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source: trunk/python/asapfitter.py@ 1028

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Last change on this file since 1028 was 1017, checked in by mar637, 19 years ago
Fix for ticket #21 - get_parameters/set_parameters inconsistent. Reworked the interface to allow this.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 17.4 KB

Rev	Line
[113]	1	import _asap
[259]	2	from asap import rcParams
[723]	3	from asap import print_log
[113]	4
	5	class fitter:
	6	"""
	7	The fitting class for ASAP.
	8	"""
[723]	9
[113]	10	def __init__(self):
	11	"""
	12	Create a fitter object. No state is set.
	13	"""
	14	self.fitter = _asap.fitter()
	15	self.x = None
	16	self.y = None
	17	self.mask = None
	18	self.fitfunc = None
[515]	19	self.fitfuncs = None
[113]	20	self.fitted = False
	21	self.data = None
[515]	22	self.components = 0
	23	self._fittedrow = 0
[113]	24	self._p = None
[515]	25	self._selection = None
[113]	26
	27	def set_data(self, xdat, ydat, mask=None):
	28	"""
[158]	29	Set the absissa and ordinate for the fit. Also set the mask
[113]	30	indicationg valid points.
	31	This can be used for data vectors retrieved from a scantable.
	32	For scantable fitting use 'fitter.set_scan(scan, mask)'.
	33	Parameters:
[158]	34	xdat: the abcissa values
[113]	35	ydat: the ordinate values
	36	mask: an optional mask
[723]	37
[113]	38	"""
	39	self.fitted = False
	40	self.x = xdat
	41	self.y = ydat
	42	if mask == None:
	43	from numarray import ones
	44	self.mask = ones(len(xdat))
	45	else:
	46	self.mask = mask
	47	return
	48
	49	def set_scan(self, thescan=None, mask=None):
	50	"""
	51	Set the 'data' (a scantable) of the fitter.
	52	Parameters:
	53	thescan: a scantable
	54	mask: a msk retireved from the scantable
	55	"""
	56	if not thescan:
[723]	57	msg = "Please give a correct scan"
	58	if rcParams['verbose']:
	59	print msg
	60	return
	61	else:
	62	raise TypeError(msg)
[113]	63	self.fitted = False
	64	self.data = thescan
	65	if mask is None:
	66	from numarray import ones
	67	self.mask = ones(self.data.nchan())
	68	else:
	69	self.mask = mask
	70	return
	71
	72	def set_function(self, **kwargs):
	73	"""
	74	Set the function to be fit.
	75	Parameters:
	76	poly: use a polynomial of the order given
	77	gauss: fit the number of gaussian specified
	78	Example:
	79	fitter.set_function(gauss=2) # will fit two gaussians
	80	fitter.set_function(poly=3) # will fit a 3rd order polynomial
	81	"""
[723]	82	#default poly order 0
[515]	83	n=0
[113]	84	if kwargs.has_key('poly'):
	85	self.fitfunc = 'poly'
	86	n = kwargs.get('poly')
[515]	87	self.components = [n]
[113]	88	elif kwargs.has_key('gauss'):
	89	n = kwargs.get('gauss')
	90	self.fitfunc = 'gauss'
[515]	91	self.fitfuncs = [ 'gauss' for i in range(n) ]
	92	self.components = [ 3 for i in range(n) ]
	93	else:
[723]	94	msg = "Invalid function type."
	95	if rcParams['verbose']:
	96	print msg
	97	return
	98	else:
	99	raise TypeError(msg)
	100
[113]	101	self.fitter.setexpression(self.fitfunc,n)
	102	return
[723]	103
[515]	104	def fit(self, row=0):
[113]	105	"""
	106	Execute the actual fitting process. All the state has to be set.
	107	Parameters:
[526]	108	row: specify the row in the scantable
[113]	109	Example:
[515]	110	s = scantable('myscan.asap')
	111	s.set_cursor(thepol=1) # select second pol
[113]	112	f = fitter()
	113	f.set_scan(s)
	114	f.set_function(poly=0)
[723]	115	f.fit(row=0) # fit first row
[113]	116	"""
	117	if ((self.x is None or self.y is None) and self.data is None) \
	118	or self.fitfunc is None:
[723]	119	msg = "Fitter not yet initialised. Please set data & fit function"
	120	if rcParams['verbose']:
	121	print msg
	122	return
	123	else:
	124	raise RuntimeError(msg)
	125
[113]	126	else:
	127	if self.data is not None:
[515]	128	self.x = self.data._getabcissa(row)
	129	self.y = self.data._getspectrum(row)
[723]	130	from asap import asaplog
	131	asaplog.push("Fitting:")
[943]	132	i = row
	133	out = "Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (self.data.getscan(i),self.data.getbeam(i),self.data.getif(i),self.data.getpol(i), self.data.getcycle(i))
[876]	134	asaplog.push(out)
[515]	135	self.fitter.setdata(self.x, self.y, self.mask)
[113]	136	if self.fitfunc == 'gauss':
	137	ps = self.fitter.getparameters()
	138	if len(ps) == 0:
	139	self.fitter.estimate()
[626]	140	try:
	141	self.fitter.fit()
	142	except RuntimeError, msg:
[723]	143	if rcParams['verbose']:
	144	print msg
	145	else:
	146	raise
[515]	147	self._fittedrow = row
[113]	148	self.fitted = True
[723]	149	print_log()
[113]	150	return
	151
[515]	152	def store_fit(self):
[526]	153	"""
	154	Store the fit parameters in the scantable.
	155	"""
[515]	156	if self.fitted and self.data is not None:
	157	pars = list(self.fitter.getparameters())
	158	fixed = list(self.fitter.getfixedparameters())
[975]	159	from asap.asapfit import asapfit
	160	fit = asapfit()
	161	fit.setparameters(pars)
	162	fit.setfixedparameters(fixed)
	163	fit.setfunctions(self.fitfuncs)
	164	fit.setcomponents(self.components)
	165	fit.setframeinfo(self.data._getcoordinfo())
	166	self.data._addfit(fit,self._fittedrow)
[515]	167
[1017]	168	#def set_parameters(self, params, fixed=None, component=None):
	169	def set_parameters(self,args,*kwargs):
[526]	170	"""
	171	Set the parameters to be fitted.
	172	Parameters:
	173	params: a vector of parameters
	174	fixed: a vector of which parameters are to be held fixed
	175	(default is none)
	176	component: in case of multiple gaussians, the index of the
	177	component
[1017]	178	"""
	179	component = None
	180	fixed = None
	181	params = None
	182
	183	if len(args) and isinstance(args[0],dict):
	184	kwargs = args[0]
	185	if kwargs.has_key("fixed"): fixed = kwargs["fixed"]
	186	if kwargs.has_key("params"): params = kwargs["params"]
	187	if len(args) == 2 and isinstance(args[1], int):
	188	component = args[1]
[515]	189	if self.fitfunc is None:
[723]	190	msg = "Please specify a fitting function first."
	191	if rcParams['verbose']:
	192	print msg
	193	return
	194	else:
	195	raise RuntimeError(msg)
[515]	196	if self.fitfunc == "gauss" and component is not None:
[1017]	197	if not self.fitted and sum(self.fitter.getparameters()) == 0:
[515]	198	from numarray import zeros
	199	pars = list(zeros(len(self.components)*3))
	200	fxd = list(zeros(len(pars)))
	201	else:
[723]	202	pars = list(self.fitter.getparameters())
[515]	203	fxd = list(self.fitter.getfixedparameters())
	204	i = 3*component
	205	pars[i:i+3] = params
	206	fxd[i:i+3] = fixed
	207	params = pars
[723]	208	fixed = fxd
[113]	209	self.fitter.setparameters(params)
	210	if fixed is not None:
	211	self.fitter.setfixedparameters(fixed)
[723]	212	print_log()
[113]	213	return
[515]	214
	215	def set_gauss_parameters(self, peak, centre, fhwm,
[1017]	216	peakfixed=0, centerfixed=0,
	217	fhwmfixed=0,
[515]	218	component=0):
[113]	219	"""
[515]	220	Set the Parameters of a 'Gaussian' component, set with set_function.
	221	Parameters:
	222	peak, centre, fhwm: The gaussian parameters
	223	peakfixed,
	224	centerfixed,
	225	fhwmfixed: Optional parameters to indicate if
	226	the paramters should be held fixed during
	227	the fitting process. The default is to keep
	228	all parameters flexible.
[526]	229	component: The number of the component (Default is the
	230	component 0)
[515]	231	"""
	232	if self.fitfunc != "gauss":
[723]	233	msg = "Function only operates on Gaussian components."
	234	if rcParams['verbose']:
	235	print msg
	236	return
	237	else:
	238	raise ValueError(msg)
[515]	239	if 0 <= component < len(self.components):
[1017]	240	d = {'params':[peak, centre, fhwm],
	241	'fixed':[peakfixed, centerfixed, fhwmfixed]}
	242	self.set_parameters(d, component)
[515]	243	else:
[723]	244	msg = "Please select a valid component."
	245	if rcParams['verbose']:
	246	print msg
	247	return
	248	else:
	249	raise ValueError(msg)
	250
[975]	251	def get_area(self, component=None):
	252	"""
	253	Return the area under the fitted gaussian component.
	254	Parameters:
	255	component: the gaussian component selection,
	256	default (None) is the sum of all components
	257	Note:
	258	This will only work for gaussian fits.
	259	"""
	260	if not self.fitted: return
	261	if self.fitfunc == "gauss":
	262	pars = list(self.fitter.getparameters())
	263	from math import log,pi,sqrt
	264	fac = sqrt(pi/log(16.0))
	265	areas = []
	266	for i in range(len(self.components)):
	267	j = i*3
	268	cpars = pars[j:j+3]
	269	areas.append(fac * cpars[0] * cpars[2])
	270	else:
	271	return None
	272	if component is not None:
	273	return areas[component]
	274	else:
	275	return sum(areas)
	276
[515]	277	def get_parameters(self, component=None):
	278	"""
[113]	279	Return the fit paramters.
[526]	280	Parameters:
	281	component: get the parameters for the specified component
	282	only, default is all components
[113]	283	"""
	284	if not self.fitted:
[723]	285	msg = "Not yet fitted."
	286	if rcParams['verbose']:
	287	print msg
	288	return
	289	else:
	290	raise RuntimeError(msg)
[113]	291	pars = list(self.fitter.getparameters())
	292	fixed = list(self.fitter.getfixedparameters())
[723]	293	if component is not None:
[515]	294	if self.fitfunc == "gauss":
	295	i = 3*component
	296	cpars = pars[i:i+3]
	297	cfixed = fixed[i:i+3]
	298	else:
	299	cpars = pars
[723]	300	cfixed = fixed
[515]	301	else:
	302	cpars = pars
	303	cfixed = fixed
[975]	304	fpars = self._format_pars(cpars, cfixed, self.get_area(component))
[723]	305	if rcParams['verbose']:
[515]	306	print fpars
[1017]	307	return {'params':cpars, 'fixed':cfixed}
[723]	308
[975]	309	def _format_pars(self, pars, fixed, area):
[113]	310	out = ''
	311	if self.fitfunc == 'poly':
	312	c = 0
[515]	313	for i in range(len(pars)):
	314	fix = ""
	315	if fixed[i]: fix = "(fixed)"
	316	out += ' p%d%s= %3.3f,' % (c,fix,pars[i])
[113]	317	c+=1
[515]	318	out = out[:-1] # remove trailing ','
[113]	319	elif self.fitfunc == 'gauss':
	320	i = 0
	321	c = 0
[515]	322	aunit = ''
	323	ounit = ''
[113]	324	if self.data:
[515]	325	aunit = self.data.get_unit()
	326	ounit = self.data.get_fluxunit()
[113]	327	while i < len(pars):
[1017]	328	if area:
	329	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,ounit,aunit)
	330	else:
	331	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]	332	c+=1
	333	i+=3
	334	return out
[723]	335
[113]	336	def get_estimate(self):
	337	"""
[515]	338	Return the parameter estimates (for non-linear functions).
[113]	339	"""
	340	pars = self.fitter.getestimate()
[943]	341	fixed = self.fitter.getfixedparameters()
[723]	342	if rcParams['verbose']:
[1017]	343	print self._format_pars(pars,fixed,None)
[113]	344	return pars
	345
	346	def get_residual(self):
	347	"""
	348	Return the residual of the fit.
	349	"""
	350	if not self.fitted:
[723]	351	msg = "Not yet fitted."
	352	if rcParams['verbose']:
	353	print msg
	354	return
	355	else:
	356	raise RuntimeError(msg)
[113]	357	return self.fitter.getresidual()
	358
	359	def get_chi2(self):
	360	"""
	361	Return chi^2.
	362	"""
	363	if not self.fitted:
[723]	364	msg = "Not yet fitted."
	365	if rcParams['verbose']:
	366	print msg
	367	return
	368	else:
	369	raise RuntimeError(msg)
[113]	370	ch2 = self.fitter.getchi2()
[723]	371	if rcParams['verbose']:
[113]	372	print 'Chi^2 = %3.3f' % (ch2)
[723]	373	return ch2
[113]	374
	375	def get_fit(self):
	376	"""
	377	Return the fitted ordinate values.
	378	"""
	379	if not self.fitted:
[723]	380	msg = "Not yet fitted."
	381	if rcParams['verbose']:
	382	print msg
	383	return
	384	else:
	385	raise RuntimeError(msg)
[113]	386	return self.fitter.getfit()
	387
	388	def commit(self):
	389	"""
[526]	390	Return a new scan where the fits have been commited (subtracted)
[113]	391	"""
	392	if not self.fitted:
	393	print "Not yet fitted."
[723]	394	msg = "Not yet fitted."
	395	if rcParams['verbose']:
	396	print msg
	397	return
	398	else:
	399	raise RuntimeError(msg)
[975]	400	from asap import scantable
	401	if not isinstance(self.data, scantable):
[723]	402	msg = "Not a scantable"
	403	if rcParams['verbose']:
	404	print msg
	405	return
	406	else:
	407	raise TypeError(msg)
[113]	408	scan = self.data.copy()
[259]	409	scan._setspectrum(self.fitter.getresidual())
[723]	410	print_log()
[113]	411
[723]	412	def plot(self, residual=False, components=None, plotparms=False, filename=None):
[113]	413	"""
	414	Plot the last fit.
	415	Parameters:
	416	residual: an optional parameter indicating if the residual
	417	should be plotted (default 'False')
[526]	418	components: a list of components to plot, e.g [0,1],
	419	-1 plots the total fit. Default is to only
	420	plot the total fit.
	421	plotparms: Inidicates if the parameter values should be present
	422	on the plot
[113]	423	"""
	424	if not self.fitted:
	425	return
[723]	426	if not self._p or self._p.is_dead:
	427	if rcParams['plotter.gui']:
	428	from asap.asaplotgui import asaplotgui as asaplot
	429	else:
	430	from asap.asaplot import asaplot
	431	self._p = asaplot()
	432	self._p.hold()
[113]	433	self._p.clear()
[515]	434	self._p.set_panels()
[652]	435	self._p.palette(0)
[113]	436	tlab = 'Spectrum'
[723]	437	xlab = 'Abcissa'
[1017]	438	ylab = 'Ordinate'
	439	m = None
[113]	440	if self.data:
[515]	441	tlab = self.data._getsourcename(self._fittedrow)
	442	xlab = self.data._getabcissalabel(self._fittedrow)
	443	m = self.data._getmask(self._fittedrow)
[626]	444	ylab = self.data._get_ordinate_label()
[515]	445
[668]	446	colours = ["#777777","#bbbbbb","red","orange","purple","green","magenta", "cyan"]
[652]	447	self._p.palette(0,colours)
[515]	448	self._p.set_line(label='Spectrum')
[113]	449	self._p.plot(self.x, self.y, m)
	450	if residual:
[652]	451	self._p.palette(1)
[515]	452	self._p.set_line(label='Residual')
[113]	453	self._p.plot(self.x, self.get_residual(), m)
[652]	454	self._p.palette(2)
[515]	455	if components is not None:
	456	cs = components
	457	if isinstance(components,int): cs = [components]
[526]	458	if plotparms:
	459	self._p.text(0.15,0.15,str(self.get_parameters()[2]),size=8)
[515]	460	n = len(self.components)
[652]	461	self._p.palette(3)
[515]	462	for c in cs:
	463	if 0 <= c < n:
	464	lab = self.fitfuncs[c]+str(c)
	465	self._p.set_line(label=lab)
	466	self._p.plot(self.x, self.fitter.evaluate(c), m)
	467	elif c == -1:
[652]	468	self._p.palette(2)
[515]	469	self._p.set_line(label="Total Fit")
[723]	470	self._p.plot(self.x, self.get_fit(), m)
[515]	471	else:
[652]	472	self._p.palette(2)
[515]	473	self._p.set_line(label='Fit')
	474	self._p.plot(self.x, self.get_fit(), m)
[723]	475	xlim=[min(self.x),max(self.x)]
	476	self._p.axes.set_xlim(xlim)
[113]	477	self._p.set_axes('xlabel',xlab)
	478	self._p.set_axes('ylabel',ylab)
	479	self._p.set_axes('title',tlab)
	480	self._p.release()
[723]	481	if (not rcParams['plotter.gui']):
	482	self._p.save(filename)
	483	print_log()
[113]	484
[876]	485	def auto_fit(self, insitu=None):
[113]	486	"""
[515]	487	Return a scan where the function is applied to all rows for
	488	all Beams/IFs/Pols.
[723]	489
[113]	490	"""
	491	from asap import scantable
[515]	492	if not isinstance(self.data, scantable) :
[723]	493	msg = "Data is not a scantable"
	494	if rcParams['verbose']:
	495	print msg
	496	return
	497	else:
	498	raise TypeError(msg)
[259]	499	if insitu is None: insitu = rcParams['insitu']
	500	if not insitu:
	501	scan = self.data.copy()
	502	else:
	503	scan = self.data
[880]	504	rows = xrange(scan.nrow())
[723]	505	from asap import asaplog
[876]	506	asaplog.push("Fitting:")
	507	for r in rows:
[880]	508	out = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (scan.getscan(r),scan.getbeam(r),scan.getif(r),scan.getpol(r), scan.getcycle(r))
	509	asaplog.push(out, False)
[876]	510	self.x = scan._getabcissa(r)
	511	self.y = scan._getspectrum(r)
	512	self.data = None
	513	self.fit()
	514	x = self.get_parameters()
[880]	515	scan._setspectrum(self.fitter.getresidual(), r)
[876]	516	print_log()
	517	return scan
[794]	518

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