter.set_function(gauss=2) # will fit two gaussians
	88	fitter.set_function(lorentz=2) # will fit two lorentzians
[113]	89	"""
[723]	90	#default poly order 0
[515]	91	n=0
[113]	92	if kwargs.has_key('poly'):
	93	self.fitfunc = 'poly'
	94	n = kwargs.get('poly')
[515]	95	self.components = [n]
[1589]	96	self.uselinear = False
[1391]	97	elif kwargs.has_key('lpoly'):
	98	self.fitfunc = 'poly'
	99	n = kwargs.get('lpoly')
	100	self.components = [n]
	101	self.uselinear = True
[113]	102	elif kwargs.has_key('gauss'):
	103	n = kwargs.get('gauss')
	104	self.fitfunc = 'gauss'
[515]	105	self.fitfuncs = [ 'gauss' for i in range(n) ]
	106	self.components = [ 3 for i in range(n) ]
[1589]	107	self.uselinear = False
[1819]	108	elif kwargs.has_key('lorentz'):
	109	n = kwargs.get('lorentz')
	110	self.fitfunc = 'lorentz'
	111	self.fitfuncs = [ 'lorentz' for i in range(n) ]
	112	self.components = [ 3 for i in range(n) ]
	113	self.uselinear = False
[515]	114	else:
[723]	115	msg = "Invalid function type."
	116	if rcParams['verbose']:
[1819]	117	#print msg
	118	asaplog.push(msg)
	119	print_log('ERROR')
[723]	120	return
	121	else:
	122	raise TypeError(msg)
	123
[113]	124	self.fitter.setexpression(self.fitfunc,n)
[1232]	125	self.fitted = False
[113]	126	return
[723]	127
[1589]	128	@print_log_dec
[1075]	129	def fit(self, row=0, estimate=False):
[113]	130	"""
	131	Execute the actual fitting process. All the state has to be set.
	132	Parameters:
[1075]	133	row: specify the row in the scantable
	134	estimate: auto-compute an initial parameter set (default False)
	135	This can be used to compute estimates even if fit was
	136	called before.
[113]	137	Example:
[515]	138	s = scantable('myscan.asap')
	139	s.set_cursor(thepol=1) # select second pol
[113]	140	f = fitter()
	141	f.set_scan(s)
	142	f.set_function(poly=0)
[723]	143	f.fit(row=0) # fit first row
[113]	144	"""
	145	if ((self.x is None or self.y is None) and self.data is None) \
	146	or self.fitfunc is None:
[723]	147	msg = "Fitter not yet initialised. Please set data & fit function"
	148	if rcParams['verbose']:
[1819]	149	#print msg
	150	asaplog.push(msg)
	151	print_log('ERROR')
[723]	152	return
	153	else:
	154	raise RuntimeError(msg)
	155
[113]	156	else:
	157	if self.data is not None:
[515]	158	self.x = self.data._getabcissa(row)
	159	self.y = self.data._getspectrum(row)
[1536]	160	self.mask = mask_and(self.mask, self.data._getmask(row))
[723]	161	asaplog.push("Fitting:")
[943]	162	i = row
[1536]	163	out = "Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (self.data.getscan(i),
	164	self.data.getbeam(i),
	165	self.data.getif(i),
[1589]	166	self.data.getpol(i),
[1536]	167	self.data.getcycle(i))
[1075]	168	asaplog.push(out,False)
[515]	169	self.fitter.setdata(self.x, self.y, self.mask)
[1819]	170	if self.fitfunc == 'gauss' or self.fitfunc == 'lorentz':
[113]	171	ps = self.fitter.getparameters()
[1075]	172	if len(ps) == 0 or estimate:
[113]	173	self.fitter.estimate()
[626]	174	try:
[1232]	175	fxdpar = list(self.fitter.getfixedparameters())
	176	if len(fxdpar) and fxdpar.count(0) == 0:
	177	raise RuntimeError,"No point fitting, if all parameters are fixed."
[1391]	178	if self.uselinear:
	179	converged = self.fitter.lfit()
	180	else:
	181	converged = self.fitter.fit()
[1075]	182	if not converged:
	183	raise RuntimeError,"Fit didn't converge."
[626]	184	except RuntimeError, msg:
[723]	185	if rcParams['verbose']:
[1819]	186	#print msg
	187	print_log()
	188	asaplog.push(str(msg))
	189	print_log('ERROR')
[723]	190	else:
	191	raise
[515]	192	self._fittedrow = row
[113]	193	self.fitted = True
[1819]	194	print_log()
[113]	195	return
	196
[1232]	197	def store_fit(self, filename=None):
[526]	198	"""
[1232]	199	Save the fit parameters.
	200	Parameters:
	201	filename: if specified save as an ASCII file, if None (default)
	202	store it in the scnatable
[526]	203	"""
[515]	204	if self.fitted and self.data is not None:
	205	pars = list(self.fitter.getparameters())
	206	fixed = list(self.fitter.getfixedparameters())
[975]	207	from asap.asapfit import asapfit
	208	fit = asapfit()
	209	fit.setparameters(pars)
	210	fit.setfixedparameters(fixed)
	211	fit.setfunctions(self.fitfuncs)
	212	fit.setcomponents(self.components)
	213	fit.setframeinfo(self.data._getcoordinfo())
[1232]	214	if filename is not None:
	215	import os
	216	filename = os.path.expandvars(os.path.expanduser(filename))
	217	if os.path.exists(filename):
	218	raise IOError("File '%s' exists." % filename)
	219	fit.save(filename)
	220	else:
	221	self.data._addfit(fit,self._fittedrow)
[515]	222
[1589]	223	@print_log_dec
[1017]	224	def set_parameters(self,args,*kwargs):
[526]	225	"""
	226	Set the parameters to be fitted.
	227	Parameters:
	228	params: a vector of parameters
	229	fixed: a vector of which parameters are to be held fixed
	230	(default is none)
	231	component: in case of multiple gaussians, the index of the
	232	component
[1017]	233	"""
	234	component = None
	235	fixed = None
	236	params = None
[1031]	237
[1017]	238	if len(args) and isinstance(args[0],dict):
	239	kwargs = args[0]
	240	if kwargs.has_key("fixed"): fixed = kwargs["fixed"]
	241	if kwargs.has_key("params"): params = kwargs["params"]
	242	if len(args) == 2 and isinstance(args[1], int):
	243	component = args[1]
[515]	244	if self.fitfunc is None:
[723]	245	msg = "Please specify a fitting function first."
	246	if rcParams['verbose']:
[1819]	247	#print msg
	248	asaplog.push(msg)
	249	print_log('ERROR')
[723]	250	return
	251	else:
	252	raise RuntimeError(msg)
[1819]	253	if (self.fitfunc == "gauss" or self.fitfunc == 'lorentz') and component is not None:
[1017]	254	if not self.fitted and sum(self.fitter.getparameters()) == 0:
[1295]	255	pars = _n_bools(len(self.components)*3, False)
	256	fxd = _n_bools(len(pars), False)
[515]	257	else:
[723]	258	pars = list(self.fitter.getparameters())
[515]	259	fxd = list(self.fitter.getfixedparameters())
	260	i = 3*component
	261	pars[i:i+3] = params
	262	fxd[i:i+3] = fixed
	263	params = pars
[723]	264	fixed = fxd
[113]	265	self.fitter.setparameters(params)
	266	if fixed is not None:
	267	self.fitter.setfixedparameters(fixed)
[1819]	268	print_log()
[113]	269	return
[515]	270
[1217]	271	def set_gauss_parameters(self, peak, centre, fwhm,
[1409]	272	peakfixed=0, centrefixed=0,
[1217]	273	fwhmfixed=0,
[515]	274	component=0):
[113]	275	"""
[515]	276	Set the Parameters of a 'Gaussian' component, set with set_function.
	277	Parameters:
[1232]	278	peak, centre, fwhm: The gaussian parameters
[515]	279	peakfixed,
[1409]	280	centrefixed,
[1217]	281	fwhmfixed: Optional parameters to indicate if
[515]	282	the paramters should be held fixed during
	283	the fitting process. The default is to keep
	284	all parameters flexible.
[526]	285	component: The number of the component (Default is the
	286	component 0)
[515]	287	"""
	288	if self.fitfunc != "gauss":
[723]	289	msg = "Function only operates on Gaussian components."
	290	if rcParams['verbose']:
[1819]	291	#print msg
	292	asaplog.push(msg)
	293	print_log('ERROR')
[723]	294	return
	295	else:
	296	raise ValueError(msg)
[515]	297	if 0 <= component < len(self.components):
[1217]	298	d = {'params':[peak, centre, fwhm],
[1409]	299	'fixed':[peakfixed, centrefixed, fwhmfixed]}
[1017]	300	self.set_parameters(d, component)
[515]	301	else:
[723]	302	msg = "Please select a valid component."
	303	if rcParams['verbose']:
[1819]	304	#print msg
	305	asaplog.push(msg)
	306	print_log('ERROR')
[723]	307	return
	308	else:
	309	raise ValueError(msg)
	310
[1819]	311	def set_lorentz_parameters(self, peak, centre, fwhm,
	312	peakfixed=0, centrefixed=0,
	313	fwhmfixed=0,
	314	component=0):
	315	"""
	316	Set the Parameters of a 'Lorentzian' component, set with set_function.
	317	Parameters:
	318	peak, centre, fwhm: The gaussian parameters
	319	peakfixed,
	320	centrefixed,
	321	fwhmfixed: Optional parameters to indicate if
	322	the paramters should be held fixed during
	323	the fitting process. The default is to keep
	324	all parameters flexible.
	325	component: The number of the component (Default is the
	326	component 0)
	327	"""
	328	if self.fitfunc != "lorentz":
	329	msg = "Function only operates on Lorentzian components."
	330	if rcParams['verbose']:
	331	#print msg
	332	asaplog.push(msg)
	333	print_log('ERROR')
	334	return
	335	else:
	336	raise ValueError(msg)
	337	if 0 <= component < len(self.components):
	338	d = {'params':[peak, centre, fwhm],
	339	'fixed':[peakfixed, centrefixed, fwhmfixed]}
	340	self.set_parameters(d, component)
	341	else:
	342	msg = "Please select a valid component."
	343	if rcParams['verbose']:
	344	#print msg
	345	asaplog.push(msg)
	346	print_log('ERROR')
	347	return
	348	else:
	349	raise ValueError(msg)
	350
[975]	351	def get_area(self, component=None):
	352	"""
[1819]	353	Return the area under the fitted gaussian/lorentzian component.
[975]	354	Parameters:
[1819]	355	component: the gaussian/lorentzian component selection,
[975]	356	default (None) is the sum of all components
	357	Note:
[1819]	358	This will only work for gaussian/lorentzian fits.
[975]	359	"""
	360	if not self.fitted: return
[1819]	361	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[975]	362	pars = list(self.fitter.getparameters())
	363	from math import log,pi,sqrt
[1819]	364	if self.fitfunc == "gauss":
	365	fac = sqrt(pi/log(16.0))
	366	elif self.fitfunc == "lorentz":
	367	fac = pi/2.0
[975]	368	areas = []
	369	for i in range(len(self.components)):
	370	j = i*3
	371	cpars = pars[j:j+3]
	372	areas.append(fac * cpars[0] * cpars[2])
	373	else:
	374	return None
	375	if component is not None:
	376	return areas[component]
	377	else:
	378	return sum(areas)
	379
[1075]	380	def get_errors(self, component=None):
[515]	381	"""
[1075]	382	Return the errors in the parameters.
	383	Parameters:
	384	component: get the errors for the specified component
	385	only, default is all components
	386	"""
	387	if not self.fitted:
	388	msg = "Not yet fitted."
	389	if rcParams['verbose']:
[1819]	390	#print msg
	391	asaplog.push(msg)
	392	print_log('ERROR')
[1075]	393	return
	394	else:
	395	raise RuntimeError(msg)
	396	errs = list(self.fitter.geterrors())
	397	cerrs = errs
	398	if component is not None:
[1819]	399	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[1075]	400	i = 3*component
	401	if i < len(errs):
	402	cerrs = errs[i:i+3]
	403	return cerrs
	404
	405	def get_parameters(self, component=None, errors=False):
	406	"""
[113]	407	Return the fit paramters.
[526]	408	Parameters:
	409	component: get the parameters for the specified component
	410	only, default is all components
[113]	411	"""
	412	if not self.fitted:
[723]	413	msg = "Not yet fitted."
	414	if rcParams['verbose']:
[1819]	415	#print msg
	416	asaplog.push(msg)
	417	print_log('ERROR')
[723]	418	return
	419	else:
	420	raise RuntimeError(msg)
[113]	421	pars = list(self.fitter.getparameters())
	422	fixed = list(self.fitter.getfixedparameters())
[1075]	423	errs = list(self.fitter.geterrors())
[1039]	424	area = []
[723]	425	if component is not None:
[1819]	426	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[515]	427	i = 3*component
	428	cpars = pars[i:i+3]
	429	cfixed = fixed[i:i+3]
[1075]	430	cerrs = errs[i:i+3]
[1039]	431	a = self.get_area(component)
	432	area = [a for i in range(3)]
[515]	433	else:
	434	cpars = pars
[723]	435	cfixed = fixed
[1075]	436	cerrs = errs
[515]	437	else:
	438	cpars = pars
	439	cfixed = fixed
[1075]	440	cerrs = errs
[1819]	441	if self.fitfunc == "gauss" or self.fitfunc == "lorentz":
[1039]	442	for c in range(len(self.components)):
	443	a = self.get_area(c)
	444	area += [a for i in range(3)]
[1088]	445	fpars = self._format_pars(cpars, cfixed, errors and cerrs, area)
[723]	446	if rcParams['verbose']:
[1819]	447	#print fpars
	448	asaplog.push(fpars)
	449	print_log()
[1075]	450	return {'params':cpars, 'fixed':cfixed, 'formatted': fpars,
	451	'errors':cerrs}
[723]	452
[1075]	453	def _format_pars(self, pars, fixed, errors, area):
[113]	454	out = ''
	455	if self.fitfunc == 'poly':
	456	c = 0
[515]	457	for i in range(len(pars)):
	458	fix = ""
[1232]	459	if len(fixed) and fixed[i]: fix = "(fixed)"
[1088]	460	if errors :
	461	out += ' p%d%s= %3.6f (%1.6f),' % (c,fix,pars[i], errors[i])
	462	else:
	463	out += ' p%d%s= %3.6f,' % (c,fix,pars[i])
[113]	464	c+=1
[515]	465	out = out[:-1] # remove trailing ','
[1819]	466	elif self.fitfunc == 'gauss' or self.fitfunc == 'lorentz':
[113]	467	i = 0
	468	c = 0
[515]	469	aunit = ''
	470	ounit = ''
[113]	471	if self.data:
[515]	472	aunit = self.data.get_unit()
	473	ounit = self.data.get_fluxunit()
[113]	474	while i < len(pars):
[1039]	475	if len(area):
	476	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]	477	else:
	478	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]	479	c+=1
	480	i+=3
	481	return out
[723]	482
[113]	483	def get_estimate(self):
	484	"""
[515]	485	Return the parameter estimates (for non-linear functions).
[113]	486	"""
	487	pars = self.fitter.getestimate()
[943]	488	fixed = self.fitter.getfixedparameters()
[723]	489	if rcParams['verbose']:
[1819]	490	#print self._format_pars(pars,fixed,None)
	491	asaplog.push(self._format_pars(pars,fixed,None))
	492	print_log()
[113]	493	return pars
	494
	495	def get_residual(self):
	496	"""
	497	Return the residual of the fit.
	498	"""
	499	if not self.fitted:
[723]	500	msg = "Not yet fitted."
	501	if rcParams['verbose']:
[1819]	502	#print msg
	503	asaplog.push(msg)
	504	print_log('ERROR')
[723]	505	return
	506	else:
	507	raise RuntimeError(msg)
[113]	508	return self.fitter.getresidual()
	509
	510	def get_chi2(self):
	511	"""
	512	Return chi^2.
	513	"""
	514	if not self.fitted:
[723]	515	msg = "Not yet fitted."
	516	if rcParams['verbose']:
[1819]	517	#print msg
	518	asaplog.push(msg)
	519	print_log('ERROR')
[723]	520	return
	521	else:
	522	raise RuntimeError(msg)
[113]	523	ch2 = self.fitter.getchi2()
[723]	524	if rcParams['verbose']:
[1819]	525	#print 'Chi^2 = %3.3f' % (ch2)
	526	asaplog.push( 'Chi^2 = %3.3f' % (ch2) )
	527	print_log()
[723]	528	return ch2
[113]	529
	530	def get_fit(self):
	531	"""
	532	Return the fitted ordinate values.
	533	"""
	534	if not self.fitted:
[723]	535	msg = "Not yet fitted."
	536	if rcParams['verbose']:
[1819]	537	#print msg
	538	asaplog.push(msg)
	539	print_log('ERROR')
[723]	540	return
	541	else:
	542	raise RuntimeError(msg)
[113]	543	return self.fitter.getfit()
	544
[1589]	545	@print_log_dec
[113]	546	def commit(self):
	547	"""
[526]	548	Return a new scan where the fits have been commited (subtracted)
[113]	549	"""
	550	if not self.fitted:
[723]	551	msg = "Not yet fitted."
	552	if rcParams['verbose']:
[1819]	553	#print msg
	554	asaplog.push(msg)
	555	print_log('ERROR')
[723]	556	return
	557	else:
	558	raise RuntimeError(msg)
[975]	559	from asap import scantable
	560	if not isinstance(self.data, scantable):
[723]	561	msg = "Not a scantable"
	562	if rcParams['verbose']:
[1819]	563	#print msg
	564	asaplog.push(msg)
	565	print_log('ERROR')
[723]	566	return
	567	else:
	568	raise TypeError(msg)
[113]	569	scan = self.data.copy()
[259]	570	scan._setspectrum(self.fitter.getresidual())
[1819]	571	print_log()
[1092]	572	return scan
[113]	573
[1589]	574	@print_log_dec
[1689]	575	def plot(self, residual=False, components=None, plotparms=False,
	576	filename=None):
[113]	577	"""
	578	Plot the last fit.
	579	Parameters:
	580	residual: an optional parameter indicating if the residual
	581	should be plotted (default 'False')
[526]	582	components: a list of components to plot, e.g [0,1],
	583	-1 plots the total fit. Default is to only
	584	plot the total fit.
	585	plotparms: Inidicates if the parameter values should be present
	586	on the plot
[113]	587	"""
	588	if not self.fitted:
	589	return
[723]	590	if not self._p or self._p.is_dead:
	591	if rcParams['plotter.gui']:
	592	from asap.asaplotgui import asaplotgui as asaplot
	593	else:
	594	from asap.asaplot import asaplot
	595	self._p = asaplot()
	596	self._p.hold()
[113]	597	self._p.clear()
[515]	598	self._p.set_panels()
[652]	599	self._p.palette(0)
[113]	600	tlab = 'Spectrum'
[723]	601	xlab = 'Abcissa'
[1017]	602	ylab = 'Ordinate'
[1739]	603	from numpy import ma,logical_not,logical_and,array
[1273]	604	m = self.mask
[113]	605	if self.data:
[515]	606	tlab = self.data._getsourcename(self._fittedrow)
	607	xlab = self.data._getabcissalabel(self._fittedrow)
[1273]	608	m = logical_and(self.mask,
[1306]	609	array(self.data._getmask(self._fittedrow),
	610	copy=False))
[1589]	611
[626]	612	ylab = self.data._get_ordinate_label()
[515]	613
[1075]	614	colours = ["#777777","#dddddd","red","orange","purple","green","magenta", "cyan"]
[1819]	615	nomask=True
	616	for i in range(len(m)):
	617	nomask = nomask and m[i]
	618	label0='Masked Region'
	619	label1='Spectrum'
	620	if ( nomask ):
	621	label0=label1
	622	else:
	623	y = ma.masked_array( self.y, mask = m )
	624	self._p.palette(1,colours)
	625	self._p.set_line( label = label1 )
	626	self._p.plot( self.x, y )
[652]	627	self._p.palette(0,colours)
[1819]	628	self._p.set_line(label=label0)
[1273]	629	y = ma.masked_array(self.y,mask=logical_not(m))
[1088]	630	self._p.plot(self.x, y)
[113]	631	if residual:
[1819]	632	self._p.palette(7)
[515]	633	self._p.set_line(label='Residual')
[1116]	634	y = ma.masked_array(self.get_residual(),
[1273]	635	mask=logical_not(m))
[1088]	636	self._p.plot(self.x, y)
[652]	637	self._p.palette(2)
[515]	638	if components is not None:
	639	cs = components
	640	if isinstance(components,int): cs = [components]
[526]	641	if plotparms:
[1031]	642	self._p.text(0.15,0.15,str(self.get_parameters()['formatted']),size=8)
[515]	643	n = len(self.components)
[652]	644	self._p.palette(3)
[515]	645	for c in cs:
	646	if 0 <= c < n:
	647	lab = self.fitfuncs[c]+str(c)
	648	self._p.set_line(label=lab)
[1116]	649	y = ma.masked_array(self.fitter.evaluate(c),
[1273]	650	mask=logical_not(m))
[1088]	651
	652	self._p.plot(self.x, y)
[515]	653	elif c == -1:
[652]	654	self._p.palette(2)
[515]	655	self._p.set_line(label="Total Fit")
[1116]	656	y = ma.masked_array(self.fitter.getfit(),
[1273]	657	mask=logical_not(m))
[1088]	658	self._p.plot(self.x, y)
[515]	659	else:
[652]	660	self._p.palette(2)
[515]	661	self._p.set_line(label='Fit')
[1116]	662	y = ma.masked_array(self.fitter.getfit(),
[1273]	663	mask=logical_not(m))
[1088]	664	self._p.plot(self.x, y)
[723]	665	xlim=[min(self.x),max(self.x)]
	666	self._p.axes.set_xlim(xlim)
[113]	667	self._p.set_axes('xlabel',xlab)
	668	self._p.set_axes('ylabel',ylab)
	669	self._p.set_axes('title',tlab)
	670	self._p.release()
[723]	671	if (not rcParams['plotter.gui']):
	672	self._p.save(filename)
[1819]	673	print_log()
[113]	674
[1589]	675	@print_log_dec
[1061]	676	def auto_fit(self, insitu=None, plot=False):
[113]	677	"""
[515]	678	Return a scan where the function is applied to all rows for
	679	all Beams/IFs/Pols.
[723]	680
[113]	681	"""
	682	from asap import scantable
[515]	683	if not isinstance(self.data, scantable) :
[723]	684	msg = "Data is not a scantable"
	685	if rcParams['verbose']:
[1819]	686	#print msg
	687	asaplog.push(msg)
	688	print_log('ERROR')
[723]	689	return
	690	else:
	691	raise TypeError(msg)
[259]	692	if insitu is None: insitu = rcParams['insitu']
	693	if not insitu:
	694	scan = self.data.copy()
	695	else:
	696	scan = self.data
[880]	697	rows = xrange(scan.nrow())
[1826]	698	# Save parameters of baseline fits as a class attribute.
[1819]	699	# NOTICE: This does not reflect changes in scantable!
	700	if len(rows) > 0: self.blpars=[]
[876]	701	asaplog.push("Fitting:")
	702	for r in rows:
[1536]	703	out = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (scan.getscan(r),
	704	scan.getbeam(r),
	705	scan.getif(r),
[1589]	706	scan.getpol(r),
[1536]	707	scan.getcycle(r))
[880]	708	asaplog.push(out, False)
[876]	709	self.x = scan._getabcissa(r)
	710	self.y = scan._getspectrum(r)
[1536]	711	self.mask = mask_and(self.mask, scan._getmask(r))
[876]	712	self.data = None
	713	self.fit()
	714	x = self.get_parameters()
[1819]	715	fpar = self.get_parameters()
[1061]	716	if plot:
	717	self.plot(residual=True)
	718	x = raw_input("Accept fit ([y]/n): ")
	719	if x.upper() == 'N':
[1819]	720	self.blpars.append(None)
[1061]	721	continue
[880]	722	scan._setspectrum(self.fitter.getresidual(), r)
[1819]	723	self.blpars.append(fpar)
[1061]	724	if plot:
	725	self._p.unmap()
	726	self._p = None
[1819]	727	print_log()
[876]	728	return scan

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