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source: trunk/GSASIIgrid.py @ 2110

Last change on this file since 2110 was 2110, checked in by vondreele, 7 years ago
add menu item for global setting of wave vary parameters - TBD split StructureFactorDeriv? over twins & incommensurate do block refl for the nontwin/powder one
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1	# -- coding: utf-8 --
2	#GSASIIgrid - data display routines
3	########### SVN repository information ###################
4	# $Date: 2016-01-03 18:40:04 +0000 (Sun, 03 Jan 2016) $
5	# $Author: vondreele $
6	# $Revision: 2110 $
7	# $URL: trunk/GSASIIgrid.py $
8	# $Id: GSASIIgrid.py 2110 2016-01-03 18:40:04Z vondreele $
9	########### SVN repository information ###################
10	'''
11	GSASIIgrid: Basic GUI routines
12	--------------------------------
13
14	'''
15	import wx
16	import wx.grid as wg
17	#import wx.wizard as wz
18	#import wx.aui
19	import wx.lib.scrolledpanel as wxscroll
20	import time
21	import copy
22	import cPickle
23	import sys
24	import os
25	import numpy as np
26	import numpy.ma as ma
27	import scipy.optimize as so
28	import GSASIIpath
29	GSASIIpath.SetVersionNumber("$Revision: 2110 $")
30	import GSASIImath as G2mth
31	import GSASIIIO as G2IO
32	import GSASIIstrIO as G2stIO
33	import GSASIIlattice as G2lat
34	import GSASIIplot as G2plt
35	import GSASIIpwdGUI as G2pdG
36	import GSASIIimgGUI as G2imG
37	import GSASIIphsGUI as G2phG
38	import GSASIIspc as G2spc
39	import GSASIImapvars as G2mv
40	import GSASIIconstrGUI as G2cnstG
41	import GSASIIrestrGUI as G2restG
42	import GSASIIpy3 as G2py3
43	import GSASIIobj as G2obj
44	import GSASIIexprGUI as G2exG
45	import GSASIIlog as log
46	import GSASIIctrls as G2G
47
48	# trig functions in degrees
49	sind = lambda x: np.sin(x*np.pi/180.)
50	tand = lambda x: np.tan(x*np.pi/180.)
51	cosd = lambda x: np.cos(x*np.pi/180.)
52
53	# Define a short name for convenience
54	WACV = wx.ALIGN_CENTER_VERTICAL
55
56	[ wxID_FOURCALC, wxID_FOURSEARCH, wxID_FOURCLEAR, wxID_PEAKSMOVE, wxID_PEAKSCLEAR,
57	wxID_CHARGEFLIP, wxID_PEAKSUNIQUE, wxID_PEAKSDELETE, wxID_PEAKSDA,
58	wxID_PEAKSDISTVP, wxID_PEAKSVIEWPT, wxID_FINDEQVPEAKS,wxID_SHOWBONDS,wxID_MULTIMCSA,
59	wxID_SINGLEMCSA,wxID_4DCHARGEFLIP,
60	] = [wx.NewId() for item in range(16)]
61
62	[ wxID_PWDRADD, wxID_HKLFADD, wxID_PWDANALYSIS, wxID_PWDCOPY, wxID_PLOTCTRLCOPY,
63	wxID_DATADELETE,wxID_DATACOPY,wxID_DATACOPYFLAGS,wxID_DATASELCOPY,
64	] = [wx.NewId() for item in range(9)]
65
66	[ wxID_ATOMSEDITADD, wxID_ATOMSEDITINSERT, wxID_ATOMSEDITDELETE, wxID_ATOMSREFINE,
67	wxID_ATOMSMODIFY, wxID_ATOMSTRANSFORM, wxID_ATOMSVIEWADD, wxID_ATOMVIEWINSERT,
68	wxID_RELOADDRAWATOMS,wxID_ATOMSDISAGL,wxID_ATOMMOVE,wxID_MAKEMOLECULE,
69	wxID_ASSIGNATMS2RB,wxID_ATOMSPDISAGL, wxID_ISODISP,wxID_ADDHATOM,wxID_UPDATEHATOM,
70	wxID_WAVEVARY,
71	] = [wx.NewId() for item in range(18)]
72
73	[ wxID_DRAWATOMSTYLE, wxID_DRAWATOMLABEL, wxID_DRAWATOMCOLOR, wxID_DRAWATOMRESETCOLOR,
74	wxID_DRAWVIEWPOINT, wxID_DRAWTRANSFORM, wxID_DRAWDELETE, wxID_DRAWFILLCELL,
75	wxID_DRAWADDEQUIV, wxID_DRAWFILLCOORD, wxID_DRAWDISAGLTOR, wxID_DRAWPLANE,
76	wxID_DRAWDISTVP,
77	] = [wx.NewId() for item in range(13)]
78
79	[ wxID_DRAWRESTRBOND, wxID_DRAWRESTRANGLE, wxID_DRAWRESTRPLANE, wxID_DRAWRESTRCHIRAL,
80	] = [wx.NewId() for item in range(4)]
81
82	[ wxID_ADDMCSAATOM,wxID_ADDMCSARB,wxID_CLEARMCSARB,wxID_MOVEMCSA,wxID_MCSACLEARRESULTS,
83	] = [wx.NewId() for item in range(5)]
84
85	[ wxID_CLEARTEXTURE,wxID_REFINETEXTURE,
86	] = [wx.NewId() for item in range(2)]
87
88	[ wxID_PAWLEYLOAD, wxID_PAWLEYESTIMATE, wxID_PAWLEYUPDATE,
89	] = [wx.NewId() for item in range(3)]
90
91	[ wxID_IMCALIBRATE,wxID_IMRECALIBRATE,wxID_IMINTEGRATE, wxID_IMCLEARCALIB,
92	wxID_IMCOPYCONTROLS, wxID_INTEGRATEALL, wxID_IMSAVECONTROLS, wxID_IMLOADCONTROLS, wxID_IMAUTOINTEG,
93	] = [wx.NewId() for item in range(9)]
94
95	[ wxID_MASKCOPY, wxID_MASKSAVE, wxID_MASKLOAD, wxID_NEWMASKSPOT,wxID_NEWMASKARC,wxID_NEWMASKRING,
96	wxID_NEWMASKFRAME, wxID_NEWMASKPOLY, wxID_MASKLOADNOT,
97	] = [wx.NewId() for item in range(9)]
98
99	[ wxID_STRSTACOPY, wxID_STRSTAFIT, wxID_STRSTASAVE, wxID_STRSTALOAD,wxID_STRSTSAMPLE,
100	wxID_APPENDDZERO,wxID_STRSTAALLFIT,wxID_UPDATEDZERO,
101	] = [wx.NewId() for item in range(8)]
102
103	[ wxID_BACKCOPY,wxID_LIMITCOPY, wxID_SAMPLECOPY, wxID_SAMPLECOPYSOME, wxID_BACKFLAGCOPY, wxID_SAMPLEFLAGCOPY,
104	wxID_SAMPLESAVE, wxID_SAMPLELOAD,wxID_ADDEXCLREGION,wxID_SETSCALE,wxID_SAMPLE1VAL,wxID_ALLSAMPLELOAD,
105	] = [wx.NewId() for item in range(12)]
106
107	[ wxID_INSTPRMRESET,wxID_CHANGEWAVETYPE,wxID_INSTCOPY, wxID_INSTFLAGCOPY, wxID_INSTLOAD,
108	wxID_INSTSAVE, wxID_INST1VAL, wxID_INSTCALIB,
109	] = [wx.NewId() for item in range(8)]
110
111	[ wxID_UNDO,wxID_LSQPEAKFIT,wxID_LSQONECYCLE,wxID_RESETSIGGAM,wxID_CLEARPEAKS,wxID_AUTOSEARCH,
112	wxID_PEAKSCOPY, wxID_SEQPEAKFIT,
113	] = [wx.NewId() for item in range(8)]
114
115	[ wxID_INDXRELOAD, wxID_INDEXPEAKS, wxID_REFINECELL, wxID_COPYCELL, wxID_MAKENEWPHASE,
116	wxID_EXPORTCELLS,
117	] = [wx.NewId() for item in range(6)]
118
119	[ wxID_CONSTRAINTADD,wxID_EQUIVADD,wxID_HOLDADD,wxID_FUNCTADD,wxID_ADDRIDING,
120	wxID_CONSPHASE, wxID_CONSHIST, wxID_CONSHAP, wxID_CONSGLOBAL,wxID_EQUIVALANCEATOMS,
121	] = [wx.NewId() for item in range(10)]
122
123	[ wxID_RESTRAINTADD, wxID_RESTSELPHASE,wxID_RESTDELETE, wxID_RESRCHANGEVAL,
124	wxID_RESTCHANGEESD,wxID_AARESTRAINTADD,wxID_AARESTRAINTPLOT,
125	] = [wx.NewId() for item in range(7)]
126
127	[ wxID_RIGIDBODYADD,wxID_DRAWDEFINERB,wxID_RIGIDBODYIMPORT,wxID_RESIDUETORSSEQ,
128	wxID_AUTOFINDRESRB,wxID_GLOBALRESREFINE,wxID_RBREMOVEALL,wxID_COPYRBPARMS,
129	wxID_GLOBALTHERM,wxID_VECTORBODYADD
130	] = [wx.NewId() for item in range(10)]
131
132	[ wxID_RENAMESEQSEL,wxID_SAVESEQSEL,wxID_SAVESEQSELCSV,wxID_SAVESEQCSV,wxID_PLOTSEQSEL,
133	wxID_ORGSEQSEL,wxADDSEQVAR,wxDELSEQVAR,wxEDITSEQVAR,wxCOPYPARFIT,wxID_AVESEQSEL,
134	wxADDPARFIT,wxDELPARFIT,wxEDITPARFIT,wxDOPARFIT,
135	] = [wx.NewId() for item in range(15)]
136
137	[ wxID_MODELCOPY,wxID_MODELFIT,wxID_MODELADD,wxID_ELEMENTADD,wxID_ELEMENTDELETE,
138	wxID_ADDSUBSTANCE,wxID_LOADSUBSTANCE,wxID_DELETESUBSTANCE,wxID_COPYSUBSTANCE,
139	wxID_MODELUNDO,wxID_MODELFITALL,wxID_MODELCOPYFLAGS,
140	] = [wx.NewId() for item in range(12)]
141
142	[ wxID_SELECTPHASE,wxID_PWDHKLPLOT,wxID_PWD3DHKLPLOT,wxID_3DALLHKLPLOT,
143	] = [wx.NewId() for item in range(4)]
144
145	[ wxID_PDFCOPYCONTROLS, wxID_PDFSAVECONTROLS, wxID_PDFLOADCONTROLS,
146	wxID_PDFCOMPUTE, wxID_PDFCOMPUTEALL, wxID_PDFADDELEMENT, wxID_PDFDELELEMENT,
147	] = [wx.NewId() for item in range(7)]
148
149	[ wxID_MCRON,wxID_MCRLIST,wxID_MCRSAVE,wxID_MCRPLAY,
150	] = [wx.NewId() for item in range(4)]
151
152	VERY_LIGHT_GREY = wx.Colour(235,235,235)
153
154	# Aliases for Classes/Functions moved to GSASIIctrls, all should be tracked down but leaving as a reminder
155	#SingleFloatDialog = G2G.SingleFloatDialog
156	#SingleStringDialog = G2G.SingleStringDialog
157	#MultiStringDialog = G2G.MultiStringDialog
158	#G2ColumnIDDialog = G2G.G2ColumnIDDialog
159	#ItemSelector = G2G.ItemSelector
160	#HorizontalLine = G2G.HorizontalLine
161	#G2LoggedButton = G2G.G2LoggedButton
162	#EnumSelector = G2G.EnumSelector
163	#G2ChoiceButton = G2G.G2ChoiceButton
164	#GSGrid = G2G.GSGrid
165	#Table = G2G.Table
166	#GridFractionEditor = G2G.GridFractionEditor
167	#GSNoteBook = G2G.GSNoteBook
168
169	# Should SGMessageBox, SymOpDialog, DisAglDialog be moved?
170
171	################################################################################
172	#### GSAS-II class definitions
173	################################################################################
174
175	class SGMessageBox(wx.Dialog):
176	''' Special version of MessageBox that displays space group & super space group text
177	in two blocks
178	'''
179	def __init__(self,parent,title,text,table,):
180	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,pos=wx.DefaultPosition,
181	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
182	self.text=text
183	self.table = table
184	self.panel = wx.Panel(self)
185	mainSizer = wx.BoxSizer(wx.VERTICAL)
186	mainSizer.Add((0,10))
187	for line in text:
188	mainSizer.Add(wx.StaticText(self.panel,label=' %s '%(line)),0,WACV)
189	ncol = self.table[0].count(',')+1
190	tableSizer = wx.FlexGridSizer(0,2*ncol+3,0,0)
191	for j,item in enumerate(self.table):
192	num,flds = item.split(')')
193	tableSizer.Add(wx.StaticText(self.panel,label=' %s '%(num+')')),0,WACV\|wx.ALIGN_LEFT)
194	flds = flds.replace(' ','').split(',')
195	for i,fld in enumerate(flds):
196	if i < ncol-1:
197	tableSizer.Add(wx.StaticText(self.panel,label='%s, '%(fld)),0,WACV\|wx.ALIGN_RIGHT)
198	else:
199	tableSizer.Add(wx.StaticText(self.panel,label='%s'%(fld)),0,WACV\|wx.ALIGN_RIGHT)
200	if not j%2:
201	tableSizer.Add((20,0))
202	mainSizer.Add(tableSizer,0,wx.ALIGN_LEFT)
203	btnsizer = wx.StdDialogButtonSizer()
204	OKbtn = wx.Button(self.panel, wx.ID_OK)
205	OKbtn.SetDefault()
206	btnsizer.AddButton(OKbtn)
207	btnsizer.Realize()
208	mainSizer.Add((0,10))
209	mainSizer.Add(btnsizer,0,wx.ALIGN_CENTER)
210	self.panel.SetSizer(mainSizer)
211	self.panel.Fit()
212	self.Fit()
213	size = self.GetSize()
214	self.SetSize([size[0]+20,size[1]])
215
216	def Show(self):
217	'''Use this method after creating the dialog to post it
218	'''
219	self.ShowModal()
220	return
221
222	################################################################################
223	class SymOpDialog(wx.Dialog):
224	'''Class to select a symmetry operator
225	'''
226	def __init__(self,parent,SGData,New=True,ForceUnit=False):
227	wx.Dialog.__init__(self,parent,-1,'Select symmetry operator',
228	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
229	panel = wx.Panel(self)
230	self.SGData = SGData
231	self.New = New
232	self.Force = ForceUnit
233	self.OpSelected = [0,0,0,[0,0,0],False,False]
234	mainSizer = wx.BoxSizer(wx.VERTICAL)
235	if ForceUnit:
236	choice = ['No','Yes']
237	self.force = wx.RadioBox(panel,-1,'Force to unit cell?',choices=choice)
238	self.force.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
239	mainSizer.Add(self.force,0,WACV\|wx.TOP,5)
240	# if SGData['SGInv']:
241	choice = ['No','Yes']
242	self.inv = wx.RadioBox(panel,-1,'Choose inversion?',choices=choice)
243	self.inv.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
244	mainSizer.Add(self.inv,0,WACV)
245	if SGData['SGLatt'] != 'P':
246	LattOp = G2spc.Latt2text(SGData['SGLatt']).split(';')
247	self.latt = wx.RadioBox(panel,-1,'Choose cell centering?',choices=LattOp)
248	self.latt.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
249	mainSizer.Add(self.latt,0,WACV)
250	if SGData['SGLaue'] in ['-1','2/m','mmm','4/m','4/mmm']:
251	Ncol = 2
252	else:
253	Ncol = 3
254	OpList = []
255	for Opr in SGData['SGOps']:
256	OpList.append(G2spc.MT2text(Opr))
257	self.oprs = wx.RadioBox(panel,-1,'Choose space group operator?',choices=OpList,
258	majorDimension=Ncol)
259	self.oprs.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
260	mainSizer.Add(self.oprs,0,WACV\|wx.BOTTOM,5)
261	mainSizer.Add(wx.StaticText(panel,-1," Choose unit cell?"),0,WACV)
262	cellSizer = wx.BoxSizer(wx.HORIZONTAL)
263	cellName = ['X','Y','Z']
264	self.cell = []
265	for i in range(3):
266	self.cell.append(wx.SpinCtrl(panel,-1,cellName[i],size=wx.Size(50,20)))
267	self.cell[-1].SetRange(-3,3)
268	self.cell[-1].SetValue(0)
269	self.cell[-1].Bind(wx.EVT_SPINCTRL, self.OnOpSelect)
270	cellSizer.Add(self.cell[-1],0,WACV)
271	mainSizer.Add(cellSizer,0,WACV\|wx.BOTTOM,5)
272	if self.New:
273	choice = ['No','Yes']
274	self.new = wx.RadioBox(panel,-1,'Generate new positions?',choices=choice)
275	self.new.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
276	mainSizer.Add(self.new,0,WACV)
277
278	OkBtn = wx.Button(panel,-1,"Ok")
279	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
280	cancelBtn = wx.Button(panel,-1,"Cancel")
281	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
282	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
283	btnSizer.Add((20,20),1)
284	btnSizer.Add(OkBtn)
285	btnSizer.Add((20,20),1)
286	btnSizer.Add(cancelBtn)
287	btnSizer.Add((20,20),1)
288
289	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
290	panel.SetSizer(mainSizer)
291	panel.Fit()
292	self.Fit()
293
294	def OnOpSelect(self,event):
295	# if self.SGData['SGInv']:
296	self.OpSelected[0] = self.inv.GetSelection()
297	if self.SGData['SGLatt'] != 'P':
298	self.OpSelected[1] = self.latt.GetSelection()
299	self.OpSelected[2] = self.oprs.GetSelection()
300	for i in range(3):
301	self.OpSelected[3][i] = float(self.cell[i].GetValue())
302	if self.New:
303	self.OpSelected[4] = self.new.GetSelection()
304	if self.Force:
305	self.OpSelected[5] = self.force.GetSelection()
306
307	def GetSelection(self):
308	return self.OpSelected
309
310	def OnOk(self,event):
311	parent = self.GetParent()
312	parent.Raise()
313	self.EndModal(wx.ID_OK)
314
315	def OnCancel(self,event):
316	parent = self.GetParent()
317	parent.Raise()
318	self.EndModal(wx.ID_CANCEL)
319
320	################################################################################
321	class AddHatomDialog(wx.Dialog):
322	'''H atom addition dialog. After :meth:`ShowModal` returns, the results
323	are found in dict :attr:`self.data`, which is accessed using :meth:`GetData`.
324
325	:param wx.Frame parent: reference to parent frame (or None)
326	:param dict Neigh: a dict of atom names with list of atom name, dist pairs for neighboring atoms
327	:param dict phase: a dict containing the phase as defined by
328	:ref:`Phase Tree Item <Phase_table>`
329	'''
330	def __init__(self,parent,Neigh,phase):
331	wx.Dialog.__init__(self,parent,wx.ID_ANY,'H atom add',
332	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
333	self.panel = wxscroll.ScrolledPanel(self) #just a dummy - gets destroyed in Draw!
334	self.Neigh = Neigh
335	self.phase = phase
336	self.Hatoms = []
337	self.Draw(self.Neigh,self.phase)
338
339	def Draw(self,Neigh,phase):
340	'''Creates the contents of the dialog. Normally called
341	by :meth:`__init__`.
342	'''
343	def OnHSelect(event):
344	Obj = event.GetEventObject()
345	item,i = Indx[Obj.GetId()]
346	for obj in Indx[item]:
347	obj.SetValue(False)
348	Obj.SetValue(True)
349	self.Neigh[item][2] = i
350
351	def OnBond(event):
352	Obj = event.GetEventObject()
353	inei,ibond = Indx[Obj.GetId()]
354	self.Neigh[inei][1][0][ibond][2] = Obj.GetValue()
355
356	self.panel.Destroy()
357	self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE)
358	mainSizer = wx.BoxSizer(wx.VERTICAL)
359	mainSizer.Add(wx.StaticText(self.panel,-1,'H atom add controls for phase %s:'%(phase['General']['Name'])),
360	0,wx.LEFT\|wx.TOP,10)
361	mainSizer.Add(wx.StaticText(self.panel,-1,'NB: Check selections as they may not be correct'),0,WACV\|wx.LEFT,10)
362	mainSizer.Add(wx.StaticText(self.panel,-1," Atom: Add # H's Use: Neighbors, dist"),0,wx.TOP\|wx.LEFT,5)
363	nHatms = ['0','1','2','3']
364	dataSizer = wx.FlexGridSizer(0,3,0,0)
365	Indx = {}
366	for inei,neigh in enumerate(Neigh):
367	dataSizer.Add(wx.StaticText(self.panel,-1,' %s: '%(neigh[0])),0,WACV)
368	nH = 1 #for O atom
369	if 'C' in neigh[0] or 'N' in neigh[0]:
370	nH = 4-len(neigh[1][0])
371	checks = wx.BoxSizer(wx.HORIZONTAL)
372	Ids = []
373	for i in range(nH+1):
374	nHs = wx.CheckBox(self.panel,-1,label=nHatms[i])
375	if i == neigh[2]:
376	nHs.SetValue(True)
377	Indx[nHs.GetId()] = [inei,i]
378	Ids.append(nHs)
379	nHs.Bind(wx.EVT_CHECKBOX, OnHSelect)
380	checks.Add(nHs,0,WACV)
381	Indx[inei] = Ids
382	dataSizer.Add(checks,0,WACV)
383	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
384	for ib,bond in enumerate(neigh[1][0]):
385	Bond = wx.CheckBox(self.panel,-1,label=': %s, %.3f'%(bond[0],bond[1]))
386	Bond.SetValue(bond[2])
387	Indx[Bond.GetId()] = [inei,ib]
388	Bond.Bind(wx.EVT_CHECKBOX,OnBond)
389	lineSizer.Add(Bond,0,WACV)
390	dataSizer.Add(lineSizer,0,WACV\|wx.RIGHT,10)
391	mainSizer.Add(dataSizer,0,wx.LEFT,5)
392
393	CancelBtn = wx.Button(self.panel,-1,'Cancel')
394	CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
395	OkBtn = wx.Button(self.panel,-1,'Ok')
396	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
397	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
398	btnSizer.Add((20,20),1)
399	btnSizer.Add(OkBtn)
400	btnSizer.Add((20,20),1)
401	btnSizer.Add(CancelBtn)
402	btnSizer.Add((20,20),1)
403	mainSizer.Add(btnSizer,0,wx.BOTTOM\|wx.TOP, 10)
404	size = np.array(self.GetSize())
405	self.panel.SetupScrolling()
406	self.panel.SetSizer(mainSizer)
407	self.panel.SetAutoLayout(1)
408	size = [size[0]-5,size[1]-20] #this fiddling is needed for older wx!
409	self.panel.SetSize(size)
410
411	def GetData(self):
412	'Returns the values from the dialog'
413	for neigh in self.Neigh:
414	for ibond,bond in enumerate(neigh[1][0]):
415	if not bond[2]:
416	neigh[1][1][1][ibond] = 0 #deselected bond
417	neigh[1][1][1] = [a for a in neigh[1][1][1] if a]
418	return self.Neigh #has #Hs to add for each entry
419
420	def OnOk(self,event):
421	'Called when the OK button is pressed'
422	parent = self.GetParent()
423	parent.Raise()
424	self.EndModal(wx.ID_OK)
425
426	def OnCancel(self,event):
427	parent = self.GetParent()
428	parent.Raise()
429	self.EndModal(wx.ID_CANCEL)
430
431	################################################################################
432	class DisAglDialog(wx.Dialog):
433	'''Distance/Angle Controls input dialog. After
434	:meth:`ShowModal` returns, the results are found in
435	dict :attr:`self.data`, which is accessed using :meth:`GetData`.
436
437	:param wx.Frame parent: reference to parent frame (or None)
438	:param dict data: a dict containing the current
439	search ranges or an empty dict, which causes default values
440	to be used.
441	Will be used to set element `DisAglCtls` in
442	:ref:`Phase Tree Item <Phase_table>`
443	:param dict default: A dict containing the default
444	search ranges for each element.
445	'''
446	def __init__(self,parent,data,default,Reset=True):
447	wx.Dialog.__init__(self,parent,wx.ID_ANY,
448	'Distance Angle Controls',
449	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
450	self.default = default
451	self.Reset = Reset
452	self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
453	self._default(data,self.default)
454	self.Draw(self.data)
455
456	def _default(self,data,default):
457	'''Set starting values for the search values, either from
458	the input array or from defaults, if input is null
459	'''
460	if data:
461	self.data = copy.deepcopy(data) # don't mess with originals
462	else:
463	self.data = {}
464	self.data['Name'] = default['Name']
465	self.data['Factors'] = [0.85,0.85]
466	self.data['AtomTypes'] = default['AtomTypes']
467	self.data['BondRadii'] = default['BondRadii'][:]
468	self.data['AngleRadii'] = default['AngleRadii'][:]
469
470	def Draw(self,data):
471	'''Creates the contents of the dialog. Normally called
472	by :meth:`__init__`.
473	'''
474	self.panel.Destroy()
475	self.panel = wx.Panel(self)
476	mainSizer = wx.BoxSizer(wx.VERTICAL)
477	mainSizer.Add(wx.StaticText(self.panel,-1,'Controls for phase '+data['Name']),
478	0,WACV\|wx.LEFT,10)
479	mainSizer.Add((10,10),1)
480
481	radiiSizer = wx.FlexGridSizer(0,3,5,5)
482	radiiSizer.Add(wx.StaticText(self.panel,-1,' Type'),0,WACV)
483	radiiSizer.Add(wx.StaticText(self.panel,-1,'Bond radii'),0,WACV)
484	radiiSizer.Add(wx.StaticText(self.panel,-1,'Angle radii'),0,WACV)
485	self.objList = {}
486	for id,item in enumerate(self.data['AtomTypes']):
487	radiiSizer.Add(wx.StaticText(self.panel,-1,' '+item),0,WACV)
488	bRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['BondRadii'][id]),style=wx.TE_PROCESS_ENTER)
489	self.objList[bRadii.GetId()] = ['BondRadii',id]
490	bRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
491	bRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
492	radiiSizer.Add(bRadii,0,WACV)
493	aRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['AngleRadii'][id]),style=wx.TE_PROCESS_ENTER)
494	self.objList[aRadii.GetId()] = ['AngleRadii',id]
495	aRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
496	aRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
497	radiiSizer.Add(aRadii,0,WACV)
498	mainSizer.Add(radiiSizer,0,wx.EXPAND)
499	factorSizer = wx.FlexGridSizer(0,2,5,5)
500	Names = ['Bond','Angle']
501	for i,name in enumerate(Names):
502	factorSizer.Add(wx.StaticText(self.panel,-1,name+' search factor'),0,WACV)
503	bondFact = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['Factors'][i]),style=wx.TE_PROCESS_ENTER)
504	self.objList[bondFact.GetId()] = ['Factors',i]
505	bondFact.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
506	bondFact.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
507	factorSizer.Add(bondFact)
508	mainSizer.Add(factorSizer,0,wx.EXPAND)
509
510	OkBtn = wx.Button(self.panel,-1,"Ok")
511	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
512	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
513	btnSizer.Add((20,20),1)
514	btnSizer.Add(OkBtn)
515	if self.Reset:
516	ResetBtn = wx.Button(self.panel,-1,'Reset')
517	ResetBtn.Bind(wx.EVT_BUTTON, self.OnReset)
518	btnSizer.Add(ResetBtn)
519	btnSizer.Add((20,20),1)
520	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
521	self.panel.SetSizer(mainSizer)
522	self.panel.Fit()
523	self.Fit()
524
525	def OnRadiiVal(self,event):
526	Obj = event.GetEventObject()
527	item = self.objList[Obj.GetId()]
528	try:
529	self.data[item[0]][item[1]] = float(Obj.GetValue())
530	except ValueError:
531	pass
532	Obj.SetValue("%.3f"%(self.data[item[0]][item[1]])) #reset in case of error
533
534	def GetData(self):
535	'Returns the values from the dialog'
536	return self.data
537
538	def OnOk(self,event):
539	'Called when the OK button is pressed'
540	parent = self.GetParent()
541	parent.Raise()
542	self.EndModal(wx.ID_OK)
543
544	def OnReset(self,event):
545	'Called when the Reset button is pressed'
546	data = {}
547	self._default(data,self.default)
548	self.Draw(self.data)
549
550	################################################################################
551	class ShowLSParms(wx.Dialog):
552	'''Create frame to show least-squares parameters
553	'''
554	def __init__(self,parent,title,parmDict,varyList,fullVaryList,
555	size=(300,430)):
556	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,size=size,
557	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
558	mainSizer = wx.BoxSizer(wx.VERTICAL)
559
560	panel = wxscroll.ScrolledPanel(
561	self, wx.ID_ANY,
562	#size=size,
563	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
564	num = len(varyList)
565	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,'Number of refined variables: '+str(num)))
566	if len(varyList) != len(fullVaryList):
567	num = len(fullVaryList) - len(varyList)
568	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,' + '+str(num)+' parameters are varied via constraints'))
569	subSizer = wx.FlexGridSizer(cols=4,hgap=2,vgap=2)
570	parmNames = parmDict.keys()
571	parmNames.sort()
572	subSizer.Add((-1,-1))
573	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'Parameter name '))
574	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'refine?'))
575	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'value'),0,wx.ALIGN_RIGHT)
576	explainRefine = False
577	for name in parmNames:
578	# skip entries without numerical values
579	if isinstance(parmDict[name],basestring): continue
580	try:
581	value = G2py3.FormatSigFigs(parmDict[name])
582	except TypeError:
583	value = str(parmDict[name])+' -?' # unexpected
584	#continue
585	v = G2obj.getVarDescr(name)
586	if v is None or v[-1] is None:
587	subSizer.Add((-1,-1))
588	else:
589	ch = G2G.HelpButton(panel,G2obj.fmtVarDescr(name))
590	subSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
591	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,str(name)))
592	if name in varyList:
593	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'R'))
594	elif name in fullVaryList:
595	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'C'))
596	explainRefine = True
597	else:
598	subSizer.Add((-1,-1))
599	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
600
601	# finish up ScrolledPanel
602	panel.SetSizer(subSizer)
603	panel.SetAutoLayout(1)
604	panel.SetupScrolling()
605	mainSizer.Add(panel,1, wx.ALL\|wx.EXPAND,1)
606
607	if explainRefine:
608	mainSizer.Add(
609	wx.StaticText(self,wx.ID_ANY,
610	'"R" indicates a refined variable\n'+
611	'"C" indicates generated from a constraint'
612	),
613	0, wx.ALL,0)
614	# make OK button
615	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
616	btn = wx.Button(self, wx.ID_CLOSE,"Close")
617	btn.Bind(wx.EVT_BUTTON,self._onClose)
618	btnsizer.Add(btn)
619	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
620	# Allow window to be enlarged but not made smaller
621	self.SetSizer(mainSizer)
622	self.SetMinSize(self.GetSize())
623
624	def _onClose(self,event):
625	self.EndModal(wx.ID_CANCEL)
626
627	################################################################################
628	class DataFrame(wx.Frame):
629	'''Create the data item window and all the entries in menus used in
630	that window. For Linux and windows, the menu entries are created for the
631	current data item window, but in the Mac the menu is accessed from all
632	windows. This means that a different menu is posted depending on which
633	data item is posted. On the Mac, all the menus contain the data tree menu
634	items, but additional menus are added specific to the data item.
635
636	Note that while the menus are created here,
637	the binding for the menus is done later in various GSASII*GUI modules,
638	where the functions to be called are defined.
639	'''
640	def Bind(self,eventtype,handler,args,*kwargs):
641	'''Override the Bind() function: on the Mac the binding is to
642	the main window, so that menus operate with any window on top.
643	For other platforms, either wrap calls that will be logged
644	or call the default wx.Frame Bind() to bind to the menu item directly.
645
646	Note that bindings can be made to objects by Id or by direct reference to the
647	object. As a convention, when bindings are to objects, they are not logged
648	but when bindings are by Id, they are logged.
649	'''
650	if sys.platform == "darwin": # mac
651	self.G2frame.Bind(eventtype,handler,args,*kwargs)
652	return
653	if eventtype == wx.EVT_MENU and 'id' in kwargs:
654	menulabels = log.SaveMenuCommand(kwargs['id'],self.G2frame,handler)
655	if menulabels:
656	#print 'intercepting bind for',handler,menulabels,kwargs['id']
657	wx.Frame.Bind(self,eventtype,self.G2frame.MenuBinding,args,*kwargs)
658	return
659	wx.Frame.Bind(self,eventtype,handler,args,*kwargs)
660
661	def PrefillDataMenu(self,menu,helpType,helpLbl=None,empty=False):
662	'''Create the "standard" part of data frame menus. Note that on Linux and
663	Windows nothing happens here. On Mac, this menu duplicates the
664	tree menu, but adds an extra help command for the data item and a separator.
665	'''
666	self.datamenu = menu
667	self.G2frame.dataMenuBars.append(menu)
668	self.helpType = helpType
669	self.helpLbl = helpLbl
670	if sys.platform == "darwin": # mac
671	self.G2frame.FillMainMenu(menu) # add the data tree menu items
672	if not empty:
673	menu.Append(wx.Menu(title=''),title='\|') # add a separator
674
675	def PostfillDataMenu(self,empty=False):
676	'''Create the "standard" part of data frame menus. Note that on Linux and
677	Windows, this is the standard help Menu. On Mac, this menu duplicates the
678	tree menu, but adds an extra help command for the data item and a separator.
679	'''
680	menu = self.datamenu
681	helpType = self.helpType
682	helpLbl = self.helpLbl
683	if sys.platform == "darwin": # mac
684	if not empty:
685	menu.Append(wx.Menu(title=''),title='\|') # add another separator
686	menu.Append(G2G.AddHelp(self.G2frame,helpType=helpType, helpLbl=helpLbl),
687	title='&Help')
688	else: # other
689	menu.Append(menu=G2G.MyHelp(self,helpType=helpType, helpLbl=helpLbl),
690	title='&Help')
691
692	def _init_menus(self):
693	'define all GSAS-II data frame menus'
694
695	# for use where no menu or data frame help is provided
696	self.BlankMenu = wx.MenuBar()
697
698	# Controls
699	self.ControlsMenu = wx.MenuBar()
700	self.PrefillDataMenu(self.ControlsMenu,helpType='Controls',empty=True)
701	self.PostfillDataMenu(empty=True)
702
703	# Notebook
704	self.DataNotebookMenu = wx.MenuBar()
705	self.PrefillDataMenu(self.DataNotebookMenu,helpType='Notebook',empty=True)
706	self.PostfillDataMenu(empty=True)
707
708	# Comments
709	self.DataCommentsMenu = wx.MenuBar()
710	self.PrefillDataMenu(self.DataCommentsMenu,helpType='Comments',empty=True)
711	self.PostfillDataMenu(empty=True)
712
713	# Constraints - something amiss here - get weird wx C++ error after refine!
714	self.ConstraintMenu = wx.MenuBar()
715	self.PrefillDataMenu(self.ConstraintMenu,helpType='Constraints')
716	self.ConstraintTab = wx.Menu(title='')
717	self.ConstraintMenu.Append(menu=self.ConstraintTab, title='Select tab')
718	for id,txt in (
719	(wxID_CONSPHASE,'Phase'),
720	(wxID_CONSHAP,'Histogram/Phase'),
721	(wxID_CONSHIST,'Histogram'),
722	(wxID_CONSGLOBAL,'Global')):
723	self.ConstraintTab.Append(
724	id=id, kind=wx.ITEM_NORMAL,text=txt,
725	help='Select '+txt+' constraint editing tab')
726	self.ConstraintEdit = wx.Menu(title='')
727	self.ConstraintMenu.Append(menu=self.ConstraintEdit, title='Edit')
728	self.ConstraintEdit.Append(id=wxID_HOLDADD, kind=wx.ITEM_NORMAL,text='Add hold',
729	help='Add hold on a parameter value')
730	self.ConstraintEdit.Append(id=wxID_EQUIVADD, kind=wx.ITEM_NORMAL,text='Add equivalence',
731	help='Add equivalence between parameter values')
732	self.ConstraintEdit.Append(id=wxID_CONSTRAINTADD, kind=wx.ITEM_NORMAL,text='Add constraint',
733	help='Add constraint on parameter values')
734	self.ConstraintEdit.Append(id=wxID_FUNCTADD, kind=wx.ITEM_NORMAL,text='Add New Var',
735	help='Add variable composed of existing parameter')
736	self.ConstraintEdit.Append(id=wxID_EQUIVALANCEATOMS, kind=wx.ITEM_NORMAL,text='Add atom equivalence',
737	help='Add equivalences between atom parameter values')
738	self.ConstraintEdit.Enable(wxID_EQUIVALANCEATOMS,False)
739	# self.ConstraintEdit.Append(id=wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add H riding constraints',
740	# help='Add H atom riding constraints between atom parameter values')
741	# self.ConstraintEdit.Enable(wxID_ADDRIDING,False)
742	self.PostfillDataMenu()
743
744	# item = self.ConstraintEdit.Append(id=wx.ID_ANY,kind=wx.ITEM_NORMAL,text='Update GUI')
745	# def UpdateGSASIIconstrGUI(event):
746	# import GSASIIconstrGUI
747	# reload(GSASIIconstrGUI)
748	# import GSASIIobj
749	# reload(GSASIIobj)
750	# self.Bind(wx.EVT_MENU,UpdateGSASIIconstrGUI,id=item.GetId())
751
752	# Rigid bodies
753	self.RigidBodyMenu = wx.MenuBar()
754	self.PrefillDataMenu(self.RigidBodyMenu,helpType='Rigid bodies')
755	self.ResidueRBMenu = wx.Menu(title='')
756	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYIMPORT, kind=wx.ITEM_NORMAL,text='Import XYZ',
757	help='Import rigid body XYZ from file')
758	self.ResidueRBMenu.Append(id=wxID_RESIDUETORSSEQ, kind=wx.ITEM_NORMAL,text='Define sequence',
759	help='Define torsion sequence')
760	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYADD, kind=wx.ITEM_NORMAL,text='Import residues',
761	help='Import residue rigid bodies from macro file')
762	self.RigidBodyMenu.Append(menu=self.ResidueRBMenu, title='Edit Body')
763	self.PostfillDataMenu()
764
765	self.VectorBodyMenu = wx.MenuBar()
766	self.PrefillDataMenu(self.VectorBodyMenu,helpType='Vector rigid bodies')
767	self.VectorRBEdit = wx.Menu(title='')
768	self.VectorRBEdit.Append(id=wxID_VECTORBODYADD, kind=wx.ITEM_NORMAL,text='Add rigid body',
769	help='Add vector rigid body')
770	self.VectorBodyMenu.Append(menu=self.VectorRBEdit, title='Edit Vector Body')
771	self.PostfillDataMenu()
772
773
774	# Restraints
775	self.RestraintTab = wx.Menu(title='')
776	self.RestraintEdit = wx.Menu(title='')
777	self.RestraintEdit.Append(id=wxID_RESTSELPHASE, kind=wx.ITEM_NORMAL,text='Select phase',
778	help='Select phase')
779	self.RestraintEdit.Append(id=wxID_RESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add restraints',
780	help='Add restraints')
781	self.RestraintEdit.Enable(wxID_RESTRAINTADD,True) #gets disabled if macromolecule phase
782	self.RestraintEdit.Append(id=wxID_AARESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add residue restraints',
783	help='Add residue based restraints for macromolecules from macro file')
784	self.RestraintEdit.Enable(wxID_AARESTRAINTADD,False) #gets enabled if macromolecule phase
785	self.RestraintEdit.Append(id=wxID_AARESTRAINTPLOT, kind=wx.ITEM_NORMAL,text='Plot residue restraints',
786	help='Plot selected residue based restraints for macromolecules from macro file')
787	self.RestraintEdit.Enable(wxID_AARESTRAINTPLOT,False) #gets enabled if macromolecule phase
788	self.RestraintEdit.Append(id=wxID_RESRCHANGEVAL, kind=wx.ITEM_NORMAL,text='Change value',
789	help='Change observed value')
790	self.RestraintEdit.Append(id=wxID_RESTCHANGEESD, kind=wx.ITEM_NORMAL,text='Change esd',
791	help='Change esd in observed value')
792	self.RestraintEdit.Append(id=wxID_RESTDELETE, kind=wx.ITEM_NORMAL,text='Delete restraints',
793	help='Delete selected restraints')
794
795	self.RestraintMenu = wx.MenuBar()
796	self.PrefillDataMenu(self.RestraintMenu,helpType='Restraints')
797	self.RestraintMenu.Append(menu=self.RestraintTab, title='Select tab')
798	self.RestraintMenu.Append(menu=self.RestraintEdit, title='Edit')
799	self.PostfillDataMenu()
800
801	# Sequential results
802	self.SequentialMenu = wx.MenuBar()
803	self.PrefillDataMenu(self.SequentialMenu,helpType='Sequential',helpLbl='Sequential Refinement')
804	self.SequentialFile = wx.Menu(title='')
805	self.SequentialMenu.Append(menu=self.SequentialFile, title='Columns')
806	self.SequentialFile.Append(id=wxID_RENAMESEQSEL, kind=wx.ITEM_NORMAL,text='Rename selected',
807	help='Rename selected sequential refinement columns')
808	self.SequentialFile.Append(id=wxID_SAVESEQSEL, kind=wx.ITEM_NORMAL,text='Save selected as text',
809	help='Save selected sequential refinement results as a text file')
810	self.SequentialFile.Append(id=wxID_SAVESEQCSV, kind=wx.ITEM_NORMAL,text='Save all as CSV',
811	help='Save all sequential refinement results as a CSV spreadsheet file')
812	self.SequentialFile.Append(id=wxID_SAVESEQSELCSV, kind=wx.ITEM_NORMAL,text='Save selected as CSV',
813	help='Save selected sequential refinement results as a CSV spreadsheet file')
814	self.SequentialFile.Append(id=wxID_PLOTSEQSEL, kind=wx.ITEM_NORMAL,text='Plot selected',
815	help='Plot selected sequential refinement results')
816	self.SequentialFile.Append(id=wxID_AVESEQSEL, kind=wx.ITEM_NORMAL,text='Compute average',
817	help='Compute average for selected parameter')
818	self.SequentialFile.Append(id=wxID_ORGSEQSEL, kind=wx.ITEM_NORMAL,text='Reorganize',
819	help='Reorganize variables where variables change')
820	self.SequentialPvars = wx.Menu(title='')
821	self.SequentialMenu.Append(menu=self.SequentialPvars, title='Pseudo Vars')
822	self.SequentialPvars.Append(
823	id=wxADDSEQVAR, kind=wx.ITEM_NORMAL,text='Add',
824	help='Add a new pseudo-variable')
825	self.SequentialPvars.Append(
826	id=wxDELSEQVAR, kind=wx.ITEM_NORMAL,text='Delete',
827	help='Delete an existing pseudo-variable')
828	self.SequentialPvars.Append(
829	id=wxEDITSEQVAR, kind=wx.ITEM_NORMAL,text='Edit',
830	help='Edit an existing pseudo-variable')
831
832	self.SequentialPfit = wx.Menu(title='')
833	self.SequentialMenu.Append(menu=self.SequentialPfit, title='Parametric Fit')
834	self.SequentialPfit.Append(
835	id=wxADDPARFIT, kind=wx.ITEM_NORMAL,text='Add equation',
836	help='Add a new equation to minimize')
837	self.SequentialPfit.Append(
838	id=wxCOPYPARFIT, kind=wx.ITEM_NORMAL,text='Copy equation',
839	help='Copy an equation to minimize - edit it next')
840	self.SequentialPfit.Append(
841	id=wxDELPARFIT, kind=wx.ITEM_NORMAL,text='Delete equation',
842	help='Delete an equation for parametric minimization')
843	self.SequentialPfit.Append(
844	id=wxEDITPARFIT, kind=wx.ITEM_NORMAL,text='Edit equation',
845	help='Edit an existing parametric minimization equation')
846	self.SequentialPfit.Append(
847	id=wxDOPARFIT, kind=wx.ITEM_NORMAL,text='Fit to equation(s)',
848	help='Perform a parametric minimization')
849	self.PostfillDataMenu()
850
851	# PWDR & SASD
852	self.PWDRMenu = wx.MenuBar()
853	self.PrefillDataMenu(self.PWDRMenu,helpType='PWDR Analysis',helpLbl='Powder Fit Error Analysis')
854	self.ErrorAnal = wx.Menu(title='')
855	self.PWDRMenu.Append(menu=self.ErrorAnal,title='Commands')
856	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
857	help='Error analysis on powder pattern')
858	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
859	help='Copy of PWDR parameters')
860	self.ErrorAnal.Append(id=wxID_PLOTCTRLCOPY,kind=wx.ITEM_NORMAL,text='Copy plot controls',
861	help='Copy of PWDR plot controls')
862
863	self.PostfillDataMenu()
864
865	# HKLF
866	self.HKLFMenu = wx.MenuBar()
867	self.PrefillDataMenu(self.HKLFMenu,helpType='HKLF Analysis',helpLbl='HKLF Fit Error Analysis')
868	self.ErrorAnal = wx.Menu(title='')
869	self.HKLFMenu.Append(menu=self.ErrorAnal,title='Commands')
870	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
871	help='Error analysis on single crystal data')
872	self.ErrorAnal.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
873	help='Plot HKLs from single crystal data in 3D')
874	self.ErrorAnal.Append(id=wxID_3DALLHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot all 3D HKLs',
875	help='Plot HKLs from all single crystal data in 3D')
876	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
877	help='Copy of HKLF parameters')
878	self.PostfillDataMenu()
879
880	# PDR / Limits
881	self.LimitMenu = wx.MenuBar()
882	self.PrefillDataMenu(self.LimitMenu,helpType='Limits')
883	self.LimitEdit = wx.Menu(title='')
884	self.LimitMenu.Append(menu=self.LimitEdit, title='Edit')
885	self.LimitEdit.Append(id=wxID_LIMITCOPY, kind=wx.ITEM_NORMAL,text='Copy',
886	help='Copy limits to other histograms')
887	self.LimitEdit.Append(id=wxID_ADDEXCLREGION, kind=wx.ITEM_NORMAL,text='Add exclude',
888	help='Add excluded region - select a point on plot; drag to adjust')
889	self.PostfillDataMenu()
890
891	# PDR / Background
892	self.BackMenu = wx.MenuBar()
893	self.PrefillDataMenu(self.BackMenu,helpType='Background')
894	self.BackEdit = wx.Menu(title='')
895	self.BackMenu.Append(menu=self.BackEdit, title='File')
896	self.BackEdit.Append(id=wxID_BACKCOPY, kind=wx.ITEM_NORMAL,text='Copy',
897	help='Copy background parameters to other histograms')
898	self.BackEdit.Append(id=wxID_BACKFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
899	help='Copy background refinement flags to other histograms')
900	self.BackEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
901	help='Move background peaks to Peak List')
902	self.BackFixed = wx.Menu(title='') # fixed background point menu
903	self.BackMenu.Append(menu=self.BackFixed, title='Fixed Points')
904	self.wxID_BackPts = {}
905	self.wxID_BackPts['Add'] = wx.NewId() # N.B. not using wxID_ global as for other menu items
906	self.BackFixed.Append(id=self.wxID_BackPts['Add'], kind=wx.ITEM_RADIO,text='Add',
907	help='Add fixed background points with mouse clicks')
908	self.wxID_BackPts['Move'] = wx.NewId()
909	item = self.BackFixed.Append(id=self.wxID_BackPts['Move'], kind=wx.ITEM_RADIO,text='Move',
910	help='Move selected fixed background points with mouse drags')
911	item.Check(True)
912	self.wxID_BackPts['Del'] = wx.NewId()
913	self.BackFixed.Append(id=self.wxID_BackPts['Del'], kind=wx.ITEM_RADIO,text='Delete',
914	help='Delete fixed background points with mouse clicks')
915	self.wxID_BackPts['Clear'] = wx.NewId()
916	self.BackFixed.Append(id=self.wxID_BackPts['Clear'], kind=wx.ITEM_NORMAL,text='Clear',
917	help='Clear fixed background points')
918	self.wxID_BackPts['Fit'] = wx.NewId()
919	self.BackFixed.Append(id=self.wxID_BackPts['Fit'], kind=wx.ITEM_NORMAL,text='Fit background',
920	help='Fit background function to fixed background points')
921	self.PostfillDataMenu()
922
923	# PDR / Instrument Parameters
924	self.InstMenu = wx.MenuBar()
925	self.PrefillDataMenu(self.InstMenu,helpType='Instrument Parameters')
926	self.InstEdit = wx.Menu(title='')
927	self.InstMenu.Append(menu=self.InstEdit, title='Operations')
928	self.InstEdit.Append(help='Calibrate from indexed peaks',
929	id=wxID_INSTCALIB, kind=wx.ITEM_NORMAL,text='Calibrate')
930	self.InstEdit.Append(help='Reset instrument profile parameters to default',
931	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
932	self.InstEdit.Append(help='Load instrument profile parameters from file',
933	id=wxID_INSTLOAD, kind=wx.ITEM_NORMAL,text='Load profile...')
934	self.InstEdit.Append(help='Save instrument profile parameters to file',
935	id=wxID_INSTSAVE, kind=wx.ITEM_NORMAL,text='Save profile...')
936	self.InstEdit.Append(help='Copy instrument profile parameters to other histograms',
937	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
938	self.InstEdit.Append(id=wxID_INSTFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
939	help='Copy instrument parameter refinement flags to other histograms')
940	# self.InstEdit.Append(help='Change radiation type (Ka12 - synch)',
941	# id=wxID_CHANGEWAVETYPE, kind=wx.ITEM_NORMAL,text='Change radiation')
942	self.InstEdit.Append(id=wxID_INST1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
943	help='Set one instrument parameter value across multiple histograms')
944
945	self.PostfillDataMenu()
946
947	# PDR / Sample Parameters
948	self.SampleMenu = wx.MenuBar()
949	self.PrefillDataMenu(self.SampleMenu,helpType='Sample Parameters')
950	self.SampleEdit = wx.Menu(title='')
951	self.SampleMenu.Append(menu=self.SampleEdit, title='Command')
952	self.SetScale = self.SampleEdit.Append(id=wxID_SETSCALE, kind=wx.ITEM_NORMAL,text='Set scale',
953	help='Set scale by matching to another histogram')
954	self.SampleEdit.Append(id=wxID_SAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load',
955	help='Load sample parameters from file')
956	self.SampleEdit.Append(id=wxID_SAMPLESAVE, kind=wx.ITEM_NORMAL,text='Save',
957	help='Save sample parameters to file')
958	self.SampleEdit.Append(id=wxID_SAMPLECOPY, kind=wx.ITEM_NORMAL,text='Copy',
959	help='Copy refinable and most other sample parameters to other histograms')
960	self.SampleEdit.Append(id=wxID_SAMPLECOPYSOME, kind=wx.ITEM_NORMAL,text='Copy selected...',
961	help='Copy selected sample parameters to other histograms')
962	self.SampleEdit.Append(id=wxID_SAMPLEFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
963	help='Copy sample parameter refinement flags to other histograms')
964	self.SampleEdit.Append(id=wxID_SAMPLE1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
965	help='Set one sample parameter value across multiple histograms')
966	self.SampleEdit.Append(id=wxID_ALLSAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load all',
967	help='Load sample parmameters over multiple histograms')
968
969	self.PostfillDataMenu()
970	self.SetScale.Enable(False)
971
972	# PDR / Peak List
973	self.PeakMenu = wx.MenuBar()
974	self.PrefillDataMenu(self.PeakMenu,helpType='Peak List')
975	self.PeakEdit = wx.Menu(title='')
976	self.PeakMenu.Append(menu=self.PeakEdit, title='Peak Fitting')
977	self.AutoSearch = self.PeakEdit.Append(help='Automatic peak search',
978	id=wxID_AUTOSEARCH, kind=wx.ITEM_NORMAL,text='Auto search')
979	self.UnDo = self.PeakEdit.Append(help='Undo last least squares refinement',
980	id=wxID_UNDO, kind=wx.ITEM_NORMAL,text='UnDo')
981	self.PeakFit = self.PeakEdit.Append(id=wxID_LSQPEAKFIT, kind=wx.ITEM_NORMAL,text='Peakfit',
982	help='Peak fitting' )
983	self.PFOneCycle = self.PeakEdit.Append(id=wxID_LSQONECYCLE, kind=wx.ITEM_NORMAL,text='Peakfit one cycle',
984	help='One cycle of Peak fitting' )
985	self.PeakEdit.Append(id=wxID_RESETSIGGAM, kind=wx.ITEM_NORMAL,
986	text='Reset sig and gam',help='Reset sigma and gamma to global fit' )
987	self.PeakCopy = self.PeakEdit.Append(help='Copy peaks to other histograms',
988	id=wxID_PEAKSCOPY, kind=wx.ITEM_NORMAL,text='Peak copy')
989	self.SeqPeakFit = self.PeakEdit.Append(id=wxID_SEQPEAKFIT, kind=wx.ITEM_NORMAL,text='Seq PeakFit',
990	help='Sequential Peak fitting for all histograms' )
991	self.PeakEdit.Append(id=wxID_CLEARPEAKS, kind=wx.ITEM_NORMAL,text='Clear peaks',
992	help='Clear the peak list' )
993	self.PostfillDataMenu()
994	self.UnDo.Enable(False)
995	self.PeakFit.Enable(False)
996	self.PFOneCycle.Enable(False)
997	self.AutoSearch.Enable(True)
998
999	# PDR / Index Peak List
1000	self.IndPeaksMenu = wx.MenuBar()
1001	self.PrefillDataMenu(self.IndPeaksMenu,helpType='Index Peak List')
1002	self.IndPeaksEdit = wx.Menu(title='')
1003	self.IndPeaksMenu.Append(menu=self.IndPeaksEdit,title='Operations')
1004	self.IndPeaksEdit.Append(help='Load/Reload index peaks from peak list',id=wxID_INDXRELOAD,
1005	kind=wx.ITEM_NORMAL,text='Load/Reload')
1006	self.PostfillDataMenu()
1007
1008	# PDR / Unit Cells List
1009	self.IndexMenu = wx.MenuBar()
1010	self.PrefillDataMenu(self.IndexMenu,helpType='Unit Cells List')
1011	self.IndexEdit = wx.Menu(title='')
1012	self.IndexMenu.Append(menu=self.IndexEdit, title='Cell Index/Refine')
1013	self.IndexPeaks = self.IndexEdit.Append(help='', id=wxID_INDEXPEAKS, kind=wx.ITEM_NORMAL,
1014	text='Index Cell')
1015	self.CopyCell = self.IndexEdit.Append( id=wxID_COPYCELL, kind=wx.ITEM_NORMAL,text='Copy Cell',
1016	help='Copy selected unit cell from indexing to cell refinement fields')
1017	self.RefineCell = self.IndexEdit.Append( id=wxID_REFINECELL, kind=wx.ITEM_NORMAL,
1018	text='Refine Cell',help='Refine unit cell parameters from indexed peaks')
1019	self.MakeNewPhase = self.IndexEdit.Append( id=wxID_MAKENEWPHASE, kind=wx.ITEM_NORMAL,
1020	text='Make new phase',help='Make new phase from selected unit cell')
1021	self.ExportCells = self.IndexEdit.Append( id=wxID_EXPORTCELLS, kind=wx.ITEM_NORMAL,
1022	text='Export cell list',help='Export cell list to csv file')
1023	self.PostfillDataMenu()
1024	self.IndexPeaks.Enable(False)
1025	self.CopyCell.Enable(False)
1026	self.RefineCell.Enable(False)
1027	self.MakeNewPhase.Enable(False)
1028
1029	# PDR / Reflection Lists
1030	self.ReflMenu = wx.MenuBar()
1031	self.PrefillDataMenu(self.ReflMenu,helpType='Reflection List')
1032	self.ReflEdit = wx.Menu(title='')
1033	self.ReflMenu.Append(menu=self.ReflEdit, title='Reflection List')
1034	self.SelectPhase = self.ReflEdit.Append(help='Select phase for reflection list',id=wxID_SELECTPHASE,
1035	kind=wx.ITEM_NORMAL,text='Select phase')
1036	self.ReflEdit.Append(id=wxID_PWDHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot HKLs',
1037	help='Plot HKLs from powder pattern')
1038	self.ReflEdit.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
1039	help='Plot HKLs from powder pattern in 3D')
1040	self.PostfillDataMenu()
1041
1042	# SASD / Instrument Parameters
1043	self.SASDInstMenu = wx.MenuBar()
1044	self.PrefillDataMenu(self.SASDInstMenu,helpType='Instrument Parameters')
1045	self.SASDInstEdit = wx.Menu(title='')
1046	self.SASDInstMenu.Append(menu=self.SASDInstEdit, title='Operations')
1047	self.InstEdit.Append(help='Reset instrument profile parameters to default',
1048	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
1049	self.SASDInstEdit.Append(help='Copy instrument profile parameters to other histograms',
1050	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
1051	self.PostfillDataMenu()
1052
1053	#SASD & REFL/ Substance editor
1054	self.SubstanceMenu = wx.MenuBar()
1055	self.PrefillDataMenu(self.SubstanceMenu,helpType='Substances')
1056	self.SubstanceEdit = wx.Menu(title='')
1057	self.SubstanceMenu.Append(menu=self.SubstanceEdit, title='Edit')
1058	self.SubstanceEdit.Append(id=wxID_LOADSUBSTANCE, kind=wx.ITEM_NORMAL,text='Load substance',
1059	help='Load substance from file')
1060	self.SubstanceEdit.Append(id=wxID_ADDSUBSTANCE, kind=wx.ITEM_NORMAL,text='Add substance',
1061	help='Add new substance to list')
1062	self.SubstanceEdit.Append(id=wxID_COPYSUBSTANCE, kind=wx.ITEM_NORMAL,text='Copy substances',
1063	help='Copy substances')
1064	self.SubstanceEdit.Append(id=wxID_DELETESUBSTANCE, kind=wx.ITEM_NORMAL,text='Delete substance',
1065	help='Delete substance from list')
1066	self.SubstanceEdit.Append(id=wxID_ELEMENTADD, kind=wx.ITEM_NORMAL,text='Add elements',
1067	help='Add elements to substance')
1068	self.SubstanceEdit.Append(id=wxID_ELEMENTDELETE, kind=wx.ITEM_NORMAL,text='Delete elements',
1069	help='Delete elements from substance')
1070	self.PostfillDataMenu()
1071
1072	# SASD/ Models
1073	self.ModelMenu = wx.MenuBar()
1074	self.PrefillDataMenu(self.ModelMenu,helpType='Models')
1075	self.ModelEdit = wx.Menu(title='')
1076	self.ModelMenu.Append(menu=self.ModelEdit, title='Models')
1077	self.ModelEdit.Append(id=wxID_MODELADD,kind=wx.ITEM_NORMAL,text='Add',
1078	help='Add new term to model')
1079	self.ModelEdit.Append(id=wxID_MODELFIT, kind=wx.ITEM_NORMAL,text='Fit',
1080	help='Fit model parameters to data')
1081	self.SasdUndo = self.ModelEdit.Append(id=wxID_MODELUNDO, kind=wx.ITEM_NORMAL,text='Undo',
1082	help='Undo model fit')
1083	self.SasdUndo.Enable(False)
1084	self.ModelEdit.Append(id=wxID_MODELFITALL, kind=wx.ITEM_NORMAL,text='Sequential fit',
1085	help='Sequential fit of model parameters to all SASD data')
1086	self.ModelEdit.Append(id=wxID_MODELCOPY, kind=wx.ITEM_NORMAL,text='Copy',
1087	help='Copy model parameters to other histograms')
1088	self.ModelEdit.Append(id=wxID_MODELCOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1089	help='Copy model refinement flags to other histograms')
1090	self.PostfillDataMenu()
1091
1092	# IMG / Image Controls
1093	self.ImageMenu = wx.MenuBar()
1094	self.PrefillDataMenu(self.ImageMenu,helpType='Image Controls')
1095	self.ImageEdit = wx.Menu(title='')
1096	self.ImageMenu.Append(menu=self.ImageEdit, title='Operations')
1097	self.ImageEdit.Append(help='Calibrate detector by fitting to calibrant lines',
1098	id=wxID_IMCALIBRATE, kind=wx.ITEM_NORMAL,text='Calibrate')
1099	self.ImageEdit.Append(help='Recalibrate detector by fitting to calibrant lines',
1100	id=wxID_IMRECALIBRATE, kind=wx.ITEM_NORMAL,text='Recalibrate')
1101	self.ImageEdit.Append(help='Clear calibration data points and rings',id=wxID_IMCLEARCALIB,
1102	kind=wx.ITEM_NORMAL,text='Clear calibration')
1103	self.ImageEdit.Append(help='Integrate selected image',id=wxID_IMINTEGRATE,
1104	kind=wx.ITEM_NORMAL,text='Integrate')
1105	self.ImageEdit.Append(help='Integrate all images selected from list',id=wxID_INTEGRATEALL,
1106	kind=wx.ITEM_NORMAL,text='Integrate all')
1107	self.ImageEdit.Append(help='Copy image controls to other images',
1108	id=wxID_IMCOPYCONTROLS, kind=wx.ITEM_NORMAL,text='Copy Controls')
1109	self.ImageEdit.Append(help='Save image controls to file',
1110	id=wxID_IMSAVECONTROLS, kind=wx.ITEM_NORMAL,text='Save Controls')
1111	self.ImageEdit.Append(help='Load image controls from file',
1112	id=wxID_IMLOADCONTROLS, kind=wx.ITEM_NORMAL,text='Load Controls')
1113	self.ImageEdit.Append(help='Open Auto-integration window to integrate a series of images',
1114	id=wxID_IMAUTOINTEG, kind=wx.ITEM_NORMAL,text='Auto Integrate')
1115	self.PostfillDataMenu()
1116
1117	# IMG / Masks
1118	self.MaskMenu = wx.MenuBar()
1119	self.PrefillDataMenu(self.MaskMenu,helpType='Image Masks')
1120	self.MaskEdit = wx.Menu(title='')
1121	self.MaskMenu.Append(menu=self.MaskEdit, title='Operations')
1122	submenu = wx.Menu()
1123	self.MaskEdit.AppendMenu(
1124	wx.ID_ANY,'Create new', submenu,
1125	help=''
1126	)
1127	self.MaskEdit.Append(help='Copy mask to other images',
1128	id=wxID_MASKCOPY, kind=wx.ITEM_NORMAL,text='Copy mask')
1129	self.MaskEdit.Append(help='Save mask to file',
1130	id=wxID_MASKSAVE, kind=wx.ITEM_NORMAL,text='Save mask')
1131	self.MaskEdit.Append(help='Load mask from file',
1132	id=wxID_MASKLOAD, kind=wx.ITEM_NORMAL,text='Load mask')
1133	self.MaskEdit.Append(help='Load mask from file; ignore threshold',
1134	id=wxID_MASKLOADNOT, kind=wx.ITEM_NORMAL,text='Load mask w/o threshold')
1135	submenu.Append(help='Create an arc mask with mouse input',
1136	id=wxID_NEWMASKARC, kind=wx.ITEM_NORMAL,text='Arc mask')
1137	submenu.Append(help='Create a frame mask with mouse input',
1138	id=wxID_NEWMASKFRAME, kind=wx.ITEM_NORMAL,text='Frame mask')
1139	submenu.Append(help='Create a polygon mask with mouse input',
1140	id=wxID_NEWMASKPOLY, kind=wx.ITEM_NORMAL,text='Polygon mask')
1141	submenu.Append(help='Create a ring mask with mouse input',
1142	id=wxID_NEWMASKRING, kind=wx.ITEM_NORMAL,text='Ring mask')
1143	submenu.Append(help='Create a spot mask with mouse input',
1144	id=wxID_NEWMASKSPOT, kind=wx.ITEM_NORMAL,text='Spot mask')
1145	self.PostfillDataMenu()
1146
1147	# IMG / Stress/Strain
1148	self.StrStaMenu = wx.MenuBar()
1149	self.PrefillDataMenu(self.StrStaMenu,helpType='Stress/Strain')
1150	self.StrStaEdit = wx.Menu(title='')
1151	self.StrStaMenu.Append(menu=self.StrStaEdit, title='Operations')
1152	self.StrStaEdit.Append(help='Append d-zero for one ring',
1153	id=wxID_APPENDDZERO, kind=wx.ITEM_NORMAL,text='Append d-zero')
1154	self.StrStaEdit.Append(help='Fit stress/strain data',
1155	id=wxID_STRSTAFIT, kind=wx.ITEM_NORMAL,text='Fit stress/strain')
1156	self.StrStaEdit.Append(help='Update d-zero from ave d-zero',
1157	id=wxID_UPDATEDZERO, kind=wx.ITEM_NORMAL,text='Update d-zero')
1158	self.StrStaEdit.Append(help='Fit stress/strain data for all images',
1159	id=wxID_STRSTAALLFIT, kind=wx.ITEM_NORMAL,text='All image fit')
1160	self.StrStaEdit.Append(help='Copy stress/strain data to other images',
1161	id=wxID_STRSTACOPY, kind=wx.ITEM_NORMAL,text='Copy stress/strain')
1162	self.StrStaEdit.Append(help='Save stress/strain data to file',
1163	id=wxID_STRSTASAVE, kind=wx.ITEM_NORMAL,text='Save stress/strain')
1164	self.StrStaEdit.Append(help='Load stress/strain data from file',
1165	id=wxID_STRSTALOAD, kind=wx.ITEM_NORMAL,text='Load stress/strain')
1166	self.StrStaEdit.Append(help='Load sample data from file',
1167	id=wxID_STRSTSAMPLE, kind=wx.ITEM_NORMAL,text='Load sample data')
1168	self.PostfillDataMenu()
1169
1170	# PDF / PDF Controls
1171	self.PDFMenu = wx.MenuBar()
1172	self.PrefillDataMenu(self.PDFMenu,helpType='PDF Controls')
1173	self.PDFEdit = wx.Menu(title='')
1174	self.PDFMenu.Append(menu=self.PDFEdit, title='PDF Controls')
1175	self.PDFEdit.Append(help='Add element to sample composition',id=wxID_PDFADDELEMENT, kind=wx.ITEM_NORMAL,
1176	text='Add element')
1177	self.PDFEdit.Append(help='Delete element from sample composition',id=wxID_PDFDELELEMENT, kind=wx.ITEM_NORMAL,
1178	text='Delete element')
1179	self.PDFEdit.Append(help='Copy PDF controls', id=wxID_PDFCOPYCONTROLS, kind=wx.ITEM_NORMAL,
1180	text='Copy controls')
1181	self.PDFEdit.Append(help='Load PDF controls from file',id=wxID_PDFLOADCONTROLS, kind=wx.ITEM_NORMAL,
1182	text='Load Controls')
1183	self.PDFEdit.Append(help='Save PDF controls to file', id=wxID_PDFSAVECONTROLS, kind=wx.ITEM_NORMAL,
1184	text='Save controls')
1185	self.PDFEdit.Append(help='Compute PDF', id=wxID_PDFCOMPUTE, kind=wx.ITEM_NORMAL,
1186	text='Compute PDF')
1187	self.PDFEdit.Append(help='Compute all PDFs', id=wxID_PDFCOMPUTEALL, kind=wx.ITEM_NORMAL,
1188	text='Compute all PDFs')
1189	self.PostfillDataMenu()
1190
1191	# Phase / General tab
1192	self.DataGeneral = wx.MenuBar()
1193	self.PrefillDataMenu(self.DataGeneral,helpType='General', helpLbl='Phase/General')
1194	self.DataGeneral.Append(menu=wx.Menu(title=''),title='Select tab')
1195	self.GeneralCalc = wx.Menu(title='')
1196	self.DataGeneral.Append(menu=self.GeneralCalc,title='Compute')
1197	self.GeneralCalc.Append(help='Compute Fourier map',id=wxID_FOURCALC, kind=wx.ITEM_NORMAL,
1198	text='Fourier map')
1199	self.GeneralCalc.Append(help='Search Fourier map',id=wxID_FOURSEARCH, kind=wx.ITEM_NORMAL,
1200	text='Search map')
1201	self.GeneralCalc.Append(help='Run charge flipping',id=wxID_CHARGEFLIP, kind=wx.ITEM_NORMAL,
1202	text='Charge flipping')
1203	self.GeneralCalc.Append(help='Run 4D charge flipping',id=wxID_4DCHARGEFLIP, kind=wx.ITEM_NORMAL,
1204	text='4D Charge flipping')
1205	self.GeneralCalc.Enable(wxID_4DCHARGEFLIP,False)
1206	self.GeneralCalc.Append(help='Clear map',id=wxID_FOURCLEAR, kind=wx.ITEM_NORMAL,
1207	text='Clear map')
1208	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing',id=wxID_SINGLEMCSA, kind=wx.ITEM_NORMAL,
1209	text='MC/SA')
1210	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing on multiprocessors',id=wxID_MULTIMCSA, kind=wx.ITEM_NORMAL,
1211	text='Multi MC/SA') #currently not useful
1212	self.PostfillDataMenu()
1213
1214	# Phase / Data tab
1215	self.DataMenu = wx.MenuBar()
1216	self.PrefillDataMenu(self.DataMenu,helpType='Data', helpLbl='Phase/Data')
1217	self.DataMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1218	self.DataEdit = wx.Menu(title='')
1219	self.DataMenu.Append(menu=self.DataEdit, title='Edit')
1220	self.DataEdit.Append(id=wxID_DATACOPY, kind=wx.ITEM_NORMAL,text='Copy data',
1221	help='Copy phase data to other histograms')
1222	self.DataEdit.Append(id=wxID_DATACOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1223	help='Copy phase data flags to other histograms')
1224	self.DataEdit.Append(id=wxID_DATASELCOPY, kind=wx.ITEM_NORMAL,text='Copy selected data',
1225	help='Copy selected phase data to other histograms')
1226	self.DataEdit.Append(id=wxID_PWDRADD, kind=wx.ITEM_NORMAL,text='Add powder histograms',
1227	help='Select new powder histograms to be used for this phase')
1228	self.DataEdit.Append(id=wxID_HKLFADD, kind=wx.ITEM_NORMAL,text='Add single crystal histograms',
1229	help='Select new single crystal histograms to be used for this phase')
1230	self.DataEdit.Append(id=wxID_DATADELETE, kind=wx.ITEM_NORMAL,text='Remove histograms',
1231	help='Remove histograms from use for this phase')
1232	self.PostfillDataMenu()
1233
1234	# Phase / Atoms tab
1235	self.AtomsMenu = wx.MenuBar()
1236	self.PrefillDataMenu(self.AtomsMenu,helpType='Atoms')
1237	self.AtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1238	self.AtomEdit = wx.Menu(title='')
1239	self.AtomCompute = wx.Menu(title='')
1240	self.AtomsMenu.Append(menu=self.AtomEdit, title='Edit')
1241	self.AtomsMenu.Append(menu=self.AtomCompute, title='Compute')
1242	self.AtomEdit.Append(id=wxID_ATOMSEDITADD, kind=wx.ITEM_NORMAL,text='Append atom',
1243	help='Appended as an H atom')
1244	self.AtomEdit.Append(id=wxID_ATOMSVIEWADD, kind=wx.ITEM_NORMAL,text='Append view point',
1245	help='Appended as an H atom')
1246	self.AtomEdit.Append(id=wxID_ATOMSEDITINSERT, kind=wx.ITEM_NORMAL,text='Insert atom',
1247	help='Select atom row to insert before; inserted as an H atom')
1248	self.AtomEdit.Append(id=wxID_ATOMVIEWINSERT, kind=wx.ITEM_NORMAL,text='Insert view point',
1249	help='Select atom row to insert before; inserted as an H atom')
1250	self.AtomEdit.Append(id=wxID_ADDHATOM, kind=wx.ITEM_NORMAL,text='Insert H atoms',
1251	help='Insert H atoms in standard positions bonded to selected atoms')
1252	self.AtomEdit.Append(id=wxID_UPDATEHATOM, kind=wx.ITEM_NORMAL,text='Update H atoms',
1253	help='Update H atoms in standard positions')
1254	self.AtomEdit.Append(id=wxID_ATOMMOVE, kind=wx.ITEM_NORMAL,text='Move atom to view point',
1255	help='Select single atom to move')
1256	self.AtomEdit.Append(id=wxID_ATOMSEDITDELETE, kind=wx.ITEM_NORMAL,text='Delete atom',
1257	help='Select atoms to delete first')
1258	self.AtomEdit.Append(id=wxID_ATOMSREFINE, kind=wx.ITEM_NORMAL,text='Set atom refinement flags',
1259	help='Select atoms to refine first')
1260	self.AtomEdit.Append(id=wxID_ATOMSMODIFY, kind=wx.ITEM_NORMAL,text='Modify atom parameters',
1261	help='Select atoms to modify first')
1262	self.AtomEdit.Append(id=wxID_ATOMSTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform atoms',
1263	help='Select atoms to transform first')
1264	self.AtomEdit.Append(id=wxID_MAKEMOLECULE, kind=wx.ITEM_NORMAL,text='Assemble molecule',
1265	help='Assemble molecule from scatterd atom positions')
1266	self.AtomEdit.Append(id=wxID_RELOADDRAWATOMS, kind=wx.ITEM_NORMAL,text='Reload draw atoms',
1267	help='Reload atom drawing list')
1268	submenu = wx.Menu()
1269	self.AtomEdit.AppendMenu(wx.ID_ANY, 'Reimport atoms', submenu,
1270	help='Reimport atoms from file; sequence must match')
1271	# setup a cascade menu for the formats that have been defined
1272	self.ReImportMenuId = {} # points to readers for each menu entry
1273	for reader in self.G2frame.ImportPhaseReaderlist:
1274	item = submenu.Append(
1275	wx.ID_ANY,help=reader.longFormatName,
1276	kind=wx.ITEM_NORMAL,text='reimport coordinates from '+reader.formatName+' file')
1277	self.ReImportMenuId[item.GetId()] = reader
1278	item = submenu.Append(
1279	wx.ID_ANY,
1280	help='Reimport coordinates, try to determine format from file',
1281	kind=wx.ITEM_NORMAL,
1282	text='guess format from file')
1283	self.ReImportMenuId[item.GetId()] = None # try all readers
1284
1285	self.AtomCompute.Append(id=wxID_ATOMSDISAGL, kind=wx.ITEM_NORMAL,text='Show Distances && Angles',
1286	help='Compute distances & angles for selected atoms')
1287	self.AtomCompute.Append(id=wxID_ATOMSPDISAGL, kind=wx.ITEM_NORMAL,text='Save Distances && Angles',
1288	help='Compute distances & angles for selected atoms')
1289	self.AtomCompute.ISOcalc = self.AtomCompute.Append(
1290	id=wxID_ISODISP, kind=wx.ITEM_NORMAL,
1291	text='Compute ISODISTORT mode values',
1292	help='Compute values of ISODISTORT modes from atom parameters')
1293	self.PostfillDataMenu()
1294
1295	# Phase / Imcommensurate "waves" tab
1296	self.WavesData = wx.MenuBar()
1297	self.PrefillDataMenu(self.WavesData,helpType='Wave Data', helpLbl='Imcommensurate wave data')
1298	self.WavesData.Append(menu=wx.Menu(title=''),title='Select tab')
1299	self.WavesDataEdit = wx.Menu(title='')
1300	self.WavesData.Append(menu=self.WavesDataEdit, title='Edit')
1301	self.WavesDataEdit.Append(id=wxID_WAVEVARY, kind=wx.ITEM_NORMAL,text='Global wave vary',
1302	help='Global setting of wave vary flags')
1303	self.PostfillDataMenu()
1304
1305	# Phase / Draw Options tab
1306	self.DataDrawOptions = wx.MenuBar()
1307	self.PrefillDataMenu(self.DataDrawOptions,helpType='Draw Options', helpLbl='Phase/Draw Options')
1308	self.DataDrawOptions.Append(menu=wx.Menu(title=''),title='Select tab')
1309	self.PostfillDataMenu()
1310
1311	# Phase / Draw Atoms tab
1312	self.DrawAtomsMenu = wx.MenuBar()
1313	self.PrefillDataMenu(self.DrawAtomsMenu,helpType='Draw Atoms')
1314	self.DrawAtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1315	self.DrawAtomEdit = wx.Menu(title='')
1316	self.DrawAtomCompute = wx.Menu(title='')
1317	self.DrawAtomRestraint = wx.Menu(title='')
1318	self.DrawAtomRigidBody = wx.Menu(title='')
1319	self.DrawAtomsMenu.Append(menu=self.DrawAtomEdit, title='Edit')
1320	self.DrawAtomsMenu.Append(menu=self.DrawAtomCompute,title='Compute')
1321	self.DrawAtomsMenu.Append(menu=self.DrawAtomRestraint, title='Restraints')
1322	self.DrawAtomsMenu.Append(menu=self.DrawAtomRigidBody, title='Rigid body')
1323	self.DrawAtomEdit.Append(id=wxID_DRAWATOMSTYLE, kind=wx.ITEM_NORMAL,text='Atom style',
1324	help='Select atoms first')
1325	self.DrawAtomEdit.Append(id=wxID_DRAWATOMLABEL, kind=wx.ITEM_NORMAL,text='Atom label',
1326	help='Select atoms first')
1327	self.DrawAtomEdit.Append(id=wxID_DRAWATOMCOLOR, kind=wx.ITEM_NORMAL,text='Atom color',
1328	help='Select atoms first')
1329	self.DrawAtomEdit.Append(id=wxID_DRAWATOMRESETCOLOR, kind=wx.ITEM_NORMAL,text='Reset atom colors',
1330	help='Resets all atom colors to defaults')
1331	self.DrawAtomEdit.Append(id=wxID_DRAWVIEWPOINT, kind=wx.ITEM_NORMAL,text='View point',
1332	help='View point is 1st atom selected')
1333	self.DrawAtomEdit.Append(id=wxID_DRAWADDEQUIV, kind=wx.ITEM_NORMAL,text='Add atoms',
1334	help='Add symmetry & cell equivalents to drawing set from selected atoms')
1335	self.DrawAtomEdit.Append(id=wxID_DRAWTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform draw atoms',
1336	help='Transform selected atoms by symmetry & cell translations')
1337	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCOORD, kind=wx.ITEM_NORMAL,text='Fill CN-sphere',
1338	help='Fill coordination sphere for selected atoms')
1339	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCELL, kind=wx.ITEM_NORMAL,text='Fill unit cell',
1340	help='Fill unit cell with selected atoms')
1341	self.DrawAtomEdit.Append(id=wxID_DRAWDELETE, kind=wx.ITEM_NORMAL,text='Delete atoms',
1342	help='Delete atoms from drawing set')
1343	self.DrawAtomCompute.Append(id=wxID_DRAWDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1344	help='Compute distance of selected atoms from view point')
1345	self.DrawAtomCompute.Append(id=wxID_DRAWDISAGLTOR, kind=wx.ITEM_NORMAL,text='Dist. Ang. Tors.',
1346	help='Compute distance, angle or torsion for 2-4 selected atoms')
1347	self.DrawAtomCompute.Append(id=wxID_DRAWPLANE, kind=wx.ITEM_NORMAL,text='Best plane',
1348	help='Compute best plane for 4+ selected atoms')
1349	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRBOND, kind=wx.ITEM_NORMAL,text='Add bond restraint',
1350	help='Add bond restraint for selected atoms (2)')
1351	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRANGLE, kind=wx.ITEM_NORMAL,text='Add angle restraint',
1352	help='Add angle restraint for selected atoms (3: one end 1st)')
1353	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRPLANE, kind=wx.ITEM_NORMAL,text='Add plane restraint',
1354	help='Add plane restraint for selected atoms (4+)')
1355	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRCHIRAL, kind=wx.ITEM_NORMAL,text='Add chiral restraint',
1356	help='Add chiral restraint for selected atoms (4: center atom 1st)')
1357	self.DrawAtomRigidBody.Append(id=wxID_DRAWDEFINERB, kind=wx.ITEM_NORMAL,text='Define rigid body',
1358	help='Define rigid body with selected atoms')
1359	self.PostfillDataMenu()
1360
1361	# Phase / MCSA tab
1362	self.MCSAMenu = wx.MenuBar()
1363	self.PrefillDataMenu(self.MCSAMenu,helpType='MC/SA')
1364	self.MCSAMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1365	self.MCSAEdit = wx.Menu(title='')
1366	self.MCSAMenu.Append(menu=self.MCSAEdit, title='MC/SA')
1367	self.MCSAEdit.Append(id=wxID_ADDMCSAATOM, kind=wx.ITEM_NORMAL,text='Add atom',
1368	help='Add single atom to MC/SA model')
1369	self.MCSAEdit.Append(id=wxID_ADDMCSARB, kind=wx.ITEM_NORMAL,text='Add rigid body',
1370	help='Add rigid body to MC/SA model' )
1371	self.MCSAEdit.Append(id=wxID_CLEARMCSARB, kind=wx.ITEM_NORMAL,text='Clear rigid bodies',
1372	help='Clear all atoms & rigid bodies from MC/SA model' )
1373	self.MCSAEdit.Append(id=wxID_MOVEMCSA, kind=wx.ITEM_NORMAL,text='Move MC/SA solution',
1374	help='Move MC/SA solution to atom list' )
1375	self.MCSAEdit.Append(id=wxID_MCSACLEARRESULTS, kind=wx.ITEM_NORMAL,text='Clear results',
1376	help='Clear table of MC/SA results' )
1377	self.PostfillDataMenu()
1378
1379	# Phase / Texture tab
1380	self.TextureMenu = wx.MenuBar()
1381	self.PrefillDataMenu(self.TextureMenu,helpType='Texture')
1382	self.TextureMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1383	self.TextureEdit = wx.Menu(title='')
1384	self.TextureMenu.Append(menu=self.TextureEdit, title='Texture')
1385	self.TextureEdit.Append(id=wxID_REFINETEXTURE, kind=wx.ITEM_NORMAL,text='Refine texture',
1386	help='Refine the texture coefficients from sequential results')
1387	# self.TextureEdit.Append(id=wxID_CLEARTEXTURE, kind=wx.ITEM_NORMAL,text='Clear texture',
1388	# help='Clear the texture coefficients' )
1389	self.PostfillDataMenu()
1390
1391	# Phase / Pawley tab
1392	self.PawleyMenu = wx.MenuBar()
1393	self.PrefillDataMenu(self.PawleyMenu,helpType='Pawley')
1394	self.PawleyMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1395	self.PawleyEdit = wx.Menu(title='')
1396	self.PawleyMenu.Append(menu=self.PawleyEdit,title='Operations')
1397	self.PawleyEdit.Append(id=wxID_PAWLEYLOAD, kind=wx.ITEM_NORMAL,text='Pawley create',
1398	help='Initialize Pawley reflection list')
1399	self.PawleyEdit.Append(id=wxID_PAWLEYESTIMATE, kind=wx.ITEM_NORMAL,text='Pawley estimate',
1400	help='Estimate initial Pawley intensities')
1401	self.PawleyEdit.Append(id=wxID_PAWLEYUPDATE, kind=wx.ITEM_NORMAL,text='Pawley update',
1402	help='Update negative Pawley intensities with -0.5*Fobs and turn off refinemnt')
1403	self.PostfillDataMenu()
1404
1405	# Phase / Map peaks tab
1406	self.MapPeaksMenu = wx.MenuBar()
1407	self.PrefillDataMenu(self.MapPeaksMenu,helpType='Map peaks')
1408	self.MapPeaksMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1409	self.MapPeaksEdit = wx.Menu(title='')
1410	self.MapPeaksMenu.Append(menu=self.MapPeaksEdit, title='Map peaks')
1411	self.MapPeaksEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
1412	help='Move selected peaks to atom list')
1413	self.MapPeaksEdit.Append(id=wxID_PEAKSVIEWPT, kind=wx.ITEM_NORMAL,text='View point',
1414	help='View point is 1st peak selected')
1415	self.MapPeaksEdit.Append(id=wxID_PEAKSDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1416	help='Compute distance of selected peaks from view point')
1417	self.MapPeaksEdit.Append(id=wxID_SHOWBONDS, kind=wx.ITEM_NORMAL,text='Hide bonds',
1418	help='Hide or show bonds between peak positions')
1419	self.MapPeaksEdit.Append(id=wxID_PEAKSDA, kind=wx.ITEM_NORMAL,text='Calc dist/ang',
1420	help='Calculate distance or angle for selection')
1421	self.MapPeaksEdit.Append(id=wxID_FINDEQVPEAKS, kind=wx.ITEM_NORMAL,text='Equivalent peaks',
1422	help='Find equivalent peaks')
1423	self.MapPeaksEdit.Append(id=wxID_PEAKSUNIQUE, kind=wx.ITEM_NORMAL,text='Unique peaks',
1424	help='Select unique set')
1425	self.MapPeaksEdit.Append(id=wxID_PEAKSDELETE, kind=wx.ITEM_NORMAL,text='Delete peaks',
1426	help='Delete selected peaks')
1427	self.MapPeaksEdit.Append(id=wxID_PEAKSCLEAR, kind=wx.ITEM_NORMAL,text='Clear peaks',
1428	help='Clear the map peak list')
1429	self.PostfillDataMenu()
1430
1431	# Phase / Rigid bodies tab
1432	self.RigidBodiesMenu = wx.MenuBar()
1433	self.PrefillDataMenu(self.RigidBodiesMenu,helpType='Rigid bodies')
1434	self.RigidBodiesMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1435	self.RigidBodiesEdit = wx.Menu(title='')
1436	self.RigidBodiesMenu.Append(menu=self.RigidBodiesEdit, title='Edit')
1437	self.RigidBodiesEdit.Append(id=wxID_ASSIGNATMS2RB, kind=wx.ITEM_NORMAL,text='Assign atoms to rigid body',
1438	help='Select & position rigid body in structure of existing atoms')
1439	self.RigidBodiesEdit.Append(id=wxID_AUTOFINDRESRB, kind=wx.ITEM_NORMAL,text='Auto find residues',
1440	help='Auto find of residue RBs in macromolecule')
1441	self.RigidBodiesEdit.Append(id=wxID_COPYRBPARMS, kind=wx.ITEM_NORMAL,text='Copy rigid body parms',
1442	help='Copy rigid body location & TLS parameters')
1443	self.RigidBodiesEdit.Append(id=wxID_GLOBALTHERM, kind=wx.ITEM_NORMAL,text='Global thermal motion',
1444	help='Global setting of residue thermal motion models')
1445	self.RigidBodiesEdit.Append(id=wxID_GLOBALRESREFINE, kind=wx.ITEM_NORMAL,text='Global residue refine',
1446	help='Global setting of residue RB refinement flags')
1447	self.RigidBodiesEdit.Append(id=wxID_RBREMOVEALL, kind=wx.ITEM_NORMAL,text='Remove all rigid bodies',
1448	help='Remove all rigid body assignment for atoms')
1449	self.PostfillDataMenu()
1450	# end of GSAS-II menu definitions
1451
1452	def _init_ctrls(self, parent,name=None,size=None,pos=None):
1453	wx.Frame.__init__(
1454	self,parent=parent,
1455	#style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX \| wx.FRAME_FLOAT_ON_PARENT ,
1456	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX,
1457	size=size,pos=pos,title='GSAS-II data display')
1458	self._init_menus()
1459	if name:
1460	self.SetLabel(name)
1461	self.Show()
1462
1463	def __init__(self,parent,frame,data=None,name=None, size=None,pos=None):
1464	self.G2frame = frame
1465	self._init_ctrls(parent,name,size,pos)
1466	self.data = data
1467	clientSize = wx.ClientDisplayRect()
1468	Size = self.GetSize()
1469	xPos = clientSize[2]-Size[0]
1470	self.SetPosition(wx.Point(xPos,clientSize[1]+250))
1471	self.AtomGrid = []
1472	self.selectedRow = 0
1473
1474	def setSizePosLeft(self,Width):
1475	clientSize = wx.ClientDisplayRect()
1476	Width[1] = min(Width[1],clientSize[2]-300)
1477	Width[0] = max(Width[0],300)
1478	self.SetSize(Width)
1479	# self.SetPosition(wx.Point(clientSize[2]-Width[0],clientSize[1]+250))
1480
1481	def Clear(self):
1482	self.ClearBackground()
1483	self.DestroyChildren()
1484
1485
1486	################################################################################
1487	##### Notebook Tree Item editor
1488	################################################################################
1489	def UpdateNotebook(G2frame,data):
1490	'''Called when the data tree notebook entry is selected. Allows for
1491	editing of the text in that tree entry
1492	'''
1493	def OnNoteBook(event):
1494	data = G2frame.dataDisplay.GetValue().split('\n')
1495	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Notebook'),data)
1496	if 'nt' not in os.name:
1497	G2frame.dataDisplay.AppendText('\n')
1498
1499	if G2frame.dataDisplay:
1500	G2frame.dataDisplay.Destroy()
1501	G2frame.dataFrame.SetLabel('Notebook')
1502	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1503	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER \| wx.TE_DONTWRAP)
1504	G2frame.dataDisplay.Bind(wx.EVT_TEXT_ENTER,OnNoteBook)
1505	G2frame.dataDisplay.Bind(wx.EVT_KILL_FOCUS,OnNoteBook)
1506	for line in data:
1507	G2frame.dataDisplay.AppendText(line+"\n")
1508	G2frame.dataDisplay.AppendText('Notebook entry @ '+time.ctime()+"\n")
1509	G2frame.dataFrame.setSizePosLeft([400,250])
1510
1511	################################################################################
1512	##### Controls Tree Item editor
1513	################################################################################
1514	def UpdateControls(G2frame,data):
1515	'''Edit overall GSAS-II controls in main Controls data tree entry
1516	'''
1517	#patch
1518	if 'deriv type' not in data:
1519	data = {}
1520	data['deriv type'] = 'analytic Hessian'
1521	data['min dM/M'] = 0.0001
1522	data['shift factor'] = 1.
1523	data['max cyc'] = 3
1524	data['F**2'] = False
1525	if 'shift factor' not in data:
1526	data['shift factor'] = 1.
1527	if 'max cyc' not in data:
1528	data['max cyc'] = 3
1529	if 'F**2' not in data:
1530	data['F**2'] = False
1531	if 'Author' not in data:
1532	data['Author'] = 'no name'
1533	if 'FreePrm1' not in data:
1534	data['FreePrm1'] = 'Sample humidity (%)'
1535	if 'FreePrm2' not in data:
1536	data['FreePrm2'] = 'Sample voltage (V)'
1537	if 'FreePrm3' not in data:
1538	data['FreePrm3'] = 'Applied load (MN)'
1539	if 'Copy2Next' not in data:
1540	data['Copy2Next'] = False
1541	if 'Reverse Seq' not in data:
1542	data['Reverse Seq'] = False
1543	if 'UsrReject' not in data:
1544	data['UsrReject'] = {'minF/sig':0,'MinExt':0.01,'MaxDF/F':20.,'MaxD':500.,'MinD':0.05}
1545	if 'HatomFix' not in data:
1546	data['HatomFix'] = False
1547
1548	#end patch
1549
1550	def SeqSizer():
1551
1552	def OnSelectData(event):
1553	choices = GetPatternTreeDataNames(G2frame,['PWDR','HKLF',])
1554	sel = []
1555	try:
1556	if 'Seq Data' in data:
1557	for item in data['Seq Data']:
1558	sel.append(choices.index(item))
1559	sel = [choices.index(item) for item in data['Seq Data']]
1560	except ValueError: #data changed somehow - start fresh
1561	sel = []
1562	dlg = G2G.G2MultiChoiceDialog(G2frame.dataFrame, 'Sequential refinement',
1563	'Select dataset to include',choices)
1564	dlg.SetSelections(sel)
1565	names = []
1566	if dlg.ShowModal() == wx.ID_OK:
1567	for sel in dlg.GetSelections():
1568	names.append(choices[sel])
1569	data['Seq Data'] = names
1570	G2frame.EnableSeqRefineMenu()
1571	dlg.Destroy()
1572	wx.CallAfter(UpdateControls,G2frame,data)
1573
1574	def OnReverse(event):
1575	data['Reverse Seq'] = reverseSel.GetValue()
1576
1577	def OnCopySel(event):
1578	data['Copy2Next'] = copySel.GetValue()
1579
1580	seqSizer = wx.BoxSizer(wx.VERTICAL)
1581	dataSizer = wx.BoxSizer(wx.HORIZONTAL)
1582	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Sequential Refinement: '),0,WACV)
1583	selSeqData = wx.Button(G2frame.dataDisplay,-1,label=' Select data')
1584	selSeqData.Bind(wx.EVT_BUTTON,OnSelectData)
1585	dataSizer.Add(selSeqData,0,WACV)
1586	SeqData = data.get('Seq Data',[])
1587	if not SeqData:
1588	lbl = ' (no data selected)'
1589	else:
1590	lbl = ' ('+str(len(SeqData))+' dataset(s) selected)'
1591
1592	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=lbl),0,WACV)
1593	seqSizer.Add(dataSizer,0)
1594	if SeqData:
1595	selSizer = wx.BoxSizer(wx.HORIZONTAL)
1596	reverseSel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Reverse order?')
1597	reverseSel.Bind(wx.EVT_CHECKBOX,OnReverse)
1598	reverseSel.SetValue(data['Reverse Seq'])
1599	selSizer.Add(reverseSel,0,WACV)
1600	copySel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Copy results to next histogram?')
1601	copySel.Bind(wx.EVT_CHECKBOX,OnCopySel)
1602	copySel.SetValue(data['Copy2Next'])
1603	selSizer.Add(copySel,0,WACV)
1604	seqSizer.Add(selSizer,0)
1605	return seqSizer
1606
1607	def LSSizer():
1608
1609	def OnDerivType(event):
1610	data['deriv type'] = derivSel.GetValue()
1611	derivSel.SetValue(data['deriv type'])
1612	wx.CallAfter(UpdateControls,G2frame,data)
1613
1614	def OnConvergence(event):
1615	try:
1616	value = max(1.e-9,min(1.0,float(Cnvrg.GetValue())))
1617	except ValueError:
1618	value = 0.0001
1619	data['min dM/M'] = value
1620	Cnvrg.SetValue('%.2g'%(value))
1621
1622	def OnMaxCycles(event):
1623	data['max cyc'] = int(maxCyc.GetValue())
1624	maxCyc.SetValue(str(data['max cyc']))
1625
1626	def OnFactor(event):
1627	try:
1628	value = min(max(float(Factr.GetValue()),0.00001),100.)
1629	except ValueError:
1630	value = 1.0
1631	data['shift factor'] = value
1632	Factr.SetValue('%.5f'%(value))
1633
1634	def OnFsqRef(event):
1635	data['F**2'] = fsqRef.GetValue()
1636
1637	def OnHatomFix(event):
1638	data['HatomFix'] = Hfix.GetValue()
1639
1640	def OnUsrRej(event):
1641	Obj = event.GetEventObject()
1642	item,limits = Indx[Obj]
1643	try:
1644	value = min(max(float(Obj.GetValue()),limits[0]),limits[1])
1645	except ValueError:
1646	value = data['UsrReject'][item]
1647	data['UsrReject'][item] = value
1648	Obj.SetValue('%.2f'%(value))
1649
1650	LSSizer = wx.FlexGridSizer(cols=4,vgap=5,hgap=5)
1651	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement derivatives: '),0,WACV)
1652	Choice=['analytic Jacobian','numeric','analytic Hessian']
1653	derivSel = wx.ComboBox(parent=G2frame.dataDisplay,value=data['deriv type'],choices=Choice,
1654	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1655	derivSel.SetValue(data['deriv type'])
1656	derivSel.Bind(wx.EVT_COMBOBOX, OnDerivType)
1657
1658	LSSizer.Add(derivSel,0,WACV)
1659	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Min delta-M/M: '),0,WACV)
1660	Cnvrg = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2g'%(data['min dM/M']),style=wx.TE_PROCESS_ENTER)
1661	Cnvrg.Bind(wx.EVT_TEXT_ENTER,OnConvergence)
1662	Cnvrg.Bind(wx.EVT_KILL_FOCUS,OnConvergence)
1663	LSSizer.Add(Cnvrg,0,WACV)
1664	Indx = {}
1665	if 'Hessian' in data['deriv type']:
1666	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Max cycles: '),0,WACV)
1667	Choice = ['0','1','2','3','5','10','15','20']
1668	maxCyc = wx.ComboBox(parent=G2frame.dataDisplay,value=str(data['max cyc']),choices=Choice,
1669	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1670	maxCyc.SetValue(str(data['max cyc']))
1671	maxCyc.Bind(wx.EVT_COMBOBOX, OnMaxCycles)
1672	LSSizer.Add(maxCyc,0,WACV)
1673	else:
1674	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Initial shift factor: '),0,WACV)
1675	Factr = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.5f'%(data['shift factor']),style=wx.TE_PROCESS_ENTER)
1676	Factr.Bind(wx.EVT_TEXT_ENTER,OnFactor)
1677	Factr.Bind(wx.EVT_KILL_FOCUS,OnFactor)
1678	LSSizer.Add(Factr,0,WACV)
1679	if G2frame.Sngl:
1680	userReject = data['UsrReject']
1681	usrRej = {'minF/sig':[' Min obs/sig (0-5): ',[0,5], ],'MinExt':[' Min extinct. (0-.9): ',[0,.9],],
1682	'MaxDF/F':[' Max delt-F/sig (3-1000): ',[3.,1000.],],'MaxD':[' Max d-spacing (3-500): ',[3,500],],
1683	'MinD':[' Min d-spacing (0.1-1.0): ',[0.1,1.0],]}
1684
1685	fsqRef = wx.CheckBox(G2frame.dataDisplay,-1,label='Refine HKLF as F^2? ')
1686	fsqRef.SetValue(data['F**2'])
1687	fsqRef.Bind(wx.EVT_CHECKBOX,OnFsqRef)
1688	LSSizer.Add(fsqRef,0,WACV)
1689	LSSizer.Add((1,0),)
1690	for item in usrRej:
1691	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,label=usrRej[item][0]),0,WACV)
1692	usrrej = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2f'%(userReject[item]),style=wx.TE_PROCESS_ENTER)
1693	Indx[usrrej] = [item,usrRej[item][1]]
1694	usrrej.Bind(wx.EVT_TEXT_ENTER,OnUsrRej)
1695	usrrej.Bind(wx.EVT_KILL_FOCUS,OnUsrRej)
1696	LSSizer.Add(usrrej,0,WACV)
1697	# Hfix = wx.CheckBox(G2frame.dataDisplay,-1,label='Regularize H atoms? ')
1698	# Hfix.SetValue(data['HatomFix'])
1699	# Hfix.Bind(wx.EVT_CHECKBOX,OnHatomFix)
1700	# LSSizer.Add(Hfix,0,WACV) #for now
1701	return LSSizer
1702
1703	def AuthSizer():
1704
1705	def OnAuthor(event):
1706	data['Author'] = auth.GetValue()
1707
1708	Author = data['Author']
1709	authSizer = wx.BoxSizer(wx.HORIZONTAL)
1710	authSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' CIF Author (last, first):'),0,WACV)
1711	auth = wx.TextCtrl(G2frame.dataDisplay,-1,value=Author,style=wx.TE_PROCESS_ENTER)
1712	auth.Bind(wx.EVT_TEXT_ENTER,OnAuthor)
1713	auth.Bind(wx.EVT_KILL_FOCUS,OnAuthor)
1714	authSizer.Add(auth,0,WACV)
1715	return authSizer
1716
1717
1718	if G2frame.dataDisplay:
1719	G2frame.dataDisplay.Destroy()
1720	if not G2frame.dataFrame.GetStatusBar():
1721	Status = G2frame.dataFrame.CreateStatusBar()
1722	Status.SetStatusText('')
1723	G2frame.dataFrame.SetLabel('Controls')
1724	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
1725	SetDataMenuBar(G2frame,G2frame.dataFrame.ControlsMenu)
1726	mainSizer = wx.BoxSizer(wx.VERTICAL)
1727	mainSizer.Add((5,5),0)
1728	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement Controls:'),0,WACV)
1729	mainSizer.Add(LSSizer())
1730	mainSizer.Add((5,5),0)
1731	mainSizer.Add(SeqSizer())
1732	mainSizer.Add((5,5),0)
1733	mainSizer.Add(AuthSizer())
1734	mainSizer.Add((5,5),0)
1735
1736	mainSizer.Layout()
1737	G2frame.dataDisplay.SetSizer(mainSizer)
1738	G2frame.dataDisplay.SetSize(mainSizer.Fit(G2frame.dataFrame))
1739	G2frame.dataFrame.setSizePosLeft(mainSizer.Fit(G2frame.dataFrame))
1740
1741	################################################################################
1742	##### Comments
1743	################################################################################
1744
1745	def UpdateComments(G2frame,data):
1746
1747	if G2frame.dataDisplay:
1748	G2frame.dataDisplay.Destroy()
1749	G2frame.dataFrame.SetLabel('Comments')
1750	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1751	style=wx.TE_MULTILINE\|wx.TE_READONLY\|wx.TE_DONTWRAP)
1752	for line in data:
1753	G2frame.dataDisplay.AppendText(line+'\n')
1754	G2frame.dataFrame.setSizePosLeft([400,250])
1755
1756	################################################################################
1757	##### Display of Sequential Results
1758	################################################################################
1759
1760	def UpdateSeqResults(G2frame,data,prevSize=None):
1761	"""
1762	Called when the Sequential Results data tree entry is selected
1763	to show results from a sequential refinement.
1764
1765	:param wx.Frame G2frame: main GSAS-II data tree windows
1766
1767	:param dict data: a dictionary containing the following items:
1768
1769	* 'histNames' - list of histogram names in order as processed by Sequential Refinement
1770	* 'varyList' - list of variables - identical over all refinements in sequence
1771	note that this is the original list of variables, prior to processing
1772	constraints.
1773	* 'variableLabels' -- a dict of labels to be applied to each parameter
1774	(this is created as an empty dict if not present in data).
1775	* keyed by histName - dictionaries for all data sets processed, which contains:
1776
1777	* 'variables'- result[0] from leastsq call
1778	* 'varyList' - list of variables passed to leastsq call (not same as above)
1779	* 'sig' - esds for variables
1780	* 'covMatrix' - covariance matrix from individual refinement
1781	* 'title' - histogram name; same as dict item name
1782	* 'newAtomDict' - new atom parameters after shifts applied
1783	* 'newCellDict' - refined cell parameters after shifts to A0-A5 from Dij terms applied'
1784	"""
1785
1786	def GetSampleParms():
1787	'''Make a dictionary of the sample parameters are not the same over the
1788	refinement series.
1789	'''
1790	if 'IMG' in histNames[0]:
1791	sampleParmDict = {'Sample load':[],}
1792	else:
1793	sampleParmDict = {'Temperature':[],'Pressure':[],'Time':[],
1794	'FreePrm1':[],'FreePrm2':[],'FreePrm3':[],'Omega':[],
1795	'Chi':[],'Phi':[],'Azimuth':[],}
1796	Controls = G2frame.PatternTree.GetItemPyData(
1797	GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
1798	sampleParm = {}
1799	for name in histNames:
1800	if 'IMG' in name:
1801	for item in sampleParmDict:
1802	sampleParmDict[item].append(data[name]['parmDict'].get(item,0))
1803	else:
1804	Id = GetPatternTreeItemId(G2frame,G2frame.root,name)
1805	sampleData = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,Id,'Sample Parameters'))
1806	for item in sampleParmDict:
1807	sampleParmDict[item].append(sampleData.get(item,0))
1808	for item in sampleParmDict:
1809	frstValue = sampleParmDict[item][0]
1810	if np.any(np.array(sampleParmDict[item])-frstValue):
1811	if item.startswith('FreePrm'):
1812	sampleParm[Controls[item]] = sampleParmDict[item]
1813	else:
1814	sampleParm[item] = sampleParmDict[item]
1815	return sampleParm
1816
1817	def GetColumnInfo(col):
1818	'''returns column label, lists of values and errors (or None) for each column in the table
1819	for plotting. The column label is reformatted from Unicode to MatPlotLib encoding
1820	'''
1821	colName = G2frame.SeqTable.GetColLabelValue(col)
1822	plotName = variableLabels.get(colName,colName)
1823	plotName = plotSpCharFix(plotName)
1824	return plotName,colList[col],colSigs[col]
1825
1826	def PlotSelect(event):
1827	'Plots a row (covariance) or column on double-click'
1828	cols = G2frame.dataDisplay.GetSelectedCols()
1829	rows = G2frame.dataDisplay.GetSelectedRows()
1830	if cols:
1831	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1832	elif rows:
1833	name = histNames[rows[0]] #only does 1st one selected
1834	G2plt.PlotCovariance(G2frame,data[name])
1835	else:
1836	G2frame.ErrorDialog(
1837	'Select row or columns',
1838	'Nothing selected in table. Click on column or row label(s) to plot. N.B. Grid selection can be a bit funky.'
1839	)
1840
1841	def OnPlotSelSeq(event):
1842	'plot the selected columns or row from menu command'
1843	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1844	rows = G2frame.dataDisplay.GetSelectedRows()
1845	if cols:
1846	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1847	elif rows:
1848	name = histNames[rows[0]] #only does 1st one selected
1849	G2plt.PlotCovariance(G2frame,data[name])
1850	else:
1851	G2frame.ErrorDialog(
1852	'Select columns',
1853	'No columns or rows selected in table. Click on row or column labels to select fields for plotting.'
1854	)
1855
1856	def OnAveSelSeq(event):
1857	'average the selected columns from menu command'
1858	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1859	if cols:
1860	for col in cols:
1861	ave = np.mean(GetColumnInfo(col)[1])
1862	sig = np.std(GetColumnInfo(col)[1])
1863	print ' Average for '+G2frame.SeqTable.GetColLabelValue(col)+': '+'%.6g'%(ave)+' +/- '+'%.6g'%(sig)
1864	else:
1865	G2frame.ErrorDialog(
1866	'Select columns',
1867	'No columns selected in table. Click on column labels to select fields for averaging.'
1868	)
1869
1870	def OnRenameSelSeq(event):
1871	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1872	colNames = [G2frame.SeqTable.GetColLabelValue(c) for c in cols]
1873	newNames = colNames[:]
1874	for i,name in enumerate(colNames):
1875	if name in variableLabels:
1876	newNames[i] = variableLabels[name]
1877	if not cols:
1878	G2frame.ErrorDialog('Select columns',
1879	'No columns selected in table. Click on column labels to select fields for rename.')
1880	return
1881	dlg = G2G.MultiStringDialog(G2frame.dataDisplay,'Set column names',colNames,newNames)
1882	if dlg.Show():
1883	newNames = dlg.GetValues()
1884	variableLabels.update(dict(zip(colNames,newNames)))
1885	data['variableLabels'] = variableLabels
1886	dlg.Destroy()
1887	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1888	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1889
1890	def OnReOrgSelSeq(event):
1891	'Reorder the columns'
1892	G2G.GetItemOrder(G2frame,VaryListChanges,vallookup,posdict)
1893	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1894
1895	def OnSaveSelSeqCSV(event):
1896	'export the selected columns to a .csv file from menu command'
1897	OnSaveSelSeq(event,csv=True)
1898
1899	def OnSaveSeqCSV(event):
1900	'export all columns to a .csv file from menu command'
1901	OnSaveSelSeq(event,csv=True,allcols=True)
1902
1903	def OnSaveSelSeq(event,csv=False,allcols=False):
1904	'export the selected columns to a .txt or .csv file from menu command'
1905	def WriteCSV():
1906	def WriteList(headerItems):
1907	line = ''
1908	for lbl in headerItems:
1909	if line: line += ','
1910	line += '"'+lbl+'"'
1911	return line
1912	head = ['name']
1913	for col in cols:
1914	item = G2frame.SeqTable.GetColLabelValue(col)
1915	# get rid of labels that have Unicode characters
1916	if not all([ord(c) < 128 and ord(c) != 0 for c in item]): item = '?'
1917	if col in havesig:
1918	head += [item,'esd-'+item]
1919	else:
1920	head += [item]
1921	SeqFile.write(WriteList(head)+'\n')
1922	for row,name in enumerate(saveNames):
1923	line = '"'+saveNames[row]+'"'
1924	for col in cols:
1925	if col in havesig:
1926	line += ','+str(saveData[col][row])+','+str(saveSigs[col][row])
1927	else:
1928	line += ','+str(saveData[col][row])
1929	SeqFile.write(line+'\n')
1930	def WriteSeq():
1931	lenName = len(saveNames[0])
1932	line = ' %s '%('name'.center(lenName))
1933	for col in cols:
1934	item = G2frame.SeqTable.GetColLabelValue(col)
1935	if col in havesig:
1936	line += ' %12s %12s '%(item.center(12),'esd'.center(12))
1937	else:
1938	line += ' %12s '%(item.center(12))
1939	SeqFile.write(line+'\n')
1940	for row,name in enumerate(saveNames):
1941	line = " '%s' "%(saveNames[row])
1942	for col in cols:
1943	if col in havesig:
1944	line += ' %12.6f %12.6f '%(saveData[col][row],saveSigs[col][row])
1945	else:
1946	line += ' %12.6f '%saveData[col][row]
1947	SeqFile.write(line+'\n')
1948
1949	# start of OnSaveSelSeq code
1950	if allcols:
1951	cols = range(G2frame.SeqTable.GetNumberCols())
1952	else:
1953	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1954	nrows = G2frame.SeqTable.GetNumberRows()
1955	if not cols:
1956	G2frame.ErrorDialog('Select columns',
1957	'No columns selected in table. Click on column labels to select fields for output.')
1958	return
1959	saveNames = [G2frame.SeqTable.GetRowLabelValue(r) for r in range(nrows)]
1960	saveData = {}
1961	saveSigs = {}
1962	havesig = []
1963	for col in cols:
1964	name,vals,sigs = GetColumnInfo(col)
1965	saveData[col] = vals
1966	if sigs:
1967	havesig.append(col)
1968	saveSigs[col] = sigs
1969	if csv:
1970	wild = 'CSV output file (.csv)\|.csv'
1971	else:
1972	wild = 'Text output file (.txt)\|.txt'
1973	pth = G2G.GetExportPath(G2frame)
1974	dlg = wx.FileDialog(
1975	G2frame,
1976	'Choose text output file for your selection', pth, '',
1977	wild,wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1978	try:
1979	if dlg.ShowModal() == wx.ID_OK:
1980	SeqTextFile = dlg.GetPath()
1981	SeqTextFile = G2IO.FileDlgFixExt(dlg,SeqTextFile)
1982	SeqFile = open(SeqTextFile,'w')
1983	if csv:
1984	WriteCSV()
1985	else:
1986	WriteSeq()
1987	SeqFile.close()
1988	finally:
1989	dlg.Destroy()
1990
1991	def striphist(var,insChar=''):
1992	'strip a histogram number from a var name'
1993	sv = var.split(':')
1994	if len(sv) <= 1: return var
1995	if sv[1]:
1996	sv[1] = insChar
1997	return ':'.join(sv)
1998
1999	def plotSpCharFix(lbl):
2000	'Change selected unicode characters to their matplotlib equivalent'
2001	for u,p in [
2002	(u'\u03B1',r'$\alpha$'),
2003	(u'\u03B2',r'$\beta$'),
2004	(u'\u03B3',r'$\gamma$'),
2005	(u'\u0394\u03C7',r'$\Delta\chi$'),
2006	]:
2007	lbl = lbl.replace(u,p)
2008	return lbl
2009
2010	def SelectXaxis():
2011	'returns a selected column number (or None) as the X-axis selection'
2012	ncols = G2frame.SeqTable.GetNumberCols()
2013	colNames = [G2frame.SeqTable.GetColLabelValue(r) for r in range(ncols)]
2014	dlg = G2G.G2SingleChoiceDialog(
2015	G2frame.dataDisplay,
2016	'Select x-axis parameter for plot or Cancel for sequence number',
2017	'Select X-axis',
2018	colNames)
2019	try:
2020	if dlg.ShowModal() == wx.ID_OK:
2021	col = dlg.GetSelection()
2022	else:
2023	col = None
2024	finally:
2025	dlg.Destroy()
2026	return col
2027
2028	def EnablePseudoVarMenus():
2029	'Enables or disables the PseudoVar menu items that require existing defs'
2030	if Controls['SeqPseudoVars']:
2031	val = True
2032	else:
2033	val = False
2034	G2frame.dataFrame.SequentialPvars.Enable(wxDELSEQVAR,val)
2035	G2frame.dataFrame.SequentialPvars.Enable(wxEDITSEQVAR,val)
2036
2037	def DelPseudoVar(event):
2038	'Ask the user to select a pseudo var expression to delete'
2039	choices = Controls['SeqPseudoVars'].keys()
2040	selected = G2G.ItemSelector(
2041	choices,G2frame.dataFrame,
2042	multiple=True,
2043	title='Select expressions to remove',
2044	header='Delete expression')
2045	if selected is None: return
2046	for item in selected:
2047	del Controls['SeqPseudoVars'][choices[item]]
2048	if selected:
2049	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2050
2051	def EditPseudoVar(event):
2052	'Edit an existing pseudo var expression'
2053	choices = Controls['SeqPseudoVars'].keys()
2054	if len(choices) == 1:
2055	selected = 0
2056	else:
2057	selected = G2G.ItemSelector(
2058	choices,G2frame.dataFrame,
2059	multiple=False,
2060	title='Select an expression to edit',
2061	header='Edit expression')
2062	if selected is not None:
2063	dlg = G2exG.ExpressionDialog(
2064	G2frame.dataDisplay,PSvarDict,
2065	Controls['SeqPseudoVars'][choices[selected]],
2066	header="Edit the PseudoVar expression",
2067	VarLabel="PseudoVar #"+str(selected+1),
2068	fit=False)
2069	newobj = dlg.Show(True)
2070	if newobj:
2071	calcobj = G2obj.ExpressionCalcObj(newobj)
2072	del Controls['SeqPseudoVars'][choices[selected]]
2073	Controls['SeqPseudoVars'][calcobj.eObj.expression] = newobj
2074	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2075
2076	def AddNewPseudoVar(event):
2077	'Create a new pseudo var expression'
2078	dlg = G2exG.ExpressionDialog(
2079	G2frame.dataDisplay,PSvarDict,
2080	header='Enter an expression for a PseudoVar here',
2081	VarLabel = "New PseudoVar",
2082	fit=False)
2083	obj = dlg.Show(True)
2084	dlg.Destroy()
2085	if obj:
2086	calcobj = G2obj.ExpressionCalcObj(obj)
2087	Controls['SeqPseudoVars'][calcobj.eObj.expression] = obj
2088	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2089
2090	def UpdateParmDict(parmDict):
2091	'''generate the atom positions and the direct & reciprocal cell values,
2092	because they might be needed to evaluate the pseudovar
2093	'''
2094	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2095	['A'+str(i) for i in range(6)])
2096	)
2097	delList = []
2098	phaselist = []
2099	for item in parmDict:
2100	if ':' not in item: continue
2101	key = item.split(':')
2102	if len(key) < 3: continue
2103	# remove the dA[xyz] terms, they would only bring confusion
2104	if key[2].startswith('dA'):
2105	delList.append(item)
2106	# compute and update the corrected reciprocal cell terms using the Dij values
2107	elif key[2] in Ddict:
2108	if key[0] not in phaselist: phaselist.append(key[0])
2109	akey = key[0]+'::'+Ddict[key[2]]
2110	parmDict[akey] -= parmDict[item]
2111	delList.append(item)
2112	for item in delList:
2113	del parmDict[item]
2114	for i in phaselist:
2115	pId = int(i)
2116	# apply cell symmetry
2117	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],parmDict,zeroDict[pId])
2118	# convert to direct cell & add the unique terms to the dictionary
2119	for i,val in enumerate(G2lat.A2cell(A)):
2120	if i in uniqCellIndx[pId]:
2121	lbl = str(pId)+'::'+cellUlbl[i]
2122	parmDict[lbl] = val
2123	lbl = str(pId)+'::'+'vol'
2124	parmDict[lbl] = G2lat.calc_V(A)
2125	return parmDict
2126
2127	def EvalPSvarDeriv(calcobj,parmDict,sampleDict,var,ESD):
2128	'''Evaluate an expression derivative with respect to a
2129	GSAS-II variable name.
2130
2131	Note this likely could be faster if the loop over calcobjs were done
2132	inside after the Dict was created.
2133	'''
2134	step = ESD/10
2135	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2136	['A'+str(i) for i in range(6)])
2137	)
2138	results = []
2139	phaselist = []
2140	VparmDict = sampleDict.copy()
2141	for incr in step,-step:
2142	VparmDict.update(parmDict.copy())
2143	# as saved, the parmDict has updated 'A[xyz]' values, but 'dA[xyz]'
2144	# values are not zeroed: fix that!
2145	VparmDict.update({item:0.0 for item in parmDict if 'dA' in item})
2146	VparmDict[var] += incr
2147	G2mv.Dict2Map(VparmDict,[]) # apply constraints
2148	# generate the atom positions and the direct & reciprocal cell values now, because they might
2149	# needed to evaluate the pseudovar
2150	for item in VparmDict:
2151	if item in sampleDict:
2152	continue
2153	if ':' not in item: continue
2154	key = item.split(':')
2155	if len(key) < 3: continue
2156	# apply any new shifts to atom positions
2157	if key[2].startswith('dA'):
2158	VparmDict[''.join(item.split('d'))] += VparmDict[item]
2159	VparmDict[item] = 0.0
2160	# compute and update the corrected reciprocal cell terms using the Dij values
2161	if key[2] in Ddict:
2162	if key[0] not in phaselist: phaselist.append(key[0])
2163	akey = key[0]+'::'+Ddict[key[2]]
2164	VparmDict[akey] -= VparmDict[item]
2165	for i in phaselist:
2166	pId = int(i)
2167	# apply cell symmetry
2168	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],VparmDict,zeroDict[pId])
2169	# convert to direct cell & add the unique terms to the dictionary
2170	for i,val in enumerate(G2lat.A2cell(A)):
2171	if i in uniqCellIndx[pId]:
2172	lbl = str(pId)+'::'+cellUlbl[i]
2173	VparmDict[lbl] = val
2174	lbl = str(pId)+'::'+'vol'
2175	VparmDict[lbl] = G2lat.calc_V(A)
2176	# dict should be fully updated, use it & calculate
2177	calcobj.SetupCalc(VparmDict)
2178	results.append(calcobj.EvalExpression())
2179	return (results[0] - results[1]) / (2.*step)
2180
2181	def EnableParFitEqMenus():
2182	'Enables or disables the Parametric Fit menu items that require existing defs'
2183	if Controls['SeqParFitEqList']:
2184	val = True
2185	else:
2186	val = False
2187	G2frame.dataFrame.SequentialPfit.Enable(wxDELPARFIT,val)
2188	G2frame.dataFrame.SequentialPfit.Enable(wxEDITPARFIT,val)
2189	G2frame.dataFrame.SequentialPfit.Enable(wxDOPARFIT,val)
2190
2191	def ParEqEval(Values,calcObjList,varyList):
2192	'''Evaluate the parametric expression(s)
2193	:param list Values: a list of values for each variable parameter
2194	:param list calcObjList: a list of :class:`GSASIIobj.ExpressionCalcObj`
2195	expression objects to evaluate
2196	:param list varyList: a list of variable names for each value in Values
2197	'''
2198	result = []
2199	for calcobj in calcObjList:
2200	calcobj.UpdateVars(varyList,Values)
2201	result.append((calcobj.depVal-calcobj.EvalExpression())/calcobj.depSig)
2202	return result
2203
2204	def DoParEqFit(event,eqObj=None):
2205	'Parametric fit minimizer'
2206	varyValueDict = {} # dict of variables and their initial values
2207	calcObjList = [] # expression objects, ready to go for each data point
2208	if eqObj is not None:
2209	eqObjList = [eqObj,]
2210	else:
2211	eqObjList = Controls['SeqParFitEqList']
2212	UseFlags = G2frame.SeqTable.GetColValues(0)
2213	for obj in eqObjList:
2214	expr = obj.expression
2215	# assemble refined vars for this equation
2216	varyValueDict.update({var:val for var,val in obj.GetVariedVarVal()})
2217	# lookup dependent var position
2218	depVar = obj.GetDepVar()
2219	if depVar in colLabels:
2220	indx = colLabels.index(depVar)
2221	else:
2222	raise Exception('Dependent variable '+depVar+' not found')
2223	# assemble a list of the independent variables
2224	indepVars = obj.GetIndependentVars()
2225	# loop over each datapoint
2226	for j,row in enumerate(zip(*colList)):
2227	if not UseFlags[j]: continue
2228	# assemble equations to fit
2229	calcobj = G2obj.ExpressionCalcObj(obj)
2230	# prepare a dict of needed independent vars for this expression
2231	indepVarDict = {var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2232	calcobj.SetupCalc(indepVarDict)
2233	# values and sigs for current value of dependent var
2234	calcobj.depVal = row[indx]
2235	calcobj.depSig = colSigs[indx][j]
2236	calcObjList.append(calcobj)
2237	# varied parameters
2238	varyList = varyValueDict.keys()
2239	values = varyValues = [varyValueDict[key] for key in varyList]
2240	if not varyList:
2241	print 'no variables to refine!'
2242	return
2243	try:
2244	result = so.leastsq(ParEqEval,varyValues,full_output=True, #ftol=Ftol,
2245	args=(calcObjList,varyList)
2246	)
2247	values = result[0]
2248	covar = result[1]
2249	if covar is None:
2250	raise Exception
2251	esdDict = {}
2252	for i,avar in enumerate(varyList):
2253	esdDict[avar] = np.sqrt(covar[i,i])
2254	except:
2255	print('====> Fit failed')
2256	return
2257	print('==== Fit Results ====')
2258	for obj in eqObjList:
2259	obj.UpdateVariedVars(varyList,values)
2260	ind = ' '
2261	print(' '+obj.GetDepVar()+' = '+obj.expression)
2262	for var in obj.assgnVars:
2263	print(ind+var+' = '+obj.assgnVars[var])
2264	for var in obj.freeVars:
2265	avar = "::"+obj.freeVars[var][0]
2266	val = obj.freeVars[var][1]
2267	if obj.freeVars[var][2]:
2268	print(ind+var+' = '+avar + " = " + G2mth.ValEsd(val,esdDict[avar]))
2269	else:
2270	print(ind+var+' = '+avar + " =" + G2mth.ValEsd(val,0))
2271	# create a plot for each parametric variable
2272	for fitnum,obj in enumerate(eqObjList):
2273	calcobj = G2obj.ExpressionCalcObj(obj)
2274	# lookup dependent var position
2275	indx = colLabels.index(obj.GetDepVar())
2276	# assemble a list of the independent variables
2277	indepVars = obj.GetIndependentVars()
2278	# loop over each datapoint
2279	fitvals = []
2280	for j,row in enumerate(zip(*colList)):
2281	calcobj.SetupCalc(
2282	{var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2283	)
2284	fitvals.append(calcobj.EvalExpression())
2285	G2plt.PlotSelectedSequence(
2286	G2frame,[indx],GetColumnInfo,SelectXaxis,
2287	fitnum,fitvals)
2288
2289	def SingleParEqFit(eqObj):
2290	DoParEqFit(None,eqObj)
2291
2292	def DelParFitEq(event):
2293	'Ask the user to select function to delete'
2294	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2295	selected = G2G.ItemSelector(
2296	txtlst,G2frame.dataFrame,
2297	multiple=True,
2298	title='Select a parametric equation(s) to remove',
2299	header='Delete equation')
2300	if selected is None: return
2301	Controls['SeqParFitEqList'] = [obj for i,obj in enumerate(Controls['SeqParFitEqList']) if i not in selected]
2302	EnableParFitEqMenus()
2303	if Controls['SeqParFitEqList']: DoParEqFit(event)
2304
2305	def EditParFitEq(event):
2306	'Edit an existing parametric equation'
2307	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2308	if len(txtlst) == 1:
2309	selected = 0
2310	else:
2311	selected = G2G.ItemSelector(
2312	txtlst,G2frame.dataFrame,
2313	multiple=False,
2314	title='Select a parametric equation to edit',
2315	header='Edit equation')
2316	if selected is not None:
2317	dlg = G2exG.ExpressionDialog(
2318	G2frame.dataDisplay,indepVarDict,
2319	Controls['SeqParFitEqList'][selected],
2320	depVarDict=depVarDict,
2321	header="Edit the formula for this minimization function",
2322	ExtraButton=['Fit',SingleParEqFit])
2323	newobj = dlg.Show(True)
2324	if newobj:
2325	calcobj = G2obj.ExpressionCalcObj(newobj)
2326	Controls['SeqParFitEqList'][selected] = newobj
2327	EnableParFitEqMenus()
2328	if Controls['SeqParFitEqList']: DoParEqFit(event)
2329
2330	def AddNewParFitEq(event):
2331	'Create a new parametric equation to be fit to sequential results'
2332
2333	# compile the variable names used in previous freevars to avoid accidental name collisions
2334	usedvarlist = []
2335	for obj in Controls['SeqParFitEqList']:
2336	for var in obj.freeVars:
2337	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2338
2339	dlg = G2exG.ExpressionDialog(
2340	G2frame.dataDisplay,indepVarDict,
2341	depVarDict=depVarDict,
2342	header='Define an equation to minimize in the parametric fit',
2343	ExtraButton=['Fit',SingleParEqFit],
2344	usedVars=usedvarlist)
2345	obj = dlg.Show(True)
2346	dlg.Destroy()
2347	if obj:
2348	Controls['SeqParFitEqList'].append(obj)
2349	EnableParFitEqMenus()
2350	if Controls['SeqParFitEqList']: DoParEqFit(event)
2351
2352	def CopyParFitEq(event):
2353	'Copy an existing parametric equation to be fit to sequential results'
2354	# compile the variable names used in previous freevars to avoid accidental name collisions
2355	usedvarlist = []
2356	for obj in Controls['SeqParFitEqList']:
2357	for var in obj.freeVars:
2358	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2359	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2360	if len(txtlst) == 1:
2361	selected = 0
2362	else:
2363	selected = G2G.ItemSelector(
2364	txtlst,G2frame.dataFrame,
2365	multiple=False,
2366	title='Select a parametric equation to copy',
2367	header='Copy equation')
2368	if selected is not None:
2369	newEqn = copy.deepcopy(Controls['SeqParFitEqList'][selected])
2370	for var in newEqn.freeVars:
2371	newEqn.freeVars[var][0] = G2obj.MakeUniqueLabel(newEqn.freeVars[var][0],usedvarlist)
2372	dlg = G2exG.ExpressionDialog(
2373	G2frame.dataDisplay,indepVarDict,
2374	newEqn,
2375	depVarDict=depVarDict,
2376	header="Edit the formula for this minimization function",
2377	ExtraButton=['Fit',SingleParEqFit])
2378	newobj = dlg.Show(True)
2379	if newobj:
2380	calcobj = G2obj.ExpressionCalcObj(newobj)
2381	Controls['SeqParFitEqList'].append(newobj)
2382	EnableParFitEqMenus()
2383	if Controls['SeqParFitEqList']: DoParEqFit(event)
2384
2385	def GridSetToolTip(row,col):
2386	'''Routine to show standard uncertainties for each element in table
2387	as a tooltip
2388	'''
2389	if colSigs[col]:
2390	return u'\u03c3 = '+str(colSigs[col][row])
2391	return ''
2392
2393	def GridColLblToolTip(col):
2394	'''Define a tooltip for a column. This will be the user-entered value
2395	(from data['variableLabels']) or the default name
2396	'''
2397	if col < 0 or col > len(colLabels):
2398	print 'Illegal column #',col
2399	return
2400	var = colLabels[col]
2401	return variableLabels.get(var,G2obj.fmtVarDescr(var))
2402
2403	def SetLabelString(event):
2404	'''Define or edit the label for a column in the table, to be used
2405	as a tooltip and for plotting
2406	'''
2407	col = event.GetCol()
2408	if col < 0 or col > len(colLabels):
2409	return
2410	var = colLabels[col]
2411	lbl = variableLabels.get(var,G2obj.fmtVarDescr(var))
2412	dlg = G2G.SingleStringDialog(G2frame.dataFrame,'Set variable label',
2413	'Set a new name for variable '+var,lbl,size=(400,-1))
2414	if dlg.Show():
2415	variableLabels[var] = dlg.GetValue()
2416	dlg.Destroy()
2417
2418	#def GridRowLblToolTip(row): return 'Row ='+str(row)
2419
2420	# lookup table for unique cell parameters by symmetry
2421	cellGUIlist = [
2422	[['m3','m3m'],(0,)],
2423	[['3R','3mR'],(0,3)],
2424	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],(0,2)],
2425	[['mmm'],(0,1,2)],
2426	[['2/m'+'a'],(0,1,2,3)],
2427	[['2/m'+'b'],(0,1,2,4)],
2428	[['2/m'+'c'],(0,1,2,5)],
2429	[['-1'],(0,1,2,3,4,5)],
2430	]
2431	# cell labels
2432	cellUlbl = ('a','b','c',u'\u03B1',u'\u03B2',u'\u03B3') # unicode a,b,c,alpha,beta,gamma
2433
2434	#======================================================================
2435	# start processing sequential results here (UpdateSeqResults)
2436	#======================================================================
2437	if not data:
2438	print 'No sequential refinement results'
2439	return
2440	variableLabels = data.get('variableLabels',{})
2441	data['variableLabels'] = variableLabels
2442	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
2443	Controls = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Controls'))
2444	# create a place to store Pseudo Vars & Parametric Fit functions, if not present
2445	if 'SeqPseudoVars' not in Controls: Controls['SeqPseudoVars'] = {}
2446	if 'SeqParFitEqList' not in Controls: Controls['SeqParFitEqList'] = []
2447	histNames = data['histNames']
2448	if G2frame.dataDisplay:
2449	G2frame.dataDisplay.Destroy()
2450	if not G2frame.dataFrame.GetStatusBar():
2451	Status = G2frame.dataFrame.CreateStatusBar()
2452	Status.SetStatusText("Select column to export; Double click on column to plot data; on row for Covariance")
2453	sampleParms = GetSampleParms()
2454
2455	# make dict of varied atom coords keyed by absolute position
2456	newAtomDict = data[histNames[0]].get('newAtomDict',{}) # dict with atom positions; relative & absolute
2457	# Possible error: the next might need to be data[histNames[0]]['varyList']
2458	# error will arise if there constraints on coordinates?
2459	atomLookup = {newAtomDict[item][0]:item for item in newAtomDict if item in data['varyList']}
2460
2461	# make dict of varied cell parameters equivalents
2462	ESDlookup = {} # provides the Dij term for each Ak term (where terms are refined)
2463	Dlookup = {} # provides the Ak term for each Dij term (where terms are refined)
2464	# N.B. These Dij vars are missing a histogram #
2465	newCellDict = data[histNames[0]].get('newCellDict',{})
2466	for item in newCellDict:
2467	if item in data['varyList']:
2468	ESDlookup[newCellDict[item][0]] = item
2469	Dlookup[item] = newCellDict[item][0]
2470	# add coordinate equivalents to lookup table
2471	for parm in atomLookup:
2472	Dlookup[atomLookup[parm]] = parm
2473	ESDlookup[parm] = atomLookup[parm]
2474
2475	# get unit cell & symmetry for all phases & initial stuff for later use
2476	RecpCellTerms = {}
2477	SGdata = {}
2478	uniqCellIndx = {}
2479	initialCell = {}
2480	RcellLbls = {}
2481	zeroDict = {}
2482	Rcelldict = {}
2483	for phase in Phases:
2484	phasedict = Phases[phase]
2485	pId = phasedict['pId']
2486	pfx = str(pId)+'::' # prefix for A values from phase
2487	RcellLbls[pId] = [pfx+'A'+str(i) for i in range(6)]
2488	RecpCellTerms[pId] = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2489	zeroDict[pId] = dict(zip(RcellLbls[pId],6*[0.,]))
2490	SGdata[pId] = phasedict['General']['SGData']
2491	Rcelldict.update({lbl:val for lbl,val in zip(RcellLbls[pId],RecpCellTerms[pId])})
2492	laue = SGdata[pId]['SGLaue']
2493	if laue == '2/m':
2494	laue += SGdata[pId]['SGUniq']
2495	for symlist,celllist in cellGUIlist:
2496	if laue in symlist:
2497	uniqCellIndx[pId] = celllist
2498	break
2499	else: # should not happen
2500	uniqCellIndx[pId] = range(6)
2501	for i in uniqCellIndx[pId]:
2502	initialCell[str(pId)+'::A'+str(i)] = RecpCellTerms[pId][i]
2503
2504	SetDataMenuBar(G2frame,G2frame.dataFrame.SequentialMenu)
2505	G2frame.dataFrame.SetLabel('Sequential refinement results')
2506	if not G2frame.dataFrame.GetStatusBar():
2507	Status = G2frame.dataFrame.CreateStatusBar()
2508	Status.SetStatusText('')
2509	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRenameSelSeq, id=wxID_RENAMESEQSEL)
2510	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeq, id=wxID_SAVESEQSEL)
2511	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeqCSV, id=wxID_SAVESEQSELCSV)
2512	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSeqCSV, id=wxID_SAVESEQCSV)
2513	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotSelSeq, id=wxID_PLOTSEQSEL)
2514	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAveSelSeq, id=wxID_AVESEQSEL)
2515	G2frame.dataFrame.Bind(wx.EVT_MENU, OnReOrgSelSeq, id=wxID_ORGSEQSEL)
2516	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewPseudoVar, id=wxADDSEQVAR)
2517	G2frame.dataFrame.Bind(wx.EVT_MENU, DelPseudoVar, id=wxDELSEQVAR)
2518	G2frame.dataFrame.Bind(wx.EVT_MENU, EditPseudoVar, id=wxEDITSEQVAR)
2519	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewParFitEq, id=wxADDPARFIT)
2520	G2frame.dataFrame.Bind(wx.EVT_MENU, CopyParFitEq, id=wxCOPYPARFIT)
2521	G2frame.dataFrame.Bind(wx.EVT_MENU, DelParFitEq, id=wxDELPARFIT)
2522	G2frame.dataFrame.Bind(wx.EVT_MENU, EditParFitEq, id=wxEDITPARFIT)
2523	G2frame.dataFrame.Bind(wx.EVT_MENU, DoParEqFit, id=wxDOPARFIT)
2524	EnablePseudoVarMenus()
2525	EnableParFitEqMenus()
2526
2527	# scan for locations where the variables change
2528	VaryListChanges = [] # histograms where there is a change
2529	combinedVaryList = []
2530	firstValueDict = {}
2531	vallookup = {}
2532	posdict = {}
2533	prevVaryList = []
2534	for i,name in enumerate(histNames):
2535	for var,val,sig in zip(data[name]['varyList'],data[name]['variables'],data[name]['sig']):
2536	svar = striphist(var,'*') # wild-carded
2537	if svar not in combinedVaryList:
2538	# add variables to list as they appear
2539	combinedVaryList.append(svar)
2540	firstValueDict[svar] = (val,sig)
2541	if prevVaryList != data[name]['varyList']: # this refinement has a different refinement list from previous
2542	prevVaryList = data[name]['varyList']
2543	vallookup[name] = dict(zip(data[name]['varyList'],data[name]['variables']))
2544	posdict[name] = {}
2545	for var in data[name]['varyList']:
2546	svar = striphist(var,'*')
2547	posdict[name][combinedVaryList.index(svar)] = svar
2548	VaryListChanges.append(name)
2549	if len(VaryListChanges) > 1:
2550	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,True)
2551	else:
2552	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,False)
2553	#-----------------------------------------------------------------------------------
2554	# build up the data table by columns -----------------------------------------------
2555	nRows = len(histNames)
2556	colList = [nRows*[True]]
2557	colSigs = [None]
2558	colLabels = ['Use']
2559	Types = [wg.GRID_VALUE_BOOL]
2560	# start with Rwp values
2561	if 'IMG ' not in histNames[0][:4]:
2562	colList += [[data[name]['Rvals']['Rwp'] for name in histNames]]
2563	colSigs += [None]
2564	colLabels += ['Rwp']
2565	Types += [wg.GRID_VALUE_FLOAT+':10,3',]
2566	# add % change in Chi^2 in last cycle
2567	if histNames[0][:4] not in ['SASD','IMG '] and Controls.get('ShowCell'):
2568	colList += [[100.*data[name]['Rvals'].get('DelChi2',-1) for name in histNames]]
2569	colSigs += [None]
2570	colLabels += [u'\u0394\u03C7\u00B2 (%)']
2571	Types += [wg.GRID_VALUE_FLOAT,]
2572	deltaChiCol = len(colLabels)-1
2573	# add changing sample parameters to table
2574	for key in sampleParms:
2575	colList += [sampleParms[key]]
2576	colSigs += [None]
2577	colLabels += [key]
2578	Types += [wg.GRID_VALUE_FLOAT,]
2579	sampleDict = {}
2580	for i,name in enumerate(histNames):
2581	sampleDict[name] = dict(zip(sampleParms.keys(),[sampleParms[key][i] for key in sampleParms.keys()]))
2582	# add unique cell parameters TODO: review this where the cell symmetry changes (when possible)
2583	if Controls.get('ShowCell',False):
2584	for pId in sorted(RecpCellTerms):
2585	pfx = str(pId)+'::' # prefix for A values from phase
2586	cells = []
2587	cellESDs = []
2588	colLabels += [pfx+cellUlbl[i] for i in uniqCellIndx[pId]]
2589	colLabels += [pfx+'Vol']
2590	Types += (1+len(uniqCellIndx[pId]))*[wg.GRID_VALUE_FLOAT,]
2591	for name in histNames:
2592	covData = {
2593	'varyList': [Dlookup.get(striphist(v),v) for v in data[name]['varyList']],
2594	'covMatrix': data[name]['covMatrix']
2595	}
2596	A = RecpCellTerms[pId][:] # make copy of starting A values
2597	# update with refined values
2598	for i in range(6):
2599	var = str(pId)+'::A'+str(i)
2600	if var in ESDlookup:
2601	val = data[name]['newCellDict'][ESDlookup[var]][1] # get refined value
2602	A[i] = val # override with updated value
2603	# apply symmetry
2604	Albls = [pfx+'A'+str(i) for i in range(6)]
2605	cellDict = dict(zip(Albls,A))
2606	A,zeros = G2stIO.cellFill(pfx,SGdata[pId],cellDict,zeroDict[pId])
2607	# convert to direct cell & add only unique values to table
2608	c = G2lat.A2cell(A)
2609	vol = G2lat.calc_V(A)
2610	cE = G2stIO.getCellEsd(pfx,SGdata[pId],A,covData)
2611	cells += [[c[i] for i in uniqCellIndx[pId]]+[vol]]
2612	cellESDs += [[cE[i] for i in uniqCellIndx[pId]]+[cE[-1]]]
2613	colList += zip(*cells)
2614	colSigs += zip(*cellESDs)
2615	# sort out the variables in their selected order
2616	varcols = 0
2617	for d in posdict.itervalues():
2618	varcols = max(varcols,max(d.keys())+1)
2619	# get labels for each column
2620	for i in range(varcols):
2621	lbl = ''
2622	for h in VaryListChanges:
2623	if posdict[h].get(i):
2624	if posdict[h].get(i) in lbl: continue
2625	if lbl != "": lbl += '/'
2626	lbl += posdict[h].get(i)
2627	colLabels.append(lbl)
2628	Types += varcols*[wg.GRID_VALUE_FLOAT]
2629	vals = []
2630	esds = []
2631	varsellist = None # will be a list of variable names in the order they are selected to appear
2632	# tabulate values for each hist, leaving None for blank columns
2633	for name in histNames:
2634	if name in posdict:
2635	varsellist = [posdict[name].get(i) for i in range(varcols)]
2636	# translate variable names to how they will be used in the headings
2637	vs = [striphist(v,'*') for v in data[name]['varyList']]
2638	# determine the index for each column (or None) in the data[]['variables'] and ['sig'] lists
2639	sellist = [vs.index(v) if v is not None else None for v in varsellist]
2640	#sellist = [i if striphist(v,'*') in varsellist else None for i,v in enumerate(data[name]['varyList'])]
2641	if not varsellist: raise Exception()
2642	vals.append([data[name]['variables'][s] if s is not None else None for s in sellist])
2643	esds.append([data[name]['sig'][s] if s is not None else None for s in sellist])
2644	#GSASIIpath.IPyBreak()
2645	colList += zip(*vals)
2646	colSigs += zip(*esds)
2647
2648	# tabulate constrained variables, removing histogram numbers if needed
2649	# from parameter label
2650	depValDict = {}
2651	depSigDict = {}
2652	for name in histNames:
2653	for var in data[name].get('depParmDict',{}):
2654	val,sig = data[name]['depParmDict'][var]
2655	svar = striphist(var,'*')
2656	if svar not in depValDict:
2657	depValDict[svar] = [val]
2658	depSigDict[svar] = [sig]
2659	else:
2660	depValDict[svar].append(val)
2661	depSigDict[svar].append(sig)
2662	# add the dependent constrained variables to the table
2663	for var in sorted(depValDict):
2664	if len(depValDict[var]) != len(histNames): continue
2665	colLabels.append(var)
2666	Types += [wg.GRID_VALUE_FLOAT,]
2667	colSigs += [depSigDict[var]]
2668	colList += [depValDict[var]]
2669
2670	# add atom parameters to table
2671	colLabels += atomLookup.keys()
2672	Types += len(atomLookup)*[wg.GRID_VALUE_FLOAT]
2673	for parm in sorted(atomLookup):
2674	colList += [[data[name]['newAtomDict'][atomLookup[parm]][1] for name in histNames]]
2675	if atomLookup[parm] in data[histNames[0]]['varyList']:
2676	col = data[histNames[0]]['varyList'].index(atomLookup[parm])
2677	colSigs += [[data[name]['sig'][col] for name in histNames]]
2678	else:
2679	colSigs += [None] # should not happen
2680	# evaluate Pseudovars, their ESDs and add them to grid
2681	for expr in Controls['SeqPseudoVars']:
2682	obj = Controls['SeqPseudoVars'][expr]
2683	calcobj = G2obj.ExpressionCalcObj(obj)
2684	valList = []
2685	esdList = []
2686	for seqnum,name in enumerate(histNames):
2687	sigs = data[name]['sig']
2688	G2mv.InitVars()
2689	parmDict = data[name].get('parmDict')
2690	badVary = data[name].get('badVary',[])
2691	constraintInfo = data[name].get('constraintInfo',[[],[],{},[],seqnum])
2692	groups,parmlist,constrDict,fixedList,ihst = constraintInfo
2693	varyList = data[name]['varyList']
2694	parmDict = data[name]['parmDict']
2695	G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmDict,SeqHist=ihst)
2696	derivs = np.array(
2697	[EvalPSvarDeriv(calcobj,parmDict.copy(),sampleDict[name],var,ESD)
2698	for var,ESD in zip(varyList,sigs)]
2699	)
2700	esdList.append(np.sqrt(
2701	np.inner(derivs,np.inner(data[name]['covMatrix'],derivs.T))
2702	))
2703	PSvarDict = parmDict.copy()
2704	PSvarDict.update(sampleDict[name])
2705	UpdateParmDict(PSvarDict)
2706	calcobj.UpdateDict(PSvarDict)
2707	valList.append(calcobj.EvalExpression())
2708	if not esdList:
2709	esdList = None
2710	colList += [valList]
2711	colSigs += [esdList]
2712	colLabels += [expr]
2713	Types += [wg.GRID_VALUE_FLOAT,]
2714	#---- table build done -------------------------------------------------------------
2715
2716	# Make dict needed for creating & editing pseudovars (PSvarDict).
2717	name = histNames[0]
2718	parmDict = data[name].get('parmDict')
2719	PSvarDict = parmDict.copy()
2720	PSvarDict.update(sampleParms)
2721	UpdateParmDict(PSvarDict)
2722	# Also dicts of dependent (depVarDict) & independent vars (indepVarDict)
2723	# for Parametric fitting from the data table
2724	parmDict = dict(zip(colLabels,zip(*colList)[0])) # scratch dict w/all values in table
2725	parmDict.update(
2726	{var:val for var,val in data[name].get('newCellDict',{}).values()} # add varied reciprocal cell terms
2727	)
2728	name = histNames[0]
2729
2730	#******************************************************************************
2731	# create a set of values for example evaluation of pseudovars and
2732	# this does not work for refinements that have differing numbers of variables.
2733	#raise Exception
2734	indepVarDict = {} # values in table w/o ESDs
2735	depVarDict = {}
2736	for i,var in enumerate(colLabels):
2737	if var == 'Use': continue
2738	if colList[i][0] is None:
2739	val,sig = firstValueDict.get(var,[None,None])
2740	elif colSigs[i]:
2741	val,sig = colList[i][0],colSigs[i][0]
2742	else:
2743	val,sig = colList[i][0],None
2744	if val is None:
2745	continue
2746	elif sig is None:
2747	indepVarDict[var] = val
2748	elif striphist(var) not in Dlookup:
2749	depVarDict[var] = val
2750	# add recip cell coeff. values
2751	depVarDict.update({var:val for var,val in data[name].get('newCellDict',{}).values()})
2752
2753	G2frame.dataDisplay = G2G.GSGrid(parent=G2frame.dataFrame)
2754	G2frame.SeqTable = G2G.Table(
2755	[list(c) for c in zip(*colList)], # convert from columns to rows
2756	colLabels=colLabels,rowLabels=histNames,types=Types)
2757	G2frame.dataDisplay.SetTable(G2frame.SeqTable, True)
2758	#G2frame.dataDisplay.EnableEditing(False)
2759	# make all but first column read-only
2760	for c in range(1,len(colLabels)):
2761	for r in range(nRows):
2762	G2frame.dataDisplay.SetCellReadOnly(r,c)
2763	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, PlotSelect)
2764	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, SetLabelString)
2765	G2frame.dataDisplay.SetRowLabelSize(8*len(histNames[0])) #pretty arbitrary 8
2766	G2frame.dataDisplay.SetMargins(0,0)
2767	G2frame.dataDisplay.AutoSizeColumns(True)
2768	if prevSize:
2769	G2frame.dataDisplay.SetSize(prevSize)
2770	else:
2771	G2frame.dataFrame.setSizePosLeft([700,350])
2772	# highlight unconverged shifts
2773	if histNames[0][:4] not in ['SASD','IMG ']:
2774	for row,name in enumerate(histNames):
2775	deltaChi = G2frame.SeqTable.GetValue(row,deltaChiCol)
2776	if deltaChi > 10.:
2777	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,0,0))
2778	elif deltaChi > 1.0:
2779	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,255,0))
2780	G2frame.dataDisplay.InstallGridToolTip(GridSetToolTip,GridColLblToolTip)
2781	G2frame.dataDisplay.SendSizeEvent() # resize needed on mac
2782	G2frame.dataDisplay.Refresh() # shows colored text on mac
2783
2784	################################################################################
2785	##### Main PWDR panel
2786	################################################################################
2787
2788	def UpdatePWHKPlot(G2frame,kind,item):
2789	'''Called when the histogram main tree entry is called. Displays the
2790	histogram weight factor, refinement statistics for the histogram
2791	and the range of data for a simulation.
2792
2793	Also invokes a plot of the histogram.
2794	'''
2795	def onEditSimRange(event):
2796	'Edit simulation range'
2797	inp = [
2798	min(data[1][0]),
2799	max(data[1][0]),
2800	None
2801	]
2802	inp[2] = (inp[1] - inp[0])/(len(data[1][0])-1.)
2803	names = ('start angle', 'end angle', 'step size')
2804	dictlst = [inp] * len(inp)
2805	elemlst = range(len(inp))
2806	dlg = G2G.ScrolledMultiEditor(
2807	G2frame,[inp] * len(inp), range(len(inp)), names,
2808	header='Edit simulation range',
2809	minvals=(0.001,0.001,0.0001),
2810	maxvals=(180.,180.,.1),
2811	)
2812	dlg.CenterOnParent()
2813	val = dlg.ShowModal()
2814	dlg.Destroy()
2815	if val != wx.ID_OK: return
2816	if inp[0] > inp[1]:
2817	end,start,step = inp
2818	else:
2819	start,end,step = inp
2820	step = abs(step)
2821	N = int((end-start)/step)+1
2822	newdata = np.linspace(start,end,N,True)
2823	if len(newdata) < 2: return # too small a range - reject
2824	data[1] = [newdata,np.zeros_like(newdata),np.ones_like(newdata),
2825	np.zeros_like(newdata),np.zeros_like(newdata),np.zeros_like(newdata)]
2826	Tmin = newdata[0]
2827	Tmax = newdata[-1]
2828	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,item,'Limits'),
2829	[(Tmin,Tmax),[Tmin,Tmax]])
2830	UpdatePWHKPlot(G2frame,kind,item) # redisplay data screen
2831
2832	def OnPlot3DHKL(event):
2833	refList = data[1]['RefList']
2834	FoMax = np.max(refList.T[8+Super])
2835	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2836	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2837	Vpoint = np.array([int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))])
2838	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,'Zone':False,'viewKey':'L',
2839	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2840	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
2841	'Scale':1.0,'oldxy':[],'viewDir':[0,0,1]},'Super':Super,'SuperVec':SuperVec}
2842	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2843
2844	def OnPlotAll3DHKL(event):
2845	choices = GetPatternTreeDataNames(G2frame,['HKLF',])
2846	dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to plot',
2847	'Use data',choices)
2848	try:
2849	if dlg.ShowModal() == wx.ID_OK:
2850	refNames = [choices[i] for i in dlg.GetSelections()]
2851	else:
2852	return
2853	finally:
2854	dlg.Destroy()
2855	refList = np.zeros(0)
2856	for name in refNames:
2857	Id = GetPatternTreeItemId(G2frame,G2frame.root, name)
2858	reflData = G2frame.PatternTree.GetItemPyData(Id)[1]
2859	if len(refList):
2860	refList = np.concatenate((refList,reflData['RefList']))
2861	else:
2862	refList = reflData['RefList']
2863
2864	FoMax = np.max(refList.T[8+Super])
2865	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2866	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2867	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2868	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,'Zone':False,'viewKey':'L',
2869	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2870	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
2871	'Scale':1.0,'oldxy':[],'viewDir':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
2872	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2873
2874
2875	def OnErrorAnalysis(event):
2876	G2plt.PlotDeltSig(G2frame,kind)
2877
2878	def OnWtFactor(event):
2879	try:
2880	val = float(wtval.GetValue())
2881	except ValueError:
2882	val = data[0]['wtFactor']
2883	data[0]['wtFactor'] = val
2884	wtval.SetValue('%.3f'%(val))
2885
2886	def OnCompression(event):
2887	data[0] = int(comp.GetValue())
2888
2889	def onCopyPlotCtrls(event):
2890	'''Respond to menu item to copy multiple sections from a histogram.
2891	Need this here to pass on the G2frame object.
2892	'''
2893	G2pdG.CopyPlotCtrls(G2frame)
2894
2895	def onCopySelectedItems(event):
2896	'''Respond to menu item to copy multiple sections from a histogram.
2897	Need this here to pass on the G2frame object.
2898	'''
2899	G2pdG.CopySelectedHistItems(G2frame)
2900
2901	data = G2frame.PatternTree.GetItemPyData(item)
2902	#patches
2903	if 'wtFactor' not in data[0]:
2904	data[0] = {'wtFactor':1.0}
2905	# if kind == 'PWDR' and 'Compression' not in data[0]:
2906	# data[0]['Compression'] = 1
2907	#if isinstance(data[1],list) and kind == 'HKLF':
2908	if 'list' in str(type(data[1])) and kind == 'HKLF':
2909	RefData = {'RefList':[],'FF':[]}
2910	for ref in data[1]:
2911	RefData['RefList'].append(ref[:11]+[ref[13],])
2912	RefData['FF'].append(ref[14])
2913	data[1] = RefData
2914	G2frame.PatternTree.SetItemPyData(item,data)
2915	#end patches
2916	if G2frame.dataDisplay:
2917	G2frame.dataDisplay.Destroy()
2918	if kind in ['PWDR','SASD']:
2919	SetDataMenuBar(G2frame,G2frame.dataFrame.PWDRMenu)
2920	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2921	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2922	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopyPlotCtrls, id=wxID_PLOTCTRLCOPY)
2923	elif kind in ['HKLF',]:
2924	SetDataMenuBar(G2frame,G2frame.dataFrame.HKLFMenu)
2925	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2926	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=wxID_PWD3DHKLPLOT)
2927	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotAll3DHKL, id=wxID_3DALLHKLPLOT)
2928	# G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2929	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
2930
2931	mainSizer = wx.BoxSizer(wx.VERTICAL)
2932	mainSizer.Add((5,5),)
2933	wtSizer = wx.BoxSizer(wx.HORIZONTAL)
2934	wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Weight factor: '),0,WACV)
2935	wtval = wx.TextCtrl(G2frame.dataDisplay,-1,'%.3f'%(data[0]['wtFactor']),style=wx.TE_PROCESS_ENTER)
2936	wtval.Bind(wx.EVT_TEXT_ENTER,OnWtFactor)
2937	wtval.Bind(wx.EVT_KILL_FOCUS,OnWtFactor)
2938	wtSizer.Add(wtval,0,WACV)
2939	# if kind == 'PWDR': #possible future compression feature; NB above patch as well
2940	# wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Compression factor: '),0,WACV)
2941	# choice = ['1','2','3','4','5','6']
2942	# comp = wx.ComboBox(parent=G2frame.dataDisplay,choices=choice,
2943	# style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2944	# comp.SetValue(str(data[0]['Compression']))
2945	# comp.Bind(wx.EVT_COMBOBOX, OnCompression)
2946	# wtSizer.Add(comp,0,WACV)
2947	mainSizer.Add(wtSizer)
2948	if data[0].get('Dummy'):
2949	simSizer = wx.BoxSizer(wx.HORIZONTAL)
2950	Tmin = min(data[1][0])
2951	Tmax = max(data[1][0])
2952	num = len(data[1][0])
2953	step = (Tmax - Tmin)/(num-1)
2954	t = u'2\u03b8' # 2theta
2955	lbl = u'Simulation range: {:.2f} to {:.2f} {:s}\nwith {:.4f} steps ({:d} points)'
2956	lbl += u'\n(Edit range resets observed intensities).'
2957	lbl = lbl.format(Tmin,Tmax,t,step,num)
2958	simSizer.Add(wx.StaticText(G2frame.dataDisplay,wx.ID_ANY,lbl),
2959	0,WACV)
2960	but = wx.Button(G2frame.dataDisplay,wx.ID_ANY,"Edit range")
2961	but.Bind(wx.EVT_BUTTON,onEditSimRange)
2962	simSizer.Add(but,0,WACV)
2963	mainSizer.Add(simSizer)
2964	if 'Nobs' in data[0]:
2965	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2966	' Data residual wR: %.3f%% on %d observations'%(data[0]['wR'],data[0]['Nobs'])))
2967	for value in data[0]:
2968	if 'Nref' in value:
2969	pfx = value.split('Nref')[0]
2970	name = data[0].get(pfx.split(':')[0]+'::Name','?')
2971	if 'SS' in value:
2972	mainSizer.Add((5,5),)
2973	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For incommensurate phase '+name+':'))
2974	for m,(Rf2,Rf,Nobs) in enumerate(zip(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])):
2975	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2976	u' m = +/- %d: RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2977	(m,Rf2,Rf,Nobs)))
2978	else:
2979	mainSizer.Add((5,5),)
2980	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For phase '+name+':'))
2981	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2982	u' Unweighted phase residuals RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2983	(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])))
2984
2985	mainSizer.Add((5,5),)
2986	mainSizer.Layout()
2987	G2frame.dataDisplay.SetSizer(mainSizer)
2988	Size = mainSizer.Fit(G2frame.dataFrame)
2989	Size[1] += 10
2990	G2frame.dataFrame.setSizePosLeft(Size)
2991	G2frame.PatternTree.SetItemPyData(item,data)
2992	if kind in ['PWDR','SASD']:
2993	if 'xylim' in dir(G2frame):
2994	NewPlot = False
2995	else:
2996
2997	NewPlot = True
2998	G2plt.PlotPatterns(G2frame,plotType=kind,newPlot=NewPlot)
2999	elif kind == 'HKLF':
3000	Name = G2frame.PatternTree.GetItemText(item)
3001	phaseName = G2pdG.IsHistogramInAnyPhase(G2frame,Name)
3002	if phaseName:
3003	pId = GetPatternTreeItemId(G2frame,G2frame.root,'Phases')
3004	phaseId = GetPatternTreeItemId(G2frame,pId,phaseName)
3005	General = G2frame.PatternTree.GetItemPyData(phaseId)['General']
3006	Super = General.get('Super',0)
3007	SuperVec = General.get('SuperVec',[])
3008	else:
3009	Super = 0
3010	SuperVec = []
3011	refList = data[1]['RefList']
3012	FoMax = np.max(refList.T[5+data[1].get('Super',0)])
3013	page = G2frame.G2plotNB.nb.GetSelection()
3014	tab = ''
3015	if page >= 0:
3016	tab = G2frame.G2plotNB.nb.GetPageText(page)
3017	if '3D' in tab:
3018	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
3019	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
3020	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
3021	Page = G2frame.G2plotNB.nb.GetPage(page)
3022	controls = Page.controls
3023	G2plt.Plot3DSngl(G2frame,newPlot=False,Data=controls,hklRef=refList,Title=phaseName)
3024	else:
3025	controls = {'Type' : 'Fo','ifFc' : True,
3026	'HKLmax' : [int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))],
3027	'HKLmin' : [int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))],
3028	'FoMax' : FoMax,'Zone' : '001','Layer' : 0,'Scale' : 1.0,'Super':Super,'SuperVec':SuperVec}
3029	G2plt.PlotSngl(G2frame,newPlot=True,Data=controls,hklRef=refList)
3030
3031	################################################################################
3032	##### Pattern tree routines
3033	################################################################################
3034
3035	def GetPatternTreeDataNames(G2frame,dataTypes):
3036	'''Finds all items in tree that match a 4 character prefix
3037
3038	:param wx.Frame G2frame: Data tree frame object
3039	:param list dataTypes: Contains one or more data tree item types to be matched
3040	such as ['IMG '] or ['PWDR','HKLF']
3041	:returns: a list of tree item names for the matching items
3042	'''
3043	names = []
3044	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3045	while item:
3046	name = G2frame.PatternTree.GetItemText(item)
3047	if name[:4] in dataTypes:
3048	names.append(name)
3049	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3050	return names
3051
3052	def GetPatternTreeItemId(G2frame, parentId, itemText):
3053	'''Needs a doc string
3054	'''
3055	item, cookie = G2frame.PatternTree.GetFirstChild(parentId)
3056	while item:
3057	if G2frame.PatternTree.GetItemText(item) == itemText:
3058	return item
3059	item, cookie = G2frame.PatternTree.GetNextChild(parentId, cookie)
3060	return 0
3061
3062	def MovePatternTreeToGrid(G2frame,item):
3063	'''Called from GSASII.OnPatternTreeSelChanged when a item is selected on the tree
3064	'''
3065	pickName = G2frame.PatternTree.GetItemText(item)
3066	if G2frame.PickIdText == pickName:
3067	return
3068
3069	oldPage = None # will be set later if already on a Phase item
3070	if G2frame.dataFrame:
3071	SetDataMenuBar(G2frame)
3072	if G2frame.dataFrame.GetLabel() == 'Comments':
3073	try:
3074	data = [G2frame.dataDisplay.GetValue()]
3075	G2frame.dataDisplay.Clear()
3076	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Comments')
3077	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3078	except: #clumsy but avoids dead window problem when opening another project
3079	pass
3080	elif G2frame.dataFrame.GetLabel() == 'Notebook':
3081	try:
3082	data = [G2frame.dataDisplay.GetValue()]
3083	G2frame.dataDisplay.Clear()
3084	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Notebook')
3085	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3086	except: #clumsy but avoids dead window problem when opening another project
3087	pass
3088	elif 'Phase Data for' in G2frame.dataFrame.GetLabel():
3089	if G2frame.dataDisplay:
3090	oldPage = G2frame.dataDisplay.GetSelection()
3091	G2frame.dataFrame.Clear()
3092	G2frame.dataFrame.SetLabel('')
3093	else:
3094	#create the frame for the data item window
3095	G2frame.dataFrame = DataFrame(parent=G2frame.mainPanel,frame=G2frame)
3096	G2frame.dataFrame.PhaseUserSize = None
3097
3098	G2frame.dataFrame.Raise()
3099	G2frame.PickId = item
3100	G2frame.PickIdText = None
3101	parentID = G2frame.root
3102	#for i in G2frame.ExportPattern: i.Enable(False)
3103	defWid = [250,150]
3104	if item != G2frame.root:
3105	parentID = G2frame.PatternTree.GetItemParent(item)
3106	if G2frame.PatternTree.GetItemParent(item) == G2frame.root:
3107	G2frame.PatternId = item
3108	if G2frame.PatternTree.GetItemText(item) == 'Notebook':
3109	SetDataMenuBar(G2frame,G2frame.dataFrame.DataNotebookMenu)
3110	G2frame.PatternId = 0
3111	#for i in G2frame.ExportPattern: i.Enable(False)
3112	data = G2frame.PatternTree.GetItemPyData(item)
3113	UpdateNotebook(G2frame,data)
3114	elif G2frame.PatternTree.GetItemText(item) == 'Controls':
3115	G2frame.PatternId = 0
3116	#for i in G2frame.ExportPattern: i.Enable(False)
3117	data = G2frame.PatternTree.GetItemPyData(item)
3118	if not data: #fill in defaults
3119	data = copy.copy(G2obj.DefaultControls) #least squares controls
3120	G2frame.PatternTree.SetItemPyData(item,data)
3121	for i in G2frame.Refine: i.Enable(True)
3122	G2frame.EnableSeqRefineMenu()
3123	UpdateControls(G2frame,data)
3124	elif G2frame.PatternTree.GetItemText(item) == 'Sequential results':
3125	data = G2frame.PatternTree.GetItemPyData(item)
3126	UpdateSeqResults(G2frame,data)
3127	elif G2frame.PatternTree.GetItemText(item) == 'Covariance':
3128	data = G2frame.PatternTree.GetItemPyData(item)
3129	G2frame.dataFrame.setSizePosLeft(defWid)
3130	text = ''
3131	if 'Rvals' in data:
3132	Nvars = len(data['varyList'])
3133	Rvals = data['Rvals']
3134	text = '\nFinal residuals: \nwR = %.3f%% \nchi**2 = %.1f \nGOF = %.2f'%(Rvals['Rwp'],Rvals['chisq'],Rvals['GOF'])
3135	text += '\nNobs = %d \nNvals = %d'%(Rvals['Nobs'],Nvars)
3136	if 'lamMax' in Rvals:
3137	text += '\nlog10 MaxLambda = %.1f'%(np.log10(Rvals['lamMax']))
3138	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3139	value='See plot window for covariance display'+text,style=wx.TE_MULTILINE)
3140	G2plt.PlotCovariance(G2frame,data)
3141	elif G2frame.PatternTree.GetItemText(item) == 'Constraints':
3142	data = G2frame.PatternTree.GetItemPyData(item)
3143	G2cnstG.UpdateConstraints(G2frame,data)
3144	elif G2frame.PatternTree.GetItemText(item) == 'Rigid bodies':
3145	data = G2frame.PatternTree.GetItemPyData(item)
3146	G2cnstG.UpdateRigidBodies(G2frame,data)
3147	elif G2frame.PatternTree.GetItemText(item) == 'Restraints':
3148	data = G2frame.PatternTree.GetItemPyData(item)
3149	Phases = G2frame.GetPhaseData()
3150	phase = ''
3151	phaseName = ''
3152	if Phases:
3153	phaseName = Phases.keys()[0]
3154	G2frame.dataFrame.setSizePosLeft(defWid)
3155	G2restG.UpdateRestraints(G2frame,data,Phases,phaseName)
3156	elif 'IMG' in G2frame.PatternTree.GetItemText(item):
3157	G2frame.Image = item
3158	G2frame.dataFrame.SetTitle('Image Data')
3159	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(
3160	G2frame,item,'Image Controls'))
3161	G2imG.UpdateImageData(G2frame,data)
3162	G2plt.PlotImage(G2frame,newPlot=True)
3163	elif 'PKS' in G2frame.PatternTree.GetItemText(item):
3164	G2plt.PlotPowderLines(G2frame)
3165	elif 'PWDR' in G2frame.PatternTree.GetItemText(item):
3166	#for i in G2frame.ExportPattern: i.Enable(True)
3167	if G2frame.EnablePlot:
3168	UpdatePWHKPlot(G2frame,'PWDR',item)
3169	elif 'SASD' in G2frame.PatternTree.GetItemText(item):
3170	#for i in G2frame.ExportPattern: i.Enable(True)
3171	if G2frame.EnablePlot:
3172	UpdatePWHKPlot(G2frame,'SASD',item)
3173	elif 'HKLF' in G2frame.PatternTree.GetItemText(item):
3174	G2frame.Sngl = True
3175	UpdatePWHKPlot(G2frame,'HKLF',item)
3176	elif 'PDF' in G2frame.PatternTree.GetItemText(item):
3177	G2frame.PatternId = item
3178	for i in G2frame.ExportPDF: i.Enable(True)
3179	G2plt.PlotISFG(G2frame,type='S(Q)')
3180	elif G2frame.PatternTree.GetItemText(item) == 'Phases':
3181	G2frame.dataFrame.setSizePosLeft(defWid)
3182	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3183	value='Select one phase to see its parameters')
3184	elif 'I(Q)' in G2frame.PatternTree.GetItemText(item):
3185	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3186	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3187	G2pdG.UpdatePDFGrid(G2frame,data)
3188	G2plt.PlotISFG(G2frame,type='I(Q)',newPlot=True)
3189	elif 'S(Q)' in G2frame.PatternTree.GetItemText(item):
3190	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3191	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3192	G2pdG.UpdatePDFGrid(G2frame,data)
3193	G2plt.PlotISFG(G2frame,type='S(Q)',newPlot=True)
3194	elif 'F(Q)' in G2frame.PatternTree.GetItemText(item):
3195	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3196	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3197	G2pdG.UpdatePDFGrid(G2frame,data)
3198	G2plt.PlotISFG(G2frame,type='F(Q)',newPlot=True)
3199	elif 'G(R)' in G2frame.PatternTree.GetItemText(item):
3200	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3201	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3202	G2pdG.UpdatePDFGrid(G2frame,data)
3203	G2plt.PlotISFG(G2frame,type='G(R)',newPlot=True)
3204	elif G2frame.PatternTree.GetItemText(parentID) == 'Phases':
3205	data = G2frame.PatternTree.GetItemPyData(item)
3206	G2phG.UpdatePhaseData(G2frame,item,data,oldPage)
3207	elif G2frame.PatternTree.GetItemText(item) == 'Comments':
3208	SetDataMenuBar(G2frame,G2frame.dataFrame.DataCommentsMenu)
3209	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3210	data = G2frame.PatternTree.GetItemPyData(item)
3211	UpdateComments(G2frame,data)
3212	elif G2frame.PatternTree.GetItemText(item) == 'Image Controls':
3213	G2frame.dataFrame.SetTitle('Image Controls')
3214	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3215	masks = G2frame.PatternTree.GetItemPyData(
3216	GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3217	data = G2frame.PatternTree.GetItemPyData(item)
3218	G2imG.UpdateImageControls(G2frame,data,masks)
3219	G2plt.PlotImage(G2frame,newPlot=True)
3220	elif G2frame.PatternTree.GetItemText(item) == 'Masks':
3221	G2frame.dataFrame.SetTitle('Masks')
3222	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3223	data = G2frame.PatternTree.GetItemPyData(item)
3224	G2imG.UpdateMasks(G2frame,data)
3225	G2plt.PlotImage(G2frame,newPlot=True)
3226	elif G2frame.PatternTree.GetItemText(item) == 'Stress/Strain':
3227	G2frame.dataFrame.SetTitle('Stress/Strain')
3228	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3229	data = G2frame.PatternTree.GetItemPyData(item)
3230	G2plt.PlotImage(G2frame,newPlot=True)
3231	G2plt.PlotStrain(G2frame,data,newPlot=True)
3232	G2imG.UpdateStressStrain(G2frame,data)
3233	elif G2frame.PatternTree.GetItemText(item) == 'PDF Controls':
3234	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3235	for i in G2frame.ExportPDF: i.Enable(True)
3236	data = G2frame.PatternTree.GetItemPyData(item)
3237	G2pdG.UpdatePDFGrid(G2frame,data)
3238	G2plt.PlotISFG(G2frame,type='I(Q)')
3239	G2plt.PlotISFG(G2frame,type='S(Q)')
3240	G2plt.PlotISFG(G2frame,type='F(Q)')
3241	G2plt.PlotISFG(G2frame,type='G(R)')
3242	elif G2frame.PatternTree.GetItemText(item) == 'Peak List':
3243	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3244	for i in G2frame.ExportPeakList: i.Enable(True)
3245	data = G2frame.PatternTree.GetItemPyData(item)
3246	#patch
3247	if 'list' in str(type(data)):
3248	data = {'peaks':data,'sigDict':{}}
3249	G2frame.PatternTree.SetItemPyData(item,data)
3250	#end patch
3251	G2pdG.UpdatePeakGrid(G2frame,data)
3252	G2plt.PlotPatterns(G2frame)
3253	elif G2frame.PatternTree.GetItemText(item) == 'Background':
3254	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3255	data = G2frame.PatternTree.GetItemPyData(item)
3256	G2pdG.UpdateBackground(G2frame,data)
3257	G2plt.PlotPatterns(G2frame)
3258	elif G2frame.PatternTree.GetItemText(item) == 'Limits':
3259	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3260	datatype = G2frame.PatternTree.GetItemText(G2frame.PatternId)[:4]
3261	data = G2frame.PatternTree.GetItemPyData(item)
3262	G2pdG.UpdateLimitsGrid(G2frame,data,datatype)
3263	G2plt.PlotPatterns(G2frame,plotType=datatype)
3264	elif G2frame.PatternTree.GetItemText(item) == 'Instrument Parameters':
3265	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3266	data = G2frame.PatternTree.GetItemPyData(item)[0]
3267	G2pdG.UpdateInstrumentGrid(G2frame,data)
3268	if 'P' in data['Type'][0]: #powder data only
3269	G2plt.PlotPeakWidths(G2frame)
3270	elif G2frame.PatternTree.GetItemText(item) == 'Models':
3271	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3272	data = G2frame.PatternTree.GetItemPyData(item)
3273	G2pdG.UpdateModelsGrid(G2frame,data)
3274	G2plt.PlotPatterns(G2frame,plotType='SASD')
3275	if len(data['Size']['Distribution']):
3276	G2plt.PlotSASDSizeDist(G2frame)
3277	elif G2frame.PatternTree.GetItemText(item) == 'Substances':
3278	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3279	data = G2frame.PatternTree.GetItemPyData(item)
3280	G2pdG.UpdateSubstanceGrid(G2frame,data)
3281	elif G2frame.PatternTree.GetItemText(item) == 'Sample Parameters':
3282	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3283	data = G2frame.PatternTree.GetItemPyData(item)
3284	datatype = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[2][:4]
3285
3286	if 'Temperature' not in data: #temp fix for old gpx files
3287	data = {'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],'DisplaceX':[0.0,False],
3288	'DisplaceY':[0.0,False],'Diffuse':[],'Temperature':300.,'Pressure':1.0,
3289	'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
3290	'Gonio. radius':200.0}
3291	G2frame.PatternTree.SetItemPyData(item,data)
3292
3293	G2pdG.UpdateSampleGrid(G2frame,data)
3294	G2plt.PlotPatterns(G2frame,plotType=datatype)
3295	elif G2frame.PatternTree.GetItemText(item) == 'Index Peak List':
3296	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3297	for i in G2frame.ExportPeakList: i.Enable(True)
3298	data = G2frame.PatternTree.GetItemPyData(item)
3299	#patch
3300	if len(data) != 2:
3301	data = [data,[]]
3302	G2frame.PatternTree.SetItemPyData(item,data)
3303	#end patch
3304	G2pdG.UpdateIndexPeaksGrid(G2frame,data)
3305	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3306	G2plt.PlotPowderLines(G2frame)
3307	else:
3308	G2plt.PlotPatterns(G2frame)
3309	elif G2frame.PatternTree.GetItemText(item) == 'Unit Cells List':
3310	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3311	data = G2frame.PatternTree.GetItemPyData(item)
3312	if not data:
3313	data.append([0,0.0,4,25.0,0,'P1',1,1,1,90,90,90]) #zero error flag, zero value, max Nc/No, start volume
3314	data.append([0,0,0,0,0,0,0,0,0,0,0,0,0,0]) #Bravais lattice flags
3315	data.append([]) #empty cell list
3316	data.append([]) #empty dmin
3317	data.append({}) #empty superlattice stuff
3318	G2frame.PatternTree.SetItemPyData(item,data)
3319	#patch
3320	if len(data) < 5:
3321	data.append({'Use':False,'ModVec':[0,0,0.1],'maxH':1,'ssSymb':''}) #empty superlattice stuff
3322	G2frame.PatternTree.SetItemPyData(item,data)
3323	#end patch
3324	G2pdG.UpdateUnitCellsGrid(G2frame,data)
3325	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3326	G2plt.PlotPowderLines(G2frame)
3327	else:
3328	G2plt.PlotPatterns(G2frame)
3329	elif G2frame.PatternTree.GetItemText(item) == 'Reflection Lists': #powder reflections
3330	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3331	data = G2frame.PatternTree.GetItemPyData(item)
3332	G2frame.RefList = ''
3333	if len(data):
3334	G2frame.RefList = data.keys()[0]
3335	G2pdG.UpdateReflectionGrid(G2frame,data)
3336	G2plt.PlotPatterns(G2frame)
3337	elif G2frame.PatternTree.GetItemText(item) == 'Reflection List': #HKLF reflections
3338	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3339	name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
3340	data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
3341	G2pdG.UpdateReflectionGrid(G2frame,data,HKLF=True,Name=name)
3342
3343	if G2frame.PickId:
3344	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
3345	G2frame.dataFrame.Raise()
3346
3347	def SetDataMenuBar(G2frame,menu=None):
3348	'''Set the menu for the data frame. On the Mac put this
3349	menu for the data tree window instead.
3350
3351	Note that data frame items do not have menus, for these (menu=None)
3352	display a blank menu or on the Mac display the standard menu for
3353	the data tree window.
3354	'''
3355	if sys.platform == "darwin":
3356	if menu is None:
3357	G2frame.SetMenuBar(G2frame.GSASIIMenu)
3358	else:
3359	G2frame.SetMenuBar(menu)
3360	else:
3361	if menu is None:
3362	G2frame.dataFrame.SetMenuBar(G2frame.dataFrame.BlankMenu)
3363	else:
3364	G2frame.dataFrame.SetMenuBar(menu)
3365
3366	def HowDidIgetHere():
3367	'''Show a traceback with calls that brought us to the current location.
3368	Used for debugging.
3369	'''
3370	import traceback
3371	print 70''
3372	for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip.rstrip())
3373	print 70''
3374

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