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source: trunk/GSASIIplot.py @ 327

Last change on this file since 327 was 327, checked in by vondreele, 12 years ago
fix to path name for atomdata.dat fix to texture display - can't have colorbars! put in bit to show #threads used
Property svn:keywords set to `Date Author Revision URL Id`
File size: 103.5 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2011-07-01 17:10:28 +0000 (Fri, 01 Jul 2011) $
4	# $Author: vondreele $
5	# $Revision: 327 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 327 2011-07-01 17:10:28Z vondreele $
8	########### SVN repository information ###################
9	import math
10	import time
11	import copy
12	import os.path
13	import numpy as np
14	import numpy.linalg as nl
15	import wx
16	import wx.aui
17	import wx.glcanvas
18	import matplotlib as mpl
19	import mpl_toolkits.mplot3d.axes3d as mp3d
20	import GSASIIpath
21	import GSASIIgrid as G2gd
22	import GSASIIimage as G2img
23	import GSASIIpwd as G2pwd
24	import GSASIIIO as G2IO
25	import GSASIIpwdGUI as G2pdG
26	import GSASIIimgGUI as G2imG
27	import GSASIIphsGUI as G2phG
28	import GSASIIlattice as G2lat
29	import GSASIIspc as G2spc
30	import pytexture as ptx
31	from OpenGL.GL import *
32	from OpenGL.GLU import *
33	from OpenGL.GLUT import *
34	from OpenGL.GLE import *
35	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
36	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
37
38	# useful degree trig functions
39	sind = lambda x: math.sin(x*math.pi/180.)
40	cosd = lambda x: math.cos(x*math.pi/180.)
41	tand = lambda x: math.tan(x*math.pi/180.)
42	asind = lambda x: 180.*math.asin(x)/math.pi
43	acosd = lambda x: 180.*math.acos(x)/math.pi
44	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
45	atand = lambda x: 180.*math.atan(x)/math.pi
46	# numpy versions
47	npsind = lambda x: np.sin(x*np.pi/180.)
48	npcosd = lambda x: np.cos(x*np.pi/180.)
49	npacosd = lambda x: 180.*np.arccos(x)/np.pi
50	npasind = lambda x: 180.*np.arcsin(x)/np.pi
51	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
52
53	class G2PlotMpl(wx.Panel):
54	def __init__(self,parent,id=-1,dpi=None,**kwargs):
55	wx.Panel.__init__(self,parent,id=id,**kwargs)
56	mpl.rcParams['legend.fontsize'] = 8
57	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
58	self.canvas = Canvas(self,-1,self.figure)
59	self.toolbar = Toolbar(self.canvas)
60
61	self.toolbar.Realize()
62
63	sizer=wx.BoxSizer(wx.VERTICAL)
64	sizer.Add(self.canvas,1,wx.EXPAND)
65	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
66	self.SetSizer(sizer)
67
68	class G2PlotOgl(wx.Panel):
69	def __init__(self,parent,id=-1,dpi=None,**kwargs):
70	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
71	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
72	self.camera = {}
73	sizer=wx.BoxSizer(wx.VERTICAL)
74	sizer.Add(self.canvas,1,wx.EXPAND)
75	self.SetSizer(sizer)
76
77	class G2Plot3D(wx.Panel):
78	def __init__(self,parent,id=-1,dpi=None,**kwargs):
79	wx.Panel.__init__(self,parent,id=id,**kwargs)
80	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
81	self.canvas = Canvas(self,-1,self.figure)
82	self.toolbar = Toolbar(self.canvas)
83
84	self.toolbar.Realize()
85
86	sizer=wx.BoxSizer(wx.VERTICAL)
87	sizer.Add(self.canvas,1,wx.EXPAND)
88	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
89	self.SetSizer(sizer)
90
91	class G2PlotNoteBook(wx.Panel):
92	def __init__(self,parent,id=-1):
93	wx.Panel.__init__(self,parent,id=id)
94	#so one can't delete a plot page!!
95	self.nb = wx.aui.AuiNotebook(self, \
96	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
97	sizer = wx.BoxSizer()
98	sizer.Add(self.nb,1,wx.EXPAND)
99	self.SetSizer(sizer)
100	self.status = parent.CreateStatusBar()
101	self.status.SetFieldsCount(2)
102	self.status.SetStatusWidths([150,-1])
103	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
104
105	self.plotList = []
106
107	def addMpl(self,name=""):
108	page = G2PlotMpl(self.nb)
109	self.nb.AddPage(page,name)
110
111	self.plotList.append(name)
112
113	return page.figure
114
115	def add3D(self,name=""):
116	page = G2Plot3D(self.nb)
117	self.nb.AddPage(page,name)
118
119	self.plotList.append(name)
120
121	return page.figure
122
123	def addOgl(self,name=""):
124	page = G2PlotOgl(self.nb)
125	self.nb.AddPage(page,name)
126
127	self.plotList.append(name)
128
129	return page.figure
130
131	def Delete(self,name):
132	try:
133	item = self.plotList.index(name)
134	del self.plotList[item]
135	self.nb.DeletePage(item)
136	except ValueError: #no plot of this name - do nothing
137	return
138
139	def clear(self):
140	while self.nb.GetPageCount():
141	self.nb.DeletePage(0)
142	self.plotList = []
143	self.status.DestroyChildren()
144
145	def Rename(self,oldName,newName):
146	try:
147	item = self.plotList.index(oldName)
148	self.plotList[item] = newName
149	self.nb.SetPageText(item,newName)
150	except ValueError: #no plot of this name - do nothing
151	return
152
153	def OnPageChanged(self,event):
154	if self.plotList:
155	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
156	self.status.DestroyChildren() #get rid of special stuff on status bar
157
158	def PlotSngl(self,newPlot=False):
159	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
160	to F, F**2, etc. as requested
161	'''
162	from matplotlib.patches import Circle
163	global HKL,HKLF
164
165	def OnSCMotion(event):
166	xpos = event.xdata
167	if xpos:
168	xpos = round(xpos) #avoid out of frame mouse position
169	ypos = round(event.ydata)
170	zpos = Data['Layer']
171	if '100' in Data['Zone']:
172	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
173	elif '010' in Data['Zone']:
174	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
175	elif '001' in Data['Zone']:
176	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
177	Page.canvas.SetToolTipString(HKLtxt)
178	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
179
180	def OnSCPick(event):
181	zpos = Data['Layer']
182	pos = event.artist.center
183	if '100' in Data['Zone']:
184	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
185	hkl = np.array([zpos,pos[0],pos[1]])
186	elif '010' in Data['Zone']:
187	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
188	hkl = np.array([pos[0],zpos,pos[1]])
189	elif '001' in Data['Zone']:
190	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
191	hkl = np.array([pos[0],pos[1],zpos])
192	h,k,l = hkl
193	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
194	if len(hklf):
195	Fosq,sig,Fcsq = hklf[0]
196	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
197	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
198
199	def OnSCKeyPress(event):
200	print event.key
201
202	try:
203	plotNum = self.G2plotNB.plotList.index('Structure Factors')
204	Page = self.G2plotNB.nb.GetPage(plotNum)
205	if not newPlot:
206	Plot = Page.figure.gca() #get previous powder plot & get limits
207	xylim = Plot.get_xlim(),Plot.get_ylim()
208	Page.figure.clf()
209	Plot = Page.figure.gca() #get a fresh plot after clf()
210	except ValueError:
211	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
212	plotNum = self.G2plotNB.plotList.index('Structure Factors')
213	Page = self.G2plotNB.nb.GetPage(plotNum)
214	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
215	Page.canvas.mpl_connect('pick_event', OnSCPick)
216	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
217	Page.SetFocus()
218
219	Plot.set_aspect(aspect='equal')
220	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
221	Data = self.PatternTree.GetItemPyData( \
222	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
223	Type = Data['Type']
224	scale = Data['Scale']
225	HKLmax = Data['HKLmax']
226	HKLmin = Data['HKLmin']
227	FosqMax = Data['FoMax']
228	FoMax = math.sqrt(FosqMax)
229	ifFc = Data['ifFc']
230	xlabel = ['k, h=','h, k=','h, l=']
231	ylabel = ['l','l','k']
232	zones = ['100','010','001']
233	pzone = [[1,2],[0,2],[0,1]]
234	izone = zones.index(Data['Zone'])
235	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
236	HKL = []
237	HKLF = []
238	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
239	HKL.append(H)
240	HKLF.append([Fosq,sig,Fcsq])
241	if H[izone] == Data['Layer']:
242	B = 0
243	if Type == 'Fosq':
244	A = scale*Fosq/FosqMax
245	B = scale*Fcsq/FosqMax
246	C = abs(A-B)
247	elif Type == 'Fo':
248	A = scale*math.sqrt(max(0,Fosq))/FoMax
249	B = scale*math.sqrt(max(0,Fcsq))/FoMax
250	C = abs(A-B)
251	elif Type == '\|DFsq\|/sig':
252	A = abs(Fosq-Fcsq)/(scale*sig)
253	elif Type == '\|DFsq\|>sig':
254	A = abs(Fosq-Fcsq)/(scale*sig)
255	if A < 1.0: A = 0
256	elif Type == '\|DFsq\|>3sig':
257	A = abs(Fosq-Fcsq)/(scale*sig)
258	if A < 3.0: A = 0
259	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
260	if A > 0.0:
261	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
262	if B:
263	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
264	radius = C
265	if radius > 0:
266	if A > B:
267	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
268	else:
269	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
270	HKL = np.array(HKL,dtype=np.int)
271	HKLF = np.array(HKLF)
272	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
273	Plot.set_ylabel(ylabel[izone],fontsize=12)
274	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
275	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
276	if not newPlot:
277	Page.toolbar.push_current()
278	Plot.set_xlim(xylim[0])
279	Plot.set_ylim(xylim[1])
280	xylim = []
281	Page.toolbar.push_current()
282	Page.toolbar.draw()
283	else:
284	Page.canvas.draw()
285
286	def PlotPatterns(self,newPlot=False):
287	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
288	2-theta or q (future TOF). Can display multiple patterns as "waterfall plots" or contour plots. Log I
289	plotting available.
290	'''
291	global HKL
292
293	def OnPick(event):
294	if self.itemPicked is not None: return
295	PatternId = self.PatternId
296	try:
297	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
298	except TypeError:
299	return
300	Parms = dict(zip(Names,Values))
301	try:
302	wave = Parms['Lam']
303	except KeyError:
304	wave = Parms['Lam1']
305	PickId = self.PickId
306	pick = event.artist
307	mouse = event.mouseevent
308	xpos = pick.get_xdata()
309	ypos = pick.get_ydata()
310	ind = event.ind
311	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
312	if self.PatternTree.GetItemText(PickId) == 'Peak List':
313	if ind.all() != [0]: #picked a data point
314	if 'C' in Parms['Type']: #CW data - TOF later in an elif
315	ins = [Parms[x] for x in ['U','V','W','X','Y']]
316	if self.qPlot: #qplot - convert back to 2-theta
317	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
318	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
319	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
320	data = self.PatternTree.GetItemPyData(self.PickId)
321	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
322	data.append(XY)
323	G2pdG.UpdatePeakGrid(self,data)
324	PlotPatterns(self)
325	else: #picked a peak list line
326	self.itemPicked = pick
327	elif self.PatternTree.GetItemText(PickId) == 'Limits':
328	if ind.all() != [0]: #picked a data point
329	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
330	data = self.PatternTree.GetItemPyData(LimitId)
331	if 'C' in Parms['Type']: #CW data - TOF later in an elif
332	if self.qPlot: #qplot - convert back to 2-theta
333	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
334	if mouse.button==1:
335	data[1][0] = min(xy[0],data[1][1])
336	if mouse.button==3:
337	data[1][1] = max(xy[0],data[1][0])
338	self.PatternTree.SetItemPyData(LimitId,data)
339	G2pdG.UpdateLimitsGrid(self,data)
340	PlotPatterns(self)
341	else: #picked a limit line
342	self.itemPicked = pick
343
344	def OnPlotKeyPress(event):
345	newPlot = False
346	if event.key == 'w':
347	if self.Weight:
348	self.Weight = False
349	else:
350	self.Weight = True
351	print 'plot weighting:',self.Weight
352	elif event.key == 'n':
353	if self.Contour:
354	pass
355	else:
356	if self.logPlot:
357	self.logPlot = False
358	else:
359	self.Offset[0] = 0
360	self.logPlot = True
361	elif event.key == 'u':
362	if self.Contour:
363	self.Cmax = min(1.0,self.Cmax*1.2)
364	elif self.logPlot:
365	pass
366	elif self.Offset[0] < 100.:
367	self.Offset[0] += 1.
368	elif event.key == 'd':
369	if self.Contour:
370	self.Cmax = max(0.0,self.Cmax*0.8)
371	elif self.logPlot:
372	pass
373	elif self.Offset[0] > 0.:
374	self.Offset[0] -= 1.
375	elif event.key == 'l':
376	self.Offset[1] -= 1.
377	elif event.key == 'r':
378	self.Offset[1] += 1.
379	elif event.key == 'o':
380	self.Offset = [0,0]
381	elif event.key == 'c':
382	newPlot = True
383	if self.Contour:
384	self.Contour = False
385	else:
386	self.Contour = True
387	self.SinglePlot = False
388	self.Offset = [0.,0.]
389	elif event.key == 'q':
390	newPlot = True
391	if self.qPlot:
392	self.qPlot = False
393	else:
394	self.qPlot = True
395	elif event.key == 's':
396	if self.Contour:
397	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
398	choice.sort()
399	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
400	if dlg.ShowModal() == wx.ID_OK:
401	sel = dlg.GetSelection()
402	self.ContourColor = choice[sel]
403	else:
404	self.ContourColor = 'Paired'
405	dlg.Destroy()
406	else:
407	if self.SinglePlot:
408	self.SinglePlot = False
409	else:
410	self.SinglePlot = True
411	elif event.key == '+':
412	if self.PickId:
413	self.PickId = False
414	elif event.key == 'i': #for smoothing contour plot
415	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
416	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
417	'mitchell','sinc','lanczos']
418	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
419	if dlg.ShowModal() == wx.ID_OK:
420	sel = dlg.GetSelection()
421	self.Interpolate = choice[sel]
422	else:
423	self.Interpolate = 'nearest'
424	dlg.Destroy()
425
426	PlotPatterns(self,newPlot=newPlot)
427
428	def OnKeyBox(event):
429	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('Powder Patterns'):
430	event.key = cb.GetValue()[0]
431	cb.SetValue(' key press')
432	OnPlotKeyPress(event)
433
434	def OnMotion(event):
435	xpos = event.xdata
436	if xpos: #avoid out of frame mouse position
437	ypos = event.ydata
438	Page.canvas.SetCursor(wx.CROSS_CURSOR)
439	try:
440	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
441	Parms = dict(zip(Names,Values))
442	try:
443	wave = Parms['Lam']
444	except KeyError:
445	wave = Parms['Lam1']
446	if self.qPlot:
447	xpos = 2.0asind(xposwave/(4*math.pi))
448	dsp = 0.0
449	if abs(xpos) > 0.: #avoid possible singularity at beam center
450	dsp = wave/(2.*sind(abs(xpos)/2.0))
451	if self.Contour:
452	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
453	else:
454	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
455	if self.itemPicked:
456	Page.canvas.SetToolTipString('%9.3f'%(xpos))
457	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
458	found = []
459	if len(HKL):
460	view = Page.toolbar._views.forward()[0][:2]
461	wid = view[1]-view[0]
462	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
463	if len(found):
464	h,k,l = found[0][:3]
465	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
466	else:
467	Page.canvas.SetToolTipString('')
468
469	except TypeError:
470	self.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
471
472	def OnRelease(event):
473	if self.itemPicked is None: return
474	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
475	Parms = dict(zip(Names,Values))
476	try:
477	wave = Parms['Lam']
478	except KeyError:
479	wave = Parms['Lam1']
480	xpos = event.xdata
481	if xpos: #avoid out of frame mouse position
482	lines = []
483	for line in self.Lines: lines.append(line.get_xdata()[0])
484	lineNo = lines.index(self.itemPicked.get_xdata()[0])
485	if lineNo in [0,1]:
486	LimitId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Limits')
487	data = self.PatternTree.GetItemPyData(LimitId)
488	# print 'limits',xpos
489	if self.qPlot:
490	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
491	else:
492	data[1][lineNo] = xpos
493	self.PatternTree.SetItemPyData(LimitId,data)
494	if self.PatternTree.GetItemText(self.PickId) == 'Limits':
495	G2pdG.UpdateLimitsGrid(self,data)
496	else:
497	PeakId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Peak List')
498	data = self.PatternTree.GetItemPyData(PeakId)
499	# print 'peaks',xpos
500	if event.button == 3:
501	del data[lineNo-2]
502	else:
503	if self.qPlot:
504	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
505	else:
506	data[lineNo-2][0] = xpos
507	self.PatternTree.SetItemPyData(PeakId,data)
508	G2pdG.UpdatePeakGrid(self,data)
509	PlotPatterns(self)
510	self.itemPicked = None
511
512	xylim = []
513	try:
514	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
515	Page = self.G2plotNB.nb.GetPage(plotNum)
516	if not newPlot:
517	Plot = Page.figure.gca() #get previous powder plot & get limits
518	xylim = Plot.get_xlim(),Plot.get_ylim()
519	Page.figure.clf()
520	Plot = Page.figure.gca() #get a fresh plot after clf()
521	except ValueError:
522	newPlot = True
523	self.Cmax = 1.0
524	Plot = self.G2plotNB.addMpl('Powder Patterns').gca()
525	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
526	Page = self.G2plotNB.nb.GetPage(plotNum)
527	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
528	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
529	Page.canvas.mpl_connect('pick_event', OnPick)
530	Page.canvas.mpl_connect('button_release_event', OnRelease)
531	Page.SetFocus()
532	self.G2plotNB.status.DestroyChildren()
533	if self.Contour:
534	Choice = (' key press','d: lower contour max','u: raise contour max',
535	'i: interpolation method','s: color scheme','c: contour off')
536	else:
537	if self.logPlot:
538	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
539	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
540	else:
541	Choice = (' key press','l: offset left','r: offset right','d: offset down',
542	'u: offset up','o: reset offset','n: log(I) on','c: contour on',
543	'q: toggle q plot','s: toggle single plot','+: no selection')
544	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
545	choices=Choice)
546	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
547	cb.SetValue(' key press')
548
549	PickId = self.PickId
550	PatternId = self.PatternId
551	colors=['b','g','r','c','m','k']
552	Lines = []
553	if self.SinglePlot:
554	Pattern = self.PatternTree.GetItemPyData(PatternId)
555	Pattern.append(self.PatternTree.GetItemText(PatternId))
556	PlotList = [Pattern,]
557	ParmList = [self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
558	self.PatternId, 'Instrument Parameters'))[1],]
559	else:
560	PlotList = []
561	ParmList = []
562	item, cookie = self.PatternTree.GetFirstChild(self.root)
563	while item:
564	if 'PWDR' in self.PatternTree.GetItemText(item):
565	Pattern = self.PatternTree.GetItemPyData(item)
566	if len(Pattern) < 3: # put name on end if needed
567	Pattern.append(self.PatternTree.GetItemText(item))
568	PlotList.append(Pattern)
569	ParmList.append(self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
570	item,'Instrument Parameters'))[1])
571	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
572	Ymax = 1.0
573	lenX = 0
574	HKL = np.array(self.HKL)
575	for Pattern in PlotList:
576	xye = Pattern[1]
577	Ymax = max(Ymax,max(xye[1]))
578	offset = self.Offset[0]*Ymax/100.0
579	Title = 'Powder Patterns: '+os.path.split(self.GSASprojectfile)[1]
580	if self.logPlot:
581	Title = 'log('+Title+')'
582	Plot.set_title(Title)
583	if self.qPlot:
584	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
585	else:
586	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
587	Plot.set_ylabel('Intensity',fontsize=12)
588	if self.Contour:
589	ContourZ = []
590	ContourY = []
591	Nseq = 0
592	for N,Pattern in enumerate(PlotList):
593	Parms = ParmList[N]
594	ifpicked = False
595	LimitId = 0
596	xye = np.array(Pattern[1])
597	if PickId:
598	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
599	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
600	if self.qPlot:
601	Id = G2gd.GetPatternTreeItemId(self,self.root, Pattern[2])
602	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
603	else:
604	X = xye[0]
605	if not lenX:
606	lenX = len(X)
607	Y = xye[1]+offset*N
608	if LimitId:
609	limits = np.array(self.PatternTree.GetItemPyData(LimitId))
610	if self.qPlot:
611	limits = 4np.pinpsind(limits/2.0)/Parms[1]
612	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
613	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
614	if self.Contour:
615
616	if lenX == len(X):
617	ContourY.append(N)
618	ContourZ.append(Y)
619	ContourX = X
620	Nseq += 1
621	Plot.set_ylabel('Data sequence',fontsize=12)
622	else:
623	X += self.Offset[1].005N
624	if ifpicked:
625	Z = xye[3]+offset*N
626	W = xye[4]+offset*N
627	D = xye[5]+offsetN-Ymax.02
628	if self.Weight:
629	W2 = np.sqrt(xye[2])
630	D = W2-Ymax.02
631	if self.logPlot:
632	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
633	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
634	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
635	else:
636	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
637	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
638	Plot.plot(X,W,colors[(N+2)%6],picker=False)
639	Plot.plot(X,D,colors[(N+3)%6],picker=False)
640	Plot.axhline(0.,color=wx.BLACK)
641	Page.canvas.SetToolTipString('')
642	if self.PatternTree.GetItemText(PickId) == 'Peak List':
643	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
644	Page.canvas.SetToolTipString(tip)
645	data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List'))
646	for item in data:
647	if self.qPlot:
648	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
649	else:
650	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
651	if self.PatternTree.GetItemText(PickId) == 'Limits':
652	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
653	Page.canvas.SetToolTipString(tip)
654	data = self.LimitsTable.GetData()
655	else:
656	if self.logPlot:
657	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
658	else:
659	Plot.plot(X,Y,colors[N%6],picker=False)
660	if PickId and self.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
661	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1::2]
662	Parms = dict(zip(Names,Values))
663	try:
664	wave = Parms['Lam']
665	except KeyError:
666	wave = Parms['Lam1']
667	peaks = np.array((self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))))
668	for peak in peaks:
669	if self.qPlot:
670	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
671	else:
672	Plot.axvline(peak[0],color='b')
673	for hkl in self.HKL:
674	if self.qPlot:
675	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
676	else:
677	Plot.axvline(hkl[5],color='r',dashes=(5,5))
678	if self.Contour:
679	acolor = mpl.cm.get_cmap(self.ContourColor)
680	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
681	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
682	Page.figure.colorbar(Img)
683	else:
684	self.Lines = Lines
685	if not newPlot:
686	Page.toolbar.push_current()
687	Plot.set_xlim(xylim[0])
688	Plot.set_ylim(xylim[1])
689	xylim = []
690	Page.toolbar.push_current()
691	Page.toolbar.draw()
692	else:
693	Page.canvas.draw()
694	self.Pwdr = True
695
696	def PlotISFG(self,newPlot=False,type=''):
697	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
698	or multiple plots with waterfall and contour plots as options
699	'''
700	if not type:
701	type = self.G2plotNB.plotList[self.G2plotNB.nb.GetSelection()]
702	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
703	return
704	superMinusOne = unichr(0xaf)+unichr(0xb9)
705
706	def OnPlotKeyPress(event):
707	newPlot = False
708	if event.key == 'u':
709	if self.Contour:
710	self.Cmax = min(1.0,self.Cmax*1.2)
711	elif self.Offset[0] < 100.:
712	self.Offset[0] += 1.
713	elif event.key == 'd':
714	if self.Contour:
715	self.Cmax = max(0.0,self.Cmax*0.8)
716	elif self.Offset[0] > 0.:
717	self.Offset[0] -= 1.
718	elif event.key == 'l':
719	self.Offset[1] -= 1.
720	elif event.key == 'r':
721	self.Offset[1] += 1.
722	elif event.key == 'o':
723	self.Offset = [0,0]
724	elif event.key == 'c':
725	newPlot = True
726	if self.Contour:
727	self.Contour = False
728	else:
729	self.Contour = True
730	self.SinglePlot = False
731	self.Offset = [0.,0.]
732	elif event.key == 's':
733	if self.Contour:
734	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
735	choice.sort()
736	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
737	if dlg.ShowModal() == wx.ID_OK:
738	sel = dlg.GetSelection()
739	self.ContourColor = choice[sel]
740	else:
741	self.ContourColor = 'Paired'
742	dlg.Destroy()
743	else:
744	if self.SinglePlot:
745	self.SinglePlot = False
746	else:
747	self.SinglePlot = True
748	elif event.key == 'i': #for smoothing contour plot
749	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
750	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
751	'mitchell','sinc','lanczos']
752	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
753	if dlg.ShowModal() == wx.ID_OK:
754	sel = dlg.GetSelection()
755	self.Interpolate = choice[sel]
756	else:
757	self.Interpolate = 'nearest'
758	dlg.Destroy()
759	elif event.key == 't' and not self.Contour:
760	if self.Legend:
761	self.Legend = False
762	else:
763	self.Legend = True
764
765
766	PlotISFG(self,newPlot=newPlot,type=type)
767
768	def OnKeyBox(event):
769	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index(type):
770	event.key = cb.GetValue()[0]
771	cb.SetValue(' key press')
772	OnPlotKeyPress(event)
773
774	def OnMotion(event):
775	xpos = event.xdata
776	if xpos: #avoid out of frame mouse position
777	ypos = event.ydata
778	Page.canvas.SetCursor(wx.CROSS_CURSOR)
779	try:
780	if self.Contour:
781	self.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
782	else:
783	self.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
784	except TypeError:
785	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
786
787	xylim = []
788	try:
789	plotNum = self.G2plotNB.plotList.index(type)
790	Page = self.G2plotNB.nb.GetPage(plotNum)
791	if not newPlot:
792	Plot = Page.figure.gca() #get previous plot & get limits
793	xylim = Plot.get_xlim(),Plot.get_ylim()
794	Page.figure.clf()
795	Plot = Page.figure.gca()
796	except ValueError:
797	newPlot = True
798	self.Cmax = 1.0
799	Plot = self.G2plotNB.addMpl(type).gca()
800	plotNum = self.G2plotNB.plotList.index(type)
801	Page = self.G2plotNB.nb.GetPage(plotNum)
802	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
803	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
804
805	Page.SetFocus()
806	self.G2plotNB.status.DestroyChildren()
807	if self.Contour:
808	Choice = (' key press','d: lower contour max','u: raise contour max',
809	'i: interpolation method','s: color scheme','c: contour off')
810	else:
811	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
812	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
813	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
814	choices=Choice)
815	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
816	cb.SetValue(' key press')
817	PatternId = self.PatternId
818	PickId = self.PickId
819	Plot.set_title(type)
820	if type == 'G(R)':
821	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
822	else:
823	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
824	Plot.set_ylabel(r''+type,fontsize=14)
825	colors=['b','g','r','c','m','k']
826	name = self.PatternTree.GetItemText(PatternId)[4:]
827	Pattern = []
828	if self.SinglePlot:
829	name = self.PatternTree.GetItemText(PatternId)
830	name = type+name[4:]
831	Id = G2gd.GetPatternTreeItemId(self,PatternId,name)
832	Pattern = self.PatternTree.GetItemPyData(Id)
833	if Pattern:
834	Pattern.append(name)
835	PlotList = [Pattern,]
836	else:
837	PlotList = []
838	item, cookie = self.PatternTree.GetFirstChild(self.root)
839	while item:
840	if 'PDF' in self.PatternTree.GetItemText(item):
841	name = type+self.PatternTree.GetItemText(item)[4:]
842	Id = G2gd.GetPatternTreeItemId(self,item,name)
843	Pattern = self.PatternTree.GetItemPyData(Id)
844	if Pattern:
845	Pattern.append(name)
846	PlotList.append(Pattern)
847	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
848	PDFdata = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'PDF Controls'))
849	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
850	Xb = [0.,10.]
851	Yb = [0.,-40.np.pinumbDen]
852	Ymax = 1.0
853	lenX = 0
854	for Pattern in PlotList:
855	xye = Pattern[1]
856	Ymax = max(Ymax,max(xye[1]))
857	offset = self.Offset[0]*Ymax/100.0
858	if self.Contour:
859	ContourZ = []
860	ContourY = []
861	Nseq = 0
862	for N,Pattern in enumerate(PlotList):
863	xye = Pattern[1]
864	if PickId:
865	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
866	X = xye[0]
867	if not lenX:
868	lenX = len(X)
869	Y = xye[1]+offset*N
870	if self.Contour:
871	if lenX == len(X):
872	ContourY.append(N)
873	ContourZ.append(Y)
874	ContourX = X
875	Nseq += 1
876	Plot.set_ylabel('Data sequence',fontsize=12)
877	else:
878	X = xye[0]+self.Offset[1].005N
879	if ifpicked:
880	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
881	Page.canvas.SetToolTipString('')
882	else:
883	if self.Legend:
884	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
885	else:
886	Plot.plot(X,Y,colors[N%6],picker=False)
887	if type == 'G(R)':
888	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
889	elif type == 'F(Q)':
890	Plot.axhline(0.,color=wx.BLACK)
891	elif type == 'S(Q)':
892	Plot.axhline(1.,color=wx.BLACK)
893	if self.Contour:
894	acolor = mpl.cm.get_cmap(self.ContourColor)
895	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
896	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
897	Page.figure.colorbar(Img)
898	elif self.Legend:
899	Plot.legend(loc='best')
900	if not newPlot:
901	Page.toolbar.push_current()
902	Plot.set_xlim(xylim[0])
903	Plot.set_ylim(xylim[1])
904	xylim = []
905	Page.toolbar.push_current()
906	Page.toolbar.draw()
907	else:
908	Page.canvas.draw()
909
910	def PlotXY(self,XY,newPlot=False,type=''):
911	'''simple plot of xy data, used for diagnostic purposes
912	'''
913	def OnMotion(event):
914	xpos = event.xdata
915	if xpos: #avoid out of frame mouse position
916	ypos = event.ydata
917	Page.canvas.SetCursor(wx.CROSS_CURSOR)
918	try:
919	self.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
920	except TypeError:
921	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
922
923	try:
924	plotNum = self.G2plotNB.plotList.index(type)
925	Page = self.G2plotNB.nb.GetPage(plotNum)
926	if not newPlot:
927	Plot = Page.figure.gca()
928	xylim = Plot.get_xlim(),Plot.get_ylim()
929	Page.figure.clf()
930	Plot = Page.figure.gca()
931	except ValueError:
932	newPlot = True
933	Plot = self.G2plotNB.addMpl(type).gca()
934	plotNum = self.G2plotNB.plotList.index(type)
935	Page = self.G2plotNB.nb.GetPage(plotNum)
936	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
937
938	Page.SetFocus()
939	self.G2plotNB.status.DestroyChildren()
940	Plot.set_title(type)
941	Plot.set_xlabel(r'X',fontsize=14)
942	Plot.set_ylabel(r''+type,fontsize=14)
943	colors=['b','g','r','c','m','k']
944	Ymax = 1.0
945	lenX = 0
946	X,Y = XY[:2]
947	Ymax = max(Ymax,max(Y))
948	Plot.plot(X,Y,'k',picker=False)
949	if not newPlot:
950	Page.toolbar.push_current()
951	Plot.set_xlim(xylim[0])
952	Plot.set_ylim(xylim[1])
953	xylim = []
954	Page.toolbar.push_current()
955	Page.toolbar.draw()
956	else:
957	Page.canvas.draw()
958
959	def PlotPowderLines(self):
960	''' plotting of powder lines (i.e. no powder pattern) as sticks
961	'''
962	global HKL
963
964	def OnMotion(event):
965	xpos = event.xdata
966	if xpos: #avoid out of frame mouse position
967	Page.canvas.SetCursor(wx.CROSS_CURSOR)
968	self.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
969	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
970	found = []
971	if len(HKL):
972	view = Page.toolbar._views.forward()[0][:2]
973	wid = view[1]-view[0]
974	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
975	if len(found):
976	h,k,l = found[0][:3]
977	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
978	else:
979	Page.canvas.SetToolTipString('')
980
981	try:
982	plotNum = self.G2plotNB.plotList.index('Powder Lines')
983	Page = self.G2plotNB.nb.GetPage(plotNum)
984	Page.figure.clf()
985	Plot = Page.figure.gca()
986	except ValueError:
987	Plot = self.G2plotNB.addMpl('Powder Lines').gca()
988	plotNum = self.G2plotNB.plotList.index('Powder Lines')
989	Page = self.G2plotNB.nb.GetPage(plotNum)
990	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
991
992	Page.SetFocus()
993	Plot.set_title('Powder Pattern Lines')
994	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
995	PickId = self.PickId
996	PatternId = self.PatternId
997	peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))
998	for peak in peaks:
999	Plot.axvline(peak[0],color='b')
1000	HKL = np.array(self.HKL)
1001	for hkl in self.HKL:
1002	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1003	xmin = peaks[0][0]
1004	xmax = peaks[-1][0]
1005	delt = xmax-xmin
1006	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1007	Plot.set_xlim(xlim)
1008	Page.canvas.draw()
1009	Page.toolbar.push_current()
1010
1011	def PlotPeakWidths(self):
1012	''' Plotting of instrument broadening terms as function of 2-theta (future TOF)
1013	Seen when "Instrument Parameters" chosen from powder pattern data tree
1014	'''
1015	PatternId = self.PatternId
1016	limitID = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
1017	if limitID:
1018	limits = self.PatternTree.GetItemPyData(limitID)
1019	else:
1020	return
1021	instParms = self.PatternTree.GetItemPyData( \
1022	G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))
1023	if instParms[0][0] == 'PXC':
1024	lam = instParms[1][1]
1025	if len(instParms[1]) == 13:
1026	GU,GV,GW,LX,LY = instParms[0][6:11]
1027	else:
1028	GU,GV,GW,LX,LY = instParms[0][4:9]
1029	peakID = G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List')
1030	if peakID:
1031	peaks = self.PatternTree.GetItemPyData(peakID)
1032	else:
1033	peaks = []
1034
1035	try:
1036	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1037	Page = self.G2plotNB.nb.GetPage(plotNum)
1038	Page.figure.clf()
1039	Plot = Page.figure.gca()
1040	except ValueError:
1041	Plot = self.G2plotNB.addMpl('Peak Widths').gca()
1042	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1043	Page = self.G2plotNB.nb.GetPage(plotNum)
1044	Page.SetFocus()
1045
1046	Page.canvas.SetToolTipString('')
1047	colors=['b','g','r','c','m','k']
1048	Xmin,Xmax = limits[1]
1049	Xmin = min(0.5,max(Xmin,1))
1050	Xmin /= 2
1051	Xmax /= 2
1052	nPts = 100
1053	delt = (Xmax-Xmin)/nPts
1054	thetas = []
1055	for i in range(nPts):
1056	thetas.append(Xmin+i*delt)
1057	X = []
1058	Y = []
1059	Z = []
1060	W = []
1061	V = []
1062	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1063	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1064	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.)
1065	gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1066	for theta in thetas:
1067	X.append(4.0math.pisind(theta)/lam) #q
1068	s = sig(theta,GU,GV,GW)
1069	g = gam(theta,LX,LY)
1070	G = gamFW(g,s)
1071	H = gamFW2(g,s)
1072	Y.append(s/tand(theta))
1073	Z.append(g/tand(theta))
1074	W.append(G/tand(theta))
1075	V.append(H/tand(theta))
1076	Plot.set_title('Instrument and sample peak widths')
1077	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1078	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1079	Plot.plot(X,Y,color='r',label='Gaussian')
1080	Plot.plot(X,Z,color='g',label='Lorentzian')
1081	Plot.plot(X,W,color='b',label='G+L')
1082	Plot.plot(X,V,color='k',label='G+L2')
1083	X = []
1084	Y = []
1085	Z = []
1086	W = []
1087	V = []
1088	for peak in peaks:
1089	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1090	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1091	g = peak[6]*math.pi/18000.
1092	G = gamFW(g,s)
1093	H = gamFW2(g,s)
1094	Y.append(s/tand(peak[0]/2.))
1095	Z.append(g/tand(peak[0]/2.))
1096	W.append(G/tand(peak[0]/2.))
1097	V.append(H/tand(peak[0]/2.))
1098	Plot.plot(X,Y,'+',color='r',label='G peak')
1099	Plot.plot(X,Z,'+',color='g',label='L peak')
1100	Plot.plot(X,W,'+',color='b',label='G+L peak')
1101	Plot.plot(X,V,'+',color='k',label='G+L2 peak')
1102	Plot.legend(loc='best')
1103	Page.canvas.draw()
1104
1105	def PlotStrain(self,data):
1106	'''Plot 3D microstrain figure. In this instance data is for a phase
1107	'''
1108	PatternId = self.PatternId
1109	generalData = data['General']
1110	SGData = generalData['SGData']
1111	MuStrKeys = G2spc.MustrainNames(SGData)
1112	cell = generalData['Cell'][1:]
1113	A,B = G2lat.cell2AB(cell[:6])
1114	Vol = cell[6]
1115	useList = data['Histograms']
1116	for item in useList:
1117	if useList[item]['Show']:
1118	break
1119	else:
1120	self.G2plotNB.Delete('Microstrain')
1121	return #nothing to show!!
1122
1123	numPlots = len(useList)
1124
1125	try:
1126	plotNum = self.G2plotNB.plotList.index('Microstrain')
1127	Page = self.G2plotNB.nb.GetPage(plotNum)
1128	Page.figure.clf()
1129	Plot = mp3d.Axes3D(Page.figure)
1130	if not Page.IsShown():
1131	Page.Show()
1132	except ValueError:
1133	Plot = mp3d.Axes3D(self.G2plotNB.add3D('Microstrain'))
1134	plotNum = self.G2plotNB.plotList.index('Microstrain')
1135	Page = self.G2plotNB.nb.GetPage(plotNum)
1136	Page.SetFocus()
1137	self.G2plotNB.status.SetStatusText('Adjust frame size to get desired aspect ratio',1)
1138
1139	for item in useList:
1140	if useList[item]['Show']:
1141	muStrain = useList[item]['Mustrain']
1142	PHI = np.linspace(0.,360.,30,True)
1143	PSI = np.linspace(0.,180.,30,True)
1144	X = np.outer(npsind(PHI),npsind(PSI))
1145	Y = np.outer(npcosd(PHI),npsind(PSI))
1146	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1147	if muStrain[0] == 'isotropic':
1148	muiso = muStrain[1][0]*math.pi/0.018 #centidegrees to radians!
1149	X *= muiso
1150	Y *= muiso
1151	Z *= muiso
1152
1153	elif muStrain[0] == 'uniaxial':
1154	def uniaxMustrain(xyz,muiso,muaniso,axes):
1155	cp = abs(np.dot(xyz,axes))
1156	S = muiso+muaniso*cp
1157	return Sxyzmath.pi/0.018 #centidegrees to radians!
1158	muiso,muaniso = muStrain[1][:2]
1159	axes = np.inner(A,np.array(muStrain[3]))
1160	axes /= nl.norm(axes)
1161	Shkl = np.array(muStrain[1])
1162	Shape = X.shape[0]
1163	XYZ = np.dstack((X,Y,Z))
1164	XYZ = np.nan_to_num(np.apply_along_axis(uniaxMustrain,2,XYZ,muiso,muaniso,axes))
1165	X,Y,Z = np.dsplit(XYZ,3)
1166	X = X[:,:,0]
1167	Y = Y[:,:,0]
1168	Z = Z[:,:,0]
1169
1170	elif muStrain[0] == 'generalized':
1171	def genMustrain(xyz,SGData,A,Shkl):
1172	uvw = np.inner(A.T,xyz)
1173	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1174	sum = np.sqrt(np.sum(np.multiply(Shkl,Strm)))*math.pi/0.018 #centidegrees to radians!
1175	return sum*xyz
1176	Shkl = np.array(muStrain[4])
1177	if np.any(Shkl):
1178	Shape = X.shape[0]
1179	XYZ = np.dstack((X,Y,Z))
1180	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1181	X,Y,Z = np.dsplit(XYZ,3)
1182	X = X[:,:,0]
1183	Y = Y[:,:,0]
1184	Z = Z[:,:,0]
1185
1186	if np.any(X) and np.any(Y) and np.any(Z):
1187	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g')
1188
1189	Plot.set_xlabel('X')
1190	Plot.set_ylabel('Y')
1191	Plot.set_zlabel('Z')
1192	Page.canvas.draw()
1193
1194	def PlotTexture(self,data,newPlot=False,Start=False):
1195	'''Pole figure, inverse pole figure(?), 3D pole distribution and 3D inverse pole distribution(?)
1196	plotting; Need way to select
1197	pole figure or pole distribution to be displayed - do in key enter menu
1198	dict generalData contains all phase info needed which is in data
1199	'''
1200
1201	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1202	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1203	PatternId = self.PatternId
1204	generalData = data['General']
1205	SGData = generalData['SGData']
1206	textureData = generalData['SH Texture']
1207	if not textureData['Order']:
1208	self.G2plotNB.Delete('Texture')
1209	return #no plot!!
1210	SHData = generalData['SH Texture']
1211	SHCoef = SHData['SH Coeff'][1]
1212	cell = generalData['Cell'][1:7]
1213
1214	def OnMotion(event):
1215	Page.canvas.SetToolTipString('')
1216	if event.xdata and event.ydata: #avoid out of frame errors
1217	if 'Pole figure' in SHData['PlotType']:
1218	xpos = event.xdata
1219	ypos = event.ydata
1220	Int = 0
1221	if xpos2+ypos2 < 1.0:
1222	r,p = 2.npasind(np.sqrt(xpos2+ypos2)0.707106782),npatan2d(ypos,xpos)
1223	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1224	self.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1225
1226	try:
1227	plotNum = self.G2plotNB.plotList.index('Texture')
1228	Page = self.G2plotNB.nb.GetPage(plotNum)
1229	Page.figure.clf()
1230	Plot = Page.figure.gca()
1231	if not Page.IsShown():
1232	Page.Show()
1233	except ValueError:
1234	Plot = self.G2plotNB.addMpl('Texture').gca()
1235	plotNum = self.G2plotNB.plotList.index('Texture')
1236	Page = self.G2plotNB.nb.GetPage(plotNum)
1237	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1238	Page.SetFocus()
1239
1240	if 'Axial' in SHData['PlotType']:
1241	PH = np.array(SHData['PFhkl'])
1242	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1243	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1244	X = np.linspace(0,90.0,26)
1245	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1246	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1247	Plot.legend(loc='best')
1248	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1249	Plot.set_xlabel(r'$\psi$',fontsize=16)
1250	Plot.set_ylabel('MRD',fontsize=14)
1251
1252	else:
1253	if 'Inverse' in SHData['PlotType']:
1254	PX = np.array(SHData['PFxyz'])
1255	gam = atan2d(PX[0],PX[1])
1256	xy = math.sqrt(PX[0]2+PX[1]2)
1257	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1258	psi = asind(xy/xyz)
1259	npts = 201
1260	ODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1261	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1262	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1263	R = np.where(R <= 1.,2.npasind(R0.70710678),0.0)
1264	Z = np.zeros_like(R)
1265	Z = G2lat.invpolfcal(ODFln,SGData,R,P)
1266	Z = np.reshape(Z,(npts,npts))
1267	CS = Plot.contour(Y,X,Z,aspect='equal')
1268	Plot.clabel(CS,fontsize=9,inline=1)
1269	Img = Plot.imshow(Z.T,aspect='equal',cmap='binary',extent=[-1,1,-1,1])
1270	if newPlot:
1271	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1272	newPlot = False
1273	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
1274
1275	else:
1276	PH = np.array(SHData['PFhkl'])
1277	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1278	npts = 201
1279	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1280	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1281	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1282	R = np.where(R <= 1.,2.npasind(R0.70710678),0.0)
1283	Z = np.zeros_like(R)
1284	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
1285	Z = np.reshape(Z,(npts,npts))
1286	CS = Plot.contour(Y,X,Z,aspect='equal')
1287	Plot.clabel(CS,fontsize=9,inline=1)
1288	Img = Plot.imshow(Z.T,aspect='equal',cmap='binary',extent=[-1,1,-1,1])
1289	if newPlot:
1290	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1291	newPlot = False
1292	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
1293	Page.canvas.draw()
1294
1295
1296	def PlotExposedImage(self,newPlot=False,event=None):
1297	'''General access module for 2D image plotting
1298	'''
1299	plotNo = self.G2plotNB.nb.GetSelection()
1300	if self.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1301	PlotImage(self,newPlot,event,newImage=True)
1302	elif self.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1303	PlotIntegration(self,newPlot,event)
1304
1305	def PlotImage(self,newPlot=False,event=None,newImage=True):
1306	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1307	masks, etc.
1308	'''
1309	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1310	import numpy.ma as ma
1311	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1312	global Data,Masks
1313	colors=['b','g','r','c','m','k']
1314	Data = self.PatternTree.GetItemPyData(
1315	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1316	Masks = self.PatternTree.GetItemPyData(
1317	G2gd.GetPatternTreeItemId(self,self.Image, 'Masks'))
1318
1319	def OnImMotion(event):
1320	Page.canvas.SetToolTipString('')
1321	sizexy = Data['size']
1322	if event.xdata and event.ydata: #avoid out of frame errors
1323	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1324	item = self.itemPicked
1325	pixelSize = Data['pixelSize']
1326	scalex = 1000./pixelSize[0]
1327	scaley = 1000./pixelSize[1]
1328	if item and self.PatternTree.GetItemText(self.PickId) == 'Image Controls':
1329	if 'Text' in str(item):
1330	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1331	else:
1332	xcent,ycent = Data['center']
1333	xpos = event.xdata-xcent
1334	ypos = event.ydata-ycent
1335	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1336	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1337	Page.canvas.SetToolTipString('%6d deg'%(azm))
1338	elif 'line1' in str(item) or 'line2' in str(item):
1339	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1340	else:
1341	xpos = event.xdata
1342	ypos = event.ydata
1343	xpix = xpos*scalex
1344	ypix = ypos*scaley
1345	Int = 0
1346	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1347	Int = self.ImageZ[ypix][xpix]
1348	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1349	Q = 2.*math.pi/dsp
1350	if self.setPoly:
1351	self.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1352	else:
1353	self.G2plotNB.status.SetFields(\
1354	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1355
1356	def OnImPlotKeyPress(event):
1357	try:
1358	PickName = self.PatternTree.GetItemText(self.PickId)
1359	except TypeError:
1360	return
1361	if PickName == 'Masks':
1362	Xpos = event.xdata
1363	if not Xpos: #got point out of frame
1364	return
1365	Ypos = event.ydata
1366	if event.key == 's':
1367	Masks['Points'].append([Xpos,Ypos,1.])
1368	elif event.key == 'r':
1369	tth = G2img.GetTth(Xpos,Ypos,Data)
1370	Masks['Rings'].append([tth,0.1])
1371	elif event.key == 'a':
1372	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1373	azm = int(azm)
1374	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1375	elif event.key == 'p':
1376	self.setPoly = True
1377	Masks['Polygons'].append([])
1378	self.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1379	G2imG.UpdateMasks(self,Masks)
1380	elif PickName == 'Image Controls':
1381	if event.key == 'c':
1382	Xpos = event.xdata
1383	if not Xpos: #got point out of frame
1384	return
1385	Ypos = event.ydata
1386	dlg = wx.MessageDialog(self,'Are you sure you want to change the center?',
1387	'Center change',style=wx.OK\|wx.CANCEL)
1388	try:
1389	if dlg.ShowModal() == wx.ID_OK:
1390	print 'move center to: ',Xpos,Ypos
1391	Data['center'] = [Xpos,Ypos]
1392	G2imG.UpdateImageControls(self,Data,Masks)
1393	finally:
1394	dlg.Destroy()
1395	elif event.key == 'l':
1396	if self.logPlot:
1397	self.logPlot = False
1398	else:
1399	self.logPlot = True
1400	PlotImage(self,newImage=True)
1401
1402	def OnKeyBox(event):
1403	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('2D Powder Image'):
1404	event.key = cb.GetValue()[0]
1405	cb.SetValue(' key press')
1406	if event.key in 'l':
1407	OnImPlotKeyPress(event)
1408
1409	def OnImPick(event):
1410	if self.PatternTree.GetItemText(self.PickId) not in ['Image Controls','Masks']:
1411	return
1412	if self.setPoly:
1413	polygon = Masks['Polygons'][-1]
1414	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1415	if xpos and ypos: #point inside image
1416	if len(polygon) > 2 and event.mouseevent.button == 3:
1417	x0,y0 = polygon[0]
1418	polygon.append([x0,y0])
1419	self.setPoly = False
1420	self.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1421	else:
1422	self.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1423	polygon.append([xpos,ypos])
1424	G2imG.UpdateMasks(self,Masks)
1425	else:
1426	if self.itemPicked is not None: return
1427	self.itemPicked = event.artist
1428	self.mousePicked = event.mouseevent
1429
1430	def OnImRelease(event):
1431	try:
1432	PickName = self.PatternTree.GetItemText(self.PickId)
1433	except TypeError:
1434	return
1435	if PickName not in ['Image Controls','Masks']:
1436	return
1437	pixelSize = Data['pixelSize']
1438	scalex = 1000./pixelSize[0]
1439	scaley = 1000./pixelSize[1]
1440	pixLimit = Data['pixLimit']
1441	if self.itemPicked is None and PickName == 'Image Controls':
1442	# sizexy = Data['size']
1443	Xpos = event.xdata
1444	if not (Xpos and self.ifGetRing): #got point out of frame
1445	return
1446	Ypos = event.ydata
1447	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1448	if event.button == 1:
1449	Xpix = Xpos*scalex
1450	Ypix = Ypos*scaley
1451	xpos,ypos,I,J = G2img.ImageLocalMax(self.ImageZ,pixLimit,Xpix,Ypix)
1452	if I and J:
1453	xpos += .5 #shift to pixel center
1454	ypos += .5
1455	xpos /= scalex #convert to mm
1456	ypos /= scaley
1457	Data['ring'].append([xpos,ypos])
1458	elif event.button == 3:
1459	self.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1460	if G2img.ImageCalibrate(self,Data):
1461	self.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1462	print 'Calibration successful'
1463	else:
1464	self.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1465	print 'Calibration failed'
1466	self.ifGetRing = False
1467	G2imG.UpdateImageControls(self,Data,Masks)
1468	return
1469	PlotImage(self,newImage=False)
1470	return
1471	else:
1472	xpos = event.xdata
1473	if xpos: #avoid out of frame mouse position
1474	ypos = event.ydata
1475	if self.ifGetRing: #delete a calibration ring pick
1476	xypos = [xpos,ypos]
1477	rings = Data['ring']
1478	for ring in rings:
1479	if np.allclose(ring,xypos,.01,0):
1480	rings.remove(ring)
1481	else:
1482	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1483	itemPicked = str(self.itemPicked)
1484	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1485	if 'line1' in itemPicked:
1486	Data['IOtth'][0] = max(tth,0.001)
1487	elif 'line2' in itemPicked:
1488	Data['IOtth'][1] = tth
1489	elif 'line3' in itemPicked:
1490	Data['LRazimuth'][0] = int(azm)
1491	if Data['fullIntegrate']:
1492	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1493	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1494	Data['LRazimuth'][1] = int(azm)
1495
1496	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1497	Data['LRazimuth'][0] -= 360
1498
1499	azLim = np.array(Data['LRazimuth'])
1500	if np.any(azLim>360):
1501	azLim -= 360
1502	Data['LRazimuth'] = list(azLim)
1503
1504	if Data['IOtth'][0] > Data['IOtth'][1]:
1505	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1506
1507	self.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1508	self.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1509	self.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1510	self.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1511	elif 'Circle' in itemPicked and PickName == 'Masks':
1512	spots = Masks['Points']
1513	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1514	newPos = np.array([float(newPos[0]),float(newPos[1])])
1515	for spot in spots:
1516	if np.allclose(np.array([spot[:2]]),newPos):
1517	spot[:2] = xpos,ypos
1518	G2imG.UpdateMasks(self,Masks)
1519	elif 'Line2D' in itemPicked and PickName == 'Masks':
1520	Obj = self.itemPicked.findobj()
1521	rings = Masks['Rings']
1522	arcs = Masks['Arcs']
1523	polygons = Masks['Polygons']
1524	for ring in self.ringList:
1525	if Obj == ring[0]:
1526	rN = ring[1]
1527	if ring[2] == 'o':
1528	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1529	else:
1530	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1531	for arc in self.arcList:
1532	if Obj == arc[0]:
1533	aN = arc[1]
1534	if arc[2] == 'o':
1535	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1536	elif arc[2] == 'i':
1537	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1538	elif arc[2] == 'l':
1539	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1540	else:
1541	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1542	for poly in self.polyList:
1543	if Obj == poly[0]:
1544	ind = self.itemPicked.contains(self.mousePicked)[1]['ind'][0]
1545	oldPos = np.array([self.mousePicked.xdata,self.mousePicked.ydata])
1546	pN = poly[1]
1547	for i,xy in enumerate(polygons[pN]):
1548	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1549	polygons[pN][i] = xpos,ypos
1550	G2imG.UpdateMasks(self,Masks)
1551	# else: #keep for future debugging
1552	# print str(self.itemPicked),event.xdata,event.ydata,event.button
1553	PlotImage(self,newImage=True)
1554	self.itemPicked = None
1555
1556	try:
1557	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1558	Page = self.G2plotNB.nb.GetPage(plotNum)
1559	if not newPlot:
1560	Plot = Page.figure.gca() #get previous powder plot & get limits
1561	xylim = Plot.get_xlim(),Plot.get_ylim()
1562	if newImage:
1563	Page.figure.clf()
1564	Plot = Page.figure.gca() #get a fresh plot after clf()
1565
1566	except ValueError:
1567	Plot = self.G2plotNB.addMpl('2D Powder Image').gca()
1568	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1569	Page = self.G2plotNB.nb.GetPage(plotNum)
1570	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1571	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1572	Page.canvas.mpl_connect('pick_event', OnImPick)
1573	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1574	xylim = []
1575	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1576	Page.SetFocus()
1577	Title = self.PatternTree.GetItemText(self.Image)[4:]
1578	self.G2plotNB.status.DestroyChildren()
1579	if self.logPlot:
1580	Title = 'log('+Title+')'
1581	Plot.set_title(Title)
1582	try:
1583	if self.PatternTree.GetItemText(self.PickId) in ['Image Controls',]:
1584	if self.logPlot:
1585	Choice = (' key press','l: log(I) off')
1586	else:
1587	Choice = (' key press','l: log(I) on')
1588	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1589	choices=Choice)
1590	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1591	cb.SetValue(' key press')
1592	except TypeError:
1593	pass
1594	size,imagefile = self.PatternTree.GetItemPyData(self.Image)
1595	if imagefile != self.oldImagefile:
1596	imagefile = G2IO.CheckImageFile(self,imagefile)
1597	if not imagefile:
1598	self.G2plotNB.Delete('2D Powder Image')
1599	return
1600	self.PatternTree.SetItemPyData(self.Image,[size,imagefile])
1601	self.ImageZ = G2IO.GetImageData(self,imagefile,imageOnly=True)
1602	# print self.ImageZ.shape,self.ImageZ.size,Data['size'] #might be useful debugging line
1603	self.oldImagefile = imagefile
1604
1605	imScale = 1
1606	if len(self.ImageZ) > 1024:
1607	imScale = len(self.ImageZ)/1024
1608	sizexy = Data['size']
1609	pixelSize = Data['pixelSize']
1610	scalex = 1000./pixelSize[0]
1611	scaley = 1000./pixelSize[1]
1612	Xmax = sizexy[0]*pixelSize[0]/1000.
1613	Ymax = sizexy[1]*pixelSize[1]/1000.
1614	xlim = (0,Xmax)
1615	ylim = (Ymax,0)
1616	Imin,Imax = Data['range'][1]
1617	acolor = mpl.cm.get_cmap(Data['color'])
1618	xcent,ycent = Data['center']
1619	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1620	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1621	#do threshold mask - "real" mask - others are just bondaries
1622	Zlim = Masks['Thresholds'][1]
1623	wx.BeginBusyCursor()
1624	try:
1625
1626	if newImage:
1627	MA = ma.masked_greater(ma.masked_less(self.ImageZ,Zlim[0]),Zlim[1])
1628	MaskA = ma.getmaskarray(MA)
1629	A = G2img.ImageCompress(MA,imScale)
1630	AM = G2img.ImageCompress(MaskA,imScale)
1631	if self.logPlot:
1632	A = np.log(A)
1633	AM = np.log(AM)
1634	Imin,Imax = [np.amin(A),np.amax(A)]
1635	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
1636	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Xmax,0])
1637	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
1638	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
1639	if self.setPoly:
1640	Img.set_picker(True)
1641
1642	Plot.plot(xcent,ycent,'x')
1643	if Data['showLines']:
1644	LRAzim = Data['LRazimuth'] #NB: integers
1645	Nazm = Data['outAzimuths']
1646	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
1647	AzmthOff = Data['azmthOff']
1648	IOtth = Data['IOtth']
1649	wave = Data['wavelength']
1650	dspI = wave/(2.0*sind(IOtth[0]/2.0))
1651	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
1652	dspO = wave/(2.0*sind(IOtth[1]/2.0))
1653	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
1654	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
1655	if ellI:
1656	xyI = []
1657	for azm in Azm:
1658	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
1659	xyI = np.array(xyI)
1660	arcxI,arcyI = xyI.T
1661	Plot.plot(arcxI,arcyI,picker=3)
1662	if ellO:
1663	xyO = []
1664	for azm in Azm:
1665	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
1666	xyO = np.array(xyO)
1667	arcxO,arcyO = xyO.T
1668	Plot.plot(arcxO,arcyO,picker=3)
1669	if ellO and ellI:
1670	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
1671	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
1672	for i in range(Nazm):
1673	cake = LRAzim[0]+i*delAzm
1674	ind = np.searchsorted(Azm,cake)
1675	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
1676
1677	for xring,yring in Data['ring']:
1678	Plot.plot(xring,yring,'r+',picker=3)
1679	if Data['setRings']:
1680	# rings = np.concatenate((Data['rings']),axis=0)
1681	N = 0
1682	for ring in Data['rings']:
1683	xring,yring = np.array(ring).T[:2]
1684	Plot.plot(xring,yring,'+',color=colors[N%6])
1685	N += 1
1686	for ellipse in Data['ellipses']:
1687	cent,phi,[width,height],col = ellipse
1688	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
1689	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
1690	#masks - mask lines numbered after integration limit lines
1691	spots = Masks['Points']
1692	rings = Masks['Rings']
1693	arcs = Masks['Arcs']
1694	polygons = Masks['Polygons']
1695	for x,y,d in spots:
1696	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
1697	self.ringList = []
1698	for iring,(tth,thick) in enumerate(rings):
1699	wave = Data['wavelength']
1700	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
1701	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
1702	self.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1703	self.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1704	self.arcList = []
1705	for iarc,(tth,azm,thick) in enumerate(arcs):
1706	wave = Data['wavelength']
1707	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
1708	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
1709	self.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1710	self.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1711	self.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1712	self.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1713	self.polyList = []
1714	for ipoly,polygon in enumerate(polygons):
1715	x,y = np.hsplit(np.array(polygon),2)
1716	self.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
1717	Plot.plot(x,y,'r')
1718	if newImage:
1719	colorBar = Page.figure.colorbar(Img)
1720	Plot.set_xlim(xlim)
1721	Plot.set_ylim(ylim)
1722	if not newPlot and xylim:
1723	Page.toolbar.push_current()
1724	Plot.set_xlim(xylim[0])
1725	Plot.set_ylim(xylim[1])
1726	xylim = []
1727	Page.toolbar.push_current()
1728	Page.toolbar.draw()
1729	else:
1730	Page.canvas.draw()
1731	finally:
1732	wx.EndBusyCursor()
1733
1734	def PlotIntegration(self,newPlot=False,event=None):
1735	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
1736	'''
1737
1738	def OnMotion(event):
1739	Page.canvas.SetToolTipString('')
1740	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1741	azm = event.ydata
1742	tth = event.xdata
1743	if azm and tth:
1744	self.G2plotNB.status.SetFields(\
1745	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1746
1747	try:
1748	plotNum = self.G2plotNB.plotList.index('2D Integration')
1749	Page = self.G2plotNB.nb.GetPage(plotNum)
1750	if not newPlot:
1751	Plot = Page.figure.gca() #get previous plot & get limits
1752	xylim = Plot.get_xlim(),Plot.get_ylim()
1753	Page.figure.clf()
1754	Plot = Page.figure.gca() #get a fresh plot after clf()
1755
1756	except ValueError:
1757	Plot = self.G2plotNB.addMpl('2D Integration').gca()
1758	plotNum = self.G2plotNB.plotList.index('2D Integration')
1759	Page = self.G2plotNB.nb.GetPage(plotNum)
1760	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1761	Page.views = False
1762	view = False
1763	if not event:
1764	Page.SetFocus()
1765
1766	Data = self.PatternTree.GetItemPyData(
1767	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1768	image = self.Integrate[0]
1769	xsc = self.Integrate[1]
1770	ysc = self.Integrate[2]
1771	Imin,Imax = Data['range'][1]
1772	acolor = mpl.cm.get_cmap(Data['color'])
1773	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1774	Plot.set_ylabel('azimuth',fontsize=12)
1775	Plot.set_xlabel('2-theta',fontsize=12)
1776	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
1777	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
1778	colorBar = Page.figure.colorbar(Img)
1779	if Data['setRings'] and Data['rings']:
1780	rings = np.concatenate((Data['rings']),axis=0)
1781	for xring,yring,dsp in rings:
1782	x,y = G2img.GetTthAzm(xring,yring,Data)
1783	Plot.plot(x,y,'r+')
1784	if Data['ellipses']:
1785	for ellipse in Data['ellipses']:
1786	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1787	x,y = np.hsplit(ring,2)
1788	tth,azm = G2img.GetTthAzm(x,y,Data)
1789	azm = np.where(azm < 0.,azm+360,azm)
1790	Plot.plot(tth,azm,'b,')
1791	if not newPlot:
1792	Page.toolbar.push_current()
1793	Plot.set_xlim(xylim[0])
1794	Plot.set_ylim(xylim[1])
1795	xylim = []
1796	Page.toolbar.push_current()
1797	Page.toolbar.draw()
1798	else:
1799	Page.canvas.draw()
1800
1801	def PlotTRImage(self,tax,tay,taz,newPlot=False):
1802	'''a test plot routine - not normally used
1803	'''
1804
1805	def OnMotion(event):
1806	Page.canvas.SetToolTipString('')
1807	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1808	azm = event.xdata
1809	tth = event.ydata
1810	if azm and tth:
1811	self.G2plotNB.status.SetFields(\
1812	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1813
1814	try:
1815	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1816	Page = self.G2plotNB.nb.GetPage(plotNum)
1817	if not newPlot:
1818	Plot = Page.figure.gca() #get previous plot & get limits
1819	xylim = Plot.get_xlim(),Plot.get_ylim()
1820	Page.figure.clf()
1821	Plot = Page.figure.gca() #get a fresh plot after clf()
1822
1823	except ValueError:
1824	Plot = self.G2plotNB.addMpl('2D Transformed Powder Image').gca()
1825	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1826	Page = self.G2plotNB.nb.GetPage(plotNum)
1827	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1828	Page.views = False
1829	view = False
1830	Page.SetFocus()
1831
1832	Data = self.PatternTree.GetItemPyData(
1833	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1834	Imin,Imax = Data['range'][1]
1835	step = (Imax-Imin)/5.
1836	V = np.arange(Imin,Imax,step)
1837	acolor = mpl.cm.get_cmap(Data['color'])
1838	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1839	Plot.set_xlabel('azimuth',fontsize=12)
1840	Plot.set_ylabel('2-theta',fontsize=12)
1841	Plot.contour(tax,tay,taz,V,cmap=acolor)
1842	if Data['showLines']:
1843	IOtth = Data['IOtth']
1844	if Data['fullIntegrate']:
1845	LRAzim = [-180,180]
1846	else:
1847	LRAzim = Data['LRazimuth'] #NB: integers
1848	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
1849	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
1850	if not Data['fullIntegrate']:
1851	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
1852	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
1853	if Data['setRings']:
1854	rings = np.concatenate((Data['rings']),axis=0)
1855	for xring,yring,dsp in rings:
1856	x,y = G2img.GetTthAzm(xring,yring,Data)
1857	Plot.plot(y,x,'r+')
1858	if Data['ellipses']:
1859	for ellipse in Data['ellipses']:
1860	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1861	x,y = np.hsplit(ring,2)
1862	tth,azm = G2img.GetTthAzm(x,y,Data)
1863	Plot.plot(azm,tth,'b,')
1864	if not newPlot:
1865	Page.toolbar.push_current()
1866	Plot.set_xlim(xylim[0])
1867	Plot.set_ylim(xylim[1])
1868	xylim = []
1869	Page.toolbar.push_current()
1870	Page.toolbar.draw()
1871	else:
1872	Page.canvas.draw()
1873
1874	def PlotStructure(self,data):
1875	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
1876	thermal motion ellipsoids and polyhedra
1877	'''
1878	generalData = data['General']
1879	cell = generalData['Cell'][1:7]
1880	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
1881	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1882	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1883	Mydir = generalData['Mydir']
1884	atomData = data['Atoms']
1885	drawingData = data['Drawing']
1886	drawAtoms = drawingData['Atoms']
1887	cx,ct,cs = drawingData['atomPtrs']
1888	Wt = [255,255,255]
1889	Rd = [255,0,0]
1890	Gr = [0,255,0]
1891	Bl = [0,0,255]
1892	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]])
1893	uEdges = np.array([
1894	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
1895	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
1896	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
1897	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
1898	altDown = False
1899	shiftDown = False
1900	ctrlDown = False
1901
1902	def OnKeyBox(event):
1903	import Image
1904	Draw() #make sure plot is fresh!!
1905	mode = cb.GetValue()
1906	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
1907	size = Page.canvas.GetSize()
1908	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
1909	if mode in ['jpeg',]:
1910	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
1911	im = Image.new("RGBA", (size[0],size[1]))
1912	else:
1913	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
1914	im = Image.new("RGB", (size[0],size[1]))
1915	im.fromstring(Pix)
1916	im.save(Fname,mode)
1917	cb.SetValue(' Save as:')
1918	self.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
1919
1920	def GetTruePosition(xy):
1921	View = glGetIntegerv(GL_VIEWPORT)
1922	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
1923	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
1924	Zmax = 1.
1925	for i,atom in enumerate(drawAtoms):
1926	x,y,z = atom[cx:cx+3]
1927	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
1928	XY = [int(X),int(View[3]-Y)]
1929	if np.allclose(xy,XY,atol=10) and Z < Zmax:
1930	Zmax = Z
1931	SetSelectedAtoms(i)
1932
1933	def OnMouseDown(event):
1934	xy = event.GetPosition()
1935	if event.ShiftDown():
1936	GetTruePosition(xy)
1937	else:
1938	drawingData['Rotation'][3] = xy
1939	Draw()
1940
1941	def OnMouseMove(event):
1942	newxy = event.GetPosition()
1943	page = getSelection()
1944	if event.ControlDown() and drawingData['showABC']:
1945	if event.LeftIsDown():
1946	SetTestRot(newxy)
1947	elif event.RightIsDown():
1948	SetTestPos(newxy)
1949	elif event.MiddleIsDown():
1950	SetTestRotZ(newxy)
1951	x,y,z = drawingData['testPos'][0]
1952	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
1953
1954
1955	if event.Dragging() and not event.ControlDown():
1956	if event.LeftIsDown():
1957	SetRotation(newxy)
1958	angX,angY,angZ = drawingData['Rotation'][:3]
1959	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
1960	elif event.RightIsDown():
1961	SetTranslation(newxy)
1962	Tx,Ty,Tz = drawingData['viewPoint'][0]
1963	self.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
1964	elif event.MiddleIsDown():
1965	SetRotationZ(newxy)
1966	angX,angY,angZ = drawingData['Rotation'][:3]
1967	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
1968	Draw()
1969
1970	def OnMouseWheel(event):
1971	drawingData['cameraPos'] += event.GetWheelRotation()/24
1972	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
1973	self.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
1974	page = getSelection()
1975	if page:
1976	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1977	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1978	names = [child.GetName() for child in panel]
1979	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
1980	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
1981	Draw()
1982
1983	def getSelection():
1984	try:
1985	return self.dataDisplay.GetSelection()
1986	except AttributeError:
1987	print self.dataDisplay.GetLabel()
1988	self.G2plotNB.status.SetStatusText('Select this from Phase data window!')
1989	return 0
1990
1991	def SetViewPointText(VP):
1992	page = getSelection()
1993	if page:
1994	if self.dataDisplay.GetPageText(page) == 'Draw Options':
1995	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
1996	names = [child.GetName() for child in panel]
1997	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
1998
1999	def ClearSelectedAtoms():
2000	page = getSelection()
2001	if page:
2002	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2003	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2004	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2005	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2006
2007	def SetSelectedAtoms(ind):
2008	page = getSelection()
2009	if page:
2010	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2011	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
2012	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2013	Id = drawAtoms[ind][-2]
2014	for i,atom in enumerate(atomData):
2015	if atom[-1] == Id:
2016	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2017
2018	def GetSelectedAtoms():
2019	page = getSelection()
2020	Ind = []
2021	if page:
2022	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2023	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2024	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2025	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2026	return Ind
2027
2028	def OnKey(event): #on key UP!!
2029	keyCode = event.GetKeyCode()
2030	if keyCode > 255:
2031	keyCode = 0
2032	key,xyz = chr(keyCode),event.GetPosition()
2033	indx = drawingData['selectedAtoms']
2034	if key in ['c','C']:
2035	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2036	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
2037	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
2038	SetViewPointText(drawingData['viewPoint'][0])
2039	elif key in ['n','N']:
2040	drawAtoms = drawingData['Atoms']
2041	pI = drawingData['viewPoint'][1]
2042	if indx:
2043	pI[0] = indx[pI[1]]
2044	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2045	pI[1] += 1
2046	if pI[1] >= len(indx):
2047	pI[1] = 0
2048	else:
2049	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2050	pI[0] += 1
2051	if pI[0] >= len(drawAtoms):
2052	pI[0] = 0
2053	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2054	SetViewPointText(drawingData['viewPoint'][0])
2055
2056	elif key in ['p','P']:
2057	drawAtoms = drawingData['Atoms']
2058	pI = drawingData['viewPoint'][1]
2059	if indx:
2060	pI[0] = indx[pI[1]]
2061	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2062	pI[1] -= 1
2063	if pI[1] < 0:
2064	pI[1] = len(indx)-1
2065	else:
2066	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2067	pI[0] -= 1
2068	if pI[0] < 0:
2069	pI[0] = len(drawAtoms)-1
2070	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2071	SetViewPointText(drawingData['viewPoint'][0])
2072	Draw()
2073
2074	def SetBackground():
2075	R,G,B,A = Page.camera['backColor']
2076	glClearColor(R,G,B,A)
2077	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2078
2079	def SetLights():
2080	glEnable(GL_DEPTH_TEST)
2081	glShadeModel(GL_SMOOTH)
2082	glEnable(GL_LIGHTING)
2083	glEnable(GL_LIGHT0)
2084	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2085	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2086	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2087
2088	def SetTranslation(newxy):
2089	Tx,Ty,Tz = drawingData['viewPoint'][0]
2090	anglex,angley,anglez,oldxy = drawingData['Rotation']
2091	Rx = G2lat.rotdMat(anglex,0)
2092	Ry = G2lat.rotdMat(angley,1)
2093	Rz = G2lat.rotdMat(anglez,2)
2094	dxy = list(newxy-oldxy)+[0,]
2095	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
2096	Tx -= dxy[0]*0.01
2097	Ty += dxy[1]*0.01
2098	Tz -= dxy[2]*0.01
2099	drawingData['Rotation'][3] = newxy
2100	drawingData['viewPoint'][0] = Tx,Ty,Tz
2101	SetViewPointText([Tx,Ty,Tz])
2102
2103	def SetTestPos(newxy):
2104	Tx,Ty,Tz = drawingData['testPos'][0]
2105	anglex,angley,anglez,oldxy = drawingData['Rotation']
2106	Rx = G2lat.rotdMat(anglex,0)
2107	Ry = G2lat.rotdMat(angley,1)
2108	Rz = G2lat.rotdMat(anglez,2)
2109	dxy = list(newxy-oldxy)+[0,]
2110	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
2111	Tx += dxy[0]*0.001
2112	Ty -= dxy[1]*0.001
2113	Tz += dxy[2]*0.001
2114	drawingData['Rotation'][3] = newxy
2115	drawingData['testPos'][0] = Tx,Ty,Tz
2116
2117	def SetTestRot(newxy):
2118	Txyz = np.array(drawingData['testPos'][0])
2119	oldxy = drawingData['testPos'][2]
2120	Ax,Ay,Az = drawingData['testPos'][1]
2121	Vxyz = np.array(drawingData['viewPoint'][0])
2122	Dxyz = np.inner(Amat,Txyz-Vxyz)
2123	dxy = list(newxy-oldxy)+[0,]
2124	Ax += dxy[1]*0.01
2125	Ay += dxy[0]*0.01
2126	Rx = G2lat.rotdMat(Ax,0)
2127	Ry = G2lat.rotdMat(Ay,1)
2128	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
2129	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2130	drawingData['testPos'][1] = [Ax,Ay,Az]
2131	drawingData['testPos'][2] = newxy
2132	drawingData['testPos'][0] = Dxyz
2133
2134	def SetTestRotZ(newxy):
2135	Txyz = np.array(drawingData['testPos'][0])
2136	oldxy = drawingData['testPos'][2]
2137	Ax,Ay,Az = drawingData['testPos'][1]
2138	Vxyz = np.array(drawingData['viewPoint'][0])
2139	Dxyz = np.inner(Amat,Txyz-Vxyz)
2140	dxy = list(newxy-oldxy)+[0,]
2141	Az += (dxy[0]+dxy[1])*.01
2142	Rz = G2lat.rotdMat(Az,2)
2143	Dxyz = np.inner(Rz,Dxyz)
2144	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2145	drawingData['testPos'][1] = [Ax,Ay,Az]
2146	drawingData['testPos'][2] = newxy
2147	drawingData['testPos'][0] = Dxyz
2148
2149	def SetRotation(newxy):
2150	anglex,angley,anglez,oldxy = drawingData['Rotation']
2151	dxy = newxy-oldxy
2152	anglex += dxy[1]*.25
2153	angley += dxy[0]*.25
2154	oldxy = newxy
2155	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2156
2157	def SetRotationZ(newxy):
2158	anglex,angley,anglez,oldxy = drawingData['Rotation']
2159	dxy = newxy-oldxy
2160	anglez += (dxy[0]+dxy[1])*.25
2161	oldxy = newxy
2162	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2163
2164	def RenderBox():
2165	glEnable(GL_COLOR_MATERIAL)
2166	glLineWidth(2)
2167	glEnable(GL_BLEND)
2168	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2169	glEnable(GL_LINE_SMOOTH)
2170	glBegin(GL_LINES)
2171	for line,color in zip(uEdges,uColors):
2172	glColor3ubv(color)
2173	glVertex3fv(line[0])
2174	glVertex3fv(line[1])
2175	glEnd()
2176	glColor4ubv([0,0,0,0])
2177	glDisable(GL_LINE_SMOOTH)
2178	glDisable(GL_BLEND)
2179	glDisable(GL_COLOR_MATERIAL)
2180
2181	def RenderUnitVectors(x,y,z):
2182	xyz = np.array([x,y,z])
2183	glEnable(GL_COLOR_MATERIAL)
2184	glLineWidth(1)
2185	glPushMatrix()
2186	glTranslate(x,y,z)
2187	glScalef(1/cell[0],1/cell[1],1/cell[2])
2188	glBegin(GL_LINES)
2189	for line,color in zip(uEdges,uColors)[:3]:
2190	glColor3ubv(color)
2191	glVertex3fv(line[0])
2192	glVertex3fv(line[1])
2193	glEnd()
2194	glPopMatrix()
2195	glColor4ubv([0,0,0,0])
2196	glDisable(GL_COLOR_MATERIAL)
2197
2198	def RenderSphere(x,y,z,radius,color):
2199	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2200	glPushMatrix()
2201	glTranslate(x,y,z)
2202	glMultMatrixf(B4mat.T)
2203	q = gluNewQuadric()
2204	gluSphere(q,radius,20,10)
2205	glPopMatrix()
2206
2207	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2208	s1,s2,s3 = E
2209	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2210	glPushMatrix()
2211	glTranslate(x,y,z)
2212	glMultMatrixf(B4mat.T)
2213	glMultMatrixf(R4.T)
2214	glEnable(GL_NORMALIZE)
2215	glScale(s1,s2,s3)
2216	q = gluNewQuadric()
2217	gluSphere(q,ellipseProb,20,10)
2218	glDisable(GL_NORMALIZE)
2219	glPopMatrix()
2220
2221	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2222	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2223	glPushMatrix()
2224	glTranslate(x,y,z)
2225	glMultMatrixf(B4mat.T)
2226	for bond in Bonds:
2227	glPushMatrix()
2228	Dx = np.inner(Amat,bond)
2229	Z = np.sqrt(np.sum(Dx**2))
2230	azm = atan2d(-Dx[1],-Dx[0])
2231	phi = acosd(Dx[2]/Z)
2232	glRotate(-azm,0,0,1)
2233	glRotate(phi,1,0,0)
2234	q = gluNewQuadric()
2235	gluCylinder(q,radius,radius,Z,slice,2)
2236	glPopMatrix()
2237	glPopMatrix()
2238
2239	def RenderLines(x,y,z,Bonds,color):
2240	xyz = np.array([x,y,z])
2241	glEnable(GL_COLOR_MATERIAL)
2242	glLineWidth(1)
2243	glColor3fv(color)
2244	glPushMatrix()
2245	glBegin(GL_LINES)
2246	for bond in Bonds:
2247	glVertex3fv(xyz)
2248	glVertex3fv(xyz+bond)
2249	glEnd()
2250	glColor4ubv([0,0,0,0])
2251	glPopMatrix()
2252	glDisable(GL_COLOR_MATERIAL)
2253
2254	def RenderPolyhedra(x,y,z,Faces,color):
2255	glPushMatrix()
2256	glTranslate(x,y,z)
2257	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2258	glShadeModel(GL_SMOOTH)
2259	glMultMatrixf(B4mat.T)
2260	for face,norm in Faces:
2261	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2262	glFrontFace(GL_CW)
2263	glNormal3fv(norm)
2264	glBegin(GL_TRIANGLES)
2265	for vert in face:
2266	glVertex3fv(vert)
2267	glEnd()
2268	glPopMatrix()
2269
2270	def RenderBackbone(Backbone,BackboneColor,radius):
2271	glPushMatrix()
2272	glMultMatrixf(B4mat.T)
2273	glEnable(GL_COLOR_MATERIAL)
2274	glShadeModel(GL_SMOOTH)
2275	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2276	glePolyCylinder(Backbone,BackboneColor,radius)
2277	glPopMatrix()
2278	glDisable(GL_COLOR_MATERIAL)
2279
2280	def RenderLabel(x,y,z,label,r):
2281	glPushMatrix()
2282	glTranslate(x,y,z)
2283	glMultMatrixf(B4mat.T)
2284	glDisable(GL_LIGHTING)
2285	glColor3f(0,1.,0)
2286	glRasterPos3f(r,r,r)
2287	for c in list(label):
2288	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2289	glEnable(GL_LIGHTING)
2290	glPopMatrix()
2291
2292	def Draw():
2293	import numpy.linalg as nl
2294	Ind = GetSelectedAtoms()
2295	VS = np.array(Page.canvas.GetSize())
2296	aspect = float(VS[0])/float(VS[1])
2297	cPos = drawingData['cameraPos']
2298	Zclip = drawingData['Zclip']*cPos/200.
2299	anglex,angley,anglez = drawingData['Rotation'][:3]
2300	Tx,Ty,Tz = drawingData['viewPoint'][0]
2301	cx,ct,cs = drawingData['atomPtrs']
2302	bondR = drawingData['bondRadius']
2303	G,g = G2lat.cell2Gmat(cell)
2304	GS = G
2305	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2306	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2307	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2308	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2309
2310	SetBackground()
2311	glInitNames()
2312	glPushName(0)
2313
2314	glMatrixMode(GL_PROJECTION)
2315	glLoadIdentity()
2316	glViewport(0,0,VS[0],VS[1])
2317	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2318	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2319	SetLights()
2320
2321	glMatrixMode(GL_MODELVIEW)
2322	glLoadIdentity()
2323	glRotate(anglez,0,0,1)
2324	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2325	glRotate(angley,sind(anglez),cosd(anglez),0)
2326	glMultMatrixf(A4mat.T)
2327	glTranslate(-Tx,-Ty,-Tz)
2328	if drawingData['unitCellBox']:
2329	RenderBox()
2330	if drawingData['showABC']:
2331	x,y,z = drawingData['testPos'][0]
2332	# if altDown:
2333	# self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2334	# else:
2335	# self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2336	RenderUnitVectors(x,y,z)
2337	Backbone = []
2338	BackboneColor = []
2339	time0 = time.time()
2340	for iat,atom in enumerate(drawingData['Atoms']):
2341	x,y,z = atom[cx:cx+3]
2342	Bonds = atom[-2]
2343	Faces = atom[-1]
2344	try:
2345	atNum = generalData['AtomTypes'].index(atom[ct])
2346	except ValueError:
2347	atNum = -1
2348	CL = atom[cs+2]
2349	color = np.array(CL)/255.
2350	if iat in Ind:
2351	color = np.array(Gr)/255.
2352	radius = 0.5
2353	if atom[cs] != '':
2354	glLoadName(atom[-3])
2355	if 'balls' in atom[cs]:
2356	vdwScale = drawingData['vdwScale']
2357	ballScale = drawingData['ballScale']
2358	if atNum < 0:
2359	radius = 0.2
2360	elif 'H' == atom[ct]:
2361	if drawingData['showHydrogen']:
2362	if 'vdW' in atom[cs] and atNum >= 0:
2363	radius = vdwScale*generalData['vdWRadii'][atNum]
2364	else:
2365	radius = ballScale*drawingData['sizeH']
2366	else:
2367	radius = 0.0
2368	else:
2369	if 'vdW' in atom[cs]:
2370	radius = vdwScale*generalData['vdWRadii'][atNum]
2371	else:
2372	radius = ballScale*generalData['BondRadii'][atNum]
2373	RenderSphere(x,y,z,radius,color)
2374	if 'sticks' in atom[cs]:
2375	RenderBonds(x,y,z,Bonds,bondR,color)
2376	elif 'ellipsoids' in atom[cs]:
2377	RenderBonds(x,y,z,Bonds,bondR,color)
2378	if atom[cs+3] == 'A':
2379	Uij = atom[cs+5:cs+11]
2380	U = np.multiply(G2spc.Uij2U(Uij),GS)
2381	U = np.inner(Amat,np.inner(U,Amat).T)
2382	E,R = nl.eigh(U)
2383	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2384	E = np.sqrt(E)
2385	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2386	pass
2387	else:
2388	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2389	else:
2390	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2391	pass
2392	else:
2393	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2394	RenderSphere(x,y,z,radius,color)
2395	elif 'lines' in atom[cs]:
2396	radius = 0.1
2397	RenderLines(x,y,z,Bonds,color)
2398	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2399	elif atom[cs] == 'sticks':
2400	radius = 0.1
2401	RenderBonds(x,y,z,Bonds,bondR,color)
2402	elif atom[cs] == 'polyhedra':
2403	RenderPolyhedra(x,y,z,Faces,color)
2404	elif atom[cs] == 'backbone':
2405	if atom[ct-1].split()[0] in ['C','N']:
2406	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2407	BackboneColor.append(list(color))
2408
2409	if atom[cs+1] == 'type':
2410	RenderLabel(x,y,z,atom[ct],radius)
2411	elif atom[cs+1] == 'name':
2412	RenderLabel(x,y,z,atom[ct-1],radius)
2413	elif atom[cs+1] == 'number':
2414	RenderLabel(x,y,z,str(iat+1),radius)
2415	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2416	RenderLabel(x,y,z,atom[ct-4],radius)
2417	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2418	RenderLabel(x,y,z,atom[ct-3],radius)
2419	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2420	RenderLabel(x,y,z,atom[ct-2],radius)
2421	if Backbone:
2422	RenderBackbone(Backbone,BackboneColor,bondR)
2423	# print time.time()-time0
2424	Page.canvas.SwapBuffers()
2425
2426	def OnSize(event):
2427	Draw()
2428
2429	def OnFocus(event):
2430	Draw()
2431
2432	try:
2433	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2434	Page = self.G2plotNB.nb.GetPage(plotNum)
2435	except ValueError:
2436	Plot = self.G2plotNB.addOgl(generalData['Name'])
2437	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2438	Page = self.G2plotNB.nb.GetPage(plotNum)
2439	Page.views = False
2440	view = False
2441	altDown = False
2442	Page.SetFocus()
2443	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2444	choices=(' save as:','jpeg','tiff','bmp'))
2445	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2446	cb.SetValue(' save as:')
2447	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2448	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2449	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2450	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2451	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2452	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2453	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2454	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2455	Page.camera['position'] = drawingData['cameraPos']
2456	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2457	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2458	Page.canvas.SetCurrent()
2459	Draw()
2460

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