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source: trunk/GSASIIgrid.py @ 1925

Last change on this file since 1925 was 1925, checked in by vondreele, 8 years ago
create AddHatomDialog? & work on OnHydAtomAdd? allow reading of .cor images made at APS 1ID
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1	# -- coding: utf-8 --
2	#GSASIIgrid - data display routines
3	########### SVN repository information ###################
4	# $Date: 2015-07-10 20:50:10 +0000 (Fri, 10 Jul 2015) $
5	# $Author: vondreele $
6	# $Revision: 1925 $
7	# $URL: trunk/GSASIIgrid.py $
8	# $Id: GSASIIgrid.py 1925 2015-07-10 20:50:10Z vondreele $
9	########### SVN repository information ###################
10	'''
11	GSASIIgrid: Basic GUI routines
12	--------------------------------
13
14	'''
15	import wx
16	import wx.grid as wg
17	#import wx.wizard as wz
18	#import wx.aui
19	import wx.lib.scrolledpanel as wxscroll
20	import time
21	import copy
22	import cPickle
23	import sys
24	import os
25	import numpy as np
26	import numpy.ma as ma
27	import scipy.optimize as so
28	import GSASIIpath
29	GSASIIpath.SetVersionNumber("$Revision: 1925 $")
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,
70	] = [wx.NewId() for item in range(16)]
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,
92	] = [wx.NewId() for item in range(8)]
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	class AddHatomDialog(wx.Dialog):
320	'''H atom addition dialog. After :meth:`ShowModal` returns, the results
321	are found in dict :attr:`self.data`, which is accessed using :meth:`GetData`.
322	:param wx.Frame parent: reference to parent frame (or None)
323	:param dict Neigh: a dict of atom names with list of atom name, dist pairs for neighboring atoms
324	:param dict phase: a dict containing the phase as defined by
325	:ref:`Phase Tree Item <Phase_table>`
326	'''
327	def __init__(self,parent,Neigh,phase):
328	wx.Dialog.__init__(self,parent,wx.ID_ANY,'H atom add',
329	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
330	self.panel = wxscroll.ScrolledPanel(self) #just a dummy - gets destroyed in Draw!
331	self.Neigh = Neigh
332	self.phase = phase
333	self.Hatoms = []
334	self.Draw(self.Neigh,self.phase)
335
336	def Draw(self,Neigh,phase):
337	'''Creates the contents of the dialog. Normally called
338	by :meth:`__init__`.
339	'''
340	def OnHSelect(event):
341	Obj = event.GetEventObject()
342	item,i = Indx[Obj.GetId()]
343	for obj in Indx[item]:
344	obj.SetValue(False)
345	Obj.SetValue(True)
346	self.Neigh[item][2] = i
347
348	self.panel.Destroy()
349	self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE)
350	mainSizer = wx.BoxSizer(wx.VERTICAL)
351	mainSizer.Add(wx.StaticText(self.panel,-1,'H atom add controls for phase %s:'%(phase['General']['Name'])),
352	0,wx.LEFT\|wx.TOP,10)
353	mainSizer.Add(wx.StaticText(self.panel,-1," Atom: Add # H's Neighbors, dist"),0,wx.TOP\|wx.LEFT,5)
354	nHatms = ['0','1','2','3']
355	dataSizer = wx.FlexGridSizer(0,3,0,0)
356	Indx = {}
357	for inei,neigh in enumerate(Neigh):
358	dataSizer.Add(wx.StaticText(self.panel,-1,' %s: '%(neigh[0])),0,WACV)
359	nH = 1 #for O atom
360	if 'C' in neigh[0] or 'N' in neigh[0]:
361	nH = 4-len(neigh[1])
362	neigh[2] = nH
363	checks = wx.BoxSizer(wx.HORIZONTAL)
364	Ids = []
365	for i in range(nH+1):
366	nHs = wx.CheckBox(self.panel,-1,label=nHatms[i])
367	if i == neigh[2]:
368	nHs.SetValue(True)
369	Indx[nHs.GetId()] = [inei,i]
370	Ids.append(nHs)
371	nHs.Bind(wx.EVT_CHECKBOX, OnHSelect)
372	checks.Add(nHs,0,WACV)
373	Indx[inei] = Ids
374	dataSizer.Add(checks,0,WACV)
375	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
376	for bond in neigh[1]:
377	lineSizer.Add(wx.StaticText(self.panel,-1,' %s, %.3f'%(bond[0],bond[1])),0,WACV)
378	dataSizer.Add(lineSizer,0,WACV)
379	mainSizer.Add(dataSizer,0,wx.LEFT,5)
380
381	CancelBtn = wx.Button(self.panel,-1,'Cancel')
382	CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
383	OkBtn = wx.Button(self.panel,-1,'Ok')
384	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
385	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
386	btnSizer.Add((20,20),1)
387	btnSizer.Add(OkBtn)
388	btnSizer.Add((20,20),1)
389	btnSizer.Add(CancelBtn)
390	btnSizer.Add((20,20),1)
391	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
392	self.panel.SetSizer(mainSizer)
393	self.panel.SetupScrolling()
394
395	def GetData(self):
396	'Returns the values from the dialog'
397	return self.Neigh #has #Hs to add for each entry
398
399	def OnOk(self,event):
400	'Called when the OK button is pressed'
401	parent = self.GetParent()
402	parent.Raise()
403	self.EndModal(wx.ID_OK)
404
405	def OnCancel(self,event):
406	parent = self.GetParent()
407	parent.Raise()
408	self.EndModal(wx.ID_CANCEL)
409
410	class DisAglDialog(wx.Dialog):
411	'''Distance/Angle Controls input dialog. After
412	:meth:`ShowModal` returns, the results are found in
413	dict :attr:`self.data`, which is accessed using :meth:`GetData`.
414
415	:param wx.Frame parent: reference to parent frame (or None)
416	:param dict data: a dict containing the current
417	search ranges or an empty dict, which causes default values
418	to be used.
419	Will be used to set element `DisAglCtls` in
420	:ref:`Phase Tree Item <Phase_table>`
421	:param dict default: A dict containing the default
422	search ranges for each element.
423	'''
424	def __init__(self,parent,data,default,Reset=True):
425	wx.Dialog.__init__(self,parent,wx.ID_ANY,
426	'Distance Angle Controls',
427	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
428	self.default = default
429	self.Reset = Reset
430	self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
431	self._default(data,self.default)
432	self.Draw(self.data)
433
434	def _default(self,data,default):
435	'''Set starting values for the search values, either from
436	the input array or from defaults, if input is null
437	'''
438	if data:
439	self.data = copy.deepcopy(data) # don't mess with originals
440	else:
441	self.data = {}
442	self.data['Name'] = default['Name']
443	self.data['Factors'] = [0.85,0.85]
444	self.data['AtomTypes'] = default['AtomTypes']
445	self.data['BondRadii'] = default['BondRadii'][:]
446	self.data['AngleRadii'] = default['AngleRadii'][:]
447
448	def Draw(self,data):
449	'''Creates the contents of the dialog. Normally called
450	by :meth:`__init__`.
451	'''
452	self.panel.Destroy()
453	self.panel = wx.Panel(self)
454	mainSizer = wx.BoxSizer(wx.VERTICAL)
455	mainSizer.Add(wx.StaticText(self.panel,-1,'Controls for phase '+data['Name']),
456	0,WACV\|wx.LEFT,10)
457	mainSizer.Add((10,10),1)
458
459	radiiSizer = wx.FlexGridSizer(0,3,5,5)
460	radiiSizer.Add(wx.StaticText(self.panel,-1,' Type'),0,WACV)
461	radiiSizer.Add(wx.StaticText(self.panel,-1,'Bond radii'),0,WACV)
462	radiiSizer.Add(wx.StaticText(self.panel,-1,'Angle radii'),0,WACV)
463	self.objList = {}
464	for id,item in enumerate(self.data['AtomTypes']):
465	radiiSizer.Add(wx.StaticText(self.panel,-1,' '+item),0,WACV)
466	bRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['BondRadii'][id]),style=wx.TE_PROCESS_ENTER)
467	self.objList[bRadii.GetId()] = ['BondRadii',id]
468	bRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
469	bRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
470	radiiSizer.Add(bRadii,0,WACV)
471	aRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['AngleRadii'][id]),style=wx.TE_PROCESS_ENTER)
472	self.objList[aRadii.GetId()] = ['AngleRadii',id]
473	aRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
474	aRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
475	radiiSizer.Add(aRadii,0,WACV)
476	mainSizer.Add(radiiSizer,0,wx.EXPAND)
477	factorSizer = wx.FlexGridSizer(0,2,5,5)
478	Names = ['Bond','Angle']
479	for i,name in enumerate(Names):
480	factorSizer.Add(wx.StaticText(self.panel,-1,name+' search factor'),0,WACV)
481	bondFact = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['Factors'][i]),style=wx.TE_PROCESS_ENTER)
482	self.objList[bondFact.GetId()] = ['Factors',i]
483	bondFact.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
484	bondFact.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
485	factorSizer.Add(bondFact)
486	mainSizer.Add(factorSizer,0,wx.EXPAND)
487
488	OkBtn = wx.Button(self.panel,-1,"Ok")
489	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
490	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
491	btnSizer.Add((20,20),1)
492	btnSizer.Add(OkBtn)
493	if self.Reset:
494	ResetBtn = wx.Button(self.panel,-1,'Reset')
495	ResetBtn.Bind(wx.EVT_BUTTON, self.OnReset)
496	btnSizer.Add(ResetBtn)
497	btnSizer.Add((20,20),1)
498	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
499	self.panel.SetSizer(mainSizer)
500	self.panel.Fit()
501	self.Fit()
502
503	def OnRadiiVal(self,event):
504	Obj = event.GetEventObject()
505	item = self.objList[Obj.GetId()]
506	try:
507	self.data[item[0]][item[1]] = float(Obj.GetValue())
508	except ValueError:
509	pass
510	Obj.SetValue("%.3f"%(self.data[item[0]][item[1]])) #reset in case of error
511
512	def GetData(self):
513	'Returns the values from the dialog'
514	return self.data
515
516	def OnOk(self,event):
517	'Called when the OK button is pressed'
518	parent = self.GetParent()
519	parent.Raise()
520	self.EndModal(wx.ID_OK)
521
522	def OnReset(self,event):
523	'Called when the Reset button is pressed'
524	data = {}
525	self._default(data,self.default)
526	self.Draw(self.data)
527
528	################################################################################
529	class ShowLSParms(wx.Dialog):
530	'''Create frame to show least-squares parameters
531	'''
532	def __init__(self,parent,title,parmDict,varyList,fullVaryList,
533	size=(300,430)):
534	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,size=size,
535	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
536	mainSizer = wx.BoxSizer(wx.VERTICAL)
537
538	panel = wxscroll.ScrolledPanel(
539	self, wx.ID_ANY,
540	#size=size,
541	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
542	num = len(varyList)
543	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,'Number of refined variables: '+str(num)))
544	if len(varyList) != len(fullVaryList):
545	num = len(fullVaryList) - len(varyList)
546	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,' + '+str(num)+' parameters are varied via constraints'))
547	subSizer = wx.FlexGridSizer(cols=4,hgap=2,vgap=2)
548	parmNames = parmDict.keys()
549	parmNames.sort()
550	subSizer.Add((-1,-1))
551	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'Parameter name '))
552	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'refine?'))
553	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'value'),0,wx.ALIGN_RIGHT)
554	explainRefine = False
555	for name in parmNames:
556	# skip entries without numerical values
557	if isinstance(parmDict[name],basestring): continue
558	try:
559	value = G2py3.FormatSigFigs(parmDict[name])
560	except TypeError:
561	value = str(parmDict[name])+' -?' # unexpected
562	#continue
563	v = G2obj.getVarDescr(name)
564	if v is None or v[-1] is None:
565	subSizer.Add((-1,-1))
566	else:
567	ch = G2G.HelpButton(panel,G2obj.fmtVarDescr(name))
568	subSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
569	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,str(name)))
570	if name in varyList:
571	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'R'))
572	elif name in fullVaryList:
573	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'C'))
574	explainRefine = True
575	else:
576	subSizer.Add((-1,-1))
577	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
578
579	# finish up ScrolledPanel
580	panel.SetSizer(subSizer)
581	panel.SetAutoLayout(1)
582	panel.SetupScrolling()
583	mainSizer.Add(panel,1, wx.ALL\|wx.EXPAND,1)
584
585	if explainRefine:
586	mainSizer.Add(
587	wx.StaticText(self,wx.ID_ANY,
588	'"R" indicates a refined variable\n'+
589	'"C" indicates generated from a constraint'
590	),
591	0, wx.ALL,0)
592	# make OK button
593	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
594	btn = wx.Button(self, wx.ID_CLOSE,"Close")
595	btn.Bind(wx.EVT_BUTTON,self._onClose)
596	btnsizer.Add(btn)
597	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
598	# Allow window to be enlarged but not made smaller
599	self.SetSizer(mainSizer)
600	self.SetMinSize(self.GetSize())
601
602	def _onClose(self,event):
603	self.EndModal(wx.ID_CANCEL)
604
605	################################################################################
606	class DataFrame(wx.Frame):
607	'''Create the data item window and all the entries in menus used in
608	that window. For Linux and windows, the menu entries are created for the
609	current data item window, but in the Mac the menu is accessed from all
610	windows. This means that a different menu is posted depending on which
611	data item is posted. On the Mac, all the menus contain the data tree menu
612	items, but additional menus are added specific to the data item.
613
614	Note that while the menus are created here,
615	the binding for the menus is done later in various GSASII*GUI modules,
616	where the functions to be called are defined.
617	'''
618	def Bind(self,eventtype,handler,args,*kwargs):
619	'''Override the Bind() function: on the Mac the binding is to
620	the main window, so that menus operate with any window on top.
621	For other platforms, either wrap calls that will be logged
622	or call the default wx.Frame Bind() to bind to the menu item directly.
623
624	Note that bindings can be made to objects by Id or by direct reference to the
625	object. As a convention, when bindings are to objects, they are not logged
626	but when bindings are by Id, they are logged.
627	'''
628	if sys.platform == "darwin": # mac
629	self.G2frame.Bind(eventtype,handler,args,*kwargs)
630	return
631	if eventtype == wx.EVT_MENU and 'id' in kwargs:
632	menulabels = log.SaveMenuCommand(kwargs['id'],self.G2frame,handler)
633	if menulabels:
634	#print 'intercepting bind for',handler,menulabels,kwargs['id']
635	wx.Frame.Bind(self,eventtype,self.G2frame.MenuBinding,args,*kwargs)
636	return
637	wx.Frame.Bind(self,eventtype,handler,args,*kwargs)
638
639	def PrefillDataMenu(self,menu,helpType,helpLbl=None,empty=False):
640	'''Create the "standard" part of data frame menus. Note that on Linux and
641	Windows nothing happens here. On Mac, this menu duplicates the
642	tree menu, but adds an extra help command for the data item and a separator.
643	'''
644	self.datamenu = menu
645	self.G2frame.dataMenuBars.append(menu)
646	self.helpType = helpType
647	self.helpLbl = helpLbl
648	if sys.platform == "darwin": # mac
649	self.G2frame.FillMainMenu(menu) # add the data tree menu items
650	if not empty:
651	menu.Append(wx.Menu(title=''),title='\|') # add a separator
652
653	def PostfillDataMenu(self,empty=False):
654	'''Create the "standard" part of data frame menus. Note that on Linux and
655	Windows, this is the standard help Menu. On Mac, this menu duplicates the
656	tree menu, but adds an extra help command for the data item and a separator.
657	'''
658	menu = self.datamenu
659	helpType = self.helpType
660	helpLbl = self.helpLbl
661	if sys.platform == "darwin": # mac
662	if not empty:
663	menu.Append(wx.Menu(title=''),title='\|') # add another separator
664	menu.Append(G2G.AddHelp(self.G2frame,helpType=helpType, helpLbl=helpLbl),
665	title='&Help')
666	else: # other
667	menu.Append(menu=G2G.MyHelp(self,helpType=helpType, helpLbl=helpLbl),
668	title='&Help')
669
670	def _init_menus(self):
671	'define all GSAS-II data frame menus'
672
673	# for use where no menu or data frame help is provided
674	self.BlankMenu = wx.MenuBar()
675
676	# Controls
677	self.ControlsMenu = wx.MenuBar()
678	self.PrefillDataMenu(self.ControlsMenu,helpType='Controls',empty=True)
679	self.PostfillDataMenu(empty=True)
680
681	# Notebook
682	self.DataNotebookMenu = wx.MenuBar()
683	self.PrefillDataMenu(self.DataNotebookMenu,helpType='Notebook',empty=True)
684	self.PostfillDataMenu(empty=True)
685
686	# Comments
687	self.DataCommentsMenu = wx.MenuBar()
688	self.PrefillDataMenu(self.DataCommentsMenu,helpType='Comments',empty=True)
689	self.PostfillDataMenu(empty=True)
690
691	# Constraints - something amiss here - get weird wx C++ error after refine!
692	self.ConstraintMenu = wx.MenuBar()
693	self.PrefillDataMenu(self.ConstraintMenu,helpType='Constraints')
694	self.ConstraintTab = wx.Menu(title='')
695	self.ConstraintMenu.Append(menu=self.ConstraintTab, title='Select tab')
696	for id,txt in (
697	(wxID_CONSPHASE,'Phase'),
698	(wxID_CONSHAP,'Histogram/Phase'),
699	(wxID_CONSHIST,'Histogram'),
700	(wxID_CONSGLOBAL,'Global')):
701	self.ConstraintTab.Append(
702	id=id, kind=wx.ITEM_NORMAL,text=txt,
703	help='Select '+txt+' constraint editing tab')
704	self.ConstraintEdit = wx.Menu(title='')
705	self.ConstraintMenu.Append(menu=self.ConstraintEdit, title='Edit')
706	self.ConstraintEdit.Append(id=wxID_HOLDADD, kind=wx.ITEM_NORMAL,text='Add hold',
707	help='Add hold on a parameter value')
708	self.ConstraintEdit.Append(id=wxID_EQUIVADD, kind=wx.ITEM_NORMAL,text='Add equivalence',
709	help='Add equivalence between parameter values')
710	self.ConstraintEdit.Append(id=wxID_CONSTRAINTADD, kind=wx.ITEM_NORMAL,text='Add constraint',
711	help='Add constraint on parameter values')
712	self.ConstraintEdit.Append(id=wxID_FUNCTADD, kind=wx.ITEM_NORMAL,text='Add New Var',
713	help='Add variable composed of existing parameter')
714	self.ConstraintEdit.Append(id=wxID_EQUIVALANCEATOMS, kind=wx.ITEM_NORMAL,text='Add atom equivalence',
715	help='Add equivalences between atom parameter values')
716	self.ConstraintEdit.Enable(wxID_EQUIVALANCEATOMS,False)
717	self.ConstraintEdit.Append(id=wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add H riding constraints',
718	help='Add H atom riding constraints between atom parameter values')
719	self.ConstraintEdit.Enable(wxID_ADDRIDING,False)
720	wxID_ADDRIDING
721	self.PostfillDataMenu()
722
723	# item = self.ConstraintEdit.Append(id=wx.ID_ANY,kind=wx.ITEM_NORMAL,text='Update GUI')
724	# def UpdateGSASIIconstrGUI(event):
725	# import GSASIIconstrGUI
726	# reload(GSASIIconstrGUI)
727	# import GSASIIobj
728	# reload(GSASIIobj)
729	# self.Bind(wx.EVT_MENU,UpdateGSASIIconstrGUI,id=item.GetId())
730
731	# Rigid bodies
732	self.RigidBodyMenu = wx.MenuBar()
733	self.PrefillDataMenu(self.RigidBodyMenu,helpType='Rigid bodies')
734	self.ResidueRBMenu = wx.Menu(title='')
735	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYIMPORT, kind=wx.ITEM_NORMAL,text='Import XYZ',
736	help='Import rigid body XYZ from file')
737	self.ResidueRBMenu.Append(id=wxID_RESIDUETORSSEQ, kind=wx.ITEM_NORMAL,text='Define sequence',
738	help='Define torsion sequence')
739	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYADD, kind=wx.ITEM_NORMAL,text='Import residues',
740	help='Import residue rigid bodies from macro file')
741	self.RigidBodyMenu.Append(menu=self.ResidueRBMenu, title='Edit Body')
742	self.PostfillDataMenu()
743
744	self.VectorBodyMenu = wx.MenuBar()
745	self.PrefillDataMenu(self.VectorBodyMenu,helpType='Vector rigid bodies')
746	self.VectorRBEdit = wx.Menu(title='')
747	self.VectorRBEdit.Append(id=wxID_VECTORBODYADD, kind=wx.ITEM_NORMAL,text='Add rigid body',
748	help='Add vector rigid body')
749	self.VectorBodyMenu.Append(menu=self.VectorRBEdit, title='Edit Vector Body')
750	self.PostfillDataMenu()
751
752
753	# Restraints
754	self.RestraintTab = wx.Menu(title='')
755	self.RestraintEdit = wx.Menu(title='')
756	self.RestraintEdit.Append(id=wxID_RESTSELPHASE, kind=wx.ITEM_NORMAL,text='Select phase',
757	help='Select phase')
758	self.RestraintEdit.Append(id=wxID_RESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add restraints',
759	help='Add restraints')
760	self.RestraintEdit.Enable(wxID_RESTRAINTADD,True) #gets disabled if macromolecule phase
761	self.RestraintEdit.Append(id=wxID_AARESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add residue restraints',
762	help='Add residue based restraints for macromolecules from macro file')
763	self.RestraintEdit.Enable(wxID_AARESTRAINTADD,False) #gets enabled if macromolecule phase
764	self.RestraintEdit.Append(id=wxID_AARESTRAINTPLOT, kind=wx.ITEM_NORMAL,text='Plot residue restraints',
765	help='Plot selected residue based restraints for macromolecules from macro file')
766	self.RestraintEdit.Enable(wxID_AARESTRAINTPLOT,False) #gets enabled if macromolecule phase
767	self.RestraintEdit.Append(id=wxID_RESRCHANGEVAL, kind=wx.ITEM_NORMAL,text='Change value',
768	help='Change observed value')
769	self.RestraintEdit.Append(id=wxID_RESTCHANGEESD, kind=wx.ITEM_NORMAL,text='Change esd',
770	help='Change esd in observed value')
771	self.RestraintEdit.Append(id=wxID_RESTDELETE, kind=wx.ITEM_NORMAL,text='Delete restraints',
772	help='Delete selected restraints')
773
774	self.RestraintMenu = wx.MenuBar()
775	self.PrefillDataMenu(self.RestraintMenu,helpType='Restraints')
776	self.RestraintMenu.Append(menu=self.RestraintTab, title='Select tab')
777	self.RestraintMenu.Append(menu=self.RestraintEdit, title='Edit')
778	self.PostfillDataMenu()
779
780	# Sequential results
781	self.SequentialMenu = wx.MenuBar()
782	self.PrefillDataMenu(self.SequentialMenu,helpType='Sequential',helpLbl='Sequential Refinement')
783	self.SequentialFile = wx.Menu(title='')
784	self.SequentialMenu.Append(menu=self.SequentialFile, title='Columns')
785	self.SequentialFile.Append(id=wxID_RENAMESEQSEL, kind=wx.ITEM_NORMAL,text='Rename selected',
786	help='Rename selected sequential refinement columns')
787	self.SequentialFile.Append(id=wxID_SAVESEQSEL, kind=wx.ITEM_NORMAL,text='Save selected as text',
788	help='Save selected sequential refinement results as a text file')
789	self.SequentialFile.Append(id=wxID_SAVESEQCSV, kind=wx.ITEM_NORMAL,text='Save all as CSV',
790	help='Save all sequential refinement results as a CSV spreadsheet file')
791	self.SequentialFile.Append(id=wxID_SAVESEQSELCSV, kind=wx.ITEM_NORMAL,text='Save selected as CSV',
792	help='Save selected sequential refinement results as a CSV spreadsheet file')
793	self.SequentialFile.Append(id=wxID_PLOTSEQSEL, kind=wx.ITEM_NORMAL,text='Plot selected',
794	help='Plot selected sequential refinement results')
795	self.SequentialFile.Append(id=wxID_AVESEQSEL, kind=wx.ITEM_NORMAL,text='Compute average',
796	help='Compute average for selected parameter')
797	self.SequentialFile.Append(id=wxID_ORGSEQSEL, kind=wx.ITEM_NORMAL,text='Reorganize',
798	help='Reorganize variables where variables change')
799	self.SequentialPvars = wx.Menu(title='')
800	self.SequentialMenu.Append(menu=self.SequentialPvars, title='Pseudo Vars')
801	self.SequentialPvars.Append(
802	id=wxADDSEQVAR, kind=wx.ITEM_NORMAL,text='Add',
803	help='Add a new pseudo-variable')
804	self.SequentialPvars.Append(
805	id=wxDELSEQVAR, kind=wx.ITEM_NORMAL,text='Delete',
806	help='Delete an existing pseudo-variable')
807	self.SequentialPvars.Append(
808	id=wxEDITSEQVAR, kind=wx.ITEM_NORMAL,text='Edit',
809	help='Edit an existing pseudo-variable')
810
811	self.SequentialPfit = wx.Menu(title='')
812	self.SequentialMenu.Append(menu=self.SequentialPfit, title='Parametric Fit')
813	self.SequentialPfit.Append(
814	id=wxADDPARFIT, kind=wx.ITEM_NORMAL,text='Add equation',
815	help='Add a new equation to minimize')
816	self.SequentialPfit.Append(
817	id=wxCOPYPARFIT, kind=wx.ITEM_NORMAL,text='Copy equation',
818	help='Copy an equation to minimize - edit it next')
819	self.SequentialPfit.Append(
820	id=wxDELPARFIT, kind=wx.ITEM_NORMAL,text='Delete equation',
821	help='Delete an equation for parametric minimization')
822	self.SequentialPfit.Append(
823	id=wxEDITPARFIT, kind=wx.ITEM_NORMAL,text='Edit equation',
824	help='Edit an existing parametric minimization equation')
825	self.SequentialPfit.Append(
826	id=wxDOPARFIT, kind=wx.ITEM_NORMAL,text='Fit to equation(s)',
827	help='Perform a parametric minimization')
828	self.PostfillDataMenu()
829
830	# PWDR & SASD
831	self.PWDRMenu = wx.MenuBar()
832	self.PrefillDataMenu(self.PWDRMenu,helpType='PWDR Analysis',helpLbl='Powder Fit Error Analysis')
833	self.ErrorAnal = wx.Menu(title='')
834	self.PWDRMenu.Append(menu=self.ErrorAnal,title='Commands')
835	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
836	help='Error analysis on powder pattern')
837	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
838	help='Copy of PWDR parameters')
839	self.ErrorAnal.Append(id=wxID_PLOTCTRLCOPY,kind=wx.ITEM_NORMAL,text='Copy plot controls',
840	help='Copy of PWDR plot controls')
841
842	self.PostfillDataMenu()
843
844	# HKLF
845	self.HKLFMenu = wx.MenuBar()
846	self.PrefillDataMenu(self.HKLFMenu,helpType='HKLF Analysis',helpLbl='HKLF Fit Error Analysis')
847	self.ErrorAnal = wx.Menu(title='')
848	self.HKLFMenu.Append(menu=self.ErrorAnal,title='Commands')
849	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
850	help='Error analysis on single crystal data')
851	self.ErrorAnal.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
852	help='Plot HKLs from single crystal data in 3D')
853	self.ErrorAnal.Append(id=wxID_3DALLHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot all 3D HKLs',
854	help='Plot HKLs from all single crystal data in 3D')
855	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
856	help='Copy of HKLF parameters')
857	self.PostfillDataMenu()
858
859	# PDR / Limits
860	self.LimitMenu = wx.MenuBar()
861	self.PrefillDataMenu(self.LimitMenu,helpType='Limits')
862	self.LimitEdit = wx.Menu(title='')
863	self.LimitMenu.Append(menu=self.LimitEdit, title='Edit')
864	self.LimitEdit.Append(id=wxID_LIMITCOPY, kind=wx.ITEM_NORMAL,text='Copy',
865	help='Copy limits to other histograms')
866	self.LimitEdit.Append(id=wxID_ADDEXCLREGION, kind=wx.ITEM_NORMAL,text='Add exclude',
867	help='Add excluded region - select a point on plot; drag to adjust')
868	self.PostfillDataMenu()
869
870	# PDR / Background
871	self.BackMenu = wx.MenuBar()
872	self.PrefillDataMenu(self.BackMenu,helpType='Background')
873	self.BackEdit = wx.Menu(title='')
874	self.BackMenu.Append(menu=self.BackEdit, title='File')
875	self.BackEdit.Append(id=wxID_BACKCOPY, kind=wx.ITEM_NORMAL,text='Copy',
876	help='Copy background parameters to other histograms')
877	self.BackEdit.Append(id=wxID_BACKFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
878	help='Copy background refinement flags to other histograms')
879	self.BackEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
880	help='Move background peaks to Peak List')
881	self.BackFixed = wx.Menu(title='') # fixed background point menu
882	self.BackMenu.Append(menu=self.BackFixed, title='Fixed Points')
883	self.wxID_BackPts = {}
884	self.wxID_BackPts['Add'] = wx.NewId() # N.B. not using wxID_ global as for other menu items
885	self.BackFixed.Append(id=self.wxID_BackPts['Add'], kind=wx.ITEM_RADIO,text='Add',
886	help='Add fixed background points with mouse clicks')
887	self.wxID_BackPts['Move'] = wx.NewId()
888	item = self.BackFixed.Append(id=self.wxID_BackPts['Move'], kind=wx.ITEM_RADIO,text='Move',
889	help='Move selected fixed background points with mouse drags')
890	item.Check(True)
891	self.wxID_BackPts['Del'] = wx.NewId()
892	self.BackFixed.Append(id=self.wxID_BackPts['Del'], kind=wx.ITEM_RADIO,text='Delete',
893	help='Delete fixed background points with mouse clicks')
894	self.wxID_BackPts['Clear'] = wx.NewId()
895	self.BackFixed.Append(id=self.wxID_BackPts['Clear'], kind=wx.ITEM_NORMAL,text='Clear',
896	help='Clear fixed background points')
897	self.wxID_BackPts['Fit'] = wx.NewId()
898	self.BackFixed.Append(id=self.wxID_BackPts['Fit'], kind=wx.ITEM_NORMAL,text='Fit background',
899	help='Fit background function to fixed background points')
900	self.PostfillDataMenu()
901
902	# PDR / Instrument Parameters
903	self.InstMenu = wx.MenuBar()
904	self.PrefillDataMenu(self.InstMenu,helpType='Instrument Parameters')
905	self.InstEdit = wx.Menu(title='')
906	self.InstMenu.Append(menu=self.InstEdit, title='Operations')
907	self.InstEdit.Append(help='Calibrate from indexed peaks',
908	id=wxID_INSTCALIB, kind=wx.ITEM_NORMAL,text='Calibrate')
909	self.InstEdit.Append(help='Reset instrument profile parameters to default',
910	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
911	self.InstEdit.Append(help='Load instrument profile parameters from file',
912	id=wxID_INSTLOAD, kind=wx.ITEM_NORMAL,text='Load profile...')
913	self.InstEdit.Append(help='Save instrument profile parameters to file',
914	id=wxID_INSTSAVE, kind=wx.ITEM_NORMAL,text='Save profile...')
915	self.InstEdit.Append(help='Copy instrument profile parameters to other histograms',
916	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
917	self.InstEdit.Append(id=wxID_INSTFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
918	help='Copy instrument parameter refinement flags to other histograms')
919	# self.InstEdit.Append(help='Change radiation type (Ka12 - synch)',
920	# id=wxID_CHANGEWAVETYPE, kind=wx.ITEM_NORMAL,text='Change radiation')
921	self.InstEdit.Append(id=wxID_INST1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
922	help='Set one instrument parameter value across multiple histograms')
923
924	self.PostfillDataMenu()
925
926	# PDR / Sample Parameters
927	self.SampleMenu = wx.MenuBar()
928	self.PrefillDataMenu(self.SampleMenu,helpType='Sample Parameters')
929	self.SampleEdit = wx.Menu(title='')
930	self.SampleMenu.Append(menu=self.SampleEdit, title='Command')
931	self.SetScale = self.SampleEdit.Append(id=wxID_SETSCALE, kind=wx.ITEM_NORMAL,text='Set scale',
932	help='Set scale by matching to another histogram')
933	self.SampleEdit.Append(id=wxID_SAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load',
934	help='Load sample parameters from file')
935	self.SampleEdit.Append(id=wxID_SAMPLESAVE, kind=wx.ITEM_NORMAL,text='Save',
936	help='Save sample parameters to file')
937	self.SampleEdit.Append(id=wxID_SAMPLECOPY, kind=wx.ITEM_NORMAL,text='Copy',
938	help='Copy refinable and most other sample parameters to other histograms')
939	self.SampleEdit.Append(id=wxID_SAMPLECOPYSOME, kind=wx.ITEM_NORMAL,text='Copy selected...',
940	help='Copy selected sample parameters to other histograms')
941	self.SampleEdit.Append(id=wxID_SAMPLEFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
942	help='Copy sample parameter refinement flags to other histograms')
943	self.SampleEdit.Append(id=wxID_SAMPLE1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
944	help='Set one sample parameter value across multiple histograms')
945	self.SampleEdit.Append(id=wxID_ALLSAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load all',
946	help='Load sample parmameters over multiple histograms')
947
948	self.PostfillDataMenu()
949	self.SetScale.Enable(False)
950
951	# PDR / Peak List
952	self.PeakMenu = wx.MenuBar()
953	self.PrefillDataMenu(self.PeakMenu,helpType='Peak List')
954	self.PeakEdit = wx.Menu(title='')
955	self.PeakMenu.Append(menu=self.PeakEdit, title='Peak Fitting')
956	self.AutoSearch = self.PeakEdit.Append(help='Automatic peak search',
957	id=wxID_AUTOSEARCH, kind=wx.ITEM_NORMAL,text='Auto search')
958	self.UnDo = self.PeakEdit.Append(help='Undo last least squares refinement',
959	id=wxID_UNDO, kind=wx.ITEM_NORMAL,text='UnDo')
960	self.PeakFit = self.PeakEdit.Append(id=wxID_LSQPEAKFIT, kind=wx.ITEM_NORMAL,text='Peakfit',
961	help='Peak fitting' )
962	self.PFOneCycle = self.PeakEdit.Append(id=wxID_LSQONECYCLE, kind=wx.ITEM_NORMAL,text='Peakfit one cycle',
963	help='One cycle of Peak fitting' )
964	self.PeakEdit.Append(id=wxID_RESETSIGGAM, kind=wx.ITEM_NORMAL,
965	text='Reset sig and gam',help='Reset sigma and gamma to global fit' )
966	self.PeakCopy = self.PeakEdit.Append(help='Copy peaks to other histograms',
967	id=wxID_PEAKSCOPY, kind=wx.ITEM_NORMAL,text='Peak copy')
968	self.SeqPeakFit = self.PeakEdit.Append(id=wxID_SEQPEAKFIT, kind=wx.ITEM_NORMAL,text='Seq PeakFit',
969	help='Sequential Peak fitting for all histograms' )
970	self.PeakEdit.Append(id=wxID_CLEARPEAKS, kind=wx.ITEM_NORMAL,text='Clear peaks',
971	help='Clear the peak list' )
972	self.PostfillDataMenu()
973	self.UnDo.Enable(False)
974	self.PeakFit.Enable(False)
975	self.PFOneCycle.Enable(False)
976	self.AutoSearch.Enable(True)
977
978	# PDR / Index Peak List
979	self.IndPeaksMenu = wx.MenuBar()
980	self.PrefillDataMenu(self.IndPeaksMenu,helpType='Index Peak List')
981	self.IndPeaksEdit = wx.Menu(title='')
982	self.IndPeaksMenu.Append(menu=self.IndPeaksEdit,title='Operations')
983	self.IndPeaksEdit.Append(help='Load/Reload index peaks from peak list',id=wxID_INDXRELOAD,
984	kind=wx.ITEM_NORMAL,text='Load/Reload')
985	self.PostfillDataMenu()
986
987	# PDR / Unit Cells List
988	self.IndexMenu = wx.MenuBar()
989	self.PrefillDataMenu(self.IndexMenu,helpType='Unit Cells List')
990	self.IndexEdit = wx.Menu(title='')
991	self.IndexMenu.Append(menu=self.IndexEdit, title='Cell Index/Refine')
992	self.IndexPeaks = self.IndexEdit.Append(help='', id=wxID_INDEXPEAKS, kind=wx.ITEM_NORMAL,
993	text='Index Cell')
994	self.CopyCell = self.IndexEdit.Append( id=wxID_COPYCELL, kind=wx.ITEM_NORMAL,text='Copy Cell',
995	help='Copy selected unit cell from indexing to cell refinement fields')
996	self.RefineCell = self.IndexEdit.Append( id=wxID_REFINECELL, kind=wx.ITEM_NORMAL,
997	text='Refine Cell',help='Refine unit cell parameters from indexed peaks')
998	self.MakeNewPhase = self.IndexEdit.Append( id=wxID_MAKENEWPHASE, kind=wx.ITEM_NORMAL,
999	text='Make new phase',help='Make new phase from selected unit cell')
1000	self.ExportCells = self.IndexEdit.Append( id=wxID_EXPORTCELLS, kind=wx.ITEM_NORMAL,
1001	text='Export cell list',help='Export cell list to csv file')
1002	self.PostfillDataMenu()
1003	self.IndexPeaks.Enable(False)
1004	self.CopyCell.Enable(False)
1005	self.RefineCell.Enable(False)
1006	self.MakeNewPhase.Enable(False)
1007
1008	# PDR / Reflection Lists
1009	self.ReflMenu = wx.MenuBar()
1010	self.PrefillDataMenu(self.ReflMenu,helpType='Reflection List')
1011	self.ReflEdit = wx.Menu(title='')
1012	self.ReflMenu.Append(menu=self.ReflEdit, title='Reflection List')
1013	self.SelectPhase = self.ReflEdit.Append(help='Select phase for reflection list',id=wxID_SELECTPHASE,
1014	kind=wx.ITEM_NORMAL,text='Select phase')
1015	self.ReflEdit.Append(id=wxID_PWDHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot HKLs',
1016	help='Plot HKLs from powder pattern')
1017	self.ReflEdit.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
1018	help='Plot HKLs from powder pattern in 3D')
1019	self.PostfillDataMenu()
1020
1021	# SASD / Instrument Parameters
1022	self.SASDInstMenu = wx.MenuBar()
1023	self.PrefillDataMenu(self.SASDInstMenu,helpType='Instrument Parameters')
1024	self.SASDInstEdit = wx.Menu(title='')
1025	self.SASDInstMenu.Append(menu=self.SASDInstEdit, title='Operations')
1026	self.InstEdit.Append(help='Reset instrument profile parameters to default',
1027	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
1028	self.SASDInstEdit.Append(help='Copy instrument profile parameters to other histograms',
1029	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
1030	self.PostfillDataMenu()
1031
1032	#SASD & REFL/ Substance editor
1033	self.SubstanceMenu = wx.MenuBar()
1034	self.PrefillDataMenu(self.SubstanceMenu,helpType='Substances')
1035	self.SubstanceEdit = wx.Menu(title='')
1036	self.SubstanceMenu.Append(menu=self.SubstanceEdit, title='Edit')
1037	self.SubstanceEdit.Append(id=wxID_LOADSUBSTANCE, kind=wx.ITEM_NORMAL,text='Load substance',
1038	help='Load substance from file')
1039	self.SubstanceEdit.Append(id=wxID_ADDSUBSTANCE, kind=wx.ITEM_NORMAL,text='Add substance',
1040	help='Add new substance to list')
1041	self.SubstanceEdit.Append(id=wxID_COPYSUBSTANCE, kind=wx.ITEM_NORMAL,text='Copy substances',
1042	help='Copy substances')
1043	self.SubstanceEdit.Append(id=wxID_DELETESUBSTANCE, kind=wx.ITEM_NORMAL,text='Delete substance',
1044	help='Delete substance from list')
1045	self.SubstanceEdit.Append(id=wxID_ELEMENTADD, kind=wx.ITEM_NORMAL,text='Add elements',
1046	help='Add elements to substance')
1047	self.SubstanceEdit.Append(id=wxID_ELEMENTDELETE, kind=wx.ITEM_NORMAL,text='Delete elements',
1048	help='Delete elements from substance')
1049	self.PostfillDataMenu()
1050
1051	# SASD/ Models
1052	self.ModelMenu = wx.MenuBar()
1053	self.PrefillDataMenu(self.ModelMenu,helpType='Models')
1054	self.ModelEdit = wx.Menu(title='')
1055	self.ModelMenu.Append(menu=self.ModelEdit, title='Models')
1056	self.ModelEdit.Append(id=wxID_MODELADD,kind=wx.ITEM_NORMAL,text='Add',
1057	help='Add new term to model')
1058	self.ModelEdit.Append(id=wxID_MODELFIT, kind=wx.ITEM_NORMAL,text='Fit',
1059	help='Fit model parameters to data')
1060	self.SasdUndo = self.ModelEdit.Append(id=wxID_MODELUNDO, kind=wx.ITEM_NORMAL,text='Undo',
1061	help='Undo model fit')
1062	self.SasdUndo.Enable(False)
1063	self.ModelEdit.Append(id=wxID_MODELFITALL, kind=wx.ITEM_NORMAL,text='Sequential fit',
1064	help='Sequential fit of model parameters to all SASD data')
1065	self.ModelEdit.Append(id=wxID_MODELCOPY, kind=wx.ITEM_NORMAL,text='Copy',
1066	help='Copy model parameters to other histograms')
1067	self.ModelEdit.Append(id=wxID_MODELCOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1068	help='Copy model refinement flags to other histograms')
1069	self.PostfillDataMenu()
1070
1071	# IMG / Image Controls
1072	self.ImageMenu = wx.MenuBar()
1073	self.PrefillDataMenu(self.ImageMenu,helpType='Image Controls')
1074	self.ImageEdit = wx.Menu(title='')
1075	self.ImageMenu.Append(menu=self.ImageEdit, title='Operations')
1076	self.ImageEdit.Append(help='Calibrate detector by fitting to calibrant lines',
1077	id=wxID_IMCALIBRATE, kind=wx.ITEM_NORMAL,text='Calibrate')
1078	self.ImageEdit.Append(help='Recalibrate detector by fitting to calibrant lines',
1079	id=wxID_IMRECALIBRATE, kind=wx.ITEM_NORMAL,text='Recalibrate')
1080	self.ImageEdit.Append(help='Clear calibration data points and rings',id=wxID_IMCLEARCALIB,
1081	kind=wx.ITEM_NORMAL,text='Clear calibration')
1082	self.ImageEdit.Append(help='Integrate selected image',id=wxID_IMINTEGRATE,
1083	kind=wx.ITEM_NORMAL,text='Integrate')
1084	self.ImageEdit.Append(help='Integrate all images selected from list',id=wxID_INTEGRATEALL,
1085	kind=wx.ITEM_NORMAL,text='Integrate all')
1086	self.ImageEdit.Append(help='Copy image controls to other images',
1087	id=wxID_IMCOPYCONTROLS, kind=wx.ITEM_NORMAL,text='Copy Controls')
1088	self.ImageEdit.Append(help='Save image controls to file',
1089	id=wxID_IMSAVECONTROLS, kind=wx.ITEM_NORMAL,text='Save Controls')
1090	self.ImageEdit.Append(help='Load image controls from file',
1091	id=wxID_IMLOADCONTROLS, kind=wx.ITEM_NORMAL,text='Load Controls')
1092	self.PostfillDataMenu()
1093
1094	# IMG / Masks
1095	self.MaskMenu = wx.MenuBar()
1096	self.PrefillDataMenu(self.MaskMenu,helpType='Image Masks')
1097	self.MaskEdit = wx.Menu(title='')
1098	self.MaskMenu.Append(menu=self.MaskEdit, title='Operations')
1099	submenu = wx.Menu()
1100	self.MaskEdit.AppendMenu(
1101	wx.ID_ANY,'Create new', submenu,
1102	help=''
1103	)
1104	self.MaskEdit.Append(help='Copy mask to other images',
1105	id=wxID_MASKCOPY, kind=wx.ITEM_NORMAL,text='Copy mask')
1106	self.MaskEdit.Append(help='Save mask to file',
1107	id=wxID_MASKSAVE, kind=wx.ITEM_NORMAL,text='Save mask')
1108	self.MaskEdit.Append(help='Load mask from file',
1109	id=wxID_MASKLOAD, kind=wx.ITEM_NORMAL,text='Load mask')
1110	self.MaskEdit.Append(help='Load mask from file; ignore threshold',
1111	id=wxID_MASKLOADNOT, kind=wx.ITEM_NORMAL,text='Load mask w/o threshold')
1112	submenu.Append(help='Create an arc mask with mouse input',
1113	id=wxID_NEWMASKARC, kind=wx.ITEM_NORMAL,text='Arc mask')
1114	submenu.Append(help='Create a frame mask with mouse input',
1115	id=wxID_NEWMASKFRAME, kind=wx.ITEM_NORMAL,text='Frame mask')
1116	submenu.Append(help='Create a polygon mask with mouse input',
1117	id=wxID_NEWMASKPOLY, kind=wx.ITEM_NORMAL,text='Polygon mask')
1118	submenu.Append(help='Create a ring mask with mouse input',
1119	id=wxID_NEWMASKRING, kind=wx.ITEM_NORMAL,text='Ring mask')
1120	submenu.Append(help='Create a spot mask with mouse input',
1121	id=wxID_NEWMASKSPOT, kind=wx.ITEM_NORMAL,text='Spot mask')
1122	self.PostfillDataMenu()
1123
1124	# IMG / Stress/Strain
1125	self.StrStaMenu = wx.MenuBar()
1126	self.PrefillDataMenu(self.StrStaMenu,helpType='Stress/Strain')
1127	self.StrStaEdit = wx.Menu(title='')
1128	self.StrStaMenu.Append(menu=self.StrStaEdit, title='Operations')
1129	self.StrStaEdit.Append(help='Append d-zero for one ring',
1130	id=wxID_APPENDDZERO, kind=wx.ITEM_NORMAL,text='Append d-zero')
1131	self.StrStaEdit.Append(help='Fit stress/strain data',
1132	id=wxID_STRSTAFIT, kind=wx.ITEM_NORMAL,text='Fit stress/strain')
1133	self.StrStaEdit.Append(help='Update d-zero from ave d-zero',
1134	id=wxID_UPDATEDZERO, kind=wx.ITEM_NORMAL,text='Update d-zero')
1135	self.StrStaEdit.Append(help='Fit stress/strain data for all images',
1136	id=wxID_STRSTAALLFIT, kind=wx.ITEM_NORMAL,text='All image fit')
1137	self.StrStaEdit.Append(help='Copy stress/strain data to other images',
1138	id=wxID_STRSTACOPY, kind=wx.ITEM_NORMAL,text='Copy stress/strain')
1139	self.StrStaEdit.Append(help='Save stress/strain data to file',
1140	id=wxID_STRSTASAVE, kind=wx.ITEM_NORMAL,text='Save stress/strain')
1141	self.StrStaEdit.Append(help='Load stress/strain data from file',
1142	id=wxID_STRSTALOAD, kind=wx.ITEM_NORMAL,text='Load stress/strain')
1143	self.StrStaEdit.Append(help='Load sample data from file',
1144	id=wxID_STRSTSAMPLE, kind=wx.ITEM_NORMAL,text='Load sample data')
1145	self.PostfillDataMenu()
1146
1147	# PDF / PDF Controls
1148	self.PDFMenu = wx.MenuBar()
1149	self.PrefillDataMenu(self.PDFMenu,helpType='PDF Controls')
1150	self.PDFEdit = wx.Menu(title='')
1151	self.PDFMenu.Append(menu=self.PDFEdit, title='PDF Controls')
1152	self.PDFEdit.Append(help='Add element to sample composition',id=wxID_PDFADDELEMENT, kind=wx.ITEM_NORMAL,
1153	text='Add element')
1154	self.PDFEdit.Append(help='Delete element from sample composition',id=wxID_PDFDELELEMENT, kind=wx.ITEM_NORMAL,
1155	text='Delete element')
1156	self.PDFEdit.Append(help='Copy PDF controls', id=wxID_PDFCOPYCONTROLS, kind=wx.ITEM_NORMAL,
1157	text='Copy controls')
1158	self.PDFEdit.Append(help='Load PDF controls from file',id=wxID_PDFLOADCONTROLS, kind=wx.ITEM_NORMAL,
1159	text='Load Controls')
1160	self.PDFEdit.Append(help='Save PDF controls to file', id=wxID_PDFSAVECONTROLS, kind=wx.ITEM_NORMAL,
1161	text='Save controls')
1162	self.PDFEdit.Append(help='Compute PDF', id=wxID_PDFCOMPUTE, kind=wx.ITEM_NORMAL,
1163	text='Compute PDF')
1164	self.PDFEdit.Append(help='Compute all PDFs', id=wxID_PDFCOMPUTEALL, kind=wx.ITEM_NORMAL,
1165	text='Compute all PDFs')
1166	self.PostfillDataMenu()
1167
1168	# Phase / General tab
1169	self.DataGeneral = wx.MenuBar()
1170	self.PrefillDataMenu(self.DataGeneral,helpType='General', helpLbl='Phase/General')
1171	self.DataGeneral.Append(menu=wx.Menu(title=''),title='Select tab')
1172	self.GeneralCalc = wx.Menu(title='')
1173	self.DataGeneral.Append(menu=self.GeneralCalc,title='Compute')
1174	self.GeneralCalc.Append(help='Compute Fourier map',id=wxID_FOURCALC, kind=wx.ITEM_NORMAL,
1175	text='Fourier map')
1176	self.GeneralCalc.Append(help='Search Fourier map',id=wxID_FOURSEARCH, kind=wx.ITEM_NORMAL,
1177	text='Search map')
1178	self.GeneralCalc.Append(help='Run charge flipping',id=wxID_CHARGEFLIP, kind=wx.ITEM_NORMAL,
1179	text='Charge flipping')
1180	self.GeneralCalc.Append(help='Run 4D charge flipping',id=wxID_4DCHARGEFLIP, kind=wx.ITEM_NORMAL,
1181	text='4D Charge flipping')
1182	self.GeneralCalc.Enable(wxID_4DCHARGEFLIP,False)
1183	self.GeneralCalc.Append(help='Clear map',id=wxID_FOURCLEAR, kind=wx.ITEM_NORMAL,
1184	text='Clear map')
1185	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing',id=wxID_SINGLEMCSA, kind=wx.ITEM_NORMAL,
1186	text='MC/SA')
1187	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing on multiprocessors',id=wxID_MULTIMCSA, kind=wx.ITEM_NORMAL,
1188	text='Multi MC/SA') #currently not useful
1189	self.PostfillDataMenu()
1190
1191	# Phase / Data tab
1192	self.DataMenu = wx.MenuBar()
1193	self.PrefillDataMenu(self.DataMenu,helpType='Data', helpLbl='Phase/Data')
1194	self.DataMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1195	self.DataEdit = wx.Menu(title='')
1196	self.DataMenu.Append(menu=self.DataEdit, title='Edit')
1197	self.DataEdit.Append(id=wxID_DATACOPY, kind=wx.ITEM_NORMAL,text='Copy data',
1198	help='Copy phase data to other histograms')
1199	self.DataEdit.Append(id=wxID_DATACOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1200	help='Copy phase data flags to other histograms')
1201	self.DataEdit.Append(id=wxID_DATASELCOPY, kind=wx.ITEM_NORMAL,text='Copy selected data',
1202	help='Copy selected phase data to other histograms')
1203	self.DataEdit.Append(id=wxID_PWDRADD, kind=wx.ITEM_NORMAL,text='Add powder histograms',
1204	help='Select new powder histograms to be used for this phase')
1205	self.DataEdit.Append(id=wxID_HKLFADD, kind=wx.ITEM_NORMAL,text='Add single crystal histograms',
1206	help='Select new single crystal histograms to be used for this phase')
1207	self.DataEdit.Append(id=wxID_DATADELETE, kind=wx.ITEM_NORMAL,text='Remove histograms',
1208	help='Remove histograms from use for this phase')
1209	self.PostfillDataMenu()
1210
1211	# Phase / Atoms tab
1212	self.AtomsMenu = wx.MenuBar()
1213	self.PrefillDataMenu(self.AtomsMenu,helpType='Atoms')
1214	self.AtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1215	self.AtomEdit = wx.Menu(title='')
1216	self.AtomCompute = wx.Menu(title='')
1217	self.AtomsMenu.Append(menu=self.AtomEdit, title='Edit')
1218	self.AtomsMenu.Append(menu=self.AtomCompute, title='Compute')
1219	self.AtomEdit.Append(id=wxID_ATOMSEDITADD, kind=wx.ITEM_NORMAL,text='Append atom',
1220	help='Appended as an H atom')
1221	self.AtomEdit.Append(id=wxID_ATOMSVIEWADD, kind=wx.ITEM_NORMAL,text='Append view point',
1222	help='Appended as an H atom')
1223	self.AtomEdit.Append(id=wxID_ATOMSEDITINSERT, kind=wx.ITEM_NORMAL,text='Insert atom',
1224	help='Select atom row to insert before; inserted as an H atom')
1225	self.AtomEdit.Append(id=wxID_ATOMVIEWINSERT, kind=wx.ITEM_NORMAL,text='Insert view point',
1226	help='Select atom row to insert before; inserted as an H atom')
1227	self.AtomEdit.Append(id=wxID_ADDHATOM, kind=wx.ITEM_NORMAL,text='Insert H atoms',
1228	help='Insert H atoms in standard positions bonded to selected atoms')
1229	self.AtomEdit.Append(id=wxID_ATOMMOVE, kind=wx.ITEM_NORMAL,text='Move atom to view point',
1230	help='Select single atom to move')
1231	self.AtomEdit.Append(id=wxID_ATOMSEDITDELETE, kind=wx.ITEM_NORMAL,text='Delete atom',
1232	help='Select atoms to delete first')
1233	self.AtomEdit.Append(id=wxID_ATOMSREFINE, kind=wx.ITEM_NORMAL,text='Set atom refinement flags',
1234	help='Select atoms to refine first')
1235	self.AtomEdit.Append(id=wxID_ATOMSMODIFY, kind=wx.ITEM_NORMAL,text='Modify atom parameters',
1236	help='Select atoms to modify first')
1237	self.AtomEdit.Append(id=wxID_ATOMSTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform atoms',
1238	help='Select atoms to transform first')
1239	self.AtomEdit.Append(id=wxID_MAKEMOLECULE, kind=wx.ITEM_NORMAL,text='Assemble molecule',
1240	help='Assemble molecule from scatterd atom positions')
1241	self.AtomEdit.Append(id=wxID_RELOADDRAWATOMS, kind=wx.ITEM_NORMAL,text='Reload draw atoms',
1242	help='Reload atom drawing list')
1243	submenu = wx.Menu()
1244	self.AtomEdit.AppendMenu(wx.ID_ANY, 'Reimport atoms', submenu,
1245	help='Reimport atoms from file; sequence must match')
1246	# setup a cascade menu for the formats that have been defined
1247	self.ReImportMenuId = {} # points to readers for each menu entry
1248	for reader in self.G2frame.ImportPhaseReaderlist:
1249	item = submenu.Append(
1250	wx.ID_ANY,help=reader.longFormatName,
1251	kind=wx.ITEM_NORMAL,text='reimport coordinates from '+reader.formatName+' file')
1252	self.ReImportMenuId[item.GetId()] = reader
1253	item = submenu.Append(
1254	wx.ID_ANY,
1255	help='Reimport coordinates, try to determine format from file',
1256	kind=wx.ITEM_NORMAL,
1257	text='guess format from file')
1258	self.ReImportMenuId[item.GetId()] = None # try all readers
1259
1260	self.AtomCompute.Append(id=wxID_ATOMSDISAGL, kind=wx.ITEM_NORMAL,text='Show Distances && Angles',
1261	help='Compute distances & angles for selected atoms')
1262	self.AtomCompute.Append(id=wxID_ATOMSPDISAGL, kind=wx.ITEM_NORMAL,text='Save Distances && Angles',
1263	help='Compute distances & angles for selected atoms')
1264	self.AtomCompute.ISOcalc = self.AtomCompute.Append(
1265	id=wxID_ISODISP, kind=wx.ITEM_NORMAL,
1266	text='Compute ISODISTORT mode values',
1267	help='Compute values of ISODISTORT modes from atom parameters')
1268	self.PostfillDataMenu()
1269
1270	# Phase / Imcommensurate "waves" tab
1271	self.WavesData = wx.MenuBar()
1272	self.PrefillDataMenu(self.WavesData,helpType='Wave Data', helpLbl='Imcommensurate wave data')
1273	self.WavesData.Append(menu=wx.Menu(title=''),title='Select tab')
1274	self.WavesDataCompute = wx.Menu(title='')
1275	self.WavesData.Append(menu=self.WavesDataCompute,title='Compute')
1276	self.WavesDataCompute.Append(id=wxID_4DMAPCOMPUTE, kind=wx.ITEM_NORMAL,text='Compute 4D map',
1277	help='Compute 4-dimensional map')
1278	self.PostfillDataMenu()
1279
1280	# Phase / Draw Options tab
1281	self.DataDrawOptions = wx.MenuBar()
1282	self.PrefillDataMenu(self.DataDrawOptions,helpType='Draw Options', helpLbl='Phase/Draw Options')
1283	self.DataDrawOptions.Append(menu=wx.Menu(title=''),title='Select tab')
1284	self.PostfillDataMenu()
1285
1286	# Phase / Draw Atoms tab
1287	self.DrawAtomsMenu = wx.MenuBar()
1288	self.PrefillDataMenu(self.DrawAtomsMenu,helpType='Draw Atoms')
1289	self.DrawAtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1290	self.DrawAtomEdit = wx.Menu(title='')
1291	self.DrawAtomCompute = wx.Menu(title='')
1292	self.DrawAtomRestraint = wx.Menu(title='')
1293	self.DrawAtomRigidBody = wx.Menu(title='')
1294	self.DrawAtomsMenu.Append(menu=self.DrawAtomEdit, title='Edit')
1295	self.DrawAtomsMenu.Append(menu=self.DrawAtomCompute,title='Compute')
1296	self.DrawAtomsMenu.Append(menu=self.DrawAtomRestraint, title='Restraints')
1297	self.DrawAtomsMenu.Append(menu=self.DrawAtomRigidBody, title='Rigid body')
1298	self.DrawAtomEdit.Append(id=wxID_DRAWATOMSTYLE, kind=wx.ITEM_NORMAL,text='Atom style',
1299	help='Select atoms first')
1300	self.DrawAtomEdit.Append(id=wxID_DRAWATOMLABEL, kind=wx.ITEM_NORMAL,text='Atom label',
1301	help='Select atoms first')
1302	self.DrawAtomEdit.Append(id=wxID_DRAWATOMCOLOR, kind=wx.ITEM_NORMAL,text='Atom color',
1303	help='Select atoms first')
1304	self.DrawAtomEdit.Append(id=wxID_DRAWATOMRESETCOLOR, kind=wx.ITEM_NORMAL,text='Reset atom colors',
1305	help='Resets all atom colors to defaults')
1306	self.DrawAtomEdit.Append(id=wxID_DRAWVIEWPOINT, kind=wx.ITEM_NORMAL,text='View point',
1307	help='View point is 1st atom selected')
1308	self.DrawAtomEdit.Append(id=wxID_DRAWADDEQUIV, kind=wx.ITEM_NORMAL,text='Add atoms',
1309	help='Add symmetry & cell equivalents to drawing set from selected atoms')
1310	self.DrawAtomEdit.Append(id=wxID_DRAWTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform draw atoms',
1311	help='Transform selected atoms by symmetry & cell translations')
1312	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCOORD, kind=wx.ITEM_NORMAL,text='Fill CN-sphere',
1313	help='Fill coordination sphere for selected atoms')
1314	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCELL, kind=wx.ITEM_NORMAL,text='Fill unit cell',
1315	help='Fill unit cell with selected atoms')
1316	self.DrawAtomEdit.Append(id=wxID_DRAWDELETE, kind=wx.ITEM_NORMAL,text='Delete atoms',
1317	help='Delete atoms from drawing set')
1318	self.DrawAtomCompute.Append(id=wxID_DRAWDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1319	help='Compute distance of selected atoms from view point')
1320	self.DrawAtomCompute.Append(id=wxID_DRAWDISAGLTOR, kind=wx.ITEM_NORMAL,text='Dist. Ang. Tors.',
1321	help='Compute distance, angle or torsion for 2-4 selected atoms')
1322	self.DrawAtomCompute.Append(id=wxID_DRAWPLANE, kind=wx.ITEM_NORMAL,text='Best plane',
1323	help='Compute best plane for 4+ selected atoms')
1324	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRBOND, kind=wx.ITEM_NORMAL,text='Add bond restraint',
1325	help='Add bond restraint for selected atoms (2)')
1326	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRANGLE, kind=wx.ITEM_NORMAL,text='Add angle restraint',
1327	help='Add angle restraint for selected atoms (3: one end 1st)')
1328	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRPLANE, kind=wx.ITEM_NORMAL,text='Add plane restraint',
1329	help='Add plane restraint for selected atoms (4+)')
1330	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRCHIRAL, kind=wx.ITEM_NORMAL,text='Add chiral restraint',
1331	help='Add chiral restraint for selected atoms (4: center atom 1st)')
1332	self.DrawAtomRigidBody.Append(id=wxID_DRAWDEFINERB, kind=wx.ITEM_NORMAL,text='Define rigid body',
1333	help='Define rigid body with selected atoms')
1334	self.PostfillDataMenu()
1335
1336	# Phase / MCSA tab
1337	self.MCSAMenu = wx.MenuBar()
1338	self.PrefillDataMenu(self.MCSAMenu,helpType='MC/SA')
1339	self.MCSAMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1340	self.MCSAEdit = wx.Menu(title='')
1341	self.MCSAMenu.Append(menu=self.MCSAEdit, title='MC/SA')
1342	self.MCSAEdit.Append(id=wxID_ADDMCSAATOM, kind=wx.ITEM_NORMAL,text='Add atom',
1343	help='Add single atom to MC/SA model')
1344	self.MCSAEdit.Append(id=wxID_ADDMCSARB, kind=wx.ITEM_NORMAL,text='Add rigid body',
1345	help='Add rigid body to MC/SA model' )
1346	self.MCSAEdit.Append(id=wxID_CLEARMCSARB, kind=wx.ITEM_NORMAL,text='Clear rigid bodies',
1347	help='Clear all atoms & rigid bodies from MC/SA model' )
1348	self.MCSAEdit.Append(id=wxID_MOVEMCSA, kind=wx.ITEM_NORMAL,text='Move MC/SA solution',
1349	help='Move MC/SA solution to atom list' )
1350	self.MCSAEdit.Append(id=wxID_MCSACLEARRESULTS, kind=wx.ITEM_NORMAL,text='Clear results',
1351	help='Clear table of MC/SA results' )
1352	self.PostfillDataMenu()
1353
1354	# Phase / Texture tab
1355	self.TextureMenu = wx.MenuBar()
1356	self.PrefillDataMenu(self.TextureMenu,helpType='Texture')
1357	self.TextureMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1358	self.TextureEdit = wx.Menu(title='')
1359	self.TextureMenu.Append(menu=self.TextureEdit, title='Texture')
1360	self.TextureEdit.Append(id=wxID_REFINETEXTURE, kind=wx.ITEM_NORMAL,text='Refine texture',
1361	help='Refine the texture coefficients from sequential results')
1362	# self.TextureEdit.Append(id=wxID_CLEARTEXTURE, kind=wx.ITEM_NORMAL,text='Clear texture',
1363	# help='Clear the texture coefficients' )
1364	self.PostfillDataMenu()
1365
1366	# Phase / Pawley tab
1367	self.PawleyMenu = wx.MenuBar()
1368	self.PrefillDataMenu(self.PawleyMenu,helpType='Pawley')
1369	self.PawleyMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1370	self.PawleyEdit = wx.Menu(title='')
1371	self.PawleyMenu.Append(menu=self.PawleyEdit,title='Operations')
1372	self.PawleyEdit.Append(id=wxID_PAWLEYLOAD, kind=wx.ITEM_NORMAL,text='Pawley create',
1373	help='Initialize Pawley reflection list')
1374	self.PawleyEdit.Append(id=wxID_PAWLEYESTIMATE, kind=wx.ITEM_NORMAL,text='Pawley estimate',
1375	help='Estimate initial Pawley intensities')
1376	self.PawleyEdit.Append(id=wxID_PAWLEYUPDATE, kind=wx.ITEM_NORMAL,text='Pawley update',
1377	help='Update negative Pawley intensities with -0.5*Fobs and turn off refinemnt')
1378	self.PostfillDataMenu()
1379
1380	# Phase / Map peaks tab
1381	self.MapPeaksMenu = wx.MenuBar()
1382	self.PrefillDataMenu(self.MapPeaksMenu,helpType='Map peaks')
1383	self.MapPeaksMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1384	self.MapPeaksEdit = wx.Menu(title='')
1385	self.MapPeaksMenu.Append(menu=self.MapPeaksEdit, title='Map peaks')
1386	self.MapPeaksEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
1387	help='Move selected peaks to atom list')
1388	self.MapPeaksEdit.Append(id=wxID_PEAKSVIEWPT, kind=wx.ITEM_NORMAL,text='View point',
1389	help='View point is 1st peak selected')
1390	self.MapPeaksEdit.Append(id=wxID_PEAKSDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1391	help='Compute distance of selected peaks from view point')
1392	self.MapPeaksEdit.Append(id=wxID_SHOWBONDS, kind=wx.ITEM_NORMAL,text='Hide bonds',
1393	help='Hide or show bonds between peak positions')
1394	self.MapPeaksEdit.Append(id=wxID_PEAKSDA, kind=wx.ITEM_NORMAL,text='Calc dist/ang',
1395	help='Calculate distance or angle for selection')
1396	self.MapPeaksEdit.Append(id=wxID_FINDEQVPEAKS, kind=wx.ITEM_NORMAL,text='Equivalent peaks',
1397	help='Find equivalent peaks')
1398	self.MapPeaksEdit.Append(id=wxID_PEAKSUNIQUE, kind=wx.ITEM_NORMAL,text='Unique peaks',
1399	help='Select unique set')
1400	self.MapPeaksEdit.Append(id=wxID_PEAKSDELETE, kind=wx.ITEM_NORMAL,text='Delete peaks',
1401	help='Delete selected peaks')
1402	self.MapPeaksEdit.Append(id=wxID_PEAKSCLEAR, kind=wx.ITEM_NORMAL,text='Clear peaks',
1403	help='Clear the map peak list')
1404	self.PostfillDataMenu()
1405
1406	# Phase / Rigid bodies tab
1407	self.RigidBodiesMenu = wx.MenuBar()
1408	self.PrefillDataMenu(self.RigidBodiesMenu,helpType='Rigid bodies')
1409	self.RigidBodiesMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1410	self.RigidBodiesEdit = wx.Menu(title='')
1411	self.RigidBodiesMenu.Append(menu=self.RigidBodiesEdit, title='Edit')
1412	self.RigidBodiesEdit.Append(id=wxID_ASSIGNATMS2RB, kind=wx.ITEM_NORMAL,text='Assign atoms to rigid body',
1413	help='Select & position rigid body in structure of existing atoms')
1414	self.RigidBodiesEdit.Append(id=wxID_AUTOFINDRESRB, kind=wx.ITEM_NORMAL,text='Auto find residues',
1415	help='Auto find of residue RBs in macromolecule')
1416	self.RigidBodiesEdit.Append(id=wxID_COPYRBPARMS, kind=wx.ITEM_NORMAL,text='Copy rigid body parms',
1417	help='Copy rigid body location & TLS parameters')
1418	self.RigidBodiesEdit.Append(id=wxID_GLOBALTHERM, kind=wx.ITEM_NORMAL,text='Global thermal motion',
1419	help='Global setting of residue thermal motion models')
1420	self.RigidBodiesEdit.Append(id=wxID_GLOBALRESREFINE, kind=wx.ITEM_NORMAL,text='Global residue refine',
1421	help='Global setting of residue RB refinement flags')
1422	self.RigidBodiesEdit.Append(id=wxID_RBREMOVEALL, kind=wx.ITEM_NORMAL,text='Remove all rigid bodies',
1423	help='Remove all rigid body assignment for atoms')
1424	self.PostfillDataMenu()
1425	# end of GSAS-II menu definitions
1426
1427	def _init_ctrls(self, parent,name=None,size=None,pos=None):
1428	wx.Frame.__init__(
1429	self,parent=parent,
1430	#style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX \| wx.FRAME_FLOAT_ON_PARENT ,
1431	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX,
1432	size=size,pos=pos,title='GSAS-II data display')
1433	self._init_menus()
1434	if name:
1435	self.SetLabel(name)
1436	self.Show()
1437
1438	def __init__(self,parent,frame,data=None,name=None, size=None,pos=None):
1439	self.G2frame = frame
1440	self._init_ctrls(parent,name,size,pos)
1441	self.data = data
1442	clientSize = wx.ClientDisplayRect()
1443	Size = self.GetSize()
1444	xPos = clientSize[2]-Size[0]
1445	self.SetPosition(wx.Point(xPos,clientSize[1]+250))
1446	self.AtomGrid = []
1447	self.selectedRow = 0
1448
1449	def setSizePosLeft(self,Width):
1450	clientSize = wx.ClientDisplayRect()
1451	Width[1] = min(Width[1],clientSize[2]-300)
1452	Width[0] = max(Width[0],300)
1453	self.SetSize(Width)
1454	# self.SetPosition(wx.Point(clientSize[2]-Width[0],clientSize[1]+250))
1455
1456	def Clear(self):
1457	self.ClearBackground()
1458	self.DestroyChildren()
1459
1460
1461	################################################################################
1462	##### Notebook Tree Item editor
1463	################################################################################
1464	def UpdateNotebook(G2frame,data):
1465	'''Called when the data tree notebook entry is selected. Allows for
1466	editing of the text in that tree entry
1467	'''
1468	def OnNoteBook(event):
1469	data = G2frame.dataDisplay.GetValue().split('\n')
1470	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Notebook'),data)
1471	if 'nt' not in os.name:
1472	G2frame.dataDisplay.AppendText('\n')
1473
1474	if G2frame.dataDisplay:
1475	G2frame.dataDisplay.Destroy()
1476	G2frame.dataFrame.SetLabel('Notebook')
1477	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1478	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER \| wx.TE_DONTWRAP)
1479	G2frame.dataDisplay.Bind(wx.EVT_TEXT_ENTER,OnNoteBook)
1480	G2frame.dataDisplay.Bind(wx.EVT_KILL_FOCUS,OnNoteBook)
1481	for line in data:
1482	G2frame.dataDisplay.AppendText(line+"\n")
1483	G2frame.dataDisplay.AppendText('Notebook entry @ '+time.ctime()+"\n")
1484	G2frame.dataFrame.setSizePosLeft([400,250])
1485
1486	################################################################################
1487	##### Controls Tree Item editor
1488	################################################################################
1489	def UpdateControls(G2frame,data):
1490	'''Edit overall GSAS-II controls in main Controls data tree entry
1491	'''
1492	#patch
1493	if 'deriv type' not in data:
1494	data = {}
1495	data['deriv type'] = 'analytic Hessian'
1496	data['min dM/M'] = 0.0001
1497	data['shift factor'] = 1.
1498	data['max cyc'] = 3
1499	data['F**2'] = False
1500	if 'shift factor' not in data:
1501	data['shift factor'] = 1.
1502	if 'max cyc' not in data:
1503	data['max cyc'] = 3
1504	if 'F**2' not in data:
1505	data['F**2'] = False
1506	if 'Author' not in data:
1507	data['Author'] = 'no name'
1508	if 'FreePrm1' not in data:
1509	data['FreePrm1'] = 'Sample humidity (%)'
1510	if 'FreePrm2' not in data:
1511	data['FreePrm2'] = 'Sample voltage (V)'
1512	if 'FreePrm3' not in data:
1513	data['FreePrm3'] = 'Applied load (MN)'
1514	if 'Copy2Next' not in data:
1515	data['Copy2Next'] = False
1516	if 'Reverse Seq' not in data:
1517	data['Reverse Seq'] = False
1518	if 'UsrReject' not in data:
1519	data['UsrReject'] = {'minF/sig':0,'MinExt':0.01,'MaxDF/F':20.,'MaxD':500.,'MinD':0.05}
1520	if 'HatomFix' not in data:
1521	data['HatomFix'] = False
1522
1523	#end patch
1524
1525	def SeqSizer():
1526
1527	def OnSelectData(event):
1528	choices = GetPatternTreeDataNames(G2frame,['PWDR','HKLF',])
1529	sel = []
1530	try:
1531	if 'Seq Data' in data:
1532	for item in data['Seq Data']:
1533	sel.append(choices.index(item))
1534	sel = [choices.index(item) for item in data['Seq Data']]
1535	except ValueError: #data changed somehow - start fresh
1536	sel = []
1537	dlg = G2G.G2MultiChoiceDialog(G2frame.dataFrame, 'Sequential refinement',
1538	'Select dataset to include',choices)
1539	dlg.SetSelections(sel)
1540	names = []
1541	if dlg.ShowModal() == wx.ID_OK:
1542	for sel in dlg.GetSelections():
1543	names.append(choices[sel])
1544	data['Seq Data'] = names
1545	G2frame.EnableSeqRefineMenu()
1546	dlg.Destroy()
1547	wx.CallAfter(UpdateControls,G2frame,data)
1548
1549	def OnReverse(event):
1550	data['Reverse Seq'] = reverseSel.GetValue()
1551
1552	def OnCopySel(event):
1553	data['Copy2Next'] = copySel.GetValue()
1554
1555	seqSizer = wx.BoxSizer(wx.VERTICAL)
1556	dataSizer = wx.BoxSizer(wx.HORIZONTAL)
1557	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Sequential Refinement: '),0,WACV)
1558	selSeqData = wx.Button(G2frame.dataDisplay,-1,label=' Select data')
1559	selSeqData.Bind(wx.EVT_BUTTON,OnSelectData)
1560	dataSizer.Add(selSeqData,0,WACV)
1561	SeqData = data.get('Seq Data',[])
1562	if not SeqData:
1563	lbl = ' (no data selected)'
1564	else:
1565	lbl = ' ('+str(len(SeqData))+' dataset(s) selected)'
1566
1567	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=lbl),0,WACV)
1568	seqSizer.Add(dataSizer,0)
1569	if SeqData:
1570	selSizer = wx.BoxSizer(wx.HORIZONTAL)
1571	reverseSel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Reverse order?')
1572	reverseSel.Bind(wx.EVT_CHECKBOX,OnReverse)
1573	reverseSel.SetValue(data['Reverse Seq'])
1574	selSizer.Add(reverseSel,0,WACV)
1575	copySel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Copy results to next histogram?')
1576	copySel.Bind(wx.EVT_CHECKBOX,OnCopySel)
1577	copySel.SetValue(data['Copy2Next'])
1578	selSizer.Add(copySel,0,WACV)
1579	seqSizer.Add(selSizer,0)
1580	return seqSizer
1581
1582	def LSSizer():
1583
1584	def OnDerivType(event):
1585	data['deriv type'] = derivSel.GetValue()
1586	derivSel.SetValue(data['deriv type'])
1587	wx.CallAfter(UpdateControls,G2frame,data)
1588
1589	def OnConvergence(event):
1590	try:
1591	value = max(1.e-9,min(1.0,float(Cnvrg.GetValue())))
1592	except ValueError:
1593	value = 0.0001
1594	data['min dM/M'] = value
1595	Cnvrg.SetValue('%.2g'%(value))
1596
1597	def OnMaxCycles(event):
1598	data['max cyc'] = int(maxCyc.GetValue())
1599	maxCyc.SetValue(str(data['max cyc']))
1600
1601	def OnFactor(event):
1602	try:
1603	value = min(max(float(Factr.GetValue()),0.00001),100.)
1604	except ValueError:
1605	value = 1.0
1606	data['shift factor'] = value
1607	Factr.SetValue('%.5f'%(value))
1608
1609	def OnFsqRef(event):
1610	data['F**2'] = fsqRef.GetValue()
1611
1612	def OnHatomFix(event):
1613	data['HatomFix'] = Hfix.GetValue()
1614
1615	def OnUsrRej(event):
1616	Obj = event.GetEventObject()
1617	item,limits = Indx[Obj]
1618	try:
1619	value = min(max(float(Obj.GetValue()),limits[0]),limits[1])
1620	except ValueError:
1621	value = data['UsrReject'][item]
1622	data['UsrReject'][item] = value
1623	Obj.SetValue('%.2f'%(value))
1624
1625	LSSizer = wx.FlexGridSizer(cols=4,vgap=5,hgap=5)
1626	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement derivatives: '),0,WACV)
1627	Choice=['analytic Jacobian','numeric','analytic Hessian']
1628	derivSel = wx.ComboBox(parent=G2frame.dataDisplay,value=data['deriv type'],choices=Choice,
1629	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1630	derivSel.SetValue(data['deriv type'])
1631	derivSel.Bind(wx.EVT_COMBOBOX, OnDerivType)
1632
1633	LSSizer.Add(derivSel,0,WACV)
1634	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Min delta-M/M: '),0,WACV)
1635	Cnvrg = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2g'%(data['min dM/M']),style=wx.TE_PROCESS_ENTER)
1636	Cnvrg.Bind(wx.EVT_TEXT_ENTER,OnConvergence)
1637	Cnvrg.Bind(wx.EVT_KILL_FOCUS,OnConvergence)
1638	LSSizer.Add(Cnvrg,0,WACV)
1639	Indx = {}
1640	if 'Hessian' in data['deriv type']:
1641	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Max cycles: '),0,WACV)
1642	Choice = ['0','1','2','3','5','10','15','20']
1643	maxCyc = wx.ComboBox(parent=G2frame.dataDisplay,value=str(data['max cyc']),choices=Choice,
1644	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1645	maxCyc.SetValue(str(data['max cyc']))
1646	maxCyc.Bind(wx.EVT_COMBOBOX, OnMaxCycles)
1647	LSSizer.Add(maxCyc,0,WACV)
1648	else:
1649	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Initial shift factor: '),0,WACV)
1650	Factr = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.5f'%(data['shift factor']),style=wx.TE_PROCESS_ENTER)
1651	Factr.Bind(wx.EVT_TEXT_ENTER,OnFactor)
1652	Factr.Bind(wx.EVT_KILL_FOCUS,OnFactor)
1653	LSSizer.Add(Factr,0,WACV)
1654	if G2frame.Sngl:
1655	userReject = data['UsrReject']
1656	usrRej = {'minF/sig':[' Min obs/sig (0-5): ',[0,5], ],'MinExt':[' Min extinct. (0-.9): ',[0,.9],],
1657	'MaxDF/F':[' Max delt-F/sig (3-1000): ',[3.,1000.],],'MaxD':[' Max d-spacing (3-500): ',[3,500],],
1658	'MinD':[' Min d-spacing (0.1-1.0): ',[0.1,1.0],]}
1659
1660	fsqRef = wx.CheckBox(G2frame.dataDisplay,-1,label='Refine HKLF as F^2? ')
1661	fsqRef.SetValue(data['F**2'])
1662	fsqRef.Bind(wx.EVT_CHECKBOX,OnFsqRef)
1663	LSSizer.Add(fsqRef,0,WACV)
1664	LSSizer.Add((1,0),)
1665	for item in usrRej:
1666	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,label=usrRej[item][0]),0,WACV)
1667	usrrej = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2f'%(userReject[item]),style=wx.TE_PROCESS_ENTER)
1668	Indx[usrrej] = [item,usrRej[item][1]]
1669	usrrej.Bind(wx.EVT_TEXT_ENTER,OnUsrRej)
1670	usrrej.Bind(wx.EVT_KILL_FOCUS,OnUsrRej)
1671	LSSizer.Add(usrrej,0,WACV)
1672	# Hfix = wx.CheckBox(G2frame.dataDisplay,-1,label='Regularize H atoms? ')
1673	# Hfix.SetValue(data['HatomFix'])
1674	# Hfix.Bind(wx.EVT_CHECKBOX,OnHatomFix)
1675	# LSSizer.Add(Hfix,0,WACV) #for now
1676	return LSSizer
1677
1678	def AuthSizer():
1679
1680	def OnAuthor(event):
1681	data['Author'] = auth.GetValue()
1682
1683	Author = data['Author']
1684	authSizer = wx.BoxSizer(wx.HORIZONTAL)
1685	authSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' CIF Author (last, first):'),0,WACV)
1686	auth = wx.TextCtrl(G2frame.dataDisplay,-1,value=Author,style=wx.TE_PROCESS_ENTER)
1687	auth.Bind(wx.EVT_TEXT_ENTER,OnAuthor)
1688	auth.Bind(wx.EVT_KILL_FOCUS,OnAuthor)
1689	authSizer.Add(auth,0,WACV)
1690	return authSizer
1691
1692
1693	if G2frame.dataDisplay:
1694	G2frame.dataDisplay.Destroy()
1695	if not G2frame.dataFrame.GetStatusBar():
1696	Status = G2frame.dataFrame.CreateStatusBar()
1697	Status.SetStatusText('')
1698	G2frame.dataFrame.SetLabel('Controls')
1699	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
1700	SetDataMenuBar(G2frame,G2frame.dataFrame.ControlsMenu)
1701	mainSizer = wx.BoxSizer(wx.VERTICAL)
1702	mainSizer.Add((5,5),0)
1703	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement Controls:'),0,WACV)
1704	mainSizer.Add(LSSizer())
1705	mainSizer.Add((5,5),0)
1706	mainSizer.Add(SeqSizer())
1707	mainSizer.Add((5,5),0)
1708	mainSizer.Add(AuthSizer())
1709	mainSizer.Add((5,5),0)
1710
1711	mainSizer.Layout()
1712	G2frame.dataDisplay.SetSizer(mainSizer)
1713	G2frame.dataDisplay.SetSize(mainSizer.Fit(G2frame.dataFrame))
1714	G2frame.dataFrame.setSizePosLeft(mainSizer.Fit(G2frame.dataFrame))
1715
1716	################################################################################
1717	##### Comments
1718	################################################################################
1719
1720	def UpdateComments(G2frame,data):
1721
1722	if G2frame.dataDisplay:
1723	G2frame.dataDisplay.Destroy()
1724	G2frame.dataFrame.SetLabel('Comments')
1725	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1726	style=wx.TE_MULTILINE\|wx.TE_READONLY\|wx.TE_DONTWRAP)
1727	for line in data:
1728	G2frame.dataDisplay.AppendText(line+'\n')
1729	G2frame.dataFrame.setSizePosLeft([400,250])
1730
1731	################################################################################
1732	##### Display of Sequential Results
1733	################################################################################
1734
1735	def UpdateSeqResults(G2frame,data,prevSize=None):
1736	"""
1737	Called when the Sequential Results data tree entry is selected
1738	to show results from a sequential refinement.
1739
1740	:param wx.Frame G2frame: main GSAS-II data tree windows
1741
1742	:param dict data: a dictionary containing the following items:
1743
1744	* 'histNames' - list of histogram names in order as processed by Sequential Refinement
1745	* 'varyList' - list of variables - identical over all refinements in sequence
1746	note that this is the original list of variables, prior to processing
1747	constraints.
1748	* 'variableLabels' -- a dict of labels to be applied to each parameter
1749	(this is created as an empty dict if not present in data).
1750	* keyed by histName - dictionaries for all data sets processed, which contains:
1751
1752	* 'variables'- result[0] from leastsq call
1753	* 'varyList' - list of variables passed to leastsq call (not same as above)
1754	* 'sig' - esds for variables
1755	* 'covMatrix' - covariance matrix from individual refinement
1756	* 'title' - histogram name; same as dict item name
1757	* 'newAtomDict' - new atom parameters after shifts applied
1758	* 'newCellDict' - refined cell parameters after shifts to A0-A5 from Dij terms applied'
1759	"""
1760
1761	def GetSampleParms():
1762	'''Make a dictionary of the sample parameters are not the same over the
1763	refinement series.
1764	'''
1765	if 'IMG' in histNames[0]:
1766	sampleParmDict = {'Sample load':[],}
1767	else:
1768	sampleParmDict = {'Temperature':[],'Pressure':[],'Time':[],
1769	'FreePrm1':[],'FreePrm2':[],'FreePrm3':[],'Omega':[],
1770	'Chi':[],'Phi':[],'Azimuth':[],}
1771	Controls = G2frame.PatternTree.GetItemPyData(
1772	GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
1773	sampleParm = {}
1774	for name in histNames:
1775	if 'IMG' in name:
1776	for item in sampleParmDict:
1777	sampleParmDict[item].append(data[name]['parmDict'].get(item,0))
1778	else:
1779	Id = GetPatternTreeItemId(G2frame,G2frame.root,name)
1780	sampleData = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,Id,'Sample Parameters'))
1781	for item in sampleParmDict:
1782	sampleParmDict[item].append(sampleData.get(item,0))
1783	for item in sampleParmDict:
1784	frstValue = sampleParmDict[item][0]
1785	if np.any(np.array(sampleParmDict[item])-frstValue):
1786	if item.startswith('FreePrm'):
1787	sampleParm[Controls[item]] = sampleParmDict[item]
1788	else:
1789	sampleParm[item] = sampleParmDict[item]
1790	return sampleParm
1791
1792	def GetColumnInfo(col):
1793	'''returns column label, lists of values and errors (or None) for each column in the table
1794	for plotting. The column label is reformatted from Unicode to MatPlotLib encoding
1795	'''
1796	colName = G2frame.SeqTable.GetColLabelValue(col)
1797	plotName = variableLabels.get(colName,colName)
1798	plotName = plotSpCharFix(plotName)
1799	return plotName,colList[col],colSigs[col]
1800
1801	def PlotSelect(event):
1802	'Plots a row (covariance) or column on double-click'
1803	cols = G2frame.dataDisplay.GetSelectedCols()
1804	rows = G2frame.dataDisplay.GetSelectedRows()
1805	if cols:
1806	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1807	elif rows:
1808	name = histNames[rows[0]] #only does 1st one selected
1809	G2plt.PlotCovariance(G2frame,data[name])
1810	else:
1811	G2frame.ErrorDialog(
1812	'Select row or columns',
1813	'Nothing selected in table. Click on column or row label(s) to plot. N.B. Grid selection can be a bit funky.'
1814	)
1815
1816	def OnPlotSelSeq(event):
1817	'plot the selected columns or row from menu command'
1818	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1819	rows = G2frame.dataDisplay.GetSelectedRows()
1820	if cols:
1821	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1822	elif rows:
1823	name = histNames[rows[0]] #only does 1st one selected
1824	G2plt.PlotCovariance(G2frame,data[name])
1825	else:
1826	G2frame.ErrorDialog(
1827	'Select columns',
1828	'No columns or rows selected in table. Click on row or column labels to select fields for plotting.'
1829	)
1830
1831	def OnAveSelSeq(event):
1832	'average the selected columns from menu command'
1833	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1834	if cols:
1835	for col in cols:
1836	ave = np.mean(GetColumnInfo(col)[1])
1837	sig = np.std(GetColumnInfo(col)[1])
1838	print ' Average for '+G2frame.SeqTable.GetColLabelValue(col)+': '+'%.6g'%(ave)+' +/- '+'%.6g'%(sig)
1839	else:
1840	G2frame.ErrorDialog(
1841	'Select columns',
1842	'No columns selected in table. Click on column labels to select fields for averaging.'
1843	)
1844
1845	def OnRenameSelSeq(event):
1846	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1847	colNames = [G2frame.SeqTable.GetColLabelValue(c) for c in cols]
1848	newNames = colNames[:]
1849	for i,name in enumerate(colNames):
1850	if name in variableLabels:
1851	newNames[i] = variableLabels[name]
1852	if not cols:
1853	G2frame.ErrorDialog('Select columns',
1854	'No columns selected in table. Click on column labels to select fields for rename.')
1855	return
1856	dlg = G2G.MultiStringDialog(G2frame.dataDisplay,'Set column names',colNames,newNames)
1857	if dlg.Show():
1858	newNames = dlg.GetValues()
1859	variableLabels.update(dict(zip(colNames,newNames)))
1860	data['variableLabels'] = variableLabels
1861	dlg.Destroy()
1862	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1863	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1864
1865	def OnReOrgSelSeq(event):
1866	'Reorder the columns'
1867	G2G.GetItemOrder(G2frame,VaryListChanges,vallookup,posdict)
1868	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1869
1870	def OnSaveSelSeqCSV(event):
1871	'export the selected columns to a .csv file from menu command'
1872	OnSaveSelSeq(event,csv=True)
1873
1874	def OnSaveSeqCSV(event):
1875	'export all columns to a .csv file from menu command'
1876	OnSaveSelSeq(event,csv=True,allcols=True)
1877
1878	def OnSaveSelSeq(event,csv=False,allcols=False):
1879	'export the selected columns to a .txt or .csv file from menu command'
1880	def WriteCSV():
1881	def WriteList(headerItems):
1882	line = ''
1883	for lbl in headerItems:
1884	if line: line += ','
1885	line += '"'+lbl+'"'
1886	return line
1887	head = ['name']
1888	for col in cols:
1889	item = G2frame.SeqTable.GetColLabelValue(col)
1890	# get rid of labels that have Unicode characters
1891	if not all([ord(c) < 128 and ord(c) != 0 for c in item]): item = '?'
1892	if col in havesig:
1893	head += [item,'esd-'+item]
1894	else:
1895	head += [item]
1896	SeqFile.write(WriteList(head)+'\n')
1897	for row,name in enumerate(saveNames):
1898	line = '"'+saveNames[row]+'"'
1899	for col in cols:
1900	if col in havesig:
1901	line += ','+str(saveData[col][row])+','+str(saveSigs[col][row])
1902	else:
1903	line += ','+str(saveData[col][row])
1904	SeqFile.write(line+'\n')
1905	def WriteSeq():
1906	lenName = len(saveNames[0])
1907	line = ' %s '%('name'.center(lenName))
1908	for col in cols:
1909	item = G2frame.SeqTable.GetColLabelValue(col)
1910	if col in havesig:
1911	line += ' %12s %12s '%(item.center(12),'esd'.center(12))
1912	else:
1913	line += ' %12s '%(item.center(12))
1914	SeqFile.write(line+'\n')
1915	for row,name in enumerate(saveNames):
1916	line = " '%s' "%(saveNames[row])
1917	for col in cols:
1918	if col in havesig:
1919	line += ' %12.6f %12.6f '%(saveData[col][row],saveSigs[col][row])
1920	else:
1921	line += ' %12.6f '%saveData[col][row]
1922	SeqFile.write(line+'\n')
1923
1924	# start of OnSaveSelSeq code
1925	if allcols:
1926	cols = range(G2frame.SeqTable.GetNumberCols())
1927	else:
1928	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1929	nrows = G2frame.SeqTable.GetNumberRows()
1930	if not cols:
1931	G2frame.ErrorDialog('Select columns',
1932	'No columns selected in table. Click on column labels to select fields for output.')
1933	return
1934	saveNames = [G2frame.SeqTable.GetRowLabelValue(r) for r in range(nrows)]
1935	saveData = {}
1936	saveSigs = {}
1937	havesig = []
1938	for col in cols:
1939	name,vals,sigs = GetColumnInfo(col)
1940	saveData[col] = vals
1941	if sigs:
1942	havesig.append(col)
1943	saveSigs[col] = sigs
1944	if csv:
1945	wild = 'CSV output file (.csv)\|.csv'
1946	else:
1947	wild = 'Text output file (.txt)\|.txt'
1948	dlg = wx.FileDialog(
1949	G2frame,
1950	'Choose text output file for your selection', '.', '',
1951	wild,wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1952	try:
1953	if dlg.ShowModal() == wx.ID_OK:
1954	SeqTextFile = dlg.GetPath()
1955	SeqTextFile = G2IO.FileDlgFixExt(dlg,SeqTextFile)
1956	SeqFile = open(SeqTextFile,'w')
1957	if csv:
1958	WriteCSV()
1959	else:
1960	WriteSeq()
1961	SeqFile.close()
1962	finally:
1963	dlg.Destroy()
1964
1965	def striphist(var,insChar=''):
1966	'strip a histogram number from a var name'
1967	sv = var.split(':')
1968	if len(sv) <= 1: return var
1969	if sv[1]:
1970	sv[1] = insChar
1971	return ':'.join(sv)
1972
1973	def plotSpCharFix(lbl):
1974	'Change selected unicode characters to their matplotlib equivalent'
1975	for u,p in [
1976	(u'\u03B1',r'$\alpha$'),
1977	(u'\u03B2',r'$\beta$'),
1978	(u'\u03B3',r'$\gamma$'),
1979	(u'\u0394\u03C7',r'$\Delta\chi$'),
1980	]:
1981	lbl = lbl.replace(u,p)
1982	return lbl
1983
1984	def SelectXaxis():
1985	'returns a selected column number (or None) as the X-axis selection'
1986	ncols = G2frame.SeqTable.GetNumberCols()
1987	colNames = [G2frame.SeqTable.GetColLabelValue(r) for r in range(ncols)]
1988	dlg = G2G.G2SingleChoiceDialog(
1989	G2frame.dataDisplay,
1990	'Select x-axis parameter for plot or Cancel for sequence number',
1991	'Select X-axis',
1992	colNames)
1993	try:
1994	if dlg.ShowModal() == wx.ID_OK:
1995	col = dlg.GetSelection()
1996	else:
1997	col = None
1998	finally:
1999	dlg.Destroy()
2000	return col
2001
2002	def EnablePseudoVarMenus():
2003	'Enables or disables the PseudoVar menu items that require existing defs'
2004	if Controls['SeqPseudoVars']:
2005	val = True
2006	else:
2007	val = False
2008	G2frame.dataFrame.SequentialPvars.Enable(wxDELSEQVAR,val)
2009	G2frame.dataFrame.SequentialPvars.Enable(wxEDITSEQVAR,val)
2010
2011	def DelPseudoVar(event):
2012	'Ask the user to select a pseudo var expression to delete'
2013	choices = Controls['SeqPseudoVars'].keys()
2014	selected = G2G.ItemSelector(
2015	choices,G2frame.dataFrame,
2016	multiple=True,
2017	title='Select expressions to remove',
2018	header='Delete expression')
2019	if selected is None: return
2020	for item in selected:
2021	del Controls['SeqPseudoVars'][choices[item]]
2022	if selected:
2023	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2024
2025	def EditPseudoVar(event):
2026	'Edit an existing pseudo var expression'
2027	choices = Controls['SeqPseudoVars'].keys()
2028	if len(choices) == 1:
2029	selected = 0
2030	else:
2031	selected = G2G.ItemSelector(
2032	choices,G2frame.dataFrame,
2033	multiple=False,
2034	title='Select an expression to edit',
2035	header='Edit expression')
2036	if selected is not None:
2037	dlg = G2exG.ExpressionDialog(
2038	G2frame.dataDisplay,PSvarDict,
2039	Controls['SeqPseudoVars'][choices[selected]],
2040	header="Edit the PseudoVar expression",
2041	VarLabel="PseudoVar #"+str(selected+1),
2042	fit=False)
2043	newobj = dlg.Show(True)
2044	if newobj:
2045	calcobj = G2obj.ExpressionCalcObj(newobj)
2046	del Controls['SeqPseudoVars'][choices[selected]]
2047	Controls['SeqPseudoVars'][calcobj.eObj.expression] = newobj
2048	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2049
2050	def AddNewPseudoVar(event):
2051	'Create a new pseudo var expression'
2052	dlg = G2exG.ExpressionDialog(
2053	G2frame.dataDisplay,PSvarDict,
2054	header='Enter an expression for a PseudoVar here',
2055	VarLabel = "New PseudoVar",
2056	fit=False)
2057	obj = dlg.Show(True)
2058	dlg.Destroy()
2059	if obj:
2060	calcobj = G2obj.ExpressionCalcObj(obj)
2061	Controls['SeqPseudoVars'][calcobj.eObj.expression] = obj
2062	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2063
2064	def UpdateParmDict(parmDict):
2065	'''generate the atom positions and the direct & reciprocal cell values,
2066	because they might be needed to evaluate the pseudovar
2067	'''
2068	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2069	['A'+str(i) for i in range(6)])
2070	)
2071	delList = []
2072	phaselist = []
2073	for item in parmDict:
2074	if ':' not in item: continue
2075	key = item.split(':')
2076	if len(key) < 3: continue
2077	# remove the dA[xyz] terms, they would only bring confusion
2078	if key[2].startswith('dA'):
2079	delList.append(item)
2080	# compute and update the corrected reciprocal cell terms using the Dij values
2081	elif key[2] in Ddict:
2082	if key[0] not in phaselist: phaselist.append(key[0])
2083	akey = key[0]+'::'+Ddict[key[2]]
2084	parmDict[akey] -= parmDict[item]
2085	delList.append(item)
2086	for item in delList:
2087	del parmDict[item]
2088	for i in phaselist:
2089	pId = int(i)
2090	# apply cell symmetry
2091	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],parmDict,zeroDict[pId])
2092	# convert to direct cell & add the unique terms to the dictionary
2093	for i,val in enumerate(G2lat.A2cell(A)):
2094	if i in uniqCellIndx[pId]:
2095	lbl = str(pId)+'::'+cellUlbl[i]
2096	parmDict[lbl] = val
2097	lbl = str(pId)+'::'+'vol'
2098	parmDict[lbl] = G2lat.calc_V(A)
2099	return parmDict
2100
2101	def EvalPSvarDeriv(calcobj,parmDict,sampleDict,var,ESD):
2102	'''Evaluate an expression derivative with respect to a
2103	GSAS-II variable name.
2104
2105	Note this likely could be faster if the loop over calcobjs were done
2106	inside after the Dict was created.
2107	'''
2108	step = ESD/10
2109	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2110	['A'+str(i) for i in range(6)])
2111	)
2112	results = []
2113	phaselist = []
2114	VparmDict = sampleDict.copy()
2115	for incr in step,-step:
2116	VparmDict.update(parmDict.copy())
2117	# as saved, the parmDict has updated 'A[xyz]' values, but 'dA[xyz]'
2118	# values are not zeroed: fix that!
2119	VparmDict.update({item:0.0 for item in parmDict if 'dA' in item})
2120	VparmDict[var] += incr
2121	G2mv.Dict2Map(VparmDict,[]) # apply constraints
2122	# generate the atom positions and the direct & reciprocal cell values now, because they might
2123	# needed to evaluate the pseudovar
2124	for item in VparmDict:
2125	if item in sampleDict:
2126	continue
2127	if ':' not in item: continue
2128	key = item.split(':')
2129	if len(key) < 3: continue
2130	# apply any new shifts to atom positions
2131	if key[2].startswith('dA'):
2132	VparmDict[''.join(item.split('d'))] += VparmDict[item]
2133	VparmDict[item] = 0.0
2134	# compute and update the corrected reciprocal cell terms using the Dij values
2135	if key[2] in Ddict:
2136	if key[0] not in phaselist: phaselist.append(key[0])
2137	akey = key[0]+'::'+Ddict[key[2]]
2138	VparmDict[akey] -= VparmDict[item]
2139	for i in phaselist:
2140	pId = int(i)
2141	# apply cell symmetry
2142	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],VparmDict,zeroDict[pId])
2143	# convert to direct cell & add the unique terms to the dictionary
2144	for i,val in enumerate(G2lat.A2cell(A)):
2145	if i in uniqCellIndx[pId]:
2146	lbl = str(pId)+'::'+cellUlbl[i]
2147	VparmDict[lbl] = val
2148	lbl = str(pId)+'::'+'vol'
2149	VparmDict[lbl] = G2lat.calc_V(A)
2150	# dict should be fully updated, use it & calculate
2151	calcobj.SetupCalc(VparmDict)
2152	results.append(calcobj.EvalExpression())
2153	return (results[0] - results[1]) / (2.*step)
2154
2155	def EnableParFitEqMenus():
2156	'Enables or disables the Parametric Fit menu items that require existing defs'
2157	if Controls['SeqParFitEqList']:
2158	val = True
2159	else:
2160	val = False
2161	G2frame.dataFrame.SequentialPfit.Enable(wxDELPARFIT,val)
2162	G2frame.dataFrame.SequentialPfit.Enable(wxEDITPARFIT,val)
2163	G2frame.dataFrame.SequentialPfit.Enable(wxDOPARFIT,val)
2164
2165	def ParEqEval(Values,calcObjList,varyList):
2166	'''Evaluate the parametric expression(s)
2167	:param list Values: a list of values for each variable parameter
2168	:param list calcObjList: a list of :class:`GSASIIobj.ExpressionCalcObj`
2169	expression objects to evaluate
2170	:param list varyList: a list of variable names for each value in Values
2171	'''
2172	result = []
2173	for calcobj in calcObjList:
2174	calcobj.UpdateVars(varyList,Values)
2175	result.append((calcobj.depVal-calcobj.EvalExpression())/calcobj.depSig)
2176	return result
2177
2178	def DoParEqFit(event,eqObj=None):
2179	'Parametric fit minimizer'
2180	varyValueDict = {} # dict of variables and their initial values
2181	calcObjList = [] # expression objects, ready to go for each data point
2182	if eqObj is not None:
2183	eqObjList = [eqObj,]
2184	else:
2185	eqObjList = Controls['SeqParFitEqList']
2186	UseFlags = G2frame.SeqTable.GetColValues(0)
2187	for obj in eqObjList:
2188	expr = obj.expression
2189	# assemble refined vars for this equation
2190	varyValueDict.update({var:val for var,val in obj.GetVariedVarVal()})
2191	# lookup dependent var position
2192	depVar = obj.GetDepVar()
2193	if depVar in colLabels:
2194	indx = colLabels.index(depVar)
2195	else:
2196	raise Exception('Dependent variable '+depVar+' not found')
2197	# assemble a list of the independent variables
2198	indepVars = obj.GetIndependentVars()
2199	# loop over each datapoint
2200	for j,row in enumerate(zip(*colList)):
2201	if not UseFlags[j]: continue
2202	# assemble equations to fit
2203	calcobj = G2obj.ExpressionCalcObj(obj)
2204	# prepare a dict of needed independent vars for this expression
2205	indepVarDict = {var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2206	calcobj.SetupCalc(indepVarDict)
2207	# values and sigs for current value of dependent var
2208	calcobj.depVal = row[indx]
2209	calcobj.depSig = colSigs[indx][j]
2210	calcObjList.append(calcobj)
2211	# varied parameters
2212	varyList = varyValueDict.keys()
2213	values = varyValues = [varyValueDict[key] for key in varyList]
2214	if not varyList:
2215	print 'no variables to refine!'
2216	return
2217	try:
2218	result = so.leastsq(ParEqEval,varyValues,full_output=True, #ftol=Ftol,
2219	args=(calcObjList,varyList)
2220	)
2221	values = result[0]
2222	covar = result[1]
2223	if covar is None:
2224	raise Exception
2225	esdDict = {}
2226	for i,avar in enumerate(varyList):
2227	esdDict[avar] = np.sqrt(covar[i,i])
2228	except:
2229	print('====> Fit failed')
2230	return
2231	print('==== Fit Results ====')
2232	for obj in eqObjList:
2233	obj.UpdateVariedVars(varyList,values)
2234	ind = ' '
2235	print(' '+obj.GetDepVar()+' = '+obj.expression)
2236	for var in obj.assgnVars:
2237	print(ind+var+' = '+obj.assgnVars[var])
2238	for var in obj.freeVars:
2239	avar = "::"+obj.freeVars[var][0]
2240	val = obj.freeVars[var][1]
2241	if obj.freeVars[var][2]:
2242	print(ind+var+' = '+avar + " = " + G2mth.ValEsd(val,esdDict[avar]))
2243	else:
2244	print(ind+var+' = '+avar + " =" + G2mth.ValEsd(val,0))
2245	# create a plot for each parametric variable
2246	for fitnum,obj in enumerate(eqObjList):
2247	calcobj = G2obj.ExpressionCalcObj(obj)
2248	# lookup dependent var position
2249	indx = colLabels.index(obj.GetDepVar())
2250	# assemble a list of the independent variables
2251	indepVars = obj.GetIndependentVars()
2252	# loop over each datapoint
2253	fitvals = []
2254	for j,row in enumerate(zip(*colList)):
2255	calcobj.SetupCalc(
2256	{var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2257	)
2258	fitvals.append(calcobj.EvalExpression())
2259	G2plt.PlotSelectedSequence(
2260	G2frame,[indx],GetColumnInfo,SelectXaxis,
2261	fitnum,fitvals)
2262
2263	def SingleParEqFit(eqObj):
2264	DoParEqFit(None,eqObj)
2265
2266	def DelParFitEq(event):
2267	'Ask the user to select function to delete'
2268	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2269	selected = G2G.ItemSelector(
2270	txtlst,G2frame.dataFrame,
2271	multiple=True,
2272	title='Select a parametric equation(s) to remove',
2273	header='Delete equation')
2274	if selected is None: return
2275	Controls['SeqParFitEqList'] = [obj for i,obj in enumerate(Controls['SeqParFitEqList']) if i not in selected]
2276	EnableParFitEqMenus()
2277	if Controls['SeqParFitEqList']: DoParEqFit(event)
2278
2279	def EditParFitEq(event):
2280	'Edit an existing parametric equation'
2281	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2282	if len(txtlst) == 1:
2283	selected = 0
2284	else:
2285	selected = G2G.ItemSelector(
2286	txtlst,G2frame.dataFrame,
2287	multiple=False,
2288	title='Select a parametric equation to edit',
2289	header='Edit equation')
2290	if selected is not None:
2291	dlg = G2exG.ExpressionDialog(
2292	G2frame.dataDisplay,indepVarDict,
2293	Controls['SeqParFitEqList'][selected],
2294	depVarDict=depVarDict,
2295	header="Edit the formula for this minimization function",
2296	ExtraButton=['Fit',SingleParEqFit])
2297	newobj = dlg.Show(True)
2298	if newobj:
2299	calcobj = G2obj.ExpressionCalcObj(newobj)
2300	Controls['SeqParFitEqList'][selected] = newobj
2301	EnableParFitEqMenus()
2302	if Controls['SeqParFitEqList']: DoParEqFit(event)
2303
2304	def AddNewParFitEq(event):
2305	'Create a new parametric equation to be fit to sequential results'
2306
2307	# compile the variable names used in previous freevars to avoid accidental name collisions
2308	usedvarlist = []
2309	for obj in Controls['SeqParFitEqList']:
2310	for var in obj.freeVars:
2311	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2312
2313	dlg = G2exG.ExpressionDialog(
2314	G2frame.dataDisplay,indepVarDict,
2315	depVarDict=depVarDict,
2316	header='Define an equation to minimize in the parametric fit',
2317	ExtraButton=['Fit',SingleParEqFit],
2318	usedVars=usedvarlist)
2319	obj = dlg.Show(True)
2320	dlg.Destroy()
2321	if obj:
2322	Controls['SeqParFitEqList'].append(obj)
2323	EnableParFitEqMenus()
2324	if Controls['SeqParFitEqList']: DoParEqFit(event)
2325
2326	def CopyParFitEq(event):
2327	'Copy an existing parametric equation to be fit to sequential results'
2328	# compile the variable names used in previous freevars to avoid accidental name collisions
2329	usedvarlist = []
2330	for obj in Controls['SeqParFitEqList']:
2331	for var in obj.freeVars:
2332	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2333	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2334	if len(txtlst) == 1:
2335	selected = 0
2336	else:
2337	selected = G2G.ItemSelector(
2338	txtlst,G2frame.dataFrame,
2339	multiple=False,
2340	title='Select a parametric equation to copy',
2341	header='Copy equation')
2342	if selected is not None:
2343	newEqn = copy.deepcopy(Controls['SeqParFitEqList'][selected])
2344	for var in newEqn.freeVars:
2345	newEqn.freeVars[var][0] = G2obj.MakeUniqueLabel(newEqn.freeVars[var][0],usedvarlist)
2346	dlg = G2exG.ExpressionDialog(
2347	G2frame.dataDisplay,indepVarDict,
2348	newEqn,
2349	depVarDict=depVarDict,
2350	header="Edit the formula for this minimization function",
2351	ExtraButton=['Fit',SingleParEqFit])
2352	newobj = dlg.Show(True)
2353	if newobj:
2354	calcobj = G2obj.ExpressionCalcObj(newobj)
2355	Controls['SeqParFitEqList'].append(newobj)
2356	EnableParFitEqMenus()
2357	if Controls['SeqParFitEqList']: DoParEqFit(event)
2358
2359	def GridSetToolTip(row,col):
2360	'''Routine to show standard uncertainties for each element in table
2361	as a tooltip
2362	'''
2363	if colSigs[col]:
2364	return u'\u03c3 = '+str(colSigs[col][row])
2365	return ''
2366
2367	def GridColLblToolTip(col):
2368	'''Define a tooltip for a column. This will be the user-entered value
2369	(from data['variableLabels']) or the default name
2370	'''
2371	if col < 0 or col > len(colLabels):
2372	print 'Illegal column #',col
2373	return
2374	var = colLabels[col]
2375	return variableLabels.get(var,G2obj.fmtVarDescr(var))
2376
2377	def SetLabelString(event):
2378	'''Define or edit the label for a column in the table, to be used
2379	as a tooltip and for plotting
2380	'''
2381	col = event.GetCol()
2382	if col < 0 or col > len(colLabels):
2383	return
2384	var = colLabels[col]
2385	lbl = variableLabels.get(var,G2obj.fmtVarDescr(var))
2386	dlg = G2G.SingleStringDialog(G2frame.dataFrame,'Set variable label',
2387	'Set a new name for variable '+var,lbl,size=(400,-1))
2388	if dlg.Show():
2389	variableLabels[var] = dlg.GetValue()
2390	dlg.Destroy()
2391
2392	#def GridRowLblToolTip(row): return 'Row ='+str(row)
2393
2394	# lookup table for unique cell parameters by symmetry
2395	cellGUIlist = [
2396	[['m3','m3m'],(0,)],
2397	[['3R','3mR'],(0,3)],
2398	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],(0,2)],
2399	[['mmm'],(0,1,2)],
2400	[['2/m'+'a'],(0,1,2,3)],
2401	[['2/m'+'b'],(0,1,2,4)],
2402	[['2/m'+'c'],(0,1,2,5)],
2403	[['-1'],(0,1,2,3,4,5)],
2404	]
2405	# cell labels
2406	cellUlbl = ('a','b','c',u'\u03B1',u'\u03B2',u'\u03B3') # unicode a,b,c,alpha,beta,gamma
2407
2408	#======================================================================
2409	# start processing sequential results here (UpdateSeqResults)
2410	#======================================================================
2411	if not data:
2412	print 'No sequential refinement results'
2413	return
2414	variableLabels = data.get('variableLabels',{})
2415	data['variableLabels'] = variableLabels
2416	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
2417	Controls = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Controls'))
2418	# create a place to store Pseudo Vars & Parametric Fit functions, if not present
2419	if 'SeqPseudoVars' not in Controls: Controls['SeqPseudoVars'] = {}
2420	if 'SeqParFitEqList' not in Controls: Controls['SeqParFitEqList'] = []
2421	histNames = data['histNames']
2422	if G2frame.dataDisplay:
2423	G2frame.dataDisplay.Destroy()
2424	if not G2frame.dataFrame.GetStatusBar():
2425	Status = G2frame.dataFrame.CreateStatusBar()
2426	Status.SetStatusText("Select column to export; Double click on column to plot data; on row for Covariance")
2427	sampleParms = GetSampleParms()
2428
2429	# make dict of varied atom coords keyed by absolute position
2430	newAtomDict = data[histNames[0]].get('newAtomDict',{}) # dict with atom positions; relative & absolute
2431	# Possible error: the next might need to be data[histNames[0]]['varyList']
2432	# error will arise if there constraints on coordinates?
2433	atomLookup = {newAtomDict[item][0]:item for item in newAtomDict if item in data['varyList']}
2434
2435	# make dict of varied cell parameters equivalents
2436	ESDlookup = {} # provides the Dij term for each Ak term (where terms are refined)
2437	Dlookup = {} # provides the Ak term for each Dij term (where terms are refined)
2438	# N.B. These Dij vars are missing a histogram #
2439	newCellDict = data[histNames[0]].get('newCellDict',{})
2440	for item in newCellDict:
2441	if item in data['varyList']:
2442	ESDlookup[newCellDict[item][0]] = item
2443	Dlookup[item] = newCellDict[item][0]
2444	# add coordinate equivalents to lookup table
2445	for parm in atomLookup:
2446	Dlookup[atomLookup[parm]] = parm
2447	ESDlookup[parm] = atomLookup[parm]
2448
2449	# get unit cell & symmetry for all phases & initial stuff for later use
2450	RecpCellTerms = {}
2451	SGdata = {}
2452	uniqCellIndx = {}
2453	initialCell = {}
2454	RcellLbls = {}
2455	zeroDict = {}
2456	Rcelldict = {}
2457	for phase in Phases:
2458	phasedict = Phases[phase]
2459	pId = phasedict['pId']
2460	pfx = str(pId)+'::' # prefix for A values from phase
2461	RcellLbls[pId] = [pfx+'A'+str(i) for i in range(6)]
2462	RecpCellTerms[pId] = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2463	zeroDict[pId] = dict(zip(RcellLbls[pId],6*[0.,]))
2464	SGdata[pId] = phasedict['General']['SGData']
2465	Rcelldict.update({lbl:val for lbl,val in zip(RcellLbls[pId],RecpCellTerms[pId])})
2466	laue = SGdata[pId]['SGLaue']
2467	if laue == '2/m':
2468	laue += SGdata[pId]['SGUniq']
2469	for symlist,celllist in cellGUIlist:
2470	if laue in symlist:
2471	uniqCellIndx[pId] = celllist
2472	break
2473	else: # should not happen
2474	uniqCellIndx[pId] = range(6)
2475	for i in uniqCellIndx[pId]:
2476	initialCell[str(pId)+'::A'+str(i)] = RecpCellTerms[pId][i]
2477
2478	SetDataMenuBar(G2frame,G2frame.dataFrame.SequentialMenu)
2479	G2frame.dataFrame.SetLabel('Sequential refinement results')
2480	if not G2frame.dataFrame.GetStatusBar():
2481	Status = G2frame.dataFrame.CreateStatusBar()
2482	Status.SetStatusText('')
2483	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRenameSelSeq, id=wxID_RENAMESEQSEL)
2484	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeq, id=wxID_SAVESEQSEL)
2485	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeqCSV, id=wxID_SAVESEQSELCSV)
2486	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSeqCSV, id=wxID_SAVESEQCSV)
2487	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotSelSeq, id=wxID_PLOTSEQSEL)
2488	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAveSelSeq, id=wxID_AVESEQSEL)
2489	G2frame.dataFrame.Bind(wx.EVT_MENU, OnReOrgSelSeq, id=wxID_ORGSEQSEL)
2490	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewPseudoVar, id=wxADDSEQVAR)
2491	G2frame.dataFrame.Bind(wx.EVT_MENU, DelPseudoVar, id=wxDELSEQVAR)
2492	G2frame.dataFrame.Bind(wx.EVT_MENU, EditPseudoVar, id=wxEDITSEQVAR)
2493	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewParFitEq, id=wxADDPARFIT)
2494	G2frame.dataFrame.Bind(wx.EVT_MENU, CopyParFitEq, id=wxCOPYPARFIT)
2495	G2frame.dataFrame.Bind(wx.EVT_MENU, DelParFitEq, id=wxDELPARFIT)
2496	G2frame.dataFrame.Bind(wx.EVT_MENU, EditParFitEq, id=wxEDITPARFIT)
2497	G2frame.dataFrame.Bind(wx.EVT_MENU, DoParEqFit, id=wxDOPARFIT)
2498	EnablePseudoVarMenus()
2499	EnableParFitEqMenus()
2500
2501	# scan for locations where the variables change
2502	VaryListChanges = [] # histograms where there is a change
2503	combinedVaryList = []
2504	firstValueDict = {}
2505	vallookup = {}
2506	posdict = {}
2507	prevVaryList = []
2508	for i,name in enumerate(histNames):
2509	for var,val,sig in zip(data[name]['varyList'],data[name]['variables'],data[name]['sig']):
2510	svar = striphist(var,'*') # wild-carded
2511	if svar not in combinedVaryList:
2512	# add variables to list as they appear
2513	combinedVaryList.append(svar)
2514	firstValueDict[svar] = (val,sig)
2515	if prevVaryList != data[name]['varyList']: # this refinement has a different refinement list from previous
2516	prevVaryList = data[name]['varyList']
2517	vallookup[name] = dict(zip(data[name]['varyList'],data[name]['variables']))
2518	posdict[name] = {}
2519	for var in data[name]['varyList']:
2520	svar = striphist(var,'*')
2521	posdict[name][combinedVaryList.index(svar)] = svar
2522	VaryListChanges.append(name)
2523	if len(VaryListChanges) > 1:
2524	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,True)
2525	else:
2526	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,False)
2527	#-----------------------------------------------------------------------------------
2528	# build up the data table by columns -----------------------------------------------
2529	nRows = len(histNames)
2530	colList = [nRows*[True]]
2531	colSigs = [None]
2532	colLabels = ['Use']
2533	Types = [wg.GRID_VALUE_BOOL]
2534	# start with Rwp values
2535	if 'IMG ' not in histNames[0][:4]:
2536	colList += [[data[name]['Rvals']['Rwp'] for name in histNames]]
2537	colSigs += [None]
2538	colLabels += ['Rwp']
2539	Types += [wg.GRID_VALUE_FLOAT+':10,3',]
2540	# add % change in Chi^2 in last cycle
2541	if histNames[0][:4] not in ['SASD','IMG '] and Controls.get('ShowCell'):
2542	colList += [[100.*data[name]['Rvals'].get('DelChi2',-1) for name in histNames]]
2543	colSigs += [None]
2544	colLabels += [u'\u0394\u03C7\u00B2 (%)']
2545	Types += [wg.GRID_VALUE_FLOAT,]
2546	deltaChiCol = len(colLabels)-1
2547	# add changing sample parameters to table
2548	for key in sampleParms:
2549	colList += [sampleParms[key]]
2550	colSigs += [None]
2551	colLabels += [key]
2552	Types += [wg.GRID_VALUE_FLOAT,]
2553	sampleDict = {}
2554	for i,name in enumerate(histNames):
2555	sampleDict[name] = dict(zip(sampleParms.keys(),[sampleParms[key][i] for key in sampleParms.keys()]))
2556	# add unique cell parameters TODO: review this where the cell symmetry changes (when possible)
2557	if Controls.get('ShowCell',False):
2558	for pId in sorted(RecpCellTerms):
2559	pfx = str(pId)+'::' # prefix for A values from phase
2560	cells = []
2561	cellESDs = []
2562	colLabels += [pfx+cellUlbl[i] for i in uniqCellIndx[pId]]
2563	colLabels += [pfx+'Vol']
2564	Types += (1+len(uniqCellIndx[pId]))*[wg.GRID_VALUE_FLOAT,]
2565	for name in histNames:
2566	covData = {
2567	'varyList': [Dlookup.get(striphist(v),v) for v in data[name]['varyList']],
2568	'covMatrix': data[name]['covMatrix']
2569	}
2570	A = RecpCellTerms[pId][:] # make copy of starting A values
2571	# update with refined values
2572	for i in range(6):
2573	var = str(pId)+'::A'+str(i)
2574	if var in ESDlookup:
2575	val = data[name]['newCellDict'][ESDlookup[var]][1] # get refined value
2576	A[i] = val # override with updated value
2577	# apply symmetry
2578	Albls = [pfx+'A'+str(i) for i in range(6)]
2579	cellDict = dict(zip(Albls,A))
2580	A,zeros = G2stIO.cellFill(pfx,SGdata[pId],cellDict,zeroDict[pId])
2581	# convert to direct cell & add only unique values to table
2582	c = G2lat.A2cell(A)
2583	vol = G2lat.calc_V(A)
2584	cE = G2stIO.getCellEsd(pfx,SGdata[pId],A,covData)
2585	cells += [[c[i] for i in uniqCellIndx[pId]]+[vol]]
2586	cellESDs += [[cE[i] for i in uniqCellIndx[pId]]+[cE[-1]]]
2587	colList += zip(*cells)
2588	colSigs += zip(*cellESDs)
2589	# sort out the variables in their selected order
2590	varcols = 0
2591	for d in posdict.itervalues():
2592	varcols = max(varcols,max(d.keys())+1)
2593	# get labels for each column
2594	for i in range(varcols):
2595	lbl = ''
2596	for h in VaryListChanges:
2597	if posdict[h].get(i):
2598	if posdict[h].get(i) in lbl: continue
2599	if lbl != "": lbl += '/'
2600	lbl += posdict[h].get(i)
2601	colLabels.append(lbl)
2602	Types += varcols*[wg.GRID_VALUE_FLOAT]
2603	vals = []
2604	esds = []
2605	varsellist = None # will be a list of variable names in the order they are selected to appear
2606	# tabulate values for each hist, leaving None for blank columns
2607	for name in histNames:
2608	if name in posdict:
2609	varsellist = [posdict[name].get(i) for i in range(varcols)]
2610	# translate variable names to how they will be used in the headings
2611	vs = [striphist(v,'*') for v in data[name]['varyList']]
2612	# determine the index for each column (or None) in the data[]['variables'] and ['sig'] lists
2613	sellist = [vs.index(v) if v is not None else None for v in varsellist]
2614	#sellist = [i if striphist(v,'*') in varsellist else None for i,v in enumerate(data[name]['varyList'])]
2615	if not varsellist: raise Exception()
2616	vals.append([data[name]['variables'][s] if s is not None else None for s in sellist])
2617	esds.append([data[name]['sig'][s] if s is not None else None for s in sellist])
2618	#GSASIIpath.IPyBreak()
2619	colList += zip(*vals)
2620	colSigs += zip(*esds)
2621
2622	# tabulate constrained variables, removing histogram numbers if needed
2623	# from parameter label
2624	depValDict = {}
2625	depSigDict = {}
2626	for name in histNames:
2627	for var in data[name].get('depParmDict',{}):
2628	val,sig = data[name]['depParmDict'][var]
2629	svar = striphist(var,'*')
2630	if svar not in depValDict:
2631	depValDict[svar] = [val]
2632	depSigDict[svar] = [sig]
2633	else:
2634	depValDict[svar].append(val)
2635	depSigDict[svar].append(sig)
2636	# add the dependent constrained variables to the table
2637	for var in sorted(depValDict):
2638	if len(depValDict[var]) != len(histNames): continue
2639	colLabels.append(var)
2640	Types += [wg.GRID_VALUE_FLOAT,]
2641	colSigs += [depSigDict[var]]
2642	colList += [depValDict[var]]
2643
2644	# add atom parameters to table
2645	colLabels += atomLookup.keys()
2646	Types += len(atomLookup)*[wg.GRID_VALUE_FLOAT]
2647	for parm in sorted(atomLookup):
2648	colList += [[data[name]['newAtomDict'][atomLookup[parm]][1] for name in histNames]]
2649	if atomLookup[parm] in data[histNames[0]]['varyList']:
2650	col = data[histNames[0]]['varyList'].index(atomLookup[parm])
2651	colSigs += [[data[name]['sig'][col] for name in histNames]]
2652	else:
2653	colSigs += [None] # should not happen
2654	# evaluate Pseudovars, their ESDs and add them to grid
2655	for expr in Controls['SeqPseudoVars']:
2656	obj = Controls['SeqPseudoVars'][expr]
2657	calcobj = G2obj.ExpressionCalcObj(obj)
2658	valList = []
2659	esdList = []
2660	for seqnum,name in enumerate(histNames):
2661	sigs = data[name]['sig']
2662	G2mv.InitVars()
2663	parmDict = data[name].get('parmDict')
2664	badVary = data[name].get('badVary',[])
2665	constraintInfo = data[name].get('constraintInfo',[[],[],{},[],seqnum])
2666	groups,parmlist,constrDict,fixedList,ihst = constraintInfo
2667	varyList = data[name]['varyList']
2668	parmDict = data[name]['parmDict']
2669	G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmDict,SeqHist=ihst)
2670	derivs = np.array(
2671	[EvalPSvarDeriv(calcobj,parmDict.copy(),sampleDict[name],var,ESD)
2672	for var,ESD in zip(varyList,sigs)]
2673	)
2674	esdList.append(np.sqrt(
2675	np.inner(derivs,np.inner(data[name]['covMatrix'],derivs.T))
2676	))
2677	PSvarDict = parmDict.copy()
2678	PSvarDict.update(sampleDict[name])
2679	UpdateParmDict(PSvarDict)
2680	calcobj.UpdateDict(PSvarDict)
2681	valList.append(calcobj.EvalExpression())
2682	if not esdList:
2683	esdList = None
2684	colList += [valList]
2685	colSigs += [esdList]
2686	colLabels += [expr]
2687	Types += [wg.GRID_VALUE_FLOAT,]
2688	#---- table build done -------------------------------------------------------------
2689
2690	# Make dict needed for creating & editing pseudovars (PSvarDict).
2691	name = histNames[0]
2692	parmDict = data[name].get('parmDict')
2693	PSvarDict = parmDict.copy()
2694	PSvarDict.update(sampleParms)
2695	UpdateParmDict(PSvarDict)
2696	# Also dicts of dependent (depVarDict) & independent vars (indepVarDict)
2697	# for Parametric fitting from the data table
2698	parmDict = dict(zip(colLabels,zip(*colList)[0])) # scratch dict w/all values in table
2699	parmDict.update(
2700	{var:val for var,val in data[name].get('newCellDict',{}).values()} # add varied reciprocal cell terms
2701	)
2702	name = histNames[0]
2703
2704	#******************************************************************************
2705	# create a set of values for example evaluation of pseudovars and
2706	# this does not work for refinements that have differing numbers of variables.
2707	#raise Exception
2708	indepVarDict = {} # values in table w/o ESDs
2709	depVarDict = {}
2710	for i,var in enumerate(colLabels):
2711	if var == 'Use': continue
2712	if colList[i][0] is None:
2713	val,sig = firstValueDict.get(var,[None,None])
2714	elif colSigs[i]:
2715	val,sig = colList[i][0],colSigs[i][0]
2716	else:
2717	val,sig = colList[i][0],None
2718	if val is None:
2719	continue
2720	elif sig is None:
2721	indepVarDict[var] = val
2722	elif striphist(var) not in Dlookup:
2723	depVarDict[var] = val
2724	# add recip cell coeff. values
2725	depVarDict.update({var:val for var,val in data[name].get('newCellDict',{}).values()})
2726
2727	G2frame.dataDisplay = G2G.GSGrid(parent=G2frame.dataFrame)
2728	G2frame.SeqTable = G2G.Table(
2729	[list(c) for c in zip(*colList)], # convert from columns to rows
2730	colLabels=colLabels,rowLabels=histNames,types=Types)
2731	G2frame.dataDisplay.SetTable(G2frame.SeqTable, True)
2732	#G2frame.dataDisplay.EnableEditing(False)
2733	# make all but first column read-only
2734	for c in range(1,len(colLabels)):
2735	for r in range(nRows):
2736	G2frame.dataDisplay.SetCellReadOnly(r,c)
2737	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, PlotSelect)
2738	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, SetLabelString)
2739	G2frame.dataDisplay.SetRowLabelSize(8*len(histNames[0])) #pretty arbitrary 8
2740	G2frame.dataDisplay.SetMargins(0,0)
2741	G2frame.dataDisplay.AutoSizeColumns(True)
2742	if prevSize:
2743	G2frame.dataDisplay.SetSize(prevSize)
2744	else:
2745	G2frame.dataFrame.setSizePosLeft([700,350])
2746	# highlight unconverged shifts
2747	if histNames[0][:4] not in ['SASD','IMG ']:
2748	for row,name in enumerate(histNames):
2749	deltaChi = G2frame.SeqTable.GetValue(row,deltaChiCol)
2750	if deltaChi > 10.:
2751	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,0,0))
2752	elif deltaChi > 1.0:
2753	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,255,0))
2754	G2frame.dataDisplay.InstallGridToolTip(GridSetToolTip,GridColLblToolTip)
2755	G2frame.dataDisplay.SendSizeEvent() # resize needed on mac
2756	G2frame.dataDisplay.Refresh() # shows colored text on mac
2757
2758	################################################################################
2759	##### Main PWDR panel
2760	################################################################################
2761
2762	def UpdatePWHKPlot(G2frame,kind,item):
2763	'''Called when the histogram main tree entry is called. Displays the
2764	histogram weight factor, refinement statistics for the histogram
2765	and the range of data for a simulation.
2766
2767	Also invokes a plot of the histogram.
2768	'''
2769	def onEditSimRange(event):
2770	'Edit simulation range'
2771	inp = [
2772	min(data[1][0]),
2773	max(data[1][0]),
2774	None
2775	]
2776	inp[2] = (inp[1] - inp[0])/(len(data[1][0])-1.)
2777	names = ('start angle', 'end angle', 'step size')
2778	dictlst = [inp] * len(inp)
2779	elemlst = range(len(inp))
2780	dlg = G2G.ScrolledMultiEditor(
2781	G2frame,[inp] * len(inp), range(len(inp)), names,
2782	header='Edit simulation range',
2783	minvals=(0.001,0.001,0.0001),
2784	maxvals=(180.,180.,.1),
2785	)
2786	dlg.CenterOnParent()
2787	val = dlg.ShowModal()
2788	dlg.Destroy()
2789	if val != wx.ID_OK: return
2790	if inp[0] > inp[1]:
2791	end,start,step = inp
2792	else:
2793	start,end,step = inp
2794	step = abs(step)
2795	N = int((end-start)/step)+1
2796	newdata = np.linspace(start,end,N,True)
2797	if len(newdata) < 2: return # too small a range - reject
2798	data[1] = [newdata,np.zeros_like(newdata),np.ones_like(newdata),
2799	np.zeros_like(newdata),np.zeros_like(newdata),np.zeros_like(newdata)]
2800	Tmin = newdata[0]
2801	Tmax = newdata[-1]
2802	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,item,'Limits'),
2803	[(Tmin,Tmax),[Tmin,Tmax]])
2804	UpdatePWHKPlot(G2frame,kind,item) # redisplay data screen
2805
2806	def OnPlot3DHKL(event):
2807	refList = data[1]['RefList']
2808	FoMax = np.max(refList.T[8+Super])
2809	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2810	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2811	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2812	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,
2813	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2814	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,
2815	'Scale':1.0,'oldxy':[],'viewDir':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
2816	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2817
2818	def OnPlotAll3DHKL(event):
2819	choices = GetPatternTreeDataNames(G2frame,['HKLF',])
2820	dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to plot',
2821	'Use data',choices)
2822	try:
2823	if dlg.ShowModal() == wx.ID_OK:
2824	refNames = [choices[i] for i in dlg.GetSelections()]
2825	else:
2826	return
2827	finally:
2828	dlg.Destroy()
2829	refList = np.zeros(0)
2830	for name in refNames:
2831	Id = GetPatternTreeItemId(G2frame,G2frame.root, name)
2832	reflData = G2frame.PatternTree.GetItemPyData(Id)[1]
2833	if len(refList):
2834	refList = np.concatenate((refList,reflData['RefList']))
2835	else:
2836	refList = reflData['RefList']
2837
2838	FoMax = np.max(refList.T[8+Super])
2839	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2840	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2841	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2842	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,
2843	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2844	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,
2845	'Scale':1.0,'oldxy':[],'viewDir':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
2846	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2847
2848
2849	def OnErrorAnalysis(event):
2850	G2plt.PlotDeltSig(G2frame,kind)
2851
2852	def OnWtFactor(event):
2853	try:
2854	val = float(wtval.GetValue())
2855	except ValueError:
2856	val = data[0]['wtFactor']
2857	data[0]['wtFactor'] = val
2858	wtval.SetValue('%.3f'%(val))
2859
2860	def OnCompression(event):
2861	data[0] = int(comp.GetValue())
2862
2863	def onCopyPlotCtrls(event):
2864	'''Respond to menu item to copy multiple sections from a histogram.
2865	Need this here to pass on the G2frame object.
2866	'''
2867	G2pdG.CopyPlotCtrls(G2frame)
2868
2869	def onCopySelectedItems(event):
2870	'''Respond to menu item to copy multiple sections from a histogram.
2871	Need this here to pass on the G2frame object.
2872	'''
2873	G2pdG.CopySelectedHistItems(G2frame)
2874
2875	data = G2frame.PatternTree.GetItemPyData(item)
2876	#patches
2877	if 'wtFactor' not in data[0]:
2878	data[0] = {'wtFactor':1.0}
2879	# if kind == 'PWDR' and 'Compression' not in data[0]:
2880	# data[0]['Compression'] = 1
2881	#if isinstance(data[1],list) and kind == 'HKLF':
2882	if 'list' in str(type(data[1])) and kind == 'HKLF':
2883	RefData = {'RefList':[],'FF':[]}
2884	for ref in data[1]:
2885	RefData['RefList'].append(ref[:11]+[ref[13],])
2886	RefData['FF'].append(ref[14])
2887	data[1] = RefData
2888	G2frame.PatternTree.SetItemPyData(item,data)
2889	#end patches
2890	if G2frame.dataDisplay:
2891	G2frame.dataDisplay.Destroy()
2892	if kind in ['PWDR','SASD']:
2893	SetDataMenuBar(G2frame,G2frame.dataFrame.PWDRMenu)
2894	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2895	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2896	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopyPlotCtrls, id=wxID_PLOTCTRLCOPY)
2897	elif kind in ['HKLF',]:
2898	SetDataMenuBar(G2frame,G2frame.dataFrame.HKLFMenu)
2899	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2900	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=wxID_PWD3DHKLPLOT)
2901	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotAll3DHKL, id=wxID_3DALLHKLPLOT)
2902	# G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2903	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
2904
2905	mainSizer = wx.BoxSizer(wx.VERTICAL)
2906	mainSizer.Add((5,5),)
2907	wtSizer = wx.BoxSizer(wx.HORIZONTAL)
2908	wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Weight factor: '),0,WACV)
2909	wtval = wx.TextCtrl(G2frame.dataDisplay,-1,'%.3f'%(data[0]['wtFactor']),style=wx.TE_PROCESS_ENTER)
2910	wtval.Bind(wx.EVT_TEXT_ENTER,OnWtFactor)
2911	wtval.Bind(wx.EVT_KILL_FOCUS,OnWtFactor)
2912	wtSizer.Add(wtval,0,WACV)
2913	# if kind == 'PWDR': #possible future compression feature; NB above patch as well
2914	# wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Compression factor: '),0,WACV)
2915	# choice = ['1','2','3','4','5','6']
2916	# comp = wx.ComboBox(parent=G2frame.dataDisplay,choices=choice,
2917	# style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2918	# comp.SetValue(str(data[0]['Compression']))
2919	# comp.Bind(wx.EVT_COMBOBOX, OnCompression)
2920	# wtSizer.Add(comp,0,WACV)
2921	mainSizer.Add(wtSizer)
2922	if data[0].get('Dummy'):
2923	simSizer = wx.BoxSizer(wx.HORIZONTAL)
2924	Tmin = min(data[1][0])
2925	Tmax = max(data[1][0])
2926	num = len(data[1][0])
2927	step = (Tmax - Tmin)/(num-1)
2928	t = u'2\u03b8' # 2theta
2929	lbl = u'Simulation range: {:.2f} to {:.2f} {:s}\nwith {:.4f} steps ({:d} points)'
2930	lbl += u'\n(Edit range resets observed intensities).'
2931	lbl = lbl.format(Tmin,Tmax,t,step,num)
2932	simSizer.Add(wx.StaticText(G2frame.dataDisplay,wx.ID_ANY,lbl),
2933	0,WACV)
2934	but = wx.Button(G2frame.dataDisplay,wx.ID_ANY,"Edit range")
2935	but.Bind(wx.EVT_BUTTON,onEditSimRange)
2936	simSizer.Add(but,0,WACV)
2937	mainSizer.Add(simSizer)
2938	if 'Nobs' in data[0]:
2939	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2940	' Data residual wR: %.3f%% on %d observations'%(data[0]['wR'],data[0]['Nobs'])))
2941	for value in data[0]:
2942	if 'Nref' in value:
2943	mainSizer.Add((5,5),)
2944	pfx = value.split('Nref')[0]
2945	name = data[0].get(pfx.split(':')[0]+'::Name','?')
2946	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For phase '+name+':'))
2947	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2948	u' Unweighted phase residuals RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2949	(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])))
2950	mainSizer.Add((5,5),)
2951	mainSizer.Layout()
2952	G2frame.dataDisplay.SetSizer(mainSizer)
2953	Size = mainSizer.Fit(G2frame.dataFrame)
2954	Size[1] += 10
2955	G2frame.dataFrame.setSizePosLeft(Size)
2956	G2frame.PatternTree.SetItemPyData(item,data)
2957	if kind in ['PWDR','SASD']:
2958	if 'xylim' in dir(G2frame):
2959	NewPlot = False
2960	else:
2961
2962	NewPlot = True
2963	G2plt.PlotPatterns(G2frame,plotType=kind,newPlot=NewPlot)
2964	elif kind == 'HKLF':
2965	Name = G2frame.PatternTree.GetItemText(item)
2966	phaseName = G2pdG.IsHistogramInAnyPhase(G2frame,Name)
2967	if phaseName:
2968	pId = GetPatternTreeItemId(G2frame,G2frame.root,'Phases')
2969	phaseId = GetPatternTreeItemId(G2frame,pId,phaseName)
2970	General = G2frame.PatternTree.GetItemPyData(phaseId)['General']
2971	Super = General.get('Super',0)
2972	SuperVec = General.get('SuperVec',[])
2973	else:
2974	Super = 0
2975	SuperVec = []
2976	refList = data[1]['RefList']
2977	FoMax = np.max(refList.T[5+data[1].get('Super',0)])
2978	page = G2frame.G2plotNB.nb.GetSelection()
2979	tab = ''
2980	if page >= 0:
2981	tab = G2frame.G2plotNB.nb.GetPageText(page)
2982	if '3D' in tab:
2983	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2984	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2985	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2986	Page = G2frame.G2plotNB.nb.GetPage(page)
2987	controls = Page.controls
2988	G2plt.Plot3DSngl(G2frame,newPlot=False,Data=controls,hklRef=refList,Title=phaseName)
2989	else:
2990	controls = {'Type' : 'Fo','ifFc' : True,
2991	'HKLmax' : [int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))],
2992	'HKLmin' : [int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))],
2993	'FoMax' : FoMax,'Zone' : '001','Layer' : 0,'Scale' : 1.0,'Super':Super,'SuperVec':SuperVec}
2994	G2plt.PlotSngl(G2frame,newPlot=True,Data=controls,hklRef=refList)
2995
2996	################################################################################
2997	##### Pattern tree routines
2998	################################################################################
2999
3000	def GetPatternTreeDataNames(G2frame,dataTypes):
3001	'''Needs a doc string
3002	'''
3003	names = []
3004	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3005	while item:
3006	name = G2frame.PatternTree.GetItemText(item)
3007	if name[:4] in dataTypes:
3008	names.append(name)
3009	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3010	return names
3011
3012	def GetPatternTreeItemId(G2frame, parentId, itemText):
3013	'''Needs a doc string
3014	'''
3015	item, cookie = G2frame.PatternTree.GetFirstChild(parentId)
3016	while item:
3017	if G2frame.PatternTree.GetItemText(item) == itemText:
3018	return item
3019	item, cookie = G2frame.PatternTree.GetNextChild(parentId, cookie)
3020	return 0
3021
3022	def MovePatternTreeToGrid(G2frame,item):
3023	'''Called from GSASII.OnPatternTreeSelChanged when a item is selected on the tree
3024	'''
3025	pickName = G2frame.PatternTree.GetItemText(item)
3026	if G2frame.PickIdText == pickName:
3027	return
3028
3029	oldPage = None # will be set later if already on a Phase item
3030	if G2frame.dataFrame:
3031	SetDataMenuBar(G2frame)
3032	if G2frame.dataFrame.GetLabel() == 'Comments':
3033	try:
3034	data = [G2frame.dataDisplay.GetValue()]
3035	G2frame.dataDisplay.Clear()
3036	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Comments')
3037	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3038	except: #clumsy but avoids dead window problem when opening another project
3039	pass
3040	elif G2frame.dataFrame.GetLabel() == 'Notebook':
3041	try:
3042	data = [G2frame.dataDisplay.GetValue()]
3043	G2frame.dataDisplay.Clear()
3044	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Notebook')
3045	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3046	except: #clumsy but avoids dead window problem when opening another project
3047	pass
3048	elif 'Phase Data for' in G2frame.dataFrame.GetLabel():
3049	if G2frame.dataDisplay:
3050	oldPage = G2frame.dataDisplay.GetSelection()
3051	G2frame.dataFrame.Clear()
3052	G2frame.dataFrame.SetLabel('')
3053	else:
3054	#create the frame for the data item window
3055	G2frame.dataFrame = DataFrame(parent=G2frame.mainPanel,frame=G2frame)
3056	G2frame.dataFrame.PhaseUserSize = None
3057
3058	G2frame.dataFrame.Raise()
3059	G2frame.PickId = item
3060	G2frame.PickIdText = None
3061	parentID = G2frame.root
3062	#for i in G2frame.ExportPattern: i.Enable(False)
3063	defWid = [250,150]
3064	if item != G2frame.root:
3065	parentID = G2frame.PatternTree.GetItemParent(item)
3066	if G2frame.PatternTree.GetItemParent(item) == G2frame.root:
3067	G2frame.PatternId = item
3068	if G2frame.PatternTree.GetItemText(item) == 'Notebook':
3069	SetDataMenuBar(G2frame,G2frame.dataFrame.DataNotebookMenu)
3070	G2frame.PatternId = 0
3071	#for i in G2frame.ExportPattern: i.Enable(False)
3072	data = G2frame.PatternTree.GetItemPyData(item)
3073	UpdateNotebook(G2frame,data)
3074	elif G2frame.PatternTree.GetItemText(item) == 'Controls':
3075	G2frame.PatternId = 0
3076	#for i in G2frame.ExportPattern: i.Enable(False)
3077	data = G2frame.PatternTree.GetItemPyData(item)
3078	if not data: #fill in defaults
3079	data = copy.copy(G2obj.DefaultControls) #least squares controls
3080	G2frame.PatternTree.SetItemPyData(item,data)
3081	for i in G2frame.Refine: i.Enable(True)
3082	G2frame.EnableSeqRefineMenu()
3083	UpdateControls(G2frame,data)
3084	elif G2frame.PatternTree.GetItemText(item) == 'Sequential results':
3085	data = G2frame.PatternTree.GetItemPyData(item)
3086	UpdateSeqResults(G2frame,data)
3087	elif G2frame.PatternTree.GetItemText(item) == 'Covariance':
3088	data = G2frame.PatternTree.GetItemPyData(item)
3089	G2frame.dataFrame.setSizePosLeft(defWid)
3090	text = ''
3091	if 'Rvals' in data:
3092	Nvars = len(data['varyList'])
3093	Rvals = data['Rvals']
3094	text = '\nFinal residuals: \nwR = %.3f%% \nchi**2 = %.1f \nGOF = %.2f'%(Rvals['Rwp'],Rvals['chisq'],Rvals['GOF'])
3095	text += '\nNobs = %d \nNvals = %d'%(Rvals['Nobs'],Nvars)
3096	if 'lamMax' in Rvals:
3097	text += '\nlog10 MaxLambda = %.1f'%(np.log10(Rvals['lamMax']))
3098	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3099	value='See plot window for covariance display'+text,style=wx.TE_MULTILINE)
3100	G2plt.PlotCovariance(G2frame,data)
3101	elif G2frame.PatternTree.GetItemText(item) == 'Constraints':
3102	data = G2frame.PatternTree.GetItemPyData(item)
3103	G2cnstG.UpdateConstraints(G2frame,data)
3104	elif G2frame.PatternTree.GetItemText(item) == 'Rigid bodies':
3105	data = G2frame.PatternTree.GetItemPyData(item)
3106	G2cnstG.UpdateRigidBodies(G2frame,data)
3107	elif G2frame.PatternTree.GetItemText(item) == 'Restraints':
3108	data = G2frame.PatternTree.GetItemPyData(item)
3109	Phases = G2frame.GetPhaseData()
3110	phase = ''
3111	phaseName = ''
3112	if Phases:
3113	phaseName = Phases.keys()[0]
3114	G2frame.dataFrame.setSizePosLeft(defWid)
3115	G2restG.UpdateRestraints(G2frame,data,Phases,phaseName)
3116	elif 'IMG' in G2frame.PatternTree.GetItemText(item):
3117	G2frame.Image = item
3118	G2frame.dataFrame.SetTitle('Image Data')
3119	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId( \
3120	G2frame,item,'Image Controls'))
3121	G2imG.UpdateImageData(G2frame,data)
3122	G2plt.PlotImage(G2frame,newPlot=True)
3123	elif 'PKS' in G2frame.PatternTree.GetItemText(item):
3124	G2plt.PlotPowderLines(G2frame)
3125	elif 'PWDR' in G2frame.PatternTree.GetItemText(item):
3126	#for i in G2frame.ExportPattern: i.Enable(True)
3127	if G2frame.EnablePlot:
3128	UpdatePWHKPlot(G2frame,'PWDR',item)
3129	elif 'SASD' in G2frame.PatternTree.GetItemText(item):
3130	#for i in G2frame.ExportPattern: i.Enable(True)
3131	if G2frame.EnablePlot:
3132	UpdatePWHKPlot(G2frame,'SASD',item)
3133	elif 'HKLF' in G2frame.PatternTree.GetItemText(item):
3134	G2frame.Sngl = True
3135	UpdatePWHKPlot(G2frame,'HKLF',item)
3136	elif 'PDF' in G2frame.PatternTree.GetItemText(item):
3137	G2frame.PatternId = item
3138	for i in G2frame.ExportPDF: i.Enable(True)
3139	G2plt.PlotISFG(G2frame,type='S(Q)')
3140	elif G2frame.PatternTree.GetItemText(item) == 'Phases':
3141	G2frame.dataFrame.setSizePosLeft(defWid)
3142	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3143	value='Select one phase to see its parameters')
3144	elif 'I(Q)' in G2frame.PatternTree.GetItemText(item):
3145	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3146	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3147	G2pdG.UpdatePDFGrid(G2frame,data)
3148	G2plt.PlotISFG(G2frame,type='I(Q)',newPlot=True)
3149	elif 'S(Q)' in G2frame.PatternTree.GetItemText(item):
3150	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3151	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3152	G2pdG.UpdatePDFGrid(G2frame,data)
3153	G2plt.PlotISFG(G2frame,type='S(Q)',newPlot=True)
3154	elif 'F(Q)' in G2frame.PatternTree.GetItemText(item):
3155	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3156	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3157	G2pdG.UpdatePDFGrid(G2frame,data)
3158	G2plt.PlotISFG(G2frame,type='F(Q)',newPlot=True)
3159	elif 'G(R)' in G2frame.PatternTree.GetItemText(item):
3160	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3161	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3162	G2pdG.UpdatePDFGrid(G2frame,data)
3163	G2plt.PlotISFG(G2frame,type='G(R)',newPlot=True)
3164	elif G2frame.PatternTree.GetItemText(parentID) == 'Phases':
3165	data = G2frame.PatternTree.GetItemPyData(item)
3166	G2phG.UpdatePhaseData(G2frame,item,data,oldPage)
3167	elif G2frame.PatternTree.GetItemText(item) == 'Comments':
3168	SetDataMenuBar(G2frame,G2frame.dataFrame.DataCommentsMenu)
3169	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3170	data = G2frame.PatternTree.GetItemPyData(item)
3171	UpdateComments(G2frame,data)
3172	elif G2frame.PatternTree.GetItemText(item) == 'Image Controls':
3173	G2frame.dataFrame.SetTitle('Image Controls')
3174	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3175	masks = G2frame.PatternTree.GetItemPyData(
3176	GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3177	data = G2frame.PatternTree.GetItemPyData(item)
3178	G2imG.UpdateImageControls(G2frame,data,masks)
3179	G2plt.PlotImage(G2frame)
3180	elif G2frame.PatternTree.GetItemText(item) == 'Masks':
3181	G2frame.dataFrame.SetTitle('Masks')
3182	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3183	data = G2frame.PatternTree.GetItemPyData(item)
3184	G2imG.UpdateMasks(G2frame,data)
3185	G2plt.PlotImage(G2frame)
3186	elif G2frame.PatternTree.GetItemText(item) == 'Stress/Strain':
3187	G2frame.dataFrame.SetTitle('Stress/Strain')
3188	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3189	data = G2frame.PatternTree.GetItemPyData(item)
3190	G2plt.PlotImage(G2frame)
3191	G2plt.PlotStrain(G2frame,data,newPlot=True)
3192	G2imG.UpdateStressStrain(G2frame,data)
3193	elif G2frame.PatternTree.GetItemText(item) == 'PDF Controls':
3194	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3195	for i in G2frame.ExportPDF: i.Enable(True)
3196	data = G2frame.PatternTree.GetItemPyData(item)
3197	G2pdG.UpdatePDFGrid(G2frame,data)
3198	G2plt.PlotISFG(G2frame,type='I(Q)')
3199	G2plt.PlotISFG(G2frame,type='S(Q)')
3200	G2plt.PlotISFG(G2frame,type='F(Q)')
3201	G2plt.PlotISFG(G2frame,type='G(R)')
3202	elif G2frame.PatternTree.GetItemText(item) == 'Peak List':
3203	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3204	for i in G2frame.ExportPeakList: i.Enable(True)
3205	data = G2frame.PatternTree.GetItemPyData(item)
3206	#patch
3207	if 'list' in str(type(data)):
3208	data = {'peaks':data,'sigDict':{}}
3209	G2frame.PatternTree.SetItemPyData(item,data)
3210	#end patch
3211	G2pdG.UpdatePeakGrid(G2frame,data)
3212	G2plt.PlotPatterns(G2frame)
3213	elif G2frame.PatternTree.GetItemText(item) == 'Background':
3214	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3215	data = G2frame.PatternTree.GetItemPyData(item)
3216	G2pdG.UpdateBackground(G2frame,data)
3217	G2plt.PlotPatterns(G2frame)
3218	elif G2frame.PatternTree.GetItemText(item) == 'Limits':
3219	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3220	datatype = G2frame.PatternTree.GetItemText(G2frame.PatternId)[:4]
3221	data = G2frame.PatternTree.GetItemPyData(item)
3222	G2pdG.UpdateLimitsGrid(G2frame,data,datatype)
3223	G2plt.PlotPatterns(G2frame,plotType=datatype)
3224	elif G2frame.PatternTree.GetItemText(item) == 'Instrument Parameters':
3225	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3226	data = G2frame.PatternTree.GetItemPyData(item)[0]
3227	G2pdG.UpdateInstrumentGrid(G2frame,data)
3228	if 'P' in data['Type'][0]: #powder data only
3229	G2plt.PlotPeakWidths(G2frame)
3230	elif G2frame.PatternTree.GetItemText(item) == 'Models':
3231	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3232	data = G2frame.PatternTree.GetItemPyData(item)
3233	G2pdG.UpdateModelsGrid(G2frame,data)
3234	G2plt.PlotPatterns(G2frame,plotType='SASD')
3235	if len(data['Size']['Distribution']):
3236	G2plt.PlotSASDSizeDist(G2frame)
3237	elif G2frame.PatternTree.GetItemText(item) == 'Substances':
3238	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3239	data = G2frame.PatternTree.GetItemPyData(item)
3240	G2pdG.UpdateSubstanceGrid(G2frame,data)
3241	elif G2frame.PatternTree.GetItemText(item) == 'Sample Parameters':
3242	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3243	data = G2frame.PatternTree.GetItemPyData(item)
3244	datatype = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[2][:4]
3245
3246	if 'Temperature' not in data: #temp fix for old gpx files
3247	data = {'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],'DisplaceX':[0.0,False],
3248	'DisplaceY':[0.0,False],'Diffuse':[],'Temperature':300.,'Pressure':1.0,
3249	'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
3250	'Gonio. radius':200.0}
3251	G2frame.PatternTree.SetItemPyData(item,data)
3252
3253	G2pdG.UpdateSampleGrid(G2frame,data)
3254	G2plt.PlotPatterns(G2frame,plotType=datatype)
3255	elif G2frame.PatternTree.GetItemText(item) == 'Index Peak List':
3256	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3257	for i in G2frame.ExportPeakList: i.Enable(True)
3258	data = G2frame.PatternTree.GetItemPyData(item)
3259	#patch
3260	if len(data) != 2:
3261	data = [data,[]]
3262	G2frame.PatternTree.SetItemPyData(item,data)
3263	#end patch
3264	G2pdG.UpdateIndexPeaksGrid(G2frame,data)
3265	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3266	G2plt.PlotPowderLines(G2frame)
3267	else:
3268	G2plt.PlotPatterns(G2frame)
3269	elif G2frame.PatternTree.GetItemText(item) == 'Unit Cells List':
3270	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3271	data = G2frame.PatternTree.GetItemPyData(item)
3272	if not data:
3273	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
3274	data.append([0,0,0,0,0,0,0,0,0,0,0,0,0,0]) #Bravais lattice flags
3275	data.append([]) #empty cell list
3276	data.append([]) #empty dmin
3277	data.append({}) #empty superlattice stuff
3278	G2frame.PatternTree.SetItemPyData(item,data)
3279	#patch
3280	if len(data) < 5:
3281	data.append({'Use':False,'ModVec':[0,0,0.1],'maxH':1,'ssSymb':''}) #empty superlattice stuff
3282	G2frame.PatternTree.SetItemPyData(item,data)
3283	#end patch
3284	G2pdG.UpdateUnitCellsGrid(G2frame,data)
3285	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3286	G2plt.PlotPowderLines(G2frame)
3287	else:
3288	G2plt.PlotPatterns(G2frame)
3289	elif G2frame.PatternTree.GetItemText(item) == 'Reflection Lists': #powder reflections
3290	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3291	data = G2frame.PatternTree.GetItemPyData(item)
3292	G2frame.RefList = ''
3293	if len(data):
3294	G2frame.RefList = data.keys()[0]
3295	G2pdG.UpdateReflectionGrid(G2frame,data)
3296	G2plt.PlotPatterns(G2frame)
3297	elif G2frame.PatternTree.GetItemText(item) == 'Reflection List': #HKLF reflections
3298	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3299	name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
3300	data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
3301	G2pdG.UpdateReflectionGrid(G2frame,data,HKLF=True,Name=name)
3302
3303	if G2frame.PickId:
3304	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
3305	G2frame.dataFrame.Raise()
3306
3307	def SetDataMenuBar(G2frame,menu=None):
3308	'''Set the menu for the data frame. On the Mac put this
3309	menu for the data tree window instead.
3310
3311	Note that data frame items do not have menus, for these (menu=None)
3312	display a blank menu or on the Mac display the standard menu for
3313	the data tree window.
3314	'''
3315	if sys.platform == "darwin":
3316	if menu is None:
3317	G2frame.SetMenuBar(G2frame.GSASIIMenu)
3318	else:
3319	G2frame.SetMenuBar(menu)
3320	else:
3321	if menu is None:
3322	G2frame.dataFrame.SetMenuBar(G2frame.dataFrame.BlankMenu)
3323	else:
3324	G2frame.dataFrame.SetMenuBar(menu)
3325
3326	def HowDidIgetHere():
3327	'''Show a traceback with calls that brought us to the current location.
3328	Used for debugging.
3329	'''
3330	import traceback
3331	print 70''
3332	for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip.rstrip())
3333	print 70''
3334

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