fitting.py @ 2d107b8

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 2d107b8 was b2c3225, checked in by Gervaise Alina <gervyh@…>, 16 years ago
fix small bugs
Property mode set to `100644`
File size: 25.4 KB

Line
1	import os,os.path, re
2	import sys, wx, logging
3	import string, numpy, math
4
5	from copy import deepcopy
6	from danse.common.plottools.plottables import Data1D, Theory1D,Data2D,Theory2D
7	from danse.common.plottools.PlotPanel import PlotPanel
8	from sans.guicomm.events import NewPlotEvent, StatusEvent
9	from sans.fit.AbstractFitEngine import Model,Data,FitData1D,FitData2D
10	from fitproblem import FitProblem
11	from fitpanel import FitPanel
12
13	import models,modelpage
14	import fitpage1D,fitpage2D
15	import park
16
17	class Plugin:
18	"""
19	Fitting plugin is used to perform fit
20	"""
21	def __init__(self):
22	## Plug-in name
23	self.sub_menu = "Fitting"
24
25	## Reference to the parent window
26	self.parent = None
27	self.menu_mng = models.ModelManager()
28	## List of panels for the simulation perspective (names)
29	self.perspective = []
30	# Start with a good default
31	self.elapsed = 0.022
32	self.fitter = None
33
34	#Flag to let the plug-in know that it is running standalone
35	self.standalone=True
36	## Fit engine
37	self._fit_engine = 'scipy'
38	self.enable_model2D=False
39	# Log startup
40	logging.info("Fitting plug-in started")
41
42	def populate_menu(self, id, owner):
43	"""
44	Create a menu for the Fitting plug-in
45	@param id: id to create a menu
46	@param owner: owner of menu
47	@ return : list of information to populate the main menu
48	"""
49	#Menu for fitting
50	self.menu1 = wx.Menu()
51	id1 = wx.NewId()
52	self.menu1.Append(id1, '&Show fit panel')
53	wx.EVT_MENU(owner, id1, self.on_perspective)
54	id3 = wx.NewId()
55	self.menu1.AppendCheckItem(id3, "park")
56	wx.EVT_MENU(owner, id3, self._onset_engine)
57
58	#menu for model
59	menu2 = wx.Menu()
60	id4 = wx.NewId()
61	menu2.AppendCheckItem(id4, "model view 2D")
62	wx.EVT_MENU(owner, id4, self.on_draw_model2D)
63
64	self.menu_mng.populate_menu(menu2, owner)
65	id2 = wx.NewId()
66	owner.Bind(models.EVT_MODEL,self._on_model_menu)
67	#owner.Bind(modelpage.EVT_MODEL,self._on_model_menu)
68	self.fit_panel.set_owner(owner)
69	self.fit_panel.set_model_list(self.menu_mng.get_model_list())
70	owner.Bind(fitpage1D.EVT_MODEL_BOX,self._on_model_panel)
71	owner.Bind(fitpage2D.EVT_MODEL_BOX,self._on_model_panel)
72	#create menubar items
73	return [(id, self.menu1, "Fitting"),(id2, menu2, "Model")]
74
75
76	def help(self, evt):
77	"""
78	Show a general help dialog.
79	TODO: replace the text with a nice image
80	"""
81	from helpDialog import HelpWindow
82	dialog = HelpWindow(None, -1, 'HelpWindow')
83	if dialog.ShowModal() == wx.ID_OK:
84	pass
85	dialog.Destroy()
86
87
88	def get_context_menu(self, graph=None):
89	"""
90	Get the context menu items available for P(r)
91	@param graph: the Graph object to which we attach the context menu
92	@return: a list of menu items with call-back function
93	"""
94	self.graph=graph
95	for item in graph.plottables:
96	if item.__class__.__name__ is "Data2D":
97	return [["Select data for Fitting",\
98	"Dialog with fitting parameters ", self._onSelect]]
99	#elif item.__class__.__name__ is "Theory2D":
100	# return [["Line Slicer [Q-view]","Sector Averaging as a function of Q",
101	# self.onLineSlicer],
102	# ["Annulus Slicer [Phi-view]","Sector Averaging as a function of Phi",
103	# self.onLineSlicer]]
104	else:
105	if item.name==graph.selected_plottable and\
106	item.__class__.__name__ is "Data1D":
107	return [["Select data for Fitting", \
108	"Dialog with fitting parameters ", self._onSelect]]
109	return []
110
111
112	def get_panels(self, parent):
113	"""
114	Create and return a list of panel objects
115	"""
116	self.parent = parent
117	# Creation of the fit panel
118	self.fit_panel = FitPanel(self.parent, -1)
119	#Set the manager forthe main panel
120	self.fit_panel.set_manager(self)
121	# List of windows used for the perspective
122	self.perspective = []
123	self.perspective.append(self.fit_panel.window_name)
124	# take care of saving data, model and page associated with each other
125	self.page_finder = {}
126	#index number to create random model name
127	self.index_model = 0
128	#create the fitting panel
129	return [self.fit_panel]
130
131
132	def get_perspective(self):
133	"""
134	Get the list of panel names for this perspective
135	"""
136	return self.perspective
137
138
139	def on_perspective(self, event):
140	"""
141	Call back function for the perspective menu item.
142	We notify the parent window that the perspective
143	has changed.
144	"""
145	self.parent.set_perspective(self.perspective)
146
147
148	def post_init(self):
149	"""
150	Post initialization call back to close the loose ends
151	[Somehow openGL needs this call]
152	"""
153	self.parent.set_perspective(self.perspective)
154
155
156	def _onSelect(self,event):
157	"""
158	when Select data to fit a new page is created .Its reference is
159	added to self.page_finder
160	"""
161	self.panel = event.GetEventObject()
162	for item in self.panel.graph.plottables:
163	if item.name == self.panel.graph.selected_plottable or\
164	item.__class__.__name__ is "Data2D":
165	#find a name for the page created for notebook
166	try:
167	page = self.fit_panel.add_fit_page(item)
168	# add data associated to the page created
169
170	if page !=None:
171
172	#create a fitproblem storing all link to data,model,page creation
173	self.page_finder[page]= FitProblem()
174	self.page_finder[page].add_data(item)
175	except:
176	wx.PostEvent(self.parent, StatusEvent(status="Creating Fit page: %s"\
177	%sys.exc_value))
178	def schedule_for_fit(self,value=0,fitproblem =None):
179	"""
180
181	"""
182	if fitproblem !=None:
183	fitproblem.schedule_tofit(value)
184	else:
185	current_pg=self.fit_panel.get_current_page()
186	for page, val in self.page_finder.iteritems():
187	if page ==current_pg :
188	val.schedule_tofit(value)
189	break
190
191
192	def get_page_finder(self):
193	""" @return self.page_finder used also by simfitpage.py"""
194	return self.page_finder
195
196
197	def set_page_finder(self,modelname,names,values):
198	"""
199	Used by simfitpage.py to reset a parameter given the string constrainst.
200	@param modelname: the name ot the model for with the parameter has to reset
201	@param value: can be a string in this case.
202	@param names: the paramter name
203	@note: expecting park used for fit.
204	"""
205	sim_page=self.fit_panel.get_page(0)
206	for page, value in self.page_finder.iteritems():
207	if page != sim_page:
208	list=value.get_model()
209	model=list[0]
210	#print "fitting",model.name,modelname
211	if model.name== modelname:
212	value.set_model_param(names,values)
213	break
214
215
216
217	def split_string(self,item):
218	"""
219	receive a word containing dot and split it. used to split parameterset
220	name into model name and parameter name example:
221	paramaterset (item) = M1.A
222	@return model_name =M1 , parameter name =A
223	"""
224	if string.find(item,".")!=-1:
225	param_names= re.split("\.",item)
226	model_name=param_names[0]
227	param_name=param_names[1]
228	return model_name,param_name
229
230
231	def _single_fit_completed(self,result,pars,cpage,qmin,qmax,ymin=None, ymax=None):
232	"""
233	Display fit result on one page of the notebook.
234	@param result: result of fit
235	@param pars: list of names of parameters fitted
236	@param current_pg: the page where information will be displayed
237	@param qmin: the minimum value of x to replot the model
238	@param qmax: the maximum value of x to replot model
239
240	"""
241	try:
242	for page, value in self.page_finder.iteritems():
243	if page==cpage :
244	#fitdata = value.get_data()
245	list = value.get_model()
246	model= list[0]
247	break
248	i = 0
249	# print "fitting: single fit pars ", pars
250	for name in pars:
251	if result.pvec.__class__==numpy.float64:
252	model.setParam(name,result.pvec)
253	else:
254	model.setParam(name,result.pvec[i])
255	# print "fitting: single fit", name, result.pvec[i]
256	i += 1
257	# print "fitting result : chisqr",result.fitness
258	# print "fitting result : pvec",result.pvec
259	# print "fitting result : stderr",result.stderr
260
261	cpage.onsetValues(result.fitness, result.pvec,result.stderr)
262	self.plot_helper(currpage=cpage,qmin=qmin,qmax=qmax,ymin=ymin, ymax=ymax)
263	except:
264	raise
265	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
266
267
268	def _simul_fit_completed(self,result,qmin,qmax,ymin=None, ymax=None):
269	"""
270	Parameter estimation completed,
271	display the results to the user
272	@param alpha: estimated best alpha
273	@param elapsed: computation time
274	"""
275	try:
276	for page, value in self.page_finder.iteritems():
277	if value.get_scheduled()==1:
278	#fitdata = value.get_data()
279	list = value.get_model()
280	model= list[0]
281
282	small_out = []
283	small_cov = []
284	i = 0
285	#Separate result in to data corresponding to each page
286	for p in result.parameters:
287	model_name,param_name = self.split_string(p.name)
288	if model.name == model_name:
289	small_out.append(p.value )
290	small_cov.append(p.stderr)
291	model.setParam(param_name,p.value)
292	# Display result on each page
293	page.onsetValues(result.fitness, small_out,small_cov)
294	#Replot model
295	self.plot_helper(currpage= page,qmin= qmin,qmax= qmax,ymin=ymin, ymax=ymax)
296	except:
297	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
298
299
300	def _on_single_fit(self,id=None,qmin=None,qmax=None,ymin=None,ymax=None):
301	"""
302	perform fit for the current page and return chisqr,out and cov
303	@param engineName: type of fit to be performed
304	@param id: unique id corresponding to a fit problem(model, set of data)
305	@param model: model to fit
306
307	"""
308	#print "in single fitting"
309	#set an engine to perform fit
310	from sans.fit.Fitting import Fit
311	self.fitter= Fit(self._fit_engine)
312	#Setting an id to store model and data in fit engine
313	if id==None:
314	id=0
315	self.id = id
316	page_fitted=None
317	fit_problem=None
318	#Get information (model , data) related to the page on
319	#with the fit will be perform
320	#current_pg=self.fit_panel.get_current_page()
321	#simul_pg=self.fit_panel.get_page(0)
322
323	for page, value in self.page_finder.iteritems():
324	if value.get_scheduled() ==1 :
325	metadata = value.get_data()
326	list=value.get_model()
327	model=list[0]
328	#Create list of parameters for fitting used
329	pars=[]
330	templist=[]
331	try:
332	#templist=current_pg.get_param_list()
333	templist=page.get_param_list()
334	for element in templist:
335	pars.append(str(element[0].GetLabelText()))
336	pars.sort()
337	#Do the single fit
338	self.fitter.set_model(Model(model), self.id, pars)
339
340	self.fitter.set_data(metadata,self.id,qmin,qmax)
341	self.fitter.select_problem_for_fit(Uid=self.id,value=value.get_scheduled())
342	page_fitted=page
343	self.id+=1
344	self.schedule_for_fit( 0,value)
345	except:
346	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
347	return
348	# make sure to keep an alphabetic order
349	#of parameter names in the list
350	try:
351	result=self.fitter.fit()
352	#self._single_fit_completed(result,pars,current_pg,qmin,qmax)
353	print "single_fit: result",result.fitness,result.pvec,result.stderr
354	#self._single_fit_completed(result,pars,page,qmin,qmax)
355	self._single_fit_completed(result,pars,page_fitted,qmin,qmax,ymin,ymax)
356	except:
357	raise
358	wx.PostEvent(self.parent, StatusEvent(status="Single Fit error: %s" % sys.exc_value))
359	return
360
361	def _on_simul_fit(self, id=None,qmin=None,qmax=None, ymin=None, ymax=None):
362	"""
363	perform fit for all the pages selected on simpage and return chisqr,out and cov
364	@param engineName: type of fit to be performed
365	@param id: unique id corresponding to a fit problem(model, set of data)
366	in park_integration
367	@param model: model to fit
368
369	"""
370	#set an engine to perform fit
371	from sans.fit.Fitting import Fit
372	self.fitter= Fit(self._fit_engine)
373
374	#Setting an id to store model and data
375	if id==None:
376	id = 0
377	self.id = id
378
379	for page, value in self.page_finder.iteritems():
380	try:
381	if value.get_scheduled()==1:
382	metadata = value.get_data()
383	list = value.get_model()
384	model= list[0]
385	#Create dictionary of parameters for fitting used
386	pars = []
387	templist = []
388	templist = page.get_param_list()
389	for element in templist:
390	try:
391	name = str(element[0].GetLabelText())
392	pars.append(name)
393	except:
394	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
395	return
396	new_model=Model(model)
397	param=value.get_model_param()
398
399	if len(param)>0:
400	for item in param:
401	param_value = item[1]
402	param_name = item[0]
403	#print "fitting ", param,param_name, param_value
404
405	#new_model.set( model.getParam(param_name[0])= param_value)
406	#new_model.set( exec"%s=%s"%(param_name[0], param_value))
407	#new_model.set( exec "%s"%(param_nam) = param_value)
408	new_model.parameterset[ param_name].set( param_value )
409
410	self.fitter.set_model(new_model, self.id, pars)
411	self.fitter.set_data(metadata,self.id,qmin,qmax,ymin,ymax)
412	self.fitter.select_problem_for_fit(Uid=self.id,value=value.get_scheduled())
413	self.id += 1
414	except:
415	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
416	return
417	#Do the simultaneous fit
418	try:
419	result=self.fitter.fit()
420	self._simul_fit_completed(result,qmin,qmax,ymin,ymax)
421	except:
422	wx.PostEvent(self.parent, StatusEvent(status="Simultaneous Fitting error: %s" % sys.exc_value))
423	return
424
425
426	def _onset_engine(self,event):
427	""" set engine to scipy"""
428	if self._fit_engine== 'park':
429	self._on_change_engine('scipy')
430	else:
431	self._on_change_engine('park')
432	wx.PostEvent(self.parent, StatusEvent(status="Engine set to: %s" % self._fit_engine))
433
434
435	def _on_change_engine(self, engine='park'):
436	"""
437	Allow to select the type of engine to perform fit
438	@param engine: the key work of the engine
439	"""
440	self._fit_engine = engine
441
442
443	def _on_model_panel(self, evt):
444	"""
445	react to model selection on any combo box or model menu.plot the model
446	"""
447
448	model = evt.model
449	name = evt.name
450	sim_page=self.fit_panel.get_page(0)
451	current_pg = self.fit_panel.get_current_page()
452	if current_pg != sim_page:
453	current_pg.set_panel(model)
454
455	try:
456	metadata=self.page_finder[current_pg].get_data()
457	M_name="M"+str(self.index_model)+"= "+name+"("+metadata.group_id+")"
458	except:
459	M_name="M"+str(self.index_model)+"= "+name
460	model.name="M"+str(self.index_model)
461	self.index_model += 1
462
463	self.page_finder[current_pg].set_model(model,M_name)
464	self.plot_helper(currpage= current_pg,qmin= None,qmax= None)
465	sim_page.add_model(self.page_finder)
466
467
468	def redraw_model(self,qmin= None,qmax= None):
469	"""
470	Draw a theory according to model changes or data range.
471	@param qmin: the minimum value plotted for theory
472	@param qmax: the maximum value plotted for theory
473	"""
474	current_pg=self.fit_panel.get_current_page()
475	for page, value in self.page_finder.iteritems():
476	if page ==current_pg :
477	break
478	self.plot_helper(currpage=page,qmin= qmin,qmax= qmax)
479
480	def plot_helper(self,currpage,qmin=None,qmax=None,ymin=None,ymax=None):
481	"""
482	Plot a theory given a model and data
483	@param model: the model from where the theory is derived
484	@param currpage: page in a dictionary referring to some data
485	"""
486	if self.fit_panel.get_page_count() >1:
487	for page in self.page_finder.iterkeys():
488	if page==currpage :
489	data=self.page_finder[page].get_data()
490	list=self.page_finder[page].get_model()
491	model=list[0]
492	break
493
494	if data!=None and data.__class__.__name__ != 'Data2D':
495	theory = Theory1D(x=[], y=[])
496	theory.name = "Model"
497	theory.group_id = data.group_id
498
499	x_name, x_units = data.get_xaxis()
500	y_name, y_units = data.get_yaxis()
501	theory.xaxis(x_name, x_units)
502	theory.yaxis(y_name, y_units)
503	if qmin == None :
504	qmin = min(data.x)
505	if qmax == None :
506	qmax = max(data.x)
507	try:
508	tempx = qmin
509	tempy = model.run(qmin)
510	theory.x.append(tempx)
511	theory.y.append(tempy)
512	except :
513	wx.PostEvent(self.parent, StatusEvent(status="fitting \
514	skipping point x %g %s" %(qmin, sys.exc_value)))
515
516	for i in range(len(data.x)):
517	try:
518	if data.x[i]> qmin and data.x[i]< qmax:
519	tempx = data.x[i]
520	tempy = model.run(tempx)
521	theory.x.append(tempx)
522	theory.y.append(tempy)
523
524	except:
525	wx.PostEvent(self.parent, StatusEvent(status="fitting \
526	skipping point x %g %s" %(data.x[i], sys.exc_value)))
527	try:
528	tempx = qmax
529	tempy = model.run(qmax)
530	theory.x.append(tempx)
531	theory.y.append(tempy)
532	except:
533	wx.PostEvent(self.parent, StatusEvent(status="fitting \
534	skipping point x %g %s" %(qmax, sys.exc_value)))
535
536	else:
537	theory=Theory2D(data.data, data.err_data)
538	#theory=Theory2D(data.image, data.err_image)
539	theory.x_bins= data.x_bins
540	theory.y_bins= data.y_bins
541	tempy=[]
542	if qmin==None:
543	qmin=data.xmin
544	if qmax==None:
545	qmax=data.xmax
546	if ymin==None:
547	ymin=data.ymin
548	if ymax==None:
549	ymax=data.ymax
550
551	theory.data = numpy.zeros((len(data.y_bins),len(data.x_bins)))
552	for i in range(len(data.y_bins)):
553	if data.y_bins[i]>= ymin and data.y_bins[i]<= ymax:
554	for j in range(len(data.x_bins)):
555	if data.x_bins[i]>= qmin and data.x_bins[i]<= qmax:
556	theory.data[j][i]=model.runXY([data.x_bins[j],data.y_bins[i]])
557
558	#print "fitting : plot_helper:", theory.image
559	#print data.image
560	#print "fitting : plot_helper:",theory.image
561	theory.detector= data.detector
562	theory.source= data.source
563	theory.zmin= data.zmin
564	theory.zmax= data.zmax
565	theory.xmin= qmin
566	theory.xmax= qmax
567	theory.ymin= ymin
568	theory.ymax= ymax
569
570	wx.PostEvent(self.parent, NewPlotEvent(plot=theory, title="Analytical model"))
571
572
573	def _on_model_menu(self, evt):
574	"""
575	Plot a theory from a model selected from the menu
576	"""
577
578	model=evt.model()
579	name="Model View"
580	print "mon menu",model.name
581	description=model.description
582	#self.fit_panel.add_model_page(model,description,model.name)
583	self.fit_panel.add_model_page(model,description,name)
584	self.draw_model(model,self.enable_model2D)
585
586	def draw_model(self,model,enable2D=False):
587	"""
588	draw model with default data value
589	"""
590	x = numpy.arange(0.001, 1.0, 0.001)
591	xlen = len(x)
592	y = numpy.zeros(xlen)
593	if not enable2D:
594	for i in range(xlen):
595	y[i] = model.run(x[i])
596
597	try:
598	new_plot = Theory1D(x, y)
599	new_plot.name = model.name
600	#new_plot.name = "Model"
601	new_plot.xaxis("\\rm{Q}", 'A^{-1}')
602	new_plot.yaxis("\\rm{Intensity} ","cm^{-1}")
603
604	new_plot.group_id ="Fitness"
605	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model 1D"))
606
607	except:
608	raise
609	else:
610	for i in range(xlen):
611	y[i] = model.run(x[i])
612
613	try:
614	new_plot = Theory1D(x, y)
615	new_plot.name = model.name
616	#new_plot.name = "Model"
617	new_plot.xaxis("\\rm{Q}", 'A^{-1}')
618	new_plot.yaxis("\\rm{Intensity} ","cm^{-1}")
619
620	new_plot.group_id ="Fitness"
621	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model 1D"))
622
623	except:
624	raise
625	def on_draw_model2D(self, event):
626	"""
627	plot view model 2D
628	"""
629
630	if self.enable_model2D== True:
631	self.enable_model2D=False
632	else:
633	self.enable_model2D=True
634	print "self.enable_model2D",self.enable_model2D
635	if __name__ == "__main__":
636	i = Plugin()
637
638
639
640

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SasView

source: sasview/sansview/perspectives/fitting/fitting.py @ 2d107b8

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