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source: trunk/GSASIIplot.py @ 755

Last change on this file since 755 was 755, checked in by vondreele, 11 years ago
fix rotation about view direction eliminate divide by zero error in quaternion stuff
Property svn:keywords set to `Date Author Revision URL Id`
File size: 132.6 KB

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1	# -- coding: utf-8 --
2	#GSASII plotting routines
3	########### SVN repository information ###################
4	# $Date: 2012-09-08 15:14:53 +0000 (Sat, 08 Sep 2012) $
5	# $Author: vondreele $
6	# $Revision: 755 $
7	# $URL: trunk/GSASIIplot.py $
8	# $Id: GSASIIplot.py 755 2012-09-08 15:14:53Z vondreele $
9	########### SVN repository information ###################
10	import math
11	import time
12	import copy
13	import os.path
14	import numpy as np
15	import numpy.ma as ma
16	import numpy.linalg as nl
17	import wx
18	import wx.aui
19	import wx.glcanvas
20	import matplotlib as mpl
21	import mpl_toolkits.mplot3d.axes3d as mp3d
22	import GSASIIpath
23	GSASIIpath.SetVersionNumber("$Revision: 755 $")
24	import GSASIIgrid as G2gd
25	import GSASIIimage as G2img
26	import GSASIIpwd as G2pwd
27	import GSASIIIO as G2IO
28	import GSASIIpwdGUI as G2pdG
29	import GSASIIimgGUI as G2imG
30	import GSASIIphsGUI as G2phG
31	import GSASIIlattice as G2lat
32	import GSASIIspc as G2spc
33	import GSASIImath as G2mth
34	import pytexture as ptx
35	from OpenGL.GL import *
36	from OpenGL.GLU import *
37	from OpenGL.GLUT import *
38	from OpenGL.GLE import *
39	from matplotlib.backends.backend_wx import _load_bitmap
40	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
41	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
42
43	# useful degree trig functions
44	sind = lambda x: math.sin(x*math.pi/180.)
45	cosd = lambda x: math.cos(x*math.pi/180.)
46	tand = lambda x: math.tan(x*math.pi/180.)
47	asind = lambda x: 180.*math.asin(x)/math.pi
48	acosd = lambda x: 180.*math.acos(x)/math.pi
49	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
50	atand = lambda x: 180.*math.atan(x)/math.pi
51	# numpy versions
52	npsind = lambda x: np.sin(x*np.pi/180.)
53	npcosd = lambda x: np.cos(x*np.pi/180.)
54	npacosd = lambda x: 180.*np.arccos(x)/np.pi
55	npasind = lambda x: 180.*np.arcsin(x)/np.pi
56	npatand = lambda x: 180.*np.arctan(x)/np.pi
57	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
58
59	class G2PlotMpl(wx.Panel):
60	def __init__(self,parent,id=-1,dpi=None,**kwargs):
61	wx.Panel.__init__(self,parent,id=id,**kwargs)
62	mpl.rcParams['legend.fontsize'] = 10
63	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,6))
64	self.canvas = Canvas(self,-1,self.figure)
65	self.toolbar = GSASIItoolbar(self.canvas)
66
67	self.toolbar.Realize()
68
69	sizer=wx.BoxSizer(wx.VERTICAL)
70	sizer.Add(self.canvas,1,wx.EXPAND)
71	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
72	self.SetSizer(sizer)
73
74	class G2PlotOgl(wx.Panel):
75	def __init__(self,parent,id=-1,dpi=None,**kwargs):
76	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
77	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
78	self.camera = {}
79	sizer=wx.BoxSizer(wx.VERTICAL)
80	sizer.Add(self.canvas,1,wx.EXPAND)
81	self.SetSizer(sizer)
82
83	class G2Plot3D(wx.Panel):
84	def __init__(self,parent,id=-1,dpi=None,**kwargs):
85	wx.Panel.__init__(self,parent,id=id,**kwargs)
86	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
87	self.canvas = Canvas(self,-1,self.figure)
88	self.toolbar = GSASIItoolbar(self.canvas)
89
90	self.toolbar.Realize()
91
92	sizer=wx.BoxSizer(wx.VERTICAL)
93	sizer.Add(self.canvas,1,wx.EXPAND)
94	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
95	self.SetSizer(sizer)
96
97	class G2PlotNoteBook(wx.Panel):
98	def __init__(self,parent,id=-1):
99	wx.Panel.__init__(self,parent,id=id)
100	#so one can't delete a plot page!!
101	self.nb = wx.aui.AuiNotebook(self, \
102	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
103	sizer = wx.BoxSizer()
104	sizer.Add(self.nb,1,wx.EXPAND)
105	self.SetSizer(sizer)
106	self.status = parent.CreateStatusBar()
107	self.status.SetFieldsCount(2)
108	self.status.SetStatusWidths([150,-1])
109	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
110
111	self.plotList = []
112
113	def addMpl(self,name=""):
114	page = G2PlotMpl(self.nb)
115	self.nb.AddPage(page,name)
116
117	self.plotList.append(name)
118
119	return page.figure
120
121	def add3D(self,name=""):
122	page = G2Plot3D(self.nb)
123	self.nb.AddPage(page,name)
124
125	self.plotList.append(name)
126
127	return page.figure
128
129	def addOgl(self,name=""):
130	page = G2PlotOgl(self.nb)
131	self.nb.AddPage(page,name)
132
133	self.plotList.append(name)
134
135	return page.figure
136
137	def Delete(self,name):
138	try:
139	item = self.plotList.index(name)
140	del self.plotList[item]
141	self.nb.DeletePage(item)
142	except ValueError: #no plot of this name - do nothing
143	return
144
145	def clear(self):
146	while self.nb.GetPageCount():
147	self.nb.DeletePage(0)
148	self.plotList = []
149	self.status.DestroyChildren()
150
151	def Rename(self,oldName,newName):
152	try:
153	item = self.plotList.index(oldName)
154	self.plotList[item] = newName
155	self.nb.SetPageText(item,newName)
156	except ValueError: #no plot of this name - do nothing
157	return
158
159	def OnPageChanged(self,event):
160	if self.plotList:
161	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
162	self.status.DestroyChildren() #get rid of special stuff on status bar
163
164	class GSASIItoolbar(Toolbar):
165	ON_MPL_HELP = wx.NewId()
166	def __init__(self,plotCanvas):
167	Toolbar.__init__(self,plotCanvas)
168	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6
169	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
170	help = os.path.join(os.path.split(__file__)[0],'help.ico')
171	self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
172	wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
173	def OnHelp(self,event):
174	Page = self.GetParent().GetParent()
175	pageNo = Page.GetSelection()
176	bookmark = Page.GetPageText(pageNo)
177	bookmark = bookmark.strip(')').replace('(','_')
178	G2gd.ShowHelp(bookmark,self.TopLevelParent)
179
180	################################################################################
181	##### PlotSngl
182	################################################################################
183
184	def PlotSngl(self,newPlot=False):
185	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
186	to F, F**2, etc. as requested
187	'''
188	from matplotlib.patches import Circle
189	global HKL,HKLF
190
191	def OnSCMotion(event):
192	xpos = event.xdata
193	if xpos:
194	xpos = round(xpos) #avoid out of frame mouse position
195	ypos = round(event.ydata)
196	zpos = Data['Layer']
197	if '100' in Data['Zone']:
198	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
199	elif '010' in Data['Zone']:
200	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
201	elif '001' in Data['Zone']:
202	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
203	Page.canvas.SetToolTipString(HKLtxt)
204	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
205
206	def OnSCPick(event):
207	zpos = Data['Layer']
208	pos = event.artist.center
209	if '100' in Data['Zone']:
210	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
211	hkl = np.array([zpos,pos[0],pos[1]])
212	elif '010' in Data['Zone']:
213	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
214	hkl = np.array([pos[0],zpos,pos[1]])
215	elif '001' in Data['Zone']:
216	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
217	hkl = np.array([pos[0],pos[1],zpos])
218	h,k,l = hkl
219	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
220	if len(hklf):
221	Fosq,sig,Fcsq = hklf[0]
222	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
223	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
224
225	def OnSCKeyPress(event):
226	print event.key
227
228	try:
229	plotNum = self.G2plotNB.plotList.index('Structure Factors')
230	Page = self.G2plotNB.nb.GetPage(plotNum)
231	if not newPlot:
232	Plot = Page.figure.gca() #get previous powder plot & get limits
233	xylim = Plot.get_xlim(),Plot.get_ylim()
234	Page.figure.clf()
235	Plot = Page.figure.gca() #get a fresh plot after clf()
236	except ValueError:
237	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
238	plotNum = self.G2plotNB.plotList.index('Structure Factors')
239	Page = self.G2plotNB.nb.GetPage(plotNum)
240	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
241	Page.canvas.mpl_connect('pick_event', OnSCPick)
242	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
243	Page.SetFocus()
244
245	Plot.set_aspect(aspect='equal')
246	HKLref = self.PatternTree.GetItemPyData(self.Sngl)[1]
247	Data = self.PatternTree.GetItemPyData(
248	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
249	Type = Data['Type']
250	scale = Data['Scale']
251	HKLmax = Data['HKLmax']
252	HKLmin = Data['HKLmin']
253	FosqMax = Data['FoMax']
254	FoMax = math.sqrt(FosqMax)
255	ifFc = Data['ifFc']
256	xlabel = ['k, h=','h, k=','h, l=']
257	ylabel = ['l','l','k']
258	zones = ['100','010','001']
259	pzone = [[1,2],[0,2],[0,1]]
260	izone = zones.index(Data['Zone'])
261	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
262	HKL = []
263	HKLF = []
264	for refl in HKLref:
265	H = np.array(refl[:3])
266	sig,Fosq,Fcsq = refl[7:10]
267	HKL.append(H)
268	HKLF.append([Fosq,sig,Fcsq])
269	if H[izone] == Data['Layer']:
270	B = 0
271	if Type == 'Fosq':
272	A = scale*Fosq/FosqMax
273	B = scale*Fcsq/FosqMax
274	C = abs(A-B)
275	elif Type == 'Fo':
276	A = scale*math.sqrt(max(0,Fosq))/FoMax
277	B = scale*math.sqrt(max(0,Fcsq))/FoMax
278	C = abs(A-B)
279	elif Type == '\|DFsq\|/sig':
280	A = abs(Fosq-Fcsq)/(scale*sig)
281	elif Type == '\|DFsq\|>sig':
282	A = abs(Fosq-Fcsq)/(scale*sig)
283	if A < 1.0: A = 0
284	elif Type == '\|DFsq\|>3sig':
285	A = abs(Fosq-Fcsq)/(scale*sig)
286	if A < 3.0: A = 0
287	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
288	if A > 0.0:
289	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
290	if B:
291	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
292	radius = C
293	if radius > 0:
294	if A > B:
295	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
296	else:
297	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
298	HKL = np.array(HKL,dtype=np.int)
299	HKLF = np.array(HKLF)
300	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
301	Plot.set_ylabel(ylabel[izone],fontsize=12)
302	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
303	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
304	if not newPlot:
305	Page.toolbar.push_current()
306	Plot.set_xlim(xylim[0])
307	Plot.set_ylim(xylim[1])
308	xylim = []
309	Page.toolbar.push_current()
310	Page.toolbar.draw()
311	else:
312	Page.canvas.draw()
313
314	################################################################################
315	##### PlotPatterns
316	################################################################################
317
318	def PlotPatterns(G2frame,newPlot=False):
319	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
320	2-theta or q (future TOF). Can display multiple patterns as "waterfall plots" or contour plots. Log I
321	plotting available.
322	'''
323	global HKL
324
325	def OnKeyBox(event):
326	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('Powder Patterns'):
327	event.key = cb.GetValue()[0]
328	cb.SetValue(' key press')
329	wx.CallAfter(OnPlotKeyPress,event)
330
331	def OnPlotKeyPress(event):
332	newPlot = False
333	if event.key == 'w':
334	if G2frame.Weight:
335	G2frame.Weight = False
336	else:
337	G2frame.Weight = True
338	G2frame.SinglePlot = True
339	newPlot = True
340	elif event.key == 'n':
341	if G2frame.Contour:
342	pass
343	else:
344	if G2frame.logPlot:
345	G2frame.logPlot = False
346	else:
347	G2frame.Offset[0] = 0
348	G2frame.logPlot = True
349	newPlot = True
350	elif event.key == 'u':
351	if G2frame.Contour:
352	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
353	elif G2frame.logPlot:
354	pass
355	elif G2frame.Offset[0] < 100.:
356	G2frame.Offset[0] += 1.
357	elif event.key == 'd':
358	if G2frame.Contour:
359	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
360	elif G2frame.logPlot:
361	pass
362	elif G2frame.Offset[0] > 0.:
363	G2frame.Offset[0] -= 1.
364	elif event.key == 'l':
365	G2frame.Offset[1] -= 1.
366	elif event.key == 'r':
367	G2frame.Offset[1] += 1.
368	elif event.key == 'o':
369	G2frame.Offset = [0,0]
370	elif event.key == 'c':
371	newPlot = True
372	if G2frame.Contour:
373	G2frame.Contour = False
374	else:
375	G2frame.Contour = True
376	G2frame.SinglePlot = False
377	G2frame.Offset = [0.,0.]
378	elif event.key == 'q':
379	newPlot = True
380	if G2frame.qPlot:
381	G2frame.qPlot = False
382	else:
383	G2frame.qPlot = True
384	elif event.key == 's':
385	if G2frame.Contour:
386	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
387	choice.sort()
388	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
389	if dlg.ShowModal() == wx.ID_OK:
390	sel = dlg.GetSelection()
391	G2frame.ContourColor = choice[sel]
392	else:
393	G2frame.ContourColor = 'Paired'
394	dlg.Destroy()
395	else:
396	if G2frame.SinglePlot:
397	G2frame.SinglePlot = False
398	else:
399	G2frame.SinglePlot = True
400	newPlot = True
401	elif event.key == '+':
402	if G2frame.PickId:
403	G2frame.PickId = False
404	elif event.key == 'i': #for smoothing contour plot
405	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
406	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
407	'mitchell','sinc','lanczos']
408	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
409	if dlg.ShowModal() == wx.ID_OK:
410	sel = dlg.GetSelection()
411	G2frame.Interpolate = choice[sel]
412	else:
413	G2frame.Interpolate = 'nearest'
414	dlg.Destroy()
415
416	PlotPatterns(G2frame,newPlot=newPlot)
417
418	def OnMotion(event):
419	xpos = event.xdata
420	if xpos: #avoid out of frame mouse position
421	ypos = event.ydata
422	Page.canvas.SetCursor(wx.CROSS_CURSOR)
423	try:
424	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
425	Parms = dict(zip(Names,Values))
426	try:
427	wave = Parms['Lam']
428	except KeyError:
429	wave = Parms['Lam1']
430	if G2frame.qPlot:
431	try:
432	xpos = 2.0asind(xposwave/(4*math.pi))
433	except ValueError: #avoid bad value in asin beyond upper limit
434	pass
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 G2frame.Contour:
439	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
440	else:
441	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
442	if G2frame.itemPicked:
443	Page.canvas.SetToolTipString('%9.3f'%(xpos))
444	if G2frame.PickId:
445	found = []
446	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists'] or \
447	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
448	if len(HKL):
449	view = Page.toolbar._views.forward()[0][:2]
450	wid = view[1]-view[0]
451	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
452	if len(found):
453	h,k,l = found[0][:3]
454	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
455	else:
456	Page.canvas.SetToolTipString('')
457
458	except TypeError:
459	G2frame.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
460
461	def OnPick(event):
462	if G2frame.itemPicked is not None: return
463	PatternId = G2frame.PatternId
464	try:
465	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
466	except TypeError:
467	return
468	Parms = dict(zip(Names,Values))
469	try:
470	wave = Parms['Lam']
471	except KeyError:
472	wave = Parms['Lam1']
473	PickId = G2frame.PickId
474	pick = event.artist
475	mouse = event.mouseevent
476	xpos = pick.get_xdata()
477	ypos = pick.get_ydata()
478	ind = event.ind
479	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
480	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
481	if ind.all() != [0]: #picked a data point
482	if 'C' in Parms['Type']: #CW data - TOF later in an elif
483	ins = [Parms[x] for x in ['U','V','W','X','Y']]
484	if G2frame.qPlot: #qplot - convert back to 2-theta
485	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
486	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
487	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
488	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
489	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
490	data.append(XY)
491	G2pdG.UpdatePeakGrid(G2frame,data)
492	PlotPatterns(G2frame)
493	else: #picked a peak list line
494	G2frame.itemPicked = pick
495	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
496	if ind.all() != [0]: #picked a data point
497	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
498	data = G2frame.PatternTree.GetItemPyData(LimitId)
499	if 'C' in Parms['Type']: #CW data - TOF later in an elif
500	if G2frame.qPlot: #qplot - convert back to 2-theta
501	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
502	if mouse.button==1:
503	data[1][0] = min(xy[0],data[1][1])
504	if mouse.button==3:
505	data[1][1] = max(xy[0],data[1][0])
506	G2frame.PatternTree.SetItemPyData(LimitId,data)
507	G2pdG.UpdateLimitsGrid(G2frame,data)
508	PlotPatterns(G2frame)
509	else: #picked a limit line
510	G2frame.itemPicked = pick
511	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
512	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
513	G2frame.itemPicked = pick
514	pick = str(pick)
515
516	def OnRelease(event):
517	if G2frame.itemPicked is None: return
518	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
519	Parms = dict(zip(Names,Values))
520	try:
521	wave = Parms['Lam']
522	except KeyError:
523	wave = Parms['Lam1']
524	xpos = event.xdata
525	PickId = G2frame.PickId
526	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
527	lines = []
528	for line in G2frame.Lines:
529	lines.append(line.get_xdata()[0])
530	# print G2frame.itemPicked.get_xdata()
531	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
532	if lineNo in [0,1]:
533	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
534	data = G2frame.PatternTree.GetItemPyData(LimitId)
535	if G2frame.qPlot:
536	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
537	else:
538	data[1][lineNo] = xpos
539	G2frame.PatternTree.SetItemPyData(LimitId,data)
540	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
541	G2pdG.UpdateLimitsGrid(G2frame,data)
542	else:
543	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
544	data = G2frame.PatternTree.GetItemPyData(PeakId)
545	# print 'peaks',xpos
546	if event.button == 3:
547	del data[lineNo-2]
548	else:
549	if G2frame.qPlot:
550	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
551	else:
552	data[lineNo-2][0] = xpos
553	G2frame.PatternTree.SetItemPyData(PeakId,data)
554	G2pdG.UpdatePeakGrid(G2frame,data)
555	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
556	'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos:
557	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
558	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
559	if 'line' not in pick: #avoid data points, etc.
560	num = Phases.keys().index(pick)
561	if num:
562	G2frame.refDelt = -(event.ydata-G2frame.refOffset)/(num*Ymax)
563	else: #1st row of refl ticks
564	G2frame.refOffset = event.ydata
565	PlotPatterns(G2frame)
566	G2frame.itemPicked = None
567
568	xylim = []
569	try:
570	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
571	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
572	if not newPlot:
573	Plot = Page.figure.gca() #get previous powder plot & get limits
574	xylim = Plot.get_xlim(),Plot.get_ylim()
575	Page.figure.clf()
576	Plot = Page.figure.gca() #get a fresh plot after clf()
577	except ValueError:
578	newPlot = True
579	G2frame.Cmax = 1.0
580	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
581	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
582	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
583	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
584	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
585	Page.canvas.mpl_connect('pick_event', OnPick)
586	Page.canvas.mpl_connect('button_release_event', OnRelease)
587	Page.SetFocus()
588	G2frame.G2plotNB.status.DestroyChildren()
589	if G2frame.Contour:
590	Choice = (' key press','d: lower contour max','u: raise contour max',
591	'i: interpolation method','s: color scheme','c: contour off')
592	else:
593	if G2frame.logPlot:
594	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
595	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
596	else:
597	Choice = (' key press','l: offset left','r: offset right','d: offset down',
598	'u: offset up','o: reset offset','n: log(I) on','c: contour on',
599	'q: toggle q plot','s: toggle single plot','w: toggle divide by sig','+: no selection')
600	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
601	choices=Choice)
602	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
603	cb.SetValue(' key press')
604
605	PickId = G2frame.PickId
606	PatternId = G2frame.PatternId
607	colors=['b','g','r','c','m','k']
608	Lines = []
609	if G2frame.SinglePlot:
610	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
611	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
612	PlotList = [Pattern,]
613	ParmList = [G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
614	G2frame.PatternId, 'Instrument Parameters'))[1],]
615	else:
616	PlotList = []
617	ParmList = []
618	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
619	while item:
620	if 'PWDR' in G2frame.PatternTree.GetItemText(item):
621	Pattern = G2frame.PatternTree.GetItemPyData(item)
622	if len(Pattern) < 3: # put name on end if needed
623	Pattern.append(G2frame.PatternTree.GetItemText(item))
624	PlotList.append(Pattern)
625	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
626	item,'Instrument Parameters'))[1])
627	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
628	Ymax = 1.0
629	lenX = 0
630	if PickId:
631	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
632	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
633	HKL = []
634	if Phases:
635	for peak in Phases[G2frame.RefList]:
636	HKL.append(peak[:6])
637	HKL = np.array(HKL)
638	else:
639	HKL = np.array(G2frame.HKL)
640	for Pattern in PlotList:
641	xye = Pattern[1]
642	Ymax = max(Ymax,max(xye[1]))
643	offset = G2frame.Offset[0]*Ymax/100.0
644	Title = 'Powder Patterns: '+os.path.split(G2frame.GSASprojectfile)[1]
645	if G2frame.logPlot:
646	Title = 'log('+Title+')'
647	Plot.set_title(Title)
648	if G2frame.qPlot:
649	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
650	else:
651	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
652	if G2frame.Weight:
653	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=14)
654	else:
655	Plot.set_ylabel('Intensity',fontsize=12)
656	if G2frame.Contour:
657	ContourZ = []
658	ContourY = []
659	Nseq = 0
660	if len(PlotList) < 2:
661	G2frame.Contour = False
662	for N,Pattern in enumerate(PlotList):
663	Parms = ParmList[N]
664	ifpicked = False
665	LimitId = 0
666	xye = np.array(Pattern[1])
667	if PickId:
668	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
669	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
670	if G2frame.qPlot:
671	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
672	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
673	else:
674	X = xye[0]
675	if not lenX:
676	lenX = len(X)
677	Y = xye[1]+offset*N
678	if LimitId:
679	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
680	if G2frame.qPlot:
681	limits = 4np.pinpsind(limits/2.0)/Parms[1]
682	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
683	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
684	if G2frame.Contour:
685
686	if lenX == len(X):
687	ContourY.append(N)
688	ContourZ.append(Y)
689	ContourX = X
690	Nseq += 1
691	Plot.set_ylabel('Data sequence',fontsize=12)
692	else:
693	X += G2frame.Offset[1].005N
694	if ifpicked:
695	Z = xye[3]+offset*N
696	W = xye[4]+offset*N
697	D = xye[5]-Ymax*G2frame.delOffset
698	if G2frame.logPlot:
699	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
700	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
701	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
702	elif G2frame.Weight:
703	DY = xye[1]*np.sqrt(xye[2])
704	DYmax = max(DY)
705	DZ = xye[3]*np.sqrt(xye[2])
706	DS = xye[5]np.sqrt(xye[2])-DYmaxG2frame.delOffset
707	Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False)
708	Plot.plot(X,DZ,colors[(N+1)%6],picker=False)
709	Plot.plot(X,DS,colors[(N+3)%6],picker=False)
710	Plot.axhline(0.,color=wx.BLACK)
711	else:
712	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
713	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
714	Plot.plot(X,W,colors[(N+2)%6],picker=False)
715	Plot.plot(X,D,colors[(N+3)%6],picker=False)
716	Plot.axhline(0.,color=wx.BLACK)
717	Page.canvas.SetToolTipString('')
718	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
719	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
720	Page.canvas.SetToolTipString(tip)
721	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
722	for item in data:
723	if G2frame.qPlot:
724	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
725	else:
726	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
727	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
728	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
729	Page.canvas.SetToolTipString(tip)
730	data = G2frame.LimitsTable.GetData()
731	else:
732	if G2frame.logPlot:
733	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
734	else:
735	Plot.plot(X,Y,colors[N%6],picker=False)
736	if PickId and not G2frame.Contour:
737	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))[1::2]
738	Parms = dict(zip(Names,Values))
739	try:
740	wave = Parms['Lam']
741	except KeyError:
742	wave = Parms['Lam1']
743	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
744	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
745	for peak in peaks:
746	if G2frame.qPlot:
747	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
748	else:
749	Plot.axvline(peak[0],color='b')
750	for hkl in G2frame.HKL:
751	if G2frame.qPlot:
752	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
753	else:
754	Plot.axvline(hkl[5],color='r',dashes=(5,5))
755	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
756	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
757	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
758	for pId,phase in enumerate(Phases):
759	peaks = Phases[phase]
760	if not peaks:
761	continue
762	peak = np.array([[peak[4],peak[5]] for peak in peaks])
763	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
764	if G2frame.qPlot:
765	Plot.plot(2*np.pi/peak.T[0],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
766	else:
767	Plot.plot(peak.T[1],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
768	if len(Phases):
769	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
770	if handles:
771	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
772
773	if G2frame.Contour:
774	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
775	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
776	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
777	Page.figure.colorbar(Img)
778	else:
779	G2frame.Lines = Lines
780	if not newPlot:
781	Page.toolbar.push_current()
782	Plot.set_xlim(xylim[0])
783	Plot.set_ylim(xylim[1])
784	xylim = []
785	Page.toolbar.push_current()
786	Page.toolbar.draw()
787	else:
788	Page.canvas.draw()
789	# G2frame.Pwdr = True
790
791	################################################################################
792	##### PlotDeltSig
793	################################################################################
794
795	def PlotDeltSig(G2frame,kind):
796	try:
797	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
798	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
799	Page.figure.clf()
800	Plot = Page.figure.gca() #get a fresh plot after clf()
801	except ValueError:
802	newPlot = True
803	G2frame.Cmax = 1.0
804	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
805	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
806	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
807	PatternId = G2frame.PatternId
808	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
809	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
810	wtFactor = Pattern[0]['wtFactor']
811	if kind == 'PWDR':
812	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
813	xye = np.array(Pattern[1])
814	xmin = np.searchsorted(xye[0],limits[0])
815	xmax = np.searchsorted(xye[0],limits[1])
816	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
817	elif kind == 'HKLF':
818	refl = Pattern[1]
819	DS = []
820	for ref in refl:
821	if ref[6] > 0.:
822	DS.append((ref[5]-ref[7])/ref[6])
823	Page.SetFocus()
824	G2frame.G2plotNB.status.DestroyChildren()
825	DS.sort()
826	EDS = np.zeros_like(DS)
827	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
828	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
829	T = np.sqrt(np.log(1.0/DX**2))
830	top = 2.515517+0.802853T+0.010328T**2
831	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
832	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
833	low1 = np.searchsorted(EDS,-1.)
834	hi1 = np.searchsorted(EDS,1.)
835	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
836	frac = 100.*(hi1-low1)/len(DS)
837	G2frame.G2plotNB.status.SetStatusText( \
838	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
839	Plot.set_title('Normal probability for '+Pattern[-1])
840	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
841	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
842	Plot.plot(EDS,DS,'r+',label='result')
843	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
844	Plot.legend(loc='upper left')
845	np.seterr(invalid='warn')
846	Page.canvas.draw()
847
848	################################################################################
849	##### PlotISFG
850	################################################################################
851
852	def PlotISFG(G2frame,newPlot=False,type=''):
853	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
854	or multiple plots with waterfall and contour plots as options
855	'''
856	if not type:
857	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
858	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
859	return
860	superMinusOne = unichr(0xaf)+unichr(0xb9)
861
862	def OnPlotKeyPress(event):
863	newPlot = False
864	if event.key == 'u':
865	if G2frame.Contour:
866	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
867	elif G2frame.Offset[0] < 100.:
868	G2frame.Offset[0] += 1.
869	elif event.key == 'd':
870	if G2frame.Contour:
871	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
872	elif G2frame.Offset[0] > 0.:
873	G2frame.Offset[0] -= 1.
874	elif event.key == 'l':
875	G2frame.Offset[1] -= 1.
876	elif event.key == 'r':
877	G2frame.Offset[1] += 1.
878	elif event.key == 'o':
879	G2frame.Offset = [0,0]
880	elif event.key == 'c':
881	newPlot = True
882	if G2frame.Contour:
883	G2frame.Contour = False
884	else:
885	G2frame.Contour = True
886	G2frame.SinglePlot = False
887	G2frame.Offset = [0.,0.]
888	elif event.key == 's':
889	if G2frame.Contour:
890	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
891	choice.sort()
892	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
893	if dlg.ShowModal() == wx.ID_OK:
894	sel = dlg.GetSelection()
895	G2frame.ContourColor = choice[sel]
896	else:
897	G2frame.ContourColor = 'Paired'
898	dlg.Destroy()
899	else:
900	if G2frame.SinglePlot:
901	G2frame.SinglePlot = False
902	else:
903	G2frame.SinglePlot = True
904	elif event.key == 'i': #for smoothing contour plot
905	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
906	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
907	'mitchell','sinc','lanczos']
908	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
909	if dlg.ShowModal() == wx.ID_OK:
910	sel = dlg.GetSelection()
911	G2frame.Interpolate = choice[sel]
912	else:
913	G2frame.Interpolate = 'nearest'
914	dlg.Destroy()
915	elif event.key == 't' and not G2frame.Contour:
916	if G2frame.Legend:
917	G2frame.Legend = False
918	else:
919	G2frame.Legend = True
920
921
922	PlotISFG(G2frame,newPlot=newPlot,type=type)
923
924	def OnKeyBox(event):
925	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
926	event.key = cb.GetValue()[0]
927	cb.SetValue(' key press')
928	wx.CallAfter(OnPlotKeyPress,event)
929
930	def OnMotion(event):
931	xpos = event.xdata
932	if xpos: #avoid out of frame mouse position
933	ypos = event.ydata
934	Page.canvas.SetCursor(wx.CROSS_CURSOR)
935	try:
936	if G2frame.Contour:
937	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
938	else:
939	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
940	except TypeError:
941	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
942
943	xylim = []
944	try:
945	plotNum = G2frame.G2plotNB.plotList.index(type)
946	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
947	if not newPlot:
948	Plot = Page.figure.gca() #get previous plot & get limits
949	xylim = Plot.get_xlim(),Plot.get_ylim()
950	Page.figure.clf()
951	Plot = Page.figure.gca()
952	except ValueError:
953	newPlot = True
954	G2frame.Cmax = 1.0
955	Plot = G2frame.G2plotNB.addMpl(type).gca()
956	plotNum = G2frame.G2plotNB.plotList.index(type)
957	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
958	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
959	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
960
961	Page.SetFocus()
962	G2frame.G2plotNB.status.DestroyChildren()
963	if G2frame.Contour:
964	Choice = (' key press','d: lower contour max','u: raise contour max',
965	'i: interpolation method','s: color scheme','c: contour off')
966	else:
967	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
968	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
969	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
970	choices=Choice)
971	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
972	cb.SetValue(' key press')
973	PatternId = G2frame.PatternId
974	PickId = G2frame.PickId
975	Plot.set_title(type)
976	if type == 'G(R)':
977	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
978	else:
979	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
980	Plot.set_ylabel(r''+type,fontsize=14)
981	colors=['b','g','r','c','m','k']
982	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
983	Pattern = []
984	if G2frame.SinglePlot:
985	name = G2frame.PatternTree.GetItemText(PatternId)
986	name = type+name[4:]
987	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
988	Pattern = G2frame.PatternTree.GetItemPyData(Id)
989	if Pattern:
990	Pattern.append(name)
991	PlotList = [Pattern,]
992	else:
993	PlotList = []
994	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
995	while item:
996	if 'PDF' in G2frame.PatternTree.GetItemText(item):
997	name = type+G2frame.PatternTree.GetItemText(item)[4:]
998	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
999	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1000	if Pattern:
1001	Pattern.append(name)
1002	PlotList.append(Pattern)
1003	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1004	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
1005	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
1006	Xb = [0.,10.]
1007	Yb = [0.,-40.np.pinumbDen]
1008	Ymax = 1.0
1009	lenX = 0
1010	for Pattern in PlotList:
1011	xye = Pattern[1]
1012	Ymax = max(Ymax,max(xye[1]))
1013	offset = G2frame.Offset[0]*Ymax/100.0
1014	if G2frame.Contour:
1015	ContourZ = []
1016	ContourY = []
1017	Nseq = 0
1018	for N,Pattern in enumerate(PlotList):
1019	xye = Pattern[1]
1020	if PickId:
1021	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1022	X = xye[0]
1023	if not lenX:
1024	lenX = len(X)
1025	Y = xye[1]+offset*N
1026	if G2frame.Contour:
1027	if lenX == len(X):
1028	ContourY.append(N)
1029	ContourZ.append(Y)
1030	ContourX = X
1031	Nseq += 1
1032	Plot.set_ylabel('Data sequence',fontsize=12)
1033	else:
1034	X = xye[0]+G2frame.Offset[1].005N
1035	if ifpicked:
1036	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1037	Page.canvas.SetToolTipString('')
1038	else:
1039	if G2frame.Legend:
1040	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1041	else:
1042	Plot.plot(X,Y,colors[N%6],picker=False)
1043	if type == 'G(R)':
1044	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1045	elif type == 'F(Q)':
1046	Plot.axhline(0.,color=wx.BLACK)
1047	elif type == 'S(Q)':
1048	Plot.axhline(1.,color=wx.BLACK)
1049	if G2frame.Contour:
1050	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1051	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1052	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1053	Page.figure.colorbar(Img)
1054	elif G2frame.Legend:
1055	Plot.legend(loc='best')
1056	if not newPlot:
1057	Page.toolbar.push_current()
1058	Plot.set_xlim(xylim[0])
1059	Plot.set_ylim(xylim[1])
1060	xylim = []
1061	Page.toolbar.push_current()
1062	Page.toolbar.draw()
1063	else:
1064	Page.canvas.draw()
1065
1066	################################################################################
1067	##### PlotXY
1068	################################################################################
1069
1070	def PlotXY(G2frame,XY,newPlot=False,type=''):
1071	'''simple plot of xy data, used for diagnostic purposes
1072	'''
1073	def OnMotion(event):
1074	xpos = event.xdata
1075	if xpos: #avoid out of frame mouse position
1076	ypos = event.ydata
1077	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1078	try:
1079	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
1080	except TypeError:
1081	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1082
1083	try:
1084	plotNum = G2frame.G2plotNB.plotList.index(type)
1085	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1086	if not newPlot:
1087	Plot = Page.figure.gca()
1088	xylim = Plot.get_xlim(),Plot.get_ylim()
1089	Page.figure.clf()
1090	Plot = Page.figure.gca()
1091	except ValueError:
1092	newPlot = True
1093	Plot = G2frame.G2plotNB.addMpl(type).gca()
1094	plotNum = G2frame.G2plotNB.plotList.index(type)
1095	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1096	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1097
1098	Page.SetFocus()
1099	G2frame.G2plotNB.status.DestroyChildren()
1100	Plot.set_title(type)
1101	Plot.set_xlabel(r'X',fontsize=14)
1102	Plot.set_ylabel(r''+type,fontsize=14)
1103	colors=['b','g','r','c','m','k']
1104	Ymax = 1.0
1105	lenX = 0
1106	X,Y = XY[:2]
1107	Ymax = max(Ymax,max(Y))
1108	Plot.plot(X,Y,'k',picker=False)
1109	if not newPlot:
1110	Page.toolbar.push_current()
1111	Plot.set_xlim(xylim[0])
1112	Plot.set_ylim(xylim[1])
1113	xylim = []
1114	Page.toolbar.push_current()
1115	Page.toolbar.draw()
1116	else:
1117	Page.canvas.draw()
1118
1119	################################################################################
1120	##### PlotPowderLines
1121	################################################################################
1122
1123	def PlotPowderLines(G2frame):
1124	''' plotting of powder lines (i.e. no powder pattern) as sticks
1125	'''
1126	global HKL
1127
1128	def OnMotion(event):
1129	xpos = event.xdata
1130	if xpos: #avoid out of frame mouse position
1131	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1132	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1133	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
1134	found = []
1135	if len(HKL):
1136	view = Page.toolbar._views.forward()[0][:2]
1137	wid = view[1]-view[0]
1138	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1139	if len(found):
1140	h,k,l = found[0][:3]
1141	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1142	else:
1143	Page.canvas.SetToolTipString('')
1144
1145	try:
1146	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1147	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1148	Page.figure.clf()
1149	Plot = Page.figure.gca()
1150	except ValueError:
1151	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
1152	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1153	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1154	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1155
1156	Page.SetFocus()
1157	Plot.set_title('Powder Pattern Lines')
1158	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1159	PickId = G2frame.PickId
1160	PatternId = G2frame.PatternId
1161	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
1162	for peak in peaks:
1163	Plot.axvline(peak[0],color='b')
1164	HKL = np.array(G2frame.HKL)
1165	for hkl in G2frame.HKL:
1166	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1167	xmin = peaks[0][0]
1168	xmax = peaks[-1][0]
1169	delt = xmax-xmin
1170	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1171	Plot.set_xlim(xlim)
1172	Page.canvas.draw()
1173	Page.toolbar.push_current()
1174
1175	################################################################################
1176	##### PlotPeakWidths
1177	################################################################################
1178
1179	def PlotPeakWidths(G2frame):
1180	''' Plotting of instrument broadening terms as function of 2-theta (future TOF)
1181	Seen when "Instrument Parameters" chosen from powder pattern data tree
1182	'''
1183	PatternId = G2frame.PatternId
1184	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1185	if limitID:
1186	limits = G2frame.PatternTree.GetItemPyData(limitID)
1187	else:
1188	return
1189	instParms = G2frame.PatternTree.GetItemPyData( \
1190	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1191	if instParms[0][0] in ['PXC','PNC']:
1192	lam = instParms[1][1]
1193	if len(instParms[1]) == 13:
1194	GU,GV,GW,LX,LY = instParms[0][6:11]
1195	else:
1196	GU,GV,GW,LX,LY = instParms[0][4:9]
1197	peakID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
1198	if peakID:
1199	peaks = G2frame.PatternTree.GetItemPyData(peakID)
1200	else:
1201	peaks = []
1202
1203	try:
1204	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1205	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1206	Page.figure.clf()
1207	Plot = Page.figure.gca()
1208	except ValueError:
1209	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
1210	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1211	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1212	Page.SetFocus()
1213
1214	Page.canvas.SetToolTipString('')
1215	colors=['b','g','r','c','m','k']
1216	Xmin,Xmax = limits[1]
1217	Xmin = min(0.5,max(Xmin,1))
1218	Xmin /= 2
1219	Xmax /= 2
1220	nPts = 100
1221	delt = (Xmax-Xmin)/nPts
1222	thetas = []
1223	for i in range(nPts):
1224	thetas.append(Xmin+i*delt)
1225	X = []
1226	Y = []
1227	Z = []
1228	W = []
1229	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1230	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1231	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.)
1232	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1233	try:
1234	for theta in thetas:
1235	X.append(4.0math.pisind(theta)/lam) #q
1236	s = sig(theta,GU,GV,GW)
1237	g = gam(theta,LX,LY)
1238	G = gamFW(g,s)
1239	Y.append(s/tand(theta))
1240	Z.append(g/tand(theta))
1241	W.append(G/tand(theta))
1242	Plot.set_title('Instrument and sample peak widths')
1243	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1244	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1245	Plot.plot(X,Y,color='r',label='Gaussian')
1246	Plot.plot(X,Z,color='g',label='Lorentzian')
1247	Plot.plot(X,W,color='b',label='G+L')
1248	X = []
1249	Y = []
1250	Z = []
1251	W = []
1252	V = []
1253	for peak in peaks:
1254	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1255	try:
1256	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1257	except ValueError:
1258	s = 0.01
1259	g = peak[6]*math.pi/18000.
1260	G = gamFW(g,s)
1261	Y.append(s/tand(peak[0]/2.))
1262	Z.append(g/tand(peak[0]/2.))
1263	W.append(G/tand(peak[0]/2.))
1264	Plot.plot(X,Y,'+',color='r',label='G peak')
1265	Plot.plot(X,Z,'+',color='g',label='L peak')
1266	Plot.plot(X,W,'+',color='b',label='G+L peak')
1267	Plot.legend(loc='best')
1268	Page.canvas.draw()
1269	except ValueError:
1270	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
1271	'%.3f'%(2*theta)
1272	G2frame.G2plotNB.Delete('Peak Widths')
1273
1274
1275	################################################################################
1276	##### PlotSizeStrainPO
1277	################################################################################
1278
1279	def PlotSizeStrainPO(G2frame,data,Start=False):
1280	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1281	'''
1282
1283	PatternId = G2frame.PatternId
1284	generalData = data['General']
1285	SGData = generalData['SGData']
1286	SGLaue = SGData['SGLaue']
1287	if Start: #initialize the spherical harmonics qlmn arrays
1288	ptx.pyqlmninit()
1289	Start = False
1290	# MuStrKeys = G2spc.MustrainNames(SGData)
1291	cell = generalData['Cell'][1:]
1292	A,B = G2lat.cell2AB(cell[:6])
1293	Vol = cell[6]
1294	useList = data['Histograms']
1295	phase = generalData['Name']
1296	plotType = generalData['Data plot type']
1297	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
1298	for ptype in plotDict:
1299	G2frame.G2plotNB.Delete(ptype)
1300	if plotType in ['None']:
1301	return
1302
1303	for item in useList:
1304	if useList[item]['Show']:
1305	break
1306	else:
1307	return #nothing to show!!
1308
1309	numPlots = len(useList)
1310
1311	if plotType in ['Mustrain','Size']:
1312	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
1313	else:
1314	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
1315	plotNum = G2frame.G2plotNB.plotList.index(plotType)
1316	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1317	Page.SetFocus()
1318	G2frame.G2plotNB.status.SetStatusText('',1)
1319	if not Page.IsShown():
1320	Page.Show()
1321
1322	for item in useList:
1323	if useList[item]['Show']:
1324	PHI = np.linspace(0.,360.,30,True)
1325	PSI = np.linspace(0.,180.,30,True)
1326	X = np.outer(npsind(PHI),npsind(PSI))
1327	Y = np.outer(npcosd(PHI),npsind(PSI))
1328	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1329	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
1330	coeff = useList[item][plotDict[plotType]]
1331	except KeyError:
1332	break
1333	if plotType in ['Mustrain','Size']:
1334	if coeff[0] == 'isotropic':
1335	X *= coeff[1][0]
1336	Y *= coeff[1][0]
1337	Z *= coeff[1][0]
1338	elif coeff[0] == 'uniaxial':
1339
1340	def uniaxCalc(xyz,iso,aniso,axes):
1341	Z = np.array(axes)
1342	cp = abs(np.dot(xyz,Z))
1343	sp = np.sqrt(1.-cp**2)
1344	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
1345	return R*xyz
1346
1347	iso,aniso = coeff[1][:2]
1348	axes = np.inner(A,np.array(coeff[3]))
1349	axes /= nl.norm(axes)
1350	Shkl = np.array(coeff[1])
1351	XYZ = np.dstack((X,Y,Z))
1352	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
1353	X,Y,Z = np.dsplit(XYZ,3)
1354	X = X[:,:,0]
1355	Y = Y[:,:,0]
1356	Z = Z[:,:,0]
1357
1358	elif coeff[0] == 'ellipsoidal':
1359
1360	def ellipseCalc(xyz,E,R):
1361	XYZ = xyz*E.T
1362	return np.inner(XYZ.T,R)
1363
1364	S6 = coeff[4]
1365	Sij = G2lat.U6toUij(S6)
1366	E,R = nl.eigh(Sij)
1367	XYZ = np.dstack((X,Y,Z))
1368	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
1369	X,Y,Z = np.dsplit(XYZ,3)
1370	X = X[:,:,0]
1371	Y = Y[:,:,0]
1372	Z = Z[:,:,0]
1373
1374	elif coeff[0] == 'generalized':
1375
1376	def genMustrain(xyz,SGData,A,Shkl):
1377	uvw = np.inner(A.T,xyz)
1378	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1379	sum = np.sum(np.multiply(Shkl,Strm))
1380	sum = np.where(sum > 0.01,sum,0.01)
1381	sum = np.sqrt(sum)*math.pi/0.018 #centidegrees to radians!
1382	return sum*xyz
1383
1384	Shkl = np.array(coeff[4])
1385	if np.any(Shkl):
1386	XYZ = np.dstack((X,Y,Z))
1387	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1388	X,Y,Z = np.dsplit(XYZ,3)
1389	X = X[:,:,0]
1390	Y = Y[:,:,0]
1391	Z = Z[:,:,0]
1392
1393	if np.any(X) and np.any(Y) and np.any(Z):
1394	errFlags = np.seterr(all='ignore')
1395	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1396	np.seterr(all='ignore')
1397	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
1398	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
1399	Plot.set_xlim3d(XYZlim)
1400	Plot.set_ylim3d(XYZlim)
1401	Plot.set_zlim3d(XYZlim)
1402	Plot.set_aspect('equal')
1403	if plotType == 'Size':
1404	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
1405	Plot.set_xlabel(r'X, $\mu$m')
1406	Plot.set_ylabel(r'Y, $\mu$m')
1407	Plot.set_zlabel(r'Z, $\mu$m')
1408	else:
1409	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
1410	Plot.set_xlabel(r'X, $\mu$strain')
1411	Plot.set_ylabel(r'Y, $\mu$strain')
1412	Plot.set_zlabel(r'Z, $\mu$strain')
1413	else:
1414	h,k,l = generalData['POhkl']
1415	if coeff[0] == 'MD':
1416	print 'March-Dollase preferred orientation plot'
1417
1418	else:
1419	PH = np.array(generalData['POhkl'])
1420	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
1421	SHCoef = {}
1422	for item in coeff[5]:
1423	L,N = eval(item.strip('C'))
1424	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
1425	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1426	X = np.linspace(0,90.0,26)
1427	Y = G2lat.polfcal(ODFln,'0',X,0.0)
1428	Plot.plot(X,Y,color='k',label=str(PH))
1429	Plot.legend(loc='best')
1430	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
1431	Plot.set_xlabel(r'$\psi$',fontsize=16)
1432	Plot.set_ylabel('MRD',fontsize=14)
1433	Page.canvas.draw()
1434
1435	################################################################################
1436	##### PlotTexture
1437	################################################################################
1438
1439	def PlotTexture(G2frame,data,Start=False):
1440	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
1441	plotting.
1442	dict generalData contains all phase info needed which is in data
1443	'''
1444
1445	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1446	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1447	PatternId = G2frame.PatternId
1448	generalData = data['General']
1449	SGData = generalData['SGData']
1450	textureData = generalData['SH Texture']
1451	G2frame.G2plotNB.Delete('Texture')
1452	if not textureData['Order']:
1453	return #no plot!!
1454	SHData = generalData['SH Texture']
1455	SHCoef = SHData['SH Coeff'][1]
1456	cell = generalData['Cell'][1:7]
1457	Amat,Bmat = G2lat.cell2AB(cell)
1458	sq2 = 1.0/math.sqrt(2.0)
1459
1460	def rp2xyz(r,p):
1461	z = npcosd(r)
1462	xy = np.sqrt(1.-z**2)
1463	return xynpsind(p),xynpcosd(p),z
1464
1465	def OnMotion(event):
1466	SHData = data['General']['SH Texture']
1467	if event.xdata and event.ydata: #avoid out of frame errors
1468	xpos = event.xdata
1469	ypos = event.ydata
1470	if 'Inverse' in SHData['PlotType']:
1471	r = xpos2+ypos2
1472	if r <= 1.0:
1473	if 'equal' in G2frame.Projection:
1474	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1475	else:
1476	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1477	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1478	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1479	y,x,z = list(xyz/np.max(np.abs(xyz)))
1480
1481	G2frame.G2plotNB.status.SetFields(['',
1482	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1483
1484	elif 'Axial' in SHData['PlotType']:
1485	pass
1486
1487	else: #ordinary pole figure
1488	z = xpos2+ypos2
1489	if z <= 1.0:
1490	z = np.sqrt(z)
1491	if 'equal' in G2frame.Projection:
1492	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1493	else:
1494	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1495	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1496	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1497
1498	try:
1499	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1500	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1501	Page.figure.clf()
1502	Plot = Page.figure.gca()
1503	if not Page.IsShown():
1504	Page.Show()
1505	except ValueError:
1506	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
1507	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1508	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1509	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1510
1511	Page.SetFocus()
1512	G2frame.G2plotNB.status.SetFields(['',''])
1513	PH = np.array(SHData['PFhkl'])
1514	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1515	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1516	PX = np.array(SHData['PFxyz'])
1517	gam = atan2d(PX[0],PX[1])
1518	xy = math.sqrt(PX[0]2+PX[1]2)
1519	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1520	psi = asind(xy/xyz)
1521	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1522	if 'Axial' in SHData['PlotType']:
1523	X = np.linspace(0,90.0,26)
1524	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1525	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1526	Plot.legend(loc='best')
1527	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1528	Plot.set_xlabel(r'$\psi$',fontsize=16)
1529	Plot.set_ylabel('MRD',fontsize=14)
1530
1531	else:
1532	npts = 201
1533	if 'Inverse' in SHData['PlotType']:
1534	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1535	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1536	if 'equal' in G2frame.Projection:
1537	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1538	else:
1539	R = np.where(R <= 1.,2.*npatand(R),0.0)
1540	Z = np.zeros_like(R)
1541	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
1542	Z = np.reshape(Z,(npts,npts))
1543	CS = Plot.contour(Y,X,Z,aspect='equal')
1544	Plot.clabel(CS,fontsize=9,inline=1)
1545	try:
1546	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
1547	except ValueError:
1548	pass
1549	Page.figure.colorbar(Img)
1550	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
1551	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
1552
1553	else:
1554	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1555	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1556	if 'equal' in G2frame.Projection:
1557	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1558	else:
1559	R = np.where(R <= 1.,2.*npatand(R),0.0)
1560	Z = np.zeros_like(R)
1561	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
1562	Z = np.reshape(Z,(npts,npts))
1563	try:
1564	CS = Plot.contour(Y,X,Z,aspect='equal')
1565	Plot.clabel(CS,fontsize=9,inline=1)
1566	except ValueError:
1567	pass
1568	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
1569	Page.figure.colorbar(Img)
1570	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
1571	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
1572	Page.canvas.draw()
1573
1574	################################################################################
1575	##### PlotCovariance
1576	################################################################################
1577
1578	def PlotCovariance(G2frame,Data={}):
1579	if not Data:
1580	Data = G2frame.PatternTree.GetItemPyData(
1581	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1582	if not Data:
1583	print 'No covariance matrix available'
1584	return
1585	varyList = Data['varyList']
1586	values = Data['variables']
1587	Xmax = len(varyList)
1588	covMatrix = Data['covMatrix']
1589	sig = np.sqrt(np.diag(covMatrix))
1590	xvar = np.outer(sig,np.ones_like(sig))
1591	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
1592	title = ' for\n'+Data['title']
1593	newAtomDict = Data['newAtomDict']
1594
1595	def OnPlotKeyPress(event):
1596	newPlot = False
1597	if event.key == 's':
1598	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1599	choice.sort()
1600	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1601	if dlg.ShowModal() == wx.ID_OK:
1602	sel = dlg.GetSelection()
1603	G2frame.VcovColor = choice[sel]
1604	else:
1605	G2frame.VcovColor = 'RdYlGn'
1606	dlg.Destroy()
1607	PlotCovariance(G2frame)
1608
1609	def OnMotion(event):
1610	if event.button:
1611	ytics = imgAx.get_yticks()
1612	ytics = np.where(ytics<len(varyList),ytics,-1)
1613	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
1614	imgAx.set_yticklabels(ylabs)
1615
1616	if event.xdata and event.ydata: #avoid out of frame errors
1617	xpos = int(event.xdata+.5)
1618	ypos = int(event.ydata+.5)
1619	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
1620	if xpos == ypos:
1621	value = values[xpos]
1622	name = varyList[xpos]
1623	if varyList[xpos] in newAtomDict:
1624	name,value = newAtomDict[name]
1625	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
1626	else:
1627	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
1628	Page.canvas.SetToolTipString(msg)
1629	G2frame.G2plotNB.status.SetFields(['Key: s to change colors',msg])
1630	try:
1631	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1632	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1633	Page.figure.clf()
1634	Plot = Page.figure.gca()
1635	if not Page.IsShown():
1636	Page.Show()
1637	except ValueError:
1638	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
1639	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1640	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1641	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1642	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1643
1644	Page.SetFocus()
1645	G2frame.G2plotNB.status.SetFields(['',''])
1646	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
1647	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower')
1648	imgAx = Img.get_axes()
1649	ytics = imgAx.get_yticks()
1650	ylabs = [varyList[int(i)] for i in ytics[:-1]]
1651	imgAx.set_yticklabels(ylabs)
1652	colorBar = Page.figure.colorbar(Img)
1653	Plot.set_title('V-Cov matrix'+title)
1654	Plot.set_xlabel('Variable number')
1655	Plot.set_ylabel('Variable name')
1656	Page.canvas.draw()
1657
1658	################################################################################
1659	##### PlotSeq
1660	################################################################################
1661
1662	def PlotSeq(G2frame,SeqData,SeqSig,SeqNames,sampleParm):
1663
1664	def OnKeyPress(event):
1665	if event.key == 's' and sampleParm:
1666	if G2frame.xAxis:
1667	G2frame.xAxis = False
1668	else:
1669	G2frame.xAxis = True
1670	Draw(False)
1671	try:
1672	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1673	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1674	Page.figure.clf()
1675	Plot = Page.figure.gca()
1676	if not Page.IsShown():
1677	Page.Show()
1678	except ValueError:
1679	Plot = G2frame.G2plotNB.addMpl('Sequential refinement').gca()
1680	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1681	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1682	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
1683	G2frame.xAxis = False
1684
1685	def Draw(newPlot):
1686	Page.SetFocus()
1687	G2frame.G2plotNB.status.SetFields(['','press s to toggle x-axis = sample environment parameter'])
1688	if len(SeqData):
1689	Plot.clear()
1690	if G2frame.xAxis:
1691	xName = sampleParm.keys()[0]
1692	X = sampleParm[xName]
1693	else:
1694	X = np.arange(0,len(SeqData[0]),1)
1695	xName = 'Data sequence number'
1696	for Y,sig,name in zip(SeqData,SeqSig,SeqNames):
1697	Plot.errorbar(X,Y,yerr=sig,label=name)
1698	Plot.legend(loc='best')
1699	Plot.set_ylabel('Parameter values')
1700	Plot.set_xlabel(xName)
1701	Page.canvas.draw()
1702	Draw(True)
1703
1704	################################################################################
1705	##### PlotExposedImage & PlotImage
1706	################################################################################
1707
1708	def PlotExposedImage(G2frame,newPlot=False,event=None):
1709	'''General access module for 2D image plotting
1710	'''
1711	plotNo = G2frame.G2plotNB.nb.GetSelection()
1712	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1713	PlotImage(G2frame,newPlot,event,newImage=True)
1714	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1715	PlotIntegration(G2frame,newPlot,event)
1716
1717	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
1718	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1719	masks, etc.
1720	'''
1721	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1722	import numpy.ma as ma
1723	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1724	global Data,Masks
1725	colors=['b','g','r','c','m','k']
1726	Data = G2frame.PatternTree.GetItemPyData(
1727	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
1728	Masks = G2frame.PatternTree.GetItemPyData(
1729	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
1730	try: #may be absent
1731	StrSta = G2frame.PatternTree.GetItemPyData(
1732	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
1733	except TypeError: #is missing
1734	StrSta = {}
1735
1736	def OnImMotion(event):
1737	Page.canvas.SetToolTipString('')
1738	sizexy = Data['size']
1739	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
1740	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1741	item = G2frame.itemPicked
1742	pixelSize = Data['pixelSize']
1743	scalex = 1000./pixelSize[0]
1744	scaley = 1000./pixelSize[1]
1745	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
1746	if 'Text' in str(item):
1747	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1748	else:
1749	xcent,ycent = Data['center']
1750	xpos = event.xdata-xcent
1751	ypos = event.ydata-ycent
1752	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1753	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1754	Page.canvas.SetToolTipString('%6d deg'%(azm))
1755	elif 'line1' in str(item) or 'line2' in str(item):
1756	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1757	else:
1758	xpos = event.xdata
1759	ypos = event.ydata
1760	xpix = xpos*scalex
1761	ypix = ypos*scaley
1762	Int = 0
1763	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1764	Int = G2frame.ImageZ[ypix][xpix]
1765	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1766	Q = 2.*math.pi/dsp
1767	if G2frame.setPoly:
1768	G2frame.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1769	else:
1770	G2frame.G2plotNB.status.SetFields(\
1771	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1772
1773	def OnImPlotKeyPress(event):
1774	try:
1775	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
1776	except TypeError:
1777	return
1778	if PickName == 'Masks':
1779	Xpos = event.xdata
1780	if not Xpos: #got point out of frame
1781	return
1782	Ypos = event.ydata
1783	if event.key == 's':
1784	Masks['Points'].append([Xpos,Ypos,1.])
1785	elif event.key == 'r':
1786	tth = G2img.GetTth(Xpos,Ypos,Data)
1787	Masks['Rings'].append([tth,0.1])
1788	elif event.key == 'a':
1789	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1790	azm = int(azm)
1791	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1792	elif event.key == 'p':
1793	G2frame.setPoly = True
1794	Masks['Polygons'].append([])
1795	G2frame.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1796	G2imG.UpdateMasks(G2frame,Masks)
1797	elif PickName == 'Image Controls':
1798	if event.key == 'c':
1799	Xpos = event.xdata
1800	if not Xpos: #got point out of frame
1801	return
1802	Ypos = event.ydata
1803	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
1804	'Center change',style=wx.OK\|wx.CANCEL)
1805	try:
1806	if dlg.ShowModal() == wx.ID_OK:
1807	print 'move center to: ',Xpos,Ypos
1808	Data['center'] = [Xpos,Ypos]
1809	G2imG.UpdateImageControls(G2frame,Data,Masks)
1810	finally:
1811	dlg.Destroy()
1812	elif event.key == 'l':
1813	if G2frame.logPlot:
1814	G2frame.logPlot = False
1815	else:
1816	G2frame.logPlot = True
1817	PlotImage(G2frame,newImage=True)
1818
1819	def OnKeyBox(event):
1820	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
1821	event.key = cb.GetValue()[0]
1822	cb.SetValue(' key press')
1823	if event.key in 'l':
1824	wx.CallAfter(OnImPlotKeyPress,event)
1825
1826	def OnImPick(event):
1827	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
1828	return
1829	if G2frame.setPoly:
1830	polygon = Masks['Polygons'][-1]
1831	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1832	if xpos and ypos: #point inside image
1833	if len(polygon) > 2 and event.mouseevent.button == 3:
1834	x0,y0 = polygon[0]
1835	polygon.append([x0,y0])
1836	G2frame.setPoly = False
1837	G2frame.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1838	else:
1839	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1840	polygon.append([xpos,ypos])
1841	G2imG.UpdateMasks(G2frame,Masks)
1842	else:
1843	if G2frame.itemPicked is not None: return
1844	G2frame.itemPicked = event.artist
1845	G2frame.mousePicked = event.mouseevent
1846
1847	def OnImRelease(event):
1848	try:
1849	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
1850	except TypeError:
1851	return
1852	if PickName not in ['Image Controls','Masks']:
1853	return
1854	pixelSize = Data['pixelSize']
1855	scalex = 1000./pixelSize[0]
1856	scaley = 1000./pixelSize[1]
1857	pixLimit = Data['pixLimit']
1858	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
1859	# sizexy = Data['size']
1860	Xpos = event.xdata
1861	if not (Xpos and G2frame.ifGetRing): #got point out of frame
1862	return
1863	Ypos = event.ydata
1864	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1865	if event.button == 1:
1866	Xpix = Xpos*scalex
1867	Ypix = Ypos*scaley
1868	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix)
1869	if I and J:
1870	xpos += .5 #shift to pixel center
1871	ypos += .5
1872	xpos /= scalex #convert to mm
1873	ypos /= scaley
1874	Data['ring'].append([xpos,ypos])
1875	elif event.button == 3:
1876	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1877	if G2img.ImageCalibrate(G2frame,Data):
1878	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1879	print 'Calibration successful'
1880	else:
1881	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1882	print 'Calibration failed'
1883	G2frame.ifGetRing = False
1884	G2imG.UpdateImageControls(G2frame,Data,Masks)
1885	return
1886	PlotImage(G2frame,newImage=False)
1887	return
1888	else:
1889	xpos = event.xdata
1890	if xpos: #avoid out of frame mouse position
1891	ypos = event.ydata
1892	if G2frame.ifGetRing: #delete a calibration ring pick
1893	xypos = [xpos,ypos]
1894	rings = Data['ring']
1895	for ring in rings:
1896	if np.allclose(ring,xypos,.01,0):
1897	rings.remove(ring)
1898	else:
1899	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1900	itemPicked = str(G2frame.itemPicked)
1901	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1902	if 'line1' in itemPicked:
1903	Data['IOtth'][0] = max(tth,0.001)
1904	elif 'line2' in itemPicked:
1905	Data['IOtth'][1] = tth
1906	elif 'line3' in itemPicked:
1907	Data['LRazimuth'][0] = int(azm)
1908	if Data['fullIntegrate']:
1909	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1910	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1911	Data['LRazimuth'][1] = int(azm)
1912
1913	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1914	Data['LRazimuth'][0] -= 360
1915
1916	azLim = np.array(Data['LRazimuth'])
1917	if np.any(azLim>360):
1918	azLim -= 360
1919	Data['LRazimuth'] = list(azLim)
1920
1921	if Data['IOtth'][0] > Data['IOtth'][1]:
1922	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1923
1924	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1925	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1926	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1927	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1928	elif 'Circle' in itemPicked and PickName == 'Masks':
1929	spots = Masks['Points']
1930	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1931	newPos = np.array([float(newPos[0]),float(newPos[1])])
1932	for spot in spots:
1933	if np.allclose(np.array([spot[:2]]),newPos):
1934	spot[:2] = xpos,ypos
1935	G2imG.UpdateMasks(G2frame,Masks)
1936	elif 'Line2D' in itemPicked and PickName == 'Masks':
1937	Obj = G2frame.itemPicked.findobj()
1938	rings = Masks['Rings']
1939	arcs = Masks['Arcs']
1940	polygons = Masks['Polygons']
1941	for ring in G2frame.ringList:
1942	if Obj == ring[0]:
1943	rN = ring[1]
1944	if ring[2] == 'o':
1945	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1946	else:
1947	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1948	for arc in G2frame.arcList:
1949	if Obj == arc[0]:
1950	aN = arc[1]
1951	if arc[2] == 'o':
1952	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1953	elif arc[2] == 'i':
1954	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1955	elif arc[2] == 'l':
1956	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1957	else:
1958	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1959	for poly in G2frame.polyList:
1960	if Obj == poly[0]:
1961	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
1962	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
1963	pN = poly[1]
1964	for i,xy in enumerate(polygons[pN]):
1965	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1966	polygons[pN][i] = xpos,ypos
1967	G2imG.UpdateMasks(G2frame,Masks)
1968	# else: #keep for future debugging
1969	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
1970	PlotImage(G2frame,newImage=True)
1971	G2frame.itemPicked = None
1972
1973	try:
1974	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
1975	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1976	if not newPlot:
1977	Plot = Page.figure.gca() #get previous powder plot & get limits
1978	xylim = Plot.get_xlim(),Plot.get_ylim()
1979	if newImage:
1980	Page.figure.clf()
1981	Plot = Page.figure.gca() #get a fresh plot after clf()
1982
1983	except ValueError:
1984	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
1985	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
1986	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1987	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1988	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1989	Page.canvas.mpl_connect('pick_event', OnImPick)
1990	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1991	xylim = []
1992	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1993	Page.SetFocus()
1994	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
1995	G2frame.G2plotNB.status.DestroyChildren()
1996	if G2frame.logPlot:
1997	Title = 'log('+Title+')'
1998	Plot.set_title(Title)
1999	try:
2000	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
2001	Choice = (' key press','l: log(I) on',)
2002	if G2frame.logPlot:
2003	Choice[1] = 'l: log(I) off'
2004	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2005	choices=Choice)
2006	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2007	cb.SetValue(' key press')
2008	except TypeError:
2009	pass
2010	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
2011	if imagefile != G2frame.oldImagefile:
2012	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
2013	if not imagefile:
2014	G2frame.G2plotNB.Delete('2D Powder Image')
2015	return
2016	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
2017	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
2018	G2frame.oldImagefile = imagefile
2019
2020	imScale = 1
2021	if len(G2frame.ImageZ) > 1024:
2022	imScale = len(G2frame.ImageZ)/1024
2023	sizexy = Data['size']
2024	pixelSize = Data['pixelSize']
2025	scalex = 1000./pixelSize[0]
2026	scaley = 1000./pixelSize[1]
2027	Xmax = sizexy[0]*pixelSize[0]/1000.
2028	Ymax = sizexy[1]*pixelSize[1]/1000.
2029	xlim = (0,Xmax)
2030	ylim = (Ymax,0)
2031	Imin,Imax = Data['range'][1]
2032	acolor = mpl.cm.get_cmap(Data['color'])
2033	xcent,ycent = Data['center']
2034	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
2035	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
2036	#do threshold mask - "real" mask - others are just bondaries
2037	Zlim = Masks['Thresholds'][1]
2038	wx.BeginBusyCursor()
2039	try:
2040
2041	if newImage:
2042	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]),Zlim[1])
2043	MaskA = ma.getmaskarray(MA)
2044	A = G2img.ImageCompress(MA,imScale)
2045	AM = G2img.ImageCompress(MaskA,imScale)
2046	if G2frame.logPlot:
2047	A = np.where(A>0,np.log(A),0)
2048	AM = np.where(AM>0,np.log(AM),0)
2049	Imin,Imax = [np.amin(A),np.amax(A)]
2050	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
2051	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
2052	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
2053	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
2054	if G2frame.setPoly:
2055	Img.set_picker(True)
2056
2057	Plot.plot(xcent,ycent,'x')
2058	#G2frame.PatternTree.GetItemText(item)
2059	if Data['showLines']:
2060	LRAzim = Data['LRazimuth'] #NB: integers
2061	Nazm = Data['outAzimuths']
2062	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
2063	AzmthOff = Data['azmthOff']
2064	IOtth = Data['IOtth']
2065	wave = Data['wavelength']
2066	dspI = wave/(2.0*sind(IOtth[0]/2.0))
2067	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
2068	dspO = wave/(2.0*sind(IOtth[1]/2.0))
2069	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
2070	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
2071	if ellI:
2072	xyI = []
2073	for azm in Azm:
2074	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
2075	xyI = np.array(xyI)
2076	arcxI,arcyI = xyI.T
2077	Plot.plot(arcxI,arcyI,picker=3)
2078	if ellO:
2079	xyO = []
2080	for azm in Azm:
2081	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
2082	xyO = np.array(xyO)
2083	arcxO,arcyO = xyO.T
2084	Plot.plot(arcxO,arcyO,picker=3)
2085	if ellO and ellI:
2086	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
2087	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
2088	for i in range(Nazm):
2089	cake = LRAzim[0]+i*delAzm-AzmthOff
2090	if Data['centerAzm']:
2091	cake += delAzm/2.
2092	ind = np.searchsorted(Azm,cake)
2093	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
2094
2095	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
2096	for xring,yring in Data['ring']:
2097	Plot.plot(xring,yring,'r+',picker=3)
2098	if Data['setRings']:
2099	# rings = np.concatenate((Data['rings']),axis=0)
2100	N = 0
2101	for ring in Data['rings']:
2102	xring,yring = np.array(ring).T[:2]
2103	Plot.plot(xring,yring,'+',color=colors[N%6])
2104	N += 1
2105	for ellipse in Data['ellipses']:
2106	cent,phi,[width,height],col = ellipse
2107	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
2108	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
2109	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
2110	print 'plot stress/strain stuff'
2111	for ring in StrSta['d-zero']:
2112	xring,yring = ring['ImxyObs']
2113	Plot.plot(xring,yring,'r+')
2114	# for xring,yring in ring['ImxyCalc'].T:
2115	# Plot.add_artist(Polygon(ring['ImxyCalc'].T,ec='b',fc='none'))
2116	# Plot.plot(xring,yring)
2117	#masks - mask lines numbered after integration limit lines
2118	spots = Masks['Points']
2119	rings = Masks['Rings']
2120	arcs = Masks['Arcs']
2121	polygons = Masks['Polygons']
2122	for x,y,d in spots:
2123	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
2124	G2frame.ringList = []
2125	for iring,(tth,thick) in enumerate(rings):
2126	wave = Data['wavelength']
2127	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
2128	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
2129	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
2130	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
2131	G2frame.arcList = []
2132	for iarc,(tth,azm,thick) in enumerate(arcs):
2133	wave = Data['wavelength']
2134	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
2135	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
2136	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
2137	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
2138	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
2139	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
2140	G2frame.polyList = []
2141	for ipoly,polygon in enumerate(polygons):
2142	x,y = np.hsplit(np.array(polygon),2)
2143	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
2144	Plot.plot(x,y,'r')
2145	if newImage:
2146	colorBar = Page.figure.colorbar(Img)
2147	Plot.set_xlim(xlim)
2148	Plot.set_ylim(ylim)
2149	Plot.invert_yaxis()
2150	if not newPlot and xylim:
2151	Page.toolbar.push_current()
2152	Plot.set_xlim(xylim[0])
2153	Plot.set_ylim(xylim[1])
2154	xylim = []
2155	Page.toolbar.push_current()
2156	Page.toolbar.draw()
2157	else:
2158	Page.canvas.draw()
2159	finally:
2160	wx.EndBusyCursor()
2161
2162	################################################################################
2163	##### PlotIntegration
2164	################################################################################
2165
2166	def PlotIntegration(G2frame,newPlot=False,event=None):
2167	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
2168	'''
2169
2170	def OnMotion(event):
2171	Page.canvas.SetToolTipString('')
2172	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2173	azm = event.ydata
2174	tth = event.xdata
2175	if azm and tth:
2176	G2frame.G2plotNB.status.SetFields(\
2177	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2178
2179	try:
2180	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2181	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2182	if not newPlot:
2183	Plot = Page.figure.gca() #get previous plot & get limits
2184	xylim = Plot.get_xlim(),Plot.get_ylim()
2185	Page.figure.clf()
2186	Plot = Page.figure.gca() #get a fresh plot after clf()
2187
2188	except ValueError:
2189	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
2190	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2191	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2192	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2193	Page.views = False
2194	view = False
2195	if not event:
2196	Page.SetFocus()
2197
2198	Data = G2frame.PatternTree.GetItemPyData(
2199	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2200	image = G2frame.Integrate[0]
2201	xsc = G2frame.Integrate[1]
2202	ysc = G2frame.Integrate[2]
2203	Imin,Imax = Data['range'][1]
2204	acolor = mpl.cm.get_cmap(Data['color'])
2205	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2206	Plot.set_ylabel('azimuth',fontsize=12)
2207	Plot.set_xlabel('2-theta',fontsize=12)
2208	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
2209	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
2210	colorBar = Page.figure.colorbar(Img)
2211	if Data['ellipses']:
2212	for ellipse in Data['ellipses']:
2213	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2214	x,y = np.hsplit(ring,2)
2215	tth,azm = G2img.GetTthAzm(x,y,Data)
2216	# azm = np.where(azm < 0.,azm+360,azm)
2217	Plot.plot(tth,azm,'b,')
2218	if not newPlot:
2219	Page.toolbar.push_current()
2220	Plot.set_xlim(xylim[0])
2221	Plot.set_ylim(xylim[1])
2222	xylim = []
2223	Page.toolbar.push_current()
2224	Page.toolbar.draw()
2225	else:
2226	Page.canvas.draw()
2227
2228	################################################################################
2229	##### PlotTRImage
2230	################################################################################
2231
2232	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
2233	'''a test plot routine - not normally used
2234	'''
2235
2236	def OnMotion(event):
2237	Page.canvas.SetToolTipString('')
2238	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2239	azm = event.xdata
2240	tth = event.ydata
2241	if azm and tth:
2242	G2frame.G2plotNB.status.SetFields(\
2243	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2244
2245	try:
2246	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2247	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2248	if not newPlot:
2249	Plot = Page.figure.gca() #get previous plot & get limits
2250	xylim = Plot.get_xlim(),Plot.get_ylim()
2251	Page.figure.clf()
2252	Plot = Page.figure.gca() #get a fresh plot after clf()
2253
2254	except ValueError:
2255	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
2256	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2257	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2258	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2259	Page.views = False
2260	view = False
2261	Page.SetFocus()
2262
2263	Data = G2frame.PatternTree.GetItemPyData(
2264	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2265	Imin,Imax = Data['range'][1]
2266	step = (Imax-Imin)/5.
2267	V = np.arange(Imin,Imax,step)
2268	acolor = mpl.cm.get_cmap(Data['color'])
2269	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2270	Plot.set_xlabel('azimuth',fontsize=12)
2271	Plot.set_ylabel('2-theta',fontsize=12)
2272	Plot.contour(tax,tay,taz,V,cmap=acolor)
2273	if Data['showLines']:
2274	IOtth = Data['IOtth']
2275	if Data['fullIntegrate']:
2276	LRAzim = [-180,180]
2277	else:
2278	LRAzim = Data['LRazimuth'] #NB: integers
2279	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
2280	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
2281	if not Data['fullIntegrate']:
2282	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
2283	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
2284	if Data['setRings']:
2285	rings = np.concatenate((Data['rings']),axis=0)
2286	for xring,yring,dsp in rings:
2287	x,y = G2img.GetTthAzm(xring,yring,Data)
2288	Plot.plot(y,x,'r+')
2289	if Data['ellipses']:
2290	for ellipse in Data['ellipses']:
2291	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2292	x,y = np.hsplit(ring,2)
2293	tth,azm = G2img.GetTthAzm(x,y,Data)
2294	Plot.plot(azm,tth,'b,')
2295	if not newPlot:
2296	Page.toolbar.push_current()
2297	Plot.set_xlim(xylim[0])
2298	Plot.set_ylim(xylim[1])
2299	xylim = []
2300	Page.toolbar.push_current()
2301	Page.toolbar.draw()
2302	else:
2303	Page.canvas.draw()
2304
2305	################################################################################
2306	##### PlotStructure
2307	################################################################################
2308
2309	def PlotStructure(G2frame,data):
2310	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
2311	thermal motion ellipsoids and polyhedra
2312	'''
2313	ForthirdPI = 4.0*math.pi/3.0
2314	generalData = data['General']
2315	cell = generalData['Cell'][1:7]
2316	Vol = generalData['Cell'][7:8][0]
2317	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
2318	Gmat,gmat = G2lat.cell2Gmat(cell)
2319	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2320	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2321	Mydir = generalData['Mydir']
2322	atomData = data['Atoms']
2323	mapPeaks = []
2324	if 'Map Peaks' in data:
2325	mapPeaks = data['Map Peaks']
2326	drawingData = data['Drawing']
2327	try:
2328	drawAtoms = drawingData['Atoms']
2329	except KeyError:
2330	drawAtoms = []
2331	mapData = {}
2332	flipData = {}
2333	rhoXYZ = []
2334	if 'Map' in generalData:
2335	mapData = generalData['Map']
2336	if 'Flip' in generalData:
2337	flipData = generalData['Flip']
2338	flipData['mapRoll'] = [0,0,0]
2339	cx,ct,cs,ci = drawingData['atomPtrs']
2340	Wt = np.array([255,255,255])
2341	Rd = np.array([255,0,0])
2342	Gr = np.array([0,255,0])
2343	Bl = np.array([0,0,255])
2344	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]])
2345	uEdges = np.array([
2346	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
2347	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
2348	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
2349	mD = 0.1
2350	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
2351	mapPeakVecs = np.inner(mV,Bmat)
2352
2353	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
2354	altDown = False
2355	shiftDown = False
2356	ctrlDown = False
2357
2358	def OnKeyBox(event):
2359	import Image
2360	Draw() #make sure plot is fresh!!
2361	mode = cb.GetValue()
2362	if mode in ['jpeg','bmp','tiff',]:
2363	Fname = os.path.joint(Mydir,generalData['Name']+'.'+mode)
2364	size = Page.canvas.GetSize()
2365	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
2366	if mode in ['jpeg',]:
2367	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
2368	im = Image.new("RGBA", (size[0],size[1]))
2369	else:
2370	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
2371	im = Image.new("RGB", (size[0],size[1]))
2372	im.fromstring(Pix)
2373	im.save(Fname,mode)
2374	cb.SetValue(' save as/key:')
2375	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
2376	else:
2377	event.key = cb.GetValue()[0]
2378	cb.SetValue(' save as/key:')
2379	wx.CallAfter(OnKey,event)
2380
2381	def OnKey(event): #on key UP!!
2382	Draw() #make sure plot is fresh!!
2383	try:
2384	keyCode = event.GetKeyCode()
2385	if keyCode > 255:
2386	keyCode = 0
2387	key = chr(keyCode)
2388	except AttributeError: #if from OnKeyBox above
2389	key = str(event.key).upper()
2390	indx = drawingData['selectedAtoms']
2391	if key in ['C']:
2392	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2393	VD = np.inner(Bmat,np.array([0,0,1]))
2394	VD /= np.sqrt(np.sum(VD**2))
2395	drawingData['viewDir'] = VD
2396	drawingData['oldxy'] = []
2397	drawingData['Quaternion'] = [0.0,0.0,1.0,0.0]
2398	SetViewPointText(drawingData['viewPoint'][0])
2399	SetViewDirText(drawingData['viewDir'])
2400	Q = drawingData['Quaternion']
2401	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
2402	elif key in ['N']:
2403	drawAtoms = drawingData['Atoms']
2404	pI = drawingData['viewPoint'][1]
2405	if indx:
2406	pI[0] = indx[pI[1]]
2407	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2408	pI[1] += 1
2409	if pI[1] >= len(indx):
2410	pI[1] = 0
2411	else:
2412	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2413	pI[0] += 1
2414	if pI[0] >= len(drawAtoms):
2415	pI[0] = 0
2416	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2417	SetViewPointText(drawingData['viewPoint'][0])
2418	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2419
2420	elif key in ['P']:
2421	drawAtoms = drawingData['Atoms']
2422	pI = drawingData['viewPoint'][1]
2423	if indx:
2424	pI[0] = indx[pI[1]]
2425	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2426	pI[1] -= 1
2427	if pI[1] < 0:
2428	pI[1] = len(indx)-1
2429	else:
2430	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2431	pI[0] -= 1
2432	if pI[0] < 0:
2433	pI[0] = len(drawAtoms)-1
2434	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2435	SetViewPointText(drawingData['viewPoint'][0])
2436	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2437	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
2438	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
2439	SetMapRoll(dirDict[key])
2440	SetPeakRoll(dirDict[key])
2441	SetMapPeaksText(mapPeaks)
2442	Draw()
2443
2444	def GetTruePosition(xy,Add=False):
2445	View = glGetIntegerv(GL_VIEWPORT)
2446	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
2447	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
2448	Zmax = 1.
2449	if Add:
2450	Indx = GetSelectedAtoms()
2451	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
2452	for i,peak in enumerate(mapPeaks):
2453	x,y,z = peak[1:4]
2454	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2455	XY = [int(X),int(View[3]-Y)]
2456	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2457	Zmax = Z
2458	try:
2459	Indx.remove(i)
2460	ClearSelectedAtoms()
2461	for id in Indx:
2462	SetSelectedAtoms(id,Add)
2463	except:
2464	SetSelectedAtoms(i,Add)
2465	else:
2466	for i,atom in enumerate(drawAtoms):
2467	x,y,z = atom[cx:cx+3]
2468	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2469	XY = [int(X),int(View[3]-Y)]
2470	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2471	Zmax = Z
2472	try:
2473	Indx.remove(i)
2474	ClearSelectedAtoms()
2475	for id in Indx:
2476	SetSelectedAtoms(id,Add)
2477	except:
2478	SetSelectedAtoms(i,Add)
2479
2480	def OnMouseDown(event):
2481	xy = event.GetPosition()
2482	if event.ShiftDown():
2483	if event.LeftIsDown():
2484	GetTruePosition(xy)
2485	elif event.RightIsDown():
2486	GetTruePosition(xy,True)
2487	else:
2488	drawingData['oldxy'] = list(xy)
2489	Draw()
2490
2491	def OnMouseMove(event):
2492	if event.ShiftDown(): #don't want any inadvertant moves when picking
2493	return
2494	newxy = event.GetPosition()
2495	page = getSelection()
2496
2497	if event.Dragging() and not event.ControlDown():
2498	if event.LeftIsDown():
2499	SetRotation(newxy)
2500	Q = drawingData['Quaternion']
2501	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
2502	elif event.RightIsDown():
2503	SetTranslation(newxy)
2504	Tx,Ty,Tz = drawingData['viewPoint'][0]
2505	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2506	elif event.MiddleIsDown():
2507	SetRotationZ(newxy)
2508	Q = drawingData['Quaternion']
2509	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
2510	Draw()
2511
2512	def OnMouseWheel(event):
2513	if event.ShiftDown():
2514	return
2515	drawingData['cameraPos'] += event.GetWheelRotation()/24
2516	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2517	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2518	page = getSelection()
2519	if page:
2520	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2521	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2522	names = [child.GetName() for child in panel]
2523	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2524	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2525	Draw()
2526
2527	def getSelection():
2528	try:
2529	return G2frame.dataDisplay.GetSelection()
2530	except AttributeError:
2531	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2532	return 0
2533
2534	def SetViewPointText(VP):
2535	page = getSelection()
2536	if page:
2537	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2538	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2539	names = [child.GetName() for child in panel]
2540	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
2541
2542	def SetViewDirText(VD):
2543	page = getSelection()
2544	if page:
2545	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2546	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2547	names = [child.GetName() for child in panel]
2548	panel[names.index('viewDir')].SetValue('%.3f, %.3f, %.3f'%(VD[0],VD[1],VD[2]))
2549
2550	def SetMapPeaksText(mapPeaks):
2551	page = getSelection()
2552	if page:
2553	if G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2554	G2frame.MapPeaksTable.SetData(mapPeaks)
2555	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
2556	names = [child.GetName() for child in panel]
2557	panel[names.index('grid window')].Refresh()
2558
2559	def ClearSelectedAtoms():
2560	page = getSelection()
2561	if page:
2562	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2563	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2564	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2565	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2566	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2567	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2568
2569
2570	def SetSelectedAtoms(ind,Add=False):
2571	page = getSelection()
2572	if page:
2573	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2574	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
2575	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2576	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add)
2577	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2578	Id = drawAtoms[ind][-2]
2579	for i,atom in enumerate(atomData):
2580	if atom[-1] == Id:
2581	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2582
2583	def GetSelectedAtoms():
2584	page = getSelection()
2585	Ind = []
2586	if page:
2587	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2588	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2589	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2590	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows()
2591	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2592	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2593	return Ind
2594
2595	def SetBackground():
2596	R,G,B,A = Page.camera['backColor']
2597	glClearColor(R,G,B,A)
2598	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2599
2600	def SetLights():
2601	glEnable(GL_DEPTH_TEST)
2602	glShadeModel(GL_SMOOTH)
2603	glEnable(GL_LIGHTING)
2604	glEnable(GL_LIGHT0)
2605	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2606	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2607	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2608
2609	def GetRoll(newxy,rho):
2610	Q = drawingData['Quaternion']
2611	dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,]))
2612	dxy = np.array(dxy*rho.shape)
2613	roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0))
2614	return roll
2615
2616	def SetMapRoll(newxy):
2617	rho = mapData['rho']
2618	roll = GetRoll(newxy,rho)
2619	mapData['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
2620	drawingData['oldxy'] = list(newxy)
2621
2622	def SetPeakRoll(newxy):
2623	rho = mapData['rho']
2624	roll = GetRoll(newxy,rho)
2625	steps = 1./np.array(rho.shape)
2626	dxy = roll*steps
2627	for peak in mapPeaks:
2628	peak[1:4] += dxy
2629	peak[1:4] %= 1.
2630	peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2))
2631
2632	def SetTranslation(newxy):
2633	#first get translation vector in screen coords.
2634	oldxy = drawingData['oldxy']
2635	if not len(oldxy): oldxy = list(newxy)
2636	dxy = newxy-oldxy
2637	drawingData['oldxy'] = list(newxy)
2638	V = np.array([-dxy[0],dxy[1],0.])
2639	#then transform to rotated crystal coordinates & apply to view point
2640	Q = drawingData['Quaternion']
2641	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
2642	Tx,Ty,Tz = drawingData['viewPoint'][0]
2643	Tx += V[0]*0.01
2644	Ty += V[1]*0.01
2645	Tz += V[2]*0.01
2646	drawingData['oldxy'] = list(newxy)
2647	drawingData['viewPoint'][0] = Tx,Ty,Tz
2648	SetViewPointText([Tx,Ty,Tz])
2649
2650	def SetRotation(newxy):
2651	#first get rotation vector in screen coords. & angle increment
2652	oldxy = drawingData['oldxy']
2653	if not len(oldxy): oldxy = list(newxy)
2654	dxy = newxy-oldxy
2655	drawingData['oldxy'] = list(newxy)
2656	V = np.array([dxy[1],dxy[0],0.])
2657	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
2658	# next transform vector back to xtal coordinates via inverse quaternion
2659	# & make new quaternion
2660	Q = drawingData['Quaternion']
2661	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
2662	DQ = G2mth.AVdeg2Q(A,V)
2663	Q = G2mth.prodQQ(Q,DQ)
2664	drawingData['Quaternion'] = Q
2665	# finally get new view vector - last row of rotation matrix
2666	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
2667	VD /= np.sqrt(np.sum(VD**2))
2668	drawingData['viewDir'] = VD
2669	SetViewDirText(VD)
2670
2671	def SetRotationZ(newxy):
2672	#first get rotation vector (= view vector) in screen coords. & angle increment
2673	View = glGetIntegerv(GL_VIEWPORT)
2674	cent = [View[2]/2,View[3]/2]
2675	oldxy = drawingData['oldxy']
2676	if not len(oldxy): oldxy = list(newxy)
2677	dxy = newxy-oldxy
2678	drawingData['oldxy'] = list(newxy)
2679	V = drawingData['viewDir']
2680	A = [0,0]
2681	A[0] = dxy[1]*.25
2682	A[1] = dxy[0]*.25
2683	if newxy[0] > cent[0]:
2684	A[0] *= -1
2685	if newxy[1] < cent[1]:
2686	A[1] *= -1
2687	# next transform vector back to xtal coordinates & make new quaternion
2688	Q = drawingData['Quaternion']
2689	V = np.inner(Amat,V)
2690	Qx = G2mth.AVdeg2Q(A[0],V)
2691	Qy = G2mth.AVdeg2Q(A[1],V)
2692	Q = G2mth.prodQQ(Q,Qx)
2693	Q = G2mth.prodQQ(Q,Qy)
2694	drawingData['Quaternion'] = Q
2695
2696	def RenderBox():
2697	glEnable(GL_COLOR_MATERIAL)
2698	glLineWidth(2)
2699	glEnable(GL_BLEND)
2700	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2701	glEnable(GL_LINE_SMOOTH)
2702	glBegin(GL_LINES)
2703	for line,color in zip(uEdges,uColors):
2704	glColor3ubv(color)
2705	glVertex3fv(line[0])
2706	glVertex3fv(line[1])
2707	glEnd()
2708	glColor4ubv([0,0,0,0])
2709	glDisable(GL_LINE_SMOOTH)
2710	glDisable(GL_BLEND)
2711	glDisable(GL_COLOR_MATERIAL)
2712
2713	def RenderUnitVectors(x,y,z):
2714	xyz = np.array([x,y,z])
2715	glEnable(GL_COLOR_MATERIAL)
2716	glLineWidth(1)
2717	glPushMatrix()
2718	glTranslate(x,y,z)
2719	glScalef(1/cell[0],1/cell[1],1/cell[2])
2720	glBegin(GL_LINES)
2721	for line,color in zip(uEdges,uColors)[:3]:
2722	glColor3ubv(color)
2723	glVertex3fv(-line[1]/2.)
2724	glVertex3fv(line[1]/2.)
2725	glEnd()
2726	glPopMatrix()
2727	glColor4ubv([0,0,0,0])
2728	glDisable(GL_COLOR_MATERIAL)
2729
2730	def RenderSphere(x,y,z,radius,color):
2731	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2732	glPushMatrix()
2733	glTranslate(x,y,z)
2734	glMultMatrixf(B4mat.T)
2735	q = gluNewQuadric()
2736	gluSphere(q,radius,20,10)
2737	glPopMatrix()
2738
2739	def RenderSmallSphere(x,y,z,radius,color):
2740	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2741	glPushMatrix()
2742	glTranslate(x,y,z)
2743	glMultMatrixf(B4mat.T)
2744	q = gluNewQuadric()
2745	gluSphere(q,radius,4,2)
2746	glPopMatrix()
2747
2748	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2749	s1,s2,s3 = E
2750	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2751	glPushMatrix()
2752	glTranslate(x,y,z)
2753	glMultMatrixf(B4mat.T)
2754	glMultMatrixf(R4.T)
2755	glEnable(GL_NORMALIZE)
2756	glScale(s1,s2,s3)
2757	q = gluNewQuadric()
2758	gluSphere(q,ellipseProb,20,10)
2759	glDisable(GL_NORMALIZE)
2760	glPopMatrix()
2761
2762	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2763	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2764	glPushMatrix()
2765	glTranslate(x,y,z)
2766	glMultMatrixf(B4mat.T)
2767	for bond in Bonds:
2768	glPushMatrix()
2769	Dx = np.inner(Amat,bond)
2770	Z = np.sqrt(np.sum(Dx**2))
2771	if Z:
2772	azm = atan2d(-Dx[1],-Dx[0])
2773	phi = acosd(Dx[2]/Z)
2774	glRotate(-azm,0,0,1)
2775	glRotate(phi,1,0,0)
2776	q = gluNewQuadric()
2777	gluCylinder(q,radius,radius,Z,slice,2)
2778	glPopMatrix()
2779	glPopMatrix()
2780
2781	def RenderLines(x,y,z,Bonds,color):
2782	xyz = np.array([x,y,z])
2783	glEnable(GL_COLOR_MATERIAL)
2784	glLineWidth(1)
2785	glColor3fv(color)
2786	glPushMatrix()
2787	glBegin(GL_LINES)
2788	for bond in Bonds:
2789	glVertex3fv(xyz)
2790	glVertex3fv(xyz+bond)
2791	glEnd()
2792	glColor4ubv([0,0,0,0])
2793	glPopMatrix()
2794	glDisable(GL_COLOR_MATERIAL)
2795
2796	def RenderPolyhedra(x,y,z,Faces,color):
2797	glPushMatrix()
2798	glTranslate(x,y,z)
2799	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2800	glShadeModel(GL_SMOOTH)
2801	glMultMatrixf(B4mat.T)
2802	for face,norm in Faces:
2803	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2804	glFrontFace(GL_CW)
2805	glNormal3fv(norm)
2806	glBegin(GL_TRIANGLES)
2807	for vert in face:
2808	glVertex3fv(vert)
2809	glEnd()
2810	glPopMatrix()
2811
2812	def RenderMapPeak(x,y,z,color):
2813	xyz = np.array([x,y,z])
2814	glEnable(GL_COLOR_MATERIAL)
2815	glLineWidth(3)
2816	glColor3fv(color)
2817	glPushMatrix()
2818	glBegin(GL_LINES)
2819	for vec in mapPeakVecs:
2820	glVertex3fv(vec[0]+xyz)
2821	glVertex3fv(vec[1]+xyz)
2822	glEnd()
2823	glColor4ubv([0,0,0,0])
2824	glPopMatrix()
2825	glDisable(GL_COLOR_MATERIAL)
2826
2827	def RenderBackbone(Backbone,BackboneColor,radius):
2828	glPushMatrix()
2829	glMultMatrixf(B4mat.T)
2830	glEnable(GL_COLOR_MATERIAL)
2831	glShadeModel(GL_SMOOTH)
2832	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2833	glePolyCylinder(Backbone,BackboneColor,radius)
2834	glPopMatrix()
2835	glDisable(GL_COLOR_MATERIAL)
2836
2837	def RenderLabel(x,y,z,label,r):
2838	glPushMatrix()
2839	glTranslate(x,y,z)
2840	glMultMatrixf(B4mat.T)
2841	glDisable(GL_LIGHTING)
2842	glColor3f(0,1.,0)
2843	glRasterPos3f(r,r,r)
2844	for c in list(label):
2845	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2846	glEnable(GL_LIGHTING)
2847	glPopMatrix()
2848
2849	def RenderMap(rho,rhoXYZ,indx,Rok):
2850	cLevel = drawingData['contourLevel']
2851	for i,xyz in enumerate(rhoXYZ):
2852	if not Rok[i]:
2853	x,y,z = xyz
2854	I,J,K = indx[i]
2855	alpha = 1.0
2856	if cLevel < 1.:
2857	alpha = (abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)
2858	if rho[I,J,K] < 0.:
2859	RenderSmallSphere(x,y,z,0.1*alpha,Rd)
2860	else:
2861	RenderSmallSphere(x,y,z,0.1*alpha,Gr)
2862
2863	def Draw():
2864	mapData = generalData['Map']
2865	pageName = ''
2866	page = getSelection()
2867	if page:
2868	pageName = G2frame.dataDisplay.GetPageText(page)
2869	rhoXYZ = []
2870	if len(mapData['rho']):
2871	VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
2872	contLevel = drawingData['contourLevel']*mapData['rhoMax']
2873	if 'delt-F' in mapData['MapType']:
2874	rho = ma.array(mapData['rho'],mask=(np.abs(mapData['rho'])<contLevel))
2875	else:
2876	rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
2877	steps = 1./np.array(rho.shape)
2878	incre = np.where(VP>=0,VP%steps,VP%steps-steps)
2879	Vsteps = -np.array(VP/steps,dtype='i')
2880	rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
2881	indx = np.array(ma.nonzero(rho)).T
2882	rhoXYZ = indx*steps+VP-incre
2883	Nc = len(rhoXYZ)
2884	rcube = 2000.Vol/(ForthirdPINc)
2885	rmax = math.exp(math.log(rcube)/3.)**2
2886	radius = min(drawingData['mapSize']**2,rmax)
2887	view = np.array(drawingData['viewPoint'][0])
2888	Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
2889	Ind = GetSelectedAtoms()
2890	VS = np.array(Page.canvas.GetSize())
2891	aspect = float(VS[0])/float(VS[1])
2892	cPos = drawingData['cameraPos']
2893	Zclip = drawingData['Zclip']*cPos/200.
2894	Q = drawingData['Quaternion']
2895	Tx,Ty,Tz = drawingData['viewPoint'][0]
2896	cx,ct,cs,ci = drawingData['atomPtrs']
2897	bondR = drawingData['bondRadius']
2898	G,g = G2lat.cell2Gmat(cell)
2899	GS = G
2900	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2901	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2902	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2903	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2904
2905	SetBackground()
2906	glInitNames()
2907	glPushName(0)
2908
2909	glMatrixMode(GL_PROJECTION)
2910	glLoadIdentity()
2911	glViewport(0,0,VS[0],VS[1])
2912	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2913	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2914	SetLights()
2915
2916	glMatrixMode(GL_MODELVIEW)
2917	glLoadIdentity()
2918	matRot = G2mth.Q2Mat(Q)
2919	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2920	glMultMatrixf(matRot.T)
2921	glMultMatrixf(A4mat.T)
2922	glTranslate(-Tx,-Ty,-Tz)
2923	if drawingData['unitCellBox']:
2924	RenderBox()
2925	if drawingData['showABC']:
2926	x,y,z = drawingData['viewPoint'][0]
2927	RenderUnitVectors(x,y,z)
2928	Backbones = {}
2929	BackboneColor = []
2930	time0 = time.time()
2931	# glEnable(GL_BLEND)
2932	# glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2933	for iat,atom in enumerate(drawingData['Atoms']):
2934	x,y,z = atom[cx:cx+3]
2935	Bonds = atom[-2]
2936	Faces = atom[-1]
2937	try:
2938	atNum = generalData['AtomTypes'].index(atom[ct])
2939	except ValueError:
2940	atNum = -1
2941	CL = atom[cs+2]
2942	color = np.array(CL)/255.
2943	if iat in Ind and G2frame.dataDisplay.GetPageText(getSelection()) != 'Map peaks':
2944	color = np.array(Gr)/255.
2945	# color += [.25,]
2946	radius = 0.5
2947	if atom[cs] != '':
2948	try:
2949	glLoadName(atom[-3])
2950	except: #problem with old files - missing code
2951	pass
2952	if 'balls' in atom[cs]:
2953	vdwScale = drawingData['vdwScale']
2954	ballScale = drawingData['ballScale']
2955	if atNum < 0:
2956	radius = 0.2
2957	elif 'H' == atom[ct]:
2958	if drawingData['showHydrogen']:
2959	if 'vdW' in atom[cs] and atNum >= 0:
2960	radius = vdwScale*generalData['vdWRadii'][atNum]
2961	else:
2962	radius = ballScale*drawingData['sizeH']
2963	else:
2964	radius = 0.0
2965	else:
2966	if 'vdW' in atom[cs]:
2967	radius = vdwScale*generalData['vdWRadii'][atNum]
2968	else:
2969	radius = ballScale*generalData['BondRadii'][atNum]
2970	RenderSphere(x,y,z,radius,color)
2971	if 'sticks' in atom[cs]:
2972	RenderBonds(x,y,z,Bonds,bondR,color)
2973	elif 'ellipsoids' in atom[cs]:
2974	RenderBonds(x,y,z,Bonds,bondR,color)
2975	if atom[cs+3] == 'A':
2976	Uij = atom[cs+5:cs+11]
2977	U = np.multiply(G2spc.Uij2U(Uij),GS)
2978	U = np.inner(Amat,np.inner(U,Amat).T)
2979	E,R = nl.eigh(U)
2980	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2981	E = np.sqrt(E)
2982	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2983	pass
2984	else:
2985	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2986	else:
2987	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2988	pass
2989	else:
2990	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2991	RenderSphere(x,y,z,radius,color)
2992	elif 'lines' in atom[cs]:
2993	radius = 0.1
2994	RenderLines(x,y,z,Bonds,color)
2995	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2996	elif atom[cs] == 'sticks':
2997	radius = 0.1
2998	RenderBonds(x,y,z,Bonds,bondR,color)
2999	elif atom[cs] == 'polyhedra':
3000	RenderPolyhedra(x,y,z,Faces,color)
3001	elif atom[cs] == 'backbone':
3002	if atom[ct-1].split()[0] in ['C','N']:
3003	if atom[2] not in Backbones:
3004	Backbones[atom[2]] = []
3005	Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
3006	BackboneColor.append(list(color))
3007
3008	if atom[cs+1] == 'type':
3009	RenderLabel(x,y,z,atom[ct],radius)
3010	elif atom[cs+1] == 'name':
3011	RenderLabel(x,y,z,atom[ct-1],radius)
3012	elif atom[cs+1] == 'number':
3013	RenderLabel(x,y,z,str(iat),radius)
3014	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
3015	RenderLabel(x,y,z,atom[ct-4],radius)
3016	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
3017	RenderLabel(x,y,z,atom[ct-3],radius)
3018	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
3019	RenderLabel(x,y,z,atom[ct-2],radius)
3020	# glDisable(GL_BLEND)
3021	if len(rhoXYZ):
3022	RenderMap(rho,rhoXYZ,indx,Rok)
3023	if len(mapPeaks):
3024	for ind,[mag,x,y,z,d] in enumerate(mapPeaks):
3025	if ind in Ind and pageName == 'Map peaks':
3026	RenderMapPeak(x,y,z,Gr)
3027	else:
3028	RenderMapPeak(x,y,z,Wt)
3029	if Backbones:
3030	for chain in Backbones:
3031	Backbone = Backbones[chain]
3032	RenderBackbone(Backbone,BackboneColor,bondR)
3033	# print time.time()-time0
3034	Page.canvas.SwapBuffers()
3035
3036	def OnSize(event):
3037	Draw()
3038
3039	def OnFocus(event):
3040	Draw()
3041
3042	try:
3043	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
3044	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3045	except ValueError:
3046	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
3047	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
3048	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3049	Page.views = False
3050	view = False
3051	altDown = False
3052	Page.SetFocus()
3053	if mapData['Flip']:
3054	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2','n: next','p: previous']
3055	else:
3056	choice = [' save as/key:','jpeg','tiff','bmp','u: roll up','d: roll down','l: roll left','r: roll right']
3057	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
3058	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
3059	cb.SetValue(' save as/key:')
3060	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
3061	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
3062	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
3063	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
3064	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
3065	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
3066	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
3067	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
3068	Page.camera['position'] = drawingData['cameraPos']
3069	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
3070	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
3071	Page.canvas.SetCurrent()
3072	Draw()
3073

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