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source: trunk/GSASIIplot.py @ 809

Last change on this file since 809 was 809, checked in by vondreele, 10 years ago
apply zero point to plot x
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1	# -- coding: utf-8 --
2	#GSASII plotting routines
3	########### SVN repository information ###################
4	# $Date: 2012-12-05 19:12:19 +0000 (Wed, 05 Dec 2012) $
5	# $Author: vondreele $
6	# $Revision: 809 $
7	# $URL: trunk/GSASIIplot.py $
8	# $Id: GSASIIplot.py 809 2012-12-05 19:12:19Z vondreele $
9	########### SVN repository information ###################
10	import math
11	import time
12	import copy
13	import os.path
14	import numpy as np
15	import numpy.ma as ma
16	import numpy.linalg as nl
17	import wx
18	import wx.aui
19	import wx.glcanvas
20	import matplotlib as mpl
21	import mpl_toolkits.mplot3d.axes3d as mp3d
22	import GSASIIpath
23	GSASIIpath.SetVersionNumber("$Revision: 809 $")
24	import GSASIIgrid as G2gd
25	import GSASIIimage as G2img
26	import GSASIIpwd as G2pwd
27	import GSASIIIO as G2IO
28	import GSASIIpwdGUI as G2pdG
29	import GSASIIimgGUI as G2imG
30	import GSASIIphsGUI as G2phG
31	import GSASIIlattice as G2lat
32	import GSASIIspc as G2spc
33	import GSASIImath as G2mth
34	import pytexture as ptx
35	from OpenGL.GL import *
36	from OpenGL.GLU import *
37	from OpenGL.GLUT import *
38	from OpenGL.GLE import *
39	from matplotlib.backends.backend_wx import _load_bitmap
40	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
41	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
42
43	# useful degree trig functions
44	sind = lambda x: math.sin(x*math.pi/180.)
45	cosd = lambda x: math.cos(x*math.pi/180.)
46	tand = lambda x: math.tan(x*math.pi/180.)
47	asind = lambda x: 180.*math.asin(x)/math.pi
48	acosd = lambda x: 180.*math.acos(x)/math.pi
49	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
50	atand = lambda x: 180.*math.atan(x)/math.pi
51	# numpy versions
52	npsind = lambda x: np.sin(x*np.pi/180.)
53	npcosd = lambda x: np.cos(x*np.pi/180.)
54	nptand = lambda x: np.tan(x*np.pi/180.)
55	npacosd = lambda x: 180.*np.arccos(x)/np.pi
56	npasind = lambda x: 180.*np.arcsin(x)/np.pi
57	npatand = lambda x: 180.*np.arctan(x)/np.pi
58	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
59
60	class G2PlotMpl(wx.Panel):
61	def __init__(self,parent,id=-1,dpi=None,**kwargs):
62	wx.Panel.__init__(self,parent,id=id,**kwargs)
63	mpl.rcParams['legend.fontsize'] = 10
64	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,6))
65	self.canvas = Canvas(self,-1,self.figure)
66	self.toolbar = GSASIItoolbar(self.canvas)
67
68	self.toolbar.Realize()
69
70	sizer=wx.BoxSizer(wx.VERTICAL)
71	sizer.Add(self.canvas,1,wx.EXPAND)
72	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
73	self.SetSizer(sizer)
74
75	class G2PlotOgl(wx.Panel):
76	def __init__(self,parent,id=-1,dpi=None,**kwargs):
77	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
78	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
79	self.camera = {}
80	sizer=wx.BoxSizer(wx.VERTICAL)
81	sizer.Add(self.canvas,1,wx.EXPAND)
82	self.SetSizer(sizer)
83
84	class G2Plot3D(wx.Panel):
85	def __init__(self,parent,id=-1,dpi=None,**kwargs):
86	wx.Panel.__init__(self,parent,id=id,**kwargs)
87	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
88	self.canvas = Canvas(self,-1,self.figure)
89	self.toolbar = GSASIItoolbar(self.canvas)
90
91	self.toolbar.Realize()
92
93	sizer=wx.BoxSizer(wx.VERTICAL)
94	sizer.Add(self.canvas,1,wx.EXPAND)
95	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
96	self.SetSizer(sizer)
97
98	class G2PlotNoteBook(wx.Panel):
99	def __init__(self,parent,id=-1):
100	wx.Panel.__init__(self,parent,id=id)
101	#so one can't delete a plot page!!
102	self.nb = wx.aui.AuiNotebook(self, \
103	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
104	sizer = wx.BoxSizer()
105	sizer.Add(self.nb,1,wx.EXPAND)
106	self.SetSizer(sizer)
107	self.status = parent.CreateStatusBar()
108	self.status.SetFieldsCount(2)
109	self.status.SetStatusWidths([150,-1])
110	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
111
112	self.plotList = []
113
114	def addMpl(self,name=""):
115	page = G2PlotMpl(self.nb)
116	self.nb.AddPage(page,name)
117
118	self.plotList.append(name)
119
120	return page.figure
121
122	def add3D(self,name=""):
123	page = G2Plot3D(self.nb)
124	self.nb.AddPage(page,name)
125
126	self.plotList.append(name)
127
128	return page.figure
129
130	def addOgl(self,name=""):
131	page = G2PlotOgl(self.nb)
132	self.nb.AddPage(page,name)
133
134	self.plotList.append(name)
135
136	return page.figure
137
138	def Delete(self,name):
139	try:
140	item = self.plotList.index(name)
141	del self.plotList[item]
142	self.nb.DeletePage(item)
143	except ValueError: #no plot of this name - do nothing
144	return
145
146	def clear(self):
147	while self.nb.GetPageCount():
148	self.nb.DeletePage(0)
149	self.plotList = []
150	self.status.DestroyChildren()
151
152	def Rename(self,oldName,newName):
153	try:
154	item = self.plotList.index(oldName)
155	self.plotList[item] = newName
156	self.nb.SetPageText(item,newName)
157	except ValueError: #no plot of this name - do nothing
158	return
159
160	def OnPageChanged(self,event):
161	if self.plotList:
162	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
163	self.status.DestroyChildren() #get rid of special stuff on status bar
164
165	class GSASIItoolbar(Toolbar):
166	ON_MPL_HELP = wx.NewId()
167	ON_MPL_KEY = wx.NewId()
168	def __init__(self,plotCanvas):
169	Toolbar.__init__(self,plotCanvas)
170	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6
171	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
172	parent = self.GetParent()
173	key = os.path.join(os.path.split(__file__)[0],'Key.ico')
174	self.AddSimpleTool(self.ON_MPL_KEY,_load_bitmap(key),'Key press','Select key press')
175	wx.EVT_TOOL(self,self.ON_MPL_KEY,self.OnKey)
176	help = os.path.join(os.path.split(__file__)[0],'help.ico')
177	self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
178	wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
179	def OnHelp(self,event):
180	Page = self.GetParent().GetParent()
181	pageNo = Page.GetSelection()
182	bookmark = Page.GetPageText(pageNo)
183	bookmark = bookmark.strip(')').replace('(','_')
184	G2gd.ShowHelp(bookmark,self.TopLevelParent)
185	def OnKey(self,event):
186	parent = self.GetParent()
187	if parent.Choice:
188	dlg = wx.SingleChoiceDialog(parent,'Select','Key press',list(parent.Choice))
189	if dlg.ShowModal() == wx.ID_OK:
190	sel = dlg.GetSelection()
191	event.key = parent.Choice[sel][0]
192	parent.keyPress(event)
193	dlg.Destroy()
194
195	################################################################################
196	##### PlotSngl
197	################################################################################
198
199	def PlotSngl(self,newPlot=False):
200	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
201	to F, F**2, etc. as requested
202	'''
203	from matplotlib.patches import Circle
204	global HKL,HKLF
205
206	def OnSCMotion(event):
207	xpos = event.xdata
208	if xpos:
209	xpos = round(xpos) #avoid out of frame mouse position
210	ypos = round(event.ydata)
211	zpos = Data['Layer']
212	if '100' in Data['Zone']:
213	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
214	elif '010' in Data['Zone']:
215	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
216	elif '001' in Data['Zone']:
217	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
218	Page.canvas.SetToolTipString(HKLtxt)
219	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
220
221	def OnSCPick(event):
222	zpos = Data['Layer']
223	pos = event.artist.center
224	if '100' in Data['Zone']:
225	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
226	hkl = np.array([zpos,pos[0],pos[1]])
227	elif '010' in Data['Zone']:
228	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
229	hkl = np.array([pos[0],zpos,pos[1]])
230	elif '001' in Data['Zone']:
231	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
232	hkl = np.array([pos[0],pos[1],zpos])
233	h,k,l = hkl
234	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
235	if len(hklf):
236	Fosq,sig,Fcsq = hklf[0]
237	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
238	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
239
240	def OnSCKeyPress(event):
241	print event.key
242
243	try:
244	plotNum = self.G2plotNB.plotList.index('Structure Factors')
245	Page = self.G2plotNB.nb.GetPage(plotNum)
246	if not newPlot:
247	Plot = Page.figure.gca() #get previous powder plot & get limits
248	xylim = Plot.get_xlim(),Plot.get_ylim()
249	Page.figure.clf()
250	Page.Choice = None
251	Plot = Page.figure.gca() #get a fresh plot after clf()
252	except ValueError:
253	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
254	plotNum = self.G2plotNB.plotList.index('Structure Factors')
255	Page = self.G2plotNB.nb.GetPage(plotNum)
256	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
257	Page.canvas.mpl_connect('pick_event', OnSCPick)
258	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
259	Page.Choice = None
260	Page.SetFocus()
261
262	Plot.set_aspect(aspect='equal')
263	HKLref = self.PatternTree.GetItemPyData(self.Sngl)[1]
264	Data = self.PatternTree.GetItemPyData(
265	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
266	Type = Data['Type']
267	scale = Data['Scale']
268	HKLmax = Data['HKLmax']
269	HKLmin = Data['HKLmin']
270	FosqMax = Data['FoMax']
271	FoMax = math.sqrt(FosqMax)
272	ifFc = Data['ifFc']
273	xlabel = ['k, h=','h, k=','h, l=']
274	ylabel = ['l','l','k']
275	zones = ['100','010','001']
276	pzone = [[1,2],[0,2],[0,1]]
277	izone = zones.index(Data['Zone'])
278	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
279	HKL = []
280	HKLF = []
281	for refl in HKLref:
282	H = np.array(refl[:3])
283	sig,Fosq,Fcsq = refl[7:10]
284	HKL.append(H)
285	HKLF.append([Fosq,sig,Fcsq])
286	if H[izone] == Data['Layer']:
287	B = 0
288	if Type == 'Fosq':
289	A = scale*Fosq/FosqMax
290	B = scale*Fcsq/FosqMax
291	C = abs(A-B)
292	elif Type == 'Fo':
293	A = scale*math.sqrt(max(0,Fosq))/FoMax
294	B = scale*math.sqrt(max(0,Fcsq))/FoMax
295	C = abs(A-B)
296	elif Type == '\|DFsq\|/sig':
297	A = abs(Fosq-Fcsq)/(scale*sig)
298	elif Type == '\|DFsq\|>sig':
299	A = abs(Fosq-Fcsq)/(scale*sig)
300	if A < 1.0: A = 0
301	elif Type == '\|DFsq\|>3sig':
302	A = abs(Fosq-Fcsq)/(scale*sig)
303	if A < 3.0: A = 0
304	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
305	if A > 0.0:
306	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
307	if B:
308	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
309	radius = C
310	if radius > 0:
311	if A > B:
312	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
313	else:
314	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
315	HKL = np.array(HKL,dtype=np.int)
316	HKLF = np.array(HKLF)
317	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
318	Plot.set_ylabel(ylabel[izone],fontsize=12)
319	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
320	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
321	if not newPlot:
322	Page.toolbar.push_current()
323	Plot.set_xlim(xylim[0])
324	Plot.set_ylim(xylim[1])
325	xylim = []
326	Page.toolbar.push_current()
327	Page.toolbar.draw()
328	else:
329	Page.canvas.draw()
330
331	################################################################################
332	##### PlotPatterns
333	################################################################################
334
335	def PlotPatterns(G2frame,newPlot=False):
336	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
337	2-theta, q or TOF. Can display multiple patterns as "waterfall plots" or contour plots. Log I
338	plotting available.
339	'''
340	global HKL
341
342	# def OnKeyBox(event):
343	# if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('Powder Patterns'):
344	# event.key = cb.GetValue()[0]
345	# cb.SetValue(' key press')
346	# wx.CallAfter(OnPlotKeyPress,event)
347	#
348	def OnPlotKeyPress(event):
349	newPlot = False
350	if event.key == 'w':
351	if G2frame.Weight:
352	G2frame.Weight = False
353	else:
354	G2frame.Weight = True
355	G2frame.SinglePlot = True
356	newPlot = True
357	elif event.key == 'b':
358	if G2frame.SubBack:
359	G2frame.SubBack = False
360	else:
361	G2frame.SubBack = True
362	G2frame.SinglePlot = True
363	elif event.key == 'n':
364	if G2frame.Contour:
365	pass
366	else:
367	if G2frame.logPlot:
368	G2frame.logPlot = False
369	else:
370	G2frame.Offset[0] = 0
371	G2frame.logPlot = True
372	newPlot = True
373	elif event.key == 'u':
374	if G2frame.Contour:
375	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
376	elif G2frame.logPlot:
377	pass
378	elif G2frame.Offset[0] < 100.:
379	G2frame.Offset[0] += 1.
380	elif event.key == 'd':
381	if G2frame.Contour:
382	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
383	elif G2frame.logPlot:
384	pass
385	elif G2frame.Offset[0] > 0.:
386	G2frame.Offset[0] -= 1.
387	elif event.key == 'l':
388	G2frame.Offset[1] -= 1.
389	elif event.key == 'r':
390	G2frame.Offset[1] += 1.
391	elif event.key == 'o':
392	G2frame.Offset = [0,0]
393	elif event.key == 'c':
394	newPlot = True
395	if G2frame.Contour:
396	G2frame.Contour = False
397	else:
398	G2frame.Contour = True
399	G2frame.SinglePlot = False
400	G2frame.Offset = [0.,0.]
401	elif event.key == 'q':
402	newPlot = True
403	if G2frame.qPlot:
404	G2frame.qPlot = False
405	else:
406	G2frame.qPlot = True
407	elif event.key == 's':
408	if G2frame.Contour:
409	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
410	choice.sort()
411	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
412	if dlg.ShowModal() == wx.ID_OK:
413	sel = dlg.GetSelection()
414	G2frame.ContourColor = choice[sel]
415	else:
416	G2frame.ContourColor = 'Paired'
417	dlg.Destroy()
418	else:
419	if G2frame.SinglePlot:
420	G2frame.SinglePlot = False
421	else:
422	G2frame.SinglePlot = True
423	newPlot = True
424	elif event.key == '+':
425	if G2frame.PickId:
426	G2frame.PickId = False
427	elif event.key == 'i': #for smoothing contour plot
428	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
429	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
430	'mitchell','sinc','lanczos']
431	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
432	if dlg.ShowModal() == wx.ID_OK:
433	sel = dlg.GetSelection()
434	G2frame.Interpolate = choice[sel]
435	else:
436	G2frame.Interpolate = 'nearest'
437	dlg.Destroy()
438
439	PlotPatterns(G2frame,newPlot=newPlot)
440
441	def OnMotion(event):
442	xpos = event.xdata
443	if xpos: #avoid out of frame mouse position
444	ypos = event.ydata
445	Page.canvas.SetCursor(wx.CROSS_CURSOR)
446	try:
447	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
448	if 'C' in Parms['Type'][0]:
449	wave = G2mth.getWave(Parms)
450	if G2frame.qPlot:
451	try:
452	xpos = 2.0asind(xposwave/(4*math.pi))
453	except ValueError: #avoid bad value in asin beyond upper limit
454	pass
455	dsp = 0.0
456	if abs(xpos) > 0.: #avoid possible singularity at beam center
457	dsp = wave/(2.*sind(abs(xpos)/2.0))
458	if G2frame.Contour:
459	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
460	else:
461	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
462	else: #TOF neutrons
463	dsp = 0.0
464	difC = Parms['difC'][1]
465	dsp = xpos/difC #rough approx.!
466	if G2frame.Contour:
467	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
468	else:
469	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
470	if G2frame.itemPicked:
471	Page.canvas.SetToolTipString('%9.3f'%(xpos))
472	if G2frame.PickId:
473	found = []
474	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists'] or \
475	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
476	if len(HKL):
477	view = Page.toolbar._views.forward()[0][:2]
478	wid = view[1]-view[0]
479	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
480	if len(found):
481	h,k,l = found[0][:3]
482	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
483	else:
484	Page.canvas.SetToolTipString('')
485
486	except TypeError:
487	G2frame.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
488
489	def OnPick(event):
490	if G2frame.itemPicked is not None: return
491	PatternId = G2frame.PatternId
492	try:
493	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
494	except TypeError:
495	return
496	if 'C' in Parms['Type'][0]:
497	wave = G2mth.getWave(Parms)
498	else:
499	difC = Parms['difC'][1]
500	PickId = G2frame.PickId
501	pick = event.artist
502	mouse = event.mouseevent
503	xpos = pick.get_xdata()
504	ypos = pick.get_ydata()
505	ind = event.ind
506	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
507	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
508	if ind.all() != [0]: #picked a data point
509	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
510	XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1]) #what happens for a q-plot???
511	data.append(XY)
512	G2pdG.UpdatePeakGrid(G2frame,data)
513	PlotPatterns(G2frame)
514	else: #picked a peak list line
515	G2frame.itemPicked = pick
516	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
517	if ind.all() != [0]: #picked a data point
518	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
519	data = G2frame.PatternTree.GetItemPyData(LimitId)
520	if 'C' in Parms['Type'][0]: #CW data - TOF later in an elif
521	if G2frame.qPlot: #qplot - convert back to 2-theta
522	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
523	if mouse.button==1:
524	data[1][0] = min(xy[0],data[1][1])
525	if mouse.button==3:
526	data[1][1] = max(xy[0],data[1][0])
527	G2frame.PatternTree.SetItemPyData(LimitId,data)
528	G2pdG.UpdateLimitsGrid(G2frame,data)
529	PlotPatterns(G2frame)
530	else: #picked a limit line
531	G2frame.itemPicked = pick
532	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
533	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
534	G2frame.itemPicked = pick
535	pick = str(pick)
536
537	def OnRelease(event):
538	if G2frame.itemPicked is None: return
539	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
540	if 'C' in Parms['Type'][0]:
541	wave = G2mth.getWave(Parms)
542	else:
543	difC = Parms['difC'][1]
544	xpos = event.xdata
545	PickId = G2frame.PickId
546	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
547	lines = []
548	for line in G2frame.Lines:
549	lines.append(line.get_xdata()[0])
550	# print G2frame.itemPicked.get_xdata()
551	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
552	if lineNo in [0,1]:
553	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
554	data = G2frame.PatternTree.GetItemPyData(LimitId)
555	if G2frame.qPlot:
556	if 'C' in Parms['Type'][0]:
557	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
558	else:
559	data[1][lineNo] = 2math.piParms['difC'][1]/xpos
560	else:
561	data[1][lineNo] = xpos
562	G2frame.PatternTree.SetItemPyData(LimitId,data)
563	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
564	G2pdG.UpdateLimitsGrid(G2frame,data)
565	else:
566	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
567	data = G2frame.PatternTree.GetItemPyData(PeakId)
568	# print 'peaks',xpos
569	if event.button == 3:
570	del data[lineNo-2]
571	else:
572	if G2frame.qPlot:
573	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
574	else:
575	data[lineNo-2][0] = xpos
576	G2frame.PatternTree.SetItemPyData(PeakId,data)
577	G2pdG.UpdatePeakGrid(G2frame,data)
578	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
579	'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos:
580	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
581	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
582	if 'line' not in pick: #avoid data points, etc.
583	num = Phases.keys().index(pick)
584	if num:
585	G2frame.refDelt = -(event.ydata-G2frame.refOffset)/(num*Ymax)
586	else: #1st row of refl ticks
587	G2frame.refOffset = event.ydata
588	PlotPatterns(G2frame)
589	G2frame.itemPicked = None
590
591	xylim = []
592	try:
593	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
594	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
595	if not newPlot:
596	Plot = Page.figure.gca() #get previous powder plot & get limits
597	xylim = Plot.get_xlim(),Plot.get_ylim()
598	Page.figure.clf()
599	Plot = Page.figure.gca() #get a fresh plot after clf()
600	except ValueError:
601	newPlot = True
602	G2frame.Cmax = 1.0
603	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
604	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
605	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
606	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
607	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
608	Page.canvas.mpl_connect('pick_event', OnPick)
609	Page.canvas.mpl_connect('button_release_event', OnRelease)
610	Page.SetFocus()
611	G2frame.G2plotNB.status.DestroyChildren()
612	if G2frame.Contour:
613	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
614	'i: interpolation method','s: color scheme','c: contour off')
615	else:
616	if G2frame.logPlot:
617	Page.Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
618	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
619	else:
620	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down',
621	'u: offset up','o: reset offset','b: toggle subtract background','n: log(I) on','c: contour on',
622	'q: toggle q plot','s: toggle single plot','w: toggle divide by sig','+: no selection')
623	Page.keyPress = OnPlotKeyPress
624
625	PickId = G2frame.PickId
626	PatternId = G2frame.PatternId
627	colors=['b','g','r','c','m','k']
628	Lines = []
629	if G2frame.SinglePlot:
630	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
631	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
632	PlotList = [Pattern,]
633	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
634	G2frame.PatternId, 'Instrument Parameters'))
635	ParmList = [Parms,]
636	else:
637	PlotList = []
638	ParmList = []
639	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
640	while item:
641	if 'PWDR' in G2frame.PatternTree.GetItemText(item):
642	Pattern = G2frame.PatternTree.GetItemPyData(item)
643	if len(Pattern) < 3: # put name on end if needed
644	Pattern.append(G2frame.PatternTree.GetItemText(item))
645	PlotList.append(Pattern)
646	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
647	item,'Instrument Parameters'))[0])
648	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
649	Ymax = 1.0
650	lenX = 0
651	if PickId:
652	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
653	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
654	HKL = []
655	if Phases:
656	for peak in Phases[G2frame.RefList]:
657	HKL.append(peak[:6])
658	HKL = np.array(HKL)
659	else:
660	HKL = np.array(G2frame.HKL)
661	for Pattern in PlotList:
662	xye = Pattern[1]
663	Ymax = max(Ymax,max(xye[1]))
664	offset = G2frame.Offset[0]*Ymax/100.0
665	Title = 'Powder Patterns: '+os.path.split(G2frame.GSASprojectfile)[1]
666	if G2frame.logPlot:
667	Title = 'log('+Title+')'
668	Plot.set_title(Title)
669	if G2frame.qPlot:
670	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
671	else:
672	if 'C' in ParmList[0]['Type'][0]:
673	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
674	else:
675	Plot.set_xlabel(r'TOF, $\mathsf{\mu}$s',fontsize=14)
676	if G2frame.Weight:
677	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=14)
678	else:
679	if 'C' in ParmList[0]['Type'][0]:
680	Plot.set_ylabel('Intensity',fontsize=14)
681	else:
682	Plot.set_ylabel('Normalized intensity',fontsize=14)
683	if G2frame.Contour:
684	ContourZ = []
685	ContourY = []
686	Nseq = 0
687	if len(PlotList) < 2:
688	G2frame.Contour = False
689	for N,Pattern in enumerate(PlotList):
690	Parms = ParmList[N]
691	if 'C' in Parms['Type'][0]:
692	wave = G2mth.getWave(Parms)
693	else:
694	difC = Parms['difC'][1]
695	ifpicked = False
696	LimitId = 0
697	xye = np.array(Pattern[1])
698	if PickId:
699	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
700	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
701	if G2frame.qPlot:
702	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
703	if 'C' in Parms['Type'][0]:
704	X = 4np.pinpsind((xye[0]-Parms['Zero'][1])/2.0)/wave
705	else:
706	X = 2np.piParms['difC'][1]/(xye[0]-Parms['Zero'][1])
707	else:
708	X = xye[0]-Parms['Zero'][1]
709	if not lenX:
710	lenX = len(X)
711	Y = xye[1]+offset*N
712	if LimitId:
713	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
714	if G2frame.qPlot:
715	if 'C' in Parms['Type'][0]:
716	limits = 4np.pinpsind(limits/2.0)/wave
717	else:
718	limits = 2np.pidifC/limits
719	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
720	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
721	if G2frame.Contour:
722
723	if lenX == len(X):
724	ContourY.append(N)
725	ContourZ.append(Y)
726	ContourX = X
727	Nseq += 1
728	Plot.set_ylabel('Data sequence',fontsize=12)
729	else:
730	X += G2frame.Offset[1].005N
731	if ifpicked:
732	Z = xye[3]+offset*N
733	W = xye[4]+offset*N
734	D = xye[5]-Ymax*G2frame.delOffset
735	if G2frame.logPlot:
736	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
737	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
738	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
739	elif G2frame.Weight:
740	DY = xye[1]*np.sqrt(xye[2])
741	DYmax = max(DY)
742	DZ = xye[3]*np.sqrt(xye[2])
743	DS = xye[5]np.sqrt(xye[2])-DYmaxG2frame.delOffset
744	Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False)
745	Plot.plot(X,DZ,colors[(N+1)%6],picker=False)
746	Plot.plot(X,DS,colors[(N+3)%6],picker=False)
747	Plot.axhline(0.,color=wx.BLACK)
748	else:
749	if G2frame.SubBack:
750	Plot.plot(X,Y-W,colors[N%6]+'+',picker=3.,clip_on=False)
751	Plot.plot(X,Z-W,colors[(N+1)%6],picker=False)
752	else:
753	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
754	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
755	Plot.plot(X,W,colors[(N+2)%6],picker=False)
756	Plot.plot(X,D,colors[(N+3)%6],picker=False)
757	Plot.axhline(0.,color=wx.BLACK)
758	Page.canvas.SetToolTipString('')
759	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
760	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
761	Page.canvas.SetToolTipString(tip)
762	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
763	for item in data:
764	if G2frame.qPlot:
765	if 'C' in Parms['Type'][0]:
766	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/wave,color=colors[N%6],picker=2.))
767	else:
768	Lines.append(Plot.axvline(2math.pidifC/item[0],color=colors[N%6],picker=2.))
769	else:
770	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
771	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
772	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
773	Page.canvas.SetToolTipString(tip)
774	data = G2frame.LimitsTable.GetData()
775	else:
776	if G2frame.logPlot:
777	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
778	else:
779	Plot.plot(X,Y,colors[N%6],picker=False)
780	if PickId and not G2frame.Contour:
781	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
782	if 'C' in Parms['Type'][0]:
783	wave = G2mth.getWave(Parms)
784	else:
785	difC = Parms['difC'][1]
786	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
787	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
788	for peak in peaks:
789	if G2frame.qPlot:
790	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
791	else:
792	Plot.axvline(peak[0],color='b')
793	for hkl in G2frame.HKL:
794	if G2frame.qPlot:
795	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
796	else:
797	Plot.axvline(hkl[5],color='r',dashes=(5,5))
798	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
799	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
800	refColors=['b','r','c','g','m','k']
801	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
802	for pId,phase in enumerate(Phases):
803	peaks = Phases[phase]
804	if not peaks:
805	continue
806	peak = np.array([[peak[4],peak[5]] for peak in peaks])
807	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
808	if G2frame.qPlot:
809	Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
810	else:
811	Plot.plot(peak.T[1],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
812	if len(Phases):
813	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
814	if handles:
815	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
816
817	if G2frame.Contour:
818	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
819	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
820	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
821	Page.figure.colorbar(Img)
822	else:
823	G2frame.Lines = Lines
824	if not newPlot:
825	Page.toolbar.push_current()
826	Plot.set_xlim(xylim[0])
827	Plot.set_ylim(xylim[1])
828	xylim = []
829	Page.toolbar.push_current()
830	Page.toolbar.draw()
831	else:
832	Page.canvas.draw()
833	# G2frame.Pwdr = True
834
835	################################################################################
836	##### PlotDeltSig
837	################################################################################
838
839	def PlotDeltSig(G2frame,kind):
840	try:
841	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
842	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
843	Page.figure.clf()
844	Plot = Page.figure.gca() #get a fresh plot after clf()
845	except ValueError:
846	newPlot = True
847	G2frame.Cmax = 1.0
848	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
849	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
850	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
851	Page.Choice = None
852	PatternId = G2frame.PatternId
853	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
854	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
855	wtFactor = Pattern[0]['wtFactor']
856	if kind == 'PWDR':
857	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
858	xye = np.array(Pattern[1])
859	xmin = np.searchsorted(xye[0],limits[0])
860	xmax = np.searchsorted(xye[0],limits[1])
861	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
862	elif kind == 'HKLF':
863	refl = Pattern[1]
864	DS = []
865	for ref in refl:
866	if ref[6] > 0.:
867	DS.append((ref[5]-ref[7])/ref[6])
868	Page.SetFocus()
869	G2frame.G2plotNB.status.DestroyChildren()
870	DS.sort()
871	EDS = np.zeros_like(DS)
872	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
873	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
874	T = np.sqrt(np.log(1.0/DX**2))
875	top = 2.515517+0.802853T+0.010328T**2
876	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
877	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
878	low1 = np.searchsorted(EDS,-1.)
879	hi1 = np.searchsorted(EDS,1.)
880	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
881	frac = 100.*(hi1-low1)/len(DS)
882	G2frame.G2plotNB.status.SetStatusText( \
883	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
884	Plot.set_title('Normal probability for '+Pattern[-1])
885	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
886	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
887	Plot.plot(EDS,DS,'r+',label='result')
888	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
889	Plot.legend(loc='upper left')
890	np.seterr(invalid='warn')
891	Page.canvas.draw()
892
893	################################################################################
894	##### PlotISFG
895	################################################################################
896
897	def PlotISFG(G2frame,newPlot=False,type=''):
898	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
899	or multiple plots with waterfall and contour plots as options
900	'''
901	if not type:
902	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
903	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
904	return
905	superMinusOne = unichr(0xaf)+unichr(0xb9)
906
907	def OnPlotKeyPress(event):
908	newPlot = False
909	if event.key == 'u':
910	if G2frame.Contour:
911	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
912	elif G2frame.Offset[0] < 100.:
913	G2frame.Offset[0] += 1.
914	elif event.key == 'd':
915	if G2frame.Contour:
916	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
917	elif G2frame.Offset[0] > 0.:
918	G2frame.Offset[0] -= 1.
919	elif event.key == 'l':
920	G2frame.Offset[1] -= 1.
921	elif event.key == 'r':
922	G2frame.Offset[1] += 1.
923	elif event.key == 'o':
924	G2frame.Offset = [0,0]
925	elif event.key == 'c':
926	newPlot = True
927	if G2frame.Contour:
928	G2frame.Contour = False
929	else:
930	G2frame.Contour = True
931	G2frame.SinglePlot = False
932	G2frame.Offset = [0.,0.]
933	elif event.key == 's':
934	if G2frame.Contour:
935	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
936	choice.sort()
937	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
938	if dlg.ShowModal() == wx.ID_OK:
939	sel = dlg.GetSelection()
940	G2frame.ContourColor = choice[sel]
941	else:
942	G2frame.ContourColor = 'Paired'
943	dlg.Destroy()
944	else:
945	if G2frame.SinglePlot:
946	G2frame.SinglePlot = False
947	else:
948	G2frame.SinglePlot = True
949	elif event.key == 'i': #for smoothing contour plot
950	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
951	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
952	'mitchell','sinc','lanczos']
953	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
954	if dlg.ShowModal() == wx.ID_OK:
955	sel = dlg.GetSelection()
956	G2frame.Interpolate = choice[sel]
957	else:
958	G2frame.Interpolate = 'nearest'
959	dlg.Destroy()
960	elif event.key == 't' and not G2frame.Contour:
961	if G2frame.Legend:
962	G2frame.Legend = False
963	else:
964	G2frame.Legend = True
965
966
967	PlotISFG(G2frame,newPlot=newPlot,type=type)
968
969	def OnKeyBox(event):
970	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
971	event.key = cb.GetValue()[0]
972	cb.SetValue(' key press')
973	wx.CallAfter(OnPlotKeyPress,event)
974
975	def OnMotion(event):
976	xpos = event.xdata
977	if xpos: #avoid out of frame mouse position
978	ypos = event.ydata
979	Page.canvas.SetCursor(wx.CROSS_CURSOR)
980	try:
981	if G2frame.Contour:
982	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
983	else:
984	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
985	except TypeError:
986	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
987
988	xylim = []
989	try:
990	plotNum = G2frame.G2plotNB.plotList.index(type)
991	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
992	if not newPlot:
993	Plot = Page.figure.gca() #get previous plot & get limits
994	xylim = Plot.get_xlim(),Plot.get_ylim()
995	Page.figure.clf()
996	Plot = Page.figure.gca()
997	except ValueError:
998	newPlot = True
999	G2frame.Cmax = 1.0
1000	Plot = G2frame.G2plotNB.addMpl(type).gca()
1001	plotNum = G2frame.G2plotNB.plotList.index(type)
1002	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1003	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1004	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1005
1006	Page.SetFocus()
1007	G2frame.G2plotNB.status.DestroyChildren()
1008	if G2frame.Contour:
1009	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
1010	'i: interpolation method','s: color scheme','c: contour off')
1011	else:
1012	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
1013	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
1014	Page.keyPress = OnPlotKeyPress
1015	PatternId = G2frame.PatternId
1016	PickId = G2frame.PickId
1017	Plot.set_title(type)
1018	if type == 'G(R)':
1019	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
1020	else:
1021	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
1022	Plot.set_ylabel(r''+type,fontsize=14)
1023	colors=['b','g','r','c','m','k']
1024	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
1025	Pattern = []
1026	if G2frame.SinglePlot:
1027	name = G2frame.PatternTree.GetItemText(PatternId)
1028	name = type+name[4:]
1029	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
1030	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1031	if Pattern:
1032	Pattern.append(name)
1033	PlotList = [Pattern,]
1034	else:
1035	PlotList = []
1036	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1037	while item:
1038	if 'PDF' in G2frame.PatternTree.GetItemText(item):
1039	name = type+G2frame.PatternTree.GetItemText(item)[4:]
1040	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
1041	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1042	if Pattern:
1043	Pattern.append(name)
1044	PlotList.append(Pattern)
1045	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1046	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
1047	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
1048	Xb = [0.,10.]
1049	Yb = [0.,-40.np.pinumbDen]
1050	Ymax = 1.0
1051	lenX = 0
1052	for Pattern in PlotList:
1053	xye = Pattern[1]
1054	Ymax = max(Ymax,max(xye[1]))
1055	offset = G2frame.Offset[0]*Ymax/100.0
1056	if G2frame.Contour:
1057	ContourZ = []
1058	ContourY = []
1059	Nseq = 0
1060	for N,Pattern in enumerate(PlotList):
1061	xye = Pattern[1]
1062	if PickId:
1063	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1064	X = xye[0]
1065	if not lenX:
1066	lenX = len(X)
1067	Y = xye[1]+offset*N
1068	if G2frame.Contour:
1069	if lenX == len(X):
1070	ContourY.append(N)
1071	ContourZ.append(Y)
1072	ContourX = X
1073	Nseq += 1
1074	Plot.set_ylabel('Data sequence',fontsize=12)
1075	else:
1076	X = xye[0]+G2frame.Offset[1].005N
1077	if ifpicked:
1078	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1079	Page.canvas.SetToolTipString('')
1080	else:
1081	if G2frame.Legend:
1082	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1083	else:
1084	Plot.plot(X,Y,colors[N%6],picker=False)
1085	if type == 'G(R)':
1086	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1087	elif type == 'F(Q)':
1088	Plot.axhline(0.,color=wx.BLACK)
1089	elif type == 'S(Q)':
1090	Plot.axhline(1.,color=wx.BLACK)
1091	if G2frame.Contour:
1092	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1093	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1094	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1095	Page.figure.colorbar(Img)
1096	elif G2frame.Legend:
1097	Plot.legend(loc='best')
1098	if not newPlot:
1099	Page.toolbar.push_current()
1100	Plot.set_xlim(xylim[0])
1101	Plot.set_ylim(xylim[1])
1102	xylim = []
1103	Page.toolbar.push_current()
1104	Page.toolbar.draw()
1105	else:
1106	Page.canvas.draw()
1107
1108	################################################################################
1109	##### PlotXY
1110	################################################################################
1111
1112	def PlotXY(G2frame,XY,newPlot=False,type=''):
1113	'''simple plot of xy data, used for diagnostic purposes
1114	'''
1115	def OnMotion(event):
1116	xpos = event.xdata
1117	if xpos: #avoid out of frame mouse position
1118	ypos = event.ydata
1119	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1120	try:
1121	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
1122	except TypeError:
1123	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1124
1125	try:
1126	plotNum = G2frame.G2plotNB.plotList.index(type)
1127	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1128	if not newPlot:
1129	Plot = Page.figure.gca()
1130	xylim = Plot.get_xlim(),Plot.get_ylim()
1131	Page.figure.clf()
1132	Plot = Page.figure.gca()
1133	except ValueError:
1134	newPlot = True
1135	Plot = G2frame.G2plotNB.addMpl(type).gca()
1136	plotNum = G2frame.G2plotNB.plotList.index(type)
1137	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1138	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1139
1140	Page.Choice = None
1141	Page.SetFocus()
1142	G2frame.G2plotNB.status.DestroyChildren()
1143	Plot.set_title(type)
1144	Plot.set_xlabel(r'X',fontsize=14)
1145	Plot.set_ylabel(r''+type,fontsize=14)
1146	colors=['b','g','r','c','m','k']
1147	Ymax = 1.0
1148	lenX = 0
1149	X,Y = XY[:2]
1150	Ymax = max(Ymax,max(Y))
1151	Plot.plot(X,Y,'k',picker=False)
1152	if not newPlot:
1153	Page.toolbar.push_current()
1154	Plot.set_xlim(xylim[0])
1155	Plot.set_ylim(xylim[1])
1156	xylim = []
1157	Page.toolbar.push_current()
1158	Page.toolbar.draw()
1159	else:
1160	Page.canvas.draw()
1161
1162	################################################################################
1163	##### PlotPowderLines
1164	################################################################################
1165
1166	def PlotPowderLines(G2frame):
1167	''' plotting of powder lines (i.e. no powder pattern) as sticks
1168	'''
1169	global HKL
1170
1171	def OnMotion(event):
1172	xpos = event.xdata
1173	if xpos: #avoid out of frame mouse position
1174	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1175	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1176	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
1177	found = []
1178	if len(HKL):
1179	view = Page.toolbar._views.forward()[0][:2]
1180	wid = view[1]-view[0]
1181	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1182	if len(found):
1183	h,k,l = found[0][:3]
1184	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1185	else:
1186	Page.canvas.SetToolTipString('')
1187
1188	try:
1189	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1190	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1191	Page.figure.clf()
1192	Plot = Page.figure.gca()
1193	except ValueError:
1194	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
1195	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1196	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1197	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1198
1199	Page.Choice = None
1200	Page.SetFocus()
1201	Plot.set_title('Powder Pattern Lines')
1202	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1203	PickId = G2frame.PickId
1204	PatternId = G2frame.PatternId
1205	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
1206	for peak in peaks:
1207	Plot.axvline(peak[0],color='b')
1208	HKL = np.array(G2frame.HKL)
1209	for hkl in G2frame.HKL:
1210	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1211	xmin = peaks[0][0]
1212	xmax = peaks[-1][0]
1213	delt = xmax-xmin
1214	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1215	Plot.set_xlim(xlim)
1216	Page.canvas.draw()
1217	Page.toolbar.push_current()
1218
1219	################################################################################
1220	##### PlotPeakWidths
1221	################################################################################
1222
1223	def PlotPeakWidths(G2frame):
1224	''' Plotting of instrument broadening terms as function of 2-theta
1225	Seen when "Instrument Parameters" chosen from powder pattern data tree
1226	'''
1227	# sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1228	# gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1229	gamFW = lambda s,g: np.exp(np.log(s*5+2.69269s*4g+2.42843s3g*2+4.47163s*2g*3+0.07842sg4+g*5)/5.)
1230	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1231	PatternId = G2frame.PatternId
1232	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1233	if limitID:
1234	limits = G2frame.PatternTree.GetItemPyData(limitID)
1235	else:
1236	return
1237	Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \
1238	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1239	if 'C' in Parms['Type'][0]:
1240	lam = G2mth.getWave(Parms)
1241	else:
1242	difC = Parms['difC'][0]
1243	peakID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
1244	if peakID:
1245	peaks = G2frame.PatternTree.GetItemPyData(peakID)
1246	else:
1247	peaks = []
1248
1249	try:
1250	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1251	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1252	Page.figure.clf()
1253	Plot = Page.figure.gca()
1254	except ValueError:
1255	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
1256	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1257	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1258	Page.Choice = None
1259	Page.SetFocus()
1260
1261	Page.canvas.SetToolTipString('')
1262	colors=['b','g','r','c','m','k']
1263	X = []
1264	Y = []
1265	Z = []
1266	W = []
1267	if 'C' in Parms['Type'][0]:
1268	Plot.set_title('Instrument and sample peak widths')
1269	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1270	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1271	try:
1272	Xmin,Xmax = limits[1]
1273	Xmin = min(0.5,max(Xmin,1))
1274	X = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1275	Q = 4.np.pinpsind(X/2.)/lam
1276	Z = np.ones_like(X)
1277	data = G2mth.setPeakparms(Parms,Parms2,X,Z)
1278	s = 1.17741np.sqrt(data[4])np.pi/18000.
1279	g = data[6]*np.pi/18000.
1280	G = gamFW(g,s)
1281	Y = s/nptand(X/2.)
1282	Z = g/nptand(X/2.)
1283	W = G/nptand(X/2.)
1284	Plot.plot(Q,Y,color='r',label='Gaussian')
1285	Plot.plot(Q,Z,color='g',label='Lorentzian')
1286	Plot.plot(Q,W,color='b',label='G+L')
1287
1288	fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True)
1289	sf = 1.17741np.sqrt(fit[4])np.pi/18000.
1290	gf = fit[6]*np.pi/18000.
1291	Gf = gamFW(gf,sf)
1292	Yf = sf/nptand(X/2.)
1293	Zf = gf/nptand(X/2.)
1294	Wf = Gf/nptand(X/2.)
1295	Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit')
1296	Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit')
1297	Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
1298
1299	X = []
1300	Y = []
1301	Z = []
1302	W = []
1303	V = []
1304	for peak in peaks:
1305	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1306	try:
1307	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1308	except ValueError:
1309	s = 0.01
1310	g = peak[6]*math.pi/18000.
1311	G = gamFW(g,s)
1312	Y.append(s/tand(peak[0]/2.))
1313	Z.append(g/tand(peak[0]/2.))
1314	W.append(G/tand(peak[0]/2.))
1315	if len(peaks):
1316	Plot.plot(X,Y,'+',color='r',label='G peak')
1317	Plot.plot(X,Z,'+',color='g',label='L peak')
1318	Plot.plot(X,W,'+',color='b',label='G+L peak')
1319	Plot.legend(loc='best')
1320	Page.canvas.draw()
1321	except ValueError:
1322	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
1323	'%.3f'%(2*theta)
1324	G2frame.G2plotNB.Delete('Peak Widths')
1325	else:
1326	Plot.set_title('Instrument and sample peak coefficients')
1327	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1328	Plot.set_ylabel(r'$\alpha, \beta, \Delta q/q, \Delta d/d$',fontsize=14)
1329	Xmin,Xmax = limits[1]
1330	T = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1331	Z = np.ones_like(T)
1332	data = G2mth.setPeakparms(Parms,Parms2,T,Z)
1333	ds = T/difC
1334	Q = 2.*np.pi/ds
1335	A = data[4]
1336	B = data[6]
1337	S = 1.17741*np.sqrt(data[8])/T
1338	G = data[10]/T
1339	Plot.plot(Q,A,color='r',label='Alpha')
1340	Plot.plot(Q,B,color='g',label='Beta')
1341	Plot.plot(Q,S,color='b',label='Gaussian')
1342	Plot.plot(Q,G,color='m',label='Lorentzian')
1343
1344	fit = G2mth.setPeakparms(Parms,Parms2,T,Z)
1345	ds = T/difC
1346	Q = 2.*np.pi/ds
1347	Af = fit[4]
1348	Bf = fit[6]
1349	Sf = 1.17741*np.sqrt(fit[8])/T
1350	Gf = fit[10]/T
1351	Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit')
1352	Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit')
1353	Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit')
1354	Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit')
1355
1356	T = []
1357	A = []
1358	B = []
1359	S = []
1360	G = []
1361	W = []
1362	Q = []
1363	V = []
1364	for peak in peaks:
1365	T.append(peak[0])
1366	A.append(peak[4])
1367	B.append(peak[6])
1368	Q.append(2.np.pidifC/peak[0])
1369	S.append(1.17741*np.sqrt(peak[8])/peak[0])
1370	G.append(peak[10]/peak[0])
1371
1372
1373	Plot.plot(Q,A,'+',color='r',label='Alpha peak')
1374	Plot.plot(Q,B,'+',color='g',label='Beta peak')
1375	Plot.plot(Q,S,'+',color='b',label='Gaussian peak')
1376	Plot.plot(Q,G,'+',color='m',label='Lorentzian peak')
1377	Plot.legend(loc='best')
1378	Page.canvas.draw()
1379
1380
1381	################################################################################
1382	##### PlotSizeStrainPO
1383	################################################################################
1384
1385	def PlotSizeStrainPO(G2frame,data,Start=False):
1386	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1387	'''
1388
1389	PatternId = G2frame.PatternId
1390	generalData = data['General']
1391	SGData = generalData['SGData']
1392	SGLaue = SGData['SGLaue']
1393	if Start: #initialize the spherical harmonics qlmn arrays
1394	ptx.pyqlmninit()
1395	Start = False
1396	# MuStrKeys = G2spc.MustrainNames(SGData)
1397	cell = generalData['Cell'][1:]
1398	A,B = G2lat.cell2AB(cell[:6])
1399	Vol = cell[6]
1400	useList = data['Histograms']
1401	phase = generalData['Name']
1402	plotType = generalData['Data plot type']
1403	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
1404	for ptype in plotDict:
1405	G2frame.G2plotNB.Delete(ptype)
1406	if plotType in ['None']:
1407	return
1408
1409	for item in useList:
1410	if useList[item]['Show']:
1411	break
1412	else:
1413	return #nothing to show!!
1414
1415	numPlots = len(useList)
1416
1417	if plotType in ['Mustrain','Size']:
1418	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
1419	else:
1420	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
1421	plotNum = G2frame.G2plotNB.plotList.index(plotType)
1422	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1423	Page.Choice = None
1424	Page.SetFocus()
1425	G2frame.G2plotNB.status.SetStatusText('',1)
1426	if not Page.IsShown():
1427	Page.Show()
1428
1429	for item in useList:
1430	if useList[item]['Show']:
1431	PHI = np.linspace(0.,360.,30,True)
1432	PSI = np.linspace(0.,180.,30,True)
1433	X = np.outer(npsind(PHI),npsind(PSI))
1434	Y = np.outer(npcosd(PHI),npsind(PSI))
1435	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1436	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
1437	coeff = useList[item][plotDict[plotType]]
1438	except KeyError:
1439	break
1440	if plotType in ['Mustrain','Size']:
1441	if coeff[0] == 'isotropic':
1442	X *= coeff[1][0]
1443	Y *= coeff[1][0]
1444	Z *= coeff[1][0]
1445	elif coeff[0] == 'uniaxial':
1446
1447	def uniaxCalc(xyz,iso,aniso,axes):
1448	Z = np.array(axes)
1449	cp = abs(np.dot(xyz,Z))
1450	sp = np.sqrt(1.-cp**2)
1451	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
1452	return R*xyz
1453
1454	iso,aniso = coeff[1][:2]
1455	axes = np.inner(A,np.array(coeff[3]))
1456	axes /= nl.norm(axes)
1457	Shkl = np.array(coeff[1])
1458	XYZ = np.dstack((X,Y,Z))
1459	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
1460	X,Y,Z = np.dsplit(XYZ,3)
1461	X = X[:,:,0]
1462	Y = Y[:,:,0]
1463	Z = Z[:,:,0]
1464
1465	elif coeff[0] == 'ellipsoidal':
1466
1467	def ellipseCalc(xyz,E,R):
1468	XYZ = xyz*E.T
1469	return np.inner(XYZ.T,R)
1470
1471	S6 = coeff[4]
1472	Sij = G2lat.U6toUij(S6)
1473	E,R = nl.eigh(Sij)
1474	XYZ = np.dstack((X,Y,Z))
1475	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
1476	X,Y,Z = np.dsplit(XYZ,3)
1477	X = X[:,:,0]
1478	Y = Y[:,:,0]
1479	Z = Z[:,:,0]
1480
1481	elif coeff[0] == 'generalized':
1482
1483	def genMustrain(xyz,SGData,A,Shkl):
1484	uvw = np.inner(A.T,xyz)
1485	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1486	sum = np.sum(np.multiply(Shkl,Strm))
1487	sum = np.where(sum > 0.01,sum,0.01)
1488	sum = np.sqrt(sum)*math.pi/0.018 #centidegrees to radians!
1489	return sum*xyz
1490
1491	Shkl = np.array(coeff[4])
1492	if np.any(Shkl):
1493	XYZ = np.dstack((X,Y,Z))
1494	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1495	X,Y,Z = np.dsplit(XYZ,3)
1496	X = X[:,:,0]
1497	Y = Y[:,:,0]
1498	Z = Z[:,:,0]
1499
1500	if np.any(X) and np.any(Y) and np.any(Z):
1501	errFlags = np.seterr(all='ignore')
1502	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1503	np.seterr(all='ignore')
1504	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
1505	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
1506	Plot.set_xlim3d(XYZlim)
1507	Plot.set_ylim3d(XYZlim)
1508	Plot.set_zlim3d(XYZlim)
1509	Plot.set_aspect('equal')
1510	if plotType == 'Size':
1511	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
1512	Plot.set_xlabel(r'X, $\mu$m')
1513	Plot.set_ylabel(r'Y, $\mu$m')
1514	Plot.set_zlabel(r'Z, $\mu$m')
1515	else:
1516	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
1517	Plot.set_xlabel(r'X, $\mu$strain')
1518	Plot.set_ylabel(r'Y, $\mu$strain')
1519	Plot.set_zlabel(r'Z, $\mu$strain')
1520	else:
1521	h,k,l = generalData['POhkl']
1522	if coeff[0] == 'MD':
1523	print 'March-Dollase preferred orientation plot'
1524
1525	else:
1526	PH = np.array(generalData['POhkl'])
1527	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
1528	SHCoef = {}
1529	for item in coeff[5]:
1530	L,N = eval(item.strip('C'))
1531	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
1532	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1533	X = np.linspace(0,90.0,26)
1534	Y = G2lat.polfcal(ODFln,'0',X,0.0)
1535	Plot.plot(X,Y,color='k',label=str(PH))
1536	Plot.legend(loc='best')
1537	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
1538	Plot.set_xlabel(r'$\psi$',fontsize=16)
1539	Plot.set_ylabel('MRD',fontsize=14)
1540	Page.canvas.draw()
1541
1542	################################################################################
1543	##### PlotTexture
1544	################################################################################
1545
1546	def PlotTexture(G2frame,data,Start=False):
1547	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
1548	plotting.
1549	dict generalData contains all phase info needed which is in data
1550	'''
1551
1552	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1553	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1554	PatternId = G2frame.PatternId
1555	generalData = data['General']
1556	SGData = generalData['SGData']
1557	textureData = generalData['SH Texture']
1558	G2frame.G2plotNB.Delete('Texture')
1559	if not textureData['Order']:
1560	return #no plot!!
1561	SHData = generalData['SH Texture']
1562	SHCoef = SHData['SH Coeff'][1]
1563	cell = generalData['Cell'][1:7]
1564	Amat,Bmat = G2lat.cell2AB(cell)
1565	sq2 = 1.0/math.sqrt(2.0)
1566
1567	def rp2xyz(r,p):
1568	z = npcosd(r)
1569	xy = np.sqrt(1.-z**2)
1570	return xynpsind(p),xynpcosd(p),z
1571
1572	def OnMotion(event):
1573	SHData = data['General']['SH Texture']
1574	if event.xdata and event.ydata: #avoid out of frame errors
1575	xpos = event.xdata
1576	ypos = event.ydata
1577	if 'Inverse' in SHData['PlotType']:
1578	r = xpos2+ypos2
1579	if r <= 1.0:
1580	if 'equal' in G2frame.Projection:
1581	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1582	else:
1583	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1584	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1585	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1586	y,x,z = list(xyz/np.max(np.abs(xyz)))
1587
1588	G2frame.G2plotNB.status.SetFields(['',
1589	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1590
1591	elif 'Axial' in SHData['PlotType']:
1592	pass
1593
1594	else: #ordinary pole figure
1595	z = xpos2+ypos2
1596	if z <= 1.0:
1597	z = np.sqrt(z)
1598	if 'equal' in G2frame.Projection:
1599	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1600	else:
1601	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1602	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1603	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1604
1605	try:
1606	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1607	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1608	Page.figure.clf()
1609	Plot = Page.figure.gca()
1610	if not Page.IsShown():
1611	Page.Show()
1612	except ValueError:
1613	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
1614	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1615	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1616	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1617
1618	Page.Choice = None
1619	Page.SetFocus()
1620	G2frame.G2plotNB.status.SetFields(['',''])
1621	PH = np.array(SHData['PFhkl'])
1622	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1623	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1624	PX = np.array(SHData['PFxyz'])
1625	gam = atan2d(PX[0],PX[1])
1626	xy = math.sqrt(PX[0]2+PX[1]2)
1627	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1628	psi = asind(xy/xyz)
1629	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1630	if 'Axial' in SHData['PlotType']:
1631	X = np.linspace(0,90.0,26)
1632	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1633	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1634	Plot.legend(loc='best')
1635	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1636	Plot.set_xlabel(r'$\psi$',fontsize=16)
1637	Plot.set_ylabel('MRD',fontsize=14)
1638
1639	else:
1640	npts = 201
1641	if 'Inverse' in SHData['PlotType']:
1642	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1643	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1644	if 'equal' in G2frame.Projection:
1645	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1646	else:
1647	R = np.where(R <= 1.,2.*npatand(R),0.0)
1648	Z = np.zeros_like(R)
1649	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
1650	Z = np.reshape(Z,(npts,npts))
1651	CS = Plot.contour(Y,X,Z,aspect='equal')
1652	Plot.clabel(CS,fontsize=9,inline=1)
1653	try:
1654	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
1655	except ValueError:
1656	pass
1657	Page.figure.colorbar(Img)
1658	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
1659	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
1660
1661	else:
1662	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1663	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1664	if 'equal' in G2frame.Projection:
1665	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1666	else:
1667	R = np.where(R <= 1.,2.*npatand(R),0.0)
1668	Z = np.zeros_like(R)
1669	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
1670	Z = np.reshape(Z,(npts,npts))
1671	try:
1672	CS = Plot.contour(Y,X,Z,aspect='equal')
1673	Plot.clabel(CS,fontsize=9,inline=1)
1674	except ValueError:
1675	pass
1676	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
1677	Page.figure.colorbar(Img)
1678	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
1679	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
1680	Page.canvas.draw()
1681
1682	################################################################################
1683	##### PlotCovariance
1684	################################################################################
1685
1686	def PlotCovariance(G2frame,Data={}):
1687	if not Data:
1688	Data = G2frame.PatternTree.GetItemPyData(
1689	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1690	if not Data:
1691	print 'No covariance matrix available'
1692	return
1693	varyList = Data['varyList']
1694	values = Data['variables']
1695	Xmax = len(varyList)
1696	covMatrix = Data['covMatrix']
1697	sig = np.sqrt(np.diag(covMatrix))
1698	xvar = np.outer(sig,np.ones_like(sig))
1699	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
1700	title = ' for\n'+Data['title']
1701	newAtomDict = Data['newAtomDict']
1702
1703	def OnPlotKeyPress(event):
1704	newPlot = False
1705	if event.key == 's':
1706	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1707	choice.sort()
1708	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1709	if dlg.ShowModal() == wx.ID_OK:
1710	sel = dlg.GetSelection()
1711	G2frame.VcovColor = choice[sel]
1712	else:
1713	G2frame.VcovColor = 'RdYlGn'
1714	dlg.Destroy()
1715	PlotCovariance(G2frame)
1716
1717	def OnMotion(event):
1718	if event.button:
1719	ytics = imgAx.get_yticks()
1720	ytics = np.where(ytics<len(varyList),ytics,-1)
1721	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
1722	imgAx.set_yticklabels(ylabs)
1723
1724	if event.xdata and event.ydata: #avoid out of frame errors
1725	xpos = int(event.xdata+.5)
1726	ypos = int(event.ydata+.5)
1727	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
1728	if xpos == ypos:
1729	value = values[xpos]
1730	name = varyList[xpos]
1731	if varyList[xpos] in newAtomDict:
1732	name,value = newAtomDict[name]
1733	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
1734	else:
1735	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
1736	Page.canvas.SetToolTipString(msg)
1737	G2frame.G2plotNB.status.SetFields(['',msg])
1738	try:
1739	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1740	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1741	Page.figure.clf()
1742	Plot = Page.figure.gca()
1743	if not Page.IsShown():
1744	Page.Show()
1745	except ValueError:
1746	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
1747	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1748	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1749	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1750	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1751
1752	Page.Choice = ['s: to change colors']
1753	Page.keyPress = OnPlotKeyPress
1754	Page.SetFocus()
1755	G2frame.G2plotNB.status.SetFields(['',''])
1756	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
1757	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower')
1758	imgAx = Img.get_axes()
1759	ytics = imgAx.get_yticks()
1760	ylabs = [varyList[int(i)] for i in ytics[:-1]]
1761	imgAx.set_yticklabels(ylabs)
1762	colorBar = Page.figure.colorbar(Img)
1763	Plot.set_title('V-Cov matrix'+title)
1764	Plot.set_xlabel('Variable number')
1765	Plot.set_ylabel('Variable name')
1766	Page.canvas.draw()
1767
1768	################################################################################
1769	##### PlotSeq
1770	################################################################################
1771
1772	def PlotSeq(G2frame,SeqData,SeqSig,SeqNames,sampleParm):
1773
1774	def OnKeyPress(event):
1775	if event.key == 's' and sampleParm:
1776	if G2frame.xAxis:
1777	G2frame.xAxis = False
1778	else:
1779	G2frame.xAxis = True
1780	Draw(False)
1781	try:
1782	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1783	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1784	Page.figure.clf()
1785	Plot = Page.figure.gca()
1786	if not Page.IsShown():
1787	Page.Show()
1788	except ValueError:
1789	Plot = G2frame.G2plotNB.addMpl('Sequential refinement').gca()
1790	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1791	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1792	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
1793	G2frame.xAxis = False
1794	Page.Choice = ['s to toggle x-axis = sample environment parameter']
1795	Page.keyPress = OnKeyPress
1796
1797	def Draw(newPlot):
1798	Page.SetFocus()
1799	G2frame.G2plotNB.status.SetFields(['','press '])
1800	if len(SeqData):
1801	Plot.clear()
1802	if G2frame.xAxis:
1803	xName = sampleParm.keys()[0]
1804	X = sampleParm[xName]
1805	else:
1806	X = np.arange(0,len(SeqData[0]),1)
1807	xName = 'Data sequence number'
1808	for Y,sig,name in zip(SeqData,SeqSig,SeqNames):
1809	Plot.errorbar(X,Y,yerr=sig,label=name)
1810	Plot.legend(loc='best')
1811	Plot.set_ylabel('Parameter values')
1812	Plot.set_xlabel(xName)
1813	Page.canvas.draw()
1814	Draw(True)
1815
1816	################################################################################
1817	##### PlotExposedImage & PlotImage
1818	################################################################################
1819
1820	def PlotExposedImage(G2frame,newPlot=False,event=None):
1821	'''General access module for 2D image plotting
1822	'''
1823	plotNo = G2frame.G2plotNB.nb.GetSelection()
1824	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1825	PlotImage(G2frame,newPlot,event,newImage=True)
1826	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1827	PlotIntegration(G2frame,newPlot,event)
1828
1829	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
1830	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1831	masks, etc.
1832	'''
1833	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1834	import numpy.ma as ma
1835	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1836	global Data,Masks
1837	colors=['b','g','r','c','m','k']
1838	Data = G2frame.PatternTree.GetItemPyData(
1839	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
1840	Masks = G2frame.PatternTree.GetItemPyData(
1841	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
1842	try: #may be absent
1843	StrSta = G2frame.PatternTree.GetItemPyData(
1844	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
1845	except TypeError: #is missing
1846	StrSta = {}
1847
1848	def OnImMotion(event):
1849	Page.canvas.SetToolTipString('')
1850	sizexy = Data['size']
1851	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
1852	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1853	item = G2frame.itemPicked
1854	pixelSize = Data['pixelSize']
1855	scalex = 1000./pixelSize[0]
1856	scaley = 1000./pixelSize[1]
1857	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
1858	if 'Text' in str(item):
1859	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1860	else:
1861	xcent,ycent = Data['center']
1862	xpos = event.xdata-xcent
1863	ypos = event.ydata-ycent
1864	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1865	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1866	Page.canvas.SetToolTipString('%6d deg'%(azm))
1867	elif 'line1' in str(item) or 'line2' in str(item):
1868	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1869	else:
1870	xpos = event.xdata
1871	ypos = event.ydata
1872	xpix = xpos*scalex
1873	ypix = ypos*scaley
1874	Int = 0
1875	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1876	Int = G2frame.ImageZ[ypix][xpix]
1877	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1878	Q = 2.*math.pi/dsp
1879	if G2frame.setPoly:
1880	G2frame.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1881	else:
1882	G2frame.G2plotNB.status.SetFields(\
1883	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1884
1885	def OnImPlotKeyPress(event):
1886	try:
1887	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
1888	except TypeError:
1889	return
1890	if PickName == 'Masks':
1891	Xpos = event.xdata
1892	if not Xpos: #got point out of frame
1893	return
1894	Ypos = event.ydata
1895	if event.key == 's':
1896	Masks['Points'].append([Xpos,Ypos,1.])
1897	elif event.key == 'r':
1898	tth = G2img.GetTth(Xpos,Ypos,Data)
1899	Masks['Rings'].append([tth,0.1])
1900	elif event.key == 'a':
1901	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1902	azm = int(azm)
1903	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1904	elif event.key == 'p':
1905	G2frame.setPoly = True
1906	Masks['Polygons'].append([])
1907	G2frame.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1908	G2imG.UpdateMasks(G2frame,Masks)
1909	elif PickName == 'Image Controls':
1910	if event.key == 'c':
1911	Xpos = event.xdata
1912	if not Xpos: #got point out of frame
1913	return
1914	Ypos = event.ydata
1915	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
1916	'Center change',style=wx.OK\|wx.CANCEL)
1917	try:
1918	if dlg.ShowModal() == wx.ID_OK:
1919	print 'move center to: ',Xpos,Ypos
1920	Data['center'] = [Xpos,Ypos]
1921	G2imG.UpdateImageControls(G2frame,Data,Masks)
1922	finally:
1923	dlg.Destroy()
1924	elif event.key == 'l':
1925	if G2frame.logPlot:
1926	G2frame.logPlot = False
1927	else:
1928	G2frame.logPlot = True
1929	PlotImage(G2frame,newImage=True)
1930
1931	def OnKeyBox(event):
1932	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
1933	event.key = cb.GetValue()[0]
1934	cb.SetValue(' key press')
1935	if event.key in 'l':
1936	wx.CallAfter(OnImPlotKeyPress,event)
1937
1938	def OnImPick(event):
1939	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
1940	return
1941	if G2frame.setPoly:
1942	polygon = Masks['Polygons'][-1]
1943	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1944	if xpos and ypos: #point inside image
1945	if len(polygon) > 2 and event.mouseevent.button == 3:
1946	x0,y0 = polygon[0]
1947	polygon.append([x0,y0])
1948	G2frame.setPoly = False
1949	G2frame.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1950	else:
1951	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1952	polygon.append([xpos,ypos])
1953	G2imG.UpdateMasks(G2frame,Masks)
1954	else:
1955	if G2frame.itemPicked is not None: return
1956	G2frame.itemPicked = event.artist
1957	G2frame.mousePicked = event.mouseevent
1958
1959	def OnImRelease(event):
1960	try:
1961	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
1962	except TypeError:
1963	return
1964	if PickName not in ['Image Controls','Masks']:
1965	return
1966	pixelSize = Data['pixelSize']
1967	scalex = 1000./pixelSize[0]
1968	scaley = 1000./pixelSize[1]
1969	pixLimit = Data['pixLimit']
1970	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
1971	# sizexy = Data['size']
1972	Xpos = event.xdata
1973	if not (Xpos and G2frame.ifGetRing): #got point out of frame
1974	return
1975	Ypos = event.ydata
1976	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1977	if event.button == 1:
1978	Xpix = Xpos*scalex
1979	Ypix = Ypos*scaley
1980	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix)
1981	if I and J:
1982	xpos += .5 #shift to pixel center
1983	ypos += .5
1984	xpos /= scalex #convert to mm
1985	ypos /= scaley
1986	Data['ring'].append([xpos,ypos])
1987	elif event.button == 3:
1988	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1989	if G2img.ImageCalibrate(G2frame,Data):
1990	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1991	print 'Calibration successful'
1992	else:
1993	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1994	print 'Calibration failed'
1995	G2frame.ifGetRing = False
1996	G2imG.UpdateImageControls(G2frame,Data,Masks)
1997	return
1998	PlotImage(G2frame,newImage=False)
1999	return
2000	else:
2001	xpos = event.xdata
2002	if xpos: #avoid out of frame mouse position
2003	ypos = event.ydata
2004	if G2frame.ifGetRing: #delete a calibration ring pick
2005	xypos = [xpos,ypos]
2006	rings = Data['ring']
2007	for ring in rings:
2008	if np.allclose(ring,xypos,.01,0):
2009	rings.remove(ring)
2010	else:
2011	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
2012	itemPicked = str(G2frame.itemPicked)
2013	if 'Line2D' in itemPicked and PickName == 'Image Controls':
2014	if 'line1' in itemPicked:
2015	Data['IOtth'][0] = max(tth,0.001)
2016	elif 'line2' in itemPicked:
2017	Data['IOtth'][1] = tth
2018	elif 'line3' in itemPicked:
2019	Data['LRazimuth'][0] = int(azm)
2020	if Data['fullIntegrate']:
2021	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
2022	elif 'line4' in itemPicked and not Data['fullIntegrate']:
2023	Data['LRazimuth'][1] = int(azm)
2024
2025	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
2026	Data['LRazimuth'][0] -= 360
2027
2028	azLim = np.array(Data['LRazimuth'])
2029	if np.any(azLim>360):
2030	azLim -= 360
2031	Data['LRazimuth'] = list(azLim)
2032
2033	if Data['IOtth'][0] > Data['IOtth'][1]:
2034	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
2035
2036	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
2037	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
2038	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
2039	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
2040	elif 'Circle' in itemPicked and PickName == 'Masks':
2041	spots = Masks['Points']
2042	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
2043	newPos = np.array([float(newPos[0]),float(newPos[1])])
2044	for spot in spots:
2045	if np.allclose(np.array([spot[:2]]),newPos):
2046	spot[:2] = xpos,ypos
2047	G2imG.UpdateMasks(G2frame,Masks)
2048	elif 'Line2D' in itemPicked and PickName == 'Masks':
2049	Obj = G2frame.itemPicked.findobj()
2050	rings = Masks['Rings']
2051	arcs = Masks['Arcs']
2052	polygons = Masks['Polygons']
2053	for ring in G2frame.ringList:
2054	if Obj == ring[0]:
2055	rN = ring[1]
2056	if ring[2] == 'o':
2057	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
2058	else:
2059	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
2060	for arc in G2frame.arcList:
2061	if Obj == arc[0]:
2062	aN = arc[1]
2063	if arc[2] == 'o':
2064	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
2065	elif arc[2] == 'i':
2066	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
2067	elif arc[2] == 'l':
2068	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
2069	else:
2070	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
2071	for poly in G2frame.polyList:
2072	if Obj == poly[0]:
2073	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
2074	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
2075	pN = poly[1]
2076	for i,xy in enumerate(polygons[pN]):
2077	if np.allclose(np.array([xy]),oldPos,atol=1.0):
2078	polygons[pN][i] = xpos,ypos
2079	G2imG.UpdateMasks(G2frame,Masks)
2080	# else: #keep for future debugging
2081	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
2082	PlotImage(G2frame,newImage=True)
2083	G2frame.itemPicked = None
2084
2085	try:
2086	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2087	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2088	if not newPlot:
2089	Plot = Page.figure.gca() #get previous powder plot & get limits
2090	xylim = Plot.get_xlim(),Plot.get_ylim()
2091	if newImage:
2092	Page.figure.clf()
2093	Plot = Page.figure.gca() #get a fresh plot after clf()
2094
2095	except ValueError:
2096	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
2097	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2098	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2099	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
2100	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
2101	Page.canvas.mpl_connect('pick_event', OnImPick)
2102	Page.canvas.mpl_connect('button_release_event', OnImRelease)
2103	xylim = []
2104	Page.Choice = None
2105	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
2106	Page.SetFocus()
2107	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
2108	G2frame.G2plotNB.status.DestroyChildren()
2109	if G2frame.logPlot:
2110	Title = 'log('+Title+')'
2111	Plot.set_title(Title)
2112	try:
2113	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
2114	Page.Choice = (' key press','l: log(I) on',)
2115	if G2frame.logPlot:
2116	Page.Choice[1] = 'l: log(I) off'
2117	Page.keyPress = OnImPlotKeyPress
2118	except TypeError:
2119	pass
2120	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
2121	if imagefile != G2frame.oldImagefile:
2122	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
2123	if not imagefile:
2124	G2frame.G2plotNB.Delete('2D Powder Image')
2125	return
2126	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
2127	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
2128	G2frame.oldImagefile = imagefile
2129
2130	imScale = 1
2131	if len(G2frame.ImageZ) > 1024:
2132	imScale = len(G2frame.ImageZ)/1024
2133	sizexy = Data['size']
2134	pixelSize = Data['pixelSize']
2135	scalex = 1000./pixelSize[0]
2136	scaley = 1000./pixelSize[1]
2137	Xmax = sizexy[0]*pixelSize[0]/1000.
2138	Ymax = sizexy[1]*pixelSize[1]/1000.
2139	xlim = (0,Xmax)
2140	ylim = (Ymax,0)
2141	Imin,Imax = Data['range'][1]
2142	acolor = mpl.cm.get_cmap(Data['color'])
2143	xcent,ycent = Data['center']
2144	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
2145	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
2146	#do threshold mask - "real" mask - others are just bondaries
2147	Zlim = Masks['Thresholds'][1]
2148	wx.BeginBusyCursor()
2149	try:
2150
2151	if newImage:
2152	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]),Zlim[1])
2153	MaskA = ma.getmaskarray(MA)
2154	A = G2img.ImageCompress(MA,imScale)
2155	AM = G2img.ImageCompress(MaskA,imScale)
2156	if G2frame.logPlot:
2157	A = np.where(A>0,np.log(A),0)
2158	AM = np.where(AM>0,np.log(AM),0)
2159	Imin,Imax = [np.amin(A),np.amax(A)]
2160	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
2161	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
2162	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
2163	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
2164	if G2frame.setPoly:
2165	Img.set_picker(True)
2166
2167	Plot.plot(xcent,ycent,'x')
2168	#G2frame.PatternTree.GetItemText(item)
2169	if Data['showLines']:
2170	LRAzim = Data['LRazimuth'] #NB: integers
2171	Nazm = Data['outAzimuths']
2172	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
2173	AzmthOff = Data['azmthOff']
2174	IOtth = Data['IOtth']
2175	wave = Data['wavelength']
2176	dspI = wave/(2.0*sind(IOtth[0]/2.0))
2177	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
2178	dspO = wave/(2.0*sind(IOtth[1]/2.0))
2179	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
2180	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
2181	if ellI:
2182	xyI = []
2183	for azm in Azm:
2184	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
2185	xyI = np.array(xyI)
2186	arcxI,arcyI = xyI.T
2187	Plot.plot(arcxI,arcyI,picker=3)
2188	if ellO:
2189	xyO = []
2190	for azm in Azm:
2191	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
2192	xyO = np.array(xyO)
2193	arcxO,arcyO = xyO.T
2194	Plot.plot(arcxO,arcyO,picker=3)
2195	if ellO and ellI:
2196	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
2197	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
2198	for i in range(Nazm):
2199	cake = LRAzim[0]+i*delAzm-AzmthOff
2200	if Data['centerAzm']:
2201	cake += delAzm/2.
2202	ind = np.searchsorted(Azm,cake)
2203	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
2204
2205	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
2206	for xring,yring in Data['ring']:
2207	Plot.plot(xring,yring,'r+',picker=3)
2208	if Data['setRings']:
2209	# rings = np.concatenate((Data['rings']),axis=0)
2210	N = 0
2211	for ring in Data['rings']:
2212	xring,yring = np.array(ring).T[:2]
2213	Plot.plot(xring,yring,'+',color=colors[N%6])
2214	N += 1
2215	for ellipse in Data['ellipses']:
2216	cent,phi,[width,height],col = ellipse
2217	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
2218	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
2219	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
2220	print 'plot stress/strain stuff'
2221	for ring in StrSta['d-zero']:
2222	xring,yring = ring['ImxyObs']
2223	Plot.plot(xring,yring,'r+')
2224	# for xring,yring in ring['ImxyCalc'].T:
2225	# Plot.add_artist(Polygon(ring['ImxyCalc'].T,ec='b',fc='none'))
2226	# Plot.plot(xring,yring)
2227	#masks - mask lines numbered after integration limit lines
2228	spots = Masks['Points']
2229	rings = Masks['Rings']
2230	arcs = Masks['Arcs']
2231	polygons = Masks['Polygons']
2232	for x,y,d in spots:
2233	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
2234	G2frame.ringList = []
2235	for iring,(tth,thick) in enumerate(rings):
2236	wave = Data['wavelength']
2237	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
2238	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
2239	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
2240	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
2241	G2frame.arcList = []
2242	for iarc,(tth,azm,thick) in enumerate(arcs):
2243	wave = Data['wavelength']
2244	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
2245	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
2246	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
2247	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
2248	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
2249	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
2250	G2frame.polyList = []
2251	for ipoly,polygon in enumerate(polygons):
2252	x,y = np.hsplit(np.array(polygon),2)
2253	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
2254	Plot.plot(x,y,'r')
2255	if newImage:
2256	colorBar = Page.figure.colorbar(Img)
2257	Plot.set_xlim(xlim)
2258	Plot.set_ylim(ylim)
2259	Plot.invert_yaxis()
2260	if not newPlot and xylim:
2261	Page.toolbar.push_current()
2262	Plot.set_xlim(xylim[0])
2263	Plot.set_ylim(xylim[1])
2264	xylim = []
2265	Page.toolbar.push_current()
2266	Page.toolbar.draw()
2267	else:
2268	Page.canvas.draw()
2269	finally:
2270	wx.EndBusyCursor()
2271
2272	################################################################################
2273	##### PlotIntegration
2274	################################################################################
2275
2276	def PlotIntegration(G2frame,newPlot=False,event=None):
2277	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
2278	'''
2279
2280	def OnMotion(event):
2281	Page.canvas.SetToolTipString('')
2282	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2283	azm = event.ydata
2284	tth = event.xdata
2285	if azm and tth:
2286	G2frame.G2plotNB.status.SetFields(\
2287	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2288
2289	try:
2290	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2291	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2292	if not newPlot:
2293	Plot = Page.figure.gca() #get previous plot & get limits
2294	xylim = Plot.get_xlim(),Plot.get_ylim()
2295	Page.figure.clf()
2296	Plot = Page.figure.gca() #get a fresh plot after clf()
2297
2298	except ValueError:
2299	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
2300	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2301	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2302	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2303	Page.views = False
2304	view = False
2305	Page.Choice = None
2306	if not event:
2307	Page.SetFocus()
2308
2309	Data = G2frame.PatternTree.GetItemPyData(
2310	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2311	image = G2frame.Integrate[0]
2312	xsc = G2frame.Integrate[1]
2313	ysc = G2frame.Integrate[2]
2314	Imin,Imax = Data['range'][1]
2315	acolor = mpl.cm.get_cmap(Data['color'])
2316	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2317	Plot.set_ylabel('azimuth',fontsize=12)
2318	Plot.set_xlabel('2-theta',fontsize=12)
2319	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
2320	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
2321	colorBar = Page.figure.colorbar(Img)
2322	if Data['ellipses']:
2323	for ellipse in Data['ellipses']:
2324	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2325	x,y = np.hsplit(ring,2)
2326	tth,azm = G2img.GetTthAzm(x,y,Data)
2327	# azm = np.where(azm < 0.,azm+360,azm)
2328	Plot.plot(tth,azm,'b,')
2329	if not newPlot:
2330	Page.toolbar.push_current()
2331	Plot.set_xlim(xylim[0])
2332	Plot.set_ylim(xylim[1])
2333	xylim = []
2334	Page.toolbar.push_current()
2335	Page.toolbar.draw()
2336	else:
2337	Page.canvas.draw()
2338
2339	################################################################################
2340	##### PlotTRImage
2341	################################################################################
2342
2343	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
2344	'''a test plot routine - not normally used
2345	'''
2346
2347	def OnMotion(event):
2348	Page.canvas.SetToolTipString('')
2349	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2350	azm = event.xdata
2351	tth = event.ydata
2352	if azm and tth:
2353	G2frame.G2plotNB.status.SetFields(\
2354	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2355
2356	try:
2357	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2358	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2359	if not newPlot:
2360	Plot = Page.figure.gca() #get previous plot & get limits
2361	xylim = Plot.get_xlim(),Plot.get_ylim()
2362	Page.figure.clf()
2363	Plot = Page.figure.gca() #get a fresh plot after clf()
2364
2365	except ValueError:
2366	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
2367	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2368	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2369	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2370	Page.views = False
2371	view = False
2372	Page.Choice = None
2373	Page.SetFocus()
2374
2375	Data = G2frame.PatternTree.GetItemPyData(
2376	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2377	Imin,Imax = Data['range'][1]
2378	step = (Imax-Imin)/5.
2379	V = np.arange(Imin,Imax,step)
2380	acolor = mpl.cm.get_cmap(Data['color'])
2381	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2382	Plot.set_xlabel('azimuth',fontsize=12)
2383	Plot.set_ylabel('2-theta',fontsize=12)
2384	Plot.contour(tax,tay,taz,V,cmap=acolor)
2385	if Data['showLines']:
2386	IOtth = Data['IOtth']
2387	if Data['fullIntegrate']:
2388	LRAzim = [-180,180]
2389	else:
2390	LRAzim = Data['LRazimuth'] #NB: integers
2391	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
2392	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
2393	if not Data['fullIntegrate']:
2394	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
2395	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
2396	if Data['setRings']:
2397	rings = np.concatenate((Data['rings']),axis=0)
2398	for xring,yring,dsp in rings:
2399	x,y = G2img.GetTthAzm(xring,yring,Data)
2400	Plot.plot(y,x,'r+')
2401	if Data['ellipses']:
2402	for ellipse in Data['ellipses']:
2403	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2404	x,y = np.hsplit(ring,2)
2405	tth,azm = G2img.GetTthAzm(x,y,Data)
2406	Plot.plot(azm,tth,'b,')
2407	if not newPlot:
2408	Page.toolbar.push_current()
2409	Plot.set_xlim(xylim[0])
2410	Plot.set_ylim(xylim[1])
2411	xylim = []
2412	Page.toolbar.push_current()
2413	Page.toolbar.draw()
2414	else:
2415	Page.canvas.draw()
2416
2417	################################################################################
2418	##### PlotStructure
2419	################################################################################
2420
2421	def PlotStructure(G2frame,data):
2422	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
2423	thermal motion ellipsoids and polyhedra
2424	'''
2425	ForthirdPI = 4.0*math.pi/3.0
2426	generalData = data['General']
2427	cell = generalData['Cell'][1:7]
2428	Vol = generalData['Cell'][7:8][0]
2429	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
2430	Gmat,gmat = G2lat.cell2Gmat(cell)
2431	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2432	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2433	Mydir = generalData['Mydir']
2434	atomData = data['Atoms']
2435	mapPeaks = []
2436	if 'Map Peaks' in data:
2437	mapPeaks = np.array(data['Map Peaks'])
2438	peakMax = 100.
2439	if len(mapPeaks):
2440	peakMax = np.max(mapPeaks.T[0])
2441	drawingData = data['Drawing']
2442	try:
2443	drawAtoms = drawingData['Atoms']
2444	except KeyError:
2445	drawAtoms = []
2446	mapData = {}
2447	flipData = {}
2448	rhoXYZ = []
2449	if 'Map' in generalData:
2450	mapData = generalData['Map']
2451	if 'Flip' in generalData:
2452	flipData = generalData['Flip']
2453	flipData['mapRoll'] = [0,0,0]
2454	cx,ct,cs,ci = drawingData['atomPtrs']
2455	Wt = np.array([255,255,255])
2456	Rd = np.array([255,0,0])
2457	Gr = np.array([0,255,0])
2458	Bl = np.array([0,0,255])
2459	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]])
2460	uEdges = np.array([
2461	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
2462	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
2463	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
2464	mD = 0.1
2465	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
2466	mapPeakVecs = np.inner(mV,Bmat)
2467
2468	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
2469	altDown = False
2470	shiftDown = False
2471	ctrlDown = False
2472
2473	def OnKeyBox(event):
2474	import Image
2475	# Draw() #make sure plot is fresh!!
2476	mode = cb.GetValue()
2477	if mode in ['jpeg','bmp','tiff',]:
2478	Fname = os.path.joint(Mydir,generalData['Name']+'.'+mode)
2479	size = Page.canvas.GetSize()
2480	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
2481	if mode in ['jpeg',]:
2482	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
2483	im = Image.new("RGBA", (size[0],size[1]))
2484	else:
2485	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
2486	im = Image.new("RGB", (size[0],size[1]))
2487	im.fromstring(Pix)
2488	im.save(Fname,mode)
2489	cb.SetValue(' save as/key:')
2490	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
2491	else:
2492	event.key = cb.GetValue()[0]
2493	cb.SetValue(' save as/key:')
2494	wx.CallAfter(OnKey,event)
2495
2496	def OnKey(event): #on key UP!!
2497	# Draw() #make sure plot is fresh!!
2498	try:
2499	keyCode = event.GetKeyCode()
2500	if keyCode > 255:
2501	keyCode = 0
2502	key = chr(keyCode)
2503	except AttributeError: #if from OnKeyBox above
2504	key = str(event.key).upper()
2505	indx = drawingData['selectedAtoms']
2506	if key in ['C']:
2507	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2508	drawingData['viewDir'] = [0,0,1]
2509	drawingData['oldxy'] = []
2510	V0 = np.array([0,0,1])
2511	V = np.inner(Amat,V0)
2512	V /= np.sqrt(np.sum(V**2))
2513	A = np.arccos(np.sum(V*V0))
2514	Q = G2mth.AV2Q(A,[0,1,0])
2515	drawingData['Quaternion'] = Q
2516	SetViewPointText(drawingData['viewPoint'][0])
2517	SetViewDirText(drawingData['viewDir'])
2518	Q = drawingData['Quaternion']
2519	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
2520	elif key in ['N']:
2521	drawAtoms = drawingData['Atoms']
2522	pI = drawingData['viewPoint'][1]
2523	if indx:
2524	pI[0] = indx[pI[1]]
2525	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2526	pI[1] += 1
2527	if pI[1] >= len(indx):
2528	pI[1] = 0
2529	else:
2530	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2531	pI[0] += 1
2532	if pI[0] >= len(drawAtoms):
2533	pI[0] = 0
2534	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2535	SetViewPointText(drawingData['viewPoint'][0])
2536	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2537
2538	elif key in ['P']:
2539	drawAtoms = drawingData['Atoms']
2540	pI = drawingData['viewPoint'][1]
2541	if indx:
2542	pI[0] = indx[pI[1]]
2543	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2544	pI[1] -= 1
2545	if pI[1] < 0:
2546	pI[1] = len(indx)-1
2547	else:
2548	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2549	pI[0] -= 1
2550	if pI[0] < 0:
2551	pI[0] = len(drawAtoms)-1
2552	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2553	SetViewPointText(drawingData['viewPoint'][0])
2554	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2555	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
2556	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
2557	SetMapRoll(dirDict[key])
2558	SetPeakRoll(dirDict[key])
2559	SetMapPeaksText(mapPeaks)
2560	Draw('key')
2561
2562	def GetTruePosition(xy,Add=False):
2563	View = glGetIntegerv(GL_VIEWPORT)
2564	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
2565	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
2566	Zmax = 1.
2567	if Add:
2568	Indx = GetSelectedAtoms()
2569	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
2570	for i,peak in enumerate(mapPeaks):
2571	x,y,z = peak[1:4]
2572	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2573	XY = [int(X),int(View[3]-Y)]
2574	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2575	Zmax = Z
2576	try:
2577	Indx.remove(i)
2578	ClearSelectedAtoms()
2579	for id in Indx:
2580	SetSelectedAtoms(id,Add)
2581	except:
2582	SetSelectedAtoms(i,Add)
2583	else:
2584	for i,atom in enumerate(drawAtoms):
2585	x,y,z = atom[cx:cx+3]
2586	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2587	XY = [int(X),int(View[3]-Y)]
2588	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2589	Zmax = Z
2590	try:
2591	Indx.remove(i)
2592	ClearSelectedAtoms()
2593	for id in Indx:
2594	SetSelectedAtoms(id,Add)
2595	except:
2596	SetSelectedAtoms(i,Add)
2597
2598	def OnMouseDown(event):
2599	xy = event.GetPosition()
2600	if event.ShiftDown():
2601	if event.LeftIsDown():
2602	GetTruePosition(xy)
2603	elif event.RightIsDown():
2604	GetTruePosition(xy,True)
2605	else:
2606	drawingData['oldxy'] = list(xy)
2607	# Draw()
2608
2609	def OnMouseMove(event):
2610	if event.ShiftDown(): #don't want any inadvertant moves when picking
2611	return
2612	newxy = event.GetPosition()
2613	page = getSelection()
2614
2615	if event.Dragging() and not event.ControlDown():
2616	if event.LeftIsDown():
2617	SetRotation(newxy)
2618	Q = drawingData['Quaternion']
2619	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
2620	elif event.RightIsDown():
2621	SetTranslation(newxy)
2622	Tx,Ty,Tz = drawingData['viewPoint'][0]
2623	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2624	elif event.MiddleIsDown():
2625	SetRotationZ(newxy)
2626	Q = drawingData['Quaternion']
2627	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
2628	Draw('move')
2629
2630	def OnMouseWheel(event):
2631	if event.ShiftDown():
2632	return
2633	drawingData['cameraPos'] += event.GetWheelRotation()/24
2634	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2635	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2636	page = getSelection()
2637	if page:
2638	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2639	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2640	names = [child.GetName() for child in panel]
2641	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2642	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2643	Draw('wheel')
2644
2645	def getSelection():
2646	try:
2647	return G2frame.dataDisplay.GetSelection()
2648	except AttributeError:
2649	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2650	return 0
2651
2652	def SetViewPointText(VP):
2653	page = getSelection()
2654	if page:
2655	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2656	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2657	names = [child.GetName() for child in panel]
2658	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2659
2660	def SetViewDirText(VD):
2661	page = getSelection()
2662	if page:
2663	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2664	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2665	names = [child.GetName() for child in panel]
2666	panel[names.index('viewDir')].SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2667
2668	def SetMapPeaksText(mapPeaks):
2669	page = getSelection()
2670	if page:
2671	if G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2672	G2frame.MapPeaksTable.SetData(mapPeaks)
2673	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
2674	names = [child.GetName() for child in panel]
2675	panel[names.index('grid window')].Refresh()
2676
2677	def ClearSelectedAtoms():
2678	page = getSelection()
2679	if page:
2680	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2681	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2682	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2683	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2684	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2685	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2686
2687
2688	def SetSelectedAtoms(ind,Add=False):
2689	page = getSelection()
2690	if page:
2691	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2692	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
2693	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2694	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add)
2695	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2696	Id = drawAtoms[ind][-3]
2697	for i,atom in enumerate(atomData):
2698	if atom[-1] == Id:
2699	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2700
2701	def GetSelectedAtoms():
2702	page = getSelection()
2703	Ind = []
2704	if page:
2705	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2706	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2707	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
2708	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows()
2709	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2710	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2711	return Ind
2712
2713	def SetBackground():
2714	R,G,B,A = Page.camera['backColor']
2715	glClearColor(R,G,B,A)
2716	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2717
2718	def SetLights():
2719	glEnable(GL_DEPTH_TEST)
2720	glShadeModel(GL_SMOOTH)
2721	glEnable(GL_LIGHTING)
2722	glEnable(GL_LIGHT0)
2723	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2724	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2725	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2726
2727	def GetRoll(newxy,rho):
2728	Q = drawingData['Quaternion']
2729	dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,]))
2730	dxy = np.array(dxy*rho.shape)
2731	roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0))
2732	return roll
2733
2734	def SetMapRoll(newxy):
2735	rho = mapData['rho']
2736	roll = GetRoll(newxy,rho)
2737	mapData['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
2738	drawingData['oldxy'] = list(newxy)
2739
2740	def SetPeakRoll(newxy):
2741	rho = mapData['rho']
2742	roll = GetRoll(newxy,rho)
2743	steps = 1./np.array(rho.shape)
2744	dxy = roll*steps
2745	for peak in mapPeaks:
2746	peak[1:4] += dxy
2747	peak[1:4] %= 1.
2748	peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2))
2749
2750	def SetTranslation(newxy):
2751	#first get translation vector in screen coords.
2752	oldxy = drawingData['oldxy']
2753	if not len(oldxy): oldxy = list(newxy)
2754	dxy = newxy-oldxy
2755	drawingData['oldxy'] = list(newxy)
2756	V = np.array([-dxy[0],dxy[1],0.])
2757	#then transform to rotated crystal coordinates & apply to view point
2758	Q = drawingData['Quaternion']
2759	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
2760	Tx,Ty,Tz = drawingData['viewPoint'][0]
2761	Tx += V[0]*0.01
2762	Ty += V[1]*0.01
2763	Tz += V[2]*0.01
2764	drawingData['oldxy'] = list(newxy)
2765	drawingData['viewPoint'][0] = Tx,Ty,Tz
2766	SetViewPointText([Tx,Ty,Tz])
2767
2768	def SetRotation(newxy):
2769	#first get rotation vector in screen coords. & angle increment
2770	oldxy = drawingData['oldxy']
2771	if not len(oldxy): oldxy = list(newxy)
2772	dxy = newxy-oldxy
2773	drawingData['oldxy'] = list(newxy)
2774	V = np.array([dxy[1],dxy[0],0.])
2775	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
2776	# next transform vector back to xtal coordinates via inverse quaternion
2777	# & make new quaternion
2778	Q = drawingData['Quaternion']
2779	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
2780	DQ = G2mth.AVdeg2Q(A,V)
2781	Q = G2mth.prodQQ(Q,DQ)
2782	drawingData['Quaternion'] = Q
2783	# finally get new view vector - last row of rotation matrix
2784	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
2785	VD /= np.sqrt(np.sum(VD**2))
2786	drawingData['viewDir'] = VD
2787	SetViewDirText(VD)
2788
2789	def SetRotationZ(newxy):
2790	#first get rotation vector (= view vector) in screen coords. & angle increment
2791	View = glGetIntegerv(GL_VIEWPORT)
2792	cent = [View[2]/2,View[3]/2]
2793	oldxy = drawingData['oldxy']
2794	if not len(oldxy): oldxy = list(newxy)
2795	dxy = newxy-oldxy
2796	drawingData['oldxy'] = list(newxy)
2797	V = drawingData['viewDir']
2798	A = [0,0]
2799	A[0] = dxy[1]*.25
2800	A[1] = dxy[0]*.25
2801	if newxy[0] > cent[0]:
2802	A[0] *= -1
2803	if newxy[1] < cent[1]:
2804	A[1] *= -1
2805	# next transform vector back to xtal coordinates & make new quaternion
2806	Q = drawingData['Quaternion']
2807	V = np.inner(Amat,V)
2808	Qx = G2mth.AVdeg2Q(A[0],V)
2809	Qy = G2mth.AVdeg2Q(A[1],V)
2810	Q = G2mth.prodQQ(Q,Qx)
2811	Q = G2mth.prodQQ(Q,Qy)
2812	drawingData['Quaternion'] = Q
2813
2814	def RenderBox():
2815	glEnable(GL_COLOR_MATERIAL)
2816	glLineWidth(2)
2817	glEnable(GL_BLEND)
2818	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2819	glEnable(GL_LINE_SMOOTH)
2820	glBegin(GL_LINES)
2821	for line,color in zip(uEdges,uColors):
2822	glColor3ubv(color)
2823	glVertex3fv(line[0])
2824	glVertex3fv(line[1])
2825	glEnd()
2826	glColor4ubv([0,0,0,0])
2827	glDisable(GL_LINE_SMOOTH)
2828	glDisable(GL_BLEND)
2829	glDisable(GL_COLOR_MATERIAL)
2830
2831	def RenderUnitVectors(x,y,z):
2832	xyz = np.array([x,y,z])
2833	glEnable(GL_COLOR_MATERIAL)
2834	glLineWidth(1)
2835	glPushMatrix()
2836	glTranslate(x,y,z)
2837	glScalef(1/cell[0],1/cell[1],1/cell[2])
2838	glBegin(GL_LINES)
2839	for line,color in zip(uEdges,uColors)[:3]:
2840	glColor3ubv(color)
2841	glVertex3fv(-line[1]/2.)
2842	glVertex3fv(line[1]/2.)
2843	glEnd()
2844	glPopMatrix()
2845	glColor4ubv([0,0,0,0])
2846	glDisable(GL_COLOR_MATERIAL)
2847
2848	def RenderSphere(x,y,z,radius,color):
2849	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2850	glPushMatrix()
2851	glTranslate(x,y,z)
2852	glMultMatrixf(B4mat.T)
2853	q = gluNewQuadric()
2854	gluSphere(q,radius,20,10)
2855	glPopMatrix()
2856
2857	def RenderDots(XYZ,RC):
2858	glEnable(GL_COLOR_MATERIAL)
2859	XYZ = np.array(XYZ)
2860	glPushMatrix()
2861	for xyz,rc in zip(XYZ,RC):
2862	x,y,z = xyz
2863	r,c = rc
2864	glColor3ubv(c)
2865	glPointSize(r*50)
2866	glBegin(GL_POINTS)
2867	glVertex3fv(xyz)
2868	glEnd()
2869	glPopMatrix()
2870	glColor4ubv([0,0,0,0])
2871	glDisable(GL_COLOR_MATERIAL)
2872
2873	def RenderSmallSphere(x,y,z,radius,color):
2874	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2875	glPushMatrix()
2876	glTranslate(x,y,z)
2877	glMultMatrixf(B4mat.T)
2878	q = gluNewQuadric()
2879	gluSphere(q,radius,4,2)
2880	glPopMatrix()
2881
2882	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2883	s1,s2,s3 = E
2884	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2885	glPushMatrix()
2886	glTranslate(x,y,z)
2887	glMultMatrixf(B4mat.T)
2888	glMultMatrixf(R4.T)
2889	glEnable(GL_NORMALIZE)
2890	glScale(s1,s2,s3)
2891	q = gluNewQuadric()
2892	gluSphere(q,ellipseProb,20,10)
2893	glDisable(GL_NORMALIZE)
2894	glPopMatrix()
2895
2896	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2897	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2898	glPushMatrix()
2899	glTranslate(x,y,z)
2900	glMultMatrixf(B4mat.T)
2901	for bond in Bonds:
2902	glPushMatrix()
2903	Dx = np.inner(Amat,bond)
2904	Z = np.sqrt(np.sum(Dx**2))
2905	if Z:
2906	azm = atan2d(-Dx[1],-Dx[0])
2907	phi = acosd(Dx[2]/Z)
2908	glRotate(-azm,0,0,1)
2909	glRotate(phi,1,0,0)
2910	q = gluNewQuadric()
2911	gluCylinder(q,radius,radius,Z,slice,2)
2912	glPopMatrix()
2913	glPopMatrix()
2914
2915	def RenderLines(x,y,z,Bonds,color):
2916	xyz = np.array([x,y,z])
2917	glEnable(GL_COLOR_MATERIAL)
2918	glLineWidth(1)
2919	glColor3fv(color)
2920	glPushMatrix()
2921	glBegin(GL_LINES)
2922	for bond in Bonds:
2923	glVertex3fv(xyz)
2924	glVertex3fv(xyz+bond)
2925	glEnd()
2926	glColor4ubv([0,0,0,0])
2927	glPopMatrix()
2928	glDisable(GL_COLOR_MATERIAL)
2929
2930	def RenderPolyhedra(x,y,z,Faces,color):
2931	glPushMatrix()
2932	glTranslate(x,y,z)
2933	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2934	glShadeModel(GL_SMOOTH)
2935	glMultMatrixf(B4mat.T)
2936	for face,norm in Faces:
2937	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2938	glFrontFace(GL_CW)
2939	glNormal3fv(norm)
2940	glBegin(GL_TRIANGLES)
2941	for vert in face:
2942	glVertex3fv(vert)
2943	glEnd()
2944	glPopMatrix()
2945
2946	def RenderMapPeak(x,y,z,color,den):
2947	xyz = np.array([x,y,z])
2948	glEnable(GL_COLOR_MATERIAL)
2949	glLineWidth(3)
2950	glColor3fv(color*den/255)
2951	glPushMatrix()
2952	glBegin(GL_LINES)
2953	for vec in mapPeakVecs:
2954	glVertex3fv(vec[0]+xyz)
2955	glVertex3fv(vec[1]+xyz)
2956	glEnd()
2957	glColor4ubv([0,0,0,0])
2958	glPopMatrix()
2959	glDisable(GL_COLOR_MATERIAL)
2960
2961	def RenderBackbone(Backbone,BackboneColor,radius):
2962	glPushMatrix()
2963	glMultMatrixf(B4mat.T)
2964	glEnable(GL_COLOR_MATERIAL)
2965	glShadeModel(GL_SMOOTH)
2966	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2967	glePolyCylinder(Backbone,BackboneColor,radius)
2968	glPopMatrix()
2969	glDisable(GL_COLOR_MATERIAL)
2970
2971	def RenderLabel(x,y,z,label,r):
2972	glPushMatrix()
2973	glTranslate(x,y,z)
2974	glMultMatrixf(B4mat.T)
2975	glDisable(GL_LIGHTING)
2976	glColor3f(0,1.,0)
2977	glRasterPos3f(r,r,r)
2978	for c in list(label):
2979	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2980	glEnable(GL_LIGHTING)
2981	glPopMatrix()
2982
2983	def RenderMap(rho,rhoXYZ,indx,Rok):
2984	cLevel = drawingData['contourLevel']
2985	XYZ = []
2986	RC = []
2987	for i,xyz in enumerate(rhoXYZ):
2988	if not Rok[i]:
2989	x,y,z = xyz
2990	I,J,K = indx[i]
2991	alpha = 1.0
2992	if cLevel < 1.:
2993	alpha = (abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)
2994	if rho[I,J,K] < 0.:
2995	XYZ.append(xyz)
2996	RC.append([0.1*alpha,Rd])
2997	else:
2998	XYZ.append(xyz)
2999	RC.append([0.1*alpha,Gr])
3000	RenderDots(XYZ,RC)
3001
3002	def Draw(caller=''):
3003	#useful debug?
3004	# if caller:
3005	# print caller
3006	# end of useful debug
3007	mapData = generalData['Map']
3008	pageName = ''
3009	page = getSelection()
3010	if page:
3011	pageName = G2frame.dataDisplay.GetPageText(page)
3012	rhoXYZ = []
3013	if len(mapData['rho']):
3014	VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
3015	contLevel = drawingData['contourLevel']*mapData['rhoMax']
3016	if 'delt-F' in mapData['MapType']:
3017	rho = ma.array(mapData['rho'],mask=(np.abs(mapData['rho'])<contLevel))
3018	else:
3019	rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
3020	steps = 1./np.array(rho.shape)
3021	incre = np.where(VP>=0,VP%steps,VP%steps-steps)
3022	Vsteps = -np.array(VP/steps,dtype='i')
3023	rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
3024	indx = np.array(ma.nonzero(rho)).T
3025	rhoXYZ = indx*steps+VP-incre
3026	Nc = len(rhoXYZ)
3027	rcube = 2000.Vol/(ForthirdPINc)
3028	rmax = math.exp(math.log(rcube)/3.)**2
3029	radius = min(drawingData['mapSize']**2,rmax)
3030	view = np.array(drawingData['viewPoint'][0])
3031	Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
3032	Ind = GetSelectedAtoms()
3033	VS = np.array(Page.canvas.GetSize())
3034	aspect = float(VS[0])/float(VS[1])
3035	cPos = drawingData['cameraPos']
3036	Zclip = drawingData['Zclip']*cPos/200.
3037	Q = drawingData['Quaternion']
3038	Tx,Ty,Tz = drawingData['viewPoint'][0]
3039	cx,ct,cs,ci = drawingData['atomPtrs']
3040	bondR = drawingData['bondRadius']
3041	G,g = G2lat.cell2Gmat(cell)
3042	GS = G
3043	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
3044	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
3045	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
3046	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
3047
3048	SetBackground()
3049	glInitNames()
3050	glPushName(0)
3051
3052	glMatrixMode(GL_PROJECTION)
3053	glLoadIdentity()
3054	glViewport(0,0,VS[0],VS[1])
3055	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
3056	gluLookAt(0,0,cPos,0,0,0,0,1,0)
3057	SetLights()
3058
3059	glMatrixMode(GL_MODELVIEW)
3060	glLoadIdentity()
3061	matRot = G2mth.Q2Mat(Q)
3062	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3063	glMultMatrixf(matRot.T)
3064	glMultMatrixf(A4mat.T)
3065	glTranslate(-Tx,-Ty,-Tz)
3066	if drawingData['unitCellBox']:
3067	RenderBox()
3068	if drawingData['showABC']:
3069	x,y,z = drawingData['viewPoint'][0]
3070	RenderUnitVectors(x,y,z)
3071	Backbones = {}
3072	BackboneColor = []
3073	time0 = time.time()
3074	# glEnable(GL_BLEND)
3075	# glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
3076	for iat,atom in enumerate(drawingData['Atoms']):
3077	x,y,z = atom[cx:cx+3]
3078	Bonds = atom[-2]
3079	Faces = atom[-1]
3080	try:
3081	atNum = generalData['AtomTypes'].index(atom[ct])
3082	except ValueError:
3083	atNum = -1
3084	CL = atom[cs+2]
3085	color = np.array(CL)/255.
3086	if iat in Ind and G2frame.dataDisplay.GetPageText(getSelection()) != 'Map peaks':
3087	color = np.array(Gr)/255.
3088	# color += [.25,]
3089	radius = 0.5
3090	if atom[cs] != '':
3091	try:
3092	glLoadName(atom[-3])
3093	except: #problem with old files - missing code
3094	pass
3095	if 'balls' in atom[cs]:
3096	vdwScale = drawingData['vdwScale']
3097	ballScale = drawingData['ballScale']
3098	if atNum < 0:
3099	radius = 0.2
3100	elif 'H' == atom[ct]:
3101	if drawingData['showHydrogen']:
3102	if 'vdW' in atom[cs] and atNum >= 0:
3103	radius = vdwScale*generalData['vdWRadii'][atNum]
3104	else:
3105	radius = ballScale*drawingData['sizeH']
3106	else:
3107	radius = 0.0
3108	else:
3109	if 'vdW' in atom[cs]:
3110	radius = vdwScale*generalData['vdWRadii'][atNum]
3111	else:
3112	radius = ballScale*generalData['BondRadii'][atNum]
3113	RenderSphere(x,y,z,radius,color)
3114	if 'sticks' in atom[cs]:
3115	RenderBonds(x,y,z,Bonds,bondR,color)
3116	elif 'ellipsoids' in atom[cs]:
3117	RenderBonds(x,y,z,Bonds,bondR,color)
3118	if atom[cs+3] == 'A':
3119	Uij = atom[cs+5:cs+11]
3120	U = np.multiply(G2spc.Uij2U(Uij),GS)
3121	U = np.inner(Amat,np.inner(U,Amat).T)
3122	E,R = nl.eigh(U)
3123	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3124	E = np.sqrt(E)
3125	if atom[ct] == 'H' and not drawingData['showHydrogen']:
3126	pass
3127	else:
3128	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
3129	else:
3130	if atom[ct] == 'H' and not drawingData['showHydrogen']:
3131	pass
3132	else:
3133	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
3134	RenderSphere(x,y,z,radius,color)
3135	elif 'lines' in atom[cs]:
3136	radius = 0.1
3137	RenderLines(x,y,z,Bonds,color)
3138	# RenderBonds(x,y,z,Bonds,0.05,color,6)
3139	elif atom[cs] == 'sticks':
3140	radius = 0.1
3141	RenderBonds(x,y,z,Bonds,bondR,color)
3142	elif atom[cs] == 'polyhedra':
3143	RenderPolyhedra(x,y,z,Faces,color)
3144	elif atom[cs] == 'backbone':
3145	if atom[ct-1].split()[0] in ['C','N']:
3146	if atom[2] not in Backbones:
3147	Backbones[atom[2]] = []
3148	Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
3149	BackboneColor.append(list(color))
3150
3151	if atom[cs+1] == 'type':
3152	RenderLabel(x,y,z,atom[ct],radius)
3153	elif atom[cs+1] == 'name':
3154	RenderLabel(x,y,z,atom[ct-1],radius)
3155	elif atom[cs+1] == 'number':
3156	RenderLabel(x,y,z,str(iat),radius)
3157	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
3158	RenderLabel(x,y,z,atom[ct-4],radius)
3159	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
3160	RenderLabel(x,y,z,atom[ct-3],radius)
3161	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
3162	RenderLabel(x,y,z,atom[ct-2],radius)
3163	# glDisable(GL_BLEND)
3164	if len(rhoXYZ):
3165	RenderMap(rho,rhoXYZ,indx,Rok)
3166	if len(mapPeaks):
3167	for ind,[mag,x,y,z,d] in enumerate(mapPeaks):
3168	if ind in Ind and pageName == 'Map peaks':
3169	RenderMapPeak(x,y,z,Gr,1.0)
3170	else:
3171	RenderMapPeak(x,y,z,Wt,mag/peakMax)
3172	if Backbones:
3173	for chain in Backbones:
3174	Backbone = Backbones[chain]
3175	RenderBackbone(Backbone,BackboneColor,bondR)
3176	# print time.time()-time0
3177	Page.canvas.SwapBuffers()
3178
3179	def OnSize(event):
3180	Draw('size')
3181
3182	def OnFocus(event): #not needed?? Bind commented out below
3183	Draw('focus')
3184
3185	try:
3186	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
3187	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3188	except ValueError:
3189	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
3190	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
3191	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3192	Page.views = False
3193	view = False
3194	altDown = False
3195	Page.SetFocus()
3196	Page.Choice = None
3197	if mapData['Flip']:
3198	choice = [' save as/key:','jpeg','tiff','bmp','u: roll up','d: roll down','l: roll left','r: roll right']
3199	else:
3200	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2','n: next','p: previous']
3201	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
3202	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
3203	cb.SetValue(' save as/key:')
3204	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
3205	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
3206	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
3207	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
3208	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
3209	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
3210	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
3211	# Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
3212	Page.camera['position'] = drawingData['cameraPos']
3213	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
3214	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
3215	Page.canvas.SetCurrent()
3216	Draw('main')
3217

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