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source: trunk/GSASIIplot.py @ 271

Last change on this file since 271 was 271, checked in by vondreele, 12 years ago
make g77 versions of fortran for binwin2.7 - faster than gfortran! fix to histogram2d.for GSASII.py - allow 2D offset in multiplots, fix for large file lists GSASIIimgGUI.py - more stuff in save/load controls GSASIIplot.py - 2D offset in multiplots, fix bad behavior in structure drawings GSASIIpwd.py - more mods to PDF calcs
Property svn:keywords set to `Date Author Revision URL Id`
File size: 96.0 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2011-04-28 18:11:32 +0000 (Thu, 28 Apr 2011) $
4	# $Author: vondreele $
5	# $Revision: 271 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 271 2011-04-28 18:11:32Z vondreele $
8	########### SVN repository information ###################
9	import math
10	import time
11	import copy
12	import os.path
13	import numpy as np
14	import numpy.linalg as nl
15	import wx
16	import wx.aui
17	import wx.glcanvas
18	import matplotlib as mpl
19	import mpl_toolkits.mplot3d.axes3d as mp3d
20	import GSASIIpath
21	import GSASIIgrid as G2gd
22	import GSASIIimage as G2img
23	import GSASIIpwd as G2pwd
24	import GSASIIIO as G2IO
25	import GSASIIpwdGUI as G2pdG
26	import GSASIIimgGUI as G2imG
27	import GSASIIphsGUI as G2phG
28	import GSASIIlattice as G2lat
29	import GSASIIspc as G2spc
30	from OpenGL.GL import *
31	from OpenGL.GLU import *
32	from OpenGL.GLUT import *
33	from OpenGL.GLE import *
34	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
35	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
36
37	# useful degree trig functions
38	sind = lambda x: math.sin(x*math.pi/180.)
39	cosd = lambda x: math.cos(x*math.pi/180.)
40	tand = lambda x: math.tan(x*math.pi/180.)
41	asind = lambda x: 180.*math.asin(x)/math.pi
42	acosd = lambda x: 180.*math.acos(x)/math.pi
43	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
44	atand = lambda x: 180.*math.atan(x)/math.pi
45	# numpy versions
46	npsind = lambda x: np.sin(x*np.pi/180.)
47	npcosd = lambda x: np.cos(x*np.pi/180.)
48	npacosd = lambda x: 180.*np.arccos(x)/np.pi
49
50	class G2PlotMpl(wx.Panel):
51	def __init__(self,parent,id=-1,dpi=None,**kwargs):
52	wx.Panel.__init__(self,parent,id=id,**kwargs)
53	mpl.rcParams['legend.fontsize'] = 8
54	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
55	self.canvas = Canvas(self,-1,self.figure)
56	self.toolbar = Toolbar(self.canvas)
57
58	self.toolbar.Realize()
59
60	sizer=wx.BoxSizer(wx.VERTICAL)
61	sizer.Add(self.canvas,1,wx.EXPAND)
62	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
63	self.SetSizer(sizer)
64
65	class G2PlotOgl(wx.Panel):
66	def __init__(self,parent,id=-1,dpi=None,**kwargs):
67	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
68	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
69	self.camera = {}
70	sizer=wx.BoxSizer(wx.VERTICAL)
71	sizer.Add(self.canvas,1,wx.EXPAND)
72	self.SetSizer(sizer)
73
74	class G2Plot3D(wx.Panel):
75	def __init__(self,parent,id=-1,dpi=None,**kwargs):
76	wx.Panel.__init__(self,parent,id=id,**kwargs)
77	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
78	self.canvas = Canvas(self,-1,self.figure)
79	self.toolbar = Toolbar(self.canvas)
80
81	self.toolbar.Realize()
82
83	sizer=wx.BoxSizer(wx.VERTICAL)
84	sizer.Add(self.canvas,1,wx.EXPAND)
85	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
86	self.SetSizer(sizer)
87
88	class G2PlotNoteBook(wx.Panel):
89	def __init__(self,parent,id=-1):
90	wx.Panel.__init__(self,parent,id=id)
91	#so one can't delete a plot page!!
92	self.nb = wx.aui.AuiNotebook(self, \
93	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
94	sizer = wx.BoxSizer()
95	sizer.Add(self.nb,1,wx.EXPAND)
96	self.SetSizer(sizer)
97	self.status = parent.CreateStatusBar()
98	self.status.SetFieldsCount(2)
99	self.status.SetStatusWidths([150,-1])
100	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
101
102	self.plotList = []
103
104	def addMpl(self,name=""):
105	page = G2PlotMpl(self.nb)
106	self.nb.AddPage(page,name)
107
108	self.plotList.append(name)
109
110	return page.figure
111
112	def add3D(self,name=""):
113	page = G2Plot3D(self.nb)
114	self.nb.AddPage(page,name)
115
116	self.plotList.append(name)
117
118	return page.figure
119
120	def addOgl(self,name=""):
121	page = G2PlotOgl(self.nb)
122	self.nb.AddPage(page,name)
123
124	self.plotList.append(name)
125
126	return page.figure
127
128	def Delete(self,name):
129	try:
130	item = self.plotList.index(name)
131	del self.plotList[item]
132	self.nb.DeletePage(item)
133	except ValueError: #no plot of this name - do nothing
134	return
135
136	def clear(self):
137	while self.nb.GetPageCount():
138	self.nb.DeletePage(0)
139	self.plotList = []
140	self.status.DestroyChildren()
141
142	def Rename(self,oldName,newName):
143	try:
144	item = self.plotList.index(oldName)
145	self.plotList[item] = newName
146	self.nb.SetPageText(item,newName)
147	except ValueError: #no plot of this name - do nothing
148	return
149
150	def OnPageChanged(self,event):
151	if self.plotList:
152	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
153	self.status.DestroyChildren() #get rid of special stuff on status bar
154
155	def PlotSngl(self,newPlot=False):
156	from matplotlib.patches import Circle
157	global HKL,HKLF
158
159	def OnSCMotion(event):
160	xpos = event.xdata
161	if xpos:
162	xpos = round(xpos) #avoid out of frame mouse position
163	ypos = round(event.ydata)
164	zpos = Data['Layer']
165	if '100' in Data['Zone']:
166	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
167	elif '010' in Data['Zone']:
168	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
169	elif '001' in Data['Zone']:
170	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
171	Page.canvas.SetToolTipString(HKLtxt)
172	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
173
174	def OnSCPick(event):
175	zpos = Data['Layer']
176	pos = event.artist.center
177	if '100' in Data['Zone']:
178	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
179	hkl = np.array([zpos,pos[0],pos[1]])
180	elif '010' in Data['Zone']:
181	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
182	hkl = np.array([pos[0],zpos,pos[1]])
183	elif '001' in Data['Zone']:
184	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
185	hkl = np.array([pos[0],pos[1],zpos])
186	h,k,l = hkl
187	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
188	if len(hklf):
189	Fosq,sig,Fcsq = hklf[0]
190	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
191	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
192
193	def OnSCKeyPress(event):
194	print event.key
195
196	try:
197	plotNum = self.G2plotNB.plotList.index('Structure Factors')
198	Page = self.G2plotNB.nb.GetPage(plotNum)
199	if not newPlot:
200	Plot = Page.figure.gca() #get previous powder plot & get limits
201	xylim = Plot.get_xlim(),Plot.get_ylim()
202	Page.figure.clf()
203	Plot = Page.figure.gca() #get a fresh plot after clf()
204	except ValueError:
205	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
206	plotNum = self.G2plotNB.plotList.index('Structure Factors')
207	Page = self.G2plotNB.nb.GetPage(plotNum)
208	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
209	Page.canvas.mpl_connect('pick_event', OnSCPick)
210	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
211	Page.SetFocus()
212
213	Plot.set_aspect(aspect='equal')
214	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
215	Data = self.PatternTree.GetItemPyData( \
216	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
217	Type = Data['Type']
218	scale = Data['Scale']
219	HKLmax = Data['HKLmax']
220	HKLmin = Data['HKLmin']
221	FosqMax = Data['FoMax']
222	FoMax = math.sqrt(FosqMax)
223	ifFc = Data['ifFc']
224	xlabel = ['k, h=','h, k=','h, l=']
225	ylabel = ['l','l','k']
226	zones = ['100','010','001']
227	pzone = [[1,2],[0,2],[0,1]]
228	izone = zones.index(Data['Zone'])
229	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
230	HKL = []
231	HKLF = []
232	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
233	HKL.append(H)
234	HKLF.append([Fosq,sig,Fcsq])
235	if H[izone] == Data['Layer']:
236	B = 0
237	if Type == 'Fosq':
238	A = scale*Fosq/FosqMax
239	B = scale*Fcsq/FosqMax
240	C = abs(A-B)
241	elif Type == 'Fo':
242	A = scale*math.sqrt(max(0,Fosq))/FoMax
243	B = scale*math.sqrt(max(0,Fcsq))/FoMax
244	C = abs(A-B)
245	elif Type == '\|DFsq\|/sig':
246	A = abs(Fosq-Fcsq)/(scale*sig)
247	elif Type == '\|DFsq\|>sig':
248	A = abs(Fosq-Fcsq)/(scale*sig)
249	if A < 1.0: A = 0
250	elif Type == '\|DFsq\|>3sig':
251	A = abs(Fosq-Fcsq)/(scale*sig)
252	if A < 3.0: A = 0
253	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
254	if A > 0.0:
255	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
256	if B:
257	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
258	radius = C
259	if radius > 0:
260	if A > B:
261	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
262	else:
263	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
264	HKL = np.array(HKL,dtype=np.int)
265	HKLF = np.array(HKLF)
266	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
267	Plot.set_ylabel(ylabel[izone],fontsize=12)
268	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
269	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
270	if not newPlot:
271	Page.toolbar.push_current()
272	Plot.set_xlim(xylim[0])
273	Plot.set_ylim(xylim[1])
274	xylim = []
275	Page.toolbar.push_current()
276	Page.toolbar.draw()
277	else:
278	Page.canvas.draw()
279
280	def PlotPatterns(self,newPlot=False):
281	global HKL
282
283	def OnPick(event):
284	if self.itemPicked is not None: return
285	PatternId = self.PatternId
286	try:
287	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
288	except TypeError:
289	return
290	Parms = dict(zip(Names,Values))
291	try:
292	wave = Parms['Lam']
293	except KeyError:
294	wave = Parms['Lam1']
295	PickId = self.PickId
296	pick = event.artist
297	mouse = event.mouseevent
298	xpos = pick.get_xdata()
299	ypos = pick.get_ydata()
300	ind = event.ind
301	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
302	if self.PatternTree.GetItemText(PickId) == 'Peak List':
303	if ind.all() != [0]: #picked a data point
304	ins = [Parms[x] for x in ['U','V','W','X','Y','SH/L']]
305	if self.qPlot: #qplot - convert back to 2-theta
306	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
307	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
308	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
309	data = self.PatternTree.GetItemPyData(self.PickId)
310	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
311	data.append(XY)
312	G2pdG.UpdatePeakGrid(self,data)
313	PlotPatterns(self)
314	else: #picked a peak list line
315	self.itemPicked = pick
316	elif self.PatternTree.GetItemText(PickId) == 'Limits':
317	if ind.all() != [0]: #picked a data point
318	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
319	data = self.PatternTree.GetItemPyData(LimitId)
320	if self.qPlot: #qplot - convert back to 2-theta
321	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
322	if mouse.button==1:
323	data[1][0] = min(xy[0],data[1][1])
324	if mouse.button==3:
325	data[1][1] = max(xy[0],data[1][0])
326	self.PatternTree.SetItemPyData(LimitId,data)
327	G2pdG.UpdateLimitsGrid(self,data)
328	PlotPatterns(self)
329	else: #picked a limit line
330	self.itemPicked = pick
331
332	def OnPlotKeyPress(event):
333	newPlot = False
334	if event.key == 'w':
335	if self.Weight:
336	self.Weight = False
337	else:
338	self.Weight = True
339	print 'plot weighting:',self.Weight
340	elif event.key == 'n':
341	if self.Contour:
342	pass
343	else:
344	if self.logPlot:
345	self.logPlot = False
346	else:
347	self.Offset[0] = 0
348	self.logPlot = True
349	elif event.key == 'u':
350	if self.Contour:
351	self.Cmax = min(1.0,self.Cmax*1.2)
352	elif self.logPlot:
353	pass
354	elif self.Offset[0] < 100.:
355	self.Offset[0] += 1.
356	elif event.key == 'd':
357	if self.Contour:
358	self.Cmax = max(0.0,self.Cmax*0.8)
359	elif self.logPlot:
360	pass
361	elif self.Offset[0] > 0.:
362	self.Offset[0] -= 1.
363	elif event.key == 'l':
364	self.Offset[1] -= 1.
365	elif event.key == 'r':
366	self.Offset[1] += 1.
367	elif event.key == 'c':
368	newPlot = True
369	if self.Contour:
370	self.Contour = False
371	else:
372	self.Contour = True
373	self.SinglePlot = False
374	self.Offset = [0.,0.]
375	elif event.key == 'q':
376	newPlot = True
377	if self.qPlot:
378	self.qPlot = False
379	else:
380	self.qPlot = True
381	elif event.key == 's':
382	if self.Contour:
383	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
384	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
385	if dlg.ShowModal() == wx.ID_OK:
386	sel = dlg.GetSelection()
387	self.ContourColor = choice[sel]
388	else:
389	self.ContourColor = 'Paired'
390	dlg.Destroy()
391	else:
392	if self.SinglePlot:
393	self.SinglePlot = False
394	else:
395	self.SinglePlot = True
396	elif event.key == '+':
397	if self.PickId:
398	self.PickId = False
399	elif event.key == 'i': #for smoothing contour plot
400	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
401	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
402	'mitchell','sinc','lanczos']
403	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
404	if dlg.ShowModal() == wx.ID_OK:
405	sel = dlg.GetSelection()
406	self.Interpolate = choice[sel]
407	else:
408	self.Interpolate = 'nearest'
409	dlg.Destroy()
410
411	PlotPatterns(self,newPlot=newPlot)
412
413	def OnKeyBox(event):
414	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('Powder Patterns'):
415	event.key = cb.GetValue()[0]
416	cb.SetValue(' key press')
417	OnPlotKeyPress(event)
418
419	def OnMotion(event):
420	xpos = event.xdata
421	if xpos: #avoid out of frame mouse position
422	ypos = event.ydata
423	Page.canvas.SetCursor(wx.CROSS_CURSOR)
424	try:
425	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
426	Parms = dict(zip(Names,Values))
427	try:
428	wave = Parms['Lam']
429	except KeyError:
430	wave = Parms['Lam1']
431	if self.qPlot:
432	xpos = 2.0asind(xposwave/(4*math.pi))
433	dsp = 0.0
434	if abs(xpos) > 0.: #avoid possible singularity at beam center
435	dsp = wave/(2.*sind(abs(xpos)/2.0))
436	if self.Contour:
437	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
438	else:
439	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
440	if self.itemPicked:
441	Page.canvas.SetToolTipString('%9.3f'%(xpos))
442	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
443	found = []
444	if len(HKL):
445	view = Page.toolbar._views.forward()[0][:2]
446	wid = view[1]-view[0]
447	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
448	if len(found):
449	h,k,l = found[0][:3]
450	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
451	else:
452	Page.canvas.SetToolTipString('')
453
454	except TypeError:
455	self.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
456
457	def OnRelease(event):
458	if self.itemPicked is None: return
459	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
460	Parms = dict(zip(Names,Values))
461	try:
462	wave = Parms['Lam']
463	except KeyError:
464	wave = Parms['Lam1']
465	xpos = event.xdata
466	if xpos: #avoid out of frame mouse position
467	lines = []
468	for line in self.Lines: lines.append(line.get_xdata()[0])
469	lineNo = lines.index(self.itemPicked.get_xdata()[0])
470	if lineNo in [0,1]:
471	LimitId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Limits')
472	data = self.PatternTree.GetItemPyData(LimitId)
473	# print 'limits',xpos
474	if self.qPlot:
475	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
476	else:
477	data[1][lineNo] = xpos
478	self.PatternTree.SetItemPyData(LimitId,data)
479	if self.PatternTree.GetItemText(self.PickId) == 'Limits':
480	G2pdG.UpdateLimitsGrid(self,data)
481	else:
482	PeakId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Peak List')
483	data = self.PatternTree.GetItemPyData(PeakId)
484	# print 'peaks',xpos
485	if event.button == 3:
486	del data[lineNo-2]
487	else:
488	if self.qPlot:
489	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
490	else:
491	data[lineNo-2][0] = xpos
492	self.PatternTree.SetItemPyData(PeakId,data)
493	G2pdG.UpdatePeakGrid(self,data)
494	PlotPatterns(self)
495	self.itemPicked = None
496
497	xylim = []
498	try:
499	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
500	Page = self.G2plotNB.nb.GetPage(plotNum)
501	if not newPlot:
502	Plot = Page.figure.gca() #get previous powder plot & get limits
503	xylim = Plot.get_xlim(),Plot.get_ylim()
504	Page.figure.clf()
505	Plot = Page.figure.gca() #get a fresh plot after clf()
506	except ValueError:
507	newPlot = True
508	self.Cmax = 1.0
509	Plot = self.G2plotNB.addMpl('Powder Patterns').gca()
510	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
511	Page = self.G2plotNB.nb.GetPage(plotNum)
512	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
513	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
514	Page.canvas.mpl_connect('pick_event', OnPick)
515	Page.canvas.mpl_connect('button_release_event', OnRelease)
516	Page.SetFocus()
517	self.G2plotNB.status.DestroyChildren()
518	if self.Contour:
519	Choice = (' key press','d: lower contour max','u: raise contour max',
520	'i: interpolation method','s: color scheme','c: contour off')
521	else:
522	if self.logPlot:
523	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
524	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
525	else:
526	Choice = (' key press','l: offset left','r: offset right','d: offset down',
527	'u: offset up','n: log(I) on','c: contour on','q: toggle q plot',
528	's: toggle single plot','+: no selection')
529	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
530	choices=Choice)
531	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
532	cb.SetValue(' key press')
533
534	PickId = self.PickId
535	PatternId = self.PatternId
536	colors=['b','g','r','c','m','k']
537	Lines = []
538	if self.SinglePlot:
539	Pattern = self.PatternTree.GetItemPyData(PatternId)
540	Pattern.append(self.PatternTree.GetItemText(PatternId))
541	PlotList = [Pattern,]
542	ParmList = [self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
543	self.PatternId, 'Instrument Parameters'))[1],]
544	else:
545	PlotList = []
546	ParmList = []
547	item, cookie = self.PatternTree.GetFirstChild(self.root)
548	while item:
549	if 'PWDR' in self.PatternTree.GetItemText(item):
550	Pattern = self.PatternTree.GetItemPyData(item)
551	if len(Pattern) < 3: # put name on end if needed
552	Pattern.append(self.PatternTree.GetItemText(item))
553	PlotList.append(Pattern)
554	ParmList.append(self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
555	item,'Instrument Parameters'))[1])
556	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
557	Ymax = 1.0
558	lenX = 0
559	HKL = np.array(self.HKL)
560	for Pattern in PlotList:
561	xye = Pattern[1]
562	Ymax = max(Ymax,max(xye[1]))
563	offset = self.Offset[0]*Ymax/100.0
564	Title = 'Powder Patterns: '+os.path.split(self.GSASprojectfile)[1]
565	if self.logPlot:
566	Title = 'log('+Title+')'
567	Plot.set_title(Title)
568	if self.qPlot:
569	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
570	else:
571	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
572	Plot.set_ylabel('Intensity',fontsize=12)
573	if self.Contour:
574	ContourZ = []
575	ContourY = []
576	Nseq = 0
577	for N,Pattern in enumerate(PlotList):
578	Parms = ParmList[N]
579	ifpicked = False
580	LimitId = 0
581	xye = np.array(Pattern[1])
582	if PickId:
583	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
584	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
585	if self.qPlot:
586	Id = G2gd.GetPatternTreeItemId(self,self.root, Pattern[2])
587	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
588	else:
589	X = xye[0]
590	if not lenX:
591	lenX = len(X)
592	Y = xye[1]+offset*N
593	if LimitId:
594	limits = np.array(self.PatternTree.GetItemPyData(LimitId))
595	if self.qPlot:
596	limits = 4np.pinpsind(limits/2.0)/Parms[1]
597	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
598	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
599	if self.Contour:
600
601	if lenX == len(X):
602	ContourY.append(N)
603	ContourZ.append(Y)
604	ContourX = X
605	Nseq += 1
606	Plot.set_ylabel('Data sequence',fontsize=12)
607	else:
608	X += self.Offset[1].005N
609	if ifpicked:
610	Z = xye[3]+offset*N
611	W = xye[4]+offset*N
612	D = xye[5]+offsetN-Ymax.02
613	if self.Weight:
614	W2 = np.sqrt(xye[2])
615	D = W2-Ymax.02
616	if self.logPlot:
617	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
618	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
619	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
620	else:
621	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
622	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
623	Plot.plot(X,W,colors[(N+2)%6],picker=False)
624	Plot.plot(X,D,colors[(N+3)%6],picker=False)
625	Plot.axhline(0.,color=wx.BLACK)
626	Page.canvas.SetToolTipString('')
627	if self.PatternTree.GetItemText(PickId) == 'Peak List':
628	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
629	Page.canvas.SetToolTipString(tip)
630	data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List'))
631	for item in data:
632	if self.qPlot:
633	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
634	else:
635	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
636	if self.PatternTree.GetItemText(PickId) == 'Limits':
637	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
638	Page.canvas.SetToolTipString(tip)
639	data = self.LimitsTable.GetData()
640	else:
641	if self.logPlot:
642	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
643	else:
644	Plot.plot(X,Y,colors[N%6],picker=False)
645	if PickId and self.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
646	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1::2]
647	Parms = dict(zip(Names,Values))
648	try:
649	wave = Parms['Lam']
650	except KeyError:
651	wave = Parms['Lam1']
652	peaks = np.array((self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))))
653	for peak in peaks:
654	if self.qPlot:
655	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
656	else:
657	Plot.axvline(peak[0],color='b')
658	for hkl in self.HKL:
659	if self.qPlot:
660	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
661	else:
662	Plot.axvline(hkl[5],color='r',dashes=(5,5))
663	if self.Contour:
664	acolor = mpl.cm.get_cmap(self.ContourColor)
665	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
666	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
667	Page.figure.colorbar(Img)
668	else:
669	self.Lines = Lines
670	if not newPlot:
671	Page.toolbar.push_current()
672	Plot.set_xlim(xylim[0])
673	Plot.set_ylim(xylim[1])
674	xylim = []
675	Page.toolbar.push_current()
676	Page.toolbar.draw()
677	else:
678	Page.canvas.draw()
679	self.Pwdr = True
680
681	def PlotISFG(self,newPlot=False,type=''):
682	if not type:
683	type = self.G2plotNB.plotList[self.G2plotNB.nb.GetSelection()]
684	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
685	return
686	superMinusOne = unichr(0xaf)+unichr(0xb9)
687
688	def OnPlotKeyPress(event):
689	newPlot = False
690	if event.key == 'u':
691	if self.Contour:
692	self.Cmax = min(1.0,self.Cmax*1.2)
693	elif self.Offset[0] < 100.:
694	self.Offset[0] += 1.
695	elif event.key == 'd':
696	if self.Contour:
697	self.Cmax = max(0.0,self.Cmax*0.8)
698	elif self.Offset[0] > 0.:
699	self.Offset[0] -= 1.
700	elif event.key == 'l':
701	self.Offset[1] -= 1.
702	elif event.key == 'r':
703	self.Offset[1] += 1.
704	elif event.key == 'c':
705	newPlot = True
706	if self.Contour:
707	self.Contour = False
708	else:
709	self.Contour = True
710	self.SinglePlot = False
711	self.Offset = [0.,0.]
712	elif event.key == 's':
713	if self.Contour:
714	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
715	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
716	if dlg.ShowModal() == wx.ID_OK:
717	sel = dlg.GetSelection()
718	self.ContourColor = choice[sel]
719	else:
720	self.ContourColor = 'Paired'
721	dlg.Destroy()
722	else:
723	if self.SinglePlot:
724	self.SinglePlot = False
725	else:
726	self.SinglePlot = True
727	elif event.key == 'i': #for smoothing contour plot
728	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
729	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
730	'mitchell','sinc','lanczos']
731	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
732	if dlg.ShowModal() == wx.ID_OK:
733	sel = dlg.GetSelection()
734	self.Interpolate = choice[sel]
735	else:
736	self.Interpolate = 'nearest'
737	dlg.Destroy()
738	elif event.key == 't' and not self.Contour:
739	if self.Legend:
740	self.Legend = False
741	else:
742	self.Legend = True
743
744
745	PlotISFG(self,newPlot=newPlot,type=type)
746
747	def OnKeyBox(event):
748	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index(type):
749	event.key = cb.GetValue()[0]
750	cb.SetValue(' key press')
751	OnPlotKeyPress(event)
752
753	def OnMotion(event):
754	xpos = event.xdata
755	if xpos: #avoid out of frame mouse position
756	ypos = event.ydata
757	Page.canvas.SetCursor(wx.CROSS_CURSOR)
758	try:
759	if self.Contour:
760	self.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
761	else:
762	self.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
763	except TypeError:
764	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
765
766	xylim = []
767	try:
768	plotNum = self.G2plotNB.plotList.index(type)
769	Page = self.G2plotNB.nb.GetPage(plotNum)
770	if not newPlot:
771	Plot = Page.figure.gca() #get previous S(Q) plot & get limits
772	xylim = Plot.get_xlim(),Plot.get_ylim()
773	Page.figure.clf()
774	Plot = Page.figure.gca()
775	except ValueError:
776	newPlot = True
777	self.Cmax = 1.0
778	Plot = self.G2plotNB.addMpl(type).gca()
779	plotNum = self.G2plotNB.plotList.index(type)
780	Page = self.G2plotNB.nb.GetPage(plotNum)
781	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
782	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
783
784	Page.SetFocus()
785	self.G2plotNB.status.DestroyChildren()
786	if self.Contour:
787	Choice = (' key press','d: lower contour max','u: raise contour max',
788	'i: interpolation method','s: color scheme','c: contour off')
789	else:
790	Choice = (' key press','l: offset left','r: offset right','d: offset down',
791	'u: offset up','t: toggle legend','c: contour on','s: toggle single plot')
792	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
793	choices=Choice)
794	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
795	cb.SetValue(' key press')
796	PatternId = self.PatternId
797	PickId = self.PickId
798	Plot.set_title(type)
799	if type == 'G(R)':
800	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
801	else:
802	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
803	Plot.set_ylabel(r''+type,fontsize=14)
804	colors=['b','g','r','c','m','k']
805	name = self.PatternTree.GetItemText(PatternId)[4:]
806	Pattern = []
807	if self.SinglePlot:
808	name = self.PatternTree.GetItemText(PatternId)
809	name = type+name[4:]
810	Id = G2gd.GetPatternTreeItemId(self,PatternId,name)
811	Pattern = self.PatternTree.GetItemPyData(Id)
812	if Pattern:
813	Pattern.append(name)
814	PlotList = [Pattern,]
815	else:
816	PlotList = []
817	item, cookie = self.PatternTree.GetFirstChild(self.root)
818	while item:
819	if 'PDF' in self.PatternTree.GetItemText(item):
820	name = type+self.PatternTree.GetItemText(item)[4:]
821	Id = G2gd.GetPatternTreeItemId(self,item,name)
822	Pattern = self.PatternTree.GetItemPyData(Id)
823	if Pattern:
824	Pattern.append(name)
825	PlotList.append(Pattern)
826	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
827	PDFdata = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'PDF Controls'))
828	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
829	Xb = [0.,10.]
830	Yb = [0.,-40.np.pinumbDen]
831	Ymax = 1.0
832	lenX = 0
833	for Pattern in PlotList:
834	xye = Pattern[1]
835	Ymax = max(Ymax,max(xye[1]))
836	offset = self.Offset[0]*Ymax/100.0
837	if self.Contour:
838	ContourZ = []
839	ContourY = []
840	Nseq = 0
841	for N,Pattern in enumerate(PlotList):
842	xye = Pattern[1]
843	if PickId:
844	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
845	X = xye[0]
846	if not lenX:
847	lenX = len(X)
848	Y = xye[1]+offset*N
849	if self.Contour:
850	if lenX == len(X):
851	ContourY.append(N)
852	ContourZ.append(Y)
853	ContourX = X
854	Nseq += 1
855	Plot.set_ylabel('Data sequence',fontsize=12)
856	else:
857	X = xye[0]+self.Offset[1].005N
858	if ifpicked:
859	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
860	Page.canvas.SetToolTipString('')
861	else:
862	if self.Legend:
863	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
864	else:
865	Plot.plot(X,Y,colors[N%6],picker=False)
866	if type == 'G(R)':
867	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
868	elif type == 'F(Q)':
869	Plot.axhline(0.,color=wx.BLACK)
870	elif type == 'S(Q)':
871	Plot.axhline(1.,color=wx.BLACK)
872	if self.Contour:
873	acolor = mpl.cm.get_cmap(self.ContourColor)
874	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
875	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
876	Page.figure.colorbar(Img)
877	elif self.Legend:
878	Plot.legend(loc='best')
879	if not newPlot:
880	Page.toolbar.push_current()
881	Plot.set_xlim(xylim[0])
882	Plot.set_ylim(xylim[1])
883	xylim = []
884	Page.toolbar.push_current()
885	Page.toolbar.draw()
886	else:
887	Page.canvas.draw()
888
889	def PlotXY(self,XY,newPlot=False,type=''):
890	#simple plot of xy data
891
892	def OnMotion(event):
893	xpos = event.xdata
894	if xpos: #avoid out of frame mouse position
895	ypos = event.ydata
896	Page.canvas.SetCursor(wx.CROSS_CURSOR)
897	try:
898	self.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
899	except TypeError:
900	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
901
902	try:
903	plotNum = self.G2plotNB.plotList.index(type)
904	Page = self.G2plotNB.nb.GetPage(plotNum)
905	if not newPlot:
906	Plot = Page.figure.gca()
907	xylim = Plot.get_xlim(),Plot.get_ylim()
908	Page.figure.clf()
909	Plot = Page.figure.gca()
910	except ValueError:
911	newPlot = True
912	Plot = self.G2plotNB.addMpl(type).gca()
913	plotNum = self.G2plotNB.plotList.index(type)
914	Page = self.G2plotNB.nb.GetPage(plotNum)
915	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
916
917	Page.SetFocus()
918	self.G2plotNB.status.DestroyChildren()
919	Plot.set_title(type)
920	Plot.set_xlabel(r'X',fontsize=14)
921	Plot.set_ylabel(r''+type,fontsize=14)
922	colors=['b','g','r','c','m','k']
923	Ymax = 1.0
924	lenX = 0
925	X,Y = XY[:2]
926	Ymax = max(Ymax,max(Y))
927	Plot.plot(X,Y,'k',picker=False)
928	if not newPlot:
929	Page.toolbar.push_current()
930	Plot.set_xlim(xylim[0])
931	Plot.set_ylim(xylim[1])
932	xylim = []
933	Page.toolbar.push_current()
934	Page.toolbar.draw()
935	else:
936	Page.canvas.draw()
937
938	def PlotPowderLines(self):
939	global HKL
940
941	def OnMotion(event):
942	xpos = event.xdata
943	if xpos: #avoid out of frame mouse position
944	Page.canvas.SetCursor(wx.CROSS_CURSOR)
945	self.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
946	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
947	found = []
948	if len(HKL):
949	view = Page.toolbar._views.forward()[0][:2]
950	wid = view[1]-view[0]
951	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
952	if len(found):
953	h,k,l = found[0][:3]
954	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
955	else:
956	Page.canvas.SetToolTipString('')
957
958	try:
959	plotNum = self.G2plotNB.plotList.index('Powder Lines')
960	Page = self.G2plotNB.nb.GetPage(plotNum)
961	Page.figure.clf()
962	Plot = Page.figure.gca()
963	except ValueError:
964	Plot = self.G2plotNB.addMpl('Powder Lines').gca()
965	plotNum = self.G2plotNB.plotList.index('Powder Lines')
966	Page = self.G2plotNB.nb.GetPage(plotNum)
967	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
968
969	Page.SetFocus()
970	Plot.set_title('Powder Pattern Lines')
971	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
972	PickId = self.PickId
973	PatternId = self.PatternId
974	peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))
975	for peak in peaks:
976	Plot.axvline(peak[0],color='b')
977	HKL = np.array(self.HKL)
978	for hkl in self.HKL:
979	Plot.axvline(hkl[5],color='r',dashes=(5,5))
980	xmin = peaks[0][0]
981	xmax = peaks[-1][0]
982	delt = xmax-xmin
983	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
984	Plot.set_xlim(xlim)
985	Page.canvas.draw()
986
987	def PlotPeakWidths(self):
988	PatternId = self.PatternId
989	limitID = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
990	if limitID:
991	limits = self.PatternTree.GetItemPyData(limitID)
992	else:
993	return
994	instParms = self.PatternTree.GetItemPyData( \
995	G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))
996	if instParms[0][0] == 'PXC':
997	lam = instParms[1][1]
998	if len(instParms[1]) == 13:
999	GU,GV,GW,LX,LY = instParms[0][6:11]
1000	else:
1001	GU,GV,GW,LX,LY = instParms[0][4:9]
1002	peakID = G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List')
1003	if peakID:
1004	peaks = self.PatternTree.GetItemPyData(peakID)
1005	else:
1006	peaks = []
1007
1008	try:
1009	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1010	Page = self.G2plotNB.nb.GetPage(plotNum)
1011	Page.figure.clf()
1012	Plot = Page.figure.gca()
1013	except ValueError:
1014	Plot = self.G2plotNB.addMpl('Peak Widths').gca()
1015	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1016	Page = self.G2plotNB.nb.GetPage(plotNum)
1017	Page.SetFocus()
1018
1019	Page.canvas.SetToolTipString('')
1020	colors=['b','g','r','c','m','k']
1021	Xmin,Xmax = limits[1]
1022	Xmin = min(0.5,max(Xmin,1))
1023	Xmin /= 2
1024	Xmax /= 2
1025	nPts = 100
1026	delt = (Xmax-Xmin)/nPts
1027	thetas = []
1028	for i in range(nPts):
1029	thetas.append(Xmin+i*delt)
1030	X = []
1031	Y = []
1032	Z = []
1033	W = []
1034	V = []
1035	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1036	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1037	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.)
1038	gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1039	for theta in thetas:
1040	X.append(4.0math.pisind(theta)/lam) #q
1041	s = sig(theta,GU,GV,GW)
1042	g = gam(theta,LX,LY)
1043	G = gamFW(g,s)
1044	H = gamFW2(g,s)
1045	Y.append(s/tand(theta))
1046	Z.append(g/tand(theta))
1047	W.append(G/tand(theta))
1048	V.append(H/tand(theta))
1049	Plot.set_title('Instrument and sample peak widths')
1050	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1051	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1052	Plot.plot(X,Y,color='r',label='Gaussian')
1053	Plot.plot(X,Z,color='g',label='Lorentzian')
1054	Plot.plot(X,W,color='b',label='G+L')
1055	Plot.plot(X,V,color='k',label='G+L2')
1056	X = []
1057	Y = []
1058	Z = []
1059	W = []
1060	V = []
1061	for peak in peaks:
1062	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1063	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1064	g = peak[6]*math.pi/18000.
1065	G = gamFW(g,s)
1066	H = gamFW2(g,s)
1067	Y.append(s/tand(peak[0]/2.))
1068	Z.append(g/tand(peak[0]/2.))
1069	W.append(G/tand(peak[0]/2.))
1070	V.append(H/tand(peak[0]/2.))
1071	Plot.plot(X,Y,'+',color='r',label='G peak')
1072	Plot.plot(X,Z,'+',color='g',label='L peak')
1073	Plot.plot(X,W,'+',color='b',label='G+L peak')
1074	Plot.plot(X,V,'+',color='k',label='G+L2 peak')
1075	Plot.legend(loc='best')
1076	Page.canvas.draw()
1077
1078	def PlotStrain(self,data):
1079	# in this instance data is for a phase
1080	PatternId = self.PatternId
1081	generalData = data['General']
1082	SGData = generalData['SGData']
1083	MuStrKeys = G2spc.MustrainNames(SGData)
1084	cell = generalData['Cell'][1:]
1085	A,B = G2lat.cell2AB(cell[:6])
1086	Vol = cell[6]
1087	useList = data['Histograms']
1088	numPlots = len(useList)
1089
1090	try:
1091	plotNum = self.G2plotNB.plotList.index('Microstrain')
1092	Page = self.G2plotNB.nb.GetPage(plotNum)
1093	Page.figure.clf()
1094	Plot = mp3d.Axes3D(Page.figure)
1095	except ValueError:
1096	Plot = mp3d.Axes3D(self.G2plotNB.add3D('Microstrain'))
1097	plotNum = self.G2plotNB.plotList.index('Microstrain')
1098	Page = self.G2plotNB.nb.GetPage(plotNum)
1099	Page.SetFocus()
1100	self.G2plotNB.status.SetStatusText('Adjust frame size to get desired aspect ratio',1)
1101
1102	for item in useList:
1103	if useList[item]['Show']:
1104	muStrain = useList[item]['Mustrain']
1105	PHI = np.linspace(0.,360.,30,True)
1106	PSI = np.linspace(0.,180.,30,True)
1107	X = np.outer(npsind(PHI),npsind(PSI))
1108	Y = np.outer(npcosd(PHI),npsind(PSI))
1109	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1110	if muStrain[0] == 'isotropic':
1111	muiso = muStrain[1][0]*math.pi/0.018 #centidegrees to radians!
1112	X *= muiso
1113	Y *= muiso
1114	Z *= muiso
1115
1116	elif muStrain[0] == 'uniaxial':
1117	def uniaxMustrain(xyz,muiso,muaniso,axes):
1118	cp = abs(np.dot(xyz,axes))
1119	S = muiso+muaniso*cp
1120	return Sxyzmath.pi/0.018 #centidegrees to radians!
1121	muiso,muaniso = muStrain[1][:2]
1122	axes = np.inner(A,np.array(muStrain[3]))
1123	axes /= nl.norm(axes)
1124	Shkl = np.array(muStrain[1])
1125	Shape = X.shape[0]
1126	XYZ = np.dstack((X,Y,Z))
1127	XYZ = np.nan_to_num(np.apply_along_axis(uniaxMustrain,2,XYZ,muiso,muaniso,axes))
1128	X,Y,Z = np.dsplit(XYZ,3)
1129	X = X[:,:,0]
1130	Y = Y[:,:,0]
1131	Z = Z[:,:,0]
1132
1133	elif muStrain[0] == 'generalized':
1134	def genMustrain(xyz,SGData,A,Shkl):
1135	uvw = np.inner(A.T,xyz)
1136	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1137	sum = np.sqrt(np.sum(np.multiply(Shkl,Strm)))*math.pi/0.018 #centidegrees to radians!
1138	return sum*xyz
1139	Shkl = np.array(muStrain[4])
1140	if np.any(Shkl):
1141	Shape = X.shape[0]
1142	XYZ = np.dstack((X,Y,Z))
1143	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1144	X,Y,Z = np.dsplit(XYZ,3)
1145	X = X[:,:,0]
1146	Y = Y[:,:,0]
1147	Z = Z[:,:,0]
1148
1149	if np.any(X) and np.any(Y) and np.any(Z):
1150	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g')
1151
1152	Plot.set_xlabel('X')
1153	Plot.set_ylabel('Y')
1154	Plot.set_zlabel('Z')
1155	Page.canvas.draw()
1156
1157	def PlotExposedImage(self,newPlot=False,event=None):
1158	plotNo = self.G2plotNB.nb.GetSelection()
1159	if self.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1160	PlotImage(self,newPlot,event,newImage=True)
1161	elif self.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1162	PlotIntegration(self,newPlot,event)
1163
1164	def PlotImage(self,newPlot=False,event=None,newImage=True):
1165	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1166	import numpy.ma as ma
1167	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1168	global Data,Masks
1169	colors=['b','g','r','c','m','k']
1170	Data = self.PatternTree.GetItemPyData(
1171	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1172	Masks = self.PatternTree.GetItemPyData(
1173	G2gd.GetPatternTreeItemId(self,self.Image, 'Masks'))
1174
1175	def OnImMotion(event):
1176	Page.canvas.SetToolTipString('')
1177	sizexy = Data['size']
1178	if event.xdata and event.ydata: #avoid out of frame errors
1179	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1180	item = self.itemPicked
1181	pixelSize = Data['pixelSize']
1182	scalex = 1000./pixelSize[0]
1183	scaley = 1000./pixelSize[1]
1184	if item and self.PatternTree.GetItemText(self.PickId) == 'Image Controls':
1185	if 'Text' in str(item):
1186	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1187	else:
1188	xcent,ycent = Data['center']
1189	xpos = event.xdata-xcent
1190	ypos = event.ydata-ycent
1191	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1192	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1193	Page.canvas.SetToolTipString('%6d deg'%(azm))
1194	elif 'line1' in str(item) or 'line2' in str(item):
1195	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1196	else:
1197	xpos = event.xdata
1198	ypos = event.ydata
1199	xpix = xpos*scalex
1200	ypix = ypos*scaley
1201	Int = 0
1202	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1203	Int = self.ImageZ[ypix][xpix]
1204	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1205	Q = 2.*math.pi/dsp
1206	if self.setPoly:
1207	self.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1208	else:
1209	self.G2plotNB.status.SetFields(\
1210	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1211
1212	def OnImPlotKeyPress(event):
1213	try:
1214	PickName = self.PatternTree.GetItemText(self.PickId)
1215	except TypeError:
1216	return
1217	if PickName == 'Masks':
1218	Xpos = event.xdata
1219	if not Xpos: #got point out of frame
1220	return
1221	Ypos = event.ydata
1222	if event.key == 's':
1223	Masks['Points'].append([Xpos,Ypos,1.])
1224	elif event.key == 'r':
1225	tth = G2img.GetTth(Xpos,Ypos,Data)
1226	Masks['Rings'].append([tth,0.1])
1227	elif event.key == 'a':
1228	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1229	azm = int(azm)
1230	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1231	elif event.key == 'p':
1232	self.setPoly = True
1233	Masks['Polygons'].append([])
1234	self.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1235	G2imG.UpdateMasks(self,Masks)
1236	elif PickName == 'Image Controls':
1237	if event.key == 'c':
1238	Xpos = event.xdata
1239	if not Xpos: #got point out of frame
1240	return
1241	Ypos = event.ydata
1242	dlg = wx.MessageDialog(self,'Are you sure you want to change the center?',
1243	'Center change',style=wx.OK\|wx.CANCEL)
1244	try:
1245	if dlg.ShowModal() == wx.ID_OK:
1246	print 'move center to: ',Xpos,Ypos
1247	Data['center'] = [Xpos,Ypos]
1248	G2imG.UpdateImageControls(self,Data,Masks)
1249	finally:
1250	dlg.Destroy()
1251	elif event.key == 'l':
1252	if self.logPlot:
1253	self.logPlot = False
1254	else:
1255	self.logPlot = True
1256	PlotImage(self,newImage=True)
1257
1258	def OnKeyBox(event):
1259	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('2D Powder Image'):
1260	event.key = cb.GetValue()[0]
1261	cb.SetValue(' key press')
1262	if event.key in 'l':
1263	OnImPlotKeyPress(event)
1264
1265	def OnImPick(event):
1266	if self.PatternTree.GetItemText(self.PickId) not in ['Image Controls','Masks']:
1267	return
1268	if self.setPoly:
1269	polygon = Masks['Polygons'][-1]
1270	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1271	if xpos and ypos: #point inside image
1272	if len(polygon) > 2 and event.mouseevent.button == 3:
1273	x0,y0 = polygon[0]
1274	polygon.append([x0,y0])
1275	self.setPoly = False
1276	self.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1277	else:
1278	self.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1279	polygon.append([xpos,ypos])
1280	G2imG.UpdateMasks(self,Masks)
1281	else:
1282	if self.itemPicked is not None: return
1283	self.itemPicked = event.artist
1284	self.mousePicked = event.mouseevent
1285
1286	def OnImRelease(event):
1287	try:
1288	PickName = self.PatternTree.GetItemText(self.PickId)
1289	except TypeError:
1290	return
1291	if PickName not in ['Image Controls','Masks']:
1292	return
1293	pixelSize = Data['pixelSize']
1294	scalex = 1000./pixelSize[0]
1295	scaley = 1000./pixelSize[1]
1296	pixLimit = Data['pixLimit']
1297	if self.itemPicked is None and PickName == 'Image Controls':
1298	# sizexy = Data['size']
1299	Xpos = event.xdata
1300	if not (Xpos and self.ifGetRing): #got point out of frame
1301	return
1302	Ypos = event.ydata
1303	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1304	if event.button == 1:
1305	Xpix = Xpos*scalex
1306	Ypix = Ypos*scaley
1307	xpos,ypos,I,J = G2img.ImageLocalMax(self.ImageZ,pixLimit,Xpix,Ypix)
1308	if I and J:
1309	xpos += .5 #shift to pixel center
1310	ypos += .5
1311	xpos /= scalex #convert to mm
1312	ypos /= scaley
1313	Data['ring'].append([xpos,ypos])
1314	elif event.button == 3:
1315	print 'LB shift'
1316	self.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1317	if G2img.ImageCalibrate(self,Data):
1318	self.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1319	print 'Calibration successful'
1320	else:
1321	self.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1322	print 'Calibration failed'
1323	self.ifGetRing = False
1324	G2imG.UpdateImageControls(self,Data,Masks)
1325	return
1326	PlotImage(self,newImage=False)
1327	return
1328	else:
1329	xpos = event.xdata
1330	if xpos: #avoid out of frame mouse position
1331	ypos = event.ydata
1332	if self.ifGetRing: #delete a calibration ring pick
1333	xypos = [xpos,ypos]
1334	rings = Data['ring']
1335	for ring in rings:
1336	if np.allclose(ring,xypos,.01,0):
1337	rings.remove(ring)
1338	else:
1339	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1340	itemPicked = str(self.itemPicked)
1341	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1342	if 'line1' in itemPicked:
1343	Data['IOtth'][0] = max(tth,0.001)
1344	elif 'line2' in itemPicked:
1345	Data['IOtth'][1] = tth
1346	elif 'line3' in itemPicked:
1347	Data['LRazimuth'][0] = int(azm)
1348	if Data['fullIntegrate']:
1349	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1350	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1351	Data['LRazimuth'][1] = int(azm)
1352
1353	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1354	Data['LRazimuth'][0] -= 360
1355
1356	azLim = np.array(Data['LRazimuth'])
1357	if np.any(azLim>360):
1358	azLim -= 360
1359	Data['LRazimuth'] = list(azLim)
1360
1361	if Data['IOtth'][0] > Data['IOtth'][1]:
1362	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1363
1364	self.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1365	self.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1366	self.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1367	self.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1368	elif 'Circle' in itemPicked and PickName == 'Masks':
1369	spots = Masks['Points']
1370	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1371	newPos = np.array([float(newPos[0]),float(newPos[1])])
1372	for spot in spots:
1373	if np.allclose(np.array([spot[:2]]),newPos):
1374	spot[:2] = xpos,ypos
1375	G2imG.UpdateMasks(self,Masks)
1376	elif 'Line2D' in itemPicked and PickName == 'Masks':
1377	Obj = self.itemPicked.findobj()
1378	rings = Masks['Rings']
1379	arcs = Masks['Arcs']
1380	polygons = Masks['Polygons']
1381	for ring in self.ringList:
1382	if Obj == ring[0]:
1383	rN = ring[1]
1384	if ring[2] == 'o':
1385	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1386	else:
1387	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1388	for arc in self.arcList:
1389	if Obj == arc[0]:
1390	aN = arc[1]
1391	if arc[2] == 'o':
1392	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1393	elif arc[2] == 'i':
1394	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1395	elif arc[2] == 'l':
1396	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1397	else:
1398	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1399	for poly in self.polyList:
1400	if Obj == poly[0]:
1401	ind = self.itemPicked.contains(self.mousePicked)[1]['ind'][0]
1402	oldPos = np.array([self.mousePicked.xdata,self.mousePicked.ydata])
1403	pN = poly[1]
1404	for i,xy in enumerate(polygons[pN]):
1405	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1406	polygons[pN][i] = xpos,ypos
1407	G2imG.UpdateMasks(self,Masks)
1408	# else: #keep for future debugging
1409	# print str(self.itemPicked),event.xdata,event.ydata,event.button
1410	PlotImage(self,newImage=True)
1411	self.itemPicked = None
1412
1413	try:
1414	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1415	Page = self.G2plotNB.nb.GetPage(plotNum)
1416	if not newPlot:
1417	Plot = Page.figure.gca() #get previous powder plot & get limits
1418	xylim = Plot.get_xlim(),Plot.get_ylim()
1419	if newImage:
1420	Page.figure.clf()
1421	Plot = Page.figure.gca() #get a fresh plot after clf()
1422
1423	except ValueError:
1424	Plot = self.G2plotNB.addMpl('2D Powder Image').gca()
1425	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1426	Page = self.G2plotNB.nb.GetPage(plotNum)
1427	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1428	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1429	Page.canvas.mpl_connect('pick_event', OnImPick)
1430	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1431	xylim = []
1432	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1433	Page.SetFocus()
1434	Title = self.PatternTree.GetItemText(self.Image)[4:]
1435	self.G2plotNB.status.DestroyChildren()
1436	if self.logPlot:
1437	Title = 'log('+Title+')'
1438	Plot.set_title(Title)
1439	try:
1440	if self.PatternTree.GetItemText(self.PickId) in ['Image Controls',]:
1441	if self.logPlot:
1442	Choice = (' key press','l: log(I) off')
1443	else:
1444	Choice = (' key press','l: log(I) on')
1445	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1446	choices=Choice)
1447	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1448	cb.SetValue(' key press')
1449	except TypeError:
1450	pass
1451	size,imagefile = self.PatternTree.GetItemPyData(self.Image)
1452	if imagefile != self.oldImagefile:
1453	imagefile = G2IO.CheckImageFile(self,imagefile)
1454	if not imagefile:
1455	self.G2plotNB.Delete('2D Powder Image')
1456	return
1457	self.PatternTree.SetItemPyData(self.Image,[size,imagefile])
1458	self.ImageZ = G2IO.GetImageData(self,imagefile,imageOnly=True)
1459	# print self.ImageZ.shape,self.ImageZ.size,Data['size'] #might be useful debugging line
1460	self.oldImagefile = imagefile
1461
1462	imScale = 1
1463	if len(self.ImageZ) > 1024:
1464	imScale = len(self.ImageZ)/1024
1465	sizexy = Data['size']
1466	pixelSize = Data['pixelSize']
1467	scalex = 1000./pixelSize[0]
1468	scaley = 1000./pixelSize[1]
1469	Xmax = sizexy[0]*pixelSize[0]/1000.
1470	Ymax = sizexy[1]*pixelSize[1]/1000.
1471	xlim = (0,Xmax)
1472	ylim = (Ymax,0)
1473	Imin,Imax = Data['range'][1]
1474	acolor = mpl.cm.get_cmap(Data['color'])
1475	xcent,ycent = Data['center']
1476	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1477	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1478	#do threshold mask - "real" mask - others are just bondaries
1479	Zlim = Masks['Thresholds'][1]
1480	wx.BeginBusyCursor()
1481	try:
1482
1483	if newImage:
1484	MA = ma.masked_greater(ma.masked_less(self.ImageZ,Zlim[0]),Zlim[1])
1485	MaskA = ma.getmaskarray(MA)
1486	A = G2img.ImageCompress(MA,imScale)
1487	AM = G2img.ImageCompress(MaskA,imScale)
1488	if self.logPlot:
1489	A = np.log(A)
1490	AM = np.log(AM)
1491	Imin,Imax = [np.amin(A),np.amax(A)]
1492	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
1493	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Xmax,0])
1494	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
1495	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
1496	if self.setPoly:
1497	Img.set_picker(True)
1498
1499	Plot.plot(xcent,ycent,'x')
1500	if Data['showLines']:
1501	LRAzim = Data['LRazimuth'] #NB: integers
1502	Nazm = Data['outAzimuths']
1503	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
1504	AzmthOff = Data['azmthOff']
1505	IOtth = Data['IOtth']
1506	wave = Data['wavelength']
1507	dspI = wave/(2.0*sind(IOtth[0]/2.0))
1508	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
1509	dspO = wave/(2.0*sind(IOtth[1]/2.0))
1510	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
1511	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
1512	if ellI:
1513	xyI = []
1514	for azm in Azm:
1515	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
1516	xyI = np.array(xyI)
1517	arcxI,arcyI = xyI.T
1518	Plot.plot(arcxI,arcyI,picker=3)
1519	if ellO:
1520	xyO = []
1521	for azm in Azm:
1522	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
1523	xyO = np.array(xyO)
1524	arcxO,arcyO = xyO.T
1525	Plot.plot(arcxO,arcyO,picker=3)
1526	if ellO and ellI:
1527	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
1528	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
1529	for i in range(Nazm):
1530	cake = LRAzim[0]+i*delAzm
1531	ind = np.searchsorted(Azm,cake)
1532	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
1533
1534	for xring,yring in Data['ring']:
1535	Plot.plot(xring,yring,'r+',picker=3)
1536	if Data['setRings']:
1537	# rings = np.concatenate((Data['rings']),axis=0)
1538	N = 0
1539	for ring in Data['rings']:
1540	xring,yring = np.array(ring).T[:2]
1541	Plot.plot(xring,yring,'+',color=colors[N%6])
1542	N += 1
1543	for ellipse in Data['ellipses']:
1544	cent,phi,[width,height],col = ellipse
1545	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
1546	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
1547	#masks - mask lines numbered after integration limit lines
1548	spots = Masks['Points']
1549	rings = Masks['Rings']
1550	arcs = Masks['Arcs']
1551	polygons = Masks['Polygons']
1552	for x,y,d in spots:
1553	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
1554	self.ringList = []
1555	for iring,(tth,thick) in enumerate(rings):
1556	wave = Data['wavelength']
1557	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
1558	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
1559	self.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1560	self.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1561	self.arcList = []
1562	for iarc,(tth,azm,thick) in enumerate(arcs):
1563	wave = Data['wavelength']
1564	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
1565	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
1566	self.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1567	self.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1568	self.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1569	self.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1570	self.polyList = []
1571	for ipoly,polygon in enumerate(polygons):
1572	x,y = np.hsplit(np.array(polygon),2)
1573	self.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
1574	Plot.plot(x,y,'r')
1575	if newImage:
1576	colorBar = Page.figure.colorbar(Img)
1577	Plot.set_xlim(xlim)
1578	Plot.set_ylim(ylim)
1579	if not newPlot and xylim:
1580	Page.toolbar.push_current()
1581	Plot.set_xlim(xylim[0])
1582	Plot.set_ylim(xylim[1])
1583	xylim = []
1584	Page.toolbar.push_current()
1585	Page.toolbar.draw()
1586	else:
1587	Page.canvas.draw()
1588	finally:
1589	wx.EndBusyCursor()
1590
1591	def PlotIntegration(self,newPlot=False,event=None):
1592
1593	def OnMotion(event):
1594	Page.canvas.SetToolTipString('')
1595	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1596	azm = event.ydata
1597	tth = event.xdata
1598	if azm and tth:
1599	self.G2plotNB.status.SetFields(\
1600	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1601
1602	try:
1603	plotNum = self.G2plotNB.plotList.index('2D Integration')
1604	Page = self.G2plotNB.nb.GetPage(plotNum)
1605	if not newPlot:
1606	Plot = Page.figure.gca() #get previous plot & get limits
1607	xylim = Plot.get_xlim(),Plot.get_ylim()
1608	Page.figure.clf()
1609	Plot = Page.figure.gca() #get a fresh plot after clf()
1610
1611	except ValueError:
1612	Plot = self.G2plotNB.addMpl('2D Integration').gca()
1613	plotNum = self.G2plotNB.plotList.index('2D Integration')
1614	Page = self.G2plotNB.nb.GetPage(plotNum)
1615	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1616	Page.views = False
1617	view = False
1618	if not event:
1619	Page.SetFocus()
1620
1621	Data = self.PatternTree.GetItemPyData(
1622	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1623	image = self.Integrate[0]
1624	xsc = self.Integrate[1]
1625	ysc = self.Integrate[2]
1626	Imin,Imax = Data['range'][1]
1627	acolor = mpl.cm.get_cmap(Data['color'])
1628	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1629	Plot.set_ylabel('azimuth',fontsize=12)
1630	Plot.set_xlabel('2-theta',fontsize=12)
1631	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
1632	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
1633	colorBar = Page.figure.colorbar(Img)
1634	if Data['setRings'] and Data['rings']:
1635	rings = np.concatenate((Data['rings']),axis=0)
1636	for xring,yring,dsp in rings:
1637	x,y = G2img.GetTthAzm(xring,yring,Data)
1638	Plot.plot(x,y,'r+')
1639	if Data['ellipses']:
1640	for ellipse in Data['ellipses']:
1641	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1642	x,y = np.hsplit(ring,2)
1643	tth,azm = G2img.GetTthAzm(x,y,Data)
1644	Plot.plot(tth,azm,'b,')
1645	if not newPlot:
1646	Page.toolbar.push_current()
1647	Plot.set_xlim(xylim[0])
1648	Plot.set_ylim(xylim[1])
1649	xylim = []
1650	Page.toolbar.push_current()
1651	Page.toolbar.draw()
1652	else:
1653	Page.canvas.draw()
1654
1655	def PlotTRImage(self,tax,tay,taz,newPlot=False):
1656	#a test plot routine - not normally used
1657
1658	def OnMotion(event):
1659	Page.canvas.SetToolTipString('')
1660	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1661	azm = event.xdata
1662	tth = event.ydata
1663	if azm and tth:
1664	self.G2plotNB.status.SetFields(\
1665	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1666
1667	try:
1668	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1669	Page = self.G2plotNB.nb.GetPage(plotNum)
1670	if not newPlot:
1671	Plot = Page.figure.gca() #get previous plot & get limits
1672	xylim = Plot.get_xlim(),Plot.get_ylim()
1673	Page.figure.clf()
1674	Plot = Page.figure.gca() #get a fresh plot after clf()
1675
1676	except ValueError:
1677	Plot = self.G2plotNB.addMpl('2D Transformed Powder Image').gca()
1678	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1679	Page = self.G2plotNB.nb.GetPage(plotNum)
1680	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1681	Page.views = False
1682	view = False
1683	Page.SetFocus()
1684
1685	Data = self.PatternTree.GetItemPyData(
1686	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1687	Imin,Imax = Data['range'][1]
1688	step = (Imax-Imin)/5.
1689	V = np.arange(Imin,Imax,step)
1690	acolor = mpl.cm.get_cmap(Data['color'])
1691	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1692	Plot.set_xlabel('azimuth',fontsize=12)
1693	Plot.set_ylabel('2-theta',fontsize=12)
1694	Plot.contour(tax,tay,taz,V,cmap=acolor)
1695	if Data['showLines']:
1696	IOtth = Data['IOtth']
1697	if Data['fullIntegrate']:
1698	LRAzim = [-180,180]
1699	else:
1700	LRAzim = Data['LRazimuth'] #NB: integers
1701	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
1702	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
1703	if not Data['fullIntegrate']:
1704	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
1705	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
1706	if Data['setRings']:
1707	rings = np.concatenate((Data['rings']),axis=0)
1708	for xring,yring,dsp in rings:
1709	x,y = G2img.GetTthAzm(xring,yring,Data)
1710	Plot.plot(y,x,'r+')
1711	if Data['ellipses']:
1712	for ellipse in Data['ellipses']:
1713	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1714	x,y = np.hsplit(ring,2)
1715	tth,azm = G2img.GetTthAzm(x,y,Data)
1716	Plot.plot(azm,tth,'b,')
1717	if not newPlot:
1718	Page.toolbar.push_current()
1719	Plot.set_xlim(xylim[0])
1720	Plot.set_ylim(xylim[1])
1721	xylim = []
1722	Page.toolbar.push_current()
1723	Page.toolbar.draw()
1724	else:
1725	Page.canvas.draw()
1726
1727	def PlotStructure(self,data):
1728	generalData = data['General']
1729	cell = generalData['Cell'][1:7]
1730	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
1731	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1732	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1733	Mydir = generalData['Mydir']
1734	atomData = data['Atoms']
1735	drawingData = data['Drawing']
1736	drawAtoms = drawingData['Atoms']
1737	cx,ct,cs = drawingData['atomPtrs']
1738	Wt = [255,255,255]
1739	Rd = [255,0,0]
1740	Gr = [0,255,0]
1741	Bl = [0,0,255]
1742	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]])
1743	uEdges = np.array([
1744	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
1745	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
1746	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
1747	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
1748	altDown = False
1749	shiftDown = False
1750	ctrlDown = False
1751
1752	def OnKeyBox(event):
1753	import Image
1754	Draw() #make sure plot is fresh!!
1755	mode = cb.GetValue()
1756	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
1757	size = Page.canvas.GetSize()
1758	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
1759	if mode in ['jpeg',]:
1760	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
1761	im = Image.new("RGBA", (size[0],size[1]))
1762	else:
1763	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
1764	im = Image.new("RGB", (size[0],size[1]))
1765	im.fromstring(Pix)
1766	im.save(Fname,mode)
1767	cb.SetValue(' Save as:')
1768	self.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
1769
1770	def GetTruePosition(xy):
1771	View = glGetIntegerv(GL_VIEWPORT)
1772	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
1773	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
1774	Zmax = 1.
1775	for i,atom in enumerate(drawAtoms):
1776	x,y,z = atom[cx:cx+3]
1777	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
1778	XY = [int(X),int(View[3]-Y)]
1779	if np.allclose(xy,XY,atol=10) and Z < Zmax:
1780	Zmax = Z
1781	SetSelectedAtoms(i)
1782
1783	def OnMouseDown(event):
1784	xy = event.GetPosition()
1785	if event.ShiftDown():
1786	GetTruePosition(xy)
1787	else:
1788	drawingData['Rotation'][3] = xy
1789	Draw()
1790
1791	def OnMouseMove(event):
1792	newxy = event.GetPosition()
1793	if event.ControlDown() and drawingData['showABC']:
1794	if event.LeftIsDown():
1795	ctrlDown = True
1796	SetTestRot(newxy)
1797	elif event.RightIsDown():
1798	SetTestPos(newxy)
1799	elif event.MiddleIsDown():
1800	SetTestRotZ(newxy)
1801
1802
1803	if event.Dragging() and not event.ControlDown():
1804	if event.LeftIsDown():
1805	SetRotation(newxy)
1806	elif event.RightIsDown():
1807	SetTranslation(newxy)
1808	elif event.MiddleIsDown():
1809	SetRotationZ(newxy)
1810	Draw()
1811
1812	def OnMouseWheel(event):
1813	drawingData['cameraPos'] += event.GetWheelRotation()/24
1814	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
1815	page = self.dataDisplay.GetSelection()
1816	if page:
1817	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1818	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1819	names = [child.GetName() for child in panel]
1820	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
1821	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
1822	Draw()
1823
1824	def getSelection():
1825	if self.dataDisplay:
1826	return self.dataDisplay.GetSelection()
1827	else:
1828	return 0
1829
1830	def SetViewPointText(VP):
1831	page = getSelection()
1832	if page:
1833	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1834	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1835	names = [child.GetName() for child in panel]
1836	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
1837
1838	def ClearSelectedAtoms():
1839	page = getSelection()
1840	if page:
1841	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1842	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
1843	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1844	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
1845
1846	def SetSelectedAtoms(ind):
1847	page = getSelection()
1848	if page:
1849	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1850	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
1851	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1852	Id = drawAtoms[ind][-2]
1853	for i,atom in enumerate(atomData):
1854	if atom[-1] == Id:
1855	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
1856
1857	def GetSelectedAtoms():
1858	page = getSelection()
1859	Ind = []
1860	if page:
1861	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
1862	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
1863	elif self.dataDisplay.GetPageText(page) == 'Atoms':
1864	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
1865	return Ind
1866
1867	def OnKey(event): #on key UP!!
1868	keyCode = event.GetKeyCode()
1869	if keyCode > 255:
1870	keyCode = 0
1871	key,xyz = chr(keyCode),event.GetPosition()
1872	indx = drawingData['selectedAtoms']
1873	if key in ['c','C']:
1874	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
1875	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
1876	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
1877	SetViewPointText(drawingData['viewPoint'][0])
1878	elif key in ['n','N']:
1879	drawAtoms = drawingData['Atoms']
1880	pI = drawingData['viewPoint'][1]
1881	if indx:
1882	pI[0] = indx[pI[1]]
1883	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1884	pI[1] += 1
1885	if pI[1] >= len(indx):
1886	pI[1] = 0
1887	else:
1888	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1889	pI[0] += 1
1890	if pI[0] >= len(drawAtoms):
1891	pI[0] = 0
1892	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
1893	SetViewPointText(drawingData['viewPoint'][0])
1894
1895	elif key in ['p','P']:
1896	drawAtoms = drawingData['Atoms']
1897	pI = drawingData['viewPoint'][1]
1898	if indx:
1899	pI[0] = indx[pI[1]]
1900	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1901	pI[1] -= 1
1902	if pI[1] < 0:
1903	pI[1] = len(indx)-1
1904	else:
1905	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
1906	pI[0] -= 1
1907	if pI[0] < 0:
1908	pI[0] = len(drawAtoms)-1
1909	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
1910	SetViewPointText(drawingData['viewPoint'][0])
1911	Draw()
1912
1913	def SetBackground():
1914	R,G,B,A = Page.camera['backColor']
1915	glClearColor(R,G,B,A)
1916	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
1917
1918	def SetLights():
1919	glEnable(GL_DEPTH_TEST)
1920	glShadeModel(GL_SMOOTH)
1921	glEnable(GL_LIGHTING)
1922	glEnable(GL_LIGHT0)
1923	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
1924	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
1925	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
1926
1927	def SetTranslation(newxy):
1928	Tx,Ty,Tz = drawingData['viewPoint'][0]
1929	anglex,angley,anglez,oldxy = drawingData['Rotation']
1930	Rx = G2lat.rotdMat(anglex,0)
1931	Ry = G2lat.rotdMat(angley,1)
1932	Rz = G2lat.rotdMat(anglez,2)
1933	dxy = list(newxy-oldxy)+[0,]
1934	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
1935	Tx -= dxy[0]*0.01
1936	Ty += dxy[1]*0.01
1937	Tz -= dxy[2]*0.01
1938	drawingData['Rotation'][3] = newxy
1939	drawingData['viewPoint'][0] = Tx,Ty,Tz
1940	SetViewPointText([Tx,Ty,Tz])
1941
1942	def SetTestPos(newxy):
1943	Tx,Ty,Tz = drawingData['testPos'][0]
1944	anglex,angley,anglez,oldxy = drawingData['Rotation']
1945	Rx = G2lat.rotdMat(anglex,0)
1946	Ry = G2lat.rotdMat(angley,1)
1947	Rz = G2lat.rotdMat(anglez,2)
1948	dxy = list(newxy-oldxy)+[0,]
1949	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
1950	Tx += dxy[0]*0.001
1951	Ty -= dxy[1]*0.001
1952	Tz += dxy[2]*0.001
1953	drawingData['Rotation'][3] = newxy
1954	drawingData['testPos'][0] = Tx,Ty,Tz
1955
1956	def SetTestRot(newxy):
1957	Txyz = np.array(drawingData['testPos'][0])
1958	oldxy = drawingData['testPos'][2]
1959	Ax,Ay,Az = drawingData['testPos'][1]
1960	Vxyz = np.array(drawingData['viewPoint'][0])
1961	Dxyz = np.inner(Amat,Txyz-Vxyz)
1962	dxy = list(newxy-oldxy)+[0,]
1963	Ax += dxy[1]*0.01
1964	Ay += dxy[0]*0.01
1965	Rx = G2lat.rotdMat(Ax,0)
1966	Ry = G2lat.rotdMat(Ay,1)
1967	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
1968	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
1969	drawingData['testPos'][1] = [Ax,Ay,Az]
1970	drawingData['testPos'][2] = newxy
1971	drawingData['testPos'][0] = Dxyz
1972
1973	def SetTestRotZ(newxy):
1974	Txyz = np.array(drawingData['testPos'][0])
1975	oldxy = drawingData['testPos'][2]
1976	Ax,Ay,Az = drawingData['testPos'][1]
1977	Vxyz = np.array(drawingData['viewPoint'][0])
1978	Dxyz = np.inner(Amat,Txyz-Vxyz)
1979	dxy = list(newxy-oldxy)+[0,]
1980	Az += (dxy[0]+dxy[1])*.01
1981	Rz = G2lat.rotdMat(Az,2)
1982	Dxyz = np.inner(Rz,Dxyz)
1983	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
1984	drawingData['testPos'][1] = [Ax,Ay,Az]
1985	drawingData['testPos'][2] = newxy
1986	drawingData['testPos'][0] = Dxyz
1987
1988	def SetRotation(newxy):
1989	anglex,angley,anglez,oldxy = drawingData['Rotation']
1990	dxy = newxy-oldxy
1991	anglex += dxy[1]*.25
1992	angley += dxy[0]*.25
1993	oldxy = newxy
1994	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
1995
1996	def SetRotationZ(newxy):
1997	anglex,angley,anglez,oldxy = drawingData['Rotation']
1998	dxy = newxy-oldxy
1999	anglez += (dxy[0]+dxy[1])*.25
2000	oldxy = newxy
2001	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2002
2003	def RenderBox():
2004	glEnable(GL_COLOR_MATERIAL)
2005	glLineWidth(2)
2006	glEnable(GL_BLEND)
2007	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2008	glEnable(GL_LINE_SMOOTH)
2009	glBegin(GL_LINES)
2010	for line,color in zip(uEdges,uColors):
2011	glColor3ubv(color)
2012	glVertex3fv(line[0])
2013	glVertex3fv(line[1])
2014	glEnd()
2015	glColor4ubv([0,0,0,0])
2016	glDisable(GL_LINE_SMOOTH)
2017	glDisable(GL_BLEND)
2018	glDisable(GL_COLOR_MATERIAL)
2019
2020	def RenderUnitVectors(x,y,z):
2021	xyz = np.array([x,y,z])
2022	glEnable(GL_COLOR_MATERIAL)
2023	glLineWidth(1)
2024	glPushMatrix()
2025	glTranslate(x,y,z)
2026	glScalef(1/cell[0],1/cell[1],1/cell[2])
2027	glBegin(GL_LINES)
2028	for line,color in zip(uEdges,uColors)[:3]:
2029	glColor3ubv(color)
2030	glVertex3fv(line[0])
2031	glVertex3fv(line[1])
2032	glEnd()
2033	glPopMatrix()
2034	glColor4ubv([0,0,0,0])
2035	glDisable(GL_COLOR_MATERIAL)
2036
2037	def RenderSphere(x,y,z,radius,color):
2038	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2039	glPushMatrix()
2040	glTranslate(x,y,z)
2041	glMultMatrixf(B4mat.T)
2042	q = gluNewQuadric()
2043	gluSphere(q,radius,20,10)
2044	glPopMatrix()
2045
2046	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2047	s1,s2,s3 = E
2048	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2049	glPushMatrix()
2050	glTranslate(x,y,z)
2051	glMultMatrixf(B4mat.T)
2052	glMultMatrixf(R4.T)
2053	glEnable(GL_NORMALIZE)
2054	glScale(s1,s2,s3)
2055	q = gluNewQuadric()
2056	gluSphere(q,ellipseProb,20,10)
2057	glDisable(GL_NORMALIZE)
2058	glPopMatrix()
2059
2060	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2061	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2062	glPushMatrix()
2063	glTranslate(x,y,z)
2064	glMultMatrixf(B4mat.T)
2065	for bond in Bonds:
2066	glPushMatrix()
2067	Dx = np.inner(Amat,bond)
2068	Z = np.sqrt(np.sum(Dx**2))
2069	azm = atan2d(-Dx[1],-Dx[0])
2070	phi = acosd(Dx[2]/Z)
2071	glRotate(-azm,0,0,1)
2072	glRotate(phi,1,0,0)
2073	q = gluNewQuadric()
2074	gluCylinder(q,radius,radius,Z,slice,2)
2075	glPopMatrix()
2076	glPopMatrix()
2077
2078	def RenderLines(x,y,z,Bonds,color):
2079	xyz = np.array([x,y,z])
2080	glEnable(GL_COLOR_MATERIAL)
2081	glLineWidth(1)
2082	glColor3fv(color)
2083	glPushMatrix()
2084	glBegin(GL_LINES)
2085	for bond in Bonds:
2086	glVertex3fv(xyz)
2087	glVertex3fv(xyz+bond)
2088	glEnd()
2089	glColor4ubv([0,0,0,0])
2090	glPopMatrix()
2091	glDisable(GL_COLOR_MATERIAL)
2092
2093	def RenderPolyhedra(x,y,z,Faces,color):
2094	glPushMatrix()
2095	glTranslate(x,y,z)
2096	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2097	glShadeModel(GL_SMOOTH)
2098	glMultMatrixf(B4mat.T)
2099	for face,norm in Faces:
2100	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2101	glFrontFace(GL_CW)
2102	glNormal3fv(norm)
2103	glBegin(GL_TRIANGLES)
2104	for vert in face:
2105	glVertex3fv(vert)
2106	glEnd()
2107	glPopMatrix()
2108
2109	def RenderBackbone(Backbone,BackboneColor,radius):
2110	glPushMatrix()
2111	glMultMatrixf(B4mat.T)
2112	glEnable(GL_COLOR_MATERIAL)
2113	glShadeModel(GL_SMOOTH)
2114	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2115	glePolyCylinder(Backbone,BackboneColor,radius)
2116	glPopMatrix()
2117	glDisable(GL_COLOR_MATERIAL)
2118
2119	def RenderLabel(x,y,z,label,r):
2120	glPushMatrix()
2121	glTranslate(x,y,z)
2122	glMultMatrixf(B4mat.T)
2123	glDisable(GL_LIGHTING)
2124	glColor3f(0,1.,0)
2125	glRasterPos3f(r,r,r)
2126	for c in list(label):
2127	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2128	glEnable(GL_LIGHTING)
2129	glPopMatrix()
2130
2131	def Draw():
2132	import numpy.linalg as nl
2133	Ind = GetSelectedAtoms()
2134	VS = np.array(Page.canvas.GetSize())
2135	aspect = float(VS[0])/float(VS[1])
2136	cPos = drawingData['cameraPos']
2137	Zclip = drawingData['Zclip']*cPos/200.
2138	anglex,angley,anglez = drawingData['Rotation'][:3]
2139	Tx,Ty,Tz = drawingData['viewPoint'][0]
2140	cx,ct,cs = drawingData['atomPtrs']
2141	bondR = drawingData['bondRadius']
2142	G,g = G2lat.cell2Gmat(cell)
2143	GS = G
2144	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2145	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2146	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2147	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2148
2149	SetBackground()
2150	glInitNames()
2151	glPushName(0)
2152
2153	glMatrixMode(GL_PROJECTION)
2154	glLoadIdentity()
2155	glViewport(0,0,VS[0],VS[1])
2156	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2157	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2158	SetLights()
2159
2160	glMatrixMode(GL_MODELVIEW)
2161	glLoadIdentity()
2162	glRotate(anglez,0,0,1)
2163	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2164	glRotate(angley,sind(anglez),cosd(anglez),0)
2165	glMultMatrixf(A4mat.T)
2166	glTranslate(-Tx,-Ty,-Tz)
2167	if drawingData['unitCellBox']:
2168	RenderBox()
2169	if drawingData['showABC']:
2170	# try: #temporary fix - not needed further?
2171	# x,y,z = drawingData['testPos'][0]
2172	# except TypeError:
2173	# x,y,z = drawingData['testPos']
2174	x,y,z = drawingData['testPos'][0]
2175	if altDown:
2176	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2177	else:
2178	self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2179	RenderUnitVectors(x,y,z)
2180	Backbone = []
2181	BackboneColor = []
2182	time0 = time.time()
2183	for iat,atom in enumerate(drawingData['Atoms']):
2184	x,y,z = atom[cx:cx+3]
2185	Bonds = atom[-2]
2186	Faces = atom[-1]
2187	try:
2188	atNum = generalData['AtomTypes'].index(atom[ct])
2189	except ValueError:
2190	atNum = -1
2191	CL = atom[cs+2]
2192	color = np.array(CL)/255.
2193	if iat in Ind:
2194	color = np.array(Gr)/255.
2195	radius = 0.5
2196	if atom[cs] != '':
2197	glLoadName(atom[-3])
2198	if 'balls' in atom[cs]:
2199	vdwScale = drawingData['vdwScale']
2200	ballScale = drawingData['ballScale']
2201	if atNum < 0:
2202	radius = 0.2
2203	elif 'H' == atom[ct]:
2204	if drawingData['showHydrogen']:
2205	if 'vdW' in atom[cs] and atNum >= 0:
2206	radius = vdwScale*generalData['vdWRadii'][atNum]
2207	else:
2208	radius = ballScale*drawingData['sizeH']
2209	else:
2210	radius = 0.0
2211	else:
2212	if 'vdW' in atom[cs]:
2213	radius = vdwScale*generalData['vdWRadii'][atNum]
2214	else:
2215	radius = ballScale*generalData['BondRadii'][atNum]
2216	RenderSphere(x,y,z,radius,color)
2217	if 'sticks' in atom[cs]:
2218	RenderBonds(x,y,z,Bonds,bondR,color)
2219	elif 'ellipsoids' in atom[cs]:
2220	RenderBonds(x,y,z,Bonds,bondR,color)
2221	if atom[cs+3] == 'A':
2222	Uij = atom[cs+5:cs+11]
2223	U = np.multiply(G2spc.Uij2U(Uij),GS)
2224	U = np.inner(Amat,np.inner(U,Amat).T)
2225	E,R = nl.eigh(U)
2226	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2227	E = np.sqrt(E)
2228	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2229	pass
2230	else:
2231	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2232	else:
2233	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2234	pass
2235	else:
2236	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2237	RenderSphere(x,y,z,radius,color)
2238	elif 'lines' in atom[cs]:
2239	radius = 0.1
2240	RenderLines(x,y,z,Bonds,color)
2241	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2242	elif atom[cs] == 'sticks':
2243	radius = 0.1
2244	RenderBonds(x,y,z,Bonds,bondR,color)
2245	elif atom[cs] == 'polyhedra':
2246	RenderPolyhedra(x,y,z,Faces,color)
2247	elif atom[cs] == 'backbone':
2248	if atom[ct-1].split()[0] in ['C','N']:
2249	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2250	BackboneColor.append(list(color))
2251
2252	if atom[cs+1] == 'type':
2253	RenderLabel(x,y,z,atom[ct],radius)
2254	elif atom[cs+1] == 'name':
2255	RenderLabel(x,y,z,atom[ct-1],radius)
2256	elif atom[cs+1] == 'number':
2257	RenderLabel(x,y,z,str(iat+1),radius)
2258	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2259	RenderLabel(x,y,z,atom[ct-4],radius)
2260	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2261	RenderLabel(x,y,z,atom[ct-3],radius)
2262	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2263	RenderLabel(x,y,z,atom[ct-2],radius)
2264	if Backbone:
2265	RenderBackbone(Backbone,BackboneColor,bondR)
2266	# print time.time()-time0
2267	Page.canvas.SwapBuffers()
2268
2269	def OnSize(event):
2270	Draw()
2271
2272	def OnFocus(event):
2273	Draw()
2274
2275	try:
2276	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2277	Page = self.G2plotNB.nb.GetPage(plotNum)
2278	except ValueError:
2279	Plot = self.G2plotNB.addOgl(generalData['Name'])
2280	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2281	Page = self.G2plotNB.nb.GetPage(plotNum)
2282	Page.views = False
2283	view = False
2284	altDown = False
2285	Page.SetFocus()
2286	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2287	choices=(' save as:','jpeg','tiff','bmp'))
2288	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2289	cb.SetValue(' save as:')
2290	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2291	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2292	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2293	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2294	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2295	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2296	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2297	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2298	Page.camera['position'] = drawingData['cameraPos']
2299	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2300	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2301	Page.canvas.SetCurrent()
2302	Draw()
2303

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