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source: trunk/GSASIIgrid.py @ 2116

Last change on this file since 2116 was 2116, checked in by vondreele, 7 years ago
change error message about 'X' space groups! add Transform stub in General Compute menu - see bottom of General stuff in G2phsGUI
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1	# -- coding: utf-8 --
2	#GSASIIgrid - data display routines
3	########### SVN repository information ###################
4	# $Date: 2016-01-07 18:40:19 +0000 (Thu, 07 Jan 2016) $
5	# $Author: vondreele $
6	# $Revision: 2116 $
7	# $URL: trunk/GSASIIgrid.py $
8	# $Id: GSASIIgrid.py 2116 2016-01-07 18:40:19Z 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: 2116 $")
30	import GSASIImath as G2mth
31	import GSASIIIO as G2IO
32	import GSASIIstrIO as G2stIO
33	import GSASIIlattice as G2lat
34	import GSASIIplot as G2plt
35	import GSASIIpwdGUI as G2pdG
36	import GSASIIimgGUI as G2imG
37	import GSASIIphsGUI as G2phG
38	import GSASIIspc as G2spc
39	import GSASIImapvars as G2mv
40	import GSASIIconstrGUI as G2cnstG
41	import GSASIIrestrGUI as G2restG
42	import GSASIIpy3 as G2py3
43	import GSASIIobj as G2obj
44	import GSASIIexprGUI as G2exG
45	import GSASIIlog as log
46	import GSASIIctrls as G2G
47
48	# trig functions in degrees
49	sind = lambda x: np.sin(x*np.pi/180.)
50	tand = lambda x: np.tan(x*np.pi/180.)
51	cosd = lambda x: np.cos(x*np.pi/180.)
52
53	# Define a short name for convenience
54	WACV = wx.ALIGN_CENTER_VERTICAL
55
56	[ wxID_FOURCALC, wxID_FOURSEARCH, wxID_FOURCLEAR, wxID_PEAKSMOVE, wxID_PEAKSCLEAR,
57	wxID_CHARGEFLIP, wxID_PEAKSUNIQUE, wxID_PEAKSDELETE, wxID_PEAKSDA,
58	wxID_PEAKSDISTVP, wxID_PEAKSVIEWPT, wxID_FINDEQVPEAKS,wxID_SHOWBONDS,wxID_MULTIMCSA,
59	wxID_SINGLEMCSA,wxID_4DCHARGEFLIP,wxID_TRANSFORMSTRUCTURE,
60	] = [wx.NewId() for item in range(17)]
61
62	[ wxID_PWDRADD, wxID_HKLFADD, wxID_PWDANALYSIS, wxID_PWDCOPY, wxID_PLOTCTRLCOPY,
63	wxID_DATADELETE,wxID_DATACOPY,wxID_DATACOPYFLAGS,wxID_DATASELCOPY,
64	] = [wx.NewId() for item in range(9)]
65
66	[ wxID_ATOMSEDITADD, wxID_ATOMSEDITINSERT, wxID_ATOMSEDITDELETE, wxID_ATOMSREFINE,
67	wxID_ATOMSMODIFY, wxID_ATOMSTRANSFORM, wxID_ATOMSVIEWADD, wxID_ATOMVIEWINSERT,
68	wxID_RELOADDRAWATOMS,wxID_ATOMSDISAGL,wxID_ATOMMOVE,wxID_MAKEMOLECULE,
69	wxID_ASSIGNATMS2RB,wxID_ATOMSPDISAGL, wxID_ISODISP,wxID_ADDHATOM,wxID_UPDATEHATOM,
70	wxID_WAVEVARY,
71	] = [wx.NewId() for item in range(18)]
72
73	[ wxID_DRAWATOMSTYLE, wxID_DRAWATOMLABEL, wxID_DRAWATOMCOLOR, wxID_DRAWATOMRESETCOLOR,
74	wxID_DRAWVIEWPOINT, wxID_DRAWTRANSFORM, wxID_DRAWDELETE, wxID_DRAWFILLCELL,
75	wxID_DRAWADDEQUIV, wxID_DRAWFILLCOORD, wxID_DRAWDISAGLTOR, wxID_DRAWPLANE,
76	wxID_DRAWDISTVP,
77	] = [wx.NewId() for item in range(13)]
78
79	[ wxID_DRAWRESTRBOND, wxID_DRAWRESTRANGLE, wxID_DRAWRESTRPLANE, wxID_DRAWRESTRCHIRAL,
80	] = [wx.NewId() for item in range(4)]
81
82	[ wxID_ADDMCSAATOM,wxID_ADDMCSARB,wxID_CLEARMCSARB,wxID_MOVEMCSA,wxID_MCSACLEARRESULTS,
83	] = [wx.NewId() for item in range(5)]
84
85	[ wxID_CLEARTEXTURE,wxID_REFINETEXTURE,
86	] = [wx.NewId() for item in range(2)]
87
88	[ wxID_PAWLEYLOAD, wxID_PAWLEYESTIMATE, wxID_PAWLEYUPDATE,
89	] = [wx.NewId() for item in range(3)]
90
91	[ wxID_IMCALIBRATE,wxID_IMRECALIBRATE,wxID_IMINTEGRATE, wxID_IMCLEARCALIB,
92	wxID_IMCOPYCONTROLS, wxID_INTEGRATEALL, wxID_IMSAVECONTROLS, wxID_IMLOADCONTROLS, wxID_IMAUTOINTEG,
93	] = [wx.NewId() for item in range(9)]
94
95	[ wxID_MASKCOPY, wxID_MASKSAVE, wxID_MASKLOAD, wxID_NEWMASKSPOT,wxID_NEWMASKARC,wxID_NEWMASKRING,
96	wxID_NEWMASKFRAME, wxID_NEWMASKPOLY, wxID_MASKLOADNOT,
97	] = [wx.NewId() for item in range(9)]
98
99	[ wxID_STRSTACOPY, wxID_STRSTAFIT, wxID_STRSTASAVE, wxID_STRSTALOAD,wxID_STRSTSAMPLE,
100	wxID_APPENDDZERO,wxID_STRSTAALLFIT,wxID_UPDATEDZERO,
101	] = [wx.NewId() for item in range(8)]
102
103	[ wxID_BACKCOPY,wxID_LIMITCOPY, wxID_SAMPLECOPY, wxID_SAMPLECOPYSOME, wxID_BACKFLAGCOPY, wxID_SAMPLEFLAGCOPY,
104	wxID_SAMPLESAVE, wxID_SAMPLELOAD,wxID_ADDEXCLREGION,wxID_SETSCALE,wxID_SAMPLE1VAL,wxID_ALLSAMPLELOAD,
105	] = [wx.NewId() for item in range(12)]
106
107	[ wxID_INSTPRMRESET,wxID_CHANGEWAVETYPE,wxID_INSTCOPY, wxID_INSTFLAGCOPY, wxID_INSTLOAD,
108	wxID_INSTSAVE, wxID_INST1VAL, wxID_INSTCALIB,
109	] = [wx.NewId() for item in range(8)]
110
111	[ wxID_UNDO,wxID_LSQPEAKFIT,wxID_LSQONECYCLE,wxID_RESETSIGGAM,wxID_CLEARPEAKS,wxID_AUTOSEARCH,
112	wxID_PEAKSCOPY, wxID_SEQPEAKFIT,
113	] = [wx.NewId() for item in range(8)]
114
115	[ wxID_INDXRELOAD, wxID_INDEXPEAKS, wxID_REFINECELL, wxID_COPYCELL, wxID_MAKENEWPHASE,
116	wxID_EXPORTCELLS,
117	] = [wx.NewId() for item in range(6)]
118
119	[ wxID_CONSTRAINTADD,wxID_EQUIVADD,wxID_HOLDADD,wxID_FUNCTADD,wxID_ADDRIDING,
120	wxID_CONSPHASE, wxID_CONSHIST, wxID_CONSHAP, wxID_CONSGLOBAL,wxID_EQUIVALANCEATOMS,
121	] = [wx.NewId() for item in range(10)]
122
123	[ wxID_RESTRAINTADD, wxID_RESTSELPHASE,wxID_RESTDELETE, wxID_RESRCHANGEVAL,
124	wxID_RESTCHANGEESD,wxID_AARESTRAINTADD,wxID_AARESTRAINTPLOT,
125	] = [wx.NewId() for item in range(7)]
126
127	[ wxID_RIGIDBODYADD,wxID_DRAWDEFINERB,wxID_RIGIDBODYIMPORT,wxID_RESIDUETORSSEQ,
128	wxID_AUTOFINDRESRB,wxID_GLOBALRESREFINE,wxID_RBREMOVEALL,wxID_COPYRBPARMS,
129	wxID_GLOBALTHERM,wxID_VECTORBODYADD
130	] = [wx.NewId() for item in range(10)]
131
132	[ wxID_RENAMESEQSEL,wxID_SAVESEQSEL,wxID_SAVESEQSELCSV,wxID_SAVESEQCSV,wxID_PLOTSEQSEL,
133	wxID_ORGSEQSEL,wxADDSEQVAR,wxDELSEQVAR,wxEDITSEQVAR,wxCOPYPARFIT,wxID_AVESEQSEL,
134	wxADDPARFIT,wxDELPARFIT,wxEDITPARFIT,wxDOPARFIT,
135	] = [wx.NewId() for item in range(15)]
136
137	[ wxID_MODELCOPY,wxID_MODELFIT,wxID_MODELADD,wxID_ELEMENTADD,wxID_ELEMENTDELETE,
138	wxID_ADDSUBSTANCE,wxID_LOADSUBSTANCE,wxID_DELETESUBSTANCE,wxID_COPYSUBSTANCE,
139	wxID_MODELUNDO,wxID_MODELFITALL,wxID_MODELCOPYFLAGS,
140	] = [wx.NewId() for item in range(12)]
141
142	[ wxID_SELECTPHASE,wxID_PWDHKLPLOT,wxID_PWD3DHKLPLOT,wxID_3DALLHKLPLOT,
143	] = [wx.NewId() for item in range(4)]
144
145	[ wxID_PDFCOPYCONTROLS, wxID_PDFSAVECONTROLS, wxID_PDFLOADCONTROLS,
146	wxID_PDFCOMPUTE, wxID_PDFCOMPUTEALL, wxID_PDFADDELEMENT, wxID_PDFDELELEMENT,
147	] = [wx.NewId() for item in range(7)]
148
149	[ wxID_MCRON,wxID_MCRLIST,wxID_MCRSAVE,wxID_MCRPLAY,
150	] = [wx.NewId() for item in range(4)]
151
152	VERY_LIGHT_GREY = wx.Colour(235,235,235)
153
154	# Aliases for Classes/Functions moved to GSASIIctrls, all should be tracked down but leaving as a reminder
155	#SingleFloatDialog = G2G.SingleFloatDialog
156	#SingleStringDialog = G2G.SingleStringDialog
157	#MultiStringDialog = G2G.MultiStringDialog
158	#G2ColumnIDDialog = G2G.G2ColumnIDDialog
159	#ItemSelector = G2G.ItemSelector
160	#HorizontalLine = G2G.HorizontalLine
161	#G2LoggedButton = G2G.G2LoggedButton
162	#EnumSelector = G2G.EnumSelector
163	#G2ChoiceButton = G2G.G2ChoiceButton
164	#GSGrid = G2G.GSGrid
165	#Table = G2G.Table
166	#GridFractionEditor = G2G.GridFractionEditor
167	#GSNoteBook = G2G.GSNoteBook
168
169	# Should SGMessageBox, SymOpDialog, DisAglDialog be moved?
170
171	################################################################################
172	#### GSAS-II class definitions
173	################################################################################
174
175	class SGMessageBox(wx.Dialog):
176	''' Special version of MessageBox that displays space group & super space group text
177	in two blocks
178	'''
179	def __init__(self,parent,title,text,table,):
180	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,pos=wx.DefaultPosition,
181	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
182	self.text=text
183	self.table = table
184	self.panel = wx.Panel(self)
185	mainSizer = wx.BoxSizer(wx.VERTICAL)
186	mainSizer.Add((0,10))
187	for line in text:
188	mainSizer.Add(wx.StaticText(self.panel,label=' %s '%(line)),0,WACV)
189	ncol = self.table[0].count(',')+1
190	tableSizer = wx.FlexGridSizer(0,2*ncol+3,0,0)
191	for j,item in enumerate(self.table):
192	num,flds = item.split(')')
193	tableSizer.Add(wx.StaticText(self.panel,label=' %s '%(num+')')),0,WACV\|wx.ALIGN_LEFT)
194	flds = flds.replace(' ','').split(',')
195	for i,fld in enumerate(flds):
196	if i < ncol-1:
197	tableSizer.Add(wx.StaticText(self.panel,label='%s, '%(fld)),0,WACV\|wx.ALIGN_RIGHT)
198	else:
199	tableSizer.Add(wx.StaticText(self.panel,label='%s'%(fld)),0,WACV\|wx.ALIGN_RIGHT)
200	if not j%2:
201	tableSizer.Add((20,0))
202	mainSizer.Add(tableSizer,0,wx.ALIGN_LEFT)
203	btnsizer = wx.StdDialogButtonSizer()
204	OKbtn = wx.Button(self.panel, wx.ID_OK)
205	OKbtn.SetDefault()
206	btnsizer.AddButton(OKbtn)
207	btnsizer.Realize()
208	mainSizer.Add((0,10))
209	mainSizer.Add(btnsizer,0,wx.ALIGN_CENTER)
210	self.panel.SetSizer(mainSizer)
211	self.panel.Fit()
212	self.Fit()
213	size = self.GetSize()
214	self.SetSize([size[0]+20,size[1]])
215
216	def Show(self):
217	'''Use this method after creating the dialog to post it
218	'''
219	self.ShowModal()
220	return
221
222	################################################################################
223	class SymOpDialog(wx.Dialog):
224	'''Class to select a symmetry operator
225	'''
226	def __init__(self,parent,SGData,New=True,ForceUnit=False):
227	wx.Dialog.__init__(self,parent,-1,'Select symmetry operator',
228	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
229	panel = wx.Panel(self)
230	self.SGData = SGData
231	self.New = New
232	self.Force = ForceUnit
233	self.OpSelected = [0,0,0,[0,0,0],False,False]
234	mainSizer = wx.BoxSizer(wx.VERTICAL)
235	if ForceUnit:
236	choice = ['No','Yes']
237	self.force = wx.RadioBox(panel,-1,'Force to unit cell?',choices=choice)
238	self.force.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
239	mainSizer.Add(self.force,0,WACV\|wx.TOP,5)
240	# if SGData['SGInv']:
241	choice = ['No','Yes']
242	self.inv = wx.RadioBox(panel,-1,'Choose inversion?',choices=choice)
243	self.inv.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
244	mainSizer.Add(self.inv,0,WACV)
245	if SGData['SGLatt'] != 'P':
246	LattOp = G2spc.Latt2text(SGData['SGLatt']).split(';')
247	self.latt = wx.RadioBox(panel,-1,'Choose cell centering?',choices=LattOp)
248	self.latt.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
249	mainSizer.Add(self.latt,0,WACV)
250	if SGData['SGLaue'] in ['-1','2/m','mmm','4/m','4/mmm']:
251	Ncol = 2
252	else:
253	Ncol = 3
254	OpList = []
255	for Opr in SGData['SGOps']:
256	OpList.append(G2spc.MT2text(Opr))
257	self.oprs = wx.RadioBox(panel,-1,'Choose space group operator?',choices=OpList,
258	majorDimension=Ncol)
259	self.oprs.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
260	mainSizer.Add(self.oprs,0,WACV\|wx.BOTTOM,5)
261	mainSizer.Add(wx.StaticText(panel,-1," Choose unit cell?"),0,WACV)
262	cellSizer = wx.BoxSizer(wx.HORIZONTAL)
263	cellName = ['X','Y','Z']
264	self.cell = []
265	for i in range(3):
266	self.cell.append(wx.SpinCtrl(panel,-1,cellName[i],size=wx.Size(50,20)))
267	self.cell[-1].SetRange(-3,3)
268	self.cell[-1].SetValue(0)
269	self.cell[-1].Bind(wx.EVT_SPINCTRL, self.OnOpSelect)
270	cellSizer.Add(self.cell[-1],0,WACV)
271	mainSizer.Add(cellSizer,0,WACV\|wx.BOTTOM,5)
272	if self.New:
273	choice = ['No','Yes']
274	self.new = wx.RadioBox(panel,-1,'Generate new positions?',choices=choice)
275	self.new.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
276	mainSizer.Add(self.new,0,WACV)
277
278	OkBtn = wx.Button(panel,-1,"Ok")
279	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
280	cancelBtn = wx.Button(panel,-1,"Cancel")
281	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
282	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
283	btnSizer.Add((20,20),1)
284	btnSizer.Add(OkBtn)
285	btnSizer.Add((20,20),1)
286	btnSizer.Add(cancelBtn)
287	btnSizer.Add((20,20),1)
288
289	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
290	panel.SetSizer(mainSizer)
291	panel.Fit()
292	self.Fit()
293
294	def OnOpSelect(self,event):
295	# if self.SGData['SGInv']:
296	self.OpSelected[0] = self.inv.GetSelection()
297	if self.SGData['SGLatt'] != 'P':
298	self.OpSelected[1] = self.latt.GetSelection()
299	self.OpSelected[2] = self.oprs.GetSelection()
300	for i in range(3):
301	self.OpSelected[3][i] = float(self.cell[i].GetValue())
302	if self.New:
303	self.OpSelected[4] = self.new.GetSelection()
304	if self.Force:
305	self.OpSelected[5] = self.force.GetSelection()
306
307	def GetSelection(self):
308	return self.OpSelected
309
310	def OnOk(self,event):
311	parent = self.GetParent()
312	parent.Raise()
313	self.EndModal(wx.ID_OK)
314
315	def OnCancel(self,event):
316	parent = self.GetParent()
317	parent.Raise()
318	self.EndModal(wx.ID_CANCEL)
319
320	################################################################################
321	class AddHatomDialog(wx.Dialog):
322	'''H atom addition dialog. After :meth:`ShowModal` returns, the results
323	are found in dict :attr:`self.data`, which is accessed using :meth:`GetData`.
324
325	:param wx.Frame parent: reference to parent frame (or None)
326	:param dict Neigh: a dict of atom names with list of atom name, dist pairs for neighboring atoms
327	:param dict phase: a dict containing the phase as defined by
328	:ref:`Phase Tree Item <Phase_table>`
329	'''
330	def __init__(self,parent,Neigh,phase):
331	wx.Dialog.__init__(self,parent,wx.ID_ANY,'H atom add',
332	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
333	self.panel = wxscroll.ScrolledPanel(self) #just a dummy - gets destroyed in Draw!
334	self.Neigh = Neigh
335	self.phase = phase
336	self.Hatoms = []
337	self.Draw(self.Neigh,self.phase)
338
339	def Draw(self,Neigh,phase):
340	'''Creates the contents of the dialog. Normally called
341	by :meth:`__init__`.
342	'''
343	def OnHSelect(event):
344	Obj = event.GetEventObject()
345	item,i = Indx[Obj.GetId()]
346	for obj in Indx[item]:
347	obj.SetValue(False)
348	Obj.SetValue(True)
349	self.Neigh[item][2] = i
350
351	def OnBond(event):
352	Obj = event.GetEventObject()
353	inei,ibond = Indx[Obj.GetId()]
354	self.Neigh[inei][1][0][ibond][2] = Obj.GetValue()
355
356	self.panel.Destroy()
357	self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE)
358	mainSizer = wx.BoxSizer(wx.VERTICAL)
359	mainSizer.Add(wx.StaticText(self.panel,-1,'H atom add controls for phase %s:'%(phase['General']['Name'])),
360	0,wx.LEFT\|wx.TOP,10)
361	mainSizer.Add(wx.StaticText(self.panel,-1,'NB: Check selections as they may not be correct'),0,WACV\|wx.LEFT,10)
362	mainSizer.Add(wx.StaticText(self.panel,-1," Atom: Add # H's Use: Neighbors, dist"),0,wx.TOP\|wx.LEFT,5)
363	nHatms = ['0','1','2','3']
364	dataSizer = wx.FlexGridSizer(0,3,0,0)
365	Indx = {}
366	for inei,neigh in enumerate(Neigh):
367	dataSizer.Add(wx.StaticText(self.panel,-1,' %s: '%(neigh[0])),0,WACV)
368	nH = 1 #for O atom
369	if 'C' in neigh[0] or 'N' in neigh[0]:
370	nH = 4-len(neigh[1][0])
371	checks = wx.BoxSizer(wx.HORIZONTAL)
372	Ids = []
373	for i in range(nH+1):
374	nHs = wx.CheckBox(self.panel,-1,label=nHatms[i])
375	if i == neigh[2]:
376	nHs.SetValue(True)
377	Indx[nHs.GetId()] = [inei,i]
378	Ids.append(nHs)
379	nHs.Bind(wx.EVT_CHECKBOX, OnHSelect)
380	checks.Add(nHs,0,WACV)
381	Indx[inei] = Ids
382	dataSizer.Add(checks,0,WACV)
383	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
384	for ib,bond in enumerate(neigh[1][0]):
385	Bond = wx.CheckBox(self.panel,-1,label=': %s, %.3f'%(bond[0],bond[1]))
386	Bond.SetValue(bond[2])
387	Indx[Bond.GetId()] = [inei,ib]
388	Bond.Bind(wx.EVT_CHECKBOX,OnBond)
389	lineSizer.Add(Bond,0,WACV)
390	dataSizer.Add(lineSizer,0,WACV\|wx.RIGHT,10)
391	mainSizer.Add(dataSizer,0,wx.LEFT,5)
392
393	CancelBtn = wx.Button(self.panel,-1,'Cancel')
394	CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
395	OkBtn = wx.Button(self.panel,-1,'Ok')
396	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
397	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
398	btnSizer.Add((20,20),1)
399	btnSizer.Add(OkBtn)
400	btnSizer.Add((20,20),1)
401	btnSizer.Add(CancelBtn)
402	btnSizer.Add((20,20),1)
403	mainSizer.Add(btnSizer,0,wx.BOTTOM\|wx.TOP, 10)
404	size = np.array(self.GetSize())
405	self.panel.SetupScrolling()
406	self.panel.SetSizer(mainSizer)
407	self.panel.SetAutoLayout(1)
408	size = [size[0]-5,size[1]-20] #this fiddling is needed for older wx!
409	self.panel.SetSize(size)
410
411	def GetData(self):
412	'Returns the values from the dialog'
413	for neigh in self.Neigh:
414	for ibond,bond in enumerate(neigh[1][0]):
415	if not bond[2]:
416	neigh[1][1][1][ibond] = 0 #deselected bond
417	neigh[1][1][1] = [a for a in neigh[1][1][1] if a]
418	return self.Neigh #has #Hs to add for each entry
419
420	def OnOk(self,event):
421	'Called when the OK button is pressed'
422	parent = self.GetParent()
423	parent.Raise()
424	self.EndModal(wx.ID_OK)
425
426	def OnCancel(self,event):
427	parent = self.GetParent()
428	parent.Raise()
429	self.EndModal(wx.ID_CANCEL)
430
431	################################################################################
432	class DisAglDialog(wx.Dialog):
433	'''Distance/Angle Controls input dialog. After
434	:meth:`ShowModal` returns, the results are found in
435	dict :attr:`self.data`, which is accessed using :meth:`GetData`.
436
437	:param wx.Frame parent: reference to parent frame (or None)
438	:param dict data: a dict containing the current
439	search ranges or an empty dict, which causes default values
440	to be used.
441	Will be used to set element `DisAglCtls` in
442	:ref:`Phase Tree Item <Phase_table>`
443	:param dict default: A dict containing the default
444	search ranges for each element.
445	'''
446	def __init__(self,parent,data,default,Reset=True):
447	wx.Dialog.__init__(self,parent,wx.ID_ANY,
448	'Distance Angle Controls',
449	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
450	self.default = default
451	self.Reset = Reset
452	self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
453	self._default(data,self.default)
454	self.Draw(self.data)
455
456	def _default(self,data,default):
457	'''Set starting values for the search values, either from
458	the input array or from defaults, if input is null
459	'''
460	if data:
461	self.data = copy.deepcopy(data) # don't mess with originals
462	else:
463	self.data = {}
464	self.data['Name'] = default['Name']
465	self.data['Factors'] = [0.85,0.85]
466	self.data['AtomTypes'] = default['AtomTypes']
467	self.data['BondRadii'] = default['BondRadii'][:]
468	self.data['AngleRadii'] = default['AngleRadii'][:]
469
470	def Draw(self,data):
471	'''Creates the contents of the dialog. Normally called
472	by :meth:`__init__`.
473	'''
474	self.panel.Destroy()
475	self.panel = wx.Panel(self)
476	mainSizer = wx.BoxSizer(wx.VERTICAL)
477	mainSizer.Add(wx.StaticText(self.panel,-1,'Controls for phase '+data['Name']),
478	0,WACV\|wx.LEFT,10)
479	mainSizer.Add((10,10),1)
480
481	radiiSizer = wx.FlexGridSizer(0,3,5,5)
482	radiiSizer.Add(wx.StaticText(self.panel,-1,' Type'),0,WACV)
483	radiiSizer.Add(wx.StaticText(self.panel,-1,'Bond radii'),0,WACV)
484	radiiSizer.Add(wx.StaticText(self.panel,-1,'Angle radii'),0,WACV)
485	self.objList = {}
486	for id,item in enumerate(self.data['AtomTypes']):
487	radiiSizer.Add(wx.StaticText(self.panel,-1,' '+item),0,WACV)
488	bRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['BondRadii'][id]),style=wx.TE_PROCESS_ENTER)
489	self.objList[bRadii.GetId()] = ['BondRadii',id]
490	bRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
491	bRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
492	radiiSizer.Add(bRadii,0,WACV)
493	aRadii = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['AngleRadii'][id]),style=wx.TE_PROCESS_ENTER)
494	self.objList[aRadii.GetId()] = ['AngleRadii',id]
495	aRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
496	aRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
497	radiiSizer.Add(aRadii,0,WACV)
498	mainSizer.Add(radiiSizer,0,wx.EXPAND)
499	factorSizer = wx.FlexGridSizer(0,2,5,5)
500	Names = ['Bond','Angle']
501	for i,name in enumerate(Names):
502	factorSizer.Add(wx.StaticText(self.panel,-1,name+' search factor'),0,WACV)
503	bondFact = wx.TextCtrl(self.panel,-1,value='%.3f'%(data['Factors'][i]),style=wx.TE_PROCESS_ENTER)
504	self.objList[bondFact.GetId()] = ['Factors',i]
505	bondFact.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
506	bondFact.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
507	factorSizer.Add(bondFact)
508	mainSizer.Add(factorSizer,0,wx.EXPAND)
509
510	OkBtn = wx.Button(self.panel,-1,"Ok")
511	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
512	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
513	btnSizer.Add((20,20),1)
514	btnSizer.Add(OkBtn)
515	if self.Reset:
516	ResetBtn = wx.Button(self.panel,-1,'Reset')
517	ResetBtn.Bind(wx.EVT_BUTTON, self.OnReset)
518	btnSizer.Add(ResetBtn)
519	btnSizer.Add((20,20),1)
520	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
521	self.panel.SetSizer(mainSizer)
522	self.panel.Fit()
523	self.Fit()
524
525	def OnRadiiVal(self,event):
526	Obj = event.GetEventObject()
527	item = self.objList[Obj.GetId()]
528	try:
529	self.data[item[0]][item[1]] = float(Obj.GetValue())
530	except ValueError:
531	pass
532	Obj.SetValue("%.3f"%(self.data[item[0]][item[1]])) #reset in case of error
533
534	def GetData(self):
535	'Returns the values from the dialog'
536	return self.data
537
538	def OnOk(self,event):
539	'Called when the OK button is pressed'
540	parent = self.GetParent()
541	parent.Raise()
542	self.EndModal(wx.ID_OK)
543
544	def OnReset(self,event):
545	'Called when the Reset button is pressed'
546	data = {}
547	self._default(data,self.default)
548	self.Draw(self.data)
549
550	################################################################################
551	class ShowLSParms(wx.Dialog):
552	'''Create frame to show least-squares parameters
553	'''
554	def __init__(self,parent,title,parmDict,varyList,fullVaryList,
555	size=(300,430)):
556	wx.Dialog.__init__(self,parent,wx.ID_ANY,title,size=size,
557	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
558	mainSizer = wx.BoxSizer(wx.VERTICAL)
559
560	panel = wxscroll.ScrolledPanel(
561	self, wx.ID_ANY,
562	#size=size,
563	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
564	num = len(varyList)
565	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,'Number of refined variables: '+str(num)))
566	if len(varyList) != len(fullVaryList):
567	num = len(fullVaryList) - len(varyList)
568	mainSizer.Add(wx.StaticText(self,wx.ID_ANY,' + '+str(num)+' parameters are varied via constraints'))
569	subSizer = wx.FlexGridSizer(cols=4,hgap=2,vgap=2)
570	parmNames = parmDict.keys()
571	parmNames.sort()
572	subSizer.Add((-1,-1))
573	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'Parameter name '))
574	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'refine?'))
575	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'value'),0,wx.ALIGN_RIGHT)
576	explainRefine = False
577	for name in parmNames:
578	# skip entries without numerical values
579	if isinstance(parmDict[name],basestring): continue
580	try:
581	value = G2py3.FormatSigFigs(parmDict[name])
582	except TypeError:
583	value = str(parmDict[name])+' -?' # unexpected
584	#continue
585	v = G2obj.getVarDescr(name)
586	if v is None or v[-1] is None:
587	subSizer.Add((-1,-1))
588	else:
589	ch = G2G.HelpButton(panel,G2obj.fmtVarDescr(name))
590	subSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
591	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,str(name)))
592	if name in varyList:
593	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'R'))
594	elif name in fullVaryList:
595	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,'C'))
596	explainRefine = True
597	else:
598	subSizer.Add((-1,-1))
599	subSizer.Add(wx.StaticText(panel,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
600
601	# finish up ScrolledPanel
602	panel.SetSizer(subSizer)
603	panel.SetAutoLayout(1)
604	panel.SetupScrolling()
605	mainSizer.Add(panel,1, wx.ALL\|wx.EXPAND,1)
606
607	if explainRefine:
608	mainSizer.Add(
609	wx.StaticText(self,wx.ID_ANY,
610	'"R" indicates a refined variable\n'+
611	'"C" indicates generated from a constraint'
612	),
613	0, wx.ALL,0)
614	# make OK button
615	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
616	btn = wx.Button(self, wx.ID_CLOSE,"Close")
617	btn.Bind(wx.EVT_BUTTON,self._onClose)
618	btnsizer.Add(btn)
619	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
620	# Allow window to be enlarged but not made smaller
621	self.SetSizer(mainSizer)
622	self.SetMinSize(self.GetSize())
623
624	def _onClose(self,event):
625	self.EndModal(wx.ID_CANCEL)
626
627	################################################################################
628	class DataFrame(wx.Frame):
629	'''Create the data item window and all the entries in menus used in
630	that window. For Linux and windows, the menu entries are created for the
631	current data item window, but in the Mac the menu is accessed from all
632	windows. This means that a different menu is posted depending on which
633	data item is posted. On the Mac, all the menus contain the data tree menu
634	items, but additional menus are added specific to the data item.
635
636	Note that while the menus are created here,
637	the binding for the menus is done later in various GSASII*GUI modules,
638	where the functions to be called are defined.
639	'''
640	def Bind(self,eventtype,handler,args,*kwargs):
641	'''Override the Bind() function: on the Mac the binding is to
642	the main window, so that menus operate with any window on top.
643	For other platforms, either wrap calls that will be logged
644	or call the default wx.Frame Bind() to bind to the menu item directly.
645
646	Note that bindings can be made to objects by Id or by direct reference to the
647	object. As a convention, when bindings are to objects, they are not logged
648	but when bindings are by Id, they are logged.
649	'''
650	if sys.platform == "darwin": # mac
651	self.G2frame.Bind(eventtype,handler,args,*kwargs)
652	return
653	if eventtype == wx.EVT_MENU and 'id' in kwargs:
654	menulabels = log.SaveMenuCommand(kwargs['id'],self.G2frame,handler)
655	if menulabels:
656	#print 'intercepting bind for',handler,menulabels,kwargs['id']
657	wx.Frame.Bind(self,eventtype,self.G2frame.MenuBinding,args,*kwargs)
658	return
659	wx.Frame.Bind(self,eventtype,handler,args,*kwargs)
660
661	def PrefillDataMenu(self,menu,helpType,helpLbl=None,empty=False):
662	'''Create the "standard" part of data frame menus. Note that on Linux and
663	Windows nothing happens here. On Mac, this menu duplicates the
664	tree menu, but adds an extra help command for the data item and a separator.
665	'''
666	self.datamenu = menu
667	self.G2frame.dataMenuBars.append(menu)
668	self.helpType = helpType
669	self.helpLbl = helpLbl
670	if sys.platform == "darwin": # mac
671	self.G2frame.FillMainMenu(menu) # add the data tree menu items
672	if not empty:
673	menu.Append(wx.Menu(title=''),title='\|') # add a separator
674
675	def PostfillDataMenu(self,empty=False):
676	'''Create the "standard" part of data frame menus. Note that on Linux and
677	Windows, this is the standard help Menu. On Mac, this menu duplicates the
678	tree menu, but adds an extra help command for the data item and a separator.
679	'''
680	menu = self.datamenu
681	helpType = self.helpType
682	helpLbl = self.helpLbl
683	if sys.platform == "darwin": # mac
684	if not empty:
685	menu.Append(wx.Menu(title=''),title='\|') # add another separator
686	menu.Append(G2G.AddHelp(self.G2frame,helpType=helpType, helpLbl=helpLbl),
687	title='&Help')
688	else: # other
689	menu.Append(menu=G2G.MyHelp(self,helpType=helpType, helpLbl=helpLbl),
690	title='&Help')
691
692	def _init_menus(self):
693	'define all GSAS-II data frame menus'
694
695	# for use where no menu or data frame help is provided
696	self.BlankMenu = wx.MenuBar()
697
698	# Controls
699	self.ControlsMenu = wx.MenuBar()
700	self.PrefillDataMenu(self.ControlsMenu,helpType='Controls',empty=True)
701	self.PostfillDataMenu(empty=True)
702
703	# Notebook
704	self.DataNotebookMenu = wx.MenuBar()
705	self.PrefillDataMenu(self.DataNotebookMenu,helpType='Notebook',empty=True)
706	self.PostfillDataMenu(empty=True)
707
708	# Comments
709	self.DataCommentsMenu = wx.MenuBar()
710	self.PrefillDataMenu(self.DataCommentsMenu,helpType='Comments',empty=True)
711	self.PostfillDataMenu(empty=True)
712
713	# Constraints - something amiss here - get weird wx C++ error after refine!
714	self.ConstraintMenu = wx.MenuBar()
715	self.PrefillDataMenu(self.ConstraintMenu,helpType='Constraints')
716	self.ConstraintTab = wx.Menu(title='')
717	self.ConstraintMenu.Append(menu=self.ConstraintTab, title='Select tab')
718	for id,txt in (
719	(wxID_CONSPHASE,'Phase'),
720	(wxID_CONSHAP,'Histogram/Phase'),
721	(wxID_CONSHIST,'Histogram'),
722	(wxID_CONSGLOBAL,'Global')):
723	self.ConstraintTab.Append(
724	id=id, kind=wx.ITEM_NORMAL,text=txt,
725	help='Select '+txt+' constraint editing tab')
726	self.ConstraintEdit = wx.Menu(title='')
727	self.ConstraintMenu.Append(menu=self.ConstraintEdit, title='Edit')
728	self.ConstraintEdit.Append(id=wxID_HOLDADD, kind=wx.ITEM_NORMAL,text='Add hold',
729	help='Add hold on a parameter value')
730	self.ConstraintEdit.Append(id=wxID_EQUIVADD, kind=wx.ITEM_NORMAL,text='Add equivalence',
731	help='Add equivalence between parameter values')
732	self.ConstraintEdit.Append(id=wxID_CONSTRAINTADD, kind=wx.ITEM_NORMAL,text='Add constraint',
733	help='Add constraint on parameter values')
734	self.ConstraintEdit.Append(id=wxID_FUNCTADD, kind=wx.ITEM_NORMAL,text='Add New Var',
735	help='Add variable composed of existing parameter')
736	self.ConstraintEdit.Append(id=wxID_EQUIVALANCEATOMS, kind=wx.ITEM_NORMAL,text='Add atom equivalence',
737	help='Add equivalences between atom parameter values')
738	self.ConstraintEdit.Enable(wxID_EQUIVALANCEATOMS,False)
739	# self.ConstraintEdit.Append(id=wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add H riding constraints',
740	# help='Add H atom riding constraints between atom parameter values')
741	# self.ConstraintEdit.Enable(wxID_ADDRIDING,False)
742	self.PostfillDataMenu()
743
744	# item = self.ConstraintEdit.Append(id=wx.ID_ANY,kind=wx.ITEM_NORMAL,text='Update GUI')
745	# def UpdateGSASIIconstrGUI(event):
746	# import GSASIIconstrGUI
747	# reload(GSASIIconstrGUI)
748	# import GSASIIobj
749	# reload(GSASIIobj)
750	# self.Bind(wx.EVT_MENU,UpdateGSASIIconstrGUI,id=item.GetId())
751
752	# Rigid bodies
753	self.RigidBodyMenu = wx.MenuBar()
754	self.PrefillDataMenu(self.RigidBodyMenu,helpType='Rigid bodies')
755	self.ResidueRBMenu = wx.Menu(title='')
756	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYIMPORT, kind=wx.ITEM_NORMAL,text='Import XYZ',
757	help='Import rigid body XYZ from file')
758	self.ResidueRBMenu.Append(id=wxID_RESIDUETORSSEQ, kind=wx.ITEM_NORMAL,text='Define sequence',
759	help='Define torsion sequence')
760	self.ResidueRBMenu.Append(id=wxID_RIGIDBODYADD, kind=wx.ITEM_NORMAL,text='Import residues',
761	help='Import residue rigid bodies from macro file')
762	self.RigidBodyMenu.Append(menu=self.ResidueRBMenu, title='Edit Body')
763	self.PostfillDataMenu()
764
765	self.VectorBodyMenu = wx.MenuBar()
766	self.PrefillDataMenu(self.VectorBodyMenu,helpType='Vector rigid bodies')
767	self.VectorRBEdit = wx.Menu(title='')
768	self.VectorRBEdit.Append(id=wxID_VECTORBODYADD, kind=wx.ITEM_NORMAL,text='Add rigid body',
769	help='Add vector rigid body')
770	self.VectorBodyMenu.Append(menu=self.VectorRBEdit, title='Edit Vector Body')
771	self.PostfillDataMenu()
772
773
774	# Restraints
775	self.RestraintTab = wx.Menu(title='')
776	self.RestraintEdit = wx.Menu(title='')
777	self.RestraintEdit.Append(id=wxID_RESTSELPHASE, kind=wx.ITEM_NORMAL,text='Select phase',
778	help='Select phase')
779	self.RestraintEdit.Append(id=wxID_RESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add restraints',
780	help='Add restraints')
781	self.RestraintEdit.Enable(wxID_RESTRAINTADD,True) #gets disabled if macromolecule phase
782	self.RestraintEdit.Append(id=wxID_AARESTRAINTADD, kind=wx.ITEM_NORMAL,text='Add residue restraints',
783	help='Add residue based restraints for macromolecules from macro file')
784	self.RestraintEdit.Enable(wxID_AARESTRAINTADD,False) #gets enabled if macromolecule phase
785	self.RestraintEdit.Append(id=wxID_AARESTRAINTPLOT, kind=wx.ITEM_NORMAL,text='Plot residue restraints',
786	help='Plot selected residue based restraints for macromolecules from macro file')
787	self.RestraintEdit.Enable(wxID_AARESTRAINTPLOT,False) #gets enabled if macromolecule phase
788	self.RestraintEdit.Append(id=wxID_RESRCHANGEVAL, kind=wx.ITEM_NORMAL,text='Change value',
789	help='Change observed value')
790	self.RestraintEdit.Append(id=wxID_RESTCHANGEESD, kind=wx.ITEM_NORMAL,text='Change esd',
791	help='Change esd in observed value')
792	self.RestraintEdit.Append(id=wxID_RESTDELETE, kind=wx.ITEM_NORMAL,text='Delete restraints',
793	help='Delete selected restraints')
794
795	self.RestraintMenu = wx.MenuBar()
796	self.PrefillDataMenu(self.RestraintMenu,helpType='Restraints')
797	self.RestraintMenu.Append(menu=self.RestraintTab, title='Select tab')
798	self.RestraintMenu.Append(menu=self.RestraintEdit, title='Edit')
799	self.PostfillDataMenu()
800
801	# Sequential results
802	self.SequentialMenu = wx.MenuBar()
803	self.PrefillDataMenu(self.SequentialMenu,helpType='Sequential',helpLbl='Sequential Refinement')
804	self.SequentialFile = wx.Menu(title='')
805	self.SequentialMenu.Append(menu=self.SequentialFile, title='Columns')
806	self.SequentialFile.Append(id=wxID_RENAMESEQSEL, kind=wx.ITEM_NORMAL,text='Rename selected',
807	help='Rename selected sequential refinement columns')
808	self.SequentialFile.Append(id=wxID_SAVESEQSEL, kind=wx.ITEM_NORMAL,text='Save selected as text',
809	help='Save selected sequential refinement results as a text file')
810	self.SequentialFile.Append(id=wxID_SAVESEQCSV, kind=wx.ITEM_NORMAL,text='Save all as CSV',
811	help='Save all sequential refinement results as a CSV spreadsheet file')
812	self.SequentialFile.Append(id=wxID_SAVESEQSELCSV, kind=wx.ITEM_NORMAL,text='Save selected as CSV',
813	help='Save selected sequential refinement results as a CSV spreadsheet file')
814	self.SequentialFile.Append(id=wxID_PLOTSEQSEL, kind=wx.ITEM_NORMAL,text='Plot selected',
815	help='Plot selected sequential refinement results')
816	self.SequentialFile.Append(id=wxID_AVESEQSEL, kind=wx.ITEM_NORMAL,text='Compute average',
817	help='Compute average for selected parameter')
818	self.SequentialFile.Append(id=wxID_ORGSEQSEL, kind=wx.ITEM_NORMAL,text='Reorganize',
819	help='Reorganize variables where variables change')
820	self.SequentialPvars = wx.Menu(title='')
821	self.SequentialMenu.Append(menu=self.SequentialPvars, title='Pseudo Vars')
822	self.SequentialPvars.Append(
823	id=wxADDSEQVAR, kind=wx.ITEM_NORMAL,text='Add',
824	help='Add a new pseudo-variable')
825	self.SequentialPvars.Append(
826	id=wxDELSEQVAR, kind=wx.ITEM_NORMAL,text='Delete',
827	help='Delete an existing pseudo-variable')
828	self.SequentialPvars.Append(
829	id=wxEDITSEQVAR, kind=wx.ITEM_NORMAL,text='Edit',
830	help='Edit an existing pseudo-variable')
831
832	self.SequentialPfit = wx.Menu(title='')
833	self.SequentialMenu.Append(menu=self.SequentialPfit, title='Parametric Fit')
834	self.SequentialPfit.Append(
835	id=wxADDPARFIT, kind=wx.ITEM_NORMAL,text='Add equation',
836	help='Add a new equation to minimize')
837	self.SequentialPfit.Append(
838	id=wxCOPYPARFIT, kind=wx.ITEM_NORMAL,text='Copy equation',
839	help='Copy an equation to minimize - edit it next')
840	self.SequentialPfit.Append(
841	id=wxDELPARFIT, kind=wx.ITEM_NORMAL,text='Delete equation',
842	help='Delete an equation for parametric minimization')
843	self.SequentialPfit.Append(
844	id=wxEDITPARFIT, kind=wx.ITEM_NORMAL,text='Edit equation',
845	help='Edit an existing parametric minimization equation')
846	self.SequentialPfit.Append(
847	id=wxDOPARFIT, kind=wx.ITEM_NORMAL,text='Fit to equation(s)',
848	help='Perform a parametric minimization')
849	self.PostfillDataMenu()
850
851	# PWDR & SASD
852	self.PWDRMenu = wx.MenuBar()
853	self.PrefillDataMenu(self.PWDRMenu,helpType='PWDR Analysis',helpLbl='Powder Fit Error Analysis')
854	self.ErrorAnal = wx.Menu(title='')
855	self.PWDRMenu.Append(menu=self.ErrorAnal,title='Commands')
856	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
857	help='Error analysis on powder pattern')
858	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
859	help='Copy of PWDR parameters')
860	self.ErrorAnal.Append(id=wxID_PLOTCTRLCOPY,kind=wx.ITEM_NORMAL,text='Copy plot controls',
861	help='Copy of PWDR plot controls')
862
863	self.PostfillDataMenu()
864
865	# HKLF
866	self.HKLFMenu = wx.MenuBar()
867	self.PrefillDataMenu(self.HKLFMenu,helpType='HKLF Analysis',helpLbl='HKLF Fit Error Analysis')
868	self.ErrorAnal = wx.Menu(title='')
869	self.HKLFMenu.Append(menu=self.ErrorAnal,title='Commands')
870	self.ErrorAnal.Append(id=wxID_PWDANALYSIS,kind=wx.ITEM_NORMAL,text='Error Analysis',
871	help='Error analysis on single crystal data')
872	self.ErrorAnal.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
873	help='Plot HKLs from single crystal data in 3D')
874	self.ErrorAnal.Append(id=wxID_3DALLHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot all 3D HKLs',
875	help='Plot HKLs from all single crystal data in 3D')
876	self.ErrorAnal.Append(id=wxID_PWDCOPY,kind=wx.ITEM_NORMAL,text='Copy params',
877	help='Copy of HKLF parameters')
878	self.PostfillDataMenu()
879
880	# PDR / Limits
881	self.LimitMenu = wx.MenuBar()
882	self.PrefillDataMenu(self.LimitMenu,helpType='Limits')
883	self.LimitEdit = wx.Menu(title='')
884	self.LimitMenu.Append(menu=self.LimitEdit, title='Edit')
885	self.LimitEdit.Append(id=wxID_LIMITCOPY, kind=wx.ITEM_NORMAL,text='Copy',
886	help='Copy limits to other histograms')
887	self.LimitEdit.Append(id=wxID_ADDEXCLREGION, kind=wx.ITEM_NORMAL,text='Add exclude',
888	help='Add excluded region - select a point on plot; drag to adjust')
889	self.PostfillDataMenu()
890
891	# PDR / Background
892	self.BackMenu = wx.MenuBar()
893	self.PrefillDataMenu(self.BackMenu,helpType='Background')
894	self.BackEdit = wx.Menu(title='')
895	self.BackMenu.Append(menu=self.BackEdit, title='File')
896	self.BackEdit.Append(id=wxID_BACKCOPY, kind=wx.ITEM_NORMAL,text='Copy',
897	help='Copy background parameters to other histograms')
898	self.BackEdit.Append(id=wxID_BACKFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
899	help='Copy background refinement flags to other histograms')
900	self.BackEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
901	help='Move background peaks to Peak List')
902	self.BackFixed = wx.Menu(title='') # fixed background point menu
903	self.BackMenu.Append(menu=self.BackFixed, title='Fixed Points')
904	self.wxID_BackPts = {}
905	self.wxID_BackPts['Add'] = wx.NewId() # N.B. not using wxID_ global as for other menu items
906	self.BackFixed.Append(id=self.wxID_BackPts['Add'], kind=wx.ITEM_RADIO,text='Add',
907	help='Add fixed background points with mouse clicks')
908	self.wxID_BackPts['Move'] = wx.NewId()
909	item = self.BackFixed.Append(id=self.wxID_BackPts['Move'], kind=wx.ITEM_RADIO,text='Move',
910	help='Move selected fixed background points with mouse drags')
911	item.Check(True)
912	self.wxID_BackPts['Del'] = wx.NewId()
913	self.BackFixed.Append(id=self.wxID_BackPts['Del'], kind=wx.ITEM_RADIO,text='Delete',
914	help='Delete fixed background points with mouse clicks')
915	self.wxID_BackPts['Clear'] = wx.NewId()
916	self.BackFixed.Append(id=self.wxID_BackPts['Clear'], kind=wx.ITEM_NORMAL,text='Clear',
917	help='Clear fixed background points')
918	self.wxID_BackPts['Fit'] = wx.NewId()
919	self.BackFixed.Append(id=self.wxID_BackPts['Fit'], kind=wx.ITEM_NORMAL,text='Fit background',
920	help='Fit background function to fixed background points')
921	self.PostfillDataMenu()
922
923	# PDR / Instrument Parameters
924	self.InstMenu = wx.MenuBar()
925	self.PrefillDataMenu(self.InstMenu,helpType='Instrument Parameters')
926	self.InstEdit = wx.Menu(title='')
927	self.InstMenu.Append(menu=self.InstEdit, title='Operations')
928	self.InstEdit.Append(help='Calibrate from indexed peaks',
929	id=wxID_INSTCALIB, kind=wx.ITEM_NORMAL,text='Calibrate')
930	self.InstEdit.Append(help='Reset instrument profile parameters to default',
931	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
932	self.InstEdit.Append(help='Load instrument profile parameters from file',
933	id=wxID_INSTLOAD, kind=wx.ITEM_NORMAL,text='Load profile...')
934	self.InstEdit.Append(help='Save instrument profile parameters to file',
935	id=wxID_INSTSAVE, kind=wx.ITEM_NORMAL,text='Save profile...')
936	self.InstEdit.Append(help='Copy instrument profile parameters to other histograms',
937	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
938	self.InstEdit.Append(id=wxID_INSTFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
939	help='Copy instrument parameter refinement flags to other histograms')
940	# self.InstEdit.Append(help='Change radiation type (Ka12 - synch)',
941	# id=wxID_CHANGEWAVETYPE, kind=wx.ITEM_NORMAL,text='Change radiation')
942	self.InstEdit.Append(id=wxID_INST1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
943	help='Set one instrument parameter value across multiple histograms')
944
945	self.PostfillDataMenu()
946
947	# PDR / Sample Parameters
948	self.SampleMenu = wx.MenuBar()
949	self.PrefillDataMenu(self.SampleMenu,helpType='Sample Parameters')
950	self.SampleEdit = wx.Menu(title='')
951	self.SampleMenu.Append(menu=self.SampleEdit, title='Command')
952	self.SetScale = self.SampleEdit.Append(id=wxID_SETSCALE, kind=wx.ITEM_NORMAL,text='Set scale',
953	help='Set scale by matching to another histogram')
954	self.SampleEdit.Append(id=wxID_SAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load',
955	help='Load sample parameters from file')
956	self.SampleEdit.Append(id=wxID_SAMPLESAVE, kind=wx.ITEM_NORMAL,text='Save',
957	help='Save sample parameters to file')
958	self.SampleEdit.Append(id=wxID_SAMPLECOPY, kind=wx.ITEM_NORMAL,text='Copy',
959	help='Copy refinable and most other sample parameters to other histograms')
960	self.SampleEdit.Append(id=wxID_SAMPLECOPYSOME, kind=wx.ITEM_NORMAL,text='Copy selected...',
961	help='Copy selected sample parameters to other histograms')
962	self.SampleEdit.Append(id=wxID_SAMPLEFLAGCOPY, kind=wx.ITEM_NORMAL,text='Copy flags',
963	help='Copy sample parameter refinement flags to other histograms')
964	self.SampleEdit.Append(id=wxID_SAMPLE1VAL, kind=wx.ITEM_NORMAL,text='Set one value',
965	help='Set one sample parameter value across multiple histograms')
966	self.SampleEdit.Append(id=wxID_ALLSAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load all',
967	help='Load sample parmameters over multiple histograms')
968
969	self.PostfillDataMenu()
970	self.SetScale.Enable(False)
971
972	# PDR / Peak List
973	self.PeakMenu = wx.MenuBar()
974	self.PrefillDataMenu(self.PeakMenu,helpType='Peak List')
975	self.PeakEdit = wx.Menu(title='')
976	self.PeakMenu.Append(menu=self.PeakEdit, title='Peak Fitting')
977	self.AutoSearch = self.PeakEdit.Append(help='Automatic peak search',
978	id=wxID_AUTOSEARCH, kind=wx.ITEM_NORMAL,text='Auto search')
979	self.UnDo = self.PeakEdit.Append(help='Undo last least squares refinement',
980	id=wxID_UNDO, kind=wx.ITEM_NORMAL,text='UnDo')
981	self.PeakFit = self.PeakEdit.Append(id=wxID_LSQPEAKFIT, kind=wx.ITEM_NORMAL,text='Peakfit',
982	help='Peak fitting' )
983	self.PFOneCycle = self.PeakEdit.Append(id=wxID_LSQONECYCLE, kind=wx.ITEM_NORMAL,text='Peakfit one cycle',
984	help='One cycle of Peak fitting' )
985	self.PeakEdit.Append(id=wxID_RESETSIGGAM, kind=wx.ITEM_NORMAL,
986	text='Reset sig and gam',help='Reset sigma and gamma to global fit' )
987	self.PeakCopy = self.PeakEdit.Append(help='Copy peaks to other histograms',
988	id=wxID_PEAKSCOPY, kind=wx.ITEM_NORMAL,text='Peak copy')
989	self.SeqPeakFit = self.PeakEdit.Append(id=wxID_SEQPEAKFIT, kind=wx.ITEM_NORMAL,text='Seq PeakFit',
990	help='Sequential Peak fitting for all histograms' )
991	self.PeakEdit.Append(id=wxID_CLEARPEAKS, kind=wx.ITEM_NORMAL,text='Clear peaks',
992	help='Clear the peak list' )
993	self.PostfillDataMenu()
994	self.UnDo.Enable(False)
995	self.PeakFit.Enable(False)
996	self.PFOneCycle.Enable(False)
997	self.AutoSearch.Enable(True)
998
999	# PDR / Index Peak List
1000	self.IndPeaksMenu = wx.MenuBar()
1001	self.PrefillDataMenu(self.IndPeaksMenu,helpType='Index Peak List')
1002	self.IndPeaksEdit = wx.Menu(title='')
1003	self.IndPeaksMenu.Append(menu=self.IndPeaksEdit,title='Operations')
1004	self.IndPeaksEdit.Append(help='Load/Reload index peaks from peak list',id=wxID_INDXRELOAD,
1005	kind=wx.ITEM_NORMAL,text='Load/Reload')
1006	self.PostfillDataMenu()
1007
1008	# PDR / Unit Cells List
1009	self.IndexMenu = wx.MenuBar()
1010	self.PrefillDataMenu(self.IndexMenu,helpType='Unit Cells List')
1011	self.IndexEdit = wx.Menu(title='')
1012	self.IndexMenu.Append(menu=self.IndexEdit, title='Cell Index/Refine')
1013	self.IndexPeaks = self.IndexEdit.Append(help='', id=wxID_INDEXPEAKS, kind=wx.ITEM_NORMAL,
1014	text='Index Cell')
1015	self.CopyCell = self.IndexEdit.Append( id=wxID_COPYCELL, kind=wx.ITEM_NORMAL,text='Copy Cell',
1016	help='Copy selected unit cell from indexing to cell refinement fields')
1017	self.RefineCell = self.IndexEdit.Append( id=wxID_REFINECELL, kind=wx.ITEM_NORMAL,
1018	text='Refine Cell',help='Refine unit cell parameters from indexed peaks')
1019	self.MakeNewPhase = self.IndexEdit.Append( id=wxID_MAKENEWPHASE, kind=wx.ITEM_NORMAL,
1020	text='Make new phase',help='Make new phase from selected unit cell')
1021	self.ExportCells = self.IndexEdit.Append( id=wxID_EXPORTCELLS, kind=wx.ITEM_NORMAL,
1022	text='Export cell list',help='Export cell list to csv file')
1023	self.PostfillDataMenu()
1024	self.IndexPeaks.Enable(False)
1025	self.CopyCell.Enable(False)
1026	self.RefineCell.Enable(False)
1027	self.MakeNewPhase.Enable(False)
1028
1029	# PDR / Reflection Lists
1030	self.ReflMenu = wx.MenuBar()
1031	self.PrefillDataMenu(self.ReflMenu,helpType='Reflection List')
1032	self.ReflEdit = wx.Menu(title='')
1033	self.ReflMenu.Append(menu=self.ReflEdit, title='Reflection List')
1034	self.SelectPhase = self.ReflEdit.Append(help='Select phase for reflection list',id=wxID_SELECTPHASE,
1035	kind=wx.ITEM_NORMAL,text='Select phase')
1036	self.ReflEdit.Append(id=wxID_PWDHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot HKLs',
1037	help='Plot HKLs from powder pattern')
1038	self.ReflEdit.Append(id=wxID_PWD3DHKLPLOT,kind=wx.ITEM_NORMAL,text='Plot 3D HKLs',
1039	help='Plot HKLs from powder pattern in 3D')
1040	self.PostfillDataMenu()
1041
1042	# SASD / Instrument Parameters
1043	self.SASDInstMenu = wx.MenuBar()
1044	self.PrefillDataMenu(self.SASDInstMenu,helpType='Instrument Parameters')
1045	self.SASDInstEdit = wx.Menu(title='')
1046	self.SASDInstMenu.Append(menu=self.SASDInstEdit, title='Operations')
1047	self.InstEdit.Append(help='Reset instrument profile parameters to default',
1048	id=wxID_INSTPRMRESET, kind=wx.ITEM_NORMAL,text='Reset profile')
1049	self.SASDInstEdit.Append(help='Copy instrument profile parameters to other histograms',
1050	id=wxID_INSTCOPY, kind=wx.ITEM_NORMAL,text='Copy')
1051	self.PostfillDataMenu()
1052
1053	#SASD & REFL/ Substance editor
1054	self.SubstanceMenu = wx.MenuBar()
1055	self.PrefillDataMenu(self.SubstanceMenu,helpType='Substances')
1056	self.SubstanceEdit = wx.Menu(title='')
1057	self.SubstanceMenu.Append(menu=self.SubstanceEdit, title='Edit')
1058	self.SubstanceEdit.Append(id=wxID_LOADSUBSTANCE, kind=wx.ITEM_NORMAL,text='Load substance',
1059	help='Load substance from file')
1060	self.SubstanceEdit.Append(id=wxID_ADDSUBSTANCE, kind=wx.ITEM_NORMAL,text='Add substance',
1061	help='Add new substance to list')
1062	self.SubstanceEdit.Append(id=wxID_COPYSUBSTANCE, kind=wx.ITEM_NORMAL,text='Copy substances',
1063	help='Copy substances')
1064	self.SubstanceEdit.Append(id=wxID_DELETESUBSTANCE, kind=wx.ITEM_NORMAL,text='Delete substance',
1065	help='Delete substance from list')
1066	self.SubstanceEdit.Append(id=wxID_ELEMENTADD, kind=wx.ITEM_NORMAL,text='Add elements',
1067	help='Add elements to substance')
1068	self.SubstanceEdit.Append(id=wxID_ELEMENTDELETE, kind=wx.ITEM_NORMAL,text='Delete elements',
1069	help='Delete elements from substance')
1070	self.PostfillDataMenu()
1071
1072	# SASD/ Models
1073	self.ModelMenu = wx.MenuBar()
1074	self.PrefillDataMenu(self.ModelMenu,helpType='Models')
1075	self.ModelEdit = wx.Menu(title='')
1076	self.ModelMenu.Append(menu=self.ModelEdit, title='Models')
1077	self.ModelEdit.Append(id=wxID_MODELADD,kind=wx.ITEM_NORMAL,text='Add',
1078	help='Add new term to model')
1079	self.ModelEdit.Append(id=wxID_MODELFIT, kind=wx.ITEM_NORMAL,text='Fit',
1080	help='Fit model parameters to data')
1081	self.SasdUndo = self.ModelEdit.Append(id=wxID_MODELUNDO, kind=wx.ITEM_NORMAL,text='Undo',
1082	help='Undo model fit')
1083	self.SasdUndo.Enable(False)
1084	self.ModelEdit.Append(id=wxID_MODELFITALL, kind=wx.ITEM_NORMAL,text='Sequential fit',
1085	help='Sequential fit of model parameters to all SASD data')
1086	self.ModelEdit.Append(id=wxID_MODELCOPY, kind=wx.ITEM_NORMAL,text='Copy',
1087	help='Copy model parameters to other histograms')
1088	self.ModelEdit.Append(id=wxID_MODELCOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1089	help='Copy model refinement flags to other histograms')
1090	self.PostfillDataMenu()
1091
1092	# IMG / Image Controls
1093	self.ImageMenu = wx.MenuBar()
1094	self.PrefillDataMenu(self.ImageMenu,helpType='Image Controls')
1095	self.ImageEdit = wx.Menu(title='')
1096	self.ImageMenu.Append(menu=self.ImageEdit, title='Operations')
1097	self.ImageEdit.Append(help='Calibrate detector by fitting to calibrant lines',
1098	id=wxID_IMCALIBRATE, kind=wx.ITEM_NORMAL,text='Calibrate')
1099	self.ImageEdit.Append(help='Recalibrate detector by fitting to calibrant lines',
1100	id=wxID_IMRECALIBRATE, kind=wx.ITEM_NORMAL,text='Recalibrate')
1101	self.ImageEdit.Append(help='Clear calibration data points and rings',id=wxID_IMCLEARCALIB,
1102	kind=wx.ITEM_NORMAL,text='Clear calibration')
1103	self.ImageEdit.Append(help='Integrate selected image',id=wxID_IMINTEGRATE,
1104	kind=wx.ITEM_NORMAL,text='Integrate')
1105	self.ImageEdit.Append(help='Integrate all images selected from list',id=wxID_INTEGRATEALL,
1106	kind=wx.ITEM_NORMAL,text='Integrate all')
1107	self.ImageEdit.Append(help='Copy image controls to other images',
1108	id=wxID_IMCOPYCONTROLS, kind=wx.ITEM_NORMAL,text='Copy Controls')
1109	self.ImageEdit.Append(help='Save image controls to file',
1110	id=wxID_IMSAVECONTROLS, kind=wx.ITEM_NORMAL,text='Save Controls')
1111	self.ImageEdit.Append(help='Load image controls from file',
1112	id=wxID_IMLOADCONTROLS, kind=wx.ITEM_NORMAL,text='Load Controls')
1113	self.ImageEdit.Append(help='Open Auto-integration window to integrate a series of images',
1114	id=wxID_IMAUTOINTEG, kind=wx.ITEM_NORMAL,text='Auto Integrate')
1115	self.PostfillDataMenu()
1116
1117	# IMG / Masks
1118	self.MaskMenu = wx.MenuBar()
1119	self.PrefillDataMenu(self.MaskMenu,helpType='Image Masks')
1120	self.MaskEdit = wx.Menu(title='')
1121	self.MaskMenu.Append(menu=self.MaskEdit, title='Operations')
1122	submenu = wx.Menu()
1123	self.MaskEdit.AppendMenu(
1124	wx.ID_ANY,'Create new', submenu,
1125	help=''
1126	)
1127	self.MaskEdit.Append(help='Copy mask to other images',
1128	id=wxID_MASKCOPY, kind=wx.ITEM_NORMAL,text='Copy mask')
1129	self.MaskEdit.Append(help='Save mask to file',
1130	id=wxID_MASKSAVE, kind=wx.ITEM_NORMAL,text='Save mask')
1131	self.MaskEdit.Append(help='Load mask from file',
1132	id=wxID_MASKLOAD, kind=wx.ITEM_NORMAL,text='Load mask')
1133	self.MaskEdit.Append(help='Load mask from file; ignore threshold',
1134	id=wxID_MASKLOADNOT, kind=wx.ITEM_NORMAL,text='Load mask w/o threshold')
1135	submenu.Append(help='Create an arc mask with mouse input',
1136	id=wxID_NEWMASKARC, kind=wx.ITEM_NORMAL,text='Arc mask')
1137	submenu.Append(help='Create a frame mask with mouse input',
1138	id=wxID_NEWMASKFRAME, kind=wx.ITEM_NORMAL,text='Frame mask')
1139	submenu.Append(help='Create a polygon mask with mouse input',
1140	id=wxID_NEWMASKPOLY, kind=wx.ITEM_NORMAL,text='Polygon mask')
1141	submenu.Append(help='Create a ring mask with mouse input',
1142	id=wxID_NEWMASKRING, kind=wx.ITEM_NORMAL,text='Ring mask')
1143	submenu.Append(help='Create a spot mask with mouse input',
1144	id=wxID_NEWMASKSPOT, kind=wx.ITEM_NORMAL,text='Spot mask')
1145	self.PostfillDataMenu()
1146
1147	# IMG / Stress/Strain
1148	self.StrStaMenu = wx.MenuBar()
1149	self.PrefillDataMenu(self.StrStaMenu,helpType='Stress/Strain')
1150	self.StrStaEdit = wx.Menu(title='')
1151	self.StrStaMenu.Append(menu=self.StrStaEdit, title='Operations')
1152	self.StrStaEdit.Append(help='Append d-zero for one ring',
1153	id=wxID_APPENDDZERO, kind=wx.ITEM_NORMAL,text='Append d-zero')
1154	self.StrStaEdit.Append(help='Fit stress/strain data',
1155	id=wxID_STRSTAFIT, kind=wx.ITEM_NORMAL,text='Fit stress/strain')
1156	self.StrStaEdit.Append(help='Update d-zero from ave d-zero',
1157	id=wxID_UPDATEDZERO, kind=wx.ITEM_NORMAL,text='Update d-zero')
1158	self.StrStaEdit.Append(help='Fit stress/strain data for all images',
1159	id=wxID_STRSTAALLFIT, kind=wx.ITEM_NORMAL,text='All image fit')
1160	self.StrStaEdit.Append(help='Copy stress/strain data to other images',
1161	id=wxID_STRSTACOPY, kind=wx.ITEM_NORMAL,text='Copy stress/strain')
1162	self.StrStaEdit.Append(help='Save stress/strain data to file',
1163	id=wxID_STRSTASAVE, kind=wx.ITEM_NORMAL,text='Save stress/strain')
1164	self.StrStaEdit.Append(help='Load stress/strain data from file',
1165	id=wxID_STRSTALOAD, kind=wx.ITEM_NORMAL,text='Load stress/strain')
1166	self.StrStaEdit.Append(help='Load sample data from file',
1167	id=wxID_STRSTSAMPLE, kind=wx.ITEM_NORMAL,text='Load sample data')
1168	self.PostfillDataMenu()
1169
1170	# PDF / PDF Controls
1171	self.PDFMenu = wx.MenuBar()
1172	self.PrefillDataMenu(self.PDFMenu,helpType='PDF Controls')
1173	self.PDFEdit = wx.Menu(title='')
1174	self.PDFMenu.Append(menu=self.PDFEdit, title='PDF Controls')
1175	self.PDFEdit.Append(help='Add element to sample composition',id=wxID_PDFADDELEMENT, kind=wx.ITEM_NORMAL,
1176	text='Add element')
1177	self.PDFEdit.Append(help='Delete element from sample composition',id=wxID_PDFDELELEMENT, kind=wx.ITEM_NORMAL,
1178	text='Delete element')
1179	self.PDFEdit.Append(help='Copy PDF controls', id=wxID_PDFCOPYCONTROLS, kind=wx.ITEM_NORMAL,
1180	text='Copy controls')
1181	self.PDFEdit.Append(help='Load PDF controls from file',id=wxID_PDFLOADCONTROLS, kind=wx.ITEM_NORMAL,
1182	text='Load Controls')
1183	self.PDFEdit.Append(help='Save PDF controls to file', id=wxID_PDFSAVECONTROLS, kind=wx.ITEM_NORMAL,
1184	text='Save controls')
1185	self.PDFEdit.Append(help='Compute PDF', id=wxID_PDFCOMPUTE, kind=wx.ITEM_NORMAL,
1186	text='Compute PDF')
1187	self.PDFEdit.Append(help='Compute all PDFs', id=wxID_PDFCOMPUTEALL, kind=wx.ITEM_NORMAL,
1188	text='Compute all PDFs')
1189	self.PostfillDataMenu()
1190
1191	# Phase / General tab
1192	self.DataGeneral = wx.MenuBar()
1193	self.PrefillDataMenu(self.DataGeneral,helpType='General', helpLbl='Phase/General')
1194	self.DataGeneral.Append(menu=wx.Menu(title=''),title='Select tab')
1195	self.GeneralCalc = wx.Menu(title='')
1196	self.DataGeneral.Append(menu=self.GeneralCalc,title='Compute')
1197	self.GeneralCalc.Append(help='Compute Fourier map',id=wxID_FOURCALC, kind=wx.ITEM_NORMAL,
1198	text='Fourier map')
1199	self.GeneralCalc.Append(help='Search Fourier map',id=wxID_FOURSEARCH, kind=wx.ITEM_NORMAL,
1200	text='Search map')
1201	self.GeneralCalc.Append(help='Run charge flipping',id=wxID_CHARGEFLIP, kind=wx.ITEM_NORMAL,
1202	text='Charge flipping')
1203	self.GeneralCalc.Append(help='Run 4D charge flipping',id=wxID_4DCHARGEFLIP, kind=wx.ITEM_NORMAL,
1204	text='4D Charge flipping')
1205	self.GeneralCalc.Enable(wxID_4DCHARGEFLIP,False)
1206	self.GeneralCalc.Append(help='Clear map',id=wxID_FOURCLEAR, kind=wx.ITEM_NORMAL,
1207	text='Clear map')
1208	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing',id=wxID_SINGLEMCSA, kind=wx.ITEM_NORMAL,
1209	text='MC/SA')
1210	self.GeneralCalc.Append(help='Run Monte Carlo - Simulated Annealing on multiprocessors',id=wxID_MULTIMCSA, kind=wx.ITEM_NORMAL,
1211	text='Multi MC/SA') #currently not useful
1212	self.GeneralCalc.Append(help='Transform crystal structure',id=wxID_TRANSFORMSTRUCTURE, kind=wx.ITEM_NORMAL,
1213	text='Transform')
1214	self.PostfillDataMenu()
1215
1216	# Phase / Data tab
1217	self.DataMenu = wx.MenuBar()
1218	self.PrefillDataMenu(self.DataMenu,helpType='Data', helpLbl='Phase/Data')
1219	self.DataMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1220	self.DataEdit = wx.Menu(title='')
1221	self.DataMenu.Append(menu=self.DataEdit, title='Edit')
1222	self.DataEdit.Append(id=wxID_DATACOPY, kind=wx.ITEM_NORMAL,text='Copy data',
1223	help='Copy phase data to other histograms')
1224	self.DataEdit.Append(id=wxID_DATACOPYFLAGS, kind=wx.ITEM_NORMAL,text='Copy flags',
1225	help='Copy phase data flags to other histograms')
1226	self.DataEdit.Append(id=wxID_DATASELCOPY, kind=wx.ITEM_NORMAL,text='Copy selected data',
1227	help='Copy selected phase data to other histograms')
1228	self.DataEdit.Append(id=wxID_PWDRADD, kind=wx.ITEM_NORMAL,text='Add powder histograms',
1229	help='Select new powder histograms to be used for this phase')
1230	self.DataEdit.Append(id=wxID_HKLFADD, kind=wx.ITEM_NORMAL,text='Add single crystal histograms',
1231	help='Select new single crystal histograms to be used for this phase')
1232	self.DataEdit.Append(id=wxID_DATADELETE, kind=wx.ITEM_NORMAL,text='Remove histograms',
1233	help='Remove histograms from use for this phase')
1234	self.PostfillDataMenu()
1235
1236	# Phase / Atoms tab
1237	self.AtomsMenu = wx.MenuBar()
1238	self.PrefillDataMenu(self.AtomsMenu,helpType='Atoms')
1239	self.AtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1240	self.AtomEdit = wx.Menu(title='')
1241	self.AtomCompute = wx.Menu(title='')
1242	self.AtomsMenu.Append(menu=self.AtomEdit, title='Edit')
1243	self.AtomsMenu.Append(menu=self.AtomCompute, title='Compute')
1244	self.AtomEdit.Append(id=wxID_ATOMSEDITADD, kind=wx.ITEM_NORMAL,text='Append atom',
1245	help='Appended as an H atom')
1246	self.AtomEdit.Append(id=wxID_ATOMSVIEWADD, kind=wx.ITEM_NORMAL,text='Append view point',
1247	help='Appended as an H atom')
1248	self.AtomEdit.Append(id=wxID_ATOMSEDITINSERT, kind=wx.ITEM_NORMAL,text='Insert atom',
1249	help='Select atom row to insert before; inserted as an H atom')
1250	self.AtomEdit.Append(id=wxID_ATOMVIEWINSERT, kind=wx.ITEM_NORMAL,text='Insert view point',
1251	help='Select atom row to insert before; inserted as an H atom')
1252	self.AtomEdit.Append(id=wxID_ADDHATOM, kind=wx.ITEM_NORMAL,text='Insert H atoms',
1253	help='Insert H atoms in standard positions bonded to selected atoms')
1254	self.AtomEdit.Append(id=wxID_UPDATEHATOM, kind=wx.ITEM_NORMAL,text='Update H atoms',
1255	help='Update H atoms in standard positions')
1256	self.AtomEdit.Append(id=wxID_ATOMMOVE, kind=wx.ITEM_NORMAL,text='Move atom to view point',
1257	help='Select single atom to move')
1258	self.AtomEdit.Append(id=wxID_ATOMSEDITDELETE, kind=wx.ITEM_NORMAL,text='Delete atom',
1259	help='Select atoms to delete first')
1260	self.AtomEdit.Append(id=wxID_ATOMSREFINE, kind=wx.ITEM_NORMAL,text='Set atom refinement flags',
1261	help='Select atoms to refine first')
1262	self.AtomEdit.Append(id=wxID_ATOMSMODIFY, kind=wx.ITEM_NORMAL,text='Modify atom parameters',
1263	help='Select atoms to modify first')
1264	self.AtomEdit.Append(id=wxID_ATOMSTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform atoms',
1265	help='Select atoms to transform first')
1266	self.AtomEdit.Append(id=wxID_MAKEMOLECULE, kind=wx.ITEM_NORMAL,text='Assemble molecule',
1267	help='Assemble molecule from scatterd atom positions')
1268	self.AtomEdit.Append(id=wxID_RELOADDRAWATOMS, kind=wx.ITEM_NORMAL,text='Reload draw atoms',
1269	help='Reload atom drawing list')
1270	submenu = wx.Menu()
1271	self.AtomEdit.AppendMenu(wx.ID_ANY, 'Reimport atoms', submenu,
1272	help='Reimport atoms from file; sequence must match')
1273	# setup a cascade menu for the formats that have been defined
1274	self.ReImportMenuId = {} # points to readers for each menu entry
1275	for reader in self.G2frame.ImportPhaseReaderlist:
1276	item = submenu.Append(
1277	wx.ID_ANY,help=reader.longFormatName,
1278	kind=wx.ITEM_NORMAL,text='reimport coordinates from '+reader.formatName+' file')
1279	self.ReImportMenuId[item.GetId()] = reader
1280	item = submenu.Append(
1281	wx.ID_ANY,
1282	help='Reimport coordinates, try to determine format from file',
1283	kind=wx.ITEM_NORMAL,
1284	text='guess format from file')
1285	self.ReImportMenuId[item.GetId()] = None # try all readers
1286
1287	self.AtomCompute.Append(id=wxID_ATOMSDISAGL, kind=wx.ITEM_NORMAL,text='Show Distances && Angles',
1288	help='Compute distances & angles for selected atoms')
1289	self.AtomCompute.Append(id=wxID_ATOMSPDISAGL, kind=wx.ITEM_NORMAL,text='Save Distances && Angles',
1290	help='Compute distances & angles for selected atoms')
1291	self.AtomCompute.ISOcalc = self.AtomCompute.Append(
1292	id=wxID_ISODISP, kind=wx.ITEM_NORMAL,
1293	text='Compute ISODISTORT mode values',
1294	help='Compute values of ISODISTORT modes from atom parameters')
1295	self.PostfillDataMenu()
1296
1297	# Phase / Imcommensurate "waves" tab
1298	self.WavesData = wx.MenuBar()
1299	self.PrefillDataMenu(self.WavesData,helpType='Wave Data', helpLbl='Imcommensurate wave data')
1300	self.WavesData.Append(menu=wx.Menu(title=''),title='Select tab')
1301	self.WavesDataEdit = wx.Menu(title='')
1302	self.WavesData.Append(menu=self.WavesDataEdit, title='Edit')
1303	self.WavesDataEdit.Append(id=wxID_WAVEVARY, kind=wx.ITEM_NORMAL,text='Global wave vary',
1304	help='Global setting of wave vary flags')
1305	self.PostfillDataMenu()
1306
1307	# Phase / Draw Options tab
1308	self.DataDrawOptions = wx.MenuBar()
1309	self.PrefillDataMenu(self.DataDrawOptions,helpType='Draw Options', helpLbl='Phase/Draw Options')
1310	self.DataDrawOptions.Append(menu=wx.Menu(title=''),title='Select tab')
1311	self.PostfillDataMenu()
1312
1313	# Phase / Draw Atoms tab
1314	self.DrawAtomsMenu = wx.MenuBar()
1315	self.PrefillDataMenu(self.DrawAtomsMenu,helpType='Draw Atoms')
1316	self.DrawAtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1317	self.DrawAtomEdit = wx.Menu(title='')
1318	self.DrawAtomCompute = wx.Menu(title='')
1319	self.DrawAtomRestraint = wx.Menu(title='')
1320	self.DrawAtomRigidBody = wx.Menu(title='')
1321	self.DrawAtomsMenu.Append(menu=self.DrawAtomEdit, title='Edit')
1322	self.DrawAtomsMenu.Append(menu=self.DrawAtomCompute,title='Compute')
1323	self.DrawAtomsMenu.Append(menu=self.DrawAtomRestraint, title='Restraints')
1324	self.DrawAtomsMenu.Append(menu=self.DrawAtomRigidBody, title='Rigid body')
1325	self.DrawAtomEdit.Append(id=wxID_DRAWATOMSTYLE, kind=wx.ITEM_NORMAL,text='Atom style',
1326	help='Select atoms first')
1327	self.DrawAtomEdit.Append(id=wxID_DRAWATOMLABEL, kind=wx.ITEM_NORMAL,text='Atom label',
1328	help='Select atoms first')
1329	self.DrawAtomEdit.Append(id=wxID_DRAWATOMCOLOR, kind=wx.ITEM_NORMAL,text='Atom color',
1330	help='Select atoms first')
1331	self.DrawAtomEdit.Append(id=wxID_DRAWATOMRESETCOLOR, kind=wx.ITEM_NORMAL,text='Reset atom colors',
1332	help='Resets all atom colors to defaults')
1333	self.DrawAtomEdit.Append(id=wxID_DRAWVIEWPOINT, kind=wx.ITEM_NORMAL,text='View point',
1334	help='View point is 1st atom selected')
1335	self.DrawAtomEdit.Append(id=wxID_DRAWADDEQUIV, kind=wx.ITEM_NORMAL,text='Add atoms',
1336	help='Add symmetry & cell equivalents to drawing set from selected atoms')
1337	self.DrawAtomEdit.Append(id=wxID_DRAWTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform draw atoms',
1338	help='Transform selected atoms by symmetry & cell translations')
1339	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCOORD, kind=wx.ITEM_NORMAL,text='Fill CN-sphere',
1340	help='Fill coordination sphere for selected atoms')
1341	self.DrawAtomEdit.Append(id=wxID_DRAWFILLCELL, kind=wx.ITEM_NORMAL,text='Fill unit cell',
1342	help='Fill unit cell with selected atoms')
1343	self.DrawAtomEdit.Append(id=wxID_DRAWDELETE, kind=wx.ITEM_NORMAL,text='Delete atoms',
1344	help='Delete atoms from drawing set')
1345	self.DrawAtomCompute.Append(id=wxID_DRAWDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1346	help='Compute distance of selected atoms from view point')
1347	self.DrawAtomCompute.Append(id=wxID_DRAWDISAGLTOR, kind=wx.ITEM_NORMAL,text='Dist. Ang. Tors.',
1348	help='Compute distance, angle or torsion for 2-4 selected atoms')
1349	self.DrawAtomCompute.Append(id=wxID_DRAWPLANE, kind=wx.ITEM_NORMAL,text='Best plane',
1350	help='Compute best plane for 4+ selected atoms')
1351	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRBOND, kind=wx.ITEM_NORMAL,text='Add bond restraint',
1352	help='Add bond restraint for selected atoms (2)')
1353	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRANGLE, kind=wx.ITEM_NORMAL,text='Add angle restraint',
1354	help='Add angle restraint for selected atoms (3: one end 1st)')
1355	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRPLANE, kind=wx.ITEM_NORMAL,text='Add plane restraint',
1356	help='Add plane restraint for selected atoms (4+)')
1357	self.DrawAtomRestraint.Append(id=wxID_DRAWRESTRCHIRAL, kind=wx.ITEM_NORMAL,text='Add chiral restraint',
1358	help='Add chiral restraint for selected atoms (4: center atom 1st)')
1359	self.DrawAtomRigidBody.Append(id=wxID_DRAWDEFINERB, kind=wx.ITEM_NORMAL,text='Define rigid body',
1360	help='Define rigid body with selected atoms')
1361	self.PostfillDataMenu()
1362
1363	# Phase / MCSA tab
1364	self.MCSAMenu = wx.MenuBar()
1365	self.PrefillDataMenu(self.MCSAMenu,helpType='MC/SA')
1366	self.MCSAMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1367	self.MCSAEdit = wx.Menu(title='')
1368	self.MCSAMenu.Append(menu=self.MCSAEdit, title='MC/SA')
1369	self.MCSAEdit.Append(id=wxID_ADDMCSAATOM, kind=wx.ITEM_NORMAL,text='Add atom',
1370	help='Add single atom to MC/SA model')
1371	self.MCSAEdit.Append(id=wxID_ADDMCSARB, kind=wx.ITEM_NORMAL,text='Add rigid body',
1372	help='Add rigid body to MC/SA model' )
1373	self.MCSAEdit.Append(id=wxID_CLEARMCSARB, kind=wx.ITEM_NORMAL,text='Clear rigid bodies',
1374	help='Clear all atoms & rigid bodies from MC/SA model' )
1375	self.MCSAEdit.Append(id=wxID_MOVEMCSA, kind=wx.ITEM_NORMAL,text='Move MC/SA solution',
1376	help='Move MC/SA solution to atom list' )
1377	self.MCSAEdit.Append(id=wxID_MCSACLEARRESULTS, kind=wx.ITEM_NORMAL,text='Clear results',
1378	help='Clear table of MC/SA results' )
1379	self.PostfillDataMenu()
1380
1381	# Phase / Texture tab
1382	self.TextureMenu = wx.MenuBar()
1383	self.PrefillDataMenu(self.TextureMenu,helpType='Texture')
1384	self.TextureMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1385	self.TextureEdit = wx.Menu(title='')
1386	self.TextureMenu.Append(menu=self.TextureEdit, title='Texture')
1387	self.TextureEdit.Append(id=wxID_REFINETEXTURE, kind=wx.ITEM_NORMAL,text='Refine texture',
1388	help='Refine the texture coefficients from sequential results')
1389	# self.TextureEdit.Append(id=wxID_CLEARTEXTURE, kind=wx.ITEM_NORMAL,text='Clear texture',
1390	# help='Clear the texture coefficients' )
1391	self.PostfillDataMenu()
1392
1393	# Phase / Pawley tab
1394	self.PawleyMenu = wx.MenuBar()
1395	self.PrefillDataMenu(self.PawleyMenu,helpType='Pawley')
1396	self.PawleyMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1397	self.PawleyEdit = wx.Menu(title='')
1398	self.PawleyMenu.Append(menu=self.PawleyEdit,title='Operations')
1399	self.PawleyEdit.Append(id=wxID_PAWLEYLOAD, kind=wx.ITEM_NORMAL,text='Pawley create',
1400	help='Initialize Pawley reflection list')
1401	self.PawleyEdit.Append(id=wxID_PAWLEYESTIMATE, kind=wx.ITEM_NORMAL,text='Pawley estimate',
1402	help='Estimate initial Pawley intensities')
1403	self.PawleyEdit.Append(id=wxID_PAWLEYUPDATE, kind=wx.ITEM_NORMAL,text='Pawley update',
1404	help='Update negative Pawley intensities with -0.5*Fobs and turn off refinemnt')
1405	self.PostfillDataMenu()
1406
1407	# Phase / Map peaks tab
1408	self.MapPeaksMenu = wx.MenuBar()
1409	self.PrefillDataMenu(self.MapPeaksMenu,helpType='Map peaks')
1410	self.MapPeaksMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1411	self.MapPeaksEdit = wx.Menu(title='')
1412	self.MapPeaksMenu.Append(menu=self.MapPeaksEdit, title='Map peaks')
1413	self.MapPeaksEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks',
1414	help='Move selected peaks to atom list')
1415	self.MapPeaksEdit.Append(id=wxID_PEAKSVIEWPT, kind=wx.ITEM_NORMAL,text='View point',
1416	help='View point is 1st peak selected')
1417	self.MapPeaksEdit.Append(id=wxID_PEAKSDISTVP, kind=wx.ITEM_NORMAL,text='View pt. dist.',
1418	help='Compute distance of selected peaks from view point')
1419	self.MapPeaksEdit.Append(id=wxID_SHOWBONDS, kind=wx.ITEM_NORMAL,text='Hide bonds',
1420	help='Hide or show bonds between peak positions')
1421	self.MapPeaksEdit.Append(id=wxID_PEAKSDA, kind=wx.ITEM_NORMAL,text='Calc dist/ang',
1422	help='Calculate distance or angle for selection')
1423	self.MapPeaksEdit.Append(id=wxID_FINDEQVPEAKS, kind=wx.ITEM_NORMAL,text='Equivalent peaks',
1424	help='Find equivalent peaks')
1425	self.MapPeaksEdit.Append(id=wxID_PEAKSUNIQUE, kind=wx.ITEM_NORMAL,text='Unique peaks',
1426	help='Select unique set')
1427	self.MapPeaksEdit.Append(id=wxID_PEAKSDELETE, kind=wx.ITEM_NORMAL,text='Delete peaks',
1428	help='Delete selected peaks')
1429	self.MapPeaksEdit.Append(id=wxID_PEAKSCLEAR, kind=wx.ITEM_NORMAL,text='Clear peaks',
1430	help='Clear the map peak list')
1431	self.PostfillDataMenu()
1432
1433	# Phase / Rigid bodies tab
1434	self.RigidBodiesMenu = wx.MenuBar()
1435	self.PrefillDataMenu(self.RigidBodiesMenu,helpType='Rigid bodies')
1436	self.RigidBodiesMenu.Append(menu=wx.Menu(title=''),title='Select tab')
1437	self.RigidBodiesEdit = wx.Menu(title='')
1438	self.RigidBodiesMenu.Append(menu=self.RigidBodiesEdit, title='Edit')
1439	self.RigidBodiesEdit.Append(id=wxID_ASSIGNATMS2RB, kind=wx.ITEM_NORMAL,text='Assign atoms to rigid body',
1440	help='Select & position rigid body in structure of existing atoms')
1441	self.RigidBodiesEdit.Append(id=wxID_AUTOFINDRESRB, kind=wx.ITEM_NORMAL,text='Auto find residues',
1442	help='Auto find of residue RBs in macromolecule')
1443	self.RigidBodiesEdit.Append(id=wxID_COPYRBPARMS, kind=wx.ITEM_NORMAL,text='Copy rigid body parms',
1444	help='Copy rigid body location & TLS parameters')
1445	self.RigidBodiesEdit.Append(id=wxID_GLOBALTHERM, kind=wx.ITEM_NORMAL,text='Global thermal motion',
1446	help='Global setting of residue thermal motion models')
1447	self.RigidBodiesEdit.Append(id=wxID_GLOBALRESREFINE, kind=wx.ITEM_NORMAL,text='Global residue refine',
1448	help='Global setting of residue RB refinement flags')
1449	self.RigidBodiesEdit.Append(id=wxID_RBREMOVEALL, kind=wx.ITEM_NORMAL,text='Remove all rigid bodies',
1450	help='Remove all rigid body assignment for atoms')
1451	self.PostfillDataMenu()
1452	# end of GSAS-II menu definitions
1453
1454	def _init_ctrls(self, parent,name=None,size=None,pos=None):
1455	wx.Frame.__init__(
1456	self,parent=parent,
1457	#style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX \| wx.FRAME_FLOAT_ON_PARENT ,
1458	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX,
1459	size=size,pos=pos,title='GSAS-II data display')
1460	self._init_menus()
1461	if name:
1462	self.SetLabel(name)
1463	self.Show()
1464
1465	def __init__(self,parent,frame,data=None,name=None, size=None,pos=None):
1466	self.G2frame = frame
1467	self._init_ctrls(parent,name,size,pos)
1468	self.data = data
1469	clientSize = wx.ClientDisplayRect()
1470	Size = self.GetSize()
1471	xPos = clientSize[2]-Size[0]
1472	self.SetPosition(wx.Point(xPos,clientSize[1]+250))
1473	self.AtomGrid = []
1474	self.selectedRow = 0
1475
1476	def setSizePosLeft(self,Width):
1477	clientSize = wx.ClientDisplayRect()
1478	Width[1] = min(Width[1],clientSize[2]-300)
1479	Width[0] = max(Width[0],300)
1480	self.SetSize(Width)
1481	# self.SetPosition(wx.Point(clientSize[2]-Width[0],clientSize[1]+250))
1482
1483	def Clear(self):
1484	self.ClearBackground()
1485	self.DestroyChildren()
1486
1487
1488	################################################################################
1489	##### Notebook Tree Item editor
1490	################################################################################
1491	def UpdateNotebook(G2frame,data):
1492	'''Called when the data tree notebook entry is selected. Allows for
1493	editing of the text in that tree entry
1494	'''
1495	def OnNoteBook(event):
1496	data = G2frame.dataDisplay.GetValue().split('\n')
1497	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Notebook'),data)
1498	if 'nt' not in os.name:
1499	G2frame.dataDisplay.AppendText('\n')
1500
1501	if G2frame.dataDisplay:
1502	G2frame.dataDisplay.Destroy()
1503	G2frame.dataFrame.SetLabel('Notebook')
1504	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1505	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER \| wx.TE_DONTWRAP)
1506	G2frame.dataDisplay.Bind(wx.EVT_TEXT_ENTER,OnNoteBook)
1507	G2frame.dataDisplay.Bind(wx.EVT_KILL_FOCUS,OnNoteBook)
1508	for line in data:
1509	G2frame.dataDisplay.AppendText(line+"\n")
1510	G2frame.dataDisplay.AppendText('Notebook entry @ '+time.ctime()+"\n")
1511	G2frame.dataFrame.setSizePosLeft([400,250])
1512
1513	################################################################################
1514	##### Controls Tree Item editor
1515	################################################################################
1516	def UpdateControls(G2frame,data):
1517	'''Edit overall GSAS-II controls in main Controls data tree entry
1518	'''
1519	#patch
1520	if 'deriv type' not in data:
1521	data = {}
1522	data['deriv type'] = 'analytic Hessian'
1523	data['min dM/M'] = 0.0001
1524	data['shift factor'] = 1.
1525	data['max cyc'] = 3
1526	data['F**2'] = False
1527	if 'shift factor' not in data:
1528	data['shift factor'] = 1.
1529	if 'max cyc' not in data:
1530	data['max cyc'] = 3
1531	if 'F**2' not in data:
1532	data['F**2'] = False
1533	if 'Author' not in data:
1534	data['Author'] = 'no name'
1535	if 'FreePrm1' not in data:
1536	data['FreePrm1'] = 'Sample humidity (%)'
1537	if 'FreePrm2' not in data:
1538	data['FreePrm2'] = 'Sample voltage (V)'
1539	if 'FreePrm3' not in data:
1540	data['FreePrm3'] = 'Applied load (MN)'
1541	if 'Copy2Next' not in data:
1542	data['Copy2Next'] = False
1543	if 'Reverse Seq' not in data:
1544	data['Reverse Seq'] = False
1545	if 'UsrReject' not in data:
1546	data['UsrReject'] = {'minF/sig':0,'MinExt':0.01,'MaxDF/F':20.,'MaxD':500.,'MinD':0.05}
1547	if 'HatomFix' not in data:
1548	data['HatomFix'] = False
1549
1550	#end patch
1551
1552	def SeqSizer():
1553
1554	def OnSelectData(event):
1555	choices = GetPatternTreeDataNames(G2frame,['PWDR','HKLF',])
1556	sel = []
1557	try:
1558	if 'Seq Data' in data:
1559	for item in data['Seq Data']:
1560	sel.append(choices.index(item))
1561	sel = [choices.index(item) for item in data['Seq Data']]
1562	except ValueError: #data changed somehow - start fresh
1563	sel = []
1564	dlg = G2G.G2MultiChoiceDialog(G2frame.dataFrame, 'Sequential refinement',
1565	'Select dataset to include',choices)
1566	dlg.SetSelections(sel)
1567	names = []
1568	if dlg.ShowModal() == wx.ID_OK:
1569	for sel in dlg.GetSelections():
1570	names.append(choices[sel])
1571	data['Seq Data'] = names
1572	G2frame.EnableSeqRefineMenu()
1573	dlg.Destroy()
1574	wx.CallAfter(UpdateControls,G2frame,data)
1575
1576	def OnReverse(event):
1577	data['Reverse Seq'] = reverseSel.GetValue()
1578
1579	def OnCopySel(event):
1580	data['Copy2Next'] = copySel.GetValue()
1581
1582	seqSizer = wx.BoxSizer(wx.VERTICAL)
1583	dataSizer = wx.BoxSizer(wx.HORIZONTAL)
1584	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Sequential Refinement: '),0,WACV)
1585	selSeqData = wx.Button(G2frame.dataDisplay,-1,label=' Select data')
1586	selSeqData.Bind(wx.EVT_BUTTON,OnSelectData)
1587	dataSizer.Add(selSeqData,0,WACV)
1588	SeqData = data.get('Seq Data',[])
1589	if not SeqData:
1590	lbl = ' (no data selected)'
1591	else:
1592	lbl = ' ('+str(len(SeqData))+' dataset(s) selected)'
1593
1594	dataSizer.Add(wx.StaticText(G2frame.dataDisplay,label=lbl),0,WACV)
1595	seqSizer.Add(dataSizer,0)
1596	if SeqData:
1597	selSizer = wx.BoxSizer(wx.HORIZONTAL)
1598	reverseSel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Reverse order?')
1599	reverseSel.Bind(wx.EVT_CHECKBOX,OnReverse)
1600	reverseSel.SetValue(data['Reverse Seq'])
1601	selSizer.Add(reverseSel,0,WACV)
1602	copySel = wx.CheckBox(G2frame.dataDisplay,-1,label=' Copy results to next histogram?')
1603	copySel.Bind(wx.EVT_CHECKBOX,OnCopySel)
1604	copySel.SetValue(data['Copy2Next'])
1605	selSizer.Add(copySel,0,WACV)
1606	seqSizer.Add(selSizer,0)
1607	return seqSizer
1608
1609	def LSSizer():
1610
1611	def OnDerivType(event):
1612	data['deriv type'] = derivSel.GetValue()
1613	derivSel.SetValue(data['deriv type'])
1614	wx.CallAfter(UpdateControls,G2frame,data)
1615
1616	def OnConvergence(event):
1617	try:
1618	value = max(1.e-9,min(1.0,float(Cnvrg.GetValue())))
1619	except ValueError:
1620	value = 0.0001
1621	data['min dM/M'] = value
1622	Cnvrg.SetValue('%.2g'%(value))
1623
1624	def OnMaxCycles(event):
1625	data['max cyc'] = int(maxCyc.GetValue())
1626	maxCyc.SetValue(str(data['max cyc']))
1627
1628	def OnFactor(event):
1629	try:
1630	value = min(max(float(Factr.GetValue()),0.00001),100.)
1631	except ValueError:
1632	value = 1.0
1633	data['shift factor'] = value
1634	Factr.SetValue('%.5f'%(value))
1635
1636	def OnFsqRef(event):
1637	data['F**2'] = fsqRef.GetValue()
1638
1639	def OnHatomFix(event):
1640	data['HatomFix'] = Hfix.GetValue()
1641
1642	def OnUsrRej(event):
1643	Obj = event.GetEventObject()
1644	item,limits = Indx[Obj]
1645	try:
1646	value = min(max(float(Obj.GetValue()),limits[0]),limits[1])
1647	except ValueError:
1648	value = data['UsrReject'][item]
1649	data['UsrReject'][item] = value
1650	Obj.SetValue('%.2f'%(value))
1651
1652	LSSizer = wx.FlexGridSizer(cols=4,vgap=5,hgap=5)
1653	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement derivatives: '),0,WACV)
1654	Choice=['analytic Jacobian','numeric','analytic Hessian']
1655	derivSel = wx.ComboBox(parent=G2frame.dataDisplay,value=data['deriv type'],choices=Choice,
1656	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1657	derivSel.SetValue(data['deriv type'])
1658	derivSel.Bind(wx.EVT_COMBOBOX, OnDerivType)
1659
1660	LSSizer.Add(derivSel,0,WACV)
1661	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Min delta-M/M: '),0,WACV)
1662	Cnvrg = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2g'%(data['min dM/M']),style=wx.TE_PROCESS_ENTER)
1663	Cnvrg.Bind(wx.EVT_TEXT_ENTER,OnConvergence)
1664	Cnvrg.Bind(wx.EVT_KILL_FOCUS,OnConvergence)
1665	LSSizer.Add(Cnvrg,0,WACV)
1666	Indx = {}
1667	if 'Hessian' in data['deriv type']:
1668	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Max cycles: '),0,WACV)
1669	Choice = ['0','1','2','3','5','10','15','20']
1670	maxCyc = wx.ComboBox(parent=G2frame.dataDisplay,value=str(data['max cyc']),choices=Choice,
1671	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1672	maxCyc.SetValue(str(data['max cyc']))
1673	maxCyc.Bind(wx.EVT_COMBOBOX, OnMaxCycles)
1674	LSSizer.Add(maxCyc,0,WACV)
1675	else:
1676	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Initial shift factor: '),0,WACV)
1677	Factr = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.5f'%(data['shift factor']),style=wx.TE_PROCESS_ENTER)
1678	Factr.Bind(wx.EVT_TEXT_ENTER,OnFactor)
1679	Factr.Bind(wx.EVT_KILL_FOCUS,OnFactor)
1680	LSSizer.Add(Factr,0,WACV)
1681	if G2frame.Sngl:
1682	userReject = data['UsrReject']
1683	usrRej = {'minF/sig':[' Min obs/sig (0-5): ',[0,5], ],'MinExt':[' Min extinct. (0-.9): ',[0,.9],],
1684	'MaxDF/F':[' Max delt-F/sig (3-1000): ',[3.,1000.],],'MaxD':[' Max d-spacing (3-500): ',[3,500],],
1685	'MinD':[' Min d-spacing (0.1-1.0): ',[0.1,1.0],]}
1686
1687	fsqRef = wx.CheckBox(G2frame.dataDisplay,-1,label='Refine HKLF as F^2? ')
1688	fsqRef.SetValue(data['F**2'])
1689	fsqRef.Bind(wx.EVT_CHECKBOX,OnFsqRef)
1690	LSSizer.Add(fsqRef,0,WACV)
1691	LSSizer.Add((1,0),)
1692	for item in usrRej:
1693	LSSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,label=usrRej[item][0]),0,WACV)
1694	usrrej = wx.TextCtrl(G2frame.dataDisplay,-1,value='%.2f'%(userReject[item]),style=wx.TE_PROCESS_ENTER)
1695	Indx[usrrej] = [item,usrRej[item][1]]
1696	usrrej.Bind(wx.EVT_TEXT_ENTER,OnUsrRej)
1697	usrrej.Bind(wx.EVT_KILL_FOCUS,OnUsrRej)
1698	LSSizer.Add(usrrej,0,WACV)
1699	# Hfix = wx.CheckBox(G2frame.dataDisplay,-1,label='Regularize H atoms? ')
1700	# Hfix.SetValue(data['HatomFix'])
1701	# Hfix.Bind(wx.EVT_CHECKBOX,OnHatomFix)
1702	# LSSizer.Add(Hfix,0,WACV) #for now
1703	return LSSizer
1704
1705	def AuthSizer():
1706
1707	def OnAuthor(event):
1708	data['Author'] = auth.GetValue()
1709
1710	Author = data['Author']
1711	authSizer = wx.BoxSizer(wx.HORIZONTAL)
1712	authSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' CIF Author (last, first):'),0,WACV)
1713	auth = wx.TextCtrl(G2frame.dataDisplay,-1,value=Author,style=wx.TE_PROCESS_ENTER)
1714	auth.Bind(wx.EVT_TEXT_ENTER,OnAuthor)
1715	auth.Bind(wx.EVT_KILL_FOCUS,OnAuthor)
1716	authSizer.Add(auth,0,WACV)
1717	return authSizer
1718
1719
1720	if G2frame.dataDisplay:
1721	G2frame.dataDisplay.Destroy()
1722	if not G2frame.dataFrame.GetStatusBar():
1723	Status = G2frame.dataFrame.CreateStatusBar()
1724	Status.SetStatusText('')
1725	G2frame.dataFrame.SetLabel('Controls')
1726	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
1727	SetDataMenuBar(G2frame,G2frame.dataFrame.ControlsMenu)
1728	mainSizer = wx.BoxSizer(wx.VERTICAL)
1729	mainSizer.Add((5,5),0)
1730	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,label=' Refinement Controls:'),0,WACV)
1731	mainSizer.Add(LSSizer())
1732	mainSizer.Add((5,5),0)
1733	mainSizer.Add(SeqSizer())
1734	mainSizer.Add((5,5),0)
1735	mainSizer.Add(AuthSizer())
1736	mainSizer.Add((5,5),0)
1737
1738	mainSizer.Layout()
1739	G2frame.dataDisplay.SetSizer(mainSizer)
1740	G2frame.dataDisplay.SetSize(mainSizer.Fit(G2frame.dataFrame))
1741	G2frame.dataFrame.setSizePosLeft(mainSizer.Fit(G2frame.dataFrame))
1742
1743	################################################################################
1744	##### Comments
1745	################################################################################
1746
1747	def UpdateComments(G2frame,data):
1748
1749	if G2frame.dataDisplay:
1750	G2frame.dataDisplay.Destroy()
1751	G2frame.dataFrame.SetLabel('Comments')
1752	G2frame.dataDisplay = wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
1753	style=wx.TE_MULTILINE\|wx.TE_READONLY\|wx.TE_DONTWRAP)
1754	for line in data:
1755	G2frame.dataDisplay.AppendText(line+'\n')
1756	G2frame.dataFrame.setSizePosLeft([400,250])
1757
1758	################################################################################
1759	##### Display of Sequential Results
1760	################################################################################
1761
1762	def UpdateSeqResults(G2frame,data,prevSize=None):
1763	"""
1764	Called when the Sequential Results data tree entry is selected
1765	to show results from a sequential refinement.
1766
1767	:param wx.Frame G2frame: main GSAS-II data tree windows
1768
1769	:param dict data: a dictionary containing the following items:
1770
1771	* 'histNames' - list of histogram names in order as processed by Sequential Refinement
1772	* 'varyList' - list of variables - identical over all refinements in sequence
1773	note that this is the original list of variables, prior to processing
1774	constraints.
1775	* 'variableLabels' -- a dict of labels to be applied to each parameter
1776	(this is created as an empty dict if not present in data).
1777	* keyed by histName - dictionaries for all data sets processed, which contains:
1778
1779	* 'variables'- result[0] from leastsq call
1780	* 'varyList' - list of variables passed to leastsq call (not same as above)
1781	* 'sig' - esds for variables
1782	* 'covMatrix' - covariance matrix from individual refinement
1783	* 'title' - histogram name; same as dict item name
1784	* 'newAtomDict' - new atom parameters after shifts applied
1785	* 'newCellDict' - refined cell parameters after shifts to A0-A5 from Dij terms applied'
1786	"""
1787
1788	def GetSampleParms():
1789	'''Make a dictionary of the sample parameters are not the same over the
1790	refinement series.
1791	'''
1792	if 'IMG' in histNames[0]:
1793	sampleParmDict = {'Sample load':[],}
1794	else:
1795	sampleParmDict = {'Temperature':[],'Pressure':[],'Time':[],
1796	'FreePrm1':[],'FreePrm2':[],'FreePrm3':[],'Omega':[],
1797	'Chi':[],'Phi':[],'Azimuth':[],}
1798	Controls = G2frame.PatternTree.GetItemPyData(
1799	GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
1800	sampleParm = {}
1801	for name in histNames:
1802	if 'IMG' in name:
1803	for item in sampleParmDict:
1804	sampleParmDict[item].append(data[name]['parmDict'].get(item,0))
1805	else:
1806	Id = GetPatternTreeItemId(G2frame,G2frame.root,name)
1807	sampleData = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,Id,'Sample Parameters'))
1808	for item in sampleParmDict:
1809	sampleParmDict[item].append(sampleData.get(item,0))
1810	for item in sampleParmDict:
1811	frstValue = sampleParmDict[item][0]
1812	if np.any(np.array(sampleParmDict[item])-frstValue):
1813	if item.startswith('FreePrm'):
1814	sampleParm[Controls[item]] = sampleParmDict[item]
1815	else:
1816	sampleParm[item] = sampleParmDict[item]
1817	return sampleParm
1818
1819	def GetColumnInfo(col):
1820	'''returns column label, lists of values and errors (or None) for each column in the table
1821	for plotting. The column label is reformatted from Unicode to MatPlotLib encoding
1822	'''
1823	colName = G2frame.SeqTable.GetColLabelValue(col)
1824	plotName = variableLabels.get(colName,colName)
1825	plotName = plotSpCharFix(plotName)
1826	return plotName,colList[col],colSigs[col]
1827
1828	def PlotSelect(event):
1829	'Plots a row (covariance) or column on double-click'
1830	cols = G2frame.dataDisplay.GetSelectedCols()
1831	rows = G2frame.dataDisplay.GetSelectedRows()
1832	if cols:
1833	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1834	elif rows:
1835	name = histNames[rows[0]] #only does 1st one selected
1836	G2plt.PlotCovariance(G2frame,data[name])
1837	else:
1838	G2frame.ErrorDialog(
1839	'Select row or columns',
1840	'Nothing selected in table. Click on column or row label(s) to plot. N.B. Grid selection can be a bit funky.'
1841	)
1842
1843	def OnPlotSelSeq(event):
1844	'plot the selected columns or row from menu command'
1845	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1846	rows = G2frame.dataDisplay.GetSelectedRows()
1847	if cols:
1848	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1849	elif rows:
1850	name = histNames[rows[0]] #only does 1st one selected
1851	G2plt.PlotCovariance(G2frame,data[name])
1852	else:
1853	G2frame.ErrorDialog(
1854	'Select columns',
1855	'No columns or rows selected in table. Click on row or column labels to select fields for plotting.'
1856	)
1857
1858	def OnAveSelSeq(event):
1859	'average the selected columns from menu command'
1860	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1861	if cols:
1862	for col in cols:
1863	ave = np.mean(GetColumnInfo(col)[1])
1864	sig = np.std(GetColumnInfo(col)[1])
1865	print ' Average for '+G2frame.SeqTable.GetColLabelValue(col)+': '+'%.6g'%(ave)+' +/- '+'%.6g'%(sig)
1866	else:
1867	G2frame.ErrorDialog(
1868	'Select columns',
1869	'No columns selected in table. Click on column labels to select fields for averaging.'
1870	)
1871
1872	def OnRenameSelSeq(event):
1873	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1874	colNames = [G2frame.SeqTable.GetColLabelValue(c) for c in cols]
1875	newNames = colNames[:]
1876	for i,name in enumerate(colNames):
1877	if name in variableLabels:
1878	newNames[i] = variableLabels[name]
1879	if not cols:
1880	G2frame.ErrorDialog('Select columns',
1881	'No columns selected in table. Click on column labels to select fields for rename.')
1882	return
1883	dlg = G2G.MultiStringDialog(G2frame.dataDisplay,'Set column names',colNames,newNames)
1884	if dlg.Show():
1885	newNames = dlg.GetValues()
1886	variableLabels.update(dict(zip(colNames,newNames)))
1887	data['variableLabels'] = variableLabels
1888	dlg.Destroy()
1889	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1890	G2plt.PlotSelectedSequence(G2frame,cols,GetColumnInfo,SelectXaxis)
1891
1892	def OnReOrgSelSeq(event):
1893	'Reorder the columns'
1894	G2G.GetItemOrder(G2frame,VaryListChanges,vallookup,posdict)
1895	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
1896
1897	def OnSaveSelSeqCSV(event):
1898	'export the selected columns to a .csv file from menu command'
1899	OnSaveSelSeq(event,csv=True)
1900
1901	def OnSaveSeqCSV(event):
1902	'export all columns to a .csv file from menu command'
1903	OnSaveSelSeq(event,csv=True,allcols=True)
1904
1905	def OnSaveSelSeq(event,csv=False,allcols=False):
1906	'export the selected columns to a .txt or .csv file from menu command'
1907	def WriteCSV():
1908	def WriteList(headerItems):
1909	line = ''
1910	for lbl in headerItems:
1911	if line: line += ','
1912	line += '"'+lbl+'"'
1913	return line
1914	head = ['name']
1915	for col in cols:
1916	item = G2frame.SeqTable.GetColLabelValue(col)
1917	# get rid of labels that have Unicode characters
1918	if not all([ord(c) < 128 and ord(c) != 0 for c in item]): item = '?'
1919	if col in havesig:
1920	head += [item,'esd-'+item]
1921	else:
1922	head += [item]
1923	SeqFile.write(WriteList(head)+'\n')
1924	for row,name in enumerate(saveNames):
1925	line = '"'+saveNames[row]+'"'
1926	for col in cols:
1927	if col in havesig:
1928	line += ','+str(saveData[col][row])+','+str(saveSigs[col][row])
1929	else:
1930	line += ','+str(saveData[col][row])
1931	SeqFile.write(line+'\n')
1932	def WriteSeq():
1933	lenName = len(saveNames[0])
1934	line = ' %s '%('name'.center(lenName))
1935	for col in cols:
1936	item = G2frame.SeqTable.GetColLabelValue(col)
1937	if col in havesig:
1938	line += ' %12s %12s '%(item.center(12),'esd'.center(12))
1939	else:
1940	line += ' %12s '%(item.center(12))
1941	SeqFile.write(line+'\n')
1942	for row,name in enumerate(saveNames):
1943	line = " '%s' "%(saveNames[row])
1944	for col in cols:
1945	if col in havesig:
1946	line += ' %12.6f %12.6f '%(saveData[col][row],saveSigs[col][row])
1947	else:
1948	line += ' %12.6f '%saveData[col][row]
1949	SeqFile.write(line+'\n')
1950
1951	# start of OnSaveSelSeq code
1952	if allcols:
1953	cols = range(G2frame.SeqTable.GetNumberCols())
1954	else:
1955	cols = sorted(G2frame.dataDisplay.GetSelectedCols()) # ignore selection order
1956	nrows = G2frame.SeqTable.GetNumberRows()
1957	if not cols:
1958	G2frame.ErrorDialog('Select columns',
1959	'No columns selected in table. Click on column labels to select fields for output.')
1960	return
1961	saveNames = [G2frame.SeqTable.GetRowLabelValue(r) for r in range(nrows)]
1962	saveData = {}
1963	saveSigs = {}
1964	havesig = []
1965	for col in cols:
1966	name,vals,sigs = GetColumnInfo(col)
1967	saveData[col] = vals
1968	if sigs:
1969	havesig.append(col)
1970	saveSigs[col] = sigs
1971	if csv:
1972	wild = 'CSV output file (.csv)\|.csv'
1973	else:
1974	wild = 'Text output file (.txt)\|.txt'
1975	pth = G2G.GetExportPath(G2frame)
1976	dlg = wx.FileDialog(
1977	G2frame,
1978	'Choose text output file for your selection', pth, '',
1979	wild,wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1980	try:
1981	if dlg.ShowModal() == wx.ID_OK:
1982	SeqTextFile = dlg.GetPath()
1983	SeqTextFile = G2IO.FileDlgFixExt(dlg,SeqTextFile)
1984	SeqFile = open(SeqTextFile,'w')
1985	if csv:
1986	WriteCSV()
1987	else:
1988	WriteSeq()
1989	SeqFile.close()
1990	finally:
1991	dlg.Destroy()
1992
1993	def striphist(var,insChar=''):
1994	'strip a histogram number from a var name'
1995	sv = var.split(':')
1996	if len(sv) <= 1: return var
1997	if sv[1]:
1998	sv[1] = insChar
1999	return ':'.join(sv)
2000
2001	def plotSpCharFix(lbl):
2002	'Change selected unicode characters to their matplotlib equivalent'
2003	for u,p in [
2004	(u'\u03B1',r'$\alpha$'),
2005	(u'\u03B2',r'$\beta$'),
2006	(u'\u03B3',r'$\gamma$'),
2007	(u'\u0394\u03C7',r'$\Delta\chi$'),
2008	]:
2009	lbl = lbl.replace(u,p)
2010	return lbl
2011
2012	def SelectXaxis():
2013	'returns a selected column number (or None) as the X-axis selection'
2014	ncols = G2frame.SeqTable.GetNumberCols()
2015	colNames = [G2frame.SeqTable.GetColLabelValue(r) for r in range(ncols)]
2016	dlg = G2G.G2SingleChoiceDialog(
2017	G2frame.dataDisplay,
2018	'Select x-axis parameter for plot or Cancel for sequence number',
2019	'Select X-axis',
2020	colNames)
2021	try:
2022	if dlg.ShowModal() == wx.ID_OK:
2023	col = dlg.GetSelection()
2024	else:
2025	col = None
2026	finally:
2027	dlg.Destroy()
2028	return col
2029
2030	def EnablePseudoVarMenus():
2031	'Enables or disables the PseudoVar menu items that require existing defs'
2032	if Controls['SeqPseudoVars']:
2033	val = True
2034	else:
2035	val = False
2036	G2frame.dataFrame.SequentialPvars.Enable(wxDELSEQVAR,val)
2037	G2frame.dataFrame.SequentialPvars.Enable(wxEDITSEQVAR,val)
2038
2039	def DelPseudoVar(event):
2040	'Ask the user to select a pseudo var expression to delete'
2041	choices = Controls['SeqPseudoVars'].keys()
2042	selected = G2G.ItemSelector(
2043	choices,G2frame.dataFrame,
2044	multiple=True,
2045	title='Select expressions to remove',
2046	header='Delete expression')
2047	if selected is None: return
2048	for item in selected:
2049	del Controls['SeqPseudoVars'][choices[item]]
2050	if selected:
2051	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2052
2053	def EditPseudoVar(event):
2054	'Edit an existing pseudo var expression'
2055	choices = Controls['SeqPseudoVars'].keys()
2056	if len(choices) == 1:
2057	selected = 0
2058	else:
2059	selected = G2G.ItemSelector(
2060	choices,G2frame.dataFrame,
2061	multiple=False,
2062	title='Select an expression to edit',
2063	header='Edit expression')
2064	if selected is not None:
2065	dlg = G2exG.ExpressionDialog(
2066	G2frame.dataDisplay,PSvarDict,
2067	Controls['SeqPseudoVars'][choices[selected]],
2068	header="Edit the PseudoVar expression",
2069	VarLabel="PseudoVar #"+str(selected+1),
2070	fit=False)
2071	newobj = dlg.Show(True)
2072	if newobj:
2073	calcobj = G2obj.ExpressionCalcObj(newobj)
2074	del Controls['SeqPseudoVars'][choices[selected]]
2075	Controls['SeqPseudoVars'][calcobj.eObj.expression] = newobj
2076	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2077
2078	def AddNewPseudoVar(event):
2079	'Create a new pseudo var expression'
2080	dlg = G2exG.ExpressionDialog(
2081	G2frame.dataDisplay,PSvarDict,
2082	header='Enter an expression for a PseudoVar here',
2083	VarLabel = "New PseudoVar",
2084	fit=False)
2085	obj = dlg.Show(True)
2086	dlg.Destroy()
2087	if obj:
2088	calcobj = G2obj.ExpressionCalcObj(obj)
2089	Controls['SeqPseudoVars'][calcobj.eObj.expression] = obj
2090	UpdateSeqResults(G2frame,data,G2frame.dataDisplay.GetSize()) # redisplay variables
2091
2092	def UpdateParmDict(parmDict):
2093	'''generate the atom positions and the direct & reciprocal cell values,
2094	because they might be needed to evaluate the pseudovar
2095	'''
2096	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2097	['A'+str(i) for i in range(6)])
2098	)
2099	delList = []
2100	phaselist = []
2101	for item in parmDict:
2102	if ':' not in item: continue
2103	key = item.split(':')
2104	if len(key) < 3: continue
2105	# remove the dA[xyz] terms, they would only bring confusion
2106	if key[2].startswith('dA'):
2107	delList.append(item)
2108	# compute and update the corrected reciprocal cell terms using the Dij values
2109	elif key[2] in Ddict:
2110	if key[0] not in phaselist: phaselist.append(key[0])
2111	akey = key[0]+'::'+Ddict[key[2]]
2112	parmDict[akey] -= parmDict[item]
2113	delList.append(item)
2114	for item in delList:
2115	del parmDict[item]
2116	for i in phaselist:
2117	pId = int(i)
2118	# apply cell symmetry
2119	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],parmDict,zeroDict[pId])
2120	# convert to direct cell & add the unique terms to the dictionary
2121	for i,val in enumerate(G2lat.A2cell(A)):
2122	if i in uniqCellIndx[pId]:
2123	lbl = str(pId)+'::'+cellUlbl[i]
2124	parmDict[lbl] = val
2125	lbl = str(pId)+'::'+'vol'
2126	parmDict[lbl] = G2lat.calc_V(A)
2127	return parmDict
2128
2129	def EvalPSvarDeriv(calcobj,parmDict,sampleDict,var,ESD):
2130	'''Evaluate an expression derivative with respect to a
2131	GSAS-II variable name.
2132
2133	Note this likely could be faster if the loop over calcobjs were done
2134	inside after the Dict was created.
2135	'''
2136	step = ESD/10
2137	Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],
2138	['A'+str(i) for i in range(6)])
2139	)
2140	results = []
2141	phaselist = []
2142	VparmDict = sampleDict.copy()
2143	for incr in step,-step:
2144	VparmDict.update(parmDict.copy())
2145	# as saved, the parmDict has updated 'A[xyz]' values, but 'dA[xyz]'
2146	# values are not zeroed: fix that!
2147	VparmDict.update({item:0.0 for item in parmDict if 'dA' in item})
2148	VparmDict[var] += incr
2149	G2mv.Dict2Map(VparmDict,[]) # apply constraints
2150	# generate the atom positions and the direct & reciprocal cell values now, because they might
2151	# needed to evaluate the pseudovar
2152	for item in VparmDict:
2153	if item in sampleDict:
2154	continue
2155	if ':' not in item: continue
2156	key = item.split(':')
2157	if len(key) < 3: continue
2158	# apply any new shifts to atom positions
2159	if key[2].startswith('dA'):
2160	VparmDict[''.join(item.split('d'))] += VparmDict[item]
2161	VparmDict[item] = 0.0
2162	# compute and update the corrected reciprocal cell terms using the Dij values
2163	if key[2] in Ddict:
2164	if key[0] not in phaselist: phaselist.append(key[0])
2165	akey = key[0]+'::'+Ddict[key[2]]
2166	VparmDict[akey] -= VparmDict[item]
2167	for i in phaselist:
2168	pId = int(i)
2169	# apply cell symmetry
2170	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata[pId],VparmDict,zeroDict[pId])
2171	# convert to direct cell & add the unique terms to the dictionary
2172	for i,val in enumerate(G2lat.A2cell(A)):
2173	if i in uniqCellIndx[pId]:
2174	lbl = str(pId)+'::'+cellUlbl[i]
2175	VparmDict[lbl] = val
2176	lbl = str(pId)+'::'+'vol'
2177	VparmDict[lbl] = G2lat.calc_V(A)
2178	# dict should be fully updated, use it & calculate
2179	calcobj.SetupCalc(VparmDict)
2180	results.append(calcobj.EvalExpression())
2181	return (results[0] - results[1]) / (2.*step)
2182
2183	def EnableParFitEqMenus():
2184	'Enables or disables the Parametric Fit menu items that require existing defs'
2185	if Controls['SeqParFitEqList']:
2186	val = True
2187	else:
2188	val = False
2189	G2frame.dataFrame.SequentialPfit.Enable(wxDELPARFIT,val)
2190	G2frame.dataFrame.SequentialPfit.Enable(wxEDITPARFIT,val)
2191	G2frame.dataFrame.SequentialPfit.Enable(wxDOPARFIT,val)
2192
2193	def ParEqEval(Values,calcObjList,varyList):
2194	'''Evaluate the parametric expression(s)
2195	:param list Values: a list of values for each variable parameter
2196	:param list calcObjList: a list of :class:`GSASIIobj.ExpressionCalcObj`
2197	expression objects to evaluate
2198	:param list varyList: a list of variable names for each value in Values
2199	'''
2200	result = []
2201	for calcobj in calcObjList:
2202	calcobj.UpdateVars(varyList,Values)
2203	result.append((calcobj.depVal-calcobj.EvalExpression())/calcobj.depSig)
2204	return result
2205
2206	def DoParEqFit(event,eqObj=None):
2207	'Parametric fit minimizer'
2208	varyValueDict = {} # dict of variables and their initial values
2209	calcObjList = [] # expression objects, ready to go for each data point
2210	if eqObj is not None:
2211	eqObjList = [eqObj,]
2212	else:
2213	eqObjList = Controls['SeqParFitEqList']
2214	UseFlags = G2frame.SeqTable.GetColValues(0)
2215	for obj in eqObjList:
2216	expr = obj.expression
2217	# assemble refined vars for this equation
2218	varyValueDict.update({var:val for var,val in obj.GetVariedVarVal()})
2219	# lookup dependent var position
2220	depVar = obj.GetDepVar()
2221	if depVar in colLabels:
2222	indx = colLabels.index(depVar)
2223	else:
2224	raise Exception('Dependent variable '+depVar+' not found')
2225	# assemble a list of the independent variables
2226	indepVars = obj.GetIndependentVars()
2227	# loop over each datapoint
2228	for j,row in enumerate(zip(*colList)):
2229	if not UseFlags[j]: continue
2230	# assemble equations to fit
2231	calcobj = G2obj.ExpressionCalcObj(obj)
2232	# prepare a dict of needed independent vars for this expression
2233	indepVarDict = {var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2234	calcobj.SetupCalc(indepVarDict)
2235	# values and sigs for current value of dependent var
2236	calcobj.depVal = row[indx]
2237	calcobj.depSig = colSigs[indx][j]
2238	calcObjList.append(calcobj)
2239	# varied parameters
2240	varyList = varyValueDict.keys()
2241	values = varyValues = [varyValueDict[key] for key in varyList]
2242	if not varyList:
2243	print 'no variables to refine!'
2244	return
2245	try:
2246	result = so.leastsq(ParEqEval,varyValues,full_output=True, #ftol=Ftol,
2247	args=(calcObjList,varyList)
2248	)
2249	values = result[0]
2250	covar = result[1]
2251	if covar is None:
2252	raise Exception
2253	esdDict = {}
2254	for i,avar in enumerate(varyList):
2255	esdDict[avar] = np.sqrt(covar[i,i])
2256	except:
2257	print('====> Fit failed')
2258	return
2259	print('==== Fit Results ====')
2260	for obj in eqObjList:
2261	obj.UpdateVariedVars(varyList,values)
2262	ind = ' '
2263	print(' '+obj.GetDepVar()+' = '+obj.expression)
2264	for var in obj.assgnVars:
2265	print(ind+var+' = '+obj.assgnVars[var])
2266	for var in obj.freeVars:
2267	avar = "::"+obj.freeVars[var][0]
2268	val = obj.freeVars[var][1]
2269	if obj.freeVars[var][2]:
2270	print(ind+var+' = '+avar + " = " + G2mth.ValEsd(val,esdDict[avar]))
2271	else:
2272	print(ind+var+' = '+avar + " =" + G2mth.ValEsd(val,0))
2273	# create a plot for each parametric variable
2274	for fitnum,obj in enumerate(eqObjList):
2275	calcobj = G2obj.ExpressionCalcObj(obj)
2276	# lookup dependent var position
2277	indx = colLabels.index(obj.GetDepVar())
2278	# assemble a list of the independent variables
2279	indepVars = obj.GetIndependentVars()
2280	# loop over each datapoint
2281	fitvals = []
2282	for j,row in enumerate(zip(*colList)):
2283	calcobj.SetupCalc(
2284	{var:row[i] for i,var in enumerate(colLabels) if var in indepVars}
2285	)
2286	fitvals.append(calcobj.EvalExpression())
2287	G2plt.PlotSelectedSequence(
2288	G2frame,[indx],GetColumnInfo,SelectXaxis,
2289	fitnum,fitvals)
2290
2291	def SingleParEqFit(eqObj):
2292	DoParEqFit(None,eqObj)
2293
2294	def DelParFitEq(event):
2295	'Ask the user to select function to delete'
2296	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2297	selected = G2G.ItemSelector(
2298	txtlst,G2frame.dataFrame,
2299	multiple=True,
2300	title='Select a parametric equation(s) to remove',
2301	header='Delete equation')
2302	if selected is None: return
2303	Controls['SeqParFitEqList'] = [obj for i,obj in enumerate(Controls['SeqParFitEqList']) if i not in selected]
2304	EnableParFitEqMenus()
2305	if Controls['SeqParFitEqList']: DoParEqFit(event)
2306
2307	def EditParFitEq(event):
2308	'Edit an existing parametric equation'
2309	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2310	if len(txtlst) == 1:
2311	selected = 0
2312	else:
2313	selected = G2G.ItemSelector(
2314	txtlst,G2frame.dataFrame,
2315	multiple=False,
2316	title='Select a parametric equation to edit',
2317	header='Edit equation')
2318	if selected is not None:
2319	dlg = G2exG.ExpressionDialog(
2320	G2frame.dataDisplay,indepVarDict,
2321	Controls['SeqParFitEqList'][selected],
2322	depVarDict=depVarDict,
2323	header="Edit the formula for this minimization function",
2324	ExtraButton=['Fit',SingleParEqFit])
2325	newobj = dlg.Show(True)
2326	if newobj:
2327	calcobj = G2obj.ExpressionCalcObj(newobj)
2328	Controls['SeqParFitEqList'][selected] = newobj
2329	EnableParFitEqMenus()
2330	if Controls['SeqParFitEqList']: DoParEqFit(event)
2331
2332	def AddNewParFitEq(event):
2333	'Create a new parametric equation to be fit to sequential results'
2334
2335	# compile the variable names used in previous freevars to avoid accidental name collisions
2336	usedvarlist = []
2337	for obj in Controls['SeqParFitEqList']:
2338	for var in obj.freeVars:
2339	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2340
2341	dlg = G2exG.ExpressionDialog(
2342	G2frame.dataDisplay,indepVarDict,
2343	depVarDict=depVarDict,
2344	header='Define an equation to minimize in the parametric fit',
2345	ExtraButton=['Fit',SingleParEqFit],
2346	usedVars=usedvarlist)
2347	obj = dlg.Show(True)
2348	dlg.Destroy()
2349	if obj:
2350	Controls['SeqParFitEqList'].append(obj)
2351	EnableParFitEqMenus()
2352	if Controls['SeqParFitEqList']: DoParEqFit(event)
2353
2354	def CopyParFitEq(event):
2355	'Copy an existing parametric equation to be fit to sequential results'
2356	# compile the variable names used in previous freevars to avoid accidental name collisions
2357	usedvarlist = []
2358	for obj in Controls['SeqParFitEqList']:
2359	for var in obj.freeVars:
2360	if obj.freeVars[var][0] not in usedvarlist: usedvarlist.append(obj.freeVars[var][0])
2361	txtlst = [obj.GetDepVar()+' = '+obj.expression for obj in Controls['SeqParFitEqList']]
2362	if len(txtlst) == 1:
2363	selected = 0
2364	else:
2365	selected = G2G.ItemSelector(
2366	txtlst,G2frame.dataFrame,
2367	multiple=False,
2368	title='Select a parametric equation to copy',
2369	header='Copy equation')
2370	if selected is not None:
2371	newEqn = copy.deepcopy(Controls['SeqParFitEqList'][selected])
2372	for var in newEqn.freeVars:
2373	newEqn.freeVars[var][0] = G2obj.MakeUniqueLabel(newEqn.freeVars[var][0],usedvarlist)
2374	dlg = G2exG.ExpressionDialog(
2375	G2frame.dataDisplay,indepVarDict,
2376	newEqn,
2377	depVarDict=depVarDict,
2378	header="Edit the formula for this minimization function",
2379	ExtraButton=['Fit',SingleParEqFit])
2380	newobj = dlg.Show(True)
2381	if newobj:
2382	calcobj = G2obj.ExpressionCalcObj(newobj)
2383	Controls['SeqParFitEqList'].append(newobj)
2384	EnableParFitEqMenus()
2385	if Controls['SeqParFitEqList']: DoParEqFit(event)
2386
2387	def GridSetToolTip(row,col):
2388	'''Routine to show standard uncertainties for each element in table
2389	as a tooltip
2390	'''
2391	if colSigs[col]:
2392	return u'\u03c3 = '+str(colSigs[col][row])
2393	return ''
2394
2395	def GridColLblToolTip(col):
2396	'''Define a tooltip for a column. This will be the user-entered value
2397	(from data['variableLabels']) or the default name
2398	'''
2399	if col < 0 or col > len(colLabels):
2400	print 'Illegal column #',col
2401	return
2402	var = colLabels[col]
2403	return variableLabels.get(var,G2obj.fmtVarDescr(var))
2404
2405	def SetLabelString(event):
2406	'''Define or edit the label for a column in the table, to be used
2407	as a tooltip and for plotting
2408	'''
2409	col = event.GetCol()
2410	if col < 0 or col > len(colLabels):
2411	return
2412	var = colLabels[col]
2413	lbl = variableLabels.get(var,G2obj.fmtVarDescr(var))
2414	dlg = G2G.SingleStringDialog(G2frame.dataFrame,'Set variable label',
2415	'Set a new name for variable '+var,lbl,size=(400,-1))
2416	if dlg.Show():
2417	variableLabels[var] = dlg.GetValue()
2418	dlg.Destroy()
2419
2420	#def GridRowLblToolTip(row): return 'Row ='+str(row)
2421
2422	# lookup table for unique cell parameters by symmetry
2423	cellGUIlist = [
2424	[['m3','m3m'],(0,)],
2425	[['3R','3mR'],(0,3)],
2426	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],(0,2)],
2427	[['mmm'],(0,1,2)],
2428	[['2/m'+'a'],(0,1,2,3)],
2429	[['2/m'+'b'],(0,1,2,4)],
2430	[['2/m'+'c'],(0,1,2,5)],
2431	[['-1'],(0,1,2,3,4,5)],
2432	]
2433	# cell labels
2434	cellUlbl = ('a','b','c',u'\u03B1',u'\u03B2',u'\u03B3') # unicode a,b,c,alpha,beta,gamma
2435
2436	#======================================================================
2437	# start processing sequential results here (UpdateSeqResults)
2438	#======================================================================
2439	if not data:
2440	print 'No sequential refinement results'
2441	return
2442	variableLabels = data.get('variableLabels',{})
2443	data['variableLabels'] = variableLabels
2444	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
2445	Controls = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.root,'Controls'))
2446	# create a place to store Pseudo Vars & Parametric Fit functions, if not present
2447	if 'SeqPseudoVars' not in Controls: Controls['SeqPseudoVars'] = {}
2448	if 'SeqParFitEqList' not in Controls: Controls['SeqParFitEqList'] = []
2449	histNames = data['histNames']
2450	if G2frame.dataDisplay:
2451	G2frame.dataDisplay.Destroy()
2452	if not G2frame.dataFrame.GetStatusBar():
2453	Status = G2frame.dataFrame.CreateStatusBar()
2454	Status.SetStatusText("Select column to export; Double click on column to plot data; on row for Covariance")
2455	sampleParms = GetSampleParms()
2456
2457	# make dict of varied atom coords keyed by absolute position
2458	newAtomDict = data[histNames[0]].get('newAtomDict',{}) # dict with atom positions; relative & absolute
2459	# Possible error: the next might need to be data[histNames[0]]['varyList']
2460	# error will arise if there constraints on coordinates?
2461	atomLookup = {newAtomDict[item][0]:item for item in newAtomDict if item in data['varyList']}
2462
2463	# make dict of varied cell parameters equivalents
2464	ESDlookup = {} # provides the Dij term for each Ak term (where terms are refined)
2465	Dlookup = {} # provides the Ak term for each Dij term (where terms are refined)
2466	# N.B. These Dij vars are missing a histogram #
2467	newCellDict = data[histNames[0]].get('newCellDict',{})
2468	for item in newCellDict:
2469	if item in data['varyList']:
2470	ESDlookup[newCellDict[item][0]] = item
2471	Dlookup[item] = newCellDict[item][0]
2472	# add coordinate equivalents to lookup table
2473	for parm in atomLookup:
2474	Dlookup[atomLookup[parm]] = parm
2475	ESDlookup[parm] = atomLookup[parm]
2476
2477	# get unit cell & symmetry for all phases & initial stuff for later use
2478	RecpCellTerms = {}
2479	SGdata = {}
2480	uniqCellIndx = {}
2481	initialCell = {}
2482	RcellLbls = {}
2483	zeroDict = {}
2484	Rcelldict = {}
2485	for phase in Phases:
2486	phasedict = Phases[phase]
2487	pId = phasedict['pId']
2488	pfx = str(pId)+'::' # prefix for A values from phase
2489	RcellLbls[pId] = [pfx+'A'+str(i) for i in range(6)]
2490	RecpCellTerms[pId] = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2491	zeroDict[pId] = dict(zip(RcellLbls[pId],6*[0.,]))
2492	SGdata[pId] = phasedict['General']['SGData']
2493	Rcelldict.update({lbl:val for lbl,val in zip(RcellLbls[pId],RecpCellTerms[pId])})
2494	laue = SGdata[pId]['SGLaue']
2495	if laue == '2/m':
2496	laue += SGdata[pId]['SGUniq']
2497	for symlist,celllist in cellGUIlist:
2498	if laue in symlist:
2499	uniqCellIndx[pId] = celllist
2500	break
2501	else: # should not happen
2502	uniqCellIndx[pId] = range(6)
2503	for i in uniqCellIndx[pId]:
2504	initialCell[str(pId)+'::A'+str(i)] = RecpCellTerms[pId][i]
2505
2506	SetDataMenuBar(G2frame,G2frame.dataFrame.SequentialMenu)
2507	G2frame.dataFrame.SetLabel('Sequential refinement results')
2508	if not G2frame.dataFrame.GetStatusBar():
2509	Status = G2frame.dataFrame.CreateStatusBar()
2510	Status.SetStatusText('')
2511	G2frame.dataFrame.Bind(wx.EVT_MENU, OnRenameSelSeq, id=wxID_RENAMESEQSEL)
2512	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeq, id=wxID_SAVESEQSEL)
2513	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSelSeqCSV, id=wxID_SAVESEQSELCSV)
2514	G2frame.dataFrame.Bind(wx.EVT_MENU, OnSaveSeqCSV, id=wxID_SAVESEQCSV)
2515	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotSelSeq, id=wxID_PLOTSEQSEL)
2516	G2frame.dataFrame.Bind(wx.EVT_MENU, OnAveSelSeq, id=wxID_AVESEQSEL)
2517	G2frame.dataFrame.Bind(wx.EVT_MENU, OnReOrgSelSeq, id=wxID_ORGSEQSEL)
2518	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewPseudoVar, id=wxADDSEQVAR)
2519	G2frame.dataFrame.Bind(wx.EVT_MENU, DelPseudoVar, id=wxDELSEQVAR)
2520	G2frame.dataFrame.Bind(wx.EVT_MENU, EditPseudoVar, id=wxEDITSEQVAR)
2521	G2frame.dataFrame.Bind(wx.EVT_MENU, AddNewParFitEq, id=wxADDPARFIT)
2522	G2frame.dataFrame.Bind(wx.EVT_MENU, CopyParFitEq, id=wxCOPYPARFIT)
2523	G2frame.dataFrame.Bind(wx.EVT_MENU, DelParFitEq, id=wxDELPARFIT)
2524	G2frame.dataFrame.Bind(wx.EVT_MENU, EditParFitEq, id=wxEDITPARFIT)
2525	G2frame.dataFrame.Bind(wx.EVT_MENU, DoParEqFit, id=wxDOPARFIT)
2526	EnablePseudoVarMenus()
2527	EnableParFitEqMenus()
2528
2529	# scan for locations where the variables change
2530	VaryListChanges = [] # histograms where there is a change
2531	combinedVaryList = []
2532	firstValueDict = {}
2533	vallookup = {}
2534	posdict = {}
2535	prevVaryList = []
2536	for i,name in enumerate(histNames):
2537	for var,val,sig in zip(data[name]['varyList'],data[name]['variables'],data[name]['sig']):
2538	svar = striphist(var,'*') # wild-carded
2539	if svar not in combinedVaryList:
2540	# add variables to list as they appear
2541	combinedVaryList.append(svar)
2542	firstValueDict[svar] = (val,sig)
2543	if prevVaryList != data[name]['varyList']: # this refinement has a different refinement list from previous
2544	prevVaryList = data[name]['varyList']
2545	vallookup[name] = dict(zip(data[name]['varyList'],data[name]['variables']))
2546	posdict[name] = {}
2547	for var in data[name]['varyList']:
2548	svar = striphist(var,'*')
2549	posdict[name][combinedVaryList.index(svar)] = svar
2550	VaryListChanges.append(name)
2551	if len(VaryListChanges) > 1:
2552	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,True)
2553	else:
2554	G2frame.dataFrame.SequentialFile.Enable(wxID_ORGSEQSEL,False)
2555	#-----------------------------------------------------------------------------------
2556	# build up the data table by columns -----------------------------------------------
2557	nRows = len(histNames)
2558	colList = [nRows*[True]]
2559	colSigs = [None]
2560	colLabels = ['Use']
2561	Types = [wg.GRID_VALUE_BOOL]
2562	# start with Rwp values
2563	if 'IMG ' not in histNames[0][:4]:
2564	colList += [[data[name]['Rvals']['Rwp'] for name in histNames]]
2565	colSigs += [None]
2566	colLabels += ['Rwp']
2567	Types += [wg.GRID_VALUE_FLOAT+':10,3',]
2568	# add % change in Chi^2 in last cycle
2569	if histNames[0][:4] not in ['SASD','IMG '] and Controls.get('ShowCell'):
2570	colList += [[100.*data[name]['Rvals'].get('DelChi2',-1) for name in histNames]]
2571	colSigs += [None]
2572	colLabels += [u'\u0394\u03C7\u00B2 (%)']
2573	Types += [wg.GRID_VALUE_FLOAT,]
2574	deltaChiCol = len(colLabels)-1
2575	# add changing sample parameters to table
2576	for key in sampleParms:
2577	colList += [sampleParms[key]]
2578	colSigs += [None]
2579	colLabels += [key]
2580	Types += [wg.GRID_VALUE_FLOAT,]
2581	sampleDict = {}
2582	for i,name in enumerate(histNames):
2583	sampleDict[name] = dict(zip(sampleParms.keys(),[sampleParms[key][i] for key in sampleParms.keys()]))
2584	# add unique cell parameters TODO: review this where the cell symmetry changes (when possible)
2585	if Controls.get('ShowCell',False):
2586	for pId in sorted(RecpCellTerms):
2587	pfx = str(pId)+'::' # prefix for A values from phase
2588	cells = []
2589	cellESDs = []
2590	colLabels += [pfx+cellUlbl[i] for i in uniqCellIndx[pId]]
2591	colLabels += [pfx+'Vol']
2592	Types += (1+len(uniqCellIndx[pId]))*[wg.GRID_VALUE_FLOAT,]
2593	for name in histNames:
2594	covData = {
2595	'varyList': [Dlookup.get(striphist(v),v) for v in data[name]['varyList']],
2596	'covMatrix': data[name]['covMatrix']
2597	}
2598	A = RecpCellTerms[pId][:] # make copy of starting A values
2599	# update with refined values
2600	for i in range(6):
2601	var = str(pId)+'::A'+str(i)
2602	if var in ESDlookup:
2603	val = data[name]['newCellDict'][ESDlookup[var]][1] # get refined value
2604	A[i] = val # override with updated value
2605	# apply symmetry
2606	Albls = [pfx+'A'+str(i) for i in range(6)]
2607	cellDict = dict(zip(Albls,A))
2608	A,zeros = G2stIO.cellFill(pfx,SGdata[pId],cellDict,zeroDict[pId])
2609	# convert to direct cell & add only unique values to table
2610	c = G2lat.A2cell(A)
2611	vol = G2lat.calc_V(A)
2612	cE = G2stIO.getCellEsd(pfx,SGdata[pId],A,covData)
2613	cells += [[c[i] for i in uniqCellIndx[pId]]+[vol]]
2614	cellESDs += [[cE[i] for i in uniqCellIndx[pId]]+[cE[-1]]]
2615	colList += zip(*cells)
2616	colSigs += zip(*cellESDs)
2617	# sort out the variables in their selected order
2618	varcols = 0
2619	for d in posdict.itervalues():
2620	varcols = max(varcols,max(d.keys())+1)
2621	# get labels for each column
2622	for i in range(varcols):
2623	lbl = ''
2624	for h in VaryListChanges:
2625	if posdict[h].get(i):
2626	if posdict[h].get(i) in lbl: continue
2627	if lbl != "": lbl += '/'
2628	lbl += posdict[h].get(i)
2629	colLabels.append(lbl)
2630	Types += varcols*[wg.GRID_VALUE_FLOAT]
2631	vals = []
2632	esds = []
2633	varsellist = None # will be a list of variable names in the order they are selected to appear
2634	# tabulate values for each hist, leaving None for blank columns
2635	for name in histNames:
2636	if name in posdict:
2637	varsellist = [posdict[name].get(i) for i in range(varcols)]
2638	# translate variable names to how they will be used in the headings
2639	vs = [striphist(v,'*') for v in data[name]['varyList']]
2640	# determine the index for each column (or None) in the data[]['variables'] and ['sig'] lists
2641	sellist = [vs.index(v) if v is not None else None for v in varsellist]
2642	#sellist = [i if striphist(v,'*') in varsellist else None for i,v in enumerate(data[name]['varyList'])]
2643	if not varsellist: raise Exception()
2644	vals.append([data[name]['variables'][s] if s is not None else None for s in sellist])
2645	esds.append([data[name]['sig'][s] if s is not None else None for s in sellist])
2646	#GSASIIpath.IPyBreak()
2647	colList += zip(*vals)
2648	colSigs += zip(*esds)
2649
2650	# tabulate constrained variables, removing histogram numbers if needed
2651	# from parameter label
2652	depValDict = {}
2653	depSigDict = {}
2654	for name in histNames:
2655	for var in data[name].get('depParmDict',{}):
2656	val,sig = data[name]['depParmDict'][var]
2657	svar = striphist(var,'*')
2658	if svar not in depValDict:
2659	depValDict[svar] = [val]
2660	depSigDict[svar] = [sig]
2661	else:
2662	depValDict[svar].append(val)
2663	depSigDict[svar].append(sig)
2664	# add the dependent constrained variables to the table
2665	for var in sorted(depValDict):
2666	if len(depValDict[var]) != len(histNames): continue
2667	colLabels.append(var)
2668	Types += [wg.GRID_VALUE_FLOAT,]
2669	colSigs += [depSigDict[var]]
2670	colList += [depValDict[var]]
2671
2672	# add atom parameters to table
2673	colLabels += atomLookup.keys()
2674	Types += len(atomLookup)*[wg.GRID_VALUE_FLOAT]
2675	for parm in sorted(atomLookup):
2676	colList += [[data[name]['newAtomDict'][atomLookup[parm]][1] for name in histNames]]
2677	if atomLookup[parm] in data[histNames[0]]['varyList']:
2678	col = data[histNames[0]]['varyList'].index(atomLookup[parm])
2679	colSigs += [[data[name]['sig'][col] for name in histNames]]
2680	else:
2681	colSigs += [None] # should not happen
2682	# evaluate Pseudovars, their ESDs and add them to grid
2683	for expr in Controls['SeqPseudoVars']:
2684	obj = Controls['SeqPseudoVars'][expr]
2685	calcobj = G2obj.ExpressionCalcObj(obj)
2686	valList = []
2687	esdList = []
2688	for seqnum,name in enumerate(histNames):
2689	sigs = data[name]['sig']
2690	G2mv.InitVars()
2691	parmDict = data[name].get('parmDict')
2692	badVary = data[name].get('badVary',[])
2693	constraintInfo = data[name].get('constraintInfo',[[],[],{},[],seqnum])
2694	groups,parmlist,constrDict,fixedList,ihst = constraintInfo
2695	varyList = data[name]['varyList']
2696	parmDict = data[name]['parmDict']
2697	G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmDict,SeqHist=ihst)
2698	derivs = np.array(
2699	[EvalPSvarDeriv(calcobj,parmDict.copy(),sampleDict[name],var,ESD)
2700	for var,ESD in zip(varyList,sigs)]
2701	)
2702	esdList.append(np.sqrt(
2703	np.inner(derivs,np.inner(data[name]['covMatrix'],derivs.T))
2704	))
2705	PSvarDict = parmDict.copy()
2706	PSvarDict.update(sampleDict[name])
2707	UpdateParmDict(PSvarDict)
2708	calcobj.UpdateDict(PSvarDict)
2709	valList.append(calcobj.EvalExpression())
2710	if not esdList:
2711	esdList = None
2712	colList += [valList]
2713	colSigs += [esdList]
2714	colLabels += [expr]
2715	Types += [wg.GRID_VALUE_FLOAT,]
2716	#---- table build done -------------------------------------------------------------
2717
2718	# Make dict needed for creating & editing pseudovars (PSvarDict).
2719	name = histNames[0]
2720	parmDict = data[name].get('parmDict')
2721	PSvarDict = parmDict.copy()
2722	PSvarDict.update(sampleParms)
2723	UpdateParmDict(PSvarDict)
2724	# Also dicts of dependent (depVarDict) & independent vars (indepVarDict)
2725	# for Parametric fitting from the data table
2726	parmDict = dict(zip(colLabels,zip(*colList)[0])) # scratch dict w/all values in table
2727	parmDict.update(
2728	{var:val for var,val in data[name].get('newCellDict',{}).values()} # add varied reciprocal cell terms
2729	)
2730	name = histNames[0]
2731
2732	#******************************************************************************
2733	# create a set of values for example evaluation of pseudovars and
2734	# this does not work for refinements that have differing numbers of variables.
2735	#raise Exception
2736	indepVarDict = {} # values in table w/o ESDs
2737	depVarDict = {}
2738	for i,var in enumerate(colLabels):
2739	if var == 'Use': continue
2740	if colList[i][0] is None:
2741	val,sig = firstValueDict.get(var,[None,None])
2742	elif colSigs[i]:
2743	val,sig = colList[i][0],colSigs[i][0]
2744	else:
2745	val,sig = colList[i][0],None
2746	if val is None:
2747	continue
2748	elif sig is None:
2749	indepVarDict[var] = val
2750	elif striphist(var) not in Dlookup:
2751	depVarDict[var] = val
2752	# add recip cell coeff. values
2753	depVarDict.update({var:val for var,val in data[name].get('newCellDict',{}).values()})
2754
2755	G2frame.dataDisplay = G2G.GSGrid(parent=G2frame.dataFrame)
2756	G2frame.SeqTable = G2G.Table(
2757	[list(c) for c in zip(*colList)], # convert from columns to rows
2758	colLabels=colLabels,rowLabels=histNames,types=Types)
2759	G2frame.dataDisplay.SetTable(G2frame.SeqTable, True)
2760	#G2frame.dataDisplay.EnableEditing(False)
2761	# make all but first column read-only
2762	for c in range(1,len(colLabels)):
2763	for r in range(nRows):
2764	G2frame.dataDisplay.SetCellReadOnly(r,c)
2765	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, PlotSelect)
2766	G2frame.dataDisplay.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, SetLabelString)
2767	G2frame.dataDisplay.SetRowLabelSize(8*len(histNames[0])) #pretty arbitrary 8
2768	G2frame.dataDisplay.SetMargins(0,0)
2769	G2frame.dataDisplay.AutoSizeColumns(True)
2770	if prevSize:
2771	G2frame.dataDisplay.SetSize(prevSize)
2772	else:
2773	G2frame.dataFrame.setSizePosLeft([700,350])
2774	# highlight unconverged shifts
2775	if histNames[0][:4] not in ['SASD','IMG ']:
2776	for row,name in enumerate(histNames):
2777	deltaChi = G2frame.SeqTable.GetValue(row,deltaChiCol)
2778	if deltaChi > 10.:
2779	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,0,0))
2780	elif deltaChi > 1.0:
2781	G2frame.dataDisplay.SetCellStyle(row,deltaChiCol,color=wx.Colour(255,255,0))
2782	G2frame.dataDisplay.InstallGridToolTip(GridSetToolTip,GridColLblToolTip)
2783	G2frame.dataDisplay.SendSizeEvent() # resize needed on mac
2784	G2frame.dataDisplay.Refresh() # shows colored text on mac
2785
2786	################################################################################
2787	##### Main PWDR panel
2788	################################################################################
2789
2790	def UpdatePWHKPlot(G2frame,kind,item):
2791	'''Called when the histogram main tree entry is called. Displays the
2792	histogram weight factor, refinement statistics for the histogram
2793	and the range of data for a simulation.
2794
2795	Also invokes a plot of the histogram.
2796	'''
2797	def onEditSimRange(event):
2798	'Edit simulation range'
2799	inp = [
2800	min(data[1][0]),
2801	max(data[1][0]),
2802	None
2803	]
2804	inp[2] = (inp[1] - inp[0])/(len(data[1][0])-1.)
2805	names = ('start angle', 'end angle', 'step size')
2806	dictlst = [inp] * len(inp)
2807	elemlst = range(len(inp))
2808	dlg = G2G.ScrolledMultiEditor(
2809	G2frame,[inp] * len(inp), range(len(inp)), names,
2810	header='Edit simulation range',
2811	minvals=(0.001,0.001,0.0001),
2812	maxvals=(180.,180.,.1),
2813	)
2814	dlg.CenterOnParent()
2815	val = dlg.ShowModal()
2816	dlg.Destroy()
2817	if val != wx.ID_OK: return
2818	if inp[0] > inp[1]:
2819	end,start,step = inp
2820	else:
2821	start,end,step = inp
2822	step = abs(step)
2823	N = int((end-start)/step)+1
2824	newdata = np.linspace(start,end,N,True)
2825	if len(newdata) < 2: return # too small a range - reject
2826	data[1] = [newdata,np.zeros_like(newdata),np.ones_like(newdata),
2827	np.zeros_like(newdata),np.zeros_like(newdata),np.zeros_like(newdata)]
2828	Tmin = newdata[0]
2829	Tmax = newdata[-1]
2830	G2frame.PatternTree.SetItemPyData(GetPatternTreeItemId(G2frame,item,'Limits'),
2831	[(Tmin,Tmax),[Tmin,Tmax]])
2832	UpdatePWHKPlot(G2frame,kind,item) # redisplay data screen
2833
2834	def OnPlot3DHKL(event):
2835	refList = data[1]['RefList']
2836	FoMax = np.max(refList.T[8+Super])
2837	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2838	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2839	Vpoint = np.array([int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))])
2840	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,'Zone':False,'viewKey':'L',
2841	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2842	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
2843	'Scale':1.0,'oldxy':[],'viewDir':[0,0,1]},'Super':Super,'SuperVec':SuperVec}
2844	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2845
2846	def OnPlotAll3DHKL(event):
2847	choices = GetPatternTreeDataNames(G2frame,['HKLF',])
2848	dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to plot',
2849	'Use data',choices)
2850	try:
2851	if dlg.ShowModal() == wx.ID_OK:
2852	refNames = [choices[i] for i in dlg.GetSelections()]
2853	else:
2854	return
2855	finally:
2856	dlg.Destroy()
2857	refList = np.zeros(0)
2858	for name in refNames:
2859	Id = GetPatternTreeItemId(G2frame,G2frame.root, name)
2860	reflData = G2frame.PatternTree.GetItemPyData(Id)[1]
2861	if len(refList):
2862	refList = np.concatenate((refList,reflData['RefList']))
2863	else:
2864	refList = reflData['RefList']
2865
2866	FoMax = np.max(refList.T[8+Super])
2867	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
2868	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
2869	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
2870	controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,'Zone':False,'viewKey':'L',
2871	'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
2872	'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
2873	'Scale':1.0,'oldxy':[],'viewDir':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
2874	G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
2875
2876
2877	def OnErrorAnalysis(event):
2878	G2plt.PlotDeltSig(G2frame,kind)
2879
2880	def OnWtFactor(event):
2881	try:
2882	val = float(wtval.GetValue())
2883	except ValueError:
2884	val = data[0]['wtFactor']
2885	data[0]['wtFactor'] = val
2886	wtval.SetValue('%.3f'%(val))
2887
2888	def OnCompression(event):
2889	data[0] = int(comp.GetValue())
2890
2891	def onCopyPlotCtrls(event):
2892	'''Respond to menu item to copy multiple sections from a histogram.
2893	Need this here to pass on the G2frame object.
2894	'''
2895	G2pdG.CopyPlotCtrls(G2frame)
2896
2897	def onCopySelectedItems(event):
2898	'''Respond to menu item to copy multiple sections from a histogram.
2899	Need this here to pass on the G2frame object.
2900	'''
2901	G2pdG.CopySelectedHistItems(G2frame)
2902
2903	data = G2frame.PatternTree.GetItemPyData(item)
2904	#patches
2905	if 'wtFactor' not in data[0]:
2906	data[0] = {'wtFactor':1.0}
2907	# if kind == 'PWDR' and 'Compression' not in data[0]:
2908	# data[0]['Compression'] = 1
2909	#if isinstance(data[1],list) and kind == 'HKLF':
2910	if 'list' in str(type(data[1])) and kind == 'HKLF':
2911	RefData = {'RefList':[],'FF':[]}
2912	for ref in data[1]:
2913	RefData['RefList'].append(ref[:11]+[ref[13],])
2914	RefData['FF'].append(ref[14])
2915	data[1] = RefData
2916	G2frame.PatternTree.SetItemPyData(item,data)
2917	#end patches
2918	if G2frame.dataDisplay:
2919	G2frame.dataDisplay.Destroy()
2920	if kind in ['PWDR','SASD']:
2921	SetDataMenuBar(G2frame,G2frame.dataFrame.PWDRMenu)
2922	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2923	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2924	G2frame.dataFrame.Bind(wx.EVT_MENU, onCopyPlotCtrls, id=wxID_PLOTCTRLCOPY)
2925	elif kind in ['HKLF',]:
2926	SetDataMenuBar(G2frame,G2frame.dataFrame.HKLFMenu)
2927	G2frame.dataFrame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=wxID_PWDANALYSIS)
2928	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=wxID_PWD3DHKLPLOT)
2929	G2frame.dataFrame.Bind(wx.EVT_MENU, OnPlotAll3DHKL, id=wxID_3DALLHKLPLOT)
2930	# G2frame.dataFrame.Bind(wx.EVT_MENU, onCopySelectedItems, id=wxID_PWDCOPY)
2931	G2frame.dataDisplay = wx.Panel(G2frame.dataFrame)
2932
2933	mainSizer = wx.BoxSizer(wx.VERTICAL)
2934	mainSizer.Add((5,5),)
2935	wtSizer = wx.BoxSizer(wx.HORIZONTAL)
2936	wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Weight factor: '),0,WACV)
2937	wtval = wx.TextCtrl(G2frame.dataDisplay,-1,'%.3f'%(data[0]['wtFactor']),style=wx.TE_PROCESS_ENTER)
2938	wtval.Bind(wx.EVT_TEXT_ENTER,OnWtFactor)
2939	wtval.Bind(wx.EVT_KILL_FOCUS,OnWtFactor)
2940	wtSizer.Add(wtval,0,WACV)
2941	# if kind == 'PWDR': #possible future compression feature; NB above patch as well
2942	# wtSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' Compression factor: '),0,WACV)
2943	# choice = ['1','2','3','4','5','6']
2944	# comp = wx.ComboBox(parent=G2frame.dataDisplay,choices=choice,
2945	# style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2946	# comp.SetValue(str(data[0]['Compression']))
2947	# comp.Bind(wx.EVT_COMBOBOX, OnCompression)
2948	# wtSizer.Add(comp,0,WACV)
2949	mainSizer.Add(wtSizer)
2950	if data[0].get('Dummy'):
2951	simSizer = wx.BoxSizer(wx.HORIZONTAL)
2952	Tmin = min(data[1][0])
2953	Tmax = max(data[1][0])
2954	num = len(data[1][0])
2955	step = (Tmax - Tmin)/(num-1)
2956	t = u'2\u03b8' # 2theta
2957	lbl = u'Simulation range: {:.2f} to {:.2f} {:s}\nwith {:.4f} steps ({:d} points)'
2958	lbl += u'\n(Edit range resets observed intensities).'
2959	lbl = lbl.format(Tmin,Tmax,t,step,num)
2960	simSizer.Add(wx.StaticText(G2frame.dataDisplay,wx.ID_ANY,lbl),
2961	0,WACV)
2962	but = wx.Button(G2frame.dataDisplay,wx.ID_ANY,"Edit range")
2963	but.Bind(wx.EVT_BUTTON,onEditSimRange)
2964	simSizer.Add(but,0,WACV)
2965	mainSizer.Add(simSizer)
2966	if 'Nobs' in data[0]:
2967	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2968	' Data residual wR: %.3f%% on %d observations'%(data[0]['wR'],data[0]['Nobs'])))
2969	for value in data[0]:
2970	if 'Nref' in value:
2971	pfx = value.split('Nref')[0]
2972	name = data[0].get(pfx.split(':')[0]+'::Name','?')
2973	if 'SS' in value:
2974	mainSizer.Add((5,5),)
2975	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For incommensurate phase '+name+':'))
2976	for m,(Rf2,Rf,Nobs) in enumerate(zip(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])):
2977	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2978	u' m = +/- %d: RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2979	(m,Rf2,Rf,Nobs)))
2980	else:
2981	mainSizer.Add((5,5),)
2982	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,' For phase '+name+':'))
2983	mainSizer.Add(wx.StaticText(G2frame.dataDisplay,-1,
2984	u' Unweighted phase residuals RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
2985	(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])))
2986
2987	mainSizer.Add((5,5),)
2988	mainSizer.Layout()
2989	G2frame.dataDisplay.SetSizer(mainSizer)
2990	Size = mainSizer.Fit(G2frame.dataFrame)
2991	Size[1] += 10
2992	G2frame.dataFrame.setSizePosLeft(Size)
2993	G2frame.PatternTree.SetItemPyData(item,data)
2994	if kind in ['PWDR','SASD']:
2995	if 'xylim' in dir(G2frame):
2996	NewPlot = False
2997	else:
2998
2999	NewPlot = True
3000	G2plt.PlotPatterns(G2frame,plotType=kind,newPlot=NewPlot)
3001	elif kind == 'HKLF':
3002	Name = G2frame.PatternTree.GetItemText(item)
3003	phaseName = G2pdG.IsHistogramInAnyPhase(G2frame,Name)
3004	if phaseName:
3005	pId = GetPatternTreeItemId(G2frame,G2frame.root,'Phases')
3006	phaseId = GetPatternTreeItemId(G2frame,pId,phaseName)
3007	General = G2frame.PatternTree.GetItemPyData(phaseId)['General']
3008	Super = General.get('Super',0)
3009	SuperVec = General.get('SuperVec',[])
3010	else:
3011	Super = 0
3012	SuperVec = []
3013	refList = data[1]['RefList']
3014	FoMax = np.max(refList.T[5+data[1].get('Super',0)])
3015	page = G2frame.G2plotNB.nb.GetSelection()
3016	tab = ''
3017	if page >= 0:
3018	tab = G2frame.G2plotNB.nb.GetPageText(page)
3019	if '3D' in tab:
3020	Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
3021	Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
3022	Vpoint = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
3023	Page = G2frame.G2plotNB.nb.GetPage(page)
3024	controls = Page.controls
3025	G2plt.Plot3DSngl(G2frame,newPlot=False,Data=controls,hklRef=refList,Title=phaseName)
3026	else:
3027	controls = {'Type' : 'Fo','ifFc' : True,
3028	'HKLmax' : [int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))],
3029	'HKLmin' : [int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))],
3030	'FoMax' : FoMax,'Zone' : '001','Layer' : 0,'Scale' : 1.0,'Super':Super,'SuperVec':SuperVec}
3031	G2plt.PlotSngl(G2frame,newPlot=True,Data=controls,hklRef=refList)
3032
3033	################################################################################
3034	##### Pattern tree routines
3035	################################################################################
3036
3037	def GetPatternTreeDataNames(G2frame,dataTypes):
3038	'''Finds all items in tree that match a 4 character prefix
3039
3040	:param wx.Frame G2frame: Data tree frame object
3041	:param list dataTypes: Contains one or more data tree item types to be matched
3042	such as ['IMG '] or ['PWDR','HKLF']
3043	:returns: a list of tree item names for the matching items
3044	'''
3045	names = []
3046	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3047	while item:
3048	name = G2frame.PatternTree.GetItemText(item)
3049	if name[:4] in dataTypes:
3050	names.append(name)
3051	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3052	return names
3053
3054	def GetPatternTreeItemId(G2frame, parentId, itemText):
3055	'''Needs a doc string
3056	'''
3057	item, cookie = G2frame.PatternTree.GetFirstChild(parentId)
3058	while item:
3059	if G2frame.PatternTree.GetItemText(item) == itemText:
3060	return item
3061	item, cookie = G2frame.PatternTree.GetNextChild(parentId, cookie)
3062	return 0
3063
3064	def MovePatternTreeToGrid(G2frame,item):
3065	'''Called from GSASII.OnPatternTreeSelChanged when a item is selected on the tree
3066	'''
3067	pickName = G2frame.PatternTree.GetItemText(item)
3068	if G2frame.PickIdText == pickName:
3069	return
3070
3071	oldPage = None # will be set later if already on a Phase item
3072	if G2frame.dataFrame:
3073	SetDataMenuBar(G2frame)
3074	if G2frame.dataFrame.GetLabel() == 'Comments':
3075	try:
3076	data = [G2frame.dataDisplay.GetValue()]
3077	G2frame.dataDisplay.Clear()
3078	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Comments')
3079	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3080	except: #clumsy but avoids dead window problem when opening another project
3081	pass
3082	elif G2frame.dataFrame.GetLabel() == 'Notebook':
3083	try:
3084	data = [G2frame.dataDisplay.GetValue()]
3085	G2frame.dataDisplay.Clear()
3086	Id = GetPatternTreeItemId(G2frame,G2frame.root, 'Notebook')
3087	if Id: G2frame.PatternTree.SetItemPyData(Id,data)
3088	except: #clumsy but avoids dead window problem when opening another project
3089	pass
3090	elif 'Phase Data for' in G2frame.dataFrame.GetLabel():
3091	if G2frame.dataDisplay:
3092	oldPage = G2frame.dataDisplay.GetSelection()
3093	G2frame.dataFrame.Clear()
3094	G2frame.dataFrame.SetLabel('')
3095	else:
3096	#create the frame for the data item window
3097	G2frame.dataFrame = DataFrame(parent=G2frame.mainPanel,frame=G2frame)
3098	G2frame.dataFrame.PhaseUserSize = None
3099
3100	G2frame.dataFrame.Raise()
3101	G2frame.PickId = item
3102	G2frame.PickIdText = None
3103	parentID = G2frame.root
3104	#for i in G2frame.ExportPattern: i.Enable(False)
3105	defWid = [250,150]
3106	if item != G2frame.root:
3107	parentID = G2frame.PatternTree.GetItemParent(item)
3108	if G2frame.PatternTree.GetItemParent(item) == G2frame.root:
3109	G2frame.PatternId = item
3110	if G2frame.PatternTree.GetItemText(item) == 'Notebook':
3111	SetDataMenuBar(G2frame,G2frame.dataFrame.DataNotebookMenu)
3112	G2frame.PatternId = 0
3113	#for i in G2frame.ExportPattern: i.Enable(False)
3114	data = G2frame.PatternTree.GetItemPyData(item)
3115	UpdateNotebook(G2frame,data)
3116	elif G2frame.PatternTree.GetItemText(item) == 'Controls':
3117	G2frame.PatternId = 0
3118	#for i in G2frame.ExportPattern: i.Enable(False)
3119	data = G2frame.PatternTree.GetItemPyData(item)
3120	if not data: #fill in defaults
3121	data = copy.copy(G2obj.DefaultControls) #least squares controls
3122	G2frame.PatternTree.SetItemPyData(item,data)
3123	for i in G2frame.Refine: i.Enable(True)
3124	G2frame.EnableSeqRefineMenu()
3125	UpdateControls(G2frame,data)
3126	elif G2frame.PatternTree.GetItemText(item) == 'Sequential results':
3127	data = G2frame.PatternTree.GetItemPyData(item)
3128	UpdateSeqResults(G2frame,data)
3129	elif G2frame.PatternTree.GetItemText(item) == 'Covariance':
3130	data = G2frame.PatternTree.GetItemPyData(item)
3131	G2frame.dataFrame.setSizePosLeft(defWid)
3132	text = ''
3133	if 'Rvals' in data:
3134	Nvars = len(data['varyList'])
3135	Rvals = data['Rvals']
3136	text = '\nFinal residuals: \nwR = %.3f%% \nchi**2 = %.1f \nGOF = %.2f'%(Rvals['Rwp'],Rvals['chisq'],Rvals['GOF'])
3137	text += '\nNobs = %d \nNvals = %d'%(Rvals['Nobs'],Nvars)
3138	if 'lamMax' in Rvals:
3139	text += '\nlog10 MaxLambda = %.1f'%(np.log10(Rvals['lamMax']))
3140	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3141	value='See plot window for covariance display'+text,style=wx.TE_MULTILINE)
3142	G2plt.PlotCovariance(G2frame,data)
3143	elif G2frame.PatternTree.GetItemText(item) == 'Constraints':
3144	data = G2frame.PatternTree.GetItemPyData(item)
3145	G2cnstG.UpdateConstraints(G2frame,data)
3146	elif G2frame.PatternTree.GetItemText(item) == 'Rigid bodies':
3147	data = G2frame.PatternTree.GetItemPyData(item)
3148	G2cnstG.UpdateRigidBodies(G2frame,data)
3149	elif G2frame.PatternTree.GetItemText(item) == 'Restraints':
3150	data = G2frame.PatternTree.GetItemPyData(item)
3151	Phases = G2frame.GetPhaseData()
3152	phase = ''
3153	phaseName = ''
3154	if Phases:
3155	phaseName = Phases.keys()[0]
3156	G2frame.dataFrame.setSizePosLeft(defWid)
3157	G2restG.UpdateRestraints(G2frame,data,Phases,phaseName)
3158	elif 'IMG' in G2frame.PatternTree.GetItemText(item):
3159	G2frame.Image = item
3160	G2frame.dataFrame.SetTitle('Image Data')
3161	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(
3162	G2frame,item,'Image Controls'))
3163	G2imG.UpdateImageData(G2frame,data)
3164	G2plt.PlotImage(G2frame,newPlot=True)
3165	elif 'PKS' in G2frame.PatternTree.GetItemText(item):
3166	G2plt.PlotPowderLines(G2frame)
3167	elif 'PWDR' in G2frame.PatternTree.GetItemText(item):
3168	#for i in G2frame.ExportPattern: i.Enable(True)
3169	if G2frame.EnablePlot:
3170	UpdatePWHKPlot(G2frame,'PWDR',item)
3171	elif 'SASD' in G2frame.PatternTree.GetItemText(item):
3172	#for i in G2frame.ExportPattern: i.Enable(True)
3173	if G2frame.EnablePlot:
3174	UpdatePWHKPlot(G2frame,'SASD',item)
3175	elif 'HKLF' in G2frame.PatternTree.GetItemText(item):
3176	G2frame.Sngl = True
3177	UpdatePWHKPlot(G2frame,'HKLF',item)
3178	elif 'PDF' in G2frame.PatternTree.GetItemText(item):
3179	G2frame.PatternId = item
3180	for i in G2frame.ExportPDF: i.Enable(True)
3181	G2plt.PlotISFG(G2frame,type='S(Q)')
3182	elif G2frame.PatternTree.GetItemText(item) == 'Phases':
3183	G2frame.dataFrame.setSizePosLeft(defWid)
3184	wx.TextCtrl(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize(),
3185	value='Select one phase to see its parameters')
3186	elif 'I(Q)' in G2frame.PatternTree.GetItemText(item):
3187	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3188	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3189	G2pdG.UpdatePDFGrid(G2frame,data)
3190	G2plt.PlotISFG(G2frame,type='I(Q)',newPlot=True)
3191	elif 'S(Q)' in G2frame.PatternTree.GetItemText(item):
3192	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3193	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3194	G2pdG.UpdatePDFGrid(G2frame,data)
3195	G2plt.PlotISFG(G2frame,type='S(Q)',newPlot=True)
3196	elif 'F(Q)' in G2frame.PatternTree.GetItemText(item):
3197	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3198	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3199	G2pdG.UpdatePDFGrid(G2frame,data)
3200	G2plt.PlotISFG(G2frame,type='F(Q)',newPlot=True)
3201	elif 'G(R)' in G2frame.PatternTree.GetItemText(item):
3202	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3203	data = G2frame.PatternTree.GetItemPyData(GetPatternTreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
3204	G2pdG.UpdatePDFGrid(G2frame,data)
3205	G2plt.PlotISFG(G2frame,type='G(R)',newPlot=True)
3206	elif G2frame.PatternTree.GetItemText(parentID) == 'Phases':
3207	data = G2frame.PatternTree.GetItemPyData(item)
3208	G2phG.UpdatePhaseData(G2frame,item,data,oldPage)
3209	elif G2frame.PatternTree.GetItemText(item) == 'Comments':
3210	SetDataMenuBar(G2frame,G2frame.dataFrame.DataCommentsMenu)
3211	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3212	data = G2frame.PatternTree.GetItemPyData(item)
3213	UpdateComments(G2frame,data)
3214	elif G2frame.PatternTree.GetItemText(item) == 'Image Controls':
3215	G2frame.dataFrame.SetTitle('Image Controls')
3216	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3217	masks = G2frame.PatternTree.GetItemPyData(
3218	GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3219	data = G2frame.PatternTree.GetItemPyData(item)
3220	G2imG.UpdateImageControls(G2frame,data,masks)
3221	G2plt.PlotImage(G2frame,newPlot=True)
3222	elif G2frame.PatternTree.GetItemText(item) == 'Masks':
3223	G2frame.dataFrame.SetTitle('Masks')
3224	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3225	data = G2frame.PatternTree.GetItemPyData(item)
3226	G2imG.UpdateMasks(G2frame,data)
3227	G2plt.PlotImage(G2frame,newPlot=True)
3228	elif G2frame.PatternTree.GetItemText(item) == 'Stress/Strain':
3229	G2frame.dataFrame.SetTitle('Stress/Strain')
3230	G2frame.Image = G2frame.PatternTree.GetItemParent(item)
3231	data = G2frame.PatternTree.GetItemPyData(item)
3232	G2plt.PlotImage(G2frame,newPlot=True)
3233	G2plt.PlotStrain(G2frame,data,newPlot=True)
3234	G2imG.UpdateStressStrain(G2frame,data)
3235	elif G2frame.PatternTree.GetItemText(item) == 'PDF Controls':
3236	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3237	for i in G2frame.ExportPDF: i.Enable(True)
3238	data = G2frame.PatternTree.GetItemPyData(item)
3239	G2pdG.UpdatePDFGrid(G2frame,data)
3240	G2plt.PlotISFG(G2frame,type='I(Q)')
3241	G2plt.PlotISFG(G2frame,type='S(Q)')
3242	G2plt.PlotISFG(G2frame,type='F(Q)')
3243	G2plt.PlotISFG(G2frame,type='G(R)')
3244	elif G2frame.PatternTree.GetItemText(item) == 'Peak List':
3245	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3246	for i in G2frame.ExportPeakList: i.Enable(True)
3247	data = G2frame.PatternTree.GetItemPyData(item)
3248	#patch
3249	if 'list' in str(type(data)):
3250	data = {'peaks':data,'sigDict':{}}
3251	G2frame.PatternTree.SetItemPyData(item,data)
3252	#end patch
3253	G2pdG.UpdatePeakGrid(G2frame,data)
3254	G2plt.PlotPatterns(G2frame)
3255	elif G2frame.PatternTree.GetItemText(item) == 'Background':
3256	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3257	data = G2frame.PatternTree.GetItemPyData(item)
3258	G2pdG.UpdateBackground(G2frame,data)
3259	G2plt.PlotPatterns(G2frame)
3260	elif G2frame.PatternTree.GetItemText(item) == 'Limits':
3261	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3262	datatype = G2frame.PatternTree.GetItemText(G2frame.PatternId)[:4]
3263	data = G2frame.PatternTree.GetItemPyData(item)
3264	G2pdG.UpdateLimitsGrid(G2frame,data,datatype)
3265	G2plt.PlotPatterns(G2frame,plotType=datatype)
3266	elif G2frame.PatternTree.GetItemText(item) == 'Instrument Parameters':
3267	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3268	data = G2frame.PatternTree.GetItemPyData(item)[0]
3269	G2pdG.UpdateInstrumentGrid(G2frame,data)
3270	if 'P' in data['Type'][0]: #powder data only
3271	G2plt.PlotPeakWidths(G2frame)
3272	elif G2frame.PatternTree.GetItemText(item) == 'Models':
3273	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3274	data = G2frame.PatternTree.GetItemPyData(item)
3275	G2pdG.UpdateModelsGrid(G2frame,data)
3276	G2plt.PlotPatterns(G2frame,plotType='SASD')
3277	if len(data['Size']['Distribution']):
3278	G2plt.PlotSASDSizeDist(G2frame)
3279	elif G2frame.PatternTree.GetItemText(item) == 'Substances':
3280	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3281	data = G2frame.PatternTree.GetItemPyData(item)
3282	G2pdG.UpdateSubstanceGrid(G2frame,data)
3283	elif G2frame.PatternTree.GetItemText(item) == 'Sample Parameters':
3284	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3285	data = G2frame.PatternTree.GetItemPyData(item)
3286	datatype = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[2][:4]
3287
3288	if 'Temperature' not in data: #temp fix for old gpx files
3289	data = {'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],'DisplaceX':[0.0,False],
3290	'DisplaceY':[0.0,False],'Diffuse':[],'Temperature':300.,'Pressure':1.0,
3291	'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
3292	'Gonio. radius':200.0}
3293	G2frame.PatternTree.SetItemPyData(item,data)
3294
3295	G2pdG.UpdateSampleGrid(G2frame,data)
3296	G2plt.PlotPatterns(G2frame,plotType=datatype)
3297	elif G2frame.PatternTree.GetItemText(item) == 'Index Peak List':
3298	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3299	for i in G2frame.ExportPeakList: i.Enable(True)
3300	data = G2frame.PatternTree.GetItemPyData(item)
3301	#patch
3302	if len(data) != 2:
3303	data = [data,[]]
3304	G2frame.PatternTree.SetItemPyData(item,data)
3305	#end patch
3306	G2pdG.UpdateIndexPeaksGrid(G2frame,data)
3307	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3308	G2plt.PlotPowderLines(G2frame)
3309	else:
3310	G2plt.PlotPatterns(G2frame)
3311	elif G2frame.PatternTree.GetItemText(item) == 'Unit Cells List':
3312	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3313	data = G2frame.PatternTree.GetItemPyData(item)
3314	if not data:
3315	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
3316	data.append([0,0,0,0,0,0,0,0,0,0,0,0,0,0]) #Bravais lattice flags
3317	data.append([]) #empty cell list
3318	data.append([]) #empty dmin
3319	data.append({}) #empty superlattice stuff
3320	G2frame.PatternTree.SetItemPyData(item,data)
3321	#patch
3322	if len(data) < 5:
3323	data.append({'Use':False,'ModVec':[0,0,0.1],'maxH':1,'ssSymb':''}) #empty superlattice stuff
3324	G2frame.PatternTree.SetItemPyData(item,data)
3325	#end patch
3326	G2pdG.UpdateUnitCellsGrid(G2frame,data)
3327	if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
3328	G2plt.PlotPowderLines(G2frame)
3329	else:
3330	G2plt.PlotPatterns(G2frame)
3331	elif G2frame.PatternTree.GetItemText(item) == 'Reflection Lists': #powder reflections
3332	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3333	data = G2frame.PatternTree.GetItemPyData(item)
3334	G2frame.RefList = ''
3335	if len(data):
3336	G2frame.RefList = data.keys()[0]
3337	G2pdG.UpdateReflectionGrid(G2frame,data)
3338	G2plt.PlotPatterns(G2frame)
3339	elif G2frame.PatternTree.GetItemText(item) == 'Reflection List': #HKLF reflections
3340	G2frame.PatternId = G2frame.PatternTree.GetItemParent(item)
3341	name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
3342	data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
3343	G2pdG.UpdateReflectionGrid(G2frame,data,HKLF=True,Name=name)
3344
3345	if G2frame.PickId:
3346	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
3347	G2frame.dataFrame.Raise()
3348
3349	def SetDataMenuBar(G2frame,menu=None):
3350	'''Set the menu for the data frame. On the Mac put this
3351	menu for the data tree window instead.
3352
3353	Note that data frame items do not have menus, for these (menu=None)
3354	display a blank menu or on the Mac display the standard menu for
3355	the data tree window.
3356	'''
3357	if sys.platform == "darwin":
3358	if menu is None:
3359	G2frame.SetMenuBar(G2frame.GSASIIMenu)
3360	else:
3361	G2frame.SetMenuBar(menu)
3362	else:
3363	if menu is None:
3364	G2frame.dataFrame.SetMenuBar(G2frame.dataFrame.BlankMenu)
3365	else:
3366	G2frame.dataFrame.SetMenuBar(menu)
3367
3368	def HowDidIgetHere():
3369	'''Show a traceback with calls that brought us to the current location.
3370	Used for debugging.
3371	'''
3372	import traceback
3373	print 70''
3374	for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip.rstrip())
3375	print 70''
3376

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