fitting.py @ 6ced1cc

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 6ced1cc was 6ced1cc, checked in by Jae Cho <jhjcho@…>, 15 years ago
changed the default qmin 0.001. Former value 0.0001 made poor plot since there was not many points near the value
Property mode set to `100644`
File size: 48.7 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
23	from sans.guicomm.events import NewPlotEvent, StatusEvent
24	from sans.guicomm.events import EVT_SLICER_PANEL,ERR_DATA,EVT_REMOVE_DATA
25	from sans.guicomm.events import EVT_SLICER_PARS_UPDATE
26
27	from sans.fit.AbstractFitEngine import Model
28	from sans.fit.AbstractFitEngine import FitAbort
29
30
31	from fitproblem import FitProblem
32	from fitpanel import FitPanel
33	from fit_thread import FitThread
34	import models
35	import fitpage
36
37	DEFAULT_BEAM = 0.005
38	DEFAULT_QMIN = 0.001
39	DEFAULT_QMAX = 0.13
40	DEFAULT_NPTS = 50
41
42	(PageInfoEvent, EVT_PAGE_INFO) = wx.lib.newevent.NewEvent()
43
44
45	class PlotInfo:
46	"""
47	store some plotting field
48	"""
49	_xunit = 'A^{-1}'
50	_xaxis= "\\rm{Q}"
51	_yunit = "cm^{-1}"
52	_yaxis= "\\rm{Intensity} "
53	id = "Model"
54	group_id = "Model"
55	title= None
56	info= None
57
58
59	class Plugin:
60	"""
61	Fitting plugin is used to perform fit
62	"""
63	def __init__(self):
64	## Plug-in name
65	self.sub_menu = "Fitting"
66
67	## Reference to the parent window
68	self.parent = None
69	#Provide list of models existing in the application
70	self.menu_mng = models.ModelManager()
71	## List of panels for the simulation perspective (names)
72	self.perspective = []
73	#list of panel to send to guiframe
74	self.mypanels=[]
75	# reference to the current running thread
76	self.calc_2D= None
77	self.calc_1D= None
78	self.calc_fit= None
79
80	# Start with a good default
81	self.elapsed = 0.022
82	# the type of optimizer selected, park or scipy
83	self.fitter = None
84	#Flag to let the plug-in know that it is running stand alone
85	self.standalone=True
86	## dictionary of page closed and id
87	self.closed_page_dict ={}
88	## Fit engine
89	self._fit_engine = 'scipy'
90	#List of selected data
91	self.selected_data_list=[]
92	## list of slicer panel created to display slicer parameters and results
93	self.slicer_panels=[]
94	# Log startup
95	logging.info("Fitting plug-in started")
96	# model 2D view
97	self.model2D_id=None
98	#keep reference of the simultaneous fit page
99	self.sim_page=None
100	#dictionary containing data name and error on dy of that data
101	self.err_dy={}
102
103
104
105	def populate_menu(self, id, owner):
106	"""
107	Create a menu for the Fitting plug-in
108	@param id: id to create a menu
109	@param owner: owner of menu
110	@ return : list of information to populate the main menu
111	"""
112	#Menu for fitting
113	self.menu1 = wx.Menu()
114
115	#Set park engine
116	id3 = wx.NewId()
117	scipy_help= "Scipy Engine: Perform Simple fit. More in Help window...."
118	self.menu1.AppendCheckItem(id3, "Simple Fit [Scipy]",scipy_help)
119	wx.EVT_MENU(owner, id3, self._onset_engine_scipy)
120
121	id3 = wx.NewId()
122	park_help = "Park Engine: Perform Complex fit. More in Help window...."
123	self.menu1.AppendCheckItem(id3, "Complex Fit [Park]",park_help)
124	wx.EVT_MENU(owner, id3, self._onset_engine_park)
125
126	self.menu1.FindItemByPosition(0).Check(True)
127	self.menu1.FindItemByPosition(1).Check(False)
128
129	self.menu1.AppendSeparator()
130	id1 = wx.NewId()
131	simul_help = "Allow to edit fit engine with multiple model and data"
132	self.menu1.Append(id1, '&Simultaneous Page',simul_help)
133	wx.EVT_MENU(owner, id1, self.on_add_sim_page)
134	#menu for SLD Calculator
135	#self.tool_menu = wx.Menu()
136	#id_tool_menu = wx.NewId()
137	#sld_id = wx.NewId()
138	#sld_help= "Compute the scattering length density of molecules"
139	#self.tool_menu.Append(sld_id, "SLD Calculator",sld_help)
140	#wx.EVT_MENU(owner,sld_id, self.onCalculateSld)
141
142	#menu for model
143	menu2 = wx.Menu()
144	self.menu_mng.populate_menu(menu2, owner)
145	id2 = wx.NewId()
146	owner.Bind(models.EVT_MODEL,self._on_model_menu)
147
148	self.fit_panel.set_owner(owner)
149	self.fit_panel.set_model_list(self.menu_mng.get_model_list())
150	owner.Bind(fitpage.EVT_MODEL_BOX,self._on_model_panel)
151
152	#create menubar items
153	return [(id, self.menu1, "Fitting"),
154	(id2, menu2, "Model")]
155
156
157	def on_add_sim_page(self, event):
158	"""
159	Create a page to access simultaneous fit option
160	"""
161	Plugin.on_perspective(self,event=event)
162	if self.sim_page !=None:
163	msg= "Simultaneous Fit page already opened"
164	wx.PostEvent(self.parent, StatusEvent(status= msg))
165	return
166
167	self.sim_page= self.fit_panel.add_sim_page()
168
169
170
171	def help(self, evt):
172	"""
173	Show a general help dialog.
174	TODO: replace the text with a nice image
175	"""
176	from helpPanel import HelpWindow
177	frame = HelpWindow(None, -1, 'HelpWindow')
178	frame.Show(True)
179
180
181	def get_context_menu(self, graph=None):
182	"""
183	Get the context menu items available for P(r)
184	@param graph: the Graph object to which we attach the context menu
185	@return: a list of menu items with call-back function
186	"""
187	#TODO: clean this up so that the string are not copied
188	# multiple times.
189	self.graph=graph
190
191	for item in graph.plottables:
192	if item.__class__.__name__ is "Data2D":
193
194	if hasattr(item,"is_data"):
195	if item.is_data:
196	return [["Select data for fitting", \
197	"Dialog with fitting parameters ", self._onSelect]]
198	else:
199	return []
200	return [["Select data for fitting",\
201	"Dialog with fitting parameters ", self._onSelect]]
202	else:
203	if item.name==graph.selected_plottable :
204	if item.name !="$I_{obs}(q)$" and item.name !="$P_{fit}(r)$":
205	if hasattr(item, "group_id"):
206	if hasattr(item,"is_data"):
207	if item.is_data:
208	return [["Select data for fitting", \
209	"Dialog with fitting parameters ", self._onSelect]]
210	else:
211	return []
212	else:
213	return [["Select data for fitting", \
214	"Dialog with fitting parameters ", self._onSelect]]
215	return []
216
217
218	def get_panels(self, parent):
219	"""
220	Create and return a list of panel objects
221	"""
222	self.parent = parent
223	# Creation of the fit panel
224	self.fit_panel = FitPanel(self.parent, -1)
225	#Set the manager for the main panel
226	self.fit_panel.set_manager(self)
227	# List of windows used for the perspective
228	self.perspective = []
229	self.perspective.append(self.fit_panel.window_name)
230	# take care of saving data, model and page associated with each other
231	self.page_finder = {}
232	#index number to create random model name
233	self.index_model = 0
234	self.index_theory= 0
235	self.parent.Bind(EVT_SLICER_PANEL, self._on_slicer_event)
236	self.parent.Bind( ERR_DATA, self._on_data_error)
237	self.parent.Bind(EVT_REMOVE_DATA, self._closed_fitpage)
238	self.parent.Bind(EVT_SLICER_PARS_UPDATE, self._onEVT_SLICER_PANEL)
239	self.parent._mgr.Bind(wx.aui.EVT_AUI_PANE_CLOSE,self._onclearslicer)
240
241
242	#Send the fitting panel to guiframe
243	self.mypanels.append(self.fit_panel)
244	return self.mypanels
245
246
247
248	def get_perspective(self):
249	"""
250	Get the list of panel names for this perspective
251	"""
252	return self.perspective
253
254
255	def on_perspective(self, event):
256	"""
257	Call back function for the perspective menu item.
258	We notify the parent window that the perspective
259	has changed.
260	"""
261	self.parent.set_perspective(self.perspective)
262
263
264	def post_init(self):
265	"""
266	Post initialization call back to close the loose ends
267	"""
268	# Do not show the fitting perspective immediately and
269	# let the application show the Welcome Page.
270	#self.parent.set_perspective(self.perspective)
271	pass
272
273
274	def copy_data(self, item, dy=None):
275	"""
276	receive a data 1D and the list of errors on dy
277	and create a new data1D data
278	@param return
279	"""
280
281	id=None
282
283	if hasattr(item,"id"):
284	id = copy.deepcopy(item.id)
285
286
287	data= Data1D(x=item.x, y=item.y,dx=None, dy=None)
288	data.copy_from_datainfo(item)
289	item.clone_without_data(clone=data)
290	data.dy=dy
291	data.name = item.name
292
293	## allow to highlight data when plotted
294	data.interactive = copy.deepcopy(item.interactive)
295	## when 2 data have the same id override the 1 st plotted
296	data.id = id
297
298	data.group_id = item.group_id
299	return data
300
301	def set_fit_range(self, page, qmin, qmax):
302	"""
303	Set the fitting range of a given page
304	"""
305	if page in self.page_finder.iterkeys():
306	fitproblem= self.page_finder[page]
307	fitproblem.set_range(qmin= qmin, qmax= qmax)
308
309	def schedule_for_fit(self,value=0,page=None,fitproblem =None):
310	"""
311	Set the fit problem field to 0 or 1 to schedule that problem to fit.
312	Schedule the specified fitproblem or get the fit problem related to
313	the current page and set value.
314	@param value : integer 0 or 1
315	@param fitproblem: fitproblem to schedule or not to fit
316	"""
317	if fitproblem !=None:
318	fitproblem.schedule_tofit(value)
319	else:
320	if page in self.page_finder.iterkeys():
321	fitproblem= self.page_finder[page]
322	fitproblem.schedule_tofit(value)
323
324
325
326	def get_page_finder(self):
327	""" @return self.page_finder used also by simfitpage.py"""
328	return self.page_finder
329
330
331	def set_page_finder(self,modelname,names,values):
332	"""
333	Used by simfitpage.py to reset a parameter given the string constrainst.
334	@param modelname: the name ot the model for with the parameter has to reset
335	@param value: can be a string in this case.
336	@param names: the paramter name
337	@note: expecting park used for fit.
338	"""
339	sim_page= self.sim_page
340	for page, value in self.page_finder.iteritems():
341	if page != sim_page:
342	list=value.get_model()
343	model = list[0]
344	if model.name== modelname:
345	value.set_model_param(names,values)
346	break
347
348
349
350	def split_string(self,item):
351	"""
352	receive a word containing dot and split it. used to split parameterset
353	name into model name and parameter name example:
354	paramaterset (item) = M1.A
355	@return model_name =M1 , parameter name =A
356	"""
357	if string.find(item,".")!=-1:
358	param_names= re.split("\.",item)
359	model_name=param_names[0]
360	param_name=param_names[1]
361	return model_name,param_name
362
363
364	def stop_fit(self):
365	"""
366	Stop the fit engine
367	"""
368	if self.calc_fit!= None and self.calc_fit.isrunning():
369	self.calc_fit.stop()
370	wx.PostEvent(self.parent, StatusEvent(status="Fitting \
371	is cancelled" , type="stop"))
372
373
374
375	def set_smearer(self,smearer, qmin=None, qmax=None):
376	"""
377	Get a smear object and store it to a fit problem
378	@param smearer: smear object to allow smearing data
379	"""
380	current_pg=self.fit_panel.get_current_page()
381	self.page_finder[current_pg].set_smearer(smearer)
382	## draw model 1D with smeared data
383	data = self.page_finder[current_pg].get_plotted_data()
384	model = self.page_finder[current_pg].get_model()
385	## if user has already selected a model to plot
386	## redraw the model with data smeared
387
388	smear =self.page_finder[current_pg].get_smearer()
389	if model!= None:
390	self.draw_model( model=model, data= data, smearer= smear,
391	qmin= qmin, qmax= qmax)
392
393
394
395	def draw_model(self, model, data= None,smearer= None,
396	enable1D= True, enable2D= False,
397	qmin= DEFAULT_QMIN, qmax= DEFAULT_QMAX, qstep= DEFAULT_NPTS):
398	"""
399	Draw model.
400	@param model: the model to draw
401	@param name: the name of the model to draw
402	@param data: the data on which the model is based to be drawn
403	@param description: model's description
404	@param enable1D: if true enable drawing model 1D
405	@param enable2D: if true enable drawing model 2D
406	@param qmin: Range's minimum value to draw model
407	@param qmax: Range's maximum value to draw model
408	@param qstep: number of step to divide the x and y-axis
409
410	"""
411	## draw model 1D with no loaded data
412	self._draw_model1D( model= model, data= data,enable1D=enable1D, smearer= smearer,
413	qmin= qmin, qmax= qmax, qstep= qstep )
414	## draw model 2D with no initial data
415	self._draw_model2D(model=model,
416	data = data,
417	enable2D= enable2D,
418	qmin=qmin,
419	qmax=qmax,
420	qstep=qstep)
421
422
423
424	def onFit(self):
425	"""
426	perform fit
427	"""
428	## count the number of fitproblem schedule to fit
429	fitproblem_count= 0
430	for value in self.page_finder.itervalues():
431	if value.get_scheduled()==1:
432	fitproblem_count += 1
433
434	## if simultaneous fit change automatically the engine to park
435	if fitproblem_count >1:
436	self._on_change_engine(engine='park')
437
438	from sans.fit.Fitting import Fit
439	self.fitter= Fit(self._fit_engine)
440
441	if self._fit_engine=="park":
442	engineType="Simultaneous Fit"
443	else:
444	engineType="Single Fit"
445
446	fproblemId = 0
447	current_pg=None
448	for page, value in self.page_finder.iteritems():
449	try:
450	if value.get_scheduled()==1:
451	#Get list of parameters name to fit
452	pars = []
453	templist = []
454	templist = page.get_param_list()
455	for element in templist:
456	name = str(element[1])
457	pars.append(name)
458	#Set Engine (model , data) related to the page on
459	self._fit_helper( current_pg=page, value=value,pars=pars,
460	id=fproblemId, title= engineType )
461	fproblemId += 1
462	current_pg= page
463	except:
464	msg= "%s error: %s" % (engineType,sys.exc_value)
465	wx.PostEvent(self.parent, StatusEvent(status= msg ))
466	return
467	#Do the simultaneous fit
468	try:
469	## If a thread is already started, stop it
470	if self.calc_fit!= None and self.calc_fit.isrunning():
471	self.calc_fit.stop()
472
473	wx.PostEvent(self.parent, StatusEvent(status="Start the computation",
474	curr_thread=self.calc_fit,type="start"))
475	wx.PostEvent(self.parent, StatusEvent(status="Computing...",
476	curr_thread=self.calc_fit,type="progress"))
477	## perform single fit
478	if self._fit_engine=="scipy":
479	qmin, qmax= current_pg.get_range()
480	self.calc_fit=FitThread(parent =self.parent,
481	fn= self.fitter,
482	cpage=current_pg,
483	pars= pars,
484	completefn= self._single_fit_completed,
485	updatefn=self._updateFit)
486
487	else:
488	## Perform more than 1 fit at the time
489	self.calc_fit=FitThread(parent =self.parent,
490	fn= self.fitter,
491	completefn= self._simul_fit_completed,
492	updatefn=self._updateFit)
493	self.calc_fit.queue()
494	self.calc_fit.ready(2.5)
495
496	except FitAbort:
497	print "in pluging"
498	except:
499	msg= "%s error: %s" % (engineType,sys.exc_value)
500	wx.PostEvent(self.parent, StatusEvent(status= msg ,type="stop"))
501	return
502
503	def onCalculateSld(self, event):
504	"""
505	Compute the scattering length density of molecula
506	"""
507	from sldPanel import SldWindow
508	frame = SldWindow(base=self.parent)
509	frame.Show(True)
510
511
512	def _onEVT_SLICER_PANEL(self, event):
513	"""
514	receive and event telling to update a panel with a name starting with
515	event.panel_name. this method update slicer panel for a given interactor.
516	@param event: contains type of slicer , paramaters for updating the panel
517	and panel_name to find the slicer 's panel concerned.
518	"""
519
520	for item in self.parent.panels:
521	if self.parent.panels[item].window_caption.startswith(event.panel_name):
522	self.parent.panels[item].set_slicer(event.type, event.params)
523
524	self.parent._mgr.Update()
525
526
527
528	def _closed_fitpage(self, event):
529	"""
530	request fitpanel to close a given page when its unique data is removed
531	from the plot
532	"""
533	self.fit_panel._close_fitpage(event.data)
534
535
536	def _add_page_onmenu(self, name,fitproblem=None):
537	"""
538	Add name of a closed page of fitpanel in a menu
539	"""
540	list = self.menu1.GetMenuItems()
541	for item in list:
542	if name == item.GetItemLabel():
543	self.closed_page_dict[name][1] = fitproblem
544
545	if not name in self.closed_page_dict.keys():
546	# Post paramters
547	event_id = wx.NewId()
548	self.menu1.Append(event_id, name, "Show %s fit panel" % name)
549	self.closed_page_dict[name]= [event_id, fitproblem]
550	wx.EVT_MENU(self.parent,event_id, self._open_closed_page)
551
552
553	def _open_closed_page(self, event):
554	"""
555	reopen a closed page
556	"""
557	for name, value in self.closed_page_dict.iteritems():
558	if event.GetId() in value:
559	id,fitproblem = value
560	if name !="Model":
561	data= fitproblem.get_fit_data()
562	page = self.fit_panel.add_fit_page(data= data,reset=True)
563	if fitproblem != None:
564	self.page_finder[page]=fitproblem
565	if self.sim_page != None:
566	self.sim_page.draw_page()
567
568	else:
569	model = fitproblem
570	self.fit_panel.add_model_page(model=model, topmenu=True,
571	reset= True)
572	break
573
574
575	def _reset_schedule_problem(self, value=0):
576	"""
577	unschedule or schedule all fitproblem to be fit
578	"""
579	for page, fitproblem in self.page_finder.iteritems():
580	fitproblem.schedule_tofit(value)
581
582	def _fit_helper(self,current_pg,pars,value, id, title="Single Fit " ):
583	"""
584	helper for fitting
585	"""
586	metadata = value.get_fit_data()
587	model = value.get_model()
588	smearer = value.get_smearer()
589	qmin , qmax = value.get_range()
590	self.fit_id =id
591	#Create list of parameters for fitting used
592	templist=[]
593	pars=pars
594	try:
595	## create a park model and reset parameter value if constraint
596	## is given
597	new_model = Model(model)
598	param = value.get_model_param()
599	if len(param)>0:
600	for item in param:
601	param_value = item[1]
602	param_name = item[0]
603	## check if constraint
604	if param_value !=None and param_name != None:
605	new_model.parameterset[ param_name].set( param_value )
606
607	#Do the single fit
608	self.fitter.set_model(new_model, self.fit_id, pars)
609
610	self.fitter.set_data(data=metadata,Uid=self.fit_id,
611	smearer=smearer,qmin= qmin,qmax=qmax )
612
613	self.fitter.select_problem_for_fit(Uid= self.fit_id,
614	value= value.get_scheduled())
615	value.clear_model_param()
616	except:
617	msg= title +" error: %s" % sys.exc_value
618	wx.PostEvent(self.parent, StatusEvent(status= msg, type="stop"))
619	return
620
621	def _onSelect(self,event):
622	"""
623	when Select data to fit a new page is created .Its reference is
624	added to self.page_finder
625	"""
626	self.panel = event.GetEventObject()
627	Plugin.on_perspective(self,event=event)
628	for plottable in self.panel.graph.plottables:
629	if plottable.name == self.panel.graph.selected_plottable:
630	#if not hasattr(plottable, "is_data"):
631
632	if plottable.__class__.__name__=="Theory1D":
633	dy=numpy.zeros(len(plottable.y))
634	if hasattr(plottable, "dy"):
635	dy= copy.deepcopy(plottable.dy)
636
637	item= self.copy_data(plottable, dy)
638	item.group_id += "data1D"
639	item.id +="data1D"
640	item.is_data= False
641	title = item.name
642	wx.PostEvent(self.parent, NewPlotEvent(plot=item, title=str(title)))
643	else:
644	item= self.copy_data(plottable, plottable.dy)
645	item.is_data=True
646
647	## put the errors values back to the model if the errors were hiden
648	## before sending them to the fit engine
649	if len(self.err_dy)>0:
650	if item.name in self.err_dy.iterkeys():
651	dy= self.err_dy[item.name]
652	data= self.copy_data(item, dy)
653	data.is_data= item.is_data
654	else:
655	data= self.copy_data(item, item.dy)
656	data.is_data= item.is_data
657
658
659	else:
660	if item.dy==None:
661	dy= numpy.zeros(len(item.y))
662	data= self.copy_data(item, dy)
663	data.is_data=item.is_data
664	else:
665	data= self.copy_data(item,item.dy)
666	data.is_data=item.is_data
667
668	else:
669	if plottable.__class__.__name__ !="Data2D":
670	return
671	## Data2D case
672	if not hasattr(plottable, "is_data"):
673	item= copy.deepcopy(plottable)
674	item.group_id += "data2D"
675	item.id +="data2D"
676	item.is_data= False
677	title = item.name
678	title += " Fit"
679	data = item
680	wx.PostEvent(self.parent, NewPlotEvent(plot=item, title=str(title)))
681	else:
682	item= copy.deepcopy(plottable )
683	data= copy.deepcopy(plottable )
684	item.is_data=True
685	data.is_data=True
686
687
688	## create anew page
689	if item.name == self.panel.graph.selected_plottable or\
690	item.__class__.__name__ is "Data2D":
691	try:
692	page = self.fit_panel.add_fit_page(data)
693	# add data associated to the page created
694	if page !=None:
695	#create a fitproblem storing all link to data,model,page creation
696	if not page in self.page_finder.keys():
697	self.page_finder[page]= FitProblem()
698	## item is almost the same as data but contains
699	## axis info for plotting
700	self.page_finder[page].add_plotted_data(item)
701	self.page_finder[page].add_fit_data(data)
702
703	wx.PostEvent(self.parent, StatusEvent(status="Page Created"))
704	else:
705	wx.PostEvent(self.parent, StatusEvent(status="Page was already Created"))
706	except:
707	wx.PostEvent(self.parent, StatusEvent(status="Creating Fit page: %s"\
708	%sys.exc_value))
709	return
710
711
712	def _updateFit(self):
713	"""
714	Is called when values of result are available
715	"""
716	##Sending a progess message to the status bar
717	wx.PostEvent(self.parent, StatusEvent(status="Computing..."))
718
719	def _single_fit_completed(self,result,pars,cpage, elapsed=None):
720	"""
721	Display fit result on one page of the notebook.
722	@param result: result of fit
723	@param pars: list of names of parameters fitted
724	@param current_pg: the page where information will be displayed
725	@param qmin: the minimum value of x to replot the model
726	@param qmax: the maximum value of x to replot model
727
728	"""
729	wx.PostEvent(self.parent, StatusEvent(status="Single fit \
730	complete! " ))
731
732	try:
733	if result ==None:
734	msg= "Simple Fitting Stop !!!"
735	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
736	return
737	if numpy.any(result.pvec ==None )or not numpy.all(numpy.isfinite(result.pvec) ):
738	msg= "Single Fitting did not converge!!!"
739	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
740	return
741	for page, value in self.page_finder.iteritems():
742	if page==cpage :
743	model= value.get_model()
744	break
745	i = 0
746	for name in pars:
747	if result.pvec.__class__==numpy.float64:
748	model.setParam(name,result.pvec)
749	else:
750	model.setParam(name,result.pvec[i])
751	i += 1
752	## Reset values of the current page to fit result
753	cpage.onsetValues(result.fitness, result.pvec,result.stderr)
754	## plot the current model with new param
755	metadata = self.page_finder[cpage].get_fit_data()
756	model = self.page_finder[cpage].get_model()
757	qmin, qmax= self.page_finder[cpage].get_range()
758	smearer =self.page_finder[cpage].get_smearer()
759	#Replot models
760	msg= "Single Fit completed. plotting... %s:"%model.name
761	wx.PostEvent(self.parent, StatusEvent(status="%s " % msg))
762	self.draw_model( model=model, data= metadata, smearer= smearer,
763	qmin= qmin, qmax= qmax)
764	wx.PostEvent(self.parent, StatusEvent(status=" " , type="stop"))
765	except:
766	msg= "Single Fit completed but Following error occurred:%s"% sys.exc_value
767	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
768	return
769
770
771	def _simul_fit_completed(self,result,pars=None,cpage=None, elapsed=None):
772	"""
773	Parameter estimation completed,
774	display the results to the user
775	@param alpha: estimated best alpha
776	@param elapsed: computation time
777	"""
778	wx.PostEvent(self.parent, StatusEvent(status="Simultaneous fit complete "))
779
780	## fit more than 1 model at the same time
781	try:
782	if result ==None:
783	msg= "Complex Fitting Stop !!!"
784	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
785	return
786	if numpy.any(result.pvec ==None )or not numpy.all(numpy.isfinite(result.pvec) ):
787	msg= "Single Fitting did not converge!!!"
788	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
789	return
790	for page, value in self.page_finder.iteritems():
791	if value.get_scheduled()==1:
792	model = value.get_model()
793	metadata = value.get_plotted_data()
794	small_out = []
795	small_cov = []
796	i = 0
797	#Separate result in to data corresponding to each page
798	for p in result.parameters:
799	model_name,param_name = self.split_string(p.name)
800	if model.name == model_name:
801	p_name= model.name+"."+param_name
802	if p.name == p_name:
803	small_out.append(p.value )
804	model.setParam(param_name,p.value)
805
806	small_cov.append(p.stderr)
807	else:
808	value= model.getParam(param_name)
809	small_out.append(value )
810	small_cov.append(None)
811	# Display result on each page
812	page.onsetValues(result.fitness, small_out,small_cov)
813	#Replot models
814	msg= "Simultaneous Fit completed. plotting... %s:"%model.name
815	wx.PostEvent(self.parent, StatusEvent(status="%s " % msg))
816	qmin, qmax= page.get_range()
817	smearer =self.page_finder[page].get_smearer()
818	self.draw_model( model=model, data= metadata, smearer=smearer,
819	qmin= qmin, qmax= qmax)
820	wx.PostEvent(self.parent, StatusEvent(status="", type="stop"))
821	except:
822	msg= "Simultaneous Fit completed"
823	msg +=" but Following error occurred:%s"%sys.exc_value
824	wx.PostEvent(self.parent, StatusEvent(status=msg,type="stop"))
825	return
826
827
828
829	def _on_show_panel(self, event):
830	print "_on_show_panel: fitting"
831
832
833	def _onset_engine_park(self,event):
834	"""
835	set engine to park
836	"""
837	self._on_change_engine('park')
838
839
840	def _onset_engine_scipy(self,event):
841	"""
842	set engine to scipy
843	"""
844	self._on_change_engine('scipy')
845
846	def _on_slicer_event(self, event):
847	"""
848	Receive a panel as event and send it to guiframe
849	@param event: event containing a panel
850	"""
851
852	if event.panel!=None:
853	new_panel = event.panel
854	self.slicer_panels.append(event.panel)
855	# Set group ID if available
856	event_id = self.parent.popup_panel(new_panel)
857	#self.menu3.Append(event_id, new_panel.window_caption,
858	# "Show %s plot panel" % new_panel.window_caption)
859	# Set UID to allow us to reference the panel later
860
861	new_panel.uid = event_id
862	self.mypanels.append(new_panel)
863	return
864
865	def _onclearslicer(self, event):
866	"""
867	Clear the boxslicer when close the panel associate with this slicer
868	"""
869	name =event.GetPane().caption
870
871	for panel in self.slicer_panels:
872	if panel.window_caption==name:
873
874	for item in self.parent.panels:
875	if hasattr(self.parent.panels[item],"uid"):
876	if self.parent.panels[item].uid ==panel.base.uid:
877	self.parent.panels[item].onClearSlicer(event)
878	self.parent._mgr.Update()
879	break
880	break
881
882
883
884
885	def _return_engine_type(self):
886	"""
887	return the current type of engine
888	"""
889	return self._fit_engine
890
891
892	def _on_change_engine(self, engine='park'):
893	"""
894	Allow to select the type of engine to perform fit
895	@param engine: the key work of the engine
896	"""
897	## saving fit engine name
898	self._fit_engine = engine
899	## change menu item state
900	if engine=="park":
901	self.menu1.FindItemByPosition(0).Check(False)
902	self.menu1.FindItemByPosition(1).Check(True)
903	else:
904	self.menu1.FindItemByPosition(0).Check(True)
905	self.menu1.FindItemByPosition(1).Check(False)
906
907	## post a message to status bar
908	wx.PostEvent(self.parent, StatusEvent(status="Engine set to: %s" % self._fit_engine))
909
910	## Bind every open fit page with a newevent to know the current fitting engine
911	import fitpage
912	event= fitpage.FitterTypeEvent()
913	event.type = self._fit_engine
914	for key in self.page_finder.keys():
915	wx.PostEvent(key, event)
916
917
918	def _on_model_panel(self, evt):
919	"""
920	react to model selection on any combo box or model menu.plot the model
921	@param evt: wx.combobox event
922	"""
923	model = evt.model
924
925	if model ==None:
926	return
927	model.origin_name = model.name
928	current_pg = self.fit_panel.get_current_page()
929	## make sure nothing is done on self.sim_page
930	## example trying to call set_panel on self.sim_page
931	if current_pg != self.sim_page :
932
933	if self.page_finder[current_pg].get_model()== None :
934
935	model.name="M"+str(self.index_model)
936	self.index_model += 1
937	else:
938	model.name= self.page_finder[current_pg].get_model().name
939
940	metadata = self.page_finder[current_pg].get_plotted_data()
941
942	# save the name containing the data name with the appropriate model
943	self.page_finder[current_pg].set_model(model)
944	qmin, qmax= current_pg.get_range()
945	self.page_finder[current_pg].set_range(qmin=qmin, qmax=qmax)
946	smearer= self.page_finder[current_pg].get_smearer()
947	# save model name
948	self.draw_model( model=model,smearer=smearer,
949	data= metadata, qmin=qmin, qmax=qmax)
950
951	if self.sim_page!=None:
952	self.sim_page.draw_page()
953
954
955
956	def _on_model_menu(self, evt):
957	"""
958	Plot a theory from a model selected from the menu
959	@param evt: wx.menu event
960	"""
961	model = evt.model
962	Plugin.on_perspective(self,event=evt)
963	# Create a model page. If a new page is created, the model
964	# will be plotted automatically. If a page already exists,
965	# the content will be updated and the plot refreshed
966	self.fit_panel.add_model_page(model,topmenu=True)
967
968
969
970
971	def _update1D(self,x, output):
972	"""
973	Update the output of plotting model 1D
974	"""
975	wx.PostEvent(self.parent, StatusEvent(status="Plot \
976	#updating ... ",type="update"))
977	self.calc_thread.ready(0.01)
978
979
980	def _fill_default_model2D(self, theory, qmax,qstep, qmin=None):
981	"""
982	fill Data2D with default value
983	@param theory: Data2D to fill
984	"""
985	from DataLoader.data_info import Detector, Source
986
987	detector = Detector()
988	theory.detector.append(detector)
989
990	theory.detector[0].distance=1e+32
991	theory.source= Source()
992	theory.source.wavelength=2*math.pi/1e+32
993
994	## Create detector for Model 2D
995	xmax=2theory.detector[0].distancemath.atan(\
996	qmax/(4*math.pi/theory.source.wavelength))
997
998	theory.detector[0].pixel_size.x= xmax/(qstep/2-0.5)
999	theory.detector[0].pixel_size.y= xmax/(qstep/2-0.5)
1000	theory.detector[0].beam_center.x= qmax
1001	theory.detector[0].beam_center.y= qmax
1002	## create x_bins and y_bins of the model 2D
1003	distance = theory.detector[0].distance
1004	pixel = qstep/2-1
1005	theta = pixel / distance / qstep#100.0
1006	wavelength = theory.source.wavelength
1007	pixel_width_x = theory.detector[0].pixel_size.x
1008	pixel_width_y = theory.detector[0].pixel_size.y
1009	center_x = theory.detector[0].beam_center.x/pixel_width_x
1010	center_y = theory.detector[0].beam_center.y/pixel_width_y
1011
1012
1013	size_x, size_y= numpy.shape(theory.data)
1014	for i_x in range(size_x):
1015	theta = (i_x-center_x)*pixel_width_x / distance
1016	qx = 4.0math.pi/wavelength math.tan(theta/2.0)
1017	theory.x_bins.append(qx)
1018	for i_y in range(size_y):
1019	theta = (i_y-center_y)*pixel_width_y / distance
1020	qy =4.0math.pi/wavelength math.tan(theta/2.0)
1021	theory.y_bins.append(qy)
1022
1023	theory.group_id ="Model"
1024	theory.id ="Model"
1025	## determine plot boundaries
1026	theory.xmin= -qmax
1027	theory.xmax= qmax
1028	theory.ymin= -qmax
1029	theory.ymax= qmax
1030
1031
1032	def _get_plotting_info(self, data=None):
1033	"""
1034	get plotting info from data if data !=None
1035	else use some default
1036	"""
1037	my_info = PlotInfo()
1038	if data !=None:
1039	if hasattr(data,"info"):
1040	x_name, x_units = data.get_xaxis()
1041	y_name, y_units = data.get_yaxis()
1042
1043	my_info._xunit = x_units
1044	my_info._xaxis = x_name
1045	my_info._yunit = y_units
1046	my_info._yaxis = y_name
1047
1048	my_info.title= data.name
1049	if hasattr(data, "info"):
1050	my_info.info= data.info
1051	if hasattr(data, "group_id"):
1052	my_info.group_id= data.group_id
1053
1054	return my_info
1055
1056
1057	def _complete1D(self, x,y, elapsed,model,data=None):
1058	"""
1059	Complete plotting 1D data
1060	"""
1061
1062	try:
1063
1064	new_plot = Theory1D(x=x, y=y)
1065	my_info = self._get_plotting_info( data)
1066	new_plot.name = model.name
1067	new_plot.id = my_info.id
1068	new_plot.group_id = my_info.group_id
1069
1070	new_plot.xaxis( my_info._xaxis, my_info._xunit)
1071	new_plot.yaxis( my_info._yaxis, my_info._yunit)
1072	if data!=None:
1073	if new_plot.id == data.id:
1074	new_plot.id += "Model"
1075	new_plot.is_data =False
1076
1077
1078	title= new_plot.name
1079
1080	# Pass the reset flag to let the plotting event handler
1081	# know that we are replacing the whole plot
1082	if title== None:
1083	title = "Analytical model 1D "
1084	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1085	title= str(title), reset=True ))
1086	else:
1087	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1088	title= str(title)))
1089	msg = "Plot 1D complete !"
1090	wx.PostEvent( self.parent, StatusEvent( status= msg , type="stop" ))
1091	except:
1092	msg= " Error occurred when drawing %s Model 1D: "%new_plot.name
1093	msg+= " %s"%sys.exc_value
1094	wx.PostEvent( self.parent, StatusEvent(status= msg, type="stop" ))
1095	return
1096
1097
1098
1099	def _update2D(self, output,time=None):
1100	"""
1101	Update the output of plotting model
1102	"""
1103	wx.PostEvent(self.parent, StatusEvent(status="Plot \
1104	#updating ... ",type="update"))
1105	self.calc_thread.ready(0.01)
1106
1107
1108	def _complete2D(self, image,data, model, elapsed,qmin, qmax,qstep=DEFAULT_NPTS):
1109	"""
1110	Complete get the result of modelthread and create model 2D
1111	that can be plot.
1112	"""
1113
1114
1115	err_image = numpy.zeros(numpy.shape(image))
1116
1117	theory= Data2D(image= image , err_image= err_image)
1118	theory.name= model.name
1119
1120	if data ==None:
1121	self._fill_default_model2D(theory= theory, qmax=qmax,qstep=qstep, qmin= qmin)
1122
1123	else:
1124	theory.id= data.id+"Model"
1125	theory.group_id= data.name+"Model"
1126	theory.x_bins= data.x_bins
1127	theory.y_bins= data.y_bins
1128	theory.detector= data.detector
1129	theory.source= data.source
1130	theory.is_data =False
1131	## plot boundaries
1132	theory.ymin= data.ymin
1133	theory.ymax= data.ymax
1134	theory.xmin= data.xmin
1135	theory.xmax= data.xmax
1136
1137
1138	## plot
1139	wx.PostEvent(self.parent, NewPlotEvent(plot=theory,
1140	title="Analytical model 2D ", reset=True ))
1141	msg = "Plot 2D complete !"
1142	wx.PostEvent( self.parent, StatusEvent( status= msg , type="stop" ))
1143
1144	def _on_data_error(self, event):
1145	"""
1146	receives and event from plotting plu-gins to store the data name and
1147	their errors of y coordinates for 1Data hide and show error
1148	"""
1149	self.err_dy= event.err_dy
1150
1151
1152	def _draw_model2D(self,model,data=None,description=None, enable2D=False,
1153	qmin=DEFAULT_QMIN, qmax=DEFAULT_QMAX, qstep=DEFAULT_NPTS):
1154	"""
1155	draw model in 2D
1156	@param model: instance of the model to draw
1157	@param description: the description of the model
1158	@param enable2D: when True allows to draw model 2D
1159	@param qmin: the minimum value to draw model 2D
1160	@param qmax: the maximum value to draw model 2D
1161	@param qstep: the number of division of Qx and Qy of the model to draw
1162
1163	"""
1164	x= numpy.linspace(start= -1*qmax,
1165	stop= qmax,
1166	num= qstep,
1167	endpoint=True )
1168	y = numpy.linspace(start= -1*qmax,
1169	stop= qmax,
1170	num= qstep,
1171	endpoint=True )
1172	## use data info instead
1173	if data !=None:
1174	## check if data2D to plot
1175	if hasattr(data, "x_bins"):
1176	enable2D = True
1177	x= data.x_bins
1178	y= data.y_bins
1179
1180	if not enable2D:
1181	return
1182	try:
1183	from model_thread import Calc2D
1184	## If a thread is already started, stop it
1185	if self.calc_2D != None and self.calc_2D.isrunning():
1186	self.calc_2D.stop()
1187	self.calc_2D = Calc2D( x= x,
1188	y= y,
1189	model= model,
1190	data = data,
1191	qmin= qmin,
1192	qmax= qmax,
1193	qstep= qstep,
1194	completefn= self._complete2D,
1195	updatefn= self._update2D )
1196	self.calc_2D.queue()
1197
1198	except:
1199	raise
1200	#msg= " Error occurred when drawing %s Model 2D: "%model.name
1201	#msg+= " %s"%sys.exc_value
1202	#wx.PostEvent( self.parent, StatusEvent(status= msg ))
1203	#return
1204
1205	def _draw_model1D(self, model, data=None, smearer= None,
1206	qmin=DEFAULT_QMIN, qmax=DEFAULT_QMAX, qstep= DEFAULT_NPTS,enable1D= True):
1207	"""
1208	Draw model 1D from loaded data1D
1209	@param data: loaded data
1210	@param model: the model to plot
1211	"""
1212
1213	x= numpy.linspace(start= qmin,
1214	stop= qmax,
1215	num= qstep,
1216	endpoint=True
1217	)
1218	if data!=None:
1219	## check for data2D
1220	if hasattr(data,"x_bins"):
1221	return
1222	x = data.x
1223	if qmin == DEFAULT_QMIN :
1224	qmin = min(data.x)
1225	if qmax == DEFAULT_QMAX:
1226	qmax = max(data.x)
1227
1228
1229	if not enable1D:
1230	return
1231
1232	try:
1233	from model_thread import Calc1D
1234	## If a thread is already started, stop it
1235	if self.calc_1D!= None and self.calc_1D.isrunning():
1236	self.calc_1D.stop()
1237	self.calc_1D= Calc1D( x= x,
1238	data = data,
1239	model= model,
1240	qmin = qmin,
1241	qmax = qmax,
1242	smearer = smearer,
1243	completefn = self._complete1D,
1244	updatefn = self._update1D )
1245	self.calc_1D.queue()
1246
1247	except:
1248	msg= " Error occurred when drawing %s Model 1D: "%model.name
1249	msg+= " %s"%sys.exc_value
1250	wx.PostEvent( self.parent, StatusEvent(status= msg ))
1251	return
1252
1253
1254	def profile(fn, args, *kw):
1255	import cProfile, pstats, os
1256	global call_result
1257	def call():
1258	global call_result
1259	call_result = fn(args, *kw)
1260	cProfile.runctx('call()', dict(call=call), {}, 'profile.out')
1261	stats = pstats.Stats('profile.out')
1262	stats.sort_stats('time')
1263	#stats.sort_stats('calls')
1264	stats.print_stats()
1265	os.unlink('profile.out')
1266	return call_result
1267	if __name__ == "__main__":
1268	i = Plugin()
1269
1270
1271
1272

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SasView

source: sasview/sansview/perspectives/fitting/fitting.py @ 6ced1cc

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