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source: trunk/GSASIIplot.py @ 412

Last change on this file since 412 was 404, checked in by vondreele, 14 years ago
put error bars on seq refinement plots add cubic elastic strain coeff make sure results are saved from seq refinements
Property svn:keywords set to `Date Author Revision URL Id`
File size: 110.9 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2011-10-28 18:59:03 +0000 (Fri, 28 Oct 2011) $
4	# $Author: vondreele $
5	# $Revision: 404 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 404 2011-10-28 18:59:03Z vondreele $
8	########### SVN repository information ###################
9	import math
10	import time
11	import copy
12	import os.path
13	import numpy as np
14	import numpy.linalg as nl
15	import wx
16	import wx.aui
17	import wx.glcanvas
18	import matplotlib as mpl
19	import mpl_toolkits.mplot3d.axes3d as mp3d
20	import GSASIIpath
21	import GSASIIgrid as G2gd
22	import GSASIIimage as G2img
23	import GSASIIpwd as G2pwd
24	import GSASIIIO as G2IO
25	import GSASIIpwdGUI as G2pdG
26	import GSASIIimgGUI as G2imG
27	import GSASIIphsGUI as G2phG
28	import GSASIIlattice as G2lat
29	import GSASIIspc as G2spc
30	import pytexture as ptx
31	from OpenGL.GL import *
32	from OpenGL.GLU import *
33	from OpenGL.GLUT import *
34	from OpenGL.GLE import *
35	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
36	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
37
38	# useful degree trig functions
39	sind = lambda x: math.sin(x*math.pi/180.)
40	cosd = lambda x: math.cos(x*math.pi/180.)
41	tand = lambda x: math.tan(x*math.pi/180.)
42	asind = lambda x: 180.*math.asin(x)/math.pi
43	acosd = lambda x: 180.*math.acos(x)/math.pi
44	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
45	atand = lambda x: 180.*math.atan(x)/math.pi
46	# numpy versions
47	npsind = lambda x: np.sin(x*np.pi/180.)
48	npcosd = lambda x: np.cos(x*np.pi/180.)
49	npacosd = lambda x: 180.*np.arccos(x)/np.pi
50	npasind = lambda x: 180.*np.arcsin(x)/np.pi
51	npatand = lambda x: 180.*np.arctan(x)/np.pi
52	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
53
54	class G2PlotMpl(wx.Panel):
55	def __init__(self,parent,id=-1,dpi=None,**kwargs):
56	wx.Panel.__init__(self,parent,id=id,**kwargs)
57	mpl.rcParams['legend.fontsize'] = 8
58	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
59	self.canvas = Canvas(self,-1,self.figure)
60	self.toolbar = Toolbar(self.canvas)
61
62	self.toolbar.Realize()
63
64	sizer=wx.BoxSizer(wx.VERTICAL)
65	sizer.Add(self.canvas,1,wx.EXPAND)
66	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
67	self.SetSizer(sizer)
68
69	class G2PlotOgl(wx.Panel):
70	def __init__(self,parent,id=-1,dpi=None,**kwargs):
71	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
72	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
73	self.camera = {}
74	sizer=wx.BoxSizer(wx.VERTICAL)
75	sizer.Add(self.canvas,1,wx.EXPAND)
76	self.SetSizer(sizer)
77
78	class G2Plot3D(wx.Panel):
79	def __init__(self,parent,id=-1,dpi=None,**kwargs):
80	wx.Panel.__init__(self,parent,id=id,**kwargs)
81	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
82	self.canvas = Canvas(self,-1,self.figure)
83	self.toolbar = Toolbar(self.canvas)
84
85	self.toolbar.Realize()
86
87	sizer=wx.BoxSizer(wx.VERTICAL)
88	sizer.Add(self.canvas,1,wx.EXPAND)
89	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
90	self.SetSizer(sizer)
91
92	class G2PlotNoteBook(wx.Panel):
93	def __init__(self,parent,id=-1):
94	wx.Panel.__init__(self,parent,id=id)
95	#so one can't delete a plot page!!
96	self.nb = wx.aui.AuiNotebook(self, \
97	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
98	sizer = wx.BoxSizer()
99	sizer.Add(self.nb,1,wx.EXPAND)
100	self.SetSizer(sizer)
101	self.status = parent.CreateStatusBar()
102	self.status.SetFieldsCount(2)
103	self.status.SetStatusWidths([150,-1])
104	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
105
106	self.plotList = []
107
108	def addMpl(self,name=""):
109	page = G2PlotMpl(self.nb)
110	self.nb.AddPage(page,name)
111
112	self.plotList.append(name)
113
114	return page.figure
115
116	def add3D(self,name=""):
117	page = G2Plot3D(self.nb)
118	self.nb.AddPage(page,name)
119
120	self.plotList.append(name)
121
122	return page.figure
123
124	def addOgl(self,name=""):
125	page = G2PlotOgl(self.nb)
126	self.nb.AddPage(page,name)
127
128	self.plotList.append(name)
129
130	return page.figure
131
132	def Delete(self,name):
133	try:
134	item = self.plotList.index(name)
135	del self.plotList[item]
136	self.nb.DeletePage(item)
137	except ValueError: #no plot of this name - do nothing
138	return
139
140	def clear(self):
141	while self.nb.GetPageCount():
142	self.nb.DeletePage(0)
143	self.plotList = []
144	self.status.DestroyChildren()
145
146	def Rename(self,oldName,newName):
147	try:
148	item = self.plotList.index(oldName)
149	self.plotList[item] = newName
150	self.nb.SetPageText(item,newName)
151	except ValueError: #no plot of this name - do nothing
152	return
153
154	def OnPageChanged(self,event):
155	if self.plotList:
156	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
157	self.status.DestroyChildren() #get rid of special stuff on status bar
158
159	def PlotSngl(self,newPlot=False):
160	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
161	to F, F**2, etc. as requested
162	'''
163	from matplotlib.patches import Circle
164	global HKL,HKLF
165
166	def OnSCMotion(event):
167	xpos = event.xdata
168	if xpos:
169	xpos = round(xpos) #avoid out of frame mouse position
170	ypos = round(event.ydata)
171	zpos = Data['Layer']
172	if '100' in Data['Zone']:
173	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
174	elif '010' in Data['Zone']:
175	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
176	elif '001' in Data['Zone']:
177	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
178	Page.canvas.SetToolTipString(HKLtxt)
179	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
180
181	def OnSCPick(event):
182	zpos = Data['Layer']
183	pos = event.artist.center
184	if '100' in Data['Zone']:
185	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
186	hkl = np.array([zpos,pos[0],pos[1]])
187	elif '010' in Data['Zone']:
188	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
189	hkl = np.array([pos[0],zpos,pos[1]])
190	elif '001' in Data['Zone']:
191	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
192	hkl = np.array([pos[0],pos[1],zpos])
193	h,k,l = hkl
194	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
195	if len(hklf):
196	Fosq,sig,Fcsq = hklf[0]
197	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
198	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
199
200	def OnSCKeyPress(event):
201	print event.key
202
203	try:
204	plotNum = self.G2plotNB.plotList.index('Structure Factors')
205	Page = self.G2plotNB.nb.GetPage(plotNum)
206	if not newPlot:
207	Plot = Page.figure.gca() #get previous powder plot & get limits
208	xylim = Plot.get_xlim(),Plot.get_ylim()
209	Page.figure.clf()
210	Plot = Page.figure.gca() #get a fresh plot after clf()
211	except ValueError:
212	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
213	plotNum = self.G2plotNB.plotList.index('Structure Factors')
214	Page = self.G2plotNB.nb.GetPage(plotNum)
215	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
216	Page.canvas.mpl_connect('pick_event', OnSCPick)
217	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
218	Page.SetFocus()
219
220	Plot.set_aspect(aspect='equal')
221	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
222	Data = self.PatternTree.GetItemPyData( \
223	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
224	Type = Data['Type']
225	scale = Data['Scale']
226	HKLmax = Data['HKLmax']
227	HKLmin = Data['HKLmin']
228	FosqMax = Data['FoMax']
229	FoMax = math.sqrt(FosqMax)
230	ifFc = Data['ifFc']
231	xlabel = ['k, h=','h, k=','h, l=']
232	ylabel = ['l','l','k']
233	zones = ['100','010','001']
234	pzone = [[1,2],[0,2],[0,1]]
235	izone = zones.index(Data['Zone'])
236	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
237	HKL = []
238	HKLF = []
239	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
240	HKL.append(H)
241	HKLF.append([Fosq,sig,Fcsq])
242	if H[izone] == Data['Layer']:
243	B = 0
244	if Type == 'Fosq':
245	A = scale*Fosq/FosqMax
246	B = scale*Fcsq/FosqMax
247	C = abs(A-B)
248	elif Type == 'Fo':
249	A = scale*math.sqrt(max(0,Fosq))/FoMax
250	B = scale*math.sqrt(max(0,Fcsq))/FoMax
251	C = abs(A-B)
252	elif Type == '\|DFsq\|/sig':
253	A = abs(Fosq-Fcsq)/(scale*sig)
254	elif Type == '\|DFsq\|>sig':
255	A = abs(Fosq-Fcsq)/(scale*sig)
256	if A < 1.0: A = 0
257	elif Type == '\|DFsq\|>3sig':
258	A = abs(Fosq-Fcsq)/(scale*sig)
259	if A < 3.0: A = 0
260	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
261	if A > 0.0:
262	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
263	if B:
264	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
265	radius = C
266	if radius > 0:
267	if A > B:
268	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
269	else:
270	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
271	HKL = np.array(HKL,dtype=np.int)
272	HKLF = np.array(HKLF)
273	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
274	Plot.set_ylabel(ylabel[izone],fontsize=12)
275	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
276	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
277	if not newPlot:
278	Page.toolbar.push_current()
279	Plot.set_xlim(xylim[0])
280	Plot.set_ylim(xylim[1])
281	xylim = []
282	Page.toolbar.push_current()
283	Page.toolbar.draw()
284	else:
285	Page.canvas.draw()
286
287	def PlotPatterns(self,newPlot=False):
288	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
289	2-theta or q (future TOF). Can display multiple patterns as "waterfall plots" or contour plots. Log I
290	plotting available.
291	'''
292	global HKL
293
294	def OnPick(event):
295	if self.itemPicked is not None: return
296	PatternId = self.PatternId
297	try:
298	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
299	except TypeError:
300	return
301	Parms = dict(zip(Names,Values))
302	try:
303	wave = Parms['Lam']
304	except KeyError:
305	wave = Parms['Lam1']
306	PickId = self.PickId
307	pick = event.artist
308	mouse = event.mouseevent
309	xpos = pick.get_xdata()
310	ypos = pick.get_ydata()
311	ind = event.ind
312	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
313	if self.PatternTree.GetItemText(PickId) == 'Peak List':
314	if ind.all() != [0]: #picked a data point
315	if 'C' in Parms['Type']: #CW data - TOF later in an elif
316	ins = [Parms[x] for x in ['U','V','W','X','Y']]
317	if self.qPlot: #qplot - convert back to 2-theta
318	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
319	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
320	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
321	data = self.PatternTree.GetItemPyData(self.PickId)
322	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
323	data.append(XY)
324	G2pdG.UpdatePeakGrid(self,data)
325	PlotPatterns(self)
326	else: #picked a peak list line
327	self.itemPicked = pick
328	elif self.PatternTree.GetItemText(PickId) == 'Limits':
329	if ind.all() != [0]: #picked a data point
330	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
331	data = self.PatternTree.GetItemPyData(LimitId)
332	if 'C' in Parms['Type']: #CW data - TOF later in an elif
333	if self.qPlot: #qplot - convert back to 2-theta
334	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
335	if mouse.button==1:
336	data[1][0] = min(xy[0],data[1][1])
337	if mouse.button==3:
338	data[1][1] = max(xy[0],data[1][0])
339	self.PatternTree.SetItemPyData(LimitId,data)
340	G2pdG.UpdateLimitsGrid(self,data)
341	PlotPatterns(self)
342	else: #picked a limit line
343	self.itemPicked = pick
344	elif self.PatternTree.GetItemText(PickId) == 'Reflection Lists':
345	if ind.all() == [0]: #picked a limit line
346	self.itemPicked = pick
347
348	def OnPlotKeyPress(event):
349	newPlot = False
350	if event.key == 'w':
351	if self.Weight:
352	self.Weight = False
353	else:
354	self.Weight = True
355	print 'plot weighting:',self.Weight
356	elif event.key == 'n':
357	if self.Contour:
358	pass
359	else:
360	if self.logPlot:
361	self.logPlot = False
362	else:
363	self.Offset[0] = 0
364	self.logPlot = True
365	elif event.key == 'u':
366	if self.Contour:
367	self.Cmax = min(1.0,self.Cmax*1.2)
368	elif self.logPlot:
369	pass
370	elif self.Offset[0] < 100.:
371	self.Offset[0] += 1.
372	elif event.key == 'd':
373	if self.Contour:
374	self.Cmax = max(0.0,self.Cmax*0.8)
375	elif self.logPlot:
376	pass
377	elif self.Offset[0] > 0.:
378	self.Offset[0] -= 1.
379	elif event.key == 'l':
380	self.Offset[1] -= 1.
381	elif event.key == 'r':
382	self.Offset[1] += 1.
383	elif event.key == 'o':
384	self.Offset = [0,0]
385	elif event.key == 'c':
386	newPlot = True
387	if self.Contour:
388	self.Contour = False
389	else:
390	self.Contour = True
391	self.SinglePlot = False
392	self.Offset = [0.,0.]
393	elif event.key == 'q':
394	newPlot = True
395	if self.qPlot:
396	self.qPlot = False
397	else:
398	self.qPlot = True
399	elif event.key == 's':
400	if self.Contour:
401	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
402	choice.sort()
403	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
404	if dlg.ShowModal() == wx.ID_OK:
405	sel = dlg.GetSelection()
406	self.ContourColor = choice[sel]
407	else:
408	self.ContourColor = 'Paired'
409	dlg.Destroy()
410	else:
411	if self.SinglePlot:
412	self.SinglePlot = False
413	else:
414	self.SinglePlot = True
415	elif event.key == '+':
416	if self.PickId:
417	self.PickId = False
418	elif event.key == 'i': #for smoothing contour plot
419	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
420	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
421	'mitchell','sinc','lanczos']
422	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
423	if dlg.ShowModal() == wx.ID_OK:
424	sel = dlg.GetSelection()
425	self.Interpolate = choice[sel]
426	else:
427	self.Interpolate = 'nearest'
428	dlg.Destroy()
429
430	PlotPatterns(self,newPlot=newPlot)
431
432	def OnKeyBox(event):
433	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('Powder Patterns'):
434	event.key = cb.GetValue()[0]
435	cb.SetValue(' key press')
436	OnPlotKeyPress(event)
437
438	def OnMotion(event):
439	xpos = event.xdata
440	if xpos: #avoid out of frame mouse position
441	ypos = event.ydata
442	Page.canvas.SetCursor(wx.CROSS_CURSOR)
443	try:
444	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
445	Parms = dict(zip(Names,Values))
446	try:
447	wave = Parms['Lam']
448	except KeyError:
449	wave = Parms['Lam1']
450	if self.qPlot:
451	xpos = 2.0asind(xposwave/(4*math.pi))
452	dsp = 0.0
453	if abs(xpos) > 0.: #avoid possible singularity at beam center
454	dsp = wave/(2.*sind(abs(xpos)/2.0))
455	if self.Contour:
456	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
457	else:
458	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
459	if self.itemPicked:
460	Page.canvas.SetToolTipString('%9.3f'%(xpos))
461	if self.PickId:
462	found = []
463	if self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists']:
464	if len(HKL):
465	view = Page.toolbar._views.forward()[0][:2]
466	wid = view[1]-view[0]
467	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
468	if len(found):
469	h,k,l = found[0][:3]
470	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
471	else:
472	Page.canvas.SetToolTipString('')
473
474	except TypeError:
475	self.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
476
477	def OnRelease(event):
478	if self.itemPicked is None: return
479	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
480	Parms = dict(zip(Names,Values))
481	try:
482	wave = Parms['Lam']
483	except KeyError:
484	wave = Parms['Lam1']
485	xpos = event.xdata
486	if xpos: #avoid out of frame mouse position
487	lines = []
488	for line in self.Lines: lines.append(line.get_xdata()[0])
489	lineNo = lines.index(self.itemPicked.get_xdata()[0])
490	if lineNo in [0,1]:
491	LimitId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Limits')
492	data = self.PatternTree.GetItemPyData(LimitId)
493	# print 'limits',xpos
494	if self.qPlot:
495	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
496	else:
497	data[1][lineNo] = xpos
498	self.PatternTree.SetItemPyData(LimitId,data)
499	if self.PatternTree.GetItemText(self.PickId) == 'Limits':
500	G2pdG.UpdateLimitsGrid(self,data)
501	else:
502	PeakId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Peak List')
503	data = self.PatternTree.GetItemPyData(PeakId)
504	# print 'peaks',xpos
505	if event.button == 3:
506	del data[lineNo-2]
507	else:
508	if self.qPlot:
509	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
510	else:
511	data[lineNo-2][0] = xpos
512	self.PatternTree.SetItemPyData(PeakId,data)
513	G2pdG.UpdatePeakGrid(self,data)
514	PlotPatterns(self)
515	self.itemPicked = None
516
517	xylim = []
518	try:
519	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
520	Page = self.G2plotNB.nb.GetPage(plotNum)
521	if not newPlot:
522	Plot = Page.figure.gca() #get previous powder plot & get limits
523	xylim = Plot.get_xlim(),Plot.get_ylim()
524	Page.figure.clf()
525	Plot = Page.figure.gca() #get a fresh plot after clf()
526	except ValueError:
527	newPlot = True
528	self.Cmax = 1.0
529	Plot = self.G2plotNB.addMpl('Powder Patterns').gca()
530	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
531	Page = self.G2plotNB.nb.GetPage(plotNum)
532	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
533	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
534	Page.canvas.mpl_connect('pick_event', OnPick)
535	Page.canvas.mpl_connect('button_release_event', OnRelease)
536	Page.SetFocus()
537	self.G2plotNB.status.DestroyChildren()
538	if self.Contour:
539	Choice = (' key press','d: lower contour max','u: raise contour max',
540	'i: interpolation method','s: color scheme','c: contour off')
541	else:
542	if self.logPlot:
543	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
544	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
545	else:
546	Choice = (' key press','l: offset left','r: offset right','d: offset down',
547	'u: offset up','o: reset offset','n: log(I) on','c: contour on',
548	'q: toggle q plot','s: toggle single plot','+: no selection')
549	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
550	choices=Choice)
551	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
552	cb.SetValue(' key press')
553
554	PickId = self.PickId
555	PatternId = self.PatternId
556	colors=['b','g','r','c','m','k']
557	Lines = []
558	if self.SinglePlot:
559	Pattern = self.PatternTree.GetItemPyData(PatternId)
560	Pattern.append(self.PatternTree.GetItemText(PatternId))
561	PlotList = [Pattern,]
562	ParmList = [self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
563	self.PatternId, 'Instrument Parameters'))[1],]
564	else:
565	PlotList = []
566	ParmList = []
567	item, cookie = self.PatternTree.GetFirstChild(self.root)
568	while item:
569	if 'PWDR' in self.PatternTree.GetItemText(item):
570	Pattern = self.PatternTree.GetItemPyData(item)
571	if len(Pattern) < 3: # put name on end if needed
572	Pattern.append(self.PatternTree.GetItemText(item))
573	PlotList.append(Pattern)
574	ParmList.append(self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
575	item,'Instrument Parameters'))[1])
576	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
577	Ymax = 1.0
578	lenX = 0
579	if self.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
580	Phases = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId,'Reflection Lists'))
581	HKL = []
582	for peak in Phases[self.RefList]:
583	HKL.append(peak[:6])
584	HKL = np.array(HKL)
585	else:
586	HKL = np.array(self.HKL)
587	for Pattern in PlotList:
588	xye = Pattern[1]
589	Ymax = max(Ymax,max(xye[1]))
590	offset = self.Offset[0]*Ymax/100.0
591	Title = 'Powder Patterns: '+os.path.split(self.GSASprojectfile)[1]
592	if self.logPlot:
593	Title = 'log('+Title+')'
594	Plot.set_title(Title)
595	if self.qPlot:
596	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
597	else:
598	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
599	Plot.set_ylabel('Intensity',fontsize=12)
600	if self.Contour:
601	ContourZ = []
602	ContourY = []
603	Nseq = 0
604	if len(PlotList) < 2:
605	self.Contour = False
606	for N,Pattern in enumerate(PlotList):
607	Parms = ParmList[N]
608	ifpicked = False
609	LimitId = 0
610	xye = np.array(Pattern[1])
611	if PickId:
612	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
613	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
614	if self.qPlot:
615	Id = G2gd.GetPatternTreeItemId(self,self.root, Pattern[2])
616	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
617	else:
618	X = xye[0]
619	if not lenX:
620	lenX = len(X)
621	Y = xye[1]+offset*N
622	if LimitId:
623	limits = np.array(self.PatternTree.GetItemPyData(LimitId))
624	if self.qPlot:
625	limits = 4np.pinpsind(limits/2.0)/Parms[1]
626	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
627	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
628	if self.Contour:
629
630	if lenX == len(X):
631	ContourY.append(N)
632	ContourZ.append(Y)
633	ContourX = X
634	Nseq += 1
635	Plot.set_ylabel('Data sequence',fontsize=12)
636	else:
637	X += self.Offset[1].005N
638	if ifpicked:
639	Z = xye[3]+offset*N
640	W = xye[4]+offset*N
641	D = xye[5]+offsetN-Ymax.02
642	if self.Weight:
643	W2 = np.sqrt(xye[2])
644	D = W2-Ymax.02
645	if self.logPlot:
646	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
647	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
648	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
649	else:
650	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
651	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
652	Plot.plot(X,W,colors[(N+2)%6],picker=False)
653	Plot.plot(X,D,colors[(N+3)%6],picker=False)
654	Plot.axhline(0.,color=wx.BLACK)
655	Page.canvas.SetToolTipString('')
656	if self.PatternTree.GetItemText(PickId) == 'Peak List':
657	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
658	Page.canvas.SetToolTipString(tip)
659	data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List'))
660	for item in data:
661	if self.qPlot:
662	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
663	else:
664	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
665	if self.PatternTree.GetItemText(PickId) == 'Limits':
666	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
667	Page.canvas.SetToolTipString(tip)
668	data = self.LimitsTable.GetData()
669	else:
670	if self.logPlot:
671	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
672	else:
673	Plot.plot(X,Y,colors[N%6],picker=False)
674	if PickId:
675	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1::2]
676	Parms = dict(zip(Names,Values))
677	try:
678	wave = Parms['Lam']
679	except KeyError:
680	wave = Parms['Lam1']
681	if self.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
682	peaks = np.array((self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))))
683	for peak in peaks:
684	if self.qPlot:
685	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
686	else:
687	Plot.axvline(peak[0],color='b')
688	for hkl in self.HKL:
689	if self.qPlot:
690	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
691	else:
692	Plot.axvline(hkl[5],color='r',dashes=(5,5))
693	elif self.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
694	Phases = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId,'Reflection Lists'))
695	for pId,phase in enumerate(Phases):
696	pId += 1
697	peaks = Phases[phase]
698	for peak in peaks:
699	if self.qPlot:
700	Plot.plot(2np.pi/peak[4],offsetN-pIdYmax.005,colors[pId%6]+'\|',mew=1,ms=8,picker=2.)
701	else:
702	Plot.plot(peak[5],offsetN-pIdYmax*.005,colors[pId%6]+'\|',mew=1,ms=8,picker=2.)
703
704	if self.Contour:
705	acolor = mpl.cm.get_cmap(self.ContourColor)
706	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
707	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
708	Page.figure.colorbar(Img)
709	else:
710	self.Lines = Lines
711	if not newPlot:
712	Page.toolbar.push_current()
713	Plot.set_xlim(xylim[0])
714	Plot.set_ylim(xylim[1])
715	xylim = []
716	Page.toolbar.push_current()
717	Page.toolbar.draw()
718	else:
719	Page.canvas.draw()
720	self.Pwdr = True
721
722	def PlotISFG(self,newPlot=False,type=''):
723	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
724	or multiple plots with waterfall and contour plots as options
725	'''
726	if not type:
727	type = self.G2plotNB.plotList[self.G2plotNB.nb.GetSelection()]
728	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
729	return
730	superMinusOne = unichr(0xaf)+unichr(0xb9)
731
732	def OnPlotKeyPress(event):
733	newPlot = False
734	if event.key == 'u':
735	if self.Contour:
736	self.Cmax = min(1.0,self.Cmax*1.2)
737	elif self.Offset[0] < 100.:
738	self.Offset[0] += 1.
739	elif event.key == 'd':
740	if self.Contour:
741	self.Cmax = max(0.0,self.Cmax*0.8)
742	elif self.Offset[0] > 0.:
743	self.Offset[0] -= 1.
744	elif event.key == 'l':
745	self.Offset[1] -= 1.
746	elif event.key == 'r':
747	self.Offset[1] += 1.
748	elif event.key == 'o':
749	self.Offset = [0,0]
750	elif event.key == 'c':
751	newPlot = True
752	if self.Contour:
753	self.Contour = False
754	else:
755	self.Contour = True
756	self.SinglePlot = False
757	self.Offset = [0.,0.]
758	elif event.key == 's':
759	if self.Contour:
760	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
761	choice.sort()
762	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
763	if dlg.ShowModal() == wx.ID_OK:
764	sel = dlg.GetSelection()
765	self.ContourColor = choice[sel]
766	else:
767	self.ContourColor = 'Paired'
768	dlg.Destroy()
769	else:
770	if self.SinglePlot:
771	self.SinglePlot = False
772	else:
773	self.SinglePlot = True
774	elif event.key == 'i': #for smoothing contour plot
775	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
776	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
777	'mitchell','sinc','lanczos']
778	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
779	if dlg.ShowModal() == wx.ID_OK:
780	sel = dlg.GetSelection()
781	self.Interpolate = choice[sel]
782	else:
783	self.Interpolate = 'nearest'
784	dlg.Destroy()
785	elif event.key == 't' and not self.Contour:
786	if self.Legend:
787	self.Legend = False
788	else:
789	self.Legend = True
790
791
792	PlotISFG(self,newPlot=newPlot,type=type)
793
794	def OnKeyBox(event):
795	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index(type):
796	event.key = cb.GetValue()[0]
797	cb.SetValue(' key press')
798	OnPlotKeyPress(event)
799
800	def OnMotion(event):
801	xpos = event.xdata
802	if xpos: #avoid out of frame mouse position
803	ypos = event.ydata
804	Page.canvas.SetCursor(wx.CROSS_CURSOR)
805	try:
806	if self.Contour:
807	self.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
808	else:
809	self.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
810	except TypeError:
811	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
812
813	xylim = []
814	try:
815	plotNum = self.G2plotNB.plotList.index(type)
816	Page = self.G2plotNB.nb.GetPage(plotNum)
817	if not newPlot:
818	Plot = Page.figure.gca() #get previous plot & get limits
819	xylim = Plot.get_xlim(),Plot.get_ylim()
820	Page.figure.clf()
821	Plot = Page.figure.gca()
822	except ValueError:
823	newPlot = True
824	self.Cmax = 1.0
825	Plot = self.G2plotNB.addMpl(type).gca()
826	plotNum = self.G2plotNB.plotList.index(type)
827	Page = self.G2plotNB.nb.GetPage(plotNum)
828	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
829	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
830
831	Page.SetFocus()
832	self.G2plotNB.status.DestroyChildren()
833	if self.Contour:
834	Choice = (' key press','d: lower contour max','u: raise contour max',
835	'i: interpolation method','s: color scheme','c: contour off')
836	else:
837	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
838	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
839	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
840	choices=Choice)
841	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
842	cb.SetValue(' key press')
843	PatternId = self.PatternId
844	PickId = self.PickId
845	Plot.set_title(type)
846	if type == 'G(R)':
847	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
848	else:
849	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
850	Plot.set_ylabel(r''+type,fontsize=14)
851	colors=['b','g','r','c','m','k']
852	name = self.PatternTree.GetItemText(PatternId)[4:]
853	Pattern = []
854	if self.SinglePlot:
855	name = self.PatternTree.GetItemText(PatternId)
856	name = type+name[4:]
857	Id = G2gd.GetPatternTreeItemId(self,PatternId,name)
858	Pattern = self.PatternTree.GetItemPyData(Id)
859	if Pattern:
860	Pattern.append(name)
861	PlotList = [Pattern,]
862	else:
863	PlotList = []
864	item, cookie = self.PatternTree.GetFirstChild(self.root)
865	while item:
866	if 'PDF' in self.PatternTree.GetItemText(item):
867	name = type+self.PatternTree.GetItemText(item)[4:]
868	Id = G2gd.GetPatternTreeItemId(self,item,name)
869	Pattern = self.PatternTree.GetItemPyData(Id)
870	if Pattern:
871	Pattern.append(name)
872	PlotList.append(Pattern)
873	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
874	PDFdata = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'PDF Controls'))
875	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
876	Xb = [0.,10.]
877	Yb = [0.,-40.np.pinumbDen]
878	Ymax = 1.0
879	lenX = 0
880	for Pattern in PlotList:
881	xye = Pattern[1]
882	Ymax = max(Ymax,max(xye[1]))
883	offset = self.Offset[0]*Ymax/100.0
884	if self.Contour:
885	ContourZ = []
886	ContourY = []
887	Nseq = 0
888	for N,Pattern in enumerate(PlotList):
889	xye = Pattern[1]
890	if PickId:
891	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
892	X = xye[0]
893	if not lenX:
894	lenX = len(X)
895	Y = xye[1]+offset*N
896	if self.Contour:
897	if lenX == len(X):
898	ContourY.append(N)
899	ContourZ.append(Y)
900	ContourX = X
901	Nseq += 1
902	Plot.set_ylabel('Data sequence',fontsize=12)
903	else:
904	X = xye[0]+self.Offset[1].005N
905	if ifpicked:
906	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
907	Page.canvas.SetToolTipString('')
908	else:
909	if self.Legend:
910	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
911	else:
912	Plot.plot(X,Y,colors[N%6],picker=False)
913	if type == 'G(R)':
914	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
915	elif type == 'F(Q)':
916	Plot.axhline(0.,color=wx.BLACK)
917	elif type == 'S(Q)':
918	Plot.axhline(1.,color=wx.BLACK)
919	if self.Contour:
920	acolor = mpl.cm.get_cmap(self.ContourColor)
921	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
922	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
923	Page.figure.colorbar(Img)
924	elif self.Legend:
925	Plot.legend(loc='best')
926	if not newPlot:
927	Page.toolbar.push_current()
928	Plot.set_xlim(xylim[0])
929	Plot.set_ylim(xylim[1])
930	xylim = []
931	Page.toolbar.push_current()
932	Page.toolbar.draw()
933	else:
934	Page.canvas.draw()
935
936	def PlotXY(self,XY,newPlot=False,type=''):
937	'''simple plot of xy data, used for diagnostic purposes
938	'''
939	def OnMotion(event):
940	xpos = event.xdata
941	if xpos: #avoid out of frame mouse position
942	ypos = event.ydata
943	Page.canvas.SetCursor(wx.CROSS_CURSOR)
944	try:
945	self.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
946	except TypeError:
947	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
948
949	try:
950	plotNum = self.G2plotNB.plotList.index(type)
951	Page = self.G2plotNB.nb.GetPage(plotNum)
952	if not newPlot:
953	Plot = Page.figure.gca()
954	xylim = Plot.get_xlim(),Plot.get_ylim()
955	Page.figure.clf()
956	Plot = Page.figure.gca()
957	except ValueError:
958	newPlot = True
959	Plot = self.G2plotNB.addMpl(type).gca()
960	plotNum = self.G2plotNB.plotList.index(type)
961	Page = self.G2plotNB.nb.GetPage(plotNum)
962	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
963
964	Page.SetFocus()
965	self.G2plotNB.status.DestroyChildren()
966	Plot.set_title(type)
967	Plot.set_xlabel(r'X',fontsize=14)
968	Plot.set_ylabel(r''+type,fontsize=14)
969	colors=['b','g','r','c','m','k']
970	Ymax = 1.0
971	lenX = 0
972	X,Y = XY[:2]
973	Ymax = max(Ymax,max(Y))
974	Plot.plot(X,Y,'k',picker=False)
975	if not newPlot:
976	Page.toolbar.push_current()
977	Plot.set_xlim(xylim[0])
978	Plot.set_ylim(xylim[1])
979	xylim = []
980	Page.toolbar.push_current()
981	Page.toolbar.draw()
982	else:
983	Page.canvas.draw()
984
985	def PlotPowderLines(self):
986	''' plotting of powder lines (i.e. no powder pattern) as sticks
987	'''
988	global HKL
989
990	def OnMotion(event):
991	xpos = event.xdata
992	if xpos: #avoid out of frame mouse position
993	Page.canvas.SetCursor(wx.CROSS_CURSOR)
994	self.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
995	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
996	found = []
997	if len(HKL):
998	view = Page.toolbar._views.forward()[0][:2]
999	wid = view[1]-view[0]
1000	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1001	if len(found):
1002	h,k,l = found[0][:3]
1003	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1004	else:
1005	Page.canvas.SetToolTipString('')
1006
1007	try:
1008	plotNum = self.G2plotNB.plotList.index('Powder Lines')
1009	Page = self.G2plotNB.nb.GetPage(plotNum)
1010	Page.figure.clf()
1011	Plot = Page.figure.gca()
1012	except ValueError:
1013	Plot = self.G2plotNB.addMpl('Powder Lines').gca()
1014	plotNum = self.G2plotNB.plotList.index('Powder Lines')
1015	Page = self.G2plotNB.nb.GetPage(plotNum)
1016	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1017
1018	Page.SetFocus()
1019	Plot.set_title('Powder Pattern Lines')
1020	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1021	PickId = self.PickId
1022	PatternId = self.PatternId
1023	peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))
1024	for peak in peaks:
1025	Plot.axvline(peak[0],color='b')
1026	HKL = np.array(self.HKL)
1027	for hkl in self.HKL:
1028	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1029	xmin = peaks[0][0]
1030	xmax = peaks[-1][0]
1031	delt = xmax-xmin
1032	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1033	Plot.set_xlim(xlim)
1034	Page.canvas.draw()
1035	Page.toolbar.push_current()
1036
1037	def PlotPeakWidths(self):
1038	''' Plotting of instrument broadening terms as function of 2-theta (future TOF)
1039	Seen when "Instrument Parameters" chosen from powder pattern data tree
1040	'''
1041	PatternId = self.PatternId
1042	limitID = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
1043	if limitID:
1044	limits = self.PatternTree.GetItemPyData(limitID)
1045	else:
1046	return
1047	instParms = self.PatternTree.GetItemPyData( \
1048	G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))
1049	if instParms[0][0] in ['PXC','PNC']:
1050	lam = instParms[1][1]
1051	if len(instParms[1]) == 13:
1052	GU,GV,GW,LX,LY = instParms[0][6:11]
1053	else:
1054	GU,GV,GW,LX,LY = instParms[0][4:9]
1055	peakID = G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List')
1056	if peakID:
1057	peaks = self.PatternTree.GetItemPyData(peakID)
1058	else:
1059	peaks = []
1060
1061	try:
1062	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1063	Page = self.G2plotNB.nb.GetPage(plotNum)
1064	Page.figure.clf()
1065	Plot = Page.figure.gca()
1066	except ValueError:
1067	Plot = self.G2plotNB.addMpl('Peak Widths').gca()
1068	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1069	Page = self.G2plotNB.nb.GetPage(plotNum)
1070	Page.SetFocus()
1071
1072	Page.canvas.SetToolTipString('')
1073	colors=['b','g','r','c','m','k']
1074	Xmin,Xmax = limits[1]
1075	Xmin = min(0.5,max(Xmin,1))
1076	Xmin /= 2
1077	Xmax /= 2
1078	nPts = 100
1079	delt = (Xmax-Xmin)/nPts
1080	thetas = []
1081	for i in range(nPts):
1082	thetas.append(Xmin+i*delt)
1083	X = []
1084	Y = []
1085	Z = []
1086	W = []
1087	# V = []
1088	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1089	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1090	gamFW = lambda s,g: math.exp(math.log(s*5+2.69269s*4g+2.42843s3g*2+4.47163s*2g*3+0.07842sg4+g*5)/5.)
1091	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1092	for theta in thetas:
1093	X.append(4.0math.pisind(theta)/lam) #q
1094	s = sig(theta,GU,GV,GW)
1095	g = gam(theta,LX,LY)
1096	G = gamFW(g,s)
1097	# H = gamFW2(g,s)
1098	Y.append(s/tand(theta))
1099	Z.append(g/tand(theta))
1100	W.append(G/tand(theta))
1101	# V.append(H/tand(theta))
1102	Plot.set_title('Instrument and sample peak widths')
1103	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1104	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1105	Plot.plot(X,Y,color='r',label='Gaussian')
1106	Plot.plot(X,Z,color='g',label='Lorentzian')
1107	Plot.plot(X,W,color='b',label='G+L')
1108	# Plot.plot(X,V,color='k',label='G+L2')
1109	X = []
1110	Y = []
1111	Z = []
1112	W = []
1113	V = []
1114	for peak in peaks:
1115	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1116	try:
1117	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1118	except ValueError:
1119	s = 0.01
1120	g = peak[6]*math.pi/18000.
1121	G = gamFW(g,s)
1122	# H = gamFW2(g,s)
1123	Y.append(s/tand(peak[0]/2.))
1124	Z.append(g/tand(peak[0]/2.))
1125	W.append(G/tand(peak[0]/2.))
1126	# V.append(H/tand(peak[0]/2.))
1127	Plot.plot(X,Y,'+',color='r',label='G peak')
1128	Plot.plot(X,Z,'+',color='g',label='L peak')
1129	Plot.plot(X,W,'+',color='b',label='G+L peak')
1130	# Plot.plot(X,V,'+',color='k',label='G+L2 peak')
1131	Plot.legend(loc='best')
1132	Page.canvas.draw()
1133
1134	def PlotStrain(self,data):
1135	'''Plot 3D microstrain figure. In this instance data is for a phase
1136	'''
1137	PatternId = self.PatternId
1138	generalData = data['General']
1139	SGData = generalData['SGData']
1140	MuStrKeys = G2spc.MustrainNames(SGData)
1141	cell = generalData['Cell'][1:]
1142	A,B = G2lat.cell2AB(cell[:6])
1143	Vol = cell[6]
1144	useList = data['Histograms']
1145	for item in useList:
1146	if useList[item]['Show']:
1147	break
1148	else:
1149	self.G2plotNB.Delete('Microstrain')
1150	return #nothing to show!!
1151
1152	numPlots = len(useList)
1153
1154	try:
1155	plotNum = self.G2plotNB.plotList.index('Microstrain')
1156	Page = self.G2plotNB.nb.GetPage(plotNum)
1157	Page.figure.clf()
1158	Plot = mp3d.Axes3D(Page.figure)
1159	if not Page.IsShown():
1160	Page.Show()
1161	except ValueError:
1162	Plot = mp3d.Axes3D(self.G2plotNB.add3D('Microstrain'))
1163	plotNum = self.G2plotNB.plotList.index('Microstrain')
1164	Page = self.G2plotNB.nb.GetPage(plotNum)
1165	Page.SetFocus()
1166	self.G2plotNB.status.SetStatusText('Adjust frame size to get desired aspect ratio',1)
1167
1168	for item in useList:
1169	if useList[item]['Show']:
1170	muStrain = useList[item]['Mustrain']
1171	PHI = np.linspace(0.,360.,30,True)
1172	PSI = np.linspace(0.,180.,30,True)
1173	X = np.outer(npsind(PHI),npsind(PSI))
1174	Y = np.outer(npcosd(PHI),npsind(PSI))
1175	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1176	if muStrain[0] == 'isotropic':
1177	muiso = muStrain[1][0]*math.pi/0.018 #centidegrees to radians!
1178	X *= muiso
1179	Y *= muiso
1180	Z *= muiso
1181
1182	elif muStrain[0] == 'uniaxial':
1183	def uniaxMustrain(xyz,muiso,muaniso,axes):
1184	Z = np.array(axes)
1185	cp = abs(np.dot(xyz,Z))
1186	sp = np.sqrt(1.-cp**2)
1187	R = muisomuaniso/np.sqrt((muisocp)*2+(muanisosp)**2)
1188	# S = muiso+muaniso*cp #old GSAS - wrong math!!
1189	return Rxyzmath.pi/0.018 #centidegrees to radians!
1190	muiso,muaniso = muStrain[1][:2]
1191	axes = np.inner(A,np.array(muStrain[3]))
1192	axes /= nl.norm(axes)
1193	Shkl = np.array(muStrain[1])
1194	Shape = X.shape[0]
1195	XYZ = np.dstack((X,Y,Z))
1196	XYZ = np.nan_to_num(np.apply_along_axis(uniaxMustrain,2,XYZ,muiso,muaniso,axes))
1197	X,Y,Z = np.dsplit(XYZ,3)
1198	X = X[:,:,0]
1199	Y = Y[:,:,0]
1200	Z = Z[:,:,0]
1201
1202	elif muStrain[0] == 'generalized':
1203	def genMustrain(xyz,SGData,A,Shkl):
1204	uvw = np.inner(A.T,xyz)
1205	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1206	sum = np.sum(np.multiply(Shkl,Strm))
1207	sum = np.where(sum > 0.01,sum,0.01)
1208	sum = np.sqrt(sum)*math.pi/0.018 #centidegrees to radians!
1209	return sum*xyz
1210	Shkl = np.array(muStrain[4])
1211	if np.any(Shkl):
1212	Shape = X.shape[0]
1213	XYZ = np.dstack((X,Y,Z))
1214	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1215	X,Y,Z = np.dsplit(XYZ,3)
1216	X = X[:,:,0]
1217	Y = Y[:,:,0]
1218	Z = Z[:,:,0]
1219
1220	if np.any(X) and np.any(Y) and np.any(Z):
1221	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1222
1223	Plot.set_xlabel('X')
1224	Plot.set_ylabel('Y')
1225	Plot.set_zlabel('Z')
1226	Page.canvas.draw()
1227
1228	def PlotTexture(self,data,newPlot=False,Start=False):
1229	'''Pole figure, inverse pole figure(?), 3D pole distribution and 3D inverse pole distribution(?)
1230	plotting; Need way to select
1231	pole figure or pole distribution to be displayed - do in key enter menu
1232	dict generalData contains all phase info needed which is in data
1233	'''
1234
1235	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1236	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1237	PatternId = self.PatternId
1238	generalData = data['General']
1239	SGData = generalData['SGData']
1240	textureData = generalData['SH Texture']
1241	if not textureData['Order']:
1242	self.G2plotNB.Delete('Texture')
1243	return #no plot!!
1244	SHData = generalData['SH Texture']
1245	SHCoef = SHData['SH Coeff'][1]
1246	cell = generalData['Cell'][1:7]
1247	Amat,Bmat = G2lat.cell2AB(cell)
1248	sq2 = 1.0/math.sqrt(2.0)
1249
1250	def rp2xyz(r,p):
1251	z = npcosd(r)
1252	xy = np.sqrt(1.-z**2)
1253	return xynpsind(p),xynpcosd(p),z
1254
1255	def OnMotion(event):
1256	SHData = data['General']['SH Texture']
1257	if event.xdata and event.ydata: #avoid out of frame errors
1258	xpos = event.xdata
1259	ypos = event.ydata
1260	if 'Inverse' in SHData['PlotType']:
1261	r = xpos2+ypos2
1262	if r <= 1.0:
1263	if 'equal' in self.Projection:
1264	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1265	else:
1266	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1267	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1268	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1269	y,x,z = list(xyz/np.max(np.abs(xyz)))
1270
1271	self.G2plotNB.status.SetFields(['',
1272	'psi =%9.3f, beta =%9.3f, MRD =%9.3f xyz=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1273
1274	elif 'Axial' in SHData['PlotType']:
1275	pass
1276
1277	else: #ordinary pole figure
1278	z = xpos2+ypos2
1279	if z <= 1.0:
1280	z = np.sqrt(z)
1281	if 'equal' in self.Projection:
1282	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1283	else:
1284	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1285	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1286	self.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1287
1288	try:
1289	plotNum = self.G2plotNB.plotList.index('Texture')
1290	Page = self.G2plotNB.nb.GetPage(plotNum)
1291	Page.figure.clf()
1292	Plot = Page.figure.gca()
1293	if not Page.IsShown():
1294	Page.Show()
1295	except ValueError:
1296	Plot = self.G2plotNB.addMpl('Texture').gca()
1297	plotNum = self.G2plotNB.plotList.index('Texture')
1298	Page = self.G2plotNB.nb.GetPage(plotNum)
1299	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1300
1301	Page.SetFocus()
1302	self.G2plotNB.status.SetFields(['',''])
1303	PH = np.array(SHData['PFhkl'])
1304	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1305	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1306	PX = np.array(SHData['PFxyz'])
1307	gam = atan2d(PX[0],PX[1])
1308	xy = math.sqrt(PX[0]2+PX[1]2)
1309	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1310	psi = asind(xy/xyz)
1311	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1312	if 'Axial' in SHData['PlotType']:
1313	X = np.linspace(0,90.0,26)
1314	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1315	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1316	Plot.legend(loc='best')
1317	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1318	Plot.set_xlabel(r'$\psi$',fontsize=16)
1319	Plot.set_ylabel('MRD',fontsize=14)
1320
1321	else:
1322	npts = 201
1323	if 'Inverse' in SHData['PlotType']:
1324	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1325	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1326	if 'equal' in self.Projection:
1327	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1328	else:
1329	R = np.where(R <= 1.,2.*npatand(R),0.0)
1330	Z = np.zeros_like(R)
1331	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
1332	Z = np.reshape(Z,(npts,npts))
1333	CS = Plot.contour(Y,X,Z,aspect='equal')
1334	Plot.clabel(CS,fontsize=9,inline=1)
1335	try:
1336	Img = Plot.imshow(Z.T,aspect='equal',cmap=self.ContourColor,extent=[-1,1,-1,1])
1337	except ValueError:
1338	pass
1339	if newPlot:
1340	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1341	newPlot = False
1342	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
1343	Plot.set_xlabel(self.Projection.capitalize()+' projection')
1344
1345	else:
1346	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1347	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1348	if 'equal' in self.Projection:
1349	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1350	else:
1351	R = np.where(R <= 1.,2.*npatand(R),0.0)
1352	Z = np.zeros_like(R)
1353	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
1354	Z = np.reshape(Z,(npts,npts))
1355	try:
1356	CS = Plot.contour(Y,X,Z,aspect='equal')
1357	Plot.clabel(CS,fontsize=9,inline=1)
1358	except ValueError:
1359	pass
1360	Img = Plot.imshow(Z.T,aspect='equal',cmap=self.ContourColor,extent=[-1,1,-1,1])
1361	if newPlot:
1362	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1363	newPlot = False
1364	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
1365	Plot.set_xlabel(self.Projection.capitalize()+' projection')
1366	Page.canvas.draw()
1367
1368	def PlotCovariance(self,Data={}):
1369	if not Data:
1370	Data = self.PatternTree.GetItemPyData(
1371	G2gd.GetPatternTreeItemId(self,self.root, 'Covariance'))
1372	if not Data:
1373	print 'No covariance matrix available'
1374	return
1375	varyList = Data['varyList']
1376	values = Data['variables']
1377	Xmax = len(varyList)
1378	covMatrix = Data['covMatrix']
1379	sig = np.sqrt(np.diag(covMatrix))
1380	xvar = np.outer(sig,np.ones_like(sig))
1381	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
1382	title = ' for\n'+Data['title']
1383	newAtomDict = Data['newAtomDict']
1384
1385	def OnPlotKeyPress(event):
1386	newPlot = False
1387	if event.key == 's':
1388	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1389	choice.sort()
1390	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
1391	if dlg.ShowModal() == wx.ID_OK:
1392	sel = dlg.GetSelection()
1393	self.VcovColor = choice[sel]
1394	else:
1395	self.VcovColor = 'RdYlGn'
1396	dlg.Destroy()
1397	PlotCovariance(self)
1398
1399	def OnMotion(event):
1400	if event.button:
1401	ytics = imgAx.get_yticks()
1402	ytics = np.where(ytics<len(varyList),ytics,-1)
1403	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
1404	imgAx.set_yticklabels(ylabs)
1405
1406	if event.xdata and event.ydata: #avoid out of frame errors
1407	xpos = int(event.xdata+.5)
1408	ypos = int(event.ydata+.5)
1409	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
1410	if xpos == ypos:
1411	value = values[xpos]
1412	name = varyList[xpos]
1413	if varyList[xpos] in newAtomDict:
1414	name,value = newAtomDict[name]
1415	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
1416	else:
1417	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
1418	Page.canvas.SetToolTipString(msg)
1419	self.G2plotNB.status.SetFields(['Key: s to change colors',msg])
1420	try:
1421	plotNum = self.G2plotNB.plotList.index('Covariance')
1422	Page = self.G2plotNB.nb.GetPage(plotNum)
1423	Page.figure.clf()
1424	Plot = Page.figure.gca()
1425	if not Page.IsShown():
1426	Page.Show()
1427	except ValueError:
1428	Plot = self.G2plotNB.addMpl('Covariance').gca()
1429	plotNum = self.G2plotNB.plotList.index('Covariance')
1430	Page = self.G2plotNB.nb.GetPage(plotNum)
1431	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1432	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1433
1434	Page.SetFocus()
1435	self.G2plotNB.status.SetFields(['',''])
1436	acolor = mpl.cm.get_cmap(self.VcovColor)
1437	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower')
1438	imgAx = Img.get_axes()
1439	ytics = imgAx.get_yticks()
1440	ylabs = [varyList[int(i)] for i in ytics[:-1]]
1441	imgAx.set_yticklabels(ylabs)
1442	colorBar = Page.figure.colorbar(Img)
1443	Plot.set_title('V-Cov matrix'+title)
1444	Plot.set_xlabel('Variable number')
1445	Plot.set_ylabel('Variable name')
1446	Page.canvas.draw()
1447
1448	def PlotSeq(self,SeqData,SeqSig,SeqNames):
1449
1450	try:
1451	plotNum = self.G2plotNB.plotList.index('Sequential refinement')
1452	Page = self.G2plotNB.nb.GetPage(plotNum)
1453	Page.figure.clf()
1454	Plot = Page.figure.gca()
1455	if not Page.IsShown():
1456	Page.Show()
1457	except ValueError:
1458	Plot = self.G2plotNB.addMpl('Sequential refinement').gca()
1459	plotNum = self.G2plotNB.plotList.index('Sequential refinement')
1460	Page = self.G2plotNB.nb.GetPage(plotNum)
1461
1462	Page.SetFocus()
1463	self.G2plotNB.status.SetFields(['',''])
1464	if len(SeqData):
1465	X = np.arange(0,len(SeqData[0]),1)
1466	for Y,sig,name in zip(SeqData,SeqSig,SeqNames):
1467	Plot.errorbar(X,Y,yerr=sig,label=name)
1468	Plot.legend(loc='best')
1469	Page.canvas.draw()
1470
1471	def PlotExposedImage(self,newPlot=False,event=None):
1472	'''General access module for 2D image plotting
1473	'''
1474	plotNo = self.G2plotNB.nb.GetSelection()
1475	if self.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1476	PlotImage(self,newPlot,event,newImage=True)
1477	elif self.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1478	PlotIntegration(self,newPlot,event)
1479
1480	def PlotImage(self,newPlot=False,event=None,newImage=True):
1481	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1482	masks, etc.
1483	'''
1484	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1485	import numpy.ma as ma
1486	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1487	global Data,Masks
1488	colors=['b','g','r','c','m','k']
1489	Data = self.PatternTree.GetItemPyData(
1490	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1491	Masks = self.PatternTree.GetItemPyData(
1492	G2gd.GetPatternTreeItemId(self,self.Image, 'Masks'))
1493
1494	def OnImMotion(event):
1495	Page.canvas.SetToolTipString('')
1496	sizexy = Data['size']
1497	if event.xdata and event.ydata: #avoid out of frame errors
1498	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1499	item = self.itemPicked
1500	pixelSize = Data['pixelSize']
1501	scalex = 1000./pixelSize[0]
1502	scaley = 1000./pixelSize[1]
1503	if item and self.PatternTree.GetItemText(self.PickId) == 'Image Controls':
1504	if 'Text' in str(item):
1505	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1506	else:
1507	xcent,ycent = Data['center']
1508	xpos = event.xdata-xcent
1509	ypos = event.ydata-ycent
1510	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1511	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1512	Page.canvas.SetToolTipString('%6d deg'%(azm))
1513	elif 'line1' in str(item) or 'line2' in str(item):
1514	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1515	else:
1516	xpos = event.xdata
1517	ypos = event.ydata
1518	xpix = xpos*scalex
1519	ypix = ypos*scaley
1520	Int = 0
1521	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1522	Int = self.ImageZ[ypix][xpix]
1523	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1524	Q = 2.*math.pi/dsp
1525	if self.setPoly:
1526	self.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1527	else:
1528	self.G2plotNB.status.SetFields(\
1529	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1530
1531	def OnImPlotKeyPress(event):
1532	try:
1533	PickName = self.PatternTree.GetItemText(self.PickId)
1534	except TypeError:
1535	return
1536	if PickName == 'Masks':
1537	Xpos = event.xdata
1538	if not Xpos: #got point out of frame
1539	return
1540	Ypos = event.ydata
1541	if event.key == 's':
1542	Masks['Points'].append([Xpos,Ypos,1.])
1543	elif event.key == 'r':
1544	tth = G2img.GetTth(Xpos,Ypos,Data)
1545	Masks['Rings'].append([tth,0.1])
1546	elif event.key == 'a':
1547	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1548	azm = int(azm)
1549	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1550	elif event.key == 'p':
1551	self.setPoly = True
1552	Masks['Polygons'].append([])
1553	self.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1554	G2imG.UpdateMasks(self,Masks)
1555	elif PickName == 'Image Controls':
1556	if event.key == 'c':
1557	Xpos = event.xdata
1558	if not Xpos: #got point out of frame
1559	return
1560	Ypos = event.ydata
1561	dlg = wx.MessageDialog(self,'Are you sure you want to change the center?',
1562	'Center change',style=wx.OK\|wx.CANCEL)
1563	try:
1564	if dlg.ShowModal() == wx.ID_OK:
1565	print 'move center to: ',Xpos,Ypos
1566	Data['center'] = [Xpos,Ypos]
1567	G2imG.UpdateImageControls(self,Data,Masks)
1568	finally:
1569	dlg.Destroy()
1570	elif event.key == 'l':
1571	if self.logPlot:
1572	self.logPlot = False
1573	else:
1574	self.logPlot = True
1575	PlotImage(self,newImage=True)
1576
1577	def OnKeyBox(event):
1578	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('2D Powder Image'):
1579	event.key = cb.GetValue()[0]
1580	cb.SetValue(' key press')
1581	if event.key in 'l':
1582	OnImPlotKeyPress(event)
1583
1584	def OnImPick(event):
1585	if self.PatternTree.GetItemText(self.PickId) not in ['Image Controls','Masks']:
1586	return
1587	if self.setPoly:
1588	polygon = Masks['Polygons'][-1]
1589	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1590	if xpos and ypos: #point inside image
1591	if len(polygon) > 2 and event.mouseevent.button == 3:
1592	x0,y0 = polygon[0]
1593	polygon.append([x0,y0])
1594	self.setPoly = False
1595	self.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1596	else:
1597	self.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1598	polygon.append([xpos,ypos])
1599	G2imG.UpdateMasks(self,Masks)
1600	else:
1601	if self.itemPicked is not None: return
1602	self.itemPicked = event.artist
1603	self.mousePicked = event.mouseevent
1604
1605	def OnImRelease(event):
1606	try:
1607	PickName = self.PatternTree.GetItemText(self.PickId)
1608	except TypeError:
1609	return
1610	if PickName not in ['Image Controls','Masks']:
1611	return
1612	pixelSize = Data['pixelSize']
1613	scalex = 1000./pixelSize[0]
1614	scaley = 1000./pixelSize[1]
1615	pixLimit = Data['pixLimit']
1616	if self.itemPicked is None and PickName == 'Image Controls':
1617	# sizexy = Data['size']
1618	Xpos = event.xdata
1619	if not (Xpos and self.ifGetRing): #got point out of frame
1620	return
1621	Ypos = event.ydata
1622	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1623	if event.button == 1:
1624	Xpix = Xpos*scalex
1625	Ypix = Ypos*scaley
1626	xpos,ypos,I,J = G2img.ImageLocalMax(self.ImageZ,pixLimit,Xpix,Ypix)
1627	if I and J:
1628	xpos += .5 #shift to pixel center
1629	ypos += .5
1630	xpos /= scalex #convert to mm
1631	ypos /= scaley
1632	Data['ring'].append([xpos,ypos])
1633	elif event.button == 3:
1634	self.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1635	if G2img.ImageCalibrate(self,Data):
1636	self.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1637	print 'Calibration successful'
1638	else:
1639	self.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1640	print 'Calibration failed'
1641	self.ifGetRing = False
1642	G2imG.UpdateImageControls(self,Data,Masks)
1643	return
1644	PlotImage(self,newImage=False)
1645	return
1646	else:
1647	xpos = event.xdata
1648	if xpos: #avoid out of frame mouse position
1649	ypos = event.ydata
1650	if self.ifGetRing: #delete a calibration ring pick
1651	xypos = [xpos,ypos]
1652	rings = Data['ring']
1653	for ring in rings:
1654	if np.allclose(ring,xypos,.01,0):
1655	rings.remove(ring)
1656	else:
1657	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1658	itemPicked = str(self.itemPicked)
1659	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1660	if 'line1' in itemPicked:
1661	Data['IOtth'][0] = max(tth,0.001)
1662	elif 'line2' in itemPicked:
1663	Data['IOtth'][1] = tth
1664	elif 'line3' in itemPicked:
1665	Data['LRazimuth'][0] = int(azm)
1666	if Data['fullIntegrate']:
1667	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1668	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1669	Data['LRazimuth'][1] = int(azm)
1670
1671	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1672	Data['LRazimuth'][0] -= 360
1673
1674	azLim = np.array(Data['LRazimuth'])
1675	if np.any(azLim>360):
1676	azLim -= 360
1677	Data['LRazimuth'] = list(azLim)
1678
1679	if Data['IOtth'][0] > Data['IOtth'][1]:
1680	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1681
1682	self.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1683	self.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1684	self.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1685	self.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1686	elif 'Circle' in itemPicked and PickName == 'Masks':
1687	spots = Masks['Points']
1688	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1689	newPos = np.array([float(newPos[0]),float(newPos[1])])
1690	for spot in spots:
1691	if np.allclose(np.array([spot[:2]]),newPos):
1692	spot[:2] = xpos,ypos
1693	G2imG.UpdateMasks(self,Masks)
1694	elif 'Line2D' in itemPicked and PickName == 'Masks':
1695	Obj = self.itemPicked.findobj()
1696	rings = Masks['Rings']
1697	arcs = Masks['Arcs']
1698	polygons = Masks['Polygons']
1699	for ring in self.ringList:
1700	if Obj == ring[0]:
1701	rN = ring[1]
1702	if ring[2] == 'o':
1703	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1704	else:
1705	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1706	for arc in self.arcList:
1707	if Obj == arc[0]:
1708	aN = arc[1]
1709	if arc[2] == 'o':
1710	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1711	elif arc[2] == 'i':
1712	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1713	elif arc[2] == 'l':
1714	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1715	else:
1716	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1717	for poly in self.polyList:
1718	if Obj == poly[0]:
1719	ind = self.itemPicked.contains(self.mousePicked)[1]['ind'][0]
1720	oldPos = np.array([self.mousePicked.xdata,self.mousePicked.ydata])
1721	pN = poly[1]
1722	for i,xy in enumerate(polygons[pN]):
1723	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1724	polygons[pN][i] = xpos,ypos
1725	G2imG.UpdateMasks(self,Masks)
1726	# else: #keep for future debugging
1727	# print str(self.itemPicked),event.xdata,event.ydata,event.button
1728	PlotImage(self,newImage=True)
1729	self.itemPicked = None
1730
1731	try:
1732	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1733	Page = self.G2plotNB.nb.GetPage(plotNum)
1734	if not newPlot:
1735	Plot = Page.figure.gca() #get previous powder plot & get limits
1736	xylim = Plot.get_xlim(),Plot.get_ylim()
1737	if newImage:
1738	Page.figure.clf()
1739	Plot = Page.figure.gca() #get a fresh plot after clf()
1740
1741	except ValueError:
1742	Plot = self.G2plotNB.addMpl('2D Powder Image').gca()
1743	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1744	Page = self.G2plotNB.nb.GetPage(plotNum)
1745	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1746	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1747	Page.canvas.mpl_connect('pick_event', OnImPick)
1748	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1749	xylim = []
1750	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1751	Page.SetFocus()
1752	Title = self.PatternTree.GetItemText(self.Image)[4:]
1753	self.G2plotNB.status.DestroyChildren()
1754	if self.logPlot:
1755	Title = 'log('+Title+')'
1756	Plot.set_title(Title)
1757	try:
1758	if self.PatternTree.GetItemText(self.PickId) in ['Image Controls',]:
1759	Choice = (' key press','l: log(I) on',)
1760	if self.logPlot:
1761	Choice[1] = 'l: log(I) off'
1762	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1763	choices=Choice)
1764	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1765	cb.SetValue(' key press')
1766	except TypeError:
1767	pass
1768	size,imagefile = self.PatternTree.GetItemPyData(self.Image)
1769	if imagefile != self.oldImagefile:
1770	imagefile = G2IO.CheckImageFile(self,imagefile)
1771	if not imagefile:
1772	self.G2plotNB.Delete('2D Powder Image')
1773	return
1774	self.PatternTree.SetItemPyData(self.Image,[size,imagefile])
1775	self.ImageZ = G2IO.GetImageData(self,imagefile,imageOnly=True)
1776	# print self.ImageZ.shape,self.ImageZ.size,Data['size'] #might be useful debugging line
1777	self.oldImagefile = imagefile
1778
1779	imScale = 1
1780	if len(self.ImageZ) > 1024:
1781	imScale = len(self.ImageZ)/1024
1782	sizexy = Data['size']
1783	pixelSize = Data['pixelSize']
1784	scalex = 1000./pixelSize[0]
1785	scaley = 1000./pixelSize[1]
1786	Xmax = sizexy[0]*pixelSize[0]/1000.
1787	Ymax = sizexy[1]*pixelSize[1]/1000.
1788	xlim = (0,Xmax)
1789	ylim = (Ymax,0)
1790	Imin,Imax = Data['range'][1]
1791	acolor = mpl.cm.get_cmap(Data['color'])
1792	xcent,ycent = Data['center']
1793	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1794	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1795	#do threshold mask - "real" mask - others are just bondaries
1796	Zlim = Masks['Thresholds'][1]
1797	wx.BeginBusyCursor()
1798	try:
1799
1800	if newImage:
1801	MA = ma.masked_greater(ma.masked_less(self.ImageZ,Zlim[0]),Zlim[1])
1802	MaskA = ma.getmaskarray(MA)
1803	A = G2img.ImageCompress(MA,imScale)
1804	AM = G2img.ImageCompress(MaskA,imScale)
1805	if self.logPlot:
1806	A = np.where(A>0,np.log(A),0)
1807	AM = np.where(AM>0,np.log(AM),0)
1808	Imin,Imax = [np.amin(A),np.amax(A)]
1809	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
1810	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Xmax,0])
1811	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
1812	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
1813	if self.setPoly:
1814	Img.set_picker(True)
1815
1816	Plot.plot(xcent,ycent,'x')
1817	if Data['showLines']:
1818	LRAzim = Data['LRazimuth'] #NB: integers
1819	Nazm = Data['outAzimuths']
1820	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
1821	AzmthOff = Data['azmthOff']
1822	IOtth = Data['IOtth']
1823	wave = Data['wavelength']
1824	dspI = wave/(2.0*sind(IOtth[0]/2.0))
1825	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
1826	dspO = wave/(2.0*sind(IOtth[1]/2.0))
1827	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
1828	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
1829	if ellI:
1830	xyI = []
1831	for azm in Azm:
1832	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
1833	xyI = np.array(xyI)
1834	arcxI,arcyI = xyI.T
1835	Plot.plot(arcxI,arcyI,picker=3)
1836	if ellO:
1837	xyO = []
1838	for azm in Azm:
1839	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
1840	xyO = np.array(xyO)
1841	arcxO,arcyO = xyO.T
1842	Plot.plot(arcxO,arcyO,picker=3)
1843	if ellO and ellI:
1844	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
1845	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
1846	for i in range(Nazm):
1847	cake = LRAzim[0]+i*delAzm-AzmthOff
1848	ind = np.searchsorted(Azm,cake)
1849	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
1850
1851	for xring,yring in Data['ring']:
1852	Plot.plot(xring,yring,'r+',picker=3)
1853	if Data['setRings']:
1854	# rings = np.concatenate((Data['rings']),axis=0)
1855	N = 0
1856	for ring in Data['rings']:
1857	xring,yring = np.array(ring).T[:2]
1858	Plot.plot(xring,yring,'+',color=colors[N%6])
1859	N += 1
1860	for ellipse in Data['ellipses']:
1861	cent,phi,[width,height],col = ellipse
1862	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
1863	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
1864	#masks - mask lines numbered after integration limit lines
1865	spots = Masks['Points']
1866	rings = Masks['Rings']
1867	arcs = Masks['Arcs']
1868	polygons = Masks['Polygons']
1869	for x,y,d in spots:
1870	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
1871	self.ringList = []
1872	for iring,(tth,thick) in enumerate(rings):
1873	wave = Data['wavelength']
1874	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
1875	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
1876	self.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1877	self.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1878	self.arcList = []
1879	for iarc,(tth,azm,thick) in enumerate(arcs):
1880	wave = Data['wavelength']
1881	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
1882	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
1883	self.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1884	self.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1885	self.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1886	self.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1887	self.polyList = []
1888	for ipoly,polygon in enumerate(polygons):
1889	x,y = np.hsplit(np.array(polygon),2)
1890	self.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
1891	Plot.plot(x,y,'r')
1892	if newImage:
1893	colorBar = Page.figure.colorbar(Img)
1894	Plot.set_xlim(xlim)
1895	Plot.set_ylim(ylim)
1896	if not newPlot and xylim:
1897	Page.toolbar.push_current()
1898	Plot.set_xlim(xylim[0])
1899	Plot.set_ylim(xylim[1])
1900	xylim = []
1901	Page.toolbar.push_current()
1902	Page.toolbar.draw()
1903	else:
1904	Page.canvas.draw()
1905	finally:
1906	wx.EndBusyCursor()
1907
1908	def PlotIntegration(self,newPlot=False,event=None):
1909	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
1910	'''
1911
1912	def OnMotion(event):
1913	Page.canvas.SetToolTipString('')
1914	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1915	azm = event.ydata
1916	tth = event.xdata
1917	if azm and tth:
1918	self.G2plotNB.status.SetFields(\
1919	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1920
1921	try:
1922	plotNum = self.G2plotNB.plotList.index('2D Integration')
1923	Page = self.G2plotNB.nb.GetPage(plotNum)
1924	if not newPlot:
1925	Plot = Page.figure.gca() #get previous plot & get limits
1926	xylim = Plot.get_xlim(),Plot.get_ylim()
1927	Page.figure.clf()
1928	Plot = Page.figure.gca() #get a fresh plot after clf()
1929
1930	except ValueError:
1931	Plot = self.G2plotNB.addMpl('2D Integration').gca()
1932	plotNum = self.G2plotNB.plotList.index('2D Integration')
1933	Page = self.G2plotNB.nb.GetPage(plotNum)
1934	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1935	Page.views = False
1936	view = False
1937	if not event:
1938	Page.SetFocus()
1939
1940	Data = self.PatternTree.GetItemPyData(
1941	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1942	image = self.Integrate[0]
1943	xsc = self.Integrate[1]
1944	ysc = self.Integrate[2]
1945	Imin,Imax = Data['range'][1]
1946	acolor = mpl.cm.get_cmap(Data['color'])
1947	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1948	Plot.set_ylabel('azimuth',fontsize=12)
1949	Plot.set_xlabel('2-theta',fontsize=12)
1950	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
1951	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
1952	colorBar = Page.figure.colorbar(Img)
1953	if Data['setRings'] and Data['rings']:
1954	rings = np.concatenate((Data['rings']),axis=0)
1955	for xring,yring,dsp in rings:
1956	x,y = G2img.GetTthAzm(xring,yring,Data)
1957	Plot.plot(x,y,'r+')
1958	if Data['ellipses']:
1959	for ellipse in Data['ellipses']:
1960	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1961	x,y = np.hsplit(ring,2)
1962	tth,azm = G2img.GetTthAzm(x,y,Data)
1963	# azm = np.where(azm < 0.,azm+360,azm)
1964	Plot.plot(tth,azm,'b,')
1965	if not newPlot:
1966	Page.toolbar.push_current()
1967	Plot.set_xlim(xylim[0])
1968	Plot.set_ylim(xylim[1])
1969	xylim = []
1970	Page.toolbar.push_current()
1971	Page.toolbar.draw()
1972	else:
1973	Page.canvas.draw()
1974
1975	def PlotTRImage(self,tax,tay,taz,newPlot=False):
1976	'''a test plot routine - not normally used
1977	'''
1978
1979	def OnMotion(event):
1980	Page.canvas.SetToolTipString('')
1981	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1982	azm = event.xdata
1983	tth = event.ydata
1984	if azm and tth:
1985	self.G2plotNB.status.SetFields(\
1986	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1987
1988	try:
1989	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1990	Page = self.G2plotNB.nb.GetPage(plotNum)
1991	if not newPlot:
1992	Plot = Page.figure.gca() #get previous plot & get limits
1993	xylim = Plot.get_xlim(),Plot.get_ylim()
1994	Page.figure.clf()
1995	Plot = Page.figure.gca() #get a fresh plot after clf()
1996
1997	except ValueError:
1998	Plot = self.G2plotNB.addMpl('2D Transformed Powder Image').gca()
1999	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
2000	Page = self.G2plotNB.nb.GetPage(plotNum)
2001	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2002	Page.views = False
2003	view = False
2004	Page.SetFocus()
2005
2006	Data = self.PatternTree.GetItemPyData(
2007	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
2008	Imin,Imax = Data['range'][1]
2009	step = (Imax-Imin)/5.
2010	V = np.arange(Imin,Imax,step)
2011	acolor = mpl.cm.get_cmap(Data['color'])
2012	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
2013	Plot.set_xlabel('azimuth',fontsize=12)
2014	Plot.set_ylabel('2-theta',fontsize=12)
2015	Plot.contour(tax,tay,taz,V,cmap=acolor)
2016	if Data['showLines']:
2017	IOtth = Data['IOtth']
2018	if Data['fullIntegrate']:
2019	LRAzim = [-180,180]
2020	else:
2021	LRAzim = Data['LRazimuth'] #NB: integers
2022	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
2023	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
2024	if not Data['fullIntegrate']:
2025	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
2026	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
2027	if Data['setRings']:
2028	rings = np.concatenate((Data['rings']),axis=0)
2029	for xring,yring,dsp in rings:
2030	x,y = G2img.GetTthAzm(xring,yring,Data)
2031	Plot.plot(y,x,'r+')
2032	if Data['ellipses']:
2033	for ellipse in Data['ellipses']:
2034	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2035	x,y = np.hsplit(ring,2)
2036	tth,azm = G2img.GetTthAzm(x,y,Data)
2037	Plot.plot(azm,tth,'b,')
2038	if not newPlot:
2039	Page.toolbar.push_current()
2040	Plot.set_xlim(xylim[0])
2041	Plot.set_ylim(xylim[1])
2042	xylim = []
2043	Page.toolbar.push_current()
2044	Page.toolbar.draw()
2045	else:
2046	Page.canvas.draw()
2047
2048	def PlotStructure(self,data):
2049	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
2050	thermal motion ellipsoids and polyhedra
2051	'''
2052	generalData = data['General']
2053	cell = generalData['Cell'][1:7]
2054	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
2055	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2056	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2057	Mydir = generalData['Mydir']
2058	atomData = data['Atoms']
2059	drawingData = data['Drawing']
2060	drawAtoms = drawingData['Atoms']
2061	cx,ct,cs = drawingData['atomPtrs']
2062	Wt = [255,255,255]
2063	Rd = [255,0,0]
2064	Gr = [0,255,0]
2065	Bl = [0,0,255]
2066	uBox = np.array([[0,0,0],[1,0,0],[1,1,0],[0,1,0],[0,0,1],[1,0,1],[1,1,1],[0,1,1]])
2067	uEdges = np.array([
2068	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
2069	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
2070	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
2071	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
2072	altDown = False
2073	shiftDown = False
2074	ctrlDown = False
2075
2076	def OnKeyBox(event):
2077	import Image
2078	Draw() #make sure plot is fresh!!
2079	mode = cb.GetValue()
2080	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
2081	size = Page.canvas.GetSize()
2082	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
2083	if mode in ['jpeg',]:
2084	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
2085	im = Image.new("RGBA", (size[0],size[1]))
2086	else:
2087	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
2088	im = Image.new("RGB", (size[0],size[1]))
2089	im.fromstring(Pix)
2090	im.save(Fname,mode)
2091	cb.SetValue(' Save as:')
2092	self.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
2093
2094	def GetTruePosition(xy):
2095	View = glGetIntegerv(GL_VIEWPORT)
2096	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
2097	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
2098	Zmax = 1.
2099	for i,atom in enumerate(drawAtoms):
2100	x,y,z = atom[cx:cx+3]
2101	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2102	XY = [int(X),int(View[3]-Y)]
2103	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2104	Zmax = Z
2105	SetSelectedAtoms(i)
2106
2107	def OnMouseDown(event):
2108	xy = event.GetPosition()
2109	if event.ShiftDown():
2110	GetTruePosition(xy)
2111	else:
2112	drawingData['Rotation'][3] = xy
2113	Draw()
2114
2115	def OnMouseMove(event):
2116	newxy = event.GetPosition()
2117	page = getSelection()
2118	if event.ControlDown() and drawingData['showABC']:
2119	if event.LeftIsDown():
2120	SetTestRot(newxy)
2121	elif event.RightIsDown():
2122	SetTestPos(newxy)
2123	elif event.MiddleIsDown():
2124	SetTestRotZ(newxy)
2125	x,y,z = drawingData['testPos'][0]
2126	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2127
2128
2129	if event.Dragging() and not event.ControlDown():
2130	if event.LeftIsDown():
2131	SetRotation(newxy)
2132	angX,angY,angZ = drawingData['Rotation'][:3]
2133	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
2134	elif event.RightIsDown():
2135	SetTranslation(newxy)
2136	Tx,Ty,Tz = drawingData['viewPoint'][0]
2137	self.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2138	elif event.MiddleIsDown():
2139	SetRotationZ(newxy)
2140	angX,angY,angZ = drawingData['Rotation'][:3]
2141	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
2142	Draw()
2143
2144	def OnMouseWheel(event):
2145	drawingData['cameraPos'] += event.GetWheelRotation()/24
2146	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2147	self.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2148	page = getSelection()
2149	if page:
2150	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2151	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2152	names = [child.GetName() for child in panel]
2153	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2154	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2155	Draw()
2156
2157	def getSelection():
2158	try:
2159	return self.dataDisplay.GetSelection()
2160	except AttributeError:
2161	print self.dataDisplay.GetLabel()
2162	self.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2163	return 0
2164
2165	def SetViewPointText(VP):
2166	page = getSelection()
2167	if page:
2168	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2169	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2170	names = [child.GetName() for child in panel]
2171	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
2172
2173	def ClearSelectedAtoms():
2174	page = getSelection()
2175	if page:
2176	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2177	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2178	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2179	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2180
2181	def SetSelectedAtoms(ind):
2182	page = getSelection()
2183	if page:
2184	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2185	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
2186	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2187	Id = drawAtoms[ind][-2]
2188	for i,atom in enumerate(atomData):
2189	if atom[-1] == Id:
2190	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2191
2192	def GetSelectedAtoms():
2193	page = getSelection()
2194	Ind = []
2195	if page:
2196	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2197	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2198	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2199	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2200	return Ind
2201
2202	def OnKey(event): #on key UP!!
2203	keyCode = event.GetKeyCode()
2204	if keyCode > 255:
2205	keyCode = 0
2206	key,xyz = chr(keyCode),event.GetPosition()
2207	indx = drawingData['selectedAtoms']
2208	if key in ['c','C']:
2209	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2210	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
2211	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
2212	SetViewPointText(drawingData['viewPoint'][0])
2213	elif key in ['n','N']:
2214	drawAtoms = drawingData['Atoms']
2215	pI = drawingData['viewPoint'][1]
2216	if indx:
2217	pI[0] = indx[pI[1]]
2218	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2219	pI[1] += 1
2220	if pI[1] >= len(indx):
2221	pI[1] = 0
2222	else:
2223	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2224	pI[0] += 1
2225	if pI[0] >= len(drawAtoms):
2226	pI[0] = 0
2227	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2228	SetViewPointText(drawingData['viewPoint'][0])
2229
2230	elif key in ['p','P']:
2231	drawAtoms = drawingData['Atoms']
2232	pI = drawingData['viewPoint'][1]
2233	if indx:
2234	pI[0] = indx[pI[1]]
2235	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2236	pI[1] -= 1
2237	if pI[1] < 0:
2238	pI[1] = len(indx)-1
2239	else:
2240	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2241	pI[0] -= 1
2242	if pI[0] < 0:
2243	pI[0] = len(drawAtoms)-1
2244	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2245	SetViewPointText(drawingData['viewPoint'][0])
2246	Draw()
2247
2248	def SetBackground():
2249	R,G,B,A = Page.camera['backColor']
2250	glClearColor(R,G,B,A)
2251	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2252
2253	def SetLights():
2254	glEnable(GL_DEPTH_TEST)
2255	glShadeModel(GL_SMOOTH)
2256	glEnable(GL_LIGHTING)
2257	glEnable(GL_LIGHT0)
2258	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2259	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2260	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2261
2262	def SetTranslation(newxy):
2263	Tx,Ty,Tz = drawingData['viewPoint'][0]
2264	anglex,angley,anglez,oldxy = drawingData['Rotation']
2265	Rx = G2lat.rotdMat(anglex,0)
2266	Ry = G2lat.rotdMat(angley,1)
2267	Rz = G2lat.rotdMat(anglez,2)
2268	dxy = list(newxy-oldxy)+[0,]
2269	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
2270	Tx -= dxy[0]*0.01
2271	Ty += dxy[1]*0.01
2272	Tz -= dxy[2]*0.01
2273	drawingData['Rotation'][3] = newxy
2274	drawingData['viewPoint'][0] = Tx,Ty,Tz
2275	SetViewPointText([Tx,Ty,Tz])
2276
2277	def SetTestPos(newxy):
2278	Tx,Ty,Tz = drawingData['testPos'][0]
2279	anglex,angley,anglez,oldxy = drawingData['Rotation']
2280	Rx = G2lat.rotdMat(anglex,0)
2281	Ry = G2lat.rotdMat(angley,1)
2282	Rz = G2lat.rotdMat(anglez,2)
2283	dxy = list(newxy-oldxy)+[0,]
2284	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
2285	Tx += dxy[0]*0.001
2286	Ty -= dxy[1]*0.001
2287	Tz += dxy[2]*0.001
2288	drawingData['Rotation'][3] = newxy
2289	drawingData['testPos'][0] = Tx,Ty,Tz
2290
2291	def SetTestRot(newxy):
2292	Txyz = np.array(drawingData['testPos'][0])
2293	oldxy = drawingData['testPos'][2]
2294	Ax,Ay,Az = drawingData['testPos'][1]
2295	Vxyz = np.array(drawingData['viewPoint'][0])
2296	Dxyz = np.inner(Amat,Txyz-Vxyz)
2297	dxy = list(newxy-oldxy)+[0,]
2298	Ax += dxy[1]*0.01
2299	Ay += dxy[0]*0.01
2300	Rx = G2lat.rotdMat(Ax,0)
2301	Ry = G2lat.rotdMat(Ay,1)
2302	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
2303	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2304	drawingData['testPos'][1] = [Ax,Ay,Az]
2305	drawingData['testPos'][2] = newxy
2306	drawingData['testPos'][0] = Dxyz
2307
2308	def SetTestRotZ(newxy):
2309	Txyz = np.array(drawingData['testPos'][0])
2310	oldxy = drawingData['testPos'][2]
2311	Ax,Ay,Az = drawingData['testPos'][1]
2312	Vxyz = np.array(drawingData['viewPoint'][0])
2313	Dxyz = np.inner(Amat,Txyz-Vxyz)
2314	dxy = list(newxy-oldxy)+[0,]
2315	Az += (dxy[0]+dxy[1])*.01
2316	Rz = G2lat.rotdMat(Az,2)
2317	Dxyz = np.inner(Rz,Dxyz)
2318	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2319	drawingData['testPos'][1] = [Ax,Ay,Az]
2320	drawingData['testPos'][2] = newxy
2321	drawingData['testPos'][0] = Dxyz
2322
2323	def SetRotation(newxy):
2324	anglex,angley,anglez,oldxy = drawingData['Rotation']
2325	dxy = newxy-oldxy
2326	anglex += dxy[1]*.25
2327	angley += dxy[0]*.25
2328	oldxy = newxy
2329	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2330
2331	def SetRotationZ(newxy):
2332	anglex,angley,anglez,oldxy = drawingData['Rotation']
2333	dxy = newxy-oldxy
2334	anglez += (dxy[0]+dxy[1])*.25
2335	oldxy = newxy
2336	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2337
2338	def RenderBox():
2339	glEnable(GL_COLOR_MATERIAL)
2340	glLineWidth(2)
2341	glEnable(GL_BLEND)
2342	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2343	glEnable(GL_LINE_SMOOTH)
2344	glBegin(GL_LINES)
2345	for line,color in zip(uEdges,uColors):
2346	glColor3ubv(color)
2347	glVertex3fv(line[0])
2348	glVertex3fv(line[1])
2349	glEnd()
2350	glColor4ubv([0,0,0,0])
2351	glDisable(GL_LINE_SMOOTH)
2352	glDisable(GL_BLEND)
2353	glDisable(GL_COLOR_MATERIAL)
2354
2355	def RenderUnitVectors(x,y,z):
2356	xyz = np.array([x,y,z])
2357	glEnable(GL_COLOR_MATERIAL)
2358	glLineWidth(1)
2359	glPushMatrix()
2360	glTranslate(x,y,z)
2361	glScalef(1/cell[0],1/cell[1],1/cell[2])
2362	glBegin(GL_LINES)
2363	for line,color in zip(uEdges,uColors)[:3]:
2364	glColor3ubv(color)
2365	glVertex3fv(line[0])
2366	glVertex3fv(line[1])
2367	glEnd()
2368	glPopMatrix()
2369	glColor4ubv([0,0,0,0])
2370	glDisable(GL_COLOR_MATERIAL)
2371
2372	def RenderSphere(x,y,z,radius,color):
2373	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2374	glPushMatrix()
2375	glTranslate(x,y,z)
2376	glMultMatrixf(B4mat.T)
2377	q = gluNewQuadric()
2378	gluSphere(q,radius,20,10)
2379	glPopMatrix()
2380
2381	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2382	s1,s2,s3 = E
2383	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2384	glPushMatrix()
2385	glTranslate(x,y,z)
2386	glMultMatrixf(B4mat.T)
2387	glMultMatrixf(R4.T)
2388	glEnable(GL_NORMALIZE)
2389	glScale(s1,s2,s3)
2390	q = gluNewQuadric()
2391	gluSphere(q,ellipseProb,20,10)
2392	glDisable(GL_NORMALIZE)
2393	glPopMatrix()
2394
2395	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2396	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2397	glPushMatrix()
2398	glTranslate(x,y,z)
2399	glMultMatrixf(B4mat.T)
2400	for bond in Bonds:
2401	glPushMatrix()
2402	Dx = np.inner(Amat,bond)
2403	Z = np.sqrt(np.sum(Dx**2))
2404	azm = atan2d(-Dx[1],-Dx[0])
2405	phi = acosd(Dx[2]/Z)
2406	glRotate(-azm,0,0,1)
2407	glRotate(phi,1,0,0)
2408	q = gluNewQuadric()
2409	gluCylinder(q,radius,radius,Z,slice,2)
2410	glPopMatrix()
2411	glPopMatrix()
2412
2413	def RenderLines(x,y,z,Bonds,color):
2414	xyz = np.array([x,y,z])
2415	glEnable(GL_COLOR_MATERIAL)
2416	glLineWidth(1)
2417	glColor3fv(color)
2418	glPushMatrix()
2419	glBegin(GL_LINES)
2420	for bond in Bonds:
2421	glVertex3fv(xyz)
2422	glVertex3fv(xyz+bond)
2423	glEnd()
2424	glColor4ubv([0,0,0,0])
2425	glPopMatrix()
2426	glDisable(GL_COLOR_MATERIAL)
2427
2428	def RenderPolyhedra(x,y,z,Faces,color):
2429	glPushMatrix()
2430	glTranslate(x,y,z)
2431	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2432	glShadeModel(GL_SMOOTH)
2433	glMultMatrixf(B4mat.T)
2434	for face,norm in Faces:
2435	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2436	glFrontFace(GL_CW)
2437	glNormal3fv(norm)
2438	glBegin(GL_TRIANGLES)
2439	for vert in face:
2440	glVertex3fv(vert)
2441	glEnd()
2442	glPopMatrix()
2443
2444	def RenderBackbone(Backbone,BackboneColor,radius):
2445	glPushMatrix()
2446	glMultMatrixf(B4mat.T)
2447	glEnable(GL_COLOR_MATERIAL)
2448	glShadeModel(GL_SMOOTH)
2449	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2450	glePolyCylinder(Backbone,BackboneColor,radius)
2451	glPopMatrix()
2452	glDisable(GL_COLOR_MATERIAL)
2453
2454	def RenderLabel(x,y,z,label,r):
2455	glPushMatrix()
2456	glTranslate(x,y,z)
2457	glMultMatrixf(B4mat.T)
2458	glDisable(GL_LIGHTING)
2459	glColor3f(0,1.,0)
2460	glRasterPos3f(r,r,r)
2461	for c in list(label):
2462	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2463	glEnable(GL_LIGHTING)
2464	glPopMatrix()
2465
2466	def Draw():
2467	import numpy.linalg as nl
2468	Ind = GetSelectedAtoms()
2469	VS = np.array(Page.canvas.GetSize())
2470	aspect = float(VS[0])/float(VS[1])
2471	cPos = drawingData['cameraPos']
2472	Zclip = drawingData['Zclip']*cPos/200.
2473	anglex,angley,anglez = drawingData['Rotation'][:3]
2474	Tx,Ty,Tz = drawingData['viewPoint'][0]
2475	cx,ct,cs = drawingData['atomPtrs']
2476	bondR = drawingData['bondRadius']
2477	G,g = G2lat.cell2Gmat(cell)
2478	GS = G
2479	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2480	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2481	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2482	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2483
2484	SetBackground()
2485	glInitNames()
2486	glPushName(0)
2487
2488	glMatrixMode(GL_PROJECTION)
2489	glLoadIdentity()
2490	glViewport(0,0,VS[0],VS[1])
2491	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2492	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2493	SetLights()
2494
2495	glMatrixMode(GL_MODELVIEW)
2496	glLoadIdentity()
2497	glRotate(anglez,0,0,1)
2498	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2499	glRotate(angley,sind(anglez),cosd(anglez),0)
2500	glMultMatrixf(A4mat.T)
2501	glTranslate(-Tx,-Ty,-Tz)
2502	if drawingData['unitCellBox']:
2503	RenderBox()
2504	if drawingData['showABC']:
2505	x,y,z = drawingData['testPos'][0]
2506	# if altDown:
2507	# self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2508	# else:
2509	# self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2510	RenderUnitVectors(x,y,z)
2511	Backbone = []
2512	BackboneColor = []
2513	time0 = time.time()
2514	for iat,atom in enumerate(drawingData['Atoms']):
2515	x,y,z = atom[cx:cx+3]
2516	Bonds = atom[-2]
2517	Faces = atom[-1]
2518	try:
2519	atNum = generalData['AtomTypes'].index(atom[ct])
2520	except ValueError:
2521	atNum = -1
2522	CL = atom[cs+2]
2523	color = np.array(CL)/255.
2524	if iat in Ind:
2525	color = np.array(Gr)/255.
2526	radius = 0.5
2527	if atom[cs] != '':
2528	glLoadName(atom[-3])
2529	if 'balls' in atom[cs]:
2530	vdwScale = drawingData['vdwScale']
2531	ballScale = drawingData['ballScale']
2532	if atNum < 0:
2533	radius = 0.2
2534	elif 'H' == atom[ct]:
2535	if drawingData['showHydrogen']:
2536	if 'vdW' in atom[cs] and atNum >= 0:
2537	radius = vdwScale*generalData['vdWRadii'][atNum]
2538	else:
2539	radius = ballScale*drawingData['sizeH']
2540	else:
2541	radius = 0.0
2542	else:
2543	if 'vdW' in atom[cs]:
2544	radius = vdwScale*generalData['vdWRadii'][atNum]
2545	else:
2546	radius = ballScale*generalData['BondRadii'][atNum]
2547	RenderSphere(x,y,z,radius,color)
2548	if 'sticks' in atom[cs]:
2549	RenderBonds(x,y,z,Bonds,bondR,color)
2550	elif 'ellipsoids' in atom[cs]:
2551	RenderBonds(x,y,z,Bonds,bondR,color)
2552	if atom[cs+3] == 'A':
2553	Uij = atom[cs+5:cs+11]
2554	U = np.multiply(G2spc.Uij2U(Uij),GS)
2555	U = np.inner(Amat,np.inner(U,Amat).T)
2556	E,R = nl.eigh(U)
2557	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2558	E = np.sqrt(E)
2559	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2560	pass
2561	else:
2562	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2563	else:
2564	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2565	pass
2566	else:
2567	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2568	RenderSphere(x,y,z,radius,color)
2569	elif 'lines' in atom[cs]:
2570	radius = 0.1
2571	RenderLines(x,y,z,Bonds,color)
2572	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2573	elif atom[cs] == 'sticks':
2574	radius = 0.1
2575	RenderBonds(x,y,z,Bonds,bondR,color)
2576	elif atom[cs] == 'polyhedra':
2577	RenderPolyhedra(x,y,z,Faces,color)
2578	elif atom[cs] == 'backbone':
2579	if atom[ct-1].split()[0] in ['C','N']:
2580	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2581	BackboneColor.append(list(color))
2582
2583	if atom[cs+1] == 'type':
2584	RenderLabel(x,y,z,atom[ct],radius)
2585	elif atom[cs+1] == 'name':
2586	RenderLabel(x,y,z,atom[ct-1],radius)
2587	elif atom[cs+1] == 'number':
2588	RenderLabel(x,y,z,str(iat+1),radius)
2589	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2590	RenderLabel(x,y,z,atom[ct-4],radius)
2591	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2592	RenderLabel(x,y,z,atom[ct-3],radius)
2593	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2594	RenderLabel(x,y,z,atom[ct-2],radius)
2595	if Backbone:
2596	RenderBackbone(Backbone,BackboneColor,bondR)
2597	# print time.time()-time0
2598	Page.canvas.SwapBuffers()
2599
2600	def OnSize(event):
2601	Draw()
2602
2603	def OnFocus(event):
2604	Draw()
2605
2606	try:
2607	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2608	Page = self.G2plotNB.nb.GetPage(plotNum)
2609	except ValueError:
2610	Plot = self.G2plotNB.addOgl(generalData['Name'])
2611	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2612	Page = self.G2plotNB.nb.GetPage(plotNum)
2613	Page.views = False
2614	view = False
2615	altDown = False
2616	Page.SetFocus()
2617	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2618	choices=(' save as:','jpeg','tiff','bmp'))
2619	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2620	cb.SetValue(' save as:')
2621	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2622	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2623	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2624	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2625	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2626	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2627	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2628	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2629	Page.camera['position'] = drawingData['cameraPos']
2630	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2631	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2632	Page.canvas.SetCurrent()
2633	Draw()
2634

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