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source: trunk/GSASIIplot.py @ 425

Last change on this file since 425 was 423, checked in by vondreele, 14 years ago
Add help to all dataDisplay menus remove ring fit points from integration image - way too slow to plot slight streamline for building of depDerivDict
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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2011-11-18 20:19:01 +0000 (Fri, 18 Nov 2011) $
4	# $Author: vondreele $
5	# $Revision: 423 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 423 2011-11-18 20:19:01Z 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'] = 10
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]-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,sampleParm):
1449
1450	def OnKeyPress(event):
1451	if event.key == 's' and sampleParm:
1452	if self.xAxis:
1453	self.xAxis = False
1454	else:
1455	self.xAxis = True
1456	Draw(False)
1457	try:
1458	plotNum = self.G2plotNB.plotList.index('Sequential refinement')
1459	Page = self.G2plotNB.nb.GetPage(plotNum)
1460	Page.figure.clf()
1461	Plot = Page.figure.gca()
1462	if not Page.IsShown():
1463	Page.Show()
1464	except ValueError:
1465	Plot = self.G2plotNB.addMpl('Sequential refinement').gca()
1466	plotNum = self.G2plotNB.plotList.index('Sequential refinement')
1467	Page = self.G2plotNB.nb.GetPage(plotNum)
1468	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
1469	self.xAxis = False
1470
1471	def Draw(newPlot):
1472	Page.SetFocus()
1473	self.G2plotNB.status.SetFields(['','press s to toggle x-axis = sample environment parameter'])
1474	if len(SeqData):
1475	Plot.clear()
1476	if self.xAxis:
1477	xName = sampleParm.keys()[0]
1478	X = sampleParm[xName]
1479	else:
1480	X = np.arange(0,len(SeqData[0]),1)
1481	xName = 'Data sequence number'
1482	for Y,sig,name in zip(SeqData,SeqSig,SeqNames):
1483	Plot.errorbar(X,Y,yerr=sig,label=name)
1484	Plot.legend(loc='best')
1485	Plot.set_ylabel('Parameter values')
1486	Plot.set_xlabel(xName)
1487	Page.canvas.draw()
1488	Draw(True)
1489
1490	def PlotExposedImage(self,newPlot=False,event=None):
1491	'''General access module for 2D image plotting
1492	'''
1493	plotNo = self.G2plotNB.nb.GetSelection()
1494	if self.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1495	PlotImage(self,newPlot,event,newImage=True)
1496	elif self.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1497	PlotIntegration(self,newPlot,event)
1498
1499	def PlotImage(self,newPlot=False,event=None,newImage=True):
1500	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1501	masks, etc.
1502	'''
1503	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1504	import numpy.ma as ma
1505	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1506	global Data,Masks
1507	colors=['b','g','r','c','m','k']
1508	Data = self.PatternTree.GetItemPyData(
1509	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1510	Masks = self.PatternTree.GetItemPyData(
1511	G2gd.GetPatternTreeItemId(self,self.Image, 'Masks'))
1512
1513	def OnImMotion(event):
1514	Page.canvas.SetToolTipString('')
1515	sizexy = Data['size']
1516	if event.xdata and event.ydata: #avoid out of frame errors
1517	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1518	item = self.itemPicked
1519	pixelSize = Data['pixelSize']
1520	scalex = 1000./pixelSize[0]
1521	scaley = 1000./pixelSize[1]
1522	if item and self.PatternTree.GetItemText(self.PickId) == 'Image Controls':
1523	if 'Text' in str(item):
1524	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1525	else:
1526	xcent,ycent = Data['center']
1527	xpos = event.xdata-xcent
1528	ypos = event.ydata-ycent
1529	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1530	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1531	Page.canvas.SetToolTipString('%6d deg'%(azm))
1532	elif 'line1' in str(item) or 'line2' in str(item):
1533	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1534	else:
1535	xpos = event.xdata
1536	ypos = event.ydata
1537	xpix = xpos*scalex
1538	ypix = ypos*scaley
1539	Int = 0
1540	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1541	Int = self.ImageZ[ypix][xpix]
1542	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1543	Q = 2.*math.pi/dsp
1544	if self.setPoly:
1545	self.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1546	else:
1547	self.G2plotNB.status.SetFields(\
1548	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1549
1550	def OnImPlotKeyPress(event):
1551	try:
1552	PickName = self.PatternTree.GetItemText(self.PickId)
1553	except TypeError:
1554	return
1555	if PickName == 'Masks':
1556	Xpos = event.xdata
1557	if not Xpos: #got point out of frame
1558	return
1559	Ypos = event.ydata
1560	if event.key == 's':
1561	Masks['Points'].append([Xpos,Ypos,1.])
1562	elif event.key == 'r':
1563	tth = G2img.GetTth(Xpos,Ypos,Data)
1564	Masks['Rings'].append([tth,0.1])
1565	elif event.key == 'a':
1566	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1567	azm = int(azm)
1568	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1569	elif event.key == 'p':
1570	self.setPoly = True
1571	Masks['Polygons'].append([])
1572	self.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1573	G2imG.UpdateMasks(self,Masks)
1574	elif PickName == 'Image Controls':
1575	if event.key == 'c':
1576	Xpos = event.xdata
1577	if not Xpos: #got point out of frame
1578	return
1579	Ypos = event.ydata
1580	dlg = wx.MessageDialog(self,'Are you sure you want to change the center?',
1581	'Center change',style=wx.OK\|wx.CANCEL)
1582	try:
1583	if dlg.ShowModal() == wx.ID_OK:
1584	print 'move center to: ',Xpos,Ypos
1585	Data['center'] = [Xpos,Ypos]
1586	G2imG.UpdateImageControls(self,Data,Masks)
1587	finally:
1588	dlg.Destroy()
1589	elif event.key == 'l':
1590	if self.logPlot:
1591	self.logPlot = False
1592	else:
1593	self.logPlot = True
1594	PlotImage(self,newImage=True)
1595
1596	def OnKeyBox(event):
1597	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('2D Powder Image'):
1598	event.key = cb.GetValue()[0]
1599	cb.SetValue(' key press')
1600	if event.key in 'l':
1601	OnImPlotKeyPress(event)
1602
1603	def OnImPick(event):
1604	if self.PatternTree.GetItemText(self.PickId) not in ['Image Controls','Masks']:
1605	return
1606	if self.setPoly:
1607	polygon = Masks['Polygons'][-1]
1608	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1609	if xpos and ypos: #point inside image
1610	if len(polygon) > 2 and event.mouseevent.button == 3:
1611	x0,y0 = polygon[0]
1612	polygon.append([x0,y0])
1613	self.setPoly = False
1614	self.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1615	else:
1616	self.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1617	polygon.append([xpos,ypos])
1618	G2imG.UpdateMasks(self,Masks)
1619	else:
1620	if self.itemPicked is not None: return
1621	self.itemPicked = event.artist
1622	self.mousePicked = event.mouseevent
1623
1624	def OnImRelease(event):
1625	try:
1626	PickName = self.PatternTree.GetItemText(self.PickId)
1627	except TypeError:
1628	return
1629	if PickName not in ['Image Controls','Masks']:
1630	return
1631	pixelSize = Data['pixelSize']
1632	scalex = 1000./pixelSize[0]
1633	scaley = 1000./pixelSize[1]
1634	pixLimit = Data['pixLimit']
1635	if self.itemPicked is None and PickName == 'Image Controls':
1636	# sizexy = Data['size']
1637	Xpos = event.xdata
1638	if not (Xpos and self.ifGetRing): #got point out of frame
1639	return
1640	Ypos = event.ydata
1641	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1642	if event.button == 1:
1643	Xpix = Xpos*scalex
1644	Ypix = Ypos*scaley
1645	xpos,ypos,I,J = G2img.ImageLocalMax(self.ImageZ,pixLimit,Xpix,Ypix)
1646	if I and J:
1647	xpos += .5 #shift to pixel center
1648	ypos += .5
1649	xpos /= scalex #convert to mm
1650	ypos /= scaley
1651	Data['ring'].append([xpos,ypos])
1652	elif event.button == 3:
1653	self.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1654	if G2img.ImageCalibrate(self,Data):
1655	self.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1656	print 'Calibration successful'
1657	else:
1658	self.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1659	print 'Calibration failed'
1660	self.ifGetRing = False
1661	G2imG.UpdateImageControls(self,Data,Masks)
1662	return
1663	PlotImage(self,newImage=False)
1664	return
1665	else:
1666	xpos = event.xdata
1667	if xpos: #avoid out of frame mouse position
1668	ypos = event.ydata
1669	if self.ifGetRing: #delete a calibration ring pick
1670	xypos = [xpos,ypos]
1671	rings = Data['ring']
1672	for ring in rings:
1673	if np.allclose(ring,xypos,.01,0):
1674	rings.remove(ring)
1675	else:
1676	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1677	itemPicked = str(self.itemPicked)
1678	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1679	if 'line1' in itemPicked:
1680	Data['IOtth'][0] = max(tth,0.001)
1681	elif 'line2' in itemPicked:
1682	Data['IOtth'][1] = tth
1683	elif 'line3' in itemPicked:
1684	Data['LRazimuth'][0] = int(azm)
1685	if Data['fullIntegrate']:
1686	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1687	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1688	Data['LRazimuth'][1] = int(azm)
1689
1690	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1691	Data['LRazimuth'][0] -= 360
1692
1693	azLim = np.array(Data['LRazimuth'])
1694	if np.any(azLim>360):
1695	azLim -= 360
1696	Data['LRazimuth'] = list(azLim)
1697
1698	if Data['IOtth'][0] > Data['IOtth'][1]:
1699	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1700
1701	self.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1702	self.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1703	self.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1704	self.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1705	elif 'Circle' in itemPicked and PickName == 'Masks':
1706	spots = Masks['Points']
1707	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1708	newPos = np.array([float(newPos[0]),float(newPos[1])])
1709	for spot in spots:
1710	if np.allclose(np.array([spot[:2]]),newPos):
1711	spot[:2] = xpos,ypos
1712	G2imG.UpdateMasks(self,Masks)
1713	elif 'Line2D' in itemPicked and PickName == 'Masks':
1714	Obj = self.itemPicked.findobj()
1715	rings = Masks['Rings']
1716	arcs = Masks['Arcs']
1717	polygons = Masks['Polygons']
1718	for ring in self.ringList:
1719	if Obj == ring[0]:
1720	rN = ring[1]
1721	if ring[2] == 'o':
1722	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1723	else:
1724	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1725	for arc in self.arcList:
1726	if Obj == arc[0]:
1727	aN = arc[1]
1728	if arc[2] == 'o':
1729	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1730	elif arc[2] == 'i':
1731	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1732	elif arc[2] == 'l':
1733	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1734	else:
1735	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1736	for poly in self.polyList:
1737	if Obj == poly[0]:
1738	ind = self.itemPicked.contains(self.mousePicked)[1]['ind'][0]
1739	oldPos = np.array([self.mousePicked.xdata,self.mousePicked.ydata])
1740	pN = poly[1]
1741	for i,xy in enumerate(polygons[pN]):
1742	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1743	polygons[pN][i] = xpos,ypos
1744	G2imG.UpdateMasks(self,Masks)
1745	# else: #keep for future debugging
1746	# print str(self.itemPicked),event.xdata,event.ydata,event.button
1747	PlotImage(self,newImage=True)
1748	self.itemPicked = None
1749
1750	try:
1751	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1752	Page = self.G2plotNB.nb.GetPage(plotNum)
1753	if not newPlot:
1754	Plot = Page.figure.gca() #get previous powder plot & get limits
1755	xylim = Plot.get_xlim(),Plot.get_ylim()
1756	if newImage:
1757	Page.figure.clf()
1758	Plot = Page.figure.gca() #get a fresh plot after clf()
1759
1760	except ValueError:
1761	Plot = self.G2plotNB.addMpl('2D Powder Image').gca()
1762	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1763	Page = self.G2plotNB.nb.GetPage(plotNum)
1764	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1765	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1766	Page.canvas.mpl_connect('pick_event', OnImPick)
1767	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1768	xylim = []
1769	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1770	Page.SetFocus()
1771	Title = self.PatternTree.GetItemText(self.Image)[4:]
1772	self.G2plotNB.status.DestroyChildren()
1773	if self.logPlot:
1774	Title = 'log('+Title+')'
1775	Plot.set_title(Title)
1776	try:
1777	if self.PatternTree.GetItemText(self.PickId) in ['Image Controls',]:
1778	Choice = (' key press','l: log(I) on',)
1779	if self.logPlot:
1780	Choice[1] = 'l: log(I) off'
1781	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1782	choices=Choice)
1783	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1784	cb.SetValue(' key press')
1785	except TypeError:
1786	pass
1787	size,imagefile = self.PatternTree.GetItemPyData(self.Image)
1788	if imagefile != self.oldImagefile:
1789	imagefile = G2IO.CheckImageFile(self,imagefile)
1790	if not imagefile:
1791	self.G2plotNB.Delete('2D Powder Image')
1792	return
1793	self.PatternTree.SetItemPyData(self.Image,[size,imagefile])
1794	self.ImageZ = G2IO.GetImageData(self,imagefile,imageOnly=True)
1795	# print self.ImageZ.shape,self.ImageZ.size,Data['size'] #might be useful debugging line
1796	self.oldImagefile = imagefile
1797
1798	imScale = 1
1799	if len(self.ImageZ) > 1024:
1800	imScale = len(self.ImageZ)/1024
1801	sizexy = Data['size']
1802	pixelSize = Data['pixelSize']
1803	scalex = 1000./pixelSize[0]
1804	scaley = 1000./pixelSize[1]
1805	Xmax = sizexy[0]*pixelSize[0]/1000.
1806	Ymax = sizexy[1]*pixelSize[1]/1000.
1807	xlim = (0,Xmax)
1808	ylim = (Ymax,0)
1809	Imin,Imax = Data['range'][1]
1810	acolor = mpl.cm.get_cmap(Data['color'])
1811	xcent,ycent = Data['center']
1812	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1813	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1814	#do threshold mask - "real" mask - others are just bondaries
1815	Zlim = Masks['Thresholds'][1]
1816	wx.BeginBusyCursor()
1817	try:
1818
1819	if newImage:
1820	MA = ma.masked_greater(ma.masked_less(self.ImageZ,Zlim[0]),Zlim[1])
1821	MaskA = ma.getmaskarray(MA)
1822	A = G2img.ImageCompress(MA,imScale)
1823	AM = G2img.ImageCompress(MaskA,imScale)
1824	if self.logPlot:
1825	A = np.where(A>0,np.log(A),0)
1826	AM = np.where(AM>0,np.log(AM),0)
1827	Imin,Imax = [np.amin(A),np.amax(A)]
1828	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
1829	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Xmax,0])
1830	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
1831	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
1832	if self.setPoly:
1833	Img.set_picker(True)
1834
1835	Plot.plot(xcent,ycent,'x')
1836	if Data['showLines']:
1837	LRAzim = Data['LRazimuth'] #NB: integers
1838	Nazm = Data['outAzimuths']
1839	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
1840	AzmthOff = Data['azmthOff']
1841	IOtth = Data['IOtth']
1842	wave = Data['wavelength']
1843	dspI = wave/(2.0*sind(IOtth[0]/2.0))
1844	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
1845	dspO = wave/(2.0*sind(IOtth[1]/2.0))
1846	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
1847	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
1848	if ellI:
1849	xyI = []
1850	for azm in Azm:
1851	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
1852	xyI = np.array(xyI)
1853	arcxI,arcyI = xyI.T
1854	Plot.plot(arcxI,arcyI,picker=3)
1855	if ellO:
1856	xyO = []
1857	for azm in Azm:
1858	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
1859	xyO = np.array(xyO)
1860	arcxO,arcyO = xyO.T
1861	Plot.plot(arcxO,arcyO,picker=3)
1862	if ellO and ellI:
1863	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
1864	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
1865	for i in range(Nazm):
1866	cake = LRAzim[0]+i*delAzm-AzmthOff
1867	ind = np.searchsorted(Azm,cake)
1868	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
1869
1870	for xring,yring in Data['ring']:
1871	Plot.plot(xring,yring,'r+',picker=3)
1872	if Data['setRings']:
1873	# rings = np.concatenate((Data['rings']),axis=0)
1874	N = 0
1875	for ring in Data['rings']:
1876	xring,yring = np.array(ring).T[:2]
1877	Plot.plot(xring,yring,'+',color=colors[N%6])
1878	N += 1
1879	for ellipse in Data['ellipses']:
1880	cent,phi,[width,height],col = ellipse
1881	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
1882	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
1883	#masks - mask lines numbered after integration limit lines
1884	spots = Masks['Points']
1885	rings = Masks['Rings']
1886	arcs = Masks['Arcs']
1887	polygons = Masks['Polygons']
1888	for x,y,d in spots:
1889	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
1890	self.ringList = []
1891	for iring,(tth,thick) in enumerate(rings):
1892	wave = Data['wavelength']
1893	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
1894	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
1895	self.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1896	self.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1897	self.arcList = []
1898	for iarc,(tth,azm,thick) in enumerate(arcs):
1899	wave = Data['wavelength']
1900	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
1901	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
1902	self.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1903	self.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1904	self.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1905	self.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1906	self.polyList = []
1907	for ipoly,polygon in enumerate(polygons):
1908	x,y = np.hsplit(np.array(polygon),2)
1909	self.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
1910	Plot.plot(x,y,'r')
1911	if newImage:
1912	colorBar = Page.figure.colorbar(Img)
1913	Plot.set_xlim(xlim)
1914	Plot.set_ylim(ylim)
1915	if not newPlot and xylim:
1916	Page.toolbar.push_current()
1917	Plot.set_xlim(xylim[0])
1918	Plot.set_ylim(xylim[1])
1919	xylim = []
1920	Page.toolbar.push_current()
1921	Page.toolbar.draw()
1922	else:
1923	Page.canvas.draw()
1924	finally:
1925	wx.EndBusyCursor()
1926
1927	def PlotIntegration(self,newPlot=False,event=None):
1928	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
1929	'''
1930
1931	def OnMotion(event):
1932	Page.canvas.SetToolTipString('')
1933	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1934	azm = event.ydata
1935	tth = event.xdata
1936	if azm and tth:
1937	self.G2plotNB.status.SetFields(\
1938	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1939
1940	try:
1941	plotNum = self.G2plotNB.plotList.index('2D Integration')
1942	Page = self.G2plotNB.nb.GetPage(plotNum)
1943	if not newPlot:
1944	Plot = Page.figure.gca() #get previous plot & get limits
1945	xylim = Plot.get_xlim(),Plot.get_ylim()
1946	Page.figure.clf()
1947	Plot = Page.figure.gca() #get a fresh plot after clf()
1948
1949	except ValueError:
1950	Plot = self.G2plotNB.addMpl('2D Integration').gca()
1951	plotNum = self.G2plotNB.plotList.index('2D Integration')
1952	Page = self.G2plotNB.nb.GetPage(plotNum)
1953	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1954	Page.views = False
1955	view = False
1956	if not event:
1957	Page.SetFocus()
1958
1959	Data = self.PatternTree.GetItemPyData(
1960	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1961	image = self.Integrate[0]
1962	xsc = self.Integrate[1]
1963	ysc = self.Integrate[2]
1964	Imin,Imax = Data['range'][1]
1965	acolor = mpl.cm.get_cmap(Data['color'])
1966	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1967	Plot.set_ylabel('azimuth',fontsize=12)
1968	Plot.set_xlabel('2-theta',fontsize=12)
1969	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
1970	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
1971	colorBar = Page.figure.colorbar(Img)
1972	if Data['ellipses']:
1973	for ellipse in Data['ellipses']:
1974	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1975	x,y = np.hsplit(ring,2)
1976	tth,azm = G2img.GetTthAzm(x,y,Data)
1977	# azm = np.where(azm < 0.,azm+360,azm)
1978	Plot.plot(tth,azm,'b,')
1979	if not newPlot:
1980	Page.toolbar.push_current()
1981	Plot.set_xlim(xylim[0])
1982	Plot.set_ylim(xylim[1])
1983	xylim = []
1984	Page.toolbar.push_current()
1985	Page.toolbar.draw()
1986	else:
1987	Page.canvas.draw()
1988
1989	def PlotTRImage(self,tax,tay,taz,newPlot=False):
1990	'''a test plot routine - not normally used
1991	'''
1992
1993	def OnMotion(event):
1994	Page.canvas.SetToolTipString('')
1995	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1996	azm = event.xdata
1997	tth = event.ydata
1998	if azm and tth:
1999	self.G2plotNB.status.SetFields(\
2000	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2001
2002	try:
2003	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
2004	Page = self.G2plotNB.nb.GetPage(plotNum)
2005	if not newPlot:
2006	Plot = Page.figure.gca() #get previous plot & get limits
2007	xylim = Plot.get_xlim(),Plot.get_ylim()
2008	Page.figure.clf()
2009	Plot = Page.figure.gca() #get a fresh plot after clf()
2010
2011	except ValueError:
2012	Plot = self.G2plotNB.addMpl('2D Transformed Powder Image').gca()
2013	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
2014	Page = self.G2plotNB.nb.GetPage(plotNum)
2015	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2016	Page.views = False
2017	view = False
2018	Page.SetFocus()
2019
2020	Data = self.PatternTree.GetItemPyData(
2021	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
2022	Imin,Imax = Data['range'][1]
2023	step = (Imax-Imin)/5.
2024	V = np.arange(Imin,Imax,step)
2025	acolor = mpl.cm.get_cmap(Data['color'])
2026	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
2027	Plot.set_xlabel('azimuth',fontsize=12)
2028	Plot.set_ylabel('2-theta',fontsize=12)
2029	Plot.contour(tax,tay,taz,V,cmap=acolor)
2030	if Data['showLines']:
2031	IOtth = Data['IOtth']
2032	if Data['fullIntegrate']:
2033	LRAzim = [-180,180]
2034	else:
2035	LRAzim = Data['LRazimuth'] #NB: integers
2036	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
2037	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
2038	if not Data['fullIntegrate']:
2039	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
2040	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
2041	if Data['setRings']:
2042	rings = np.concatenate((Data['rings']),axis=0)
2043	for xring,yring,dsp in rings:
2044	x,y = G2img.GetTthAzm(xring,yring,Data)
2045	Plot.plot(y,x,'r+')
2046	if Data['ellipses']:
2047	for ellipse in Data['ellipses']:
2048	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2049	x,y = np.hsplit(ring,2)
2050	tth,azm = G2img.GetTthAzm(x,y,Data)
2051	Plot.plot(azm,tth,'b,')
2052	if not newPlot:
2053	Page.toolbar.push_current()
2054	Plot.set_xlim(xylim[0])
2055	Plot.set_ylim(xylim[1])
2056	xylim = []
2057	Page.toolbar.push_current()
2058	Page.toolbar.draw()
2059	else:
2060	Page.canvas.draw()
2061
2062	def PlotStructure(self,data):
2063	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
2064	thermal motion ellipsoids and polyhedra
2065	'''
2066	generalData = data['General']
2067	cell = generalData['Cell'][1:7]
2068	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
2069	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2070	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2071	Mydir = generalData['Mydir']
2072	atomData = data['Atoms']
2073	drawingData = data['Drawing']
2074	drawAtoms = drawingData['Atoms']
2075	cx,ct,cs = drawingData['atomPtrs']
2076	Wt = [255,255,255]
2077	Rd = [255,0,0]
2078	Gr = [0,255,0]
2079	Bl = [0,0,255]
2080	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]])
2081	uEdges = np.array([
2082	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
2083	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
2084	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
2085	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
2086	altDown = False
2087	shiftDown = False
2088	ctrlDown = False
2089
2090	def OnKeyBox(event):
2091	import Image
2092	Draw() #make sure plot is fresh!!
2093	mode = cb.GetValue()
2094	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
2095	size = Page.canvas.GetSize()
2096	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
2097	if mode in ['jpeg',]:
2098	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
2099	im = Image.new("RGBA", (size[0],size[1]))
2100	else:
2101	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
2102	im = Image.new("RGB", (size[0],size[1]))
2103	im.fromstring(Pix)
2104	im.save(Fname,mode)
2105	cb.SetValue(' Save as:')
2106	self.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
2107
2108	def GetTruePosition(xy):
2109	View = glGetIntegerv(GL_VIEWPORT)
2110	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
2111	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
2112	Zmax = 1.
2113	for i,atom in enumerate(drawAtoms):
2114	x,y,z = atom[cx:cx+3]
2115	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2116	XY = [int(X),int(View[3]-Y)]
2117	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2118	Zmax = Z
2119	SetSelectedAtoms(i)
2120
2121	def OnMouseDown(event):
2122	xy = event.GetPosition()
2123	if event.ShiftDown():
2124	GetTruePosition(xy)
2125	else:
2126	drawingData['Rotation'][3] = xy
2127	Draw()
2128
2129	def OnMouseMove(event):
2130	newxy = event.GetPosition()
2131	page = getSelection()
2132	if event.ControlDown() and drawingData['showABC']:
2133	if event.LeftIsDown():
2134	SetTestRot(newxy)
2135	elif event.RightIsDown():
2136	SetTestPos(newxy)
2137	elif event.MiddleIsDown():
2138	SetTestRotZ(newxy)
2139	x,y,z = drawingData['testPos'][0]
2140	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2141
2142
2143	if event.Dragging() and not event.ControlDown():
2144	if event.LeftIsDown():
2145	SetRotation(newxy)
2146	angX,angY,angZ = drawingData['Rotation'][:3]
2147	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
2148	elif event.RightIsDown():
2149	SetTranslation(newxy)
2150	Tx,Ty,Tz = drawingData['viewPoint'][0]
2151	self.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2152	elif event.MiddleIsDown():
2153	SetRotationZ(newxy)
2154	angX,angY,angZ = drawingData['Rotation'][:3]
2155	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
2156	Draw()
2157
2158	def OnMouseWheel(event):
2159	drawingData['cameraPos'] += event.GetWheelRotation()/24
2160	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2161	self.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2162	page = getSelection()
2163	if page:
2164	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2165	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2166	names = [child.GetName() for child in panel]
2167	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2168	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2169	Draw()
2170
2171	def getSelection():
2172	try:
2173	return self.dataDisplay.GetSelection()
2174	except AttributeError:
2175	print self.dataDisplay.GetLabel()
2176	self.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2177	return 0
2178
2179	def SetViewPointText(VP):
2180	page = getSelection()
2181	if page:
2182	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2183	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2184	names = [child.GetName() for child in panel]
2185	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
2186
2187	def ClearSelectedAtoms():
2188	page = getSelection()
2189	if page:
2190	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2191	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2192	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2193	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2194
2195	def SetSelectedAtoms(ind):
2196	page = getSelection()
2197	if page:
2198	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2199	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
2200	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2201	Id = drawAtoms[ind][-2]
2202	for i,atom in enumerate(atomData):
2203	if atom[-1] == Id:
2204	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2205
2206	def GetSelectedAtoms():
2207	page = getSelection()
2208	Ind = []
2209	if page:
2210	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2211	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2212	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2213	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2214	return Ind
2215
2216	def OnKey(event): #on key UP!!
2217	keyCode = event.GetKeyCode()
2218	if keyCode > 255:
2219	keyCode = 0
2220	key,xyz = chr(keyCode),event.GetPosition()
2221	indx = drawingData['selectedAtoms']
2222	if key in ['c','C']:
2223	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2224	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
2225	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
2226	SetViewPointText(drawingData['viewPoint'][0])
2227	elif key in ['n','N']:
2228	drawAtoms = drawingData['Atoms']
2229	pI = drawingData['viewPoint'][1]
2230	if indx:
2231	pI[0] = indx[pI[1]]
2232	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2233	pI[1] += 1
2234	if pI[1] >= len(indx):
2235	pI[1] = 0
2236	else:
2237	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2238	pI[0] += 1
2239	if pI[0] >= len(drawAtoms):
2240	pI[0] = 0
2241	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2242	SetViewPointText(drawingData['viewPoint'][0])
2243
2244	elif key in ['p','P']:
2245	drawAtoms = drawingData['Atoms']
2246	pI = drawingData['viewPoint'][1]
2247	if indx:
2248	pI[0] = indx[pI[1]]
2249	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2250	pI[1] -= 1
2251	if pI[1] < 0:
2252	pI[1] = len(indx)-1
2253	else:
2254	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2255	pI[0] -= 1
2256	if pI[0] < 0:
2257	pI[0] = len(drawAtoms)-1
2258	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2259	SetViewPointText(drawingData['viewPoint'][0])
2260	Draw()
2261
2262	def SetBackground():
2263	R,G,B,A = Page.camera['backColor']
2264	glClearColor(R,G,B,A)
2265	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2266
2267	def SetLights():
2268	glEnable(GL_DEPTH_TEST)
2269	glShadeModel(GL_SMOOTH)
2270	glEnable(GL_LIGHTING)
2271	glEnable(GL_LIGHT0)
2272	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2273	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2274	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2275
2276	def SetTranslation(newxy):
2277	Tx,Ty,Tz = drawingData['viewPoint'][0]
2278	anglex,angley,anglez,oldxy = drawingData['Rotation']
2279	Rx = G2lat.rotdMat(anglex,0)
2280	Ry = G2lat.rotdMat(angley,1)
2281	Rz = G2lat.rotdMat(anglez,2)
2282	dxy = list(newxy-oldxy)+[0,]
2283	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
2284	Tx -= dxy[0]*0.01
2285	Ty += dxy[1]*0.01
2286	Tz -= dxy[2]*0.01
2287	drawingData['Rotation'][3] = newxy
2288	drawingData['viewPoint'][0] = Tx,Ty,Tz
2289	SetViewPointText([Tx,Ty,Tz])
2290
2291	def SetTestPos(newxy):
2292	Tx,Ty,Tz = drawingData['testPos'][0]
2293	anglex,angley,anglez,oldxy = drawingData['Rotation']
2294	Rx = G2lat.rotdMat(anglex,0)
2295	Ry = G2lat.rotdMat(angley,1)
2296	Rz = G2lat.rotdMat(anglez,2)
2297	dxy = list(newxy-oldxy)+[0,]
2298	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
2299	Tx += dxy[0]*0.001
2300	Ty -= dxy[1]*0.001
2301	Tz += dxy[2]*0.001
2302	drawingData['Rotation'][3] = newxy
2303	drawingData['testPos'][0] = Tx,Ty,Tz
2304
2305	def SetTestRot(newxy):
2306	Txyz = np.array(drawingData['testPos'][0])
2307	oldxy = drawingData['testPos'][2]
2308	Ax,Ay,Az = drawingData['testPos'][1]
2309	Vxyz = np.array(drawingData['viewPoint'][0])
2310	Dxyz = np.inner(Amat,Txyz-Vxyz)
2311	dxy = list(newxy-oldxy)+[0,]
2312	Ax += dxy[1]*0.01
2313	Ay += dxy[0]*0.01
2314	Rx = G2lat.rotdMat(Ax,0)
2315	Ry = G2lat.rotdMat(Ay,1)
2316	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
2317	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2318	drawingData['testPos'][1] = [Ax,Ay,Az]
2319	drawingData['testPos'][2] = newxy
2320	drawingData['testPos'][0] = Dxyz
2321
2322	def SetTestRotZ(newxy):
2323	Txyz = np.array(drawingData['testPos'][0])
2324	oldxy = drawingData['testPos'][2]
2325	Ax,Ay,Az = drawingData['testPos'][1]
2326	Vxyz = np.array(drawingData['viewPoint'][0])
2327	Dxyz = np.inner(Amat,Txyz-Vxyz)
2328	dxy = list(newxy-oldxy)+[0,]
2329	Az += (dxy[0]+dxy[1])*.01
2330	Rz = G2lat.rotdMat(Az,2)
2331	Dxyz = np.inner(Rz,Dxyz)
2332	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2333	drawingData['testPos'][1] = [Ax,Ay,Az]
2334	drawingData['testPos'][2] = newxy
2335	drawingData['testPos'][0] = Dxyz
2336
2337	def SetRotation(newxy):
2338	anglex,angley,anglez,oldxy = drawingData['Rotation']
2339	dxy = newxy-oldxy
2340	anglex += dxy[1]*.25
2341	angley += dxy[0]*.25
2342	oldxy = newxy
2343	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2344
2345	def SetRotationZ(newxy):
2346	anglex,angley,anglez,oldxy = drawingData['Rotation']
2347	dxy = newxy-oldxy
2348	anglez += (dxy[0]+dxy[1])*.25
2349	oldxy = newxy
2350	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2351
2352	def RenderBox():
2353	glEnable(GL_COLOR_MATERIAL)
2354	glLineWidth(2)
2355	glEnable(GL_BLEND)
2356	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2357	glEnable(GL_LINE_SMOOTH)
2358	glBegin(GL_LINES)
2359	for line,color in zip(uEdges,uColors):
2360	glColor3ubv(color)
2361	glVertex3fv(line[0])
2362	glVertex3fv(line[1])
2363	glEnd()
2364	glColor4ubv([0,0,0,0])
2365	glDisable(GL_LINE_SMOOTH)
2366	glDisable(GL_BLEND)
2367	glDisable(GL_COLOR_MATERIAL)
2368
2369	def RenderUnitVectors(x,y,z):
2370	xyz = np.array([x,y,z])
2371	glEnable(GL_COLOR_MATERIAL)
2372	glLineWidth(1)
2373	glPushMatrix()
2374	glTranslate(x,y,z)
2375	glScalef(1/cell[0],1/cell[1],1/cell[2])
2376	glBegin(GL_LINES)
2377	for line,color in zip(uEdges,uColors)[:3]:
2378	glColor3ubv(color)
2379	glVertex3fv(line[0])
2380	glVertex3fv(line[1])
2381	glEnd()
2382	glPopMatrix()
2383	glColor4ubv([0,0,0,0])
2384	glDisable(GL_COLOR_MATERIAL)
2385
2386	def RenderSphere(x,y,z,radius,color):
2387	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2388	glPushMatrix()
2389	glTranslate(x,y,z)
2390	glMultMatrixf(B4mat.T)
2391	q = gluNewQuadric()
2392	gluSphere(q,radius,20,10)
2393	glPopMatrix()
2394
2395	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2396	s1,s2,s3 = E
2397	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2398	glPushMatrix()
2399	glTranslate(x,y,z)
2400	glMultMatrixf(B4mat.T)
2401	glMultMatrixf(R4.T)
2402	glEnable(GL_NORMALIZE)
2403	glScale(s1,s2,s3)
2404	q = gluNewQuadric()
2405	gluSphere(q,ellipseProb,20,10)
2406	glDisable(GL_NORMALIZE)
2407	glPopMatrix()
2408
2409	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2410	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2411	glPushMatrix()
2412	glTranslate(x,y,z)
2413	glMultMatrixf(B4mat.T)
2414	for bond in Bonds:
2415	glPushMatrix()
2416	Dx = np.inner(Amat,bond)
2417	Z = np.sqrt(np.sum(Dx**2))
2418	azm = atan2d(-Dx[1],-Dx[0])
2419	phi = acosd(Dx[2]/Z)
2420	glRotate(-azm,0,0,1)
2421	glRotate(phi,1,0,0)
2422	q = gluNewQuadric()
2423	gluCylinder(q,radius,radius,Z,slice,2)
2424	glPopMatrix()
2425	glPopMatrix()
2426
2427	def RenderLines(x,y,z,Bonds,color):
2428	xyz = np.array([x,y,z])
2429	glEnable(GL_COLOR_MATERIAL)
2430	glLineWidth(1)
2431	glColor3fv(color)
2432	glPushMatrix()
2433	glBegin(GL_LINES)
2434	for bond in Bonds:
2435	glVertex3fv(xyz)
2436	glVertex3fv(xyz+bond)
2437	glEnd()
2438	glColor4ubv([0,0,0,0])
2439	glPopMatrix()
2440	glDisable(GL_COLOR_MATERIAL)
2441
2442	def RenderPolyhedra(x,y,z,Faces,color):
2443	glPushMatrix()
2444	glTranslate(x,y,z)
2445	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2446	glShadeModel(GL_SMOOTH)
2447	glMultMatrixf(B4mat.T)
2448	for face,norm in Faces:
2449	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2450	glFrontFace(GL_CW)
2451	glNormal3fv(norm)
2452	glBegin(GL_TRIANGLES)
2453	for vert in face:
2454	glVertex3fv(vert)
2455	glEnd()
2456	glPopMatrix()
2457
2458	def RenderBackbone(Backbone,BackboneColor,radius):
2459	glPushMatrix()
2460	glMultMatrixf(B4mat.T)
2461	glEnable(GL_COLOR_MATERIAL)
2462	glShadeModel(GL_SMOOTH)
2463	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2464	glePolyCylinder(Backbone,BackboneColor,radius)
2465	glPopMatrix()
2466	glDisable(GL_COLOR_MATERIAL)
2467
2468	def RenderLabel(x,y,z,label,r):
2469	glPushMatrix()
2470	glTranslate(x,y,z)
2471	glMultMatrixf(B4mat.T)
2472	glDisable(GL_LIGHTING)
2473	glColor3f(0,1.,0)
2474	glRasterPos3f(r,r,r)
2475	for c in list(label):
2476	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2477	glEnable(GL_LIGHTING)
2478	glPopMatrix()
2479
2480	def Draw():
2481	import numpy.linalg as nl
2482	Ind = GetSelectedAtoms()
2483	VS = np.array(Page.canvas.GetSize())
2484	aspect = float(VS[0])/float(VS[1])
2485	cPos = drawingData['cameraPos']
2486	Zclip = drawingData['Zclip']*cPos/200.
2487	anglex,angley,anglez = drawingData['Rotation'][:3]
2488	Tx,Ty,Tz = drawingData['viewPoint'][0]
2489	cx,ct,cs = drawingData['atomPtrs']
2490	bondR = drawingData['bondRadius']
2491	G,g = G2lat.cell2Gmat(cell)
2492	GS = G
2493	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2494	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2495	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2496	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2497
2498	SetBackground()
2499	glInitNames()
2500	glPushName(0)
2501
2502	glMatrixMode(GL_PROJECTION)
2503	glLoadIdentity()
2504	glViewport(0,0,VS[0],VS[1])
2505	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2506	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2507	SetLights()
2508
2509	glMatrixMode(GL_MODELVIEW)
2510	glLoadIdentity()
2511	glRotate(anglez,0,0,1)
2512	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2513	glRotate(angley,sind(anglez),cosd(anglez),0)
2514	glMultMatrixf(A4mat.T)
2515	glTranslate(-Tx,-Ty,-Tz)
2516	if drawingData['unitCellBox']:
2517	RenderBox()
2518	if drawingData['showABC']:
2519	x,y,z = drawingData['testPos'][0]
2520	# if altDown:
2521	# self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2522	# else:
2523	# self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2524	RenderUnitVectors(x,y,z)
2525	Backbone = []
2526	BackboneColor = []
2527	time0 = time.time()
2528	for iat,atom in enumerate(drawingData['Atoms']):
2529	x,y,z = atom[cx:cx+3]
2530	Bonds = atom[-2]
2531	Faces = atom[-1]
2532	try:
2533	atNum = generalData['AtomTypes'].index(atom[ct])
2534	except ValueError:
2535	atNum = -1
2536	CL = atom[cs+2]
2537	color = np.array(CL)/255.
2538	if iat in Ind:
2539	color = np.array(Gr)/255.
2540	radius = 0.5
2541	if atom[cs] != '':
2542	glLoadName(atom[-3])
2543	if 'balls' in atom[cs]:
2544	vdwScale = drawingData['vdwScale']
2545	ballScale = drawingData['ballScale']
2546	if atNum < 0:
2547	radius = 0.2
2548	elif 'H' == atom[ct]:
2549	if drawingData['showHydrogen']:
2550	if 'vdW' in atom[cs] and atNum >= 0:
2551	radius = vdwScale*generalData['vdWRadii'][atNum]
2552	else:
2553	radius = ballScale*drawingData['sizeH']
2554	else:
2555	radius = 0.0
2556	else:
2557	if 'vdW' in atom[cs]:
2558	radius = vdwScale*generalData['vdWRadii'][atNum]
2559	else:
2560	radius = ballScale*generalData['BondRadii'][atNum]
2561	RenderSphere(x,y,z,radius,color)
2562	if 'sticks' in atom[cs]:
2563	RenderBonds(x,y,z,Bonds,bondR,color)
2564	elif 'ellipsoids' in atom[cs]:
2565	RenderBonds(x,y,z,Bonds,bondR,color)
2566	if atom[cs+3] == 'A':
2567	Uij = atom[cs+5:cs+11]
2568	U = np.multiply(G2spc.Uij2U(Uij),GS)
2569	U = np.inner(Amat,np.inner(U,Amat).T)
2570	E,R = nl.eigh(U)
2571	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2572	E = np.sqrt(E)
2573	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2574	pass
2575	else:
2576	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2577	else:
2578	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2579	pass
2580	else:
2581	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2582	RenderSphere(x,y,z,radius,color)
2583	elif 'lines' in atom[cs]:
2584	radius = 0.1
2585	RenderLines(x,y,z,Bonds,color)
2586	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2587	elif atom[cs] == 'sticks':
2588	radius = 0.1
2589	RenderBonds(x,y,z,Bonds,bondR,color)
2590	elif atom[cs] == 'polyhedra':
2591	RenderPolyhedra(x,y,z,Faces,color)
2592	elif atom[cs] == 'backbone':
2593	if atom[ct-1].split()[0] in ['C','N']:
2594	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2595	BackboneColor.append(list(color))
2596
2597	if atom[cs+1] == 'type':
2598	RenderLabel(x,y,z,atom[ct],radius)
2599	elif atom[cs+1] == 'name':
2600	RenderLabel(x,y,z,atom[ct-1],radius)
2601	elif atom[cs+1] == 'number':
2602	RenderLabel(x,y,z,str(iat+1),radius)
2603	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2604	RenderLabel(x,y,z,atom[ct-4],radius)
2605	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2606	RenderLabel(x,y,z,atom[ct-3],radius)
2607	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2608	RenderLabel(x,y,z,atom[ct-2],radius)
2609	if Backbone:
2610	RenderBackbone(Backbone,BackboneColor,bondR)
2611	# print time.time()-time0
2612	Page.canvas.SwapBuffers()
2613
2614	def OnSize(event):
2615	Draw()
2616
2617	def OnFocus(event):
2618	Draw()
2619
2620	try:
2621	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2622	Page = self.G2plotNB.nb.GetPage(plotNum)
2623	except ValueError:
2624	Plot = self.G2plotNB.addOgl(generalData['Name'])
2625	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2626	Page = self.G2plotNB.nb.GetPage(plotNum)
2627	Page.views = False
2628	view = False
2629	altDown = False
2630	Page.SetFocus()
2631	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2632	choices=(' save as:','jpeg','tiff','bmp'))
2633	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2634	cb.SetValue(' save as:')
2635	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2636	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2637	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2638	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2639	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2640	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2641	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2642	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2643	Page.camera['position'] = drawingData['cameraPos']
2644	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2645	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2646	Page.canvas.SetCurrent()
2647	Draw()
2648

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