fitting.py @ 0c4bca6

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 0c4bca6 was fd5ac0d, checked in by krzywon, 10 years ago
I have completed the removal of all SANS references. I will build, run, and run all unit tests before pushing.
Property mode set to `100644`
File size: 92.6 KB

Line
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 sas.dataloader.loader import Loader
24	from sas.guiframe.dataFitting import Data2D
25	from sas.guiframe.dataFitting import Data1D
26	from sas.guiframe.dataFitting import check_data_validity
27	from sas.guiframe.events import NewPlotEvent
28	from sas.guiframe.events import StatusEvent
29	from sas.guiframe.events import EVT_SLICER_PANEL
30	from sas.guiframe.events import EVT_SLICER_PARS_UPDATE
31	from sas.guiframe.gui_style import GUIFRAME_ID
32	from sas.guiframe.plugin_base import PluginBase
33	from sas.guiframe.data_processor import BatchCell
34	from sas.fit.Fitting import Fit
35	from sas.perspectives.fitting.console import ConsoleUpdate
36	from sas.perspectives.fitting.fitproblem import FitProblemDictionary
37	from sas.perspectives.fitting.fitpanel import FitPanel
38	from sas.perspectives.fitting.resultpanel import ResultPanel, PlotResultEvent
39
40	from sas.perspectives.fitting.fit_thread import FitThread
41	from sas.perspectives.fitting.pagestate import Reader
42	from sas.perspectives.fitting.fitpage import Chi2UpdateEvent
43	from sas.perspectives.calculator.model_editor import TextDialog
44	from sas.perspectives.calculator.model_editor import EditorWindow
45	from sas.guiframe.gui_manager import MDIFrame
46
47	# TODO: remove globals from interface to bumps options!
48	# Default bumps to use the levenberg-marquardt optimizer
49	import bumps.fitters
50	bumps.fitters.FIT_DEFAULT = 'lm'
51
52	MAX_NBR_DATA = 4
53	SAS_F_TOL = 5e-05
54
55	(PageInfoEvent, EVT_PAGE_INFO) = wx.lib.newevent.NewEvent()
56
57
58	if sys.platform == "win32":
59	ON_MAC = False
60	else:
61	ON_MAC = True
62
63
64
65	class Plugin(PluginBase):
66	"""
67	Fitting plugin is used to perform fit
68	"""
69	def __init__(self, standalone=False):
70	PluginBase.__init__(self, name="Fitting", standalone=standalone)
71
72	#list of panel to send to guiframe
73	self.mypanels = []
74	# reference to the current running thread
75	self.calc_2D = None
76	self.calc_1D = None
77
78	self.color_dict = {}
79
80	self.fit_thread_list = {}
81	self.residuals = None
82	self.weight = None
83	self.fit_panel = None
84	self.plot_panel = None
85	# Start with a good default
86	self.elapsed = 0.022
87	self.fit_panel = None
88	#Flag to let the plug-in know that it is running stand alone
89	self.standalone = True
90	## dictionary of page closed and id
91	self.closed_page_dict = {}
92	## Fit engine
93	self._fit_engine = 'bumps'
94	self._gui_engine = None
95	## Relative error desired in the sum of squares (float); scipy only
96	self.ftol = SAS_F_TOL
97	self.batch_reset_flag = True
98	#List of selected data
99	self.selected_data_list = []
100	## list of slicer panel created to display slicer parameters and results
101	self.slicer_panels = []
102	# model 2D view
103	self.model2D_id = None
104	#keep reference of the simultaneous fit page
105	self.sim_page = None
106	self.sim_menu = None
107	self.batch_page = None
108	self.batch_menu = None
109	self.index_model = 0
110	self.test_model_color = None
111	#Create a reader for fit page's state
112	self.state_reader = None
113	self._extensions = '.fitv'
114	self.scipy_id = wx.NewId()
115	self.park_id = wx.NewId()
116	self.bumps_id = wx.NewId()
117	self.menu1 = None
118	self.new_model_frame = None
119
120	self.temp_state = []
121	self.state_index = 0
122	self.sfile_ext = None
123	# take care of saving data, model and page associated with each other
124	self.page_finder = {}
125	# Log startup
126	logging.info("Fitting plug-in started")
127	self.batch_capable = self.get_batch_capable()
128
129	def get_batch_capable(self):
130	"""
131	Check if the plugin has a batch capability
132	"""
133	return True
134
135	def create_fit_problem(self, page_id):
136	"""
137	Given an ID create a fitproblem container
138	"""
139	self.page_finder[page_id] = FitProblemDictionary()
140
141	def delete_fit_problem(self, page_id):
142	"""
143	Given an ID create a fitproblem container
144	"""
145	if page_id in self.page_finder.iterkeys():
146	del self.page_finder[page_id]
147
148	def add_color(self, color, id):
149	"""
150	adds a color as a key with a plot id as its value to a dictionary
151	"""
152	self.color_dict[id] = color
153
154	def on_batch_selection(self, flag):
155	"""
156	switch the the notebook of batch mode or not
157	"""
158	self.batch_on = flag
159	if self.fit_panel is not None:
160	self.fit_panel.batch_on = self.batch_on
161
162	def populate_menu(self, owner):
163	"""
164	Create a menu for the Fitting plug-in
165
166	:param id: id to create a menu
167	:param owner: owner of menu
168
169	:return: list of information to populate the main menu
170
171	"""
172	#Menu for fitting
173	self.menu1 = wx.Menu()
174	id1 = wx.NewId()
175	simul_help = "Add new fit panel"
176	self.menu1.Append(id1, '&New Fit Page', simul_help)
177	wx.EVT_MENU(owner, id1, self.on_add_new_page)
178	self.menu1.AppendSeparator()
179	self.id_simfit = wx.NewId()
180	simul_help = "Constrained or Simultaneous Fit"
181	self.menu1.Append(self.id_simfit, '&Constrained or Simultaneous Fit', simul_help)
182	wx.EVT_MENU(owner, self.id_simfit, self.on_add_sim_page)
183	self.sim_menu = self.menu1.FindItemById(self.id_simfit)
184	self.sim_menu.Enable(False)
185	#combined Batch
186	self.id_batchfit = wx.NewId()
187	batch_help = "Combined Batch"
188	self.menu1.Append(self.id_batchfit, '&Combine Batch Fit', batch_help)
189	wx.EVT_MENU(owner, self.id_batchfit, self.on_add_sim_page)
190	self.batch_menu = self.menu1.FindItemById(self.id_batchfit)
191	self.batch_menu.Enable(False)
192	self.menu1.AppendSeparator()
193	#Set park engine
194	scipy_help = "Scipy Engine: Perform Simple fit. More in Help window...."
195	self.menu1.AppendCheckItem(self.scipy_id, "Simple FitEngine [LeastSq]",
196	scipy_help)
197	wx.EVT_MENU(owner, self.scipy_id, self._onset_engine_scipy)
198
199	park_help = "Park Engine: Perform Complex fit. More in Help window...."
200	self.menu1.AppendCheckItem(self.park_id, "Complex FitEngine [ParkMC]",
201	park_help)
202	wx.EVT_MENU(owner, self.park_id, self._onset_engine_park)
203
204	bumps_help = "Bumps: fitting and uncertainty analysis. More in Help window...."
205	self.menu1.AppendCheckItem(self.bumps_id, "Bumps fit",
206	bumps_help)
207	wx.EVT_MENU(owner, self.bumps_id, self._onset_engine_bumps)
208
209	self.menu1.FindItemById(self.scipy_id).Check(self._fit_engine=="scipy")
210	self.menu1.FindItemById(self.park_id).Check(self._fit_engine=="park")
211	self.menu1.FindItemById(self.bumps_id).Check(self._fit_engine=="bumps")
212	self.menu1.AppendSeparator()
213	self.id_tol = wx.NewId()
214	ftol_help = "Change the current FTolerance (=%s) " % str(self.ftol)
215	ftol_help += "of Simple FitEngine..."
216	self.menu1.Append(self.id_tol, "Change FTolerance",
217	ftol_help)
218	wx.EVT_MENU(owner, self.id_tol, self.show_ftol_dialog)
219
220	self.id_bumps_options = wx.NewId()
221	bopts_help = "Bumps fitting options"
222	self.menu1.Append(self.id_bumps_options, 'Bumps &Options', bopts_help)
223	wx.EVT_MENU(owner, self.id_bumps_options, self.on_bumps_options)
224	self.bumps_options_menu = self.menu1.FindItemById(self.id_bumps_options)
225	self.bumps_options_menu.Enable(True)
226
227	self.id_result_panel = wx.NewId()
228	self.menu1.Append(self.id_result_panel, "Fit Results", "Show fit results panel")
229	wx.EVT_MENU(owner, self.id_result_panel, lambda ev: self.result_frame.Show())
230	self.menu1.AppendSeparator()
231
232	self.id_reset_flag = wx.NewId()
233	resetf_help = "BatchFit: If checked, the initial param values will be "
234	resetf_help += "propagated from the previous results. "
235	resetf_help += "Otherwise, the same initial param values will be used "
236	resetf_help += "for all fittings."
237	self.menu1.AppendCheckItem(self.id_reset_flag,
238	"Chain Fitting [BatchFit Only]",
239	resetf_help)
240	wx.EVT_MENU(owner, self.id_reset_flag, self.on_reset_batch_flag)
241	chain_menu = self.menu1.FindItemById(self.id_reset_flag)
242	chain_menu.Check(not self.batch_reset_flag)
243	chain_menu.Enable(self.batch_on)
244
245	self.menu1.AppendSeparator()
246	self.edit_model_menu = wx.Menu()
247	# Find and put files name in menu
248	try:
249	self.set_edit_menu(owner=owner)
250	except:
251	raise
252
253	self.id_edit = wx.NewId()
254	editmodel_help = "Edit customized model sample file"
255	self.menu1.AppendMenu(self.id_edit, "Edit Custom Model",
256	self.edit_model_menu, editmodel_help)
257	#create menubar items
258	return [(self.menu1, self.sub_menu)]
259
260	def edit_custom_model(self, event):
261	"""
262	Get the python editor panel
263	"""
264	id = event.GetId()
265	label = self.edit_menu.GetLabel(id)
266	from sas.perspectives.calculator.pyconsole import PyConsole
267	filename = os.path.join(models.find_plugins_dir(), label)
268	frame = PyConsole(parent=self.parent, manager=self,
269	panel=self.fit_panel,
270	title='Advanced Custom Model Editor',
271	filename=filename)
272	self.put_icon(frame)
273	frame.Show(True)
274
275	def delete_custom_model(self, event):
276	"""
277	Delete custom model file
278	"""
279	id = event.GetId()
280	label = self.delete_menu.GetLabel(id)
281	toks = os.path.splitext(label)
282	path = os.path.join(models.find_plugins_dir(), toks[0])
283	try:
284	for ext in ['.py', '.pyc']:
285	p_path = path + ext
286	os.remove(p_path)
287	self.update_custom_combo()
288	if os.path.isfile(p_path):
289	msg = "Sorry! Could not be able to delete the default "
290	msg += "custom model... \n"
291	msg += "Please manually remove the files (.py, .pyc) "
292	msg += "in the 'plugin_models' folder \n"
293	msg += "inside of the SasView application, "
294	msg += "and try it again."
295	wx.MessageBox(msg, 'Info')
296	#wx.PostEvent(self.parent, StatusEvent(status=msg, type='stop',
297	# info='warning'))
298	else:
299	self.delete_menu.Delete(id)
300	for item in self.edit_menu.GetMenuItems():
301	if item.GetLabel() == label:
302	self.edit_menu.DeleteItem(item)
303	msg = "The custom model, %s, has been deleted."% label
304	wx.PostEvent(self.parent, StatusEvent(status=msg,
305	type='stop', info='info'))
306	break
307	except:
308	msg ='Delete Error: \nCould not delete the file; Check if in use.'
309	wx.MessageBox(msg, 'Error')
310
311	def make_sum_model(self, event):
312	"""
313	Edit summodel template and make one
314	"""
315	id = event.GetId()
316	model_manager = models.ModelManager()
317	model_list = model_manager.get_model_name_list()
318	plug_dir = models.find_plugins_dir()
319	textdial = TextDialog(None, self, -1, 'Easy Sum/Multi(p1, p2) Editor',
320	model_list, plug_dir)
321	self.put_icon(textdial)
322	textdial.ShowModal()
323	textdial.Destroy()
324
325	def make_new_model(self, event):
326	"""
327	Make new model
328	"""
329	if self.new_model_frame != None:
330	self.new_model_frame.Show(False)
331	self.new_model_frame.Show(True)
332	else:
333	id = event.GetId()
334	dir_path = models.find_plugins_dir()
335	title = "New Custom Model Function"
336	self.new_model_frame = EditorWindow(parent=self, base=self,
337	path=dir_path, title=title)
338	self.put_icon(self.new_model_frame)
339	self.new_model_frame.Show(True)
340
341	def update_custom_combo(self):
342	"""
343	Update custom model list in the fitpage combo box
344	"""
345	custom_model = 'Customized Models'
346	try:
347	# Update edit menus
348	self.set_edit_menu_helper(self.parent, self.edit_custom_model)
349	self.set_edit_menu_helper(self.parent, self.delete_custom_model)
350	temp = self.fit_panel.reset_pmodel_list()
351	if temp:
352	# Set the new custom model list for all fit pages
353	for uid, page in self.fit_panel.opened_pages.iteritems():
354	if hasattr(page, "formfactorbox"):
355	page.model_list_box = temp
356	current_val = page.formfactorbox.GetLabel()
357	#if page.plugin_rbutton.GetValue():
358	mod_cat = page.categorybox.GetStringSelection()
359	if mod_cat == custom_model:
360	#pos = page.formfactorbox.GetSelection()
361	page._show_combox_helper()
362	new_val = page.formfactorbox.GetLabel()
363	if current_val != new_val and new_val != '':
364	page.formfactorbox.SetLabel(new_val)
365	else:
366	page.formfactorbox.SetLabel(current_val)
367	except:
368	pass
369
370
371	def set_edit_menu(self, owner):
372	"""
373	Set list of the edit model menu labels
374	"""
375	id = wx.NewId()
376	#new_model_menu = wx.Menu()
377	self.edit_model_menu.Append(id, 'New',
378	'Add a new model function')
379	wx.EVT_MENU(owner, id, self.make_new_model)
380	id = wx.NewId()
381	self.edit_model_menu.Append(id, 'Sum\|Multi(p1, p2)',
382	'Sum of two model functions')
383	wx.EVT_MENU(owner, id, self.make_sum_model)
384	e_id = wx.NewId()
385	self.edit_menu = wx.Menu()
386	self.edit_model_menu.AppendMenu(e_id,
387	'Advanced', self.edit_menu)
388	self.set_edit_menu_helper(owner, self.edit_custom_model)
389
390	d_id = wx.NewId()
391	self.delete_menu = wx.Menu()
392	self.edit_model_menu.AppendMenu(d_id,
393	'Delete', self.delete_menu)
394	self.set_edit_menu_helper(owner, self.delete_custom_model)
395
396	def set_edit_menu_helper(self, owner=None, menu=None):
397	"""
398	help for setting list of the edit model menu labels
399	"""
400	if menu == None:
401	menu = self.edit_custom_model
402	list_fnames = os.listdir(models.find_plugins_dir())
403	list_fnames.sort()
404	for f_item in list_fnames:
405	name = os.path.basename(f_item)
406	toks = os.path.splitext(name)
407	if toks[-1] == '.py' and not toks[0] == '__init__':
408	if menu == self.edit_custom_model:
409	if toks[0] == 'easy_sum_of_p1_p2':
410	continue
411	submenu = self.edit_menu
412	else:
413	submenu = self.delete_menu
414	has_file = False
415	for item in submenu.GetMenuItems():
416	if name == submenu.GetLabel(item.GetId()):
417	has_file = True
418	if not has_file:
419	id = wx.NewId()
420	submenu.Append(id, name)
421	wx.EVT_MENU(owner, id, menu)
422	has_file = False
423
424	def put_icon(self, frame):
425	"""
426	Put icon in the frame title bar
427	"""
428	if hasattr(frame, "IsIconized"):
429	if not frame.IsIconized():
430	try:
431	icon = self.parent.GetIcon()
432	frame.SetIcon(icon)
433	except:
434	pass
435
436	def on_add_sim_page(self, event):
437	"""
438	Create a page to access simultaneous fit option
439	"""
440	id = event.GetId()
441	caption = "Const & Simul Fit"
442	page = self.sim_page
443	if id == self.id_batchfit:
444	caption = "Combined Batch"
445	page = self.batch_page
446
447	def set_focus_page(page):
448	page.Show(True)
449	page.Refresh()
450	page.SetFocus()
451	#self.parent._mgr.Update()
452	msg = "%s already opened\n" % str(page.window_caption)
453	wx.PostEvent(self.parent, StatusEvent(status=msg))
454
455	if page != None:
456	return set_focus_page(page)
457	if caption == "Const & Simul Fit":
458	self.sim_page = self.fit_panel.add_sim_page(caption=caption)
459	else:
460	self.batch_page = self.fit_panel.add_sim_page(caption=caption)
461
462	def help(self, evt):
463	"""
464	Show a general help dialog.
465	"""
466	from help_panel import HelpWindow
467	frame = HelpWindow(None, -1, 'HelpWindow')
468	if hasattr(frame, "IsIconized"):
469	if not frame.IsIconized():
470	try:
471	icon = self.parent.GetIcon()
472	frame.SetIcon(icon)
473	except:
474	pass
475	frame.Show(True)
476
477	def get_context_menu(self, plotpanel=None):
478	"""
479	Get the context menu items available for P(r).them allow fitting option
480	for Data2D and Data1D only.
481
482	:param graph: the Graph object to which we attach the context menu
483
484	:return: a list of menu items with call-back function
485
486	:note: if Data1D was generated from Theory1D
487	the fitting option is not allowed
488
489	"""
490	self.plot_panel = plotpanel
491	graph = plotpanel.graph
492	fit_option = "Select data for fitting"
493	fit_hint = "Dialog with fitting parameters "
494
495	if graph.selected_plottable not in plotpanel.plots:
496	return []
497	item = plotpanel.plots[graph.selected_plottable]
498	if item.__class__.__name__ is "Data2D":
499	if hasattr(item, "is_data"):
500	if item.is_data:
501	return [[fit_option, fit_hint, self._onSelect]]
502	else:
503	return []
504	return [[fit_option, fit_hint, self._onSelect]]
505	else:
506
507	# if is_data is true , this in an actual data loaded
508	#else it is a data created from a theory model
509	if hasattr(item, "is_data"):
510	if item.is_data:
511	return [[fit_option, fit_hint, self._onSelect]]
512	else:
513	return []
514	return [[fit_option, fit_hint, self._onSelect]]
515	return []
516
517	def get_panels(self, parent):
518	"""
519	Create and return a list of panel objects
520	"""
521	self.parent = parent
522	#self.parent.Bind(EVT_FITSTATE_UPDATE, self.on_set_state_helper)
523	# Creation of the fit panel
524	self.frame = MDIFrame(self.parent, None, 'None', (100, 200))
525	self.fit_panel = FitPanel(parent=self.frame, manager=self)
526	self.frame.set_panel(self.fit_panel)
527	self._frame_set_helper()
528	self.on_add_new_page(event=None)
529	#Set the manager for the main panel
530	self.fit_panel.set_manager(self)
531	# List of windows used for the perspective
532	self.perspective = []
533	self.perspective.append(self.fit_panel.window_name)
534
535	self.result_frame = MDIFrame(self.parent, None, ResultPanel.window_caption, (220, 200))
536	self.result_panel = ResultPanel(parent=self.result_frame, manager=self)
537	self.perspective.append(self.result_panel.window_name)
538
539	#index number to create random model name
540	self.index_model = 0
541	self.index_theory = 0
542	self.parent.Bind(EVT_SLICER_PANEL, self._on_slicer_event)
543	self.parent.Bind(EVT_SLICER_PARS_UPDATE, self._onEVT_SLICER_PANEL)
544	#self.parent._mgr.Bind(wx.aui.EVT_AUI_PANE_CLOSE,self._onclearslicer)
545	#Create reader when fitting panel are created
546	self.state_reader = Reader(self.set_state)
547	#append that reader to list of available reader
548	loader = Loader()
549	loader.associate_file_reader(".fitv", self.state_reader)
550	#Send the fitting panel to guiframe
551	self.mypanels.append(self.fit_panel)
552	self.mypanels.append(self.result_panel)
553	return self.mypanels
554
555	def clear_panel(self):
556	"""
557	"""
558	self.fit_panel.clear_panel()
559
560	def set_default_perspective(self):
561	"""
562	Call back method that True to notify the parent that the current plug-in
563	can be set as default perspective.
564	when returning False, the plug-in is not candidate for an automatic
565	default perspective setting
566	"""
567	return True
568
569	def delete_data(self, data):
570	"""
571	delete the given data from panel
572	"""
573	self.fit_panel.delete_data(data)
574
575	def set_data(self, data_list=None):
576	"""
577	receive a list of data to fit
578	"""
579	if data_list is None:
580	data_list = []
581	selected_data_list = []
582	if self.batch_on:
583	page = self.add_fit_page(data=data_list)
584	else:
585	if len(data_list) > MAX_NBR_DATA:
586	from fitting_widgets import DataDialog
587	dlg = DataDialog(data_list=data_list, nb_data=MAX_NBR_DATA)
588	if dlg.ShowModal() == wx.ID_OK:
589	selected_data_list = dlg.get_data()
590	dlg.Destroy()
591
592	else:
593	selected_data_list = data_list
594	try:
595	group_id = wx.NewId()
596	for data in selected_data_list:
597	if data is not None:
598	# 2D has no same group_id
599	if data.__class__.__name__ == 'Data2D':
600	group_id = wx.NewId()
601	data.group_id = group_id
602	if group_id not in data.list_group_id:
603	data.list_group_id.append(group_id)
604	page = self.add_fit_page(data=[data])
605	except:
606	msg = "Fitting Set_data: " + str(sys.exc_value)
607	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
608
609	def set_theory(self, theory_list=None):
610	"""
611	"""
612	#set the model state for a given theory_state:
613	for item in theory_list:
614	try:
615	_, theory_state = item
616	self.fit_panel.set_model_state(theory_state)
617	except:
618	msg = "Fitting: cannot deal with the theory received"
619	logging.error("set_theory " + msg + "\n" + str(sys.exc_value))
620	wx.PostEvent(self.parent,
621	StatusEvent(status=msg, info="error"))
622
623	def set_state(self, state=None, datainfo=None, format=None):
624	"""
625	Call-back method for the fit page state reader.
626	This method is called when a .fitv/.svs file is loaded.
627
628	: param state: PageState object
629	: param datainfo: data
630	"""
631	#state = self.state_reader.get_state()
632	if state != None:
633	state = state.clone()
634	# store fitting state in temp_state
635	self.temp_state.append(state)
636	else:
637	self.temp_state = []
638	# index to start with for a new set_state
639	self.state_index = 0
640	# state file format
641	self.sfile_ext = format
642
643	self.on_set_state_helper(event=None)
644
645	def on_set_state_helper(self, event=None):
646	"""
647	Set_state_helper. This actually sets state
648	after plotting data from state file.
649
650	: event: FitStateUpdateEvent called
651	by dataloader.plot_data from guiframe
652	"""
653	if len(self.temp_state) == 0:
654	if self.state_index == 0 and len(self.mypanels) <= 0 \
655	and self.sfile_ext == '.svs':
656	self.temp_state = []
657	self.state_index = 0
658	return
659
660	try:
661	# Load fitting state
662	state = self.temp_state[self.state_index]
663	#panel state should have model selection to set_state
664	if state.formfactorcombobox != None:
665	#set state
666	data = self.parent.create_gui_data(state.data)
667	data.group_id = state.data.group_id
668	self.parent.add_data(data_list={data.id: data})
669	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
670	title=data.title))
671	#need to be fix later make sure we are sendind guiframe.data
672	#to panel
673	state.data = data
674	page = self.fit_panel.set_state(state)
675	else:
676	#just set data because set_state won't work
677	data = self.parent.create_gui_data(state.data)
678	data.group_id = state.data.group_id
679	self.parent.add_data(data_list={data.id: data})
680	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
681	title=data.title))
682	page = self.add_fit_page([data])
683	caption = page.window_caption
684	self.store_data(uid=page.uid, data_list=page.get_data_list(),
685	caption=caption)
686	self.mypanels.append(page)
687
688	# get ready for the next set_state
689	self.state_index += 1
690
691	#reset state variables to default when all set_state is finished.
692	if len(self.temp_state) == self.state_index:
693
694	self.temp_state = []
695	#self.state_index = 0
696	# Make sure the user sees the fitting panel after loading
697	#self.parent.set_perspective(self.perspective)
698	self.on_perspective(event=None)
699	except:
700	self.state_index = 0
701	self.temp_state = []
702	raise
703
704	def set_param2fit(self, uid, param2fit):
705	"""
706	Set the list of param names to fit for fitprobelm
707	"""
708	self.page_finder[uid].set_param2fit(param2fit)
709
710	def set_graph_id(self, uid, graph_id):
711	"""
712	Set graph_id for fitprobelm
713	"""
714	self.page_finder[uid].set_graph_id(graph_id)
715
716	def get_graph_id(self, uid):
717	"""
718	Set graph_id for fitprobelm
719	"""
720	return self.page_finder[uid].get_graph_id()
721
722	def save_fit_state(self, filepath, fitstate):
723	"""
724	save fit page state into file
725	"""
726	self.state_reader.write(filename=filepath, fitstate=fitstate)
727
728	def set_fit_weight(self, uid, flag, is2d=False, fid=None):
729	"""
730	Set the fit weights of a given page for all
731	its data by default. If fid is provide then set the range
732	only for the data with fid as id
733	:param uid: id corresponding to a fit page
734	:param fid: id corresponding to a fit problem (data, model)
735	:param weight: current dy data
736	"""
737	if uid in self.page_finder.keys():
738	self.page_finder[uid].set_weight(flag=flag, is2d=is2d)
739
740	def set_fit_range(self, uid, qmin, qmax, fid=None):
741	"""
742	Set the fitting range of a given page for all
743	its data by default. If fid is provide then set the range
744	only for the data with fid as id
745	:param uid: id corresponding to a fit page
746	:param fid: id corresponding to a fit problem (data, model)
747	:param qmin: minimum value of the fit range
748	:param qmax: maximum value of the fit range
749	"""
750	if uid in self.page_finder.keys():
751	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax, fid=fid)
752
753	def schedule_for_fit(self, value=0, uid=None):
754	"""
755	Set the fit problem field to 0 or 1 to schedule that problem to fit.
756	Schedule the specified fitproblem or get the fit problem related to
757	the current page and set value.
758	:param value: integer 0 or 1
759	:param uid: the id related to a page contaning fitting information
760	"""
761	if uid in self.page_finder.keys():
762	self.page_finder[uid].schedule_tofit(value)
763
764	def get_page_finder(self):
765	"""
766	return self.page_finder used also by simfitpage.py
767	"""
768	return self.page_finder
769
770	def set_page_finder(self, modelname, names, values):
771	"""
772	Used by simfitpage.py to reset a parameter given the string constrainst.
773
774	:param modelname: the name ot the model for with the parameter
775	has to reset
776	:param value: can be a string in this case.
777	:param names: the paramter name
778
779	:note: expecting park used for fit.
780
781	"""
782	sim_page_id = self.sim_page.uid
783	for uid, value in self.page_finder.iteritems():
784	if uid != sim_page_id and uid != self.batch_page.uid:
785	list = value.get_model()
786	model = list[0]
787	if model.name == modelname:
788	value.set_model_param(names, values)
789	break
790
791	def split_string(self, item):
792	"""
793	receive a word containing dot and split it. used to split parameterset
794	name into model name and parameter name example: ::
795
796	paramaterset (item) = M1.A
797	Will return model_name = M1 , parameter name = A
798
799	"""
800	if item.find(".") >= 0:
801	param_names = re.split("\.", item)
802	model_name = param_names[0]
803	##Assume max len is 3; eg., M0.radius.width
804	if len(param_names) == 3:
805	param_name = param_names[1] + "." + param_names[2]
806	else:
807	param_name = param_names[1]
808	return model_name, param_name
809
810	def set_ftol(self, ftol=None):
811	"""
812	Set ftol: Relative error desired in the sum of chi squares.
813	"""
814	# check if it is flaot
815	try:
816	f_tol = float(ftol)
817	except:
818	# default
819	f_tol = SAS_F_TOL
820
821	self.ftol = f_tol
822	# update ftol menu help strings
823	ftol_help = "Change the current FTolerance (=%s) " % str(self.ftol)
824	ftol_help += "of Simple FitEngine..."
825	if self.menu1 != None:
826	self.menu1.SetHelpString(self.id_tol, ftol_help)
827
828	def show_ftol_dialog(self, event=None):
829	"""
830	Dialog to select ftol for Scipy
831	"""
832	from ftol_dialog import ChangeFtol
833	dialog = ChangeFtol(self.parent, self)
834	result = dialog.ShowModal()
835	if result == wx.ID_OK:
836	value = dialog.get_ftol()
837	if value is not None:
838	self.set_ftol(value)
839	msg = "The ftol (LeastSq) is set to %s." % value
840	else:
841	msg = "Error in the selection... No change in ftol."
842	# post event for info
843	wx.PostEvent(self.parent,
844	StatusEvent(status=msg, info='warning'))
845	dialog.Destroy()
846
847	def on_bumps_options(self, event=None):
848	from bumps.gui.fit_dialog import OpenFitOptions
849	OpenFitOptions()
850
851	def stop_fit(self, uid):
852	"""
853	Stop the fit engine
854	"""
855	if uid in self.fit_thread_list.keys():
856	calc_fit = self.fit_thread_list[uid]
857	if calc_fit is not None and calc_fit.isrunning():
858	calc_fit.stop()
859	msg = "Fit stop!"
860	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
861	del self.fit_thread_list[uid]
862	#set the fit button label of page when fit stop is trigger from
863	#simultaneous fit pane
864	sim_flag = self.sim_page is not None and uid == self.sim_page.uid
865	batch_flag = self.batch_page is not None and uid == self.batch_page.uid
866	if sim_flag or batch_flag:
867	for uid, value in self.page_finder.iteritems():
868	if value.get_scheduled() == 1:
869	if uid in self.fit_panel.opened_pages.keys():
870	panel = self.fit_panel.opened_pages[uid]
871	panel._on_fit_complete()
872
873	def set_smearer(self, uid, smearer, fid, qmin=None, qmax=None, draw=True,
874	enable_smearer=False):
875	"""
876	Get a smear object and store it to a fit problem of fid as id. If proper
877	flag is enable , will plot the theory with smearing information.
878
879	:param smearer: smear object to allow smearing data of id fid
880	:param enable_smearer: Define whether or not all (data, model) contained
881	in the structure of id uid will be smeared before fitting.
882	:param qmin: the maximum value of the theory plotting range
883	:param qmax: the maximum value of the theory plotting range
884	:param draw: Determine if the theory needs to be plot
885	"""
886	if uid not in self.page_finder.keys():
887	return
888	self.page_finder[uid].enable_smearing(flag=enable_smearer)
889	self.page_finder[uid].set_smearer(smearer, fid=fid)
890	if draw:
891	## draw model 1D with smeared data
892	data = self.page_finder[uid].get_fit_data(fid=fid)
893	if data is None:
894	msg = "set_mearer requires at least data.\n"
895	msg += "Got data = %s .\n" % str(data)
896	return
897	#raise ValueError, msg
898	model = self.page_finder[uid].get_model(fid=fid)
899	if model is None:
900	return
901	enable1D = issubclass(data.__class__, Data1D)
902	enable2D = issubclass(data.__class__, Data2D)
903	## if user has already selected a model to plot
904	## redraw the model with data smeared
905	smear = self.page_finder[uid].get_smearer(fid=fid)
906
907	# compute weight for the current data
908	weight = self.page_finder[uid].get_weight(fid=fid)
909
910	self.draw_model(model=model, data=data, page_id=uid, smearer=smear,
911	enable1D=enable1D, enable2D=enable2D,
912	qmin=qmin, qmax=qmax, weight=weight)
913	self._mac_sleep(0.2)
914
915	def _mac_sleep(self, sec=0.2):
916	"""
917	Give sleep to MAC
918	"""
919	if ON_MAC:
920	time.sleep(sec)
921
922	def draw_model(self, model, page_id, data=None, smearer=None,
923	enable1D=True, enable2D=False,
924	state=None,
925	fid=None,
926	toggle_mode_on=False,
927	qmin=None, qmax=None,
928	update_chisqr=True, weight=None, source='model'):
929	"""
930	Draw model.
931
932	:param model: the model to draw
933	:param name: the name of the model to draw
934	:param data: the data on which the model is based to be drawn
935	:param description: model's description
936	:param enable1D: if true enable drawing model 1D
937	:param enable2D: if true enable drawing model 2D
938	:param qmin: Range's minimum value to draw model
939	:param qmax: Range's maximum value to draw model
940	:param qstep: number of step to divide the x and y-axis
941	:param update_chisqr: update chisqr [bool]
942
943	"""
944	#self.weight = weight
945	if issubclass(data.__class__, Data1D) or not enable2D:
946	## draw model 1D with no loaded data
947	self._draw_model1D(model=model,
948	data=data,
949	page_id=page_id,
950	enable1D=enable1D,
951	smearer=smearer,
952	qmin=qmin,
953	qmax=qmax,
954	fid=fid,
955	weight=weight,
956	toggle_mode_on=toggle_mode_on,
957	state=state,
958	update_chisqr=update_chisqr,
959	source=source)
960	else:
961	## draw model 2D with no initial data
962	self._draw_model2D(model=model,
963	page_id=page_id,
964	data=data,
965	enable2D=enable2D,
966	smearer=smearer,
967	qmin=qmin,
968	qmax=qmax,
969	fid=fid,
970	weight=weight,
971	state=state,
972	toggle_mode_on=toggle_mode_on,
973	update_chisqr=update_chisqr,
974	source=source)
975
976	def onFit(self, uid):
977	"""
978	Get series of data, model, associates parameters and range and send then
979	to series of fit engines. Fit data and model, display result to
980	corresponding panels.
981	:param uid: id related to the panel currently calling this fit function.
982	"""
983	if uid is None: raise RuntimeError("no page to fit") # Should never happen
984
985	# Remember the user selected fit engine before the fit. Simultaneous
986	# fitting may change the selected engine, so it needs to be restored
987	# when the fit is complete.
988	self._gui_engine = self._fit_engine
989
990	sim_page_uid = getattr(self.sim_page, 'uid', None)
991	batch_page_uid = getattr(self.batch_page, 'uid', None)
992
993	if uid == sim_page_uid:
994	fit_type = 'simultaneous'
995	elif uid == batch_page_uid:
996	fit_type = 'combined_batch'
997	else:
998	fit_type = 'single'
999
1000	# if constrained fit, don't use scipy leastsq directly
1001	if fit_type == 'simultaneous':
1002	if self._fit_engine not in ("park","bumps"):
1003	self._on_change_engine(engine='bumps')
1004
1005
1006	fitter_list = []
1007	sim_fitter = None
1008	if fit_type == 'simultaneous':
1009	#simulatanous fit only one engine need to be created
1010	sim_fitter = Fit(self._fit_engine)
1011	sim_fitter.fitter_id = self.sim_page.uid
1012	fitter_list.append(sim_fitter)
1013
1014	self.current_pg = None
1015	list_page_id = []
1016	fit_id = 0
1017	for page_id, page_info in self.page_finder.iteritems():
1018	# For simulfit (uid give with None), do for-loop
1019	# if uid is specified (singlefit), do it only on the page.
1020	if page_id in (sim_page_uid, batch_page_uid): continue
1021	if fit_type == "single" and page_id != uid: continue
1022
1023	try:
1024	if page_info.get_scheduled() == 1:
1025	page_info.nbr_residuals_computed = 0
1026	page = self.fit_panel.get_page_by_id(page_id)
1027	self.set_fit_weight(uid=page.uid,
1028	flag=page.get_weight_flag(),
1029	is2d=page._is_2D())
1030	if not page.param_toFit:
1031	msg = "No fitting parameters for %s"%page.window_caption
1032	wx.PostEvent(page.parent.parent,
1033	StatusEvent(status=msg, info="error",
1034	type="stop"))
1035	return False
1036	if not page._update_paramv_on_fit():
1037	msg = "Fitting range or parameter values are"
1038	msg += " invalid in %s" % \
1039	page.window_caption
1040	wx.PostEvent(page.parent.parent,
1041	StatusEvent(status=msg, info="error",
1042	type="stop"))
1043	return False
1044
1045	pars = [str(element[1]) for element in page.param_toFit]
1046	fitproblem_list = page_info.values()
1047	for fitproblem in fitproblem_list:
1048	if sim_fitter is None:
1049	fitter = Fit(self._fit_engine)
1050	fitter.fitter_id = page_id
1051	fitter_list.append(fitter)
1052	else:
1053	fitter = sim_fitter
1054	self._add_problem_to_fit(fitproblem=fitproblem,
1055	pars=pars,
1056	fitter=fitter,
1057	fit_id=fit_id)
1058	fit_id += 1
1059	list_page_id.append(page_id)
1060	page_info.clear_model_param()
1061	except KeyboardInterrupt:
1062	msg = "Fitting terminated"
1063	wx.PostEvent(self.parent, StatusEvent(status=msg, info="info",
1064	type="stop"))
1065	return True
1066	except:
1067	msg = "Fitting error: %s" % str(sys.exc_value)
1068	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error",
1069	type="stop"))
1070	return False
1071	## If a thread is already started, stop it
1072	#if self.calc_fit!= None and self.calc_fit.isrunning():
1073	# self.calc_fit.stop()
1074	msg = "Fitting is in progress..."
1075	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1076
1077	#Handler used for park engine displayed message
1078	handler = ConsoleUpdate(parent=self.parent,
1079	manager=self,
1080	improvement_delta=0.1)
1081	self._mac_sleep(0.2)
1082
1083	# batch fit
1084	batch_inputs = {}
1085	batch_outputs = {}
1086	if fit_type == "simultaneous":
1087	page = self.sim_page
1088	elif fit_type == "combined_batch":
1089	page = self.batch_page
1090	else:
1091	page = self.fit_panel.get_page_by_id(uid)
1092	if page.batch_on:
1093	calc_fit = FitThread(handler=handler,
1094	fn=fitter_list,
1095	pars=pars,
1096	batch_inputs=batch_inputs,
1097	batch_outputs=batch_outputs,
1098	page_id=list_page_id,
1099	completefn=self._batch_fit_complete,
1100	ftol=self.ftol,
1101	reset_flag=self.batch_reset_flag)
1102	else:
1103	## Perform more than 1 fit at the time
1104	calc_fit = FitThread(handler=handler,
1105	fn=fitter_list,
1106	batch_inputs=batch_inputs,
1107	batch_outputs=batch_outputs,
1108	page_id=list_page_id,
1109	updatefn=handler.update_fit,
1110	completefn=self._fit_completed,
1111	ftol=self.ftol)
1112	#self.fit_thread_list[current_page_id] = calc_fit
1113	self.fit_thread_list[uid] = calc_fit
1114	calc_fit.queue()
1115	calc_fit.ready(2.5)
1116	msg = "Fitting is in progress..."
1117	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1118
1119	return True
1120
1121	def remove_plot(self, uid, fid=None, theory=False):
1122	"""
1123	remove model plot when a fit page is closed
1124	:param uid: the id related to the fitpage to close
1125	:param fid: the id of the fitproblem(data, model, range,etc)
1126	"""
1127	if uid not in self.page_finder.keys():
1128	return
1129	fitproblemList = self.page_finder[uid].get_fit_problem(fid)
1130	for fitproblem in fitproblemList:
1131	data = fitproblem.get_fit_data()
1132	model = fitproblem.get_model()
1133	plot_id = None
1134	if model is not None:
1135	plot_id = data.id + model.name
1136	if theory:
1137	plot_id = data.id + model.name
1138	group_id = data.group_id
1139	wx.PostEvent(self.parent, NewPlotEvent(id=plot_id,
1140	group_id=group_id,
1141	action='remove'))
1142
1143	def store_data(self, uid, data_list=None, caption=None):
1144	"""
1145	Recieve a list of data and store them ans well as a caption of
1146	the fit page where they come from.
1147	:param uid: if related to a fit page
1148	:param data_list: list of data to fit
1149	:param caption: caption of the window related to these data
1150	"""
1151	if data_list is None:
1152	data_list = []
1153
1154	self.page_finder[uid].set_fit_data(data=data_list)
1155	if caption is not None:
1156	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1157
1158	def on_add_new_page(self, event=None):
1159	"""
1160	ask fit panel to create a new empty page
1161	"""
1162	try:
1163	page = self.fit_panel.add_empty_page()
1164	# add data associated to the page created
1165	if page != None:
1166	wx.PostEvent(self.parent, StatusEvent(status="Page Created",
1167	info="info"))
1168	else:
1169	msg = "Page was already Created"
1170	wx.PostEvent(self.parent, StatusEvent(status=msg,
1171	info="warning"))
1172	except:
1173	msg = "Creating Fit page: %s"%sys.exc_value
1174	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1175
1176	def add_fit_page(self, data):
1177	"""
1178	given a data, ask to the fitting panel to create a new fitting page,
1179	get this page and store it into the page_finder of this plug-in
1180	:param data: is a list of data
1181	"""
1182	page = self.fit_panel.set_data(data)
1183	# page could be None when loading state files
1184	if page == None:
1185	return page
1186	#append Data1D to the panel containing its theory
1187	#if theory already plotted
1188	if page.uid in self.page_finder:
1189	data = page.get_data()
1190	theory_data = self.page_finder[page.uid].get_theory_data(data.id)
1191	if issubclass(data.__class__, Data2D):
1192	data.group_id = wx.NewId()
1193	if theory_data is not None:
1194	group_id = str(page.uid) + " Model1D"
1195	wx.PostEvent(self.parent,
1196	NewPlotEvent(group_id=group_id,
1197	action="delete"))
1198	self.parent.update_data(prev_data=theory_data,
1199	new_data=data)
1200	else:
1201	if theory_data is not None:
1202	group_id = str(page.uid) + " Model2D"
1203	data.group_id = theory_data.group_id
1204	wx.PostEvent(self.parent,
1205	NewPlotEvent(group_id=group_id,
1206	action="delete"))
1207	self.parent.update_data(prev_data=theory_data,
1208	new_data=data)
1209	self.store_data(uid=page.uid, data_list=page.get_data_list(),
1210	caption=page.window_caption)
1211	if self.sim_page is not None and not self.batch_on:
1212	self.sim_page.draw_page()
1213	if self.batch_page is not None and self.batch_on:
1214	self.batch_page.draw_page()
1215
1216	return page
1217
1218	def _onEVT_SLICER_PANEL(self, event):
1219	"""
1220	receive and event telling to update a panel with a name starting with
1221	event.panel_name. this method update slicer panel
1222	for a given interactor.
1223
1224	:param event: contains type of slicer , paramaters for updating
1225	the panel and panel_name to find the slicer 's panel concerned.
1226	"""
1227	event.panel_name
1228	for item in self.parent.panels:
1229	name = event.panel_name
1230	if self.parent.panels[item].window_caption.startswith(name):
1231	self.parent.panels[item].set_slicer(event.type, event.params)
1232
1233	#self.parent._mgr.Update()
1234
1235	def _closed_fitpage(self, event):
1236	"""
1237	request fitpanel to close a given page when its unique data is removed
1238	from the plot. close fitpage only when the a loaded data is removed
1239	"""
1240	if event is None or event.data is None:
1241	return
1242	if hasattr(event.data, "is_data"):
1243	if not event.data.is_data or \
1244	event.data.__class__.__name__ == "Data1D":
1245	self.fit_panel.close_page_with_data(event.data)
1246
1247	def _reset_schedule_problem(self, value=0, uid=None):
1248	"""
1249	unschedule or schedule all fitproblem to be fit
1250	"""
1251	# case that uid is not specified
1252	if uid == None:
1253	for page_id in self.page_finder.keys():
1254	self.page_finder[page_id].schedule_tofit(value)
1255	# when uid is given
1256	else:
1257	if uid in self.page_finder.keys():
1258	self.page_finder[uid].schedule_tofit(value)
1259
1260	def _add_problem_to_fit(self, fitproblem, pars, fitter, fit_id):
1261	"""
1262	Create and set fit engine with series of data and model
1263	:param pars: list of fittable parameters
1264	:param fitter_list: list of fit engine
1265	:param value: structure storing data mapped to their model, range etc.
1266	"""
1267	data = fitproblem.get_fit_data()
1268	model = fitproblem.get_model()
1269	smearer = fitproblem.get_smearer()
1270	qmin, qmax = fitproblem.get_range()
1271
1272	#Extra list of parameters and their constraints
1273	listOfConstraint = []
1274	param = fitproblem.get_model_param()
1275	if len(param) > 0:
1276	for item in param:
1277	## check if constraint
1278	if item[0] != None and item[1] != None:
1279	listOfConstraint.append((item[0], item[1]))
1280	new_model = model
1281	fitter.set_model(new_model, fit_id, pars, data=data,
1282	constraints=listOfConstraint)
1283	fitter.set_data(data=data, id=fit_id, smearer=smearer, qmin=qmin,
1284	qmax=qmax)
1285	fitter.select_problem_for_fit(id=fit_id, value=1)
1286
1287	def _onSelect(self, event):
1288	"""
1289	when Select data to fit a new page is created .Its reference is
1290	added to self.page_finder
1291	"""
1292	panel = self.plot_panel
1293	if panel == None:
1294	raise ValueError, "Fitting:_onSelect: NonType panel"
1295	Plugin.on_perspective(self, event=event)
1296	self.select_data(panel)
1297
1298	def select_data(self, panel):
1299	"""
1300	"""
1301	for plottable in panel.graph.plottables:
1302	if plottable.__class__.__name__ in ["Data1D", "Theory1D"]:
1303	data_id = panel.graph.selected_plottable
1304	if plottable == panel.plots[data_id]:
1305	data = plottable
1306	self.add_fit_page(data=[data])
1307	return
1308	else:
1309	data = plottable
1310	self.add_fit_page(data=[data])
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, "sas_data"):
1376	data = data.sas_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 sas.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	wx.PostEvent(self.result_panel, PlotResultEvent(result=result))
1570	# reset fit_engine if changed by simul_fit
1571	if self._fit_engine != self._gui_engine:
1572	self._on_change_engine(self._gui_engine)
1573	self._update_fit_button(page_id)
1574	result = result[0]
1575	self.fit_thread_list = {}
1576	if page_id is None:
1577	page_id = []
1578	## fit more than 1 model at the same time
1579	self._mac_sleep(0.2)
1580	try:
1581	index = 0
1582	for uid in page_id:
1583	res = result[index]
1584	if res.fitness is None or \
1585	not numpy.isfinite(res.fitness) or \
1586	numpy.any(res.pvec == None) or \
1587	not numpy.all(numpy.isfinite(res.pvec)):
1588	msg = "Fitting did not converge!!!"
1589	wx.PostEvent(self.parent,
1590	StatusEvent(status=msg,
1591	info="warning",
1592	type="stop"))
1593	self._update_fit_button(page_id)
1594	else:
1595	#set the panel when fit result are float not list
1596	if res.pvec.__class__ == numpy.float64:
1597	pvec = [res.pvec]
1598	else:
1599	pvec = res.pvec
1600	if res.stderr.__class__ == numpy.float64:
1601	stderr = [res.stderr]
1602	else:
1603	stderr = res.stderr
1604	cpage = self.fit_panel.get_page_by_id(uid)
1605	# Make sure we got all results
1606	#(CallAfter is important to MAC)
1607	try:
1608	#if res != None:
1609	wx.CallAfter(cpage.onsetValues, res.fitness,
1610	res.param_list,
1611	pvec, stderr)
1612	index += 1
1613	wx.CallAfter(cpage._on_fit_complete)
1614	except KeyboardInterrupt:
1615	msg = "Singular point: Fitting Stoped."
1616	wx.PostEvent(self.parent, StatusEvent(status=msg,
1617	info="info",
1618	type="stop"))
1619	except:
1620	msg = "Singular point: Fitting Error occurred."
1621	wx.PostEvent(self.parent, StatusEvent(status=msg,
1622	info="error",
1623	type="stop"))
1624
1625	except:
1626	msg = "Fit completed but Following"
1627	msg += " warning occurred: %s" % sys.exc_value
1628	wx.PostEvent(self.parent, StatusEvent(status=msg, info="warning",
1629	type="stop"))
1630
1631	def _update_fit_button(self, page_id):
1632	"""
1633	Update Fit button when fit stopped
1634
1635	: parameter page_id: fitpage where the button is
1636	"""
1637	if page_id.__class__.__name__ != 'list':
1638	page_id = [page_id]
1639	for uid in page_id:
1640	page = self.fit_panel.get_page_by_id(uid)
1641	page._on_fit_complete()
1642
1643	def _on_show_panel(self, event):
1644	"""
1645	"""
1646	pass
1647
1648	def on_reset_batch_flag(self, event):
1649	"""
1650	Set batch_reset_flag
1651	"""
1652	event.Skip()
1653	if self.menu1 == None:
1654	return
1655	menu_item = self.menu1.FindItemById(self.id_reset_flag)
1656	flag = menu_item.IsChecked()
1657	if not flag:
1658	menu_item.Check(False)
1659	self.batch_reset_flag = True
1660	else:
1661	menu_item.Check(True)
1662	self.batch_reset_flag = False
1663
1664	## post a message to status bar
1665	msg = "Set Chain Fitting: %s" % str(not self.batch_reset_flag)
1666	wx.PostEvent(self.parent,
1667	StatusEvent(status=msg))
1668
1669	def _onset_engine_park(self, event):
1670	"""
1671	set engine to park
1672	"""
1673	self._on_change_engine('park')
1674
1675	def _onset_engine_scipy(self, event):
1676	"""
1677	set engine to scipy
1678	"""
1679	self._on_change_engine('scipy')
1680
1681	def _onset_engine_bumps(self, event):
1682	"""
1683	set engine to bumps
1684	"""
1685	self._on_change_engine('bumps')
1686
1687	def _on_slicer_event(self, event):
1688	"""
1689	Receive a panel as event and send it to guiframe
1690
1691	:param event: event containing a panel
1692
1693	"""
1694	if event.panel is not None:
1695	new_panel = event.panel
1696	self.slicer_panels.append(event.panel)
1697	# Set group ID if available
1698	event_id = self.parent.popup_panel(event.panel)
1699	event.panel.uid = event_id
1700	self.mypanels.append(event.panel)
1701
1702	def _onclearslicer(self, event):
1703	"""
1704	Clear the boxslicer when close the panel associate with this slicer
1705	"""
1706	name = event.GetEventObject().frame.GetTitle()
1707	print "name", name
1708	for panel in self.slicer_panels:
1709	if panel.window_caption == name:
1710
1711	for item in self.parent.panels:
1712	if hasattr(self.parent.panels[item], "uid"):
1713	if self.parent.panels[item].uid == panel.base.uid:
1714	self.parent.panels[item].onClearSlicer(event)
1715	#self.parent._mgr.Update()
1716	break
1717	break
1718
1719	def _on_change_engine(self, engine='park'):
1720	"""
1721	Allow to select the type of engine to perform fit
1722
1723	:param engine: the key work of the engine
1724
1725	"""
1726	## saving fit engine name
1727	self._fit_engine = engine
1728	## change menu item state
1729	if engine == "park":
1730	self.menu1.FindItemById(self.park_id).Check(True)
1731	self.menu1.FindItemById(self.scipy_id).Check(False)
1732	self.menu1.FindItemById(self.bumps_id).Check(False)
1733	elif engine == "scipy":
1734	self.menu1.FindItemById(self.park_id).Check(False)
1735	self.menu1.FindItemById(self.scipy_id).Check(True)
1736	self.menu1.FindItemById(self.bumps_id).Check(False)
1737	else:
1738	self.menu1.FindItemById(self.park_id).Check(False)
1739	self.menu1.FindItemById(self.scipy_id).Check(False)
1740	self.menu1.FindItemById(self.bumps_id).Check(True)
1741	## post a message to status bar
1742	msg = "Engine set to: %s" % self._fit_engine
1743	wx.PostEvent(self.parent,
1744	StatusEvent(status=msg))
1745	## send the current engine type to fitpanel
1746	self.fit_panel._on_engine_change(name=self._fit_engine)
1747
1748	def _on_model_panel(self, evt):
1749	"""
1750	react to model selection on any combo box or model menu.plot the model
1751
1752	:param evt: wx.combobox event
1753
1754	"""
1755	model = evt.model
1756	uid = evt.uid
1757	qmin = evt.qmin
1758	qmax = evt.qmax
1759	caption = evt.caption
1760	enable_smearer = evt.enable_smearer
1761	if model == None:
1762	return
1763	if uid not in self.page_finder.keys():
1764	return
1765	# save the name containing the data name with the appropriate model
1766	self.page_finder[uid].set_model(model)
1767	self.page_finder[uid].enable_smearing(enable_smearer)
1768	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax)
1769	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1770	if self.sim_page is not None and not self.batch_on:
1771	self.sim_page.draw_page()
1772	if self.batch_page is not None and self.batch_on:
1773	self.batch_page.draw_page()
1774
1775	def _update1D(self, x, output):
1776	"""
1777	Update the output of plotting model 1D
1778	"""
1779	msg = "Plot updating ... "
1780	wx.PostEvent(self.parent, StatusEvent(status=msg, type="update"))
1781
1782	def _complete1D(self, x, y, page_id, elapsed, index, model,
1783	weight=None, fid=None,
1784	toggle_mode_on=False, state=None,
1785	data=None, update_chisqr=True,
1786	source='model', plot_result=True):
1787	"""
1788	Complete plotting 1D data
1789	"""
1790	try:
1791	numpy.nan_to_num(y)
1792
1793	new_plot = Data1D(x=x, y=y)
1794	new_plot.is_data = False
1795	new_plot.dy = numpy.zeros(len(y))
1796	new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
1797	_yaxis, _yunit = data.get_yaxis()
1798	_xaxis, _xunit = data.get_xaxis()
1799	new_plot.title = data.name
1800
1801	new_plot.group_id = data.group_id
1802	if new_plot.group_id == None:
1803	new_plot.group_id = data.group_id
1804	new_plot.id = str(page_id) + " " + data.name
1805	#if new_plot.id in self.color_dict:
1806	# new_plot.custom_color = self.color_dict[new_plot.id]
1807	#find if this theory was already plotted and replace that plot given
1808	#the same id
1809	theory_data = self.page_finder[page_id].get_theory_data(fid=data.id)
1810
1811	if data.is_data:
1812	data_name = str(data.name)
1813	else:
1814	data_name = str(model.__class__.__name__)
1815
1816	new_plot.name = model.name + " [" + data_name +"]"
1817	new_plot.xaxis(_xaxis, _xunit)
1818	new_plot.yaxis(_yaxis, _yunit)
1819	self.page_finder[page_id].set_theory_data(data=new_plot,
1820	fid=data.id)
1821	self.parent.update_theory(data_id=data.id, theory=new_plot,
1822	state=state)
1823	current_pg = self.fit_panel.get_page_by_id(page_id)
1824	title = new_plot.title
1825	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
1826	if not batch_on:
1827	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1828	title=str(title)))
1829	elif plot_result:
1830	top_data_id = self.fit_panel.get_page_by_id(page_id).data.id
1831	if data.id == top_data_id:
1832	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1833	title=str(title)))
1834	caption = current_pg.window_caption
1835	self.page_finder[page_id].set_fit_tab_caption(caption=caption)
1836
1837	self.page_finder[page_id].set_theory_data(data=new_plot,
1838	fid=data.id)
1839	if toggle_mode_on:
1840	wx.PostEvent(self.parent,
1841	NewPlotEvent(group_id=str(page_id) + " Model2D",
1842	action="Hide"))
1843	else:
1844	if update_chisqr:
1845	wx.PostEvent(current_pg,
1846	Chi2UpdateEvent(output=self._cal_chisqr(
1847	data=data,
1848	fid=fid,
1849	weight=weight,
1850	page_id=page_id,
1851	index=index)))
1852	else:
1853	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1854	index=index, weight=weight)
1855
1856	msg = "Computation completed!"
1857	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1858	except:
1859	raise
1860
1861	def _update2D(self, output, time=None):
1862	"""
1863	Update the output of plotting model
1864	"""
1865	wx.PostEvent(self.parent, StatusEvent(status="Plot \
1866	#updating ... ", type="update"))
1867	#self.ready_fit()
1868
1869	def _complete2D(self, image, data, model, page_id, elapsed, index, qmin,
1870	qmax, fid=None, weight=None, toggle_mode_on=False, state=None,
1871	update_chisqr=True, source='model', plot_result=True):
1872	"""
1873	Complete get the result of modelthread and create model 2D
1874	that can be plot.
1875	"""
1876	numpy.nan_to_num(image)
1877	new_plot = Data2D(image=image, err_image=data.err_data)
1878	new_plot.name = model.name + '2d'
1879	new_plot.title = "Analytical model 2D "
1880	new_plot.id = str(page_id) + " " + data.name
1881	new_plot.group_id = str(page_id) + " Model2D"
1882	new_plot.detector = data.detector
1883	new_plot.source = data.source
1884	new_plot.is_data = False
1885	new_plot.qx_data = data.qx_data
1886	new_plot.qy_data = data.qy_data
1887	new_plot.q_data = data.q_data
1888	new_plot.mask = data.mask
1889	## plot boundaries
1890	new_plot.ymin = data.ymin
1891	new_plot.ymax = data.ymax
1892	new_plot.xmin = data.xmin
1893	new_plot.xmax = data.xmax
1894	title = data.title
1895
1896	new_plot.is_data = False
1897	if data.is_data:
1898	data_name = str(data.name)
1899	else:
1900	data_name = str(model.__class__.__name__) + '2d'
1901
1902	if len(title) > 1:
1903	new_plot.title = "Model2D for %s "% model.name + data_name
1904	new_plot.name = model.name + " [" + \
1905	data_name + "]"
1906	theory_data = deepcopy(new_plot)
1907
1908	self.page_finder[page_id].set_theory_data(data=theory_data,
1909	fid=data.id)
1910	self.parent.update_theory(data_id=data.id,
1911	theory=new_plot,
1912	state=state)
1913	current_pg = self.fit_panel.get_page_by_id(page_id)
1914	title = new_plot.title
1915	if not source == 'fit' and plot_result:
1916	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
1917	title=title))
1918	if toggle_mode_on:
1919	wx.PostEvent(self.parent,
1920	NewPlotEvent(group_id=str(page_id) + " Model1D",
1921	action="Hide"))
1922	else:
1923	# Chisqr in fitpage
1924	if update_chisqr:
1925	wx.PostEvent(current_pg,
1926	Chi2UpdateEvent(output=self._cal_chisqr(data=data,
1927	weight=weight,
1928	fid=fid,
1929	page_id=page_id,
1930	index=index)))
1931	else:
1932	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1933	index=index, weight=weight)
1934	msg = "Computation completed!"
1935	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1936
1937	def _draw_model2D(self, model, page_id, qmin,
1938	qmax,
1939	data=None, smearer=None,
1940	description=None, enable2D=False,
1941	state=None,
1942	fid=None,
1943	weight=None,
1944	toggle_mode_on=False,
1945	update_chisqr=True, source='model'):
1946	"""
1947	draw model in 2D
1948
1949	:param model: instance of the model to draw
1950	:param description: the description of the model
1951	:param enable2D: when True allows to draw model 2D
1952	:param qmin: the minimum value to draw model 2D
1953	:param qmax: the maximum value to draw model 2D
1954	:param qstep: the number of division of Qx and Qy of the model to draw
1955
1956	"""
1957	if not enable2D:
1958	return None
1959	try:
1960	from model_thread import Calc2D
1961	## If a thread is already started, stop it
1962	if (self.calc_2D is not None) and self.calc_2D.isrunning():
1963	self.calc_2D.stop()
1964	## stop just raises a flag to tell the thread to kill
1965	## itself -- see the fix in Calc1D implemented to fix
1966	## an actual problem. Seems the fix should also go here
1967	## and may be the cause of other noted instabilities
1968	##
1969	## -PDB August 12, 2014
1970	while self.calc_2D.isrunning():
1971	time.sleep(0.1)
1972	self.calc_2D = Calc2D(model=model,
1973	data=data,
1974	page_id=page_id,
1975	smearer=smearer,
1976	qmin=qmin,
1977	qmax=qmax,
1978	weight=weight,
1979	fid=fid,
1980	toggle_mode_on=toggle_mode_on,
1981	state=state,
1982	completefn=self._complete2D,
1983	update_chisqr=update_chisqr, source=source)
1984	self.calc_2D.queue()
1985	except:
1986	raise
1987
1988	def _draw_model1D(self, model, page_id, data,
1989	qmin, qmax, smearer=None,
1990	state=None,
1991	weight=None,
1992	fid=None,
1993	toggle_mode_on=False, update_chisqr=True, source='model',
1994	enable1D=True):
1995	"""
1996	Draw model 1D from loaded data1D
1997
1998	:param data: loaded data
1999	:param model: the model to plot
2000
2001	"""
2002	if not enable1D:
2003	return
2004	try:
2005	from model_thread import Calc1D
2006	## If a thread is already started, stop it
2007	if (self.calc_1D is not None) and self.calc_1D.isrunning():
2008	self.calc_1D.stop()
2009	## stop just raises the flag -- the thread is supposed to
2010	## then kill itself but cannot. Paul Kienzle came up with
2011	## this fix to prevent threads from stepping on each other
2012	## which was causing a simple custom model to crash Sasview.
2013	## We still don't know why the fit sometimes lauched a second
2014	## thread -- something which should also be investigated.
2015	## The thread approach was implemented in order to be able
2016	## to lauch a computation in a separate thread from the GUI so
2017	## that the GUI can still respond to user input including
2018	## a request to stop the computation.
2019	## It seems thus that the whole thread approach used here
2020	## May need rethinking
2021	##
2022	## -PDB August 12, 2014
2023	while self.calc_1D.isrunning():
2024	time.sleep(0.1)
2025	self.calc_1D = Calc1D(data=data,
2026	model=model,
2027	page_id=page_id,
2028	qmin=qmin,
2029	qmax=qmax,
2030	smearer=smearer,
2031	state=state,
2032	weight=weight,
2033	fid=fid,
2034	toggle_mode_on=toggle_mode_on,
2035	completefn=self._complete1D,
2036	#updatefn = self._update1D,
2037	update_chisqr=update_chisqr,
2038	source=source)
2039	self.calc_1D.queue()
2040	except:
2041	msg = " Error occurred when drawing %s Model 1D: " % model.name
2042	msg += " %s" % sys.exc_value
2043	wx.PostEvent(self.parent, StatusEvent(status=msg))
2044
2045	def _cal_chisqr(self, page_id, data, weight, fid=None, index=None):
2046	"""
2047	Get handy Chisqr using the output from draw1D and 2D,
2048	instead of calling expansive CalcChisqr in guithread
2049	"""
2050	try:
2051	data_copy = deepcopy(data)
2052	except:
2053	return
2054	# default chisqr
2055	chisqr = None
2056	#to compute chisq make sure data has valid data
2057	# return None if data == None
2058	if not check_data_validity(data_copy) or data_copy == None:
2059	return chisqr
2060
2061	# Get data: data I, theory I, and data dI in order
2062	if data_copy.__class__.__name__ == "Data2D":
2063	if index == None:
2064	index = numpy.ones(len(data_copy.data), dtype=bool)
2065	if weight != None:
2066	data_copy.err_data = weight
2067	# get rid of zero error points
2068	index = index & (data_copy.err_data != 0)
2069	index = index & (numpy.isfinite(data_copy.data))
2070	fn = data_copy.data[index]
2071	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2072	if theory_data == None:
2073	return chisqr
2074	gn = theory_data.data[index]
2075	en = data_copy.err_data[index]
2076	else:
2077	# 1 d theory from model_thread is only in the range of index
2078	if index == None:
2079	index = numpy.ones(len(data_copy.y), dtype=bool)
2080	if weight != None:
2081	data_copy.dy = weight
2082	if data_copy.dy == None or data_copy.dy == []:
2083	dy = numpy.ones(len(data_copy.y))
2084	else:
2085	## Set consitently w/AbstractFitengine:
2086	# But this should be corrected later.
2087	dy = deepcopy(data_copy.dy)
2088	dy[dy == 0] = 1
2089	fn = data_copy.y[index]
2090
2091	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2092	if theory_data == None:
2093	return chisqr
2094	gn = theory_data.y
2095	en = dy[index]
2096
2097	# residual
2098	try:
2099	res = (fn - gn) / en
2100	except ValueError:
2101	print "Unmatch lengths %s, %s, %s"% (len(fn), len(gn), len(en))
2102	return
2103
2104	residuals = res[numpy.isfinite(res)]
2105	# get chisqr only w/finite
2106	chisqr = numpy.average(residuals * residuals)
2107
2108	self._plot_residuals(page_id=page_id, data=data_copy,
2109	fid=fid,
2110	weight=weight, index=index)
2111
2112	return chisqr
2113
2114	def _plot_residuals(self, page_id, weight, fid=None,
2115	data=None, index=None):
2116	"""
2117	Plot the residuals
2118
2119	:param data: data
2120	:param index: index array (bool)
2121	: Note: this is different from the residuals in cal_chisqr()
2122	"""
2123	data_copy = deepcopy(data)
2124	# Get data: data I, theory I, and data dI in order
2125	if data_copy.__class__.__name__ == "Data2D":
2126	# build residuals
2127	residuals = Data2D()
2128	#residuals.copy_from_datainfo(data)
2129	# Not for trunk the line below, instead use the line above
2130	data_copy.clone_without_data(len(data_copy.data), residuals)
2131	residuals.data = None
2132	fn = data_copy.data
2133	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2134	gn = theory_data.data
2135	if weight == None:
2136	en = data_copy.err_data
2137	else:
2138	en = weight
2139	residuals.data = (fn - gn) / en
2140	residuals.qx_data = data_copy.qx_data
2141	residuals.qy_data = data_copy.qy_data
2142	residuals.q_data = data_copy.q_data
2143	residuals.err_data = numpy.ones(len(residuals.data))
2144	residuals.xmin = min(residuals.qx_data)
2145	residuals.xmax = max(residuals.qx_data)
2146	residuals.ymin = min(residuals.qy_data)
2147	residuals.ymax = max(residuals.qy_data)
2148	residuals.q_data = data_copy.q_data
2149	residuals.mask = data_copy.mask
2150	residuals.scale = 'linear'
2151	# check the lengths
2152	if len(residuals.data) != len(residuals.q_data):
2153	return
2154	else:
2155	# 1 d theory from model_thread is only in the range of index
2156	if data_copy.dy == None or data_copy.dy == []:
2157	dy = numpy.ones(len(data_copy.y))
2158	else:
2159	if weight == None:
2160	dy = numpy.ones(len(data_copy.y))
2161	## Set consitently w/AbstractFitengine:
2162	## But this should be corrected later.
2163	else:
2164	dy = weight
2165	dy[dy == 0] = 1
2166	fn = data_copy.y[index]
2167	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2168	gn = theory_data.y
2169	en = dy[index]
2170	# build residuals
2171	residuals = Data1D()
2172	try:
2173	residuals.y = (fn - gn) / en
2174	except:
2175	msg = "ResidualPlot Error: different # of data points in theory"
2176	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
2177	residuals.y = (fn - gn[index]) / en
2178	residuals.x = data_copy.x[index]
2179	residuals.dy = numpy.ones(len(residuals.y))
2180	residuals.dx = None
2181	residuals.dxl = None
2182	residuals.dxw = None
2183	residuals.ytransform = 'y'
2184	# For latter scale changes
2185	residuals.xaxis('\\rm{Q} ', 'A^{-1}')
2186	residuals.yaxis('\\rm{Residuals} ', 'normalized')
2187	theory_name = str(theory_data.name.split()[0])
2188	new_plot = residuals
2189	new_plot.name = "Residuals for " + str(theory_name) + "[" +\
2190	str(data.name) +"]"
2191	## allow to highlight data when plotted
2192	new_plot.interactive = True
2193	## when 2 data have the same id override the 1 st plotted
2194	new_plot.id = "res" + str(data_copy.id) + str(theory_name)
2195	##group_id specify on which panel to plot this data
2196	group_id = self.page_finder[page_id].get_graph_id()
2197	if group_id == None:
2198	group_id = data.group_id
2199	new_plot.group_id = "res" + str(group_id)
2200	#new_plot.is_data = True
2201	##post data to plot
2202	title = new_plot.name
2203	self.page_finder[page_id].set_residuals(residuals=new_plot,
2204	fid=data.id)
2205	self.parent.update_theory(data_id=data.id, theory=new_plot)
2206	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
2207	if not batch_on:
2208	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))

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SasView

source: sasview/src/sas/perspectives/fitting/fitting.py @ 0c4bca6

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