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source: trunk/python/asapfitter.py @ 943

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Last change on this file since 943 was 943, checked in by mar637, 18 years ago
fixed a couple of variable mix ups
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 15.5 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())
	159	self.data._addfit(self._fittedrow, pars, fixed,
	160	self.fitfuncs, self.components)
	161
	162	def set_parameters(self, params, fixed=None, component=None):
[526]	163	"""
	164	Set the parameters to be fitted.
	165	Parameters:
	166	params: a vector of parameters
	167	fixed: a vector of which parameters are to be held fixed
	168	(default is none)
	169	component: in case of multiple gaussians, the index of the
	170	component
	171	"""
[515]	172	if self.fitfunc is None:
[723]	173	msg = "Please specify a fitting function first."
	174	if rcParams['verbose']:
	175	print msg
	176	return
	177	else:
	178	raise RuntimeError(msg)
[515]	179	if self.fitfunc == "gauss" and component is not None:
	180	if not self.fitted:
	181	from numarray import zeros
	182	pars = list(zeros(len(self.components)*3))
	183	fxd = list(zeros(len(pars)))
	184	else:
[723]	185	pars = list(self.fitter.getparameters())
[515]	186	fxd = list(self.fitter.getfixedparameters())
	187	i = 3*component
	188	pars[i:i+3] = params
	189	fxd[i:i+3] = fixed
	190	params = pars
[723]	191	fixed = fxd
[113]	192	self.fitter.setparameters(params)
	193	if fixed is not None:
	194	self.fitter.setfixedparameters(fixed)
[723]	195	print_log()
[113]	196	return
[515]	197
	198	def set_gauss_parameters(self, peak, centre, fhwm,
	199	peakfixed=False, centerfixed=False,
	200	fhwmfixed=False,
	201	component=0):
[113]	202	"""
[515]	203	Set the Parameters of a 'Gaussian' component, set with set_function.
	204	Parameters:
	205	peak, centre, fhwm: The gaussian parameters
	206	peakfixed,
	207	centerfixed,
	208	fhwmfixed: Optional parameters to indicate if
	209	the paramters should be held fixed during
	210	the fitting process. The default is to keep
	211	all parameters flexible.
[526]	212	component: The number of the component (Default is the
	213	component 0)
[515]	214	"""
	215	if self.fitfunc != "gauss":
[723]	216	msg = "Function only operates on Gaussian components."
	217	if rcParams['verbose']:
	218	print msg
	219	return
	220	else:
	221	raise ValueError(msg)
[515]	222	if 0 <= component < len(self.components):
	223	self.set_parameters([peak, centre, fhwm],
	224	[peakfixed, centerfixed, fhwmfixed],
	225	component)
	226	else:
[723]	227	msg = "Please select a valid component."
	228	if rcParams['verbose']:
	229	print msg
	230	return
	231	else:
	232	raise ValueError(msg)
	233
[515]	234	def get_parameters(self, component=None):
	235	"""
[113]	236	Return the fit paramters.
[526]	237	Parameters:
	238	component: get the parameters for the specified component
	239	only, default is all components
[113]	240	"""
	241	if not self.fitted:
[723]	242	msg = "Not yet fitted."
	243	if rcParams['verbose']:
	244	print msg
	245	return
	246	else:
	247	raise RuntimeError(msg)
[113]	248	pars = list(self.fitter.getparameters())
	249	fixed = list(self.fitter.getfixedparameters())
[723]	250	if component is not None:
[515]	251	if self.fitfunc == "gauss":
	252	i = 3*component
	253	cpars = pars[i:i+3]
	254	cfixed = fixed[i:i+3]
	255	else:
	256	cpars = pars
[723]	257	cfixed = fixed
[515]	258	else:
	259	cpars = pars
	260	cfixed = fixed
	261	fpars = self._format_pars(cpars, cfixed)
[723]	262	if rcParams['verbose']:
[515]	263	print fpars
	264	return cpars, cfixed, fpars
[723]	265
[515]	266	def _format_pars(self, pars, fixed):
[113]	267	out = ''
	268	if self.fitfunc == 'poly':
	269	c = 0
[515]	270	for i in range(len(pars)):
	271	fix = ""
	272	if fixed[i]: fix = "(fixed)"
	273	out += ' p%d%s= %3.3f,' % (c,fix,pars[i])
[113]	274	c+=1
[515]	275	out = out[:-1] # remove trailing ','
[113]	276	elif self.fitfunc == 'gauss':
	277	i = 0
	278	c = 0
[515]	279	aunit = ''
	280	ounit = ''
[113]	281	if self.data:
[515]	282	aunit = self.data.get_unit()
	283	ounit = self.data.get_fluxunit()
[113]	284	while i < len(pars):
[515]	285	out += ' %d: 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)
[113]	286	c+=1
	287	i+=3
	288	return out
[723]	289
[113]	290	def get_estimate(self):
	291	"""
[515]	292	Return the parameter estimates (for non-linear functions).
[113]	293	"""
	294	pars = self.fitter.getestimate()
[943]	295	fixed = self.fitter.getfixedparameters()
[723]	296	if rcParams['verbose']:
[943]	297	print self._format_pars(pars,fixed)
[113]	298	return pars
	299
	300	def get_residual(self):
	301	"""
	302	Return the residual of the fit.
	303	"""
	304	if not self.fitted:
[723]	305	msg = "Not yet fitted."
	306	if rcParams['verbose']:
	307	print msg
	308	return
	309	else:
	310	raise RuntimeError(msg)
[113]	311	return self.fitter.getresidual()
	312
	313	def get_chi2(self):
	314	"""
	315	Return chi^2.
	316	"""
	317	if not self.fitted:
[723]	318	msg = "Not yet fitted."
	319	if rcParams['verbose']:
	320	print msg
	321	return
	322	else:
	323	raise RuntimeError(msg)
[113]	324	ch2 = self.fitter.getchi2()
[723]	325	if rcParams['verbose']:
[113]	326	print 'Chi^2 = %3.3f' % (ch2)
[723]	327	return ch2
[113]	328
	329	def get_fit(self):
	330	"""
	331	Return the fitted ordinate values.
	332	"""
	333	if not self.fitted:
[723]	334	msg = "Not yet fitted."
	335	if rcParams['verbose']:
	336	print msg
	337	return
	338	else:
	339	raise RuntimeError(msg)
[113]	340	return self.fitter.getfit()
	341
	342	def commit(self):
	343	"""
[526]	344	Return a new scan where the fits have been commited (subtracted)
[113]	345	"""
	346	if not self.fitted:
	347	print "Not yet fitted."
[723]	348	msg = "Not yet fitted."
	349	if rcParams['verbose']:
	350	print msg
	351	return
	352	else:
	353	raise RuntimeError(msg)
[113]	354	if self.data is not scantable:
[723]	355	msg = "Not a scantable"
	356	if rcParams['verbose']:
	357	print msg
	358	return
	359	else:
	360	raise TypeError(msg)
[113]	361	scan = self.data.copy()
[259]	362	scan._setspectrum(self.fitter.getresidual())
[723]	363	print_log()
[113]	364
[723]	365	def plot(self, residual=False, components=None, plotparms=False, filename=None):
[113]	366	"""
	367	Plot the last fit.
	368	Parameters:
	369	residual: an optional parameter indicating if the residual
	370	should be plotted (default 'False')
[526]	371	components: a list of components to plot, e.g [0,1],
	372	-1 plots the total fit. Default is to only
	373	plot the total fit.
	374	plotparms: Inidicates if the parameter values should be present
	375	on the plot
[113]	376	"""
	377	if not self.fitted:
	378	return
[723]	379	if not self._p or self._p.is_dead:
	380	if rcParams['plotter.gui']:
	381	from asap.asaplotgui import asaplotgui as asaplot
	382	else:
	383	from asap.asaplot import asaplot
	384	self._p = asaplot()
	385	self._p.hold()
[113]	386	self._p.clear()
[515]	387	self._p.set_panels()
[652]	388	self._p.palette(0)
[113]	389	tlab = 'Spectrum'
[723]	390	xlab = 'Abcissa'
[515]	391	m = ()
[113]	392	if self.data:
[515]	393	tlab = self.data._getsourcename(self._fittedrow)
	394	xlab = self.data._getabcissalabel(self._fittedrow)
	395	m = self.data._getmask(self._fittedrow)
[626]	396	ylab = self.data._get_ordinate_label()
[515]	397
[668]	398	colours = ["#777777","#bbbbbb","red","orange","purple","green","magenta", "cyan"]
[652]	399	self._p.palette(0,colours)
[515]	400	self._p.set_line(label='Spectrum')
[113]	401	self._p.plot(self.x, self.y, m)
	402	if residual:
[652]	403	self._p.palette(1)
[515]	404	self._p.set_line(label='Residual')
[113]	405	self._p.plot(self.x, self.get_residual(), m)
[652]	406	self._p.palette(2)
[515]	407	if components is not None:
	408	cs = components
	409	if isinstance(components,int): cs = [components]
[526]	410	if plotparms:
	411	self._p.text(0.15,0.15,str(self.get_parameters()[2]),size=8)
[515]	412	n = len(self.components)
[652]	413	self._p.palette(3)
[515]	414	for c in cs:
	415	if 0 <= c < n:
	416	lab = self.fitfuncs[c]+str(c)
	417	self._p.set_line(label=lab)
	418	self._p.plot(self.x, self.fitter.evaluate(c), m)
	419	elif c == -1:
[652]	420	self._p.palette(2)
[515]	421	self._p.set_line(label="Total Fit")
[723]	422	self._p.plot(self.x, self.get_fit(), m)
[515]	423	else:
[652]	424	self._p.palette(2)
[515]	425	self._p.set_line(label='Fit')
	426	self._p.plot(self.x, self.get_fit(), m)
[723]	427	xlim=[min(self.x),max(self.x)]
	428	self._p.axes.set_xlim(xlim)
[113]	429	self._p.set_axes('xlabel',xlab)
	430	self._p.set_axes('ylabel',ylab)
	431	self._p.set_axes('title',tlab)
	432	self._p.release()
[723]	433	if (not rcParams['plotter.gui']):
	434	self._p.save(filename)
	435	print_log()
[113]	436
[876]	437	def auto_fit(self, insitu=None):
[113]	438	"""
[515]	439	Return a scan where the function is applied to all rows for
	440	all Beams/IFs/Pols.
[723]	441
[113]	442	"""
	443	from asap import scantable
[515]	444	if not isinstance(self.data, scantable) :
[723]	445	msg = "Data is not a scantable"
	446	if rcParams['verbose']:
	447	print msg
	448	return
	449	else:
	450	raise TypeError(msg)
[259]	451	if insitu is None: insitu = rcParams['insitu']
	452	if not insitu:
	453	scan = self.data.copy()
	454	else:
	455	scan = self.data
[880]	456	rows = xrange(scan.nrow())
[723]	457	from asap import asaplog
[876]	458	asaplog.push("Fitting:")
	459	for r in rows:
[880]	460	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))
	461	asaplog.push(out, False)
[876]	462	self.x = scan._getabcissa(r)
	463	self.y = scan._getspectrum(r)
	464	self.data = None
	465	self.fit()
	466	x = self.get_parameters()
[880]	467	scan._setspectrum(self.fitter.getresidual(), r)
[876]	468	print_log()
	469	return scan
[794]	470

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