fitting.py @ 3b19ac9

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 3b19ac9 was 3b19ac9, checked in by Gervaise Alina <gervyh@…>, 16 years ago
working on simultaneous fit and scipy/park fit added on menubar
Property mode set to `100644`
File size: 21.0 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
[3b19ac9]	15
[d89f09b]	16	class PlottableData(Data,Data1D):
[3b19ac9]	17	""" class plottable data: class allowing to plot Data type on panel"""
[d89f09b]	18	def __init__(self,data,data1d):
	19	self.x = data1d.x
	20	self.y = data1d.y
[3b19ac9]	21	self.dx = data1d.dx
	22	self.dy = data1d.dy
[d89f09b]	23
[3b19ac9]	24	self.group_id = data1d.group_id
[d89f09b]	25	x_name, x_units = data1d.get_xaxis()
	26	y_name, y_units = data1d.get_yaxis()
	27	self.xaxis( x_name, x_units)
	28	self.yaxis( y_name, y_units )
[3b19ac9]	29	self.qmin = data.qmin
	30	self.qmax = data.qmax
	31
[d89f09b]	32	class Plugin:
	33	"""
	34	"""
	35	def __init__(self):
	36	## Plug-in name
	37	self.sub_menu = "Fitting"
	38
	39	## Reference to the parent window
	40	self.parent = None
	41	self.menu_mng = models.ModelManager()
	42	## List of panels for the simulation perspective (names)
	43	self.perspective = []
	44	# Start with a good default
	45	self.elapsed = 0.022
	46	self.fitter = None
	47
	48	#Flag to let the plug-in know that it is running standalone
	49	self.standalone=True
	50	## Fit engine
[3b19ac9]	51	self._fit_engine = 'scipy'
[d89f09b]	52	# Log startup
	53	logging.info("Fitting plug-in started")
	54
	55	def populate_menu(self, id, owner):
	56	"""
	57	Create a menu for the Fitting plug-in
	58	@param id: id to create a menu
	59	@param owner: owner of menu
	60	@ return : list of information to populate the main menu
	61	"""
	62	#Menu for fitting
	63	self.menu1 = wx.Menu()
	64	id1 = wx.NewId()
	65	self.menu1.Append(id1, '&Show fit panel')
	66	wx.EVT_MENU(owner, id1, self.on_perspective)
[3b19ac9]	67	id3 = wx.NewId()
	68	self.menu1.Append(id3,'&scipy \ park','toggle engine to park or scipy')
	69	wx.EVT_MENU(owner, id3, self._onset_engine)
[d89f09b]	70
	71	#menu for model
	72	menu2 = wx.Menu()
	73	self.menu_mng.populate_menu(menu2, owner)
	74	id2 = wx.NewId()
	75	owner.Bind(models.EVT_MODEL,self._on_model_menu)
	76	self.fit_panel.set_owner(owner)
	77	self.fit_panel.set_model_list(self.menu_mng.get_model_list())
	78	owner.Bind(fitpage.EVT_MODEL_BOX,self._on_model_panel)
[3b19ac9]	79	#create menubar items
[d89f09b]	80	return [(id, self.menu1, "Fitting"),(id2, menu2, "Model")]
	81
	82
	83	def help(self, evt):
	84	"""
	85	Show a general help dialog.
	86	TODO: replace the text with a nice image
	87	"""
	88	pass
	89
	90	def get_context_menu(self, graph=None):
	91	"""
	92	Get the context menu items available for P(r)
	93	@param graph: the Graph object to which we attach the context menu
	94	@return: a list of menu items with call-back function
	95	"""
	96
	97	self.graph=graph
	98	for item in graph.plottables:
	99	if item.name==graph.selected_plottable and item.__class__.__name__ is not "Theory1D":
	100	return [["Select Data", "Dialog with fitting parameters ", self._onSelect]]
	101	return []
	102
	103
	104	def get_panels(self, parent):
	105	"""
	106	Create and return a list of panel objects
	107	"""
	108	self.parent = parent
	109	# Creation of the fit panel
	110	self.fit_panel = FitPanel(self.parent, -1)
	111	#Set the manager forthe main panel
	112	self.fit_panel.set_manager(self)
	113	# List of windows used for the perspective
	114	self.perspective = []
	115	self.perspective.append(self.fit_panel.window_name)
	116	# take care of saving data, model and page associated with each other
[3b19ac9]	117	self.page_finder = {}
	118	#index number to create random model name
	119	self.index_model = 0
	120	#create the fitting panel
[d89f09b]	121	return [self.fit_panel]
	122
	123
	124	def get_perspective(self):
	125	"""
	126	Get the list of panel names for this perspective
	127	"""
	128	return self.perspective
	129
	130
	131	def on_perspective(self, event):
	132	"""
	133	Call back function for the perspective menu item.
	134	We notify the parent window that the perspective
	135	has changed.
	136	"""
	137	self.parent.set_perspective(self.perspective)
	138
	139
	140	def post_init(self):
	141	"""
	142	Post initialization call back to close the loose ends
	143	[Somehow openGL needs this call]
	144	"""
	145	self.parent.set_perspective(self.perspective)
	146
	147
	148	def _onSelect(self,event):
	149	"""
	150	when Select data to fit a new page is created .Its reference is
	151	added to self.page_finder
	152	"""
	153	self.panel = event.GetEventObject()
	154	for item in self.panel.graph.plottables:
	155	if item.name == self.panel.graph.selected_plottable:
[3b19ac9]	156	#find a name for the page created for notebook
[d89f09b]	157	try:
	158	name = item.group_id # item in Data1D
	159	except:
	160	name = 'Fit'
	161	try:
[1b07935d]	162	page = self.fit_panel.add_fit_page(name)
[3b19ac9]	163	# add data associated to the page created
[d89f09b]	164	page.set_data_name(item)
[3b19ac9]	165	#create a fitproblem storing all link to data,model,page creation
[d89f09b]	166	self.page_finder[page]= FitProblem()
[3b19ac9]	167	data_for_park= Data(sans_data=item)
	168	datap=PlottableData(data=data_for_park,data1d=item)
	169	self.page_finder[page].add_data(datap)
[d89f09b]	170	except:
	171	raise
	172	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: \
	173	data already Selected "))
	174
	175
	176	def get_page_finder(self):
	177	""" @return self.page_finder used also by simfitpage.py"""
	178	return self.page_finder
	179
	180
[3b19ac9]	181	def set_page_finder(self,modelname,names,values):
[d89f09b]	182	"""
	183	Used by simfitpage.py to reset a parameter given the string constrainst.
	184	@param modelname: the name ot the model for with the parameter has to reset
	185	@param value: can be a string in this case.
[3b19ac9]	186	@param names: the paramter name
[d89f09b]	187	@note: expecting park used for fit.
	188	"""
	189	sim_page=self.fit_panel.get_page(0)
	190	for page, value in self.page_finder.iteritems():
	191	if page != sim_page:
	192	list=value.get_model()
	193	model=list[0]
	194	if model.name== modelname:
[3b19ac9]	195	value.set_model_param(names,values)
	196
[d89f09b]	197	break
	198
	199
	200
	201	def split_string(self,item):
	202	"""
[3b19ac9]	203	receive a word containing dot and split it. used to split parameterset
	204	name into model name and parameter name example:
	205	paramaterset (item) = M1.A
	206	@return model_name =M1 , parameter name =A
[d89f09b]	207	"""
	208	if string.find(item,".")!=-1:
	209	param_names= re.split("\.",item)
	210	model_name=param_names[0]
	211	param_name=param_names[1]
	212	return model_name,param_name
	213
	214
	215	def _single_fit_completed(self,result,pars,current_pg,qmin,qmax):
	216	"""
[3b19ac9]	217	Display fit result on one page of the notebook.
	218	@param result: result of fit
	219	@param pars: list of names of parameters fitted
	220	@param current_pg: the page where information will be displayed
	221	@param qmin: the minimum value of x to replot the model
	222	@param qmax: the maximum value of x to replot model
[d89f09b]	223
	224	"""
	225	try:
	226	for page, value in self.page_finder.iteritems():
	227	if page== current_pg:
	228	data = value.get_data()
	229	list = value.get_model()
	230	model= list[0]
	231	break
	232	i = 0
	233	for name in pars:
	234	if result.pvec.__class__==numpy.float64:
[1b07935d]	235	model.setParam(name,result.pvec)
[d89f09b]	236	else:
[1b07935d]	237	model.setParam(name,result.pvec[i])
[d89f09b]	238	i += 1
[3b19ac9]	239	current_pg.onsetValues(result.fitness, result.pvec,result.stderr)
[d89f09b]	240	self.plot_helper(currpage=current_pg,qmin=qmin,qmax=qmax)
	241	except:
[060b857]	242	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
[d89f09b]	243
	244
	245	def _simul_fit_completed(self,result,qmin,qmax):
	246	"""
	247	Parameter estimation completed,
	248	display the results to the user
	249	@param alpha: estimated best alpha
	250	@param elapsed: computation time
	251	"""
	252	try:
	253	for page, value in self.page_finder.iteritems():
[3b19ac9]	254	print "fitting : simultaneous scheduled ",value.get_scheduled()
	255	if value.get_scheduled()=='True':
	256	data = value.get_data()
	257	list = value.get_model()
	258	model= list[0]
	259
	260	small_out = []
	261	small_cov = []
	262	i = 0
	263	#Separate result in to data corresponding to each page
	264	for p in result.parameters:
	265	model_name,param_name = self.split_string(p.name)
	266	if model.name == model_name:
	267	small_out.append(p.value )
	268	small_cov.append(p.stderr)
	269	model.setParam(param_name,p.value)
	270	# Display result on each page
	271	page.onsetValues(result.fitness, small_out,small_cov)
	272	#Replot model
	273	self.plot_helper(currpage= page,qmin= qmin,qmax= qmax)
[d89f09b]	274	except:
	275	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	276
[4fc6dbf]	277
[d89f09b]	278	def _on_single_fit(self,id=None,qmin=None,qmax=None):
	279	"""
	280	perform fit for the current page and return chisqr,out and cov
	281	@param engineName: type of fit to be performed
	282	@param id: unique id corresponding to a fit problem(model, set of data)
	283	@param model: model to fit
	284
	285	"""
	286	#set an engine to perform fit
	287	from sans.fit.Fitting import Fit
	288	self.fitter= Fit(self._fit_engine)
[3b19ac9]	289	#Setting an id to store model and data in fit engine
[d89f09b]	290	if id==None:
	291	id=0
[3b19ac9]	292	self.id = id
	293	#Get information (model , data) related to the page on
	294	#with the fit will be perform
[d89f09b]	295	current_pg=self.fit_panel.get_current_page()
	296	for page, value in self.page_finder.iteritems():
	297	if page ==current_pg :
	298	data = value.get_data()
	299	list=value.get_model()
	300	model=list[0]
	301
[3b19ac9]	302	#Create list of parameters for fitting used
[d89f09b]	303	pars=[]
	304	templist=[]
	305	try:
	306	templist=current_pg.get_param_list()
	307	except:
	308	raise
	309	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	310	return
[3b19ac9]	311
[d89f09b]	312	for element in templist:
	313	try:
	314	pars.append(str(element[0].GetLabelText()))
	315	except:
	316	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	317	return
[3b19ac9]	318	# make sure to keep an alphabetic order
	319	#of parameter names in the list
[d89f09b]	320	pars.sort()
[3b19ac9]	321	#Do the single fit
[d89f09b]	322	try:
[3b19ac9]	323	self.fitter.set_model(Model(model), self.id, pars)
	324	self.fitter.set_data(data,self.id,qmin,qmax)
	325
[d89f09b]	326	result=self.fitter.fit()
	327	self._single_fit_completed(result,pars,current_pg,qmin,qmax)
	328
	329	except:
	330	wx.PostEvent(self.parent, StatusEvent(status="Single Fit error: %s" % sys.exc_value))
	331	return
	332
	333	def _on_simul_fit(self, id=None,qmin=None,qmax=None):
	334	"""
	335	perform fit for all the pages selected on simpage and return chisqr,out and cov
	336	@param engineName: type of fit to be performed
	337	@param id: unique id corresponding to a fit problem(model, set of data)
	338	in park_integration
	339	@param model: model to fit
	340
	341	"""
	342	#set an engine to perform fit
	343	from sans.fit.Fitting import Fit
	344	self.fitter= Fit(self._fit_engine)
[3b19ac9]	345
[d89f09b]	346	#Setting an id to store model and data
	347	if id==None:
	348	id = 0
	349	self.id = id
[3b19ac9]	350
[d89f09b]	351	for page, value in self.page_finder.iteritems():
	352	try:
[3b19ac9]	353	print "fitting : simultaneous scheduled ",value.get_scheduled(),value.schedule
	354	if value.get_scheduled()=='True':
	355	print "fitting: self.page_finder",value.get_scheduled()
	356	data = value.get_data()
	357	#print "fitting: data",data
	358	list = value.get_model()
	359	model= list[0]
[d89f09b]	360	#Create dictionary of parameters for fitting used
	361	pars = []
	362	templist = []
[3b19ac9]	363	templist = page.get_param_list()
[d89f09b]	364	for element in templist:
	365	try:
	366	name = str(element[0].GetLabelText())
	367	pars.append(name)
	368	except:
	369	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	370	return
[3b19ac9]	371	self.fitter.set_model(Model(model), self.id, pars)
[d89f09b]	372	self.fitter.set_data(data,self.id,qmin,qmax)
[3b19ac9]	373
	374	self.id += 1
[d89f09b]	375	except:
[3b19ac9]	376	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
	377	return
	378	#Do the simultaneous fit
[d89f09b]	379	try:
	380	result=self.fitter.fit()
	381	self._simul_fit_completed(result,qmin,qmax)
	382	except:
	383	wx.PostEvent(self.parent, StatusEvent(status="Simultaneous Fitting error: %s" % sys.exc_value))
	384	return
[3b19ac9]	385
	386
	387	def _onset_engine(self,event):
	388	""" set engine to scipy"""
	389	if self._fit_engine== 'park':
	390	self._on_change_engine('scipy')
	391	else:
	392	self._on_change_engine('park')
	393	wx.PostEvent(self.parent, StatusEvent(status="Engine set to: %s" % self._fit_engine))
	394
	395
	396
[d89f09b]	397	def _on_change_engine(self, engine='park'):
	398	"""
	399	Allow to select the type of engine to perform fit
	400	@param engine: the key work of the engine
	401	"""
	402	self._fit_engine = engine
	403
	404
	405	def _on_model_panel(self, evt):
	406	"""
	407	react to model selection on any combo box or model menu.plot the model
	408	"""
	409	model = evt.model
	410	name = evt.name
	411	sim_page=self.fit_panel.get_page(0)
	412	current_pg = self.fit_panel.get_current_page()
	413	if current_pg != sim_page:
	414	current_pg.set_model_name(name)
	415	current_pg.set_panel(model)
	416	try:
	417	data=self.page_finder[current_pg].get_data()
	418	M_name="M"+str(self.index_model)+"= "+name+"("+data.group_id+")"
	419	except:
	420	raise
	421	M_name="M"+str(self.index_model)+"= "+name
	422	model.name="M"+str(self.index_model)
	423	self.index_model += 1
	424	self.page_finder[current_pg].set_theory("Fitness")
	425	#print "on model",model.name
[1b07935d]	426	self.page_finder[current_pg].set_model(model,M_name)
[d89f09b]	427	self.plot_helper(currpage= current_pg,qmin= None,qmax= None)
	428	sim_page.add_model(self.page_finder)
	429
	430
	431	def redraw_model(self,qmin= None,qmax= None):
	432	"""
	433	Draw a theory according to model changes or data range.
	434	@param qmin: the minimum value plotted for theory
	435	@param qmax: the maximum value plotted for theory
	436	"""
	437	current_pg=self.fit_panel.get_current_page()
	438	for page, value in self.page_finder.iteritems():
	439	if page ==current_pg :
	440	break
	441	self.plot_helper(currpage=page,qmin= qmin,qmax= qmax)
	442
	443	def plot_helper(self,currpage,qmin=None,qmax=None):
	444	"""
	445	Plot a theory given a model and data
	446	@param model: the model from where the theory is derived
	447	@param currpage: page in a dictionary referring to some data
	448	"""
	449	if self.fit_panel.get_page_count() >1:
	450	for page in self.page_finder.iterkeys():
	451	if page==currpage :
	452	break
	453
	454	data=self.page_finder[page].get_data()
	455	list=self.page_finder[page].get_model()
	456	model=list[0]
	457	if data!=None:
	458	theory = Theory1D(x=[], y=[])
	459	theory.name = self.page_finder[page].get_theory()
	460	theory.group_id = data.group_id
	461
	462	x_name, x_units = data.get_xaxis()
	463	y_name, y_units = data.get_yaxis()
	464	theory.xaxis(x_name, x_units)
	465	theory.yaxis(y_name, y_units)
	466
	467	if qmin == None :
	468	qmin = min(data.x)
	469	if qmax == None :
	470	qmax = max(data.x)
	471	try:
	472	tempx = qmin
[1b07935d]	473	tempy = model.run(qmin)
[d89f09b]	474	theory.x.append(tempx)
	475	theory.y.append(tempy)
	476	except :
	477	wx.PostEvent(self.parent, StatusEvent(status="fitting \
	478	skipping point x %g %s" %(qmin, sys.exc_value)))
	479
	480	for i in range(len(data.x)):
	481	try:
	482	if data.x[i]> qmin and data.x[i]< qmax:
	483	tempx = data.x[i]
[1b07935d]	484	tempy = model.run(tempx)
[d89f09b]	485
	486	theory.x.append(tempx)
	487	theory.y.append(tempy)
	488	except:
	489	wx.PostEvent(self.parent, StatusEvent(status="fitting \
	490	skipping point x %g %s" %(data.x[i], sys.exc_value)))
	491	try:
	492	tempx = qmax
[1b07935d]	493	tempy = model.run(qmax)
[d89f09b]	494	theory.x.append(tempx)
	495	theory.y.append(tempy)
	496	except:
	497	wx.PostEvent(self.parent, StatusEvent(status="fitting \
	498	skipping point x %g %s" %(qmax, sys.exc_value)))
	499	try:
	500	from sans.guicomm.events import NewPlotEvent
	501	wx.PostEvent(self.parent, NewPlotEvent(plot=theory, title="Analytical model"))
	502	except:
	503	raise
	504	print "SimView.complete1D: could not import sans.guicomm.events"
	505
	506
	507	def _on_model_menu(self, evt):
	508	"""
	509	Plot a theory from a model selected from the menu
	510	"""
[1b07935d]	511	name="Model View"
[49b7efa]	512	model=evt.modelinfo.model()
	513	description=evt.modelinfo.description
	514	self.fit_panel.add_model_page(model,description,name)
	515	self.draw_model(model)
[1b07935d]	516
	517	def draw_model(self,model):
[3b19ac9]	518	"""
	519	draw model with default data value
	520	"""
[d89f09b]	521	x = pylab.arange(0.001, 0.1, 0.001)
	522	xlen = len(x)
	523	dy = numpy.zeros(xlen)
	524	y = numpy.zeros(xlen)
	525
	526	for i in range(xlen):
[1b07935d]	527	y[i] = model.run(x[i])
[d89f09b]	528	dy[i] = math.sqrt(math.fabs(y[i]))
	529	try:
	530
	531	new_plot = Theory1D(x, y)
	532	new_plot.name ="Fitness"
	533	new_plot.xaxis("\\rm{Q}", 'A^{-1}')
	534	new_plot.yaxis("\\rm{Intensity} ","cm^{-1}")
	535
	536	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model"))
	537	except:
	538	print "SimView.complete1D: could not import sans.guicomm.events"
	539
	540	if __name__ == "__main__":
	541	i = Plugin()
	542
	543
	544
	545

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/sansview/perspectives/fitting/fitting.py @ 3b19ac9

Download in other formats: