fitting.py @ 415bc97

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 415bc97 was d7d143b0, checked in by Gervaise Alina <gervyh@…>, 16 years ago
need to fix help html
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1	import os,os.path, re
2	import sys, wx, logging
3	import string, numpy, pylab, math
4
5	from copy import deepcopy
6	from danse.common.plottools.plottables import Data1D, Theory1D, Data2D
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	class Theory2D(Data2D):
17	def __init__(self,image=None,err_image=None,xmin=None,
18	xmax=None,ymin=None,ymax=None,zmin=None,zmax=None):
19	Data2D.__init__(self,image,err_image,xmin,
20	xmax,ymin,ymax,zmin,zmax)
21	class Plugin:
22	"""
23	Fitting plugin is used to perform fit
24	"""
25	def __init__(self):
26	## Plug-in name
27	self.sub_menu = "Fitting"
28
29	## Reference to the parent window
30	self.parent = None
31	self.menu_mng = models.ModelManager()
32	## List of panels for the simulation perspective (names)
33	self.perspective = []
34	# Start with a good default
35	self.elapsed = 0.022
36	self.fitter = None
37
38	#Flag to let the plug-in know that it is running standalone
39	self.standalone=True
40	## Fit engine
41	self._fit_engine = 'scipy'
42	# Log startup
43	logging.info("Fitting plug-in started")
44
45	def populate_menu(self, id, owner):
46	"""
47	Create a menu for the Fitting plug-in
48	@param id: id to create a menu
49	@param owner: owner of menu
50	@ return : list of information to populate the main menu
51	"""
52	#Menu for fitting
53	self.menu1 = wx.Menu()
54	id1 = wx.NewId()
55	self.menu1.Append(id1, '&Show fit panel')
56	wx.EVT_MENU(owner, id1, self.on_perspective)
57	id3 = wx.NewId()
58	self.menu1.AppendCheckItem(id3, "park")
59	wx.EVT_MENU(owner, id3, self._onset_engine)
60
61	#menu for model
62	menu2 = wx.Menu()
63	self.menu_mng.populate_menu(menu2, owner)
64	id2 = wx.NewId()
65	owner.Bind(models.EVT_MODEL,self._on_model_menu)
66	#owner.Bind(modelpage.EVT_MODEL,self._on_model_menu)
67	self.fit_panel.set_owner(owner)
68	self.fit_panel.set_model_list(self.menu_mng.get_model_list())
69	owner.Bind(fitpage1D.EVT_MODEL_BOX,self._on_model_panel)
70	owner.Bind(fitpage2D.EVT_MODEL_BOX,self._on_model_panel)
71	#create menubar items
72	return [(id, self.menu1, "Fitting"),(id2, menu2, "Model")]
73
74
75	def help(self, evt):
76	"""
77	Show a general help dialog.
78	TODO: replace the text with a nice image
79	"""
80	from helpDialog import HelpWindow
81	dialog = HelpWindow(None, -1, 'HelpWindow')
82	if dialog.ShowModal() == wx.ID_OK:
83	pass
84	dialog.Destroy()
85
86
87	def get_context_menu(self, graph=None):
88	"""
89	Get the context menu items available for P(r)
90	@param graph: the Graph object to which we attach the context menu
91	@return: a list of menu items with call-back function
92	"""
93	self.graph=graph
94	for item in graph.plottables:
95	if item.__class__.__name__ is "Data2D":
96	return [["Select data for Fitting",\
97	"Dialog with fitting parameters ", self._onSelect]]
98	else:
99	if item.name==graph.selected_plottable and\
100	item.__class__.__name__ is "Data1D":
101	return [["Select data for Fitting", \
102	"Dialog with fitting parameters ", self._onSelect]]
103	return []
104
105
106	def get_panels(self, parent):
107	"""
108	Create and return a list of panel objects
109	"""
110	self.parent = parent
111	# Creation of the fit panel
112	self.fit_panel = FitPanel(self.parent, -1)
113	#Set the manager forthe main panel
114	self.fit_panel.set_manager(self)
115	# List of windows used for the perspective
116	self.perspective = []
117	self.perspective.append(self.fit_panel.window_name)
118	# take care of saving data, model and page associated with each other
119	self.page_finder = {}
120	#index number to create random model name
121	self.index_model = 0
122	#create the fitting panel
123	return [self.fit_panel]
124
125
126	def get_perspective(self):
127	"""
128	Get the list of panel names for this perspective
129	"""
130	return self.perspective
131
132
133	def on_perspective(self, event):
134	"""
135	Call back function for the perspective menu item.
136	We notify the parent window that the perspective
137	has changed.
138	"""
139	self.parent.set_perspective(self.perspective)
140
141
142	def post_init(self):
143	"""
144	Post initialization call back to close the loose ends
145	[Somehow openGL needs this call]
146	"""
147	self.parent.set_perspective(self.perspective)
148
149
150	def _onSelect(self,event):
151	"""
152	when Select data to fit a new page is created .Its reference is
153	added to self.page_finder
154	"""
155	self.panel = event.GetEventObject()
156	for item in self.panel.graph.plottables:
157	if item.name == self.panel.graph.selected_plottable or\
158	item.__class__.__name__ is "Data2D":
159	#find a name for the page created for notebook
160	try:
161	page = self.fit_panel.add_fit_page(item)
162	# add data associated to the page created
163
164	if page !=None:
165
166	#create a fitproblem storing all link to data,model,page creation
167	self.page_finder[page]= FitProblem()
168	self.page_finder[page].add_data(item)
169	except:
170	wx.PostEvent(self.parent, StatusEvent(status="Creating Fit page: %s"\
171	%sys.exc_value))
172	def schedule_for_fit(self,value=0,fitproblem =None):
173	"""
174
175	"""
176	if fitproblem !=None:
177	fitproblem.schedule_tofit(value)
178	else:
179	current_pg=self.fit_panel.get_current_page()
180	for page, val in self.page_finder.iteritems():
181	if page ==current_pg :
182	val.schedule_tofit(value)
183	break
184
185
186	def get_page_finder(self):
187	""" @return self.page_finder used also by simfitpage.py"""
188	return self.page_finder
189
190
191	def set_page_finder(self,modelname,names,values):
192	"""
193	Used by simfitpage.py to reset a parameter given the string constrainst.
194	@param modelname: the name ot the model for with the parameter has to reset
195	@param value: can be a string in this case.
196	@param names: the paramter name
197	@note: expecting park used for fit.
198	"""
199	sim_page=self.fit_panel.get_page(0)
200	for page, value in self.page_finder.iteritems():
201	if page != sim_page:
202	list=value.get_model()
203	model=list[0]
204	#print "fitting",model.name,modelname
205	if model.name== modelname:
206	value.set_model_param(names,values)
207	break
208
209
210
211	def split_string(self,item):
212	"""
213	receive a word containing dot and split it. used to split parameterset
214	name into model name and parameter name example:
215	paramaterset (item) = M1.A
216	@return model_name =M1 , parameter name =A
217	"""
218	if string.find(item,".")!=-1:
219	param_names= re.split("\.",item)
220	model_name=param_names[0]
221	param_name=param_names[1]
222	return model_name,param_name
223
224
225	def _single_fit_completed(self,result,pars,cpage,qmin,qmax,ymin=None, ymax=None):
226	"""
227	Display fit result on one page of the notebook.
228	@param result: result of fit
229	@param pars: list of names of parameters fitted
230	@param current_pg: the page where information will be displayed
231	@param qmin: the minimum value of x to replot the model
232	@param qmax: the maximum value of x to replot model
233
234	"""
235	try:
236	for page, value in self.page_finder.iteritems():
237	if page==cpage :
238	#fitdata = value.get_data()
239	list = value.get_model()
240	model= list[0]
241	break
242	i = 0
243	# print "fitting: single fit pars ", pars
244	for name in pars:
245	if result.pvec.__class__==numpy.float64:
246	model.setParam(name,result.pvec)
247	else:
248	model.setParam(name,result.pvec[i])
249	# print "fitting: single fit", name, result.pvec[i]
250	i += 1
251	# print "fitting result : chisqr",result.fitness
252	# print "fitting result : pvec",result.pvec
253	# print "fitting result : stderr",result.stderr
254
255	cpage.onsetValues(result.fitness, result.pvec,result.stderr)
256	self.plot_helper(currpage=cpage,qmin=qmin,qmax=qmax,ymin=ymin, ymax=ymax)
257	except:
258	raise
259	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
260
261
262	def _simul_fit_completed(self,result,qmin,qmax,ymin=None, ymax=None):
263	"""
264	Parameter estimation completed,
265	display the results to the user
266	@param alpha: estimated best alpha
267	@param elapsed: computation time
268	"""
269	try:
270	for page, value in self.page_finder.iteritems():
271	if value.get_scheduled()==1:
272	#fitdata = value.get_data()
273	list = value.get_model()
274	model= list[0]
275
276	small_out = []
277	small_cov = []
278	i = 0
279	#Separate result in to data corresponding to each page
280	for p in result.parameters:
281	model_name,param_name = self.split_string(p.name)
282	if model.name == model_name:
283	small_out.append(p.value )
284	small_cov.append(p.stderr)
285	model.setParam(param_name,p.value)
286	# Display result on each page
287	page.onsetValues(result.fitness, small_out,small_cov)
288	#Replot model
289	self.plot_helper(currpage= page,qmin= qmin,qmax= qmax,ymin=ymin, ymax=ymax)
290	except:
291	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
292
293
294	def _on_single_fit(self,id=None,qmin=None,qmax=None,ymin=None,ymax=None):
295	"""
296	perform fit for the current page and return chisqr,out and cov
297	@param engineName: type of fit to be performed
298	@param id: unique id corresponding to a fit problem(model, set of data)
299	@param model: model to fit
300
301	"""
302	#print "in single fitting"
303	#set an engine to perform fit
304	from sans.fit.Fitting import Fit
305	self.fitter= Fit(self._fit_engine)
306	#Setting an id to store model and data in fit engine
307	if id==None:
308	id=0
309	self.id = id
310	page_fitted=None
311	fit_problem=None
312	#Get information (model , data) related to the page on
313	#with the fit will be perform
314	#current_pg=self.fit_panel.get_current_page()
315	#simul_pg=self.fit_panel.get_page(0)
316
317	for page, value in self.page_finder.iteritems():
318	if value.get_scheduled() ==1 :
319	metadata = value.get_data()
320	list=value.get_model()
321	model=list[0]
322	#Create list of parameters for fitting used
323	pars=[]
324	templist=[]
325	try:
326	#templist=current_pg.get_param_list()
327	templist=page.get_param_list()
328	for element in templist:
329	pars.append(str(element[0].GetLabelText()))
330	pars.sort()
331	#Do the single fit
332	self.fitter.set_model(Model(model), self.id, pars)
333	self.fitter.set_data(metadata,self.id,qmin,qmax)
334	self.fitter.select_problem_for_fit(Uid=self.id,value=value.get_scheduled())
335	page_fitted=page
336	self.id+=1
337	self.schedule_for_fit( 0,value)
338	except:
339	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
340	return
341	# make sure to keep an alphabetic order
342	#of parameter names in the list
343	try:
344	result=self.fitter.fit()
345	#self._single_fit_completed(result,pars,current_pg,qmin,qmax)
346	print "single_fit: result",result.fitness,result.pvec,result.stderr
347	#self._single_fit_completed(result,pars,page,qmin,qmax)
348	self._single_fit_completed(result,pars,page_fitted,qmin,qmax,ymin,ymax)
349	except:
350	raise
351	wx.PostEvent(self.parent, StatusEvent(status="Single Fit error: %s" % sys.exc_value))
352	return
353
354	def _on_simul_fit(self, id=None,qmin=None,qmax=None, ymin=None, ymax=None):
355	"""
356	perform fit for all the pages selected on simpage and return chisqr,out and cov
357	@param engineName: type of fit to be performed
358	@param id: unique id corresponding to a fit problem(model, set of data)
359	in park_integration
360	@param model: model to fit
361
362	"""
363	#set an engine to perform fit
364	from sans.fit.Fitting import Fit
365	self.fitter= Fit(self._fit_engine)
366
367	#Setting an id to store model and data
368	if id==None:
369	id = 0
370	self.id = id
371
372	for page, value in self.page_finder.iteritems():
373	try:
374	if value.get_scheduled()==1:
375	metadata = value.get_data()
376	list = value.get_model()
377	model= list[0]
378	#Create dictionary of parameters for fitting used
379	pars = []
380	templist = []
381	templist = page.get_param_list()
382	for element in templist:
383	try:
384	name = str(element[0].GetLabelText())
385	pars.append(name)
386	except:
387	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
388	return
389	new_model=Model(model)
390	param=value.get_model_param()
391
392	if len(param)>0:
393	for item in param:
394	param_value = item[1]
395	param_name = item[0]
396	#print "fitting ", param,param_name, param_value
397
398	#new_model.set( model.getParam(param_name[0])= param_value)
399	#new_model.set( exec"%s=%s"%(param_name[0], param_value))
400	#new_model.set( exec "%s"%(param_nam) = param_value)
401	new_model.parameterset[ param_name].set( param_value )
402
403	self.fitter.set_model(new_model, self.id, pars)
404	self.fitter.set_data(metadata,self.id,qmin,qmax,ymin,ymax)
405	self.fitter.select_problem_for_fit(Uid=self.id,value=value.get_scheduled())
406	self.id += 1
407	except:
408	wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value))
409	return
410	#Do the simultaneous fit
411	try:
412	result=self.fitter.fit()
413	self._simul_fit_completed(result,qmin,qmax,ymin,ymax)
414	except:
415	wx.PostEvent(self.parent, StatusEvent(status="Simultaneous Fitting error: %s" % sys.exc_value))
416	return
417
418
419	def _onset_engine(self,event):
420	""" set engine to scipy"""
421	if self._fit_engine== 'park':
422	self._on_change_engine('scipy')
423	else:
424	self._on_change_engine('park')
425	wx.PostEvent(self.parent, StatusEvent(status="Engine set to: %s" % self._fit_engine))
426
427
428	def _on_change_engine(self, engine='park'):
429	"""
430	Allow to select the type of engine to perform fit
431	@param engine: the key work of the engine
432	"""
433	self._fit_engine = engine
434
435
436	def _on_model_panel(self, evt):
437	"""
438	react to model selection on any combo box or model menu.plot the model
439	"""
440
441	model = evt.model
442	name = evt.name
443	sim_page=self.fit_panel.get_page(0)
444	current_pg = self.fit_panel.get_current_page()
445	if current_pg != sim_page:
446	current_pg.set_panel(model)
447
448	try:
449	metadata=self.page_finder[current_pg].get_data()
450	M_name="M"+str(self.index_model)+"= "+name+"("+metadata.group_id+")"
451	except:
452	M_name="M"+str(self.index_model)+"= "+name
453	model.name="M"+str(self.index_model)
454	self.index_model += 1
455
456	self.page_finder[current_pg].set_model(model,M_name)
457	self.plot_helper(currpage= current_pg,qmin= None,qmax= None)
458	sim_page.add_model(self.page_finder)
459
460
461	def redraw_model(self,qmin= None,qmax= None):
462	"""
463	Draw a theory according to model changes or data range.
464	@param qmin: the minimum value plotted for theory
465	@param qmax: the maximum value plotted for theory
466	"""
467	current_pg=self.fit_panel.get_current_page()
468	for page, value in self.page_finder.iteritems():
469	if page ==current_pg :
470	break
471	self.plot_helper(currpage=page,qmin= qmin,qmax= qmax)
472
473	def plot_helper(self,currpage,qmin=None,qmax=None,ymin=None,ymax=None):
474	"""
475	Plot a theory given a model and data
476	@param model: the model from where the theory is derived
477	@param currpage: page in a dictionary referring to some data
478	"""
479	if self.fit_panel.get_page_count() >1:
480	for page in self.page_finder.iterkeys():
481	if page==currpage :
482	data=self.page_finder[page].get_data()
483	list=self.page_finder[page].get_model()
484	model=list[0]
485	break
486
487	if data!=None and data.__class__.__name__ != 'Data2D':
488	theory = Theory1D(x=[], y=[])
489	theory.name = "Model"
490	theory.group_id = data.group_id
491
492	x_name, x_units = data.get_xaxis()
493	y_name, y_units = data.get_yaxis()
494	theory.xaxis(x_name, x_units)
495	theory.yaxis(y_name, y_units)
496	if qmin == None :
497	qmin = min(data.x)
498	if qmax == None :
499	qmax = max(data.x)
500	try:
501	tempx = qmin
502	tempy = model.run(qmin)
503	theory.x.append(tempx)
504	theory.y.append(tempy)
505	except :
506	wx.PostEvent(self.parent, StatusEvent(status="fitting \
507	skipping point x %g %s" %(qmin, sys.exc_value)))
508
509	for i in range(len(data.x)):
510	try:
511	if data.x[i]> qmin and data.x[i]< qmax:
512	tempx = data.x[i]
513	tempy = model.run(tempx)
514	theory.x.append(tempx)
515	theory.y.append(tempy)
516
517	except:
518	wx.PostEvent(self.parent, StatusEvent(status="fitting \
519	skipping point x %g %s" %(data.x[i], sys.exc_value)))
520	try:
521	tempx = qmax
522	tempy = model.run(qmax)
523	theory.x.append(tempx)
524	theory.y.append(tempy)
525	except:
526	wx.PostEvent(self.parent, StatusEvent(status="fitting \
527	skipping point x %g %s" %(qmax, sys.exc_value)))
528
529	else:
530	theory=Data2D(data.image, data.err_image)
531	#theory=Theory2D(data.image, data.err_image)
532	theory.x_bins= data.x_bins
533	theory.y_bins= data.y_bins
534	tempy=[]
535	if qmin==None:
536	qmin=data.xmin
537	if qmax==None:
538	qmax=data.xmax
539	if ymin==None:
540	ymin=data.ymin
541	if ymax==None:
542	ymax=data.ymax
543
544	theory.image = numpy.zeros((len(data.y_bins),len(data.x_bins)))
545	for i in range(len(data.y_bins)):
546	if data.y_bins[i]>= ymin and data.y_bins[i]<= ymax:
547	for j in range(len(data.x_bins)):
548	if data.x_bins[i]>= qmin and data.x_bins[i]<= qmax:
549	theory.image[j][i]=model.runXY([data.x_bins[j],data.y_bins[i]])
550
551	#print "fitting : plot_helper:", theory.image
552	#print data.image
553	#print "fitting : plot_helper:",theory.image
554	theory.zmin= data.zmin
555	theory.zmax= data.zmax
556	theory.xmin= qmin
557	theory.xmax= qmax
558	theory.ymin= ymin
559	theory.ymax= ymax
560
561	wx.PostEvent(self.parent, NewPlotEvent(plot=theory, title="Analytical model"))
562
563
564	def _on_model_menu(self, evt):
565	"""
566	Plot a theory from a model selected from the menu
567	"""
568	name="Model View"
569	model=evt.model()
570
571	description=model.description
572	self.fit_panel.add_model_page(model,description,name)
573	self.draw_model(model)
574
575	def draw_model(self,model):
576	"""
577	draw model with default data value
578	"""
579	x = pylab.arange(0.001, 0.1, 0.001)
580	xlen = len(x)
581	dy = numpy.zeros(xlen)
582	y = numpy.zeros(xlen)
583
584	for i in range(xlen):
585	y[i] = model.run(x[i])
586	dy[i] = math.sqrt(math.fabs(y[i]))
587	try:
588	new_plot = Theory1D(x, y)
589	new_plot.name = "Model"
590	new_plot.xaxis("\\rm{Q}", 'A^{-1}')
591	new_plot.yaxis("\\rm{Intensity} ","cm^{-1}")
592	new_plot.group_id ="Fitness"
593	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model"))
594	except:
595	raise
596	if __name__ == "__main__":
597	i = Plugin()
598
599
600
601

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source: sasview/sansview/perspectives/fitting/fitting.py @ 415bc97

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