fitting.py @ 5ae083b

Last change on this file since 5ae083b was aba4559, checked in by Paul Kienzle <pkienzle@…>, 6 years ago
fix comments
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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	from __future__ import print_function
14
15	import re
16	import sys
17	import os
18	import wx
19	import logging
20	import numpy as np
21	import time
22	from copy import deepcopy
23	import traceback
24
25	import bumps.options
26	from bumps.gui.fit_dialog import show_fit_config
27	try:
28	from bumps.gui.fit_dialog import EVT_FITTER_CHANGED
29	except ImportError:
30	# CRUFT: bumps 0.7.5.8 and below
31	EVT_FITTER_CHANGED = None # type: wx.PyCommandEvent
32
33	from sas.sascalc.dataloader.loader import Loader
34	from sas.sascalc.fit.BumpsFitting import BumpsFit as Fit
35	from sas.sascalc.fit.pagestate import Reader, PageState, SimFitPageState
36	from sas.sascalc.fit import models
37
38	from sas.sasgui.guiframe.dataFitting import Data2D
39	from sas.sasgui.guiframe.dataFitting import Data1D
40	from sas.sasgui.guiframe.dataFitting import check_data_validity
41	from sas.sasgui.guiframe.events import NewPlotEvent
42	from sas.sasgui.guiframe.events import StatusEvent
43	from sas.sasgui.guiframe.events import EVT_SLICER_PANEL
44	from sas.sasgui.guiframe.events import EVT_SLICER_PARS_UPDATE
45	from sas.sasgui.guiframe.gui_style import GUIFRAME_ID
46	from sas.sasgui.guiframe.plugin_base import PluginBase
47	from sas.sasgui.guiframe.data_processor import BatchCell
48	from sas.sasgui.guiframe.gui_manager import MDIFrame
49	from sas.sasgui.guiframe.documentation_window import DocumentationWindow
50
51	from sas.sasgui.perspectives.calculator.model_editor import TextDialog
52	from sas.sasgui.perspectives.calculator.model_editor import EditorWindow
53	from sas.sasgui.perspectives.calculator.pyconsole import PyConsole
54
55	from .fitting_widgets import DataDialog
56	from .fit_thread import FitThread
57	from .fitpage import Chi2UpdateEvent
58	from .console import ConsoleUpdate
59	from .fitproblem import FitProblemDictionary
60	from .fitpanel import FitPanel
61	from .model_thread import Calc1D, Calc2D
62	from .resultpanel import ResultPanel, PlotResultEvent
63	from .gpu_options import GpuOptions
64
65	logger = logging.getLogger(__name__)
66
67	MAX_NBR_DATA = 4
68
69	(PageInfoEvent, EVT_PAGE_INFO) = wx.lib.newevent.NewEvent()
70
71
72	if sys.platform == "win32":
73	ON_MAC = False
74	else:
75	ON_MAC = True
76
77
78	class Plugin(PluginBase):
79	"""
80	Fitting plugin is used to perform fit
81	"""
82	def __init__(self):
83	PluginBase.__init__(self, name="Fitting")
84
85	#list of panel to send to guiframe
86	self.mypanels = []
87	# reference to the current running thread
88	self.calc_2D = None
89	self.calc_1D = None
90
91	self.color_dict = {}
92
93	self.fit_thread_list = {}
94	self.residuals = None
95	self.weight = None
96	self.fit_panel = None
97	self.plot_panel = None
98	# Start with a good default
99	self.elapsed = 0.022
100	self.fit_panel = None
101	## dictionary of page closed and id
102	self.closed_page_dict = {}
103	## Relative error desired in the sum of squares (float)
104	self.batch_reset_flag = True
105	#List of selected data
106	self.selected_data_list = []
107	## list of slicer panel created to display slicer parameters and results
108	self.slicer_panels = []
109	# model 2D view
110	self.model2D_id = None
111	#keep reference of the simultaneous fit page
112	self.sim_page = None
113	self.sim_menu = None
114	self.batch_page = None
115	self.batch_menu = None
116	self.index_model = 0
117	self.test_model_color = None
118	#Create a reader for fit page's state
119	self.state_reader = None
120	self._extensions = '.fitv'
121	self.menu1 = None
122	self.new_model_frame = None
123
124	self.temp_state = []
125	self.state_index = 0
126	self.sfile_ext = None
127	# take care of saving data, model and page associated with each other
128	self.page_finder = {}
129	# Log startup
130	logger.info("Fitting plug-in started")
131	self.batch_capable = self.get_batch_capable()
132
133	def get_batch_capable(self):
134	"""
135	Check if the plugin has a batch capability
136	"""
137	return True
138
139	def create_fit_problem(self, page_id):
140	"""
141	Given an ID create a fitproblem container
142	"""
143	self.page_finder[page_id] = FitProblemDictionary()
144
145	def delete_fit_problem(self, page_id):
146	"""
147	Given an ID create a fitproblem container
148	"""
149	if page_id in self.page_finder.iterkeys():
150	del self.page_finder[page_id]
151
152	def add_color(self, color, id):
153	"""
154	adds a color as a key with a plot id as its value to a dictionary
155	"""
156	self.color_dict[id] = color
157
158	def on_batch_selection(self, flag):
159	"""
160	switch the the notebook of batch mode or not
161	"""
162	self.batch_on = flag
163	if self.fit_panel is not None:
164	self.fit_panel.batch_on = self.batch_on
165
166	def populate_menu(self, owner):
167	"""
168	Create a menu for the Fitting plug-in
169
170	:param id: id to create a menu
171	:param owner: owner of menu
172
173	:return: list of information to populate the main menu
174
175	"""
176	#Menu for fitting
177	self.menu1 = wx.Menu()
178	id1 = wx.NewId()
179	simul_help = "Add new fit panel"
180	self.menu1.Append(id1, '&New Fit Page', simul_help)
181	wx.EVT_MENU(owner, id1, self.on_add_new_page)
182	self.menu1.AppendSeparator()
183	self.id_simfit = wx.NewId()
184	simul_help = "Constrained or Simultaneous Fit"
185	self.menu1.Append(self.id_simfit, '&Constrained or Simultaneous Fit', simul_help)
186	wx.EVT_MENU(owner, self.id_simfit, self.on_add_sim_page)
187	self.sim_menu = self.menu1.FindItemById(self.id_simfit)
188	self.sim_menu.Enable(False)
189	#combined Batch
190	self.id_batchfit = wx.NewId()
191	batch_help = "Combined Batch"
192	self.menu1.Append(self.id_batchfit, '&Combine Batch Fit', batch_help)
193	wx.EVT_MENU(owner, self.id_batchfit, self.on_add_sim_page)
194	self.batch_menu = self.menu1.FindItemById(self.id_batchfit)
195	self.batch_menu.Enable(False)
196
197	self.menu1.AppendSeparator()
198	self.id_bumps_options = wx.NewId()
199	bopts_help = "Fitting options"
200	self.menu1.Append(self.id_bumps_options, 'Fit &Options', bopts_help)
201	wx.EVT_MENU(owner, self.id_bumps_options, self.on_bumps_options)
202	self.bumps_options_menu = self.menu1.FindItemById(self.id_bumps_options)
203	self.bumps_options_menu.Enable(True)
204
205	self.id_gpu_options_panel = wx.NewId()
206	self.menu1.Append(self.id_gpu_options_panel, "OpenCL Options", "Choose OpenCL driver or turn it off")
207	wx.EVT_MENU(owner, self.id_gpu_options_panel, self.on_gpu_options)
208
209	self.id_result_panel = wx.NewId()
210	self.menu1.Append(self.id_result_panel, "Fit Results", "Show fit results panel")
211	wx.EVT_MENU(owner, self.id_result_panel, self.on_fit_results)
212	self.menu1.AppendSeparator()
213
214	self.id_reset_flag = wx.NewId()
215	resetf_help = "BatchFit: If checked, the initial param values will be "
216	resetf_help += "propagated from the previous results. "
217	resetf_help += "Otherwise, the same initial param values will be used "
218	resetf_help += "for all fittings."
219	self.menu1.AppendCheckItem(self.id_reset_flag,
220	"Chain Fitting [BatchFit Only]",
221	resetf_help)
222	wx.EVT_MENU(owner, self.id_reset_flag, self.on_reset_batch_flag)
223	chain_menu = self.menu1.FindItemById(self.id_reset_flag)
224	chain_menu.Check(not self.batch_reset_flag)
225	chain_menu.Enable(self.batch_on)
226
227	self.menu1.AppendSeparator()
228	self.edit_model_menu = wx.Menu()
229	# Find and put files name in menu
230	try:
231	self.set_edit_menu(owner=owner)
232	except:
233	raise
234
235	self.id_edit = wx.NewId()
236	self.menu1.AppendMenu(self.id_edit, "Plugin Model Operations",
237	self.edit_model_menu)
238	#create menubar items
239	return [(self.menu1, self.sub_menu)]
240
241	def edit_custom_model(self, event):
242	"""
243	Get the python editor panel
244	"""
245	event_id = event.GetId()
246	label = self.edit_menu.GetLabel(event_id)
247	filename = os.path.join(models.find_plugins_dir(), label)
248	frame = PyConsole(parent=self.parent, manager=self,
249	panel=self.fit_panel,
250	title='Advanced Plugin Model Editor',
251	filename=filename)
252	self.put_icon(frame)
253	frame.Show(True)
254
255	def delete_custom_model(self, event):
256	"""
257	Delete custom model file
258	"""
259	event_id = event.GetId()
260	label = self.delete_menu.GetLabel(event_id)
261	toks = os.path.splitext(label)
262	path = os.path.join(models.find_plugins_dir(), toks[0])
263	message = "Are you sure you want to delete the file {}?".format(path)
264	dlg = wx.MessageDialog(self.frame, message, '', wx.YES_NO \| wx.ICON_QUESTION)
265	if not dlg.ShowModal() == wx.ID_YES:
266	return
267	try:
268	for ext in ['.py', '.pyc']:
269	p_path = path + ext
270	if ext == '.pyc' and not os.path.isfile(path + ext):
271	# If model is invalid, .pyc file may not exist as model has
272	# never been compiled. Don't try and delete it
273	continue
274	os.remove(p_path)
275	self.update_custom_combo()
276	if os.path.isfile(p_path):
277	msg = "Sorry! unable to delete the default "
278	msg += "plugin model... \n"
279	msg += "Please manually remove the files (.py, .pyc) "
280	msg += "in the 'plugin_models' folder \n"
281	msg += "inside of the SasView application, "
282	msg += "and try it again."
283	wx.MessageBox(msg, 'Info')
284	#evt = StatusEvent(status=msg, type='stop', info='warning')
285	#wx.PostEvent(self.parent, evt)
286	else:
287	self.delete_menu.Delete(event_id)
288	for item in self.edit_menu.GetMenuItems():
289	if item.GetLabel() == label:
290	self.edit_menu.DeleteItem(item)
291	msg = "The plugin model, %s, has been deleted." % label
292	evt = StatusEvent(status=msg, type='stop', info='info')
293	wx.PostEvent(self.parent, evt)
294	break
295	except Exception:
296	traceback.print_exc()
297	msg = 'Delete Error: \nCould not delete the file; Check if in use.'
298	wx.MessageBox(msg, 'Error')
299
300	def make_sum_model(self, event):
301	"""
302	Edit summodel template and make one
303	"""
304	event_id = event.GetId()
305	model_manager = models.ModelManager()
306	model_list = model_manager.composable_models()
307	plug_dir = models.find_plugins_dir()
308	textdial = TextDialog(None, self, wx.ID_ANY, 'Easy Sum/Multi(p1, p2) Editor',
309	model_list, plug_dir)
310	self.put_icon(textdial)
311	textdial.ShowModal()
312	textdial.Destroy()
313
314	def make_new_model(self, event):
315	"""
316	Make new model
317	"""
318	if self.new_model_frame is not None:
319	self.new_model_frame.Show(False)
320	self.new_model_frame.Show(True)
321	else:
322	event_id = event.GetId()
323	dir_path = models.find_plugins_dir()
324	title = "New Plugin Model Function"
325	self.new_model_frame = EditorWindow(parent=self, base=self,
326	path=dir_path, title=title)
327	self.put_icon(self.new_model_frame)
328	self.new_model_frame.Show(True)
329
330	def load_plugin_models(self, event):
331	"""
332	Update of models in plugin_models folder
333	"""
334	event_id = event.GetId()
335	self.update_custom_combo()
336
337	def update_custom_combo(self):
338	"""
339	Update custom model list in the fitpage combo box
340	"""
341	try:
342	# Update edit menus
343	self.set_edit_menu_helper(self.parent, self.edit_custom_model)
344	self.set_edit_menu_helper(self.parent, self.delete_custom_model)
345	new_pmodel_list = self.fit_panel.reset_pmodel_list()
346	if not new_pmodel_list:
347	return
348
349	# Redraws to a page not in focus are showing up as if they are
350	# in the current page tab.
351	current_page_index = self.fit_panel.GetSelection()
352	current_page = self.fit_panel.GetCurrentPage()
353	last_drawn_page = current_page
354
355	# Set the new plugin model list for all fit pages; anticipating
356	# categories, the updated plugin may be in either the form factor
357	# or the structure factor combo boxes
358	for uid, page in self.fit_panel.opened_pages.iteritems():
359	pbox = getattr(page, "formfactorbox", None)
360	sbox = getattr(page, "structurebox", None)
361	if pbox is None:
362	continue
363
364	# Set the new model list for the page
365	page.model_list_box = new_pmodel_list
366
367	# Grab names of the P and S models from the page. Need to do
368	# this before resetting the form factor box since that clears
369	# the structure factor box.
370	old_struct = old_form = None
371	form_name = pbox.GetValue()
372	struct_name = sbox.GetStringSelection()
373	if form_name:
374	old_form = pbox.GetClientData(pbox.GetCurrentSelection())
375	if struct_name:
376	old_struct = sbox.GetClientData(sbox.GetCurrentSelection())
377
378	# Reset form factor combo box. We are doing this for all
379	# categories not just plugins since eventually the category
380	# manager will allow plugin models to be anywhere.
381	page._show_combox_helper()
382	form_index = pbox.FindString(form_name)
383	pbox.SetSelection(form_index)
384	new_form = (pbox.GetClientData(form_index)
385	if form_index != wx.NOT_FOUND else None)
386	#print("form: %r"%form_name, old_form, new_form)
387
388	# Reset structure factor combo box; even if the model list
389	# hasn't changed, the model may have. Show the structure
390	# factor combobox if the selected model is a form factor.
391	sbox.Clear()
392	page.initialize_combox()
393	if new_form is not None and getattr(new_form, 'is_form_factor', False):
394	sbox.Show()
395	sbox.Enable()
396	page.text2.Show()
397	page.text2.Enable()
398	struct_index = sbox.FindString(struct_name)
399	sbox.SetSelection(struct_index)
400	new_struct = (sbox.GetClientData(struct_index)
401	if struct_index != wx.NOT_FOUND else None)
402	#print("struct: %r"%struct_name, old_struct, new_struct)
403
404	# Update the page if P or S has changed
405	if old_form != new_form or old_struct != new_struct:
406	#print("triggering model update")
407	page._on_select_model(keep_pars=True)
408	last_drawn_page = page
409
410	# If last drawn is not the current, then switch the current to the
411	# last drawn then switch back. Very ugly.
412	if last_drawn_page != current_page:
413	for page_index in range(self.fit_panel.PageCount):
414	if self.fit_panel.GetPage(page_index) == last_drawn_page:
415	self.fit_panel.SetSelection(page_index)
416	break
417	self.fit_panel.SetSelection(current_page_index)
418
419	except Exception:
420	logger.error("update_custom_combo: %s", sys.exc_value)
421
422	def set_edit_menu(self, owner):
423	"""
424	Set list of the edit model menu labels
425	"""
426	wx_id = wx.NewId()
427	#new_model_menu = wx.Menu()
428	self.edit_model_menu.Append(wx_id, 'New Plugin Model',
429	'Add a new model function')
430	wx.EVT_MENU(owner, wx_id, self.make_new_model)
431
432	wx_id = wx.NewId()
433	self.edit_model_menu.Append(wx_id, 'Sum\|Multi(p1, p2)',
434	'Sum of two model functions')
435	wx.EVT_MENU(owner, wx_id, self.make_sum_model)
436
437	e_id = wx.NewId()
438	self.edit_menu = wx.Menu()
439	self.edit_model_menu.AppendMenu(e_id,
440	'Advanced Plugin Editor', self.edit_menu)
441	self.set_edit_menu_helper(owner, self.edit_custom_model)
442
443	d_id = wx.NewId()
444	self.delete_menu = wx.Menu()
445	self.edit_model_menu.AppendMenu(d_id,
446	'Delete Plugin Models', self.delete_menu)
447	self.set_edit_menu_helper(owner, self.delete_custom_model)
448
449	wx_id = wx.NewId()
450	self.edit_model_menu.Append(wx_id, 'Load Plugin Models',
451	'(Re)Load all models present in user plugin_models folder')
452	wx.EVT_MENU(owner, wx_id, self.load_plugin_models)
453
454	def set_edit_menu_helper(self, owner=None, menu=None):
455	"""
456	help for setting list of the edit model menu labels
457	"""
458	if menu is None:
459	menu = self.edit_custom_model
460	list_fnames = os.listdir(models.find_plugins_dir())
461	list_fnames.sort()
462	for f_item in list_fnames:
463	name = os.path.basename(f_item)
464	toks = os.path.splitext(name)
465	if toks[-1] == '.py' and not toks[0] == '__init__':
466	if menu == self.edit_custom_model:
467	if toks[0] == 'easy_sum_of_p1_p2':
468	continue
469	submenu = self.edit_menu
470	else:
471	submenu = self.delete_menu
472	has_file = False
473	for item in submenu.GetMenuItems():
474	if name == submenu.GetLabel(item.GetId()):
475	has_file = True
476	if not has_file:
477	wx_id = wx.NewId()
478	submenu.Append(wx_id, name)
479	wx.EVT_MENU(owner, wx_id, menu)
480	has_file = False
481
482	def put_icon(self, frame):
483	"""
484	Put icon in the frame title bar
485	"""
486	if hasattr(frame, "IsIconized"):
487	if not frame.IsIconized():
488	try:
489	icon = self.parent.GetIcon()
490	frame.SetIcon(icon)
491	except:
492	pass
493
494	def on_add_sim_page(self, event):
495	"""
496	Create a page to access simultaneous fit option
497	"""
498	event_id = event.GetId()
499	caption = "Const & Simul Fit"
500	page = self.sim_page
501	if event_id == self.id_batchfit:
502	caption = "Combined Batch"
503	page = self.batch_page
504
505	def set_focus_page(page):
506	page.Show(True)
507	page.Refresh()
508	page.SetFocus()
509	#self.parent._mgr.Update()
510	msg = "%s already opened\n" % str(page.window_caption)
511	wx.PostEvent(self.parent, StatusEvent(status=msg))
512
513	if page is not None:
514	return set_focus_page(page)
515	if caption == "Const & Simul Fit":
516	self.sim_page = self.fit_panel.add_sim_page(caption=caption)
517	else:
518	self.batch_page = self.fit_panel.add_sim_page(caption=caption)
519
520	def get_context_menu(self, plotpanel=None):
521	"""
522	Get the context menu items available for P(r).them allow fitting option
523	for Data2D and Data1D only.
524
525	:param graph: the Graph object to which we attach the context menu
526
527	:return: a list of menu items with call-back function
528
529	:note: if Data1D was generated from Theory1D
530	the fitting option is not allowed
531
532	"""
533	self.plot_panel = plotpanel
534	graph = plotpanel.graph
535	fit_option = "Select data for fitting"
536	fit_hint = "Dialog with fitting parameters "
537
538	if graph.selected_plottable not in plotpanel.plots:
539	return []
540	item = plotpanel.plots[graph.selected_plottable]
541	if item.__class__.__name__ is "Data2D":
542	if hasattr(item, "is_data"):
543	if item.is_data:
544	return [[fit_option, fit_hint, self._onSelect]]
545	else:
546	return []
547	return [[fit_option, fit_hint, self._onSelect]]
548	else:
549
550	# if is_data is true , this in an actual data loaded
551	#else it is a data created from a theory model
552	if hasattr(item, "is_data"):
553	if item.is_data:
554	return [[fit_option, fit_hint, self._onSelect]]
555	else:
556	return []
557	return [[fit_option, fit_hint, self._onSelect]]
558	return []
559
560	def get_panels(self, parent):
561	"""
562	Create and return a list of panel objects
563	"""
564	self.parent = parent
565	#self.parent.Bind(EVT_FITSTATE_UPDATE, self.on_set_state_helper)
566	# Creation of the fit panel
567	self.frame = MDIFrame(self.parent, None, 'None', (100, 200))
568	self.fit_panel = FitPanel(parent=self.frame, manager=self)
569	self.frame.set_panel(self.fit_panel)
570	self._frame_set_helper()
571	self.on_add_new_page(event=None)
572	#Set the manager for the main panel
573	self.fit_panel.set_manager(self)
574	# List of windows used for the perspective
575	self.perspective = []
576	self.perspective.append(self.fit_panel.window_name)
577
578	self.result_frame = MDIFrame(self.parent, None, ResultPanel.window_caption, (220, 200))
579	self.result_panel = ResultPanel(parent=self.result_frame, manager=self)
580	self.perspective.append(self.result_panel.window_name)
581
582	#index number to create random model name
583	self.index_model = 0
584	self.index_theory = 0
585	self.parent.Bind(EVT_SLICER_PANEL, self._on_slicer_event)
586	self.parent.Bind(EVT_SLICER_PARS_UPDATE, self._onEVT_SLICER_PANEL)
587
588	# CRUFT: EVT_FITTER_CHANGED is not None for bumps 0.7.5.9 and above
589	if EVT_FITTER_CHANGED is not None:
590	self.parent.Bind(EVT_FITTER_CHANGED, self.on_fitter_changed)
591	self._set_fitter_label(bumps.options.FIT_CONFIG)
592
593	#self.parent._mgr.Bind(wx.aui.EVT_AUI_PANE_CLOSE,self._onclearslicer)
594	#Create reader when fitting panel are created
595	self.state_reader = Reader(self.set_state)
596	#append that reader to list of available reader
597	loader = Loader()
598	loader.associate_file_reader(".fitv", self.state_reader)
599	#Send the fitting panel to guiframe
600	self.mypanels.append(self.fit_panel)
601	self.mypanels.append(self.result_panel)
602	return self.mypanels
603
604	def clear_panel(self):
605	"""
606	"""
607	self.fit_panel.clear_panel()
608
609	def delete_data(self, data):
610	"""
611	delete the given data from panel
612	"""
613	self.fit_panel.delete_data(data)
614
615	def set_data(self, data_list=None):
616	"""
617	receive a list of data to fit
618	"""
619	if data_list is None:
620	data_list = []
621	selected_data_list = []
622	if self.batch_on:
623	self.add_fit_page(data=data_list)
624	else:
625	if len(data_list) > MAX_NBR_DATA:
626	dlg = DataDialog(data_list=data_list, nb_data=MAX_NBR_DATA)
627	if dlg.ShowModal() == wx.ID_OK:
628	selected_data_list = dlg.get_data()
629	dlg.Destroy()
630
631	else:
632	selected_data_list = data_list
633	try:
634	group_id = wx.NewId()
635	for data in selected_data_list:
636	if data is not None:
637	# 2D has no same group_id
638	if data.__class__.__name__ == 'Data2D':
639	group_id = wx.NewId()
640	data.group_id = group_id
641	if group_id not in data.list_group_id:
642	data.list_group_id.append(group_id)
643	self.add_fit_page(data=[data])
644	except:
645	msg = "Fitting set_data: " + str(sys.exc_value)
646	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
647
648	def set_theory(self, theory_list=None):
649	"""
650	"""
651	#set the model state for a given theory_state:
652	for item in theory_list:
653	try:
654	_, theory_state = item
655	self.fit_panel.set_model_state(theory_state)
656	except Exception:
657	msg = "Fitting: cannot deal with the theory received"
658	evt = StatusEvent(status=msg, info="error")
659	logger.error("set_theory " + msg + "\n" + str(sys.exc_value))
660	wx.PostEvent(self.parent, evt)
661
662	def set_state(self, state=None, datainfo=None, format=None):
663	"""
664	Call-back method for the fit page state reader.
665	This method is called when a .fitv/.svs file is loaded.
666
667	: param state: PageState object
668	: param datainfo: data
669	"""
670	if isinstance(state, PageState):
671	state = state.clone()
672	self.temp_state.append(state)
673	elif isinstance(state, SimFitPageState):
674	if self.fit_panel.sim_page is None:
675	self.fit_panel.add_sim_page()
676	self.fit_panel.sim_page.load_from_save_state(state)
677	else:
678	self.temp_state = []
679	# index to start with for a new set_state
680	self.state_index = 0
681	# state file format
682	self.sfile_ext = format
683
684	self.on_set_state_helper(event=None)
685
686	def on_set_state_helper(self, event=None):
687	"""
688	Set_state_helper. This actually sets state
689	after plotting data from state file.
690
691	: event: FitStateUpdateEvent called
692	by dataloader.plot_data from guiframe
693	"""
694	if len(self.temp_state) == 0:
695	if self.state_index == 0 and len(self.mypanels) <= 0 \
696	and self.sfile_ext == '.svs':
697	self.temp_state = []
698	self.state_index = 0
699	return
700
701	try:
702	# Load fitting state
703	state = self.temp_state[self.state_index]
704	#panel state should have model selection to set_state
705	if state.formfactorcombobox is not None:
706	#set state
707	data = self.parent.create_gui_data(state.data)
708	data.group_id = state.data.group_id
709	self.parent.add_data(data_list={data.id: data})
710	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
711	title=data.title))
712	#need to be fix later make sure we are sendind guiframe.data
713	#to panel
714	state.data = data
715	page = self.fit_panel.set_state(state)
716	else:
717	#just set data because set_state won't work
718	data = self.parent.create_gui_data(state.data)
719	data.group_id = state.data.group_id
720	self.parent.add_data(data_list={data.id: data})
721	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
722	title=data.title))
723	page = self.add_fit_page([data])
724	caption = page.window_caption
725	self.store_data(uid=page.uid, data_list=page.get_data_list(),
726	caption=caption)
727	self.mypanels.append(page)
728
729	# get ready for the next set_state
730	self.state_index += 1
731
732	#reset state variables to default when all set_state is finished.
733	if len(self.temp_state) == self.state_index:
734
735	self.temp_state = []
736	#self.state_index = 0
737	# Make sure the user sees the fitting panel after loading
738	#self.parent.set_perspective(self.perspective)
739	self.on_perspective(event=None)
740	except:
741	self.state_index = 0
742	self.temp_state = []
743	raise
744
745	def set_param2fit(self, uid, param2fit):
746	"""
747	Set the list of param names to fit for fitprobelm
748	"""
749	self.page_finder[uid].set_param2fit(param2fit)
750
751	def set_graph_id(self, uid, graph_id):
752	"""
753	Set graph_id for fitprobelm
754	"""
755	self.page_finder[uid].set_graph_id(graph_id)
756
757	def get_graph_id(self, uid):
758	"""
759	Set graph_id for fitprobelm
760	"""
761	return self.page_finder[uid].get_graph_id()
762
763	def save_fit_state(self, filepath, fitstate):
764	"""
765	save fit page state into file
766	"""
767	self.state_reader.write(filename=filepath, fitstate=fitstate)
768
769	def set_fit_weight(self, uid, flag, is2d=False, fid=None):
770	"""
771	Set the fit weights of a given page for all
772	its data by default. If fid is provide then set the range
773	only for the data with fid as id
774	:param uid: id corresponding to a fit page
775	:param fid: id corresponding to a fit problem (data, model)
776	:param weight: current dy data
777	"""
778	# If we are not dealing with a specific fit problem, then
779	# there is no point setting the weights.
780	if fid is None:
781	return
782	if uid in self.page_finder.keys():
783	self.page_finder[uid].set_weight(flag=flag, is2d=is2d)
784
785	def set_fit_range(self, uid, qmin, qmax, fid=None):
786	"""
787	Set the fitting range of a given page for all
788	its data by default. If fid is provide then set the range
789	only for the data with fid as id
790	:param uid: id corresponding to a fit page
791	:param fid: id corresponding to a fit problem (data, model)
792	:param qmin: minimum value of the fit range
793	:param qmax: maximum value of the fit range
794	"""
795	if uid in self.page_finder.keys():
796	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax, fid=fid)
797
798	def schedule_for_fit(self, value=0, uid=None):
799	"""
800	Set the fit problem field to 0 or 1 to schedule that problem to fit.
801	Schedule the specified fitproblem or get the fit problem related to
802	the current page and set value.
803	:param value: integer 0 or 1
804	:param uid: the id related to a page containing fitting information
805	"""
806	if uid in self.page_finder.keys():
807	self.page_finder[uid].schedule_tofit(value)
808
809	def get_page_finder(self):
810	"""
811	return self.page_finder used also by simfitpage.py
812	"""
813	return self.page_finder
814
815	def set_page_finder(self, modelname, names, values):
816	"""
817	Used by simfitpage.py to reset a parameter given the string constrainst.
818
819	:param modelname: the name of the model for with the parameter
820	has to reset
821	:param value: can be a string in this case.
822	:param names: the parameter name
823	"""
824	sim_page_id = self.sim_page.uid
825	for uid, value in self.page_finder.iteritems():
826	if uid != sim_page_id and uid != self.batch_page.uid:
827	model_list = value.get_model()
828	model = model_list[0]
829	if model.name == modelname:
830	value.set_model_param(names, values)
831	break
832
833	def split_string(self, item):
834	"""
835	receive a word containing dot and split it. used to split parameterset
836	name into model name and parameter name example: ::
837
838	parameterset (item) = M1.A
839	Will return model_name = M1 , parameter name = A
840
841	"""
842	if item.find(".") >= 0:
843	param_names = re.split(r"\.", item)
844	model_name = param_names[0]
845	##Assume max len is 3; eg., M0.radius.width
846	if len(param_names) == 3:
847	param_name = param_names[1] + "." + param_names[2]
848	else:
849	param_name = param_names[1]
850	return model_name, param_name
851
852	def on_bumps_options(self, event=None):
853	"""
854	Open the bumps options panel.
855	"""
856	show_fit_config(self.parent, help=self.on_help)
857
858	def on_fitter_changed(self, event):
859	self._set_fitter_label(event.config)
860
861	def _set_fitter_label(self, config):
862	self.fit_panel.parent.SetTitle(self.fit_panel.window_name
863	+ " - Active Fitting Optimizer: "
864	+ config.selected_name)
865
866	def on_help(self, algorithm_id):
867	_TreeLocation = "user/sasgui/perspectives/fitting/optimizer.html"
868	_anchor = "#fit-"+algorithm_id
869	DocumentationWindow(self.parent, wx.ID_ANY, _TreeLocation, _anchor, "Optimizer Help")
870
871
872	def on_fit_results(self, event=None):
873	"""
874	Make the Fit Results panel visible.
875	"""
876	self.result_frame.Show()
877	self.result_frame.Raise()
878
879	def on_gpu_options(self, event=None):
880	"""
881	Make the Fit Results panel visible.
882	"""
883	dialog = GpuOptions(None, wx.ID_ANY, "")
884	dialog.Show()
885
886	def stop_fit(self, uid):
887	"""
888	Stop the fit
889	"""
890	if uid in self.fit_thread_list.keys():
891	calc_fit = self.fit_thread_list[uid]
892	if calc_fit is not None and calc_fit.isrunning():
893	calc_fit.stop()
894	msg = "Fit stop!"
895	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
896	del self.fit_thread_list[uid]
897	#set the fit button label of page when fit stop is trigger from
898	#simultaneous fit pane
899	sim_flag = self.sim_page is not None and uid == self.sim_page.uid
900	batch_flag = self.batch_page is not None and uid == self.batch_page.uid
901	if sim_flag or batch_flag:
902	for uid, value in self.page_finder.iteritems():
903	if value.get_scheduled() == 1:
904	if uid in self.fit_panel.opened_pages.keys():
905	panel = self.fit_panel.opened_pages[uid]
906	panel._on_fit_complete()
907
908	def set_smearer(self, uid, smearer, fid, qmin=None, qmax=None, draw=True,
909	enable_smearer=False):
910	"""
911	Get a smear object and store it to a fit problem of fid as id. If proper
912	flag is enable , will plot the theory with smearing information.
913
914	:param smearer: smear object to allow smearing data of id fid
915	:param enable_smearer: Define whether or not all (data, model) contained
916	in the structure of id uid will be smeared before fitting.
917	:param qmin: the maximum value of the theory plotting range
918	:param qmax: the maximum value of the theory plotting range
919	:param draw: Determine if the theory needs to be plot
920	"""
921	if uid not in self.page_finder.keys():
922	return
923	self.page_finder[uid].enable_smearing(flag=enable_smearer)
924	self.page_finder[uid].set_smearer(smearer, fid=fid)
925	if draw:
926	## draw model 1D with smeared data
927	data = self.page_finder[uid].get_fit_data(fid=fid)
928	if data is None:
929	msg = "set_mearer requires at least data.\n"
930	msg += "Got data = %s .\n" % str(data)
931	return
932	#raise ValueError, msg
933	model = self.page_finder[uid].get_model(fid=fid)
934	if model is None:
935	return
936	enable1D = issubclass(data.__class__, Data1D)
937	enable2D = issubclass(data.__class__, Data2D)
938	## if user has already selected a model to plot
939	## redraw the model with data smeared
940	smear = self.page_finder[uid].get_smearer(fid=fid)
941
942	# compute weight for the current data
943	weight = self.page_finder[uid].get_weight(fid=fid)
944
945	self.draw_model(model=model, data=data, page_id=uid, smearer=smear,
946	enable1D=enable1D, enable2D=enable2D,
947	qmin=qmin, qmax=qmax, weight=weight)
948
949	def draw_model(self, model, page_id, data=None, smearer=None,
950	enable1D=True, enable2D=False,
951	state=None,
952	fid=None,
953	toggle_mode_on=False,
954	qmin=None, qmax=None,
955	update_chisqr=True, weight=None, source='model'):
956	"""
957	Draw model.
958
959	:param model: the model to draw
960	:param name: the name of the model to draw
961	:param data: the data on which the model is based to be drawn
962	:param description: model's description
963	:param enable1D: if true enable drawing model 1D
964	:param enable2D: if true enable drawing model 2D
965	:param qmin: Range's minimum value to draw model
966	:param qmax: Range's maximum value to draw model
967	:param qstep: number of step to divide the x and y-axis
968	:param update_chisqr: update chisqr [bool]
969
970	"""
971	#self.weight = weight
972	if issubclass(data.__class__, Data1D) or not enable2D:
973	## draw model 1D with no loaded data
974	self._draw_model1D(model=model,
975	data=data,
976	page_id=page_id,
977	enable1D=enable1D,
978	smearer=smearer,
979	qmin=qmin,
980	qmax=qmax,
981	fid=fid,
982	weight=weight,
983	toggle_mode_on=toggle_mode_on,
984	state=state,
985	update_chisqr=update_chisqr,
986	source=source)
987	else:
988	## draw model 2D with no initial data
989	self._draw_model2D(model=model,
990	page_id=page_id,
991	data=data,
992	enable2D=enable2D,
993	smearer=smearer,
994	qmin=qmin,
995	qmax=qmax,
996	fid=fid,
997	weight=weight,
998	state=state,
999	toggle_mode_on=toggle_mode_on,
1000	update_chisqr=update_chisqr,
1001	source=source)
1002
1003	def onFit(self, uid):
1004	"""
1005	Get series of data, model, associates parameters and range and send then
1006	to series of fitters. Fit data and model, display result to
1007	corresponding panels.
1008	:param uid: id related to the panel currently calling this fit function.
1009	"""
1010	if uid is None:
1011	raise RuntimeError("no page to fit") # Should never happen
1012
1013	sim_page_uid = getattr(self.sim_page, 'uid', None)
1014	batch_page_uid = getattr(self.batch_page, 'uid', None)
1015
1016	if uid == sim_page_uid:
1017	fit_type = 'simultaneous'
1018	elif uid == batch_page_uid:
1019	fit_type = 'combined_batch'
1020	else:
1021	fit_type = 'single'
1022
1023	fitter_list = []
1024	sim_fitter = None
1025	if fit_type == 'simultaneous':
1026	# for simultaneous fitting only one fitter is needed
1027	sim_fitter = Fit()
1028	sim_fitter.fitter_id = self.sim_page.uid
1029	fitter_list.append(sim_fitter)
1030
1031	self.current_pg = None
1032	list_page_id = []
1033	fit_id = 0
1034	for page_id, page_info in self.page_finder.iteritems():
1035	# For simulfit (uid give with None), do for-loop
1036	# if uid is specified (singlefit), do it only on the page.
1037	if page_id in (sim_page_uid, batch_page_uid): continue
1038	if fit_type == "single" and page_id != uid: continue
1039
1040	try:
1041	if page_info.get_scheduled() == 1:
1042	page_info.nbr_residuals_computed = 0
1043	page = self.fit_panel.get_page_by_id(page_id)
1044	self.set_fit_weight(uid=page.uid,
1045	flag=page.get_weight_flag(),
1046	is2d=page._is_2D())
1047	if not page.param_toFit:
1048	msg = "No fitting parameters for %s" % page.window_caption
1049	evt = StatusEvent(status=msg, info="error", type="stop")
1050	wx.PostEvent(page.parent.parent, evt)
1051	return False
1052	if not page._update_paramv_on_fit():
1053	msg = "Fitting range or parameter values are"
1054	msg += " invalid in %s" % \
1055	page.window_caption
1056	evt = StatusEvent(status=msg, info="error", type="stop")
1057	wx.PostEvent(page.parent.parent, evt)
1058	return False
1059
1060	pars = [str(element[1]) for element in page.param_toFit]
1061	fitproblem_list = page_info.values()
1062	for fitproblem in fitproblem_list:
1063	if sim_fitter is None:
1064	fitter = Fit()
1065	fitter.fitter_id = page_id
1066	fitter_list.append(fitter)
1067	else:
1068	fitter = sim_fitter
1069	self._add_problem_to_fit(fitproblem=fitproblem,
1070	pars=pars,
1071	fitter=fitter,
1072	fit_id=fit_id)
1073	fit_id += 1
1074	list_page_id.append(page_id)
1075	page_info.clear_model_param()
1076	except KeyboardInterrupt:
1077	msg = "Fitting terminated"
1078	evt = StatusEvent(status=msg, info="info", type="stop")
1079	wx.PostEvent(self.parent, evt)
1080	return True
1081	except:
1082	raise
1083	msg = "Fitting error: %s" % str(sys.exc_value)
1084	evt = StatusEvent(status=msg, info="error", type="stop")
1085	wx.PostEvent(self.parent, evt)
1086	return False
1087	## If a thread is already started, stop it
1088	#if self.calc_fitis not None and self.calc_fit.isrunning():
1089	# self.calc_fit.stop()
1090	msg = "Fitting is in progress..."
1091	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1092
1093	#Handler used to display fit message
1094	handler = ConsoleUpdate(parent=self.parent,
1095	manager=self,
1096	improvement_delta=0.1)
1097
1098	# batch fit
1099	batch_inputs = {}
1100	batch_outputs = {}
1101	if fit_type == "simultaneous":
1102	page = self.sim_page
1103	elif fit_type == "combined_batch":
1104	page = self.batch_page
1105	else:
1106	page = self.fit_panel.get_page_by_id(uid)
1107	if page.batch_on:
1108	calc_fit = FitThread(handler=handler,
1109	fn=fitter_list,
1110	pars=pars,
1111	batch_inputs=batch_inputs,
1112	batch_outputs=batch_outputs,
1113	page_id=list_page_id,
1114	completefn=self._batch_fit_complete,
1115	reset_flag=self.batch_reset_flag)
1116	else:
1117	## Perform more than 1 fit at the time
1118	calc_fit = FitThread(handler=handler,
1119	fn=fitter_list,
1120	batch_inputs=batch_inputs,
1121	batch_outputs=batch_outputs,
1122	page_id=list_page_id,
1123	updatefn=handler.update_fit,
1124	completefn=self._fit_completed)
1125	#self.fit_thread_list[current_page_id] = calc_fit
1126	self.fit_thread_list[uid] = calc_fit
1127	calc_fit.queue()
1128	calc_fit.ready(2.5)
1129	msg = "Fitting is in progress..."
1130	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1131
1132	return True
1133
1134	def remove_plot(self, uid, fid=None, theory=False):
1135	"""
1136	remove model plot when a fit page is closed
1137	:param uid: the id related to the fitpage to close
1138	:param fid: the id of the fitproblem(data, model, range,etc)
1139	"""
1140	if uid not in self.page_finder.keys():
1141	return
1142	fitproblemList = self.page_finder[uid].get_fit_problem(fid)
1143	for fitproblem in fitproblemList:
1144	data = fitproblem.get_fit_data()
1145	model = fitproblem.get_model()
1146	plot_id = None
1147	if model is not None:
1148	plot_id = data.id + model.name
1149	if theory:
1150	plot_id = data.id + model.name
1151	group_id = data.group_id
1152	wx.PostEvent(self.parent, NewPlotEvent(id=plot_id,
1153	group_id=group_id,
1154	action='remove'))
1155
1156	def store_data(self, uid, data_list=None, caption=None):
1157	"""
1158	Receive a list of data and store them ans well as a caption of
1159	the fit page where they come from.
1160	:param uid: if related to a fit page
1161	:param data_list: list of data to fit
1162	:param caption: caption of the window related to these data
1163	"""
1164	if data_list is None:
1165	data_list = []
1166
1167	self.page_finder[uid].set_fit_data(data=data_list)
1168	if caption is not None:
1169	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1170
1171	def on_add_new_page(self, event=None):
1172	"""
1173	ask fit panel to create a new empty page
1174	"""
1175	try:
1176	page = self.fit_panel.add_empty_page()
1177	# add data associated to the page created
1178	if page is not None:
1179	evt = StatusEvent(status="Page Created", info="info")
1180	wx.PostEvent(self.parent, evt)
1181	else:
1182	msg = "Page was already Created"
1183	evt = StatusEvent(status=msg, info="warning")
1184	wx.PostEvent(self.parent, evt)
1185	except Exception:
1186	msg = "Creating Fit page: %s" % sys.exc_value
1187	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1188
1189	def add_fit_page(self, data):
1190	"""
1191	given a data, ask to the fitting panel to create a new fitting page,
1192	get this page and store it into the page_finder of this plug-in
1193	:param data: is a list of data
1194	"""
1195	page = self.fit_panel.set_data(data)
1196	# page could be None when loading state files
1197	if page is None:
1198	return page
1199	#append Data1D to the panel containing its theory
1200	#if theory already plotted
1201	if page.uid in self.page_finder:
1202	data = page.get_data()
1203	theory_data = self.page_finder[page.uid].get_theory_data(data.id)
1204	if issubclass(data.__class__, Data2D):
1205	data.group_id = wx.NewId()
1206	if theory_data is not None:
1207	group_id = str(page.uid) + " Model1D"
1208	wx.PostEvent(self.parent,
1209	NewPlotEvent(group_id=group_id,
1210	action="delete"))
1211	self.parent.update_data(prev_data=theory_data,
1212	new_data=data)
1213	else:
1214	if theory_data is not None:
1215	group_id = str(page.uid) + " Model2D"
1216	data.group_id = theory_data.group_id
1217	wx.PostEvent(self.parent,
1218	NewPlotEvent(group_id=group_id,
1219	action="delete"))
1220	self.parent.update_data(prev_data=theory_data,
1221	new_data=data)
1222	self.store_data(uid=page.uid, data_list=page.get_data_list(),
1223	caption=page.window_caption)
1224	if self.sim_page is not None and not self.batch_on:
1225	self.sim_page.draw_page()
1226	if self.batch_page is not None and self.batch_on:
1227	self.batch_page.draw_page()
1228
1229	return page
1230
1231	def _onEVT_SLICER_PANEL(self, event):
1232	"""
1233	receive and event telling to update a panel with a name starting with
1234	event.panel_name. this method update slicer panel
1235	for a given interactor.
1236
1237	:param event: contains type of slicer , parameters for updating
1238	the panel and panel_name to find the slicer 's panel concerned.
1239	"""
1240	event.panel_name
1241	for item in self.parent.panels:
1242	name = event.panel_name
1243	if self.parent.panels[item].window_caption.startswith(name):
1244	self.parent.panels[item].set_slicer(event.type, event.params)
1245
1246	#self.parent._mgr.Update()
1247
1248	def _closed_fitpage(self, event):
1249	"""
1250	request fitpanel to close a given page when its unique data is removed
1251	from the plot. close fitpage only when the a loaded data is removed
1252	"""
1253	if event is None or event.data is None:
1254	return
1255	if hasattr(event.data, "is_data"):
1256	if not event.data.is_data or \
1257	event.data.__class__.__name__ == "Data1D":
1258	self.fit_panel.close_page_with_data(event.data)
1259
1260	def _reset_schedule_problem(self, value=0, uid=None):
1261	"""
1262	unschedule or schedule all fitproblem to be fit
1263	"""
1264	# case that uid is not specified
1265	if uid is None:
1266	for page_id in self.page_finder.keys():
1267	self.page_finder[page_id].schedule_tofit(value)
1268	# when uid is given
1269	else:
1270	if uid in self.page_finder.keys():
1271	self.page_finder[uid].schedule_tofit(value)
1272
1273	def _add_problem_to_fit(self, fitproblem, pars, fitter, fit_id):
1274	"""
1275	Create and set fitter with series of data and model
1276	"""
1277	data = fitproblem.get_fit_data()
1278	model = fitproblem.get_model()
1279	smearer = fitproblem.get_smearer()
1280	qmin, qmax = fitproblem.get_range()
1281
1282	#Extra list of parameters and their constraints
1283	listOfConstraint = []
1284	param = fitproblem.get_model_param()
1285	if len(param) > 0:
1286	for item in param:
1287	## check if constraint
1288	if item[0] is not None and item[1] is not None:
1289	listOfConstraint.append((item[0], item[1]))
1290	new_model = model
1291	fitter.set_model(new_model, fit_id, pars, data=data,
1292	constraints=listOfConstraint)
1293	fitter.set_data(data=data, id=fit_id, smearer=smearer, qmin=qmin,
1294	qmax=qmax)
1295	fitter.select_problem_for_fit(id=fit_id, value=1)
1296
1297	def _onSelect(self, event):
1298	"""
1299	when Select data to fit a new page is created .Its reference is
1300	added to self.page_finder
1301	"""
1302	panel = self.plot_panel
1303	if panel is None:
1304	raise ValueError, "Fitting:_onSelect: NonType panel"
1305	Plugin.on_perspective(self, event=event)
1306	self.select_data(panel)
1307
1308	def select_data(self, panel):
1309	"""
1310	"""
1311	for plottable in panel.graph.plottables:
1312	if plottable.__class__.__name__ in ["Data1D", "Theory1D"]:
1313	data_id = panel.graph.selected_plottable
1314	if plottable == panel.plots[data_id]:
1315	data = plottable
1316	self.add_fit_page(data=[data])
1317	return
1318	else:
1319	data = plottable
1320	self.add_fit_page(data=[data])
1321
1322	def update_fit(self, result=None, msg=""):
1323	"""
1324	"""
1325	print("update_fit result", result)
1326
1327	def _batch_fit_complete(self, result, pars, page_id,
1328	batch_outputs, batch_inputs, elapsed=None):
1329	"""
1330	Display fit result in batch
1331	:param result: list of objects received from fitters
1332	:param pars: list of fitted parameters names
1333	:param page_id: list of page ids which called fit function
1334	:param elapsed: time spent at the fitting level
1335	"""
1336	uid = page_id[0]
1337	if uid in self.fit_thread_list.keys():
1338	del self.fit_thread_list[uid]
1339
1340	wx.CallAfter(self._update_fit_button, page_id)
1341	t1 = time.time()
1342	str_time = time.strftime("%a, %d %b %Y %H:%M:%S ", time.localtime(t1))
1343	msg = "Fit completed on %s \n" % str_time
1344	msg += "Duration time: %s s.\n" % str(elapsed)
1345	evt = StatusEvent(status=msg, info="info", type="stop")
1346	wx.PostEvent(self.parent, evt)
1347
1348	if batch_outputs is None:
1349	batch_outputs = {}
1350
1351	# format batch_outputs
1352	batch_outputs["Chi2"] = []
1353	#Don't like these loops
1354	# Need to create dictionary of all fitted parameters
1355	# since the number of parameters can differ between each fit result
1356	for list_res in result:
1357	for res in list_res:
1358	model, data = res.inputs[0]
1359	if model is not None and hasattr(model, "model"):
1360	model = model.model
1361	#get all fittable parameters of the current model
1362	for param in model.getParamList():
1363	if param not in batch_outputs.keys():
1364	batch_outputs[param] = []
1365	for param in model.getDispParamList():
1366	if not model.is_fittable(param) and \
1367	param in batch_outputs.keys():
1368	del batch_outputs[param]
1369	# Add fitted parameters and their error
1370	for param in res.param_list:
1371	if param not in batch_outputs.keys():
1372	batch_outputs[param] = []
1373	err_param = "error on %s" % str(param)
1374	if err_param not in batch_inputs.keys():
1375	batch_inputs[err_param] = []
1376	msg = ""
1377	for list_res in result:
1378	for res in list_res:
1379	pid = res.fitter_id
1380	model, data = res.inputs[0]
1381	correct_result = False
1382	if model is not None and hasattr(model, "model"):
1383	model = model.model
1384	if data is not None and hasattr(data, "sas_data"):
1385	data = data.sas_data
1386
1387	is_data2d = issubclass(data.__class__, Data2D)
1388	# Check consistency of arrays
1389	if not is_data2d:
1390	if len(res.theory) == len(res.index[res.index]) and \
1391	len(res.index) == len(data.y):
1392	correct_result = True
1393	else:
1394	copy_data = deepcopy(data)
1395	new_theory = copy_data.data
1396	new_theory[res.index] = res.theory
1397	new_theory[res.index == False] = np.nan
1398	correct_result = True
1399	# Get all fittable parameters of the current model
1400	param_list = model.getParamList()
1401	for param in model.getDispParamList():
1402	if '.' in param and param in param_list:
1403	# Ensure polydispersity results are displayed
1404	p1, p2 = param.split('.')
1405	if not model.is_fittable(p1) and not (p2 == 'width' and param in res.param_list)\
1406	and param in param_list:
1407	param_list.remove(param)
1408	elif not model.is_fittable(param) and \
1409	param in param_list:
1410	param_list.remove(param)
1411	if not correct_result or res.fitness is None or \
1412	not np.isfinite(res.fitness) or \
1413	np.any(res.pvec is None) or not \
1414	np.all(np.isfinite(res.pvec)):
1415	data_name = str(None)
1416	if data is not None:
1417	data_name = str(data.name)
1418	model_name = str(None)
1419	if model is not None:
1420	model_name = str(model.name)
1421	msg += "Data %s and Model %s did not fit.\n" % (data_name,
1422	model_name)
1423	ERROR = np.NAN
1424	cell = BatchCell()
1425	cell.label = res.fitness
1426	cell.value = res.fitness
1427	batch_outputs["Chi2"].append(ERROR)
1428	for param in param_list:
1429	# Save value of fixed parameters
1430	if param not in res.param_list:
1431	batch_outputs[str(param)].append(ERROR)
1432	else:
1433	# Save only fitted values
1434	batch_outputs[param].append(ERROR)
1435	batch_inputs["error on %s" % str(param)].append(ERROR)
1436	else:
1437	# TODO: Why sometimes res.pvec comes with np.float64?
1438	# probably from scipy lmfit
1439	if res.pvec.__class__ == np.float64:
1440	res.pvec = [res.pvec]
1441
1442	cell = BatchCell()
1443	cell.label = res.fitness
1444	cell.value = res.fitness
1445	batch_outputs["Chi2"].append(cell)
1446	# add parameters to batch_results
1447	for param in param_list:
1448	# save value of fixed parameters
1449	if param not in res.param_list:
1450	batch_outputs[str(param)].append(model.getParam(param))
1451	else:
1452	index = res.param_list.index(param)
1453	#save only fitted values
1454	batch_outputs[param].append(res.pvec[index])
1455	if res.stderr is not None and \
1456	len(res.stderr) == len(res.param_list):
1457	item = res.stderr[index]
1458	batch_inputs["error on %s" % param].append(item)
1459	else:
1460	batch_inputs["error on %s" % param].append('-')
1461	model.setParam(param, res.pvec[index])
1462	#fill the batch result with emtpy value if not in the current
1463	#model
1464	EMPTY = "-"
1465	for key in batch_outputs.keys():
1466	if key not in param_list and key not in ["Chi2", "Data"]:
1467	batch_outputs[key].append(EMPTY)
1468
1469	self.page_finder[pid].set_batch_result(batch_inputs=batch_inputs,
1470	batch_outputs=batch_outputs)
1471
1472	cpage = self.fit_panel.get_page_by_id(pid)
1473	cpage._on_fit_complete()
1474	self.page_finder[pid][data.id].set_result(res)
1475	fitproblem = self.page_finder[pid][data.id]
1476	qmin, qmax = fitproblem.get_range()
1477	plot_result = False
1478	if correct_result:
1479	if not is_data2d:
1480	self._complete1D(x=data.x[res.index], y=res.theory, page_id=pid,
1481	elapsed=None,
1482	index=res.index, model=model,
1483	weight=None, fid=data.id,
1484	toggle_mode_on=False, state=None,
1485	data=data, update_chisqr=False,
1486	source='fit', plot_result=plot_result)
1487	else:
1488	self._complete2D(image=new_theory, data=data,
1489	model=model,
1490	page_id=pid, elapsed=None,
1491	index=res.index,
1492	qmin=qmin,
1493	qmax=qmax, fid=data.id, weight=None,
1494	toggle_mode_on=False, state=None,
1495	update_chisqr=False,
1496	source='fit', plot_result=plot_result)
1497	self.on_set_batch_result(page_id=pid,
1498	fid=data.id,
1499	batch_outputs=batch_outputs,
1500	batch_inputs=batch_inputs)
1501
1502	evt = StatusEvent(status=msg, error="info", type="stop")
1503	wx.PostEvent(self.parent, evt)
1504	# Remove parameters that are not shown
1505	cpage = self.fit_panel.get_page_by_id(uid)
1506	tbatch_outputs = {}
1507	shownkeystr = cpage.get_copy_params()
1508	for key in batch_outputs.keys():
1509	if key in ["Chi2", "Data"] or shownkeystr.count(key) > 0:
1510	tbatch_outputs[key] = batch_outputs[key]
1511
1512	wx.CallAfter(self.parent.on_set_batch_result, tbatch_outputs,
1513	batch_inputs, self.sub_menu)
1514
1515	def on_set_batch_result(self, page_id, fid, batch_outputs, batch_inputs):
1516	"""
1517	"""
1518	pid = page_id
1519	if fid not in self.page_finder[pid]:
1520	return
1521	fitproblem = self.page_finder[pid][fid]
1522	index = self.page_finder[pid].nbr_residuals_computed - 1
1523	residuals = fitproblem.get_residuals()
1524	theory_data = fitproblem.get_theory_data()
1525	data = fitproblem.get_fit_data()
1526	model = fitproblem.get_model()
1527	#fill batch result information
1528	if "Data" not in batch_outputs.keys():
1529	batch_outputs["Data"] = []
1530	cell = BatchCell()
1531	cell.label = data.name
1532	cell.value = index
1533
1534	if theory_data is not None:
1535	#Suucessful fit
1536	theory_data.id = wx.NewId()
1537	theory_data.name = model.name + "[%s]" % str(data.name)
1538	if issubclass(theory_data.__class__, Data2D):
1539	group_id = wx.NewId()
1540	theory_data.group_id = group_id
1541	if group_id not in theory_data.list_group_id:
1542	theory_data.list_group_id.append(group_id)
1543
1544	try:
1545	# associate residuals plot
1546	if issubclass(residuals.__class__, Data2D):
1547	group_id = wx.NewId()
1548	residuals.group_id = group_id
1549	if group_id not in residuals.list_group_id:
1550	residuals.list_group_id.append(group_id)
1551	batch_outputs["Chi2"][index].object = [residuals]
1552	except:
1553	pass
1554
1555	cell.object = [data, theory_data]
1556	batch_outputs["Data"].append(cell)
1557	for key, value in data.meta_data.iteritems():
1558	if key not in batch_inputs.keys():
1559	batch_inputs[key] = []
1560	#if key.lower().strip() != "loader":
1561	batch_inputs[key].append(value)
1562	param = "temperature"
1563	if hasattr(data.sample, param):
1564	if param not in batch_inputs.keys():
1565	batch_inputs[param] = []
1566	batch_inputs[param].append(data.sample.temperature)
1567
1568	def _fit_completed(self, result, page_id, batch_outputs,
1569	batch_inputs=None, pars=None, elapsed=None):
1570	"""
1571	Display result of the fit on related panel(s).
1572	:param result: list of object generated when fit ends
1573	:param pars: list of names of parameters fitted
1574	:param page_id: list of page ids which called fit function
1575	:param elapsed: time spent at the fitting level
1576	"""
1577	t1 = time.time()
1578	str_time = time.strftime("%a, %d %b %Y %H:%M:%S ", time.localtime(t1))
1579	msg = "Fit completed on %s \n" % str_time
1580	msg += "Duration time: %s s.\n" % str(elapsed)
1581	evt = StatusEvent(status=msg, info="info", type="stop")
1582	wx.PostEvent(self.parent, evt)
1583	wx.PostEvent(self.result_panel, PlotResultEvent(result=result))
1584	wx.CallAfter(self._update_fit_button, page_id)
1585	result = result[0]
1586	self.fit_thread_list = {}
1587	if page_id is None:
1588	page_id = []
1589	## fit more than 1 model at the same time
1590	try:
1591	index = 0
1592	# Update potential simfit page(s)
1593	if self.sim_page is not None:
1594	self.sim_page._on_fit_complete()
1595	if self.batch_page:
1596	self.batch_page._on_fit_complete()
1597	# Update all fit pages
1598	for uid in page_id:
1599	res = result[index]
1600	fit_msg = res.mesg
1601	if res.fitness is None or \
1602	not np.isfinite(res.fitness) or \
1603	np.any(res.pvec is None) or \
1604	not np.all(np.isfinite(res.pvec)):
1605	fit_msg += "\nFitting did not converge!!!"
1606	wx.CallAfter(self._update_fit_button, page_id)
1607	else:
1608	#set the panel when fit result are float not list
1609	if res.pvec.__class__ == np.float64:
1610	pvec = [res.pvec]
1611	else:
1612	pvec = res.pvec
1613	if res.stderr.__class__ == np.float64:
1614	stderr = [res.stderr]
1615	else:
1616	stderr = res.stderr
1617	cpage = self.fit_panel.get_page_by_id(uid)
1618	# Make sure we got all results
1619	#(CallAfter is important to MAC)
1620	try:
1621	#if res is not None:
1622	wx.CallAfter(cpage.onsetValues, res.fitness,
1623	res.param_list,
1624	pvec, stderr)
1625	index += 1
1626	wx.CallAfter(cpage._on_fit_complete)
1627	except KeyboardInterrupt:
1628	fit_msg += "\nSingular point: Fitting stopped."
1629	except Exception:
1630	fit_msg += "\nSingular point: Fitting error occurred."
1631	if fit_msg:
1632	evt = StatusEvent(status=fit_msg, info="warning", type="stop")
1633	wx.PostEvent(self.parent, evt)
1634
1635	except Exception:
1636	msg = ("Fit completed but the following error occurred: %s"
1637	% sys.exc_value)
1638	#msg = "\n".join((traceback.format_exc(), msg))
1639	evt = StatusEvent(status=msg, info="warning", type="stop")
1640	wx.PostEvent(self.parent, evt)
1641
1642	def _update_fit_button(self, page_id):
1643	"""
1644	Update Fit button when fit stopped
1645
1646	: parameter page_id: fitpage where the button is
1647	"""
1648	if page_id.__class__.__name__ != 'list':
1649	page_id = [page_id]
1650	for uid in page_id:
1651	page = self.fit_panel.get_page_by_id(uid)
1652	page._on_fit_complete()
1653
1654	def _on_show_panel(self, event):
1655	"""
1656	"""
1657	pass
1658
1659	def on_reset_batch_flag(self, event):
1660	"""
1661	Set batch_reset_flag
1662	"""
1663	event.Skip()
1664	if self.menu1 is None:
1665	return
1666	menu_item = self.menu1.FindItemById(self.id_reset_flag)
1667	flag = menu_item.IsChecked()
1668	if not flag:
1669	menu_item.Check(False)
1670	self.batch_reset_flag = True
1671	else:
1672	menu_item.Check(True)
1673	self.batch_reset_flag = False
1674
1675	## post a message to status bar
1676	msg = "Set Chain Fitting: %s" % str(not self.batch_reset_flag)
1677	wx.PostEvent(self.parent, StatusEvent(status=msg))
1678
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	self.slicer_panels.append(event.panel)
1689	# Set group ID if available
1690	event_id = self.parent.popup_panel(event.panel)
1691	event.panel.uid = event_id
1692	self.mypanels.append(event.panel)
1693
1694	def _onclearslicer(self, event):
1695	"""
1696	Clear the boxslicer when close the panel associate with this slicer
1697	"""
1698	name = event.GetEventObject().frame.GetTitle()
1699	for panel in self.slicer_panels:
1700	if panel.window_caption == name:
1701
1702	for item in self.parent.panels:
1703	if hasattr(self.parent.panels[item], "uid"):
1704	if self.parent.panels[item].uid == panel.base.uid:
1705	self.parent.panels[item].onClearSlicer(event)
1706	#self.parent._mgr.Update()
1707	break
1708	break
1709
1710	def _on_model_panel(self, evt):
1711	"""
1712	react to model selection on any combo box or model menu.plot the model
1713
1714	:param evt: wx.combobox event
1715
1716	"""
1717	model = evt.model
1718	uid = evt.uid
1719	qmin = evt.qmin
1720	qmax = evt.qmax
1721	caption = evt.caption
1722	enable_smearer = evt.enable_smearer
1723	if model is None:
1724	return
1725	if uid not in self.page_finder.keys():
1726	return
1727	# save the name containing the data name with the appropriate model
1728	self.page_finder[uid].set_model(model)
1729	self.page_finder[uid].enable_smearing(enable_smearer)
1730	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax)
1731	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1732	if self.sim_page is not None and not self.batch_on:
1733	self.sim_page.draw_page()
1734	if self.batch_page is not None and self.batch_on:
1735	self.batch_page.draw_page()
1736
1737	def _update1D(self, x, output):
1738	"""
1739	Update the output of plotting model 1D
1740	"""
1741	msg = "Plot updating ... "
1742	wx.PostEvent(self.parent, StatusEvent(status=msg, type="update"))
1743
1744	def create_theory_1D(self, x, y, page_id, model, data, state,
1745	data_description, data_id, dy=None):
1746	"""
1747	Create a theory object associate with an existing Data1D
1748	and add it to the data manager.
1749	@param x: x-values of the data
1750	@param y: y_values of the data
1751	@param page_id: fit page ID
1752	@param model: model used for fitting
1753	@param data: Data1D object to create the theory for
1754	@param state: model state
1755	@param data_description: title to use in the data manager
1756	@param data_id: unique data ID
1757	"""
1758	new_plot = Data1D(x=x, y=y)
1759	if dy is None:
1760	new_plot.is_data = False
1761	new_plot.dy = np.zeros(len(y))
1762	# If this is a theory curve, pick the proper symbol to make it a curve
1763	new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
1764	else:
1765	new_plot.is_data = True
1766	new_plot.dy = dy
1767	new_plot.interactive = True
1768	new_plot.dx = None
1769	new_plot.dxl = None
1770	new_plot.dxw = None
1771	_yaxis, _yunit = data.get_yaxis()
1772	_xaxis, _xunit = data.get_xaxis()
1773	new_plot.title = data.name
1774	new_plot.group_id = data.group_id
1775	if new_plot.group_id is None:
1776	new_plot.group_id = data.group_id
1777	new_plot.id = data_id
1778	# Find if this theory was already plotted and replace that plot given
1779	# the same id
1780	self.page_finder[page_id].get_theory_data(fid=data.id)
1781
1782	if data.is_data:
1783	data_name = str(data.name)
1784	else:
1785	data_name = str(model.__class__.__name__)
1786
1787	new_plot.name = data_description + " [" + data_name + "]"
1788	new_plot.xaxis(_xaxis, _xunit)
1789	new_plot.yaxis(_yaxis, _yunit)
1790	self.page_finder[page_id].set_theory_data(data=new_plot,
1791	fid=data.id)
1792	self.parent.update_theory(data_id=data.id, theory=new_plot,
1793	state=state)
1794	return new_plot
1795
1796	def _complete1D(self, x, y, page_id, elapsed, index, model,
1797	weight=None, fid=None,
1798	toggle_mode_on=False, state=None,
1799	data=None, update_chisqr=True,
1800	source='model', plot_result=True,
1801	unsmeared_model=None, unsmeared_data=None,
1802	unsmeared_error=None, sq_model=None, pq_model=None):
1803	"""
1804	Complete plotting 1D data
1805	@param unsmeared_model: fit model, without smearing
1806	@param unsmeared_data: data, rescaled to unsmeared model
1807	@param unsmeared_error: data error, rescaled to unsmeared model
1808	"""
1809	number_finite = np.count_nonzero(np.isfinite(y))
1810	np.nan_to_num(y)
1811	new_plot = self.create_theory_1D(x, y, page_id, model, data, state,
1812	data_description=model.name,
1813	data_id=str(page_id) + " " + data.name)
1814	plots_to_update = [] # List of plottables that have changed since last calculation
1815	# Create the new theories
1816	if unsmeared_model is not None:
1817	unsmeared_model_plot = self.create_theory_1D(x, unsmeared_model,
1818	page_id, model, data, state,
1819	data_description=model.name + " unsmeared",
1820	data_id=str(page_id) + " " + data.name + " unsmeared")
1821	plots_to_update.append(unsmeared_model_plot)
1822
1823	if unsmeared_data is not None and unsmeared_error is not None:
1824	unsmeared_data_plot = self.create_theory_1D(x, unsmeared_data,
1825	page_id, model, data, state,
1826	data_description="Data unsmeared",
1827	data_id="Data " + data.name + " unsmeared",
1828	dy=unsmeared_error)
1829	plots_to_update.append(unsmeared_data_plot)
1830	if sq_model is not None and pq_model is not None:
1831	sq_id = str(page_id) + " " + data.name + " S(q)"
1832	sq_plot = self.create_theory_1D(x, sq_model, page_id, model, data, state,
1833	data_description=model.name + " S(q)",
1834	data_id=sq_id)
1835	plots_to_update.append(sq_plot)
1836	pq_id = str(page_id) + " " + data.name + " P(q)"
1837	pq_plot = self.create_theory_1D(x, pq_model, page_id, model, data, state,
1838	data_description=model.name + " P(q)",
1839	data_id=pq_id)
1840	plots_to_update.append(pq_plot)
1841	# Update the P(Q), S(Q) and unsmeared theory plots if they exist
1842	wx.PostEvent(self.parent, NewPlotEvent(plots=plots_to_update,
1843	action='update'))
1844
1845	current_pg = self.fit_panel.get_page_by_id(page_id)
1846	title = new_plot.title
1847	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
1848	if not batch_on:
1849	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=str(title)))
1850	elif plot_result:
1851	top_data_id = self.fit_panel.get_page_by_id(page_id).data.id
1852	if data.id == top_data_id:
1853	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=str(title)))
1854	caption = current_pg.window_caption
1855	self.page_finder[page_id].set_fit_tab_caption(caption=caption)
1856
1857	self.page_finder[page_id].set_theory_data(data=new_plot,
1858	fid=data.id)
1859	if toggle_mode_on:
1860	wx.PostEvent(self.parent,
1861	NewPlotEvent(group_id=str(page_id) + " Model2D",
1862	action="Hide"))
1863	else:
1864	if update_chisqr:
1865	output = self._cal_chisqr(data=data,
1866	fid=fid,
1867	weight=weight,
1868	page_id=page_id,
1869	index=index)
1870	wx.PostEvent(current_pg, Chi2UpdateEvent(output=output))
1871	else:
1872	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1873	index=index, weight=weight)
1874
1875	if not number_finite:
1876	logger.error("Using the present parameters the model does not return any finite value. ")
1877	msg = "Computing Error: Model did not return any finite value."
1878	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1879	else:
1880	msg = "Computation completed!"
1881	if number_finite != y.size:
1882	msg += ' PROBLEM: For some Q values the model returns non finite intensities!'
1883	logger.error("For some Q values the model returns non finite intensities.")
1884	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1885
1886	def _calc_exception(self, etype, value, tb):
1887	"""
1888	Handle exception from calculator by posting it as an error.
1889	"""
1890	logger.error("".join(traceback.format_exception(etype, value, tb)))
1891	msg = traceback.format_exception(etype, value, tb, limit=1)
1892	evt = StatusEvent(status="".join(msg), type="stop", info="error")
1893	wx.PostEvent(self.parent, evt)
1894
1895	def _update2D(self, output, time=None):
1896	"""
1897	Update the output of plotting model
1898	"""
1899	msg = "Plot updating ... "
1900	wx.PostEvent(self.parent, StatusEvent(msg, type="update"))
1901
1902	def _complete2D(self, image, data, model, page_id, elapsed, index, qmin,
1903	qmax, fid=None, weight=None, toggle_mode_on=False, state=None,
1904	update_chisqr=True, source='model', plot_result=True):
1905	"""
1906	Complete get the result of modelthread and create model 2D
1907	that can be plot.
1908	"""
1909	number_finite = np.count_nonzero(np.isfinite(image))
1910	np.nan_to_num(image)
1911	new_plot = Data2D(image=image, err_image=data.err_data)
1912	new_plot.name = model.name + '2d'
1913	new_plot.title = "Analytical model 2D "
1914	new_plot.id = str(page_id) + " " + data.name
1915	new_plot.group_id = str(page_id) + " Model2D"
1916	new_plot.detector = data.detector
1917	new_plot.source = data.source
1918	new_plot.is_data = False
1919	new_plot.qx_data = data.qx_data
1920	new_plot.qy_data = data.qy_data
1921	new_plot.q_data = data.q_data
1922	new_plot.mask = data.mask
1923	## plot boundaries
1924	new_plot.ymin = data.ymin
1925	new_plot.ymax = data.ymax
1926	new_plot.xmin = data.xmin
1927	new_plot.xmax = data.xmax
1928	title = data.title
1929
1930	new_plot.is_data = False
1931	if data.is_data:
1932	data_name = str(data.name)
1933	else:
1934	data_name = str(model.__class__.__name__) + '2d'
1935
1936	if len(title) > 1:
1937	new_plot.title = "Model2D for %s " % model.name + data_name
1938	new_plot.name = model.name + " [" + \
1939	data_name + "]"
1940	theory_data = deepcopy(new_plot)
1941
1942	self.page_finder[page_id].set_theory_data(data=theory_data,
1943	fid=data.id)
1944	self.parent.update_theory(data_id=data.id,
1945	theory=new_plot,
1946	state=state)
1947	current_pg = self.fit_panel.get_page_by_id(page_id)
1948	title = new_plot.title
1949	if not source == 'fit' and plot_result:
1950	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))
1951	if toggle_mode_on:
1952	wx.PostEvent(self.parent,
1953	NewPlotEvent(group_id=str(page_id) + " Model1D",
1954	action="Hide"))
1955	else:
1956	# Chisqr in fitpage
1957	if update_chisqr:
1958	output = self._cal_chisqr(data=data,
1959	weight=weight,
1960	fid=fid,
1961	page_id=page_id,
1962	index=index)
1963	wx.PostEvent(current_pg, Chi2UpdateEvent(output=output))
1964	else:
1965	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1966	index=index, weight=weight)
1967
1968	if not number_finite:
1969	logger.error("Using the present parameters the model does not return any finite value. ")
1970	msg = "Computing Error: Model did not return any finite value."
1971	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1972	else:
1973	msg = "Computation completed!"
1974	if number_finite != image.size:
1975	msg += ' PROBLEM: For some Qx,Qy values the model returns non finite intensities!'
1976	logger.error("For some Qx,Qy values the model returns non finite intensities.")
1977	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1978
1979	def _draw_model2D(self, model, page_id, qmin,
1980	qmax,
1981	data=None, smearer=None,
1982	description=None, enable2D=False,
1983	state=None,
1984	fid=None,
1985	weight=None,
1986	toggle_mode_on=False,
1987	update_chisqr=True, source='model'):
1988	"""
1989	draw model in 2D
1990
1991	:param model: instance of the model to draw
1992	:param description: the description of the model
1993	:param enable2D: when True allows to draw model 2D
1994	:param qmin: the minimum value to draw model 2D
1995	:param qmax: the maximum value to draw model 2D
1996	:param qstep: the number of division of Qx and Qy of the model to draw
1997
1998	"""
1999	if not enable2D:
2000	return None
2001	try:
2002	## If a thread is already started, stop it
2003	if (self.calc_2D is not None) and self.calc_2D.isrunning():
2004	self.calc_2D.stop()
2005	## stop just raises a flag to tell the thread to kill
2006	## itself -- see the fix in Calc1D implemented to fix
2007	## an actual problem. Seems the fix should also go here
2008	## and may be the cause of other noted instabilities
2009	##
2010	## -PDB August 12, 2014
2011	while self.calc_2D.isrunning():
2012	time.sleep(0.1)
2013	self.calc_2D = Calc2D(model=model,
2014	data=data,
2015	page_id=page_id,
2016	smearer=smearer,
2017	qmin=qmin,
2018	qmax=qmax,
2019	weight=weight,
2020	fid=fid,
2021	toggle_mode_on=toggle_mode_on,
2022	state=state,
2023	completefn=self._complete2D,
2024	update_chisqr=update_chisqr,
2025	exception_handler=self._calc_exception,
2026	source=source)
2027	self.calc_2D.queue()
2028	except:
2029	raise
2030
2031	def _draw_model1D(self, model, page_id, data,
2032	qmin, qmax, smearer=None,
2033	state=None, weight=None, fid=None,
2034	toggle_mode_on=False, update_chisqr=True, source='model',
2035	enable1D=True):
2036	"""
2037	Draw model 1D from loaded data1D
2038
2039	:param data: loaded data
2040	:param model: the model to plot
2041
2042	"""
2043	if not enable1D:
2044	return
2045	try:
2046	## If a thread is already started, stop it
2047	if (self.calc_1D is not None) and self.calc_1D.isrunning():
2048	self.calc_1D.stop()
2049	## stop just raises the flag -- the thread is supposed to
2050	## then kill itself but cannot. Paul Kienzle came up with
2051	## this fix to prevent threads from stepping on each other
2052	## which was causing a simple custom plugin model to crash
2053	##Sasview.
2054	## We still don't know why the fit sometimes lauched a second
2055	## thread -- something which should also be investigated.
2056	## The thread approach was implemented in order to be able
2057	## to lauch a computation in a separate thread from the GUI so
2058	## that the GUI can still respond to user input including
2059	## a request to stop the computation.
2060	## It seems thus that the whole thread approach used here
2061	## May need rethinking
2062	##
2063	## -PDB August 12, 2014
2064	while self.calc_1D.isrunning():
2065	time.sleep(0.1)
2066	self.calc_1D = Calc1D(data=data,
2067	model=model,
2068	page_id=page_id,
2069	qmin=qmin,
2070	qmax=qmax,
2071	smearer=smearer,
2072	state=state,
2073	weight=weight,
2074	fid=fid,
2075	toggle_mode_on=toggle_mode_on,
2076	completefn=self._complete1D,
2077	#updatefn = self._update1D,
2078	update_chisqr=update_chisqr,
2079	exception_handler=self._calc_exception,
2080	source=source)
2081	self.calc_1D.queue()
2082	except:
2083	msg = " Error occurred when drawing %s Model 1D: " % model.name
2084	msg += " %s" % sys.exc_value
2085	wx.PostEvent(self.parent, StatusEvent(status=msg))
2086
2087	def _cal_chisqr(self, page_id, data, weight, fid=None, index=None):
2088	"""
2089	Get handy Chisqr using the output from draw1D and 2D,
2090	instead of calling expansive CalcChisqr in guithread
2091	"""
2092	try:
2093	data_copy = deepcopy(data)
2094	except:
2095	return
2096	# default chisqr
2097	chisqr = None
2098	#to compute chisq make sure data has valid data
2099	# return None if data is None
2100	if not check_data_validity(data_copy) or data_copy is None:
2101	return chisqr
2102
2103	# Get data: data I, theory I, and data dI in order
2104	if data_copy.__class__.__name__ == "Data2D":
2105	if index is None:
2106	index = np.ones(len(data_copy.data), dtype=bool)
2107	if weight is not None:
2108	data_copy.err_data = weight
2109	# get rid of zero error points
2110	index = index & (data_copy.err_data != 0)
2111	index = index & (np.isfinite(data_copy.data))
2112	fn = data_copy.data[index]
2113	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2114	if theory_data is None:
2115	return chisqr
2116	gn = theory_data.data[index]
2117	en = data_copy.err_data[index]
2118	else:
2119	# 1 d theory from model_thread is only in the range of index
2120	if index is None:
2121	index = np.ones(len(data_copy.y), dtype=bool)
2122	if weight is not None:
2123	data_copy.dy = weight
2124	if data_copy.dy is None or data_copy.dy == []:
2125	dy = np.ones(len(data_copy.y))
2126	else:
2127	## Set consistently w/AbstractFitengine:
2128	# But this should be corrected later.
2129	dy = deepcopy(data_copy.dy)
2130	dy[dy == 0] = 1
2131	fn = data_copy.y[index]
2132
2133	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2134	if theory_data is None:
2135	return chisqr
2136	gn = theory_data.y
2137	en = dy[index]
2138
2139	# residual
2140	try:
2141	res = (fn - gn) / en
2142	except ValueError:
2143	print("Unmatch lengths %s, %s, %s" % (len(fn), len(gn), len(en)))
2144	return
2145
2146	residuals = res[np.isfinite(res)]
2147	# get chisqr only w/finite
2148	chisqr = np.average(residuals * residuals)
2149
2150	self._plot_residuals(page_id=page_id, data=data_copy,
2151	fid=fid,
2152	weight=weight, index=index)
2153
2154	return chisqr
2155
2156	def _plot_residuals(self, page_id, weight, fid=None,
2157	data=None, index=None):
2158	"""
2159	Plot the residuals
2160
2161	:param data: data
2162	:param index: index array (bool)
2163	: Note: this is different from the residuals in cal_chisqr()
2164	"""
2165	data_copy = deepcopy(data)
2166	# Get data: data I, theory I, and data dI in order
2167	if data_copy.__class__.__name__ == "Data2D":
2168	# build residuals
2169	residuals = Data2D()
2170	#residuals.copy_from_datainfo(data)
2171	# Not for trunk the line below, instead use the line above
2172	data_copy.clone_without_data(len(data_copy.data), residuals)
2173	residuals.data = None
2174	fn = data_copy.data
2175	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2176	gn = theory_data.data
2177	if weight is None:
2178	en = data_copy.err_data
2179	else:
2180	en = weight
2181	residuals.data = (fn - gn) / en
2182	residuals.qx_data = data_copy.qx_data
2183	residuals.qy_data = data_copy.qy_data
2184	residuals.q_data = data_copy.q_data
2185	residuals.err_data = np.ones(len(residuals.data))
2186	residuals.xmin = min(residuals.qx_data)
2187	residuals.xmax = max(residuals.qx_data)
2188	residuals.ymin = min(residuals.qy_data)
2189	residuals.ymax = max(residuals.qy_data)
2190	residuals.q_data = data_copy.q_data
2191	residuals.mask = data_copy.mask
2192	residuals.scale = 'linear'
2193	# check the lengths
2194	if len(residuals.data) != len(residuals.q_data):
2195	return
2196	else:
2197	# 1 d theory from model_thread is only in the range of index
2198	if data_copy.dy is None or data_copy.dy == []:
2199	dy = np.ones(len(data_copy.y))
2200	else:
2201	if weight is None:
2202	dy = np.ones(len(data_copy.y))
2203	## Set consitently w/AbstractFitengine:
2204	## But this should be corrected later.
2205	else:
2206	dy = weight
2207	dy[dy == 0] = 1
2208	fn = data_copy.y[index]
2209	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2210	gn = theory_data.y
2211	en = dy[index]
2212	# build residuals
2213	residuals = Data1D()
2214	try:
2215	residuals.y = (fn - gn) / en
2216	except:
2217	msg = "ResidualPlot Error: different # of data points in theory"
2218	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
2219	residuals.y = (fn - gn[index]) / en
2220	residuals.x = data_copy.x[index]
2221	residuals.dy = np.ones(len(residuals.y))
2222	residuals.dx = None
2223	residuals.dxl = None
2224	residuals.dxw = None
2225	residuals.ytransform = 'y'
2226	# For latter scale changes
2227	residuals.xaxis('\\rm{Q} ', 'A^{-1}')
2228	residuals.yaxis('\\rm{Residuals} ', 'normalized')
2229	theory_name = str(theory_data.name.split()[0])
2230	new_plot = residuals
2231	new_plot.name = "Residuals for " + str(theory_name) + "[" + \
2232	str(data.name) + "]"
2233	## allow to highlight data when plotted
2234	new_plot.interactive = True
2235	## when 2 data have the same id override the 1 st plotted
2236	new_plot.id = "res" + str(data_copy.id) + str(theory_name)
2237	##group_id specify on which panel to plot this data
2238	group_id = self.page_finder[page_id].get_graph_id()
2239	if group_id is None:
2240	group_id = data.group_id
2241	new_plot.group_id = "res" + str(group_id)
2242	#new_plot.is_data = True
2243	##post data to plot
2244	title = new_plot.name
2245	self.page_finder[page_id].set_residuals(residuals=new_plot,
2246	fid=data.id)
2247	self.parent.update_theory(data_id=data.id, theory=new_plot)
2248	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
2249	if not batch_on:
2250	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))

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SasView

source: sasview/src/sas/sasgui/perspectives/fitting/fitting.py @ 5ae083b

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