fitting.py @ d250f7d

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 d250f7d was d250f7d, checked in by Gervaise Alina <gervyh@…>, 16 years ago
model 2D changed
Property mode set to `100644`
File size: 27.1 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	DEFAULT_BEAM = 0.005
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
61	self.menu_mng.populate_menu(menu2, owner)
62	id2 = wx.NewId()
63	owner.Bind(models.EVT_MODEL,self._on_model_menu)
64	#owner.Bind(modelpage.EVT_MODEL,self._on_model_menu)
65	self.fit_panel.set_owner(owner)
66	self.fit_panel.set_model_list(self.menu_mng.get_model_list())
67	owner.Bind(fitpage1D.EVT_MODEL_BOX,self._on_model_panel)
68	owner.Bind(fitpage2D.EVT_MODEL_BOX,self._on_model_panel)
69	#create menubar items
70	return [(id, self.menu1, "Fitting"),(id2, menu2, "Model")]
71
72
73	def help(self, evt):
74	"""
75	Show a general help dialog.
76	TODO: replace the text with a nice image
77	"""
78	from helpDialog import HelpWindow
79	dialog = HelpWindow(None, -1, 'HelpWindow')
80	if dialog.ShowModal() == wx.ID_OK:
81	pass
82	dialog.Destroy()
83
84
85	def get_context_menu(self, graph=None):
86	"""
87	Get the context menu items available for P(r)
88	@param graph: the Graph object to which we attach the context menu
89	@return: a list of menu items with call-back function
90	"""
91	self.graph=graph
92	for item in graph.plottables:
93	if item.__class__.__name__ is "Data2D":
94	return [["Select data for Fitting",\
95	"Dialog with fitting parameters ", self._onSelect]]
96	#elif item.__class__.__name__ is "Theory2D":
97	# return [["Line Slicer [Q-view]","Sector Averaging as a function of Q",
98	# self.onLineSlicer],
99	# ["Annulus Slicer [Phi-view]","Sector Averaging as a function of Phi",
100	# self.onLineSlicer]]
101	else:
102	if item.name==graph.selected_plottable and\
103	item.__class__.__name__ is "Data1D":
104	return [["Select data for Fitting", \
105	"Dialog with fitting parameters ", self._onSelect]]
106	return []
107
108
109	def get_panels(self, parent):
110	"""
111	Create and return a list of panel objects
112	"""
113	self.parent = parent
114	# Creation of the fit panel
115	self.fit_panel = FitPanel(self.parent, -1)
116	#Set the manager forthe main panel
117	self.fit_panel.set_manager(self)
118	# List of windows used for the perspective
119	self.perspective = []
120	self.perspective.append(self.fit_panel.window_name)
121	# take care of saving data, model and page associated with each other
122	self.page_finder = {}
123	#index number to create random model name
124	self.index_model = 0
125	#create the fitting panel
126	return [self.fit_panel]
127
128
129	def get_perspective(self):
130	"""
131	Get the list of panel names for this perspective
132	"""
133	return self.perspective
134
135
136	def on_perspective(self, event):
137	"""
138	Call back function for the perspective menu item.
139	We notify the parent window that the perspective
140	has changed.
141	"""
142	self.parent.set_perspective(self.perspective)
143
144
145	def post_init(self):
146	"""
147	Post initialization call back to close the loose ends
148	[Somehow openGL needs this call]
149	"""
150	self.parent.set_perspective(self.perspective)
151
152
153	def _onSelect(self,event):
154	"""
155	when Select data to fit a new page is created .Its reference is
156	added to self.page_finder
157	"""
158	self.panel = event.GetEventObject()
159	for item in self.panel.graph.plottables:
160	if item.name == self.panel.graph.selected_plottable or\
161	item.__class__.__name__ is "Data2D":
162	#find a name for the page created for notebook
163	try:
164	page = self.fit_panel.add_fit_page(item)
165	# add data associated to the page created
166
167	if page !=None:
168
169	#create a fitproblem storing all link to data,model,page creation
170	self.page_finder[page]= FitProblem()
171	self.page_finder[page].add_data(item)
172	except:
173	wx.PostEvent(self.parent, StatusEvent(status="Creating Fit page: %s"\
174	%sys.exc_value))
175	def schedule_for_fit(self,value=0,fitproblem =None):
176	"""
177
178	"""
179	if fitproblem !=None:
180	fitproblem.schedule_tofit(value)
181	else:
182	current_pg=self.fit_panel.get_current_page()
183	for page, val in self.page_finder.iteritems():
184	if page ==current_pg :
185	val.schedule_tofit(value)
186	break
187
188
189	def get_page_finder(self):
190	""" @return self.page_finder used also by simfitpage.py"""
191	return self.page_finder
192
193
194	def set_page_finder(self,modelname,names,values):
195	"""
196	Used by simfitpage.py to reset a parameter given the string constrainst.
197	@param modelname: the name ot the model for with the parameter has to reset
198	@param value: can be a string in this case.
199	@param names: the paramter name
200	@note: expecting park used for fit.
201	"""
202	sim_page=self.fit_panel.get_page(0)
203	for page, value in self.page_finder.iteritems():
204	if page != sim_page:
205	list=value.get_model()
206	model=list[0]
207	#print "fitting",model.name,modelname
208	if model.name== modelname:
209	value.set_model_param(names,values)
210	break
211
212
213
214	def split_string(self,item):
215	"""
216	receive a word containing dot and split it. used to split parameterset
217	name into model name and parameter name example:
218	paramaterset (item) = M1.A
219	@return model_name =M1 , parameter name =A
220	"""
221	if string.find(item,".")!=-1:
222	param_names= re.split("\.",item)
223	model_name=param_names[0]
224	param_name=param_names[1]
225	return model_name,param_name
226
227
228	def _single_fit_completed(self,result,pars,cpage,qmin,qmax,ymin=None, ymax=None):
229	"""
230	Display fit result on one page of the notebook.
231	@param result: result of fit
232	@param pars: list of names of parameters fitted
233	@param current_pg: the page where information will be displayed
234	@param qmin: the minimum value of x to replot the model
235	@param qmax: the maximum value of x to replot model
236
237	"""
238	try:
239	for page, value in self.page_finder.iteritems():
240	if page==cpage :
241	#fitdata = value.get_data()
242	list = value.get_model()
243	model= list[0]
244	break
245	i = 0
246	# print "fitting: single fit pars ", pars
247	for name in pars:
248	if result.pvec.__class__==numpy.float64:
249	model.setParam(name,result.pvec)
250	else:
251	model.setParam(name,result.pvec[i])
252	# print "fitting: single fit", name, result.pvec[i]
253	i += 1
254	# print "fitting result : chisqr",result.fitness
255	# print "fitting result : pvec",result.pvec
256	# print "fitting result : stderr",result.stderr
257
258	cpage.onsetValues(result.fitness, result.pvec,result.stderr)
259	self.plot_helper(currpage=cpage,qmin=qmin,qmax=qmax,ymin=ymin, ymax=ymax)
260	except:
261	raise
262	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
263
264
265	def _simul_fit_completed(self,result,qmin,qmax,ymin=None, ymax=None):
266	"""
267	Parameter estimation completed,
268	display the results to the user
269	@param alpha: estimated best alpha
270	@param elapsed: computation time
271	"""
272	try:
273	for page, value in self.page_finder.iteritems():
274	if value.get_scheduled()==1:
275	#fitdata = value.get_data()
276	list = value.get_model()
277	model= list[0]
278
279	small_out = []
280	small_cov = []
281	i = 0
282	#Separate result in to data corresponding to each page
283	for p in result.parameters:
284	model_name,param_name = self.split_string(p.name)
285	if model.name == model_name:
286	small_out.append(p.value )
287	small_cov.append(p.stderr)
288	model.setParam(param_name,p.value)
289	# Display result on each page
290	page.onsetValues(result.fitness, small_out,small_cov)
291	#Replot model
292	self.plot_helper(currpage= page,qmin= qmin,qmax= qmax,ymin=ymin, ymax=ymax)
293	except:
294	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
295
296
297	def _on_single_fit(self,id=None,qmin=None,qmax=None,ymin=None,ymax=None):
298	"""
299	perform fit for the current page and return chisqr,out and cov
300	@param engineName: type of fit to be performed
301	@param id: unique id corresponding to a fit problem(model, set of data)
302	@param model: model to fit
303
304	"""
305	#print "in single fitting"
306	#set an engine to perform fit
307	from sans.fit.Fitting import Fit
308	self.fitter= Fit(self._fit_engine)
309	#Setting an id to store model and data in fit engine
310	if id==None:
311	id=0
312	self.id = id
313	page_fitted=None
314	fit_problem=None
315	#Get information (model , data) related to the page on
316	#with the fit will be perform
317	#current_pg=self.fit_panel.get_current_page()
318	#simul_pg=self.fit_panel.get_page(0)
319
320	for page, value in self.page_finder.iteritems():
321	if value.get_scheduled() ==1 :
322	metadata = value.get_data()
323	list=value.get_model()
324	model=list[0]
325	#Create list of parameters for fitting used
326	pars=[]
327	templist=[]
328	try:
329	#templist=current_pg.get_param_list()
330	templist=page.get_param_list()
331	for element in templist:
332	pars.append(str(element[0].GetLabelText()))
333	pars.sort()
334	#Do the single fit
335	self.fitter.set_model(Model(model), self.id, pars)
336
337	self.fitter.set_data(metadata,self.id,qmin,qmax)
338	self.fitter.select_problem_for_fit(Uid=self.id,value=value.get_scheduled())
339	page_fitted=page
340	self.id+=1
341	self.schedule_for_fit( 0,value)
342	except:
343	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
344	return
345	# make sure to keep an alphabetic order
346	#of parameter names in the list
347	try:
348	result=self.fitter.fit()
349	#self._single_fit_completed(result,pars,current_pg,qmin,qmax)
350	#print "single_fit: result",result.fitness,result.pvec,result.stderr
351	#self._single_fit_completed(result,pars,page,qmin,qmax)
352	self._single_fit_completed(result,pars,page_fitted,qmin,qmax,ymin,ymax)
353	except:
354	raise
355	wx.PostEvent(self.parent, StatusEvent(status="Single Fit error: %s" % sys.exc_value))
356	return
357
358	def _on_simul_fit(self, id=None,qmin=None,qmax=None, ymin=None, ymax=None):
359	"""
360	perform fit for all the pages selected on simpage and return chisqr,out and cov
361	@param engineName: type of fit to be performed
362	@param id: unique id corresponding to a fit problem(model, set of data)
363	in park_integration
364	@param model: model to fit
365
366	"""
367	#set an engine to perform fit
368	from sans.fit.Fitting import Fit
369	self.fitter= Fit(self._fit_engine)
370
371	#Setting an id to store model and data
372	if id==None:
373	id = 0
374	self.id = id
375
376	for page, value in self.page_finder.iteritems():
377	try:
378	if value.get_scheduled()==1:
379	metadata = value.get_data()
380	list = value.get_model()
381	model= list[0]
382	#Create dictionary of parameters for fitting used
383	pars = []
384	templist = []
385	templist = page.get_param_list()
386	for element in templist:
387	try:
388	name = str(element[0].GetLabelText())
389	pars.append(name)
390	except:
391	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
392	return
393	new_model=Model(model)
394	param=value.get_model_param()
395
396	if len(param)>0:
397	for item in param:
398	param_value = item[1]
399	param_name = item[0]
400	#print "fitting ", param,param_name, param_value
401
402	#new_model.set( model.getParam(param_name[0])= param_value)
403	#new_model.set( exec"%s=%s"%(param_name[0], param_value))
404	#new_model.set( exec "%s"%(param_nam) = param_value)
405	new_model.parameterset[ param_name].set( param_value )
406
407	self.fitter.set_model(new_model, self.id, pars)
408	self.fitter.set_data(metadata,self.id,qmin,qmax,ymin,ymax)
409	self.fitter.select_problem_for_fit(Uid=self.id,value=value.get_scheduled())
410	self.id += 1
411	except:
412	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
413	return
414	#Do the simultaneous fit
415	try:
416	result=self.fitter.fit()
417	self._simul_fit_completed(result,qmin,qmax,ymin,ymax)
418	except:
419	wx.PostEvent(self.parent, StatusEvent(status="Simultaneous Fitting error: %s" % sys.exc_value))
420	return
421
422
423	def _onset_engine(self,event):
424	""" set engine to scipy"""
425	if self._fit_engine== 'park':
426	self._on_change_engine('scipy')
427	else:
428	self._on_change_engine('park')
429	wx.PostEvent(self.parent, StatusEvent(status="Engine set to: %s" % self._fit_engine))
430
431
432	def _on_change_engine(self, engine='park'):
433	"""
434	Allow to select the type of engine to perform fit
435	@param engine: the key work of the engine
436	"""
437	self._fit_engine = engine
438
439
440	def _on_model_panel(self, evt):
441	"""
442	react to model selection on any combo box or model menu.plot the model
443	"""
444
445	model = evt.model
446	name = evt.name
447	sim_page=self.fit_panel.get_page(0)
448	current_pg = self.fit_panel.get_current_page()
449	if current_pg != sim_page:
450	current_pg.set_panel(model)
451
452	try:
453	metadata=self.page_finder[current_pg].get_data()
454	M_name="M"+str(self.index_model)+"= "+name+"("+metadata.group_id+")"
455	except:
456	M_name="M"+str(self.index_model)+"= "+name
457	model.name="M"+str(self.index_model)
458	self.index_model += 1
459
460	self.page_finder[current_pg].set_model(model,M_name)
461	self.plot_helper(currpage= current_pg,qmin= None,qmax= None)
462	sim_page.add_model(self.page_finder)
463
464
465	def redraw_model(self,qmin= None,qmax= None):
466	"""
467	Draw a theory according to model changes or data range.
468	@param qmin: the minimum value plotted for theory
469	@param qmax: the maximum value plotted for theory
470	"""
471	current_pg=self.fit_panel.get_current_page()
472	for page, value in self.page_finder.iteritems():
473	if page ==current_pg :
474	break
475	self.plot_helper(currpage=page,qmin= qmin,qmax= qmax)
476
477	def plot_helper(self,currpage,qmin=None,qmax=None,ymin=None,ymax=None):
478	"""
479	Plot a theory given a model and data
480	@param model: the model from where the theory is derived
481	@param currpage: page in a dictionary referring to some data
482	"""
483	if self.fit_panel.get_page_count() >1:
484	for page in self.page_finder.iterkeys():
485	if page==currpage :
486	data=self.page_finder[page].get_data()
487	list=self.page_finder[page].get_model()
488	model=list[0]
489	break
490
491	if data!=None and data.__class__.__name__ != 'Data2D':
492	theory = Theory1D(x=[], y=[])
493	theory.name = "Model"
494	theory.group_id = data.group_id
495
496	x_name, x_units = data.get_xaxis()
497	y_name, y_units = data.get_yaxis()
498	theory.xaxis(x_name, x_units)
499	theory.yaxis(y_name, y_units)
500	if qmin == None :
501	qmin = min(data.x)
502	if qmax == None :
503	qmax = max(data.x)
504	try:
505	tempx = qmin
506	tempy = model.run(qmin)
507	theory.x.append(tempx)
508	theory.y.append(tempy)
509	except :
510	wx.PostEvent(self.parent, StatusEvent(status="fitting \
511	skipping point x %g %s" %(qmin, sys.exc_value)))
512
513	for i in range(len(data.x)):
514	try:
515	if data.x[i]> qmin and data.x[i]< qmax:
516	tempx = data.x[i]
517	tempy = model.run(tempx)
518	theory.x.append(tempx)
519	theory.y.append(tempy)
520
521	except:
522	wx.PostEvent(self.parent, StatusEvent(status="fitting \
523	skipping point x %g %s" %(data.x[i], sys.exc_value)))
524	try:
525	tempx = qmax
526	tempy = model.run(qmax)
527	theory.x.append(tempx)
528	theory.y.append(tempy)
529	except:
530	wx.PostEvent(self.parent, StatusEvent(status="fitting \
531	skipping point x %g %s" %(qmax, sys.exc_value)))
532
533	else:
534	theory=Theory2D(data.data, data.err_data)
535	#theory=Theory2D(data.image, data.err_image)
536	theory.x_bins= data.x_bins
537	theory.y_bins= data.y_bins
538	tempy=[]
539	if qmin==None:
540	qmin=data.xmin
541	if qmax==None:
542	qmax=data.xmax
543	if ymin==None:
544	ymin=data.ymin
545	if ymax==None:
546	ymax=data.ymax
547
548	theory.data = numpy.zeros((len(data.y_bins),len(data.x_bins)))
549	for i in range(len(data.y_bins)):
550	if data.y_bins[i]>= ymin and data.y_bins[i]<= ymax:
551	for j in range(len(data.x_bins)):
552	if data.x_bins[i]>= qmin and data.x_bins[i]<= qmax:
553	theory.data[j][i]=model.runXY([data.x_bins[j],data.y_bins[i]])
554
555	#print "fitting : plot_helper:", theory.image
556	#print data.image
557	#print "fitting : plot_helper:",theory.image
558	theory.detector= data.detector
559	theory.source= data.source
560	theory.zmin= data.zmin
561	theory.zmax= data.zmax
562	theory.xmin= qmin
563	theory.xmax= qmax
564	theory.ymin= ymin
565	theory.ymax= ymax
566
567	wx.PostEvent(self.parent, NewPlotEvent(plot=theory, title="Analytical model"))
568
569
570	def _on_model_menu(self, evt):
571	"""
572	Plot a theory from a model selected from the menu
573	"""
574
575	model=evt.model()
576	#name="Model View"
577	#print "mon menu",model.name
578	description=model.description
579	#self.fit_panel.add_model_page(model,description,name)
580
581	self.draw_model(model,self.enable_model2D)
582
583	def draw_model(self,model,description=None,enable1D=True, enable2D=False,qmin=None, qmax=None,qstep=None):
584	"""
585	draw model with default data value
586	"""
587	self.fit_panel.add_model_page(model,model.description,model.name)
588	self._draw_model2D(model,model.description, enable2D,qmin,qmax,qstep)
589	self._draw_model1D(model,model.description, enable1D,qmin,qmax, qstep)
590
591	def _draw_model1D(self,model,description=None, enable1D=True,qmin=None,qmax=None, qstep=None):
592
593	if enable1D:
594	if qmin==None:
595	qmin= 0.001
596	if qmax==None:
597	qmax= 1.0
598	if qstep ==None:
599	qstep =0.001
600
601
602	x = numpy.arange(qmin, qmax, qstep)
603	xlen= len(x)
604	y = numpy.zeros(xlen)
605	if not enable1D:
606	for i in range(xlen):
607	y[i] = model.run(x[i])
608
609	try:
610	new_plot = Theory1D(x, y)
611	#new_plot.name = model.name
612	new_plot.name = "Model"
613	new_plot.xaxis("\\rm{Q}", 'A^{-1}')
614	new_plot.yaxis("\\rm{Intensity} ","cm^{-1}")
615
616	new_plot.group_id ="Fitness"
617	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model 1D"))
618
619	except:
620	raise
621	else:
622	for i in range(xlen):
623	y[i] = model.run(x[i])
624
625	try:
626	new_plot = Theory1D(x, y)
627	new_plot.name = model.name
628	#new_plot.name = "Model"
629	new_plot.xaxis("\\rm{Q}", 'A^{-1}')
630	new_plot.yaxis("\\rm{Intensity} ","cm^{-1}")
631
632	new_plot.group_id ="Fitness"
633	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model 1D"))
634
635	except:
636	raise
637
638
639
640	def _draw_model2D(self,model,description=None, enable2D=False,qmin=None,qmax=None, qstep=None):
641	if qmin==None:
642	qmin= -0.05
643	if qmax==None:
644	qmax= 0.05
645	if qstep ==None:
646	qstep =0.001
647	x = numpy.arange(qmin,qmax, qstep)
648	y = numpy.arange(qmin,qmax,qstep)
649
650	if enable2D:
651	data=numpy.zeros([len(x),len(y)])
652	for i in range(len(x)):
653	for j in range(len(x)):
654	try:
655	data[i][j]=model.runXY([j,i])
656	except:
657	wx.PostEvent(self.parent, StatusEvent(status="\
658	Model 2D cannot be plot %g %s %s" %(data[i][j],model.name, sys.exc_value)))
659	theory = Theory2D(data)
660	theory.group_id =str(model.name)+" 2D"
661	theory.xmin= qmin
662	theory.xmax= qmax
663	theory.ymin= qmin
664	theory.ymax= qmax
665	wx.PostEvent(self.parent, NewPlotEvent(plot=theory, title="Analytical model 2D"))
666	def on_draw_model2D(self, event):
667	"""
668	plot view model 2D
669	"""
670
671	if self.enable_model2D== True:
672	self.enable_model2D=False
673	else:
674	self.enable_model2D=True
675	print "self.enable_model2D",self.enable_model2D
676	if __name__ == "__main__":
677	i = Plugin()
678
679
680
681

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SasView

source: sasview/sansview/perspectives/fitting/fitting.py @ d250f7d

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