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source: trunk/GSASIIplot.py @ 273

Last change on this file since 273 was 273, checked in by vondreele, 13 years ago
output of S(Q) and G(R) as files for other use some effort to fix graphics tab behavior
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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2011-05-02 22:16:06 +0000 (Mon, 02 May 2011) $
4	# $Author: vondreele $
5	# $Revision: 273 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 273 2011-05-02 22:16:06Z 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	from OpenGL.GL import *
31	from OpenGL.GLU import *
32	from OpenGL.GLUT import *
33	from OpenGL.GLE import *
34	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
35	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
36
37	# useful degree trig functions
38	sind = lambda x: math.sin(x*math.pi/180.)
39	cosd = lambda x: math.cos(x*math.pi/180.)
40	tand = lambda x: math.tan(x*math.pi/180.)
41	asind = lambda x: 180.*math.asin(x)/math.pi
42	acosd = lambda x: 180.*math.acos(x)/math.pi
43	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
44	atand = lambda x: 180.*math.atan(x)/math.pi
45	# numpy versions
46	npsind = lambda x: np.sin(x*np.pi/180.)
47	npcosd = lambda x: np.cos(x*np.pi/180.)
48	npacosd = lambda x: 180.*np.arccos(x)/np.pi
49
50	class G2PlotMpl(wx.Panel):
51	def __init__(self,parent,id=-1,dpi=None,**kwargs):
52	wx.Panel.__init__(self,parent,id=id,**kwargs)
53	mpl.rcParams['legend.fontsize'] = 8
54	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
55	self.canvas = Canvas(self,-1,self.figure)
56	self.toolbar = Toolbar(self.canvas)
57
58	self.toolbar.Realize()
59
60	sizer=wx.BoxSizer(wx.VERTICAL)
61	sizer.Add(self.canvas,1,wx.EXPAND)
62	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
63	self.SetSizer(sizer)
64
65	class G2PlotOgl(wx.Panel):
66	def __init__(self,parent,id=-1,dpi=None,**kwargs):
67	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
68	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
69	self.camera = {}
70	sizer=wx.BoxSizer(wx.VERTICAL)
71	sizer.Add(self.canvas,1,wx.EXPAND)
72	self.SetSizer(sizer)
73
74	class G2Plot3D(wx.Panel):
75	def __init__(self,parent,id=-1,dpi=None,**kwargs):
76	wx.Panel.__init__(self,parent,id=id,**kwargs)
77	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
78	self.canvas = Canvas(self,-1,self.figure)
79	self.toolbar = Toolbar(self.canvas)
80
81	self.toolbar.Realize()
82
83	sizer=wx.BoxSizer(wx.VERTICAL)
84	sizer.Add(self.canvas,1,wx.EXPAND)
85	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
86	self.SetSizer(sizer)
87
88	class G2PlotNoteBook(wx.Panel):
89	def __init__(self,parent,id=-1):
90	wx.Panel.__init__(self,parent,id=id)
91	#so one can't delete a plot page!!
92	self.nb = wx.aui.AuiNotebook(self, \
93	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
94	sizer = wx.BoxSizer()
95	sizer.Add(self.nb,1,wx.EXPAND)
96	self.SetSizer(sizer)
97	self.status = parent.CreateStatusBar()
98	self.status.SetFieldsCount(2)
99	self.status.SetStatusWidths([150,-1])
100	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
101
102	self.plotList = []
103
104	def addMpl(self,name=""):
105	page = G2PlotMpl(self.nb)
106	self.nb.AddPage(page,name)
107
108	self.plotList.append(name)
109
110	return page.figure
111
112	def add3D(self,name=""):
113	page = G2Plot3D(self.nb)
114	self.nb.AddPage(page,name)
115
116	self.plotList.append(name)
117
118	return page.figure
119
120	def addOgl(self,name=""):
121	page = G2PlotOgl(self.nb)
122	self.nb.AddPage(page,name)
123
124	self.plotList.append(name)
125
126	return page.figure
127
128	def Delete(self,name):
129	try:
130	item = self.plotList.index(name)
131	del self.plotList[item]
132	self.nb.DeletePage(item)
133	except ValueError: #no plot of this name - do nothing
134	return
135
136	def clear(self):
137	while self.nb.GetPageCount():
138	self.nb.DeletePage(0)
139	self.plotList = []
140	self.status.DestroyChildren()
141
142	def Rename(self,oldName,newName):
143	try:
144	item = self.plotList.index(oldName)
145	self.plotList[item] = newName
146	self.nb.SetPageText(item,newName)
147	except ValueError: #no plot of this name - do nothing
148	return
149
150	def OnPageChanged(self,event):
151	if self.plotList:
152	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
153	self.status.DestroyChildren() #get rid of special stuff on status bar
154
155	def PlotSngl(self,newPlot=False):
156	from matplotlib.patches import Circle
157	global HKL,HKLF
158
159	def OnSCMotion(event):
160	xpos = event.xdata
161	if xpos:
162	xpos = round(xpos) #avoid out of frame mouse position
163	ypos = round(event.ydata)
164	zpos = Data['Layer']
165	if '100' in Data['Zone']:
166	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
167	elif '010' in Data['Zone']:
168	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
169	elif '001' in Data['Zone']:
170	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
171	Page.canvas.SetToolTipString(HKLtxt)
172	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
173
174	def OnSCPick(event):
175	zpos = Data['Layer']
176	pos = event.artist.center
177	if '100' in Data['Zone']:
178	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
179	hkl = np.array([zpos,pos[0],pos[1]])
180	elif '010' in Data['Zone']:
181	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
182	hkl = np.array([pos[0],zpos,pos[1]])
183	elif '001' in Data['Zone']:
184	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
185	hkl = np.array([pos[0],pos[1],zpos])
186	h,k,l = hkl
187	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
188	if len(hklf):
189	Fosq,sig,Fcsq = hklf[0]
190	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
191	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
192
193	def OnSCKeyPress(event):
194	print event.key
195
196	try:
197	plotNum = self.G2plotNB.plotList.index('Structure Factors')
198	Page = self.G2plotNB.nb.GetPage(plotNum)
199	if not newPlot:
200	Plot = Page.figure.gca() #get previous powder plot & get limits
201	xylim = Plot.get_xlim(),Plot.get_ylim()
202	Page.figure.clf()
203	Plot = Page.figure.gca() #get a fresh plot after clf()
204	except ValueError:
205	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
206	plotNum = self.G2plotNB.plotList.index('Structure Factors')
207	Page = self.G2plotNB.nb.GetPage(plotNum)
208	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
209	Page.canvas.mpl_connect('pick_event', OnSCPick)
210	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
211	Page.SetFocus()
212
213	Plot.set_aspect(aspect='equal')
214	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
215	Data = self.PatternTree.GetItemPyData( \
216	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
217	Type = Data['Type']
218	scale = Data['Scale']
219	HKLmax = Data['HKLmax']
220	HKLmin = Data['HKLmin']
221	FosqMax = Data['FoMax']
222	FoMax = math.sqrt(FosqMax)
223	ifFc = Data['ifFc']
224	xlabel = ['k, h=','h, k=','h, l=']
225	ylabel = ['l','l','k']
226	zones = ['100','010','001']
227	pzone = [[1,2],[0,2],[0,1]]
228	izone = zones.index(Data['Zone'])
229	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
230	HKL = []
231	HKLF = []
232	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
233	HKL.append(H)
234	HKLF.append([Fosq,sig,Fcsq])
235	if H[izone] == Data['Layer']:
236	B = 0
237	if Type == 'Fosq':
238	A = scale*Fosq/FosqMax
239	B = scale*Fcsq/FosqMax
240	C = abs(A-B)
241	elif Type == 'Fo':
242	A = scale*math.sqrt(max(0,Fosq))/FoMax
243	B = scale*math.sqrt(max(0,Fcsq))/FoMax
244	C = abs(A-B)
245	elif Type == '\|DFsq\|/sig':
246	A = abs(Fosq-Fcsq)/(scale*sig)
247	elif Type == '\|DFsq\|>sig':
248	A = abs(Fosq-Fcsq)/(scale*sig)
249	if A < 1.0: A = 0
250	elif Type == '\|DFsq\|>3sig':
251	A = abs(Fosq-Fcsq)/(scale*sig)
252	if A < 3.0: A = 0
253	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
254	if A > 0.0:
255	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
256	if B:
257	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
258	radius = C
259	if radius > 0:
260	if A > B:
261	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
262	else:
263	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
264	HKL = np.array(HKL,dtype=np.int)
265	HKLF = np.array(HKLF)
266	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
267	Plot.set_ylabel(ylabel[izone],fontsize=12)
268	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
269	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
270	if not newPlot:
271	Page.toolbar.push_current()
272	Plot.set_xlim(xylim[0])
273	Plot.set_ylim(xylim[1])
274	xylim = []
275	Page.toolbar.push_current()
276	Page.toolbar.draw()
277	else:
278	Page.canvas.draw()
279
280	def PlotPatterns(self,newPlot=False):
281	global HKL
282
283	def OnPick(event):
284	if self.itemPicked is not None: return
285	PatternId = self.PatternId
286	try:
287	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
288	except TypeError:
289	return
290	Parms = dict(zip(Names,Values))
291	try:
292	wave = Parms['Lam']
293	except KeyError:
294	wave = Parms['Lam1']
295	PickId = self.PickId
296	pick = event.artist
297	mouse = event.mouseevent
298	xpos = pick.get_xdata()
299	ypos = pick.get_ydata()
300	ind = event.ind
301	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
302	if self.PatternTree.GetItemText(PickId) == 'Peak List':
303	if ind.all() != [0]: #picked a data point
304	ins = [Parms[x] for x in ['U','V','W','X','Y','SH/L']]
305	if self.qPlot: #qplot - convert back to 2-theta
306	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
307	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
308	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
309	data = self.PatternTree.GetItemPyData(self.PickId)
310	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
311	data.append(XY)
312	G2pdG.UpdatePeakGrid(self,data)
313	PlotPatterns(self)
314	else: #picked a peak list line
315	self.itemPicked = pick
316	elif self.PatternTree.GetItemText(PickId) == 'Limits':
317	if ind.all() != [0]: #picked a data point
318	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
319	data = self.PatternTree.GetItemPyData(LimitId)
320	if self.qPlot: #qplot - convert back to 2-theta
321	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
322	if mouse.button==1:
323	data[1][0] = min(xy[0],data[1][1])
324	if mouse.button==3:
325	data[1][1] = max(xy[0],data[1][0])
326	self.PatternTree.SetItemPyData(LimitId,data)
327	G2pdG.UpdateLimitsGrid(self,data)
328	PlotPatterns(self)
329	else: #picked a limit line
330	self.itemPicked = pick
331
332	def OnPlotKeyPress(event):
333	newPlot = False
334	if event.key == 'w':
335	if self.Weight:
336	self.Weight = False
337	else:
338	self.Weight = True
339	print 'plot weighting:',self.Weight
340	elif event.key == 'n':
341	if self.Contour:
342	pass
343	else:
344	if self.logPlot:
345	self.logPlot = False
346	else:
347	self.Offset[0] = 0
348	self.logPlot = True
349	elif event.key == 'u':
350	if self.Contour:
351	self.Cmax = min(1.0,self.Cmax*1.2)
352	elif self.logPlot:
353	pass
354	elif self.Offset[0] < 100.:
355	self.Offset[0] += 1.
356	elif event.key == 'd':
357	if self.Contour:
358	self.Cmax = max(0.0,self.Cmax*0.8)
359	elif self.logPlot:
360	pass
361	elif self.Offset[0] > 0.:
362	self.Offset[0] -= 1.
363	elif event.key == 'l':
364	self.Offset[1] -= 1.
365	elif event.key == 'r':
366	self.Offset[1] += 1.
367	elif event.key == 'o':
368	self.Offset = [0,0]
369	elif event.key == 'c':
370	newPlot = True
371	if self.Contour:
372	self.Contour = False
373	else:
374	self.Contour = True
375	self.SinglePlot = False
376	self.Offset = [0.,0.]
377	elif event.key == 'q':
378	newPlot = True
379	if self.qPlot:
380	self.qPlot = False
381	else:
382	self.qPlot = True
383	elif event.key == 's':
384	if self.Contour:
385	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
386	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
387	if dlg.ShowModal() == wx.ID_OK:
388	sel = dlg.GetSelection()
389	self.ContourColor = choice[sel]
390	else:
391	self.ContourColor = 'Paired'
392	dlg.Destroy()
393	else:
394	if self.SinglePlot:
395	self.SinglePlot = False
396	else:
397	self.SinglePlot = True
398	elif event.key == '+':
399	if self.PickId:
400	self.PickId = False
401	elif event.key == 'i': #for smoothing contour plot
402	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
403	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
404	'mitchell','sinc','lanczos']
405	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
406	if dlg.ShowModal() == wx.ID_OK:
407	sel = dlg.GetSelection()
408	self.Interpolate = choice[sel]
409	else:
410	self.Interpolate = 'nearest'
411	dlg.Destroy()
412
413	PlotPatterns(self,newPlot=newPlot)
414
415	def OnKeyBox(event):
416	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('Powder Patterns'):
417	event.key = cb.GetValue()[0]
418	cb.SetValue(' key press')
419	OnPlotKeyPress(event)
420
421	def OnMotion(event):
422	xpos = event.xdata
423	if xpos: #avoid out of frame mouse position
424	ypos = event.ydata
425	Page.canvas.SetCursor(wx.CROSS_CURSOR)
426	try:
427	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
428	Parms = dict(zip(Names,Values))
429	try:
430	wave = Parms['Lam']
431	except KeyError:
432	wave = Parms['Lam1']
433	if self.qPlot:
434	xpos = 2.0asind(xposwave/(4*math.pi))
435	dsp = 0.0
436	if abs(xpos) > 0.: #avoid possible singularity at beam center
437	dsp = wave/(2.*sind(abs(xpos)/2.0))
438	if self.Contour:
439	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
440	else:
441	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
442	if self.itemPicked:
443	Page.canvas.SetToolTipString('%9.3f'%(xpos))
444	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
445	found = []
446	if len(HKL):
447	view = Page.toolbar._views.forward()[0][:2]
448	wid = view[1]-view[0]
449	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
450	if len(found):
451	h,k,l = found[0][:3]
452	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
453	else:
454	Page.canvas.SetToolTipString('')
455
456	except TypeError:
457	self.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
458
459	def OnRelease(event):
460	if self.itemPicked is None: return
461	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
462	Parms = dict(zip(Names,Values))
463	try:
464	wave = Parms['Lam']
465	except KeyError:
466	wave = Parms['Lam1']
467	xpos = event.xdata
468	if xpos: #avoid out of frame mouse position
469	lines = []
470	for line in self.Lines: lines.append(line.get_xdata()[0])
471	lineNo = lines.index(self.itemPicked.get_xdata()[0])
472	if lineNo in [0,1]:
473	LimitId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Limits')
474	data = self.PatternTree.GetItemPyData(LimitId)
475	# print 'limits',xpos
476	if self.qPlot:
477	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
478	else:
479	data[1][lineNo] = xpos
480	self.PatternTree.SetItemPyData(LimitId,data)
481	if self.PatternTree.GetItemText(self.PickId) == 'Limits':
482	G2pdG.UpdateLimitsGrid(self,data)
483	else:
484	PeakId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Peak List')
485	data = self.PatternTree.GetItemPyData(PeakId)
486	# print 'peaks',xpos
487	if event.button == 3:
488	del data[lineNo-2]
489	else:
490	if self.qPlot:
491	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
492	else:
493	data[lineNo-2][0] = xpos
494	self.PatternTree.SetItemPyData(PeakId,data)
495	G2pdG.UpdatePeakGrid(self,data)
496	PlotPatterns(self)
497	self.itemPicked = None
498
499	xylim = []
500	try:
501	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
502	Page = self.G2plotNB.nb.GetPage(plotNum)
503	if not newPlot:
504	Plot = Page.figure.gca() #get previous powder plot & get limits
505	xylim = Plot.get_xlim(),Plot.get_ylim()
506	Page.figure.clf()
507	Plot = Page.figure.gca() #get a fresh plot after clf()
508	except ValueError:
509	newPlot = True
510	self.Cmax = 1.0
511	Plot = self.G2plotNB.addMpl('Powder Patterns').gca()
512	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
513	Page = self.G2plotNB.nb.GetPage(plotNum)
514	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
515	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
516	Page.canvas.mpl_connect('pick_event', OnPick)
517	Page.canvas.mpl_connect('button_release_event', OnRelease)
518	Page.SetFocus()
519	self.G2plotNB.status.DestroyChildren()
520	if self.Contour:
521	Choice = (' key press','d: lower contour max','u: raise contour max',
522	'i: interpolation method','s: color scheme','c: contour off')
523	else:
524	if self.logPlot:
525	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
526	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
527	else:
528	Choice = (' key press','l: offset left','r: offset right','d: offset down',
529	'u: offset up','0: reset offset','n: log(I) on','c: contour on',
530	'q: toggle q plot','s: toggle single plot','+: no selection')
531	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
532	choices=Choice)
533	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
534	cb.SetValue(' key press')
535
536	PickId = self.PickId
537	PatternId = self.PatternId
538	colors=['b','g','r','c','m','k']
539	Lines = []
540	if self.SinglePlot:
541	Pattern = self.PatternTree.GetItemPyData(PatternId)
542	Pattern.append(self.PatternTree.GetItemText(PatternId))
543	PlotList = [Pattern,]
544	ParmList = [self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
545	self.PatternId, 'Instrument Parameters'))[1],]
546	else:
547	PlotList = []
548	ParmList = []
549	item, cookie = self.PatternTree.GetFirstChild(self.root)
550	while item:
551	if 'PWDR' in self.PatternTree.GetItemText(item):
552	Pattern = self.PatternTree.GetItemPyData(item)
553	if len(Pattern) < 3: # put name on end if needed
554	Pattern.append(self.PatternTree.GetItemText(item))
555	PlotList.append(Pattern)
556	ParmList.append(self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
557	item,'Instrument Parameters'))[1])
558	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
559	Ymax = 1.0
560	lenX = 0
561	HKL = np.array(self.HKL)
562	for Pattern in PlotList:
563	xye = Pattern[1]
564	Ymax = max(Ymax,max(xye[1]))
565	offset = self.Offset[0]*Ymax/100.0
566	Title = 'Powder Patterns: '+os.path.split(self.GSASprojectfile)[1]
567	if self.logPlot:
568	Title = 'log('+Title+')'
569	Plot.set_title(Title)
570	if self.qPlot:
571	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
572	else:
573	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
574	Plot.set_ylabel('Intensity',fontsize=12)
575	if self.Contour:
576	ContourZ = []
577	ContourY = []
578	Nseq = 0
579	for N,Pattern in enumerate(PlotList):
580	Parms = ParmList[N]
581	ifpicked = False
582	LimitId = 0
583	xye = np.array(Pattern[1])
584	if PickId:
585	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
586	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
587	if self.qPlot:
588	Id = G2gd.GetPatternTreeItemId(self,self.root, Pattern[2])
589	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
590	else:
591	X = xye[0]
592	if not lenX:
593	lenX = len(X)
594	Y = xye[1]+offset*N
595	if LimitId:
596	limits = np.array(self.PatternTree.GetItemPyData(LimitId))
597	if self.qPlot:
598	limits = 4np.pinpsind(limits/2.0)/Parms[1]
599	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
600	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
601	if self.Contour:
602
603	if lenX == len(X):
604	ContourY.append(N)
605	ContourZ.append(Y)
606	ContourX = X
607	Nseq += 1
608	Plot.set_ylabel('Data sequence',fontsize=12)
609	else:
610	X += self.Offset[1].005N
611	if ifpicked:
612	Z = xye[3]+offset*N
613	W = xye[4]+offset*N
614	D = xye[5]+offsetN-Ymax.02
615	if self.Weight:
616	W2 = np.sqrt(xye[2])
617	D = W2-Ymax.02
618	if self.logPlot:
619	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
620	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
621	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
622	else:
623	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
624	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
625	Plot.plot(X,W,colors[(N+2)%6],picker=False)
626	Plot.plot(X,D,colors[(N+3)%6],picker=False)
627	Plot.axhline(0.,color=wx.BLACK)
628	Page.canvas.SetToolTipString('')
629	if self.PatternTree.GetItemText(PickId) == 'Peak List':
630	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
631	Page.canvas.SetToolTipString(tip)
632	data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List'))
633	for item in data:
634	if self.qPlot:
635	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
636	else:
637	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
638	if self.PatternTree.GetItemText(PickId) == 'Limits':
639	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
640	Page.canvas.SetToolTipString(tip)
641	data = self.LimitsTable.GetData()
642	else:
643	if self.logPlot:
644	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
645	else:
646	Plot.plot(X,Y,colors[N%6],picker=False)
647	if PickId and self.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
648	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1::2]
649	Parms = dict(zip(Names,Values))
650	try:
651	wave = Parms['Lam']
652	except KeyError:
653	wave = Parms['Lam1']
654	peaks = np.array((self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))))
655	for peak in peaks:
656	if self.qPlot:
657	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
658	else:
659	Plot.axvline(peak[0],color='b')
660	for hkl in self.HKL:
661	if self.qPlot:
662	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
663	else:
664	Plot.axvline(hkl[5],color='r',dashes=(5,5))
665	if self.Contour:
666	acolor = mpl.cm.get_cmap(self.ContourColor)
667	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
668	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
669	Page.figure.colorbar(Img)
670	else:
671	self.Lines = Lines
672	if not newPlot:
673	Page.toolbar.push_current()
674	Plot.set_xlim(xylim[0])
675	Plot.set_ylim(xylim[1])
676	xylim = []
677	Page.toolbar.push_current()
678	Page.toolbar.draw()
679	else:
680	Page.canvas.draw()
681	self.Pwdr = True
682
683	def PlotISFG(self,newPlot=False,type=''):
684	if not type:
685	type = self.G2plotNB.plotList[self.G2plotNB.nb.GetSelection()]
686	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
687	return
688	superMinusOne = unichr(0xaf)+unichr(0xb9)
689
690	def OnPlotKeyPress(event):
691	newPlot = False
692	if event.key == 'u':
693	if self.Contour:
694	self.Cmax = min(1.0,self.Cmax*1.2)
695	elif self.Offset[0] < 100.:
696	self.Offset[0] += 1.
697	elif event.key == 'd':
698	if self.Contour:
699	self.Cmax = max(0.0,self.Cmax*0.8)
700	elif self.Offset[0] > 0.:
701	self.Offset[0] -= 1.
702	elif event.key == 'l':
703	self.Offset[1] -= 1.
704	elif event.key == 'r':
705	self.Offset[1] += 1.
706	elif event.key == 'o':
707	self.Offset = [0,0]
708	elif event.key == 'c':
709	newPlot = True
710	if self.Contour:
711	self.Contour = False
712	else:
713	self.Contour = True
714	self.SinglePlot = False
715	self.Offset = [0.,0.]
716	elif event.key == 's':
717	if self.Contour:
718	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
719	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
720	if dlg.ShowModal() == wx.ID_OK:
721	sel = dlg.GetSelection()
722	self.ContourColor = choice[sel]
723	else:
724	self.ContourColor = 'Paired'
725	dlg.Destroy()
726	else:
727	if self.SinglePlot:
728	self.SinglePlot = False
729	else:
730	self.SinglePlot = True
731	elif event.key == 'i': #for smoothing contour plot
732	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
733	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
734	'mitchell','sinc','lanczos']
735	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
736	if dlg.ShowModal() == wx.ID_OK:
737	sel = dlg.GetSelection()
738	self.Interpolate = choice[sel]
739	else:
740	self.Interpolate = 'nearest'
741	dlg.Destroy()
742	elif event.key == 't' and not self.Contour:
743	if self.Legend:
744	self.Legend = False
745	else:
746	self.Legend = True
747
748
749	PlotISFG(self,newPlot=newPlot,type=type)
750
751	def OnKeyBox(event):
752	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index(type):
753	event.key = cb.GetValue()[0]
754	cb.SetValue(' key press')
755	OnPlotKeyPress(event)
756
757	def OnMotion(event):
758	xpos = event.xdata
759	if xpos: #avoid out of frame mouse position
760	ypos = event.ydata
761	Page.canvas.SetCursor(wx.CROSS_CURSOR)
762	try:
763	if self.Contour:
764	self.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
765	else:
766	self.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
767	except TypeError:
768	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
769
770	xylim = []
771	try:
772	plotNum = self.G2plotNB.plotList.index(type)
773	Page = self.G2plotNB.nb.GetPage(plotNum)
774	if not newPlot:
775	Plot = Page.figure.gca() #get previous plot & get limits
776	xylim = Plot.get_xlim(),Plot.get_ylim()
777	Page.figure.clf()
778	Plot = Page.figure.gca()
779	except ValueError:
780	newPlot = True
781	self.Cmax = 1.0
782	Plot = self.G2plotNB.addMpl(type).gca()
783	plotNum = self.G2plotNB.plotList.index(type)
784	Page = self.G2plotNB.nb.GetPage(plotNum)
785	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
786	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
787
788	Page.SetFocus()
789	self.G2plotNB.status.DestroyChildren()
790	if self.Contour:
791	Choice = (' key press','d: lower contour max','u: raise contour max',
792	'i: interpolation method','s: color scheme','c: contour off')
793	else:
794	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
795	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
796	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
797	choices=Choice)
798	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
799	cb.SetValue(' key press')
800	PatternId = self.PatternId
801	PickId = self.PickId
802	Plot.set_title(type)
803	if type == 'G(R)':
804	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
805	else:
806	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
807	Plot.set_ylabel(r''+type,fontsize=14)
808	colors=['b','g','r','c','m','k']
809	name = self.PatternTree.GetItemText(PatternId)[4:]
810	Pattern = []
811	if self.SinglePlot:
812	name = self.PatternTree.GetItemText(PatternId)
813	name = type+name[4:]
814	Id = G2gd.GetPatternTreeItemId(self,PatternId,name)
815	Pattern = self.PatternTree.GetItemPyData(Id)
816	if Pattern:
817	Pattern.append(name)
818	PlotList = [Pattern,]
819	else:
820	PlotList = []
821	item, cookie = self.PatternTree.GetFirstChild(self.root)
822	while item:
823	if 'PDF' in self.PatternTree.GetItemText(item):
824	name = type+self.PatternTree.GetItemText(item)[4:]
825	Id = G2gd.GetPatternTreeItemId(self,item,name)
826	Pattern = self.PatternTree.GetItemPyData(Id)
827	if Pattern:
828	Pattern.append(name)
829	PlotList.append(Pattern)
830	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
831	PDFdata = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'PDF Controls'))
832	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
833	Xb = [0.,10.]
834	Yb = [0.,-40.np.pinumbDen]
835	Ymax = 1.0
836	lenX = 0
837	for Pattern in PlotList:
838	xye = Pattern[1]
839	Ymax = max(Ymax,max(xye[1]))
840	offset = self.Offset[0]*Ymax/100.0
841	if self.Contour:
842	ContourZ = []
843	ContourY = []
844	Nseq = 0
845	for N,Pattern in enumerate(PlotList):
846	xye = Pattern[1]
847	if PickId:
848	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
849	X = xye[0]
850	if not lenX:
851	lenX = len(X)
852	Y = xye[1]+offset*N
853	if self.Contour:
854	if lenX == len(X):
855	ContourY.append(N)
856	ContourZ.append(Y)
857	ContourX = X
858	Nseq += 1
859	Plot.set_ylabel('Data sequence',fontsize=12)
860	else:
861	X = xye[0]+self.Offset[1].005N
862	if ifpicked:
863	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
864	Page.canvas.SetToolTipString('')
865	else:
866	if self.Legend:
867	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
868	else:
869	Plot.plot(X,Y,colors[N%6],picker=False)
870	if type == 'G(R)':
871	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
872	elif type == 'F(Q)':
873	Plot.axhline(0.,color=wx.BLACK)
874	elif type == 'S(Q)':
875	Plot.axhline(1.,color=wx.BLACK)
876	if self.Contour:
877	acolor = mpl.cm.get_cmap(self.ContourColor)
878	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
879	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
880	Page.figure.colorbar(Img)
881	elif self.Legend:
882	Plot.legend(loc='best')
883	if not newPlot:
884	Page.toolbar.push_current()
885	Plot.set_xlim(xylim[0])
886	Plot.set_ylim(xylim[1])
887	xylim = []
888	Page.toolbar.push_current()
889	Page.toolbar.draw()
890	else:
891	Page.canvas.draw()
892
893	def PlotXY(self,XY,newPlot=False,type=''):
894	#simple plot of xy data
895
896	def OnMotion(event):
897	xpos = event.xdata
898	if xpos: #avoid out of frame mouse position
899	ypos = event.ydata
900	Page.canvas.SetCursor(wx.CROSS_CURSOR)
901	try:
902	self.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
903	except TypeError:
904	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
905
906	try:
907	plotNum = self.G2plotNB.plotList.index(type)
908	Page = self.G2plotNB.nb.GetPage(plotNum)
909	if not newPlot:
910	Plot = Page.figure.gca()
911	xylim = Plot.get_xlim(),Plot.get_ylim()
912	Page.figure.clf()
913	Plot = Page.figure.gca()
914	except ValueError:
915	newPlot = True
916	Plot = self.G2plotNB.addMpl(type).gca()
917	plotNum = self.G2plotNB.plotList.index(type)
918	Page = self.G2plotNB.nb.GetPage(plotNum)
919	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
920
921	Page.SetFocus()
922	self.G2plotNB.status.DestroyChildren()
923	Plot.set_title(type)
924	Plot.set_xlabel(r'X',fontsize=14)
925	Plot.set_ylabel(r''+type,fontsize=14)
926	colors=['b','g','r','c','m','k']
927	Ymax = 1.0
928	lenX = 0
929	X,Y = XY[:2]
930	Ymax = max(Ymax,max(Y))
931	Plot.plot(X,Y,'k',picker=False)
932	if not newPlot:
933	Page.toolbar.push_current()
934	Plot.set_xlim(xylim[0])
935	Plot.set_ylim(xylim[1])
936	xylim = []
937	Page.toolbar.push_current()
938	Page.toolbar.draw()
939	else:
940	Page.canvas.draw()
941
942	def PlotPowderLines(self):
943	global HKL
944
945	def OnMotion(event):
946	xpos = event.xdata
947	if xpos: #avoid out of frame mouse position
948	Page.canvas.SetCursor(wx.CROSS_CURSOR)
949	self.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
950	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
951	found = []
952	if len(HKL):
953	view = Page.toolbar._views.forward()[0][:2]
954	wid = view[1]-view[0]
955	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
956	if len(found):
957	h,k,l = found[0][:3]
958	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
959	else:
960	Page.canvas.SetToolTipString('')
961
962	try:
963	plotNum = self.G2plotNB.plotList.index('Powder Lines')
964	Page = self.G2plotNB.nb.GetPage(plotNum)
965	Page.figure.clf()
966	Plot = Page.figure.gca()
967	except ValueError:
968	Plot = self.G2plotNB.addMpl('Powder Lines').gca()
969	plotNum = self.G2plotNB.plotList.index('Powder Lines')
970	Page = self.G2plotNB.nb.GetPage(plotNum)
971	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
972
973	Page.SetFocus()
974	Plot.set_title('Powder Pattern Lines')
975	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
976	PickId = self.PickId
977	PatternId = self.PatternId
978	peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))
979	for peak in peaks:
980	Plot.axvline(peak[0],color='b')
981	HKL = np.array(self.HKL)
982	for hkl in self.HKL:
983	Plot.axvline(hkl[5],color='r',dashes=(5,5))
984	xmin = peaks[0][0]
985	xmax = peaks[-1][0]
986	delt = xmax-xmin
987	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
988	Plot.set_xlim(xlim)
989	Page.canvas.draw()
990
991	def PlotPeakWidths(self):
992	PatternId = self.PatternId
993	limitID = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
994	if limitID:
995	limits = self.PatternTree.GetItemPyData(limitID)
996	else:
997	return
998	instParms = self.PatternTree.GetItemPyData( \
999	G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))
1000	if instParms[0][0] == 'PXC':
1001	lam = instParms[1][1]
1002	if len(instParms[1]) == 13:
1003	GU,GV,GW,LX,LY = instParms[0][6:11]
1004	else:
1005	GU,GV,GW,LX,LY = instParms[0][4:9]
1006	peakID = G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List')
1007	if peakID:
1008	peaks = self.PatternTree.GetItemPyData(peakID)
1009	else:
1010	peaks = []
1011
1012	try:
1013	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1014	Page = self.G2plotNB.nb.GetPage(plotNum)
1015	Page.figure.clf()
1016	Plot = Page.figure.gca()
1017	except ValueError:
1018	Plot = self.G2plotNB.addMpl('Peak Widths').gca()
1019	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1020	Page = self.G2plotNB.nb.GetPage(plotNum)
1021	Page.SetFocus()
1022
1023	Page.canvas.SetToolTipString('')
1024	colors=['b','g','r','c','m','k']
1025	Xmin,Xmax = limits[1]
1026	Xmin = min(0.5,max(Xmin,1))
1027	Xmin /= 2
1028	Xmax /= 2
1029	nPts = 100
1030	delt = (Xmax-Xmin)/nPts
1031	thetas = []
1032	for i in range(nPts):
1033	thetas.append(Xmin+i*delt)
1034	X = []
1035	Y = []
1036	Z = []
1037	W = []
1038	V = []
1039	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1040	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1041	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.)
1042	gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1043	for theta in thetas:
1044	X.append(4.0math.pisind(theta)/lam) #q
1045	s = sig(theta,GU,GV,GW)
1046	g = gam(theta,LX,LY)
1047	G = gamFW(g,s)
1048	H = gamFW2(g,s)
1049	Y.append(s/tand(theta))
1050	Z.append(g/tand(theta))
1051	W.append(G/tand(theta))
1052	V.append(H/tand(theta))
1053	Plot.set_title('Instrument and sample peak widths')
1054	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1055	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1056	Plot.plot(X,Y,color='r',label='Gaussian')
1057	Plot.plot(X,Z,color='g',label='Lorentzian')
1058	Plot.plot(X,W,color='b',label='G+L')
1059	Plot.plot(X,V,color='k',label='G+L2')
1060	X = []
1061	Y = []
1062	Z = []
1063	W = []
1064	V = []
1065	for peak in peaks:
1066	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1067	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1068	g = peak[6]*math.pi/18000.
1069	G = gamFW(g,s)
1070	H = gamFW2(g,s)
1071	Y.append(s/tand(peak[0]/2.))
1072	Z.append(g/tand(peak[0]/2.))
1073	W.append(G/tand(peak[0]/2.))
1074	V.append(H/tand(peak[0]/2.))
1075	Plot.plot(X,Y,'+',color='r',label='G peak')
1076	Plot.plot(X,Z,'+',color='g',label='L peak')
1077	Plot.plot(X,W,'+',color='b',label='G+L peak')
1078	Plot.plot(X,V,'+',color='k',label='G+L2 peak')
1079	Plot.legend(loc='best')
1080	Page.canvas.draw()
1081
1082	def PlotStrain(self,data):
1083	# in this instance data is for a phase
1084	PatternId = self.PatternId
1085	generalData = data['General']
1086	SGData = generalData['SGData']
1087	MuStrKeys = G2spc.MustrainNames(SGData)
1088	cell = generalData['Cell'][1:]
1089	A,B = G2lat.cell2AB(cell[:6])
1090	Vol = cell[6]
1091	useList = data['Histograms']
1092	numPlots = len(useList)
1093
1094	try:
1095	plotNum = self.G2plotNB.plotList.index('Microstrain')
1096	Page = self.G2plotNB.nb.GetPage(plotNum)
1097	Page.figure.clf()
1098	Plot = mp3d.Axes3D(Page.figure)
1099	except ValueError:
1100	Plot = mp3d.Axes3D(self.G2plotNB.add3D('Microstrain'))
1101	plotNum = self.G2plotNB.plotList.index('Microstrain')
1102	Page = self.G2plotNB.nb.GetPage(plotNum)
1103	Page.SetFocus()
1104	self.G2plotNB.status.SetStatusText('Adjust frame size to get desired aspect ratio',1)
1105
1106	for item in useList:
1107	if useList[item]['Show']:
1108	muStrain = useList[item]['Mustrain']
1109	PHI = np.linspace(0.,360.,30,True)
1110	PSI = np.linspace(0.,180.,30,True)
1111	X = np.outer(npsind(PHI),npsind(PSI))
1112	Y = np.outer(npcosd(PHI),npsind(PSI))
1113	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1114	if muStrain[0] == 'isotropic':
1115	muiso = muStrain[1][0]*math.pi/0.018 #centidegrees to radians!
1116	X *= muiso
1117	Y *= muiso
1118	Z *= muiso
1119
1120	elif muStrain[0] == 'uniaxial':
1121	def uniaxMustrain(xyz,muiso,muaniso,axes):
1122	cp = abs(np.dot(xyz,axes))
1123	S = muiso+muaniso*cp
1124	return Sxyzmath.pi/0.018 #centidegrees to radians!
1125	muiso,muaniso = muStrain[1][:2]
1126	axes = np.inner(A,np.array(muStrain[3]))
1127	axes /= nl.norm(axes)
1128	Shkl = np.array(muStrain[1])
1129	Shape = X.shape[0]
1130	XYZ = np.dstack((X,Y,Z))
1131	XYZ = np.nan_to_num(np.apply_along_axis(uniaxMustrain,2,XYZ,muiso,muaniso,axes))
1132	X,Y,Z = np.dsplit(XYZ,3)
1133	X = X[:,:,0]
1134	Y = Y[:,:,0]
1135	Z = Z[:,:,0]
1136
1137	elif muStrain[0] == 'generalized':
1138	def genMustrain(xyz,SGData,A,Shkl):
1139	uvw = np.inner(A.T,xyz)
1140	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1141	sum = np.sqrt(np.sum(np.multiply(Shkl,Strm)))*math.pi/0.018 #centidegrees to radians!
1142	return sum*xyz
1143	Shkl = np.array(muStrain[4])
1144	if np.any(Shkl):
1145	Shape = X.shape[0]
1146	XYZ = np.dstack((X,Y,Z))
1147	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1148	X,Y,Z = np.dsplit(XYZ,3)
1149	X = X[:,:,0]
1150	Y = Y[:,:,0]
1151	Z = Z[:,:,0]
1152
1153	if np.any(X) and np.any(Y) and np.any(Z):
1154	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g')
1155
1156	Plot.set_xlabel('X')
1157	Plot.set_ylabel('Y')
1158	Plot.set_zlabel('Z')
1159	Page.canvas.draw()
1160
1161	def PlotExposedImage(self,newPlot=False,event=None):
1162	plotNo = self.G2plotNB.nb.GetSelection()
1163	if self.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1164	PlotImage(self,newPlot,event,newImage=True)
1165	elif self.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1166	PlotIntegration(self,newPlot,event)
1167
1168	def PlotImage(self,newPlot=False,event=None,newImage=True):
1169	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1170	import numpy.ma as ma
1171	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1172	global Data,Masks
1173	colors=['b','g','r','c','m','k']
1174	Data = self.PatternTree.GetItemPyData(
1175	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1176	Masks = self.PatternTree.GetItemPyData(
1177	G2gd.GetPatternTreeItemId(self,self.Image, 'Masks'))
1178
1179	def OnImMotion(event):
1180	Page.canvas.SetToolTipString('')
1181	sizexy = Data['size']
1182	if event.xdata and event.ydata: #avoid out of frame errors
1183	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1184	item = self.itemPicked
1185	pixelSize = Data['pixelSize']
1186	scalex = 1000./pixelSize[0]
1187	scaley = 1000./pixelSize[1]
1188	if item and self.PatternTree.GetItemText(self.PickId) == 'Image Controls':
1189	if 'Text' in str(item):
1190	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1191	else:
1192	xcent,ycent = Data['center']
1193	xpos = event.xdata-xcent
1194	ypos = event.ydata-ycent
1195	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1196	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1197	Page.canvas.SetToolTipString('%6d deg'%(azm))
1198	elif 'line1' in str(item) or 'line2' in str(item):
1199	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1200	else:
1201	xpos = event.xdata
1202	ypos = event.ydata
1203	xpix = xpos*scalex
1204	ypix = ypos*scaley
1205	Int = 0
1206	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1207	Int = self.ImageZ[ypix][xpix]
1208	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1209	Q = 2.*math.pi/dsp
1210	if self.setPoly:
1211	self.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1212	else:
1213	self.G2plotNB.status.SetFields(\
1214	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1215
1216	def OnImPlotKeyPress(event):
1217	try:
1218	PickName = self.PatternTree.GetItemText(self.PickId)
1219	except TypeError:
1220	return
1221	if PickName == 'Masks':
1222	Xpos = event.xdata
1223	if not Xpos: #got point out of frame
1224	return
1225	Ypos = event.ydata
1226	if event.key == 's':
1227	Masks['Points'].append([Xpos,Ypos,1.])
1228	elif event.key == 'r':
1229	tth = G2img.GetTth(Xpos,Ypos,Data)
1230	Masks['Rings'].append([tth,0.1])
1231	elif event.key == 'a':
1232	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1233	azm = int(azm)
1234	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1235	elif event.key == 'p':
1236	self.setPoly = True
1237	Masks['Polygons'].append([])
1238	self.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1239	G2imG.UpdateMasks(self,Masks)
1240	elif PickName == 'Image Controls':
1241	if event.key == 'c':
1242	Xpos = event.xdata
1243	if not Xpos: #got point out of frame
1244	return
1245	Ypos = event.ydata
1246	dlg = wx.MessageDialog(self,'Are you sure you want to change the center?',
1247	'Center change',style=wx.OK\|wx.CANCEL)
1248	try:
1249	if dlg.ShowModal() == wx.ID_OK:
1250	print 'move center to: ',Xpos,Ypos
1251	Data['center'] = [Xpos,Ypos]
1252	G2imG.UpdateImageControls(self,Data,Masks)
1253	finally:
1254	dlg.Destroy()
1255	elif event.key == 'l':
1256	if self.logPlot:
1257	self.logPlot = False
1258	else:
1259	self.logPlot = True
1260	PlotImage(self,newImage=True)
1261
1262	def OnKeyBox(event):
1263	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('2D Powder Image'):
1264	event.key = cb.GetValue()[0]
1265	cb.SetValue(' key press')
1266	if event.key in 'l':
1267	OnImPlotKeyPress(event)
1268
1269	def OnImPick(event):
1270	if self.PatternTree.GetItemText(self.PickId) not in ['Image Controls','Masks']:
1271	return
1272	if self.setPoly:
1273	polygon = Masks['Polygons'][-1]
1274	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1275	if xpos and ypos: #point inside image
1276	if len(polygon) > 2 and event.mouseevent.button == 3:
1277	x0,y0 = polygon[0]
1278	polygon.append([x0,y0])
1279	self.setPoly = False
1280	self.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1281	else:
1282	self.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1283	polygon.append([xpos,ypos])
1284	G2imG.UpdateMasks(self,Masks)
1285	else:
1286	if self.itemPicked is not None: return
1287	self.itemPicked = event.artist
1288	self.mousePicked = event.mouseevent
1289
1290	def OnImRelease(event):
1291	try:
1292	PickName = self.PatternTree.GetItemText(self.PickId)
1293	except TypeError:
1294	return
1295	if PickName not in ['Image Controls','Masks']:
1296	return
1297	pixelSize = Data['pixelSize']
1298	scalex = 1000./pixelSize[0]
1299	scaley = 1000./pixelSize[1]
1300	pixLimit = Data['pixLimit']
1301	if self.itemPicked is None and PickName == 'Image Controls':
1302	# sizexy = Data['size']
1303	Xpos = event.xdata
1304	if not (Xpos and self.ifGetRing): #got point out of frame
1305	return
1306	Ypos = event.ydata
1307	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1308	if event.button == 1:
1309	Xpix = Xpos*scalex
1310	Ypix = Ypos*scaley
1311	xpos,ypos,I,J = G2img.ImageLocalMax(self.ImageZ,pixLimit,Xpix,Ypix)
1312	if I and J:
1313	xpos += .5 #shift to pixel center
1314	ypos += .5
1315	xpos /= scalex #convert to mm
1316	ypos /= scaley
1317	Data['ring'].append([xpos,ypos])
1318	elif event.button == 3:
1319	print 'LB shift'
1320	self.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1321	if G2img.ImageCalibrate(self,Data):
1322	self.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1323	print 'Calibration successful'
1324	else:
1325	self.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1326	print 'Calibration failed'
1327	self.ifGetRing = False
1328	G2imG.UpdateImageControls(self,Data,Masks)
1329	return
1330	PlotImage(self,newImage=False)
1331	return
1332	else:
1333	xpos = event.xdata
1334	if xpos: #avoid out of frame mouse position
1335	ypos = event.ydata
1336	if self.ifGetRing: #delete a calibration ring pick
1337	xypos = [xpos,ypos]
1338	rings = Data['ring']
1339	for ring in rings:
1340	if np.allclose(ring,xypos,.01,0):
1341	rings.remove(ring)
1342	else:
1343	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1344	itemPicked = str(self.itemPicked)
1345	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1346	if 'line1' in itemPicked:
1347	Data['IOtth'][0] = max(tth,0.001)
1348	elif 'line2' in itemPicked:
1349	Data['IOtth'][1] = tth
1350	elif 'line3' in itemPicked:
1351	Data['LRazimuth'][0] = int(azm)
1352	if Data['fullIntegrate']:
1353	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1354	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1355	Data['LRazimuth'][1] = int(azm)
1356
1357	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1358	Data['LRazimuth'][0] -= 360
1359
1360	azLim = np.array(Data['LRazimuth'])
1361	if np.any(azLim>360):
1362	azLim -= 360
1363	Data['LRazimuth'] = list(azLim)
1364
1365	if Data['IOtth'][0] > Data['IOtth'][1]:
1366	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1367
1368	self.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1369	self.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1370	self.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1371	self.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1372	elif 'Circle' in itemPicked and PickName == 'Masks':
1373	spots = Masks['Points']
1374	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1375	newPos = np.array([float(newPos[0]),float(newPos[1])])
1376	for spot in spots:
1377	if np.allclose(np.array([spot[:2]]),newPos):
1378	spot[:2] = xpos,ypos
1379	G2imG.UpdateMasks(self,Masks)
1380	elif 'Line2D' in itemPicked and PickName == 'Masks':
1381	Obj = self.itemPicked.findobj()
1382	rings = Masks['Rings']
1383	arcs = Masks['Arcs']
1384	polygons = Masks['Polygons']
1385	for ring in self.ringList:
1386	if Obj == ring[0]:
1387	rN = ring[1]
1388	if ring[2] == 'o':
1389	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1390	else:
1391	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1392	for arc in self.arcList:
1393	if Obj == arc[0]:
1394	aN = arc[1]
1395	if arc[2] == 'o':
1396	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1397	elif arc[2] == 'i':
1398	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1399	elif arc[2] == 'l':
1400	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1401	else:
1402	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1403	for poly in self.polyList:
1404	if Obj == poly[0]:
1405	ind = self.itemPicked.contains(self.mousePicked)[1]['ind'][0]
1406	oldPos = np.array([self.mousePicked.xdata,self.mousePicked.ydata])
1407	pN = poly[1]
1408	for i,xy in enumerate(polygons[pN]):
1409	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1410	polygons[pN][i] = xpos,ypos
1411	G2imG.UpdateMasks(self,Masks)
1412	# else: #keep for future debugging
1413	# print str(self.itemPicked),event.xdata,event.ydata,event.button
1414	PlotImage(self,newImage=True)
1415	self.itemPicked = None
1416
1417	try:
1418	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1419	Page = self.G2plotNB.nb.GetPage(plotNum)
1420	if not newPlot:
1421	Plot = Page.figure.gca() #get previous powder plot & get limits
1422	xylim = Plot.get_xlim(),Plot.get_ylim()
1423	if newImage:
1424	Page.figure.clf()
1425	Plot = Page.figure.gca() #get a fresh plot after clf()
1426
1427	except ValueError:
1428	Plot = self.G2plotNB.addMpl('2D Powder Image').gca()
1429	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1430	Page = self.G2plotNB.nb.GetPage(plotNum)
1431	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1432	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1433	Page.canvas.mpl_connect('pick_event', OnImPick)
1434	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1435	xylim = []
1436	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1437	Page.SetFocus()
1438	Title = self.PatternTree.GetItemText(self.Image)[4:]
1439	self.G2plotNB.status.DestroyChildren()
1440	if self.logPlot:
1441	Title = 'log('+Title+')'
1442	Plot.set_title(Title)
1443	try:
1444	if self.PatternTree.GetItemText(self.PickId) in ['Image Controls',]:
1445	if self.logPlot:
1446	Choice = (' key press','l: log(I) off')
1447	else:
1448	Choice = (' key press','l: log(I) on')
1449	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1450	choices=Choice)
1451	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1452	cb.SetValue(' key press')
1453	except TypeError:
1454	pass
1455	size,imagefile = self.PatternTree.GetItemPyData(self.Image)
1456	if imagefile != self.oldImagefile:
1457	imagefile = G2IO.CheckImageFile(self,imagefile)
1458	if not imagefile:
1459	self.G2plotNB.Delete('2D Powder Image')
1460	return
1461	self.PatternTree.SetItemPyData(self.Image,[size,imagefile])
1462	self.ImageZ = G2IO.GetImageData(self,imagefile,imageOnly=True)
1463	# print self.ImageZ.shape,self.ImageZ.size,Data['size'] #might be useful debugging line
1464	self.oldImagefile = imagefile
1465
1466	imScale = 1
1467	if len(self.ImageZ) > 1024:
1468	imScale = len(self.ImageZ)/1024
1469	sizexy = Data['size']
1470	pixelSize = Data['pixelSize']
1471	scalex = 1000./pixelSize[0]
1472	scaley = 1000./pixelSize[1]
1473	Xmax = sizexy[0]*pixelSize[0]/1000.
1474	Ymax = sizexy[1]*pixelSize[1]/1000.
1475	xlim = (0,Xmax)
1476	ylim = (Ymax,0)
1477	Imin,Imax = Data['range'][1]
1478	acolor = mpl.cm.get_cmap(Data['color'])
1479	xcent,ycent = Data['center']
1480	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1481	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1482	#do threshold mask - "real" mask - others are just bondaries
1483	Zlim = Masks['Thresholds'][1]
1484	wx.BeginBusyCursor()
1485	try:
1486
1487	if newImage:
1488	MA = ma.masked_greater(ma.masked_less(self.ImageZ,Zlim[0]),Zlim[1])
1489	MaskA = ma.getmaskarray(MA)
1490	A = G2img.ImageCompress(MA,imScale)
1491	AM = G2img.ImageCompress(MaskA,imScale)
1492	if self.logPlot:
1493	A = np.log(A)
1494	AM = np.log(AM)
1495	Imin,Imax = [np.amin(A),np.amax(A)]
1496	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
1497	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Xmax,0])
1498	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
1499	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
1500	if self.setPoly:
1501	Img.set_picker(True)
1502
1503	Plot.plot(xcent,ycent,'x')
1504	if Data['showLines']:
1505	LRAzim = Data['LRazimuth'] #NB: integers
1506	Nazm = Data['outAzimuths']
1507	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
1508	AzmthOff = Data['azmthOff']
1509	IOtth = Data['IOtth']
1510	wave = Data['wavelength']
1511	dspI = wave/(2.0*sind(IOtth[0]/2.0))
1512	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
1513	dspO = wave/(2.0*sind(IOtth[1]/2.0))
1514	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
1515	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
1516	if ellI:
1517	xyI = []
1518	for azm in Azm:
1519	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
1520	xyI = np.array(xyI)
1521	arcxI,arcyI = xyI.T
1522	Plot.plot(arcxI,arcyI,picker=3)
1523	if ellO:
1524	xyO = []
1525	for azm in Azm:
1526	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
1527	xyO = np.array(xyO)
1528	arcxO,arcyO = xyO.T
1529	Plot.plot(arcxO,arcyO,picker=3)
1530	if ellO and ellI:
1531	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
1532	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
1533	for i in range(Nazm):
1534	cake = LRAzim[0]+i*delAzm
1535	ind = np.searchsorted(Azm,cake)
1536	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
1537
1538	for xring,yring in Data['ring']:
1539	Plot.plot(xring,yring,'r+',picker=3)
1540	if Data['setRings']:
1541	# rings = np.concatenate((Data['rings']),axis=0)
1542	N = 0
1543	for ring in Data['rings']:
1544	xring,yring = np.array(ring).T[:2]
1545	Plot.plot(xring,yring,'+',color=colors[N%6])
1546	N += 1
1547	for ellipse in Data['ellipses']:
1548	cent,phi,[width,height],col = ellipse
1549	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
1550	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
1551	#masks - mask lines numbered after integration limit lines
1552	spots = Masks['Points']
1553	rings = Masks['Rings']
1554	arcs = Masks['Arcs']
1555	polygons = Masks['Polygons']
1556	for x,y,d in spots:
1557	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
1558	self.ringList = []
1559	for iring,(tth,thick) in enumerate(rings):
1560	wave = Data['wavelength']
1561	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
1562	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
1563	self.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1564	self.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1565	self.arcList = []
1566	for iarc,(tth,azm,thick) in enumerate(arcs):
1567	wave = Data['wavelength']
1568	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
1569	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
1570	self.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1571	self.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1572	self.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1573	self.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1574	self.polyList = []
1575	for ipoly,polygon in enumerate(polygons):
1576	x,y = np.hsplit(np.array(polygon),2)
1577	self.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
1578	Plot.plot(x,y,'r')
1579	if newImage:
1580	colorBar = Page.figure.colorbar(Img)
1581	Plot.set_xlim(xlim)
1582	Plot.set_ylim(ylim)
1583	if not newPlot and xylim:
1584	Page.toolbar.push_current()
1585	Plot.set_xlim(xylim[0])
1586	Plot.set_ylim(xylim[1])
1587	xylim = []
1588	Page.toolbar.push_current()
1589	Page.toolbar.draw()
1590	else:
1591	Page.canvas.draw()
1592	finally:
1593	wx.EndBusyCursor()
1594
1595	def PlotIntegration(self,newPlot=False,event=None):
1596
1597	def OnMotion(event):
1598	Page.canvas.SetToolTipString('')
1599	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1600	azm = event.ydata
1601	tth = event.xdata
1602	if azm and tth:
1603	self.G2plotNB.status.SetFields(\
1604	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1605
1606	try:
1607	plotNum = self.G2plotNB.plotList.index('2D Integration')
1608	Page = self.G2plotNB.nb.GetPage(plotNum)
1609	if not newPlot:
1610	Plot = Page.figure.gca() #get previous plot & get limits
1611	xylim = Plot.get_xlim(),Plot.get_ylim()
1612	Page.figure.clf()
1613	Plot = Page.figure.gca() #get a fresh plot after clf()
1614
1615	except ValueError:
1616	Plot = self.G2plotNB.addMpl('2D Integration').gca()
1617	plotNum = self.G2plotNB.plotList.index('2D Integration')
1618	Page = self.G2plotNB.nb.GetPage(plotNum)
1619	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1620	Page.views = False
1621	view = False
1622	if not event:
1623	Page.SetFocus()
1624
1625	Data = self.PatternTree.GetItemPyData(
1626	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1627	image = self.Integrate[0]
1628	xsc = self.Integrate[1]
1629	ysc = self.Integrate[2]
1630	Imin,Imax = Data['range'][1]
1631	acolor = mpl.cm.get_cmap(Data['color'])
1632	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1633	Plot.set_ylabel('azimuth',fontsize=12)
1634	Plot.set_xlabel('2-theta',fontsize=12)
1635	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
1636	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
1637	colorBar = Page.figure.colorbar(Img)
1638	if Data['setRings'] and Data['rings']:
1639	rings = np.concatenate((Data['rings']),axis=0)
1640	for xring,yring,dsp in rings:
1641	x,y = G2img.GetTthAzm(xring,yring,Data)
1642	Plot.plot(x,y,'r+')
1643	if Data['ellipses']:
1644	for ellipse in Data['ellipses']:
1645	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1646	x,y = np.hsplit(ring,2)
1647	tth,azm = G2img.GetTthAzm(x,y,Data)
1648	Plot.plot(tth,azm,'b,')
1649	if not newPlot:
1650	Page.toolbar.push_current()
1651	Plot.set_xlim(xylim[0])
1652	Plot.set_ylim(xylim[1])
1653	xylim = []
1654	Page.toolbar.push_current()
1655	Page.toolbar.draw()
1656	else:
1657	Page.canvas.draw()
1658
1659	def PlotTRImage(self,tax,tay,taz,newPlot=False):
1660	#a test plot routine - not normally used
1661
1662	def OnMotion(event):
1663	Page.canvas.SetToolTipString('')
1664	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1665	azm = event.xdata
1666	tth = event.ydata
1667	if azm and tth:
1668	self.G2plotNB.status.SetFields(\
1669	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1670
1671	try:
1672	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1673	Page = self.G2plotNB.nb.GetPage(plotNum)
1674	if not newPlot:
1675	Plot = Page.figure.gca() #get previous plot & get limits
1676	xylim = Plot.get_xlim(),Plot.get_ylim()
1677	Page.figure.clf()
1678	Plot = Page.figure.gca() #get a fresh plot after clf()
1679
1680	except ValueError:
1681	Plot = self.G2plotNB.addMpl('2D Transformed Powder Image').gca()
1682	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1683	Page = self.G2plotNB.nb.GetPage(plotNum)
1684	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1685	Page.views = False
1686	view = False
1687	Page.SetFocus()
1688
1689	Data = self.PatternTree.GetItemPyData(
1690	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1691	Imin,Imax = Data['range'][1]
1692	step = (Imax-Imin)/5.
1693	V = np.arange(Imin,Imax,step)
1694	acolor = mpl.cm.get_cmap(Data['color'])
1695	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1696	Plot.set_xlabel('azimuth',fontsize=12)
1697	Plot.set_ylabel('2-theta',fontsize=12)
1698	Plot.contour(tax,tay,taz,V,cmap=acolor)
1699	if Data['showLines']:
1700	IOtth = Data['IOtth']
1701	if Data['fullIntegrate']:
1702	LRAzim = [-180,180]
1703	else:
1704	LRAzim = Data['LRazimuth'] #NB: integers
1705	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
1706	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
1707	if not Data['fullIntegrate']:
1708	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
1709	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
1710	if Data['setRings']:
1711	rings = np.concatenate((Data['rings']),axis=0)
1712	for xring,yring,dsp in rings:
1713	x,y = G2img.GetTthAzm(xring,yring,Data)
1714	Plot.plot(y,x,'r+')
1715	if Data['ellipses']:
1716	for ellipse in Data['ellipses']:
1717	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1718	x,y = np.hsplit(ring,2)
1719	tth,azm = G2img.GetTthAzm(x,y,Data)
1720	Plot.plot(azm,tth,'b,')
1721	if not newPlot:
1722	Page.toolbar.push_current()
1723	Plot.set_xlim(xylim[0])
1724	Plot.set_ylim(xylim[1])
1725	xylim = []
1726	Page.toolbar.push_current()
1727	Page.toolbar.draw()
1728	else:
1729	Page.canvas.draw()
1730
1731	def PlotStructure(self,data):
1732	generalData = data['General']
1733	cell = generalData['Cell'][1:7]
1734	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
1735	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1736	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1737	Mydir = generalData['Mydir']
1738	atomData = data['Atoms']
1739	drawingData = data['Drawing']
1740	drawAtoms = drawingData['Atoms']
1741	cx,ct,cs = drawingData['atomPtrs']
1742	Wt = [255,255,255]
1743	Rd = [255,0,0]
1744	Gr = [0,255,0]
1745	Bl = [0,0,255]
1746	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]])
1747	uEdges = np.array([
1748	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
1749	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
1750	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
1751	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
1752	altDown = False
1753	shiftDown = False
1754	ctrlDown = False
1755
1756	def OnKeyBox(event):
1757	import Image
1758	Draw() #make sure plot is fresh!!
1759	mode = cb.GetValue()
1760	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
1761	size = Page.canvas.GetSize()
1762	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
1763	if mode in ['jpeg',]:
1764	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
1765	im = Image.new("RGBA", (size[0],size[1]))
1766	else:
1767	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
1768	im = Image.new("RGB", (size[0],size[1]))
1769	im.fromstring(Pix)
1770	im.save(Fname,mode)
1771	cb.SetValue(' Save as:')
1772	self.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
1773
1774	def GetTruePosition(xy):
1775	View = glGetIntegerv(GL_VIEWPORT)
1776	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
1777	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
1778	Zmax = 1.
1779	for i,atom in enumerate(drawAtoms):
1780	x,y,z = atom[cx:cx+3]
1781	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
1782	XY = [int(X),int(View[3]-Y)]
1783	if np.allclose(xy,XY,atol=10) and Z < Zmax:
1784	Zmax = Z
1785	SetSelectedAtoms(i)
1786
1787	def OnMouseDown(event):
1788	xy = event.GetPosition()
1789	if event.ShiftDown():
1790	GetTruePosition(xy)
1791	else:
1792	drawingData['Rotation'][3] = xy
1793	Draw()
1794
1795	def OnMouseMove(event):
1796	newxy = event.GetPosition()
1797	page = getSelection()
1798	if event.ControlDown() and drawingData['showABC']:
1799	if event.LeftIsDown():
1800	SetTestRot(newxy)
1801	elif event.RightIsDown():
1802	SetTestPos(newxy)
1803	elif event.MiddleIsDown():
1804	SetTestRotZ(newxy)
1805	x,y,z = drawingData['testPos'][0]
1806	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
1807
1808
1809	if event.Dragging() and not event.ControlDown():
1810	if event.LeftIsDown():
1811	SetRotation(newxy)
1812	angX,angY,angZ = drawingData['Rotation'][:3]
1813	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
1814	elif event.RightIsDown():
1815	SetTranslation(newxy)
1816	Tx,Ty,Tz = drawingData['viewPoint'][0]
1817	self.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
1818	elif event.MiddleIsDown():
1819	SetRotationZ(newxy)
1820	angX,angY,angZ = drawingData['Rotation'][:3]
1821	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
1822	Draw()
1823
1824	def OnMouseWheel(event):
1825	drawingData['cameraPos'] += event.GetWheelRotation()/24
1826	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
1827	self.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
1828	page = getSelection()
1829	if page:
1830	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1831	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1832	names = [child.GetName() for child in panel]
1833	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
1834	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
1835	Draw()
1836
1837	def getSelection():
1838	try:
1839	return self.dataDisplay.GetSelection()
1840	except AttributeError:
1841	print self.dataDisplay.GetLabel()
1842	self.G2plotNB.status.SetStatusText('Select this from Phase data window!')
1843	return 0
1844
1845	def SetViewPointText(VP):
1846	page = getSelection()
1847	if page:
1848	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1849	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1850	names = [child.GetName() for child in panel]
1851	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
1852
1853	def ClearSelectedAtoms():
1854	page = getSelection()
1855	if page:
1856	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1857	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
1858	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1859	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
1860
1861	def SetSelectedAtoms(ind):
1862	page = getSelection()
1863	if page:
1864	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1865	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
1866	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1867	Id = drawAtoms[ind][-2]
1868	for i,atom in enumerate(atomData):
1869	if atom[-1] == Id:
1870	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
1871
1872	def GetSelectedAtoms():
1873	page = getSelection()
1874	Ind = []
1875	if page:
1876	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1877	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
1878	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1879	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
1880	return Ind
1881
1882	def OnKey(event): #on key UP!!
1883	keyCode = event.GetKeyCode()
1884	if keyCode > 255:
1885	keyCode = 0
1886	key,xyz = chr(keyCode),event.GetPosition()
1887	indx = drawingData['selectedAtoms']
1888	if key in ['c','C']:
1889	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
1890	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
1891	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
1892	SetViewPointText(drawingData['viewPoint'][0])
1893	elif key in ['n','N']:
1894	drawAtoms = drawingData['Atoms']
1895	pI = drawingData['viewPoint'][1]
1896	if indx:
1897	pI[0] = indx[pI[1]]
1898	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1899	pI[1] += 1
1900	if pI[1] >= len(indx):
1901	pI[1] = 0
1902	else:
1903	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1904	pI[0] += 1
1905	if pI[0] >= len(drawAtoms):
1906	pI[0] = 0
1907	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
1908	SetViewPointText(drawingData['viewPoint'][0])
1909
1910	elif key in ['p','P']:
1911	drawAtoms = drawingData['Atoms']
1912	pI = drawingData['viewPoint'][1]
1913	if indx:
1914	pI[0] = indx[pI[1]]
1915	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1916	pI[1] -= 1
1917	if pI[1] < 0:
1918	pI[1] = len(indx)-1
1919	else:
1920	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1921	pI[0] -= 1
1922	if pI[0] < 0:
1923	pI[0] = len(drawAtoms)-1
1924	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
1925	SetViewPointText(drawingData['viewPoint'][0])
1926	Draw()
1927
1928	def SetBackground():
1929	R,G,B,A = Page.camera['backColor']
1930	glClearColor(R,G,B,A)
1931	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
1932
1933	def SetLights():
1934	glEnable(GL_DEPTH_TEST)
1935	glShadeModel(GL_SMOOTH)
1936	glEnable(GL_LIGHTING)
1937	glEnable(GL_LIGHT0)
1938	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
1939	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
1940	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
1941
1942	def SetTranslation(newxy):
1943	Tx,Ty,Tz = drawingData['viewPoint'][0]
1944	anglex,angley,anglez,oldxy = drawingData['Rotation']
1945	Rx = G2lat.rotdMat(anglex,0)
1946	Ry = G2lat.rotdMat(angley,1)
1947	Rz = G2lat.rotdMat(anglez,2)
1948	dxy = list(newxy-oldxy)+[0,]
1949	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
1950	Tx -= dxy[0]*0.01
1951	Ty += dxy[1]*0.01
1952	Tz -= dxy[2]*0.01
1953	drawingData['Rotation'][3] = newxy
1954	drawingData['viewPoint'][0] = Tx,Ty,Tz
1955	SetViewPointText([Tx,Ty,Tz])
1956
1957	def SetTestPos(newxy):
1958	Tx,Ty,Tz = drawingData['testPos'][0]
1959	anglex,angley,anglez,oldxy = drawingData['Rotation']
1960	Rx = G2lat.rotdMat(anglex,0)
1961	Ry = G2lat.rotdMat(angley,1)
1962	Rz = G2lat.rotdMat(anglez,2)
1963	dxy = list(newxy-oldxy)+[0,]
1964	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
1965	Tx += dxy[0]*0.001
1966	Ty -= dxy[1]*0.001
1967	Tz += dxy[2]*0.001
1968	drawingData['Rotation'][3] = newxy
1969	drawingData['testPos'][0] = Tx,Ty,Tz
1970
1971	def SetTestRot(newxy):
1972	Txyz = np.array(drawingData['testPos'][0])
1973	oldxy = drawingData['testPos'][2]
1974	Ax,Ay,Az = drawingData['testPos'][1]
1975	Vxyz = np.array(drawingData['viewPoint'][0])
1976	Dxyz = np.inner(Amat,Txyz-Vxyz)
1977	dxy = list(newxy-oldxy)+[0,]
1978	Ax += dxy[1]*0.01
1979	Ay += dxy[0]*0.01
1980	Rx = G2lat.rotdMat(Ax,0)
1981	Ry = G2lat.rotdMat(Ay,1)
1982	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
1983	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
1984	drawingData['testPos'][1] = [Ax,Ay,Az]
1985	drawingData['testPos'][2] = newxy
1986	drawingData['testPos'][0] = Dxyz
1987
1988	def SetTestRotZ(newxy):
1989	Txyz = np.array(drawingData['testPos'][0])
1990	oldxy = drawingData['testPos'][2]
1991	Ax,Ay,Az = drawingData['testPos'][1]
1992	Vxyz = np.array(drawingData['viewPoint'][0])
1993	Dxyz = np.inner(Amat,Txyz-Vxyz)
1994	dxy = list(newxy-oldxy)+[0,]
1995	Az += (dxy[0]+dxy[1])*.01
1996	Rz = G2lat.rotdMat(Az,2)
1997	Dxyz = np.inner(Rz,Dxyz)
1998	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
1999	drawingData['testPos'][1] = [Ax,Ay,Az]
2000	drawingData['testPos'][2] = newxy
2001	drawingData['testPos'][0] = Dxyz
2002
2003	def SetRotation(newxy):
2004	anglex,angley,anglez,oldxy = drawingData['Rotation']
2005	dxy = newxy-oldxy
2006	anglex += dxy[1]*.25
2007	angley += dxy[0]*.25
2008	oldxy = newxy
2009	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2010
2011	def SetRotationZ(newxy):
2012	anglex,angley,anglez,oldxy = drawingData['Rotation']
2013	dxy = newxy-oldxy
2014	anglez += (dxy[0]+dxy[1])*.25
2015	oldxy = newxy
2016	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2017
2018	def RenderBox():
2019	glEnable(GL_COLOR_MATERIAL)
2020	glLineWidth(2)
2021	glEnable(GL_BLEND)
2022	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2023	glEnable(GL_LINE_SMOOTH)
2024	glBegin(GL_LINES)
2025	for line,color in zip(uEdges,uColors):
2026	glColor3ubv(color)
2027	glVertex3fv(line[0])
2028	glVertex3fv(line[1])
2029	glEnd()
2030	glColor4ubv([0,0,0,0])
2031	glDisable(GL_LINE_SMOOTH)
2032	glDisable(GL_BLEND)
2033	glDisable(GL_COLOR_MATERIAL)
2034
2035	def RenderUnitVectors(x,y,z):
2036	xyz = np.array([x,y,z])
2037	glEnable(GL_COLOR_MATERIAL)
2038	glLineWidth(1)
2039	glPushMatrix()
2040	glTranslate(x,y,z)
2041	glScalef(1/cell[0],1/cell[1],1/cell[2])
2042	glBegin(GL_LINES)
2043	for line,color in zip(uEdges,uColors)[:3]:
2044	glColor3ubv(color)
2045	glVertex3fv(line[0])
2046	glVertex3fv(line[1])
2047	glEnd()
2048	glPopMatrix()
2049	glColor4ubv([0,0,0,0])
2050	glDisable(GL_COLOR_MATERIAL)
2051
2052	def RenderSphere(x,y,z,radius,color):
2053	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2054	glPushMatrix()
2055	glTranslate(x,y,z)
2056	glMultMatrixf(B4mat.T)
2057	q = gluNewQuadric()
2058	gluSphere(q,radius,20,10)
2059	glPopMatrix()
2060
2061	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2062	s1,s2,s3 = E
2063	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2064	glPushMatrix()
2065	glTranslate(x,y,z)
2066	glMultMatrixf(B4mat.T)
2067	glMultMatrixf(R4.T)
2068	glEnable(GL_NORMALIZE)
2069	glScale(s1,s2,s3)
2070	q = gluNewQuadric()
2071	gluSphere(q,ellipseProb,20,10)
2072	glDisable(GL_NORMALIZE)
2073	glPopMatrix()
2074
2075	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2076	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2077	glPushMatrix()
2078	glTranslate(x,y,z)
2079	glMultMatrixf(B4mat.T)
2080	for bond in Bonds:
2081	glPushMatrix()
2082	Dx = np.inner(Amat,bond)
2083	Z = np.sqrt(np.sum(Dx**2))
2084	azm = atan2d(-Dx[1],-Dx[0])
2085	phi = acosd(Dx[2]/Z)
2086	glRotate(-azm,0,0,1)
2087	glRotate(phi,1,0,0)
2088	q = gluNewQuadric()
2089	gluCylinder(q,radius,radius,Z,slice,2)
2090	glPopMatrix()
2091	glPopMatrix()
2092
2093	def RenderLines(x,y,z,Bonds,color):
2094	xyz = np.array([x,y,z])
2095	glEnable(GL_COLOR_MATERIAL)
2096	glLineWidth(1)
2097	glColor3fv(color)
2098	glPushMatrix()
2099	glBegin(GL_LINES)
2100	for bond in Bonds:
2101	glVertex3fv(xyz)
2102	glVertex3fv(xyz+bond)
2103	glEnd()
2104	glColor4ubv([0,0,0,0])
2105	glPopMatrix()
2106	glDisable(GL_COLOR_MATERIAL)
2107
2108	def RenderPolyhedra(x,y,z,Faces,color):
2109	glPushMatrix()
2110	glTranslate(x,y,z)
2111	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2112	glShadeModel(GL_SMOOTH)
2113	glMultMatrixf(B4mat.T)
2114	for face,norm in Faces:
2115	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2116	glFrontFace(GL_CW)
2117	glNormal3fv(norm)
2118	glBegin(GL_TRIANGLES)
2119	for vert in face:
2120	glVertex3fv(vert)
2121	glEnd()
2122	glPopMatrix()
2123
2124	def RenderBackbone(Backbone,BackboneColor,radius):
2125	glPushMatrix()
2126	glMultMatrixf(B4mat.T)
2127	glEnable(GL_COLOR_MATERIAL)
2128	glShadeModel(GL_SMOOTH)
2129	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2130	glePolyCylinder(Backbone,BackboneColor,radius)
2131	glPopMatrix()
2132	glDisable(GL_COLOR_MATERIAL)
2133
2134	def RenderLabel(x,y,z,label,r):
2135	glPushMatrix()
2136	glTranslate(x,y,z)
2137	glMultMatrixf(B4mat.T)
2138	glDisable(GL_LIGHTING)
2139	glColor3f(0,1.,0)
2140	glRasterPos3f(r,r,r)
2141	for c in list(label):
2142	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2143	glEnable(GL_LIGHTING)
2144	glPopMatrix()
2145
2146	def Draw():
2147	import numpy.linalg as nl
2148	Ind = GetSelectedAtoms()
2149	VS = np.array(Page.canvas.GetSize())
2150	aspect = float(VS[0])/float(VS[1])
2151	cPos = drawingData['cameraPos']
2152	Zclip = drawingData['Zclip']*cPos/200.
2153	anglex,angley,anglez = drawingData['Rotation'][:3]
2154	Tx,Ty,Tz = drawingData['viewPoint'][0]
2155	cx,ct,cs = drawingData['atomPtrs']
2156	bondR = drawingData['bondRadius']
2157	G,g = G2lat.cell2Gmat(cell)
2158	GS = G
2159	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2160	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2161	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2162	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2163
2164	SetBackground()
2165	glInitNames()
2166	glPushName(0)
2167
2168	glMatrixMode(GL_PROJECTION)
2169	glLoadIdentity()
2170	glViewport(0,0,VS[0],VS[1])
2171	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2172	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2173	SetLights()
2174
2175	glMatrixMode(GL_MODELVIEW)
2176	glLoadIdentity()
2177	glRotate(anglez,0,0,1)
2178	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2179	glRotate(angley,sind(anglez),cosd(anglez),0)
2180	glMultMatrixf(A4mat.T)
2181	glTranslate(-Tx,-Ty,-Tz)
2182	if drawingData['unitCellBox']:
2183	RenderBox()
2184	if drawingData['showABC']:
2185	x,y,z = drawingData['testPos'][0]
2186	# if altDown:
2187	# self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2188	# else:
2189	# self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2190	RenderUnitVectors(x,y,z)
2191	Backbone = []
2192	BackboneColor = []
2193	time0 = time.time()
2194	for iat,atom in enumerate(drawingData['Atoms']):
2195	x,y,z = atom[cx:cx+3]
2196	Bonds = atom[-2]
2197	Faces = atom[-1]
2198	try:
2199	atNum = generalData['AtomTypes'].index(atom[ct])
2200	except ValueError:
2201	atNum = -1
2202	CL = atom[cs+2]
2203	color = np.array(CL)/255.
2204	if iat in Ind:
2205	color = np.array(Gr)/255.
2206	radius = 0.5
2207	if atom[cs] != '':
2208	glLoadName(atom[-3])
2209	if 'balls' in atom[cs]:
2210	vdwScale = drawingData['vdwScale']
2211	ballScale = drawingData['ballScale']
2212	if atNum < 0:
2213	radius = 0.2
2214	elif 'H' == atom[ct]:
2215	if drawingData['showHydrogen']:
2216	if 'vdW' in atom[cs] and atNum >= 0:
2217	radius = vdwScale*generalData['vdWRadii'][atNum]
2218	else:
2219	radius = ballScale*drawingData['sizeH']
2220	else:
2221	radius = 0.0
2222	else:
2223	if 'vdW' in atom[cs]:
2224	radius = vdwScale*generalData['vdWRadii'][atNum]
2225	else:
2226	radius = ballScale*generalData['BondRadii'][atNum]
2227	RenderSphere(x,y,z,radius,color)
2228	if 'sticks' in atom[cs]:
2229	RenderBonds(x,y,z,Bonds,bondR,color)
2230	elif 'ellipsoids' in atom[cs]:
2231	RenderBonds(x,y,z,Bonds,bondR,color)
2232	if atom[cs+3] == 'A':
2233	Uij = atom[cs+5:cs+11]
2234	U = np.multiply(G2spc.Uij2U(Uij),GS)
2235	U = np.inner(Amat,np.inner(U,Amat).T)
2236	E,R = nl.eigh(U)
2237	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2238	E = np.sqrt(E)
2239	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2240	pass
2241	else:
2242	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2243	else:
2244	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2245	pass
2246	else:
2247	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2248	RenderSphere(x,y,z,radius,color)
2249	elif 'lines' in atom[cs]:
2250	radius = 0.1
2251	RenderLines(x,y,z,Bonds,color)
2252	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2253	elif atom[cs] == 'sticks':
2254	radius = 0.1
2255	RenderBonds(x,y,z,Bonds,bondR,color)
2256	elif atom[cs] == 'polyhedra':
2257	RenderPolyhedra(x,y,z,Faces,color)
2258	elif atom[cs] == 'backbone':
2259	if atom[ct-1].split()[0] in ['C','N']:
2260	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2261	BackboneColor.append(list(color))
2262
2263	if atom[cs+1] == 'type':
2264	RenderLabel(x,y,z,atom[ct],radius)
2265	elif atom[cs+1] == 'name':
2266	RenderLabel(x,y,z,atom[ct-1],radius)
2267	elif atom[cs+1] == 'number':
2268	RenderLabel(x,y,z,str(iat+1),radius)
2269	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2270	RenderLabel(x,y,z,atom[ct-4],radius)
2271	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2272	RenderLabel(x,y,z,atom[ct-3],radius)
2273	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2274	RenderLabel(x,y,z,atom[ct-2],radius)
2275	if Backbone:
2276	RenderBackbone(Backbone,BackboneColor,bondR)
2277	# print time.time()-time0
2278	Page.canvas.SwapBuffers()
2279
2280	def OnSize(event):
2281	Draw()
2282
2283	def OnFocus(event):
2284	Draw()
2285
2286	try:
2287	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2288	Page = self.G2plotNB.nb.GetPage(plotNum)
2289	except ValueError:
2290	Plot = self.G2plotNB.addOgl(generalData['Name'])
2291	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2292	Page = self.G2plotNB.nb.GetPage(plotNum)
2293	Page.views = False
2294	view = False
2295	altDown = False
2296	Page.SetFocus()
2297	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2298	choices=(' save as:','jpeg','tiff','bmp'))
2299	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2300	cb.SetValue(' save as:')
2301	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2302	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2303	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2304	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2305	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2306	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2307	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2308	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2309	Page.camera['position'] = drawingData['cameraPos']
2310	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2311	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2312	Page.canvas.SetCurrent()
2313	Draw()
2314

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