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source: trunk/GSASIIplot.py @ 272

Last change on this file since 272 was 272, checked in by vondreele, 12 years ago
add slider for "Ruland" coeff. add 'o' option for undoing offset in powder plots
Property svn:keywords set to `Date Author Revision URL Id`
File size: 96.2 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2011-04-29 19:20:30 +0000 (Fri, 29 Apr 2011) $
4	# $Author: vondreele $
5	# $Revision: 272 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 272 2011-04-29 19:20:30Z 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	if event.ControlDown() and drawingData['showABC']:
1798	if event.LeftIsDown():
1799	ctrlDown = True
1800	SetTestRot(newxy)
1801	elif event.RightIsDown():
1802	SetTestPos(newxy)
1803	elif event.MiddleIsDown():
1804	SetTestRotZ(newxy)
1805
1806
1807	if event.Dragging() and not event.ControlDown():
1808	if event.LeftIsDown():
1809	SetRotation(newxy)
1810	elif event.RightIsDown():
1811	SetTranslation(newxy)
1812	elif event.MiddleIsDown():
1813	SetRotationZ(newxy)
1814	Draw()
1815
1816	def OnMouseWheel(event):
1817	drawingData['cameraPos'] += event.GetWheelRotation()/24
1818	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
1819	page = self.dataDisplay.GetSelection()
1820	if page:
1821	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1822	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1823	names = [child.GetName() for child in panel]
1824	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
1825	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
1826	Draw()
1827
1828	def getSelection():
1829	if self.dataDisplay:
1830	return self.dataDisplay.GetSelection()
1831	else:
1832	return 0
1833
1834	def SetViewPointText(VP):
1835	page = getSelection()
1836	if page:
1837	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1838	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1839	names = [child.GetName() for child in panel]
1840	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
1841
1842	def ClearSelectedAtoms():
1843	page = getSelection()
1844	if page:
1845	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1846	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
1847	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1848	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
1849
1850	def SetSelectedAtoms(ind):
1851	page = getSelection()
1852	if page:
1853	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1854	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
1855	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1856	Id = drawAtoms[ind][-2]
1857	for i,atom in enumerate(atomData):
1858	if atom[-1] == Id:
1859	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
1860
1861	def GetSelectedAtoms():
1862	page = getSelection()
1863	Ind = []
1864	if page:
1865	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1866	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
1867	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1868	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
1869	return Ind
1870
1871	def OnKey(event): #on key UP!!
1872	keyCode = event.GetKeyCode()
1873	if keyCode > 255:
1874	keyCode = 0
1875	key,xyz = chr(keyCode),event.GetPosition()
1876	indx = drawingData['selectedAtoms']
1877	if key in ['c','C']:
1878	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
1879	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
1880	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
1881	SetViewPointText(drawingData['viewPoint'][0])
1882	elif key in ['n','N']:
1883	drawAtoms = drawingData['Atoms']
1884	pI = drawingData['viewPoint'][1]
1885	if indx:
1886	pI[0] = indx[pI[1]]
1887	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1888	pI[1] += 1
1889	if pI[1] >= len(indx):
1890	pI[1] = 0
1891	else:
1892	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1893	pI[0] += 1
1894	if pI[0] >= len(drawAtoms):
1895	pI[0] = 0
1896	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
1897	SetViewPointText(drawingData['viewPoint'][0])
1898
1899	elif key in ['p','P']:
1900	drawAtoms = drawingData['Atoms']
1901	pI = drawingData['viewPoint'][1]
1902	if indx:
1903	pI[0] = indx[pI[1]]
1904	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1905	pI[1] -= 1
1906	if pI[1] < 0:
1907	pI[1] = len(indx)-1
1908	else:
1909	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1910	pI[0] -= 1
1911	if pI[0] < 0:
1912	pI[0] = len(drawAtoms)-1
1913	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
1914	SetViewPointText(drawingData['viewPoint'][0])
1915	Draw()
1916
1917	def SetBackground():
1918	R,G,B,A = Page.camera['backColor']
1919	glClearColor(R,G,B,A)
1920	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
1921
1922	def SetLights():
1923	glEnable(GL_DEPTH_TEST)
1924	glShadeModel(GL_SMOOTH)
1925	glEnable(GL_LIGHTING)
1926	glEnable(GL_LIGHT0)
1927	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
1928	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
1929	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
1930
1931	def SetTranslation(newxy):
1932	Tx,Ty,Tz = drawingData['viewPoint'][0]
1933	anglex,angley,anglez,oldxy = drawingData['Rotation']
1934	Rx = G2lat.rotdMat(anglex,0)
1935	Ry = G2lat.rotdMat(angley,1)
1936	Rz = G2lat.rotdMat(anglez,2)
1937	dxy = list(newxy-oldxy)+[0,]
1938	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
1939	Tx -= dxy[0]*0.01
1940	Ty += dxy[1]*0.01
1941	Tz -= dxy[2]*0.01
1942	drawingData['Rotation'][3] = newxy
1943	drawingData['viewPoint'][0] = Tx,Ty,Tz
1944	SetViewPointText([Tx,Ty,Tz])
1945
1946	def SetTestPos(newxy):
1947	Tx,Ty,Tz = drawingData['testPos'][0]
1948	anglex,angley,anglez,oldxy = drawingData['Rotation']
1949	Rx = G2lat.rotdMat(anglex,0)
1950	Ry = G2lat.rotdMat(angley,1)
1951	Rz = G2lat.rotdMat(anglez,2)
1952	dxy = list(newxy-oldxy)+[0,]
1953	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
1954	Tx += dxy[0]*0.001
1955	Ty -= dxy[1]*0.001
1956	Tz += dxy[2]*0.001
1957	drawingData['Rotation'][3] = newxy
1958	drawingData['testPos'][0] = Tx,Ty,Tz
1959
1960	def SetTestRot(newxy):
1961	Txyz = np.array(drawingData['testPos'][0])
1962	oldxy = drawingData['testPos'][2]
1963	Ax,Ay,Az = drawingData['testPos'][1]
1964	Vxyz = np.array(drawingData['viewPoint'][0])
1965	Dxyz = np.inner(Amat,Txyz-Vxyz)
1966	dxy = list(newxy-oldxy)+[0,]
1967	Ax += dxy[1]*0.01
1968	Ay += dxy[0]*0.01
1969	Rx = G2lat.rotdMat(Ax,0)
1970	Ry = G2lat.rotdMat(Ay,1)
1971	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
1972	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
1973	drawingData['testPos'][1] = [Ax,Ay,Az]
1974	drawingData['testPos'][2] = newxy
1975	drawingData['testPos'][0] = Dxyz
1976
1977	def SetTestRotZ(newxy):
1978	Txyz = np.array(drawingData['testPos'][0])
1979	oldxy = drawingData['testPos'][2]
1980	Ax,Ay,Az = drawingData['testPos'][1]
1981	Vxyz = np.array(drawingData['viewPoint'][0])
1982	Dxyz = np.inner(Amat,Txyz-Vxyz)
1983	dxy = list(newxy-oldxy)+[0,]
1984	Az += (dxy[0]+dxy[1])*.01
1985	Rz = G2lat.rotdMat(Az,2)
1986	Dxyz = np.inner(Rz,Dxyz)
1987	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
1988	drawingData['testPos'][1] = [Ax,Ay,Az]
1989	drawingData['testPos'][2] = newxy
1990	drawingData['testPos'][0] = Dxyz
1991
1992	def SetRotation(newxy):
1993	anglex,angley,anglez,oldxy = drawingData['Rotation']
1994	dxy = newxy-oldxy
1995	anglex += dxy[1]*.25
1996	angley += dxy[0]*.25
1997	oldxy = newxy
1998	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
1999
2000	def SetRotationZ(newxy):
2001	anglex,angley,anglez,oldxy = drawingData['Rotation']
2002	dxy = newxy-oldxy
2003	anglez += (dxy[0]+dxy[1])*.25
2004	oldxy = newxy
2005	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2006
2007	def RenderBox():
2008	glEnable(GL_COLOR_MATERIAL)
2009	glLineWidth(2)
2010	glEnable(GL_BLEND)
2011	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2012	glEnable(GL_LINE_SMOOTH)
2013	glBegin(GL_LINES)
2014	for line,color in zip(uEdges,uColors):
2015	glColor3ubv(color)
2016	glVertex3fv(line[0])
2017	glVertex3fv(line[1])
2018	glEnd()
2019	glColor4ubv([0,0,0,0])
2020	glDisable(GL_LINE_SMOOTH)
2021	glDisable(GL_BLEND)
2022	glDisable(GL_COLOR_MATERIAL)
2023
2024	def RenderUnitVectors(x,y,z):
2025	xyz = np.array([x,y,z])
2026	glEnable(GL_COLOR_MATERIAL)
2027	glLineWidth(1)
2028	glPushMatrix()
2029	glTranslate(x,y,z)
2030	glScalef(1/cell[0],1/cell[1],1/cell[2])
2031	glBegin(GL_LINES)
2032	for line,color in zip(uEdges,uColors)[:3]:
2033	glColor3ubv(color)
2034	glVertex3fv(line[0])
2035	glVertex3fv(line[1])
2036	glEnd()
2037	glPopMatrix()
2038	glColor4ubv([0,0,0,0])
2039	glDisable(GL_COLOR_MATERIAL)
2040
2041	def RenderSphere(x,y,z,radius,color):
2042	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2043	glPushMatrix()
2044	glTranslate(x,y,z)
2045	glMultMatrixf(B4mat.T)
2046	q = gluNewQuadric()
2047	gluSphere(q,radius,20,10)
2048	glPopMatrix()
2049
2050	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2051	s1,s2,s3 = E
2052	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2053	glPushMatrix()
2054	glTranslate(x,y,z)
2055	glMultMatrixf(B4mat.T)
2056	glMultMatrixf(R4.T)
2057	glEnable(GL_NORMALIZE)
2058	glScale(s1,s2,s3)
2059	q = gluNewQuadric()
2060	gluSphere(q,ellipseProb,20,10)
2061	glDisable(GL_NORMALIZE)
2062	glPopMatrix()
2063
2064	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2065	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2066	glPushMatrix()
2067	glTranslate(x,y,z)
2068	glMultMatrixf(B4mat.T)
2069	for bond in Bonds:
2070	glPushMatrix()
2071	Dx = np.inner(Amat,bond)
2072	Z = np.sqrt(np.sum(Dx**2))
2073	azm = atan2d(-Dx[1],-Dx[0])
2074	phi = acosd(Dx[2]/Z)
2075	glRotate(-azm,0,0,1)
2076	glRotate(phi,1,0,0)
2077	q = gluNewQuadric()
2078	gluCylinder(q,radius,radius,Z,slice,2)
2079	glPopMatrix()
2080	glPopMatrix()
2081
2082	def RenderLines(x,y,z,Bonds,color):
2083	xyz = np.array([x,y,z])
2084	glEnable(GL_COLOR_MATERIAL)
2085	glLineWidth(1)
2086	glColor3fv(color)
2087	glPushMatrix()
2088	glBegin(GL_LINES)
2089	for bond in Bonds:
2090	glVertex3fv(xyz)
2091	glVertex3fv(xyz+bond)
2092	glEnd()
2093	glColor4ubv([0,0,0,0])
2094	glPopMatrix()
2095	glDisable(GL_COLOR_MATERIAL)
2096
2097	def RenderPolyhedra(x,y,z,Faces,color):
2098	glPushMatrix()
2099	glTranslate(x,y,z)
2100	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2101	glShadeModel(GL_SMOOTH)
2102	glMultMatrixf(B4mat.T)
2103	for face,norm in Faces:
2104	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2105	glFrontFace(GL_CW)
2106	glNormal3fv(norm)
2107	glBegin(GL_TRIANGLES)
2108	for vert in face:
2109	glVertex3fv(vert)
2110	glEnd()
2111	glPopMatrix()
2112
2113	def RenderBackbone(Backbone,BackboneColor,radius):
2114	glPushMatrix()
2115	glMultMatrixf(B4mat.T)
2116	glEnable(GL_COLOR_MATERIAL)
2117	glShadeModel(GL_SMOOTH)
2118	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2119	glePolyCylinder(Backbone,BackboneColor,radius)
2120	glPopMatrix()
2121	glDisable(GL_COLOR_MATERIAL)
2122
2123	def RenderLabel(x,y,z,label,r):
2124	glPushMatrix()
2125	glTranslate(x,y,z)
2126	glMultMatrixf(B4mat.T)
2127	glDisable(GL_LIGHTING)
2128	glColor3f(0,1.,0)
2129	glRasterPos3f(r,r,r)
2130	for c in list(label):
2131	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2132	glEnable(GL_LIGHTING)
2133	glPopMatrix()
2134
2135	def Draw():
2136	import numpy.linalg as nl
2137	Ind = GetSelectedAtoms()
2138	VS = np.array(Page.canvas.GetSize())
2139	aspect = float(VS[0])/float(VS[1])
2140	cPos = drawingData['cameraPos']
2141	Zclip = drawingData['Zclip']*cPos/200.
2142	anglex,angley,anglez = drawingData['Rotation'][:3]
2143	Tx,Ty,Tz = drawingData['viewPoint'][0]
2144	cx,ct,cs = drawingData['atomPtrs']
2145	bondR = drawingData['bondRadius']
2146	G,g = G2lat.cell2Gmat(cell)
2147	GS = G
2148	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2149	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2150	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2151	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2152
2153	SetBackground()
2154	glInitNames()
2155	glPushName(0)
2156
2157	glMatrixMode(GL_PROJECTION)
2158	glLoadIdentity()
2159	glViewport(0,0,VS[0],VS[1])
2160	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2161	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2162	SetLights()
2163
2164	glMatrixMode(GL_MODELVIEW)
2165	glLoadIdentity()
2166	glRotate(anglez,0,0,1)
2167	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2168	glRotate(angley,sind(anglez),cosd(anglez),0)
2169	glMultMatrixf(A4mat.T)
2170	glTranslate(-Tx,-Ty,-Tz)
2171	if drawingData['unitCellBox']:
2172	RenderBox()
2173	if drawingData['showABC']:
2174	# try: #temporary fix - not needed further?
2175	# x,y,z = drawingData['testPos'][0]
2176	# except TypeError:
2177	# x,y,z = drawingData['testPos']
2178	x,y,z = drawingData['testPos'][0]
2179	if altDown:
2180	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2181	else:
2182	self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2183	RenderUnitVectors(x,y,z)
2184	Backbone = []
2185	BackboneColor = []
2186	time0 = time.time()
2187	for iat,atom in enumerate(drawingData['Atoms']):
2188	x,y,z = atom[cx:cx+3]
2189	Bonds = atom[-2]
2190	Faces = atom[-1]
2191	try:
2192	atNum = generalData['AtomTypes'].index(atom[ct])
2193	except ValueError:
2194	atNum = -1
2195	CL = atom[cs+2]
2196	color = np.array(CL)/255.
2197	if iat in Ind:
2198	color = np.array(Gr)/255.
2199	radius = 0.5
2200	if atom[cs] != '':
2201	glLoadName(atom[-3])
2202	if 'balls' in atom[cs]:
2203	vdwScale = drawingData['vdwScale']
2204	ballScale = drawingData['ballScale']
2205	if atNum < 0:
2206	radius = 0.2
2207	elif 'H' == atom[ct]:
2208	if drawingData['showHydrogen']:
2209	if 'vdW' in atom[cs] and atNum >= 0:
2210	radius = vdwScale*generalData['vdWRadii'][atNum]
2211	else:
2212	radius = ballScale*drawingData['sizeH']
2213	else:
2214	radius = 0.0
2215	else:
2216	if 'vdW' in atom[cs]:
2217	radius = vdwScale*generalData['vdWRadii'][atNum]
2218	else:
2219	radius = ballScale*generalData['BondRadii'][atNum]
2220	RenderSphere(x,y,z,radius,color)
2221	if 'sticks' in atom[cs]:
2222	RenderBonds(x,y,z,Bonds,bondR,color)
2223	elif 'ellipsoids' in atom[cs]:
2224	RenderBonds(x,y,z,Bonds,bondR,color)
2225	if atom[cs+3] == 'A':
2226	Uij = atom[cs+5:cs+11]
2227	U = np.multiply(G2spc.Uij2U(Uij),GS)
2228	U = np.inner(Amat,np.inner(U,Amat).T)
2229	E,R = nl.eigh(U)
2230	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2231	E = np.sqrt(E)
2232	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2233	pass
2234	else:
2235	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2236	else:
2237	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2238	pass
2239	else:
2240	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2241	RenderSphere(x,y,z,radius,color)
2242	elif 'lines' in atom[cs]:
2243	radius = 0.1
2244	RenderLines(x,y,z,Bonds,color)
2245	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2246	elif atom[cs] == 'sticks':
2247	radius = 0.1
2248	RenderBonds(x,y,z,Bonds,bondR,color)
2249	elif atom[cs] == 'polyhedra':
2250	RenderPolyhedra(x,y,z,Faces,color)
2251	elif atom[cs] == 'backbone':
2252	if atom[ct-1].split()[0] in ['C','N']:
2253	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2254	BackboneColor.append(list(color))
2255
2256	if atom[cs+1] == 'type':
2257	RenderLabel(x,y,z,atom[ct],radius)
2258	elif atom[cs+1] == 'name':
2259	RenderLabel(x,y,z,atom[ct-1],radius)
2260	elif atom[cs+1] == 'number':
2261	RenderLabel(x,y,z,str(iat+1),radius)
2262	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2263	RenderLabel(x,y,z,atom[ct-4],radius)
2264	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2265	RenderLabel(x,y,z,atom[ct-3],radius)
2266	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2267	RenderLabel(x,y,z,atom[ct-2],radius)
2268	if Backbone:
2269	RenderBackbone(Backbone,BackboneColor,bondR)
2270	# print time.time()-time0
2271	Page.canvas.SwapBuffers()
2272
2273	def OnSize(event):
2274	Draw()
2275
2276	def OnFocus(event):
2277	Draw()
2278
2279	try:
2280	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2281	Page = self.G2plotNB.nb.GetPage(plotNum)
2282	except ValueError:
2283	Plot = self.G2plotNB.addOgl(generalData['Name'])
2284	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2285	Page = self.G2plotNB.nb.GetPage(plotNum)
2286	Page.views = False
2287	view = False
2288	altDown = False
2289	Page.SetFocus()
2290	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2291	choices=(' save as:','jpeg','tiff','bmp'))
2292	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2293	cb.SetValue(' save as:')
2294	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2295	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2296	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2297	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2298	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2299	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2300	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2301	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2302	Page.camera['position'] = drawingData['cameraPos']
2303	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2304	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2305	Page.canvas.SetCurrent()
2306	Draw()
2307

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