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source: trunk/GSASIIgrid.py @ 1998

Last change on this file since 1998 was 1998, checked in by toby, 7 years ago
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1	# -- coding: utf-8 --
2	#GSASIIgrid - data display routines
3	########### SVN repository information ###################
4	# $Date: 2015-10-11 02:59:34 +0000 (Sun, 11 Oct 2015) $
5	# $Author: toby $
6	# $Revision: 1998 $
7	# $URL: trunk/GSASIIgrid.py $
8	# $Id: GSASIIgrid.py 1998 2015-10-11 02:59:34Z toby $
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: 1998 $")
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_4DMAPCOMPUTE,wxID_4DCHARGEFLIP,
60	] = [wx.NewId() for item in range(17)]
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	] = [wx.NewId() for item in range(17)]
71
72	[ wxID_DRAWATOMSTYLE, wxID_DRAWATOMLABEL, wxID_DRAWATOMCOLOR, wxID_DRAWATOMRESETCOLOR,
73	wxID_DRAWVIEWPOINT, wxID_DRAWTRANSFORM, wxID_DRAWDELETE, wxID_DRAWFILLCELL,
74	wxID_DRAWADDEQUIV, wxID_DRAWFILLCOORD, wxID_DRAWDISAGLTOR, wxID_DRAWPLANE,
75	wxID_DRAWDISTVP,
76	] = [wx.NewId() for item in range(13)]
77
78	[ wxID_DRAWRESTRBOND, wxID_DRAWRESTRANGLE, wxID_DRAWRESTRPLANE, wxID_DRAWRESTRCHIRAL,
79	] = [wx.NewId() for item in range(4)]
80
81	[ wxID_ADDMCSAATOM,wxID_ADDMCSARB,wxID_CLEARMCSARB,wxID_MOVEMCSA,wxID_MCSACLEARRESULTS,
82	] = [wx.NewId() for item in range(5)]
83
84	[ wxID_CLEARTEXTURE,wxID_REFINETEXTURE,
85	] = [wx.NewId() for item in range(2)]
86
87	[ wxID_PAWLEYLOAD, wxID_PAWLEYESTIMATE, wxID_PAWLEYUPDATE,
88	] = [wx.NewId() for item in range(3)]
89
90	[ wxID_IMCALIBRATE,wxID_IMRECALIBRATE,wxID_IMINTEGRATE, wxID_IMCLEARCALIB,
91	wxID_IMCOPYCONTROLS, wxID_INTEGRATEALL, wxID_IMSAVECONTROLS, wxID_IMLOADCONTROLS, wxID_IMAUTOINTEG,
92	] = [wx.NewId() for item in range(9)]
93
94	[ wxID_MASKCOPY, wxID_MASKSAVE, wxID_MASKLOAD, wxID_NEWMASKSPOT,wxID_NEWMASKARC,wxID_NEWMASKRING,
95	wxID_NEWMASKFRAME, wxID_NEWMASKPOLY, wxID_MASKLOADNOT,
96	] = [wx.NewId() for item in range(9)]
97
98	[ wxID_STRSTACOPY, wxID_STRSTAFIT, wxID_STRSTASAVE, wxID_STRSTALOAD,wxID_STRSTSAMPLE,
99	wxID_APPENDDZERO,wxID_STRSTAALLFIT,wxID_UPDATEDZERO,
100	] = [wx.NewId() for item in range(8)]
101
102	[ wxID_BACKCOPY,wxID_LIMITCOPY, wxID_SAMPLECOPY, wxID_SAMPLECOPYSOME, wxID_BACKFLAGCOPY, wxID_SAMPLEFLAGCOPY,
103	wxID_SAMPLESAVE, wxID_SAMPLELOAD,wxID_ADDEXCLREGION,wxID_SETSCALE,wxID_SAMPLE1VAL,wxID_ALLSAMPLELOAD,
104	] = [wx.NewId() for item in range(12)]
105
106	[ wxID_INSTPRMRESET,wxID_CHANGEWAVETYPE,wxID_INSTCOPY, wxID_INSTFLAGCOPY, wxID_INSTLOAD,
107	wxID_INSTSAVE, wxID_INST1VAL, wxID_INSTCALIB,
108	] = [wx.NewId() for item in range(8)]
109
110	[ wxID_UNDO,wxID_LSQPEAKFIT,wxID_LSQONECYCLE,wxID_RESETSIGGAM,wxID_CLEARPEAKS,wxID_AUTOSEARCH,
111	wxID_PEAKSCOPY, wxID_SEQPEAKFIT,
112	] = [wx.NewId() for item in range(8)]
113
114	[ wxID_INDXRELOAD, wxID_INDEXPEAKS, wxID_REFINECELL, wxID_COPYCELL, wxID_MAKENEWPHASE,
115	wxID_EXPORTCELLS,
116	] = [wx.NewId() for item in range(6)]
117
118	[ wxID_CONSTRAINTADD,wxID_EQUIVADD,wxID_HOLDADD,wxID_FUNCTADD,wxID_ADDRIDING,
119	wxID_CONSPHASE, wxID_CONSHIST, wxID_CONSHAP, wxID_CONSGLOBAL,wxID_EQUIVALANCEATOMS,
120	] = [wx.NewId() for item in range(10)]
121
122	[ wxID_RESTRAINTADD, wxID_RESTSELPHASE,wxID_RESTDELETE, wxID_RESRCHANGEVAL,
123	wxID_RESTCHANGEESD,wxID_AARESTRAINTADD,wxID_AARESTRAINTPLOT,
124	] = [wx.NewId() for item in range(7)]
125
126	[ wxID_RIGIDBODYADD,wxID_DRAWDEFINERB,wxID_RIGIDBODYIMPORT,wxID_RESIDUETORSSEQ,
127	wxID_AUTOFINDRESRB,wxID_GLOBALRESREFINE,wxID_RBREMOVEALL,wxID_COPYRBPARMS,
128	wxID_GLOBALTHERM,wxID_VECTORBODYADD
129	] = [wx.NewId() for item in range(10)]
130
131	[ wxID_RENAMESEQSEL,wxID_SAVESEQSEL,wxID_SAVESEQSELCSV,wxID_SAVESEQCSV,wxID_PLOTSEQSEL,
132	wxID_ORGSEQSEL,wxADDSEQVAR,wxDELSEQVAR,wxEDITSEQVAR,wxCOPYPARFIT,wxID_AVESEQSEL,
133	wxADDPARFIT,wxDELPARFIT,wxEDITPARFIT,wxDOPARFIT,
134	] = [wx.NewId() for item in range(15)]
135
136	[ wxID_MODELCOPY,wxID_MODELFIT,wxID_MODELADD,wxID_ELEMENTADD,wxID_ELEMENTDELETE,
137	wxID_ADDSUBSTANCE,wxID_LOADSUBSTANCE,wxID_DELETESUBSTANCE,wxID_COPYSUBSTANCE,
138	wxID_MODELUNDO,wxID_MODELFITALL,wxID_MODELCOPYFLAGS,
139	] = [wx.NewId() for item in range(12)]
140
141	[ wxID_SELECTPHASE,wxID_PWDHKLPLOT,wxID_PWD3DHKLPLOT,wxID_3DALLHKLPLOT,
142	] = [wx.NewId() for item in range(4)]
143
144	[ wxID_PDFCOPYCONTROLS, wxID_PDFSAVECONTROLS, wxID_PDFLOADCONTROLS,
145	wxID_PDFCOMPUTE, wxID_PDFCOMPUTEALL, wxID_PDFADDELEMENT, wxID_PDFDELELEMENT,
146	] = [wx.NewId() for item in range(7)]
147
148	[ wxID_MCRON,wxID_MCRLIST,wxID_MCRSAVE,wxID_MCRPLAY,
149	] = [wx.NewId() for item in range(4)]
150
151	VERY_LIGHT_GREY = wx.Colour(235,235,235)
152
153	# Aliases for Classes/Functions moved to GSASIIctrls, all should be tracked down but leaving as a reminder
154	#SingleFloatDialog = G2G.SingleFloatDialog
155	#SingleStringDialog = G2G.SingleStringDialog
156	#MultiStringDialog = G2G.MultiStringDialog
157	#G2ColumnIDDialog = G2G.G2ColumnIDDialog
158	#ItemSelector = G2G.ItemSelector
159	#HorizontalLine = G2G.HorizontalLine
160	#G2LoggedButton = G2G.G2LoggedButton
161	#EnumSelector = G2G.EnumSelector
162	#G2ChoiceButton = G2G.G2ChoiceButton
163	#GSGrid = G2G.GSGrid
164	#Table = G2G.Table
165	#GridFractionEditor = G2G.GridFractionEditor
166	#GSNoteBook = G2G.GSNoteBook
167
168	# Should SGMessageBox, SymOpDialog, DisAglDialog be moved?
169
170	################################################################################
171	#### GSAS-II class definitions
172	################################################################################
173
174	class SGMessageBox(wx.Dialog):
175	''' Special version of MessageBox that displays space group & super space group text
176	in two blocks
177	'''
178	def __init__(self,parent,title,text,table,):
179	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,pos=wx.DefaultPosition,
180	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
181	self.text=text
182	self.table = table
183	self.panel = wx.Panel(self)
184	mainSizer = wx.BoxSizer(wx.VERTICAL)
185	mainSizer.Add((0,10))
186	for line in text:
187	mainSizer.Add(wx.StaticText(self.panel,label=' %s '%(line)),0,WACV)
188	ncol = self.table[0].count(',')+1
189	tableSizer = wx.FlexGridSizer(0,2*ncol+3,0,0)
190	for j,item in enumerate(self.table):
191	num,flds = item.split(')')
192	tableSizer.Add(wx.StaticText(self.panel,label=' %s '%(num+')')),0,WACV\|wx.ALIGN_LEFT)
193	flds = flds.replace(' ','').split(',')
194	for i,fld in enumerate(flds):
195	if i < ncol-1:
196	tableSizer.Add(wx.StaticText(self.panel,label='%s, '%(fld)),0,WACV\|wx.ALIGN_RIGHT)
197	else:
198	tableSizer.Add(wx.StaticText(self.panel,label='%s'%(fld)),0,WACV\|wx.ALIGN_RIGHT)
199	if not j%2:
200	tableSizer.Add((20,0))
201	mainSizer.Add(tableSizer,0,wx.ALIGN_LEFT)
202	btnsizer = wx.StdDialogButtonSizer()
203	OKbtn = wx.Button(self.panel, wx.ID_OK)
204	OKbtn.SetDefault()
205	btnsizer.AddButton(OKbtn)
206	btnsizer.Realize()
207	mainSizer.Add((0,10))
208	mainSizer.Add(btnsizer,0,wx.ALIGN_CENTER)
209	self.panel.SetSizer(mainSizer)
210	self.panel.Fit()
211	self.Fit()
212	size = self.GetSize()
213	self.SetSize([size[0]+20,size[1]])
214
215	def Show(self):
216	'''Use this method after creating the dialog to post it
217	'''
218	self.ShowModal()
219	return
220
221	################################################################################
222	class SymOpDialog(wx.Dialog):
223	'''Class to select a symmetry operator
224	'''
225	def __init__(self,parent,SGData,New=True,ForceUnit=False):
226	wx.Dialog.__init__(self,parent,-1,'Select symmetry operator',
227	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
228	panel = wx.Panel(self)
229	self.SGData = SGData
230	self.New = New
231	self.Force = ForceUnit
232	self.OpSelected = [0,0,0,[0,0,0],False,False]
233	mainSizer = wx.BoxSizer(wx.VERTICAL)
234	if ForceUnit:
235	choice = ['No','Yes']
236	self.force = wx.RadioBox(panel,-1,'Force to unit cell?',choices=choice)
237	self.force.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
238	mainSizer.Add(self.force,0,WACV\|wx.TOP,5)
239	# if SGData['SGInv']:
240	choice = ['No','Yes']
241	self.inv = wx.RadioBox(panel,-1,'Choose inversion?',choices=choice)
242	self.inv.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
243	mainSizer.Add(self.inv,0,WACV)
244	if SGData['SGLatt'] != 'P':
245	LattOp = G2spc.Latt2text(SGData['SGLatt']).split(';')
246	self.latt = wx.RadioBox(panel,-1,'Choose cell centering?',choices=LattOp)
247	self.latt.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
248	mainSizer.Add(self.latt,0,WACV)
249	if SGData['SGLaue'] in ['-1','2/m','mmm','4/m','4/mmm']:
250	Ncol = 2
251	else:
252	Ncol = 3
253	OpList = []
254	for Opr in SGData['SGOps']:
255	OpList.append(G2spc.MT2text(Opr))
256	self.oprs = wx.RadioBox(panel,-1,'Choose space group operator?',choices=OpList,
257	majorDimension=Ncol)
258	self.oprs.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
259	mainSizer.Add(self.oprs,0,WACV\|wx.BOTTOM,5)
260	mainSizer.Add(wx.StaticText(panel,-1," Choose unit cell?"),0,WACV)
261	cellSizer = wx.BoxSizer(wx.HORIZONTAL)
262	cellName = ['X','Y','Z']
263	self.cell = []
264	for i in range(3):
265	self.cell.append(wx.SpinCtrl(panel,-1,cellName[i],size=wx.Size(50,20)))
266	self.cell[-1].SetRange(-3,3)
267	self.cell[-1].SetValue(0)
268	self.cell[-1].Bind(wx.EVT_SPINCTRL, self.OnOpSelect)
269	cellSizer.Add(self.cell[-1],0,WACV)
270	mainSizer.Add(cellSizer,0,WACV\|wx.BOTTOM,5)
271	if self.New:
272	choice = ['No','Yes']
273	self.new = wx.RadioBox(panel,-1,'Generate new positions?',choices=choice)
274	self.new.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
275	mainSizer.Add(self.new,0,WACV)
276
277	OkBtn = wx.Button(panel,-1,"Ok")
278	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
279	cancelBtn = wx.Button(panel,-1,"Cancel")
280	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
281	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
282	btnSizer.Add((20,20),1)
283	btnSizer.Add(OkBtn)
284	btnSizer.Add((20,20),1)
285	btnSizer.Add(cancelBtn)
286	btnSizer.Add((20,20),1)
287
288	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
289	panel.SetSizer(mainSizer)
290	panel.Fit()
291	self.Fit()
292
293	def OnOpSelect(self,event):
294	# if self.SGData['SGInv']:
295	self.OpSelected[0] = self.inv.GetSelection()
296	if self.SGData['SGLatt'] != 'P':
297	self.OpSelected[1] = self.latt.GetSelection()
298	self.OpSelected[2] = self.oprs.GetSelection()
299	for i in range(3):
300	self.OpSelected[3][i] = float(self.cell[i].GetValue())
301	if self.New:
302	self.OpSelected[4] = self.new.GetSelection()
303	if self.Force:
304	self.OpSelected[5] = self.force.GetSelection()
305
306	def GetSelection(self):
307	return self.OpSelected
308
309	def OnOk(self,event):
310	parent = self.GetParent()
311	parent.Raise()
312	self.EndModal(wx.ID_OK)
313
314	def OnCancel(self,event):
315	parent = self.GetParent()
316	parent.Raise()
317	self.EndModal(wx.ID_CANCEL)
318
319	################################################################################
320	class AddHatomDialog(wx.Dialog):
321	'''H atom addition dialog. After :meth:`ShowModal` returns, the results
322	are found in dict :attr:`self.data`, which is accessed using :meth:`GetData`.
323
324	:param wx.Frame parent: reference to parent frame (or None)
325	:param dict Neigh: a dict of atom names with list of atom name, dist pairs for neighboring atoms
326	:param dict phase: a dict containing the phase as defined by
327	:ref:`Phase Tree Item <Phase_table>`
328	'''
329	def __init__(self,parent,Neigh,phase):
330	wx.Dialog.__init__(self,parent,wx.ID_ANY,'H atom add',
331	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
332	self.panel = wxscroll.ScrolledPanel(self) #just a dummy - gets destroyed in Draw!
333	self.Neigh = Neigh
334	self.phase = phase
335	self.Hatoms = []
336	self.Draw(self.Neigh,self.phase)
337
338	def Draw(self,Neigh,phase):
339	'''Creates the contents of the dialog. Normally called
340	by :meth:`__init__`.
341	'''
342	def OnHSelect(event):
343	Obj = event.GetEventObject()
344	item,i = Indx[Obj.GetId()]
345	for obj in Indx[item]:
346	obj.SetValue(False)
347	Obj.SetValue(True)
348	self.Neigh[item][2] = i
349
350	def OnBond(event):
351	Obj = event.GetEventObject()
352	inei,ibond = Indx[Obj.GetId()]
353	self.Neigh[inei][1][0][ibond][2] = Obj.GetValue()
354
355	self.panel.Destroy()
356	self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE)
357	mainSizer = wx.BoxSizer(wx.VERTICAL)
358	mainSizer.Add(wx.StaticText(self.panel,-1,'H atom add controls for phase %s:'%(phase['General']['Name'])),
359	0,wx.LEFT\|wx.TOP,10)
360	mainSizer.Add(wx.StaticText(self.panel,-1,'NB: Check selections as they may not be correct'),0,WACV\|wx.LEFT,10)
361	mainSizer.Add(wx.StaticText(self.panel,-1," Atom: Add # H's Use: Neighbors, dist"),0,wx.TOP\|wx.LEFT,5)
362	nHatms = ['0','1','2','3']
363	dataSizer = wx.FlexGridSizer(0,3,0,0)
364	Indx = {}
365	for inei,neigh in enumerate(Neigh):
366	dataSizer.Add(wx.StaticText(self.panel,-1,' %s: '%(neigh[0])),0,WACV)
367	nH = 1 #for O atom
368	if 'C' in neigh[0] or 'N' in neigh[0]:
369	nH = 4-len(neigh[1][0])
370	checks = wx.BoxSizer(wx.HORIZONTAL)
371	Ids = []
372	for i in range(nH+1):
373	nHs = wx.CheckBox(self.panel,-1,label=nHatms[i])
374	if i == neigh[2]:
375	nHs.SetValue(True)
376	Indx[nHs.GetId()] = [inei,i]
377	Ids.append(nHs)
378	nHs.Bind(wx.EVT_CHECKBOX, OnHSelect)
379	checks.Add(nHs,0,WACV)
380	Indx[inei] = Ids
381	dataSizer.Add(checks,0,WACV)
382	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
383	for ib,bond in enumerate(neigh[1][0]):
384	Bond = wx.CheckBox(self.panel,-1,label=': %s, %.3f'%(bond[0],bond[1]))
385	Bond.SetValue(bond[2])
386	Indx[Bond.GetId()] = [inei,ib]
387	Bond.Bind(wx.EVT_CHECKBOX,OnBond)
388	lineSizer.Add(Bond,0,WACV)
389	dataSizer.Add(lineSizer,0,WACV\|wx.RIGHT,10)
390	mainSizer.Add(dataSizer,0,wx.LEFT,5)
391
392	CancelBtn = wx.Button(self.panel,-1,'Cancel')
393	CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
394	OkBtn = wx.Button(self.panel,-1,'Ok')
395	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
396	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
397	btnSizer.Add((20,20),1)
398	btnSizer.Add(OkBtn)
399	btnSizer.Add((20,20),1)
400	btnSizer.Add(CancelBtn)
401	btnSizer.Add((20,20),1)
402	mainSizer.Add(btnSizer,0,wx.BOTTOM\|wx.TOP, 10)
403	size = np.array(self.GetSize())
404	self.panel.SetupScrolling()
405	self.panel.SetSizer(mainSizer)
406	self.panel.SetAutoLayout(1)
407	size = [size[0]-5,size[1]-20] #this fiddling is needed for older wx!
408	self.panel.SetSize(size)
409
410	def GetData(self):
411	'Returns the values from the dialog'
412	for neigh in self.Neigh:
413	for ibond,bond in enumerate(neigh[1][0]):
414	if not bond[2]:
415	neigh[1][1][1][ibond] = 0 #deselected bond
416	neigh[1][1][1] = [a for a in neigh[1][1][1] if a]
417	return self.Neigh #has #Hs to add for each entry
418
419	def OnOk(self,event):
420	'Called when the OK button is pressed'
421	parent = self.GetParent()
422	parent.Raise()
423	self.EndModal(wx.ID_OK)
424
425	def OnCancel(self,event):
426	parent = self.GetParent()
427	parent.Raise()
428	self.EndModal(wx.ID_CANCEL)
429
430	################################################################################
431	class DisAglDialog(wx.Dialog):
432	'''Distance/Angle Controls input dialog. After
433	:meth:`ShowModal` returns, the results are found in
434	dict :attr:`self.data`, which is accessed using :meth:`GetData`.
435
436	:param wx.Frame parent: reference to parent frame (or None)
437	:param dict data: a dict containing the current
438	search ranges or an empty dict, which causes default values
439	to be used.
440	Will be used to set element `DisAglCtls` in
441	:ref:`Phase Tree Item <Phase_table>`
442	:param dict default: A dict containing the default
443	search ranges for each element.
444	'''
445	def __init__(self,parent,data,default,Reset=True):
446	wx.Dialog.__init__(self,parent,wx.ID_ANY,
447	'Distance Angle Controls',
448	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
449	self.default = default
450	self.Reset = Reset
451	self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
452	self._default(data,self.default)
453	self.Draw(self.data)
454
455	def _default(self,data,default):
456	'''Set starting values for the search values, either from
457	the input array or from defaults, if input is null
458	'''
459	if data:
460	self.data = copy.deepcopy(data) # don't mess with originals
461	else:
462	self.data = {}
463	self.data['Name'] = default['Name']
464	self.data['Factors'] = [0.85,0.85]
465	self.data['AtomTypes'] = default['AtomTypes']
466	self.data['BondRadii'] = default['BondRadii'][:]
467	self.data['AngleRadii'] = default['AngleRadii'][:]
468
469	def Draw(self,data):
470	'''Creates the contents of the dialog. Normally called
471	by :meth:`__init__`.
472	'''
473	self.panel.Destroy()
474	self.panel = wx.Panel(self)
475	mainSizer = wx.BoxSizer(wx.VERTICAL)
476	mainSizer.Add(wx.StaticText(self.panel,-1,'Controls for phase '+data['Name']),
477	0,WACV\|wx.LEFT,10)
478	mainSizer.Add((10,10),1)
479
480	radiiSizer = wx.FlexGridSizer(0,3,5,5)
481	radiiSizer.Add(wx.StaticText(self.panel,-1,' Type'),0,WACV)
482	radiiSizer.Add(wx.StaticText(self.panel,-1,'Bond radii'),0,WACV)
483	radiiSizer.Add(wx.StaticText(self.panel,-1,'Angle radii'),0,WACV)
484	self.objList = {}
485	for id,item in enumerate(self.data['AtomTypes']):
486	radiiSizer.Add(wx.StaticText(self.panel,-1,' '+item),0,WACV)
487	bRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['BondRadii'][id]),style=wx.TE_PROCESS_ENTER)
488	self.objList[bRadii.GetId()] = ['BondRadii',id]
489	bRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
490	bRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
491	radiiSizer.Add(bRadii,0,WACV)
492	aRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['AngleRadii'][id]),style=wx.TE_PROCESS_ENTER)
493	self.objList[aRadii.GetId()] = ['AngleRadii',id]
494	aRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
495	aRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
496	radiiSizer.Add(aRadii,0,WACV)
497	mainSizer.Add(radiiSizer,0,wx.EXPAND)
498	factorSizer = wx.FlexGridSizer(0,2,5,5)
499	Names = ['Bond','Angle']
500	for i,name in enumerate(Names):
501	factorSizer.Add(wx.StaticText(self.panel,-1,name+' search factor'),0,WACV)
502	bondFact = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['Factors'][i]),style=wx.TE_PROCESS_ENTER)
503	self.objList[bondFact.GetId()] = ['Factors',i]
504	bondFact.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
505	bondFact.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
506	factorSizer.Add(bondFact)
507	mainSizer.Add(factorSizer,0,wx.EXPAND)
508
509	OkBtn = wx.Button(self.panel,-1,"Ok")
510	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
511	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
512	btnSizer.Add((20,20),1)
513	btnSizer.Add(OkBtn)
514	if self.Reset:
515	ResetBtn = wx.Button(self.panel,-1,'Reset')
516	ResetBtn.Bind(wx.EVT_BUTTON, self.OnReset)
517	btnSizer.Add(ResetBtn)
518	btnSizer.Add((20,20),1)
519	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
520	self.panel.SetSizer(mainSizer)
521	self.panel.Fit()
522	self.Fit()
523
524	def OnRadiiVal(self,event):
525	Obj = event.GetEventObject()
526	item = self.objList[Obj.GetId()]
527	try:
528	self.data[item[0]][item[1]] = float(Obj.GetValue())
529	except ValueError:
530	pass
531	Obj.SetValue("%.3f"%(self.data[item[0]][item[1]])) #reset in case of error
532
533	def GetData(self):
534	'Returns the values from the dialog'
535	return self.data
536
537	def OnOk(self,event):
538	'Called when the OK button is pressed'
539	parent = self.GetParent()
540	parent.Raise()
541	self.EndModal(wx.ID_OK)
542
543	def OnReset(self,event):
544	'Called when the Reset button is pressed'
545	data = {}
546	self._default(data,self.default)
547	self.Draw(self.data)
548
549	################################################################################
550	class ShowLSParms(wx.Dialog):
551	'''Create frame to show least-squares parameters
552	'''
553	def __init__(self,parent,title,parmDict,varyList,fullVaryList,
554	size=(300,430)):
555	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,size=size,
556	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
557	mainSizer = wx.BoxSizer(wx.VERTICAL)
558
559	panel = wxscroll.ScrolledPanel(
560	self, wx.ID_ANY,
561	#size=size,
562	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
563	num = len(varyList)
564	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,'Number of refined variables: '+str(num)))
565	if len(varyList) != len(fullVaryList):
566	num = len(fullVaryList) - len(varyList)
567	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,' + '+str(num)+' parameters are varied via constraints'))
568	subSizer = wx.FlexGridSizer(cols=4,hgap=2,vgap=2)
569	parmNames = parmDict.keys()
570	parmNames.sort()
571	subSizer.Add((-1,-1))
572	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'Parameter name '))
573	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'refine?'))
574	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'value'),0,wx.ALIGN_RIGHT)
575	explainRefine = False
576	for name in parmNames:
577	# skip entries without numerical values
578	if isinstance(parmDict[name],basestring): continue
579	try:
580	value = G2py3.FormatSigFigs(parmDict[name])
581	except TypeError:
582	value = str(parmDict[name])+' -?' # unexpected
583	#continue
584	v = G2obj.getVarDescr(name)
585	if v is None or v[-1] is None:
586	subSizer.Add((-1,-1))
587	else:
588	ch = G2G.HelpButton(panel,G2obj.fmtVarDescr(name))
589	subSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
590	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,str(name)))
591	if name in varyList:
592	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'R'))
593	elif name in fullVaryList:
594	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'C'))
595	explainRefine = True
596	else:
597	subSizer.Add((-1,-1))
598	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
599
600	# finish up ScrolledPanel
601	panel.SetSizer(subSizer)
602	panel.SetAutoLayout(1)
603	panel.SetupScrolling()
604	mainSizer.Add(panel,1, wx.ALL\|wx.EXPAND,1)
605
606	if explainRefine:
607	mainSizer.Add(
608	wx.StaticText(self,wx.ID_ANY,
609	'"R" indicates a refined variable\n'+
610	'"C" indicates generated from a constraint'
611	),
612	0, wx.ALL,0)
613	# make OK button
614	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
615	btn = wx.Button(self, wx.ID_CLOSE,"Close")
616	btn.Bind(wx.EVT_BUTTON,self._onClose)
617	btnsizer.Add(btn)
618	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
619	# Allow window to be enlarged but not made smaller
620	self.SetSizer(mainSizer)
621	self.SetMinSize(self.GetSize())
622
623	def _onClose(self,event):
624	self.EndModal(wx.ID_CANCEL)
625
626	################################################################################
627	class DataFrame(wx.Frame):
628	'''Create the data item window and all the entries in menus used in
629	that window. For Linux and windows, the menu entries are created for the
630	current data item window, but in the Mac the menu is accessed from all
631	windows. This means that a different menu is posted depending on which
632	data item is posted. On the Mac, all the menus contain the data tree menu
633	items, but additional menus are added specific to the data item.
634
635	Note that while the menus are created here,
636	the binding for the menus is done later in various GSASII*GUI modules,
637	where the functions to be called are defined.
638	'''
639	def Bind(self,eventtype,handler,args,*kwargs):
640	'''Override the Bind() function: on the Mac the binding is to
641	the main window, so that menus operate with any window on top.
642	For other platforms, either wrap calls that will be logged
643	or call the default wx.Frame Bind() to bind to the menu item directly.
644
645	Note that bindings can be made to objects by Id or by direct reference to the
646	object. As a convention, when bindings are to objects, they are not logged
647	but when bindings are by Id, they are logged.
648	'''
649	if sys.platform == "darwin": # mac
650	self.G2frame.Bind(eventtype,handler,args,*kwargs)
651	return
652	if eventtype == wx.EVT_MENU and 'id' in kwargs:
653	menulabels = log.SaveMenuCommand(kwargs['id'],self.G2frame,handler)
654	if menulabels:
655	#print 'intercepting bind for',handler,menulabels,kwargs['id']
656	wx.Frame.Bind(self,eventtype,self.G2frame.MenuBinding,args,*kwargs)
657	return
658	wx.Frame.Bind(self,eventtype,handler,args,*kwargs)
659
660	def PrefillDataMenu(self,menu,helpType,helpLbl=None,empty=False):
661	'''Create the "standard" part of data frame menus. Note that on Linux and
662	Windows nothing happens here. On Mac, this menu duplicates the
663	tree menu, but adds an extra help command for the data item and a separator.
664	'''
665	self.datamenu = menu
666	self.G2frame.dataMenuBars.append(menu)
667	self.helpType = helpType
668	self.helpLbl = helpLbl
669	if sys.platform == "darwin": # mac
670	self.G2frame.FillMainMenu(menu) # add the data tree menu items
671	if not empty:
672	menu.Append(wx.Menu(title=''),title='\|') # add a separator
673
674	def PostfillDataMenu(self,empty=False):
675	'''Create the "standard" part of data frame menus. Note that on Linux and
676	Windows, this is the standard help Menu. On Mac, this menu duplicates the
677	tree menu, but adds an extra help command for the data item and a separator.
678	'''
679	menu = self.datamenu
680	helpType = self.helpType
681	helpLbl = self.helpLbl
682	if sys.platform == "darwin": # mac
683	if not empty:
684	menu.Append(wx.Menu(title=''),title='\|') # add another separator
685	menu.Append(G2G.AddHelp(self.G2frame,helpType=helpType, helpLbl=helpLbl),
686	title='&Help')
687	else: # other
688	menu.Append(menu=G2G.MyHelp(self,helpType=helpType, helpLbl=helpLbl),
689	title='&Help')
690
691	def _init_menus(self):
692	'define all GSAS-II data frame menus'
693
694	# for use where no menu or data frame help is provided
695	self.BlankMenu = wx.MenuBar()
696
697	# Controls
698	self.ControlsMenu = wx.MenuBar()
699	self.PrefillDataMenu(self.ControlsMenu,helpType='Controls',empty=True)
700	self.PostfillDataMenu(empty=True)
701
702	# Notebook
703	self.DataNotebookMenu = wx.MenuBar()
704	self.PrefillDataMenu(self.DataNotebookMenu,helpType='Notebook',empty=True)
705	self.PostfillDataMenu(empty=True)
706
707	# Comments
708	self.DataCommentsMenu = wx.MenuBar()
709	self.PrefillDataMenu(self.DataCommentsMenu,helpType='Comments',empty=True)
710	self.PostfillDataMenu(empty=True)
711
712	# Constraints - something amiss here - get weird wx C++ error after refine!
713	self.ConstraintMenu = wx.MenuBar()
714	self.PrefillDataMenu(self.ConstraintMenu,helpType='Constraints')
715	self.ConstraintTab = wx.Menu(title='')
716	self.ConstraintMenu.Append(menu=self.ConstraintTab, title='Select tab')
717	for id,txt in (
718	(wxID_CONSPHASE,'Phase'),
719	(wxID_CONSHAP,'Histogram/Phase'),
720	(wxID_CONSHIST,'Histogram'),
721	(wxID_CONSGLOBAL,'Global')):
722	self.ConstraintTab.Append(
723	id=id, kind=wx.ITEM_NORMAL,text=txt,
724	help='Select '+txt+' constraint editing tab')
725	self.ConstraintEdit = wx.Menu(title='')
726	self.ConstraintMenu.Append(menu=self.ConstraintEdit, title='Edit')
727	self.ConstraintEdit.Append(id=wxID_HOLDADD, kind=wx.ITEM_NORMAL,text='Add hold',
728	help='Add hold on a parameter value')
729	self.ConstraintEdit.Append(id=wxID_EQUIVADD, kind=wx.ITEM_NORMAL,text='Add equivalence',
730	help='Add equivalence between parameter values')
731	self.ConstraintEdit.Append(id=wxID_CONSTRAINTADD, kind=wx.ITEM_NORMAL,text='Add constraint',
732	help='Add constraint on parameter values')
733	self.ConstraintEdit.Append(id=wxID_FUNCTADD, kind=wx.ITEM_NORMAL,text='Add New Var',
734	help='Add variable composed of existing parameter')
735	self.ConstraintEdit.Append(id=wxID_EQUIVALANCEATOMS, kind=wx.ITEM_NORMAL,text='Add atom equivalence',
736	help='Add equivalences between atom parameter values')
737	self.ConstraintEdit.Enable(wxID_EQUIVALANCEATOMS,False)
738	# self.ConstraintEdit.Append(id=wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add H riding constraints',
739	# help='Add H atom riding constraints between atom parameter values')
740	# self.ConstraintEdit.Enable(wxID_ADDRIDING,False)
741	self.PostfillDataMenu()
742
743	# item = self.ConstraintEdit.Append(id=wx.ID_ANY,kind=wx.ITEM_NORMAL,text='Update GUI')
744	# def UpdateGSASIIconstrGUI(event):
745	# import GSASIIconstrGUI
746	# reload(GSASIIconstrGUI)
747	# import GSASIIobj
748	# reload(GSASIIobj)
749	# self.Bind(wx.EVT_MENU,UpdateGSASIIconstrGUI,id=item.GetId())
750
751	# Rigid bodies
752	self.RigidBodyMenu = wx.MenuBar()
753	self.PrefillDataMenu(self.RigidBodyMenu,helpType='Rigid bodies')
754	self.ResidueRBMenu = wx.Menu(title='')
755	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYIMPORT, kind=wx.ITEM_NORMAL,text='Import XYZ',
756	help='Import rigid body XYZ from file')
757	self.ResidueRBMenu.Append(id=wxID_RESIDUETORSSEQ, kind=wx.ITEM_NORMAL,text='Define sequence',
758	help='Define torsion sequence')
759	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYADD, kind=wx.ITEM_NORMAL,text='Import residues',
760	help='Import residue rigid bodies from macro file')
761	self.RigidBodyMenu.Append(menu=self.ResidueRBMenu, title='Edit Body')
762	self.PostfillDataMenu()
763
764	self.VectorBodyMenu = wx.MenuBar()
765	self.PrefillDataMenu(self.VectorBodyMenu,helpType='Vector rigid bodies')
766	self.VectorRBEdit = wx.Menu(title='')
767	self.VectorRBEdit.Append(id=wxID_VECTORBODYADD, kind=wx.ITEM_NORMAL,text='Add rigid body',
768	help='Add vector rigid body')
769	self.VectorBodyMenu.Append(menu=self.VectorRBEdit, title='Edit Vector Body')
770	self.PostfillDataMenu()
771
772
773	# Restraints
774	self.RestraintTab = wx.Menu(title='')
775	self.RestraintEdit = wx.Menu(title='')
776	self.RestraintEdit.Append(id=wxID_RESTSELPHASE, kind=wx.ITEM_NORMAL,text='Select phase',
777	help='Select phase')
778	self.RestraintEdit.Append(id=wxID_RESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add restraints',
779	help='Add restraints')
780	self.RestraintEdit.Enable(wxID_RESTRAINTADD,True) #gets disabled if macromolecule phase
781	self.RestraintEdit.Append(id=wxID_AARESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add residue restraints',
782	help='Add residue based restraints for macromolecules from macro file')
783	self.RestraintEdit.Enable(wxID_AARESTRAINTADD,False) #gets enabled if macromolecule phase
784	self.RestraintEdit.Append(id=wxID_AARESTRAINTPLOT, kind=wx.ITEM_NORMAL,text='Plot residue restraints',
785	help='Plot selected residue based restraints for macromolecules from macro file')
786	self.RestraintEdit.Enable(wxID_AARESTRAINTPLOT,False) #gets enabled if macromolecule phase
787	self.RestraintEdit.Append(id=wxID_RESRCHANGEVAL, kind=wx.ITEM_NORMAL,text='Change value',
788	help='Change observed value')
789	self.RestraintEdit.Append(id=wxID_RESTCHANGEESD, kind=wx.ITEM_NORMAL,text='Change esd',
790	help='Change esd in observed value')
791	self.RestraintEdit.Append(id=wxID_RESTDELETE, kind=wx.ITEM_NORMAL,text='Delete restraints',
792	help='Delete selected restraints')
793
794	self.RestraintMenu = wx.MenuBar()
795	self.PrefillDataMenu(self.RestraintMenu,helpType='Restraints')
796	self.RestraintMenu.Append(menu=self.RestraintTab, title='Select tab')
797	self.RestraintMenu.Append(menu=self.RestraintEdit, title='Edit')
798	self.PostfillDataMenu()
799
800	# Sequential results
801	self.SequentialMenu = wx.MenuBar()
802	self.PrefillDataMenu(self.SequentialMenu,helpType='Sequential',helpLbl='Sequential Refinement')
803	self.SequentialFile = wx.Menu(title='')
804	self.SequentialMenu.Append(menu=self.SequentialFile, title='Columns')
805	self.SequentialFile.Append(id=wxID_RENAMESEQSEL, kind=wx.ITEM_NORMAL,text='Rename selected',
806	help='Rename selected sequential refinement columns')
807	self.SequentialFile.Append(id=wxID_SAVESEQSEL, kind=wx.ITEM_NORMAL,text='Save selected as text',
808	help='Save selected sequential refinement results as a text file')
809	self.SequentialFile.Append(id=wxID_SAVESEQCSV, kind=wx.ITEM_NORMAL,text='Save all as CSV',
810	help='Save all sequential refinement results as a CSV spreadsheet file')
811	self.SequentialFile.Append(id=wxID_SAVESEQSELCSV, kind=wx.ITEM_NORMAL,text='Save selected as CSV',
812	help='Save selected sequential refinement results as a CSV spreadsheet file')
813	self.SequentialFile.Append(id=wxID_PLOTSEQSEL, kind=wx.ITEM_NORMAL,text='Plot selected',
814	help='Plot selected sequential refinement results')
815	self.SequentialFile.Append(id=wxID_AVESEQSEL, kind=wx.ITEM_NORMAL,text='Compute average',
816	help='Compute average for selected parameter')
817	self.SequentialFile.Append(id=wxID_ORGSEQSEL, kind=wx.ITEM_NORMAL,text='Reorganize',
818	help='Reorganize variables where variables change')
819	self.SequentialPvars = wx.Menu(title='')
820	self.SequentialMenu.Append(menu=self.SequentialPvars, title='Pseudo Vars')
821	self.SequentialPvars.Append(
822	id=wxADDSEQVAR, kind=wx.ITEM_NORMAL,text='Add',
823	help='Add a new pseudo-variable')
824	self.SequentialPvars.Append(
825	id=wxDELSEQVAR, kind=wx.ITEM_NORMAL,text='Delete',
826	help='Delete an existing pseudo-variable')
827	self.SequentialPvars.Append(
828	id=wxEDITSEQVAR, kind=wx.ITEM_NORMAL,text='Edit',
829	help='Edit an existing pseudo-variable')
830
831	self.SequentialPfit = wx.Menu(title='')
832	self.SequentialMenu.Append(menu=self.SequentialPfit, title='Parametric Fit')
833	self.SequentialPfit.Append(
834	id=wxADDPARFIT, kind=wx.ITEM_NORMAL,text='Add equation',
835	help='Add a new equation to minimize')
836	self.SequentialPfit.Append(
837	id=wxCOPYPARFIT, kind=wx.ITEM_NORMAL,text='Copy equation',
838	help='Copy an equation to minimize - edit it next')
839	self.SequentialPfit.Append(
840	id=wxDELPARFIT, kind=wx.ITEM_NORMAL,text='Delete equation',
841	help='Delete an equation for parametric minimization')
842	self.SequentialPfit.Append(
843	id=wxEDITPARFIT, kind=wx.ITEM_NORMAL,text='Edit equation',
844	help='Edit an existing parametric minimization equation')
845	self.SequentialPfit.Append(
846	id=wxDOPARFIT, kind=wx.ITEM_NORMAL,text='Fit to equation(s)',
847	help='Perform a parametric minimization')
848	self.PostfillDataMenu()
849
850	# PWDR & SASD
851	self.PWDRMenu = wx.MenuBar()
852	self.PrefillDataMenu(self.PWDRMenu,helpType='PWDR Analysis',helpLbl='Powder Fit Error Analysis')
853	self.ErrorAnal = wx.Menu(title='')
854	self.PWDRMenu.Append(menu=self.ErrorAnal,title='Commands')
855	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
856	help='Error analysis on powder pattern')
857	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
858	help='Copy of PWDR parameters')
859	self.ErrorAnal.Append(id=wxID_PLOTCTRLCOPY,kind=wx.ITEM_NORMAL,text='Copy plot controls',
860	help='Copy of PWDR plot controls')
861
862	self.PostfillDataMenu()
863
864	# HKLF
865	self.HKLFMenu = wx.MenuBar()
866	self.PrefillDataMenu(self.HKLFMenu,helpType='HKLF Analysis',helpLbl='HKLF Fit Error Analysis')
867	self.ErrorAnal = wx.Menu(title='')
868	self.HKLFMenu.Append(menu=self.ErrorAnal,title='Commands')
869	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
870	help='Error analysis on single crystal data')
871	self.ErrorAnal.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
872	help='Plot HKLs from single crystal data in 3D')
873	self.ErrorAnal.Append(id=wxID_3DALLHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot all 3D HKLs',
874	help='Plot HKLs from all single crystal data in 3D')
875	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
876	help='Copy of HKLF parameters')
877	self.PostfillDataMenu()
878
879	# PDR / Limits
880	self.LimitMenu = wx.MenuBar()
881	self.PrefillDataMenu(self.LimitMenu,helpType='Limits')
882	self.LimitEdit = wx.Menu(title='')
883	self.LimitMenu.Append(menu=self.LimitEdit, title='Edit')
884	self.LimitEdit.Append(id=wxID_LIMITCOPY, kind=wx.ITEM_NORMAL,text='Copy',
885	help='Copy limits to other histograms')
886	self.LimitEdit.Append(id=wxID_ADDEXCLREGION, kind=wx.ITEM_NORMAL,text='Add exclude',
887	help='Add excluded region - select a point on plot; drag to adjust')
888	self.PostfillDataMenu()
889
890	# PDR / Background
891	self.BackMenu = wx.MenuBar()
892	self.PrefillDataMenu(self.BackMenu,helpType='Background')
893	self.BackEdit = wx.Menu(title='')
894	self.BackMenu.Append(menu=self.BackEdit, title='File')
895	self.BackEdit.Append(id=wxID_BACKCOPY, kind=wx.ITEM_NORMAL,text='Copy',
896	help='Copy background parameters to other histograms')
897	self.BackEdit.Append(id=wxID_BACKFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
898	help='Copy background refinement flags to other histograms')
899	self.BackEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
900	help='Move background peaks to Peak List')
901	self.BackFixed = wx.Menu(title='') # fixed background point menu
902	self.BackMenu.Append(menu=self.BackFixed, title='Fixed Points')
903	self.wxID_BackPts = {}
904	self.wxID_BackPts['Add'] = wx.NewId() # N.B. not using wxID_ global as for other menu items
905	self.BackFixed.Append(id=self.wxID_BackPts['Add'], kind=wx.ITEM_RADIO,text='Add',
906	help='Add fixed background points with mouse clicks')
907	self.wxID_BackPts['Move'] = wx.NewId()
908	item = self.BackFixed.Append(id=self.wxID_BackPts['Move'], kind=wx.ITEM_RADIO,text='Move',
909	help='Move selected fixed background points with mouse drags')
910	item.Check(True)
911	self.wxID_BackPts['Del'] = wx.NewId()
912	self.BackFixed.Append(id=self.wxID_BackPts['Del'], kind=wx.ITEM_RADIO,text='Delete',
913	help='Delete fixed background points with mouse clicks')
914	self.wxID_BackPts['Clear'] = wx.NewId()
915	self.BackFixed.Append(id=self.wxID_BackPts['Clear'], kind=wx.ITEM_NORMAL,text='Clear',
916	help='Clear fixed background points')
917	self.wxID_BackPts['Fit'] = wx.NewId()
918	self.BackFixed.Append(id=self.wxID_BackPts['Fit'], kind=wx.ITEM_NORMAL,text='Fit background',
919	help='Fit background function to fixed background points')
920	self.PostfillDataMenu()
921
922	# PDR / Instrument Parameters
923	self.InstMenu = wx.MenuBar()
924	self.PrefillDataMenu(self.InstMenu,helpType='Instrument Parameters')
925	self.InstEdit = wx.Menu(title='')
926	self.InstMenu.Append(menu=self.InstEdit, title='Operations')
927	self.InstEdit.Append(help='Calibrate from indexed peaks',
928	id=wxID_INSTCALIB, kind=wx.ITEM_NORMAL,text='Calibrate')
929	self.InstEdit.Append(help='Reset instrument profile parameters to default',
930	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
931	self.InstEdit.Append(help='Load instrument profile parameters from file',
932	id=wxID_INSTLOAD, kind=wx.ITEM_NORMAL,text='Load profile...')
933	self.InstEdit.Append(help='Save instrument profile parameters to file',
934	id=wxID_INSTSAVE, kind=wx.ITEM_NORMAL,text='Save profile...')
935	self.InstEdit.Append(help='Copy instrument profile parameters to other histograms',
936	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
937	self.InstEdit.Append(id=wxID_INSTFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
938	help='Copy instrument parameter refinement flags to other histograms')
939	# self.InstEdit.Append(help='Change radiation type (Ka12 - synch)',
940	# id=wxID_CHANGEWAVETYPE, kind=wx.ITEM_NORMAL,text='Change radiation')
941	self.InstEdit.Append(id=wxID_INST1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
942	help='Set one instrument parameter value across multiple histograms')
943
944	self.PostfillDataMenu()
945
946	# PDR / Sample Parameters
947	self.SampleMenu = wx.MenuBar()
948	self.PrefillDataMenu(self.SampleMenu,helpType='Sample Parameters')
949	self.SampleEdit = wx.Menu(title='')
950	self.SampleMenu.Append(menu=self.SampleEdit, title='Command')
951	self.SetScale = self.SampleEdit.Append(id=wxID_SETSCALE, kind=wx.ITEM_NORMAL,text='Set scale',
952	help='Set scale by matching to another histogram')
953	self.SampleEdit.Append(id=wxID_SAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load',
954	help='Load sample parameters from file')
955	self.SampleEdit.Append(id=wxID_SAMPLESAVE, kind=wx.ITEM_NORMAL,text='Save',
956	help='Save sample parameters to file')
957	self.SampleEdit.Append(id=wxID_SAMPLECOPY, kind=wx.ITEM_NORMAL,text='Copy',
958	help='Copy refinable and most other sample parameters to other histograms')
959	self.SampleEdit.Append(id=wxID_SAMPLECOPYSOME, kind=wx.ITEM_NORMAL,text='Copy selected...',
960	help='Copy selected sample parameters to other histograms')
961	self.SampleEdit.Append(id=wxID_SAMPLEFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
962	help='Copy sample parameter refinement flags to other histograms')
963	self.SampleEdit.Append(id=wxID_SAMPLE1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
964	help='Set one sample parameter value across multiple histograms')
965	self.SampleEdit.Append(id=wxID_ALLSAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load all',
966	help='Load sample parmameters over multiple histograms')
967
968	self.PostfillDataMenu()
969	self.SetScale.Enable(False)
970
971	# PDR / Peak List
972	self.PeakMenu = wx.MenuBar()
973	self.PrefillDataMenu(self.PeakMenu,helpType='Peak List')
974	self.PeakEdit = wx.Menu(title='')
975	self.PeakMenu.Append(menu=self.PeakEdit, title='Peak Fitting')
976	self.AutoSearch = self.PeakEdit.Append(help='Automatic peak search',
977	id=wxID_AUTOSEARCH, kind=wx.ITEM_NORMAL,text='Auto search')
978	self.UnDo = self.PeakEdit.Append(help='Undo last least squares refinement',
979	id=wxID_UNDO, kind=wx.ITEM_NORMAL,text='UnDo')
980	self.PeakFit = self.PeakEdit.Append(id=wxID_LSQPEAKFIT, kind=wx.ITEM_NORMAL,text='Peakfit',
981	help='Peak fitting' )
982	self.PFOneCycle = self.PeakEdit.Append(id=wxID_LSQONECYCLE, kind=wx.ITEM_NORMAL,text='Peakfit one cycle',
983	help='One cycle of Peak fitting' )
984	self.PeakEdit.Append(id=wxID_RESETSIGGAM, kind=wx.ITEM_NORMAL,
985	text='Reset sig and gam',help='Reset sigma and gamma to global fit' )
986	self.PeakCopy = self.PeakEdit.Append(help='Copy peaks to other histograms',
987	id=wxID_PEAKSCOPY, kind=wx.ITEM_NORMAL,text='Peak copy')
988	self.SeqPeakFit = self.PeakEdit.Append(id=wxID_SEQPEAKFIT, kind=wx.ITEM_NORMAL,text='Seq PeakFit',
989	help='Sequential Peak fitting for all histograms' )
990	self.PeakEdit.Append(id=wxID_CLEARPEAKS, kind=wx.ITEM_NORMAL,text='Clear peaks',
991	help='Clear the peak list' )
992	self.PostfillDataMenu()
993	self.UnDo.Enable(False)
994	self.PeakFit.Enable(False)
995	self.PFOneCycle.Enable(False)
996	self.AutoSearch.Enable(True)
997
998	# PDR / Index Peak List
999	self.IndPeaksMenu = wx.MenuBar()
1000	self.PrefillDataMenu(self.IndPeaksMenu,helpType='Index Peak List')
1001	self.IndPeaksEdit = wx.Menu(title='')
1002	self.IndPeaksMenu.Append(menu=self.IndPeaksEdit,title='Operations')
1003	self.IndPeaksEdit.Append(help='Load/Reload index peaks from peak list',id=wxID_INDXRELOAD,
1004	kind=wx.ITEM_NORMAL,text='Load/Reload')
1005	self.PostfillDataMenu()
1006
1007	# PDR / Unit Cells List
1008	self.IndexMenu = wx.MenuBar()
1009	self.PrefillDataMenu(self.IndexMenu,helpType='Unit Cells List')
1010	self.IndexEdit = wx.Menu(title='')
1011	self.IndexMenu.Append(menu=self.IndexEdit, title='Cell Index/Refine')
1012	self.IndexPeaks = self.IndexEdit.Append(help='', id=wxID_INDEXPEAKS, kind=wx.ITEM_NORMAL,
1013	text='Index Cell')
1014	self.CopyCell = self.IndexEdit.Append( id=wxID_COPYCELL, kind=wx.ITEM_NORMAL,text='Copy Cell',
1015	help='Copy selected unit cell from indexing to cell refinement fields')
1016	self.RefineCell = self.IndexEdit.Append( id=wxID_REFINECELL, kind=wx.ITEM_NORMAL,
1017	text='Refine Cell',help='Refine unit cell parameters from indexed peaks')
1018	self.MakeNewPhase = self.IndexEdit.Append( id=wxID_MAKENEWPHASE, kind=wx.ITEM_NORMAL,
1019	text='Make new phase',help='Make new phase from selected unit cell')
1020	self.ExportCells = self.IndexEdit.Append( id=wxID_EXPORTCELLS, kind=wx.ITEM_NORMAL,
1021	text='Export cell list',help='Export cell list to csv file')
1022	self.PostfillDataMenu()
1023	self.IndexPeaks.Enable(False)
1024	self.CopyCell.Enable(False)
1025	self.RefineCell.Enable(False)
1026	self.MakeNewPhase.Enable(False)
1027
1028	# PDR / Reflection Lists
1029	self.ReflMenu = wx.MenuBar()
1030	self.PrefillDataMenu(self.ReflMenu,helpType='Reflection List')
1031	self.ReflEdit = wx.Menu(title='')
1032	self.ReflMenu.Append(menu=self.ReflEdit, title='Reflection List')
1033	self.SelectPhase = self.ReflEdit.Append(help='Select phase for reflection list',id=wxID_SELECTPHASE,
1034	kind=wx.ITEM_NORMAL,text='Select phase')
1035	self.ReflEdit.Append(id=wxID_PWDHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot HKLs',
1036	help='Plot HKLs from powder pattern')
1037	self.ReflEdit.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
1038	help='Plot HKLs from powder pattern in 3D')
1039	self.PostfillDataMenu()
1040
1041	# SASD / Instrument Parameters
1042	self.SASDInstMenu = wx.MenuBar()
1043	self.PrefillDataMenu(self.SASDInstMenu,helpType='Instrument Parameters')
1044	self.SASDInstEdit = wx.Menu(title='')
1045	self.SASDInstMenu.Append(menu=self.SASDInstEdit, title='Operations')
1046	self.InstEdit.Append(help='Reset instrument profile parameters to default',
1047	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
1048	self.SASDInstEdit.Append(help='Copy instrument profile parameters to other histograms',
1049	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
1050	self.PostfillDataMenu()
1051
1052	#SASD & REFL/ Substance editor
1053	self.SubstanceMenu = wx.MenuBar()
1054	self.PrefillDataMenu(self.SubstanceMenu,helpType='Substances')
1055	self.SubstanceEdit = wx.Menu(title='')
1056	self.SubstanceMenu.Append(menu=self.SubstanceEdit, title='Edit')
1057	self.SubstanceEdit.Append(id=wxID_LOADSUBSTANCE, kind=wx.ITEM_NORMAL,text='Load substance',
1058	help='Load substance from file')
1059	self.SubstanceEdit.Append(id=wxID_ADDSUBSTANCE, kind=wx.ITEM_NORMAL,text='Add substance',
1060	help='Add new substance to list')
1061	self.SubstanceEdit.Append(id=wxID_COPYSUBSTANCE, kind=wx.ITEM_NORMAL,text='Copy substances',
1062	help='Copy substances')
1063	self.SubstanceEdit.Append(id=wxID_DELETESUBSTANCE, kind=wx.ITEM_NORMAL,text='Delete substance',
1064	help='Delete substance from list')
1065	self.SubstanceEdit.Append(id=wxID_ELEMENTADD, kind=wx.ITEM_NORMAL,text='Add elements',
1066	help='Add elements to substance')
1067	self.SubstanceEdit.Append(id=wxID_ELEMENTDELETE, kind=wx.ITEM_NORMAL,text='Delete elements',
1068	help='Delete elements from substance')
1069	self.PostfillDataMenu()
1070
1071	# SASD/ Models
1072	self.ModelMenu = wx.MenuBar()
1073	self.PrefillDataMenu(self.ModelMenu,helpType='Models')
1074	self.ModelEdit = wx.Menu(title='')
1075	self.ModelMenu.Append(menu=self.ModelEdit, title='Models')
1076	self.ModelEdit.Append(id=wxID_MODELADD,kind=wx.ITEM_NORMAL,text='Add',
1077	help='Add new term to model')
1078	self.ModelEdit.Append(id=wxID_MODELFIT, kind=wx.ITEM_NORMAL,text='Fit',
1079	help='Fit model parameters to data')
1080	self.SasdUndo = self.ModelEdit.Append(id=wxID_MODELUNDO, kind=wx.ITEM_NORMAL,text='Undo',
1081	help='Undo model fit')
1082	self.SasdUndo.Enable(False)
1083	self.ModelEdit.Append(id=wxID_MODELFITALL, kind=wx.ITEM_NORMAL,text='Sequential fit',
1084	help='Sequential fit of model parameters to all SASD data')
1085	self.ModelEdit.Append(id=wxID_MODELCOPY, kind=wx.ITEM_NORMAL,text='Copy',
1086	help='Copy model parameters to other histograms')
1087	self.ModelEdit.Append(id=wxID_MODELCOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1088	help='Copy model refinement flags to other histograms')
1089	self.PostfillDataMenu()
1090
1091	# IMG / Image Controls
1092	self.ImageMenu = wx.MenuBar()
1093	self.PrefillDataMenu(self.ImageMenu,helpType='Image Controls')
1094	self.ImageEdit = wx.Menu(title='')
1095	self.ImageMenu.Append(menu=self.ImageEdit, title='Operations')
1096	self.ImageEdit.Append(help='Calibrate detector by fitting to calibrant lines',
1097	id=wxID_IMCALIBRATE, kind=wx.ITEM_NORMAL,text='Calibrate')
1098	self.ImageEdit.Append(help='Recalibrate detector by fitting to calibrant lines',
1099	id=wxID_IMRECALIBRATE, kind=wx.ITEM_NORMAL,text='Recalibrate')
1100	self.ImageEdit.Append(help='Clear calibration data points and rings',id=wxID_IMCLEARCALIB,
1101	kind=wx.ITEM_NORMAL,text='Clear calibration')
1102	self.ImageEdit.Append(help='Integrate selected image',id=wxID_IMINTEGRATE,
1103	kind=wx.ITEM_NORMAL,text='Integrate')
1104	self.ImageEdit.Append(help='Integrate all images selected from list',id=wxID_INTEGRATEALL,
1105	kind=wx.ITEM_NORMAL,text='Integrate all')
1106	self.ImageEdit.Append(help='Copy image controls to other images',
1107	id=wxID_IMCOPYCONTROLS, kind=wx.ITEM_NORMAL,text='Copy Controls')
1108	self.ImageEdit.Append(help='Save image controls to file',
1109	id=wxID_IMSAVECONTROLS, kind=wx.ITEM_NORMAL,text='Save Controls')
1110	self.ImageEdit.Append(help='Load image controls from file',
1111	id=wxID_IMLOADCONTROLS, kind=wx.ITEM_NORMAL,text='Load Controls')
1112	try: # remove after AutoInt is completed
1113	import autoint
1114	self.ImageEdit.Append(help='Open Auto-integration window to integrate a series of images',
1115	id=wxID_IMAUTOINTEG, kind=wx.ITEM_NORMAL,text='Auto Integrate')
1116	print "development code: AutoInt found"
1117	except ImportError:
1118	pass
1119	self.PostfillDataMenu()
1120
1121	# IMG / Masks
1122	self.MaskMenu = wx.MenuBar()
1123	self.PrefillDataMenu(self.MaskMenu,helpType='Image Masks')
1124	self.MaskEdit = wx.Menu(title='')
1125	self.MaskMenu.Append(menu=self.MaskEdit, title='Operations')
1126	submenu = wx.Menu()
1127	self.MaskEdit.AppendMenu(
1128	wx.ID_ANY,'Create new', submenu,
1129	help=''
1130	)
1131	self.MaskEdit.Append(help='Copy mask to other images',
1132	id=wxID_MASKCOPY, kind=wx.ITEM_NORMAL,text='Copy mask')
1133	self.MaskEdit.Append(help='Save mask to file',
1134	id=wxID_MASKSAVE, kind=wx.ITEM_NORMAL,text='Save mask')
1135	self.MaskEdit.Append(help='Load mask from file',
1136	id=wxID_MASKLOAD, kind=wx.ITEM_NORMAL,text='Load mask')
1137	self.MaskEdit.Append(help='Load mask from file; ignore threshold',
1138	id=wxID_MASKLOADNOT, kind=wx.ITEM_NORMAL,text='Load mask w/o threshold')
1139	submenu.Append(help='Create an arc mask with mouse input',
1140	id=wxID_NEWMASKARC, kind=wx.ITEM_NORMAL,text='Arc mask')
1141	submenu.Append(help='Create a frame mask with mouse input',
1142	id=wxID_NEWMASKFRAME, kind=wx.ITEM_NORMAL,text='Frame mask')
1143	submenu.Append(help='Create a polygon mask with mouse input',
1144	id=wxID_NEWMASKPOLY, kind=wx.ITEM_NORMAL,text='Polygon mask')
1145	submenu.Append(help='Create a ring mask with mouse input',
1146	id=wxID_NEWMASKRING, kind=wx.ITEM_NORMAL,text='Ring mask')
1147	submenu.Append(help='Create a spot mask with mouse input',
1148	id=wxID_NEWMASKSPOT, kind=wx.ITEM_NORMAL,text='Spot mask')
1149	self.PostfillDataMenu()
1150
1151	# IMG / Stress/Strain
1152	self.StrStaMenu = wx.MenuBar()
1153	self.PrefillDataMenu(self.StrStaMenu,helpType='Stress/Strain')
1154	self.StrStaEdit = wx.Menu(title='')
1155	self.StrStaMenu.Append(menu=self.StrStaEdit, title='Operations')
1156	self.StrStaEdit.Append(help='Append d-zero for one ring',
1157	id=wxID_APPENDDZERO, kind=wx.ITEM_NORMAL,text='Append d-zero')
1158	self.StrStaEdit.Append(help='Fit stress/strain data',
1159	id=wxID_STRSTAFIT, kind=wx.ITEM_NORMAL,text='Fit stress/strain')
1160	self.StrStaEdit.Append(help='Update d-zero from ave d-zero',
1161	id=wxID_UPDATEDZERO, kind=wx.ITEM_NORMAL,text='Update d-zero')
1162	self.StrStaEdit.Append(help='Fit stress/strain data for all images',
1163	id=wxID_STRSTAALLFIT, kind=wx.ITEM_NORMAL,text='All image fit')
1164	self.StrStaEdit.Append(help='Copy stress/strain data to other images',
1165	id=wxID_STRSTACOPY, kind=wx.ITEM_NORMAL,text='Copy stress/strain')
1166	self.StrStaEdit.Append(help='Save stress/strain data to file',
1167	id=wxID_STRSTASAVE, kind=wx.ITEM_NORMAL,text='Save stress/strain')
1168	self.StrStaEdit.Append(help='Load stress/strain data from file',
1169	id=wxID_STRSTALOAD, kind=wx.ITEM_NORMAL,text='Load stress/strain')
1170	self.StrStaEdit.Append(help='Load sample data from file',
1171	id=wxID_STRSTSAMPLE, kind=wx.ITEM_NORMAL,text='Load sample data')
1172	self.PostfillDataMenu()
1173
1174	# PDF / PDF Controls
1175	self.PDFMenu = wx.MenuBar()
1176	self.PrefillDataMenu(self.PDFMenu,helpType='PDF Controls')
1177	self.PDFEdit = wx.Menu(title='')
1178	self.PDFMenu.Append(menu=self.PDFEdit, title='PDF Controls')
1179	self.PDFEdit.Append(help='Add element to sample composition',id=wxID_PDFADDELEMENT, kind=wx.ITEM_NORMAL,
1180	text='Add element')
1181	self.PDFEdit.Append(help='Delete element from sample composition',id=wxID_PDFDELELEMENT, kind=wx.ITEM_NORMAL,
1182	text='Delete element')
1183	self.PDFEdit.Append(help='Copy PDF controls', id=wxID_PDFCOPYCONTROLS, kind=wx.ITEM_NORMAL,
1184	text='Copy controls')
1185	self.PDFEdit.Append(help='Load PDF controls from file',id=wxID_PDFLOADCONTROLS, kind=wx.ITEM_NORMAL,
1186	text='Load Controls')
1187	self.PDFEdit.Append(help='Save PDF controls to file', id=wxID_PDFSAVECONTROLS, kind=wx.ITEM_NORMAL,
1188	text='Save controls')
1189	self.PDFEdit.Append(help='Compute PDF', id=wxID_PDFCOMPUTE, kind=wx.ITEM_NORMAL,
1190	text='Compute PDF')
1191	self.PDFEdit.Append(help='Compute all PDFs', id=wxID_PDFCOMPUTEALL, kind=wx.ITEM_NORMAL,
1192	text='Compute all PDFs')
1193	self.PostfillDataMenu()
1194
1195	# Phase / General tab
1196	self.DataGeneral = wx.MenuBar()
1197	self.PrefillDataMenu(self.DataGeneral,helpType='General', helpLbl='Phase/General')
1198	self.DataGeneral.Append(menu=wx.Menu(title=''),title='Select tab')
1199	self.GeneralCalc = wx.Menu(title='')
1200	self.DataGeneral.Append(menu=self.GeneralCalc,title='Compute')
1201	self.GeneralCalc.Append(help='Compute Fourier map',id=wxID_FOURCALC, kind=wx.ITEM_NORMAL,
1202	text='Fourier map')
1203	self.GeneralCalc.Append(help='Search Fourier map',id=wxID_FOURSEARCH, kind=wx.ITEM_NORMAL,
1204	text='Search map')
1205	self.GeneralCalc.Append(help='Run charge flipping',id=wxID_CHARGEFLIP, kind=wx.ITEM_NORMAL,
1206	text='Charge flipping')
1207	self.GeneralCalc.Append(help='Run 4D charge flipping',id=wxID_4DCHARGEFLIP, kind=wx.ITEM_NORMAL,
1208	text='4D Charge flipping')
1209	self.GeneralCalc.Enable(wxID_4DCHARGEFLIP,False)
1210	self.GeneralCalc.Append(help='Clear map',id=wxID_FOURCLEAR, kind=wx.ITEM_NORMAL,
1211	text='Clear map')
1212	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing',id=wxID_SINGLEMCSA, kind=wx.ITEM_NORMAL,
1213	text='MC/SA')
1214	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing on multiprocessors',id=wxID_MULTIMCSA, kind=wx.ITEM_NORMAL,
1215	text='Multi MC/SA') #currently not useful
1216	self.PostfillDataMenu()
1217
1218	# Phase / Data tab
1219	self.DataMenu = wx.MenuBar()
1220	self.PrefillDataMenu(self.DataMenu,helpType='Data', helpLbl='Phase/Data')
1221	self.DataMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1222	self.DataEdit = wx.Menu(title='')
1223	self.DataMenu.Append(menu=self.DataEdit, title='Edit')
1224	self.DataEdit.Append(id=wxID_DATACOPY, kind=wx.ITEM_NORMAL,text='Copy data',
1225	help='Copy phase data to other histograms')
1226	self.DataEdit.Append(id=wxID_DATACOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1227	help='Copy phase data flags to other histograms')
1228	self.DataEdit.Append(id=wxID_DATASELCOPY, kind=wx.ITEM_NORMAL,text='Copy selected data',
1229	help='Copy selected phase data to other histograms')
1230	self.DataEdit.Append(id=wxID_PWDRADD, kind=wx.ITEM_NORMAL,text='Add powder histograms',
1231	help='Select new powder histograms to be used for this phase')
1232	self.DataEdit.Append(id=wxID_HKLFADD, kind=wx.ITEM_NORMAL,text='Add single crystal histograms',
1233	help='Select new single crystal histograms to be used for this phase')
1234	self.DataEdit.Append(id=wxID_DATADELETE, kind=wx.ITEM_NORMAL,text='Remove histograms',
1235	help='Remove histograms from use for this phase')
1236	self.PostfillDataMenu()
1237
1238	# Phase / Atoms tab
1239	self.AtomsMenu = wx.MenuBar()
1240	self.PrefillDataMenu(self.AtomsMenu,helpType='Atoms')
1241	self.AtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1242	self.AtomEdit = wx.Menu(title='')
1243	self.AtomCompute = wx.Menu(title='')
1244	self.AtomsMenu.Append(menu=self.AtomEdit, title='Edit')
1245	self.AtomsMenu.Append(menu=self.AtomCompute, title='Compute')
1246	self.AtomEdit.Append(id=wxID_ATOMSEDITADD, kind=wx.ITEM_NORMAL,text='Append atom',
1247	help='Appended as an H atom')
1248	self.AtomEdit.Append(id=wxID_ATOMSVIEWADD, kind=wx.ITEM_NORMAL,text='Append view point',
1249	help='Appended as an H atom')
1250	self.AtomEdit.Append(id=wxID_ATOMSEDITINSERT, kind=wx.ITEM_NORMAL,text='Insert atom',
1251	help='Select atom row to insert before; inserted as an H atom')
1252	self.AtomEdit.Append(id=wxID_ATOMVIEWINSERT, kind=wx.ITEM_NORMAL,text='Insert view point',
1253	help='Select atom row to insert before; inserted as an H atom')
1254	self.AtomEdit.Append(id=wxID_ADDHATOM, kind=wx.ITEM_NORMAL,text='Insert H atoms',
1255	help='Insert H atoms in standard positions bonded to selected atoms')
1256	self.AtomEdit.Append(id=wxID_UPDATEHATOM, kind=wx.ITEM_NORMAL,text='Update H atoms',
1257	help='Update H atoms in standard positions')
1258	self.AtomEdit.Append(id=wxID_ATOMMOVE, kind=wx.ITEM_NORMAL,text='Move atom to view point',
1259	help='Select single atom to move')
1260	self.AtomEdit.Append(id=wxID_ATOMSEDITDELETE, kind=wx.ITEM_NORMAL,text='Delete atom',
1261	help='Select atoms to delete first')
1262	self.AtomEdit.Append(id=wxID_ATOMSREFINE, kind=wx.ITEM_NORMAL,text='Set atom refinement flags',
1263	help='Select atoms to refine first')
1264	self.AtomEdit.Append(id=wxID_ATOMSMODIFY, kind=wx.ITEM_NORMAL,text='Modify atom parameters',
1265	help='Select atoms to modify first')
1266	self.AtomEdit.Append(id=wxID_ATOMSTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform atoms',
1267	help='Select atoms to transform first')
1268	self.AtomEdit.Append(id=wxID_MAKEMOLECULE, kind=wx.ITEM_NORMAL,text='Assemble molecule',
1269	help='Assemble molecule from scatterd atom positions')
1270	self.AtomEdit.Append(id=wxID_RELOADDRAWATOMS, kind=wx.ITEM_NORMAL,text='Reload draw atoms',
1271	help='Reload atom drawing list')
1272	submenu = wx.Menu()
1273	self.AtomEdit.AppendMenu(wx.ID_ANY, 'Reimport atoms', submenu,
1274	help='Reimport atoms from file; sequence must match')
1275	# setup a cascade menu for the formats that have been defined
1276	self.ReImportMenuId = {} # points to readers for each menu entry
1277	for reader in self.G2frame.ImportPhaseReaderlist:
1278	item = submenu.Append(
1279	wx.ID_ANY,help=reader.longFormatName,
1280	kind=wx.ITEM_NORMAL,text='reimport coordinates from '+reader.formatName+' file')
1281	self.ReImportMenuId[item.GetId()] = reader
1282	item = submenu.Append(
1283	wx.ID_ANY,
1284	help='Reimport coordinates, try to determine format from file',
1285	kind=wx.ITEM_NORMAL,
1286	text='guess format from file')
1287	self.ReImportMenuId[item.GetId()] = None # try all readers
1288
1289	self.AtomCompute.Append(id=wxID_ATOMSDISAGL, kind=wx.ITEM_NORMAL,text='Show Distances && Angles',
1290	help='Compute distances & angles for selected atoms')
1291	self.AtomCompute.Append(id=wxID_ATOMSPDISAGL, kind=wx.ITEM_NORMAL,text='Save Distances && Angles',
1292	help='Compute distances & angles for selected atoms')
1293	self.AtomCompute.ISOcalc = self.AtomCompute.Append(
1294	id=wxID_ISODISP, kind=wx.ITEM_NORMAL,
1295	text='Compute ISODISTORT mode values',
1296	help='Compute values of ISODISTORT modes from atom parameters')
1297	self.PostfillDataMenu()
1298
1299	# Phase / Imcommensurate "waves" tab
1300	self.WavesData = wx.MenuBar()
1301	self.PrefillDataMenu(self.WavesData,helpType='Wave Data', helpLbl='Imcommensurate wave data')
1302	self.WavesData.Append(menu=wx.Menu(title=''),title='Select tab')
1303	self.WavesDataCompute = wx.Menu(title='')
1304	self.WavesData.Append(menu=self.WavesDataCompute,title='Compute')
1305	self.WavesDataCompute.Append(id=wxID_4DMAPCOMPUTE, kind=wx.ITEM_NORMAL,text='Compute 4D map',
1306	help='Compute 4-dimensional map')
1307	self.PostfillDataMenu()
1308
1309	# Phase / Draw Options tab
1310	self.DataDrawOptions = wx.MenuBar()
1311	self.PrefillDataMenu(self.DataDrawOptions,helpType='Draw Options', helpLbl='Phase/Draw Options')
1312	self.DataDrawOptions.Append(menu=wx.Menu(title=''),title='Select tab')
1313	self.PostfillDataMenu()
1314
1315	# Phase / Draw Atoms tab
1316	self.DrawAtomsMenu = wx.MenuBar()
1317	self.PrefillDataMenu(self.DrawAtomsMenu,helpType='Draw Atoms')
1318	self.DrawAtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1319	self.DrawAtomEdit = wx.Menu(title='')
1320	self.DrawAtomCompute = wx.Menu(title='')
1321	self.DrawAtomRestraint = wx.Menu(title='')
1322	self.DrawAtomRigidBody = wx.Menu(title='')
1323	self.DrawAtomsMenu.Append(menu=self.DrawAtomEdit, title='Edit')
1324	self.DrawAtomsMenu.Append(menu=self.DrawAtomCompute,title='Compute')
1325	self.DrawAtomsMenu.Append(menu=self.DrawAtomRestraint, title='Restraints')
1326	self.DrawAtomsMenu.Append(menu=self.DrawAtomRigidBody, title='Rigid body')
1327	self.DrawAtomEdit.Append(id=wxID_DRAWATOMSTYLE, kind=wx.ITEM_NORMAL,text='Atom style',
1328	help='Select atoms first')
1329	self.DrawAtomEdit.Append(id=wxID_DRAWATOMLABEL, kind=wx.ITEM_NORMAL,text='Atom label',
1330	help='Select atoms first')
1331	self.DrawAtomEdit.Append(id=wxID_DRAWATOMCOLOR, kind=wx.ITEM_NORMAL,text='Atom color',
1332	help='Select atoms first')
1333	self.DrawAtomEdit.Append(id=wxID_DRAWATOMRESETCOLOR, kind=wx.ITEM_NORMAL,text='Reset atom colors',
1334	help='Resets all atom colors to defaults')
1335	self.DrawAtomEdit.Append(id=wxID_DRAWVIEWPOINT, kind=wx.ITEM_NORMAL,text='View point',
1336	help='View point is 1st atom selected')
1337	self.DrawAtomEdit.Append(id=wxID_DRAWADDEQUIV, kind=wx.ITEM_NORMAL,text='Add atoms',
1338	help='Add symmetry & cell equivalents to drawing set from selected atoms')
1339	self.DrawAtomEdit.Append(id=wxID_DRAWTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform draw atoms',
1340	help='Transform selected atoms by symmetry & cell translations')
1341	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCOORD, kind=wx.ITEM_NORMAL,text='Fill CN-sphere',
1342	help='Fill coordination sphere for selected atoms')
1343	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCELL, kind=wx.ITEM_NORMAL,text='Fill unit cell',
1344	help='Fill unit cell with selected atoms')
1345	self.DrawAtomEdit.Append(id=wxID_DRAWDELETE, kind=wx.ITEM_NORMAL,text='Delete atoms',
1346	help='Delete atoms from drawing set')
1347	self.DrawAtomCompute.Append(id=wxID_DRAWDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1348	help='Compute distance of selected atoms from view point')
1349	self.DrawAtomCompute.Append(id=wxID_DRAWDISAGLTOR, kind=wx.ITEM_NORMAL,text='Dist. Ang. Tors.',
1350	help='Compute distance, angle or torsion for 2-4 selected atoms')
1351	self.DrawAtomCompute.Append(id=wxID_DRAWPLANE, kind=wx.ITEM_NORMAL,text='Best plane',
1352	help='Compute best plane for 4+ selected atoms')
1353	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRBOND, kind=wx.ITEM_NORMAL,text='Add bond restraint',
1354	help='Add bond restraint for selected atoms (2)')
1355	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRANGLE, kind=wx.ITEM_NORMAL,text='Add angle restraint',
1356	help='Add angle restraint for selected atoms (3: one end 1st)')
1357	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRPLANE, kind=wx.ITEM_NORMAL,text='Add plane restraint',
1358	help='Add plane restraint for selected atoms (4+)')
1359	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRCHIRAL, kind=wx.ITEM_NORMAL,text='Add chiral restraint',
1360	help='Add chiral restraint for selected atoms (4: center atom 1st)')
1361	self.DrawAtomRigidBody.Append(id=wxID_DRAWDEFINERB, kind=wx.ITEM_NORMAL,text='Define rigid body',
1362	help='Define rigid body with selected atoms')
1363	self.PostfillDataMenu()
1364
1365	# Phase / MCSA tab
1366	self.MCSAMenu = wx.MenuBar()
1367	self.PrefillDataMenu(self.MCSAMenu,helpType='MC/SA')
1368	self.MCSAMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1369	self.MCSAEdit = wx.Menu(title='')
1370	self.MCSAMenu.Append(menu=self.MCSAEdit, title='MC/SA')
1371	self.MCSAEdit.Append(id=wxID_ADDMCSAATOM, kind=wx.ITEM_NORMAL,text='Add atom',
1372	help='Add single atom to MC/SA model')
1373	self.MCSAEdit.Append(id=wxID_ADDMCSARB, kind=wx.ITEM_NORMAL,text='Add rigid body',
1374	help='Add rigid body to MC/SA model' )
1375	self.MCSAEdit.Append(id=wxID_CLEARMCSARB, kind=wx.ITEM_NORMAL,text='Clear rigid bodies',
1376	help='Clear all atoms & rigid bodies from MC/SA model' )
1377	self.MCSAEdit.Append(id=wxID_MOVEMCSA, kind=wx.ITEM_NORMAL,text='Move MC/SA solution',
1378	help='Move MC/SA solution to atom list' )
1379	self.MCSAEdit.Append(id=wxID_MCSACLEARRESULTS, kind=wx.ITEM_NORMAL,text='Clear results',
1380	help='Clear table of MC/SA results' )
1381	self.PostfillDataMenu()
1382
1383	# Phase / Texture tab
1384	self.TextureMenu = wx.MenuBar()
1385	self.PrefillDataMenu(self.TextureMenu,helpType='Texture')
1386	self.TextureMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1387	self.TextureEdit = wx.Menu(title='')
1388	self.TextureMenu.Append(menu=self.TextureEdit, title='Texture')
1389	self.TextureEdit.Append(id=wxID_REFINETEXTURE, kind=wx.ITEM_NORMAL,text='Refine texture',
1390	help='Refine the texture coefficients from sequential results')
1391	# self.TextureEdit.Append(id=wxID_CLEARTEXTURE, kind=wx.ITEM_NORMAL,text='Clear texture',
1392	# help='Clear the texture coefficients' )
1393	self.PostfillDataMenu()
1394
1395	# Phase / Pawley tab
1396	self.PawleyMenu = wx.MenuBar()
1397	self.PrefillDataMenu(self.PawleyMenu,helpType='Pawley')
1398	self.PawleyMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1399	self.PawleyEdit = wx.Menu(title='')
1400	self.PawleyMenu.Append(menu=self.PawleyEdit,title='Operations')
1401	self.PawleyEdit.Append(id=wxID_PAWLEYLOAD, kind=wx.ITEM_NORMAL,text='Pawley create',
1402	help='Initialize Pawley reflection list')
1403	self.PawleyEdit.Append(id=wxID_PAWLEYESTIMATE, kind=wx.ITEM_NORMAL,text='Pawley estimate',
1404	help='Estimate initial Pawley intensities')
1405	self.PawleyEdit.Append(id=wxID_PAWLEYUPDATE, kind=wx.ITEM_NORMAL,text='Pawley update',
1406	help='Update negative Pawley intensities with -0.5*Fobs and turn off refinemnt')
1407	self.PostfillDataMenu()
1408
1409	# Phase / Map peaks tab
1410	self.MapPeaksMenu = wx.MenuBar()
1411	self.PrefillDataMenu(self.MapPeaksMenu,helpType='Map peaks')
1412	self.MapPeaksMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1413	self.MapPeaksEdit = wx.Menu(title='')
1414	self.MapPeaksMenu.Append(menu=self.MapPeaksEdit, title='Map peaks')
1415	self.MapPeaksEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
1416	help='Move selected peaks to atom list')
1417	self.MapPeaksEdit.Append(id=wxID_PEAKSVIEWPT, kind=wx.ITEM_NORMAL,text='View point',
1418	help='View point is 1st peak selected')
1419	self.MapPeaksEdit.Append(id=wxID_PEAKSDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1420	help='Compute distance of selected peaks from view point')
1421	self.MapPeaksEdit.Append(id=wxID_SHOWBONDS, kind=wx.ITEM_NORMAL,text='Hide bonds',
1422	help='Hide or show bonds between peak positions')
1423	self.MapPeaksEdit.Append(id=wxID_PEAKSDA, kind=wx.ITEM_NORMAL,text='Calc dist/ang',
1424	help='Calculate distance or angle for selection')
1425	self.MapPeaksEdit.Append(id=wxID_FINDEQVPEAKS, kind=wx.ITEM_NORMAL,text='Equivalent peaks',
1426	help='Find equivalent peaks')
1427	self.MapPeaksEdit.Append(id=wxID_PEAKSUNIQUE, kind=wx.ITEM_NORMAL,text='Unique peaks',
1428	help='Select unique set')
1429	self.MapPeaksEdit.Append(id=wxID_PEAKSDELETE, kind=wx.ITEM_NORMAL,text='Delete peaks',
1430	help='Delete selected peaks')
1431	self.MapPeaksEdit.Append(id=wxID_PEAKSCLEAR, kind=wx.ITEM_NORMAL,text='Clear peaks',
1432	help='Clear the map peak list')
1433	self.PostfillDataMenu()
1434
1435	# Phase / Rigid bodies tab
1436	self.RigidBodiesMenu = wx.MenuBar()
1437	self.PrefillDataMenu(self.RigidBodiesMenu,helpType='Rigid bodies')
1438	self.RigidBodiesMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1439	self.RigidBodiesEdit = wx.Menu(title='')
1440	self.RigidBodiesMenu.Append(menu=self.RigidBodiesEdit, title='Edit')
1441	self.RigidBodiesEdit.Append(id=wxID_ASSIGNATMS2RB, kind=wx.ITEM_NORMAL,text='Assign atoms to rigid body',
1442	help='Select & position rigid body in structure of existing atoms')
1443	self.RigidBodiesEdit.Append(id=wxID_AUTOFINDRESRB, kind=wx.ITEM_NORMAL,text='Auto find residues',
1444	help='Auto find of residue RBs in macromolecule')
1445	self.RigidBodiesEdit.Append(id=wxID_COPYRBPARMS, kind=wx.ITEM_NORMAL,text='Copy rigid body parms',
1446	help='Copy rigid body location & TLS parameters')
1447	self.RigidBodiesEdit.Append(id=wxID_GLOBALTHERM, kind=wx.ITEM_NORMAL,text='Global thermal motion',
1448	help='Global setting of residue thermal motion models')
1449	self.RigidBodiesEdit.Append(id=wxID_GLOBALRESREFINE, kind=wx.ITEM_NORMAL,text='Global residue refine',
1450	help='Global setting of residue RB refinement flags')
1451	self.RigidBodiesEdit.Append(id=wxID_RBREMOVEALL, kind=wx.ITEM_NORMAL,text='Remove all rigid bodies',
1452	help='Remove all rigid body assignment for atoms')
1453	self.PostfillDataMenu()
1454	# end of GSAS-II menu definitions
1455
1456	def _init_ctrls(self, parent,name=None,size=None,pos=None):
1457	wx.Frame.__init__(
1458	self,parent=parent,
1459	#style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX \| wx.FRAME_FLOAT_ON_PARENT ,
1460	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX,
1461	size=size,pos=pos,title='GSAS-II data display')
1462	self._init_menus()
1463	if name:
1464	self.SetLabel(name)
1465	self.Show()
1466
1467	def __init__(self,parent,frame,data=None,name=None, size=None,pos=None):
1468	self.G2frame = frame
1469	self._init_ctrls(parent,name,size,pos)
1470	self.data = data
1471	clientSize = wx.ClientDisplayRect()
1472	Size = self.GetSize()
1473	xPos = clientSize[2]-Size[0]
1474	self.SetPosition(wx.Point(xPos,clientSize[1]+250))
1475	self.AtomGrid = []
1476	self.selectedRow = 0
1477
1478	def setSizePosLeft(self,Width):
1479	clientSize = wx.ClientDisplayRect()
1480	Width[1] = min(Width[1],clientSize[2]-300)
1481	Width[0] = max(Width[0],300)
1482	self.SetSize(Width)
1483	# self.SetPosition(wx.Point(clientSize[2]-Width[0],clientSize[1]+250))
1484
1485	def Clear(self):
1486	self.ClearBackground()
1487	self.DestroyChildren()
1488
1489
1490	################################################################################
1491	##### Notebook Tree Item editor
1492	################################################################################
1493	def UpdateNotebook(G2frame,data):
1494	'''Called when the data tree notebook entry is selected. Allows for
1495	editing of the text in that tree entry
1496	'''
1497	def OnNoteBook(event):
1498	data = G2frame.dataDisplay.GetValue().split('\n')
1499	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Notebook'),data)
1500	if 'nt' not in os.name:
1501	G2frame.dataDisplay.AppendText('\n')
1502
1503	if G2frame.dataDisplay:
1504	G2frame.dataDisplay.Destroy()
1505	G2frame.dataFrame.SetLabel('Notebook')
1506	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1507	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER \| wx.TE_DONTWRAP)
1508	G2frame.dataDisplay.Bind(wx.EVT_TEXT_ENTER,OnNoteBook)
1509	G2frame.dataDisplay.Bind(wx.EVT_KILL_FOCUS,OnNoteBook)
1510	for line in data:
1511	G2frame.dataDisplay.AppendText(line+"\n")
1512	G2frame.dataDisplay.AppendText('Notebook entry @ '+time.ctime()+"\n")
1513	G2frame.dataFrame.setSizePosLeft([400,250])
1514
1515	################################################################################
1516	##### Controls Tree Item editor
1517	################################################################################
1518	def UpdateControls(G2frame,data):
1519	'''Edit overall GSAS-II controls in main Controls data tree entry
1520	'''
1521	#patch
1522	if 'deriv type' not in data:
1523	data = {}
1524	data['deriv type'] = 'analytic Hessian'
1525	data['min dM/M'] = 0.0001
1526	data['shift factor'] = 1.
1527	data['max cyc'] = 3
1528	data['F**2'] = False
1529	if 'shift factor' not in data:
1530	data['shift factor'] = 1.
1531	if 'max cyc' not in data:
1532	data['max cyc'] = 3
1533	if 'F**2' not in data:
1534	data['F**2'] = False
1535	if 'Author' not in data:
1536	data['Author'] = 'no name'
1537	if 'FreePrm1' not in data:
1538	data['FreePrm1'] = 'Sample humidity (%)'
1539	if 'FreePrm2' not in data:
1540	data['FreePrm2'] = 'Sample voltage (V)'
1541	if 'FreePrm3' not in data:
1542	data['FreePrm3'] = 'Applied load (MN)'
1543	if 'Copy2Next' not in data:
1544	data['Copy2Next'] = False
1545	if 'Reverse Seq' not in data:
1546	data['Reverse Seq'] = False
1547	if 'UsrReject' not in data:
1548	data['UsrReject'] = {'minF/sig':0,'MinExt':0.01,'MaxDF/F':20.,'MaxD':500.,'MinD':0.05}
1549	if 'HatomFix' not in data:
1550	data['HatomFix'] = False
1551
1552	#end patch
1553
1554	def SeqSizer():
1555
1556	def OnSelectData(event):
1557	choices = GetPatternTreeDataNames(G2frame,['PWDR','HKLF',])
1558	sel = []
1559	try:
1560	if 'Seq Data' in data:
1561	for item in data['Seq Data']:
1562	sel.append(choices.index(item))
1563	sel = [choices.index(item) for item in data['Seq Data']]
1564	except ValueError: #data changed somehow - start fresh
1565	sel = []
1566	dlg = G2G.G2MultiChoiceDialog(G2frame.dataFrame, 'Sequential refinement',
1567	'Select dataset to include',choices)
1568	dlg.SetSelections(sel)
1569	names = []
1570	if dlg.ShowModal() == wx.ID_OK:
1571	for sel in dlg.GetSelections():
1572	names.append(choices[sel])
1573	data['Seq Data'] = names
1574	G2frame.EnableSeqRefineMenu()
1575	dlg.Destroy()
1576	wx.CallAfter(UpdateControls,G2frame,data)
1577
1578	def OnReverse(event):
1579	data['Reverse Seq'] = reverseSel.GetValue()
1580
1581	def OnCopySel(event):
1582	data['Copy2Next'] = copySel.GetValue()
1583
1584	seqSizer = wx.BoxSizer(wx.VERTICAL)
1585	dataSizer = wx.BoxSizer(wx.HORIZONTAL)
1586	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Sequential Refinement: '),0,WACV)
1587	selSeqData = wx.Button(G2frame.dataDisplay,-1,label=' Select data')
1588	selSeqData.Bind(wx.EVT_BUTTON,OnSelectData)
1589	dataSizer.Add(selSeqData,0,WACV)
1590	SeqData = data.get('Seq Data',[])
1591	if not SeqData:
1592	lbl = ' (no data selected)'
1593	else:
1594	lbl = ' ('+str(len(SeqData))+' dataset(s) selected)'
1595
1596	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=lbl),0,WACV)
1597	seqSizer.Add(dataSizer,0)
1598	if SeqData:
1599	selSizer = wx.BoxSizer(wx.HORIZONTAL)
1600	reverseSel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Reverse order?')
1601	reverseSel.Bind(wx.EVT_CHECKBOX,OnReverse)
1602	reverseSel.SetValue(data['Reverse Seq'])
1603	selSizer.Add(reverseSel,0,WACV)
1604	copySel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Copy results to next histogram?')
1605	copySel.Bind(wx.EVT_CHECKBOX,OnCopySel)
1606	copySel.SetValue(data['Copy2Next'])
1607	selSizer.Add(copySel,0,WACV)
1608	seqSizer.Add(selSizer,0)
1609	return seqSizer
1610
1611	def LSSizer():
1612
1613	def OnDerivType(event):
1614	data['deriv type'] = derivSel.GetValue()
1615	derivSel.SetValue(data['deriv type'])
1616	wx.CallAfter(UpdateControls,G2frame,data)
1617
1618	def OnConvergence(event):
1619	try:
1620	value = max(1.e-9,min(1.0,float(Cnvrg.GetValue())))
1621	except ValueError:
1622	value = 0.0001
1623	data['min dM/M'] = value
1624	Cnvrg.SetValue('%.2g'%(value))
1625
1626	def OnMaxCycles(event):
1627	data['max cyc'] = int(maxCyc.GetValue())
1628	maxCyc.SetValue(str(data['max cyc']))
1629
1630	def OnFactor(event):
1631	try:
1632	value = min(max(float(Factr.GetValue()),0.00001),100.)
1633	except ValueError:
1634	value = 1.0
1635	data['shift factor'] = value
1636	Factr.SetValue('%.5f'%(value))
1637
1638	def OnFsqRef(event):
1639	data['F**2'] = fsqRef.GetValue()
1640
1641	def OnHatomFix(event):
1642	data['HatomFix'] = Hfix.GetValue()
1643
1644	def OnUsrRej(event):
1645	Obj = event.GetEventObject()
1646	item,limits = Indx[Obj]
1647	try:
1648	value = min(max(float(Obj.GetValue()),limits[0]),limits[1])
1649	except ValueError:
1650	value = data['UsrReject'][item]
1651	data['UsrReject'][item] = value
1652	Obj.SetValue('%.2f'%(value))
1653
1654	LSSizer = wx.FlexGridSizer(cols=4,vgap=5,hgap=5)
1655	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement derivatives: '),0,WACV)
1656	Choice=['analytic Jacobian','numeric','analytic Hessian']
1657	derivSel = wx.ComboBox(parent=G2frame.dataDisplay,value=data['deriv type'],choices=Choice,
1658	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1659	derivSel.SetValue(data['deriv type'])
1660	derivSel.Bind(wx.EVT_COMBOBOX, OnDerivType)
1661
1662	LSSizer.Add(derivSel,0,WACV)
1663	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Min delta-M/M: '),0,WACV)
1664	Cnvrg = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2g'%(data['min dM/M']),style=wx.TE_PROCESS_ENTER)
1665	Cnvrg.Bind(wx.EVT_TEXT_ENTER,OnConvergence)
1666	Cnvrg.Bind(wx.EVT_KILL_FOCUS,OnConvergence)
1667	LSSizer.Add(Cnvrg,0,WACV)
1668	Indx = {}
1669	if 'Hessian' in data['deriv type']:
1670	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Max cycles: '),0,WACV)
1671	Choice = ['0','1','2','3','5','10','15','20']
1672	maxCyc = wx.ComboBox(parent=G2frame.dataDisplay,value=str(data['max cyc']),choices=Choice,
1673	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1674	maxCyc.SetValue(str(data['max cyc']))
1675	maxCyc.Bind(wx.EVT_COMBOBOX, OnMaxCycles)
1676	LSSizer.Add(maxCyc,0,WACV)
1677	else:
1678	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Initial shift factor: '),0,WACV)
1679	Factr = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.5f'%(data['shift factor']),style=wx.TE_PROCESS_ENTER)
1680	Factr.Bind(wx.EVT_TEXT_ENTER,OnFactor)
1681	Factr.Bind(wx.EVT_KILL_FOCUS,OnFactor)
1682	LSSizer.Add(Factr,0,WACV)
1683	if G2frame.Sngl:
1684	userReject = data['UsrReject']
1685	usrRej = {'minF/sig':[' Min obs/sig (0-5): ',[0,5], ],'MinExt':[' Min extinct. (0-.9): ',[0,.9],],
1686	'MaxDF/F':[' Max delt-F/sig (3-1000): ',[3.,1000.],],'MaxD':[' Max d-spacing (3-500): ',[3,500],],
1687	'MinD':[' Min d-spacing (0.1-1.0): ',[0.1,1.0],]}
1688
1689	fsqRef = wx.CheckBox(G2frame.dataDisplay,-1,label='Refine HKLF as F^2? ')
1690	fsqRef.SetValue(data['F**2'])
1691	fsqRef.Bind(wx.EVT_CHECKBOX,OnFsqRef)
1692	LSSizer.Add(fsqRef,0,WACV)
1693	LSSizer.Add((1,0),)
1694	for item in usrRej:
1695	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,label=usrRej[item][0]),0,WACV)
1696	usrrej = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2f'%(userReject[item]),style=wx.TE_PROCESS_ENTER)
1697	Indx[usrrej] = [item,usrRej[item][1]]
1698	usrrej.Bind(wx.EVT_TEXT_ENTER,OnUsrRej)
1699	usrrej.Bind(wx.EVT_KILL_FOCUS,OnUsrRej)
1700	LSSizer.Add(usrrej,0,WACV)
1701	# Hfix = wx.CheckBox(G2frame.dataDisplay,-1,label='Regularize H atoms? ')
1702	# Hfix.SetValue(data['HatomFix'])
1703	# Hfix.Bind(wx.EVT_CHECKBOX,OnHatomFix)
1704	# LSSizer.Add(Hfix,0,WACV) #for now
1705	return LSSizer
1706
1707	def AuthSizer():
1708
1709	def OnAuthor(event):
1710	data['Author'] = auth.GetValue()
1711
1712	Author = data['Author']
1713	authSizer = wx.BoxSizer(wx.HORIZONTAL)
1714	authSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' CIF Author (last, first):'),0,WACV)
1715	auth = wx.TextCtrl(G2frame.dataDisplay,-1,value=Author,style=wx.TE_PROCESS_ENTER)
1716	auth.Bind(wx.EVT_TEXT_ENTER,OnAuthor)
1717	auth.Bind(wx.EVT_KILL_FOCUS,OnAuthor)
1718	authSizer.Add(auth,0,WACV)
1719	return authSizer
1720
1721
1722	if G2frame.dataDisplay:
1723	G2frame.dataDisplay.Destroy()
1724	if not G2frame.dataFrame.GetStatusBar():
1725	Status = G2frame.dataFrame.CreateStatusBar()
1726	Status.SetStatusText('')
1727	G2frame.dataFrame.SetLabel('Controls')
1728	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
1729	SetDataMenuBar(G2frame,G2frame.dataFrame.ControlsMenu)
1730	mainSizer = wx.BoxSizer(wx.VERTICAL)
1731	mainSizer.Add((5,5),0)
1732	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement Controls:'),0,WACV)
1733	mainSizer.Add(LSSizer())
1734	mainSizer.Add((5,5),0)
1735	mainSizer.Add(SeqSizer())
1736	mainSizer.Add((5,5),0)
1737	mainSizer.Add(AuthSizer())
1738	mainSizer.Add((5,5),0)
1739
1740	mainSizer.Layout()
1741	G2frame.dataDisplay.SetSizer(mainSizer)
1742	G2frame.dataDisplay.SetSize(mainSizer.Fit(G2frame.dataFrame))
1743	G2frame.dataFrame.setSizePosLeft(mainSizer.Fit(G2frame.dataFrame))
1744
1745	################################################################################
1746	##### Comments
1747	################################################################################
1748
1749	def UpdateComments(G2frame,data):
1750
1751	if G2frame.dataDisplay:
1752	G2frame.dataDisplay.Destroy()
1753	G2frame.dataFrame.SetLabel('Comments')
1754	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1755	style=wx.TE_MULTILINE\|wx.TE_READONLY\|wx.TE_DONTWRAP)
1756	for line in data:
1757	G2frame.dataDisplay.AppendText(line+'\n')
1758	G2frame.dataFrame.setSizePosLeft([400,250])
1759
1760	################################################################################
1761	##### Display of Sequential Results
1762	################################################################################
1763
1764	def UpdateSeqResults(G2frame,data,prevSize=None):
1765	"""
1766	Called when the Sequential Results data tree entry is selected
1767	to show results from a sequential refinement.
1768
1769	:param wx.Frame G2frame: main GSAS-II data tree windows
1770
1771	:param dict data: a dictionary containing the following items:
1772
1773	* 'histNames' - list of histogram names in order as processed by Sequential Refinement
1774	* 'varyList' - list of variables - identical over all refinements in sequence
1775	note that this is the original list of variables, prior to processing
1776	constraints.
1777	* 'variableLabels' -- a dict of labels to be applied to each parameter
1778	(this is created as an empty dict if not present in data).
1779	* keyed by histName - dictionaries for all data sets processed, which contains:
1780
1781	* 'variables'- result[0] from leastsq call
1782	* 'varyList' - list of variables passed to leastsq call (not same as above)
1783	* 'sig' - esds for variables
1784	* 'covMatrix' - covariance matrix from individual refinement
1785	* 'title' - histogram name; same as dict item name
1786	* 'newAtomDict' - new atom parameters after shifts applied
1787	* 'newCellDict' - refined cell parameters after shifts to A0-A5 from Dij terms applied'
1788	"""
1789
1790	def GetSampleParms():
1791	'''Make a dictionary of the sample parameters are not the same over the
1792	refinement series.
1793	'''
1794	if 'IMG' in histNames[0]:
1795	sampleParmDict = {'Sample load':[],}
1796	else:
1797	sampleParmDict = {'Temperature':[],'Pressure':[],'Time':[],
1798	'FreePrm1':[],'FreePrm2':[],'FreePrm3':[],'Omega':[],
1799	'Chi':[],'Phi':[],'Azimuth':[],}
1800	Controls = G2frame.PatternTree.GetItemPyData(
1801	GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
1802	sampleParm = {}
1803	for name in histNames:
1804	if 'IMG' in name:
1805	for item in sampleParmDict:
1806	sampleParmDict[item].append(data[name]['parmDict'].get(item,0))
1807	else:
1808	Id = GetPatternTreeItemId(G2frame,G2frame.root,name)
1809	sampleData = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,Id,'Sample Parameters'))
1810	for item in sampleParmDict:
1811	sampleParmDict[item].append(sampleData.get(item,0))
1812	for item in sampleParmDict:
1813	frstValue = sampleParmDict[item][0]
1814	if np.any(np.array(sampleParmDict[item])-frstValue):
1815	if item.startswith('FreePrm'):
1816	sampleParm[Controls[item]] = sampleParmDict[item]
1817	else:
1818	sampleParm[item] = sampleParmDict[item]
1819	return sampleParm
1820
1821	def GetColumnInfo(col):
1822	'''returns column label, lists of values and errors (or None) for each column in the table
1823	for plotting. The column label is reformatted from Unicode to MatPlotLib encoding
1824	'''
1825	colName = G2frame.SeqTable.GetColLabelValue(col)
1826	plotName = variableLabels.get(colName,colName)
1827	plotName = plotSpCharFix(plotName)
1828	return plotName,colList[col],colSigs[col]
1829
1830	def PlotSelect(event):
1831	'Plots a row (covariance) or column on double-click'
1832	cols = G2frame.dataDisplay.GetSelectedCols()
1833	rows = G2frame.dataDisplay.GetSelectedRows()
1834	if cols:
1835	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1836	elif rows:
1837	name = histNames[rows[0]] #only does 1st one selected
1838	G2plt.PlotCovariance(G2frame,data[name])
1839	else:
1840	G2frame.ErrorDialog(
1841	'Select row or columns',
1842	'Nothing selected in table. Click on column or row label(s) to plot. N.B. Grid selection can be a bit funky.'
1843	)
1844
1845	def OnPlotSelSeq(event):
1846	'plot the selected columns or row from menu command'
1847	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1848	rows = G2frame.dataDisplay.GetSelectedRows()
1849	if cols:
1850	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1851	elif rows:
1852	name = histNames[rows[0]] #only does 1st one selected
1853	G2plt.PlotCovariance(G2frame,data[name])
1854	else:
1855	G2frame.ErrorDialog(
1856	'Select columns',
1857	'No columns or rows selected in table. Click on row or column labels to select fields for plotting.'
1858	)
1859
1860	def OnAveSelSeq(event):
1861	'average the selected columns from menu command'
1862	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1863	if cols:
1864	for col in cols:
1865	ave = np.mean(GetColumnInfo(col)[1])
1866	sig = np.std(GetColumnInfo(col)[1])
1867	print ' Average for '+G2frame.SeqTable.GetColLabelValue(col)+': '+'%.6g'%(ave)+' +/- '+'%.6g'%(sig)
1868	else:
1869	G2frame.ErrorDialog(
1870	'Select columns',
1871	'No columns selected in table. Click on column labels to select fields for averaging.'
1872	)
1873
1874	def OnRenameSelSeq(event):
1875	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1876	colNames = [G2frame.SeqTable.GetColLabelValue(c) for c in cols]
1877	newNames = colNames[:]
1878	for i,name in enumerate(colNames):
1879	if name in variableLabels:
1880	newNames[i] = variableLabels[name]
1881	if not cols:
1882	G2frame.ErrorDialog('Select columns',
1883	'No columns selected in table. Click on column labels to select fields for rename.')
1884	return
1885	dlg = G2G.MultiStringDialog(G2frame.dataDisplay,'Set column names',colNames,newNames)
1886	if dlg.Show():
1887	newNames = dlg.GetValues()
1888	variableLabels.update(dict(zip(colNames,newNames)))
1889	data['variableLabels'] = variableLabels
1890	dlg.Destroy()
1891	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1892	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1893
1894	def OnReOrgSelSeq(event):
1895	'Reorder the columns'
1896	G2G.GetItemOrder(G2frame,VaryListChanges,vallookup,posdict)
1897	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1898
1899	def OnSaveSelSeqCSV(event):
1900	'export the selected columns to a .csv file from menu command'
1901	OnSaveSelSeq(event,csv=True)
1902
1903	def OnSaveSeqCSV(event):
1904	'export all columns to a .csv file from menu command'
1905	OnSaveSelSeq(event,csv=True,allcols=True)
1906
1907	def OnSaveSelSeq(event,csv=False,allcols=False):
1908	'export the selected columns to a .txt or .csv file from menu command'
1909	def WriteCSV():
1910	def WriteList(headerItems):
1911	line = ''
1912	for lbl in headerItems:
1913	if line: line += ','
1914	line += '"'+lbl+'"'
1915	return line
1916	head = ['name']
1917	for col in cols:
1918	item = G2frame.SeqTable.GetColLabelValue(col)
1919	# get rid of labels that have Unicode characters
1920	if not all([ord(c) < 128 and ord(c) != 0 for c in item]): item = '?'
1921	if col in havesig:
1922	head += [item,'esd-'+item]
1923	else:
1924	head += [item]
1925	SeqFile.write(WriteList(head)+'\n')
1926	for row,name in enumerate(saveNames):
1927	line = '"'+saveNames[row]+'"'
1928	for col in cols:
1929	if col in havesig:
1930	line += ','+str(saveData[col][row])+','+str(saveSigs[col][row])
1931	else:
1932	line += ','+str(saveData[col][row])
1933	SeqFile.write(line+'\n')
1934	def WriteSeq():
1935	lenName = len(saveNames[0])
1936	line = ' %s '%('name'.center(lenName))
1937	for col in cols:
1938	item = G2frame.SeqTable.GetColLabelValue(col)
1939	if col in havesig:
1940	line += ' %12s %12s '%(item.center(12),'esd'.center(12))
1941	else:
1942	line += ' %12s '%(item.center(12))
1943	SeqFile.write(line+'\n')
1944	for row,name in enumerate(saveNames):
1945	line = " '%s' "%(saveNames[row])
1946	for col in cols:
1947	if col in havesig:
1948	line += ' %12.6f %12.6f '%(saveData[col][row],saveSigs[col][row])
1949	else:
1950	line += ' %12.6f '%saveData[col][row]
1951	SeqFile.write(line+'\n')
1952
1953	# start of OnSaveSelSeq code
1954	if allcols:
1955	cols = range(G2frame.SeqTable.GetNumberCols())
1956	else:
1957	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1958	nrows = G2frame.SeqTable.GetNumberRows()
1959	if not cols:
1960	G2frame.ErrorDialog('Select columns',
1961	'No columns selected in table. Click on column labels to select fields for output.')
1962	return
1963	saveNames = [G2frame.SeqTable.GetRowLabelValue(r) for r in range(nrows)]
1964	saveData = {}
1965	saveSigs = {}
1966	havesig = []
1967	for col in cols:
1968	name,vals,sigs = GetColumnInfo(col)
1969	saveData[col] = vals
1970	if sigs:
1971	havesig.append(col)
1972	saveSigs[col] = sigs
1973	if csv:
1974	wild = 'CSV output file (.csv)\|.csv'
1975	else:
1976	wild = 'Text output file (.txt)\|.txt'
1977	dlg = wx.FileDialog(
1978	G2frame,
1979	'Choose text output file for your selection', '.', '',
1980	wild,wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1981	try:
1982	if dlg.ShowModal() == wx.ID_OK:
1983	SeqTextFile = dlg.GetPath()
1984	SeqTextFile = G2IO.FileDlgFixExt(dlg,SeqTextFile)
1985	SeqFile = open(SeqTextFile,'w')
1986	if csv:
1987	WriteCSV()
1988	else:
1989	WriteSeq()
1990	SeqFile.close()
1991	finally:
1992	dlg.Destroy()
1993
1994	def striphist(var,insChar=''):
1995	'strip a histogram number from a var name'
1996	sv = var.split(':')
1997	if len(sv) <= 1: return var
1998	if sv[1]:
1999	sv[1] = insChar
2000	return ':'.join(sv)
2001
2002	def plotSpCharFix(lbl):
2003	'Change selected unicode characters to their matplotlib equivalent'
2004	for u,p in [
2005	(u'\u03B1',r'$\alpha$'),
2006	(u'\u03B2',r'$\beta$'),
2007	(u'\u03B3',r'$\gamma$'),
2008	(u'\u0394\u03C7',r'$\Delta\chi$'),
2009	]:
2010	lbl = lbl.replace(u,p)
2011	return lbl
2012
2013	def SelectXaxis():
2014	'returns a selected column number (or None) as the X-axis selection'
2015	ncols = G2frame.SeqTable.GetNumberCols()
2016	colNames = [G2frame.SeqTable.GetColLabelValue(r) for r in range(ncols)]
2017	dlg = G2G.G2SingleChoiceDialog(
2018	G2frame.dataDisplay,
2019	'Select x-axis parameter for plot or Cancel for sequence number',
2020	'Select X-axis',
2021	colNames)
2022	try:
2023	if dlg.ShowModal() == wx.ID_OK:
2024	col = dlg.GetSelection()
2025	else:
2026	col = None
2027	finally:
2028	dlg.Destroy()
2029	return col
2030
2031	def EnablePseudoVarMenus():
2032	'Enables or disables the PseudoVar menu items that require existing defs'
2033	if Controls['SeqPseudoVars']:
2034	val = True
2035	else:
2036	val = False
2037	G2frame.dataFrame.SequentialPvars.Enable(wxDELSEQVAR,val)
2038	G2frame.dataFrame.SequentialPvars.Enable(wxEDITSEQVAR,val)
2039
2040	def DelPseudoVar(event):
2041	'Ask the user to select a pseudo var expression to delete'
2042	choices = Controls['SeqPseudoVars'].keys()
2043	selected = G2G.ItemSelector(
2044	choices,G2frame.dataFrame,
2045	multiple=True,
2046	title='Select expressions to remove',
2047	header='Delete expression')
2048	if selected is None: return
2049	for item in selected:
2050	del Controls['SeqPseudoVars'][choices[item]]
2051	if selected:
2052	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2053
2054	def EditPseudoVar(event):
2055	'Edit an existing pseudo var expression'
2056	choices = Controls['SeqPseudoVars'].keys()
2057	if len(choices) == 1:
2058	selected = 0
2059	else:
2060	selected = G2G.ItemSelector(
2061	choices,G2frame.dataFrame,
2062	multiple=False,
2063	title='Select an expression to edit',
2064	header='Edit expression')
2065	if selected is not None:
2066	dlg = G2exG.ExpressionDialog(
2067	G2frame.dataDisplay,PSvarDict,
2068	Controls['SeqPseudoVars'][choices[selected]],
2069	header="Edit the PseudoVar expression",
2070	VarLabel="PseudoVar #"+str(selected+1),
2071	fit=False)
2072	newobj = dlg.Show(True)
2073	if newobj:
2074	calcobj = G2obj.ExpressionCalcObj(newobj)
2075	del Controls['SeqPseudoVars'][choices[selected]]
2076	Controls['SeqPseudoVars'][calcobj.eObj.expression] = newobj
2077	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2078
2079	def AddNewPseudoVar(event):
2080	'Create a new pseudo var expression'
2081	dlg = G2exG.ExpressionDialog(
2082	G2frame.dataDisplay,PSvarDict,
2083	header='Enter an expression for a PseudoVar here',
2084	VarLabel = "New PseudoVar",
2085	fit=False)
2086	obj = dlg.Show(True)
2087	dlg.Destroy()
2088	if obj:
2089	calcobj = G2obj.ExpressionCalcObj(obj)
2090	Controls['SeqPseudoVars'][calcobj.eObj.expression] = obj
2091	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2092
2093	def UpdateParmDict(parmDict):
2094	'''generate the atom positions and the direct & reciprocal cell values,
2095	because they might be needed to evaluate the pseudovar
2096	'''
2097	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2098	['A'+str(i) for i in range(6)])
2099	)
2100	delList = []
2101	phaselist = []
2102	for item in parmDict:
2103	if ':' not in item: continue
2104	key = item.split(':')
2105	if len(key) < 3: continue
2106	# remove the dA[xyz] terms, they would only bring confusion
2107	if key[2].startswith('dA'):
2108	delList.append(item)
2109	# compute and update the corrected reciprocal cell terms using the Dij values
2110	elif key[2] in Ddict:
2111	if key[0] not in phaselist: phaselist.append(key[0])
2112	akey = key[0]+'::'+Ddict[key[2]]
2113	parmDict[akey] -= parmDict[item]
2114	delList.append(item)
2115	for item in delList:
2116	del parmDict[item]
2117	for i in phaselist:
2118	pId = int(i)
2119	# apply cell symmetry
2120	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],parmDict,zeroDict[pId])
2121	# convert to direct cell & add the unique terms to the dictionary
2122	for i,val in enumerate(G2lat.A2cell(A)):
2123	if i in uniqCellIndx[pId]:
2124	lbl = str(pId)+'::'+cellUlbl[i]
2125	parmDict[lbl] = val
2126	lbl = str(pId)+'::'+'vol'
2127	parmDict[lbl] = G2lat.calc_V(A)
2128	return parmDict
2129
2130	def EvalPSvarDeriv(calcobj,parmDict,sampleDict,var,ESD):
2131	'''Evaluate an expression derivative with respect to a
2132	GSAS-II variable name.
2133
2134	Note this likely could be faster if the loop over calcobjs were done
2135	inside after the Dict was created.
2136	'''
2137	step = ESD/10
2138	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2139	['A'+str(i) for i in range(6)])
2140	)
2141	results = []
2142	phaselist = []
2143	VparmDict = sampleDict.copy()
2144	for incr in step,-step:
2145	VparmDict.update(parmDict.copy())
2146	# as saved, the parmDict has updated 'A[xyz]' values, but 'dA[xyz]'
2147	# values are not zeroed: fix that!
2148	VparmDict.update({item:0.0 for item in parmDict if 'dA' in item})
2149	VparmDict[var] += incr
2150	G2mv.Dict2Map(VparmDict,[]) # apply constraints
2151	# generate the atom positions and the direct & reciprocal cell values now, because they might
2152	# needed to evaluate the pseudovar
2153	for item in VparmDict:
2154	if item in sampleDict:
2155	continue
2156	if ':' not in item: continue
2157	key = item.split(':')
2158	if len(key) < 3: continue
2159	# apply any new shifts to atom positions
2160	if key[2].startswith('dA'):
2161	VparmDict[''.join(item.split('d'))] += VparmDict[item]
2162	VparmDict[item] = 0.0
2163	# compute and update the corrected reciprocal cell terms using the Dij values
2164	if key[2] in Ddict:
2165	if key[0] not in phaselist: phaselist.append(key[0])
2166	akey = key[0]+'::'+Ddict[key[2]]
2167	VparmDict[akey] -= VparmDict[item]
2168	for i in phaselist:
2169	pId = int(i)
2170	# apply cell symmetry
2171	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],VparmDict,zeroDict[pId])
2172	# convert to direct cell & add the unique terms to the dictionary
2173	for i,val in enumerate(G2lat.A2cell(A)):
2174	if i in uniqCellIndx[pId]:
2175	lbl = str(pId)+'::'+cellUlbl[i]
2176	VparmDict[lbl] = val
2177	lbl = str(pId)+'::'+'vol'
2178	VparmDict[lbl] = G2lat.calc_V(A)
2179	# dict should be fully updated, use it & calculate
2180	calcobj.SetupCalc(VparmDict)
2181	results.append(calcobj.EvalExpression())
2182	return (results[0] - results[1]) / (2.*step)
2183
2184	def EnableParFitEqMenus():
2185	'Enables or disables the Parametric Fit menu items that require existing defs'
2186	if Controls['SeqParFitEqList']:
2187	val = True
2188	else:
2189	val = False
2190	G2frame.dataFrame.SequentialPfit.Enable(wxDELPARFIT,val)
2191	G2frame.dataFrame.SequentialPfit.Enable(wxEDITPARFIT,val)
2192	G2frame.dataFrame.SequentialPfit.Enable(wxDOPARFIT,val)
2193
2194	def ParEqEval(Values,calcObjList,varyList):
2195	'''Evaluate the parametric expression(s)
2196	:param list Values: a list of values for each variable parameter
2197	:param list calcObjList: a list of :class:`GSASIIobj.ExpressionCalcObj`
2198	expression objects to evaluate
2199	:param list varyList: a list of variable names for each value in Values
2200	'''
2201	result = []
2202	for calcobj in calcObjList:
2203	calcobj.UpdateVars(varyList,Values)
2204	result.append((calcobj.depVal-calcobj.EvalExpression())/calcobj.depSig)
2205	return result
2206
2207	def DoParEqFit(event,eqObj=None):
2208	'Parametric fit minimizer'
2209	varyValueDict = {} # dict of variables and their initial values
2210	calcObjList = [] # expression objects, ready to go for each data point
2211	if eqObj is not None:
2212	eqObjList = [eqObj,]
2213	else:
2214	eqObjList = Controls['SeqParFitEqList']
2215	UseFlags = G2frame.SeqTable.GetColValues(0)
2216	for obj in eqObjList:
2217	expr = obj.expression
2218	# assemble refined vars for this equation
2219	varyValueDict.update({var:val for var,val in obj.GetVariedVarVal()})
2220	# lookup dependent var position
2221	depVar = obj.GetDepVar()
2222	if depVar in colLabels:
2223	indx = colLabels.index(depVar)
2224	else:
2225	raise Exception('Dependent variable '+depVar+' not found')
2226	# assemble a list of the independent variables
2227	indepVars = obj.GetIndependentVars()
2228	# loop over each datapoint
2229	for j,row in enumerate(zip(*colList)):
2230	if not UseFlags[j]: continue
2231	# assemble equations to fit
2232	calcobj = G2obj.ExpressionCalcObj(obj)
2233	# prepare a dict of needed independent vars for this expression
2234	indepVarDict = {var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2235	calcobj.SetupCalc(indepVarDict)
2236	# values and sigs for current value of dependent var
2237	calcobj.depVal = row[indx]
2238	calcobj.depSig = colSigs[indx][j]
2239	calcObjList.append(calcobj)
2240	# varied parameters
2241	varyList = varyValueDict.keys()
2242	values = varyValues = [varyValueDict[key] for key in varyList]
2243	if not varyList:
2244	print 'no variables to refine!'
2245	return
2246	try:
2247	result = so.leastsq(ParEqEval,varyValues,full_output=True, #ftol=Ftol,
2248	args=(calcObjList,varyList)
2249	)
2250	values = result[0]
2251	covar = result[1]
2252	if covar is None:
2253	raise Exception
2254	esdDict = {}
2255	for i,avar in enumerate(varyList):
2256	esdDict[avar] = np.sqrt(covar[i,i])
2257	except:
2258	print('====> Fit failed')
2259	return
2260	print('==== Fit Results ====')
2261	for obj in eqObjList:
2262	obj.UpdateVariedVars(varyList,values)
2263	ind = ' '
2264	print(' '+obj.GetDepVar()+' = '+obj.expression)
2265	for var in obj.assgnVars:
2266	print(ind+var+' = '+obj.assgnVars[var])
2267	for var in obj.freeVars:
2268	avar = "::"+obj.freeVars[var][0]
2269	val = obj.freeVars[var][1]
2270	if obj.freeVars[var][2]:
2271	print(ind+var+' = '+avar + " = " + G2mth.ValEsd(val,esdDict[avar]))
2272	else:
2273	print(ind+var+' = '+avar + " =" + G2mth.ValEsd(val,0))
2274	# create a plot for each parametric variable
2275	for fitnum,obj in enumerate(eqObjList):
2276	calcobj = G2obj.ExpressionCalcObj(obj)
2277	# lookup dependent var position
2278	indx = colLabels.index(obj.GetDepVar())
2279	# assemble a list of the independent variables
2280	indepVars = obj.GetIndependentVars()
2281	# loop over each datapoint
2282	fitvals = []
2283	for j,row in enumerate(zip(*colList)):
2284	calcobj.SetupCalc(
2285	{var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2286	)
2287	fitvals.append(calcobj.EvalExpression())
2288	G2plt.PlotSelectedSequence(
2289	G2frame,[indx],GetColumnInfo,SelectXaxis,
2290	fitnum,fitvals)
2291
2292	def SingleParEqFit(eqObj):
2293	DoParEqFit(None,eqObj)
2294
2295	def DelParFitEq(event):
2296	'Ask the user to select function to delete'
2297	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2298	selected = G2G.ItemSelector(
2299	txtlst,G2frame.dataFrame,
2300	multiple=True,
2301	title='Select a parametric equation(s) to remove',
2302	header='Delete equation')
2303	if selected is None: return
2304	Controls['SeqParFitEqList'] = [obj for i,obj in enumerate(Controls['SeqParFitEqList']) if i not in selected]
2305	EnableParFitEqMenus()
2306	if Controls['SeqParFitEqList']: DoParEqFit(event)
2307
2308	def EditParFitEq(event):
2309	'Edit an existing parametric equation'
2310	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2311	if len(txtlst) == 1:
2312	selected = 0
2313	else:
2314	selected = G2G.ItemSelector(
2315	txtlst,G2frame.dataFrame,
2316	multiple=False,
2317	title='Select a parametric equation to edit',
2318	header='Edit equation')
2319	if selected is not None:
2320	dlg = G2exG.ExpressionDialog(
2321	G2frame.dataDisplay,indepVarDict,
2322	Controls['SeqParFitEqList'][selected],
2323	depVarDict=depVarDict,
2324	header="Edit the formula for this minimization function",
2325	ExtraButton=['Fit',SingleParEqFit])
2326	newobj = dlg.Show(True)
2327	if newobj:
2328	calcobj = G2obj.ExpressionCalcObj(newobj)
2329	Controls['SeqParFitEqList'][selected] = newobj
2330	EnableParFitEqMenus()
2331	if Controls['SeqParFitEqList']: DoParEqFit(event)
2332
2333	def AddNewParFitEq(event):
2334	'Create a new parametric equation to be fit to sequential results'
2335
2336	# compile the variable names used in previous freevars to avoid accidental name collisions
2337	usedvarlist = []
2338	for obj in Controls['SeqParFitEqList']:
2339	for var in obj.freeVars:
2340	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2341
2342	dlg = G2exG.ExpressionDialog(
2343	G2frame.dataDisplay,indepVarDict,
2344	depVarDict=depVarDict,
2345	header='Define an equation to minimize in the parametric fit',
2346	ExtraButton=['Fit',SingleParEqFit],
2347	usedVars=usedvarlist)
2348	obj = dlg.Show(True)
2349	dlg.Destroy()
2350	if obj:
2351	Controls['SeqParFitEqList'].append(obj)
2352	EnableParFitEqMenus()
2353	if Controls['SeqParFitEqList']: DoParEqFit(event)
2354
2355	def CopyParFitEq(event):
2356	'Copy an existing parametric equation to be fit to sequential results'
2357	# compile the variable names used in previous freevars to avoid accidental name collisions
2358	usedvarlist = []
2359	for obj in Controls['SeqParFitEqList']:
2360	for var in obj.freeVars:
2361	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2362	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2363	if len(txtlst) == 1:
2364	selected = 0
2365	else:
2366	selected = G2G.ItemSelector(
2367	txtlst,G2frame.dataFrame,
2368	multiple=False,
2369	title='Select a parametric equation to copy',
2370	header='Copy equation')
2371	if selected is not None:
2372	newEqn = copy.deepcopy(Controls['SeqParFitEqList'][selected])
2373	for var in newEqn.freeVars:
2374	newEqn.freeVars[var][0] = G2obj.MakeUniqueLabel(newEqn.freeVars[var][0],usedvarlist)
2375	dlg = G2exG.ExpressionDialog(
2376	G2frame.dataDisplay,indepVarDict,
2377	newEqn,
2378	depVarDict=depVarDict,
2379	header="Edit the formula for this minimization function",
2380	ExtraButton=['Fit',SingleParEqFit])
2381	newobj = dlg.Show(True)
2382	if newobj:
2383	calcobj = G2obj.ExpressionCalcObj(newobj)
2384	Controls['SeqParFitEqList'].append(newobj)
2385	EnableParFitEqMenus()
2386	if Controls['SeqParFitEqList']: DoParEqFit(event)
2387
2388	def GridSetToolTip(row,col):
2389	'''Routine to show standard uncertainties for each element in table
2390	as a tooltip
2391	'''
2392	if colSigs[col]:
2393	return u'\u03c3 = '+str(colSigs[col][row])
2394	return ''
2395
2396	def GridColLblToolTip(col):
2397	'''Define a tooltip for a column. This will be the user-entered value
2398	(from data['variableLabels']) or the default name
2399	'''
2400	if col < 0 or col > len(colLabels):
2401	print 'Illegal column #',col
2402	return
2403	var = colLabels[col]
2404	return variableLabels.get(var,G2obj.fmtVarDescr(var))
2405
2406	def SetLabelString(event):
2407	'''Define or edit the label for a column in the table, to be used
2408	as a tooltip and for plotting
2409	'''
2410	col = event.GetCol()
2411	if col < 0 or col > len(colLabels):
2412	return
2413	var = colLabels[col]
2414	lbl = variableLabels.get(var,G2obj.fmtVarDescr(var))
2415	dlg = G2G.SingleStringDialog(G2frame.dataFrame,'Set variable label',
2416	'Set a new name for variable '+var,lbl,size=(400,-1))
2417	if dlg.Show():
2418	variableLabels[var] = dlg.GetValue()
2419	dlg.Destroy()
2420
2421	#def GridRowLblToolTip(row): return 'Row ='+str(row)
2422
2423	# lookup table for unique cell parameters by symmetry
2424	cellGUIlist = [
2425	[['m3','m3m'],(0,)],
2426	[['3R','3mR'],(0,3)],
2427	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],(0,2)],
2428	[['mmm'],(0,1,2)],
2429	[['2/m'+'a'],(0,1,2,3)],
2430	[['2/m'+'b'],(0,1,2,4)],
2431	[['2/m'+'c'],(0,1,2,5)],
2432	[['-1'],(0,1,2,3,4,5)],
2433	]
2434	# cell labels
2435	cellUlbl = ('a','b','c',u'\u03B1',u'\u03B2',u'\u03B3') # unicode a,b,c,alpha,beta,gamma
2436
2437	#======================================================================
2438	# start processing sequential results here (UpdateSeqResults)
2439	#======================================================================
2440	if not data:
2441	print 'No sequential refinement results'
2442	return
2443	variableLabels = data.get('variableLabels',{})
2444	data['variableLabels'] = variableLabels
2445	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
2446	Controls = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Controls'))
2447	# create a place to store Pseudo Vars & Parametric Fit functions, if not present
2448	if 'SeqPseudoVars' not in Controls: Controls['SeqPseudoVars'] = {}
2449	if 'SeqParFitEqList' not in Controls: Controls['SeqParFitEqList'] = []
2450	histNames = data['histNames']
2451	if G2frame.dataDisplay:
2452	G2frame.dataDisplay.Destroy()
2453	if not G2frame.dataFrame.GetStatusBar():
2454	Status = G2frame.dataFrame.CreateStatusBar()
2455	Status.SetStatusText("Select column to export; Double click on column to plot data; on row for Covariance")
2456	sampleParms = GetSampleParms()
2457
2458	# make dict of varied atom coords keyed by absolute position
2459	newAtomDict = data[histNames[0]].get('newAtomDict',{}) # dict with atom positions; relative & absolute
2460	# Possible error: the next might need to be data[histNames[0]]['varyList']
2461	# error will arise if there constraints on coordinates?
2462	atomLookup = {newAtomDict[item][0]:item for item in newAtomDict if item in data['varyList']}
2463
2464	# make dict of varied cell parameters equivalents
2465	ESDlookup = {} # provides the Dij term for each Ak term (where terms are refined)
2466	Dlookup = {} # provides the Ak term for each Dij term (where terms are refined)
2467	# N.B. These Dij vars are missing a histogram #
2468	newCellDict = data[histNames[0]].get('newCellDict',{})
2469	for item in newCellDict:
2470	if item in data['varyList']:
2471	ESDlookup[newCellDict[item][0]] = item
2472	Dlookup[item] = newCellDict[item][0]
2473	# add coordinate equivalents to lookup table
2474	for parm in atomLookup:
2475	Dlookup[atomLookup[parm]] = parm
2476	ESDlookup[parm] = atomLookup[parm]
2477
2478	# get unit cell & symmetry for all phases & initial stuff for later use
2479	RecpCellTerms = {}
2480	SGdata = {}
2481	uniqCellIndx = {}
2482	initialCell = {}
2483	RcellLbls = {}
2484	zeroDict = {}
2485	Rcelldict = {}
2486	for phase in Phases:
2487	phasedict = Phases[phase]
2488	pId = phasedict['pId']
2489	pfx = str(pId)+'::' # prefix for A values from phase
2490	RcellLbls[pId] = [pfx+'A'+str(i) for i in range(6)]
2491	RecpCellTerms[pId] = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2492	zeroDict[pId] = dict(zip(RcellLbls[pId],6*[0.,]))
2493	SGdata[pId] = phasedict['General']['SGData']
2494	Rcelldict.update({lbl:val for lbl,val in zip(RcellLbls[pId],RecpCellTerms[pId])})
2495	laue = SGdata[pId]['SGLaue']
2496	if laue == '2/m':
2497	laue += SGdata[pId]['SGUniq']
2498	for symlist,celllist in cellGUIlist:
2499	if laue in symlist:
2500	uniqCellIndx[pId] = celllist
2501	break
2502	else: # should not happen
2503	uniqCellIndx[pId] = range(6)
2504	for i in uniqCellIndx[pId]:
2505	initialCell[str(pId)+'::A'+str(i)] = RecpCellTerms[pId][i]
2506
2507	SetDataMenuBar(G2frame,G2frame.dataFrame.SequentialMenu)
2508	G2frame.dataFrame.SetLabel('Sequential refinement results')
2509	if not G2frame.dataFrame.GetStatusBar():
2510	Status = G2frame.dataFrame.CreateStatusBar()
2511	Status.SetStatusText('')
2512	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRenameSelSeq, id=wxID_RENAMESEQSEL)
2513	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeq, id=wxID_SAVESEQSEL)
2514	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeqCSV, id=wxID_SAVESEQSELCSV)
2515	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSeqCSV, id=wxID_SAVESEQCSV)
2516	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotSelSeq, id=wxID_PLOTSEQSEL)
2517	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAveSelSeq, id=wxID_AVESEQSEL)
2518	G2frame.dataFrame.Bind(wx.EVT_MENU, OnReOrgSelSeq, id=wxID_ORGSEQSEL)
2519	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewPseudoVar, id=wxADDSEQVAR)
2520	G2frame.dataFrame.Bind(wx.EVT_MENU, DelPseudoVar, id=wxDELSEQVAR)
2521	G2frame.dataFrame.Bind(wx.EVT_MENU, EditPseudoVar, id=wxEDITSEQVAR)
2522	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewParFitEq, id=wxADDPARFIT)
2523	G2frame.dataFrame.Bind(wx.EVT_MENU, CopyParFitEq, id=wxCOPYPARFIT)
2524	G2frame.dataFrame.Bind(wx.EVT_MENU, DelParFitEq, id=wxDELPARFIT)
2525	G2frame.dataFrame.Bind(wx.EVT_MENU, EditParFitEq, id=wxEDITPARFIT)
2526	G2frame.dataFrame.Bind(wx.EVT_MENU, DoParEqFit, id=wxDOPARFIT)
2527	EnablePseudoVarMenus()
2528	EnableParFitEqMenus()
2529
2530	# scan for locations where the variables change
2531	VaryListChanges = [] # histograms where there is a change
2532	combinedVaryList = []
2533	firstValueDict = {}
2534	vallookup = {}
2535	posdict = {}
2536	prevVaryList = []
2537	for i,name in enumerate(histNames):
2538	for var,val,sig in zip(data[name]['varyList'],data[name]['variables'],data[name]['sig']):
2539	svar = striphist(var,'*') # wild-carded
2540	if svar not in combinedVaryList:
2541	# add variables to list as they appear
2542	combinedVaryList.append(svar)
2543	firstValueDict[svar] = (val,sig)
2544	if prevVaryList != data[name]['varyList']: # this refinement has a different refinement list from previous
2545	prevVaryList = data[name]['varyList']
2546	vallookup[name] = dict(zip(data[name]['varyList'],data[name]['variables']))
2547	posdict[name] = {}
2548	for var in data[name]['varyList']:
2549	svar = striphist(var,'*')
2550	posdict[name][combinedVaryList.index(svar)] = svar
2551	VaryListChanges.append(name)
2552	if len(VaryListChanges) > 1:
2553	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,True)
2554	else:
2555	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,False)
2556	#-----------------------------------------------------------------------------------
2557	# build up the data table by columns -----------------------------------------------
2558	nRows = len(histNames)
2559	colList = [nRows*[True]]
2560	colSigs = [None]
2561	colLabels = ['Use']
2562	Types = [wg.GRID_VALUE_BOOL]
2563	# start with Rwp values
2564	if 'IMG ' not in histNames[0][:4]:
2565	colList += [[data[name]['Rvals']['Rwp'] for name in histNames]]
2566	colSigs += [None]
2567	colLabels += ['Rwp']
2568	Types += [wg.GRID_VALUE_FLOAT+':10,3',]
2569	# add % change in Chi^2 in last cycle
2570	if histNames[0][:4] not in ['SASD','IMG '] and Controls.get('ShowCell'):
2571	colList += [[100.*data[name]['Rvals'].get('DelChi2',-1) for name in histNames]]
2572	colSigs += [None]
2573	colLabels += [u'\u0394\u03C7\u00B2 (%)']
2574	Types += [wg.GRID_VALUE_FLOAT,]
2575	deltaChiCol = len(colLabels)-1
2576	# add changing sample parameters to table
2577	for key in sampleParms:
2578	colList += [sampleParms[key]]
2579	colSigs += [None]
2580	colLabels += [key]
2581	Types += [wg.GRID_VALUE_FLOAT,]
2582	sampleDict = {}
2583	for i,name in enumerate(histNames):
2584	sampleDict[name] = dict(zip(sampleParms.keys(),[sampleParms[key][i] for key in sampleParms.keys()]))
2585	# add unique cell parameters TODO: review this where the cell symmetry changes (when possible)
2586	if Controls.get('ShowCell',False):
2587	for pId in sorted(RecpCellTerms):
2588	pfx = str(pId)+'::' # prefix for A values from phase
2589	cells = []
2590	cellESDs = []
2591	colLabels += [pfx+cellUlbl[i] for i in uniqCellIndx[pId]]
2592	colLabels += [pfx+'Vol']
2593	Types += (1+len(uniqCellIndx[pId]))*[wg.GRID_VALUE_FLOAT,]
2594	for name in histNames:
2595	covData = {
2596	'varyList': [Dlookup.get(striphist(v),v) for v in data[name]['varyList']],
2597	'covMatrix': data[name]['covMatrix']
2598	}
2599	A = RecpCellTerms[pId][:] # make copy of starting A values
2600	# update with refined values
2601	for i in range(6):
2602	var = str(pId)+'::A'+str(i)
2603	if var in ESDlookup:
2604	val = data[name]['newCellDict'][ESDlookup[var]][1] # get refined value
2605	A[i] = val # override with updated value
2606	# apply symmetry
2607	Albls = [pfx+'A'+str(i) for i in range(6)]
2608	cellDict = dict(zip(Albls,A))
2609	A,zeros = G2stIO.cellFill(pfx,SGdata[pId],cellDict,zeroDict[pId])
2610	# convert to direct cell & add only unique values to table
2611	c = G2lat.A2cell(A)
2612	vol = G2lat.calc_V(A)
2613	cE = G2stIO.getCellEsd(pfx,SGdata[pId],A,covData)
2614	cells += [[c[i] for i in uniqCellIndx[pId]]+[vol]]
2615	cellESDs += [[cE[i] for i in uniqCellIndx[pId]]+[cE[-1]]]
2616	colList += zip(*cells)
2617	colSigs += zip(*cellESDs)
2618	# sort out the variables in their selected order
2619	varcols = 0
2620	for d in posdict.itervalues():
2621	varcols = max(varcols,max(d.keys())+1)
2622	# get labels for each column
2623	for i in range(varcols):
2624	lbl = ''
2625	for h in VaryListChanges:
2626	if posdict[h].get(i):
2627	if posdict[h].get(i) in lbl: continue
2628	if lbl != "": lbl += '/'
2629	lbl += posdict[h].get(i)
2630	colLabels.append(lbl)
2631	Types += varcols*[wg.GRID_VALUE_FLOAT]
2632	vals = []
2633	esds = []
2634	varsellist = None # will be a list of variable names in the order they are selected to appear
2635	# tabulate values for each hist, leaving None for blank columns
2636	for name in histNames:
2637	if name in posdict:
2638	varsellist = [posdict[name].get(i) for i in range(varcols)]
2639	# translate variable names to how they will be used in the headings
2640	vs = [striphist(v,'*') for v in data[name]['varyList']]
2641	# determine the index for each column (or None) in the data[]['variables'] and ['sig'] lists
2642	sellist = [vs.index(v) if v is not None else None for v in varsellist]
2643	#sellist = [i if striphist(v,'*') in varsellist else None for i,v in enumerate(data[name]['varyList'])]
2644	if not varsellist: raise Exception()
2645	vals.append([data[name]['variables'][s] if s is not None else None for s in sellist])
2646	esds.append([data[name]['sig'][s] if s is not None else None for s in sellist])
2647	#GSASIIpath.IPyBreak()
2648	colList += zip(*vals)
2649	colSigs += zip(*esds)
2650
2651	# tabulate constrained variables, removing histogram numbers if needed
2652	# from parameter label
2653	depValDict = {}
2654	depSigDict = {}
2655	for name in histNames:
2656	for var in data[name].get('depParmDict',{}):
2657	val,sig = data[name]['depParmDict'][var]
2658	svar = striphist(var,'*')
2659	if svar not in depValDict:
2660	depValDict[svar] = [val]
2661	depSigDict[svar] = [sig]
2662	else:
2663	depValDict[svar].append(val)
2664	depSigDict[svar].append(sig)
2665	# add the dependent constrained variables to the table
2666	for var in sorted(depValDict):
2667	if len(depValDict[var]) != len(histNames): continue
2668	colLabels.append(var)
2669	Types += [wg.GRID_VALUE_FLOAT,]
2670	colSigs += [depSigDict[var]]
2671	colList += [depValDict[var]]
2672
2673	# add atom parameters to table
2674	colLabels += atomLookup.keys()
2675	Types += len(atomLookup)*[wg.GRID_VALUE_FLOAT]
2676	for parm in sorted(atomLookup):
2677	colList += [[data[name]['newAtomDict'][atomLookup[parm]][1] for name in histNames]]
2678	if atomLookup[parm] in data[histNames[0]]['varyList']:
2679	col = data[histNames[0]]['varyList'].index(atomLookup[parm])
2680	colSigs += [[data[name]['sig'][col] for name in histNames]]
2681	else:
2682	colSigs += [None] # should not happen
2683	# evaluate Pseudovars, their ESDs and add them to grid
2684	for expr in Controls['SeqPseudoVars']:
2685	obj = Controls['SeqPseudoVars'][expr]
2686	calcobj = G2obj.ExpressionCalcObj(obj)
2687	valList = []
2688	esdList = []
2689	for seqnum,name in enumerate(histNames):
2690	sigs = data[name]['sig']
2691	G2mv.InitVars()
2692	parmDict = data[name].get('parmDict')
2693	badVary = data[name].get('badVary',[])
2694	constraintInfo = data[name].get('constraintInfo',[[],[],{},[],seqnum])
2695	groups,parmlist,constrDict,fixedList,ihst = constraintInfo
2696	varyList = data[name]['varyList']
2697	parmDict = data[name]['parmDict']
2698	G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmDict,SeqHist=ihst)
2699	derivs = np.array(
2700	[EvalPSvarDeriv(calcobj,parmDict.copy(),sampleDict[name],var,ESD)
2701	for var,ESD in zip(varyList,sigs)]
2702	)
2703	esdList.append(np.sqrt(
2704	np.inner(derivs,np.inner(data[name]['covMatrix'],derivs.T))
2705	))
2706	PSvarDict = parmDict.copy()
2707	PSvarDict.update(sampleDict[name])
2708	UpdateParmDict(PSvarDict)
2709	calcobj.UpdateDict(PSvarDict)
2710	valList.append(calcobj.EvalExpression())
2711	if not esdList:
2712	esdList = None
2713	colList += [valList]
2714	colSigs += [esdList]
2715	colLabels += [expr]
2716	Types += [wg.GRID_VALUE_FLOAT,]
2717	#---- table build done -------------------------------------------------------------
2718
2719	# Make dict needed for creating & editing pseudovars (PSvarDict).
2720	name = histNames[0]
2721	parmDict = data[name].get('parmDict')
2722	PSvarDict = parmDict.copy()
2723	PSvarDict.update(sampleParms)
2724	UpdateParmDict(PSvarDict)
2725	# Also dicts of dependent (depVarDict) & independent vars (indepVarDict)
2726	# for Parametric fitting from the data table
2727	parmDict = dict(zip(colLabels,zip(*colList)[0])) # scratch dict w/all values in table
2728	parmDict.update(
2729	{var:val for var,val in data[name].get('newCellDict',{}).values()} # add varied reciprocal cell terms
2730	)
2731	name = histNames[0]
2732
2733	#******************************************************************************
2734	# create a set of values for example evaluation of pseudovars and
2735	# this does not work for refinements that have differing numbers of variables.
2736	#raise Exception
2737	indepVarDict = {} # values in table w/o ESDs
2738	depVarDict = {}
2739	for i,var in enumerate(colLabels):
2740	if var == 'Use': continue
2741	if colList[i][0] is None:
2742	val,sig = firstValueDict.get(var,[None,None])
2743	elif colSigs[i]:
2744	val,sig = colList[i][0],colSigs[i][0]
2745	else:
2746	val,sig = colList[i][0],None
2747	if val is None:
2748	continue
2749	elif sig is None:
2750	indepVarDict[var] = val
2751	elif striphist(var) not in Dlookup:
2752	depVarDict[var] = val
2753	# add recip cell coeff. values
2754	depVarDict.update({var:val for var,val in data[name].get('newCellDict',{}).values()})
2755
2756	G2frame.dataDisplay = G2G.GSGrid(parent=G2frame.dataFrame)
2757	G2frame.SeqTable = G2G.Table(
2758	[list(c) for c in zip(*colList)], # convert from columns to rows
2759	colLabels=colLabels,rowLabels=histNames,types=Types)
2760	G2frame.dataDisplay.SetTable(G2frame.SeqTable, True)
2761	#G2frame.dataDisplay.EnableEditing(False)
2762	# make all but first column read-only
2763	for c in range(1,len(colLabels)):
2764	for r in range(nRows):
2765	G2frame.dataDisplay.SetCellReadOnly(r,c)
2766	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, PlotSelect)
2767	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, SetLabelString)
2768	G2frame.dataDisplay.SetRowLabelSize(8*len(histNames[0])) #pretty arbitrary 8
2769	G2frame.dataDisplay.SetMargins(0,0)
2770	G2frame.dataDisplay.AutoSizeColumns(True)
2771	if prevSize:
2772	G2frame.dataDisplay.SetSize(prevSize)
2773	else:
2774	G2frame.dataFrame.setSizePosLeft([700,350])
2775	# highlight unconverged shifts
2776	if histNames[0][:4] not in ['SASD','IMG ']:
2777	for row,name in enumerate(histNames):
2778	deltaChi = G2frame.SeqTable.GetValue(row,deltaChiCol)
2779	if deltaChi > 10.:
2780	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,0,0))
2781	elif deltaChi > 1.0:
2782	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,255,0))
2783	G2frame.dataDisplay.InstallGridToolTip(GridSetToolTip,GridColLblToolTip)
2784	G2frame.dataDisplay.SendSizeEvent() # resize needed on mac
2785	G2frame.dataDisplay.Refresh() # shows colored text on mac
2786
2787	################################################################################
2788	##### Main PWDR panel
2789	################################################################################
2790
2791	def UpdatePWHKPlot(G2frame,kind,item):
2792	'''Called when the histogram main tree entry is called. Displays the
2793	histogram weight factor, refinement statistics for the histogram
2794	and the range of data for a simulation.
2795
2796	Also invokes a plot of the histogram.
2797	'''
2798	def onEditSimRange(event):
2799	'Edit simulation range'
2800	inp = [
2801	min(data[1][0]),
2802	max(data[1][0]),
2803	None
2804	]
2805	inp[2] = (inp[1] - inp[0])/(len(data[1][0])-1.)
2806	names = ('start angle', 'end angle', 'step size')
2807	dictlst = [inp] * len(inp)
2808	elemlst = range(len(inp))
2809	dlg = G2G.ScrolledMultiEditor(
2810	G2frame,[inp] * len(inp), range(len(inp)), names,
2811	header='Edit simulation range',
2812	minvals=(0.001,0.001,0.0001),
2813	maxvals=(180.,180.,.1),
2814	)
2815	dlg.CenterOnParent()
2816	val = dlg.ShowModal()
2817	dlg.Destroy()
2818	if val != wx.ID_OK: return
2819	if inp[0] > inp[1]:
2820	end,start,step = inp
2821	else:
2822	start,end,step = inp
2823	step = abs(step)
2824	N = int((end-start)/step)+1
2825	newdata = np.linspace(start,end,N,True)
2826	if len(newdata) < 2: return # too small a range - reject
2827	data[1] = [newdata,np.zeros_like(newdata),np.ones_like(newdata),
2828	np.zeros_like(newdata),np.zeros_like(newdata),np.zeros_like(newdata)]
2829	Tmin = newdata[0]
2830	Tmax = newdata[-1]
2831	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,item,'Limits'),
2832	[(Tmin,Tmax),[Tmin,Tmax]])
2833	UpdatePWHKPlot(G2frame,kind,item) # redisplay data screen
2834
2835	def OnPlot3DHKL(event):
2836	refList = data[1]['RefList']
2837	FoMax = np.max(refList.T[8+Super])
2838	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2839	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2840	Vpoint = np.array([int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))])
2841	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,'Zone':False,'viewKey':'L',
2842	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2843	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
2844	'Scale':1.0,'oldxy':[],'viewDir':[0,0,1]},'Super':Super,'SuperVec':SuperVec}
2845	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2846
2847	def OnPlotAll3DHKL(event):
2848	choices = GetPatternTreeDataNames(G2frame,['HKLF',])
2849	dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to plot',
2850	'Use data',choices)
2851	try:
2852	if dlg.ShowModal() == wx.ID_OK:
2853	refNames = [choices[i] for i in dlg.GetSelections()]
2854	else:
2855	return
2856	finally:
2857	dlg.Destroy()
2858	refList = np.zeros(0)
2859	for name in refNames:
2860	Id = GetPatternTreeItemId(G2frame,G2frame.root, name)
2861	reflData = G2frame.PatternTree.GetItemPyData(Id)[1]
2862	if len(refList):
2863	refList = np.concatenate((refList,reflData['RefList']))
2864	else:
2865	refList = reflData['RefList']
2866
2867	FoMax = np.max(refList.T[8+Super])
2868	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2869	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2870	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2871	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,'Zone':False,'viewKey':'L',
2872	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2873	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
2874	'Scale':1.0,'oldxy':[],'viewDir':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
2875	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2876
2877
2878	def OnErrorAnalysis(event):
2879	G2plt.PlotDeltSig(G2frame,kind)
2880
2881	def OnWtFactor(event):
2882	try:
2883	val = float(wtval.GetValue())
2884	except ValueError:
2885	val = data[0]['wtFactor']
2886	data[0]['wtFactor'] = val
2887	wtval.SetValue('%.3f'%(val))
2888
2889	def OnCompression(event):
2890	data[0] = int(comp.GetValue())
2891
2892	def onCopyPlotCtrls(event):
2893	'''Respond to menu item to copy multiple sections from a histogram.
2894	Need this here to pass on the G2frame object.
2895	'''
2896	G2pdG.CopyPlotCtrls(G2frame)
2897
2898	def onCopySelectedItems(event):
2899	'''Respond to menu item to copy multiple sections from a histogram.
2900	Need this here to pass on the G2frame object.
2901	'''
2902	G2pdG.CopySelectedHistItems(G2frame)
2903
2904	data = G2frame.PatternTree.GetItemPyData(item)
2905	#patches
2906	if 'wtFactor' not in data[0]:
2907	data[0] = {'wtFactor':1.0}
2908	# if kind == 'PWDR' and 'Compression' not in data[0]:
2909	# data[0]['Compression'] = 1
2910	#if isinstance(data[1],list) and kind == 'HKLF':
2911	if 'list' in str(type(data[1])) and kind == 'HKLF':
2912	RefData = {'RefList':[],'FF':[]}
2913	for ref in data[1]:
2914	RefData['RefList'].append(ref[:11]+[ref[13],])
2915	RefData['FF'].append(ref[14])
2916	data[1] = RefData
2917	G2frame.PatternTree.SetItemPyData(item,data)
2918	#end patches
2919	if G2frame.dataDisplay:
2920	G2frame.dataDisplay.Destroy()
2921	if kind in ['PWDR','SASD']:
2922	SetDataMenuBar(G2frame,G2frame.dataFrame.PWDRMenu)
2923	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2924	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2925	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopyPlotCtrls, id=wxID_PLOTCTRLCOPY)
2926	elif kind in ['HKLF',]:
2927	SetDataMenuBar(G2frame,G2frame.dataFrame.HKLFMenu)
2928	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2929	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=wxID_PWD3DHKLPLOT)
2930	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotAll3DHKL, id=wxID_3DALLHKLPLOT)
2931	# G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2932	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
2933
2934	mainSizer = wx.BoxSizer(wx.VERTICAL)
2935	mainSizer.Add((5,5),)
2936	wtSizer = wx.BoxSizer(wx.HORIZONTAL)
2937	wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Weight factor: '),0,WACV)
2938	wtval = wx.TextCtrl(G2frame.dataDisplay,-1,'%.3f'%(data[0]['wtFactor']),style=wx.TE_PROCESS_ENTER)
2939	wtval.Bind(wx.EVT_TEXT_ENTER,OnWtFactor)
2940	wtval.Bind(wx.EVT_KILL_FOCUS,OnWtFactor)
2941	wtSizer.Add(wtval,0,WACV)
2942	# if kind == 'PWDR': #possible future compression feature; NB above patch as well
2943	# wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Compression factor: '),0,WACV)
2944	# choice = ['1','2','3','4','5','6']
2945	# comp = wx.ComboBox(parent=G2frame.dataDisplay,choices=choice,
2946	# style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2947	# comp.SetValue(str(data[0]['Compression']))
2948	# comp.Bind(wx.EVT_COMBOBOX, OnCompression)
2949	# wtSizer.Add(comp,0,WACV)
2950	mainSizer.Add(wtSizer)
2951	if data[0].get('Dummy'):
2952	simSizer = wx.BoxSizer(wx.HORIZONTAL)
2953	Tmin = min(data[1][0])
2954	Tmax = max(data[1][0])
2955	num = len(data[1][0])
2956	step = (Tmax - Tmin)/(num-1)
2957	t = u'2\u03b8' # 2theta
2958	lbl = u'Simulation range: {:.2f} to {:.2f} {:s}\nwith {:.4f} steps ({:d} points)'
2959	lbl += u'\n(Edit range resets observed intensities).'
2960	lbl = lbl.format(Tmin,Tmax,t,step,num)
2961	simSizer.Add(wx.StaticText(G2frame.dataDisplay,wx.ID_ANY,lbl),
2962	0,WACV)
2963	but = wx.Button(G2frame.dataDisplay,wx.ID_ANY,"Edit range")
2964	but.Bind(wx.EVT_BUTTON,onEditSimRange)
2965	simSizer.Add(but,0,WACV)
2966	mainSizer.Add(simSizer)
2967	if 'Nobs' in data[0]:
2968	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2969	' Data residual wR: %.3f%% on %d observations'%(data[0]['wR'],data[0]['Nobs'])))
2970	for value in data[0]:
2971	if 'Nref' in value:
2972	pfx = value.split('Nref')[0]
2973	name = data[0].get(pfx.split(':')[0]+'::Name','?')
2974	if 'SS' in value:
2975	mainSizer.Add((5,5),)
2976	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For incommensurate phase '+name+':'))
2977	for m,(Rf2,Rf,Nobs) in enumerate(zip(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])):
2978	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2979	u' m = +/- %d: RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2980	(m,Rf2,Rf,Nobs)))
2981	else:
2982	mainSizer.Add((5,5),)
2983	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For phase '+name+':'))
2984	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2985	u' Unweighted phase residuals RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2986	(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])))
2987
2988	mainSizer.Add((5,5),)
2989	mainSizer.Layout()
2990	G2frame.dataDisplay.SetSizer(mainSizer)
2991	Size = mainSizer.Fit(G2frame.dataFrame)
2992	Size[1] += 10
2993	G2frame.dataFrame.setSizePosLeft(Size)
2994	G2frame.PatternTree.SetItemPyData(item,data)
2995	if kind in ['PWDR','SASD']:
2996	if 'xylim' in dir(G2frame):
2997	NewPlot = False
2998	else:
2999
3000	NewPlot = True
3001	G2plt.PlotPatterns(G2frame,plotType=kind,newPlot=NewPlot)
3002	elif kind == 'HKLF':
3003	Name = G2frame.PatternTree.GetItemText(item)
3004	phaseName = G2pdG.IsHistogramInAnyPhase(G2frame,Name)
3005	if phaseName:
3006	pId = GetPatternTreeItemId(G2frame,G2frame.root,'Phases')
3007	phaseId = GetPatternTreeItemId(G2frame,pId,phaseName)
3008	General = G2frame.PatternTree.GetItemPyData(phaseId)['General']
3009	Super = General.get('Super',0)
3010	SuperVec = General.get('SuperVec',[])
3011	else:
3012	Super = 0
3013	SuperVec = []
3014	refList = data[1]['RefList']
3015	FoMax = np.max(refList.T[5+data[1].get('Super',0)])
3016	page = G2frame.G2plotNB.nb.GetSelection()
3017	tab = ''
3018	if page >= 0:
3019	tab = G2frame.G2plotNB.nb.GetPageText(page)
3020	if '3D' in tab:
3021	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
3022	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
3023	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
3024	Page = G2frame.G2plotNB.nb.GetPage(page)
3025	controls = Page.controls
3026	G2plt.Plot3DSngl(G2frame,newPlot=False,Data=controls,hklRef=refList,Title=phaseName)
3027	else:
3028	controls = {'Type' : 'Fo','ifFc' : True,
3029	'HKLmax' : [int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))],
3030	'HKLmin' : [int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))],
3031	'FoMax' : FoMax,'Zone' : '001','Layer' : 0,'Scale' : 1.0,'Super':Super,'SuperVec':SuperVec}
3032	G2plt.PlotSngl(G2frame,newPlot=True,Data=controls,hklRef=refList)
3033
3034	################################################################################
3035	##### Pattern tree routines
3036	################################################################################
3037
3038	def GetPatternTreeDataNames(G2frame,dataTypes):
3039	'''Needs a doc string
3040	'''
3041	names = []
3042	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3043	while item:
3044	name = G2frame.PatternTree.GetItemText(item)
3045	if name[:4] in dataTypes:
3046	names.append(name)
3047	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3048	return names
3049
3050	def GetPatternTreeItemId(G2frame, parentId, itemText):
3051	'''Needs a doc string
3052	'''
3053	item, cookie = G2frame.PatternTree.GetFirstChild(parentId)
3054	while item:
3055	if G2frame.PatternTree.GetItemText(item) == itemText:
3056	return item
3057	item, cookie = G2frame.PatternTree.GetNextChild(parentId, cookie)
3058	return 0
3059
3060	def MovePatternTreeToGrid(G2frame,item):
3061	'''Called from GSASII.OnPatternTreeSelChanged when a item is selected on the tree
3062	'''
3063	pickName = G2frame.PatternTree.GetItemText(item)
3064	if G2frame.PickIdText == pickName:
3065	return
3066
3067	oldPage = None # will be set later if already on a Phase item
3068	if G2frame.dataFrame:
3069	SetDataMenuBar(G2frame)
3070	if G2frame.dataFrame.GetLabel() == 'Comments':
3071	try:
3072	data = [G2frame.dataDisplay.GetValue()]
3073	G2frame.dataDisplay.Clear()
3074	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Comments')
3075	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3076	except: #clumsy but avoids dead window problem when opening another project
3077	pass
3078	elif G2frame.dataFrame.GetLabel() == 'Notebook':
3079	try:
3080	data = [G2frame.dataDisplay.GetValue()]
3081	G2frame.dataDisplay.Clear()
3082	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Notebook')
3083	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3084	except: #clumsy but avoids dead window problem when opening another project
3085	pass
3086	elif 'Phase Data for' in G2frame.dataFrame.GetLabel():
3087	if G2frame.dataDisplay:
3088	oldPage = G2frame.dataDisplay.GetSelection()
3089	G2frame.dataFrame.Clear()
3090	G2frame.dataFrame.SetLabel('')
3091	else:
3092	#create the frame for the data item window
3093	G2frame.dataFrame = DataFrame(parent=G2frame.mainPanel,frame=G2frame)
3094	G2frame.dataFrame.PhaseUserSize = None
3095
3096	G2frame.dataFrame.Raise()
3097	G2frame.PickId = item
3098	G2frame.PickIdText = None
3099	parentID = G2frame.root
3100	#for i in G2frame.ExportPattern: i.Enable(False)
3101	defWid = [250,150]
3102	if item != G2frame.root:
3103	parentID = G2frame.PatternTree.GetItemParent(item)
3104	if G2frame.PatternTree.GetItemParent(item) == G2frame.root:
3105	G2frame.PatternId = item
3106	if G2frame.PatternTree.GetItemText(item) == 'Notebook':
3107	SetDataMenuBar(G2frame,G2frame.dataFrame.DataNotebookMenu)
3108	G2frame.PatternId = 0
3109	#for i in G2frame.ExportPattern: i.Enable(False)
3110	data = G2frame.PatternTree.GetItemPyData(item)
3111	UpdateNotebook(G2frame,data)
3112	elif G2frame.PatternTree.GetItemText(item) == 'Controls':
3113	G2frame.PatternId = 0
3114	#for i in G2frame.ExportPattern: i.Enable(False)
3115	data = G2frame.PatternTree.GetItemPyData(item)
3116	if not data: #fill in defaults
3117	data = copy.copy(G2obj.DefaultControls) #least squares controls
3118	G2frame.PatternTree.SetItemPyData(item,data)
3119	for i in G2frame.Refine: i.Enable(True)
3120	G2frame.EnableSeqRefineMenu()
3121	UpdateControls(G2frame,data)
3122	elif G2frame.PatternTree.GetItemText(item) == 'Sequential results':
3123	data = G2frame.PatternTree.GetItemPyData(item)
3124	UpdateSeqResults(G2frame,data)
3125	elif G2frame.PatternTree.GetItemText(item) == 'Covariance':
3126	data = G2frame.PatternTree.GetItemPyData(item)
3127	G2frame.dataFrame.setSizePosLeft(defWid)
3128	text = ''
3129	if 'Rvals' in data:
3130	Nvars = len(data['varyList'])
3131	Rvals = data['Rvals']
3132	text = '\nFinal residuals: \nwR = %.3f%% \nchi**2 = %.1f \nGOF = %.2f'%(Rvals['Rwp'],Rvals['chisq'],Rvals['GOF'])
3133	text += '\nNobs = %d \nNvals = %d'%(Rvals['Nobs'],Nvars)
3134	if 'lamMax' in Rvals:
3135	text += '\nlog10 MaxLambda = %.1f'%(np.log10(Rvals['lamMax']))
3136	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3137	value='See plot window for covariance display'+text,style=wx.TE_MULTILINE)
3138	G2plt.PlotCovariance(G2frame,data)
3139	elif G2frame.PatternTree.GetItemText(item) == 'Constraints':
3140	data = G2frame.PatternTree.GetItemPyData(item)
3141	G2cnstG.UpdateConstraints(G2frame,data)
3142	elif G2frame.PatternTree.GetItemText(item) == 'Rigid bodies':
3143	data = G2frame.PatternTree.GetItemPyData(item)
3144	G2cnstG.UpdateRigidBodies(G2frame,data)
3145	elif G2frame.PatternTree.GetItemText(item) == 'Restraints':
3146	data = G2frame.PatternTree.GetItemPyData(item)
3147	Phases = G2frame.GetPhaseData()
3148	phase = ''
3149	phaseName = ''
3150	if Phases:
3151	phaseName = Phases.keys()[0]
3152	G2frame.dataFrame.setSizePosLeft(defWid)
3153	G2restG.UpdateRestraints(G2frame,data,Phases,phaseName)
3154	elif 'IMG' in G2frame.PatternTree.GetItemText(item):
3155	G2frame.Image = item
3156	G2frame.dataFrame.SetTitle('Image Data')
3157	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId( \
3158	G2frame,item,'Image Controls'))
3159	G2imG.UpdateImageData(G2frame,data)
3160	G2plt.PlotImage(G2frame,newPlot=True)
3161	elif 'PKS' in G2frame.PatternTree.GetItemText(item):
3162	G2plt.PlotPowderLines(G2frame)
3163	elif 'PWDR' in G2frame.PatternTree.GetItemText(item):
3164	#for i in G2frame.ExportPattern: i.Enable(True)
3165	if G2frame.EnablePlot:
3166	UpdatePWHKPlot(G2frame,'PWDR',item)
3167	elif 'SASD' in G2frame.PatternTree.GetItemText(item):
3168	#for i in G2frame.ExportPattern: i.Enable(True)
3169	if G2frame.EnablePlot:
3170	UpdatePWHKPlot(G2frame,'SASD',item)
3171	elif 'HKLF' in G2frame.PatternTree.GetItemText(item):
3172	G2frame.Sngl = True
3173	UpdatePWHKPlot(G2frame,'HKLF',item)
3174	elif 'PDF' in G2frame.PatternTree.GetItemText(item):
3175	G2frame.PatternId = item
3176	for i in G2frame.ExportPDF: i.Enable(True)
3177	G2plt.PlotISFG(G2frame,type='S(Q)')
3178	elif G2frame.PatternTree.GetItemText(item) == 'Phases':
3179	G2frame.dataFrame.setSizePosLeft(defWid)
3180	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3181	value='Select one phase to see its parameters')
3182	elif 'I(Q)' in G2frame.PatternTree.GetItemText(item):
3183	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3184	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3185	G2pdG.UpdatePDFGrid(G2frame,data)
3186	G2plt.PlotISFG(G2frame,type='I(Q)',newPlot=True)
3187	elif 'S(Q)' in G2frame.PatternTree.GetItemText(item):
3188	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3189	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3190	G2pdG.UpdatePDFGrid(G2frame,data)
3191	G2plt.PlotISFG(G2frame,type='S(Q)',newPlot=True)
3192	elif 'F(Q)' in G2frame.PatternTree.GetItemText(item):
3193	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3194	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3195	G2pdG.UpdatePDFGrid(G2frame,data)
3196	G2plt.PlotISFG(G2frame,type='F(Q)',newPlot=True)
3197	elif 'G(R)' in G2frame.PatternTree.GetItemText(item):
3198	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3199	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3200	G2pdG.UpdatePDFGrid(G2frame,data)
3201	G2plt.PlotISFG(G2frame,type='G(R)',newPlot=True)
3202	elif G2frame.PatternTree.GetItemText(parentID) == 'Phases':
3203	data = G2frame.PatternTree.GetItemPyData(item)
3204	G2phG.UpdatePhaseData(G2frame,item,data,oldPage)
3205	elif G2frame.PatternTree.GetItemText(item) == 'Comments':
3206	SetDataMenuBar(G2frame,G2frame.dataFrame.DataCommentsMenu)
3207	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3208	data = G2frame.PatternTree.GetItemPyData(item)
3209	UpdateComments(G2frame,data)
3210	elif G2frame.PatternTree.GetItemText(item) == 'Image Controls':
3211	G2frame.dataFrame.SetTitle('Image Controls')
3212	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3213	masks = G2frame.PatternTree.GetItemPyData(
3214	GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3215	data = G2frame.PatternTree.GetItemPyData(item)
3216	G2imG.UpdateImageControls(G2frame,data,masks)
3217	G2plt.PlotImage(G2frame)
3218	elif G2frame.PatternTree.GetItemText(item) == 'Masks':
3219	G2frame.dataFrame.SetTitle('Masks')
3220	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3221	data = G2frame.PatternTree.GetItemPyData(item)
3222	G2imG.UpdateMasks(G2frame,data)
3223	G2plt.PlotImage(G2frame)
3224	elif G2frame.PatternTree.GetItemText(item) == 'Stress/Strain':
3225	G2frame.dataFrame.SetTitle('Stress/Strain')
3226	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3227	data = G2frame.PatternTree.GetItemPyData(item)
3228	G2plt.PlotImage(G2frame)
3229	G2plt.PlotStrain(G2frame,data,newPlot=True)
3230	G2imG.UpdateStressStrain(G2frame,data)
3231	elif G2frame.PatternTree.GetItemText(item) == 'PDF Controls':
3232	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3233	for i in G2frame.ExportPDF: i.Enable(True)
3234	data = G2frame.PatternTree.GetItemPyData(item)
3235	G2pdG.UpdatePDFGrid(G2frame,data)
3236	G2plt.PlotISFG(G2frame,type='I(Q)')
3237	G2plt.PlotISFG(G2frame,type='S(Q)')
3238	G2plt.PlotISFG(G2frame,type='F(Q)')
3239	G2plt.PlotISFG(G2frame,type='G(R)')
3240	elif G2frame.PatternTree.GetItemText(item) == 'Peak List':
3241	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3242	for i in G2frame.ExportPeakList: i.Enable(True)
3243	data = G2frame.PatternTree.GetItemPyData(item)
3244	#patch
3245	if 'list' in str(type(data)):
3246	data = {'peaks':data,'sigDict':{}}
3247	G2frame.PatternTree.SetItemPyData(item,data)
3248	#end patch
3249	G2pdG.UpdatePeakGrid(G2frame,data)
3250	G2plt.PlotPatterns(G2frame)
3251	elif G2frame.PatternTree.GetItemText(item) == 'Background':
3252	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3253	data = G2frame.PatternTree.GetItemPyData(item)
3254	G2pdG.UpdateBackground(G2frame,data)
3255	G2plt.PlotPatterns(G2frame)
3256	elif G2frame.PatternTree.GetItemText(item) == 'Limits':
3257	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3258	datatype = G2frame.PatternTree.GetItemText(G2frame.PatternId)[:4]
3259	data = G2frame.PatternTree.GetItemPyData(item)
3260	G2pdG.UpdateLimitsGrid(G2frame,data,datatype)
3261	G2plt.PlotPatterns(G2frame,plotType=datatype)
3262	elif G2frame.PatternTree.GetItemText(item) == 'Instrument Parameters':
3263	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3264	data = G2frame.PatternTree.GetItemPyData(item)[0]
3265	G2pdG.UpdateInstrumentGrid(G2frame,data)
3266	if 'P' in data['Type'][0]: #powder data only
3267	G2plt.PlotPeakWidths(G2frame)
3268	elif G2frame.PatternTree.GetItemText(item) == 'Models':
3269	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3270	data = G2frame.PatternTree.GetItemPyData(item)
3271	G2pdG.UpdateModelsGrid(G2frame,data)
3272	G2plt.PlotPatterns(G2frame,plotType='SASD')
3273	if len(data['Size']['Distribution']):
3274	G2plt.PlotSASDSizeDist(G2frame)
3275	elif G2frame.PatternTree.GetItemText(item) == 'Substances':
3276	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3277	data = G2frame.PatternTree.GetItemPyData(item)
3278	G2pdG.UpdateSubstanceGrid(G2frame,data)
3279	elif G2frame.PatternTree.GetItemText(item) == 'Sample Parameters':
3280	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3281	data = G2frame.PatternTree.GetItemPyData(item)
3282	datatype = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[2][:4]
3283
3284	if 'Temperature' not in data: #temp fix for old gpx files
3285	data = {'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],'DisplaceX':[0.0,False],
3286	'DisplaceY':[0.0,False],'Diffuse':[],'Temperature':300.,'Pressure':1.0,
3287	'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
3288	'Gonio. radius':200.0}
3289	G2frame.PatternTree.SetItemPyData(item,data)
3290
3291	G2pdG.UpdateSampleGrid(G2frame,data)
3292	G2plt.PlotPatterns(G2frame,plotType=datatype)
3293	elif G2frame.PatternTree.GetItemText(item) == 'Index Peak List':
3294	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3295	for i in G2frame.ExportPeakList: i.Enable(True)
3296	data = G2frame.PatternTree.GetItemPyData(item)
3297	#patch
3298	if len(data) != 2:
3299	data = [data,[]]
3300	G2frame.PatternTree.SetItemPyData(item,data)
3301	#end patch
3302	G2pdG.UpdateIndexPeaksGrid(G2frame,data)
3303	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3304	G2plt.PlotPowderLines(G2frame)
3305	else:
3306	G2plt.PlotPatterns(G2frame)
3307	elif G2frame.PatternTree.GetItemText(item) == 'Unit Cells List':
3308	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3309	data = G2frame.PatternTree.GetItemPyData(item)
3310	if not data:
3311	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
3312	data.append([0,0,0,0,0,0,0,0,0,0,0,0,0,0]) #Bravais lattice flags
3313	data.append([]) #empty cell list
3314	data.append([]) #empty dmin
3315	data.append({}) #empty superlattice stuff
3316	G2frame.PatternTree.SetItemPyData(item,data)
3317	#patch
3318	if len(data) < 5:
3319	data.append({'Use':False,'ModVec':[0,0,0.1],'maxH':1,'ssSymb':''}) #empty superlattice stuff
3320	G2frame.PatternTree.SetItemPyData(item,data)
3321	#end patch
3322	G2pdG.UpdateUnitCellsGrid(G2frame,data)
3323	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3324	G2plt.PlotPowderLines(G2frame)
3325	else:
3326	G2plt.PlotPatterns(G2frame)
3327	elif G2frame.PatternTree.GetItemText(item) == 'Reflection Lists': #powder reflections
3328	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3329	data = G2frame.PatternTree.GetItemPyData(item)
3330	G2frame.RefList = ''
3331	if len(data):
3332	G2frame.RefList = data.keys()[0]
3333	G2pdG.UpdateReflectionGrid(G2frame,data)
3334	G2plt.PlotPatterns(G2frame)
3335	elif G2frame.PatternTree.GetItemText(item) == 'Reflection List': #HKLF reflections
3336	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3337	name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
3338	data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
3339	G2pdG.UpdateReflectionGrid(G2frame,data,HKLF=True,Name=name)
3340
3341	if G2frame.PickId:
3342	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
3343	G2frame.dataFrame.Raise()
3344
3345	def SetDataMenuBar(G2frame,menu=None):
3346	'''Set the menu for the data frame. On the Mac put this
3347	menu for the data tree window instead.
3348
3349	Note that data frame items do not have menus, for these (menu=None)
3350	display a blank menu or on the Mac display the standard menu for
3351	the data tree window.
3352	'''
3353	if sys.platform == "darwin":
3354	if menu is None:
3355	G2frame.SetMenuBar(G2frame.GSASIIMenu)
3356	else:
3357	G2frame.SetMenuBar(menu)
3358	else:
3359	if menu is None:
3360	G2frame.dataFrame.SetMenuBar(G2frame.dataFrame.BlankMenu)
3361	else:
3362	G2frame.dataFrame.SetMenuBar(menu)
3363
3364	def HowDidIgetHere():
3365	'''Show a traceback with calls that brought us to the current location.
3366	Used for debugging.
3367	'''
3368	import traceback
3369	print 70''
3370	for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip.rstrip())
3371	print 70''
3372

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