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source: trunk/GSASIIgrid.py @ 1926

Last change on this file since 1926 was 1926, checked in by vondreele, 8 years ago
Work on add Hydrogens
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1	# -- coding: utf-8 --
2	#GSASIIgrid - data display routines
3	########### SVN repository information ###################
4	# $Date: 2015-07-13 21:10:42 +0000 (Mon, 13 Jul 2015) $
5	# $Author: vondreele $
6	# $Revision: 1926 $
7	# $URL: trunk/GSASIIgrid.py $
8	# $Id: GSASIIgrid.py 1926 2015-07-13 21:10:42Z vondreele $
9	########### SVN repository information ###################
10	'''
11	GSASIIgrid: Basic GUI routines
12	--------------------------------
13
14	'''
15	import wx
16	import wx.grid as wg
17	#import wx.wizard as wz
18	#import wx.aui
19	import wx.lib.scrolledpanel as wxscroll
20	import time
21	import copy
22	import cPickle
23	import sys
24	import os
25	import numpy as np
26	import numpy.ma as ma
27	import scipy.optimize as so
28	import GSASIIpath
29	GSASIIpath.SetVersionNumber("$Revision: 1926 $")
30	import GSASIImath as G2mth
31	import GSASIIIO as G2IO
32	import GSASIIstrIO as G2stIO
33	import GSASIIlattice as G2lat
34	import GSASIIplot as G2plt
35	import GSASIIpwdGUI as G2pdG
36	import GSASIIimgGUI as G2imG
37	import GSASIIphsGUI as G2phG
38	import GSASIIspc as G2spc
39	import GSASIImapvars as G2mv
40	import GSASIIconstrGUI as G2cnstG
41	import GSASIIrestrGUI as G2restG
42	import GSASIIpy3 as G2py3
43	import GSASIIobj as G2obj
44	import GSASIIexprGUI as G2exG
45	import GSASIIlog as log
46	import GSASIIctrls as G2G
47
48	# trig functions in degrees
49	sind = lambda x: np.sin(x*np.pi/180.)
50	tand = lambda x: np.tan(x*np.pi/180.)
51	cosd = lambda x: np.cos(x*np.pi/180.)
52
53	# Define a short name for convenience
54	WACV = wx.ALIGN_CENTER_VERTICAL
55
56	[ wxID_FOURCALC, wxID_FOURSEARCH, wxID_FOURCLEAR, wxID_PEAKSMOVE, wxID_PEAKSCLEAR,
57	wxID_CHARGEFLIP, wxID_PEAKSUNIQUE, wxID_PEAKSDELETE, wxID_PEAKSDA,
58	wxID_PEAKSDISTVP, wxID_PEAKSVIEWPT, wxID_FINDEQVPEAKS,wxID_SHOWBONDS,wxID_MULTIMCSA,
59	wxID_SINGLEMCSA, wxID_4DMAPCOMPUTE,wxID_4DCHARGEFLIP,
60	] = [wx.NewId() for item in range(17)]
61
62	[ wxID_PWDRADD, wxID_HKLFADD, wxID_PWDANALYSIS, wxID_PWDCOPY, wxID_PLOTCTRLCOPY,
63	wxID_DATADELETE,wxID_DATACOPY,wxID_DATACOPYFLAGS,wxID_DATASELCOPY,
64	] = [wx.NewId() for item in range(9)]
65
66	[ wxID_ATOMSEDITADD, wxID_ATOMSEDITINSERT, wxID_ATOMSEDITDELETE, wxID_ATOMSREFINE,
67	wxID_ATOMSMODIFY, wxID_ATOMSTRANSFORM, wxID_ATOMSVIEWADD, wxID_ATOMVIEWINSERT,
68	wxID_RELOADDRAWATOMS,wxID_ATOMSDISAGL,wxID_ATOMMOVE,wxID_MAKEMOLECULE,
69	wxID_ASSIGNATMS2RB,wxID_ATOMSPDISAGL, wxID_ISODISP,wxID_ADDHATOM,
70	] = [wx.NewId() for item in range(16)]
71
72	[ wxID_DRAWATOMSTYLE, wxID_DRAWATOMLABEL, wxID_DRAWATOMCOLOR, wxID_DRAWATOMRESETCOLOR,
73	wxID_DRAWVIEWPOINT, wxID_DRAWTRANSFORM, wxID_DRAWDELETE, wxID_DRAWFILLCELL,
74	wxID_DRAWADDEQUIV, wxID_DRAWFILLCOORD, wxID_DRAWDISAGLTOR, wxID_DRAWPLANE,
75	wxID_DRAWDISTVP,
76	] = [wx.NewId() for item in range(13)]
77
78	[ wxID_DRAWRESTRBOND, wxID_DRAWRESTRANGLE, wxID_DRAWRESTRPLANE, wxID_DRAWRESTRCHIRAL,
79	] = [wx.NewId() for item in range(4)]
80
81	[ wxID_ADDMCSAATOM,wxID_ADDMCSARB,wxID_CLEARMCSARB,wxID_MOVEMCSA,wxID_MCSACLEARRESULTS,
82	] = [wx.NewId() for item in range(5)]
83
84	[ wxID_CLEARTEXTURE,wxID_REFINETEXTURE,
85	] = [wx.NewId() for item in range(2)]
86
87	[ wxID_PAWLEYLOAD, wxID_PAWLEYESTIMATE, wxID_PAWLEYUPDATE,
88	] = [wx.NewId() for item in range(3)]
89
90	[ wxID_IMCALIBRATE,wxID_IMRECALIBRATE,wxID_IMINTEGRATE, wxID_IMCLEARCALIB,
91	wxID_IMCOPYCONTROLS, wxID_INTEGRATEALL, wxID_IMSAVECONTROLS, wxID_IMLOADCONTROLS,
92	] = [wx.NewId() for item in range(8)]
93
94	[ wxID_MASKCOPY, wxID_MASKSAVE, wxID_MASKLOAD, wxID_NEWMASKSPOT,wxID_NEWMASKARC,wxID_NEWMASKRING,
95	wxID_NEWMASKFRAME, wxID_NEWMASKPOLY, wxID_MASKLOADNOT,
96	] = [wx.NewId() for item in range(9)]
97
98	[ wxID_STRSTACOPY, wxID_STRSTAFIT, wxID_STRSTASAVE, wxID_STRSTALOAD,wxID_STRSTSAMPLE,
99	wxID_APPENDDZERO,wxID_STRSTAALLFIT,wxID_UPDATEDZERO,
100	] = [wx.NewId() for item in range(8)]
101
102	[ wxID_BACKCOPY,wxID_LIMITCOPY, wxID_SAMPLECOPY, wxID_SAMPLECOPYSOME, wxID_BACKFLAGCOPY, wxID_SAMPLEFLAGCOPY,
103	wxID_SAMPLESAVE, wxID_SAMPLELOAD,wxID_ADDEXCLREGION,wxID_SETSCALE,wxID_SAMPLE1VAL,wxID_ALLSAMPLELOAD,
104	] = [wx.NewId() for item in range(12)]
105
106	[ wxID_INSTPRMRESET,wxID_CHANGEWAVETYPE,wxID_INSTCOPY, wxID_INSTFLAGCOPY, wxID_INSTLOAD,
107	wxID_INSTSAVE, wxID_INST1VAL, wxID_INSTCALIB,
108	] = [wx.NewId() for item in range(8)]
109
110	[ wxID_UNDO,wxID_LSQPEAKFIT,wxID_LSQONECYCLE,wxID_RESETSIGGAM,wxID_CLEARPEAKS,wxID_AUTOSEARCH,
111	wxID_PEAKSCOPY, wxID_SEQPEAKFIT,
112	] = [wx.NewId() for item in range(8)]
113
114	[ wxID_INDXRELOAD, wxID_INDEXPEAKS, wxID_REFINECELL, wxID_COPYCELL, wxID_MAKENEWPHASE,
115	wxID_EXPORTCELLS,
116	] = [wx.NewId() for item in range(6)]
117
118	[ wxID_CONSTRAINTADD,wxID_EQUIVADD,wxID_HOLDADD,wxID_FUNCTADD,wxID_ADDRIDING,
119	wxID_CONSPHASE, wxID_CONSHIST, wxID_CONSHAP, wxID_CONSGLOBAL,wxID_EQUIVALANCEATOMS,
120	] = [wx.NewId() for item in range(10)]
121
122	[ wxID_RESTRAINTADD, wxID_RESTSELPHASE,wxID_RESTDELETE, wxID_RESRCHANGEVAL,
123	wxID_RESTCHANGEESD,wxID_AARESTRAINTADD,wxID_AARESTRAINTPLOT,
124	] = [wx.NewId() for item in range(7)]
125
126	[ wxID_RIGIDBODYADD,wxID_DRAWDEFINERB,wxID_RIGIDBODYIMPORT,wxID_RESIDUETORSSEQ,
127	wxID_AUTOFINDRESRB,wxID_GLOBALRESREFINE,wxID_RBREMOVEALL,wxID_COPYRBPARMS,
128	wxID_GLOBALTHERM,wxID_VECTORBODYADD
129	] = [wx.NewId() for item in range(10)]
130
131	[ wxID_RENAMESEQSEL,wxID_SAVESEQSEL,wxID_SAVESEQSELCSV,wxID_SAVESEQCSV,wxID_PLOTSEQSEL,
132	wxID_ORGSEQSEL,wxADDSEQVAR,wxDELSEQVAR,wxEDITSEQVAR,wxCOPYPARFIT,wxID_AVESEQSEL,
133	wxADDPARFIT,wxDELPARFIT,wxEDITPARFIT,wxDOPARFIT,
134	] = [wx.NewId() for item in range(15)]
135
136	[ wxID_MODELCOPY,wxID_MODELFIT,wxID_MODELADD,wxID_ELEMENTADD,wxID_ELEMENTDELETE,
137	wxID_ADDSUBSTANCE,wxID_LOADSUBSTANCE,wxID_DELETESUBSTANCE,wxID_COPYSUBSTANCE,
138	wxID_MODELUNDO,wxID_MODELFITALL,wxID_MODELCOPYFLAGS,
139	] = [wx.NewId() for item in range(12)]
140
141	[ wxID_SELECTPHASE,wxID_PWDHKLPLOT,wxID_PWD3DHKLPLOT,wxID_3DALLHKLPLOT,
142	] = [wx.NewId() for item in range(4)]
143
144	[ wxID_PDFCOPYCONTROLS, wxID_PDFSAVECONTROLS, wxID_PDFLOADCONTROLS,
145	wxID_PDFCOMPUTE, wxID_PDFCOMPUTEALL, wxID_PDFADDELEMENT, wxID_PDFDELELEMENT,
146	] = [wx.NewId() for item in range(7)]
147
148	[ wxID_MCRON,wxID_MCRLIST,wxID_MCRSAVE,wxID_MCRPLAY,
149	] = [wx.NewId() for item in range(4)]
150
151	VERY_LIGHT_GREY = wx.Colour(235,235,235)
152
153	# Aliases for Classes/Functions moved to GSASIIctrls, all should be tracked down but leaving as a reminder
154	#SingleFloatDialog = G2G.SingleFloatDialog
155	#SingleStringDialog = G2G.SingleStringDialog
156	#MultiStringDialog = G2G.MultiStringDialog
157	#G2ColumnIDDialog = G2G.G2ColumnIDDialog
158	#ItemSelector = G2G.ItemSelector
159	#HorizontalLine = G2G.HorizontalLine
160	#G2LoggedButton = G2G.G2LoggedButton
161	#EnumSelector = G2G.EnumSelector
162	#G2ChoiceButton = G2G.G2ChoiceButton
163	#GSGrid = G2G.GSGrid
164	#Table = G2G.Table
165	#GridFractionEditor = G2G.GridFractionEditor
166	#GSNoteBook = G2G.GSNoteBook
167
168	# Should SGMessageBox, SymOpDialog, DisAglDialog be moved?
169
170	################################################################################
171	#### GSAS-II class definitions
172	################################################################################
173
174	class SGMessageBox(wx.Dialog):
175	''' Special version of MessageBox that displays space group & super space group text
176	in two blocks
177	'''
178	def __init__(self,parent,title,text,table,):
179	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,pos=wx.DefaultPosition,
180	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
181	self.text=text
182	self.table = table
183	self.panel = wx.Panel(self)
184	mainSizer = wx.BoxSizer(wx.VERTICAL)
185	mainSizer.Add((0,10))
186	for line in text:
187	mainSizer.Add(wx.StaticText(self.panel,label=' %s '%(line)),0,WACV)
188	ncol = self.table[0].count(',')+1
189	tableSizer = wx.FlexGridSizer(0,2*ncol+3,0,0)
190	for j,item in enumerate(self.table):
191	num,flds = item.split(')')
192	tableSizer.Add(wx.StaticText(self.panel,label=' %s '%(num+')')),0,WACV\|wx.ALIGN_LEFT)
193	flds = flds.replace(' ','').split(',')
194	for i,fld in enumerate(flds):
195	if i < ncol-1:
196	tableSizer.Add(wx.StaticText(self.panel,label='%s, '%(fld)),0,WACV\|wx.ALIGN_RIGHT)
197	else:
198	tableSizer.Add(wx.StaticText(self.panel,label='%s'%(fld)),0,WACV\|wx.ALIGN_RIGHT)
199	if not j%2:
200	tableSizer.Add((20,0))
201	mainSizer.Add(tableSizer,0,wx.ALIGN_LEFT)
202	btnsizer = wx.StdDialogButtonSizer()
203	OKbtn = wx.Button(self.panel, wx.ID_OK)
204	OKbtn.SetDefault()
205	btnsizer.AddButton(OKbtn)
206	btnsizer.Realize()
207	mainSizer.Add((0,10))
208	mainSizer.Add(btnsizer,0,wx.ALIGN_CENTER)
209	self.panel.SetSizer(mainSizer)
210	self.panel.Fit()
211	self.Fit()
212	size = self.GetSize()
213	self.SetSize([size[0]+20,size[1]])
214
215	def Show(self):
216	'''Use this method after creating the dialog to post it
217	'''
218	self.ShowModal()
219	return
220
221	################################################################################
222	class SymOpDialog(wx.Dialog):
223	'''Class to select a symmetry operator
224	'''
225	def __init__(self,parent,SGData,New=True,ForceUnit=False):
226	wx.Dialog.__init__(self,parent,-1,'Select symmetry operator',
227	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
228	panel = wx.Panel(self)
229	self.SGData = SGData
230	self.New = New
231	self.Force = ForceUnit
232	self.OpSelected = [0,0,0,[0,0,0],False,False]
233	mainSizer = wx.BoxSizer(wx.VERTICAL)
234	if ForceUnit:
235	choice = ['No','Yes']
236	self.force = wx.RadioBox(panel,-1,'Force to unit cell?',choices=choice)
237	self.force.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
238	mainSizer.Add(self.force,0,WACV\|wx.TOP,5)
239	# if SGData['SGInv']:
240	choice = ['No','Yes']
241	self.inv = wx.RadioBox(panel,-1,'Choose inversion?',choices=choice)
242	self.inv.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
243	mainSizer.Add(self.inv,0,WACV)
244	if SGData['SGLatt'] != 'P':
245	LattOp = G2spc.Latt2text(SGData['SGLatt']).split(';')
246	self.latt = wx.RadioBox(panel,-1,'Choose cell centering?',choices=LattOp)
247	self.latt.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
248	mainSizer.Add(self.latt,0,WACV)
249	if SGData['SGLaue'] in ['-1','2/m','mmm','4/m','4/mmm']:
250	Ncol = 2
251	else:
252	Ncol = 3
253	OpList = []
254	for Opr in SGData['SGOps']:
255	OpList.append(G2spc.MT2text(Opr))
256	self.oprs = wx.RadioBox(panel,-1,'Choose space group operator?',choices=OpList,
257	majorDimension=Ncol)
258	self.oprs.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
259	mainSizer.Add(self.oprs,0,WACV\|wx.BOTTOM,5)
260	mainSizer.Add(wx.StaticText(panel,-1," Choose unit cell?"),0,WACV)
261	cellSizer = wx.BoxSizer(wx.HORIZONTAL)
262	cellName = ['X','Y','Z']
263	self.cell = []
264	for i in range(3):
265	self.cell.append(wx.SpinCtrl(panel,-1,cellName[i],size=wx.Size(50,20)))
266	self.cell[-1].SetRange(-3,3)
267	self.cell[-1].SetValue(0)
268	self.cell[-1].Bind(wx.EVT_SPINCTRL, self.OnOpSelect)
269	cellSizer.Add(self.cell[-1],0,WACV)
270	mainSizer.Add(cellSizer,0,WACV\|wx.BOTTOM,5)
271	if self.New:
272	choice = ['No','Yes']
273	self.new = wx.RadioBox(panel,-1,'Generate new positions?',choices=choice)
274	self.new.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
275	mainSizer.Add(self.new,0,WACV)
276
277	OkBtn = wx.Button(panel,-1,"Ok")
278	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
279	cancelBtn = wx.Button(panel,-1,"Cancel")
280	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
281	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
282	btnSizer.Add((20,20),1)
283	btnSizer.Add(OkBtn)
284	btnSizer.Add((20,20),1)
285	btnSizer.Add(cancelBtn)
286	btnSizer.Add((20,20),1)
287
288	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
289	panel.SetSizer(mainSizer)
290	panel.Fit()
291	self.Fit()
292
293	def OnOpSelect(self,event):
294	# if self.SGData['SGInv']:
295	self.OpSelected[0] = self.inv.GetSelection()
296	if self.SGData['SGLatt'] != 'P':
297	self.OpSelected[1] = self.latt.GetSelection()
298	self.OpSelected[2] = self.oprs.GetSelection()
299	for i in range(3):
300	self.OpSelected[3][i] = float(self.cell[i].GetValue())
301	if self.New:
302	self.OpSelected[4] = self.new.GetSelection()
303	if self.Force:
304	self.OpSelected[5] = self.force.GetSelection()
305
306	def GetSelection(self):
307	return self.OpSelected
308
309	def OnOk(self,event):
310	parent = self.GetParent()
311	parent.Raise()
312	self.EndModal(wx.ID_OK)
313
314	def OnCancel(self,event):
315	parent = self.GetParent()
316	parent.Raise()
317	self.EndModal(wx.ID_CANCEL)
318
319	class AddHatomDialog(wx.Dialog):
320	'''H atom addition dialog. After :meth:`ShowModal` returns, the results
321	are found in dict :attr:`self.data`, which is accessed using :meth:`GetData`.
322	:param wx.Frame parent: reference to parent frame (or None)
323	:param dict Neigh: a dict of atom names with list of atom name, dist pairs for neighboring atoms
324	:param dict phase: a dict containing the phase as defined by
325	:ref:`Phase Tree Item <Phase_table>`
326	'''
327	def __init__(self,parent,Neigh,phase):
328	wx.Dialog.__init__(self,parent,wx.ID_ANY,'H atom add',
329	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
330	self.panel = wxscroll.ScrolledPanel(self) #just a dummy - gets destroyed in Draw!
331	self.Neigh = Neigh
332	self.phase = phase
333	self.Hatoms = []
334	self.Draw(self.Neigh,self.phase)
335
336	def Draw(self,Neigh,phase):
337	'''Creates the contents of the dialog. Normally called
338	by :meth:`__init__`.
339	'''
340	def OnHSelect(event):
341	Obj = event.GetEventObject()
342	item,i = Indx[Obj.GetId()]
343	for obj in Indx[item]:
344	obj.SetValue(False)
345	Obj.SetValue(True)
346	self.Neigh[item][2] = i
347
348	self.panel.Destroy()
349	self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE)
350	mainSizer = wx.BoxSizer(wx.VERTICAL)
351	mainSizer.Add(wx.StaticText(self.panel,-1,'H atom add controls for phase %s:'%(phase['General']['Name'])),
352	0,wx.LEFT\|wx.TOP,10)
353	mainSizer.Add(wx.StaticText(self.panel,-1,'NB: Check selections as they may not be correct'),0,WACV\|wx.LEFT,10)
354	mainSizer.Add(wx.StaticText(self.panel,-1," Atom: Add # H's Neighbors, dist"),0,wx.TOP\|wx.LEFT,5)
355	nHatms = ['0','1','2','3']
356	dataSizer = wx.FlexGridSizer(0,3,0,0)
357	Indx = {}
358	for inei,neigh in enumerate(Neigh):
359	dataSizer.Add(wx.StaticText(self.panel,-1,' %s: '%(neigh[0])),0,WACV)
360	nH = 1 #for O atom
361	if 'C' in neigh[0] or 'N' in neigh[0]:
362	nH = 4-len(neigh[1][0])
363	checks = wx.BoxSizer(wx.HORIZONTAL)
364	Ids = []
365	for i in range(nH+1):
366	nHs = wx.CheckBox(self.panel,-1,label=nHatms[i])
367	if i == neigh[2]:
368	nHs.SetValue(True)
369	Indx[nHs.GetId()] = [inei,i]
370	Ids.append(nHs)
371	nHs.Bind(wx.EVT_CHECKBOX, OnHSelect)
372	checks.Add(nHs,0,WACV)
373	Indx[inei] = Ids
374	dataSizer.Add(checks,0,WACV)
375	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
376	for bond in neigh[1][0]:
377	lineSizer.Add(wx.StaticText(self.panel,-1,' %s, %.3f'%(bond[0],bond[1])),0,WACV)
378	dataSizer.Add(lineSizer,0,WACV\|wx.RIGHT,10)
379	mainSizer.Add(dataSizer,0,wx.LEFT,5)
380
381	CancelBtn = wx.Button(self.panel,-1,'Cancel')
382	CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
383	OkBtn = wx.Button(self.panel,-1,'Ok')
384	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
385	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
386	btnSizer.Add((20,20),1)
387	btnSizer.Add(OkBtn)
388	btnSizer.Add((20,20),1)
389	btnSizer.Add(CancelBtn)
390	btnSizer.Add((20,20),1)
391	mainSizer.Add(btnSizer,0,wx.BOTTOM\|wx.TOP, 10)
392	size = np.array(self.GetSize())
393	self.panel.SetupScrolling()
394	self.panel.SetSizer(mainSizer)
395	self.panel.SetAutoLayout(1)
396	size = [size[0]-5,size[1]-20] #this fiddling is needed for older wx!
397	self.panel.SetSize(size)
398
399	def GetData(self):
400	'Returns the values from the dialog'
401	return self.Neigh #has #Hs to add for each entry
402
403	def OnOk(self,event):
404	'Called when the OK button is pressed'
405	parent = self.GetParent()
406	parent.Raise()
407	self.EndModal(wx.ID_OK)
408
409	def OnCancel(self,event):
410	parent = self.GetParent()
411	parent.Raise()
412	self.EndModal(wx.ID_CANCEL)
413
414	class DisAglDialog(wx.Dialog):
415	'''Distance/Angle Controls input dialog. After
416	:meth:`ShowModal` returns, the results are found in
417	dict :attr:`self.data`, which is accessed using :meth:`GetData`.
418
419	:param wx.Frame parent: reference to parent frame (or None)
420	:param dict data: a dict containing the current
421	search ranges or an empty dict, which causes default values
422	to be used.
423	Will be used to set element `DisAglCtls` in
424	:ref:`Phase Tree Item <Phase_table>`
425	:param dict default: A dict containing the default
426	search ranges for each element.
427	'''
428	def __init__(self,parent,data,default,Reset=True):
429	wx.Dialog.__init__(self,parent,wx.ID_ANY,
430	'Distance Angle Controls',
431	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
432	self.default = default
433	self.Reset = Reset
434	self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
435	self._default(data,self.default)
436	self.Draw(self.data)
437
438	def _default(self,data,default):
439	'''Set starting values for the search values, either from
440	the input array or from defaults, if input is null
441	'''
442	if data:
443	self.data = copy.deepcopy(data) # don't mess with originals
444	else:
445	self.data = {}
446	self.data['Name'] = default['Name']
447	self.data['Factors'] = [0.85,0.85]
448	self.data['AtomTypes'] = default['AtomTypes']
449	self.data['BondRadii'] = default['BondRadii'][:]
450	self.data['AngleRadii'] = default['AngleRadii'][:]
451
452	def Draw(self,data):
453	'''Creates the contents of the dialog. Normally called
454	by :meth:`__init__`.
455	'''
456	self.panel.Destroy()
457	self.panel = wx.Panel(self)
458	mainSizer = wx.BoxSizer(wx.VERTICAL)
459	mainSizer.Add(wx.StaticText(self.panel,-1,'Controls for phase '+data['Name']),
460	0,WACV\|wx.LEFT,10)
461	mainSizer.Add((10,10),1)
462
463	radiiSizer = wx.FlexGridSizer(0,3,5,5)
464	radiiSizer.Add(wx.StaticText(self.panel,-1,' Type'),0,WACV)
465	radiiSizer.Add(wx.StaticText(self.panel,-1,'Bond radii'),0,WACV)
466	radiiSizer.Add(wx.StaticText(self.panel,-1,'Angle radii'),0,WACV)
467	self.objList = {}
468	for id,item in enumerate(self.data['AtomTypes']):
469	radiiSizer.Add(wx.StaticText(self.panel,-1,' '+item),0,WACV)
470	bRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['BondRadii'][id]),style=wx.TE_PROCESS_ENTER)
471	self.objList[bRadii.GetId()] = ['BondRadii',id]
472	bRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
473	bRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
474	radiiSizer.Add(bRadii,0,WACV)
475	aRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['AngleRadii'][id]),style=wx.TE_PROCESS_ENTER)
476	self.objList[aRadii.GetId()] = ['AngleRadii',id]
477	aRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
478	aRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
479	radiiSizer.Add(aRadii,0,WACV)
480	mainSizer.Add(radiiSizer,0,wx.EXPAND)
481	factorSizer = wx.FlexGridSizer(0,2,5,5)
482	Names = ['Bond','Angle']
483	for i,name in enumerate(Names):
484	factorSizer.Add(wx.StaticText(self.panel,-1,name+' search factor'),0,WACV)
485	bondFact = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['Factors'][i]),style=wx.TE_PROCESS_ENTER)
486	self.objList[bondFact.GetId()] = ['Factors',i]
487	bondFact.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
488	bondFact.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
489	factorSizer.Add(bondFact)
490	mainSizer.Add(factorSizer,0,wx.EXPAND)
491
492	OkBtn = wx.Button(self.panel,-1,"Ok")
493	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
494	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
495	btnSizer.Add((20,20),1)
496	btnSizer.Add(OkBtn)
497	if self.Reset:
498	ResetBtn = wx.Button(self.panel,-1,'Reset')
499	ResetBtn.Bind(wx.EVT_BUTTON, self.OnReset)
500	btnSizer.Add(ResetBtn)
501	btnSizer.Add((20,20),1)
502	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
503	self.panel.SetSizer(mainSizer)
504	self.panel.Fit()
505	self.Fit()
506
507	def OnRadiiVal(self,event):
508	Obj = event.GetEventObject()
509	item = self.objList[Obj.GetId()]
510	try:
511	self.data[item[0]][item[1]] = float(Obj.GetValue())
512	except ValueError:
513	pass
514	Obj.SetValue("%.3f"%(self.data[item[0]][item[1]])) #reset in case of error
515
516	def GetData(self):
517	'Returns the values from the dialog'
518	return self.data
519
520	def OnOk(self,event):
521	'Called when the OK button is pressed'
522	parent = self.GetParent()
523	parent.Raise()
524	self.EndModal(wx.ID_OK)
525
526	def OnReset(self,event):
527	'Called when the Reset button is pressed'
528	data = {}
529	self._default(data,self.default)
530	self.Draw(self.data)
531
532	################################################################################
533	class ShowLSParms(wx.Dialog):
534	'''Create frame to show least-squares parameters
535	'''
536	def __init__(self,parent,title,parmDict,varyList,fullVaryList,
537	size=(300,430)):
538	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,size=size,
539	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
540	mainSizer = wx.BoxSizer(wx.VERTICAL)
541
542	panel = wxscroll.ScrolledPanel(
543	self, wx.ID_ANY,
544	#size=size,
545	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
546	num = len(varyList)
547	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,'Number of refined variables: '+str(num)))
548	if len(varyList) != len(fullVaryList):
549	num = len(fullVaryList) - len(varyList)
550	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,' + '+str(num)+' parameters are varied via constraints'))
551	subSizer = wx.FlexGridSizer(cols=4,hgap=2,vgap=2)
552	parmNames = parmDict.keys()
553	parmNames.sort()
554	subSizer.Add((-1,-1))
555	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'Parameter name '))
556	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'refine?'))
557	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'value'),0,wx.ALIGN_RIGHT)
558	explainRefine = False
559	for name in parmNames:
560	# skip entries without numerical values
561	if isinstance(parmDict[name],basestring): continue
562	try:
563	value = G2py3.FormatSigFigs(parmDict[name])
564	except TypeError:
565	value = str(parmDict[name])+' -?' # unexpected
566	#continue
567	v = G2obj.getVarDescr(name)
568	if v is None or v[-1] is None:
569	subSizer.Add((-1,-1))
570	else:
571	ch = G2G.HelpButton(panel,G2obj.fmtVarDescr(name))
572	subSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
573	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,str(name)))
574	if name in varyList:
575	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'R'))
576	elif name in fullVaryList:
577	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'C'))
578	explainRefine = True
579	else:
580	subSizer.Add((-1,-1))
581	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
582
583	# finish up ScrolledPanel
584	panel.SetSizer(subSizer)
585	panel.SetAutoLayout(1)
586	panel.SetupScrolling()
587	mainSizer.Add(panel,1, wx.ALL\|wx.EXPAND,1)
588
589	if explainRefine:
590	mainSizer.Add(
591	wx.StaticText(self,wx.ID_ANY,
592	'"R" indicates a refined variable\n'+
593	'"C" indicates generated from a constraint'
594	),
595	0, wx.ALL,0)
596	# make OK button
597	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
598	btn = wx.Button(self, wx.ID_CLOSE,"Close")
599	btn.Bind(wx.EVT_BUTTON,self._onClose)
600	btnsizer.Add(btn)
601	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
602	# Allow window to be enlarged but not made smaller
603	self.SetSizer(mainSizer)
604	self.SetMinSize(self.GetSize())
605
606	def _onClose(self,event):
607	self.EndModal(wx.ID_CANCEL)
608
609	################################################################################
610	class DataFrame(wx.Frame):
611	'''Create the data item window and all the entries in menus used in
612	that window. For Linux and windows, the menu entries are created for the
613	current data item window, but in the Mac the menu is accessed from all
614	windows. This means that a different menu is posted depending on which
615	data item is posted. On the Mac, all the menus contain the data tree menu
616	items, but additional menus are added specific to the data item.
617
618	Note that while the menus are created here,
619	the binding for the menus is done later in various GSASII*GUI modules,
620	where the functions to be called are defined.
621	'''
622	def Bind(self,eventtype,handler,args,*kwargs):
623	'''Override the Bind() function: on the Mac the binding is to
624	the main window, so that menus operate with any window on top.
625	For other platforms, either wrap calls that will be logged
626	or call the default wx.Frame Bind() to bind to the menu item directly.
627
628	Note that bindings can be made to objects by Id or by direct reference to the
629	object. As a convention, when bindings are to objects, they are not logged
630	but when bindings are by Id, they are logged.
631	'''
632	if sys.platform == "darwin": # mac
633	self.G2frame.Bind(eventtype,handler,args,*kwargs)
634	return
635	if eventtype == wx.EVT_MENU and 'id' in kwargs:
636	menulabels = log.SaveMenuCommand(kwargs['id'],self.G2frame,handler)
637	if menulabels:
638	#print 'intercepting bind for',handler,menulabels,kwargs['id']
639	wx.Frame.Bind(self,eventtype,self.G2frame.MenuBinding,args,*kwargs)
640	return
641	wx.Frame.Bind(self,eventtype,handler,args,*kwargs)
642
643	def PrefillDataMenu(self,menu,helpType,helpLbl=None,empty=False):
644	'''Create the "standard" part of data frame menus. Note that on Linux and
645	Windows nothing happens here. On Mac, this menu duplicates the
646	tree menu, but adds an extra help command for the data item and a separator.
647	'''
648	self.datamenu = menu
649	self.G2frame.dataMenuBars.append(menu)
650	self.helpType = helpType
651	self.helpLbl = helpLbl
652	if sys.platform == "darwin": # mac
653	self.G2frame.FillMainMenu(menu) # add the data tree menu items
654	if not empty:
655	menu.Append(wx.Menu(title=''),title='\|') # add a separator
656
657	def PostfillDataMenu(self,empty=False):
658	'''Create the "standard" part of data frame menus. Note that on Linux and
659	Windows, this is the standard help Menu. On Mac, this menu duplicates the
660	tree menu, but adds an extra help command for the data item and a separator.
661	'''
662	menu = self.datamenu
663	helpType = self.helpType
664	helpLbl = self.helpLbl
665	if sys.platform == "darwin": # mac
666	if not empty:
667	menu.Append(wx.Menu(title=''),title='\|') # add another separator
668	menu.Append(G2G.AddHelp(self.G2frame,helpType=helpType, helpLbl=helpLbl),
669	title='&Help')
670	else: # other
671	menu.Append(menu=G2G.MyHelp(self,helpType=helpType, helpLbl=helpLbl),
672	title='&Help')
673
674	def _init_menus(self):
675	'define all GSAS-II data frame menus'
676
677	# for use where no menu or data frame help is provided
678	self.BlankMenu = wx.MenuBar()
679
680	# Controls
681	self.ControlsMenu = wx.MenuBar()
682	self.PrefillDataMenu(self.ControlsMenu,helpType='Controls',empty=True)
683	self.PostfillDataMenu(empty=True)
684
685	# Notebook
686	self.DataNotebookMenu = wx.MenuBar()
687	self.PrefillDataMenu(self.DataNotebookMenu,helpType='Notebook',empty=True)
688	self.PostfillDataMenu(empty=True)
689
690	# Comments
691	self.DataCommentsMenu = wx.MenuBar()
692	self.PrefillDataMenu(self.DataCommentsMenu,helpType='Comments',empty=True)
693	self.PostfillDataMenu(empty=True)
694
695	# Constraints - something amiss here - get weird wx C++ error after refine!
696	self.ConstraintMenu = wx.MenuBar()
697	self.PrefillDataMenu(self.ConstraintMenu,helpType='Constraints')
698	self.ConstraintTab = wx.Menu(title='')
699	self.ConstraintMenu.Append(menu=self.ConstraintTab, title='Select tab')
700	for id,txt in (
701	(wxID_CONSPHASE,'Phase'),
702	(wxID_CONSHAP,'Histogram/Phase'),
703	(wxID_CONSHIST,'Histogram'),
704	(wxID_CONSGLOBAL,'Global')):
705	self.ConstraintTab.Append(
706	id=id, kind=wx.ITEM_NORMAL,text=txt,
707	help='Select '+txt+' constraint editing tab')
708	self.ConstraintEdit = wx.Menu(title='')
709	self.ConstraintMenu.Append(menu=self.ConstraintEdit, title='Edit')
710	self.ConstraintEdit.Append(id=wxID_HOLDADD, kind=wx.ITEM_NORMAL,text='Add hold',
711	help='Add hold on a parameter value')
712	self.ConstraintEdit.Append(id=wxID_EQUIVADD, kind=wx.ITEM_NORMAL,text='Add equivalence',
713	help='Add equivalence between parameter values')
714	self.ConstraintEdit.Append(id=wxID_CONSTRAINTADD, kind=wx.ITEM_NORMAL,text='Add constraint',
715	help='Add constraint on parameter values')
716	self.ConstraintEdit.Append(id=wxID_FUNCTADD, kind=wx.ITEM_NORMAL,text='Add New Var',
717	help='Add variable composed of existing parameter')
718	self.ConstraintEdit.Append(id=wxID_EQUIVALANCEATOMS, kind=wx.ITEM_NORMAL,text='Add atom equivalence',
719	help='Add equivalences between atom parameter values')
720	self.ConstraintEdit.Enable(wxID_EQUIVALANCEATOMS,False)
721	self.ConstraintEdit.Append(id=wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add H riding constraints',
722	help='Add H atom riding constraints between atom parameter values')
723	self.ConstraintEdit.Enable(wxID_ADDRIDING,False)
724	wxID_ADDRIDING
725	self.PostfillDataMenu()
726
727	# item = self.ConstraintEdit.Append(id=wx.ID_ANY,kind=wx.ITEM_NORMAL,text='Update GUI')
728	# def UpdateGSASIIconstrGUI(event):
729	# import GSASIIconstrGUI
730	# reload(GSASIIconstrGUI)
731	# import GSASIIobj
732	# reload(GSASIIobj)
733	# self.Bind(wx.EVT_MENU,UpdateGSASIIconstrGUI,id=item.GetId())
734
735	# Rigid bodies
736	self.RigidBodyMenu = wx.MenuBar()
737	self.PrefillDataMenu(self.RigidBodyMenu,helpType='Rigid bodies')
738	self.ResidueRBMenu = wx.Menu(title='')
739	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYIMPORT, kind=wx.ITEM_NORMAL,text='Import XYZ',
740	help='Import rigid body XYZ from file')
741	self.ResidueRBMenu.Append(id=wxID_RESIDUETORSSEQ, kind=wx.ITEM_NORMAL,text='Define sequence',
742	help='Define torsion sequence')
743	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYADD, kind=wx.ITEM_NORMAL,text='Import residues',
744	help='Import residue rigid bodies from macro file')
745	self.RigidBodyMenu.Append(menu=self.ResidueRBMenu, title='Edit Body')
746	self.PostfillDataMenu()
747
748	self.VectorBodyMenu = wx.MenuBar()
749	self.PrefillDataMenu(self.VectorBodyMenu,helpType='Vector rigid bodies')
750	self.VectorRBEdit = wx.Menu(title='')
751	self.VectorRBEdit.Append(id=wxID_VECTORBODYADD, kind=wx.ITEM_NORMAL,text='Add rigid body',
752	help='Add vector rigid body')
753	self.VectorBodyMenu.Append(menu=self.VectorRBEdit, title='Edit Vector Body')
754	self.PostfillDataMenu()
755
756
757	# Restraints
758	self.RestraintTab = wx.Menu(title='')
759	self.RestraintEdit = wx.Menu(title='')
760	self.RestraintEdit.Append(id=wxID_RESTSELPHASE, kind=wx.ITEM_NORMAL,text='Select phase',
761	help='Select phase')
762	self.RestraintEdit.Append(id=wxID_RESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add restraints',
763	help='Add restraints')
764	self.RestraintEdit.Enable(wxID_RESTRAINTADD,True) #gets disabled if macromolecule phase
765	self.RestraintEdit.Append(id=wxID_AARESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add residue restraints',
766	help='Add residue based restraints for macromolecules from macro file')
767	self.RestraintEdit.Enable(wxID_AARESTRAINTADD,False) #gets enabled if macromolecule phase
768	self.RestraintEdit.Append(id=wxID_AARESTRAINTPLOT, kind=wx.ITEM_NORMAL,text='Plot residue restraints',
769	help='Plot selected residue based restraints for macromolecules from macro file')
770	self.RestraintEdit.Enable(wxID_AARESTRAINTPLOT,False) #gets enabled if macromolecule phase
771	self.RestraintEdit.Append(id=wxID_RESRCHANGEVAL, kind=wx.ITEM_NORMAL,text='Change value',
772	help='Change observed value')
773	self.RestraintEdit.Append(id=wxID_RESTCHANGEESD, kind=wx.ITEM_NORMAL,text='Change esd',
774	help='Change esd in observed value')
775	self.RestraintEdit.Append(id=wxID_RESTDELETE, kind=wx.ITEM_NORMAL,text='Delete restraints',
776	help='Delete selected restraints')
777
778	self.RestraintMenu = wx.MenuBar()
779	self.PrefillDataMenu(self.RestraintMenu,helpType='Restraints')
780	self.RestraintMenu.Append(menu=self.RestraintTab, title='Select tab')
781	self.RestraintMenu.Append(menu=self.RestraintEdit, title='Edit')
782	self.PostfillDataMenu()
783
784	# Sequential results
785	self.SequentialMenu = wx.MenuBar()
786	self.PrefillDataMenu(self.SequentialMenu,helpType='Sequential',helpLbl='Sequential Refinement')
787	self.SequentialFile = wx.Menu(title='')
788	self.SequentialMenu.Append(menu=self.SequentialFile, title='Columns')
789	self.SequentialFile.Append(id=wxID_RENAMESEQSEL, kind=wx.ITEM_NORMAL,text='Rename selected',
790	help='Rename selected sequential refinement columns')
791	self.SequentialFile.Append(id=wxID_SAVESEQSEL, kind=wx.ITEM_NORMAL,text='Save selected as text',
792	help='Save selected sequential refinement results as a text file')
793	self.SequentialFile.Append(id=wxID_SAVESEQCSV, kind=wx.ITEM_NORMAL,text='Save all as CSV',
794	help='Save all sequential refinement results as a CSV spreadsheet file')
795	self.SequentialFile.Append(id=wxID_SAVESEQSELCSV, kind=wx.ITEM_NORMAL,text='Save selected as CSV',
796	help='Save selected sequential refinement results as a CSV spreadsheet file')
797	self.SequentialFile.Append(id=wxID_PLOTSEQSEL, kind=wx.ITEM_NORMAL,text='Plot selected',
798	help='Plot selected sequential refinement results')
799	self.SequentialFile.Append(id=wxID_AVESEQSEL, kind=wx.ITEM_NORMAL,text='Compute average',
800	help='Compute average for selected parameter')
801	self.SequentialFile.Append(id=wxID_ORGSEQSEL, kind=wx.ITEM_NORMAL,text='Reorganize',
802	help='Reorganize variables where variables change')
803	self.SequentialPvars = wx.Menu(title='')
804	self.SequentialMenu.Append(menu=self.SequentialPvars, title='Pseudo Vars')
805	self.SequentialPvars.Append(
806	id=wxADDSEQVAR, kind=wx.ITEM_NORMAL,text='Add',
807	help='Add a new pseudo-variable')
808	self.SequentialPvars.Append(
809	id=wxDELSEQVAR, kind=wx.ITEM_NORMAL,text='Delete',
810	help='Delete an existing pseudo-variable')
811	self.SequentialPvars.Append(
812	id=wxEDITSEQVAR, kind=wx.ITEM_NORMAL,text='Edit',
813	help='Edit an existing pseudo-variable')
814
815	self.SequentialPfit = wx.Menu(title='')
816	self.SequentialMenu.Append(menu=self.SequentialPfit, title='Parametric Fit')
817	self.SequentialPfit.Append(
818	id=wxADDPARFIT, kind=wx.ITEM_NORMAL,text='Add equation',
819	help='Add a new equation to minimize')
820	self.SequentialPfit.Append(
821	id=wxCOPYPARFIT, kind=wx.ITEM_NORMAL,text='Copy equation',
822	help='Copy an equation to minimize - edit it next')
823	self.SequentialPfit.Append(
824	id=wxDELPARFIT, kind=wx.ITEM_NORMAL,text='Delete equation',
825	help='Delete an equation for parametric minimization')
826	self.SequentialPfit.Append(
827	id=wxEDITPARFIT, kind=wx.ITEM_NORMAL,text='Edit equation',
828	help='Edit an existing parametric minimization equation')
829	self.SequentialPfit.Append(
830	id=wxDOPARFIT, kind=wx.ITEM_NORMAL,text='Fit to equation(s)',
831	help='Perform a parametric minimization')
832	self.PostfillDataMenu()
833
834	# PWDR & SASD
835	self.PWDRMenu = wx.MenuBar()
836	self.PrefillDataMenu(self.PWDRMenu,helpType='PWDR Analysis',helpLbl='Powder Fit Error Analysis')
837	self.ErrorAnal = wx.Menu(title='')
838	self.PWDRMenu.Append(menu=self.ErrorAnal,title='Commands')
839	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
840	help='Error analysis on powder pattern')
841	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
842	help='Copy of PWDR parameters')
843	self.ErrorAnal.Append(id=wxID_PLOTCTRLCOPY,kind=wx.ITEM_NORMAL,text='Copy plot controls',
844	help='Copy of PWDR plot controls')
845
846	self.PostfillDataMenu()
847
848	# HKLF
849	self.HKLFMenu = wx.MenuBar()
850	self.PrefillDataMenu(self.HKLFMenu,helpType='HKLF Analysis',helpLbl='HKLF Fit Error Analysis')
851	self.ErrorAnal = wx.Menu(title='')
852	self.HKLFMenu.Append(menu=self.ErrorAnal,title='Commands')
853	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
854	help='Error analysis on single crystal data')
855	self.ErrorAnal.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
856	help='Plot HKLs from single crystal data in 3D')
857	self.ErrorAnal.Append(id=wxID_3DALLHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot all 3D HKLs',
858	help='Plot HKLs from all single crystal data in 3D')
859	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
860	help='Copy of HKLF parameters')
861	self.PostfillDataMenu()
862
863	# PDR / Limits
864	self.LimitMenu = wx.MenuBar()
865	self.PrefillDataMenu(self.LimitMenu,helpType='Limits')
866	self.LimitEdit = wx.Menu(title='')
867	self.LimitMenu.Append(menu=self.LimitEdit, title='Edit')
868	self.LimitEdit.Append(id=wxID_LIMITCOPY, kind=wx.ITEM_NORMAL,text='Copy',
869	help='Copy limits to other histograms')
870	self.LimitEdit.Append(id=wxID_ADDEXCLREGION, kind=wx.ITEM_NORMAL,text='Add exclude',
871	help='Add excluded region - select a point on plot; drag to adjust')
872	self.PostfillDataMenu()
873
874	# PDR / Background
875	self.BackMenu = wx.MenuBar()
876	self.PrefillDataMenu(self.BackMenu,helpType='Background')
877	self.BackEdit = wx.Menu(title='')
878	self.BackMenu.Append(menu=self.BackEdit, title='File')
879	self.BackEdit.Append(id=wxID_BACKCOPY, kind=wx.ITEM_NORMAL,text='Copy',
880	help='Copy background parameters to other histograms')
881	self.BackEdit.Append(id=wxID_BACKFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
882	help='Copy background refinement flags to other histograms')
883	self.BackEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
884	help='Move background peaks to Peak List')
885	self.BackFixed = wx.Menu(title='') # fixed background point menu
886	self.BackMenu.Append(menu=self.BackFixed, title='Fixed Points')
887	self.wxID_BackPts = {}
888	self.wxID_BackPts['Add'] = wx.NewId() # N.B. not using wxID_ global as for other menu items
889	self.BackFixed.Append(id=self.wxID_BackPts['Add'], kind=wx.ITEM_RADIO,text='Add',
890	help='Add fixed background points with mouse clicks')
891	self.wxID_BackPts['Move'] = wx.NewId()
892	item = self.BackFixed.Append(id=self.wxID_BackPts['Move'], kind=wx.ITEM_RADIO,text='Move',
893	help='Move selected fixed background points with mouse drags')
894	item.Check(True)
895	self.wxID_BackPts['Del'] = wx.NewId()
896	self.BackFixed.Append(id=self.wxID_BackPts['Del'], kind=wx.ITEM_RADIO,text='Delete',
897	help='Delete fixed background points with mouse clicks')
898	self.wxID_BackPts['Clear'] = wx.NewId()
899	self.BackFixed.Append(id=self.wxID_BackPts['Clear'], kind=wx.ITEM_NORMAL,text='Clear',
900	help='Clear fixed background points')
901	self.wxID_BackPts['Fit'] = wx.NewId()
902	self.BackFixed.Append(id=self.wxID_BackPts['Fit'], kind=wx.ITEM_NORMAL,text='Fit background',
903	help='Fit background function to fixed background points')
904	self.PostfillDataMenu()
905
906	# PDR / Instrument Parameters
907	self.InstMenu = wx.MenuBar()
908	self.PrefillDataMenu(self.InstMenu,helpType='Instrument Parameters')
909	self.InstEdit = wx.Menu(title='')
910	self.InstMenu.Append(menu=self.InstEdit, title='Operations')
911	self.InstEdit.Append(help='Calibrate from indexed peaks',
912	id=wxID_INSTCALIB, kind=wx.ITEM_NORMAL,text='Calibrate')
913	self.InstEdit.Append(help='Reset instrument profile parameters to default',
914	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
915	self.InstEdit.Append(help='Load instrument profile parameters from file',
916	id=wxID_INSTLOAD, kind=wx.ITEM_NORMAL,text='Load profile...')
917	self.InstEdit.Append(help='Save instrument profile parameters to file',
918	id=wxID_INSTSAVE, kind=wx.ITEM_NORMAL,text='Save profile...')
919	self.InstEdit.Append(help='Copy instrument profile parameters to other histograms',
920	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
921	self.InstEdit.Append(id=wxID_INSTFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
922	help='Copy instrument parameter refinement flags to other histograms')
923	# self.InstEdit.Append(help='Change radiation type (Ka12 - synch)',
924	# id=wxID_CHANGEWAVETYPE, kind=wx.ITEM_NORMAL,text='Change radiation')
925	self.InstEdit.Append(id=wxID_INST1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
926	help='Set one instrument parameter value across multiple histograms')
927
928	self.PostfillDataMenu()
929
930	# PDR / Sample Parameters
931	self.SampleMenu = wx.MenuBar()
932	self.PrefillDataMenu(self.SampleMenu,helpType='Sample Parameters')
933	self.SampleEdit = wx.Menu(title='')
934	self.SampleMenu.Append(menu=self.SampleEdit, title='Command')
935	self.SetScale = self.SampleEdit.Append(id=wxID_SETSCALE, kind=wx.ITEM_NORMAL,text='Set scale',
936	help='Set scale by matching to another histogram')
937	self.SampleEdit.Append(id=wxID_SAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load',
938	help='Load sample parameters from file')
939	self.SampleEdit.Append(id=wxID_SAMPLESAVE, kind=wx.ITEM_NORMAL,text='Save',
940	help='Save sample parameters to file')
941	self.SampleEdit.Append(id=wxID_SAMPLECOPY, kind=wx.ITEM_NORMAL,text='Copy',
942	help='Copy refinable and most other sample parameters to other histograms')
943	self.SampleEdit.Append(id=wxID_SAMPLECOPYSOME, kind=wx.ITEM_NORMAL,text='Copy selected...',
944	help='Copy selected sample parameters to other histograms')
945	self.SampleEdit.Append(id=wxID_SAMPLEFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
946	help='Copy sample parameter refinement flags to other histograms')
947	self.SampleEdit.Append(id=wxID_SAMPLE1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
948	help='Set one sample parameter value across multiple histograms')
949	self.SampleEdit.Append(id=wxID_ALLSAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load all',
950	help='Load sample parmameters over multiple histograms')
951
952	self.PostfillDataMenu()
953	self.SetScale.Enable(False)
954
955	# PDR / Peak List
956	self.PeakMenu = wx.MenuBar()
957	self.PrefillDataMenu(self.PeakMenu,helpType='Peak List')
958	self.PeakEdit = wx.Menu(title='')
959	self.PeakMenu.Append(menu=self.PeakEdit, title='Peak Fitting')
960	self.AutoSearch = self.PeakEdit.Append(help='Automatic peak search',
961	id=wxID_AUTOSEARCH, kind=wx.ITEM_NORMAL,text='Auto search')
962	self.UnDo = self.PeakEdit.Append(help='Undo last least squares refinement',
963	id=wxID_UNDO, kind=wx.ITEM_NORMAL,text='UnDo')
964	self.PeakFit = self.PeakEdit.Append(id=wxID_LSQPEAKFIT, kind=wx.ITEM_NORMAL,text='Peakfit',
965	help='Peak fitting' )
966	self.PFOneCycle = self.PeakEdit.Append(id=wxID_LSQONECYCLE, kind=wx.ITEM_NORMAL,text='Peakfit one cycle',
967	help='One cycle of Peak fitting' )
968	self.PeakEdit.Append(id=wxID_RESETSIGGAM, kind=wx.ITEM_NORMAL,
969	text='Reset sig and gam',help='Reset sigma and gamma to global fit' )
970	self.PeakCopy = self.PeakEdit.Append(help='Copy peaks to other histograms',
971	id=wxID_PEAKSCOPY, kind=wx.ITEM_NORMAL,text='Peak copy')
972	self.SeqPeakFit = self.PeakEdit.Append(id=wxID_SEQPEAKFIT, kind=wx.ITEM_NORMAL,text='Seq PeakFit',
973	help='Sequential Peak fitting for all histograms' )
974	self.PeakEdit.Append(id=wxID_CLEARPEAKS, kind=wx.ITEM_NORMAL,text='Clear peaks',
975	help='Clear the peak list' )
976	self.PostfillDataMenu()
977	self.UnDo.Enable(False)
978	self.PeakFit.Enable(False)
979	self.PFOneCycle.Enable(False)
980	self.AutoSearch.Enable(True)
981
982	# PDR / Index Peak List
983	self.IndPeaksMenu = wx.MenuBar()
984	self.PrefillDataMenu(self.IndPeaksMenu,helpType='Index Peak List')
985	self.IndPeaksEdit = wx.Menu(title='')
986	self.IndPeaksMenu.Append(menu=self.IndPeaksEdit,title='Operations')
987	self.IndPeaksEdit.Append(help='Load/Reload index peaks from peak list',id=wxID_INDXRELOAD,
988	kind=wx.ITEM_NORMAL,text='Load/Reload')
989	self.PostfillDataMenu()
990
991	# PDR / Unit Cells List
992	self.IndexMenu = wx.MenuBar()
993	self.PrefillDataMenu(self.IndexMenu,helpType='Unit Cells List')
994	self.IndexEdit = wx.Menu(title='')
995	self.IndexMenu.Append(menu=self.IndexEdit, title='Cell Index/Refine')
996	self.IndexPeaks = self.IndexEdit.Append(help='', id=wxID_INDEXPEAKS, kind=wx.ITEM_NORMAL,
997	text='Index Cell')
998	self.CopyCell = self.IndexEdit.Append( id=wxID_COPYCELL, kind=wx.ITEM_NORMAL,text='Copy Cell',
999	help='Copy selected unit cell from indexing to cell refinement fields')
1000	self.RefineCell = self.IndexEdit.Append( id=wxID_REFINECELL, kind=wx.ITEM_NORMAL,
1001	text='Refine Cell',help='Refine unit cell parameters from indexed peaks')
1002	self.MakeNewPhase = self.IndexEdit.Append( id=wxID_MAKENEWPHASE, kind=wx.ITEM_NORMAL,
1003	text='Make new phase',help='Make new phase from selected unit cell')
1004	self.ExportCells = self.IndexEdit.Append( id=wxID_EXPORTCELLS, kind=wx.ITEM_NORMAL,
1005	text='Export cell list',help='Export cell list to csv file')
1006	self.PostfillDataMenu()
1007	self.IndexPeaks.Enable(False)
1008	self.CopyCell.Enable(False)
1009	self.RefineCell.Enable(False)
1010	self.MakeNewPhase.Enable(False)
1011
1012	# PDR / Reflection Lists
1013	self.ReflMenu = wx.MenuBar()
1014	self.PrefillDataMenu(self.ReflMenu,helpType='Reflection List')
1015	self.ReflEdit = wx.Menu(title='')
1016	self.ReflMenu.Append(menu=self.ReflEdit, title='Reflection List')
1017	self.SelectPhase = self.ReflEdit.Append(help='Select phase for reflection list',id=wxID_SELECTPHASE,
1018	kind=wx.ITEM_NORMAL,text='Select phase')
1019	self.ReflEdit.Append(id=wxID_PWDHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot HKLs',
1020	help='Plot HKLs from powder pattern')
1021	self.ReflEdit.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
1022	help='Plot HKLs from powder pattern in 3D')
1023	self.PostfillDataMenu()
1024
1025	# SASD / Instrument Parameters
1026	self.SASDInstMenu = wx.MenuBar()
1027	self.PrefillDataMenu(self.SASDInstMenu,helpType='Instrument Parameters')
1028	self.SASDInstEdit = wx.Menu(title='')
1029	self.SASDInstMenu.Append(menu=self.SASDInstEdit, title='Operations')
1030	self.InstEdit.Append(help='Reset instrument profile parameters to default',
1031	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
1032	self.SASDInstEdit.Append(help='Copy instrument profile parameters to other histograms',
1033	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
1034	self.PostfillDataMenu()
1035
1036	#SASD & REFL/ Substance editor
1037	self.SubstanceMenu = wx.MenuBar()
1038	self.PrefillDataMenu(self.SubstanceMenu,helpType='Substances')
1039	self.SubstanceEdit = wx.Menu(title='')
1040	self.SubstanceMenu.Append(menu=self.SubstanceEdit, title='Edit')
1041	self.SubstanceEdit.Append(id=wxID_LOADSUBSTANCE, kind=wx.ITEM_NORMAL,text='Load substance',
1042	help='Load substance from file')
1043	self.SubstanceEdit.Append(id=wxID_ADDSUBSTANCE, kind=wx.ITEM_NORMAL,text='Add substance',
1044	help='Add new substance to list')
1045	self.SubstanceEdit.Append(id=wxID_COPYSUBSTANCE, kind=wx.ITEM_NORMAL,text='Copy substances',
1046	help='Copy substances')
1047	self.SubstanceEdit.Append(id=wxID_DELETESUBSTANCE, kind=wx.ITEM_NORMAL,text='Delete substance',
1048	help='Delete substance from list')
1049	self.SubstanceEdit.Append(id=wxID_ELEMENTADD, kind=wx.ITEM_NORMAL,text='Add elements',
1050	help='Add elements to substance')
1051	self.SubstanceEdit.Append(id=wxID_ELEMENTDELETE, kind=wx.ITEM_NORMAL,text='Delete elements',
1052	help='Delete elements from substance')
1053	self.PostfillDataMenu()
1054
1055	# SASD/ Models
1056	self.ModelMenu = wx.MenuBar()
1057	self.PrefillDataMenu(self.ModelMenu,helpType='Models')
1058	self.ModelEdit = wx.Menu(title='')
1059	self.ModelMenu.Append(menu=self.ModelEdit, title='Models')
1060	self.ModelEdit.Append(id=wxID_MODELADD,kind=wx.ITEM_NORMAL,text='Add',
1061	help='Add new term to model')
1062	self.ModelEdit.Append(id=wxID_MODELFIT, kind=wx.ITEM_NORMAL,text='Fit',
1063	help='Fit model parameters to data')
1064	self.SasdUndo = self.ModelEdit.Append(id=wxID_MODELUNDO, kind=wx.ITEM_NORMAL,text='Undo',
1065	help='Undo model fit')
1066	self.SasdUndo.Enable(False)
1067	self.ModelEdit.Append(id=wxID_MODELFITALL, kind=wx.ITEM_NORMAL,text='Sequential fit',
1068	help='Sequential fit of model parameters to all SASD data')
1069	self.ModelEdit.Append(id=wxID_MODELCOPY, kind=wx.ITEM_NORMAL,text='Copy',
1070	help='Copy model parameters to other histograms')
1071	self.ModelEdit.Append(id=wxID_MODELCOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1072	help='Copy model refinement flags to other histograms')
1073	self.PostfillDataMenu()
1074
1075	# IMG / Image Controls
1076	self.ImageMenu = wx.MenuBar()
1077	self.PrefillDataMenu(self.ImageMenu,helpType='Image Controls')
1078	self.ImageEdit = wx.Menu(title='')
1079	self.ImageMenu.Append(menu=self.ImageEdit, title='Operations')
1080	self.ImageEdit.Append(help='Calibrate detector by fitting to calibrant lines',
1081	id=wxID_IMCALIBRATE, kind=wx.ITEM_NORMAL,text='Calibrate')
1082	self.ImageEdit.Append(help='Recalibrate detector by fitting to calibrant lines',
1083	id=wxID_IMRECALIBRATE, kind=wx.ITEM_NORMAL,text='Recalibrate')
1084	self.ImageEdit.Append(help='Clear calibration data points and rings',id=wxID_IMCLEARCALIB,
1085	kind=wx.ITEM_NORMAL,text='Clear calibration')
1086	self.ImageEdit.Append(help='Integrate selected image',id=wxID_IMINTEGRATE,
1087	kind=wx.ITEM_NORMAL,text='Integrate')
1088	self.ImageEdit.Append(help='Integrate all images selected from list',id=wxID_INTEGRATEALL,
1089	kind=wx.ITEM_NORMAL,text='Integrate all')
1090	self.ImageEdit.Append(help='Copy image controls to other images',
1091	id=wxID_IMCOPYCONTROLS, kind=wx.ITEM_NORMAL,text='Copy Controls')
1092	self.ImageEdit.Append(help='Save image controls to file',
1093	id=wxID_IMSAVECONTROLS, kind=wx.ITEM_NORMAL,text='Save Controls')
1094	self.ImageEdit.Append(help='Load image controls from file',
1095	id=wxID_IMLOADCONTROLS, kind=wx.ITEM_NORMAL,text='Load Controls')
1096	self.PostfillDataMenu()
1097
1098	# IMG / Masks
1099	self.MaskMenu = wx.MenuBar()
1100	self.PrefillDataMenu(self.MaskMenu,helpType='Image Masks')
1101	self.MaskEdit = wx.Menu(title='')
1102	self.MaskMenu.Append(menu=self.MaskEdit, title='Operations')
1103	submenu = wx.Menu()
1104	self.MaskEdit.AppendMenu(
1105	wx.ID_ANY,'Create new', submenu,
1106	help=''
1107	)
1108	self.MaskEdit.Append(help='Copy mask to other images',
1109	id=wxID_MASKCOPY, kind=wx.ITEM_NORMAL,text='Copy mask')
1110	self.MaskEdit.Append(help='Save mask to file',
1111	id=wxID_MASKSAVE, kind=wx.ITEM_NORMAL,text='Save mask')
1112	self.MaskEdit.Append(help='Load mask from file',
1113	id=wxID_MASKLOAD, kind=wx.ITEM_NORMAL,text='Load mask')
1114	self.MaskEdit.Append(help='Load mask from file; ignore threshold',
1115	id=wxID_MASKLOADNOT, kind=wx.ITEM_NORMAL,text='Load mask w/o threshold')
1116	submenu.Append(help='Create an arc mask with mouse input',
1117	id=wxID_NEWMASKARC, kind=wx.ITEM_NORMAL,text='Arc mask')
1118	submenu.Append(help='Create a frame mask with mouse input',
1119	id=wxID_NEWMASKFRAME, kind=wx.ITEM_NORMAL,text='Frame mask')
1120	submenu.Append(help='Create a polygon mask with mouse input',
1121	id=wxID_NEWMASKPOLY, kind=wx.ITEM_NORMAL,text='Polygon mask')
1122	submenu.Append(help='Create a ring mask with mouse input',
1123	id=wxID_NEWMASKRING, kind=wx.ITEM_NORMAL,text='Ring mask')
1124	submenu.Append(help='Create a spot mask with mouse input',
1125	id=wxID_NEWMASKSPOT, kind=wx.ITEM_NORMAL,text='Spot mask')
1126	self.PostfillDataMenu()
1127
1128	# IMG / Stress/Strain
1129	self.StrStaMenu = wx.MenuBar()
1130	self.PrefillDataMenu(self.StrStaMenu,helpType='Stress/Strain')
1131	self.StrStaEdit = wx.Menu(title='')
1132	self.StrStaMenu.Append(menu=self.StrStaEdit, title='Operations')
1133	self.StrStaEdit.Append(help='Append d-zero for one ring',
1134	id=wxID_APPENDDZERO, kind=wx.ITEM_NORMAL,text='Append d-zero')
1135	self.StrStaEdit.Append(help='Fit stress/strain data',
1136	id=wxID_STRSTAFIT, kind=wx.ITEM_NORMAL,text='Fit stress/strain')
1137	self.StrStaEdit.Append(help='Update d-zero from ave d-zero',
1138	id=wxID_UPDATEDZERO, kind=wx.ITEM_NORMAL,text='Update d-zero')
1139	self.StrStaEdit.Append(help='Fit stress/strain data for all images',
1140	id=wxID_STRSTAALLFIT, kind=wx.ITEM_NORMAL,text='All image fit')
1141	self.StrStaEdit.Append(help='Copy stress/strain data to other images',
1142	id=wxID_STRSTACOPY, kind=wx.ITEM_NORMAL,text='Copy stress/strain')
1143	self.StrStaEdit.Append(help='Save stress/strain data to file',
1144	id=wxID_STRSTASAVE, kind=wx.ITEM_NORMAL,text='Save stress/strain')
1145	self.StrStaEdit.Append(help='Load stress/strain data from file',
1146	id=wxID_STRSTALOAD, kind=wx.ITEM_NORMAL,text='Load stress/strain')
1147	self.StrStaEdit.Append(help='Load sample data from file',
1148	id=wxID_STRSTSAMPLE, kind=wx.ITEM_NORMAL,text='Load sample data')
1149	self.PostfillDataMenu()
1150
1151	# PDF / PDF Controls
1152	self.PDFMenu = wx.MenuBar()
1153	self.PrefillDataMenu(self.PDFMenu,helpType='PDF Controls')
1154	self.PDFEdit = wx.Menu(title='')
1155	self.PDFMenu.Append(menu=self.PDFEdit, title='PDF Controls')
1156	self.PDFEdit.Append(help='Add element to sample composition',id=wxID_PDFADDELEMENT, kind=wx.ITEM_NORMAL,
1157	text='Add element')
1158	self.PDFEdit.Append(help='Delete element from sample composition',id=wxID_PDFDELELEMENT, kind=wx.ITEM_NORMAL,
1159	text='Delete element')
1160	self.PDFEdit.Append(help='Copy PDF controls', id=wxID_PDFCOPYCONTROLS, kind=wx.ITEM_NORMAL,
1161	text='Copy controls')
1162	self.PDFEdit.Append(help='Load PDF controls from file',id=wxID_PDFLOADCONTROLS, kind=wx.ITEM_NORMAL,
1163	text='Load Controls')
1164	self.PDFEdit.Append(help='Save PDF controls to file', id=wxID_PDFSAVECONTROLS, kind=wx.ITEM_NORMAL,
1165	text='Save controls')
1166	self.PDFEdit.Append(help='Compute PDF', id=wxID_PDFCOMPUTE, kind=wx.ITEM_NORMAL,
1167	text='Compute PDF')
1168	self.PDFEdit.Append(help='Compute all PDFs', id=wxID_PDFCOMPUTEALL, kind=wx.ITEM_NORMAL,
1169	text='Compute all PDFs')
1170	self.PostfillDataMenu()
1171
1172	# Phase / General tab
1173	self.DataGeneral = wx.MenuBar()
1174	self.PrefillDataMenu(self.DataGeneral,helpType='General', helpLbl='Phase/General')
1175	self.DataGeneral.Append(menu=wx.Menu(title=''),title='Select tab')
1176	self.GeneralCalc = wx.Menu(title='')
1177	self.DataGeneral.Append(menu=self.GeneralCalc,title='Compute')
1178	self.GeneralCalc.Append(help='Compute Fourier map',id=wxID_FOURCALC, kind=wx.ITEM_NORMAL,
1179	text='Fourier map')
1180	self.GeneralCalc.Append(help='Search Fourier map',id=wxID_FOURSEARCH, kind=wx.ITEM_NORMAL,
1181	text='Search map')
1182	self.GeneralCalc.Append(help='Run charge flipping',id=wxID_CHARGEFLIP, kind=wx.ITEM_NORMAL,
1183	text='Charge flipping')
1184	self.GeneralCalc.Append(help='Run 4D charge flipping',id=wxID_4DCHARGEFLIP, kind=wx.ITEM_NORMAL,
1185	text='4D Charge flipping')
1186	self.GeneralCalc.Enable(wxID_4DCHARGEFLIP,False)
1187	self.GeneralCalc.Append(help='Clear map',id=wxID_FOURCLEAR, kind=wx.ITEM_NORMAL,
1188	text='Clear map')
1189	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing',id=wxID_SINGLEMCSA, kind=wx.ITEM_NORMAL,
1190	text='MC/SA')
1191	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing on multiprocessors',id=wxID_MULTIMCSA, kind=wx.ITEM_NORMAL,
1192	text='Multi MC/SA') #currently not useful
1193	self.PostfillDataMenu()
1194
1195	# Phase / Data tab
1196	self.DataMenu = wx.MenuBar()
1197	self.PrefillDataMenu(self.DataMenu,helpType='Data', helpLbl='Phase/Data')
1198	self.DataMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1199	self.DataEdit = wx.Menu(title='')
1200	self.DataMenu.Append(menu=self.DataEdit, title='Edit')
1201	self.DataEdit.Append(id=wxID_DATACOPY, kind=wx.ITEM_NORMAL,text='Copy data',
1202	help='Copy phase data to other histograms')
1203	self.DataEdit.Append(id=wxID_DATACOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1204	help='Copy phase data flags to other histograms')
1205	self.DataEdit.Append(id=wxID_DATASELCOPY, kind=wx.ITEM_NORMAL,text='Copy selected data',
1206	help='Copy selected phase data to other histograms')
1207	self.DataEdit.Append(id=wxID_PWDRADD, kind=wx.ITEM_NORMAL,text='Add powder histograms',
1208	help='Select new powder histograms to be used for this phase')
1209	self.DataEdit.Append(id=wxID_HKLFADD, kind=wx.ITEM_NORMAL,text='Add single crystal histograms',
1210	help='Select new single crystal histograms to be used for this phase')
1211	self.DataEdit.Append(id=wxID_DATADELETE, kind=wx.ITEM_NORMAL,text='Remove histograms',
1212	help='Remove histograms from use for this phase')
1213	self.PostfillDataMenu()
1214
1215	# Phase / Atoms tab
1216	self.AtomsMenu = wx.MenuBar()
1217	self.PrefillDataMenu(self.AtomsMenu,helpType='Atoms')
1218	self.AtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1219	self.AtomEdit = wx.Menu(title='')
1220	self.AtomCompute = wx.Menu(title='')
1221	self.AtomsMenu.Append(menu=self.AtomEdit, title='Edit')
1222	self.AtomsMenu.Append(menu=self.AtomCompute, title='Compute')
1223	self.AtomEdit.Append(id=wxID_ATOMSEDITADD, kind=wx.ITEM_NORMAL,text='Append atom',
1224	help='Appended as an H atom')
1225	self.AtomEdit.Append(id=wxID_ATOMSVIEWADD, kind=wx.ITEM_NORMAL,text='Append view point',
1226	help='Appended as an H atom')
1227	self.AtomEdit.Append(id=wxID_ATOMSEDITINSERT, kind=wx.ITEM_NORMAL,text='Insert atom',
1228	help='Select atom row to insert before; inserted as an H atom')
1229	self.AtomEdit.Append(id=wxID_ATOMVIEWINSERT, kind=wx.ITEM_NORMAL,text='Insert view point',
1230	help='Select atom row to insert before; inserted as an H atom')
1231	self.AtomEdit.Append(id=wxID_ADDHATOM, kind=wx.ITEM_NORMAL,text='Insert H atoms',
1232	help='Insert H atoms in standard positions bonded to selected atoms')
1233	self.AtomEdit.Append(id=wxID_ATOMMOVE, kind=wx.ITEM_NORMAL,text='Move atom to view point',
1234	help='Select single atom to move')
1235	self.AtomEdit.Append(id=wxID_ATOMSEDITDELETE, kind=wx.ITEM_NORMAL,text='Delete atom',
1236	help='Select atoms to delete first')
1237	self.AtomEdit.Append(id=wxID_ATOMSREFINE, kind=wx.ITEM_NORMAL,text='Set atom refinement flags',
1238	help='Select atoms to refine first')
1239	self.AtomEdit.Append(id=wxID_ATOMSMODIFY, kind=wx.ITEM_NORMAL,text='Modify atom parameters',
1240	help='Select atoms to modify first')
1241	self.AtomEdit.Append(id=wxID_ATOMSTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform atoms',
1242	help='Select atoms to transform first')
1243	self.AtomEdit.Append(id=wxID_MAKEMOLECULE, kind=wx.ITEM_NORMAL,text='Assemble molecule',
1244	help='Assemble molecule from scatterd atom positions')
1245	self.AtomEdit.Append(id=wxID_RELOADDRAWATOMS, kind=wx.ITEM_NORMAL,text='Reload draw atoms',
1246	help='Reload atom drawing list')
1247	submenu = wx.Menu()
1248	self.AtomEdit.AppendMenu(wx.ID_ANY, 'Reimport atoms', submenu,
1249	help='Reimport atoms from file; sequence must match')
1250	# setup a cascade menu for the formats that have been defined
1251	self.ReImportMenuId = {} # points to readers for each menu entry
1252	for reader in self.G2frame.ImportPhaseReaderlist:
1253	item = submenu.Append(
1254	wx.ID_ANY,help=reader.longFormatName,
1255	kind=wx.ITEM_NORMAL,text='reimport coordinates from '+reader.formatName+' file')
1256	self.ReImportMenuId[item.GetId()] = reader
1257	item = submenu.Append(
1258	wx.ID_ANY,
1259	help='Reimport coordinates, try to determine format from file',
1260	kind=wx.ITEM_NORMAL,
1261	text='guess format from file')
1262	self.ReImportMenuId[item.GetId()] = None # try all readers
1263
1264	self.AtomCompute.Append(id=wxID_ATOMSDISAGL, kind=wx.ITEM_NORMAL,text='Show Distances && Angles',
1265	help='Compute distances & angles for selected atoms')
1266	self.AtomCompute.Append(id=wxID_ATOMSPDISAGL, kind=wx.ITEM_NORMAL,text='Save Distances && Angles',
1267	help='Compute distances & angles for selected atoms')
1268	self.AtomCompute.ISOcalc = self.AtomCompute.Append(
1269	id=wxID_ISODISP, kind=wx.ITEM_NORMAL,
1270	text='Compute ISODISTORT mode values',
1271	help='Compute values of ISODISTORT modes from atom parameters')
1272	self.PostfillDataMenu()
1273
1274	# Phase / Imcommensurate "waves" tab
1275	self.WavesData = wx.MenuBar()
1276	self.PrefillDataMenu(self.WavesData,helpType='Wave Data', helpLbl='Imcommensurate wave data')
1277	self.WavesData.Append(menu=wx.Menu(title=''),title='Select tab')
1278	self.WavesDataCompute = wx.Menu(title='')
1279	self.WavesData.Append(menu=self.WavesDataCompute,title='Compute')
1280	self.WavesDataCompute.Append(id=wxID_4DMAPCOMPUTE, kind=wx.ITEM_NORMAL,text='Compute 4D map',
1281	help='Compute 4-dimensional map')
1282	self.PostfillDataMenu()
1283
1284	# Phase / Draw Options tab
1285	self.DataDrawOptions = wx.MenuBar()
1286	self.PrefillDataMenu(self.DataDrawOptions,helpType='Draw Options', helpLbl='Phase/Draw Options')
1287	self.DataDrawOptions.Append(menu=wx.Menu(title=''),title='Select tab')
1288	self.PostfillDataMenu()
1289
1290	# Phase / Draw Atoms tab
1291	self.DrawAtomsMenu = wx.MenuBar()
1292	self.PrefillDataMenu(self.DrawAtomsMenu,helpType='Draw Atoms')
1293	self.DrawAtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1294	self.DrawAtomEdit = wx.Menu(title='')
1295	self.DrawAtomCompute = wx.Menu(title='')
1296	self.DrawAtomRestraint = wx.Menu(title='')
1297	self.DrawAtomRigidBody = wx.Menu(title='')
1298	self.DrawAtomsMenu.Append(menu=self.DrawAtomEdit, title='Edit')
1299	self.DrawAtomsMenu.Append(menu=self.DrawAtomCompute,title='Compute')
1300	self.DrawAtomsMenu.Append(menu=self.DrawAtomRestraint, title='Restraints')
1301	self.DrawAtomsMenu.Append(menu=self.DrawAtomRigidBody, title='Rigid body')
1302	self.DrawAtomEdit.Append(id=wxID_DRAWATOMSTYLE, kind=wx.ITEM_NORMAL,text='Atom style',
1303	help='Select atoms first')
1304	self.DrawAtomEdit.Append(id=wxID_DRAWATOMLABEL, kind=wx.ITEM_NORMAL,text='Atom label',
1305	help='Select atoms first')
1306	self.DrawAtomEdit.Append(id=wxID_DRAWATOMCOLOR, kind=wx.ITEM_NORMAL,text='Atom color',
1307	help='Select atoms first')
1308	self.DrawAtomEdit.Append(id=wxID_DRAWATOMRESETCOLOR, kind=wx.ITEM_NORMAL,text='Reset atom colors',
1309	help='Resets all atom colors to defaults')
1310	self.DrawAtomEdit.Append(id=wxID_DRAWVIEWPOINT, kind=wx.ITEM_NORMAL,text='View point',
1311	help='View point is 1st atom selected')
1312	self.DrawAtomEdit.Append(id=wxID_DRAWADDEQUIV, kind=wx.ITEM_NORMAL,text='Add atoms',
1313	help='Add symmetry & cell equivalents to drawing set from selected atoms')
1314	self.DrawAtomEdit.Append(id=wxID_DRAWTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform draw atoms',
1315	help='Transform selected atoms by symmetry & cell translations')
1316	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCOORD, kind=wx.ITEM_NORMAL,text='Fill CN-sphere',
1317	help='Fill coordination sphere for selected atoms')
1318	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCELL, kind=wx.ITEM_NORMAL,text='Fill unit cell',
1319	help='Fill unit cell with selected atoms')
1320	self.DrawAtomEdit.Append(id=wxID_DRAWDELETE, kind=wx.ITEM_NORMAL,text='Delete atoms',
1321	help='Delete atoms from drawing set')
1322	self.DrawAtomCompute.Append(id=wxID_DRAWDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1323	help='Compute distance of selected atoms from view point')
1324	self.DrawAtomCompute.Append(id=wxID_DRAWDISAGLTOR, kind=wx.ITEM_NORMAL,text='Dist. Ang. Tors.',
1325	help='Compute distance, angle or torsion for 2-4 selected atoms')
1326	self.DrawAtomCompute.Append(id=wxID_DRAWPLANE, kind=wx.ITEM_NORMAL,text='Best plane',
1327	help='Compute best plane for 4+ selected atoms')
1328	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRBOND, kind=wx.ITEM_NORMAL,text='Add bond restraint',
1329	help='Add bond restraint for selected atoms (2)')
1330	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRANGLE, kind=wx.ITEM_NORMAL,text='Add angle restraint',
1331	help='Add angle restraint for selected atoms (3: one end 1st)')
1332	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRPLANE, kind=wx.ITEM_NORMAL,text='Add plane restraint',
1333	help='Add plane restraint for selected atoms (4+)')
1334	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRCHIRAL, kind=wx.ITEM_NORMAL,text='Add chiral restraint',
1335	help='Add chiral restraint for selected atoms (4: center atom 1st)')
1336	self.DrawAtomRigidBody.Append(id=wxID_DRAWDEFINERB, kind=wx.ITEM_NORMAL,text='Define rigid body',
1337	help='Define rigid body with selected atoms')
1338	self.PostfillDataMenu()
1339
1340	# Phase / MCSA tab
1341	self.MCSAMenu = wx.MenuBar()
1342	self.PrefillDataMenu(self.MCSAMenu,helpType='MC/SA')
1343	self.MCSAMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1344	self.MCSAEdit = wx.Menu(title='')
1345	self.MCSAMenu.Append(menu=self.MCSAEdit, title='MC/SA')
1346	self.MCSAEdit.Append(id=wxID_ADDMCSAATOM, kind=wx.ITEM_NORMAL,text='Add atom',
1347	help='Add single atom to MC/SA model')
1348	self.MCSAEdit.Append(id=wxID_ADDMCSARB, kind=wx.ITEM_NORMAL,text='Add rigid body',
1349	help='Add rigid body to MC/SA model' )
1350	self.MCSAEdit.Append(id=wxID_CLEARMCSARB, kind=wx.ITEM_NORMAL,text='Clear rigid bodies',
1351	help='Clear all atoms & rigid bodies from MC/SA model' )
1352	self.MCSAEdit.Append(id=wxID_MOVEMCSA, kind=wx.ITEM_NORMAL,text='Move MC/SA solution',
1353	help='Move MC/SA solution to atom list' )
1354	self.MCSAEdit.Append(id=wxID_MCSACLEARRESULTS, kind=wx.ITEM_NORMAL,text='Clear results',
1355	help='Clear table of MC/SA results' )
1356	self.PostfillDataMenu()
1357
1358	# Phase / Texture tab
1359	self.TextureMenu = wx.MenuBar()
1360	self.PrefillDataMenu(self.TextureMenu,helpType='Texture')
1361	self.TextureMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1362	self.TextureEdit = wx.Menu(title='')
1363	self.TextureMenu.Append(menu=self.TextureEdit, title='Texture')
1364	self.TextureEdit.Append(id=wxID_REFINETEXTURE, kind=wx.ITEM_NORMAL,text='Refine texture',
1365	help='Refine the texture coefficients from sequential results')
1366	# self.TextureEdit.Append(id=wxID_CLEARTEXTURE, kind=wx.ITEM_NORMAL,text='Clear texture',
1367	# help='Clear the texture coefficients' )
1368	self.PostfillDataMenu()
1369
1370	# Phase / Pawley tab
1371	self.PawleyMenu = wx.MenuBar()
1372	self.PrefillDataMenu(self.PawleyMenu,helpType='Pawley')
1373	self.PawleyMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1374	self.PawleyEdit = wx.Menu(title='')
1375	self.PawleyMenu.Append(menu=self.PawleyEdit,title='Operations')
1376	self.PawleyEdit.Append(id=wxID_PAWLEYLOAD, kind=wx.ITEM_NORMAL,text='Pawley create',
1377	help='Initialize Pawley reflection list')
1378	self.PawleyEdit.Append(id=wxID_PAWLEYESTIMATE, kind=wx.ITEM_NORMAL,text='Pawley estimate',
1379	help='Estimate initial Pawley intensities')
1380	self.PawleyEdit.Append(id=wxID_PAWLEYUPDATE, kind=wx.ITEM_NORMAL,text='Pawley update',
1381	help='Update negative Pawley intensities with -0.5*Fobs and turn off refinemnt')
1382	self.PostfillDataMenu()
1383
1384	# Phase / Map peaks tab
1385	self.MapPeaksMenu = wx.MenuBar()
1386	self.PrefillDataMenu(self.MapPeaksMenu,helpType='Map peaks')
1387	self.MapPeaksMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1388	self.MapPeaksEdit = wx.Menu(title='')
1389	self.MapPeaksMenu.Append(menu=self.MapPeaksEdit, title='Map peaks')
1390	self.MapPeaksEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
1391	help='Move selected peaks to atom list')
1392	self.MapPeaksEdit.Append(id=wxID_PEAKSVIEWPT, kind=wx.ITEM_NORMAL,text='View point',
1393	help='View point is 1st peak selected')
1394	self.MapPeaksEdit.Append(id=wxID_PEAKSDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1395	help='Compute distance of selected peaks from view point')
1396	self.MapPeaksEdit.Append(id=wxID_SHOWBONDS, kind=wx.ITEM_NORMAL,text='Hide bonds',
1397	help='Hide or show bonds between peak positions')
1398	self.MapPeaksEdit.Append(id=wxID_PEAKSDA, kind=wx.ITEM_NORMAL,text='Calc dist/ang',
1399	help='Calculate distance or angle for selection')
1400	self.MapPeaksEdit.Append(id=wxID_FINDEQVPEAKS, kind=wx.ITEM_NORMAL,text='Equivalent peaks',
1401	help='Find equivalent peaks')
1402	self.MapPeaksEdit.Append(id=wxID_PEAKSUNIQUE, kind=wx.ITEM_NORMAL,text='Unique peaks',
1403	help='Select unique set')
1404	self.MapPeaksEdit.Append(id=wxID_PEAKSDELETE, kind=wx.ITEM_NORMAL,text='Delete peaks',
1405	help='Delete selected peaks')
1406	self.MapPeaksEdit.Append(id=wxID_PEAKSCLEAR, kind=wx.ITEM_NORMAL,text='Clear peaks',
1407	help='Clear the map peak list')
1408	self.PostfillDataMenu()
1409
1410	# Phase / Rigid bodies tab
1411	self.RigidBodiesMenu = wx.MenuBar()
1412	self.PrefillDataMenu(self.RigidBodiesMenu,helpType='Rigid bodies')
1413	self.RigidBodiesMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1414	self.RigidBodiesEdit = wx.Menu(title='')
1415	self.RigidBodiesMenu.Append(menu=self.RigidBodiesEdit, title='Edit')
1416	self.RigidBodiesEdit.Append(id=wxID_ASSIGNATMS2RB, kind=wx.ITEM_NORMAL,text='Assign atoms to rigid body',
1417	help='Select & position rigid body in structure of existing atoms')
1418	self.RigidBodiesEdit.Append(id=wxID_AUTOFINDRESRB, kind=wx.ITEM_NORMAL,text='Auto find residues',
1419	help='Auto find of residue RBs in macromolecule')
1420	self.RigidBodiesEdit.Append(id=wxID_COPYRBPARMS, kind=wx.ITEM_NORMAL,text='Copy rigid body parms',
1421	help='Copy rigid body location & TLS parameters')
1422	self.RigidBodiesEdit.Append(id=wxID_GLOBALTHERM, kind=wx.ITEM_NORMAL,text='Global thermal motion',
1423	help='Global setting of residue thermal motion models')
1424	self.RigidBodiesEdit.Append(id=wxID_GLOBALRESREFINE, kind=wx.ITEM_NORMAL,text='Global residue refine',
1425	help='Global setting of residue RB refinement flags')
1426	self.RigidBodiesEdit.Append(id=wxID_RBREMOVEALL, kind=wx.ITEM_NORMAL,text='Remove all rigid bodies',
1427	help='Remove all rigid body assignment for atoms')
1428	self.PostfillDataMenu()
1429	# end of GSAS-II menu definitions
1430
1431	def _init_ctrls(self, parent,name=None,size=None,pos=None):
1432	wx.Frame.__init__(
1433	self,parent=parent,
1434	#style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX \| wx.FRAME_FLOAT_ON_PARENT ,
1435	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX,
1436	size=size,pos=pos,title='GSAS-II data display')
1437	self._init_menus()
1438	if name:
1439	self.SetLabel(name)
1440	self.Show()
1441
1442	def __init__(self,parent,frame,data=None,name=None, size=None,pos=None):
1443	self.G2frame = frame
1444	self._init_ctrls(parent,name,size,pos)
1445	self.data = data
1446	clientSize = wx.ClientDisplayRect()
1447	Size = self.GetSize()
1448	xPos = clientSize[2]-Size[0]
1449	self.SetPosition(wx.Point(xPos,clientSize[1]+250))
1450	self.AtomGrid = []
1451	self.selectedRow = 0
1452
1453	def setSizePosLeft(self,Width):
1454	clientSize = wx.ClientDisplayRect()
1455	Width[1] = min(Width[1],clientSize[2]-300)
1456	Width[0] = max(Width[0],300)
1457	self.SetSize(Width)
1458	# self.SetPosition(wx.Point(clientSize[2]-Width[0],clientSize[1]+250))
1459
1460	def Clear(self):
1461	self.ClearBackground()
1462	self.DestroyChildren()
1463
1464
1465	################################################################################
1466	##### Notebook Tree Item editor
1467	################################################################################
1468	def UpdateNotebook(G2frame,data):
1469	'''Called when the data tree notebook entry is selected. Allows for
1470	editing of the text in that tree entry
1471	'''
1472	def OnNoteBook(event):
1473	data = G2frame.dataDisplay.GetValue().split('\n')
1474	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Notebook'),data)
1475	if 'nt' not in os.name:
1476	G2frame.dataDisplay.AppendText('\n')
1477
1478	if G2frame.dataDisplay:
1479	G2frame.dataDisplay.Destroy()
1480	G2frame.dataFrame.SetLabel('Notebook')
1481	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1482	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER \| wx.TE_DONTWRAP)
1483	G2frame.dataDisplay.Bind(wx.EVT_TEXT_ENTER,OnNoteBook)
1484	G2frame.dataDisplay.Bind(wx.EVT_KILL_FOCUS,OnNoteBook)
1485	for line in data:
1486	G2frame.dataDisplay.AppendText(line+"\n")
1487	G2frame.dataDisplay.AppendText('Notebook entry @ '+time.ctime()+"\n")
1488	G2frame.dataFrame.setSizePosLeft([400,250])
1489
1490	################################################################################
1491	##### Controls Tree Item editor
1492	################################################################################
1493	def UpdateControls(G2frame,data):
1494	'''Edit overall GSAS-II controls in main Controls data tree entry
1495	'''
1496	#patch
1497	if 'deriv type' not in data:
1498	data = {}
1499	data['deriv type'] = 'analytic Hessian'
1500	data['min dM/M'] = 0.0001
1501	data['shift factor'] = 1.
1502	data['max cyc'] = 3
1503	data['F**2'] = False
1504	if 'shift factor' not in data:
1505	data['shift factor'] = 1.
1506	if 'max cyc' not in data:
1507	data['max cyc'] = 3
1508	if 'F**2' not in data:
1509	data['F**2'] = False
1510	if 'Author' not in data:
1511	data['Author'] = 'no name'
1512	if 'FreePrm1' not in data:
1513	data['FreePrm1'] = 'Sample humidity (%)'
1514	if 'FreePrm2' not in data:
1515	data['FreePrm2'] = 'Sample voltage (V)'
1516	if 'FreePrm3' not in data:
1517	data['FreePrm3'] = 'Applied load (MN)'
1518	if 'Copy2Next' not in data:
1519	data['Copy2Next'] = False
1520	if 'Reverse Seq' not in data:
1521	data['Reverse Seq'] = False
1522	if 'UsrReject' not in data:
1523	data['UsrReject'] = {'minF/sig':0,'MinExt':0.01,'MaxDF/F':20.,'MaxD':500.,'MinD':0.05}
1524	if 'HatomFix' not in data:
1525	data['HatomFix'] = False
1526
1527	#end patch
1528
1529	def SeqSizer():
1530
1531	def OnSelectData(event):
1532	choices = GetPatternTreeDataNames(G2frame,['PWDR','HKLF',])
1533	sel = []
1534	try:
1535	if 'Seq Data' in data:
1536	for item in data['Seq Data']:
1537	sel.append(choices.index(item))
1538	sel = [choices.index(item) for item in data['Seq Data']]
1539	except ValueError: #data changed somehow - start fresh
1540	sel = []
1541	dlg = G2G.G2MultiChoiceDialog(G2frame.dataFrame, 'Sequential refinement',
1542	'Select dataset to include',choices)
1543	dlg.SetSelections(sel)
1544	names = []
1545	if dlg.ShowModal() == wx.ID_OK:
1546	for sel in dlg.GetSelections():
1547	names.append(choices[sel])
1548	data['Seq Data'] = names
1549	G2frame.EnableSeqRefineMenu()
1550	dlg.Destroy()
1551	wx.CallAfter(UpdateControls,G2frame,data)
1552
1553	def OnReverse(event):
1554	data['Reverse Seq'] = reverseSel.GetValue()
1555
1556	def OnCopySel(event):
1557	data['Copy2Next'] = copySel.GetValue()
1558
1559	seqSizer = wx.BoxSizer(wx.VERTICAL)
1560	dataSizer = wx.BoxSizer(wx.HORIZONTAL)
1561	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Sequential Refinement: '),0,WACV)
1562	selSeqData = wx.Button(G2frame.dataDisplay,-1,label=' Select data')
1563	selSeqData.Bind(wx.EVT_BUTTON,OnSelectData)
1564	dataSizer.Add(selSeqData,0,WACV)
1565	SeqData = data.get('Seq Data',[])
1566	if not SeqData:
1567	lbl = ' (no data selected)'
1568	else:
1569	lbl = ' ('+str(len(SeqData))+' dataset(s) selected)'
1570
1571	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=lbl),0,WACV)
1572	seqSizer.Add(dataSizer,0)
1573	if SeqData:
1574	selSizer = wx.BoxSizer(wx.HORIZONTAL)
1575	reverseSel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Reverse order?')
1576	reverseSel.Bind(wx.EVT_CHECKBOX,OnReverse)
1577	reverseSel.SetValue(data['Reverse Seq'])
1578	selSizer.Add(reverseSel,0,WACV)
1579	copySel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Copy results to next histogram?')
1580	copySel.Bind(wx.EVT_CHECKBOX,OnCopySel)
1581	copySel.SetValue(data['Copy2Next'])
1582	selSizer.Add(copySel,0,WACV)
1583	seqSizer.Add(selSizer,0)
1584	return seqSizer
1585
1586	def LSSizer():
1587
1588	def OnDerivType(event):
1589	data['deriv type'] = derivSel.GetValue()
1590	derivSel.SetValue(data['deriv type'])
1591	wx.CallAfter(UpdateControls,G2frame,data)
1592
1593	def OnConvergence(event):
1594	try:
1595	value = max(1.e-9,min(1.0,float(Cnvrg.GetValue())))
1596	except ValueError:
1597	value = 0.0001
1598	data['min dM/M'] = value
1599	Cnvrg.SetValue('%.2g'%(value))
1600
1601	def OnMaxCycles(event):
1602	data['max cyc'] = int(maxCyc.GetValue())
1603	maxCyc.SetValue(str(data['max cyc']))
1604
1605	def OnFactor(event):
1606	try:
1607	value = min(max(float(Factr.GetValue()),0.00001),100.)
1608	except ValueError:
1609	value = 1.0
1610	data['shift factor'] = value
1611	Factr.SetValue('%.5f'%(value))
1612
1613	def OnFsqRef(event):
1614	data['F**2'] = fsqRef.GetValue()
1615
1616	def OnHatomFix(event):
1617	data['HatomFix'] = Hfix.GetValue()
1618
1619	def OnUsrRej(event):
1620	Obj = event.GetEventObject()
1621	item,limits = Indx[Obj]
1622	try:
1623	value = min(max(float(Obj.GetValue()),limits[0]),limits[1])
1624	except ValueError:
1625	value = data['UsrReject'][item]
1626	data['UsrReject'][item] = value
1627	Obj.SetValue('%.2f'%(value))
1628
1629	LSSizer = wx.FlexGridSizer(cols=4,vgap=5,hgap=5)
1630	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement derivatives: '),0,WACV)
1631	Choice=['analytic Jacobian','numeric','analytic Hessian']
1632	derivSel = wx.ComboBox(parent=G2frame.dataDisplay,value=data['deriv type'],choices=Choice,
1633	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1634	derivSel.SetValue(data['deriv type'])
1635	derivSel.Bind(wx.EVT_COMBOBOX, OnDerivType)
1636
1637	LSSizer.Add(derivSel,0,WACV)
1638	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Min delta-M/M: '),0,WACV)
1639	Cnvrg = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2g'%(data['min dM/M']),style=wx.TE_PROCESS_ENTER)
1640	Cnvrg.Bind(wx.EVT_TEXT_ENTER,OnConvergence)
1641	Cnvrg.Bind(wx.EVT_KILL_FOCUS,OnConvergence)
1642	LSSizer.Add(Cnvrg,0,WACV)
1643	Indx = {}
1644	if 'Hessian' in data['deriv type']:
1645	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Max cycles: '),0,WACV)
1646	Choice = ['0','1','2','3','5','10','15','20']
1647	maxCyc = wx.ComboBox(parent=G2frame.dataDisplay,value=str(data['max cyc']),choices=Choice,
1648	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1649	maxCyc.SetValue(str(data['max cyc']))
1650	maxCyc.Bind(wx.EVT_COMBOBOX, OnMaxCycles)
1651	LSSizer.Add(maxCyc,0,WACV)
1652	else:
1653	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Initial shift factor: '),0,WACV)
1654	Factr = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.5f'%(data['shift factor']),style=wx.TE_PROCESS_ENTER)
1655	Factr.Bind(wx.EVT_TEXT_ENTER,OnFactor)
1656	Factr.Bind(wx.EVT_KILL_FOCUS,OnFactor)
1657	LSSizer.Add(Factr,0,WACV)
1658	if G2frame.Sngl:
1659	userReject = data['UsrReject']
1660	usrRej = {'minF/sig':[' Min obs/sig (0-5): ',[0,5], ],'MinExt':[' Min extinct. (0-.9): ',[0,.9],],
1661	'MaxDF/F':[' Max delt-F/sig (3-1000): ',[3.,1000.],],'MaxD':[' Max d-spacing (3-500): ',[3,500],],
1662	'MinD':[' Min d-spacing (0.1-1.0): ',[0.1,1.0],]}
1663
1664	fsqRef = wx.CheckBox(G2frame.dataDisplay,-1,label='Refine HKLF as F^2? ')
1665	fsqRef.SetValue(data['F**2'])
1666	fsqRef.Bind(wx.EVT_CHECKBOX,OnFsqRef)
1667	LSSizer.Add(fsqRef,0,WACV)
1668	LSSizer.Add((1,0),)
1669	for item in usrRej:
1670	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,label=usrRej[item][0]),0,WACV)
1671	usrrej = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2f'%(userReject[item]),style=wx.TE_PROCESS_ENTER)
1672	Indx[usrrej] = [item,usrRej[item][1]]
1673	usrrej.Bind(wx.EVT_TEXT_ENTER,OnUsrRej)
1674	usrrej.Bind(wx.EVT_KILL_FOCUS,OnUsrRej)
1675	LSSizer.Add(usrrej,0,WACV)
1676	# Hfix = wx.CheckBox(G2frame.dataDisplay,-1,label='Regularize H atoms? ')
1677	# Hfix.SetValue(data['HatomFix'])
1678	# Hfix.Bind(wx.EVT_CHECKBOX,OnHatomFix)
1679	# LSSizer.Add(Hfix,0,WACV) #for now
1680	return LSSizer
1681
1682	def AuthSizer():
1683
1684	def OnAuthor(event):
1685	data['Author'] = auth.GetValue()
1686
1687	Author = data['Author']
1688	authSizer = wx.BoxSizer(wx.HORIZONTAL)
1689	authSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' CIF Author (last, first):'),0,WACV)
1690	auth = wx.TextCtrl(G2frame.dataDisplay,-1,value=Author,style=wx.TE_PROCESS_ENTER)
1691	auth.Bind(wx.EVT_TEXT_ENTER,OnAuthor)
1692	auth.Bind(wx.EVT_KILL_FOCUS,OnAuthor)
1693	authSizer.Add(auth,0,WACV)
1694	return authSizer
1695
1696
1697	if G2frame.dataDisplay:
1698	G2frame.dataDisplay.Destroy()
1699	if not G2frame.dataFrame.GetStatusBar():
1700	Status = G2frame.dataFrame.CreateStatusBar()
1701	Status.SetStatusText('')
1702	G2frame.dataFrame.SetLabel('Controls')
1703	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
1704	SetDataMenuBar(G2frame,G2frame.dataFrame.ControlsMenu)
1705	mainSizer = wx.BoxSizer(wx.VERTICAL)
1706	mainSizer.Add((5,5),0)
1707	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement Controls:'),0,WACV)
1708	mainSizer.Add(LSSizer())
1709	mainSizer.Add((5,5),0)
1710	mainSizer.Add(SeqSizer())
1711	mainSizer.Add((5,5),0)
1712	mainSizer.Add(AuthSizer())
1713	mainSizer.Add((5,5),0)
1714
1715	mainSizer.Layout()
1716	G2frame.dataDisplay.SetSizer(mainSizer)
1717	G2frame.dataDisplay.SetSize(mainSizer.Fit(G2frame.dataFrame))
1718	G2frame.dataFrame.setSizePosLeft(mainSizer.Fit(G2frame.dataFrame))
1719
1720	################################################################################
1721	##### Comments
1722	################################################################################
1723
1724	def UpdateComments(G2frame,data):
1725
1726	if G2frame.dataDisplay:
1727	G2frame.dataDisplay.Destroy()
1728	G2frame.dataFrame.SetLabel('Comments')
1729	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1730	style=wx.TE_MULTILINE\|wx.TE_READONLY\|wx.TE_DONTWRAP)
1731	for line in data:
1732	G2frame.dataDisplay.AppendText(line+'\n')
1733	G2frame.dataFrame.setSizePosLeft([400,250])
1734
1735	################################################################################
1736	##### Display of Sequential Results
1737	################################################################################
1738
1739	def UpdateSeqResults(G2frame,data,prevSize=None):
1740	"""
1741	Called when the Sequential Results data tree entry is selected
1742	to show results from a sequential refinement.
1743
1744	:param wx.Frame G2frame: main GSAS-II data tree windows
1745
1746	:param dict data: a dictionary containing the following items:
1747
1748	* 'histNames' - list of histogram names in order as processed by Sequential Refinement
1749	* 'varyList' - list of variables - identical over all refinements in sequence
1750	note that this is the original list of variables, prior to processing
1751	constraints.
1752	* 'variableLabels' -- a dict of labels to be applied to each parameter
1753	(this is created as an empty dict if not present in data).
1754	* keyed by histName - dictionaries for all data sets processed, which contains:
1755
1756	* 'variables'- result[0] from leastsq call
1757	* 'varyList' - list of variables passed to leastsq call (not same as above)
1758	* 'sig' - esds for variables
1759	* 'covMatrix' - covariance matrix from individual refinement
1760	* 'title' - histogram name; same as dict item name
1761	* 'newAtomDict' - new atom parameters after shifts applied
1762	* 'newCellDict' - refined cell parameters after shifts to A0-A5 from Dij terms applied'
1763	"""
1764
1765	def GetSampleParms():
1766	'''Make a dictionary of the sample parameters are not the same over the
1767	refinement series.
1768	'''
1769	if 'IMG' in histNames[0]:
1770	sampleParmDict = {'Sample load':[],}
1771	else:
1772	sampleParmDict = {'Temperature':[],'Pressure':[],'Time':[],
1773	'FreePrm1':[],'FreePrm2':[],'FreePrm3':[],'Omega':[],
1774	'Chi':[],'Phi':[],'Azimuth':[],}
1775	Controls = G2frame.PatternTree.GetItemPyData(
1776	GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
1777	sampleParm = {}
1778	for name in histNames:
1779	if 'IMG' in name:
1780	for item in sampleParmDict:
1781	sampleParmDict[item].append(data[name]['parmDict'].get(item,0))
1782	else:
1783	Id = GetPatternTreeItemId(G2frame,G2frame.root,name)
1784	sampleData = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,Id,'Sample Parameters'))
1785	for item in sampleParmDict:
1786	sampleParmDict[item].append(sampleData.get(item,0))
1787	for item in sampleParmDict:
1788	frstValue = sampleParmDict[item][0]
1789	if np.any(np.array(sampleParmDict[item])-frstValue):
1790	if item.startswith('FreePrm'):
1791	sampleParm[Controls[item]] = sampleParmDict[item]
1792	else:
1793	sampleParm[item] = sampleParmDict[item]
1794	return sampleParm
1795
1796	def GetColumnInfo(col):
1797	'''returns column label, lists of values and errors (or None) for each column in the table
1798	for plotting. The column label is reformatted from Unicode to MatPlotLib encoding
1799	'''
1800	colName = G2frame.SeqTable.GetColLabelValue(col)
1801	plotName = variableLabels.get(colName,colName)
1802	plotName = plotSpCharFix(plotName)
1803	return plotName,colList[col],colSigs[col]
1804
1805	def PlotSelect(event):
1806	'Plots a row (covariance) or column on double-click'
1807	cols = G2frame.dataDisplay.GetSelectedCols()
1808	rows = G2frame.dataDisplay.GetSelectedRows()
1809	if cols:
1810	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1811	elif rows:
1812	name = histNames[rows[0]] #only does 1st one selected
1813	G2plt.PlotCovariance(G2frame,data[name])
1814	else:
1815	G2frame.ErrorDialog(
1816	'Select row or columns',
1817	'Nothing selected in table. Click on column or row label(s) to plot. N.B. Grid selection can be a bit funky.'
1818	)
1819
1820	def OnPlotSelSeq(event):
1821	'plot the selected columns or row from menu command'
1822	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1823	rows = G2frame.dataDisplay.GetSelectedRows()
1824	if cols:
1825	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1826	elif rows:
1827	name = histNames[rows[0]] #only does 1st one selected
1828	G2plt.PlotCovariance(G2frame,data[name])
1829	else:
1830	G2frame.ErrorDialog(
1831	'Select columns',
1832	'No columns or rows selected in table. Click on row or column labels to select fields for plotting.'
1833	)
1834
1835	def OnAveSelSeq(event):
1836	'average the selected columns from menu command'
1837	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1838	if cols:
1839	for col in cols:
1840	ave = np.mean(GetColumnInfo(col)[1])
1841	sig = np.std(GetColumnInfo(col)[1])
1842	print ' Average for '+G2frame.SeqTable.GetColLabelValue(col)+': '+'%.6g'%(ave)+' +/- '+'%.6g'%(sig)
1843	else:
1844	G2frame.ErrorDialog(
1845	'Select columns',
1846	'No columns selected in table. Click on column labels to select fields for averaging.'
1847	)
1848
1849	def OnRenameSelSeq(event):
1850	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1851	colNames = [G2frame.SeqTable.GetColLabelValue(c) for c in cols]
1852	newNames = colNames[:]
1853	for i,name in enumerate(colNames):
1854	if name in variableLabels:
1855	newNames[i] = variableLabels[name]
1856	if not cols:
1857	G2frame.ErrorDialog('Select columns',
1858	'No columns selected in table. Click on column labels to select fields for rename.')
1859	return
1860	dlg = G2G.MultiStringDialog(G2frame.dataDisplay,'Set column names',colNames,newNames)
1861	if dlg.Show():
1862	newNames = dlg.GetValues()
1863	variableLabels.update(dict(zip(colNames,newNames)))
1864	data['variableLabels'] = variableLabels
1865	dlg.Destroy()
1866	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1867	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1868
1869	def OnReOrgSelSeq(event):
1870	'Reorder the columns'
1871	G2G.GetItemOrder(G2frame,VaryListChanges,vallookup,posdict)
1872	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1873
1874	def OnSaveSelSeqCSV(event):
1875	'export the selected columns to a .csv file from menu command'
1876	OnSaveSelSeq(event,csv=True)
1877
1878	def OnSaveSeqCSV(event):
1879	'export all columns to a .csv file from menu command'
1880	OnSaveSelSeq(event,csv=True,allcols=True)
1881
1882	def OnSaveSelSeq(event,csv=False,allcols=False):
1883	'export the selected columns to a .txt or .csv file from menu command'
1884	def WriteCSV():
1885	def WriteList(headerItems):
1886	line = ''
1887	for lbl in headerItems:
1888	if line: line += ','
1889	line += '"'+lbl+'"'
1890	return line
1891	head = ['name']
1892	for col in cols:
1893	item = G2frame.SeqTable.GetColLabelValue(col)
1894	# get rid of labels that have Unicode characters
1895	if not all([ord(c) < 128 and ord(c) != 0 for c in item]): item = '?'
1896	if col in havesig:
1897	head += [item,'esd-'+item]
1898	else:
1899	head += [item]
1900	SeqFile.write(WriteList(head)+'\n')
1901	for row,name in enumerate(saveNames):
1902	line = '"'+saveNames[row]+'"'
1903	for col in cols:
1904	if col in havesig:
1905	line += ','+str(saveData[col][row])+','+str(saveSigs[col][row])
1906	else:
1907	line += ','+str(saveData[col][row])
1908	SeqFile.write(line+'\n')
1909	def WriteSeq():
1910	lenName = len(saveNames[0])
1911	line = ' %s '%('name'.center(lenName))
1912	for col in cols:
1913	item = G2frame.SeqTable.GetColLabelValue(col)
1914	if col in havesig:
1915	line += ' %12s %12s '%(item.center(12),'esd'.center(12))
1916	else:
1917	line += ' %12s '%(item.center(12))
1918	SeqFile.write(line+'\n')
1919	for row,name in enumerate(saveNames):
1920	line = " '%s' "%(saveNames[row])
1921	for col in cols:
1922	if col in havesig:
1923	line += ' %12.6f %12.6f '%(saveData[col][row],saveSigs[col][row])
1924	else:
1925	line += ' %12.6f '%saveData[col][row]
1926	SeqFile.write(line+'\n')
1927
1928	# start of OnSaveSelSeq code
1929	if allcols:
1930	cols = range(G2frame.SeqTable.GetNumberCols())
1931	else:
1932	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1933	nrows = G2frame.SeqTable.GetNumberRows()
1934	if not cols:
1935	G2frame.ErrorDialog('Select columns',
1936	'No columns selected in table. Click on column labels to select fields for output.')
1937	return
1938	saveNames = [G2frame.SeqTable.GetRowLabelValue(r) for r in range(nrows)]
1939	saveData = {}
1940	saveSigs = {}
1941	havesig = []
1942	for col in cols:
1943	name,vals,sigs = GetColumnInfo(col)
1944	saveData[col] = vals
1945	if sigs:
1946	havesig.append(col)
1947	saveSigs[col] = sigs
1948	if csv:
1949	wild = 'CSV output file (.csv)\|.csv'
1950	else:
1951	wild = 'Text output file (.txt)\|.txt'
1952	dlg = wx.FileDialog(
1953	G2frame,
1954	'Choose text output file for your selection', '.', '',
1955	wild,wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1956	try:
1957	if dlg.ShowModal() == wx.ID_OK:
1958	SeqTextFile = dlg.GetPath()
1959	SeqTextFile = G2IO.FileDlgFixExt(dlg,SeqTextFile)
1960	SeqFile = open(SeqTextFile,'w')
1961	if csv:
1962	WriteCSV()
1963	else:
1964	WriteSeq()
1965	SeqFile.close()
1966	finally:
1967	dlg.Destroy()
1968
1969	def striphist(var,insChar=''):
1970	'strip a histogram number from a var name'
1971	sv = var.split(':')
1972	if len(sv) <= 1: return var
1973	if sv[1]:
1974	sv[1] = insChar
1975	return ':'.join(sv)
1976
1977	def plotSpCharFix(lbl):
1978	'Change selected unicode characters to their matplotlib equivalent'
1979	for u,p in [
1980	(u'\u03B1',r'$\alpha$'),
1981	(u'\u03B2',r'$\beta$'),
1982	(u'\u03B3',r'$\gamma$'),
1983	(u'\u0394\u03C7',r'$\Delta\chi$'),
1984	]:
1985	lbl = lbl.replace(u,p)
1986	return lbl
1987
1988	def SelectXaxis():
1989	'returns a selected column number (or None) as the X-axis selection'
1990	ncols = G2frame.SeqTable.GetNumberCols()
1991	colNames = [G2frame.SeqTable.GetColLabelValue(r) for r in range(ncols)]
1992	dlg = G2G.G2SingleChoiceDialog(
1993	G2frame.dataDisplay,
1994	'Select x-axis parameter for plot or Cancel for sequence number',
1995	'Select X-axis',
1996	colNames)
1997	try:
1998	if dlg.ShowModal() == wx.ID_OK:
1999	col = dlg.GetSelection()
2000	else:
2001	col = None
2002	finally:
2003	dlg.Destroy()
2004	return col
2005
2006	def EnablePseudoVarMenus():
2007	'Enables or disables the PseudoVar menu items that require existing defs'
2008	if Controls['SeqPseudoVars']:
2009	val = True
2010	else:
2011	val = False
2012	G2frame.dataFrame.SequentialPvars.Enable(wxDELSEQVAR,val)
2013	G2frame.dataFrame.SequentialPvars.Enable(wxEDITSEQVAR,val)
2014
2015	def DelPseudoVar(event):
2016	'Ask the user to select a pseudo var expression to delete'
2017	choices = Controls['SeqPseudoVars'].keys()
2018	selected = G2G.ItemSelector(
2019	choices,G2frame.dataFrame,
2020	multiple=True,
2021	title='Select expressions to remove',
2022	header='Delete expression')
2023	if selected is None: return
2024	for item in selected:
2025	del Controls['SeqPseudoVars'][choices[item]]
2026	if selected:
2027	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2028
2029	def EditPseudoVar(event):
2030	'Edit an existing pseudo var expression'
2031	choices = Controls['SeqPseudoVars'].keys()
2032	if len(choices) == 1:
2033	selected = 0
2034	else:
2035	selected = G2G.ItemSelector(
2036	choices,G2frame.dataFrame,
2037	multiple=False,
2038	title='Select an expression to edit',
2039	header='Edit expression')
2040	if selected is not None:
2041	dlg = G2exG.ExpressionDialog(
2042	G2frame.dataDisplay,PSvarDict,
2043	Controls['SeqPseudoVars'][choices[selected]],
2044	header="Edit the PseudoVar expression",
2045	VarLabel="PseudoVar #"+str(selected+1),
2046	fit=False)
2047	newobj = dlg.Show(True)
2048	if newobj:
2049	calcobj = G2obj.ExpressionCalcObj(newobj)
2050	del Controls['SeqPseudoVars'][choices[selected]]
2051	Controls['SeqPseudoVars'][calcobj.eObj.expression] = newobj
2052	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2053
2054	def AddNewPseudoVar(event):
2055	'Create a new pseudo var expression'
2056	dlg = G2exG.ExpressionDialog(
2057	G2frame.dataDisplay,PSvarDict,
2058	header='Enter an expression for a PseudoVar here',
2059	VarLabel = "New PseudoVar",
2060	fit=False)
2061	obj = dlg.Show(True)
2062	dlg.Destroy()
2063	if obj:
2064	calcobj = G2obj.ExpressionCalcObj(obj)
2065	Controls['SeqPseudoVars'][calcobj.eObj.expression] = obj
2066	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2067
2068	def UpdateParmDict(parmDict):
2069	'''generate the atom positions and the direct & reciprocal cell values,
2070	because they might be needed to evaluate the pseudovar
2071	'''
2072	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2073	['A'+str(i) for i in range(6)])
2074	)
2075	delList = []
2076	phaselist = []
2077	for item in parmDict:
2078	if ':' not in item: continue
2079	key = item.split(':')
2080	if len(key) < 3: continue
2081	# remove the dA[xyz] terms, they would only bring confusion
2082	if key[2].startswith('dA'):
2083	delList.append(item)
2084	# compute and update the corrected reciprocal cell terms using the Dij values
2085	elif key[2] in Ddict:
2086	if key[0] not in phaselist: phaselist.append(key[0])
2087	akey = key[0]+'::'+Ddict[key[2]]
2088	parmDict[akey] -= parmDict[item]
2089	delList.append(item)
2090	for item in delList:
2091	del parmDict[item]
2092	for i in phaselist:
2093	pId = int(i)
2094	# apply cell symmetry
2095	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],parmDict,zeroDict[pId])
2096	# convert to direct cell & add the unique terms to the dictionary
2097	for i,val in enumerate(G2lat.A2cell(A)):
2098	if i in uniqCellIndx[pId]:
2099	lbl = str(pId)+'::'+cellUlbl[i]
2100	parmDict[lbl] = val
2101	lbl = str(pId)+'::'+'vol'
2102	parmDict[lbl] = G2lat.calc_V(A)
2103	return parmDict
2104
2105	def EvalPSvarDeriv(calcobj,parmDict,sampleDict,var,ESD):
2106	'''Evaluate an expression derivative with respect to a
2107	GSAS-II variable name.
2108
2109	Note this likely could be faster if the loop over calcobjs were done
2110	inside after the Dict was created.
2111	'''
2112	step = ESD/10
2113	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2114	['A'+str(i) for i in range(6)])
2115	)
2116	results = []
2117	phaselist = []
2118	VparmDict = sampleDict.copy()
2119	for incr in step,-step:
2120	VparmDict.update(parmDict.copy())
2121	# as saved, the parmDict has updated 'A[xyz]' values, but 'dA[xyz]'
2122	# values are not zeroed: fix that!
2123	VparmDict.update({item:0.0 for item in parmDict if 'dA' in item})
2124	VparmDict[var] += incr
2125	G2mv.Dict2Map(VparmDict,[]) # apply constraints
2126	# generate the atom positions and the direct & reciprocal cell values now, because they might
2127	# needed to evaluate the pseudovar
2128	for item in VparmDict:
2129	if item in sampleDict:
2130	continue
2131	if ':' not in item: continue
2132	key = item.split(':')
2133	if len(key) < 3: continue
2134	# apply any new shifts to atom positions
2135	if key[2].startswith('dA'):
2136	VparmDict[''.join(item.split('d'))] += VparmDict[item]
2137	VparmDict[item] = 0.0
2138	# compute and update the corrected reciprocal cell terms using the Dij values
2139	if key[2] in Ddict:
2140	if key[0] not in phaselist: phaselist.append(key[0])
2141	akey = key[0]+'::'+Ddict[key[2]]
2142	VparmDict[akey] -= VparmDict[item]
2143	for i in phaselist:
2144	pId = int(i)
2145	# apply cell symmetry
2146	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],VparmDict,zeroDict[pId])
2147	# convert to direct cell & add the unique terms to the dictionary
2148	for i,val in enumerate(G2lat.A2cell(A)):
2149	if i in uniqCellIndx[pId]:
2150	lbl = str(pId)+'::'+cellUlbl[i]
2151	VparmDict[lbl] = val
2152	lbl = str(pId)+'::'+'vol'
2153	VparmDict[lbl] = G2lat.calc_V(A)
2154	# dict should be fully updated, use it & calculate
2155	calcobj.SetupCalc(VparmDict)
2156	results.append(calcobj.EvalExpression())
2157	return (results[0] - results[1]) / (2.*step)
2158
2159	def EnableParFitEqMenus():
2160	'Enables or disables the Parametric Fit menu items that require existing defs'
2161	if Controls['SeqParFitEqList']:
2162	val = True
2163	else:
2164	val = False
2165	G2frame.dataFrame.SequentialPfit.Enable(wxDELPARFIT,val)
2166	G2frame.dataFrame.SequentialPfit.Enable(wxEDITPARFIT,val)
2167	G2frame.dataFrame.SequentialPfit.Enable(wxDOPARFIT,val)
2168
2169	def ParEqEval(Values,calcObjList,varyList):
2170	'''Evaluate the parametric expression(s)
2171	:param list Values: a list of values for each variable parameter
2172	:param list calcObjList: a list of :class:`GSASIIobj.ExpressionCalcObj`
2173	expression objects to evaluate
2174	:param list varyList: a list of variable names for each value in Values
2175	'''
2176	result = []
2177	for calcobj in calcObjList:
2178	calcobj.UpdateVars(varyList,Values)
2179	result.append((calcobj.depVal-calcobj.EvalExpression())/calcobj.depSig)
2180	return result
2181
2182	def DoParEqFit(event,eqObj=None):
2183	'Parametric fit minimizer'
2184	varyValueDict = {} # dict of variables and their initial values
2185	calcObjList = [] # expression objects, ready to go for each data point
2186	if eqObj is not None:
2187	eqObjList = [eqObj,]
2188	else:
2189	eqObjList = Controls['SeqParFitEqList']
2190	UseFlags = G2frame.SeqTable.GetColValues(0)
2191	for obj in eqObjList:
2192	expr = obj.expression
2193	# assemble refined vars for this equation
2194	varyValueDict.update({var:val for var,val in obj.GetVariedVarVal()})
2195	# lookup dependent var position
2196	depVar = obj.GetDepVar()
2197	if depVar in colLabels:
2198	indx = colLabels.index(depVar)
2199	else:
2200	raise Exception('Dependent variable '+depVar+' not found')
2201	# assemble a list of the independent variables
2202	indepVars = obj.GetIndependentVars()
2203	# loop over each datapoint
2204	for j,row in enumerate(zip(*colList)):
2205	if not UseFlags[j]: continue
2206	# assemble equations to fit
2207	calcobj = G2obj.ExpressionCalcObj(obj)
2208	# prepare a dict of needed independent vars for this expression
2209	indepVarDict = {var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2210	calcobj.SetupCalc(indepVarDict)
2211	# values and sigs for current value of dependent var
2212	calcobj.depVal = row[indx]
2213	calcobj.depSig = colSigs[indx][j]
2214	calcObjList.append(calcobj)
2215	# varied parameters
2216	varyList = varyValueDict.keys()
2217	values = varyValues = [varyValueDict[key] for key in varyList]
2218	if not varyList:
2219	print 'no variables to refine!'
2220	return
2221	try:
2222	result = so.leastsq(ParEqEval,varyValues,full_output=True, #ftol=Ftol,
2223	args=(calcObjList,varyList)
2224	)
2225	values = result[0]
2226	covar = result[1]
2227	if covar is None:
2228	raise Exception
2229	esdDict = {}
2230	for i,avar in enumerate(varyList):
2231	esdDict[avar] = np.sqrt(covar[i,i])
2232	except:
2233	print('====> Fit failed')
2234	return
2235	print('==== Fit Results ====')
2236	for obj in eqObjList:
2237	obj.UpdateVariedVars(varyList,values)
2238	ind = ' '
2239	print(' '+obj.GetDepVar()+' = '+obj.expression)
2240	for var in obj.assgnVars:
2241	print(ind+var+' = '+obj.assgnVars[var])
2242	for var in obj.freeVars:
2243	avar = "::"+obj.freeVars[var][0]
2244	val = obj.freeVars[var][1]
2245	if obj.freeVars[var][2]:
2246	print(ind+var+' = '+avar + " = " + G2mth.ValEsd(val,esdDict[avar]))
2247	else:
2248	print(ind+var+' = '+avar + " =" + G2mth.ValEsd(val,0))
2249	# create a plot for each parametric variable
2250	for fitnum,obj in enumerate(eqObjList):
2251	calcobj = G2obj.ExpressionCalcObj(obj)
2252	# lookup dependent var position
2253	indx = colLabels.index(obj.GetDepVar())
2254	# assemble a list of the independent variables
2255	indepVars = obj.GetIndependentVars()
2256	# loop over each datapoint
2257	fitvals = []
2258	for j,row in enumerate(zip(*colList)):
2259	calcobj.SetupCalc(
2260	{var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2261	)
2262	fitvals.append(calcobj.EvalExpression())
2263	G2plt.PlotSelectedSequence(
2264	G2frame,[indx],GetColumnInfo,SelectXaxis,
2265	fitnum,fitvals)
2266
2267	def SingleParEqFit(eqObj):
2268	DoParEqFit(None,eqObj)
2269
2270	def DelParFitEq(event):
2271	'Ask the user to select function to delete'
2272	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2273	selected = G2G.ItemSelector(
2274	txtlst,G2frame.dataFrame,
2275	multiple=True,
2276	title='Select a parametric equation(s) to remove',
2277	header='Delete equation')
2278	if selected is None: return
2279	Controls['SeqParFitEqList'] = [obj for i,obj in enumerate(Controls['SeqParFitEqList']) if i not in selected]
2280	EnableParFitEqMenus()
2281	if Controls['SeqParFitEqList']: DoParEqFit(event)
2282
2283	def EditParFitEq(event):
2284	'Edit an existing parametric equation'
2285	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2286	if len(txtlst) == 1:
2287	selected = 0
2288	else:
2289	selected = G2G.ItemSelector(
2290	txtlst,G2frame.dataFrame,
2291	multiple=False,
2292	title='Select a parametric equation to edit',
2293	header='Edit equation')
2294	if selected is not None:
2295	dlg = G2exG.ExpressionDialog(
2296	G2frame.dataDisplay,indepVarDict,
2297	Controls['SeqParFitEqList'][selected],
2298	depVarDict=depVarDict,
2299	header="Edit the formula for this minimization function",
2300	ExtraButton=['Fit',SingleParEqFit])
2301	newobj = dlg.Show(True)
2302	if newobj:
2303	calcobj = G2obj.ExpressionCalcObj(newobj)
2304	Controls['SeqParFitEqList'][selected] = newobj
2305	EnableParFitEqMenus()
2306	if Controls['SeqParFitEqList']: DoParEqFit(event)
2307
2308	def AddNewParFitEq(event):
2309	'Create a new parametric equation to be fit to sequential results'
2310
2311	# compile the variable names used in previous freevars to avoid accidental name collisions
2312	usedvarlist = []
2313	for obj in Controls['SeqParFitEqList']:
2314	for var in obj.freeVars:
2315	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2316
2317	dlg = G2exG.ExpressionDialog(
2318	G2frame.dataDisplay,indepVarDict,
2319	depVarDict=depVarDict,
2320	header='Define an equation to minimize in the parametric fit',
2321	ExtraButton=['Fit',SingleParEqFit],
2322	usedVars=usedvarlist)
2323	obj = dlg.Show(True)
2324	dlg.Destroy()
2325	if obj:
2326	Controls['SeqParFitEqList'].append(obj)
2327	EnableParFitEqMenus()
2328	if Controls['SeqParFitEqList']: DoParEqFit(event)
2329
2330	def CopyParFitEq(event):
2331	'Copy an existing parametric equation to be fit to sequential results'
2332	# compile the variable names used in previous freevars to avoid accidental name collisions
2333	usedvarlist = []
2334	for obj in Controls['SeqParFitEqList']:
2335	for var in obj.freeVars:
2336	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2337	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2338	if len(txtlst) == 1:
2339	selected = 0
2340	else:
2341	selected = G2G.ItemSelector(
2342	txtlst,G2frame.dataFrame,
2343	multiple=False,
2344	title='Select a parametric equation to copy',
2345	header='Copy equation')
2346	if selected is not None:
2347	newEqn = copy.deepcopy(Controls['SeqParFitEqList'][selected])
2348	for var in newEqn.freeVars:
2349	newEqn.freeVars[var][0] = G2obj.MakeUniqueLabel(newEqn.freeVars[var][0],usedvarlist)
2350	dlg = G2exG.ExpressionDialog(
2351	G2frame.dataDisplay,indepVarDict,
2352	newEqn,
2353	depVarDict=depVarDict,
2354	header="Edit the formula for this minimization function",
2355	ExtraButton=['Fit',SingleParEqFit])
2356	newobj = dlg.Show(True)
2357	if newobj:
2358	calcobj = G2obj.ExpressionCalcObj(newobj)
2359	Controls['SeqParFitEqList'].append(newobj)
2360	EnableParFitEqMenus()
2361	if Controls['SeqParFitEqList']: DoParEqFit(event)
2362
2363	def GridSetToolTip(row,col):
2364	'''Routine to show standard uncertainties for each element in table
2365	as a tooltip
2366	'''
2367	if colSigs[col]:
2368	return u'\u03c3 = '+str(colSigs[col][row])
2369	return ''
2370
2371	def GridColLblToolTip(col):
2372	'''Define a tooltip for a column. This will be the user-entered value
2373	(from data['variableLabels']) or the default name
2374	'''
2375	if col < 0 or col > len(colLabels):
2376	print 'Illegal column #',col
2377	return
2378	var = colLabels[col]
2379	return variableLabels.get(var,G2obj.fmtVarDescr(var))
2380
2381	def SetLabelString(event):
2382	'''Define or edit the label for a column in the table, to be used
2383	as a tooltip and for plotting
2384	'''
2385	col = event.GetCol()
2386	if col < 0 or col > len(colLabels):
2387	return
2388	var = colLabels[col]
2389	lbl = variableLabels.get(var,G2obj.fmtVarDescr(var))
2390	dlg = G2G.SingleStringDialog(G2frame.dataFrame,'Set variable label',
2391	'Set a new name for variable '+var,lbl,size=(400,-1))
2392	if dlg.Show():
2393	variableLabels[var] = dlg.GetValue()
2394	dlg.Destroy()
2395
2396	#def GridRowLblToolTip(row): return 'Row ='+str(row)
2397
2398	# lookup table for unique cell parameters by symmetry
2399	cellGUIlist = [
2400	[['m3','m3m'],(0,)],
2401	[['3R','3mR'],(0,3)],
2402	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],(0,2)],
2403	[['mmm'],(0,1,2)],
2404	[['2/m'+'a'],(0,1,2,3)],
2405	[['2/m'+'b'],(0,1,2,4)],
2406	[['2/m'+'c'],(0,1,2,5)],
2407	[['-1'],(0,1,2,3,4,5)],
2408	]
2409	# cell labels
2410	cellUlbl = ('a','b','c',u'\u03B1',u'\u03B2',u'\u03B3') # unicode a,b,c,alpha,beta,gamma
2411
2412	#======================================================================
2413	# start processing sequential results here (UpdateSeqResults)
2414	#======================================================================
2415	if not data:
2416	print 'No sequential refinement results'
2417	return
2418	variableLabels = data.get('variableLabels',{})
2419	data['variableLabels'] = variableLabels
2420	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
2421	Controls = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Controls'))
2422	# create a place to store Pseudo Vars & Parametric Fit functions, if not present
2423	if 'SeqPseudoVars' not in Controls: Controls['SeqPseudoVars'] = {}
2424	if 'SeqParFitEqList' not in Controls: Controls['SeqParFitEqList'] = []
2425	histNames = data['histNames']
2426	if G2frame.dataDisplay:
2427	G2frame.dataDisplay.Destroy()
2428	if not G2frame.dataFrame.GetStatusBar():
2429	Status = G2frame.dataFrame.CreateStatusBar()
2430	Status.SetStatusText("Select column to export; Double click on column to plot data; on row for Covariance")
2431	sampleParms = GetSampleParms()
2432
2433	# make dict of varied atom coords keyed by absolute position
2434	newAtomDict = data[histNames[0]].get('newAtomDict',{}) # dict with atom positions; relative & absolute
2435	# Possible error: the next might need to be data[histNames[0]]['varyList']
2436	# error will arise if there constraints on coordinates?
2437	atomLookup = {newAtomDict[item][0]:item for item in newAtomDict if item in data['varyList']}
2438
2439	# make dict of varied cell parameters equivalents
2440	ESDlookup = {} # provides the Dij term for each Ak term (where terms are refined)
2441	Dlookup = {} # provides the Ak term for each Dij term (where terms are refined)
2442	# N.B. These Dij vars are missing a histogram #
2443	newCellDict = data[histNames[0]].get('newCellDict',{})
2444	for item in newCellDict:
2445	if item in data['varyList']:
2446	ESDlookup[newCellDict[item][0]] = item
2447	Dlookup[item] = newCellDict[item][0]
2448	# add coordinate equivalents to lookup table
2449	for parm in atomLookup:
2450	Dlookup[atomLookup[parm]] = parm
2451	ESDlookup[parm] = atomLookup[parm]
2452
2453	# get unit cell & symmetry for all phases & initial stuff for later use
2454	RecpCellTerms = {}
2455	SGdata = {}
2456	uniqCellIndx = {}
2457	initialCell = {}
2458	RcellLbls = {}
2459	zeroDict = {}
2460	Rcelldict = {}
2461	for phase in Phases:
2462	phasedict = Phases[phase]
2463	pId = phasedict['pId']
2464	pfx = str(pId)+'::' # prefix for A values from phase
2465	RcellLbls[pId] = [pfx+'A'+str(i) for i in range(6)]
2466	RecpCellTerms[pId] = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2467	zeroDict[pId] = dict(zip(RcellLbls[pId],6*[0.,]))
2468	SGdata[pId] = phasedict['General']['SGData']
2469	Rcelldict.update({lbl:val for lbl,val in zip(RcellLbls[pId],RecpCellTerms[pId])})
2470	laue = SGdata[pId]['SGLaue']
2471	if laue == '2/m':
2472	laue += SGdata[pId]['SGUniq']
2473	for symlist,celllist in cellGUIlist:
2474	if laue in symlist:
2475	uniqCellIndx[pId] = celllist
2476	break
2477	else: # should not happen
2478	uniqCellIndx[pId] = range(6)
2479	for i in uniqCellIndx[pId]:
2480	initialCell[str(pId)+'::A'+str(i)] = RecpCellTerms[pId][i]
2481
2482	SetDataMenuBar(G2frame,G2frame.dataFrame.SequentialMenu)
2483	G2frame.dataFrame.SetLabel('Sequential refinement results')
2484	if not G2frame.dataFrame.GetStatusBar():
2485	Status = G2frame.dataFrame.CreateStatusBar()
2486	Status.SetStatusText('')
2487	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRenameSelSeq, id=wxID_RENAMESEQSEL)
2488	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeq, id=wxID_SAVESEQSEL)
2489	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeqCSV, id=wxID_SAVESEQSELCSV)
2490	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSeqCSV, id=wxID_SAVESEQCSV)
2491	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotSelSeq, id=wxID_PLOTSEQSEL)
2492	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAveSelSeq, id=wxID_AVESEQSEL)
2493	G2frame.dataFrame.Bind(wx.EVT_MENU, OnReOrgSelSeq, id=wxID_ORGSEQSEL)
2494	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewPseudoVar, id=wxADDSEQVAR)
2495	G2frame.dataFrame.Bind(wx.EVT_MENU, DelPseudoVar, id=wxDELSEQVAR)
2496	G2frame.dataFrame.Bind(wx.EVT_MENU, EditPseudoVar, id=wxEDITSEQVAR)
2497	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewParFitEq, id=wxADDPARFIT)
2498	G2frame.dataFrame.Bind(wx.EVT_MENU, CopyParFitEq, id=wxCOPYPARFIT)
2499	G2frame.dataFrame.Bind(wx.EVT_MENU, DelParFitEq, id=wxDELPARFIT)
2500	G2frame.dataFrame.Bind(wx.EVT_MENU, EditParFitEq, id=wxEDITPARFIT)
2501	G2frame.dataFrame.Bind(wx.EVT_MENU, DoParEqFit, id=wxDOPARFIT)
2502	EnablePseudoVarMenus()
2503	EnableParFitEqMenus()
2504
2505	# scan for locations where the variables change
2506	VaryListChanges = [] # histograms where there is a change
2507	combinedVaryList = []
2508	firstValueDict = {}
2509	vallookup = {}
2510	posdict = {}
2511	prevVaryList = []
2512	for i,name in enumerate(histNames):
2513	for var,val,sig in zip(data[name]['varyList'],data[name]['variables'],data[name]['sig']):
2514	svar = striphist(var,'*') # wild-carded
2515	if svar not in combinedVaryList:
2516	# add variables to list as they appear
2517	combinedVaryList.append(svar)
2518	firstValueDict[svar] = (val,sig)
2519	if prevVaryList != data[name]['varyList']: # this refinement has a different refinement list from previous
2520	prevVaryList = data[name]['varyList']
2521	vallookup[name] = dict(zip(data[name]['varyList'],data[name]['variables']))
2522	posdict[name] = {}
2523	for var in data[name]['varyList']:
2524	svar = striphist(var,'*')
2525	posdict[name][combinedVaryList.index(svar)] = svar
2526	VaryListChanges.append(name)
2527	if len(VaryListChanges) > 1:
2528	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,True)
2529	else:
2530	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,False)
2531	#-----------------------------------------------------------------------------------
2532	# build up the data table by columns -----------------------------------------------
2533	nRows = len(histNames)
2534	colList = [nRows*[True]]
2535	colSigs = [None]
2536	colLabels = ['Use']
2537	Types = [wg.GRID_VALUE_BOOL]
2538	# start with Rwp values
2539	if 'IMG ' not in histNames[0][:4]:
2540	colList += [[data[name]['Rvals']['Rwp'] for name in histNames]]
2541	colSigs += [None]
2542	colLabels += ['Rwp']
2543	Types += [wg.GRID_VALUE_FLOAT+':10,3',]
2544	# add % change in Chi^2 in last cycle
2545	if histNames[0][:4] not in ['SASD','IMG '] and Controls.get('ShowCell'):
2546	colList += [[100.*data[name]['Rvals'].get('DelChi2',-1) for name in histNames]]
2547	colSigs += [None]
2548	colLabels += [u'\u0394\u03C7\u00B2 (%)']
2549	Types += [wg.GRID_VALUE_FLOAT,]
2550	deltaChiCol = len(colLabels)-1
2551	# add changing sample parameters to table
2552	for key in sampleParms:
2553	colList += [sampleParms[key]]
2554	colSigs += [None]
2555	colLabels += [key]
2556	Types += [wg.GRID_VALUE_FLOAT,]
2557	sampleDict = {}
2558	for i,name in enumerate(histNames):
2559	sampleDict[name] = dict(zip(sampleParms.keys(),[sampleParms[key][i] for key in sampleParms.keys()]))
2560	# add unique cell parameters TODO: review this where the cell symmetry changes (when possible)
2561	if Controls.get('ShowCell',False):
2562	for pId in sorted(RecpCellTerms):
2563	pfx = str(pId)+'::' # prefix for A values from phase
2564	cells = []
2565	cellESDs = []
2566	colLabels += [pfx+cellUlbl[i] for i in uniqCellIndx[pId]]
2567	colLabels += [pfx+'Vol']
2568	Types += (1+len(uniqCellIndx[pId]))*[wg.GRID_VALUE_FLOAT,]
2569	for name in histNames:
2570	covData = {
2571	'varyList': [Dlookup.get(striphist(v),v) for v in data[name]['varyList']],
2572	'covMatrix': data[name]['covMatrix']
2573	}
2574	A = RecpCellTerms[pId][:] # make copy of starting A values
2575	# update with refined values
2576	for i in range(6):
2577	var = str(pId)+'::A'+str(i)
2578	if var in ESDlookup:
2579	val = data[name]['newCellDict'][ESDlookup[var]][1] # get refined value
2580	A[i] = val # override with updated value
2581	# apply symmetry
2582	Albls = [pfx+'A'+str(i) for i in range(6)]
2583	cellDict = dict(zip(Albls,A))
2584	A,zeros = G2stIO.cellFill(pfx,SGdata[pId],cellDict,zeroDict[pId])
2585	# convert to direct cell & add only unique values to table
2586	c = G2lat.A2cell(A)
2587	vol = G2lat.calc_V(A)
2588	cE = G2stIO.getCellEsd(pfx,SGdata[pId],A,covData)
2589	cells += [[c[i] for i in uniqCellIndx[pId]]+[vol]]
2590	cellESDs += [[cE[i] for i in uniqCellIndx[pId]]+[cE[-1]]]
2591	colList += zip(*cells)
2592	colSigs += zip(*cellESDs)
2593	# sort out the variables in their selected order
2594	varcols = 0
2595	for d in posdict.itervalues():
2596	varcols = max(varcols,max(d.keys())+1)
2597	# get labels for each column
2598	for i in range(varcols):
2599	lbl = ''
2600	for h in VaryListChanges:
2601	if posdict[h].get(i):
2602	if posdict[h].get(i) in lbl: continue
2603	if lbl != "": lbl += '/'
2604	lbl += posdict[h].get(i)
2605	colLabels.append(lbl)
2606	Types += varcols*[wg.GRID_VALUE_FLOAT]
2607	vals = []
2608	esds = []
2609	varsellist = None # will be a list of variable names in the order they are selected to appear
2610	# tabulate values for each hist, leaving None for blank columns
2611	for name in histNames:
2612	if name in posdict:
2613	varsellist = [posdict[name].get(i) for i in range(varcols)]
2614	# translate variable names to how they will be used in the headings
2615	vs = [striphist(v,'*') for v in data[name]['varyList']]
2616	# determine the index for each column (or None) in the data[]['variables'] and ['sig'] lists
2617	sellist = [vs.index(v) if v is not None else None for v in varsellist]
2618	#sellist = [i if striphist(v,'*') in varsellist else None for i,v in enumerate(data[name]['varyList'])]
2619	if not varsellist: raise Exception()
2620	vals.append([data[name]['variables'][s] if s is not None else None for s in sellist])
2621	esds.append([data[name]['sig'][s] if s is not None else None for s in sellist])
2622	#GSASIIpath.IPyBreak()
2623	colList += zip(*vals)
2624	colSigs += zip(*esds)
2625
2626	# tabulate constrained variables, removing histogram numbers if needed
2627	# from parameter label
2628	depValDict = {}
2629	depSigDict = {}
2630	for name in histNames:
2631	for var in data[name].get('depParmDict',{}):
2632	val,sig = data[name]['depParmDict'][var]
2633	svar = striphist(var,'*')
2634	if svar not in depValDict:
2635	depValDict[svar] = [val]
2636	depSigDict[svar] = [sig]
2637	else:
2638	depValDict[svar].append(val)
2639	depSigDict[svar].append(sig)
2640	# add the dependent constrained variables to the table
2641	for var in sorted(depValDict):
2642	if len(depValDict[var]) != len(histNames): continue
2643	colLabels.append(var)
2644	Types += [wg.GRID_VALUE_FLOAT,]
2645	colSigs += [depSigDict[var]]
2646	colList += [depValDict[var]]
2647
2648	# add atom parameters to table
2649	colLabels += atomLookup.keys()
2650	Types += len(atomLookup)*[wg.GRID_VALUE_FLOAT]
2651	for parm in sorted(atomLookup):
2652	colList += [[data[name]['newAtomDict'][atomLookup[parm]][1] for name in histNames]]
2653	if atomLookup[parm] in data[histNames[0]]['varyList']:
2654	col = data[histNames[0]]['varyList'].index(atomLookup[parm])
2655	colSigs += [[data[name]['sig'][col] for name in histNames]]
2656	else:
2657	colSigs += [None] # should not happen
2658	# evaluate Pseudovars, their ESDs and add them to grid
2659	for expr in Controls['SeqPseudoVars']:
2660	obj = Controls['SeqPseudoVars'][expr]
2661	calcobj = G2obj.ExpressionCalcObj(obj)
2662	valList = []
2663	esdList = []
2664	for seqnum,name in enumerate(histNames):
2665	sigs = data[name]['sig']
2666	G2mv.InitVars()
2667	parmDict = data[name].get('parmDict')
2668	badVary = data[name].get('badVary',[])
2669	constraintInfo = data[name].get('constraintInfo',[[],[],{},[],seqnum])
2670	groups,parmlist,constrDict,fixedList,ihst = constraintInfo
2671	varyList = data[name]['varyList']
2672	parmDict = data[name]['parmDict']
2673	G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmDict,SeqHist=ihst)
2674	derivs = np.array(
2675	[EvalPSvarDeriv(calcobj,parmDict.copy(),sampleDict[name],var,ESD)
2676	for var,ESD in zip(varyList,sigs)]
2677	)
2678	esdList.append(np.sqrt(
2679	np.inner(derivs,np.inner(data[name]['covMatrix'],derivs.T))
2680	))
2681	PSvarDict = parmDict.copy()
2682	PSvarDict.update(sampleDict[name])
2683	UpdateParmDict(PSvarDict)
2684	calcobj.UpdateDict(PSvarDict)
2685	valList.append(calcobj.EvalExpression())
2686	if not esdList:
2687	esdList = None
2688	colList += [valList]
2689	colSigs += [esdList]
2690	colLabels += [expr]
2691	Types += [wg.GRID_VALUE_FLOAT,]
2692	#---- table build done -------------------------------------------------------------
2693
2694	# Make dict needed for creating & editing pseudovars (PSvarDict).
2695	name = histNames[0]
2696	parmDict = data[name].get('parmDict')
2697	PSvarDict = parmDict.copy()
2698	PSvarDict.update(sampleParms)
2699	UpdateParmDict(PSvarDict)
2700	# Also dicts of dependent (depVarDict) & independent vars (indepVarDict)
2701	# for Parametric fitting from the data table
2702	parmDict = dict(zip(colLabels,zip(*colList)[0])) # scratch dict w/all values in table
2703	parmDict.update(
2704	{var:val for var,val in data[name].get('newCellDict',{}).values()} # add varied reciprocal cell terms
2705	)
2706	name = histNames[0]
2707
2708	#******************************************************************************
2709	# create a set of values for example evaluation of pseudovars and
2710	# this does not work for refinements that have differing numbers of variables.
2711	#raise Exception
2712	indepVarDict = {} # values in table w/o ESDs
2713	depVarDict = {}
2714	for i,var in enumerate(colLabels):
2715	if var == 'Use': continue
2716	if colList[i][0] is None:
2717	val,sig = firstValueDict.get(var,[None,None])
2718	elif colSigs[i]:
2719	val,sig = colList[i][0],colSigs[i][0]
2720	else:
2721	val,sig = colList[i][0],None
2722	if val is None:
2723	continue
2724	elif sig is None:
2725	indepVarDict[var] = val
2726	elif striphist(var) not in Dlookup:
2727	depVarDict[var] = val
2728	# add recip cell coeff. values
2729	depVarDict.update({var:val for var,val in data[name].get('newCellDict',{}).values()})
2730
2731	G2frame.dataDisplay = G2G.GSGrid(parent=G2frame.dataFrame)
2732	G2frame.SeqTable = G2G.Table(
2733	[list(c) for c in zip(*colList)], # convert from columns to rows
2734	colLabels=colLabels,rowLabels=histNames,types=Types)
2735	G2frame.dataDisplay.SetTable(G2frame.SeqTable, True)
2736	#G2frame.dataDisplay.EnableEditing(False)
2737	# make all but first column read-only
2738	for c in range(1,len(colLabels)):
2739	for r in range(nRows):
2740	G2frame.dataDisplay.SetCellReadOnly(r,c)
2741	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, PlotSelect)
2742	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, SetLabelString)
2743	G2frame.dataDisplay.SetRowLabelSize(8*len(histNames[0])) #pretty arbitrary 8
2744	G2frame.dataDisplay.SetMargins(0,0)
2745	G2frame.dataDisplay.AutoSizeColumns(True)
2746	if prevSize:
2747	G2frame.dataDisplay.SetSize(prevSize)
2748	else:
2749	G2frame.dataFrame.setSizePosLeft([700,350])
2750	# highlight unconverged shifts
2751	if histNames[0][:4] not in ['SASD','IMG ']:
2752	for row,name in enumerate(histNames):
2753	deltaChi = G2frame.SeqTable.GetValue(row,deltaChiCol)
2754	if deltaChi > 10.:
2755	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,0,0))
2756	elif deltaChi > 1.0:
2757	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,255,0))
2758	G2frame.dataDisplay.InstallGridToolTip(GridSetToolTip,GridColLblToolTip)
2759	G2frame.dataDisplay.SendSizeEvent() # resize needed on mac
2760	G2frame.dataDisplay.Refresh() # shows colored text on mac
2761
2762	################################################################################
2763	##### Main PWDR panel
2764	################################################################################
2765
2766	def UpdatePWHKPlot(G2frame,kind,item):
2767	'''Called when the histogram main tree entry is called. Displays the
2768	histogram weight factor, refinement statistics for the histogram
2769	and the range of data for a simulation.
2770
2771	Also invokes a plot of the histogram.
2772	'''
2773	def onEditSimRange(event):
2774	'Edit simulation range'
2775	inp = [
2776	min(data[1][0]),
2777	max(data[1][0]),
2778	None
2779	]
2780	inp[2] = (inp[1] - inp[0])/(len(data[1][0])-1.)
2781	names = ('start angle', 'end angle', 'step size')
2782	dictlst = [inp] * len(inp)
2783	elemlst = range(len(inp))
2784	dlg = G2G.ScrolledMultiEditor(
2785	G2frame,[inp] * len(inp), range(len(inp)), names,
2786	header='Edit simulation range',
2787	minvals=(0.001,0.001,0.0001),
2788	maxvals=(180.,180.,.1),
2789	)
2790	dlg.CenterOnParent()
2791	val = dlg.ShowModal()
2792	dlg.Destroy()
2793	if val != wx.ID_OK: return
2794	if inp[0] > inp[1]:
2795	end,start,step = inp
2796	else:
2797	start,end,step = inp
2798	step = abs(step)
2799	N = int((end-start)/step)+1
2800	newdata = np.linspace(start,end,N,True)
2801	if len(newdata) < 2: return # too small a range - reject
2802	data[1] = [newdata,np.zeros_like(newdata),np.ones_like(newdata),
2803	np.zeros_like(newdata),np.zeros_like(newdata),np.zeros_like(newdata)]
2804	Tmin = newdata[0]
2805	Tmax = newdata[-1]
2806	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,item,'Limits'),
2807	[(Tmin,Tmax),[Tmin,Tmax]])
2808	UpdatePWHKPlot(G2frame,kind,item) # redisplay data screen
2809
2810	def OnPlot3DHKL(event):
2811	refList = data[1]['RefList']
2812	FoMax = np.max(refList.T[8+Super])
2813	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2814	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2815	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2816	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,
2817	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2818	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,
2819	'Scale':1.0,'oldxy':[],'viewDir':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
2820	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2821
2822	def OnPlotAll3DHKL(event):
2823	choices = GetPatternTreeDataNames(G2frame,['HKLF',])
2824	dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to plot',
2825	'Use data',choices)
2826	try:
2827	if dlg.ShowModal() == wx.ID_OK:
2828	refNames = [choices[i] for i in dlg.GetSelections()]
2829	else:
2830	return
2831	finally:
2832	dlg.Destroy()
2833	refList = np.zeros(0)
2834	for name in refNames:
2835	Id = GetPatternTreeItemId(G2frame,G2frame.root, name)
2836	reflData = G2frame.PatternTree.GetItemPyData(Id)[1]
2837	if len(refList):
2838	refList = np.concatenate((refList,reflData['RefList']))
2839	else:
2840	refList = reflData['RefList']
2841
2842	FoMax = np.max(refList.T[8+Super])
2843	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2844	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2845	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2846	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,
2847	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2848	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,
2849	'Scale':1.0,'oldxy':[],'viewDir':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
2850	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2851
2852
2853	def OnErrorAnalysis(event):
2854	G2plt.PlotDeltSig(G2frame,kind)
2855
2856	def OnWtFactor(event):
2857	try:
2858	val = float(wtval.GetValue())
2859	except ValueError:
2860	val = data[0]['wtFactor']
2861	data[0]['wtFactor'] = val
2862	wtval.SetValue('%.3f'%(val))
2863
2864	def OnCompression(event):
2865	data[0] = int(comp.GetValue())
2866
2867	def onCopyPlotCtrls(event):
2868	'''Respond to menu item to copy multiple sections from a histogram.
2869	Need this here to pass on the G2frame object.
2870	'''
2871	G2pdG.CopyPlotCtrls(G2frame)
2872
2873	def onCopySelectedItems(event):
2874	'''Respond to menu item to copy multiple sections from a histogram.
2875	Need this here to pass on the G2frame object.
2876	'''
2877	G2pdG.CopySelectedHistItems(G2frame)
2878
2879	data = G2frame.PatternTree.GetItemPyData(item)
2880	#patches
2881	if 'wtFactor' not in data[0]:
2882	data[0] = {'wtFactor':1.0}
2883	# if kind == 'PWDR' and 'Compression' not in data[0]:
2884	# data[0]['Compression'] = 1
2885	#if isinstance(data[1],list) and kind == 'HKLF':
2886	if 'list' in str(type(data[1])) and kind == 'HKLF':
2887	RefData = {'RefList':[],'FF':[]}
2888	for ref in data[1]:
2889	RefData['RefList'].append(ref[:11]+[ref[13],])
2890	RefData['FF'].append(ref[14])
2891	data[1] = RefData
2892	G2frame.PatternTree.SetItemPyData(item,data)
2893	#end patches
2894	if G2frame.dataDisplay:
2895	G2frame.dataDisplay.Destroy()
2896	if kind in ['PWDR','SASD']:
2897	SetDataMenuBar(G2frame,G2frame.dataFrame.PWDRMenu)
2898	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2899	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2900	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopyPlotCtrls, id=wxID_PLOTCTRLCOPY)
2901	elif kind in ['HKLF',]:
2902	SetDataMenuBar(G2frame,G2frame.dataFrame.HKLFMenu)
2903	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2904	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=wxID_PWD3DHKLPLOT)
2905	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotAll3DHKL, id=wxID_3DALLHKLPLOT)
2906	# G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2907	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
2908
2909	mainSizer = wx.BoxSizer(wx.VERTICAL)
2910	mainSizer.Add((5,5),)
2911	wtSizer = wx.BoxSizer(wx.HORIZONTAL)
2912	wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Weight factor: '),0,WACV)
2913	wtval = wx.TextCtrl(G2frame.dataDisplay,-1,'%.3f'%(data[0]['wtFactor']),style=wx.TE_PROCESS_ENTER)
2914	wtval.Bind(wx.EVT_TEXT_ENTER,OnWtFactor)
2915	wtval.Bind(wx.EVT_KILL_FOCUS,OnWtFactor)
2916	wtSizer.Add(wtval,0,WACV)
2917	# if kind == 'PWDR': #possible future compression feature; NB above patch as well
2918	# wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Compression factor: '),0,WACV)
2919	# choice = ['1','2','3','4','5','6']
2920	# comp = wx.ComboBox(parent=G2frame.dataDisplay,choices=choice,
2921	# style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2922	# comp.SetValue(str(data[0]['Compression']))
2923	# comp.Bind(wx.EVT_COMBOBOX, OnCompression)
2924	# wtSizer.Add(comp,0,WACV)
2925	mainSizer.Add(wtSizer)
2926	if data[0].get('Dummy'):
2927	simSizer = wx.BoxSizer(wx.HORIZONTAL)
2928	Tmin = min(data[1][0])
2929	Tmax = max(data[1][0])
2930	num = len(data[1][0])
2931	step = (Tmax - Tmin)/(num-1)
2932	t = u'2\u03b8' # 2theta
2933	lbl = u'Simulation range: {:.2f} to {:.2f} {:s}\nwith {:.4f} steps ({:d} points)'
2934	lbl += u'\n(Edit range resets observed intensities).'
2935	lbl = lbl.format(Tmin,Tmax,t,step,num)
2936	simSizer.Add(wx.StaticText(G2frame.dataDisplay,wx.ID_ANY,lbl),
2937	0,WACV)
2938	but = wx.Button(G2frame.dataDisplay,wx.ID_ANY,"Edit range")
2939	but.Bind(wx.EVT_BUTTON,onEditSimRange)
2940	simSizer.Add(but,0,WACV)
2941	mainSizer.Add(simSizer)
2942	if 'Nobs' in data[0]:
2943	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2944	' Data residual wR: %.3f%% on %d observations'%(data[0]['wR'],data[0]['Nobs'])))
2945	for value in data[0]:
2946	if 'Nref' in value:
2947	mainSizer.Add((5,5),)
2948	pfx = value.split('Nref')[0]
2949	name = data[0].get(pfx.split(':')[0]+'::Name','?')
2950	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For phase '+name+':'))
2951	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2952	u' Unweighted phase residuals RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2953	(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])))
2954	mainSizer.Add((5,5),)
2955	mainSizer.Layout()
2956	G2frame.dataDisplay.SetSizer(mainSizer)
2957	Size = mainSizer.Fit(G2frame.dataFrame)
2958	Size[1] += 10
2959	G2frame.dataFrame.setSizePosLeft(Size)
2960	G2frame.PatternTree.SetItemPyData(item,data)
2961	if kind in ['PWDR','SASD']:
2962	if 'xylim' in dir(G2frame):
2963	NewPlot = False
2964	else:
2965
2966	NewPlot = True
2967	G2plt.PlotPatterns(G2frame,plotType=kind,newPlot=NewPlot)
2968	elif kind == 'HKLF':
2969	Name = G2frame.PatternTree.GetItemText(item)
2970	phaseName = G2pdG.IsHistogramInAnyPhase(G2frame,Name)
2971	if phaseName:
2972	pId = GetPatternTreeItemId(G2frame,G2frame.root,'Phases')
2973	phaseId = GetPatternTreeItemId(G2frame,pId,phaseName)
2974	General = G2frame.PatternTree.GetItemPyData(phaseId)['General']
2975	Super = General.get('Super',0)
2976	SuperVec = General.get('SuperVec',[])
2977	else:
2978	Super = 0
2979	SuperVec = []
2980	refList = data[1]['RefList']
2981	FoMax = np.max(refList.T[5+data[1].get('Super',0)])
2982	page = G2frame.G2plotNB.nb.GetSelection()
2983	tab = ''
2984	if page >= 0:
2985	tab = G2frame.G2plotNB.nb.GetPageText(page)
2986	if '3D' in tab:
2987	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2988	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2989	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2990	Page = G2frame.G2plotNB.nb.GetPage(page)
2991	controls = Page.controls
2992	G2plt.Plot3DSngl(G2frame,newPlot=False,Data=controls,hklRef=refList,Title=phaseName)
2993	else:
2994	controls = {'Type' : 'Fo','ifFc' : True,
2995	'HKLmax' : [int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))],
2996	'HKLmin' : [int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))],
2997	'FoMax' : FoMax,'Zone' : '001','Layer' : 0,'Scale' : 1.0,'Super':Super,'SuperVec':SuperVec}
2998	G2plt.PlotSngl(G2frame,newPlot=True,Data=controls,hklRef=refList)
2999
3000	################################################################################
3001	##### Pattern tree routines
3002	################################################################################
3003
3004	def GetPatternTreeDataNames(G2frame,dataTypes):
3005	'''Needs a doc string
3006	'''
3007	names = []
3008	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3009	while item:
3010	name = G2frame.PatternTree.GetItemText(item)
3011	if name[:4] in dataTypes:
3012	names.append(name)
3013	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3014	return names
3015
3016	def GetPatternTreeItemId(G2frame, parentId, itemText):
3017	'''Needs a doc string
3018	'''
3019	item, cookie = G2frame.PatternTree.GetFirstChild(parentId)
3020	while item:
3021	if G2frame.PatternTree.GetItemText(item) == itemText:
3022	return item
3023	item, cookie = G2frame.PatternTree.GetNextChild(parentId, cookie)
3024	return 0
3025
3026	def MovePatternTreeToGrid(G2frame,item):
3027	'''Called from GSASII.OnPatternTreeSelChanged when a item is selected on the tree
3028	'''
3029	pickName = G2frame.PatternTree.GetItemText(item)
3030	if G2frame.PickIdText == pickName:
3031	return
3032
3033	oldPage = None # will be set later if already on a Phase item
3034	if G2frame.dataFrame:
3035	SetDataMenuBar(G2frame)
3036	if G2frame.dataFrame.GetLabel() == 'Comments':
3037	try:
3038	data = [G2frame.dataDisplay.GetValue()]
3039	G2frame.dataDisplay.Clear()
3040	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Comments')
3041	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3042	except: #clumsy but avoids dead window problem when opening another project
3043	pass
3044	elif G2frame.dataFrame.GetLabel() == 'Notebook':
3045	try:
3046	data = [G2frame.dataDisplay.GetValue()]
3047	G2frame.dataDisplay.Clear()
3048	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Notebook')
3049	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3050	except: #clumsy but avoids dead window problem when opening another project
3051	pass
3052	elif 'Phase Data for' in G2frame.dataFrame.GetLabel():
3053	if G2frame.dataDisplay:
3054	oldPage = G2frame.dataDisplay.GetSelection()
3055	G2frame.dataFrame.Clear()
3056	G2frame.dataFrame.SetLabel('')
3057	else:
3058	#create the frame for the data item window
3059	G2frame.dataFrame = DataFrame(parent=G2frame.mainPanel,frame=G2frame)
3060	G2frame.dataFrame.PhaseUserSize = None
3061
3062	G2frame.dataFrame.Raise()
3063	G2frame.PickId = item
3064	G2frame.PickIdText = None
3065	parentID = G2frame.root
3066	#for i in G2frame.ExportPattern: i.Enable(False)
3067	defWid = [250,150]
3068	if item != G2frame.root:
3069	parentID = G2frame.PatternTree.GetItemParent(item)
3070	if G2frame.PatternTree.GetItemParent(item) == G2frame.root:
3071	G2frame.PatternId = item
3072	if G2frame.PatternTree.GetItemText(item) == 'Notebook':
3073	SetDataMenuBar(G2frame,G2frame.dataFrame.DataNotebookMenu)
3074	G2frame.PatternId = 0
3075	#for i in G2frame.ExportPattern: i.Enable(False)
3076	data = G2frame.PatternTree.GetItemPyData(item)
3077	UpdateNotebook(G2frame,data)
3078	elif G2frame.PatternTree.GetItemText(item) == 'Controls':
3079	G2frame.PatternId = 0
3080	#for i in G2frame.ExportPattern: i.Enable(False)
3081	data = G2frame.PatternTree.GetItemPyData(item)
3082	if not data: #fill in defaults
3083	data = copy.copy(G2obj.DefaultControls) #least squares controls
3084	G2frame.PatternTree.SetItemPyData(item,data)
3085	for i in G2frame.Refine: i.Enable(True)
3086	G2frame.EnableSeqRefineMenu()
3087	UpdateControls(G2frame,data)
3088	elif G2frame.PatternTree.GetItemText(item) == 'Sequential results':
3089	data = G2frame.PatternTree.GetItemPyData(item)
3090	UpdateSeqResults(G2frame,data)
3091	elif G2frame.PatternTree.GetItemText(item) == 'Covariance':
3092	data = G2frame.PatternTree.GetItemPyData(item)
3093	G2frame.dataFrame.setSizePosLeft(defWid)
3094	text = ''
3095	if 'Rvals' in data:
3096	Nvars = len(data['varyList'])
3097	Rvals = data['Rvals']
3098	text = '\nFinal residuals: \nwR = %.3f%% \nchi**2 = %.1f \nGOF = %.2f'%(Rvals['Rwp'],Rvals['chisq'],Rvals['GOF'])
3099	text += '\nNobs = %d \nNvals = %d'%(Rvals['Nobs'],Nvars)
3100	if 'lamMax' in Rvals:
3101	text += '\nlog10 MaxLambda = %.1f'%(np.log10(Rvals['lamMax']))
3102	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3103	value='See plot window for covariance display'+text,style=wx.TE_MULTILINE)
3104	G2plt.PlotCovariance(G2frame,data)
3105	elif G2frame.PatternTree.GetItemText(item) == 'Constraints':
3106	data = G2frame.PatternTree.GetItemPyData(item)
3107	G2cnstG.UpdateConstraints(G2frame,data)
3108	elif G2frame.PatternTree.GetItemText(item) == 'Rigid bodies':
3109	data = G2frame.PatternTree.GetItemPyData(item)
3110	G2cnstG.UpdateRigidBodies(G2frame,data)
3111	elif G2frame.PatternTree.GetItemText(item) == 'Restraints':
3112	data = G2frame.PatternTree.GetItemPyData(item)
3113	Phases = G2frame.GetPhaseData()
3114	phase = ''
3115	phaseName = ''
3116	if Phases:
3117	phaseName = Phases.keys()[0]
3118	G2frame.dataFrame.setSizePosLeft(defWid)
3119	G2restG.UpdateRestraints(G2frame,data,Phases,phaseName)
3120	elif 'IMG' in G2frame.PatternTree.GetItemText(item):
3121	G2frame.Image = item
3122	G2frame.dataFrame.SetTitle('Image Data')
3123	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId( \
3124	G2frame,item,'Image Controls'))
3125	G2imG.UpdateImageData(G2frame,data)
3126	G2plt.PlotImage(G2frame,newPlot=True)
3127	elif 'PKS' in G2frame.PatternTree.GetItemText(item):
3128	G2plt.PlotPowderLines(G2frame)
3129	elif 'PWDR' in G2frame.PatternTree.GetItemText(item):
3130	#for i in G2frame.ExportPattern: i.Enable(True)
3131	if G2frame.EnablePlot:
3132	UpdatePWHKPlot(G2frame,'PWDR',item)
3133	elif 'SASD' in G2frame.PatternTree.GetItemText(item):
3134	#for i in G2frame.ExportPattern: i.Enable(True)
3135	if G2frame.EnablePlot:
3136	UpdatePWHKPlot(G2frame,'SASD',item)
3137	elif 'HKLF' in G2frame.PatternTree.GetItemText(item):
3138	G2frame.Sngl = True
3139	UpdatePWHKPlot(G2frame,'HKLF',item)
3140	elif 'PDF' in G2frame.PatternTree.GetItemText(item):
3141	G2frame.PatternId = item
3142	for i in G2frame.ExportPDF: i.Enable(True)
3143	G2plt.PlotISFG(G2frame,type='S(Q)')
3144	elif G2frame.PatternTree.GetItemText(item) == 'Phases':
3145	G2frame.dataFrame.setSizePosLeft(defWid)
3146	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3147	value='Select one phase to see its parameters')
3148	elif 'I(Q)' in G2frame.PatternTree.GetItemText(item):
3149	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3150	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3151	G2pdG.UpdatePDFGrid(G2frame,data)
3152	G2plt.PlotISFG(G2frame,type='I(Q)',newPlot=True)
3153	elif 'S(Q)' in G2frame.PatternTree.GetItemText(item):
3154	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3155	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3156	G2pdG.UpdatePDFGrid(G2frame,data)
3157	G2plt.PlotISFG(G2frame,type='S(Q)',newPlot=True)
3158	elif 'F(Q)' in G2frame.PatternTree.GetItemText(item):
3159	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3160	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3161	G2pdG.UpdatePDFGrid(G2frame,data)
3162	G2plt.PlotISFG(G2frame,type='F(Q)',newPlot=True)
3163	elif 'G(R)' in G2frame.PatternTree.GetItemText(item):
3164	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3165	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3166	G2pdG.UpdatePDFGrid(G2frame,data)
3167	G2plt.PlotISFG(G2frame,type='G(R)',newPlot=True)
3168	elif G2frame.PatternTree.GetItemText(parentID) == 'Phases':
3169	data = G2frame.PatternTree.GetItemPyData(item)
3170	G2phG.UpdatePhaseData(G2frame,item,data,oldPage)
3171	elif G2frame.PatternTree.GetItemText(item) == 'Comments':
3172	SetDataMenuBar(G2frame,G2frame.dataFrame.DataCommentsMenu)
3173	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3174	data = G2frame.PatternTree.GetItemPyData(item)
3175	UpdateComments(G2frame,data)
3176	elif G2frame.PatternTree.GetItemText(item) == 'Image Controls':
3177	G2frame.dataFrame.SetTitle('Image Controls')
3178	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3179	masks = G2frame.PatternTree.GetItemPyData(
3180	GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3181	data = G2frame.PatternTree.GetItemPyData(item)
3182	G2imG.UpdateImageControls(G2frame,data,masks)
3183	G2plt.PlotImage(G2frame)
3184	elif G2frame.PatternTree.GetItemText(item) == 'Masks':
3185	G2frame.dataFrame.SetTitle('Masks')
3186	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3187	data = G2frame.PatternTree.GetItemPyData(item)
3188	G2imG.UpdateMasks(G2frame,data)
3189	G2plt.PlotImage(G2frame)
3190	elif G2frame.PatternTree.GetItemText(item) == 'Stress/Strain':
3191	G2frame.dataFrame.SetTitle('Stress/Strain')
3192	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3193	data = G2frame.PatternTree.GetItemPyData(item)
3194	G2plt.PlotImage(G2frame)
3195	G2plt.PlotStrain(G2frame,data,newPlot=True)
3196	G2imG.UpdateStressStrain(G2frame,data)
3197	elif G2frame.PatternTree.GetItemText(item) == 'PDF Controls':
3198	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3199	for i in G2frame.ExportPDF: i.Enable(True)
3200	data = G2frame.PatternTree.GetItemPyData(item)
3201	G2pdG.UpdatePDFGrid(G2frame,data)
3202	G2plt.PlotISFG(G2frame,type='I(Q)')
3203	G2plt.PlotISFG(G2frame,type='S(Q)')
3204	G2plt.PlotISFG(G2frame,type='F(Q)')
3205	G2plt.PlotISFG(G2frame,type='G(R)')
3206	elif G2frame.PatternTree.GetItemText(item) == 'Peak List':
3207	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3208	for i in G2frame.ExportPeakList: i.Enable(True)
3209	data = G2frame.PatternTree.GetItemPyData(item)
3210	#patch
3211	if 'list' in str(type(data)):
3212	data = {'peaks':data,'sigDict':{}}
3213	G2frame.PatternTree.SetItemPyData(item,data)
3214	#end patch
3215	G2pdG.UpdatePeakGrid(G2frame,data)
3216	G2plt.PlotPatterns(G2frame)
3217	elif G2frame.PatternTree.GetItemText(item) == 'Background':
3218	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3219	data = G2frame.PatternTree.GetItemPyData(item)
3220	G2pdG.UpdateBackground(G2frame,data)
3221	G2plt.PlotPatterns(G2frame)
3222	elif G2frame.PatternTree.GetItemText(item) == 'Limits':
3223	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3224	datatype = G2frame.PatternTree.GetItemText(G2frame.PatternId)[:4]
3225	data = G2frame.PatternTree.GetItemPyData(item)
3226	G2pdG.UpdateLimitsGrid(G2frame,data,datatype)
3227	G2plt.PlotPatterns(G2frame,plotType=datatype)
3228	elif G2frame.PatternTree.GetItemText(item) == 'Instrument Parameters':
3229	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3230	data = G2frame.PatternTree.GetItemPyData(item)[0]
3231	G2pdG.UpdateInstrumentGrid(G2frame,data)
3232	if 'P' in data['Type'][0]: #powder data only
3233	G2plt.PlotPeakWidths(G2frame)
3234	elif G2frame.PatternTree.GetItemText(item) == 'Models':
3235	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3236	data = G2frame.PatternTree.GetItemPyData(item)
3237	G2pdG.UpdateModelsGrid(G2frame,data)
3238	G2plt.PlotPatterns(G2frame,plotType='SASD')
3239	if len(data['Size']['Distribution']):
3240	G2plt.PlotSASDSizeDist(G2frame)
3241	elif G2frame.PatternTree.GetItemText(item) == 'Substances':
3242	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3243	data = G2frame.PatternTree.GetItemPyData(item)
3244	G2pdG.UpdateSubstanceGrid(G2frame,data)
3245	elif G2frame.PatternTree.GetItemText(item) == 'Sample Parameters':
3246	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3247	data = G2frame.PatternTree.GetItemPyData(item)
3248	datatype = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[2][:4]
3249
3250	if 'Temperature' not in data: #temp fix for old gpx files
3251	data = {'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],'DisplaceX':[0.0,False],
3252	'DisplaceY':[0.0,False],'Diffuse':[],'Temperature':300.,'Pressure':1.0,
3253	'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
3254	'Gonio. radius':200.0}
3255	G2frame.PatternTree.SetItemPyData(item,data)
3256
3257	G2pdG.UpdateSampleGrid(G2frame,data)
3258	G2plt.PlotPatterns(G2frame,plotType=datatype)
3259	elif G2frame.PatternTree.GetItemText(item) == 'Index Peak List':
3260	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3261	for i in G2frame.ExportPeakList: i.Enable(True)
3262	data = G2frame.PatternTree.GetItemPyData(item)
3263	#patch
3264	if len(data) != 2:
3265	data = [data,[]]
3266	G2frame.PatternTree.SetItemPyData(item,data)
3267	#end patch
3268	G2pdG.UpdateIndexPeaksGrid(G2frame,data)
3269	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3270	G2plt.PlotPowderLines(G2frame)
3271	else:
3272	G2plt.PlotPatterns(G2frame)
3273	elif G2frame.PatternTree.GetItemText(item) == 'Unit Cells List':
3274	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3275	data = G2frame.PatternTree.GetItemPyData(item)
3276	if not data:
3277	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
3278	data.append([0,0,0,0,0,0,0,0,0,0,0,0,0,0]) #Bravais lattice flags
3279	data.append([]) #empty cell list
3280	data.append([]) #empty dmin
3281	data.append({}) #empty superlattice stuff
3282	G2frame.PatternTree.SetItemPyData(item,data)
3283	#patch
3284	if len(data) < 5:
3285	data.append({'Use':False,'ModVec':[0,0,0.1],'maxH':1,'ssSymb':''}) #empty superlattice stuff
3286	G2frame.PatternTree.SetItemPyData(item,data)
3287	#end patch
3288	G2pdG.UpdateUnitCellsGrid(G2frame,data)
3289	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3290	G2plt.PlotPowderLines(G2frame)
3291	else:
3292	G2plt.PlotPatterns(G2frame)
3293	elif G2frame.PatternTree.GetItemText(item) == 'Reflection Lists': #powder reflections
3294	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3295	data = G2frame.PatternTree.GetItemPyData(item)
3296	G2frame.RefList = ''
3297	if len(data):
3298	G2frame.RefList = data.keys()[0]
3299	G2pdG.UpdateReflectionGrid(G2frame,data)
3300	G2plt.PlotPatterns(G2frame)
3301	elif G2frame.PatternTree.GetItemText(item) == 'Reflection List': #HKLF reflections
3302	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3303	name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
3304	data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
3305	G2pdG.UpdateReflectionGrid(G2frame,data,HKLF=True,Name=name)
3306
3307	if G2frame.PickId:
3308	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
3309	G2frame.dataFrame.Raise()
3310
3311	def SetDataMenuBar(G2frame,menu=None):
3312	'''Set the menu for the data frame. On the Mac put this
3313	menu for the data tree window instead.
3314
3315	Note that data frame items do not have menus, for these (menu=None)
3316	display a blank menu or on the Mac display the standard menu for
3317	the data tree window.
3318	'''
3319	if sys.platform == "darwin":
3320	if menu is None:
3321	G2frame.SetMenuBar(G2frame.GSASIIMenu)
3322	else:
3323	G2frame.SetMenuBar(menu)
3324	else:
3325	if menu is None:
3326	G2frame.dataFrame.SetMenuBar(G2frame.dataFrame.BlankMenu)
3327	else:
3328	G2frame.dataFrame.SetMenuBar(menu)
3329
3330	def HowDidIgetHere():
3331	'''Show a traceback with calls that brought us to the current location.
3332	Used for debugging.
3333	'''
3334	import traceback
3335	print 70''
3336	for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip.rstrip())
3337	print 70''
3338

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