fitting.py @ 442895f

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 442895f was 442895f, checked in by Gervaise Alina <gervyh@…>, 16 years ago
models added
Property mode set to `100644`
File size: 22.6 KB

Rev	Line
[d89f09b]	1	import os,os.path, re
	2	import sys, wx, logging
	3	import string, numpy, pylab, math
	4
[3b19ac9]	5	from copy import deepcopy
[d89f09b]	6	from sans.guitools.plottables import Data1D, Theory1D
	7	from sans.guitools.PlotPanel import PlotPanel
	8	from sans.guicomm.events import NewPlotEvent, StatusEvent
[3b19ac9]	9	from sans.fit.AbstractFitEngine import Model,Data
[d89f09b]	10	from fitproblem import FitProblem
	11	from fitpanel import FitPanel
	12
	13	import models
	14	import fitpage
[dabb633]	15	import park
[442895f]	16	class PlottableDatas(Data,Data1D):
	17	""" class plottable data: class allowing to plot Data type on panel"""
	18
	19	def __init__(self,data=None,data1d=None):
	20	Data.__init__(self,sans_data=data1d)
	21	Data1D.__init__(self,x=data1d.x,y = data1d.y,dx = data1d.dx,dy = data1d.dy)
	22	#self.x = data1d.x
	23	#self.y = data1d.y
	24	#self.dx = data1d.dx
	25	#self.dy = data1d.dy
	26	#self.data=data
	27	self.group_id = data1d.group_id
	28	#x_name, x_units = data1d.get_xaxis()
	29	#y_name, y_units = data1d.get_yaxis()
	30	#self.xaxis( x_name, x_units)
	31	#self.yaxis( y_name, y_units )
	32	#self.qmin = data.qmin
	33	#self.qmax = data.qmax
	34
[3b19ac9]	35
[d89f09b]	36	class PlottableData(Data,Data1D):
[3b19ac9]	37	""" class plottable data: class allowing to plot Data type on panel"""
[442895f]	38
	39	def __init__(self,data=None,data1d=None):
	40	#Data.__init__(self,*args)
	41	#Data1D.__init__(self,**kw)
[d89f09b]	42	self.x = data1d.x
	43	self.y = data1d.y
[3b19ac9]	44	self.dx = data1d.dx
	45	self.dy = data1d.dy
[442895f]	46	self.data=data
[3b19ac9]	47	self.group_id = data1d.group_id
[d89f09b]	48	x_name, x_units = data1d.get_xaxis()
	49	y_name, y_units = data1d.get_yaxis()
	50	self.xaxis( x_name, x_units)
	51	self.yaxis( y_name, y_units )
[3b19ac9]	52	self.qmin = data.qmin
	53	self.qmax = data.qmax
[442895f]	54	def residuals(self, fn):
	55	return self.data.residuals(fn)
[3b19ac9]	56
[d89f09b]	57	class Plugin:
	58	"""
[dabb633]	59	Fitting plugin is used to perform fit
[d89f09b]	60	"""
	61	def __init__(self):
	62	## Plug-in name
	63	self.sub_menu = "Fitting"
	64
	65	## Reference to the parent window
	66	self.parent = None
	67	self.menu_mng = models.ModelManager()
	68	## List of panels for the simulation perspective (names)
	69	self.perspective = []
	70	# Start with a good default
	71	self.elapsed = 0.022
	72	self.fitter = None
	73
	74	#Flag to let the plug-in know that it is running standalone
	75	self.standalone=True
	76	## Fit engine
[3b19ac9]	77	self._fit_engine = 'scipy'
[d89f09b]	78	# Log startup
	79	logging.info("Fitting plug-in started")
	80
	81	def populate_menu(self, id, owner):
	82	"""
	83	Create a menu for the Fitting plug-in
	84	@param id: id to create a menu
	85	@param owner: owner of menu
	86	@ return : list of information to populate the main menu
	87	"""
	88	#Menu for fitting
	89	self.menu1 = wx.Menu()
	90	id1 = wx.NewId()
	91	self.menu1.Append(id1, '&Show fit panel')
	92	wx.EVT_MENU(owner, id1, self.on_perspective)
[3b19ac9]	93	id3 = wx.NewId()
[442895f]	94	self.menu1.AppendCheckItem(id3, "park")
[3b19ac9]	95	wx.EVT_MENU(owner, id3, self._onset_engine)
[d89f09b]	96
	97	#menu for model
	98	menu2 = wx.Menu()
	99	self.menu_mng.populate_menu(menu2, owner)
	100	id2 = wx.NewId()
	101	owner.Bind(models.EVT_MODEL,self._on_model_menu)
	102	self.fit_panel.set_owner(owner)
	103	self.fit_panel.set_model_list(self.menu_mng.get_model_list())
	104	owner.Bind(fitpage.EVT_MODEL_BOX,self._on_model_panel)
[3b19ac9]	105	#create menubar items
[d89f09b]	106	return [(id, self.menu1, "Fitting"),(id2, menu2, "Model")]
	107
	108
	109	def help(self, evt):
	110	"""
	111	Show a general help dialog.
	112	TODO: replace the text with a nice image
	113	"""
	114	pass
	115
	116	def get_context_menu(self, graph=None):
	117	"""
	118	Get the context menu items available for P(r)
	119	@param graph: the Graph object to which we attach the context menu
	120	@return: a list of menu items with call-back function
	121	"""
	122	self.graph=graph
	123	for item in graph.plottables:
	124	if item.name==graph.selected_plottable and item.__class__.__name__ is not "Theory1D":
	125	return [["Select Data", "Dialog with fitting parameters ", self._onSelect]]
	126	return []
	127
	128
	129	def get_panels(self, parent):
	130	"""
	131	Create and return a list of panel objects
	132	"""
	133	self.parent = parent
	134	# Creation of the fit panel
	135	self.fit_panel = FitPanel(self.parent, -1)
	136	#Set the manager forthe main panel
	137	self.fit_panel.set_manager(self)
	138	# List of windows used for the perspective
	139	self.perspective = []
	140	self.perspective.append(self.fit_panel.window_name)
	141	# take care of saving data, model and page associated with each other
[3b19ac9]	142	self.page_finder = {}
	143	#index number to create random model name
	144	self.index_model = 0
	145	#create the fitting panel
[d89f09b]	146	return [self.fit_panel]
	147
	148
	149	def get_perspective(self):
	150	"""
	151	Get the list of panel names for this perspective
	152	"""
	153	return self.perspective
	154
	155
	156	def on_perspective(self, event):
	157	"""
	158	Call back function for the perspective menu item.
	159	We notify the parent window that the perspective
	160	has changed.
	161	"""
	162	self.parent.set_perspective(self.perspective)
	163
	164
	165	def post_init(self):
	166	"""
	167	Post initialization call back to close the loose ends
	168	[Somehow openGL needs this call]
	169	"""
	170	self.parent.set_perspective(self.perspective)
	171
	172
	173	def _onSelect(self,event):
	174	"""
	175	when Select data to fit a new page is created .Its reference is
	176	added to self.page_finder
	177	"""
	178	self.panel = event.GetEventObject()
	179	for item in self.panel.graph.plottables:
	180	if item.name == self.panel.graph.selected_plottable:
[3b19ac9]	181	#find a name for the page created for notebook
[d89f09b]	182	try:
	183	name = item.group_id # item in Data1D
	184	except:
	185	name = 'Fit'
	186	try:
[1b07935d]	187	page = self.fit_panel.add_fit_page(name)
[3b19ac9]	188	# add data associated to the page created
[d89f09b]	189	page.set_data_name(item)
[3b19ac9]	190	#create a fitproblem storing all link to data,model,page creation
[d89f09b]	191	self.page_finder[page]= FitProblem()
[442895f]	192	#data_for_park= Data(sans_data=item)
	193	#datap = PlottableData(data=data_for_park,data1d=item)
	194	#self.page_finder[page].add_data(datap)
	195	self.page_finder[page].add_data(item)
[d89f09b]	196	except:
[442895f]	197	#raise
[d89f09b]	198	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: \
	199	data already Selected "))
	200
	201
	202	def get_page_finder(self):
	203	""" @return self.page_finder used also by simfitpage.py"""
	204	return self.page_finder
	205
	206
[3b19ac9]	207	def set_page_finder(self,modelname,names,values):
[d89f09b]	208	"""
	209	Used by simfitpage.py to reset a parameter given the string constrainst.
	210	@param modelname: the name ot the model for with the parameter has to reset
	211	@param value: can be a string in this case.
[3b19ac9]	212	@param names: the paramter name
[d89f09b]	213	@note: expecting park used for fit.
	214	"""
	215	sim_page=self.fit_panel.get_page(0)
	216	for page, value in self.page_finder.iteritems():
	217	if page != sim_page:
	218	list=value.get_model()
	219	model=list[0]
	220	if model.name== modelname:
[3b19ac9]	221	value.set_model_param(names,values)
[d89f09b]	222	break
	223
	224
	225
	226	def split_string(self,item):
	227	"""
[3b19ac9]	228	receive a word containing dot and split it. used to split parameterset
	229	name into model name and parameter name example:
	230	paramaterset (item) = M1.A
	231	@return model_name =M1 , parameter name =A
[d89f09b]	232	"""
	233	if string.find(item,".")!=-1:
	234	param_names= re.split("\.",item)
	235	model_name=param_names[0]
	236	param_name=param_names[1]
	237	return model_name,param_name
	238
	239
	240	def _single_fit_completed(self,result,pars,current_pg,qmin,qmax):
	241	"""
[3b19ac9]	242	Display fit result on one page of the notebook.
	243	@param result: result of fit
	244	@param pars: list of names of parameters fitted
	245	@param current_pg: the page where information will be displayed
	246	@param qmin: the minimum value of x to replot the model
	247	@param qmax: the maximum value of x to replot model
[d89f09b]	248
	249	"""
	250	try:
	251	for page, value in self.page_finder.iteritems():
	252	if page== current_pg:
	253	data = value.get_data()
	254	list = value.get_model()
	255	model= list[0]
	256	break
	257	i = 0
[442895f]	258	# print "fitting: single fit pars ", pars
[d89f09b]	259	for name in pars:
	260	if result.pvec.__class__==numpy.float64:
[1b07935d]	261	model.setParam(name,result.pvec)
[d89f09b]	262	else:
[1b07935d]	263	model.setParam(name,result.pvec[i])
[442895f]	264	# print "fitting: single fit", name, result.pvec[i]
[d89f09b]	265	i += 1
[442895f]	266	# print "fitting result : chisqr",result.fitness
	267	# print "fitting result : pvec",result.pvec
	268	# print "fitting result : stderr",result.stderr
	269
[3b19ac9]	270	current_pg.onsetValues(result.fitness, result.pvec,result.stderr)
[d89f09b]	271	self.plot_helper(currpage=current_pg,qmin=qmin,qmax=qmax)
	272	except:
[442895f]	273	raise
[060b857]	274	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
[d89f09b]	275
	276
	277	def _simul_fit_completed(self,result,qmin,qmax):
	278	"""
	279	Parameter estimation completed,
	280	display the results to the user
	281	@param alpha: estimated best alpha
	282	@param elapsed: computation time
	283	"""
	284	try:
	285	for page, value in self.page_finder.iteritems():
[3b19ac9]	286	if value.get_scheduled()=='True':
	287	data = value.get_data()
	288	list = value.get_model()
	289	model= list[0]
	290
	291	small_out = []
	292	small_cov = []
	293	i = 0
	294	#Separate result in to data corresponding to each page
	295	for p in result.parameters:
	296	model_name,param_name = self.split_string(p.name)
	297	if model.name == model_name:
	298	small_out.append(p.value )
	299	small_cov.append(p.stderr)
	300	model.setParam(param_name,p.value)
	301	# Display result on each page
	302	page.onsetValues(result.fitness, small_out,small_cov)
	303	#Replot model
	304	self.plot_helper(currpage= page,qmin= qmin,qmax= qmax)
[d89f09b]	305	except:
	306	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	307
[4fc6dbf]	308
[d89f09b]	309	def _on_single_fit(self,id=None,qmin=None,qmax=None):
	310	"""
	311	perform fit for the current page and return chisqr,out and cov
	312	@param engineName: type of fit to be performed
	313	@param id: unique id corresponding to a fit problem(model, set of data)
	314	@param model: model to fit
	315
	316	"""
	317	#set an engine to perform fit
	318	from sans.fit.Fitting import Fit
	319	self.fitter= Fit(self._fit_engine)
[3b19ac9]	320	#Setting an id to store model and data in fit engine
[d89f09b]	321	if id==None:
	322	id=0
[3b19ac9]	323	self.id = id
	324	#Get information (model , data) related to the page on
	325	#with the fit will be perform
[d89f09b]	326	current_pg=self.fit_panel.get_current_page()
	327	for page, value in self.page_finder.iteritems():
	328	if page ==current_pg :
	329	data = value.get_data()
	330	list=value.get_model()
	331	model=list[0]
	332
[3b19ac9]	333	#Create list of parameters for fitting used
[d89f09b]	334	pars=[]
	335	templist=[]
	336	try:
	337	templist=current_pg.get_param_list()
	338	except:
	339	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	340	return
[3b19ac9]	341
[d89f09b]	342	for element in templist:
	343	try:
	344	pars.append(str(element[0].GetLabelText()))
	345	except:
	346	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	347	return
[3b19ac9]	348	# make sure to keep an alphabetic order
	349	#of parameter names in the list
[d89f09b]	350	pars.sort()
[3b19ac9]	351	#Do the single fit
[d89f09b]	352	try:
[3b19ac9]	353	self.fitter.set_model(Model(model), self.id, pars)
[442895f]	354	#print "fitting: data .x",data.x
	355	#print "fitting: data .y",data.y
	356	#print "fitting: data .dy",data.dy
	357	self.fitter.set_data(Data(sans_data=data),self.id,qmin,qmax)
[3b19ac9]	358
[d89f09b]	359	result=self.fitter.fit()
	360	self._single_fit_completed(result,pars,current_pg,qmin,qmax)
	361
	362	except:
[442895f]	363	raise
[d89f09b]	364	wx.PostEvent(self.parent, StatusEvent(status="Single Fit error: %s" % sys.exc_value))
	365	return
	366
	367	def _on_simul_fit(self, id=None,qmin=None,qmax=None):
	368	"""
	369	perform fit for all the pages selected on simpage and return chisqr,out and cov
	370	@param engineName: type of fit to be performed
	371	@param id: unique id corresponding to a fit problem(model, set of data)
	372	in park_integration
	373	@param model: model to fit
	374
	375	"""
	376	#set an engine to perform fit
	377	from sans.fit.Fitting import Fit
	378	self.fitter= Fit(self._fit_engine)
[3b19ac9]	379
[d89f09b]	380	#Setting an id to store model and data
	381	if id==None:
	382	id = 0
	383	self.id = id
[3b19ac9]	384
[d89f09b]	385	for page, value in self.page_finder.iteritems():
	386	try:
[3b19ac9]	387	if value.get_scheduled()=='True':
	388	data = value.get_data()
	389	list = value.get_model()
	390	model= list[0]
[d89f09b]	391	#Create dictionary of parameters for fitting used
	392	pars = []
	393	templist = []
[3b19ac9]	394	templist = page.get_param_list()
[d89f09b]	395	for element in templist:
	396	try:
	397	name = str(element[0].GetLabelText())
	398	pars.append(name)
	399	except:
	400	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	401	return
[3b19ac9]	402	self.fitter.set_model(Model(model), self.id, pars)
[442895f]	403	self.fitter.set_data(Data(sans_data=data),self.id,qmin,qmax)
[3b19ac9]	404
	405	self.id += 1
[d89f09b]	406	except:
[3b19ac9]	407	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	408	return
[dabb633]	409	#Do the simultaneous fit
[d89f09b]	410	try:
	411	result=self.fitter.fit()
	412	self._simul_fit_completed(result,qmin,qmax)
	413	except:
	414	wx.PostEvent(self.parent, StatusEvent(status="Simultaneous Fitting error: %s" % sys.exc_value))
	415	return
[3b19ac9]	416
	417
	418	def _onset_engine(self,event):
	419	""" set engine to scipy"""
	420	if self._fit_engine== 'park':
	421	self._on_change_engine('scipy')
	422	else:
	423	self._on_change_engine('park')
	424	wx.PostEvent(self.parent, StatusEvent(status="Engine set to: %s" % self._fit_engine))
	425
	426
[d89f09b]	427	def _on_change_engine(self, engine='park'):
	428	"""
	429	Allow to select the type of engine to perform fit
	430	@param engine: the key work of the engine
	431	"""
	432	self._fit_engine = engine
	433
	434
	435	def _on_model_panel(self, evt):
	436	"""
	437	react to model selection on any combo box or model menu.plot the model
	438	"""
	439	model = evt.model
	440	name = evt.name
	441	sim_page=self.fit_panel.get_page(0)
	442	current_pg = self.fit_panel.get_current_page()
	443	if current_pg != sim_page:
	444	current_pg.set_model_name(name)
	445	current_pg.set_panel(model)
	446	try:
	447	data=self.page_finder[current_pg].get_data()
	448	M_name="M"+str(self.index_model)+"= "+name+"("+data.group_id+")"
	449	except:
	450	raise
	451	M_name="M"+str(self.index_model)+"= "+name
	452	model.name="M"+str(self.index_model)
	453	self.index_model += 1
[442895f]	454
[1b07935d]	455	self.page_finder[current_pg].set_model(model,M_name)
[d89f09b]	456	self.plot_helper(currpage= current_pg,qmin= None,qmax= None)
	457	sim_page.add_model(self.page_finder)
	458
	459
	460	def redraw_model(self,qmin= None,qmax= None):
	461	"""
	462	Draw a theory according to model changes or data range.
	463	@param qmin: the minimum value plotted for theory
	464	@param qmax: the maximum value plotted for theory
	465	"""
	466	current_pg=self.fit_panel.get_current_page()
	467	for page, value in self.page_finder.iteritems():
	468	if page ==current_pg :
	469	break
	470	self.plot_helper(currpage=page,qmin= qmin,qmax= qmax)
	471
	472	def plot_helper(self,currpage,qmin=None,qmax=None):
	473	"""
	474	Plot a theory given a model and data
	475	@param model: the model from where the theory is derived
	476	@param currpage: page in a dictionary referring to some data
	477	"""
	478	if self.fit_panel.get_page_count() >1:
	479	for page in self.page_finder.iterkeys():
	480	if page==currpage :
	481	break
	482	data=self.page_finder[page].get_data()
	483	list=self.page_finder[page].get_model()
	484	model=list[0]
	485	if data!=None:
	486	theory = Theory1D(x=[], y=[])
[442895f]	487	theory.name = "Model"
[d89f09b]	488	theory.group_id = data.group_id
	489
	490	x_name, x_units = data.get_xaxis()
	491	y_name, y_units = data.get_yaxis()
	492	theory.xaxis(x_name, x_units)
	493	theory.yaxis(y_name, y_units)
[442895f]	494	#print"fitting : redraw data.x",data.x
	495	#print"fitting : redraw data.y",data.y
	496	#print"fitting : redraw data.dy",data.dy
[d89f09b]	497	if qmin == None :
	498	qmin = min(data.x)
	499	if qmax == None :
	500	qmax = max(data.x)
	501	try:
	502	tempx = qmin
[1b07935d]	503	tempy = model.run(qmin)
[d89f09b]	504	theory.x.append(tempx)
	505	theory.y.append(tempy)
	506	except :
	507	wx.PostEvent(self.parent, StatusEvent(status="fitting \
	508	skipping point x %g %s" %(qmin, sys.exc_value)))
	509
	510	for i in range(len(data.x)):
	511	try:
	512	if data.x[i]> qmin and data.x[i]< qmax:
	513	tempx = data.x[i]
[1b07935d]	514	tempy = model.run(tempx)
[d89f09b]	515
	516	theory.x.append(tempx)
	517	theory.y.append(tempy)
	518	except:
	519	wx.PostEvent(self.parent, StatusEvent(status="fitting \
	520	skipping point x %g %s" %(data.x[i], sys.exc_value)))
	521	try:
	522	tempx = qmax
[1b07935d]	523	tempy = model.run(qmax)
[d89f09b]	524	theory.x.append(tempx)
	525	theory.y.append(tempy)
	526	except:
	527	wx.PostEvent(self.parent, StatusEvent(status="fitting \
	528	skipping point x %g %s" %(qmax, sys.exc_value)))
	529	try:
[442895f]	530	#print "fitting redraw for plot thoery .x",theory.x
	531	#print "fitting redraw for plot thoery .y",theory.y
	532	#print "fitting redraw for plot thoery .dy",theory.dy
	533	#rom sans.guicomm.events import NewPlotEvent
[d89f09b]	534	wx.PostEvent(self.parent, NewPlotEvent(plot=theory, title="Analytical model"))
	535	except:
[442895f]	536	raise
[d89f09b]	537	print "SimView.complete1D: could not import sans.guicomm.events"
	538
	539
	540	def _on_model_menu(self, evt):
	541	"""
	542	Plot a theory from a model selected from the menu
	543	"""
[1b07935d]	544	name="Model View"
[49b7efa]	545	model=evt.modelinfo.model()
	546	description=evt.modelinfo.description
	547	self.fit_panel.add_model_page(model,description,name)
	548	self.draw_model(model)
[1b07935d]	549
	550	def draw_model(self,model):
[3b19ac9]	551	"""
	552	draw model with default data value
	553	"""
[d89f09b]	554	x = pylab.arange(0.001, 0.1, 0.001)
	555	xlen = len(x)
	556	dy = numpy.zeros(xlen)
	557	y = numpy.zeros(xlen)
	558
	559	for i in range(xlen):
[1b07935d]	560	y[i] = model.run(x[i])
[d89f09b]	561	dy[i] = math.sqrt(math.fabs(y[i]))
	562	try:
	563
	564	new_plot = Theory1D(x, y)
[442895f]	565	new_plot.name = "Model"
[d89f09b]	566	new_plot.xaxis("\\rm{Q}", 'A^{-1}')
	567	new_plot.yaxis("\\rm{Intensity} ","cm^{-1}")
[55fd102]	568	new_plot.group_id ="Fitness"
[d89f09b]	569
	570	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model"))
	571	except:
[4c530a5]	572	print "SimView.complete1D: could not import sans.guicomm.events\n %s" % sys.exc_value
	573	logging.error("SimView.complete1D: could not import sans.guicomm.events\n %s" % sys.exc_value)
[d89f09b]	574
	575	if __name__ == "__main__":
	576	i = Plugin()
	577
	578
	579
	580

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SasView

source: sasview/sansview/perspectives/fitting/fitting.py @ 442895f

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