fitting.py @ b11e127

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 b11e127 was bca2cb9, checked in by Jae Cho <jhjcho@…>, 12 years ago
minor fix
Property mode set to `100644`
File size: 90.2 KB

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1	"""
2	Fitting perspective
3	"""
4	################################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#
9	#See the license text in license.txt
10	#
11	#copyright 2009, University of Tennessee
12	################################################################################
13	import re
14	import sys
15	import os
16	import wx
17	import logging
18	import numpy
19	import time
20	from copy import deepcopy
21	import models
22
23	from sans.dataloader.loader import Loader
24	from sans.guiframe.dataFitting import Data2D
25	from sans.guiframe.dataFitting import Data1D
26	from sans.guiframe.dataFitting import check_data_validity
27	from sans.guiframe.events import NewPlotEvent
28	from sans.guiframe.events import StatusEvent
29	from sans.guiframe.events import EVT_SLICER_PANEL
30	from sans.guiframe.events import EVT_SLICER_PARS_UPDATE
31	from sans.guiframe.gui_style import GUIFRAME_ID
32	from sans.guiframe.plugin_base import PluginBase
33	from sans.guiframe.data_processor import BatchCell
34	from sans.fit.Fitting import Fit
35	from .console import ConsoleUpdate
36	from .fitproblem import FitProblemDictionary
37	from .fitpanel import FitPanel
38	from .fit_thread import FitThread
39	from .pagestate import Reader
40	from .fitpage import Chi2UpdateEvent
41	from sans.perspectives.calculator.model_editor import TextDialog
42	from sans.perspectives.calculator.model_editor import EditorWindow
43
44	MAX_NBR_DATA = 4
45	SANS_F_TOL = 5e-05
46
47	(PageInfoEvent, EVT_PAGE_INFO) = wx.lib.newevent.NewEvent()
48
49
50	if sys.platform == "win32":
51	ON_MAC = False
52	else:
53	ON_MAC = True
54
55
56
57	class Plugin(PluginBase):
58	"""
59	Fitting plugin is used to perform fit
60	"""
61	def __init__(self, standalone=False):
62	PluginBase.__init__(self, name="Fitting", standalone=standalone)
63
64	#list of panel to send to guiframe
65	self.mypanels = []
66	# reference to the current running thread
67	self.calc_2D = None
68	self.calc_1D = None
69
70	self.color_dict = {}
71
72	self.fit_thread_list = {}
73	self.residuals = None
74	self.weight = None
75	self.fit_panel = None
76	self.plot_panel = None
77	# Start with a good default
78	self.elapsed = 0.022
79	# the type of optimizer selected, park or scipy
80	self.fitter = None
81	self.fit_panel = None
82	#let fit ready
83	self.fitproblem_count = 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	self._gui_engine = None
91	## Relative error desired in the sum of squares (float); scipy only
92	self.ftol = SANS_F_TOL
93	self.batch_reset_flag = True
94	#List of selected data
95	self.selected_data_list = []
96	## list of slicer panel created to display slicer parameters and results
97	self.slicer_panels = []
98	# model 2D view
99	self.model2D_id = None
100	#keep reference of the simultaneous fit page
101	self.sim_page = None
102	self.sim_menu = None
103	self.batch_page = None
104	self.batch_menu = None
105	self.index_model = 0
106	self.test_model_color = None
107	#Create a reader for fit page's state
108	self.state_reader = None
109	self._extensions = '.fitv'
110	self.scipy_id = wx.NewId()
111	self.park_id = wx.NewId()
112	self.menu1 = None
113	self.new_model_frame = None
114
115	self.temp_state = []
116	self.state_index = 0
117	self.sfile_ext = None
118	# take care of saving data, model and page associated with each other
119	self.page_finder = {}
120	# Log startup
121	logging.info("Fitting plug-in started")
122	self.batch_capable = self.get_batch_capable()
123
124	def get_batch_capable(self):
125	"""
126	Check if the plugin has a batch capability
127	"""
128	return True
129
130	def create_fit_problem(self, page_id):
131	"""
132	Given an ID create a fitproblem container
133	"""
134	self.page_finder[page_id] = FitProblemDictionary()
135
136	def delete_fit_problem(self, page_id):
137	"""
138	Given an ID create a fitproblem container
139	"""
140	if page_id in self.page_finder.iterkeys():
141	del self.page_finder[page_id]
142
143	def add_color(self, color, id):
144	"""
145	adds a color as a key with a plot id as its value to a dictionary
146	"""
147	self.color_dict[id] = color
148
149	def on_batch_selection(self, flag):
150	"""
151	switch the the notebook of batch mode or not
152	"""
153	self.batch_on = flag
154	if self.fit_panel is not None:
155	self.fit_panel.batch_on = self.batch_on
156
157	def populate_menu(self, owner):
158	"""
159	Create a menu for the Fitting plug-in
160
161	:param id: id to create a menu
162	:param owner: owner of menu
163
164	:return: list of information to populate the main menu
165
166	"""
167	#Menu for fitting
168	self.menu1 = wx.Menu()
169	id1 = wx.NewId()
170	simul_help = "Add new fit panel"
171	self.menu1.Append(id1, '&New Fit Page', simul_help)
172	wx.EVT_MENU(owner, id1, self.on_add_new_page)
173	self.menu1.AppendSeparator()
174	self.id_simfit = wx.NewId()
175	simul_help = "Simultaneous Fit"
176	self.menu1.Append(self.id_simfit, '&Simultaneous Fit', simul_help)
177	wx.EVT_MENU(owner, self.id_simfit, self.on_add_sim_page)
178	self.sim_menu = self.menu1.FindItemById(self.id_simfit)
179	self.sim_menu.Enable(False)
180	#combined Batch
181	self.id_batchfit = wx.NewId()
182	batch_help = "Combined Batch"
183	self.menu1.Append(self.id_batchfit, '&Combine Batch Fit', batch_help)
184	wx.EVT_MENU(owner, self.id_batchfit, self.on_add_sim_page)
185	self.batch_menu = self.menu1.FindItemById(self.id_batchfit)
186	self.batch_menu.Enable(False)
187	self.menu1.AppendSeparator()
188	#Set park engine
189	scipy_help = "Scipy Engine: Perform Simple fit. More in Help window...."
190	self.menu1.AppendCheckItem(self.scipy_id, "Simple FitEngine [LeastSq]",
191	scipy_help)
192	wx.EVT_MENU(owner, self.scipy_id, self._onset_engine_scipy)
193
194	park_help = "Park Engine: Perform Complex fit. More in Help window...."
195	self.menu1.AppendCheckItem(self.park_id, "Complex FitEngine [ParkMC]",
196	park_help)
197	wx.EVT_MENU(owner, self.park_id, self._onset_engine_park)
198
199	self.menu1.FindItemById(self.scipy_id).Check(True)
200	self.menu1.FindItemById(self.park_id).Check(False)
201	self.menu1.AppendSeparator()
202	self.id_tol = wx.NewId()
203	ftol_help = "Change the current FTolerance (=%s) " % str(self.ftol)
204	ftol_help += "of Simple FitEngine..."
205	self.menu1.Append(self.id_tol, "Change FTolerance",
206	ftol_help)
207	wx.EVT_MENU(owner, self.id_tol, self.show_ftol_dialog)
208	self.menu1.AppendSeparator()
209
210	self.id_reset_flag = wx.NewId()
211	resetf_help = "BatchFit: If checked, the initial param values will be "
212	resetf_help += "propagated from the previous results. "
213	resetf_help += "Otherwise, the same initial param values will be used "
214	resetf_help += "for all fittings."
215	self.menu1.AppendCheckItem(self.id_reset_flag,
216	"Chain Fitting [BatchFit Only]",
217	resetf_help)
218	wx.EVT_MENU(owner, self.id_reset_flag, self.on_reset_batch_flag)
219	chain_menu = self.menu1.FindItemById(self.id_reset_flag)
220	chain_menu.Check(not self.batch_reset_flag)
221	chain_menu.Enable(self.batch_on)
222
223	self.menu1.AppendSeparator()
224	self.edit_model_menu = wx.Menu()
225	# Find and put files name in menu
226	try:
227	self.set_edit_menu(owner=owner)
228	except:
229	raise
230
231	self.id_edit = wx.NewId()
232	editmodel_help = "Edit customized model sample file"
233	self.menu1.AppendMenu(self.id_edit, "Edit Custom Model",
234	self.edit_model_menu, editmodel_help)
235	#create menubar items
236	return [(self.menu1, self.sub_menu)]
237
238	def edit_custom_model(self, event):
239	"""
240	Get the python editor panel
241	"""
242	id = event.GetId()
243	label = self.edit_menu.GetLabel(id)
244	from sans.perspectives.calculator.pyconsole import PyConsole
245	filename = os.path.join(models.find_plugins_dir(), label)
246	frame = PyConsole(parent=self.parent, manager=self,
247	panel=self.fit_panel,
248	title='Advanced Custom Model Editor',
249	filename=filename)
250	self.put_icon(frame)
251	frame.Show(True)
252
253	def delete_custom_model(self, event):
254	"""
255	Delete custom model file
256	"""
257	id = event.GetId()
258	label = self.delete_menu.GetLabel(id)
259	toks = os.path.splitext(label)
260	path = os.path.join(models.find_plugins_dir(), toks[0])
261	try:
262	for ext in ['.py', '.pyc']:
263	p_path = path + ext
264	os.remove(p_path)
265	self.update_custom_combo()
266	if os.path.isfile(p_path):
267	msg = "Sorry! Could not be able to delete the default "
268	msg += "custom model... \n"
269	msg += "Please manually remove the files (.py, .pyc) "
270	msg += "in the 'plugin_models' folder \n"
271	msg += "inside of the SansView application, "
272	msg += "and try it again."
273	wx.MessageBox(msg, 'Info')
274	#wx.PostEvent(self.parent, StatusEvent(status=msg, type='stop',
275	# info='warning'))
276	else:
277	self.delete_menu.Delete(id)
278	for item in self.edit_menu.GetMenuItems():
279	if item.GetLabel() == label:
280	self.edit_menu.DeleteItem(item)
281	msg = "The custom model, %s, has been deleted."% label
282	wx.PostEvent(self.parent, StatusEvent(status=msg,
283	type='stop', info='info'))
284	break
285	except:
286	msg ='Delete Error: \nCould not delete the file; Check if in use.'
287	wx.MessageBox(msg, 'Error')
288
289	def make_sum_model(self, event):
290	"""
291	Edit summodel template and make one
292	"""
293	id = event.GetId()
294	model_manager = models.ModelManager()
295	model_list = model_manager.get_model_name_list()
296	plug_dir = models.find_plugins_dir()
297	textdial = TextDialog(None, self, -1, 'Easy Sum/Multi(p1, p2) Editor',
298	model_list, plug_dir)
299	self.put_icon(textdial)
300	textdial.ShowModal()
301	textdial.Destroy()
302
303	def make_new_model(self, event):
304	"""
305	Make new model
306	"""
307	if self.new_model_frame != None:
308	self.new_model_frame.Show(False)
309	self.new_model_frame.Show(True)
310	else:
311	id = event.GetId()
312	dir_path = models.find_plugins_dir()
313	title = "New Custom Model Function"
314	self.new_model_frame = EditorWindow(parent=self, base=self,
315	path=dir_path, title=title)
316	self.put_icon(self.new_model_frame)
317	self.new_model_frame.Show(True)
318
319	def update_custom_combo(self):
320	"""
321	Update custom model list in the fitpage combo box
322	"""
323	custom_model = 'Customized Models'
324	try:
325	# Update edit menus
326	self.set_edit_menu_helper(self.parent, self.edit_custom_model)
327	self.set_edit_menu_helper(self.parent, self.delete_custom_model)
328	temp = self.fit_panel.reset_pmodel_list()
329	if temp:
330	# Set the new custom model list for all fit pages
331	for uid, page in self.fit_panel.opened_pages.iteritems():
332	if hasattr(page, "formfactorbox"):
333	page.model_list_box = temp
334	current_val = page.formfactorbox.GetLabel()
335	#if page.plugin_rbutton.GetValue():
336	mod_cat = page.categorybox.GetStringSelection()
337	if mod_cat == custom_model:
338	#pos = page.formfactorbox.GetSelection()
339	page._show_combox_helper()
340	new_val = page.formfactorbox.GetLabel()
341	if current_val != new_val and new_val != '':
342	page.formfactorbox.SetLabel(new_val)
343	else:
344	page.formfactorbox.SetLabel(current_val)
345	except:
346	pass
347
348
349	def set_edit_menu(self, owner):
350	"""
351	Set list of the edit model menu labels
352	"""
353	id = wx.NewId()
354	#new_model_menu = wx.Menu()
355	self.edit_model_menu.Append(id, 'New',
356	'Add a new model function')
357	wx.EVT_MENU(owner, id, self.make_new_model)
358	id = wx.NewId()
359	self.edit_model_menu.Append(id, 'Sum\|Multi(p1, p2)',
360	'Sum of two model functions')
361	wx.EVT_MENU(owner, id, self.make_sum_model)
362	e_id = wx.NewId()
363	self.edit_menu = wx.Menu()
364	self.edit_model_menu.AppendMenu(e_id,
365	'Advanced', self.edit_menu)
366	self.set_edit_menu_helper(owner, self.edit_custom_model)
367
368	d_id = wx.NewId()
369	self.delete_menu = wx.Menu()
370	self.edit_model_menu.AppendMenu(d_id,
371	'Delete', self.delete_menu)
372	self.set_edit_menu_helper(owner, self.delete_custom_model)
373
374	def set_edit_menu_helper(self, owner=None, menu=None):
375	"""
376	help for setting list of the edit model menu labels
377	"""
378	if menu == None:
379	menu = self.edit_custom_model
380	list_fnames = os.listdir(models.find_plugins_dir())
381	list_fnames.sort()
382	for f_item in list_fnames:
383	name = os.path.basename(f_item)
384	toks = os.path.splitext(name)
385	if toks[-1] == '.py' and not toks[0] == '__init__':
386	if menu == self.edit_custom_model:
387	if toks[0] == 'easy_sum_of_p1_p2':
388	continue
389	submenu = self.edit_menu
390	else:
391	submenu = self.delete_menu
392	has_file = False
393	for item in submenu.GetMenuItems():
394	if name == submenu.GetLabel(item.GetId()):
395	has_file = True
396	if not has_file:
397	id = wx.NewId()
398	submenu.Append(id, name)
399	wx.EVT_MENU(owner, id, menu)
400	has_file = False
401
402	def put_icon(self, frame):
403	"""
404	Put icon in the frame title bar
405	"""
406	if hasattr(frame, "IsIconized"):
407	if not frame.IsIconized():
408	try:
409	icon = self.parent.GetIcon()
410	frame.SetIcon(icon)
411	except:
412	pass
413
414	def on_add_sim_page(self, event):
415	"""
416	Create a page to access simultaneous fit option
417	"""
418	id = event.GetId()
419	caption = "Simultaneous Fit"
420	page = self.sim_page
421	if id == self.id_batchfit:
422	caption = "Combined Batch"
423	page = self.batch_page
424
425	def set_focus_page(page):
426	page.Show(True)
427	page.Refresh()
428	page.SetFocus()
429	self.parent._mgr.Update()
430	msg = "%s already opened\n" % str(page.window_caption)
431	wx.PostEvent(self.parent, StatusEvent(status=msg))
432
433	if page != None:
434	return set_focus_page(page)
435	if caption == "Simultaneous Fit":
436	self.sim_page = self.fit_panel.add_sim_page(caption=caption)
437	else:
438	self.batch_page = self.fit_panel.add_sim_page(caption=caption)
439
440	def help(self, evt):
441	"""
442	Show a general help dialog.
443	"""
444	from help_panel import HelpWindow
445	frame = HelpWindow(None, -1, 'HelpWindow')
446	if hasattr(frame, "IsIconized"):
447	if not frame.IsIconized():
448	try:
449	icon = self.parent.GetIcon()
450	frame.SetIcon(icon)
451	except:
452	pass
453	frame.Show(True)
454
455	def get_context_menu(self, plotpanel=None):
456	"""
457	Get the context menu items available for P(r).them allow fitting option
458	for Data2D and Data1D only.
459
460	:param graph: the Graph object to which we attach the context menu
461
462	:return: a list of menu items with call-back function
463
464	:note: if Data1D was generated from Theory1D
465	the fitting option is not allowed
466
467	"""
468	self.plot_panel = plotpanel
469	graph = plotpanel.graph
470	fit_option = "Select data for fitting"
471	fit_hint = "Dialog with fitting parameters "
472
473	if graph.selected_plottable not in plotpanel.plots:
474	return []
475	item = plotpanel.plots[graph.selected_plottable]
476	if item.__class__.__name__ is "Data2D":
477	if hasattr(item, "is_data"):
478	if item.is_data:
479	return [[fit_option, fit_hint, self._onSelect]]
480	else:
481	return []
482	return [[fit_option, fit_hint, self._onSelect]]
483	else:
484
485	# if is_data is true , this in an actual data loaded
486	#else it is a data created from a theory model
487	if hasattr(item, "is_data"):
488	if item.is_data:
489	return [[fit_option, fit_hint, self._onSelect]]
490	else:
491	return []
492	return [[fit_option, fit_hint, self._onSelect]]
493	return []
494
495	def get_panels(self, parent):
496	"""
497	Create and return a list of panel objects
498	"""
499	self.parent = parent
500	#self.parent.Bind(EVT_FITSTATE_UPDATE, self.on_set_state_helper)
501	# Creation of the fit panel
502	self.fit_panel = FitPanel(parent=self.parent, manager=self)
503	self.on_add_new_page(event=None)
504	#Set the manager for the main panel
505	self.fit_panel.set_manager(self)
506	# List of windows used for the perspective
507	self.perspective = []
508	self.perspective.append(self.fit_panel.window_name)
509
510	#index number to create random model name
511	self.index_model = 0
512	self.index_theory = 0
513	self.parent.Bind(EVT_SLICER_PANEL, self._on_slicer_event)
514	self.parent.Bind(EVT_SLICER_PARS_UPDATE, self._onEVT_SLICER_PANEL)
515	self.parent._mgr.Bind(wx.aui.EVT_AUI_PANE_CLOSE,self._onclearslicer)
516	#Create reader when fitting panel are created
517	self.state_reader = Reader(self.set_state)
518	#append that reader to list of available reader
519	loader = Loader()
520	loader.associate_file_reader(".fitv", self.state_reader)
521	#Send the fitting panel to guiframe
522	self.mypanels.append(self.fit_panel)
523	return self.mypanels
524
525	def clear_panel(self):
526	"""
527	"""
528	self.fit_panel.clear_panel()
529
530	def set_default_perspective(self):
531	"""
532	Call back method that True to notify the parent that the current plug-in
533	can be set as default perspective.
534	when returning False, the plug-in is not candidate for an automatic
535	default perspective setting
536	"""
537	return True
538
539	def delete_data(self, data):
540	"""
541	delete the given data from panel
542	"""
543	self.fit_panel.delete_data(data)
544
545	def set_data(self, data_list=None):
546	"""
547	receive a list of data to fit
548	"""
549	if data_list is None:
550	data_list = []
551	selected_data_list = []
552	if self.batch_on:
553	page = self.add_fit_page(data=data_list)
554	else:
555	if len(data_list) > MAX_NBR_DATA:
556	from fitting_widgets import DataDialog
557	dlg = DataDialog(data_list=data_list, nb_data=MAX_NBR_DATA)
558	if dlg.ShowModal() == wx.ID_OK:
559	selected_data_list = dlg.get_data()
560	dlg.Destroy()
561
562	else:
563	selected_data_list = data_list
564	try:
565	group_id = wx.NewId()
566	for data in selected_data_list:
567	if data is not None:
568	# 2D has no same group_id
569	if data.__class__.__name__ == 'Data2D':
570	group_id = wx.NewId()
571	data.group_id = group_id
572	if group_id not in data.list_group_id:
573	data.list_group_id.append(group_id)
574	page = self.add_fit_page(data=[data])
575	except:
576	msg = "Fitting Set_data: " + str(sys.exc_value)
577	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
578
579	def set_top_panel(self):
580	"""
581	Close default (welcome) panel
582	"""
583	if 'default' in self.parent.panels:
584	self.parent.on_close_welcome_panel()
585
586
587	def set_theory(self, theory_list=None):
588	"""
589	"""
590	#set the model state for a given theory_state:
591	for item in theory_list:
592	try:
593	_, theory_state = item
594	self.fit_panel.set_model_state(theory_state)
595	except:
596	msg = "Fitting: cannot deal with the theory received"
597	logging.error("set_theory " + msg + "\n" + str(sys.exc_value))
598	wx.PostEvent(self.parent,
599	StatusEvent(status=msg, info="error"))
600
601	def set_state(self, state=None, datainfo=None, format=None):
602	"""
603	Call-back method for the fit page state reader.
604	This method is called when a .fitv/.svs file is loaded.
605
606	: param state: PageState object
607	: param datainfo: data
608	"""
609	#state = self.state_reader.get_state()
610	if state != None:
611	state = state.clone()
612	# store fitting state in temp_state
613	self.temp_state.append(state)
614	else:
615	self.temp_state = []
616	# index to start with for a new set_state
617	self.state_index = 0
618	# state file format
619	self.sfile_ext = format
620
621	self.on_set_state_helper(event=None)
622
623	def on_set_state_helper(self, event=None):
624	"""
625	Set_state_helper. This actually sets state
626	after plotting data from state file.
627
628	: event: FitStateUpdateEvent called
629	by dataloader.plot_data from guiframe
630	"""
631	if len(self.temp_state) == 0:
632	if self.state_index == 0 and len(self.mypanels) <= 0 \
633	and self.sfile_ext == '.svs':
634	self.temp_state = []
635	self.state_index = 0
636	return
637
638	try:
639	# Load fitting state
640	state = self.temp_state[self.state_index]
641	#panel state should have model selection to set_state
642	if state.formfactorcombobox != None:
643	#set state
644	data = self.parent.create_gui_data(state.data)
645	data.group_id = state.data.group_id
646	self.parent.add_data(data_list={data.id: data})
647	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
648	title=data.title))
649	#need to be fix later make sure we are sendind guiframe.data
650	#to panel
651	state.data = data
652	page = self.fit_panel.set_state(state)
653	else:
654	#just set data because set_state won't work
655	data = self.parent.create_gui_data(state.data)
656	data.group_id = state.data.group_id
657	self.parent.add_data(data_list={data.id: data})
658	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
659	title=data.title))
660	page = self.add_fit_page([data])
661	caption = page.window_caption
662	self.store_data(uid=page.uid, data_list=page.get_data_list(),
663	caption=caption)
664	self.mypanels.append(page)
665
666	# get ready for the next set_state
667	self.state_index += 1
668
669	#reset state variables to default when all set_state is finished.
670	if len(self.temp_state) == self.state_index:
671
672	self.temp_state = []
673	#self.state_index = 0
674	# Make sure the user sees the fitting panel after loading
675	#self.parent.set_perspective(self.perspective)
676	self.on_perspective(event=None)
677	except:
678	self.state_index = 0
679	self.temp_state = []
680	raise
681
682	def set_param2fit(self, uid, param2fit):
683	"""
684	Set the list of param names to fit for fitprobelm
685	"""
686	self.page_finder[uid].set_param2fit(param2fit)
687
688	def set_graph_id(self, uid, graph_id):
689	"""
690	Set graph_id for fitprobelm
691	"""
692	self.page_finder[uid].set_graph_id(graph_id)
693
694	def get_graph_id(self, uid):
695	"""
696	Set graph_id for fitprobelm
697	"""
698	return self.page_finder[uid].get_graph_id()
699
700	def save_fit_state(self, filepath, fitstate):
701	"""
702	save fit page state into file
703	"""
704	self.state_reader.write(filename=filepath, fitstate=fitstate)
705
706	def set_fit_weight(self, uid, flag, is2d=False, fid=None):
707	"""
708	Set the fit weights of a given page for all
709	its data by default. If fid is provide then set the range
710	only for the data with fid as id
711	:param uid: id corresponding to a fit page
712	:param fid: id corresponding to a fit problem (data, model)
713	:param weight: current dy data
714	"""
715	if uid in self.page_finder.keys():
716	self.page_finder[uid].set_weight(flag=flag, is2d=is2d)
717
718	def set_fit_range(self, uid, qmin, qmax, fid=None):
719	"""
720	Set the fitting range of a given page for all
721	its data by default. If fid is provide then set the range
722	only for the data with fid as id
723	:param uid: id corresponding to a fit page
724	:param fid: id corresponding to a fit problem (data, model)
725	:param qmin: minimum value of the fit range
726	:param qmax: maximum value of the fit range
727	"""
728	if uid in self.page_finder.keys():
729	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax, fid=fid)
730
731	def schedule_for_fit(self, value=0, uid=None):
732	"""
733	Set the fit problem field to 0 or 1 to schedule that problem to fit.
734	Schedule the specified fitproblem or get the fit problem related to
735	the current page and set value.
736	:param value: integer 0 or 1
737	:param uid: the id related to a page contaning fitting information
738	"""
739	if uid in self.page_finder.keys():
740	self.page_finder[uid].schedule_tofit(value)
741
742	def get_page_finder(self):
743	"""
744	return self.page_finder used also by simfitpage.py
745	"""
746	return self.page_finder
747
748	def set_page_finder(self, modelname, names, values):
749	"""
750	Used by simfitpage.py to reset a parameter given the string constrainst.
751
752	:param modelname: the name ot the model for with the parameter
753	has to reset
754	:param value: can be a string in this case.
755	:param names: the paramter name
756
757	:note: expecting park used for fit.
758
759	"""
760	sim_page_id = self.sim_page.uid
761	for uid, value in self.page_finder.iteritems():
762	if uid != sim_page_id and uid != self.batch_page.uid:
763	list = value.get_model()
764	model = list[0]
765	if model.name == modelname:
766	value.set_model_param(names, values)
767	break
768
769	def split_string(self, item):
770	"""
771	receive a word containing dot and split it. used to split parameterset
772	name into model name and parameter name example: ::
773
774	paramaterset (item) = M1.A
775	Will return model_name = M1 , parameter name = A
776
777	"""
778	if item.find(".") >= 0:
779	param_names = re.split("\.", item)
780	model_name = param_names[0]
781	##Assume max len is 3; eg., M0.radius.width
782	if len(param_names) == 3:
783	param_name = param_names[1] + "." + param_names[2]
784	else:
785	param_name = param_names[1]
786	return model_name, param_name
787
788	def set_ftol(self, ftol=None):
789	"""
790	Set ftol: Relative error desired in the sum of chi squares.
791	"""
792	# check if it is flaot
793	try:
794	f_tol = float(ftol)
795	except:
796	# default
797	f_tol = SANS_F_TOL
798
799	self.ftol = f_tol
800	# update ftol menu help strings
801	ftol_help = "Change the current FTolerance (=%s) " % str(self.ftol)
802	ftol_help += "of Simple FitEngine..."
803	if self.menu1 != None:
804	self.menu1.SetHelpString(self.id_tol, ftol_help)
805
806	def show_ftol_dialog(self, event=None):
807	"""
808	Dialog to select ftol for Scipy
809	"""
810	#if event != None:
811	# event.Skip()
812	from ftol_dialog import ChangeFtol
813	panel = ChangeFtol(self.parent, self)
814	panel.ShowModal()
815
816	def stop_fit(self, uid):
817	"""
818	Stop the fit engine
819	"""
820	if uid in self.fit_thread_list.keys():
821	calc_fit = self.fit_thread_list[uid]
822	if calc_fit is not None and calc_fit.isrunning():
823	calc_fit.stop()
824	msg = "Fit stop!"
825	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
826	del self.fit_thread_list[uid]
827	#set the fit button label of page when fit stop is trigger from
828	#simultaneous fit pane
829	sim_flag = self.sim_page is not None and uid == self.sim_page.uid
830	batch_flag = self.batch_page is not None and uid == self.batch_page.uid
831	if sim_flag or batch_flag:
832	for uid, value in self.page_finder.iteritems():
833	if value.get_scheduled() == 1:
834	if uid in self.fit_panel.opened_pages.keys():
835	panel = self.fit_panel.opened_pages[uid]
836	panel._on_fit_complete()
837
838	def set_smearer(self, uid, smearer, fid, qmin=None, qmax=None, draw=True,
839	enable_smearer=False):
840	"""
841	Get a smear object and store it to a fit problem of fid as id. If proper
842	flag is enable , will plot the theory with smearing information.
843
844	:param smearer: smear object to allow smearing data of id fid
845	:param enable_smearer: Define whether or not all (data, model) contained
846	in the structure of id uid will be smeared before fitting.
847	:param qmin: the maximum value of the theory plotting range
848	:param qmax: the maximum value of the theory plotting range
849	:param draw: Determine if the theory needs to be plot
850	"""
851	if uid not in self.page_finder.keys():
852	return
853	self.page_finder[uid].enable_smearing(flag=enable_smearer)
854	self.page_finder[uid].set_smearer(smearer, fid=fid)
855	if draw:
856	## draw model 1D with smeared data
857	data = self.page_finder[uid].get_fit_data(fid=fid)
858	if data is None:
859	msg = "set_mearer requires at least data.\n"
860	msg += "Got data = %s .\n" % str(data)
861	return
862	#raise ValueError, msg
863	model = self.page_finder[uid].get_model(fid=fid)
864	if model is None:
865	return
866	enable1D = issubclass(data.__class__, Data1D)
867	enable2D = issubclass(data.__class__, Data2D)
868	## if user has already selected a model to plot
869	## redraw the model with data smeared
870	smear = self.page_finder[uid].get_smearer(fid=fid)
871
872	# compute weight for the current data
873	weight = self.page_finder[uid].get_weight(fid=fid)
874
875	self.draw_model(model=model, data=data, page_id=uid, smearer=smear,
876	enable1D=enable1D, enable2D=enable2D,
877	qmin=qmin, qmax=qmax, weight=weight)
878	self._mac_sleep(0.2)
879
880	def _mac_sleep(self, sec=0.2):
881	"""
882	Give sleep to MAC
883	"""
884	if ON_MAC:
885	time.sleep(sec)
886
887	def draw_model(self, model, page_id, data=None, smearer=None,
888	enable1D=True, enable2D=False,
889	state=None,
890	fid=None,
891	toggle_mode_on=False,
892	qmin=None, qmax=None,
893	update_chisqr=True, weight=None, source='model'):
894	"""
895	Draw model.
896
897	:param model: the model to draw
898	:param name: the name of the model to draw
899	:param data: the data on which the model is based to be drawn
900	:param description: model's description
901	:param enable1D: if true enable drawing model 1D
902	:param enable2D: if true enable drawing model 2D
903	:param qmin: Range's minimum value to draw model
904	:param qmax: Range's maximum value to draw model
905	:param qstep: number of step to divide the x and y-axis
906	:param update_chisqr: update chisqr [bool]
907
908	"""
909	#self.weight = weight
910	if issubclass(data.__class__, Data1D) or not enable2D:
911	## draw model 1D with no loaded data
912	self._draw_model1D(model=model,
913	data=data,
914	page_id=page_id,
915	enable1D=enable1D,
916	smearer=smearer,
917	qmin=qmin,
918	qmax=qmax,
919	fid=fid,
920	weight=weight,
921	toggle_mode_on=toggle_mode_on,
922	state=state,
923	update_chisqr=update_chisqr,
924	source=source)
925	else:
926	## draw model 2D with no initial data
927	self._draw_model2D(model=model,
928	page_id=page_id,
929	data=data,
930	enable2D=enable2D,
931	smearer=smearer,
932	qmin=qmin,
933	qmax=qmax,
934	fid=fid,
935	weight=weight,
936	state=state,
937	toggle_mode_on=toggle_mode_on,
938	update_chisqr=update_chisqr,
939	source=source)
940
941	def onFit(self, uid):
942	"""
943	Get series of data, model, associates parameters and range and send then
944	to series of fit engines. Fit data and model, display result to
945	corresponding panels.
946	:param uid: id related to the panel currently calling this fit function.
947	"""
948	flag = True
949	## count the number of fitproblem schedule to fit
950	fitproblem_count = 0
951	for value in self.page_finder.values():
952	if value.get_scheduled() == 1:
953	fitproblem_count += 1
954	self._gui_engine = self._return_engine_type()
955	self.fitproblem_count = fitproblem_count
956	if self._fit_engine == "park":
957	engineType = "Simultaneous Fit"
958	else:
959	engineType = "Single Fit"
960	fitter_list = []
961	sim_fitter = None
962	is_single_fit = True
963	batch_on = False
964	if self.sim_page is not None and self.sim_page.uid == uid:
965	#simulatanous fit only one engine need to be created
966	## if simultaneous fit change automatically the engine to park
967	self._on_change_engine(engine='park')
968	sim_fitter = Fit(self._fit_engine)
969	sim_fitter.fitter_id = self.sim_page.uid
970	fitter_list.append(sim_fitter)
971	is_single_fit = False
972	batch_on = self.sim_page.batch_on
973
974	self.fitproblem_count = fitproblem_count
975	if self._fit_engine == "park":
976	engineType = "Simultaneous Fit"
977	else:
978	engineType = "Single Fit"
979
980	self.current_pg = None
981	list_page_id = []
982	fit_id = 0
983	batch_inputs = {}
984	batch_outputs = {}
985	for page_id, value in self.page_finder.iteritems():
986	# For simulfit (uid give with None), do for-loop
987	# if uid is specified (singlefit), do it only on the page.
988	if engineType == "Single Fit":
989	#combine more than 1 batch page on single mode
990	if self.batch_page is None or self.batch_page.uid != uid:
991	if page_id != uid:
992	continue
993	try:
994	if value.get_scheduled() == 1:
995	value.nbr_residuals_computed = 0
996	#Get list of parameters name to fit
997	pars = []
998	templist = []
999	page = self.fit_panel.get_page_by_id(page_id)
1000	self.set_fit_weight(uid=page.uid,
1001	flag=page.get_weight_flag(),
1002	is2d=page._is_2D())
1003	templist = page.get_param_list()
1004	flag = page._update_paramv_on_fit()
1005	if not flag:
1006	msg = "Fitting range or parameter values are"
1007	msg += " invalid in %s" % \
1008	page.window_caption
1009	wx.PostEvent(page.parent.parent,
1010	StatusEvent(status=msg, info="error",
1011	type="stop"))
1012	return flag
1013	for element in templist:
1014	name = str(element[1])
1015	pars.append(name)
1016	fitproblem_list = value.values()
1017	for fitproblem in fitproblem_list:
1018	if sim_fitter is None:
1019	fitter = Fit(self._fit_engine)
1020	fitter.fitter_id = page_id
1021	self._fit_helper(fitproblem=fitproblem,
1022	pars=pars,
1023	fitter=fitter,
1024	fit_id=fit_id,
1025	batch_inputs=batch_inputs,
1026	batch_outputs=batch_outputs)
1027	fitter_list.append(fitter)
1028	else:
1029	fitter = sim_fitter
1030	self._fit_helper(fitproblem=fitproblem,
1031	pars=pars,
1032	fitter=fitter,
1033	fit_id=fit_id,
1034	batch_inputs=batch_inputs,
1035	batch_outputs=batch_outputs)
1036	fit_id += 1
1037	list_page_id.append(page_id)
1038	current_page_id = page_id
1039	value.clear_model_param()
1040	except KeyboardInterrupt:
1041	flag = True
1042	msg = "Fitting terminated"
1043	wx.PostEvent(self.parent, StatusEvent(status=msg, info="info",
1044	type="stop"))
1045	return flag
1046	except:
1047	flag = False
1048	msg = "%s error: %s" % (engineType, sys.exc_value)
1049	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error",
1050	type="stop"))
1051	return flag
1052	## If a thread is already started, stop it
1053	#if self.calc_fit!= None and self.calc_fit.isrunning():
1054	# self.calc_fit.stop()
1055	msg = "Fitting is in progress..."
1056	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1057
1058	#Handler used for park engine displayed message
1059	handler = ConsoleUpdate(parent=self.parent,
1060	manager=self,
1061	improvement_delta=0.1)
1062	self._mac_sleep(0.2)
1063	## perform single fit
1064	try:
1065	page = self.fit_panel.get_page_by_id(uid)
1066	batch_on = page.batch_on
1067	except:
1068	try:
1069	#if the id cannot be found then we deal with a self.sim_page
1070	#or a self.batch_page
1071	if self.sim_page is not None and uid == self.sim_page.uid:
1072	batch_on = self.sim_page.batch_on
1073	if self.batch_page is not None and uid == self.batch_page.uid:
1074	batch_on = self.batch_page.batch_on
1075	except:
1076	batch_on = False
1077
1078	# batch fit
1079	if batch_on:
1080	calc_fit = FitThread(handler=handler,
1081	fn=fitter_list,
1082	pars=pars,
1083	batch_inputs=batch_inputs,
1084	batch_outputs=batch_outputs,
1085	page_id=list_page_id,
1086	completefn=self._batch_fit_complete,
1087	ftol=self.ftol,
1088	reset_flag=self.batch_reset_flag)
1089	else:
1090	# single fit: not batch and not simul fit
1091	if not is_single_fit:
1092	current_page_id = self.sim_page.uid
1093	## Perform more than 1 fit at the time
1094	calc_fit = FitThread(handler=handler,
1095	fn=fitter_list,
1096	batch_inputs=batch_inputs,
1097	batch_outputs=batch_outputs,
1098	page_id=list_page_id,
1099	updatefn=handler.update_fit,
1100	completefn=self._fit_completed,
1101	ftol=self.ftol)
1102	self.fit_thread_list[current_page_id] = calc_fit
1103	calc_fit.queue()
1104	msg = "Fitting is in progress..."
1105	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1106
1107	self.ready_fit(calc_fit=calc_fit)
1108	return flag
1109
1110	def ready_fit(self, calc_fit):
1111	"""
1112	Ready for another fit
1113	"""
1114	if self.fitproblem_count != None and self.fitproblem_count > 1:
1115	calc_fit.ready(2.5)
1116	else:
1117	time.sleep(0.4)
1118
1119	def remove_plot(self, uid, fid=None, theory=False):
1120	"""
1121	remove model plot when a fit page is closed
1122	:param uid: the id related to the fitpage to close
1123	:param fid: the id of the fitproblem(data, model, range,etc)
1124	"""
1125	if uid not in self.page_finder.keys():
1126	return
1127	fitproblemList = self.page_finder[uid].get_fit_problem(fid)
1128	for fitproblem in fitproblemList:
1129	data = fitproblem.get_fit_data()
1130	model = fitproblem.get_model()
1131	plot_id = None
1132	if model is not None:
1133	plot_id = data.id + model.name
1134	if theory:
1135	plot_id = data.id + model.name
1136	group_id = data.group_id
1137	wx.PostEvent(self.parent, NewPlotEvent(id=plot_id,
1138	group_id=group_id,
1139	action='remove'))
1140
1141	def store_data(self, uid, data_list=None, caption=None):
1142	"""
1143	Recieve a list of data and store them ans well as a caption of
1144	the fit page where they come from.
1145	:param uid: if related to a fit page
1146	:param data_list: list of data to fit
1147	:param caption: caption of the window related to these data
1148	"""
1149	if data_list is None:
1150	data_list = []
1151
1152	self.page_finder[uid].set_fit_data(data=data_list)
1153	if caption is not None:
1154	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1155
1156	def on_add_new_page(self, event=None):
1157	"""
1158	ask fit panel to create a new empty page
1159	"""
1160	try:
1161	page = self.fit_panel.add_empty_page()
1162	# add data associated to the page created
1163	if page != None:
1164	wx.PostEvent(self.parent, StatusEvent(status="Page Created",
1165	info="info"))
1166	else:
1167	msg = "Page was already Created"
1168	wx.PostEvent(self.parent, StatusEvent(status=msg,
1169	info="warning"))
1170	self.set_top_panel()
1171	except:
1172	msg = "Creating Fit page: %s"%sys.exc_value
1173	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1174
1175	def add_fit_page(self, data):
1176	"""
1177	given a data, ask to the fitting panel to create a new fitting page,
1178	get this page and store it into the page_finder of this plug-in
1179	:param data: is a list of data
1180	"""
1181	page = self.fit_panel.set_data(data)
1182	# page could be None when loading state files
1183	if page == None:
1184	return page
1185	#append Data1D to the panel containing its theory
1186	#if theory already plotted
1187	if page.uid in self.page_finder:
1188	data = page.get_data()
1189	theory_data = self.page_finder[page.uid].get_theory_data(data.id)
1190	if issubclass(data.__class__, Data2D):
1191	data.group_id = wx.NewId()
1192	if theory_data is not None:
1193	group_id = str(page.uid) + " Model1D"
1194	wx.PostEvent(self.parent,
1195	NewPlotEvent(group_id=group_id,
1196	action="delete"))
1197	self.parent.update_data(prev_data=theory_data,
1198	new_data=data)
1199	else:
1200	if theory_data is not None:
1201	group_id = str(page.uid) + " Model2D"
1202	data.group_id = theory_data.group_id
1203	wx.PostEvent(self.parent,
1204	NewPlotEvent(group_id=group_id,
1205	action="delete"))
1206	self.parent.update_data(prev_data=theory_data,
1207	new_data=data)
1208	self.store_data(uid=page.uid, data_list=page.get_data_list(),
1209	caption=page.window_caption)
1210	if self.sim_page is not None and not self.batch_on:
1211	self.sim_page.draw_page()
1212	if self.batch_page is not None and self.batch_on:
1213	self.batch_page.draw_page()
1214
1215	return page
1216
1217	def _onEVT_SLICER_PANEL(self, event):
1218	"""
1219	receive and event telling to update a panel with a name starting with
1220	event.panel_name. this method update slicer panel
1221	for a given interactor.
1222
1223	:param event: contains type of slicer , paramaters for updating
1224	the panel and panel_name to find the slicer 's panel concerned.
1225	"""
1226	for item in self.parent.panels:
1227	name = event.panel_name
1228	if self.parent.panels[item].window_caption.startswith(name):
1229	self.parent.panels[item].set_slicer(event.type, event.params)
1230
1231	self.parent._mgr.Update()
1232
1233	def _closed_fitpage(self, event):
1234	"""
1235	request fitpanel to close a given page when its unique data is removed
1236	from the plot. close fitpage only when the a loaded data is removed
1237	"""
1238	if event is None or event.data is None:
1239	return
1240	if hasattr(event.data, "is_data"):
1241	if not event.data.is_data or \
1242	event.data.__class__.__name__ == "Data1D":
1243	self.fit_panel.close_page_with_data(event.data)
1244
1245	def _reset_schedule_problem(self, value=0, uid=None):
1246	"""
1247	unschedule or schedule all fitproblem to be fit
1248	"""
1249	# case that uid is not specified
1250	if uid == None:
1251	for page_id in self.page_finder.keys():
1252	self.page_finder[page_id].schedule_tofit(value)
1253	# when uid is given
1254	else:
1255	if uid in self.page_finder.keys():
1256	self.page_finder[uid].schedule_tofit(value)
1257
1258	def _fit_helper(self, fitproblem, pars, fitter, fit_id,
1259	batch_inputs, batch_outputs):
1260	"""
1261	Create and set fit engine with series of data and model
1262	:param pars: list of fittable parameters
1263	:param fitter_list: list of fit engine
1264	:param value: structure storing data mapped to their model, range etc.
1265	"""
1266	data = fitproblem.get_fit_data()
1267	model = fitproblem.get_model()
1268	smearer = fitproblem.get_smearer()
1269	qmin, qmax = fitproblem.get_range()
1270
1271	#Extra list of parameters and their constraints
1272	listOfConstraint = []
1273	param = fitproblem.get_model_param()
1274	if len(param) > 0:
1275	for item in param:
1276	## check if constraint
1277	if item[0] != None and item[1] != None:
1278	listOfConstraint.append((item[0], item[1]))
1279	new_model = model
1280	fitter.set_model(new_model, fit_id, pars, data=data,
1281	constraints=listOfConstraint)
1282	fitter.set_data(data=data, id=fit_id, smearer=smearer, qmin=qmin,
1283	qmax=qmax)
1284	fitter.select_problem_for_fit(id=fit_id, value=1)
1285
1286	def _onSelect(self, event):
1287	"""
1288	when Select data to fit a new page is created .Its reference is
1289	added to self.page_finder
1290	"""
1291	panel = self.plot_panel
1292	if panel == None:
1293	raise ValueError, "Fitting:_onSelect: NonType panel"
1294	Plugin.on_perspective(self, event=event)
1295	self.select_data(panel)
1296
1297	def select_data(self, panel):
1298	"""
1299	"""
1300	for plottable in panel.graph.plottables:
1301	if plottable.__class__.__name__ in ["Data1D", "Theory1D"]:
1302	data_id = panel.graph.selected_plottable
1303	if plottable == panel.plots[data_id]:
1304	data = plottable
1305	self.add_fit_page(data=[data])
1306	return
1307	else:
1308	data = plottable
1309	self.add_fit_page(data=[data])
1310	self.set_top_panel()
1311
1312	def update_fit(self, result=None, msg=""):
1313	"""
1314	"""
1315	print "update_fit result", result
1316
1317	def _batch_fit_complete(self, result, pars, page_id,
1318	batch_outputs, batch_inputs, elapsed=None):
1319	"""
1320	Display fit result in batch
1321	:param result: list of objects received fromt fit engines
1322	:param pars: list of fitted parameters names
1323	:param page_id: list of page ids which called fit function
1324	:param elapsed: time spent at the fitting level
1325	"""
1326	self._mac_sleep(0.2)
1327	uid = page_id[0]
1328	if uid in self.fit_thread_list.keys():
1329	del self.fit_thread_list[uid]
1330
1331	self._update_fit_button(page_id)
1332	t1 = time.time()
1333	str_time = time.strftime("%a, %d %b %Y %H:%M:%S ", time.localtime(t1))
1334	msg = "Fit completed on %s \n" % str_time
1335	msg += "Duration time: %s s.\n" % str(elapsed)
1336	wx.PostEvent(self.parent, StatusEvent(status=msg, info="info",
1337	type="stop"))
1338
1339	if batch_outputs is None:
1340	batch_outputs = {}
1341
1342	# format batch_outputs
1343	batch_outputs["Chi2"] = []
1344	#Don't like these loops
1345	# Need to create dictionary of all fitted parameters
1346	# since the number of parameters can differ between each fit result
1347	for list_res in result:
1348	for res in list_res:
1349	model, data = res.inputs[0]
1350	if model is not None and hasattr(model, "model"):
1351	model = model.model
1352	#get all fittable parameters of the current model
1353	for param in model.getParamList():
1354	if param not in batch_outputs.keys():
1355	batch_outputs[param] = []
1356	for param in model.getDispParamList():
1357	if not model.is_fittable(param) and \
1358	param in batch_outputs.keys():
1359	del batch_outputs[param]
1360	# Add fitted parameters and their error
1361	for param in res.param_list:
1362	if param not in batch_outputs.keys():
1363	batch_outputs[param] = []
1364	err_param = "error on %s" % str(param)
1365	if err_param not in batch_inputs.keys():
1366	batch_inputs[err_param] = []
1367	msg = ""
1368	for list_res in result:
1369	for res in list_res:
1370	pid = res.fitter_id
1371	model, data = res.inputs[0]
1372	correct_result = False
1373	if model is not None and hasattr(model, "model"):
1374	model = model.model
1375	if data is not None and hasattr(data, "sans_data"):
1376	data = data.sans_data
1377
1378	is_data2d = issubclass(data.__class__, Data2D)
1379	#check consistency of arrays
1380	if not is_data2d:
1381	if len(res.theory) == len(res.index[res.index]) and \
1382	len(res.index) == len(data.y):
1383	correct_result = True
1384	else:
1385	copy_data = deepcopy(data)
1386	new_theory = copy_data.data
1387	new_theory[res.index] = res.theory
1388	new_theory[res.index == False] = numpy.nan
1389	correct_result = True
1390	#get all fittable parameters of the current model
1391	param_list = model.getParamList()
1392	for param in model.getDispParamList():
1393	if not model.is_fittable(param) and \
1394	param in param_list:
1395	param_list.remove(param)
1396	if not correct_result or res.fitness is None or \
1397	not numpy.isfinite(res.fitness) or \
1398	numpy.any(res.pvec == None) or not \
1399	numpy.all(numpy.isfinite(res.pvec)):
1400	data_name = str(None)
1401	if data is not None:
1402	data_name = str(data.name)
1403	model_name = str(None)
1404	if model is not None:
1405	model_name = str(model.name)
1406	msg += "Data %s and Model %s did not fit.\n" % (data_name,
1407	model_name)
1408	ERROR = numpy.NAN
1409	cell = BatchCell()
1410	cell.label = res.fitness
1411	cell.value = res.fitness
1412	batch_outputs["Chi2"].append(ERROR)
1413	for param in param_list:
1414	# save value of fixed parameters
1415	if param not in res.param_list:
1416	batch_outputs[str(param)].append(ERROR)
1417	else:
1418	#save only fitted values
1419	batch_outputs[param].append(ERROR)
1420	batch_inputs["error on %s" % str(param)].append(ERROR)
1421	else:
1422	# ToDo: Why sometimes res.pvec comes with numpy.float64?
1423	# Need to fix it within ScipyEngine
1424	if res.pvec.__class__ == numpy.float64:
1425	res.pvec = [res.pvec]
1426
1427	cell = BatchCell()
1428	cell.label = res.fitness
1429	cell.value = res.fitness
1430	batch_outputs["Chi2"].append(cell)
1431	# add parameters to batch_results
1432	for param in param_list:
1433	# save value of fixed parameters
1434	if param not in res.param_list:
1435	batch_outputs[str(param)].append(model.getParam(param))
1436	else:
1437	index = res.param_list.index(param)
1438	#save only fitted values
1439	batch_outputs[param].append(res.pvec[index])
1440	if res.stderr is not None and \
1441	len(res.stderr) == len(res.param_list):
1442	item = res.stderr[index]
1443	batch_inputs["error on %s" % param].append(item)
1444	else:
1445	batch_inputs["error on %s" % param].append('-')
1446	model.setParam(param, res.pvec[index])
1447	#fill the batch result with emtpy value if not in the current
1448	#model
1449	EMPTY = "-"
1450	for key in batch_outputs.keys():
1451	if key not in param_list and key not in ["Chi2", "Data"]:
1452	batch_outputs[key].append(EMPTY)
1453
1454	self.page_finder[pid].set_batch_result(batch_inputs=batch_inputs,
1455	batch_outputs=batch_outputs)
1456
1457	cpage = self.fit_panel.get_page_by_id(pid)
1458	cpage._on_fit_complete()
1459	self.page_finder[pid][data.id].set_result(res)
1460	fitproblem = self.page_finder[pid][data.id]
1461	qmin, qmax = fitproblem.get_range()
1462	plot_result = False
1463	if correct_result:
1464	if not is_data2d:
1465	self._complete1D(x=data.x[res.index], y=res.theory, page_id=pid,
1466	elapsed=None,
1467	index=res.index, model=model,
1468	weight=None, fid=data.id,
1469	toggle_mode_on=False, state=None,
1470	data=data, update_chisqr=False,
1471	source='fit', plot_result=plot_result)
1472	else:
1473	self._complete2D(image=new_theory, data=data,
1474	model=model,
1475	page_id=pid, elapsed=None,
1476	index=res.index,
1477	qmin=qmin,
1478	qmax=qmax, fid=data.id, weight=None,
1479	toggle_mode_on=False, state=None,
1480	update_chisqr=False,
1481	source='fit', plot_result=plot_result)
1482	self.on_set_batch_result(page_id=pid,
1483	fid=data.id,
1484	batch_outputs=batch_outputs,
1485	batch_inputs=batch_inputs)
1486
1487	wx.PostEvent(self.parent, StatusEvent(status=msg, error="info",
1488	type="stop"))
1489	# Remove parameters that are not shown
1490	cpage = self.fit_panel.get_page_by_id(uid)
1491	tbatch_outputs = {}
1492	shownkeystr = cpage.get_copy_params()
1493	for key in batch_outputs.keys():
1494	if key in ["Chi2", "Data"] or shownkeystr.count(key) > 0:
1495	tbatch_outputs[key] = batch_outputs[key]
1496
1497	wx.CallAfter(self.parent.on_set_batch_result, tbatch_outputs,
1498	batch_inputs, self.sub_menu)
1499
1500	def on_set_batch_result(self, page_id, fid, batch_outputs, batch_inputs):
1501	"""
1502	"""
1503	pid = page_id
1504	if fid not in self.page_finder[pid]:
1505	return
1506	fitproblem = self.page_finder[pid][fid]
1507	index = self.page_finder[pid].nbr_residuals_computed - 1
1508	residuals = fitproblem.get_residuals()
1509	theory_data = fitproblem.get_theory_data()
1510	data = fitproblem.get_fit_data()
1511	model = fitproblem.get_model()
1512	#fill batch result information
1513	if "Data" not in batch_outputs.keys():
1514	batch_outputs["Data"] = []
1515	from sans.guiframe.data_processor import BatchCell
1516	cell = BatchCell()
1517	cell.label = data.name
1518	cell.value = index
1519
1520	if theory_data != None:
1521	#Suucessful fit
1522	theory_data.id = wx.NewId()
1523	theory_data.name = model.name + "[%s]" % str(data.name)
1524	if issubclass(theory_data.__class__, Data2D):
1525	group_id = wx.NewId()
1526	theory_data.group_id = group_id
1527	if group_id not in theory_data.list_group_id:
1528	theory_data.list_group_id.append(group_id)
1529
1530	try:
1531	# associate residuals plot
1532	if issubclass(residuals.__class__, Data2D):
1533	group_id = wx.NewId()
1534	residuals.group_id = group_id
1535	if group_id not in residuals.list_group_id:
1536	residuals.list_group_id.append(group_id)
1537	batch_outputs["Chi2"][index].object = [residuals]
1538	except:
1539	pass
1540
1541	cell.object = [data, theory_data]
1542	batch_outputs["Data"].append(cell)
1543	for key, value in data.meta_data.iteritems():
1544	if key not in batch_inputs.keys():
1545	batch_inputs[key] = []
1546	#if key.lower().strip() != "loader":
1547	batch_inputs[key].append(value)
1548	param = "temperature"
1549	if hasattr(data.sample, param):
1550	if param not in batch_inputs.keys():
1551	batch_inputs[param] = []
1552	batch_inputs[param].append(data.sample.temperature)
1553
1554	def _fit_completed(self, result, page_id, batch_outputs,
1555	batch_inputs=None, pars=None, elapsed=None):
1556	"""
1557	Display result of the fit on related panel(s).
1558	:param result: list of object generated when fit ends
1559	:param pars: list of names of parameters fitted
1560	:param page_id: list of page ids which called fit function
1561	:param elapsed: time spent at the fitting level
1562	"""
1563	t1 = time.time()
1564	str_time = time.strftime("%a, %d %b %Y %H:%M:%S ", time.localtime(t1))
1565	msg = "Fit completed on %s \n" % str_time
1566	msg += "Duration time: %s s.\n" % str(elapsed)
1567	wx.PostEvent(self.parent, StatusEvent(status=msg, info="info",
1568	type="stop"))
1569	# reset fit_engine if changed by simul_fit
1570	if self._fit_engine != self._gui_engine:
1571	self._on_change_engine(self._gui_engine)
1572	self._update_fit_button(page_id)
1573	result = result[0]
1574	self.fit_thread_list = {}
1575	if page_id is None:
1576	page_id = []
1577	## fit more than 1 model at the same time
1578	self._mac_sleep(0.2)
1579	try:
1580	index = 0
1581	for uid in page_id:
1582	res = result[index]
1583	if res.fitness is None or \
1584	not numpy.isfinite(res.fitness) or \
1585	numpy.any(res.pvec == None) or \
1586	not numpy.all(numpy.isfinite(res.pvec)):
1587	msg = "Fitting did not converge!!!"
1588	wx.PostEvent(self.parent,
1589	StatusEvent(status=msg,
1590	info="warning",
1591	type="stop"))
1592	self._update_fit_button(page_id)
1593	else:
1594	#set the panel when fit result are float not list
1595	if res.pvec.__class__ == numpy.float64:
1596	pvec = [res.pvec]
1597	else:
1598	pvec = res.pvec
1599	if res.stderr.__class__ == numpy.float64:
1600	stderr = [res.stderr]
1601	else:
1602	stderr = res.stderr
1603	cpage = self.fit_panel.get_page_by_id(uid)
1604	# Make sure we got all results
1605	#(CallAfter is important to MAC)
1606	try:
1607	#if res != None:
1608	wx.CallAfter(cpage.onsetValues, res.fitness,
1609	res.param_list,
1610	pvec, stderr)
1611	index += 1
1612	wx.CallAfter(cpage._on_fit_complete)
1613	except KeyboardInterrupt:
1614	msg = "Singular point: Fitting Stoped."
1615	wx.PostEvent(self.parent, StatusEvent(status=msg,
1616	info="info",
1617	type="stop"))
1618	except:
1619	msg = "Singular point: Fitting Error occurred."
1620	wx.PostEvent(self.parent, StatusEvent(status=msg,
1621	info="error",
1622	type="stop"))
1623
1624	except:
1625	msg = "Fit completed but Following"
1626	msg += " warning occurred: %s" % sys.exc_value
1627	wx.PostEvent(self.parent, StatusEvent(status=msg, info="warning",
1628	type="stop"))
1629
1630	def _update_fit_button(self, page_id):
1631	"""
1632	Update Fit button when fit stopped
1633
1634	: parameter page_id: fitpage where the button is
1635	"""
1636	if page_id.__class__.__name__ != 'list':
1637	page_id = [page_id]
1638	for uid in page_id:
1639	page = self.fit_panel.get_page_by_id(uid)
1640	page._on_fit_complete()
1641
1642	def _on_show_panel(self, event):
1643	"""
1644	"""
1645	pass
1646
1647	def on_reset_batch_flag(self, event):
1648	"""
1649	Set batch_reset_flag
1650	"""
1651	event.Skip()
1652	if self.menu1 == None:
1653	return
1654	menu_item = self.menu1.FindItemById(self.id_reset_flag)
1655	flag = menu_item.IsChecked()
1656	if not flag:
1657	menu_item.Check(False)
1658	self.batch_reset_flag = True
1659	else:
1660	menu_item.Check(True)
1661	self.batch_reset_flag = False
1662
1663	## post a message to status bar
1664	msg = "Set Chain Fitting: %s" % str(not self.batch_reset_flag)
1665	wx.PostEvent(self.parent,
1666	StatusEvent(status=msg))
1667
1668	def _onset_engine_park(self, event):
1669	"""
1670	set engine to park
1671	"""
1672	self._on_change_engine('park')
1673
1674	def _onset_engine_scipy(self, event):
1675	"""
1676	set engine to scipy
1677	"""
1678	self._on_change_engine('scipy')
1679
1680	def _on_slicer_event(self, event):
1681	"""
1682	Receive a panel as event and send it to guiframe
1683
1684	:param event: event containing a panel
1685
1686	"""
1687	if event.panel is not None:
1688	new_panel = event.panel
1689	self.slicer_panels.append(event.panel)
1690	# Set group ID if available
1691	event_id = self.parent.popup_panel(new_panel)
1692	new_panel.uid = event_id
1693	self.mypanels.append(new_panel)
1694
1695	def _onclearslicer(self, event):
1696	"""
1697	Clear the boxslicer when close the panel associate with this slicer
1698	"""
1699	name = event.GetPane().caption
1700
1701	for panel in self.slicer_panels:
1702	if panel.window_caption == name:
1703
1704	for item in self.parent.panels:
1705	if hasattr(self.parent.panels[item], "uid"):
1706	if self.parent.panels[item].uid == panel.base.uid:
1707	self.parent.panels[item].onClearSlicer(event)
1708	self.parent._mgr.Update()
1709	break
1710	break
1711
1712	def _return_engine_type(self):
1713	"""
1714	return the current type of engine
1715	"""
1716	return self._fit_engine
1717
1718	def _on_change_engine(self, engine='park'):
1719	"""
1720	Allow to select the type of engine to perform fit
1721
1722	:param engine: the key work of the engine
1723
1724	"""
1725	## saving fit engine name
1726	self._fit_engine = engine
1727	## change menu item state
1728	if engine == "park":
1729	self.menu1.FindItemById(self.park_id).Check(True)
1730	self.menu1.FindItemById(self.scipy_id).Check(False)
1731	else:
1732	self.menu1.FindItemById(self.park_id).Check(False)
1733	self.menu1.FindItemById(self.scipy_id).Check(True)
1734	## post a message to status bar
1735	msg = "Engine set to: %s" % self._fit_engine
1736	wx.PostEvent(self.parent,
1737	StatusEvent(status=msg))
1738	## send the current engine type to fitpanel
1739	self.fit_panel._on_engine_change(name=self._fit_engine)
1740
1741	def _on_model_panel(self, evt):
1742	"""
1743	react to model selection on any combo box or model menu.plot the model
1744
1745	:param evt: wx.combobox event
1746
1747	"""
1748	model = evt.model
1749	uid = evt.uid
1750	qmin = evt.qmin
1751	qmax = evt.qmax
1752	caption = evt.caption
1753	enable_smearer = evt.enable_smearer
1754	if model == None:
1755	return
1756	if uid not in self.page_finder.keys():
1757	return
1758	# save the name containing the data name with the appropriate model
1759	self.page_finder[uid].set_model(model)
1760	self.page_finder[uid].enable_smearing(enable_smearer)
1761	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax)
1762	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1763	if self.sim_page is not None and not self.batch_on:
1764	self.sim_page.draw_page()
1765	if self.batch_page is not None and self.batch_on:
1766	self.batch_page.draw_page()
1767
1768	def _update1D(self, x, output):
1769	"""
1770	Update the output of plotting model 1D
1771	"""
1772	msg = "Plot updating ... "
1773	wx.PostEvent(self.parent, StatusEvent(status=msg, type="update"))
1774
1775	def _complete1D(self, x, y, page_id, elapsed, index, model,
1776	weight=None, fid=None,
1777	toggle_mode_on=False, state=None,
1778	data=None, update_chisqr=True,
1779	source='model', plot_result=True):
1780	"""
1781	Complete plotting 1D data
1782	"""
1783	try:
1784	numpy.nan_to_num(y)
1785
1786	new_plot = Data1D(x=x, y=y)
1787	new_plot.is_data = False
1788	new_plot.dy = numpy.zeros(len(y))
1789	new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
1790	_yaxis, _yunit = data.get_yaxis()
1791	_xaxis, _xunit = data.get_xaxis()
1792	new_plot.title = data.name
1793
1794	new_plot.group_id = data.group_id
1795	if new_plot.group_id == None:
1796	new_plot.group_id = data.group_id
1797	new_plot.id = str(page_id) + " " + data.name
1798	#if new_plot.id in self.color_dict:
1799	# new_plot.custom_color = self.color_dict[new_plot.id]
1800	#find if this theory was already plotted and replace that plot given
1801	#the same id
1802	theory_data = self.page_finder[page_id].get_theory_data(fid=data.id)
1803
1804	if data.is_data:
1805	data_name = str(data.name)
1806	else:
1807	data_name = str(model.__class__.__name__)
1808
1809	new_plot.name = model.name + " [" + data_name +"]"
1810	new_plot.xaxis(_xaxis, _xunit)
1811	new_plot.yaxis(_yaxis, _yunit)
1812	self.page_finder[page_id].set_theory_data(data=new_plot,
1813	fid=data.id)
1814	self.parent.update_theory(data_id=data.id, theory=new_plot,
1815	state=state)
1816	current_pg = self.fit_panel.get_page_by_id(page_id)
1817	title = new_plot.title
1818	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
1819	if not batch_on:
1820	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1821	title=str(title)))
1822	elif plot_result:
1823	top_data_id = self.fit_panel.get_page_by_id(page_id).data.id
1824	if data.id == top_data_id:
1825	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1826	title=str(title)))
1827	caption = current_pg.window_caption
1828	self.page_finder[page_id].set_fit_tab_caption(caption=caption)
1829
1830	self.page_finder[page_id].set_theory_data(data=new_plot,
1831	fid=data.id)
1832	if toggle_mode_on:
1833	wx.PostEvent(self.parent,
1834	NewPlotEvent(group_id=str(page_id) + " Model2D",
1835	action="Hide"))
1836	else:
1837	if update_chisqr:
1838	wx.PostEvent(current_pg,
1839	Chi2UpdateEvent(output=self._cal_chisqr(
1840	data=data,
1841	fid=fid,
1842	weight=weight,
1843	page_id=page_id,
1844	index=index)))
1845	else:
1846	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1847	index=index, weight=weight)
1848
1849	msg = "Computation completed!"
1850	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1851	except:
1852	raise
1853
1854	def _update2D(self, output, time=None):
1855	"""
1856	Update the output of plotting model
1857	"""
1858	wx.PostEvent(self.parent, StatusEvent(status="Plot \
1859	#updating ... ", type="update"))
1860	#self.ready_fit()
1861
1862	def _complete2D(self, image, data, model, page_id, elapsed, index, qmin,
1863	qmax, fid=None, weight=None, toggle_mode_on=False, state=None,
1864	update_chisqr=True, source='model', plot_result=True):
1865	"""
1866	Complete get the result of modelthread and create model 2D
1867	that can be plot.
1868	"""
1869	numpy.nan_to_num(image)
1870	new_plot = Data2D(image=image, err_image=data.err_data)
1871	new_plot.name = model.name + '2d'
1872	new_plot.title = "Analytical model 2D "
1873	new_plot.id = str(page_id) + " " + data.name
1874	new_plot.group_id = str(page_id) + " Model2D"
1875	new_plot.detector = data.detector
1876	new_plot.source = data.source
1877	new_plot.is_data = False
1878	new_plot.qx_data = data.qx_data
1879	new_plot.qy_data = data.qy_data
1880	new_plot.q_data = data.q_data
1881	new_plot.mask = data.mask
1882	## plot boundaries
1883	new_plot.ymin = data.ymin
1884	new_plot.ymax = data.ymax
1885	new_plot.xmin = data.xmin
1886	new_plot.xmax = data.xmax
1887	title = data.title
1888
1889	new_plot.is_data = False
1890	if data.is_data:
1891	data_name = str(data.name)
1892	else:
1893	data_name = str(model.__class__.__name__) + '2d'
1894
1895	if len(title) > 1:
1896	new_plot.title = "Model2D for %s "% model.name + data_name
1897	new_plot.name = model.name + " [" + \
1898	data_name + "]"
1899	theory_data = deepcopy(new_plot)
1900
1901	self.page_finder[page_id].set_theory_data(data=theory_data,
1902	fid=data.id)
1903	self.parent.update_theory(data_id=data.id,
1904	theory=new_plot,
1905	state=state)
1906	current_pg = self.fit_panel.get_page_by_id(page_id)
1907	title = new_plot.title
1908	if not source == 'fit' and plot_result:
1909	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1910	title=title))
1911	if toggle_mode_on:
1912	wx.PostEvent(self.parent,
1913	NewPlotEvent(group_id=str(page_id) + " Model1D",
1914	action="Hide"))
1915	else:
1916	# Chisqr in fitpage
1917	if update_chisqr:
1918	wx.PostEvent(current_pg,
1919	Chi2UpdateEvent(output=self._cal_chisqr(data=data,
1920	weight=weight,
1921	fid=fid,
1922	page_id=page_id,
1923	index=index)))
1924	else:
1925	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1926	index=index, weight=weight)
1927	msg = "Computation completed!"
1928	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1929
1930	def _draw_model2D(self, model, page_id, qmin,
1931	qmax,
1932	data=None, smearer=None,
1933	description=None, enable2D=False,
1934	state=None,
1935	fid=None,
1936	weight=None,
1937	toggle_mode_on=False,
1938	update_chisqr=True, source='model'):
1939	"""
1940	draw model in 2D
1941
1942	:param model: instance of the model to draw
1943	:param description: the description of the model
1944	:param enable2D: when True allows to draw model 2D
1945	:param qmin: the minimum value to draw model 2D
1946	:param qmax: the maximum value to draw model 2D
1947	:param qstep: the number of division of Qx and Qy of the model to draw
1948
1949	"""
1950	if not enable2D:
1951	return None
1952	try:
1953	from model_thread import Calc2D
1954	## If a thread is already started, stop it
1955	if (self.calc_2D is not None) and self.calc_2D.isrunning():
1956	self.calc_2D.stop()
1957	self.calc_2D = Calc2D(model=model,
1958	data=data,
1959	page_id=page_id,
1960	smearer=smearer,
1961	qmin=qmin,
1962	qmax=qmax,
1963	weight=weight,
1964	fid=fid,
1965	toggle_mode_on=toggle_mode_on,
1966	state=state,
1967	completefn=self._complete2D,
1968	update_chisqr=update_chisqr, source=source)
1969	self.calc_2D.queue()
1970	except:
1971	raise
1972
1973	def _draw_model1D(self, model, page_id, data,
1974	qmin, qmax, smearer=None,
1975	state=None,
1976	weight=None,
1977	fid=None,
1978	toggle_mode_on=False, update_chisqr=True, source='model',
1979	enable1D=True):
1980	"""
1981	Draw model 1D from loaded data1D
1982
1983	:param data: loaded data
1984	:param model: the model to plot
1985
1986	"""
1987	if not enable1D:
1988	return
1989	try:
1990	from model_thread import Calc1D
1991	## If a thread is already started, stop it
1992	if (self.calc_1D is not None) and self.calc_1D.isrunning():
1993	self.calc_1D.stop()
1994	self.calc_1D = Calc1D(data=data,
1995	model=model,
1996	page_id=page_id,
1997	qmin=qmin,
1998	qmax=qmax,
1999	smearer=smearer,
2000	state=state,
2001	weight=weight,
2002	fid=fid,
2003	toggle_mode_on=toggle_mode_on,
2004	completefn=self._complete1D,
2005	#updatefn = self._update1D,
2006	update_chisqr=update_chisqr,
2007	source=source)
2008	self.calc_1D.queue()
2009	except:
2010	msg = " Error occurred when drawing %s Model 1D: " % model.name
2011	msg += " %s" % sys.exc_value
2012	wx.PostEvent(self.parent, StatusEvent(status=msg))
2013
2014	def _cal_chisqr(self, page_id, data, weight, fid=None, index=None):
2015	"""
2016	Get handy Chisqr using the output from draw1D and 2D,
2017	instead of calling expansive CalcChisqr in guithread
2018	"""
2019	try:
2020	data_copy = deepcopy(data)
2021	except:
2022	return
2023	# default chisqr
2024	chisqr = None
2025	#to compute chisq make sure data has valid data
2026	# return None if data == None
2027	if not check_data_validity(data_copy) or data_copy == None:
2028	return chisqr
2029
2030	# Get data: data I, theory I, and data dI in order
2031	if data_copy.__class__.__name__ == "Data2D":
2032	if index == None:
2033	index = numpy.ones(len(data_copy.data), dtype=bool)
2034	if weight != None:
2035	data_copy.err_data = weight
2036	# get rid of zero error points
2037	index = index & (data_copy.err_data != 0)
2038	index = index & (numpy.isfinite(data_copy.data))
2039	fn = data_copy.data[index]
2040	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2041	if theory_data == None:
2042	return chisqr
2043	gn = theory_data.data[index]
2044	en = data_copy.err_data[index]
2045	else:
2046	# 1 d theory from model_thread is only in the range of index
2047	if index == None:
2048	index = numpy.ones(len(data_copy.y), dtype=bool)
2049	if weight != None:
2050	data_copy.dy = weight
2051	if data_copy.dy == None or data_copy.dy == []:
2052	dy = numpy.ones(len(data_copy.y))
2053	else:
2054	## Set consitently w/AbstractFitengine:
2055	# But this should be corrected later.
2056	dy = deepcopy(data_copy.dy)
2057	dy[dy == 0] = 1
2058	fn = data_copy.y[index]
2059
2060	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2061	if theory_data == None:
2062	return chisqr
2063	gn = theory_data.y
2064	en = dy[index]
2065
2066	# residual
2067	try:
2068	res = (fn - gn) / en
2069	except ValueError:
2070	print "Unmatch lengths %s, %s, %s"% (len(fn), len(gn), len(en))
2071	return
2072
2073	residuals = res[numpy.isfinite(res)]
2074	# get chisqr only w/finite
2075	chisqr = numpy.average(residuals * residuals)
2076
2077	self._plot_residuals(page_id=page_id, data=data_copy,
2078	fid=fid,
2079	weight=weight, index=index)
2080
2081	return chisqr
2082
2083	def _plot_residuals(self, page_id, weight, fid=None,
2084	data=None, index=None):
2085	"""
2086	Plot the residuals
2087
2088	:param data: data
2089	:param index: index array (bool)
2090	: Note: this is different from the residuals in cal_chisqr()
2091	"""
2092	data_copy = deepcopy(data)
2093	# Get data: data I, theory I, and data dI in order
2094	if data_copy.__class__.__name__ == "Data2D":
2095	# build residuals
2096	residuals = Data2D()
2097	#residuals.copy_from_datainfo(data)
2098	# Not for trunk the line below, instead use the line above
2099	data_copy.clone_without_data(len(data_copy.data), residuals)
2100	residuals.data = None
2101	fn = data_copy.data
2102	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2103	gn = theory_data.data
2104	if weight == None:
2105	en = data_copy.err_data
2106	else:
2107	en = weight
2108	residuals.data = (fn - gn) / en
2109	residuals.qx_data = data_copy.qx_data
2110	residuals.qy_data = data_copy.qy_data
2111	residuals.q_data = data_copy.q_data
2112	residuals.err_data = numpy.ones(len(residuals.data))
2113	residuals.xmin = min(residuals.qx_data)
2114	residuals.xmax = max(residuals.qx_data)
2115	residuals.ymin = min(residuals.qy_data)
2116	residuals.ymax = max(residuals.qy_data)
2117	residuals.q_data = data_copy.q_data
2118	residuals.mask = data_copy.mask
2119	residuals.scale = 'linear'
2120	# check the lengths
2121	if len(residuals.data) != len(residuals.q_data):
2122	return
2123	else:
2124	# 1 d theory from model_thread is only in the range of index
2125	if data_copy.dy == None or data_copy.dy == []:
2126	dy = numpy.ones(len(data_copy.y))
2127	else:
2128	if weight == None:
2129	dy = numpy.ones(len(data_copy.y))
2130	## Set consitently w/AbstractFitengine:
2131	## But this should be corrected later.
2132	else:
2133	dy = weight
2134	dy[dy == 0] = 1
2135	fn = data_copy.y[index]
2136	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2137	gn = theory_data.y
2138	en = dy[index]
2139	# build residuals
2140	residuals = Data1D()
2141	try:
2142	residuals.y = (fn - gn) / en
2143	except:
2144	msg = "ResidualPlot Error: different # of data points in theory"
2145	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
2146	residuals.y = (fn - gn[index]) / en
2147	residuals.x = data_copy.x[index]
2148	residuals.dy = numpy.ones(len(residuals.y))
2149	residuals.dx = None
2150	residuals.dxl = None
2151	residuals.dxw = None
2152	residuals.ytransform = 'y'
2153	# For latter scale changes
2154	residuals.xaxis('\\rm{Q} ', 'A^{-1}')
2155	residuals.yaxis('\\rm{Residuals} ', 'normalized')
2156	theory_name = str(theory_data.name.split()[0])
2157	new_plot = residuals
2158	new_plot.name = "Residuals for " + str(theory_name) + "[" +\
2159	str(data.name) +"]"
2160	## allow to highlight data when plotted
2161	new_plot.interactive = True
2162	## when 2 data have the same id override the 1 st plotted
2163	new_plot.id = "res" + str(data_copy.id) + str(theory_name)
2164	##group_id specify on which panel to plot this data
2165	group_id = self.page_finder[page_id].get_graph_id()
2166	if group_id == None:
2167	group_id = data.group_id
2168	new_plot.group_id = "res" + str(group_id)
2169	#new_plot.is_data = True
2170	##post data to plot
2171	title = new_plot.name
2172	self.page_finder[page_id].set_residuals(residuals=new_plot,
2173	fid=data.id)
2174	self.parent.update_theory(data_id=data.id, theory=new_plot)
2175	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
2176	if not batch_on:
2177	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/fitting.py @ b11e127

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