fitting.py @ 6ef7ac5a

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 6ef7ac5a was 7975f2b, checked in by Jae Cho <jhjcho@…>, 15 years ago
correction of chi2 value from park, cleaned unnecessary calculation, reduced mac crash by placing sleep(0.5) between layouts.
Property mode set to `100644`
File size: 48.9 KB

Line
1	"""
2	This software was developed by the University of Tennessee as part of the
3	Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
4	project funded by the US National Science Foundation.
5
6	See the license text in license.txt
7
8	copyright 2009, University of Tennessee
9	"""
10	import re,copy
11	import sys, wx, logging
12	import string, numpy, math
13	import time
14	import thread
15	#from danse.common.plottools.plottables import Theory1D
16	from danse.common.plottools.PlotPanel import PlotPanel
17
18	from sans.guiframe.dataFitting import Data2D
19	from sans.guiframe.dataFitting import Data1D
20	from sans.guiframe.dataFitting import Theory1D
21	from sans.guiframe import dataFitting
22	from sans.guiframe.utils import format_number
23
24	from sans.guicomm.events import NewPlotEvent, StatusEvent
25	from sans.guicomm.events import EVT_SLICER_PANEL,ERR_DATA,EVT_REMOVE_DATA
26	from sans.guicomm.events import EVT_SLICER_PARS_UPDATE
27
28	from sans.fit.AbstractFitEngine import Model
29	from sans.fit.AbstractFitEngine import FitAbort
30
31
32	from fitproblem import FitProblem
33	from fitpanel import FitPanel
34	from fit_thread import FitThread
35	import models
36	import fitpage
37
38	DEFAULT_BEAM = 0.005
39	DEFAULT_QMIN = 0.001
40	DEFAULT_QMAX = 0.13
41	DEFAULT_NPTS = 50
42
43	(PageInfoEvent, EVT_PAGE_INFO) = wx.lib.newevent.NewEvent()
44
45
46	class PlotInfo:
47	"""
48	store some plotting field
49	"""
50	_xunit = 'A^{-1}'
51	_xaxis= "\\rm{Q}"
52	_yunit = "cm^{-1}"
53	_yaxis= "\\rm{Intensity} "
54	id = "Model"
55	group_id = "Model"
56	title= None
57	info= None
58
59
60	class Plugin:
61	"""
62	Fitting plugin is used to perform fit
63	"""
64	def __init__(self):
65	## Plug-in name
66	self.sub_menu = "Fitting"
67
68	## Reference to the parent window
69	self.parent = None
70	#Provide list of models existing in the application
71	self.menu_mng = models.ModelManager()
72	## List of panels for the simulation perspective (names)
73	self.perspective = []
74	#list of panel to send to guiframe
75	self.mypanels=[]
76	# reference to the current running thread
77	self.calc_2D= None
78	self.calc_1D= None
79	self.calc_fit= None
80
81	# Start with a good default
82	self.elapsed = 0.022
83	# the type of optimizer selected, park or scipy
84	self.fitter = None
85	#let fit ready
86	self.fitproblem_count = None
87	#Flag to let the plug-in know that it is running stand alone
88	self.standalone=True
89	## dictionary of page closed and id
90	self.closed_page_dict ={}
91	## Fit engine
92	self._fit_engine = 'scipy'
93	#List of selected data
94	self.selected_data_list=[]
95	## list of slicer panel created to display slicer parameters and results
96	self.slicer_panels=[]
97	# Log startup
98	logging.info("Fitting plug-in started")
99	# model 2D view
100	self.model2D_id=None
101	#keep reference of the simultaneous fit page
102	self.sim_page=None
103	#dictionary containing data name and error on dy of that data
104	self.err_dy={}
105
106
107
108	def populate_menu(self, id, owner):
109	"""
110	Create a menu for the Fitting plug-in
111	@param id: id to create a menu
112	@param owner: owner of menu
113	@ return : list of information to populate the main menu
114	"""
115	#Menu for fitting
116	self.menu1 = wx.Menu()
117
118	#Set park engine
119	id3 = wx.NewId()
120	scipy_help= "Scipy Engine: Perform Simple fit. More in Help window...."
121	self.menu1.AppendCheckItem(id3, "Simple Fit [Scipy]",scipy_help)
122	wx.EVT_MENU(owner, id3, self._onset_engine_scipy)
123
124	id3 = wx.NewId()
125	park_help = "Park Engine: Perform Complex fit. More in Help window...."
126	self.menu1.AppendCheckItem(id3, "Complex Fit [Park]",park_help)
127	wx.EVT_MENU(owner, id3, self._onset_engine_park)
128
129	self.menu1.FindItemByPosition(0).Check(True)
130	self.menu1.FindItemByPosition(1).Check(False)
131
132	self.menu1.AppendSeparator()
133	id1 = wx.NewId()
134	simul_help = "Allow to edit fit engine with multiple model and data"
135	self.menu1.Append(id1, '&Simultaneous Page',simul_help)
136	wx.EVT_MENU(owner, id1, self.on_add_sim_page)
137	#menu for SLD Calculator
138	self.tool_menu = wx.Menu()
139	id_tool_menu = wx.NewId()
140	sld_id = wx.NewId()
141	sld_help= "Compute the scattering length density of molecules"
142	self.tool_menu.Append(sld_id, "SLD Calculator",sld_help)
143	wx.EVT_MENU(owner,sld_id, self.onCalculateSld)
144
145	#menu for model
146	menu2 = wx.Menu()
147	self.menu_mng.populate_menu(menu2, owner)
148	id2 = wx.NewId()
149	owner.Bind(models.EVT_MODEL,self._on_model_menu)
150
151	self.fit_panel.set_owner(owner)
152	self.fit_panel.set_model_list(self.menu_mng.get_model_list())
153	owner.Bind(fitpage.EVT_MODEL_BOX,self._on_model_panel)
154
155	#create menubar items
156	return [(id, self.menu1, "Fitting"),
157	(id_tool_menu, self.tool_menu,"Tools" ),
158	(id2, menu2, "Model")]
159
160
161	def on_add_sim_page(self, event):
162	"""
163	Create a page to access simultaneous fit option
164	"""
165	Plugin.on_perspective(self,event=event)
166	if self.sim_page !=None:
167	msg= "Simultaneous Fit page already opened"
168	wx.PostEvent(self.parent, StatusEvent(status= msg))
169	return
170
171	self.sim_page= self.fit_panel.add_sim_page()
172
173
174
175	def help(self, evt):
176	"""
177	Show a general help dialog.
178	TODO: replace the text with a nice image
179	"""
180	from helpPanel import HelpWindow
181	frame = HelpWindow(None, -1, 'HelpWindow')
182	frame.Show(True)
183
184
185	def get_context_menu(self, graph=None):
186	"""
187	Get the context menu items available for P(r).them allow fitting option
188	for Data2D and Data1D only.
189
190	@param graph: the Graph object to which we attach the context menu
191	@return: a list of menu items with call-back function
192	@note: if Data1D was generated from Theory1D
193	the fitting option is not allowed
194	"""
195	self.graph = graph
196	fitOption = "Select data for fitting"
197	fitOpenHint = "Dialog with fitting parameters "
198
199	for item in graph.plottables:
200	if item.__class__.__name__ is "Data2D":
201
202	if hasattr(item,"is_data"):
203	if item.is_data:
204	return [[fitOption, fitOpenHint, self._onSelect]]
205	else:
206	return []
207	return [[fitOption, fitOpenHint, self._onSelect]]
208	else:
209	if item.name==graph.selected_plottable :
210	if item.name !="$I_{obs}(q)$" and item.name !="$P_{fit}(r)$":
211	if hasattr(item, "group_id"):
212	# if is_data is true , this in an actual data loaded
213	#else it is a data created from a theory model
214	if hasattr(item,"is_data"):
215	if item.is_data:
216	return [[fitOption, fitOpenHint, self._onSelect]]
217	else:
218	return []
219	else:
220	return [[fitOption, fitOpenHint, self._onSelect]]
221	return []
222
223
224	def get_panels(self, parent):
225	"""
226	Create and return a list of panel objects
227	"""
228	self.parent = parent
229	# Creation of the fit panel
230	self.fit_panel = FitPanel(self.parent, -1)
231	#Set the manager for the main panel
232	self.fit_panel.set_manager(self)
233	# List of windows used for the perspective
234	self.perspective = []
235	self.perspective.append(self.fit_panel.window_name)
236	# take care of saving data, model and page associated with each other
237	self.page_finder = {}
238	#index number to create random model name
239	self.index_model = 0
240	self.index_theory= 0
241	self.parent.Bind(EVT_SLICER_PANEL, self._on_slicer_event)
242	self.parent.Bind( ERR_DATA, self._on_data_error)
243	self.parent.Bind(EVT_REMOVE_DATA, self._closed_fitpage)
244	self.parent.Bind(EVT_SLICER_PARS_UPDATE, self._onEVT_SLICER_PANEL)
245	self.parent._mgr.Bind(wx.aui.EVT_AUI_PANE_CLOSE,self._onclearslicer)
246
247
248	#Send the fitting panel to guiframe
249	self.mypanels.append(self.fit_panel)
250	return self.mypanels
251
252
253
254	def get_perspective(self):
255	"""
256	Get the list of panel names for this perspective
257	"""
258	return self.perspective
259
260
261	def on_perspective(self, event):
262	"""
263	Call back function for the perspective menu item.
264	We notify the parent window that the perspective
265	has changed.
266	"""
267	self.parent.set_perspective(self.perspective)
268
269
270	def post_init(self):
271	"""
272	Post initialization call back to close the loose ends
273	"""
274	# Do not show the fitting perspective immediately and
275	# let the application show the Welcome Page.
276	#self.parent.set_perspective(self.perspective)
277	pass
278
279
280	def copy_data(self, item, dy=None):
281	"""
282	receive a data 1D and the list of errors on dy
283	and create a new data1D data
284	@param return
285	"""
286	id=None
287	if hasattr(item,"id"):
288	id = copy.deepcopy(item.id)
289
290	data= Data1D(x=item.x, y=item.y,dx=None, dy=None)
291	data.copy_from_datainfo(item)
292	item.clone_without_data(clone=data)
293	data.dy=dy
294	data.name = item.name
295	## allow to highlight data when plotted
296	data.interactive = copy.deepcopy(item.interactive)
297	## when 2 data have the same id override the 1 st plotted
298	data.id = id
299	data.group_id = item.group_id
300	return data
301
302	def set_fit_range(self, page, qmin, qmax):
303	"""
304	Set the fitting range of a given page
305	"""
306	if page in self.page_finder.iterkeys():
307	fitproblem= self.page_finder[page]
308	fitproblem.set_range(qmin= qmin, qmax= qmax)
309
310	def schedule_for_fit(self,value=0,page=None,fitproblem =None):
311	"""
312	Set the fit problem field to 0 or 1 to schedule that problem to fit.
313	Schedule the specified fitproblem or get the fit problem related to
314	the current page and set value.
315	@param value : integer 0 or 1
316	@param fitproblem: fitproblem to schedule or not to fit
317	"""
318	if fitproblem !=None:
319	fitproblem.schedule_tofit(value)
320	else:
321	if page in self.page_finder.iterkeys():
322	fitproblem= self.page_finder[page]
323	fitproblem.schedule_tofit(value)
324
325
326
327	def get_page_finder(self):
328	""" @return self.page_finder used also by simfitpage.py"""
329	return self.page_finder
330
331
332	def set_page_finder(self,modelname,names,values):
333	"""
334	Used by simfitpage.py to reset a parameter given the string constrainst.
335	@param modelname: the name ot the model for with the parameter has to reset
336	@param value: can be a string in this case.
337	@param names: the paramter name
338	@note: expecting park used for fit.
339	"""
340	sim_page= self.sim_page
341	for page, value in self.page_finder.iteritems():
342	if page != sim_page:
343	list=value.get_model()
344	model = list[0]
345	if model.name== modelname:
346	value.set_model_param(names,values)
347	break
348
349
350
351	def split_string(self,item):
352	"""
353	receive a word containing dot and split it. used to split parameterset
354	name into model name and parameter name example:
355	paramaterset (item) = M1.A
356	@return model_name =M1 , parameter name =A
357	"""
358	if string.find(item,".")!=-1:
359	param_names= re.split("\.",item)
360	model_name=param_names[0]
361	##Assume max len is 3; eg., M0.radius.width
362	if len(param_names) == 3:
363	param_name=param_names[1]+"."+param_names[2]
364	else:
365	param_name=param_names[1]
366	return model_name,param_name
367
368
369	def stop_fit(self):
370	"""
371	Stop the fit engine
372	"""
373	if self.calc_fit!= None and self.calc_fit.isrunning():
374	self.calc_fit.stop()
375	wx.PostEvent(self.parent, StatusEvent(status="Fitting \
376	is cancelled" , type="stop"))
377
378
379
380	def set_smearer(self,smearer, qmin=None, qmax=None):
381	"""
382	Get a smear object and store it to a fit problem
383	@param smearer: smear object to allow smearing data
384	"""
385	self.current_pg=self.fit_panel.get_current_page()
386	self.page_finder[self.current_pg].set_smearer(smearer)
387	## draw model 1D with smeared data
388	data = self.page_finder[self.current_pg].get_plotted_data()
389	model = self.page_finder[self.current_pg].get_model()
390	## if user has already selected a model to plot
391	## redraw the model with data smeared
392
393	smear =self.page_finder[self.current_pg].get_smearer()
394	if model!= None:
395	self.draw_model( model=model, data= data, smearer= smear,
396	qmin= qmin, qmax= qmax)
397
398
399
400	def draw_model(self, model, data= None,smearer= None,
401	enable1D= True, enable2D= False,
402	qmin= DEFAULT_QMIN, qmax= DEFAULT_QMAX, qstep= DEFAULT_NPTS):
403	"""
404	Draw model.
405	@param model: the model to draw
406	@param name: the name of the model to draw
407	@param data: the data on which the model is based to be drawn
408	@param description: model's description
409	@param enable1D: if true enable drawing model 1D
410	@param enable2D: if true enable drawing model 2D
411	@param qmin: Range's minimum value to draw model
412	@param qmax: Range's maximum value to draw model
413	@param qstep: number of step to divide the x and y-axis
414
415	"""
416	## draw model 1D with no loaded data
417	self._draw_model1D( model= model, data= data,enable1D=enable1D, smearer= smearer,
418	qmin= qmin, qmax= qmax, qstep= qstep )
419	## draw model 2D with no initial data
420	self._draw_model2D(model=model,
421	data = data,
422	enable2D= enable2D,
423	qmin=qmin,
424	qmax=qmax,
425	qstep=qstep)
426
427
428
429	def onFit(self):
430	"""
431	perform fit
432	"""
433	## count the number of fitproblem schedule to fit
434	fitproblem_count= 0
435	for value in self.page_finder.itervalues():
436	if value.get_scheduled()==1:
437	fitproblem_count += 1
438
439	## if simultaneous fit change automatically the engine to park
440	if fitproblem_count >1:
441	self._on_change_engine(engine='park')
442
443	self.fitproblem_count = fitproblem_count
444
445	from sans.fit.Fitting import Fit
446	self.fitter= Fit(self._fit_engine)
447
448	if self._fit_engine=="park":
449	engineType="Simultaneous Fit"
450	else:
451	engineType="Single Fit"
452
453	fproblemId = 0
454	self.current_pg=None
455	for page, value in self.page_finder.iteritems():
456	try:
457	if value.get_scheduled()==1:
458	#Get list of parameters name to fit
459	pars = []
460	templist = []
461	templist = page.get_param_list()
462	for element in templist:
463	name = str(element[1])
464	pars.append(name)
465	#Set Engine (model , data) related to the page on
466	self._fit_helper( value=value,pars=pars,
467	id=fproblemId, title= engineType )
468	fproblemId += 1
469	self.current_pg= page
470	except:
471	msg= "%s error: %s" % (engineType,sys.exc_value)
472	wx.PostEvent(self.parent, StatusEvent(status= msg ))
473	return
474
475	#Do the simultaneous fit
476	try:
477	## If a thread is already started, stop it
478	if self.calc_fit!= None and self.calc_fit.isrunning():
479	return
480	self.calc_fit.stop()
481
482	wx.PostEvent(self.parent, StatusEvent(status="Start the computation",
483	curr_thread=self.calc_fit,type="start"))
484	time.sleep(0.5)
485	wx.PostEvent(self.parent, StatusEvent(status="Computing...",
486	curr_thread=self.calc_fit,type="progress"))
487	time.sleep(0.5)
488	## perform single fit
489	if self._fit_engine=="scipy":
490	#qmin, qmax= self.current_pg.get_range()
491	self.calc_fit=FitThread(parent =self.parent,
492	fn= self.fitter,
493	cpage=self.current_pg,
494	pars= pars,
495	completefn= self._single_fit_completed,
496	updatefn=self._updateFit)
497
498	else:
499	## Perform more than 1 fit at the time
500	self.calc_fit=FitThread(parent =self.parent,
501	fn= self.fitter,
502	completefn= self._simul_fit_completed,
503	updatefn=self._updateFit)
504
505	self.calc_fit.queue()
506	self.ready_fit()
507
508	except FitAbort:
509	print "in pluging"
510	except:
511	msg= "%s error: %s" % (engineType,sys.exc_value)
512	wx.PostEvent(self.parent, StatusEvent(status= msg ,type="stop"))
513	return
514
515
516	def ready_fit(self):
517	"""
518	Ready for another fit
519	"""
520	if self.fitproblem_count != None and self.fitproblem_count > 1:
521	self.calc_fit.ready(2.5)
522
523	else:
524	time.sleep(0.4)
525
526	def onCalculateSld(self, event):
527	"""
528	Compute the scattering length density of molecula
529	"""
530	from sldPanel import SldWindow
531	frame = SldWindow(base=self.parent)
532	frame.Show(True)
533
534
535	def _onEVT_SLICER_PANEL(self, event):
536	"""
537	receive and event telling to update a panel with a name starting with
538	event.panel_name. this method update slicer panel for a given interactor.
539	@param event: contains type of slicer , paramaters for updating the panel
540	and panel_name to find the slicer 's panel concerned.
541	"""
542
543	for item in self.parent.panels:
544	if self.parent.panels[item].window_caption.startswith(event.panel_name):
545	self.parent.panels[item].set_slicer(event.type, event.params)
546
547	self.parent._mgr.Update()
548
549
550
551	def _closed_fitpage(self, event):
552	"""
553	request fitpanel to close a given page when its unique data is removed
554	from the plot
555	"""
556	self.fit_panel._close_fitpage(event.data)
557
558
559	def _add_page_onmenu(self, name,fitproblem=None):
560	"""
561	Add name of a closed page of fitpanel in a menu
562	"""
563	list = self.menu1.GetMenuItems()
564	for item in list:
565	if name == item.GetItemLabel():
566	self.closed_page_dict[name][1] = fitproblem
567
568	if not name in self.closed_page_dict.keys():
569	# Post paramters
570	event_id = wx.NewId()
571	self.menu1.Append(event_id, name, "Show %s fit panel" % name)
572	self.closed_page_dict[name]= [event_id, fitproblem]
573	wx.EVT_MENU(self.parent,event_id, self._open_closed_page)
574
575
576	def _open_closed_page(self, event):
577	"""
578	reopen a closed page
579	"""
580	for name, value in self.closed_page_dict.iteritems():
581	if event.GetId() in value:
582	id,fitproblem = value
583	if name !="Model":
584	data= fitproblem.get_fit_data()
585	page = self.fit_panel.add_fit_page(data= data,reset=True)
586	if fitproblem != None:
587	self.page_finder[page]=fitproblem
588	if self.sim_page != None:
589	self.sim_page.draw_page()
590
591	else:
592	model = fitproblem
593	self.fit_panel.add_model_page(model=model, topmenu=True,
594	reset= True)
595	break
596
597
598	def _reset_schedule_problem(self, value=0):
599	"""
600	unschedule or schedule all fitproblem to be fit
601	"""
602	for page, fitproblem in self.page_finder.iteritems():
603	fitproblem.schedule_tofit(value)
604
605	def _fit_helper(self,pars,value, id, title="Single Fit " ):
606	"""
607	helper for fitting
608	"""
609	metadata = value.get_fit_data()
610	model = value.get_model()
611	smearer = value.get_smearer()
612	qmin , qmax = value.get_range()
613	self.fit_id =id
614	#Create list of parameters for fitting used
615	templist=[]
616
617	try:
618	#Extra list of parameters and their constraints
619	listOfConstraint= []
620
621	param = value.get_model_param()
622	if len(param)>0:
623	for item in param:
624	## check if constraint
625	if item[0] !=None and item[1] != None:
626	listOfConstraint.append((item[0],item[1]))
627
628	#Do the single fit
629	self.fitter.set_model(model, self.fit_id,
630	pars,constraints = listOfConstraint)
631
632	self.fitter.set_data(data=metadata,Uid=self.fit_id,
633	smearer=smearer,qmin= qmin,qmax=qmax )
634
635	self.fitter.select_problem_for_fit(Uid= self.fit_id,
636	value= value.get_scheduled())
637	value.clear_model_param()
638	except:
639	msg= title +" error: %s" % sys.exc_value
640	wx.PostEvent(self.parent, StatusEvent(status= msg, type="stop"))
641	return
642
643	def _onSelect(self,event):
644	"""
645	when Select data to fit a new page is created .Its reference is
646	added to self.page_finder
647	"""
648	self.panel = event.GetEventObject()
649	Plugin.on_perspective(self,event=event)
650	for plottable in self.panel.graph.plottables:
651	if plottable.name == self.panel.graph.selected_plottable:
652	#if not hasattr(plottable, "is_data"):
653
654	if plottable.__class__.__name__=="Theory1D":
655	dy=numpy.zeros(len(plottable.y))
656	if hasattr(plottable, "dy"):
657	dy= copy.deepcopy(plottable.dy)
658
659	item= self.copy_data(plottable, dy)
660	item.group_id += "data1D"
661	item.id +="data1D"
662	item.is_data= False
663	title = item.name
664	wx.PostEvent(self.parent, NewPlotEvent(plot=item, title=str(title)))
665	else:
666	item= self.copy_data(plottable, plottable.dy)
667	item.is_data=True
668
669	## put the errors values back to the model if the errors were hiden
670	## before sending them to the fit engine
671	if len(self.err_dy)>0:
672	if item.name in self.err_dy.iterkeys():
673	dy= self.err_dy[item.name]
674	data= self.copy_data(item, dy)
675	data.is_data= item.is_data
676	else:
677	data= self.copy_data(item, item.dy)
678	data.is_data= item.is_data
679
680
681	else:
682	if item.dy==None:
683	dy= numpy.zeros(len(item.y))
684	data= self.copy_data(item, dy)
685	data.is_data=item.is_data
686	else:
687	data= self.copy_data(item,item.dy)
688	data.is_data=item.is_data
689
690	else:
691	if plottable.__class__.__name__ !="Data2D":
692	return
693	## Data2D case
694	if not hasattr(plottable, "is_data"):
695	item= copy.deepcopy(plottable)
696	item.group_id += "data2D"
697	item.id +="data2D"
698	item.is_data= False
699	title = item.name
700	title += " Fit"
701	data = item
702	wx.PostEvent(self.parent, NewPlotEvent(plot=item, title=str(title)))
703	else:
704	item= copy.deepcopy(plottable )
705	data= copy.deepcopy(plottable )
706	item.is_data=True
707	data.is_data=True
708
709
710	## create anew page
711	if item.name == self.panel.graph.selected_plottable or\
712	item.__class__.__name__ is "Data2D":
713	try:
714	page = self.fit_panel.add_fit_page(data)
715	# add data associated to the page created
716	if page !=None:
717	#create a fitproblem storing all link to data,model,page creation
718	if not page in self.page_finder.keys():
719	self.page_finder[page]= FitProblem()
720	## item is almost the same as data but contains
721	## axis info for plotting
722	self.page_finder[page].add_plotted_data(item)
723	self.page_finder[page].add_fit_data(data)
724
725	wx.PostEvent(self.parent, StatusEvent(status="Page Created"))
726	else:
727	wx.PostEvent(self.parent, StatusEvent(status="Page was already Created"))
728	except:
729	wx.PostEvent(self.parent, StatusEvent(status="Creating Fit page: %s"\
730	%sys.exc_value))
731	return
732
733
734	def _updateFit(self):
735	"""
736	Is called when values of result are available
737	"""
738	##Sending a progess message to the status bar
739	wx.PostEvent(self.parent, StatusEvent(status="Computing..."))
740
741	def _single_fit_completed(self,result,pars,cpage, elapsed=None):
742	"""
743	Display fit result on one page of the notebook.
744	@param result: result of fit
745	@param pars: list of names of parameters fitted
746	@param current_pg: the page where information will be displayed
747	@param qmin: the minimum value of x to replot the model
748	@param qmax: the maximum value of x to replot model
749
750	"""
751	try:
752	if result ==None:
753	msg= "Simple Fitting Stop !!!"
754	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
755	return
756	if not numpy.isfinite(result.fitness) or numpy.any(result.pvec ==None )or not numpy.all(numpy.isfinite(result.pvec) ):
757	msg= "Single Fitting did not converge!!!"
758	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
759	return
760	for page, value in self.page_finder.iteritems():
761	if page==cpage :
762	model= value.get_model()
763	break
764	param_name = []
765	i = 0
766	for name in pars:
767	param_name.append(name)
768
769	cpage.onsetValues(result.fitness,param_name, result.pvec,result.stderr)
770	"""
771	## plot the current model with new param
772	metadata = self.page_finder[cpage].get_fit_data()
773	model = self.page_finder[cpage].get_model()
774	qmin, qmax= self.page_finder[cpage].get_range()
775	smearer =self.page_finder[cpage].get_smearer()
776	#Replot models
777	msg= "Single Fit completed. plotting... %s:"%model.name
778	wx.PostEvent(self.parent, StatusEvent(status="%s " % msg))
779	self.draw_model( model=model, data= metadata, smearer= smearer,
780	qmin= qmin, qmax= qmax)
781	"""
782	except:
783	msg= "Single Fit completed but Following error occurred:%s"% sys.exc_value
784	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
785	return
786
787
788	def _simul_fit_completed(self,result,pars=None,cpage=None, elapsed=None):
789	"""
790	Parameter estimation completed,
791	display the results to the user
792	@param alpha: estimated best alpha
793	@param elapsed: computation time
794	"""
795	## fit more than 1 model at the same time
796	try:
797	msg = ""
798	if result ==None:
799	msg= "Complex Fitting Stop !!!"
800	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
801	return
802	if not numpy.isfinite(result.fitness) or numpy.any(result.pvec ==None )or not numpy.all(numpy.isfinite(result.pvec) ):
803	msg= "Single Fitting did not converge!!!"
804	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
805	return
806
807	for page, value in self.page_finder.iteritems():
808	"""
809	if format_number(result.fitness) == page.get_chi2():
810	#ToDo: Compare parameter inputs with outputs too.
811	wx.PostEvent(self.parent, StatusEvent(status="%s " % msg))
812	break
813	"""
814	if value.get_scheduled()==1:
815	model = value.get_model()
816	metadata = value.get_plotted_data()
817	small_param_name = []
818	small_out = []
819	small_cov = []
820	i = 0
821	#Separate result in to data corresponding to each page
822	for p in result.parameters:
823	model_name,param_name = self.split_string(p.name)
824	if model.name == model_name:
825	p_name= model.name+"."+param_name
826	if p.name == p_name:
827	if p.value != None and numpy.isfinite(p.value):
828	small_out.append(p.value )
829	small_param_name.append(param_name)
830	small_cov.append(p.stderr)
831
832	# Display result on each page
833	page.onsetValues(result.fitness, small_param_name,small_out,small_cov)
834	except:
835	msg= "Simultaneous Fit completed"
836	msg +=" but Following error occurred:%s"%sys.exc_value
837	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
838	return
839
840
841
842	def _on_show_panel(self, event):
843	print "_on_show_panel: fitting"
844
845
846	def _onset_engine_park(self,event):
847	"""
848	set engine to park
849	"""
850	self._on_change_engine('park')
851
852
853	def _onset_engine_scipy(self,event):
854	"""
855	set engine to scipy
856	"""
857	self._on_change_engine('scipy')
858
859	def _on_slicer_event(self, event):
860	"""
861	Receive a panel as event and send it to guiframe
862	@param event: event containing a panel
863	"""
864
865	if event.panel!=None:
866	new_panel = event.panel
867	self.slicer_panels.append(event.panel)
868	# Set group ID if available
869	event_id = self.parent.popup_panel(new_panel)
870	#self.menu3.Append(event_id, new_panel.window_caption,
871	# "Show %s plot panel" % new_panel.window_caption)
872	# Set UID to allow us to reference the panel later
873
874	new_panel.uid = event_id
875	self.mypanels.append(new_panel)
876	return
877
878	def _onclearslicer(self, event):
879	"""
880	Clear the boxslicer when close the panel associate with this slicer
881	"""
882	name =event.GetPane().caption
883
884	for panel in self.slicer_panels:
885	if panel.window_caption==name:
886
887	for item in self.parent.panels:
888	if hasattr(self.parent.panels[item],"uid"):
889	if self.parent.panels[item].uid ==panel.base.uid:
890	self.parent.panels[item].onClearSlicer(event)
891	self.parent._mgr.Update()
892	break
893	break
894
895
896
897
898	def _return_engine_type(self):
899	"""
900	return the current type of engine
901	"""
902	return self._fit_engine
903
904
905	def _on_change_engine(self, engine='park'):
906	"""
907	Allow to select the type of engine to perform fit
908	@param engine: the key work of the engine
909	"""
910	## saving fit engine name
911	self._fit_engine = engine
912	## change menu item state
913	if engine=="park":
914	self.menu1.FindItemByPosition(0).Check(False)
915	self.menu1.FindItemByPosition(1).Check(True)
916	else:
917	self.menu1.FindItemByPosition(0).Check(True)
918	self.menu1.FindItemByPosition(1).Check(False)
919
920	## post a message to status bar
921	wx.PostEvent(self.parent, StatusEvent(status="Engine set to: %s" % self._fit_engine))
922
923	## Bind every open fit page with a newevent to know the current fitting engine
924	import fitpage
925	event= fitpage.FitterTypeEvent()
926	event.type = self._fit_engine
927	for key in self.page_finder.keys():
928	wx.PostEvent(key, event)
929
930
931	def _on_model_panel(self, evt):
932	"""
933	react to model selection on any combo box or model menu.plot the model
934	@param evt: wx.combobox event
935	"""
936	model = evt.model
937
938	if model ==None:
939	return
940	model.origin_name = model.name
941	self.current_pg = self.fit_panel.get_current_page()
942	## make sure nothing is done on self.sim_page
943	## example trying to call set_panel on self.sim_page
944	if self.current_pg != self.sim_page :
945
946	if self.page_finder[self.current_pg].get_model()== None :
947
948	model.name="M"+str(self.index_model)
949	self.index_model += 1
950	else:
951	model.name= self.page_finder[self.current_pg].get_model().name
952
953	metadata = self.page_finder[self.current_pg].get_plotted_data()
954
955	# save the name containing the data name with the appropriate model
956	self.page_finder[self.current_pg].set_model(model)
957	qmin, qmax= self.current_pg.get_range()
958	self.page_finder[self.current_pg].set_range(qmin=qmin, qmax=qmax)
959	smearer= self.page_finder[self.current_pg].get_smearer()
960	# save model name
961	self.draw_model( model=model,smearer=smearer,
962	data= metadata, qmin=qmin, qmax=qmax)
963
964	if self.sim_page!=None:
965	self.sim_page.draw_page()
966
967
968
969	def _on_model_menu(self, evt):
970	"""
971	Plot a theory from a model selected from the menu
972	@param evt: wx.menu event
973	"""
974	model = evt.model
975	Plugin.on_perspective(self,event=evt)
976	# Create a model page. If a new page is created, the model
977	# will be plotted automatically. If a page already exists,
978	# the content will be updated and the plot refreshed
979	self.fit_panel.add_model_page(model,topmenu=True)
980
981
982
983
984	def _update1D(self,x, output):
985	"""
986	Update the output of plotting model 1D
987	"""
988	wx.PostEvent(self.parent, StatusEvent(status="Plot \
989	#updating ... ",type="update"))
990	self.ready_fit()
991	#self.calc_thread.ready(0.01)
992
993
994	def _fill_default_model2D(self, theory, qmax,qstep, qmin=None):
995	"""
996	fill Data2D with default value
997	@param theory: Data2D to fill
998	"""
999	from DataLoader.data_info import Detector, Source
1000
1001	detector = Detector()
1002	theory.detector.append(detector)
1003
1004	theory.detector[0].distance=1e+32
1005	theory.source= Source()
1006	theory.source.wavelength=2*math.pi/1e+32
1007
1008	## Create detector for Model 2D
1009	xmax=2theory.detector[0].distancemath.atan(\
1010	qmax/(4*math.pi/theory.source.wavelength))
1011
1012	theory.detector[0].pixel_size.x= xmax/(qstep/2-0.5)
1013	theory.detector[0].pixel_size.y= xmax/(qstep/2-0.5)
1014	theory.detector[0].beam_center.x= qmax
1015	theory.detector[0].beam_center.y= qmax
1016	## create x_bins and y_bins of the model 2D
1017	distance = theory.detector[0].distance
1018	pixel = qstep/2-1
1019	theta = pixel / distance / qstep#100.0
1020	wavelength = theory.source.wavelength
1021	pixel_width_x = theory.detector[0].pixel_size.x
1022	pixel_width_y = theory.detector[0].pixel_size.y
1023	center_x = theory.detector[0].beam_center.x/pixel_width_x
1024	center_y = theory.detector[0].beam_center.y/pixel_width_y
1025
1026
1027	size_x, size_y= numpy.shape(theory.data)
1028	for i_x in range(size_x):
1029	theta = (i_x-center_x)*pixel_width_x / distance
1030	qx = 4.0math.pi/wavelength math.tan(theta/2.0)
1031	theory.x_bins.append(qx)
1032	for i_y in range(size_y):
1033	theta = (i_y-center_y)*pixel_width_y / distance
1034	qy =4.0math.pi/wavelength math.tan(theta/2.0)
1035	theory.y_bins.append(qy)
1036
1037	theory.group_id ="Model"
1038	theory.id ="Model"
1039	## determine plot boundaries
1040	theory.xmin= -qmax
1041	theory.xmax= qmax
1042	theory.ymin= -qmax
1043	theory.ymax= qmax
1044
1045
1046	def _get_plotting_info(self, data=None):
1047	"""
1048	get plotting info from data if data !=None
1049	else use some default
1050	"""
1051	my_info = PlotInfo()
1052	if data !=None:
1053	if hasattr(data,"info"):
1054	x_name, x_units = data.get_xaxis()
1055	y_name, y_units = data.get_yaxis()
1056
1057	my_info._xunit = x_units
1058	my_info._xaxis = x_name
1059	my_info._yunit = y_units
1060	my_info._yaxis = y_name
1061
1062	my_info.title= data.name
1063	if hasattr(data, "info"):
1064	my_info.info= data.info
1065	if hasattr(data, "group_id"):
1066	my_info.group_id= data.group_id
1067
1068	return my_info
1069
1070
1071	def _complete1D(self, x,y, elapsed,model,data=None):
1072	"""
1073	Complete plotting 1D data
1074	"""
1075
1076	try:
1077	new_plot = Theory1D(x=x, y=y)
1078	my_info = self._get_plotting_info( data)
1079	new_plot.name = model.name
1080	new_plot.id = my_info.id
1081	new_plot.group_id = my_info.group_id
1082
1083	new_plot.xaxis( my_info._xaxis, my_info._xunit)
1084	new_plot.yaxis( my_info._yaxis, my_info._yunit)
1085	if data!=None:
1086	if new_plot.id == data.id:
1087	new_plot.id += "Model"
1088	new_plot.is_data =False
1089
1090
1091	title= new_plot.name
1092
1093	# Pass the reset flag to let the plotting event handler
1094	# know that we are replacing the whole plot
1095	if title== None:
1096	title = "Analytical model 1D "
1097	if data ==None:
1098	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1099	title= str(title), reset=True ))
1100	else:
1101	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1102	title= str(title)))
1103	msg = "Plot 1D complete !"
1104	wx.PostEvent( self.parent, StatusEvent( status= msg , type="stop" ))
1105	except:
1106	msg= " Error occurred when drawing %s Model 1D: "%new_plot.name
1107	msg+= " %s"%sys.exc_value
1108	wx.PostEvent( self.parent, StatusEvent(status= msg, type="stop" ))
1109	return
1110
1111
1112
1113	def _update2D(self, output,time=None):
1114	"""
1115	Update the output of plotting model
1116	"""
1117	wx.PostEvent(self.parent, StatusEvent(status="Plot \
1118	#updating ... ",type="update"))
1119	self.ready_fit()
1120	#self.calc_thread.ready(0.01)
1121
1122
1123	def _complete2D(self, image,data, model, elapsed,qmin, qmax,qstep=DEFAULT_NPTS):
1124	"""
1125	Complete get the result of modelthread and create model 2D
1126	that can be plot.
1127	"""
1128
1129
1130	err_image = numpy.zeros(numpy.shape(image))
1131
1132	theory= Data2D(image= image , err_image= err_image)
1133	theory.name= model.name
1134
1135	if data ==None:
1136	self._fill_default_model2D(theory= theory, qmax=qmax,qstep=qstep, qmin= qmin)
1137
1138	else:
1139	theory.id= data.id+"Model"
1140	theory.group_id= data.name+"Model"
1141	theory.x_bins= data.x_bins
1142	theory.y_bins= data.y_bins
1143	theory.detector= data.detector
1144	theory.source= data.source
1145	theory.is_data =False
1146	## plot boundaries
1147	theory.ymin= data.ymin
1148	theory.ymax= data.ymax
1149	theory.xmin= data.xmin
1150	theory.xmax= data.xmax
1151
1152
1153	## plot
1154	wx.PostEvent(self.parent, NewPlotEvent(plot=theory,
1155	title="Analytical model 2D ", reset=True ))
1156	msg = "Plot 2D complete !"
1157	wx.PostEvent( self.parent, StatusEvent( status= msg , type="stop" ))
1158
1159	def _on_data_error(self, event):
1160	"""
1161	receives and event from plotting plu-gins to store the data name and
1162	their errors of y coordinates for 1Data hide and show error
1163	"""
1164	self.err_dy= event.err_dy
1165
1166
1167	def _draw_model2D(self,model,data=None,description=None, enable2D=False,
1168	qmin=DEFAULT_QMIN, qmax=DEFAULT_QMAX, qstep=DEFAULT_NPTS):
1169	"""
1170	draw model in 2D
1171	@param model: instance of the model to draw
1172	@param description: the description of the model
1173	@param enable2D: when True allows to draw model 2D
1174	@param qmin: the minimum value to draw model 2D
1175	@param qmax: the maximum value to draw model 2D
1176	@param qstep: the number of division of Qx and Qy of the model to draw
1177
1178	"""
1179	x= numpy.linspace(start= -1*qmax,
1180	stop= qmax,
1181	num= qstep,
1182	endpoint=True )
1183	y = numpy.linspace(start= -1*qmax,
1184	stop= qmax,
1185	num= qstep,
1186	endpoint=True )
1187	## use data info instead
1188	if data !=None:
1189	## check if data2D to plot
1190	if hasattr(data, "x_bins"):
1191	enable2D = True
1192	x= data.x_bins
1193	y= data.y_bins
1194
1195	if not enable2D:
1196	return
1197	try:
1198	from model_thread import Calc2D
1199	## If a thread is already started, stop it
1200	if self.calc_2D != None and self.calc_2D.isrunning():
1201	self.calc_2D.stop()
1202	self.calc_2D = Calc2D( x= x,
1203	y= y,
1204	model= model,
1205	data = data,
1206	qmin= qmin,
1207	qmax= qmax,
1208	qstep= qstep,
1209	completefn= self._complete2D,
1210	updatefn= self._update2D )
1211	self.calc_2D.queue()
1212
1213	except:
1214	raise
1215	#msg= " Error occurred when drawing %s Model 2D: "%model.name
1216	#msg+= " %s"%sys.exc_value
1217	#wx.PostEvent( self.parent, StatusEvent(status= msg ))
1218	#return
1219
1220	def _draw_model1D(self, model, data=None, smearer= None,
1221	qmin=DEFAULT_QMIN, qmax=DEFAULT_QMAX, qstep= DEFAULT_NPTS,enable1D= True):
1222	"""
1223	Draw model 1D from loaded data1D
1224	@param data: loaded data
1225	@param model: the model to plot
1226	"""
1227	x= numpy.linspace(start= qmin,
1228	stop= qmax,
1229	num= qstep,
1230	endpoint=True
1231	)
1232	if data!=None:
1233	## check for data2D
1234	if hasattr(data,"x_bins"):
1235	return
1236	x = data.x
1237	if qmin == DEFAULT_QMIN :
1238	qmin = min(data.x)
1239	if qmax == DEFAULT_QMAX:
1240	qmax = max(data.x)
1241
1242
1243	if not enable1D:
1244	return
1245
1246	try:
1247	from model_thread import Calc1D
1248	## If a thread is already started, stop it
1249	if self.calc_1D!= None and self.calc_1D.isrunning():
1250	self.calc_1D.stop()
1251	self.calc_1D= Calc1D( x= x,
1252	data = data,
1253	model= model,
1254	qmin = qmin,
1255	qmax = qmax,
1256	smearer = smearer,
1257	completefn = self._complete1D,
1258	updatefn = self._update1D )
1259	self.calc_1D.queue()
1260
1261	except:
1262	msg= " Error occurred when drawing %s Model 1D: "%model.name
1263	msg+= " %s"%sys.exc_value
1264	wx.PostEvent( self.parent, StatusEvent(status= msg ))
1265	return
1266
1267
1268	def profile(fn, args, *kw):
1269	import cProfile, pstats, os
1270	global call_result
1271	def call():
1272	global call_result
1273	call_result = fn(args, *kw)
1274	cProfile.runctx('call()', dict(call=call), {}, 'profile.out')
1275	stats = pstats.Stats('profile.out')
1276	stats.sort_stats('time')
1277	#stats.sort_stats('calls')
1278	stats.print_stats()
1279	os.unlink('profile.out')
1280	return call_result
1281	if __name__ == "__main__":
1282	i = Plugin()
1283
1284
1285
1286

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SasView

source: sasview/sansview/perspectives/fitting/fitting.py @ 6ef7ac5a

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