fitting.py @ 1c206d9

magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 1c206d9 was 9706d88, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
merge fixups
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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	custom_model = 'Plugin Models'
342	try:
343	# Update edit menus
344	self.set_edit_menu_helper(self.parent, self.edit_custom_model)
345	self.set_edit_menu_helper(self.parent, self.delete_custom_model)
346	new_pmodel_list = self.fit_panel.reset_pmodel_list()
347	if not new_pmodel_list:
348	return
349	# Set the new plugin model list for all fit pages
350	for uid, page in self.fit_panel.opened_pages.iteritems():
351	if hasattr(page, "formfactorbox"):
352	page.model_list_box = new_pmodel_list
353	mod_cat = page.categorybox.GetStringSelection()
354	if mod_cat == custom_model:
355	box = page.formfactorbox
356	model_name = box.GetValue()
357	model = (box.GetClientData(box.GetCurrentSelection())
358	if model_name else None)
359	page._show_combox_helper()
360	new_index = box.FindString(model_name)
361	new_model = (box.GetClientData(new_index)
362	if new_index >= 0 else None)
363	if new_index >= 0:
364	box.SetStringSelection(model_name)
365	else:
366	box.SetStringSelection('')
367	if model and new_model != model:
368	page._on_select_model(keep_pars=True)
369	if hasattr(page, "structurebox"):
370	selected_name = page.structurebox.GetStringSelection()
371
372	page.structurebox.Clear()
373	page.initialize_combox()
374
375	index = page.structurebox.FindString(selected_name)
376	if index == -1:
377	index = 0
378	page.structurebox.SetSelection(index)
379	page._on_select_model()
380	except Exception:
381	logger.error("update_custom_combo: %s", sys.exc_value)
382
383	def set_edit_menu(self, owner):
384	"""
385	Set list of the edit model menu labels
386	"""
387	wx_id = wx.NewId()
388	#new_model_menu = wx.Menu()
389	self.edit_model_menu.Append(wx_id, 'New Plugin Model',
390	'Add a new model function')
391	wx.EVT_MENU(owner, wx_id, self.make_new_model)
392
393	wx_id = wx.NewId()
394	self.edit_model_menu.Append(wx_id, 'Sum\|Multi(p1, p2)',
395	'Sum of two model functions')
396	wx.EVT_MENU(owner, wx_id, self.make_sum_model)
397
398	e_id = wx.NewId()
399	self.edit_menu = wx.Menu()
400	self.edit_model_menu.AppendMenu(e_id,
401	'Advanced Plugin Editor', self.edit_menu)
402	self.set_edit_menu_helper(owner, self.edit_custom_model)
403
404	d_id = wx.NewId()
405	self.delete_menu = wx.Menu()
406	self.edit_model_menu.AppendMenu(d_id,
407	'Delete Plugin Models', self.delete_menu)
408	self.set_edit_menu_helper(owner, self.delete_custom_model)
409
410	wx_id = wx.NewId()
411	self.edit_model_menu.Append(wx_id, 'Load Plugin Models',
412	'(Re)Load all models present in user plugin_models folder')
413	wx.EVT_MENU(owner, wx_id, self.load_plugin_models)
414
415	def set_edit_menu_helper(self, owner=None, menu=None):
416	"""
417	help for setting list of the edit model menu labels
418	"""
419	if menu is None:
420	menu = self.edit_custom_model
421	list_fnames = os.listdir(models.find_plugins_dir())
422	list_fnames.sort()
423	for f_item in list_fnames:
424	name = os.path.basename(f_item)
425	toks = os.path.splitext(name)
426	if toks[-1] == '.py' and not toks[0] == '__init__':
427	if menu == self.edit_custom_model:
428	if toks[0] == 'easy_sum_of_p1_p2':
429	continue
430	submenu = self.edit_menu
431	else:
432	submenu = self.delete_menu
433	has_file = False
434	for item in submenu.GetMenuItems():
435	if name == submenu.GetLabel(item.GetId()):
436	has_file = True
437	if not has_file:
438	wx_id = wx.NewId()
439	submenu.Append(wx_id, name)
440	wx.EVT_MENU(owner, wx_id, menu)
441	has_file = False
442
443	def put_icon(self, frame):
444	"""
445	Put icon in the frame title bar
446	"""
447	if hasattr(frame, "IsIconized"):
448	if not frame.IsIconized():
449	try:
450	icon = self.parent.GetIcon()
451	frame.SetIcon(icon)
452	except:
453	pass
454
455	def on_add_sim_page(self, event):
456	"""
457	Create a page to access simultaneous fit option
458	"""
459	event_id = event.GetId()
460	caption = "Const & Simul Fit"
461	page = self.sim_page
462	if event_id == self.id_batchfit:
463	caption = "Combined Batch"
464	page = self.batch_page
465
466	def set_focus_page(page):
467	page.Show(True)
468	page.Refresh()
469	page.SetFocus()
470	#self.parent._mgr.Update()
471	msg = "%s already opened\n" % str(page.window_caption)
472	wx.PostEvent(self.parent, StatusEvent(status=msg))
473
474	if page is not None:
475	return set_focus_page(page)
476	if caption == "Const & Simul Fit":
477	self.sim_page = self.fit_panel.add_sim_page(caption=caption)
478	else:
479	self.batch_page = self.fit_panel.add_sim_page(caption=caption)
480
481	def get_context_menu(self, plotpanel=None):
482	"""
483	Get the context menu items available for P(r).them allow fitting option
484	for Data2D and Data1D only.
485
486	:param graph: the Graph object to which we attach the context menu
487
488	:return: a list of menu items with call-back function
489
490	:note: if Data1D was generated from Theory1D
491	the fitting option is not allowed
492
493	"""
494	self.plot_panel = plotpanel
495	graph = plotpanel.graph
496	fit_option = "Select data for fitting"
497	fit_hint = "Dialog with fitting parameters "
498
499	if graph.selected_plottable not in plotpanel.plots:
500	return []
501	item = plotpanel.plots[graph.selected_plottable]
502	if item.__class__.__name__ is "Data2D":
503	if hasattr(item, "is_data"):
504	if item.is_data:
505	return [[fit_option, fit_hint, self._onSelect]]
506	else:
507	return []
508	return [[fit_option, fit_hint, self._onSelect]]
509	else:
510
511	# if is_data is true , this in an actual data loaded
512	#else it is a data created from a theory model
513	if hasattr(item, "is_data"):
514	if item.is_data:
515	return [[fit_option, fit_hint, self._onSelect]]
516	else:
517	return []
518	return [[fit_option, fit_hint, self._onSelect]]
519	return []
520
521	def get_panels(self, parent):
522	"""
523	Create and return a list of panel objects
524	"""
525	self.parent = parent
526	#self.parent.Bind(EVT_FITSTATE_UPDATE, self.on_set_state_helper)
527	# Creation of the fit panel
528	self.frame = MDIFrame(self.parent, None, 'None', (100, 200))
529	self.fit_panel = FitPanel(parent=self.frame, manager=self)
530	self.frame.set_panel(self.fit_panel)
531	self._frame_set_helper()
532	self.on_add_new_page(event=None)
533	#Set the manager for the main panel
534	self.fit_panel.set_manager(self)
535	# List of windows used for the perspective
536	self.perspective = []
537	self.perspective.append(self.fit_panel.window_name)
538
539	self.result_frame = MDIFrame(self.parent, None, ResultPanel.window_caption, (220, 200))
540	self.result_panel = ResultPanel(parent=self.result_frame, manager=self)
541	self.perspective.append(self.result_panel.window_name)
542
543	#index number to create random model name
544	self.index_model = 0
545	self.index_theory = 0
546	self.parent.Bind(EVT_SLICER_PANEL, self._on_slicer_event)
547	self.parent.Bind(EVT_SLICER_PARS_UPDATE, self._onEVT_SLICER_PANEL)
548
549	# CRUFT: EVT_FITTER_CHANGED is not None for bumps 0.7.5.9 and above
550	if EVT_FITTER_CHANGED is not None:
551	self.parent.Bind(EVT_FITTER_CHANGED, self.on_fitter_changed)
552	self._set_fitter_label(bumps.options.FIT_CONFIG)
553
554	#self.parent._mgr.Bind(wx.aui.EVT_AUI_PANE_CLOSE,self._onclearslicer)
555	#Create reader when fitting panel are created
556	self.state_reader = Reader(self.set_state)
557	#append that reader to list of available reader
558	loader = Loader()
559	loader.associate_file_reader(".fitv", self.state_reader)
560	#Send the fitting panel to guiframe
561	self.mypanels.append(self.fit_panel)
562	self.mypanels.append(self.result_panel)
563	return self.mypanels
564
565	def clear_panel(self):
566	"""
567	"""
568	self.fit_panel.clear_panel()
569
570	def delete_data(self, data):
571	"""
572	delete the given data from panel
573	"""
574	self.fit_panel.delete_data(data)
575
576	def set_data(self, data_list=None):
577	"""
578	receive a list of data to fit
579	"""
580	if data_list is None:
581	data_list = []
582	selected_data_list = []
583	if self.batch_on:
584	self.add_fit_page(data=data_list)
585	else:
586	if len(data_list) > MAX_NBR_DATA:
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	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 Exception:
618	msg = "Fitting: cannot deal with the theory received"
619	evt = StatusEvent(status=msg, info="error")
620	logger.error("set_theory " + msg + "\n" + str(sys.exc_value))
621	wx.PostEvent(self.parent, evt)
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	if isinstance(state, PageState):
632	state = state.clone()
633	self.temp_state.append(state)
634	elif isinstance(state, SimFitPageState):
635	if self.fit_panel.sim_page is None:
636	self.fit_panel.add_sim_page()
637	self.fit_panel.sim_page.load_from_save_state(state)
638	else:
639	self.temp_state = []
640	# index to start with for a new set_state
641	self.state_index = 0
642	# state file format
643	self.sfile_ext = format
644
645	self.on_set_state_helper(event=None)
646
647	def on_set_state_helper(self, event=None):
648	"""
649	Set_state_helper. This actually sets state
650	after plotting data from state file.
651
652	: event: FitStateUpdateEvent called
653	by dataloader.plot_data from guiframe
654	"""
655	if len(self.temp_state) == 0:
656	if self.state_index == 0 and len(self.mypanels) <= 0 \
657	and self.sfile_ext == '.svs':
658	self.temp_state = []
659	self.state_index = 0
660	return
661
662	try:
663	# Load fitting state
664	state = self.temp_state[self.state_index]
665	#panel state should have model selection to set_state
666	if state.formfactorcombobox is not None:
667	#set state
668	data = self.parent.create_gui_data(state.data)
669	data.group_id = state.data.group_id
670	self.parent.add_data(data_list={data.id: data})
671	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
672	title=data.title))
673	#need to be fix later make sure we are sendind guiframe.data
674	#to panel
675	state.data = data
676	page = self.fit_panel.set_state(state)
677	else:
678	#just set data because set_state won't work
679	data = self.parent.create_gui_data(state.data)
680	data.group_id = state.data.group_id
681	self.parent.add_data(data_list={data.id: data})
682	wx.PostEvent(self.parent, NewPlotEvent(plot=data,
683	title=data.title))
684	page = self.add_fit_page([data])
685	caption = page.window_caption
686	self.store_data(uid=page.uid, data_list=page.get_data_list(),
687	caption=caption)
688	self.mypanels.append(page)
689
690	# get ready for the next set_state
691	self.state_index += 1
692
693	#reset state variables to default when all set_state is finished.
694	if len(self.temp_state) == self.state_index:
695
696	self.temp_state = []
697	#self.state_index = 0
698	# Make sure the user sees the fitting panel after loading
699	#self.parent.set_perspective(self.perspective)
700	self.on_perspective(event=None)
701	except:
702	self.state_index = 0
703	self.temp_state = []
704	raise
705
706	def set_param2fit(self, uid, param2fit):
707	"""
708	Set the list of param names to fit for fitprobelm
709	"""
710	self.page_finder[uid].set_param2fit(param2fit)
711
712	def set_graph_id(self, uid, graph_id):
713	"""
714	Set graph_id for fitprobelm
715	"""
716	self.page_finder[uid].set_graph_id(graph_id)
717
718	def get_graph_id(self, uid):
719	"""
720	Set graph_id for fitprobelm
721	"""
722	return self.page_finder[uid].get_graph_id()
723
724	def save_fit_state(self, filepath, fitstate):
725	"""
726	save fit page state into file
727	"""
728	self.state_reader.write(filename=filepath, fitstate=fitstate)
729
730	def set_fit_weight(self, uid, flag, is2d=False, fid=None):
731	"""
732	Set the fit weights of a given page for all
733	its data by default. If fid is provide then set the range
734	only for the data with fid as id
735	:param uid: id corresponding to a fit page
736	:param fid: id corresponding to a fit problem (data, model)
737	:param weight: current dy data
738	"""
739	# If we are not dealing with a specific fit problem, then
740	# there is no point setting the weights.
741	if fid is None:
742	return
743	if uid in self.page_finder.keys():
744	self.page_finder[uid].set_weight(flag=flag, is2d=is2d)
745
746	def set_fit_range(self, uid, qmin, qmax, fid=None):
747	"""
748	Set the fitting range of a given page for all
749	its data by default. If fid is provide then set the range
750	only for the data with fid as id
751	:param uid: id corresponding to a fit page
752	:param fid: id corresponding to a fit problem (data, model)
753	:param qmin: minimum value of the fit range
754	:param qmax: maximum value of the fit range
755	"""
756	if uid in self.page_finder.keys():
757	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax, fid=fid)
758
759	def schedule_for_fit(self, value=0, uid=None):
760	"""
761	Set the fit problem field to 0 or 1 to schedule that problem to fit.
762	Schedule the specified fitproblem or get the fit problem related to
763	the current page and set value.
764	:param value: integer 0 or 1
765	:param uid: the id related to a page contaning fitting information
766	"""
767	if uid in self.page_finder.keys():
768	self.page_finder[uid].schedule_tofit(value)
769
770	def get_page_finder(self):
771	"""
772	return self.page_finder used also by simfitpage.py
773	"""
774	return self.page_finder
775
776	def set_page_finder(self, modelname, names, values):
777	"""
778	Used by simfitpage.py to reset a parameter given the string constrainst.
779
780	:param modelname: the name ot the model for with the parameter
781	has to reset
782	:param value: can be a string in this case.
783	:param names: the paramter name
784	"""
785	sim_page_id = self.sim_page.uid
786	for uid, value in self.page_finder.iteritems():
787	if uid != sim_page_id and uid != self.batch_page.uid:
788	model_list = value.get_model()
789	model = model_list[0]
790	if model.name == modelname:
791	value.set_model_param(names, values)
792	break
793
794	def split_string(self, item):
795	"""
796	receive a word containing dot and split it. used to split parameterset
797	name into model name and parameter name example: ::
798
799	paramaterset (item) = M1.A
800	Will return model_name = M1 , parameter name = A
801
802	"""
803	if item.find(".") >= 0:
804	param_names = re.split(r"\.", item)
805	model_name = param_names[0]
806	##Assume max len is 3; eg., M0.radius.width
807	if len(param_names) == 3:
808	param_name = param_names[1] + "." + param_names[2]
809	else:
810	param_name = param_names[1]
811	return model_name, param_name
812
813	def on_bumps_options(self, event=None):
814	"""
815	Open the bumps options panel.
816	"""
817	show_fit_config(self.parent, help=self.on_help)
818
819	def on_fitter_changed(self, event):
820	self._set_fitter_label(event.config)
821
822	def _set_fitter_label(self, config):
823	self.fit_panel.parent.SetTitle(self.fit_panel.window_name
824	+ " - Active Fitting Optimizer: "
825	+ config.selected_name)
826
827	def on_help(self, algorithm_id):
828	_TreeLocation = "user/sasgui/perspectives/fitting/optimizer.html"
829	_anchor = "#fit-"+algorithm_id
830	DocumentationWindow(self.parent, wx.ID_ANY, _TreeLocation, _anchor, "Optimizer Help")
831
832
833	def on_fit_results(self, event=None):
834	"""
835	Make the Fit Results panel visible.
836	"""
837	self.result_frame.Show()
838	self.result_frame.Raise()
839
840	def on_gpu_options(self, event=None):
841	"""
842	Make the Fit Results panel visible.
843	"""
844	dialog = GpuOptions(None, wx.ID_ANY, "")
845	dialog.Show()
846
847	def stop_fit(self, uid):
848	"""
849	Stop the fit
850	"""
851	if uid in self.fit_thread_list.keys():
852	calc_fit = self.fit_thread_list[uid]
853	if calc_fit is not None and calc_fit.isrunning():
854	calc_fit.stop()
855	msg = "Fit stop!"
856	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
857	del self.fit_thread_list[uid]
858	#set the fit button label of page when fit stop is trigger from
859	#simultaneous fit pane
860	sim_flag = self.sim_page is not None and uid == self.sim_page.uid
861	batch_flag = self.batch_page is not None and uid == self.batch_page.uid
862	if sim_flag or batch_flag:
863	for uid, value in self.page_finder.iteritems():
864	if value.get_scheduled() == 1:
865	if uid in self.fit_panel.opened_pages.keys():
866	panel = self.fit_panel.opened_pages[uid]
867	panel._on_fit_complete()
868
869	def set_smearer(self, uid, smearer, fid, qmin=None, qmax=None, draw=True,
870	enable_smearer=False):
871	"""
872	Get a smear object and store it to a fit problem of fid as id. If proper
873	flag is enable , will plot the theory with smearing information.
874
875	:param smearer: smear object to allow smearing data of id fid
876	:param enable_smearer: Define whether or not all (data, model) contained
877	in the structure of id uid will be smeared before fitting.
878	:param qmin: the maximum value of the theory plotting range
879	:param qmax: the maximum value of the theory plotting range
880	:param draw: Determine if the theory needs to be plot
881	"""
882	if uid not in self.page_finder.keys():
883	return
884	self.page_finder[uid].enable_smearing(flag=enable_smearer)
885	self.page_finder[uid].set_smearer(smearer, fid=fid)
886	if draw:
887	## draw model 1D with smeared data
888	data = self.page_finder[uid].get_fit_data(fid=fid)
889	if data is None:
890	msg = "set_mearer requires at least data.\n"
891	msg += "Got data = %s .\n" % str(data)
892	return
893	#raise ValueError, msg
894	model = self.page_finder[uid].get_model(fid=fid)
895	if model is None:
896	return
897	enable1D = issubclass(data.__class__, Data1D)
898	enable2D = issubclass(data.__class__, Data2D)
899	## if user has already selected a model to plot
900	## redraw the model with data smeared
901	smear = self.page_finder[uid].get_smearer(fid=fid)
902
903	# compute weight for the current data
904	weight = self.page_finder[uid].get_weight(fid=fid)
905
906	self.draw_model(model=model, data=data, page_id=uid, smearer=smear,
907	enable1D=enable1D, enable2D=enable2D,
908	qmin=qmin, qmax=qmax, weight=weight)
909
910	def draw_model(self, model, page_id, data=None, smearer=None,
911	enable1D=True, enable2D=False,
912	state=None,
913	fid=None,
914	toggle_mode_on=False,
915	qmin=None, qmax=None,
916	update_chisqr=True, weight=None, source='model'):
917	"""
918	Draw model.
919
920	:param model: the model to draw
921	:param name: the name of the model to draw
922	:param data: the data on which the model is based to be drawn
923	:param description: model's description
924	:param enable1D: if true enable drawing model 1D
925	:param enable2D: if true enable drawing model 2D
926	:param qmin: Range's minimum value to draw model
927	:param qmax: Range's maximum value to draw model
928	:param qstep: number of step to divide the x and y-axis
929	:param update_chisqr: update chisqr [bool]
930
931	"""
932	#self.weight = weight
933	if issubclass(data.__class__, Data1D) or not enable2D:
934	## draw model 1D with no loaded data
935	self._draw_model1D(model=model,
936	data=data,
937	page_id=page_id,
938	enable1D=enable1D,
939	smearer=smearer,
940	qmin=qmin,
941	qmax=qmax,
942	fid=fid,
943	weight=weight,
944	toggle_mode_on=toggle_mode_on,
945	state=state,
946	update_chisqr=update_chisqr,
947	source=source)
948	else:
949	## draw model 2D with no initial data
950	self._draw_model2D(model=model,
951	page_id=page_id,
952	data=data,
953	enable2D=enable2D,
954	smearer=smearer,
955	qmin=qmin,
956	qmax=qmax,
957	fid=fid,
958	weight=weight,
959	state=state,
960	toggle_mode_on=toggle_mode_on,
961	update_chisqr=update_chisqr,
962	source=source)
963
964	def onFit(self, uid):
965	"""
966	Get series of data, model, associates parameters and range and send then
967	to series of fitters. Fit data and model, display result to
968	corresponding panels.
969	:param uid: id related to the panel currently calling this fit function.
970	"""
971	if uid is None:
972	raise RuntimeError("no page to fit") # Should never happen
973
974	sim_page_uid = getattr(self.sim_page, 'uid', None)
975	batch_page_uid = getattr(self.batch_page, 'uid', None)
976
977	if uid == sim_page_uid:
978	fit_type = 'simultaneous'
979	elif uid == batch_page_uid:
980	fit_type = 'combined_batch'
981	else:
982	fit_type = 'single'
983
984	fitter_list = []
985	sim_fitter = None
986	if fit_type == 'simultaneous':
987	# for simultaneous fitting only one fitter is needed
988	sim_fitter = Fit()
989	sim_fitter.fitter_id = self.sim_page.uid
990	fitter_list.append(sim_fitter)
991
992	self.current_pg = None
993	list_page_id = []
994	fit_id = 0
995	for page_id, page_info in self.page_finder.iteritems():
996	# For simulfit (uid give with None), do for-loop
997	# if uid is specified (singlefit), do it only on the page.
998	if page_id in (sim_page_uid, batch_page_uid): continue
999	if fit_type == "single" and page_id != uid: continue
1000
1001	try:
1002	if page_info.get_scheduled() == 1:
1003	page_info.nbr_residuals_computed = 0
1004	page = self.fit_panel.get_page_by_id(page_id)
1005	self.set_fit_weight(uid=page.uid,
1006	flag=page.get_weight_flag(),
1007	is2d=page._is_2D())
1008	if not page.param_toFit:
1009	msg = "No fitting parameters for %s" % page.window_caption
1010	evt = StatusEvent(status=msg, info="error", type="stop")
1011	wx.PostEvent(page.parent.parent, evt)
1012	return False
1013	if not page._update_paramv_on_fit():
1014	msg = "Fitting range or parameter values are"
1015	msg += " invalid in %s" % \
1016	page.window_caption
1017	evt = StatusEvent(status=msg, info="error", type="stop")
1018	wx.PostEvent(page.parent.parent, evt)
1019	return False
1020
1021	pars = [str(element[1]) for element in page.param_toFit]
1022	fitproblem_list = page_info.values()
1023	for fitproblem in fitproblem_list:
1024	if sim_fitter is None:
1025	fitter = Fit()
1026	fitter.fitter_id = page_id
1027	fitter_list.append(fitter)
1028	else:
1029	fitter = sim_fitter
1030	self._add_problem_to_fit(fitproblem=fitproblem,
1031	pars=pars,
1032	fitter=fitter,
1033	fit_id=fit_id)
1034	fit_id += 1
1035	list_page_id.append(page_id)
1036	page_info.clear_model_param()
1037	except KeyboardInterrupt:
1038	msg = "Fitting terminated"
1039	evt = StatusEvent(status=msg, info="info", type="stop")
1040	wx.PostEvent(self.parent, evt)
1041	return True
1042	except:
1043	raise
1044	msg = "Fitting error: %s" % str(sys.exc_value)
1045	evt = StatusEvent(status=msg, info="error", type="stop")
1046	wx.PostEvent(self.parent, evt)
1047	return False
1048	## If a thread is already started, stop it
1049	#if self.calc_fitis not None and self.calc_fit.isrunning():
1050	# self.calc_fit.stop()
1051	msg = "Fitting is in progress..."
1052	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1053
1054	#Handler used to display fit message
1055	handler = ConsoleUpdate(parent=self.parent,
1056	manager=self,
1057	improvement_delta=0.1)
1058
1059	# batch fit
1060	batch_inputs = {}
1061	batch_outputs = {}
1062	if fit_type == "simultaneous":
1063	page = self.sim_page
1064	elif fit_type == "combined_batch":
1065	page = self.batch_page
1066	else:
1067	page = self.fit_panel.get_page_by_id(uid)
1068	if page.batch_on:
1069	calc_fit = FitThread(handler=handler,
1070	fn=fitter_list,
1071	pars=pars,
1072	batch_inputs=batch_inputs,
1073	batch_outputs=batch_outputs,
1074	page_id=list_page_id,
1075	completefn=self._batch_fit_complete,
1076	reset_flag=self.batch_reset_flag)
1077	else:
1078	## Perform more than 1 fit at the time
1079	calc_fit = FitThread(handler=handler,
1080	fn=fitter_list,
1081	batch_inputs=batch_inputs,
1082	batch_outputs=batch_outputs,
1083	page_id=list_page_id,
1084	updatefn=handler.update_fit,
1085	completefn=self._fit_completed)
1086	#self.fit_thread_list[current_page_id] = calc_fit
1087	self.fit_thread_list[uid] = calc_fit
1088	calc_fit.queue()
1089	calc_fit.ready(2.5)
1090	msg = "Fitting is in progress..."
1091	wx.PostEvent(self.parent, StatusEvent(status=msg, type="progress"))
1092
1093	return True
1094
1095	def remove_plot(self, uid, fid=None, theory=False):
1096	"""
1097	remove model plot when a fit page is closed
1098	:param uid: the id related to the fitpage to close
1099	:param fid: the id of the fitproblem(data, model, range,etc)
1100	"""
1101	if uid not in self.page_finder.keys():
1102	return
1103	fitproblemList = self.page_finder[uid].get_fit_problem(fid)
1104	for fitproblem in fitproblemList:
1105	data = fitproblem.get_fit_data()
1106	model = fitproblem.get_model()
1107	plot_id = None
1108	if model is not None:
1109	plot_id = data.id + model.name
1110	if theory:
1111	plot_id = data.id + model.name
1112	group_id = data.group_id
1113	wx.PostEvent(self.parent, NewPlotEvent(id=plot_id,
1114	group_id=group_id,
1115	action='remove'))
1116
1117	def store_data(self, uid, data_list=None, caption=None):
1118	"""
1119	Recieve a list of data and store them ans well as a caption of
1120	the fit page where they come from.
1121	:param uid: if related to a fit page
1122	:param data_list: list of data to fit
1123	:param caption: caption of the window related to these data
1124	"""
1125	if data_list is None:
1126	data_list = []
1127
1128	self.page_finder[uid].set_fit_data(data=data_list)
1129	if caption is not None:
1130	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1131
1132	def on_add_new_page(self, event=None):
1133	"""
1134	ask fit panel to create a new empty page
1135	"""
1136	try:
1137	page = self.fit_panel.add_empty_page()
1138	# add data associated to the page created
1139	if page is not None:
1140	evt = StatusEvent(status="Page Created", info="info")
1141	wx.PostEvent(self.parent, evt)
1142	else:
1143	msg = "Page was already Created"
1144	evt = StatusEvent(status=msg, info="warning")
1145	wx.PostEvent(self.parent, evt)
1146	except Exception:
1147	msg = "Creating Fit page: %s" % sys.exc_value
1148	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1149
1150	def add_fit_page(self, data):
1151	"""
1152	given a data, ask to the fitting panel to create a new fitting page,
1153	get this page and store it into the page_finder of this plug-in
1154	:param data: is a list of data
1155	"""
1156	page = self.fit_panel.set_data(data)
1157	# page could be None when loading state files
1158	if page is None:
1159	return page
1160	#append Data1D to the panel containing its theory
1161	#if theory already plotted
1162	if page.uid in self.page_finder:
1163	data = page.get_data()
1164	theory_data = self.page_finder[page.uid].get_theory_data(data.id)
1165	if issubclass(data.__class__, Data2D):
1166	data.group_id = wx.NewId()
1167	if theory_data is not None:
1168	group_id = str(page.uid) + " Model1D"
1169	wx.PostEvent(self.parent,
1170	NewPlotEvent(group_id=group_id,
1171	action="delete"))
1172	self.parent.update_data(prev_data=theory_data,
1173	new_data=data)
1174	else:
1175	if theory_data is not None:
1176	group_id = str(page.uid) + " Model2D"
1177	data.group_id = theory_data.group_id
1178	wx.PostEvent(self.parent,
1179	NewPlotEvent(group_id=group_id,
1180	action="delete"))
1181	self.parent.update_data(prev_data=theory_data,
1182	new_data=data)
1183	self.store_data(uid=page.uid, data_list=page.get_data_list(),
1184	caption=page.window_caption)
1185	if self.sim_page is not None and not self.batch_on:
1186	self.sim_page.draw_page()
1187	if self.batch_page is not None and self.batch_on:
1188	self.batch_page.draw_page()
1189
1190	return page
1191
1192	def _onEVT_SLICER_PANEL(self, event):
1193	"""
1194	receive and event telling to update a panel with a name starting with
1195	event.panel_name. this method update slicer panel
1196	for a given interactor.
1197
1198	:param event: contains type of slicer , paramaters for updating
1199	the panel and panel_name to find the slicer 's panel concerned.
1200	"""
1201	event.panel_name
1202	for item in self.parent.panels:
1203	name = event.panel_name
1204	if self.parent.panels[item].window_caption.startswith(name):
1205	self.parent.panels[item].set_slicer(event.type, event.params)
1206
1207	#self.parent._mgr.Update()
1208
1209	def _closed_fitpage(self, event):
1210	"""
1211	request fitpanel to close a given page when its unique data is removed
1212	from the plot. close fitpage only when the a loaded data is removed
1213	"""
1214	if event is None or event.data is None:
1215	return
1216	if hasattr(event.data, "is_data"):
1217	if not event.data.is_data or \
1218	event.data.__class__.__name__ == "Data1D":
1219	self.fit_panel.close_page_with_data(event.data)
1220
1221	def _reset_schedule_problem(self, value=0, uid=None):
1222	"""
1223	unschedule or schedule all fitproblem to be fit
1224	"""
1225	# case that uid is not specified
1226	if uid is None:
1227	for page_id in self.page_finder.keys():
1228	self.page_finder[page_id].schedule_tofit(value)
1229	# when uid is given
1230	else:
1231	if uid in self.page_finder.keys():
1232	self.page_finder[uid].schedule_tofit(value)
1233
1234	def _add_problem_to_fit(self, fitproblem, pars, fitter, fit_id):
1235	"""
1236	Create and set fitter with series of data and model
1237	"""
1238	data = fitproblem.get_fit_data()
1239	model = fitproblem.get_model()
1240	smearer = fitproblem.get_smearer()
1241	qmin, qmax = fitproblem.get_range()
1242
1243	#Extra list of parameters and their constraints
1244	listOfConstraint = []
1245	param = fitproblem.get_model_param()
1246	if len(param) > 0:
1247	for item in param:
1248	## check if constraint
1249	if item[0] is not None and item[1] is not None:
1250	listOfConstraint.append((item[0], item[1]))
1251	new_model = model
1252	fitter.set_model(new_model, fit_id, pars, data=data,
1253	constraints=listOfConstraint)
1254	fitter.set_data(data=data, id=fit_id, smearer=smearer, qmin=qmin,
1255	qmax=qmax)
1256	fitter.select_problem_for_fit(id=fit_id, value=1)
1257
1258	def _onSelect(self, event):
1259	"""
1260	when Select data to fit a new page is created .Its reference is
1261	added to self.page_finder
1262	"""
1263	panel = self.plot_panel
1264	if panel is None:
1265	raise ValueError, "Fitting:_onSelect: NonType panel"
1266	Plugin.on_perspective(self, event=event)
1267	self.select_data(panel)
1268
1269	def select_data(self, panel):
1270	"""
1271	"""
1272	for plottable in panel.graph.plottables:
1273	if plottable.__class__.__name__ in ["Data1D", "Theory1D"]:
1274	data_id = panel.graph.selected_plottable
1275	if plottable == panel.plots[data_id]:
1276	data = plottable
1277	self.add_fit_page(data=[data])
1278	return
1279	else:
1280	data = plottable
1281	self.add_fit_page(data=[data])
1282
1283	def update_fit(self, result=None, msg=""):
1284	"""
1285	"""
1286	print("update_fit result", result)
1287
1288	def _batch_fit_complete(self, result, pars, page_id,
1289	batch_outputs, batch_inputs, elapsed=None):
1290	"""
1291	Display fit result in batch
1292	:param result: list of objects received from fitters
1293	:param pars: list of fitted parameters names
1294	:param page_id: list of page ids which called fit function
1295	:param elapsed: time spent at the fitting level
1296	"""
1297	uid = page_id[0]
1298	if uid in self.fit_thread_list.keys():
1299	del self.fit_thread_list[uid]
1300
1301	wx.CallAfter(self._update_fit_button, page_id)
1302	t1 = time.time()
1303	str_time = time.strftime("%a, %d %b %Y %H:%M:%S ", time.localtime(t1))
1304	msg = "Fit completed on %s \n" % str_time
1305	msg += "Duration time: %s s.\n" % str(elapsed)
1306	evt = StatusEvent(status=msg, info="info", type="stop")
1307	wx.PostEvent(self.parent, evt)
1308
1309	if batch_outputs is None:
1310	batch_outputs = {}
1311
1312	# format batch_outputs
1313	batch_outputs["Chi2"] = []
1314	#Don't like these loops
1315	# Need to create dictionary of all fitted parameters
1316	# since the number of parameters can differ between each fit result
1317	for list_res in result:
1318	for res in list_res:
1319	model, data = res.inputs[0]
1320	if model is not None and hasattr(model, "model"):
1321	model = model.model
1322	#get all fittable parameters of the current model
1323	for param in model.getParamList():
1324	if param not in batch_outputs.keys():
1325	batch_outputs[param] = []
1326	for param in model.getDispParamList():
1327	if not model.is_fittable(param) and \
1328	param in batch_outputs.keys():
1329	del batch_outputs[param]
1330	# Add fitted parameters and their error
1331	for param in res.param_list:
1332	if param not in batch_outputs.keys():
1333	batch_outputs[param] = []
1334	err_param = "error on %s" % str(param)
1335	if err_param not in batch_inputs.keys():
1336	batch_inputs[err_param] = []
1337	msg = ""
1338	for list_res in result:
1339	for res in list_res:
1340	pid = res.fitter_id
1341	model, data = res.inputs[0]
1342	correct_result = False
1343	if model is not None and hasattr(model, "model"):
1344	model = model.model
1345	if data is not None and hasattr(data, "sas_data"):
1346	data = data.sas_data
1347
1348	is_data2d = issubclass(data.__class__, Data2D)
1349	# Check consistency of arrays
1350	if not is_data2d:
1351	if len(res.theory) == len(res.index[res.index]) and \
1352	len(res.index) == len(data.y):
1353	correct_result = True
1354	else:
1355	copy_data = deepcopy(data)
1356	new_theory = copy_data.data
1357	new_theory[res.index] = res.theory
1358	new_theory[res.index == False] = np.nan
1359	correct_result = True
1360	# Get all fittable parameters of the current model
1361	param_list = model.getParamList()
1362	for param in model.getDispParamList():
1363	if '.' in param and param in param_list:
1364	# Ensure polydispersity results are displayed
1365	p1, p2 = param.split('.')
1366	if not model.is_fittable(p1) and not (p2 == 'width' and param in res.param_list)\
1367	and param in param_list:
1368	param_list.remove(param)
1369	elif not model.is_fittable(param) and \
1370	param in param_list:
1371	param_list.remove(param)
1372	if not correct_result or res.fitness is None or \
1373	not np.isfinite(res.fitness) or \
1374	np.any(res.pvec is None) or not \
1375	np.all(np.isfinite(res.pvec)):
1376	data_name = str(None)
1377	if data is not None:
1378	data_name = str(data.name)
1379	model_name = str(None)
1380	if model is not None:
1381	model_name = str(model.name)
1382	msg += "Data %s and Model %s did not fit.\n" % (data_name,
1383	model_name)
1384	ERROR = np.NAN
1385	cell = BatchCell()
1386	cell.label = res.fitness
1387	cell.value = res.fitness
1388	batch_outputs["Chi2"].append(ERROR)
1389	for param in param_list:
1390	# Save value of fixed parameters
1391	if param not in res.param_list:
1392	batch_outputs[str(param)].append(ERROR)
1393	else:
1394	# Save only fitted values
1395	batch_outputs[param].append(ERROR)
1396	batch_inputs["error on %s" % str(param)].append(ERROR)
1397	else:
1398	# TODO: Why sometimes res.pvec comes with np.float64?
1399	# probably from scipy lmfit
1400	if res.pvec.__class__ == np.float64:
1401	res.pvec = [res.pvec]
1402
1403	cell = BatchCell()
1404	cell.label = res.fitness
1405	cell.value = res.fitness
1406	batch_outputs["Chi2"].append(cell)
1407	# add parameters to batch_results
1408	for param in param_list:
1409	# save value of fixed parameters
1410	if param not in res.param_list:
1411	batch_outputs[str(param)].append(model.getParam(param))
1412	else:
1413	index = res.param_list.index(param)
1414	#save only fitted values
1415	batch_outputs[param].append(res.pvec[index])
1416	if res.stderr is not None and \
1417	len(res.stderr) == len(res.param_list):
1418	item = res.stderr[index]
1419	batch_inputs["error on %s" % param].append(item)
1420	else:
1421	batch_inputs["error on %s" % param].append('-')
1422	model.setParam(param, res.pvec[index])
1423	#fill the batch result with emtpy value if not in the current
1424	#model
1425	EMPTY = "-"
1426	for key in batch_outputs.keys():
1427	if key not in param_list and key not in ["Chi2", "Data"]:
1428	batch_outputs[key].append(EMPTY)
1429
1430	self.page_finder[pid].set_batch_result(batch_inputs=batch_inputs,
1431	batch_outputs=batch_outputs)
1432
1433	cpage = self.fit_panel.get_page_by_id(pid)
1434	cpage._on_fit_complete()
1435	self.page_finder[pid][data.id].set_result(res)
1436	fitproblem = self.page_finder[pid][data.id]
1437	qmin, qmax = fitproblem.get_range()
1438	plot_result = False
1439	if correct_result:
1440	if not is_data2d:
1441	self._complete1D(x=data.x[res.index], y=res.theory, page_id=pid,
1442	elapsed=None,
1443	index=res.index, model=model,
1444	weight=None, fid=data.id,
1445	toggle_mode_on=False, state=None,
1446	data=data, update_chisqr=False,
1447	source='fit', plot_result=plot_result)
1448	else:
1449	self._complete2D(image=new_theory, data=data,
1450	model=model,
1451	page_id=pid, elapsed=None,
1452	index=res.index,
1453	qmin=qmin,
1454	qmax=qmax, fid=data.id, weight=None,
1455	toggle_mode_on=False, state=None,
1456	update_chisqr=False,
1457	source='fit', plot_result=plot_result)
1458	self.on_set_batch_result(page_id=pid,
1459	fid=data.id,
1460	batch_outputs=batch_outputs,
1461	batch_inputs=batch_inputs)
1462
1463	evt = StatusEvent(status=msg, error="info", type="stop")
1464	wx.PostEvent(self.parent, evt)
1465	# Remove parameters that are not shown
1466	cpage = self.fit_panel.get_page_by_id(uid)
1467	tbatch_outputs = {}
1468	shownkeystr = cpage.get_copy_params()
1469	for key in batch_outputs.keys():
1470	if key in ["Chi2", "Data"] or shownkeystr.count(key) > 0:
1471	tbatch_outputs[key] = batch_outputs[key]
1472
1473	wx.CallAfter(self.parent.on_set_batch_result, tbatch_outputs,
1474	batch_inputs, self.sub_menu)
1475
1476	def on_set_batch_result(self, page_id, fid, batch_outputs, batch_inputs):
1477	"""
1478	"""
1479	pid = page_id
1480	if fid not in self.page_finder[pid]:
1481	return
1482	fitproblem = self.page_finder[pid][fid]
1483	index = self.page_finder[pid].nbr_residuals_computed - 1
1484	residuals = fitproblem.get_residuals()
1485	theory_data = fitproblem.get_theory_data()
1486	data = fitproblem.get_fit_data()
1487	model = fitproblem.get_model()
1488	#fill batch result information
1489	if "Data" not in batch_outputs.keys():
1490	batch_outputs["Data"] = []
1491	cell = BatchCell()
1492	cell.label = data.name
1493	cell.value = index
1494
1495	if theory_data is not None:
1496	#Suucessful fit
1497	theory_data.id = wx.NewId()
1498	theory_data.name = model.name + "[%s]" % str(data.name)
1499	if issubclass(theory_data.__class__, Data2D):
1500	group_id = wx.NewId()
1501	theory_data.group_id = group_id
1502	if group_id not in theory_data.list_group_id:
1503	theory_data.list_group_id.append(group_id)
1504
1505	try:
1506	# associate residuals plot
1507	if issubclass(residuals.__class__, Data2D):
1508	group_id = wx.NewId()
1509	residuals.group_id = group_id
1510	if group_id not in residuals.list_group_id:
1511	residuals.list_group_id.append(group_id)
1512	batch_outputs["Chi2"][index].object = [residuals]
1513	except:
1514	pass
1515
1516	cell.object = [data, theory_data]
1517	batch_outputs["Data"].append(cell)
1518	for key, value in data.meta_data.iteritems():
1519	if key not in batch_inputs.keys():
1520	batch_inputs[key] = []
1521	#if key.lower().strip() != "loader":
1522	batch_inputs[key].append(value)
1523	param = "temperature"
1524	if hasattr(data.sample, param):
1525	if param not in batch_inputs.keys():
1526	batch_inputs[param] = []
1527	batch_inputs[param].append(data.sample.temperature)
1528
1529	def _fit_completed(self, result, page_id, batch_outputs,
1530	batch_inputs=None, pars=None, elapsed=None):
1531	"""
1532	Display result of the fit on related panel(s).
1533	:param result: list of object generated when fit ends
1534	:param pars: list of names of parameters fitted
1535	:param page_id: list of page ids which called fit function
1536	:param elapsed: time spent at the fitting level
1537	"""
1538	t1 = time.time()
1539	str_time = time.strftime("%a, %d %b %Y %H:%M:%S ", time.localtime(t1))
1540	msg = "Fit completed on %s \n" % str_time
1541	msg += "Duration time: %s s.\n" % str(elapsed)
1542	evt = StatusEvent(status=msg, info="info", type="stop")
1543	wx.PostEvent(self.parent, evt)
1544	wx.PostEvent(self.result_panel, PlotResultEvent(result=result))
1545	wx.CallAfter(self._update_fit_button, page_id)
1546	result = result[0]
1547	self.fit_thread_list = {}
1548	if page_id is None:
1549	page_id = []
1550	## fit more than 1 model at the same time
1551	try:
1552	index = 0
1553	# Update potential simfit page(s)
1554	if self.sim_page is not None:
1555	self.sim_page._on_fit_complete()
1556	if self.batch_page:
1557	self.batch_page._on_fit_complete()
1558	# Update all fit pages
1559	for uid in page_id:
1560	res = result[index]
1561	fit_msg = res.mesg
1562	if res.fitness is None or \
1563	not np.isfinite(res.fitness) or \
1564	np.any(res.pvec is None) or \
1565	not np.all(np.isfinite(res.pvec)):
1566	fit_msg += "\nFitting did not converge!!!"
1567	wx.CallAfter(self._update_fit_button, page_id)
1568	else:
1569	#set the panel when fit result are float not list
1570	if res.pvec.__class__ == np.float64:
1571	pvec = [res.pvec]
1572	else:
1573	pvec = res.pvec
1574	if res.stderr.__class__ == np.float64:
1575	stderr = [res.stderr]
1576	else:
1577	stderr = res.stderr
1578	cpage = self.fit_panel.get_page_by_id(uid)
1579	# Make sure we got all results
1580	#(CallAfter is important to MAC)
1581	try:
1582	#if res is not None:
1583	wx.CallAfter(cpage.onsetValues, res.fitness,
1584	res.param_list,
1585	pvec, stderr)
1586	index += 1
1587	wx.CallAfter(cpage._on_fit_complete)
1588	except KeyboardInterrupt:
1589	fit_msg += "\nSingular point: Fitting stopped."
1590	except Exception:
1591	fit_msg += "\nSingular point: Fitting error occurred."
1592	if fit_msg:
1593	evt = StatusEvent(status=fit_msg, info="warning", type="stop")
1594	wx.PostEvent(self.parent, evt)
1595
1596	except Exception:
1597	msg = ("Fit completed but the following error occurred: %s"
1598	% sys.exc_value)
1599	#msg = "\n".join((traceback.format_exc(), msg))
1600	evt = StatusEvent(status=msg, info="warning", type="stop")
1601	wx.PostEvent(self.parent, evt)
1602
1603	def _update_fit_button(self, page_id):
1604	"""
1605	Update Fit button when fit stopped
1606
1607	: parameter page_id: fitpage where the button is
1608	"""
1609	if page_id.__class__.__name__ != 'list':
1610	page_id = [page_id]
1611	for uid in page_id:
1612	page = self.fit_panel.get_page_by_id(uid)
1613	page._on_fit_complete()
1614
1615	def _on_show_panel(self, event):
1616	"""
1617	"""
1618	pass
1619
1620	def on_reset_batch_flag(self, event):
1621	"""
1622	Set batch_reset_flag
1623	"""
1624	event.Skip()
1625	if self.menu1 is None:
1626	return
1627	menu_item = self.menu1.FindItemById(self.id_reset_flag)
1628	flag = menu_item.IsChecked()
1629	if not flag:
1630	menu_item.Check(False)
1631	self.batch_reset_flag = True
1632	else:
1633	menu_item.Check(True)
1634	self.batch_reset_flag = False
1635
1636	## post a message to status bar
1637	msg = "Set Chain Fitting: %s" % str(not self.batch_reset_flag)
1638	wx.PostEvent(self.parent, StatusEvent(status=msg))
1639
1640
1641	def _on_slicer_event(self, event):
1642	"""
1643	Receive a panel as event and send it to guiframe
1644
1645	:param event: event containing a panel
1646
1647	"""
1648	if event.panel is not None:
1649	self.slicer_panels.append(event.panel)
1650	# Set group ID if available
1651	event_id = self.parent.popup_panel(event.panel)
1652	event.panel.uid = event_id
1653	self.mypanels.append(event.panel)
1654
1655	def _onclearslicer(self, event):
1656	"""
1657	Clear the boxslicer when close the panel associate with this slicer
1658	"""
1659	name = event.GetEventObject().frame.GetTitle()
1660	for panel in self.slicer_panels:
1661	if panel.window_caption == name:
1662
1663	for item in self.parent.panels:
1664	if hasattr(self.parent.panels[item], "uid"):
1665	if self.parent.panels[item].uid == panel.base.uid:
1666	self.parent.panels[item].onClearSlicer(event)
1667	#self.parent._mgr.Update()
1668	break
1669	break
1670
1671	def _on_model_panel(self, evt):
1672	"""
1673	react to model selection on any combo box or model menu.plot the model
1674
1675	:param evt: wx.combobox event
1676
1677	"""
1678	model = evt.model
1679	uid = evt.uid
1680	qmin = evt.qmin
1681	qmax = evt.qmax
1682	caption = evt.caption
1683	enable_smearer = evt.enable_smearer
1684	if model is None:
1685	return
1686	if uid not in self.page_finder.keys():
1687	return
1688	# save the name containing the data name with the appropriate model
1689	self.page_finder[uid].set_model(model)
1690	self.page_finder[uid].enable_smearing(enable_smearer)
1691	self.page_finder[uid].set_range(qmin=qmin, qmax=qmax)
1692	self.page_finder[uid].set_fit_tab_caption(caption=caption)
1693	if self.sim_page is not None and not self.batch_on:
1694	self.sim_page.draw_page()
1695	if self.batch_page is not None and self.batch_on:
1696	self.batch_page.draw_page()
1697
1698	def _update1D(self, x, output):
1699	"""
1700	Update the output of plotting model 1D
1701	"""
1702	msg = "Plot updating ... "
1703	wx.PostEvent(self.parent, StatusEvent(status=msg, type="update"))
1704
1705	def create_theory_1D(self, x, y, page_id, model, data, state,
1706	data_description, data_id, dy=None):
1707	"""
1708	Create a theory object associate with an existing Data1D
1709	and add it to the data manager.
1710	@param x: x-values of the data
1711	@param y: y_values of the data
1712	@param page_id: fit page ID
1713	@param model: model used for fitting
1714	@param data: Data1D object to create the theory for
1715	@param state: model state
1716	@param data_description: title to use in the data manager
1717	@param data_id: unique data ID
1718	"""
1719	new_plot = Data1D(x=x, y=y)
1720	if dy is None:
1721	new_plot.is_data = False
1722	new_plot.dy = np.zeros(len(y))
1723	# If this is a theory curve, pick the proper symbol to make it a curve
1724	new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
1725	else:
1726	new_plot.is_data = True
1727	new_plot.dy = dy
1728	new_plot.interactive = True
1729	new_plot.dx = None
1730	new_plot.dxl = None
1731	new_plot.dxw = None
1732	_yaxis, _yunit = data.get_yaxis()
1733	_xaxis, _xunit = data.get_xaxis()
1734	new_plot.title = data.name
1735	new_plot.group_id = data.group_id
1736	if new_plot.group_id is None:
1737	new_plot.group_id = data.group_id
1738	new_plot.id = data_id
1739	# Find if this theory was already plotted and replace that plot given
1740	# the same id
1741	self.page_finder[page_id].get_theory_data(fid=data.id)
1742
1743	if data.is_data:
1744	data_name = str(data.name)
1745	else:
1746	data_name = str(model.__class__.__name__)
1747
1748	new_plot.name = data_description + " [" + data_name + "]"
1749	new_plot.xaxis(_xaxis, _xunit)
1750	new_plot.yaxis(_yaxis, _yunit)
1751	self.page_finder[page_id].set_theory_data(data=new_plot,
1752	fid=data.id)
1753	self.parent.update_theory(data_id=data.id, theory=new_plot,
1754	state=state)
1755	return new_plot
1756
1757	def _complete1D(self, x, y, page_id, elapsed, index, model,
1758	weight=None, fid=None,
1759	toggle_mode_on=False, state=None,
1760	data=None, update_chisqr=True,
1761	source='model', plot_result=True,
1762	unsmeared_model=None, unsmeared_data=None,
1763	unsmeared_error=None, sq_model=None, pq_model=None):
1764	"""
1765	Complete plotting 1D data
1766	@param unsmeared_model: fit model, without smearing
1767	@param unsmeared_data: data, rescaled to unsmeared model
1768	@param unsmeared_error: data error, rescaled to unsmeared model
1769	"""
1770	number_finite = np.count_nonzero(np.isfinite(y))
1771	np.nan_to_num(y)
1772	new_plot = self.create_theory_1D(x, y, page_id, model, data, state,
1773	data_description=model.name,
1774	data_id=str(page_id) + " " + data.name)
1775	plots_to_update = [] # List of plottables that have changed since last calculation
1776	# Create the new theories
1777	if unsmeared_model is not None:
1778	unsmeared_model_plot = self.create_theory_1D(x, unsmeared_model,
1779	page_id, model, data, state,
1780	data_description=model.name + " unsmeared",
1781	data_id=str(page_id) + " " + data.name + " unsmeared")
1782	plots_to_update.append(unsmeared_model_plot)
1783
1784	if unsmeared_data is not None and unsmeared_error is not None:
1785	unsmeared_data_plot = self.create_theory_1D(x, unsmeared_data,
1786	page_id, model, data, state,
1787	data_description="Data unsmeared",
1788	data_id="Data " + data.name + " unsmeared",
1789	dy=unsmeared_error)
1790	plots_to_update.append(unsmeared_data_plot)
1791	if sq_model is not None and pq_model is not None:
1792	sq_id = str(page_id) + " " + data.name + " S(q)"
1793	sq_plot = self.create_theory_1D(x, sq_model, page_id, model, data, state,
1794	data_description=model.name + " S(q)",
1795	data_id=sq_id)
1796	plots_to_update.append(sq_plot)
1797	pq_id = str(page_id) + " " + data.name + " P(q)"
1798	pq_plot = self.create_theory_1D(x, pq_model, page_id, model, data, state,
1799	data_description=model.name + " P(q)",
1800	data_id=pq_id)
1801	plots_to_update.append(pq_plot)
1802	# Update the P(Q), S(Q) and unsmeared theory plots if they exist
1803	wx.PostEvent(self.parent, NewPlotEvent(plots=plots_to_update,
1804	action='update'))
1805
1806	current_pg = self.fit_panel.get_page_by_id(page_id)
1807	title = new_plot.title
1808	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
1809	if not batch_on:
1810	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=str(title)))
1811	elif plot_result:
1812	top_data_id = self.fit_panel.get_page_by_id(page_id).data.id
1813	if data.id == top_data_id:
1814	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=str(title)))
1815	caption = current_pg.window_caption
1816	self.page_finder[page_id].set_fit_tab_caption(caption=caption)
1817
1818	self.page_finder[page_id].set_theory_data(data=new_plot,
1819	fid=data.id)
1820	if toggle_mode_on:
1821	wx.PostEvent(self.parent,
1822	NewPlotEvent(group_id=str(page_id) + " Model2D",
1823	action="Hide"))
1824	else:
1825	if update_chisqr:
1826	output = self._cal_chisqr(data=data,
1827	fid=fid,
1828	weight=weight,
1829	page_id=page_id,
1830	index=index)
1831	wx.PostEvent(current_pg, Chi2UpdateEvent(output=output))
1832	else:
1833	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1834	index=index, weight=weight)
1835
1836	if not number_finite:
1837	logger.error("Using the present parameters the model does not return any finite value. ")
1838	msg = "Computing Error: Model did not return any finite value."
1839	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1840	else:
1841	msg = "Computation completed!"
1842	if number_finite != y.size:
1843	msg += ' PROBLEM: For some Q values the model returns non finite intensities!'
1844	logger.error("For some Q values the model returns non finite intensities.")
1845	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1846
1847	def _calc_exception(self, etype, value, tb):
1848	"""
1849	Handle exception from calculator by posting it as an error.
1850	"""
1851	logger.error("".join(traceback.format_exception(etype, value, tb)))
1852	msg = traceback.format_exception(etype, value, tb, limit=1)
1853	evt = StatusEvent(status="".join(msg), type="stop", info="error")
1854	wx.PostEvent(self.parent, evt)
1855
1856	def _update2D(self, output, time=None):
1857	"""
1858	Update the output of plotting model
1859	"""
1860	msg = "Plot updating ... "
1861	wx.PostEvent(self.parent, StatusEvent(msg, type="update"))
1862
1863	def _complete2D(self, image, data, model, page_id, elapsed, index, qmin,
1864	qmax, fid=None, weight=None, toggle_mode_on=False, state=None,
1865	update_chisqr=True, source='model', plot_result=True):
1866	"""
1867	Complete get the result of modelthread and create model 2D
1868	that can be plot.
1869	"""
1870	number_finite = np.count_nonzero(np.isfinite(image))
1871	np.nan_to_num(image)
1872	new_plot = Data2D(image=image, err_image=data.err_data)
1873	new_plot.name = model.name + '2d'
1874	new_plot.title = "Analytical model 2D "
1875	new_plot.id = str(page_id) + " " + data.name
1876	new_plot.group_id = str(page_id) + " Model2D"
1877	new_plot.detector = data.detector
1878	new_plot.source = data.source
1879	new_plot.is_data = False
1880	new_plot.qx_data = data.qx_data
1881	new_plot.qy_data = data.qy_data
1882	new_plot.q_data = data.q_data
1883	new_plot.mask = data.mask
1884	## plot boundaries
1885	new_plot.ymin = data.ymin
1886	new_plot.ymax = data.ymax
1887	new_plot.xmin = data.xmin
1888	new_plot.xmax = data.xmax
1889	title = data.title
1890
1891	new_plot.is_data = False
1892	if data.is_data:
1893	data_name = str(data.name)
1894	else:
1895	data_name = str(model.__class__.__name__) + '2d'
1896
1897	if len(title) > 1:
1898	new_plot.title = "Model2D for %s " % model.name + data_name
1899	new_plot.name = model.name + " [" + \
1900	data_name + "]"
1901	theory_data = deepcopy(new_plot)
1902
1903	self.page_finder[page_id].set_theory_data(data=theory_data,
1904	fid=data.id)
1905	self.parent.update_theory(data_id=data.id,
1906	theory=new_plot,
1907	state=state)
1908	current_pg = self.fit_panel.get_page_by_id(page_id)
1909	title = new_plot.title
1910	if not source == 'fit' and plot_result:
1911	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))
1912	if toggle_mode_on:
1913	wx.PostEvent(self.parent,
1914	NewPlotEvent(group_id=str(page_id) + " Model1D",
1915	action="Hide"))
1916	else:
1917	# Chisqr in fitpage
1918	if update_chisqr:
1919	output = self._cal_chisqr(data=data,
1920	weight=weight,
1921	fid=fid,
1922	page_id=page_id,
1923	index=index)
1924	wx.PostEvent(current_pg, Chi2UpdateEvent(output=output))
1925	else:
1926	self._plot_residuals(page_id=page_id, data=data, fid=fid,
1927	index=index, weight=weight)
1928
1929	if not number_finite:
1930	logger.error("Using the present parameters the model does not return any finite value. ")
1931	msg = "Computing Error: Model did not return any finite value."
1932	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
1933	else:
1934	msg = "Computation completed!"
1935	if number_finite != image.size:
1936	msg += ' PROBLEM: For some Qx,Qy values the model returns non finite intensities!'
1937	logger.error("For some Qx,Qy values the model returns non finite intensities.")
1938	wx.PostEvent(self.parent, StatusEvent(status=msg, type="stop"))
1939
1940	def _draw_model2D(self, model, page_id, qmin,
1941	qmax,
1942	data=None, smearer=None,
1943	description=None, enable2D=False,
1944	state=None,
1945	fid=None,
1946	weight=None,
1947	toggle_mode_on=False,
1948	update_chisqr=True, source='model'):
1949	"""
1950	draw model in 2D
1951
1952	:param model: instance of the model to draw
1953	:param description: the description of the model
1954	:param enable2D: when True allows to draw model 2D
1955	:param qmin: the minimum value to draw model 2D
1956	:param qmax: the maximum value to draw model 2D
1957	:param qstep: the number of division of Qx and Qy of the model to draw
1958
1959	"""
1960	if not enable2D:
1961	return None
1962	try:
1963	## If a thread is already started, stop it
1964	if (self.calc_2D is not None) and self.calc_2D.isrunning():
1965	self.calc_2D.stop()
1966	## stop just raises a flag to tell the thread to kill
1967	## itself -- see the fix in Calc1D implemented to fix
1968	## an actual problem. Seems the fix should also go here
1969	## and may be the cause of other noted instabilities
1970	##
1971	## -PDB August 12, 2014
1972	while self.calc_2D.isrunning():
1973	time.sleep(0.1)
1974	self.calc_2D = Calc2D(model=model,
1975	data=data,
1976	page_id=page_id,
1977	smearer=smearer,
1978	qmin=qmin,
1979	qmax=qmax,
1980	weight=weight,
1981	fid=fid,
1982	toggle_mode_on=toggle_mode_on,
1983	state=state,
1984	completefn=self._complete2D,
1985	update_chisqr=update_chisqr,
1986	exception_handler=self._calc_exception,
1987	source=source)
1988	self.calc_2D.queue()
1989	except:
1990	raise
1991
1992	def _draw_model1D(self, model, page_id, data,
1993	qmin, qmax, smearer=None,
1994	state=None, weight=None, fid=None,
1995	toggle_mode_on=False, update_chisqr=True, source='model',
1996	enable1D=True):
1997	"""
1998	Draw model 1D from loaded data1D
1999
2000	:param data: loaded data
2001	:param model: the model to plot
2002
2003	"""
2004	if not enable1D:
2005	return
2006	try:
2007	## If a thread is already started, stop it
2008	if (self.calc_1D is not None) and self.calc_1D.isrunning():
2009	self.calc_1D.stop()
2010	## stop just raises the flag -- the thread is supposed to
2011	## then kill itself but cannot. Paul Kienzle came up with
2012	## this fix to prevent threads from stepping on each other
2013	## which was causing a simple custom plugin model to crash
2014	##Sasview.
2015	## We still don't know why the fit sometimes lauched a second
2016	## thread -- something which should also be investigated.
2017	## The thread approach was implemented in order to be able
2018	## to lauch a computation in a separate thread from the GUI so
2019	## that the GUI can still respond to user input including
2020	## a request to stop the computation.
2021	## It seems thus that the whole thread approach used here
2022	## May need rethinking
2023	##
2024	## -PDB August 12, 2014
2025	while self.calc_1D.isrunning():
2026	time.sleep(0.1)
2027	self.calc_1D = Calc1D(data=data,
2028	model=model,
2029	page_id=page_id,
2030	qmin=qmin,
2031	qmax=qmax,
2032	smearer=smearer,
2033	state=state,
2034	weight=weight,
2035	fid=fid,
2036	toggle_mode_on=toggle_mode_on,
2037	completefn=self._complete1D,
2038	#updatefn = self._update1D,
2039	update_chisqr=update_chisqr,
2040	exception_handler=self._calc_exception,
2041	source=source)
2042	self.calc_1D.queue()
2043	except:
2044	msg = " Error occurred when drawing %s Model 1D: " % model.name
2045	msg += " %s" % sys.exc_value
2046	wx.PostEvent(self.parent, StatusEvent(status=msg))
2047
2048	def _cal_chisqr(self, page_id, data, weight, fid=None, index=None):
2049	"""
2050	Get handy Chisqr using the output from draw1D and 2D,
2051	instead of calling expansive CalcChisqr in guithread
2052	"""
2053	try:
2054	data_copy = deepcopy(data)
2055	except:
2056	return
2057	# default chisqr
2058	chisqr = None
2059	#to compute chisq make sure data has valid data
2060	# return None if data is None
2061	if not check_data_validity(data_copy) or data_copy is None:
2062	return chisqr
2063
2064	# Get data: data I, theory I, and data dI in order
2065	if data_copy.__class__.__name__ == "Data2D":
2066	if index is None:
2067	index = np.ones(len(data_copy.data), dtype=bool)
2068	if weight is not None:
2069	data_copy.err_data = weight
2070	# get rid of zero error points
2071	index = index & (data_copy.err_data != 0)
2072	index = index & (np.isfinite(data_copy.data))
2073	fn = data_copy.data[index]
2074	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2075	if theory_data is None:
2076	return chisqr
2077	gn = theory_data.data[index]
2078	en = data_copy.err_data[index]
2079	else:
2080	# 1 d theory from model_thread is only in the range of index
2081	if index is None:
2082	index = np.ones(len(data_copy.y), dtype=bool)
2083	if weight is not None:
2084	data_copy.dy = weight
2085	if data_copy.dy is None or data_copy.dy == []:
2086	dy = np.ones(len(data_copy.y))
2087	else:
2088	## Set consistently w/AbstractFitengine:
2089	# But this should be corrected later.
2090	dy = deepcopy(data_copy.dy)
2091	dy[dy == 0] = 1
2092	fn = data_copy.y[index]
2093
2094	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2095	if theory_data is None:
2096	return chisqr
2097	gn = theory_data.y
2098	en = dy[index]
2099
2100	# residual
2101	try:
2102	res = (fn - gn) / en
2103	except ValueError:
2104	print("Unmatch lengths %s, %s, %s" % (len(fn), len(gn), len(en)))
2105	return
2106
2107	residuals = res[np.isfinite(res)]
2108	# get chisqr only w/finite
2109	chisqr = np.average(residuals * residuals)
2110
2111	self._plot_residuals(page_id=page_id, data=data_copy,
2112	fid=fid,
2113	weight=weight, index=index)
2114
2115	return chisqr
2116
2117	def _plot_residuals(self, page_id, weight, fid=None,
2118	data=None, index=None):
2119	"""
2120	Plot the residuals
2121
2122	:param data: data
2123	:param index: index array (bool)
2124	: Note: this is different from the residuals in cal_chisqr()
2125	"""
2126	data_copy = deepcopy(data)
2127	# Get data: data I, theory I, and data dI in order
2128	if data_copy.__class__.__name__ == "Data2D":
2129	# build residuals
2130	residuals = Data2D()
2131	#residuals.copy_from_datainfo(data)
2132	# Not for trunk the line below, instead use the line above
2133	data_copy.clone_without_data(len(data_copy.data), residuals)
2134	residuals.data = None
2135	fn = data_copy.data
2136	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2137	gn = theory_data.data
2138	if weight is None:
2139	en = data_copy.err_data
2140	else:
2141	en = weight
2142	residuals.data = (fn - gn) / en
2143	residuals.qx_data = data_copy.qx_data
2144	residuals.qy_data = data_copy.qy_data
2145	residuals.q_data = data_copy.q_data
2146	residuals.err_data = np.ones(len(residuals.data))
2147	residuals.xmin = min(residuals.qx_data)
2148	residuals.xmax = max(residuals.qx_data)
2149	residuals.ymin = min(residuals.qy_data)
2150	residuals.ymax = max(residuals.qy_data)
2151	residuals.q_data = data_copy.q_data
2152	residuals.mask = data_copy.mask
2153	residuals.scale = 'linear'
2154	# check the lengths
2155	if len(residuals.data) != len(residuals.q_data):
2156	return
2157	else:
2158	# 1 d theory from model_thread is only in the range of index
2159	if data_copy.dy is None or data_copy.dy == []:
2160	dy = np.ones(len(data_copy.y))
2161	else:
2162	if weight is None:
2163	dy = np.ones(len(data_copy.y))
2164	## Set consitently w/AbstractFitengine:
2165	## But this should be corrected later.
2166	else:
2167	dy = weight
2168	dy[dy == 0] = 1
2169	fn = data_copy.y[index]
2170	theory_data = self.page_finder[page_id].get_theory_data(fid=data_copy.id)
2171	gn = theory_data.y
2172	en = dy[index]
2173	# build residuals
2174	residuals = Data1D()
2175	try:
2176	residuals.y = (fn - gn) / en
2177	except:
2178	msg = "ResidualPlot Error: different # of data points in theory"
2179	wx.PostEvent(self.parent, StatusEvent(status=msg, info="error"))
2180	residuals.y = (fn - gn[index]) / en
2181	residuals.x = data_copy.x[index]
2182	residuals.dy = np.ones(len(residuals.y))
2183	residuals.dx = None
2184	residuals.dxl = None
2185	residuals.dxw = None
2186	residuals.ytransform = 'y'
2187	# For latter scale changes
2188	residuals.xaxis('\\rm{Q} ', 'A^{-1}')
2189	residuals.yaxis('\\rm{Residuals} ', 'normalized')
2190	theory_name = str(theory_data.name.split()[0])
2191	new_plot = residuals
2192	new_plot.name = "Residuals for " + str(theory_name) + "[" + \
2193	str(data.name) + "]"
2194	## allow to highlight data when plotted
2195	new_plot.interactive = True
2196	## when 2 data have the same id override the 1 st plotted
2197	new_plot.id = "res" + str(data_copy.id) + str(theory_name)
2198	##group_id specify on which panel to plot this data
2199	group_id = self.page_finder[page_id].get_graph_id()
2200	if group_id is None:
2201	group_id = data.group_id
2202	new_plot.group_id = "res" + str(group_id)
2203	#new_plot.is_data = True
2204	##post data to plot
2205	title = new_plot.name
2206	self.page_finder[page_id].set_residuals(residuals=new_plot,
2207	fid=data.id)
2208	self.parent.update_theory(data_id=data.id, theory=new_plot)
2209	batch_on = self.fit_panel.get_page_by_id(page_id).batch_on
2210	if not batch_on:
2211	wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))

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SasView

source: sasview/src/sas/sasgui/perspectives/fitting/fitting.py @ 1c206d9

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