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source: trunk/GSASIIgrid.py @ 2018

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

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