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source: trunk/GSASIIplot.py @ 515

Last change on this file since 515 was 515, checked in by vondreele, 11 years ago
add num variables to ViewLSparams final fixup of error analysis plots add to help file
Property svn:keywords set to `Date Author Revision URL Id`
File size: 123.4 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2012-03-07 16:30:29 +0000 (Wed, 07 Mar 2012) $
4	# $Author: vondreele $
5	# $Revision: 515 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 515 2012-03-07 16:30:29Z vondreele $
8	########### SVN repository information ###################
9	import math
10	import time
11	import copy
12	import os.path
13	import numpy as np
14	import numpy.linalg as nl
15	import wx
16	import wx.aui
17	import wx.glcanvas
18	import matplotlib as mpl
19	import mpl_toolkits.mplot3d.axes3d as mp3d
20	import GSASIIpath
21	import GSASIIgrid as G2gd
22	import GSASIIimage as G2img
23	import GSASIIpwd as G2pwd
24	import GSASIIIO as G2IO
25	import GSASIIpwdGUI as G2pdG
26	import GSASIIimgGUI as G2imG
27	import GSASIIphsGUI as G2phG
28	import GSASIIlattice as G2lat
29	import GSASIIspc as G2spc
30	import pytexture as ptx
31	from OpenGL.GL import *
32	from OpenGL.GLU import *
33	from OpenGL.GLUT import *
34	from OpenGL.GLE import *
35	from matplotlib.backends.backend_wx import _load_bitmap
36	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
37	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
38
39	# useful degree trig functions
40	sind = lambda x: math.sin(x*math.pi/180.)
41	cosd = lambda x: math.cos(x*math.pi/180.)
42	tand = lambda x: math.tan(x*math.pi/180.)
43	asind = lambda x: 180.*math.asin(x)/math.pi
44	acosd = lambda x: 180.*math.acos(x)/math.pi
45	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
46	atand = lambda x: 180.*math.atan(x)/math.pi
47	# numpy versions
48	npsind = lambda x: np.sin(x*np.pi/180.)
49	npcosd = lambda x: np.cos(x*np.pi/180.)
50	npacosd = lambda x: 180.*np.arccos(x)/np.pi
51	npasind = lambda x: 180.*np.arcsin(x)/np.pi
52	npatand = lambda x: 180.*np.arctan(x)/np.pi
53	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
54
55	class G2PlotMpl(wx.Panel):
56	def __init__(self,parent,id=-1,dpi=None,**kwargs):
57	wx.Panel.__init__(self,parent,id=id,**kwargs)
58	mpl.rcParams['legend.fontsize'] = 10
59	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
60	self.canvas = Canvas(self,-1,self.figure)
61	self.toolbar = GSASIItoolbar(self.canvas)
62
63	self.toolbar.Realize()
64
65	sizer=wx.BoxSizer(wx.VERTICAL)
66	sizer.Add(self.canvas,1,wx.EXPAND)
67	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
68	self.SetSizer(sizer)
69
70	class G2PlotOgl(wx.Panel):
71	def __init__(self,parent,id=-1,dpi=None,**kwargs):
72	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
73	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
74	self.camera = {}
75	sizer=wx.BoxSizer(wx.VERTICAL)
76	sizer.Add(self.canvas,1,wx.EXPAND)
77	self.SetSizer(sizer)
78
79	class G2Plot3D(wx.Panel):
80	def __init__(self,parent,id=-1,dpi=None,**kwargs):
81	wx.Panel.__init__(self,parent,id=id,**kwargs)
82	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
83	self.canvas = Canvas(self,-1,self.figure)
84	self.toolbar = GSASIItoolbar(self.canvas)
85
86	self.toolbar.Realize()
87
88	sizer=wx.BoxSizer(wx.VERTICAL)
89	sizer.Add(self.canvas,1,wx.EXPAND)
90	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
91	self.SetSizer(sizer)
92
93	class G2PlotNoteBook(wx.Panel):
94	def __init__(self,parent,id=-1):
95	wx.Panel.__init__(self,parent,id=id)
96	#so one can't delete a plot page!!
97	self.nb = wx.aui.AuiNotebook(self, \
98	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
99	sizer = wx.BoxSizer()
100	sizer.Add(self.nb,1,wx.EXPAND)
101	self.SetSizer(sizer)
102	self.status = parent.CreateStatusBar()
103	self.status.SetFieldsCount(2)
104	self.status.SetStatusWidths([150,-1])
105	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
106
107	self.plotList = []
108
109	def addMpl(self,name=""):
110	page = G2PlotMpl(self.nb)
111	self.nb.AddPage(page,name)
112
113	self.plotList.append(name)
114
115	return page.figure
116
117	def add3D(self,name=""):
118	page = G2Plot3D(self.nb)
119	self.nb.AddPage(page,name)
120
121	self.plotList.append(name)
122
123	return page.figure
124
125	def addOgl(self,name=""):
126	page = G2PlotOgl(self.nb)
127	self.nb.AddPage(page,name)
128
129	self.plotList.append(name)
130
131	return page.figure
132
133	def Delete(self,name):
134	try:
135	item = self.plotList.index(name)
136	del self.plotList[item]
137	self.nb.DeletePage(item)
138	except ValueError: #no plot of this name - do nothing
139	return
140
141	def clear(self):
142	while self.nb.GetPageCount():
143	self.nb.DeletePage(0)
144	self.plotList = []
145	self.status.DestroyChildren()
146
147	def Rename(self,oldName,newName):
148	try:
149	item = self.plotList.index(oldName)
150	self.plotList[item] = newName
151	self.nb.SetPageText(item,newName)
152	except ValueError: #no plot of this name - do nothing
153	return
154
155	def OnPageChanged(self,event):
156	if self.plotList:
157	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
158	self.status.DestroyChildren() #get rid of special stuff on status bar
159
160	class GSASIItoolbar(Toolbar):
161	ON_MPL_HELP = wx.NewId()
162	def __init__(self,plotCanvas):
163	Toolbar.__init__(self,plotCanvas)
164	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6
165	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
166	help = os.path.join(os.path.split(__file__)[0],'help.ico')
167	self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
168	wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
169	def OnHelp(self,event):
170	Page = self.GetParent().GetParent()
171	pageNo = Page.GetSelection()
172	bookmark = Page.GetPageText(pageNo)
173	bookmark = bookmark.strip(')').replace('(','_')
174	G2gd.ShowHelp(bookmark,self.TopLevelParent)
175
176	################################################################################
177	##### PlotSngl
178	################################################################################
179
180	def PlotSngl(self,newPlot=False):
181	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
182	to F, F**2, etc. as requested
183	'''
184	from matplotlib.patches import Circle
185	global HKL,HKLF
186
187	def OnSCMotion(event):
188	xpos = event.xdata
189	if xpos:
190	xpos = round(xpos) #avoid out of frame mouse position
191	ypos = round(event.ydata)
192	zpos = Data['Layer']
193	if '100' in Data['Zone']:
194	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
195	elif '010' in Data['Zone']:
196	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
197	elif '001' in Data['Zone']:
198	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
199	Page.canvas.SetToolTipString(HKLtxt)
200	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
201
202	def OnSCPick(event):
203	zpos = Data['Layer']
204	pos = event.artist.center
205	if '100' in Data['Zone']:
206	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
207	hkl = np.array([zpos,pos[0],pos[1]])
208	elif '010' in Data['Zone']:
209	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
210	hkl = np.array([pos[0],zpos,pos[1]])
211	elif '001' in Data['Zone']:
212	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
213	hkl = np.array([pos[0],pos[1],zpos])
214	h,k,l = hkl
215	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
216	if len(hklf):
217	Fosq,sig,Fcsq = hklf[0]
218	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
219	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
220
221	def OnSCKeyPress(event):
222	print event.key
223
224	try:
225	plotNum = self.G2plotNB.plotList.index('Structure Factors')
226	Page = self.G2plotNB.nb.GetPage(plotNum)
227	if not newPlot:
228	Plot = Page.figure.gca() #get previous powder plot & get limits
229	xylim = Plot.get_xlim(),Plot.get_ylim()
230	Page.figure.clf()
231	Plot = Page.figure.gca() #get a fresh plot after clf()
232	except ValueError:
233	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
234	plotNum = self.G2plotNB.plotList.index('Structure Factors')
235	Page = self.G2plotNB.nb.GetPage(plotNum)
236	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
237	Page.canvas.mpl_connect('pick_event', OnSCPick)
238	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
239	Page.SetFocus()
240
241	Plot.set_aspect(aspect='equal')
242	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
243	Data = self.PatternTree.GetItemPyData( \
244	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
245	Type = Data['Type']
246	scale = Data['Scale']
247	HKLmax = Data['HKLmax']
248	HKLmin = Data['HKLmin']
249	FosqMax = Data['FoMax']
250	FoMax = math.sqrt(FosqMax)
251	ifFc = Data['ifFc']
252	xlabel = ['k, h=','h, k=','h, l=']
253	ylabel = ['l','l','k']
254	zones = ['100','010','001']
255	pzone = [[1,2],[0,2],[0,1]]
256	izone = zones.index(Data['Zone'])
257	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
258	HKL = []
259	HKLF = []
260	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
261	HKL.append(H)
262	HKLF.append([Fosq,sig,Fcsq])
263	if H[izone] == Data['Layer']:
264	B = 0
265	if Type == 'Fosq':
266	A = scale*Fosq/FosqMax
267	B = scale*Fcsq/FosqMax
268	C = abs(A-B)
269	elif Type == 'Fo':
270	A = scale*math.sqrt(max(0,Fosq))/FoMax
271	B = scale*math.sqrt(max(0,Fcsq))/FoMax
272	C = abs(A-B)
273	elif Type == '\|DFsq\|/sig':
274	A = abs(Fosq-Fcsq)/(scale*sig)
275	elif Type == '\|DFsq\|>sig':
276	A = abs(Fosq-Fcsq)/(scale*sig)
277	if A < 1.0: A = 0
278	elif Type == '\|DFsq\|>3sig':
279	A = abs(Fosq-Fcsq)/(scale*sig)
280	if A < 3.0: A = 0
281	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
282	if A > 0.0:
283	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
284	if B:
285	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
286	radius = C
287	if radius > 0:
288	if A > B:
289	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
290	else:
291	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
292	HKL = np.array(HKL,dtype=np.int)
293	HKLF = np.array(HKLF)
294	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
295	Plot.set_ylabel(ylabel[izone],fontsize=12)
296	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
297	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
298	if not newPlot:
299	Page.toolbar.push_current()
300	Plot.set_xlim(xylim[0])
301	Plot.set_ylim(xylim[1])
302	xylim = []
303	Page.toolbar.push_current()
304	Page.toolbar.draw()
305	else:
306	Page.canvas.draw()
307
308	################################################################################
309	##### PlotPatterns
310	################################################################################
311
312	def PlotPatterns(G2frame,newPlot=False):
313	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
314	2-theta or q (future TOF). Can display multiple patterns as "waterfall plots" or contour plots. Log I
315	plotting available.
316	'''
317	global HKL
318
319	def OnKeyBox(event):
320	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('Powder Patterns'):
321	event.key = cb.GetValue()[0]
322	cb.SetValue(' key press')
323	OnPlotKeyPress(event)
324
325	def OnPlotKeyPress(event):
326	newPlot = False
327	if event.key == 'w':
328	if G2frame.Weight:
329	G2frame.Weight = False
330	else:
331	G2frame.Weight = True
332	G2frame.SinglePlot = True
333	newPlot = True
334	elif event.key == 'n':
335	if G2frame.Contour:
336	pass
337	else:
338	if G2frame.logPlot:
339	G2frame.logPlot = False
340	else:
341	G2frame.Offset[0] = 0
342	G2frame.logPlot = True
343	newPlot = True
344	elif event.key == 'u':
345	if G2frame.Contour:
346	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
347	elif G2frame.logPlot:
348	pass
349	elif G2frame.Offset[0] < 100.:
350	G2frame.Offset[0] += 1.
351	elif event.key == 'd':
352	if G2frame.Contour:
353	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
354	elif G2frame.logPlot:
355	pass
356	elif G2frame.Offset[0] > 0.:
357	G2frame.Offset[0] -= 1.
358	elif event.key == 'l':
359	G2frame.Offset[1] -= 1.
360	elif event.key == 'r':
361	G2frame.Offset[1] += 1.
362	elif event.key == 'o':
363	G2frame.Offset = [0,0]
364	elif event.key == 'c':
365	newPlot = True
366	if G2frame.Contour:
367	G2frame.Contour = False
368	else:
369	G2frame.Contour = True
370	G2frame.SinglePlot = False
371	G2frame.Offset = [0.,0.]
372	elif event.key == 'q':
373	newPlot = True
374	if G2frame.qPlot:
375	G2frame.qPlot = False
376	else:
377	G2frame.qPlot = True
378	elif event.key == 's':
379	if G2frame.Contour:
380	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
381	choice.sort()
382	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
383	if dlg.ShowModal() == wx.ID_OK:
384	sel = dlg.GetSelection()
385	G2frame.ContourColor = choice[sel]
386	else:
387	G2frame.ContourColor = 'Paired'
388	dlg.Destroy()
389	else:
390	if G2frame.SinglePlot:
391	G2frame.SinglePlot = False
392	else:
393	G2frame.SinglePlot = True
394	newPlot = True
395	elif event.key == '+':
396	if G2frame.PickId:
397	G2frame.PickId = False
398	elif event.key == 'i': #for smoothing contour plot
399	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
400	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
401	'mitchell','sinc','lanczos']
402	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
403	if dlg.ShowModal() == wx.ID_OK:
404	sel = dlg.GetSelection()
405	G2frame.Interpolate = choice[sel]
406	else:
407	G2frame.Interpolate = 'nearest'
408	dlg.Destroy()
409
410	PlotPatterns(G2frame,newPlot=newPlot)
411
412	def OnMotion(event):
413	xpos = event.xdata
414	if xpos: #avoid out of frame mouse position
415	ypos = event.ydata
416	Page.canvas.SetCursor(wx.CROSS_CURSOR)
417	try:
418	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
419	Parms = dict(zip(Names,Values))
420	try:
421	wave = Parms['Lam']
422	except KeyError:
423	wave = Parms['Lam1']
424	if G2frame.qPlot:
425	xpos = 2.0asind(xposwave/(4*math.pi))
426	dsp = 0.0
427	if abs(xpos) > 0.: #avoid possible singularity at beam center
428	dsp = wave/(2.*sind(abs(xpos)/2.0))
429	if G2frame.Contour:
430	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
431	else:
432	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
433	if G2frame.itemPicked:
434	Page.canvas.SetToolTipString('%9.3f'%(xpos))
435	if G2frame.PickId:
436	found = []
437	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists']:
438	if len(HKL):
439	view = Page.toolbar._views.forward()[0][:2]
440	wid = view[1]-view[0]
441	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
442	if len(found):
443	h,k,l = found[0][:3]
444	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
445	else:
446	Page.canvas.SetToolTipString('')
447
448	except TypeError:
449	G2frame.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
450
451	def OnPick(event):
452	if G2frame.itemPicked is not None: return
453	PatternId = G2frame.PatternId
454	try:
455	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
456	except TypeError:
457	return
458	Parms = dict(zip(Names,Values))
459	try:
460	wave = Parms['Lam']
461	except KeyError:
462	wave = Parms['Lam1']
463	PickId = G2frame.PickId
464	pick = event.artist
465	mouse = event.mouseevent
466	xpos = pick.get_xdata()
467	ypos = pick.get_ydata()
468	ind = event.ind
469	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
470	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
471	if ind.all() != [0]: #picked a data point
472	if 'C' in Parms['Type']: #CW data - TOF later in an elif
473	ins = [Parms[x] for x in ['U','V','W','X','Y']]
474	if G2frame.qPlot: #qplot - convert back to 2-theta
475	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
476	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
477	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
478	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
479	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
480	data.append(XY)
481	G2pdG.UpdatePeakGrid(G2frame,data)
482	PlotPatterns(G2frame)
483	else: #picked a peak list line
484	G2frame.itemPicked = pick
485	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
486	if ind.all() != [0]: #picked a data point
487	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
488	data = G2frame.PatternTree.GetItemPyData(LimitId)
489	if 'C' in Parms['Type']: #CW data - TOF later in an elif
490	if G2frame.qPlot: #qplot - convert back to 2-theta
491	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
492	if mouse.button==1:
493	data[1][0] = min(xy[0],data[1][1])
494	if mouse.button==3:
495	data[1][1] = max(xy[0],data[1][0])
496	G2frame.PatternTree.SetItemPyData(LimitId,data)
497	G2pdG.UpdateLimitsGrid(G2frame,data)
498	PlotPatterns(G2frame)
499	else: #picked a limit line
500	G2frame.itemPicked = pick
501	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists':
502	G2frame.itemPicked = pick
503	pick = str(pick)
504
505	def OnRelease(event):
506	if G2frame.itemPicked is None: return
507	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
508	Parms = dict(zip(Names,Values))
509	try:
510	wave = Parms['Lam']
511	except KeyError:
512	wave = Parms['Lam1']
513	xpos = event.xdata
514	PickId = G2frame.PickId
515	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
516	lines = []
517	for line in G2frame.Lines: lines.append(line.get_xdata()[0])
518	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
519	if lineNo in [0,1]:
520	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
521	data = G2frame.PatternTree.GetItemPyData(LimitId)
522	if G2frame.qPlot:
523	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
524	else:
525	data[1][lineNo] = xpos
526	G2frame.PatternTree.SetItemPyData(LimitId,data)
527	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
528	G2pdG.UpdateLimitsGrid(G2frame,data)
529	else:
530	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
531	data = G2frame.PatternTree.GetItemPyData(PeakId)
532	# print 'peaks',xpos
533	if event.button == 3:
534	del data[lineNo-2]
535	else:
536	if G2frame.qPlot:
537	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
538	else:
539	data[lineNo-2][0] = xpos
540	G2frame.PatternTree.SetItemPyData(PeakId,data)
541	G2pdG.UpdatePeakGrid(G2frame,data)
542	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' and xpos:
543	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
544	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
545	if 'Line' not in pick: #avoid data points, etc.
546	num = Phases.keys().index(pick)
547	if num:
548	G2frame.refDelt = -(event.ydata-G2frame.refOffset)/(num*Ymax)
549	else: #1st row of refl ticks
550	G2frame.refOffset = event.ydata
551	PlotPatterns(G2frame)
552	G2frame.itemPicked = None
553
554	xylim = []
555	try:
556	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
557	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
558	if not newPlot:
559	Plot = Page.figure.gca() #get previous powder plot & get limits
560	xylim = Plot.get_xlim(),Plot.get_ylim()
561	Page.figure.clf()
562	Plot = Page.figure.gca() #get a fresh plot after clf()
563	except ValueError:
564	newPlot = True
565	G2frame.Cmax = 1.0
566	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
567	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
568	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
569	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
570	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
571	Page.canvas.mpl_connect('pick_event', OnPick)
572	Page.canvas.mpl_connect('button_release_event', OnRelease)
573	Page.SetFocus()
574	G2frame.G2plotNB.status.DestroyChildren()
575	if G2frame.Contour:
576	Choice = (' key press','d: lower contour max','u: raise contour max',
577	'i: interpolation method','s: color scheme','c: contour off')
578	else:
579	if G2frame.logPlot:
580	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
581	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
582	else:
583	Choice = (' key press','l: offset left','r: offset right','d: offset down',
584	'u: offset up','o: reset offset','n: log(I) on','c: contour on',
585	'q: toggle q plot','s: toggle single plot','w: toggle divide by sig','+: no selection')
586	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
587	choices=Choice)
588	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
589	cb.SetValue(' key press')
590
591	PickId = G2frame.PickId
592	PatternId = G2frame.PatternId
593	colors=['b','g','r','c','m','k']
594	Lines = []
595	if G2frame.SinglePlot:
596	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
597	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
598	PlotList = [Pattern,]
599	ParmList = [G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
600	G2frame.PatternId, 'Instrument Parameters'))[1],]
601	else:
602	PlotList = []
603	ParmList = []
604	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
605	while item:
606	if 'PWDR' in G2frame.PatternTree.GetItemText(item):
607	Pattern = G2frame.PatternTree.GetItemPyData(item)
608	if len(Pattern) < 3: # put name on end if needed
609	Pattern.append(G2frame.PatternTree.GetItemText(item))
610	PlotList.append(Pattern)
611	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
612	item,'Instrument Parameters'))[1])
613	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
614	Ymax = 1.0
615	lenX = 0
616	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
617	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
618	HKL = []
619	if Phases:
620	for peak in Phases[G2frame.RefList]:
621	HKL.append(peak[:6])
622	HKL = np.array(HKL)
623	else:
624	HKL = np.array(G2frame.HKL)
625	for Pattern in PlotList:
626	xye = Pattern[1]
627	Ymax = max(Ymax,max(xye[1]))
628	offset = G2frame.Offset[0]*Ymax/100.0
629	Title = 'Powder Patterns: '+os.path.split(G2frame.GSASprojectfile)[1]
630	if G2frame.logPlot:
631	Title = 'log('+Title+')'
632	Plot.set_title(Title)
633	if G2frame.qPlot:
634	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
635	else:
636	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
637	if G2frame.Weight:
638	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=14)
639	else:
640	Plot.set_ylabel('Intensity',fontsize=12)
641	if G2frame.Contour:
642	ContourZ = []
643	ContourY = []
644	Nseq = 0
645	if len(PlotList) < 2:
646	G2frame.Contour = False
647	for N,Pattern in enumerate(PlotList):
648	Parms = ParmList[N]
649	ifpicked = False
650	LimitId = 0
651	xye = np.array(Pattern[1])
652	if PickId:
653	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
654	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
655	if G2frame.qPlot:
656	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
657	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
658	else:
659	X = xye[0]
660	if not lenX:
661	lenX = len(X)
662	Y = xye[1]+offset*N
663	if LimitId:
664	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
665	if G2frame.qPlot:
666	limits = 4np.pinpsind(limits/2.0)/Parms[1]
667	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
668	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
669	if G2frame.Contour:
670
671	if lenX == len(X):
672	ContourY.append(N)
673	ContourZ.append(Y)
674	ContourX = X
675	Nseq += 1
676	Plot.set_ylabel('Data sequence',fontsize=12)
677	else:
678	X += G2frame.Offset[1].005N
679	if ifpicked:
680	Z = xye[3]+offset*N
681	W = xye[4]+offset*N
682	D = xye[5]-Ymax*G2frame.delOffset
683	if G2frame.logPlot:
684	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
685	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
686	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
687	elif G2frame.Weight:
688	DY = xye[1]*np.sqrt(xye[2])
689	DYmax = max(DY)
690	DZ = xye[3]*np.sqrt(xye[2])
691	DS = xye[5]np.sqrt(xye[2])-DYmaxG2frame.delOffset
692	Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False)
693	Plot.plot(X,DZ,colors[(N+1)%6],picker=False)
694	Plot.plot(X,DS,colors[(N+3)%6],picker=False)
695	Plot.axhline(0.,color=wx.BLACK)
696	else:
697	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
698	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
699	Plot.plot(X,W,colors[(N+2)%6],picker=False)
700	Plot.plot(X,D,colors[(N+3)%6],picker=False)
701	Plot.axhline(0.,color=wx.BLACK)
702	Page.canvas.SetToolTipString('')
703	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
704	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
705	Page.canvas.SetToolTipString(tip)
706	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
707	for item in data:
708	if G2frame.qPlot:
709	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
710	else:
711	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
712	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
713	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
714	Page.canvas.SetToolTipString(tip)
715	data = G2frame.LimitsTable.GetData()
716	else:
717	if G2frame.logPlot:
718	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
719	else:
720	Plot.plot(X,Y,colors[N%6],picker=False)
721	if PickId and not G2frame.Contour:
722	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))[1::2]
723	Parms = dict(zip(Names,Values))
724	try:
725	wave = Parms['Lam']
726	except KeyError:
727	wave = Parms['Lam1']
728	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
729	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
730	for peak in peaks:
731	if G2frame.qPlot:
732	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
733	else:
734	Plot.axvline(peak[0],color='b')
735	for hkl in G2frame.HKL:
736	if G2frame.qPlot:
737	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
738	else:
739	Plot.axvline(hkl[5],color='r',dashes=(5,5))
740	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
741	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
742	for pId,phase in enumerate(Phases):
743	peaks = Phases[phase]
744	peak = np.array([[peak[4],peak[5]] for peak in peaks])
745	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
746	if G2frame.qPlot:
747	Plot.plot(2*np.pi/peak.T[0],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
748	else:
749	Plot.plot(peak.T[1],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
750	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
751	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
752
753	if G2frame.Contour:
754	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
755	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
756	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
757	Page.figure.colorbar(Img)
758	else:
759	G2frame.Lines = Lines
760	if not newPlot:
761	Page.toolbar.push_current()
762	Plot.set_xlim(xylim[0])
763	Plot.set_ylim(xylim[1])
764	xylim = []
765	Page.toolbar.push_current()
766	Page.toolbar.draw()
767	else:
768	Page.canvas.draw()
769	G2frame.Pwdr = True
770
771	################################################################################
772	##### PlotDeltSig
773	################################################################################
774
775	def PlotDeltSig(G2frame):
776	try:
777	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
778	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
779	Page.figure.clf()
780	Plot = Page.figure.gca() #get a fresh plot after clf()
781	except ValueError:
782	newPlot = True
783	G2frame.Cmax = 1.0
784	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
785	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
786	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
787	PatternId = G2frame.PatternId
788	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
789	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
790	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
791	xye = np.array(Pattern[1])
792	xmin = np.searchsorted(xye[0],limits[0])
793	xmax = np.searchsorted(xye[0],limits[1])
794	X = xye[0][xmin:xmax]
795	DS = xye[5][xmin:xmax]*np.sqrt(xye[2][xmin:xmax])
796	Page.SetFocus()
797	G2frame.G2plotNB.status.DestroyChildren()
798	DS.sort()
799	EDS = np.zeros_like(DS)
800	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
801	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
802	T = np.sqrt(np.log(1.0/DX**2))
803	top = 2.515517+0.802853T+0.010328T**2
804	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
805	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
806	low1 = np.searchsorted(EDS,-1.)
807	hi1 = np.searchsorted(EDS,1.)
808	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
809	frac = 100.*(hi1-low1)/len(DS)
810	G2frame.G2plotNB.status.SetStatusText( \
811	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
812	Plot.set_title('Normal probability for '+Pattern[-1])
813	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
814	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
815	Plot.plot(EDS,DS,'r+',label='result')
816	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
817	Plot.legend(loc='upper left')
818	np.seterr(invalid='warn')
819	Page.canvas.draw()
820
821	################################################################################
822	##### PlotISFG
823	################################################################################
824
825	def PlotISFG(G2frame,newPlot=False,type=''):
826	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
827	or multiple plots with waterfall and contour plots as options
828	'''
829	if not type:
830	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
831	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
832	return
833	superMinusOne = unichr(0xaf)+unichr(0xb9)
834
835	def OnPlotKeyPress(event):
836	newPlot = False
837	if event.key == 'u':
838	if G2frame.Contour:
839	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
840	elif G2frame.Offset[0] < 100.:
841	G2frame.Offset[0] += 1.
842	elif event.key == 'd':
843	if G2frame.Contour:
844	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
845	elif G2frame.Offset[0] > 0.:
846	G2frame.Offset[0] -= 1.
847	elif event.key == 'l':
848	G2frame.Offset[1] -= 1.
849	elif event.key == 'r':
850	G2frame.Offset[1] += 1.
851	elif event.key == 'o':
852	G2frame.Offset = [0,0]
853	elif event.key == 'c':
854	newPlot = True
855	if G2frame.Contour:
856	G2frame.Contour = False
857	else:
858	G2frame.Contour = True
859	G2frame.SinglePlot = False
860	G2frame.Offset = [0.,0.]
861	elif event.key == 's':
862	if G2frame.Contour:
863	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
864	choice.sort()
865	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
866	if dlg.ShowModal() == wx.ID_OK:
867	sel = dlg.GetSelection()
868	G2frame.ContourColor = choice[sel]
869	else:
870	G2frame.ContourColor = 'Paired'
871	dlg.Destroy()
872	else:
873	if G2frame.SinglePlot:
874	G2frame.SinglePlot = False
875	else:
876	G2frame.SinglePlot = True
877	elif event.key == 'i': #for smoothing contour plot
878	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
879	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
880	'mitchell','sinc','lanczos']
881	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
882	if dlg.ShowModal() == wx.ID_OK:
883	sel = dlg.GetSelection()
884	G2frame.Interpolate = choice[sel]
885	else:
886	G2frame.Interpolate = 'nearest'
887	dlg.Destroy()
888	elif event.key == 't' and not G2frame.Contour:
889	if G2frame.Legend:
890	G2frame.Legend = False
891	else:
892	G2frame.Legend = True
893
894
895	PlotISFG(G2frame,newPlot=newPlot,type=type)
896
897	def OnKeyBox(event):
898	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
899	event.key = cb.GetValue()[0]
900	cb.SetValue(' key press')
901	OnPlotKeyPress(event)
902
903	def OnMotion(event):
904	xpos = event.xdata
905	if xpos: #avoid out of frame mouse position
906	ypos = event.ydata
907	Page.canvas.SetCursor(wx.CROSS_CURSOR)
908	try:
909	if G2frame.Contour:
910	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
911	else:
912	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
913	except TypeError:
914	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
915
916	xylim = []
917	try:
918	plotNum = G2frame.G2plotNB.plotList.index(type)
919	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
920	if not newPlot:
921	Plot = Page.figure.gca() #get previous plot & get limits
922	xylim = Plot.get_xlim(),Plot.get_ylim()
923	Page.figure.clf()
924	Plot = Page.figure.gca()
925	except ValueError:
926	newPlot = True
927	G2frame.Cmax = 1.0
928	Plot = G2frame.G2plotNB.addMpl(type).gca()
929	plotNum = G2frame.G2plotNB.plotList.index(type)
930	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
931	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
932	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
933
934	Page.SetFocus()
935	G2frame.G2plotNB.status.DestroyChildren()
936	if G2frame.Contour:
937	Choice = (' key press','d: lower contour max','u: raise contour max',
938	'i: interpolation method','s: color scheme','c: contour off')
939	else:
940	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
941	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
942	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
943	choices=Choice)
944	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
945	cb.SetValue(' key press')
946	PatternId = G2frame.PatternId
947	PickId = G2frame.PickId
948	Plot.set_title(type)
949	if type == 'G(R)':
950	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
951	else:
952	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
953	Plot.set_ylabel(r''+type,fontsize=14)
954	colors=['b','g','r','c','m','k']
955	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
956	Pattern = []
957	if G2frame.SinglePlot:
958	name = G2frame.PatternTree.GetItemText(PatternId)
959	name = type+name[4:]
960	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
961	Pattern = G2frame.PatternTree.GetItemPyData(Id)
962	if Pattern:
963	Pattern.append(name)
964	PlotList = [Pattern,]
965	else:
966	PlotList = []
967	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
968	while item:
969	if 'PDF' in G2frame.PatternTree.GetItemText(item):
970	name = type+G2frame.PatternTree.GetItemText(item)[4:]
971	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
972	Pattern = G2frame.PatternTree.GetItemPyData(Id)
973	if Pattern:
974	Pattern.append(name)
975	PlotList.append(Pattern)
976	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
977	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
978	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
979	Xb = [0.,10.]
980	Yb = [0.,-40.np.pinumbDen]
981	Ymax = 1.0
982	lenX = 0
983	for Pattern in PlotList:
984	xye = Pattern[1]
985	Ymax = max(Ymax,max(xye[1]))
986	offset = G2frame.Offset[0]*Ymax/100.0
987	if G2frame.Contour:
988	ContourZ = []
989	ContourY = []
990	Nseq = 0
991	for N,Pattern in enumerate(PlotList):
992	xye = Pattern[1]
993	if PickId:
994	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
995	X = xye[0]
996	if not lenX:
997	lenX = len(X)
998	Y = xye[1]+offset*N
999	if G2frame.Contour:
1000	if lenX == len(X):
1001	ContourY.append(N)
1002	ContourZ.append(Y)
1003	ContourX = X
1004	Nseq += 1
1005	Plot.set_ylabel('Data sequence',fontsize=12)
1006	else:
1007	X = xye[0]+G2frame.Offset[1].005N
1008	if ifpicked:
1009	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1010	Page.canvas.SetToolTipString('')
1011	else:
1012	if G2frame.Legend:
1013	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1014	else:
1015	Plot.plot(X,Y,colors[N%6],picker=False)
1016	if type == 'G(R)':
1017	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1018	elif type == 'F(Q)':
1019	Plot.axhline(0.,color=wx.BLACK)
1020	elif type == 'S(Q)':
1021	Plot.axhline(1.,color=wx.BLACK)
1022	if G2frame.Contour:
1023	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1024	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1025	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1026	Page.figure.colorbar(Img)
1027	elif G2frame.Legend:
1028	Plot.legend(loc='best')
1029	if not newPlot:
1030	Page.toolbar.push_current()
1031	Plot.set_xlim(xylim[0])
1032	Plot.set_ylim(xylim[1])
1033	xylim = []
1034	Page.toolbar.push_current()
1035	Page.toolbar.draw()
1036	else:
1037	Page.canvas.draw()
1038
1039	################################################################################
1040	##### PlotXY
1041	################################################################################
1042
1043	def PlotXY(G2frame,XY,newPlot=False,type=''):
1044	'''simple plot of xy data, used for diagnostic purposes
1045	'''
1046	def OnMotion(event):
1047	xpos = event.xdata
1048	if xpos: #avoid out of frame mouse position
1049	ypos = event.ydata
1050	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1051	try:
1052	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
1053	except TypeError:
1054	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1055
1056	try:
1057	plotNum = G2frame.G2plotNB.plotList.index(type)
1058	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1059	if not newPlot:
1060	Plot = Page.figure.gca()
1061	xylim = Plot.get_xlim(),Plot.get_ylim()
1062	Page.figure.clf()
1063	Plot = Page.figure.gca()
1064	except ValueError:
1065	newPlot = True
1066	Plot = G2frame.G2plotNB.addMpl(type).gca()
1067	plotNum = G2frame.G2plotNB.plotList.index(type)
1068	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1069	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1070
1071	Page.SetFocus()
1072	G2frame.G2plotNB.status.DestroyChildren()
1073	Plot.set_title(type)
1074	Plot.set_xlabel(r'X',fontsize=14)
1075	Plot.set_ylabel(r''+type,fontsize=14)
1076	colors=['b','g','r','c','m','k']
1077	Ymax = 1.0
1078	lenX = 0
1079	X,Y = XY[:2]
1080	Ymax = max(Ymax,max(Y))
1081	Plot.plot(X,Y,'k',picker=False)
1082	if not newPlot:
1083	Page.toolbar.push_current()
1084	Plot.set_xlim(xylim[0])
1085	Plot.set_ylim(xylim[1])
1086	xylim = []
1087	Page.toolbar.push_current()
1088	Page.toolbar.draw()
1089	else:
1090	Page.canvas.draw()
1091
1092	################################################################################
1093	##### PlotPowderLines
1094	################################################################################
1095
1096	def PlotPowderLines(G2frame):
1097	''' plotting of powder lines (i.e. no powder pattern) as sticks
1098	'''
1099	global HKL
1100
1101	def OnMotion(event):
1102	xpos = event.xdata
1103	if xpos: #avoid out of frame mouse position
1104	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1105	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1106	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
1107	found = []
1108	if len(HKL):
1109	view = Page.toolbar._views.forward()[0][:2]
1110	wid = view[1]-view[0]
1111	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1112	if len(found):
1113	h,k,l = found[0][:3]
1114	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1115	else:
1116	Page.canvas.SetToolTipString('')
1117
1118	try:
1119	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1120	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1121	Page.figure.clf()
1122	Plot = Page.figure.gca()
1123	except ValueError:
1124	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
1125	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1126	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1127	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1128
1129	Page.SetFocus()
1130	Plot.set_title('Powder Pattern Lines')
1131	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1132	PickId = G2frame.PickId
1133	PatternId = G2frame.PatternId
1134	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
1135	for peak in peaks:
1136	Plot.axvline(peak[0],color='b')
1137	HKL = np.array(G2frame.HKL)
1138	for hkl in G2frame.HKL:
1139	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1140	xmin = peaks[0][0]
1141	xmax = peaks[-1][0]
1142	delt = xmax-xmin
1143	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1144	Plot.set_xlim(xlim)
1145	Page.canvas.draw()
1146	Page.toolbar.push_current()
1147
1148	################################################################################
1149	##### PlotPeakWidths
1150	################################################################################
1151
1152	def PlotPeakWidths(G2frame):
1153	''' Plotting of instrument broadening terms as function of 2-theta (future TOF)
1154	Seen when "Instrument Parameters" chosen from powder pattern data tree
1155	'''
1156	PatternId = G2frame.PatternId
1157	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1158	if limitID:
1159	limits = G2frame.PatternTree.GetItemPyData(limitID)
1160	else:
1161	return
1162	instParms = G2frame.PatternTree.GetItemPyData( \
1163	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1164	if instParms[0][0] in ['PXC','PNC']:
1165	lam = instParms[1][1]
1166	if len(instParms[1]) == 13:
1167	GU,GV,GW,LX,LY = instParms[0][6:11]
1168	else:
1169	GU,GV,GW,LX,LY = instParms[0][4:9]
1170	peakID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
1171	if peakID:
1172	peaks = G2frame.PatternTree.GetItemPyData(peakID)
1173	else:
1174	peaks = []
1175
1176	try:
1177	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1178	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1179	Page.figure.clf()
1180	Plot = Page.figure.gca()
1181	except ValueError:
1182	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
1183	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1184	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1185	Page.SetFocus()
1186
1187	Page.canvas.SetToolTipString('')
1188	colors=['b','g','r','c','m','k']
1189	Xmin,Xmax = limits[1]
1190	Xmin = min(0.5,max(Xmin,1))
1191	Xmin /= 2
1192	Xmax /= 2
1193	nPts = 100
1194	delt = (Xmax-Xmin)/nPts
1195	thetas = []
1196	for i in range(nPts):
1197	thetas.append(Xmin+i*delt)
1198	X = []
1199	Y = []
1200	Z = []
1201	W = []
1202	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1203	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1204	gamFW = lambda s,g: math.exp(math.log(s*5+2.69269s*4g+2.42843s3g*2+4.47163s*2g*3+0.07842sg4+g*5)/5.)
1205	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1206	for theta in thetas:
1207	X.append(4.0math.pisind(theta)/lam) #q
1208	s = sig(theta,GU,GV,GW)
1209	g = gam(theta,LX,LY)
1210	G = gamFW(g,s)
1211	Y.append(s/tand(theta))
1212	Z.append(g/tand(theta))
1213	W.append(G/tand(theta))
1214	Plot.set_title('Instrument and sample peak widths')
1215	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1216	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1217	Plot.plot(X,Y,color='r',label='Gaussian')
1218	Plot.plot(X,Z,color='g',label='Lorentzian')
1219	Plot.plot(X,W,color='b',label='G+L')
1220	X = []
1221	Y = []
1222	Z = []
1223	W = []
1224	V = []
1225	for peak in peaks:
1226	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1227	try:
1228	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1229	except ValueError:
1230	s = 0.01
1231	g = peak[6]*math.pi/18000.
1232	G = gamFW(g,s)
1233	Y.append(s/tand(peak[0]/2.))
1234	Z.append(g/tand(peak[0]/2.))
1235	W.append(G/tand(peak[0]/2.))
1236	Plot.plot(X,Y,'+',color='r',label='G peak')
1237	Plot.plot(X,Z,'+',color='g',label='L peak')
1238	Plot.plot(X,W,'+',color='b',label='G+L peak')
1239	Plot.legend(loc='best')
1240	Page.canvas.draw()
1241
1242	################################################################################
1243	##### PlotSizeStrainPO
1244	################################################################################
1245
1246	def PlotSizeStrainPO(G2frame,data,Start=False):
1247	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1248	'''
1249
1250	PatternId = G2frame.PatternId
1251	generalData = data['General']
1252	SGData = generalData['SGData']
1253	SGLaue = SGData['SGLaue']
1254	if Start: #initialize the spherical harmonics qlmn arrays
1255	ptx.pyqlmninit()
1256	Start = False
1257	# MuStrKeys = G2spc.MustrainNames(SGData)
1258	cell = generalData['Cell'][1:]
1259	A,B = G2lat.cell2AB(cell[:6])
1260	Vol = cell[6]
1261	useList = data['Histograms']
1262	phase = generalData['Name']
1263	plotType = generalData['Data plot type']
1264	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
1265	for ptype in plotDict:
1266	G2frame.G2plotNB.Delete(ptype)
1267
1268	for item in useList:
1269	if useList[item]['Show']:
1270	break
1271	else:
1272	return #nothing to show!!
1273
1274	numPlots = len(useList)
1275
1276	if plotType in ['Mustrain','Size']:
1277	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
1278	else:
1279	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
1280	plotNum = G2frame.G2plotNB.plotList.index(plotType)
1281	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1282	Page.SetFocus()
1283	G2frame.G2plotNB.status.SetStatusText('',1)
1284	if not Page.IsShown():
1285	Page.Show()
1286
1287	for item in useList:
1288	if useList[item]['Show']:
1289	PHI = np.linspace(0.,360.,30,True)
1290	PSI = np.linspace(0.,180.,30,True)
1291	X = np.outer(npsind(PHI),npsind(PSI))
1292	Y = np.outer(npcosd(PHI),npsind(PSI))
1293	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1294	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
1295	coeff = useList[item][plotDict[plotType]]
1296	except KeyError:
1297	break
1298	if plotType in ['Mustrain','Size']:
1299	if coeff[0] == 'isotropic':
1300	X *= coeff[1][0]
1301	Y *= coeff[1][0]
1302	Z *= coeff[1][0]
1303	elif coeff[0] == 'uniaxial':
1304
1305	def uniaxCalc(xyz,iso,aniso,axes):
1306	Z = np.array(axes)
1307	cp = abs(np.dot(xyz,Z))
1308	sp = np.sqrt(1.-cp**2)
1309	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
1310	return R*xyz
1311
1312	iso,aniso = coeff[1][:2]
1313	axes = np.inner(A,np.array(coeff[3]))
1314	axes /= nl.norm(axes)
1315	Shkl = np.array(coeff[1])
1316	XYZ = np.dstack((X,Y,Z))
1317	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
1318	X,Y,Z = np.dsplit(XYZ,3)
1319	X = X[:,:,0]
1320	Y = Y[:,:,0]
1321	Z = Z[:,:,0]
1322
1323	elif coeff[0] == 'ellipsoidal':
1324
1325	def ellipseCalc(xyz,E,R):
1326	XYZ = xyz*E.T
1327	return np.inner(XYZ.T,R)
1328
1329	S6 = coeff[4]
1330	Sij = G2lat.U6toUij(S6)
1331	E,R = nl.eigh(Sij)
1332	XYZ = np.dstack((X,Y,Z))
1333	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
1334	X,Y,Z = np.dsplit(XYZ,3)
1335	X = X[:,:,0]
1336	Y = Y[:,:,0]
1337	Z = Z[:,:,0]
1338
1339	elif coeff[0] == 'generalized':
1340
1341	def genMustrain(xyz,SGData,A,Shkl):
1342	uvw = np.inner(A.T,xyz)
1343	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1344	sum = np.sum(np.multiply(Shkl,Strm))
1345	sum = np.where(sum > 0.01,sum,0.01)
1346	sum = np.sqrt(sum)*math.pi/0.018 #centidegrees to radians!
1347	return sum*xyz
1348
1349	Shkl = np.array(coeff[4])
1350	if np.any(Shkl):
1351	XYZ = np.dstack((X,Y,Z))
1352	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1353	X,Y,Z = np.dsplit(XYZ,3)
1354	X = X[:,:,0]
1355	Y = Y[:,:,0]
1356	Z = Z[:,:,0]
1357
1358	if np.any(X) and np.any(Y) and np.any(Z):
1359	errFlags = np.seterr(all='ignore')
1360	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1361	np.seterr(all='ignore')
1362	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
1363	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
1364	Plot.set_xlim3d(XYZlim)
1365	Plot.set_ylim3d(XYZlim)
1366	Plot.set_zlim3d(XYZlim)
1367	Plot.set_aspect('equal')
1368	if plotType == 'Size':
1369	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
1370	Plot.set_xlabel(r'X, $\mu$m')
1371	Plot.set_ylabel(r'Y, $\mu$m')
1372	Plot.set_zlabel(r'Z, $\mu$m')
1373	else:
1374	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
1375	Plot.set_xlabel(r'X, $\mu$strain')
1376	Plot.set_ylabel(r'Y, $\mu$strain')
1377	Plot.set_zlabel(r'Z, $\mu$strain')
1378	else:
1379	h,k,l = generalData['POhkl']
1380	if coeff[0] == 'MD':
1381	print 'March-Dollase preferred orientation plot'
1382
1383	else:
1384	PH = np.array(generalData['POhkl'])
1385	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
1386	SHCoef = {}
1387	for item in coeff[5]:
1388	L,N = eval(item.strip('C'))
1389	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
1390	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1391	X = np.linspace(0,90.0,26)
1392	Y = G2lat.polfcal(ODFln,'0',X,0.0)
1393	Plot.plot(X,Y,color='k',label=str(PH))
1394	Plot.legend(loc='best')
1395	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
1396	Plot.set_xlabel(r'$\psi$',fontsize=16)
1397	Plot.set_ylabel('MRD',fontsize=14)
1398	Page.canvas.draw()
1399
1400	################################################################################
1401	##### PlotTexture
1402	################################################################################
1403
1404	def PlotTexture(G2frame,data,newPlot=False,Start=False):
1405	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
1406	plotting.
1407	dict generalData contains all phase info needed which is in data
1408	'''
1409
1410	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1411	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1412	PatternId = G2frame.PatternId
1413	generalData = data['General']
1414	SGData = generalData['SGData']
1415	textureData = generalData['SH Texture']
1416	G2frame.G2plotNB.Delete('Texture')
1417	if not textureData['Order']:
1418	return #no plot!!
1419	SHData = generalData['SH Texture']
1420	SHCoef = SHData['SH Coeff'][1]
1421	cell = generalData['Cell'][1:7]
1422	Amat,Bmat = G2lat.cell2AB(cell)
1423	sq2 = 1.0/math.sqrt(2.0)
1424
1425	def rp2xyz(r,p):
1426	z = npcosd(r)
1427	xy = np.sqrt(1.-z**2)
1428	return xynpsind(p),xynpcosd(p),z
1429
1430	def OnMotion(event):
1431	SHData = data['General']['SH Texture']
1432	if event.xdata and event.ydata: #avoid out of frame errors
1433	xpos = event.xdata
1434	ypos = event.ydata
1435	if 'Inverse' in SHData['PlotType']:
1436	r = xpos2+ypos2
1437	if r <= 1.0:
1438	if 'equal' in G2frame.Projection:
1439	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1440	else:
1441	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1442	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1443	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1444	y,x,z = list(xyz/np.max(np.abs(xyz)))
1445
1446	G2frame.G2plotNB.status.SetFields(['',
1447	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1448
1449	elif 'Axial' in SHData['PlotType']:
1450	pass
1451
1452	else: #ordinary pole figure
1453	z = xpos2+ypos2
1454	if z <= 1.0:
1455	z = np.sqrt(z)
1456	if 'equal' in G2frame.Projection:
1457	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1458	else:
1459	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1460	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1461	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1462
1463	if G2frame.Projection == '3D display' and 'Axial' not in SHData['PlotType']:
1464	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D('Texture'))
1465	else:
1466	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
1467	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1468	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1469	if G2frame.Projection == '3D display':
1470	pass
1471	else:
1472	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1473
1474	Page.SetFocus()
1475	G2frame.G2plotNB.status.SetFields(['',''])
1476	PH = np.array(SHData['PFhkl'])
1477	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1478	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1479	PX = np.array(SHData['PFxyz'])
1480	gam = atan2d(PX[0],PX[1])
1481	xy = math.sqrt(PX[0]2+PX[1]2)
1482	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1483	psi = asind(xy/xyz)
1484	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1485	if 'Axial' in SHData['PlotType']:
1486	X = np.linspace(0,90.0,26)
1487	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1488	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1489	Plot.legend(loc='best')
1490	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1491	Plot.set_xlabel(r'$\psi$',fontsize=16)
1492	Plot.set_ylabel('MRD',fontsize=14)
1493
1494	else:
1495	npts = 201
1496	if 'Inverse' in SHData['PlotType']:
1497	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1498	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1499	if 'equal' in G2frame.Projection:
1500	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1501	else:
1502	R = np.where(R <= 1.,2.*npatand(R),0.0)
1503	Z = np.zeros_like(R)
1504	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
1505	Z = np.reshape(Z,(npts,npts))
1506	CS = Plot.contour(Y,X,Z,aspect='equal')
1507	Plot.clabel(CS,fontsize=9,inline=1)
1508	try:
1509	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
1510	except ValueError:
1511	pass
1512	if newPlot:
1513	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1514	newPlot = False
1515	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
1516	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
1517
1518	else:
1519	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1520	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1521	if 'equal' in G2frame.Projection:
1522	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1523	else:
1524	R = np.where(R <= 1.,2.*npatand(R),0.0)
1525	Z = np.zeros_like(R)
1526	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
1527	Z = np.reshape(Z,(npts,npts))
1528	try:
1529	CS = Plot.contour(Y,X,Z,aspect='equal')
1530	Plot.clabel(CS,fontsize=9,inline=1)
1531	except ValueError:
1532	pass
1533	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
1534	if newPlot:
1535	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1536	newPlot = False
1537	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
1538	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
1539	Page.canvas.draw()
1540
1541	################################################################################
1542	##### PlotCovariance
1543	################################################################################
1544
1545	def PlotCovariance(G2frame,Data={}):
1546	if not Data:
1547	Data = G2frame.PatternTree.GetItemPyData(
1548	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1549	if not Data:
1550	print 'No covariance matrix available'
1551	return
1552	varyList = Data['varyList']
1553	values = Data['variables']
1554	Xmax = len(varyList)
1555	covMatrix = Data['covMatrix']
1556	sig = np.sqrt(np.diag(covMatrix))
1557	xvar = np.outer(sig,np.ones_like(sig))
1558	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
1559	title = ' for\n'+Data['title']
1560	newAtomDict = Data['newAtomDict']
1561
1562	def OnPlotKeyPress(event):
1563	newPlot = False
1564	if event.key == 's':
1565	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1566	choice.sort()
1567	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1568	if dlg.ShowModal() == wx.ID_OK:
1569	sel = dlg.GetSelection()
1570	G2frame.VcovColor = choice[sel]
1571	else:
1572	G2frame.VcovColor = 'RdYlGn'
1573	dlg.Destroy()
1574	PlotCovariance(G2frame)
1575
1576	def OnMotion(event):
1577	if event.button:
1578	ytics = imgAx.get_yticks()
1579	ytics = np.where(ytics<len(varyList),ytics,-1)
1580	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
1581	imgAx.set_yticklabels(ylabs)
1582
1583	if event.xdata and event.ydata: #avoid out of frame errors
1584	xpos = int(event.xdata+.5)
1585	ypos = int(event.ydata+.5)
1586	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
1587	if xpos == ypos:
1588	value = values[xpos]
1589	name = varyList[xpos]
1590	if varyList[xpos] in newAtomDict:
1591	name,value = newAtomDict[name]
1592	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
1593	else:
1594	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
1595	Page.canvas.SetToolTipString(msg)
1596	G2frame.G2plotNB.status.SetFields(['Key: s to change colors',msg])
1597	try:
1598	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1599	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1600	Page.figure.clf()
1601	Plot = Page.figure.gca()
1602	if not Page.IsShown():
1603	Page.Show()
1604	except ValueError:
1605	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
1606	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1607	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1608	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1609	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1610
1611	Page.SetFocus()
1612	G2frame.G2plotNB.status.SetFields(['',''])
1613	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
1614	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower')
1615	imgAx = Img.get_axes()
1616	ytics = imgAx.get_yticks()
1617	ylabs = [varyList[int(i)] for i in ytics[:-1]]
1618	imgAx.set_yticklabels(ylabs)
1619	colorBar = Page.figure.colorbar(Img)
1620	Plot.set_title('V-Cov matrix'+title)
1621	Plot.set_xlabel('Variable number')
1622	Plot.set_ylabel('Variable name')
1623	Page.canvas.draw()
1624
1625	################################################################################
1626	##### PlotSeq
1627	################################################################################
1628
1629	def PlotSeq(G2frame,SeqData,SeqSig,SeqNames,sampleParm):
1630
1631	def OnKeyPress(event):
1632	if event.key == 's' and sampleParm:
1633	if G2frame.xAxis:
1634	G2frame.xAxis = False
1635	else:
1636	G2frame.xAxis = True
1637	Draw(False)
1638	try:
1639	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1640	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1641	Page.figure.clf()
1642	Plot = Page.figure.gca()
1643	if not Page.IsShown():
1644	Page.Show()
1645	except ValueError:
1646	Plot = G2frame.G2plotNB.addMpl('Sequential refinement').gca()
1647	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1648	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1649	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
1650	G2frame.xAxis = False
1651
1652	def Draw(newPlot):
1653	Page.SetFocus()
1654	G2frame.G2plotNB.status.SetFields(['','press s to toggle x-axis = sample environment parameter'])
1655	if len(SeqData):
1656	Plot.clear()
1657	if G2frame.xAxis:
1658	xName = sampleParm.keys()[0]
1659	X = sampleParm[xName]
1660	else:
1661	X = np.arange(0,len(SeqData[0]),1)
1662	xName = 'Data sequence number'
1663	for Y,sig,name in zip(SeqData,SeqSig,SeqNames):
1664	Plot.errorbar(X,Y,yerr=sig,label=name)
1665	Plot.legend(loc='best')
1666	Plot.set_ylabel('Parameter values')
1667	Plot.set_xlabel(xName)
1668	Page.canvas.draw()
1669	Draw(True)
1670
1671	################################################################################
1672	##### PlotExposedImage & PlotImage
1673	################################################################################
1674
1675	def PlotExposedImage(G2frame,newPlot=False,event=None):
1676	'''General access module for 2D image plotting
1677	'''
1678	plotNo = G2frame.G2plotNB.nb.GetSelection()
1679	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1680	PlotImage(G2frame,newPlot,event,newImage=True)
1681	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1682	PlotIntegration(G2frame,newPlot,event)
1683
1684	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
1685	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1686	masks, etc.
1687	'''
1688	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1689	import numpy.ma as ma
1690	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1691	global Data,Masks
1692	colors=['b','g','r','c','m','k']
1693	Data = G2frame.PatternTree.GetItemPyData(
1694	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
1695	Masks = G2frame.PatternTree.GetItemPyData(
1696	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
1697
1698	def OnImMotion(event):
1699	Page.canvas.SetToolTipString('')
1700	sizexy = Data['size']
1701	if event.xdata and event.ydata: #avoid out of frame errors
1702	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1703	item = G2frame.itemPicked
1704	pixelSize = Data['pixelSize']
1705	scalex = 1000./pixelSize[0]
1706	scaley = 1000./pixelSize[1]
1707	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
1708	if 'Text' in str(item):
1709	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1710	else:
1711	xcent,ycent = Data['center']
1712	xpos = event.xdata-xcent
1713	ypos = event.ydata-ycent
1714	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1715	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1716	Page.canvas.SetToolTipString('%6d deg'%(azm))
1717	elif 'line1' in str(item) or 'line2' in str(item):
1718	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1719	else:
1720	xpos = event.xdata
1721	ypos = event.ydata
1722	xpix = xpos*scalex
1723	ypix = ypos*scaley
1724	Int = 0
1725	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1726	Int = G2frame.ImageZ[ypix][xpix]
1727	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1728	Q = 2.*math.pi/dsp
1729	if G2frame.setPoly:
1730	G2frame.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1731	else:
1732	G2frame.G2plotNB.status.SetFields(\
1733	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1734
1735	def OnImPlotKeyPress(event):
1736	try:
1737	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
1738	except TypeError:
1739	return
1740	if PickName == 'Masks':
1741	Xpos = event.xdata
1742	if not Xpos: #got point out of frame
1743	return
1744	Ypos = event.ydata
1745	if event.key == 's':
1746	Masks['Points'].append([Xpos,Ypos,1.])
1747	elif event.key == 'r':
1748	tth = G2img.GetTth(Xpos,Ypos,Data)
1749	Masks['Rings'].append([tth,0.1])
1750	elif event.key == 'a':
1751	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1752	azm = int(azm)
1753	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1754	elif event.key == 'p':
1755	G2frame.setPoly = True
1756	Masks['Polygons'].append([])
1757	G2frame.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1758	G2imG.UpdateMasks(G2frame,Masks)
1759	elif PickName == 'Image Controls':
1760	if event.key == 'c':
1761	Xpos = event.xdata
1762	if not Xpos: #got point out of frame
1763	return
1764	Ypos = event.ydata
1765	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
1766	'Center change',style=wx.OK\|wx.CANCEL)
1767	try:
1768	if dlg.ShowModal() == wx.ID_OK:
1769	print 'move center to: ',Xpos,Ypos
1770	Data['center'] = [Xpos,Ypos]
1771	G2imG.UpdateImageControls(G2frame,Data,Masks)
1772	finally:
1773	dlg.Destroy()
1774	elif event.key == 'l':
1775	if G2frame.logPlot:
1776	G2frame.logPlot = False
1777	else:
1778	G2frame.logPlot = True
1779	PlotImage(G2frame,newImage=True)
1780
1781	def OnKeyBox(event):
1782	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
1783	event.key = cb.GetValue()[0]
1784	cb.SetValue(' key press')
1785	if event.key in 'l':
1786	OnImPlotKeyPress(event)
1787
1788	def OnImPick(event):
1789	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
1790	return
1791	if G2frame.setPoly:
1792	polygon = Masks['Polygons'][-1]
1793	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1794	if xpos and ypos: #point inside image
1795	if len(polygon) > 2 and event.mouseevent.button == 3:
1796	x0,y0 = polygon[0]
1797	polygon.append([x0,y0])
1798	G2frame.setPoly = False
1799	G2frame.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1800	else:
1801	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1802	polygon.append([xpos,ypos])
1803	G2imG.UpdateMasks(G2frame,Masks)
1804	else:
1805	if G2frame.itemPicked is not None: return
1806	G2frame.itemPicked = event.artist
1807	G2frame.mousePicked = event.mouseevent
1808
1809	def OnImRelease(event):
1810	try:
1811	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
1812	except TypeError:
1813	return
1814	if PickName not in ['Image Controls','Masks']:
1815	return
1816	pixelSize = Data['pixelSize']
1817	scalex = 1000./pixelSize[0]
1818	scaley = 1000./pixelSize[1]
1819	pixLimit = Data['pixLimit']
1820	if G2frame.itemPicked is None and PickName == 'Image Controls':
1821	# sizexy = Data['size']
1822	Xpos = event.xdata
1823	if not (Xpos and G2frame.ifGetRing): #got point out of frame
1824	return
1825	Ypos = event.ydata
1826	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1827	if event.button == 1:
1828	Xpix = Xpos*scalex
1829	Ypix = Ypos*scaley
1830	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix)
1831	if I and J:
1832	xpos += .5 #shift to pixel center
1833	ypos += .5
1834	xpos /= scalex #convert to mm
1835	ypos /= scaley
1836	Data['ring'].append([xpos,ypos])
1837	elif event.button == 3:
1838	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1839	if G2img.ImageCalibrate(G2frame,Data):
1840	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1841	print 'Calibration successful'
1842	else:
1843	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1844	print 'Calibration failed'
1845	G2frame.ifGetRing = False
1846	G2imG.UpdateImageControls(G2frame,Data,Masks)
1847	return
1848	PlotImage(G2frame,newImage=False)
1849	return
1850	else:
1851	xpos = event.xdata
1852	if xpos: #avoid out of frame mouse position
1853	ypos = event.ydata
1854	if G2frame.ifGetRing: #delete a calibration ring pick
1855	xypos = [xpos,ypos]
1856	rings = Data['ring']
1857	for ring in rings:
1858	if np.allclose(ring,xypos,.01,0):
1859	rings.remove(ring)
1860	else:
1861	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1862	itemPicked = str(G2frame.itemPicked)
1863	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1864	if 'line1' in itemPicked:
1865	Data['IOtth'][0] = max(tth,0.001)
1866	elif 'line2' in itemPicked:
1867	Data['IOtth'][1] = tth
1868	elif 'line3' in itemPicked:
1869	Data['LRazimuth'][0] = int(azm)
1870	if Data['fullIntegrate']:
1871	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1872	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1873	Data['LRazimuth'][1] = int(azm)
1874
1875	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1876	Data['LRazimuth'][0] -= 360
1877
1878	azLim = np.array(Data['LRazimuth'])
1879	if np.any(azLim>360):
1880	azLim -= 360
1881	Data['LRazimuth'] = list(azLim)
1882
1883	if Data['IOtth'][0] > Data['IOtth'][1]:
1884	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1885
1886	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1887	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1888	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1889	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1890	elif 'Circle' in itemPicked and PickName == 'Masks':
1891	spots = Masks['Points']
1892	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1893	newPos = np.array([float(newPos[0]),float(newPos[1])])
1894	for spot in spots:
1895	if np.allclose(np.array([spot[:2]]),newPos):
1896	spot[:2] = xpos,ypos
1897	G2imG.UpdateMasks(G2frame,Masks)
1898	elif 'Line2D' in itemPicked and PickName == 'Masks':
1899	Obj = G2frame.itemPicked.findobj()
1900	rings = Masks['Rings']
1901	arcs = Masks['Arcs']
1902	polygons = Masks['Polygons']
1903	for ring in G2frame.ringList:
1904	if Obj == ring[0]:
1905	rN = ring[1]
1906	if ring[2] == 'o':
1907	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1908	else:
1909	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1910	for arc in G2frame.arcList:
1911	if Obj == arc[0]:
1912	aN = arc[1]
1913	if arc[2] == 'o':
1914	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1915	elif arc[2] == 'i':
1916	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1917	elif arc[2] == 'l':
1918	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1919	else:
1920	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1921	for poly in G2frame.polyList:
1922	if Obj == poly[0]:
1923	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
1924	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
1925	pN = poly[1]
1926	for i,xy in enumerate(polygons[pN]):
1927	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1928	polygons[pN][i] = xpos,ypos
1929	G2imG.UpdateMasks(G2frame,Masks)
1930	# else: #keep for future debugging
1931	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
1932	PlotImage(G2frame,newImage=True)
1933	G2frame.itemPicked = None
1934
1935	try:
1936	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
1937	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1938	if not newPlot:
1939	Plot = Page.figure.gca() #get previous powder plot & get limits
1940	xylim = Plot.get_xlim(),Plot.get_ylim()
1941	if newImage:
1942	Page.figure.clf()
1943	Plot = Page.figure.gca() #get a fresh plot after clf()
1944
1945	except ValueError:
1946	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
1947	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
1948	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1949	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1950	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1951	Page.canvas.mpl_connect('pick_event', OnImPick)
1952	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1953	xylim = []
1954	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1955	Page.SetFocus()
1956	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
1957	G2frame.G2plotNB.status.DestroyChildren()
1958	if G2frame.logPlot:
1959	Title = 'log('+Title+')'
1960	Plot.set_title(Title)
1961	try:
1962	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
1963	Choice = (' key press','l: log(I) on',)
1964	if G2frame.logPlot:
1965	Choice[1] = 'l: log(I) off'
1966	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1967	choices=Choice)
1968	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1969	cb.SetValue(' key press')
1970	except TypeError:
1971	pass
1972	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
1973	if imagefile != G2frame.oldImagefile:
1974	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
1975	if not imagefile:
1976	G2frame.G2plotNB.Delete('2D Powder Image')
1977	return
1978	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
1979	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
1980	# print G2frame.ImageZ.shape,G2frame.ImageZ.size,Data['size'] #might be useful debugging line
1981	G2frame.oldImagefile = imagefile
1982
1983	imScale = 1
1984	if len(G2frame.ImageZ) > 1024:
1985	imScale = len(G2frame.ImageZ)/1024
1986	sizexy = Data['size']
1987	pixelSize = Data['pixelSize']
1988	scalex = 1000./pixelSize[0]
1989	scaley = 1000./pixelSize[1]
1990	Xmax = sizexy[0]*pixelSize[0]/1000.
1991	Ymax = sizexy[1]*pixelSize[1]/1000.
1992	xlim = (0,Xmax)
1993	ylim = (Ymax,0)
1994	Imin,Imax = Data['range'][1]
1995	acolor = mpl.cm.get_cmap(Data['color'])
1996	xcent,ycent = Data['center']
1997	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1998	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1999	#do threshold mask - "real" mask - others are just bondaries
2000	Zlim = Masks['Thresholds'][1]
2001	wx.BeginBusyCursor()
2002	try:
2003
2004	if newImage:
2005	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]),Zlim[1])
2006	MaskA = ma.getmaskarray(MA)
2007	A = G2img.ImageCompress(MA,imScale)
2008	AM = G2img.ImageCompress(MaskA,imScale)
2009	if G2frame.logPlot:
2010	A = np.where(A>0,np.log(A),0)
2011	AM = np.where(AM>0,np.log(AM),0)
2012	Imin,Imax = [np.amin(A),np.amax(A)]
2013	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
2014	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
2015	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
2016	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
2017	if G2frame.setPoly:
2018	Img.set_picker(True)
2019
2020	Plot.plot(xcent,ycent,'x')
2021	if Data['showLines']:
2022	LRAzim = Data['LRazimuth'] #NB: integers
2023	Nazm = Data['outAzimuths']
2024	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
2025	AzmthOff = Data['azmthOff']
2026	IOtth = Data['IOtth']
2027	wave = Data['wavelength']
2028	dspI = wave/(2.0*sind(IOtth[0]/2.0))
2029	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
2030	dspO = wave/(2.0*sind(IOtth[1]/2.0))
2031	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
2032	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
2033	if ellI:
2034	xyI = []
2035	for azm in Azm:
2036	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
2037	xyI = np.array(xyI)
2038	arcxI,arcyI = xyI.T
2039	Plot.plot(arcxI,arcyI,picker=3)
2040	if ellO:
2041	xyO = []
2042	for azm in Azm:
2043	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
2044	xyO = np.array(xyO)
2045	arcxO,arcyO = xyO.T
2046	Plot.plot(arcxO,arcyO,picker=3)
2047	if ellO and ellI:
2048	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
2049	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
2050	for i in range(Nazm):
2051	cake = LRAzim[0]+i*delAzm-AzmthOff
2052	ind = np.searchsorted(Azm,cake)
2053	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
2054
2055	for xring,yring in Data['ring']:
2056	Plot.plot(xring,yring,'r+',picker=3)
2057	if Data['setRings']:
2058	# rings = np.concatenate((Data['rings']),axis=0)
2059	N = 0
2060	for ring in Data['rings']:
2061	xring,yring = np.array(ring).T[:2]
2062	Plot.plot(xring,yring,'+',color=colors[N%6])
2063	N += 1
2064	for ellipse in Data['ellipses']:
2065	cent,phi,[width,height],col = ellipse
2066	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
2067	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
2068	#masks - mask lines numbered after integration limit lines
2069	spots = Masks['Points']
2070	rings = Masks['Rings']
2071	arcs = Masks['Arcs']
2072	polygons = Masks['Polygons']
2073	for x,y,d in spots:
2074	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
2075	G2frame.ringList = []
2076	for iring,(tth,thick) in enumerate(rings):
2077	wave = Data['wavelength']
2078	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
2079	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
2080	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
2081	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
2082	G2frame.arcList = []
2083	for iarc,(tth,azm,thick) in enumerate(arcs):
2084	wave = Data['wavelength']
2085	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
2086	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
2087	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
2088	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
2089	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
2090	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
2091	G2frame.polyList = []
2092	for ipoly,polygon in enumerate(polygons):
2093	x,y = np.hsplit(np.array(polygon),2)
2094	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
2095	Plot.plot(x,y,'r')
2096	if newImage:
2097	colorBar = Page.figure.colorbar(Img)
2098	Plot.set_xlim(xlim)
2099	Plot.set_ylim(ylim)
2100	Plot.invert_yaxis()
2101	if not newPlot and xylim:
2102	Page.toolbar.push_current()
2103	Plot.set_xlim(xylim[0])
2104	Plot.set_ylim(xylim[1])
2105	xylim = []
2106	Page.toolbar.push_current()
2107	Page.toolbar.draw()
2108	else:
2109	Page.canvas.draw()
2110	finally:
2111	wx.EndBusyCursor()
2112
2113	################################################################################
2114	##### PlotIntegration
2115	################################################################################
2116
2117	def PlotIntegration(G2frame,newPlot=False,event=None):
2118	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
2119	'''
2120
2121	def OnMotion(event):
2122	Page.canvas.SetToolTipString('')
2123	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2124	azm = event.ydata
2125	tth = event.xdata
2126	if azm and tth:
2127	G2frame.G2plotNB.status.SetFields(\
2128	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2129
2130	try:
2131	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2132	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2133	if not newPlot:
2134	Plot = Page.figure.gca() #get previous plot & get limits
2135	xylim = Plot.get_xlim(),Plot.get_ylim()
2136	Page.figure.clf()
2137	Plot = Page.figure.gca() #get a fresh plot after clf()
2138
2139	except ValueError:
2140	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
2141	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2142	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2143	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2144	Page.views = False
2145	view = False
2146	if not event:
2147	Page.SetFocus()
2148
2149	Data = G2frame.PatternTree.GetItemPyData(
2150	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2151	image = G2frame.Integrate[0]
2152	xsc = G2frame.Integrate[1]
2153	ysc = G2frame.Integrate[2]
2154	Imin,Imax = Data['range'][1]
2155	acolor = mpl.cm.get_cmap(Data['color'])
2156	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2157	Plot.set_ylabel('azimuth',fontsize=12)
2158	Plot.set_xlabel('2-theta',fontsize=12)
2159	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
2160	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
2161	colorBar = Page.figure.colorbar(Img)
2162	if Data['ellipses']:
2163	for ellipse in Data['ellipses']:
2164	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2165	x,y = np.hsplit(ring,2)
2166	tth,azm = G2img.GetTthAzm(x,y,Data)
2167	# azm = np.where(azm < 0.,azm+360,azm)
2168	Plot.plot(tth,azm,'b,')
2169	if not newPlot:
2170	Page.toolbar.push_current()
2171	Plot.set_xlim(xylim[0])
2172	Plot.set_ylim(xylim[1])
2173	xylim = []
2174	Page.toolbar.push_current()
2175	Page.toolbar.draw()
2176	else:
2177	Page.canvas.draw()
2178
2179	################################################################################
2180	##### PlotTRImage
2181	################################################################################
2182
2183	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
2184	'''a test plot routine - not normally used
2185	'''
2186
2187	def OnMotion(event):
2188	Page.canvas.SetToolTipString('')
2189	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2190	azm = event.xdata
2191	tth = event.ydata
2192	if azm and tth:
2193	G2frame.G2plotNB.status.SetFields(\
2194	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2195
2196	try:
2197	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2198	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2199	if not newPlot:
2200	Plot = Page.figure.gca() #get previous plot & get limits
2201	xylim = Plot.get_xlim(),Plot.get_ylim()
2202	Page.figure.clf()
2203	Plot = Page.figure.gca() #get a fresh plot after clf()
2204
2205	except ValueError:
2206	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
2207	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2208	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2209	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2210	Page.views = False
2211	view = False
2212	Page.SetFocus()
2213
2214	Data = G2frame.PatternTree.GetItemPyData(
2215	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2216	Imin,Imax = Data['range'][1]
2217	step = (Imax-Imin)/5.
2218	V = np.arange(Imin,Imax,step)
2219	acolor = mpl.cm.get_cmap(Data['color'])
2220	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2221	Plot.set_xlabel('azimuth',fontsize=12)
2222	Plot.set_ylabel('2-theta',fontsize=12)
2223	Plot.contour(tax,tay,taz,V,cmap=acolor)
2224	if Data['showLines']:
2225	IOtth = Data['IOtth']
2226	if Data['fullIntegrate']:
2227	LRAzim = [-180,180]
2228	else:
2229	LRAzim = Data['LRazimuth'] #NB: integers
2230	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
2231	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
2232	if not Data['fullIntegrate']:
2233	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
2234	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
2235	if Data['setRings']:
2236	rings = np.concatenate((Data['rings']),axis=0)
2237	for xring,yring,dsp in rings:
2238	x,y = G2img.GetTthAzm(xring,yring,Data)
2239	Plot.plot(y,x,'r+')
2240	if Data['ellipses']:
2241	for ellipse in Data['ellipses']:
2242	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2243	x,y = np.hsplit(ring,2)
2244	tth,azm = G2img.GetTthAzm(x,y,Data)
2245	Plot.plot(azm,tth,'b,')
2246	if not newPlot:
2247	Page.toolbar.push_current()
2248	Plot.set_xlim(xylim[0])
2249	Plot.set_ylim(xylim[1])
2250	xylim = []
2251	Page.toolbar.push_current()
2252	Page.toolbar.draw()
2253	else:
2254	Page.canvas.draw()
2255
2256	################################################################################
2257	##### PlotStructure
2258	################################################################################
2259
2260	def PlotStructure(G2frame,data):
2261	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
2262	thermal motion ellipsoids and polyhedra
2263	'''
2264	generalData = data['General']
2265	cell = generalData['Cell'][1:7]
2266	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
2267	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2268	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2269	Mydir = generalData['Mydir']
2270	atomData = data['Atoms']
2271	drawingData = data['Drawing']
2272	drawAtoms = drawingData['Atoms']
2273	cx,ct,cs = drawingData['atomPtrs']
2274	Wt = [255,255,255]
2275	Rd = [255,0,0]
2276	Gr = [0,255,0]
2277	Bl = [0,0,255]
2278	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]])
2279	uEdges = np.array([
2280	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
2281	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
2282	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
2283	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
2284	altDown = False
2285	shiftDown = False
2286	ctrlDown = False
2287
2288	def OnKeyBox(event):
2289	import Image
2290	Draw() #make sure plot is fresh!!
2291	mode = cb.GetValue()
2292	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
2293	size = Page.canvas.GetSize()
2294	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
2295	if mode in ['jpeg',]:
2296	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
2297	im = Image.new("RGBA", (size[0],size[1]))
2298	else:
2299	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
2300	im = Image.new("RGB", (size[0],size[1]))
2301	im.fromstring(Pix)
2302	im.save(Fname,mode)
2303	cb.SetValue(' Save as:')
2304	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
2305
2306	def GetTruePosition(xy,Add=False):
2307	View = glGetIntegerv(GL_VIEWPORT)
2308	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
2309	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
2310	Zmax = 1.
2311	if Add:
2312	Indx = GetSelectedAtoms()
2313	for i,atom in enumerate(drawAtoms):
2314	x,y,z = atom[cx:cx+3]
2315	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2316	XY = [int(X),int(View[3]-Y)]
2317	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2318	Zmax = Z
2319	try:
2320	Indx.remove(i)
2321	ClearSelectedAtoms()
2322	for id in Indx:
2323	SetSelectedAtoms(id,Add)
2324	except:
2325	SetSelectedAtoms(i,Add)
2326
2327	def OnMouseDown(event):
2328	xy = event.GetPosition()
2329	if event.ShiftDown():
2330	if event.LeftIsDown():
2331	GetTruePosition(xy)
2332	elif event.RightIsDown():
2333	GetTruePosition(xy,True)
2334	else:
2335	drawingData['Rotation'][3] = list(xy)
2336	Draw()
2337
2338	def OnMouseMove(event):
2339	if event.ShiftDown():
2340	return
2341	newxy = event.GetPosition()
2342	page = getSelection()
2343	if event.ControlDown() and drawingData['showABC']:
2344	if event.LeftIsDown():
2345	SetTestRot(newxy)
2346	elif event.RightIsDown():
2347	SetTestPos(newxy)
2348	elif event.MiddleIsDown():
2349	SetTestRotZ(newxy)
2350	x,y,z = drawingData['testPos'][0]
2351	G2frame.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2352	Draw()
2353
2354	if event.Dragging() and not event.ControlDown():
2355	if event.LeftIsDown():
2356	SetRotation(newxy)
2357	angX,angY,angZ = drawingData['Rotation'][:3]
2358	G2frame.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
2359	elif event.RightIsDown():
2360	SetTranslation(newxy)
2361	Tx,Ty,Tz = drawingData['viewPoint'][0]
2362	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2363	elif event.MiddleIsDown():
2364	SetRotationZ(newxy)
2365	angX,angY,angZ = drawingData['Rotation'][:3]
2366	G2frame.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
2367	Draw()
2368
2369	def OnMouseWheel(event):
2370	if event.ShiftDown():
2371	return
2372	drawingData['cameraPos'] += event.GetWheelRotation()/24
2373	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2374	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2375	page = getSelection()
2376	if page:
2377	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2378	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2379	names = [child.GetName() for child in panel]
2380	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2381	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2382	Draw()
2383
2384	def getSelection():
2385	try:
2386	return G2frame.dataDisplay.GetSelection()
2387	except AttributeError:
2388	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2389	return 0
2390
2391	def SetViewPointText(VP):
2392	page = getSelection()
2393	if page:
2394	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2395	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2396	names = [child.GetName() for child in panel]
2397	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
2398
2399	def ClearSelectedAtoms():
2400	page = getSelection()
2401	if page:
2402	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2403	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2404	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2405	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2406
2407	def SetSelectedAtoms(ind,Add=False):
2408	page = getSelection()
2409	if page:
2410	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2411	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
2412	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2413	Id = drawAtoms[ind][-2]
2414	for i,atom in enumerate(atomData):
2415	if atom[-1] == Id:
2416	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2417
2418	def GetSelectedAtoms():
2419	page = getSelection()
2420	Ind = []
2421	if page:
2422	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2423	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2424	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2425	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2426	return Ind
2427
2428	def OnKey(event): #on key UP!!
2429	keyCode = event.GetKeyCode()
2430	if keyCode > 255:
2431	keyCode = 0
2432	key,xyz = chr(keyCode),event.GetPosition()
2433	indx = drawingData['selectedAtoms']
2434	if key in ['c','C']:
2435	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2436	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
2437	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
2438	SetViewPointText(drawingData['viewPoint'][0])
2439	elif key in ['n','N']:
2440	drawAtoms = drawingData['Atoms']
2441	pI = drawingData['viewPoint'][1]
2442	if indx:
2443	pI[0] = indx[pI[1]]
2444	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2445	pI[1] += 1
2446	if pI[1] >= len(indx):
2447	pI[1] = 0
2448	else:
2449	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2450	pI[0] += 1
2451	if pI[0] >= len(drawAtoms):
2452	pI[0] = 0
2453	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2454	SetViewPointText(drawingData['viewPoint'][0])
2455	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2456
2457	elif key in ['p','P']:
2458	drawAtoms = drawingData['Atoms']
2459	pI = drawingData['viewPoint'][1]
2460	if indx:
2461	pI[0] = indx[pI[1]]
2462	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2463	pI[1] -= 1
2464	if pI[1] < 0:
2465	pI[1] = len(indx)-1
2466	else:
2467	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2468	pI[0] -= 1
2469	if pI[0] < 0:
2470	pI[0] = len(drawAtoms)-1
2471	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2472	SetViewPointText(drawingData['viewPoint'][0])
2473	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2474	Draw()
2475
2476	def SetBackground():
2477	R,G,B,A = Page.camera['backColor']
2478	glClearColor(R,G,B,A)
2479	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2480
2481	def SetLights():
2482	glEnable(GL_DEPTH_TEST)
2483	glShadeModel(GL_SMOOTH)
2484	glEnable(GL_LIGHTING)
2485	glEnable(GL_LIGHT0)
2486	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2487	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2488	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2489
2490	def SetTranslation(newxy):
2491	Tx,Ty,Tz = drawingData['viewPoint'][0]
2492	anglex,angley,anglez,oldxy = drawingData['Rotation']
2493	Rx = G2lat.rotdMat(anglex,0)
2494	Ry = G2lat.rotdMat(angley,1)
2495	Rz = G2lat.rotdMat(anglez,2)
2496	dxy = list(newxy-oldxy)+[0,]
2497	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
2498	Tx -= dxy[0]*0.01
2499	Ty += dxy[1]*0.01
2500	Tz -= dxy[2]*0.01
2501	drawingData['Rotation'][3] = list(newxy)
2502	drawingData['viewPoint'][0] = Tx,Ty,Tz
2503	SetViewPointText([Tx,Ty,Tz])
2504
2505	def SetTestPos(newxy):
2506	Tx,Ty,Tz = drawingData['testPos'][0]
2507	anglex,angley,anglez,oldxy = drawingData['Rotation']
2508	Rx = G2lat.rotdMat(anglex,0)
2509	Ry = G2lat.rotdMat(angley,1)
2510	Rz = G2lat.rotdMat(anglez,2)
2511	dxy = list(newxy-oldxy)+[0,]
2512	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
2513	Tx += dxy[0]*0.001
2514	Ty -= dxy[1]*0.001
2515	Tz += dxy[2]*0.001
2516	drawingData['Rotation'][3] = list(newxy)
2517	drawingData['testPos'][0] = Tx,Ty,Tz
2518
2519	def SetTestRot(newxy):
2520	Txyz = np.array(drawingData['testPos'][0])
2521	oldxy = drawingData['testPos'][2]
2522	Ax,Ay,Az = drawingData['testPos'][1]
2523	Vxyz = np.array(drawingData['viewPoint'][0])
2524	Dxyz = np.inner(Amat,Txyz-Vxyz)
2525	dxy = list(newxy-oldxy)+[0,]
2526	Ax += dxy[1]*0.01
2527	Ay += dxy[0]*0.01
2528	Rx = G2lat.rotdMat(Ax,0)
2529	Ry = G2lat.rotdMat(Ay,1)
2530	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
2531	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2532	drawingData['testPos'][1] = [Ax,Ay,Az]
2533	drawingData['testPos'][2] = newxy
2534	drawingData['testPos'][0] = Dxyz
2535
2536	def SetTestRotZ(newxy):
2537	Txyz = np.array(drawingData['testPos'][0])
2538	oldxy = drawingData['testPos'][2]
2539	Ax,Ay,Az = drawingData['testPos'][1]
2540	Vxyz = np.array(drawingData['viewPoint'][0])
2541	Dxyz = np.inner(Amat,Txyz-Vxyz)
2542	dxy = list(newxy-oldxy)+[0,]
2543	Az += (dxy[0]+dxy[1])*.01
2544	Rz = G2lat.rotdMat(Az,2)
2545	Dxyz = np.inner(Rz,Dxyz)
2546	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2547	drawingData['testPos'][1] = [Ax,Ay,Az]
2548	drawingData['testPos'][2] = newxy
2549	drawingData['testPos'][0] = Dxyz
2550
2551	def SetRotation(newxy):
2552	anglex,angley,anglez,oldxy = drawingData['Rotation']
2553	dxy = newxy-oldxy
2554	anglex += dxy[1]*.25
2555	angley += dxy[0]*.25
2556	oldxy = newxy
2557	drawingData['Rotation'] = [anglex,angley,anglez,list(oldxy)]
2558
2559	def SetRotationZ(newxy):
2560	anglex,angley,anglez,oldxy = drawingData['Rotation']
2561	dxy = newxy-oldxy
2562	anglez += (dxy[0]+dxy[1])*.25
2563	oldxy = newxy
2564	drawingData['Rotation'] = [anglex,angley,anglez,list(oldxy)]
2565
2566	def RenderBox():
2567	glEnable(GL_COLOR_MATERIAL)
2568	glLineWidth(2)
2569	glEnable(GL_BLEND)
2570	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2571	glEnable(GL_LINE_SMOOTH)
2572	glBegin(GL_LINES)
2573	for line,color in zip(uEdges,uColors):
2574	glColor3ubv(color)
2575	glVertex3fv(line[0])
2576	glVertex3fv(line[1])
2577	glEnd()
2578	glColor4ubv([0,0,0,0])
2579	glDisable(GL_LINE_SMOOTH)
2580	glDisable(GL_BLEND)
2581	glDisable(GL_COLOR_MATERIAL)
2582
2583	def RenderUnitVectors(x,y,z):
2584	xyz = np.array([x,y,z])
2585	glEnable(GL_COLOR_MATERIAL)
2586	glLineWidth(1)
2587	glPushMatrix()
2588	glTranslate(x,y,z)
2589	glScalef(1/cell[0],1/cell[1],1/cell[2])
2590	glBegin(GL_LINES)
2591	for line,color in zip(uEdges,uColors)[:3]:
2592	glColor3ubv(color)
2593	glVertex3fv(line[0])
2594	glVertex3fv(line[1])
2595	glEnd()
2596	glPopMatrix()
2597	glColor4ubv([0,0,0,0])
2598	glDisable(GL_COLOR_MATERIAL)
2599
2600	def RenderSphere(x,y,z,radius,color):
2601	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2602	glPushMatrix()
2603	glTranslate(x,y,z)
2604	glMultMatrixf(B4mat.T)
2605	q = gluNewQuadric()
2606	gluSphere(q,radius,20,10)
2607	glPopMatrix()
2608
2609	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2610	s1,s2,s3 = E
2611	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2612	glPushMatrix()
2613	glTranslate(x,y,z)
2614	glMultMatrixf(B4mat.T)
2615	glMultMatrixf(R4.T)
2616	glEnable(GL_NORMALIZE)
2617	glScale(s1,s2,s3)
2618	q = gluNewQuadric()
2619	gluSphere(q,ellipseProb,20,10)
2620	glDisable(GL_NORMALIZE)
2621	glPopMatrix()
2622
2623	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2624	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2625	glPushMatrix()
2626	glTranslate(x,y,z)
2627	glMultMatrixf(B4mat.T)
2628	for bond in Bonds:
2629	glPushMatrix()
2630	Dx = np.inner(Amat,bond)
2631	Z = np.sqrt(np.sum(Dx**2))
2632	azm = atan2d(-Dx[1],-Dx[0])
2633	phi = acosd(Dx[2]/Z)
2634	glRotate(-azm,0,0,1)
2635	glRotate(phi,1,0,0)
2636	q = gluNewQuadric()
2637	gluCylinder(q,radius,radius,Z,slice,2)
2638	glPopMatrix()
2639	glPopMatrix()
2640
2641	def RenderLines(x,y,z,Bonds,color):
2642	xyz = np.array([x,y,z])
2643	glEnable(GL_COLOR_MATERIAL)
2644	glLineWidth(1)
2645	glColor3fv(color)
2646	glPushMatrix()
2647	glBegin(GL_LINES)
2648	for bond in Bonds:
2649	glVertex3fv(xyz)
2650	glVertex3fv(xyz+bond)
2651	glEnd()
2652	glColor4ubv([0,0,0,0])
2653	glPopMatrix()
2654	glDisable(GL_COLOR_MATERIAL)
2655
2656	def RenderPolyhedra(x,y,z,Faces,color):
2657	glPushMatrix()
2658	glTranslate(x,y,z)
2659	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2660	glShadeModel(GL_SMOOTH)
2661	glMultMatrixf(B4mat.T)
2662	for face,norm in Faces:
2663	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2664	glFrontFace(GL_CW)
2665	glNormal3fv(norm)
2666	glBegin(GL_TRIANGLES)
2667	for vert in face:
2668	glVertex3fv(vert)
2669	glEnd()
2670	glPopMatrix()
2671
2672	def RenderBackbone(Backbone,BackboneColor,radius):
2673	glPushMatrix()
2674	glMultMatrixf(B4mat.T)
2675	glEnable(GL_COLOR_MATERIAL)
2676	glShadeModel(GL_SMOOTH)
2677	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2678	glePolyCylinder(Backbone,BackboneColor,radius)
2679	glPopMatrix()
2680	glDisable(GL_COLOR_MATERIAL)
2681
2682	def RenderLabel(x,y,z,label,r):
2683	glPushMatrix()
2684	glTranslate(x,y,z)
2685	glMultMatrixf(B4mat.T)
2686	glDisable(GL_LIGHTING)
2687	glColor3f(0,1.,0)
2688	glRasterPos3f(r,r,r)
2689	for c in list(label):
2690	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2691	glEnable(GL_LIGHTING)
2692	glPopMatrix()
2693
2694	def Draw():
2695	Ind = GetSelectedAtoms()
2696	VS = np.array(Page.canvas.GetSize())
2697	aspect = float(VS[0])/float(VS[1])
2698	cPos = drawingData['cameraPos']
2699	Zclip = drawingData['Zclip']*cPos/200.
2700	anglex,angley,anglez = drawingData['Rotation'][:3]
2701	Tx,Ty,Tz = drawingData['viewPoint'][0]
2702	cx,ct,cs = drawingData['atomPtrs']
2703	bondR = drawingData['bondRadius']
2704	G,g = G2lat.cell2Gmat(cell)
2705	GS = G
2706	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2707	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2708	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2709	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2710
2711	SetBackground()
2712	glInitNames()
2713	glPushName(0)
2714
2715	glMatrixMode(GL_PROJECTION)
2716	glLoadIdentity()
2717	glViewport(0,0,VS[0],VS[1])
2718	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2719	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2720	SetLights()
2721
2722	glMatrixMode(GL_MODELVIEW)
2723	glLoadIdentity()
2724	glRotate(anglez,0,0,1)
2725	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2726	glRotate(angley,sind(anglez),cosd(anglez),0)
2727	glMultMatrixf(A4mat.T)
2728	glTranslate(-Tx,-Ty,-Tz)
2729	if drawingData['unitCellBox']:
2730	RenderBox()
2731	if drawingData['showABC']:
2732	x,y,z = drawingData['testPos'][0]
2733	# if altDown:
2734	# G2frame.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2735	# else:
2736	# G2frame.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2737	RenderUnitVectors(x,y,z)
2738	Backbone = []
2739	BackboneColor = []
2740	time0 = time.time()
2741	for iat,atom in enumerate(drawingData['Atoms']):
2742	x,y,z = atom[cx:cx+3]
2743	Bonds = atom[-2]
2744	Faces = atom[-1]
2745	try:
2746	atNum = generalData['AtomTypes'].index(atom[ct])
2747	except ValueError:
2748	atNum = -1
2749	CL = atom[cs+2]
2750	color = np.array(CL)/255.
2751	if iat in Ind:
2752	color = np.array(Gr)/255.
2753	radius = 0.5
2754	if atom[cs] != '':
2755	glLoadName(atom[-3])
2756	if 'balls' in atom[cs]:
2757	vdwScale = drawingData['vdwScale']
2758	ballScale = drawingData['ballScale']
2759	if atNum < 0:
2760	radius = 0.2
2761	elif 'H' == atom[ct]:
2762	if drawingData['showHydrogen']:
2763	if 'vdW' in atom[cs] and atNum >= 0:
2764	radius = vdwScale*generalData['vdWRadii'][atNum]
2765	else:
2766	radius = ballScale*drawingData['sizeH']
2767	else:
2768	radius = 0.0
2769	else:
2770	if 'vdW' in atom[cs]:
2771	radius = vdwScale*generalData['vdWRadii'][atNum]
2772	else:
2773	radius = ballScale*generalData['BondRadii'][atNum]
2774	RenderSphere(x,y,z,radius,color)
2775	if 'sticks' in atom[cs]:
2776	RenderBonds(x,y,z,Bonds,bondR,color)
2777	elif 'ellipsoids' in atom[cs]:
2778	RenderBonds(x,y,z,Bonds,bondR,color)
2779	if atom[cs+3] == 'A':
2780	Uij = atom[cs+5:cs+11]
2781	U = np.multiply(G2spc.Uij2U(Uij),GS)
2782	U = np.inner(Amat,np.inner(U,Amat).T)
2783	E,R = nl.eigh(U)
2784	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2785	E = np.sqrt(E)
2786	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2787	pass
2788	else:
2789	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2790	else:
2791	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2792	pass
2793	else:
2794	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2795	RenderSphere(x,y,z,radius,color)
2796	elif 'lines' in atom[cs]:
2797	radius = 0.1
2798	RenderLines(x,y,z,Bonds,color)
2799	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2800	elif atom[cs] == 'sticks':
2801	radius = 0.1
2802	RenderBonds(x,y,z,Bonds,bondR,color)
2803	elif atom[cs] == 'polyhedra':
2804	RenderPolyhedra(x,y,z,Faces,color)
2805	elif atom[cs] == 'backbone':
2806	if atom[ct-1].split()[0] in ['C','N']:
2807	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2808	BackboneColor.append(list(color))
2809
2810	if atom[cs+1] == 'type':
2811	RenderLabel(x,y,z,atom[ct],radius)
2812	elif atom[cs+1] == 'name':
2813	RenderLabel(x,y,z,atom[ct-1],radius)
2814	elif atom[cs+1] == 'number':
2815	RenderLabel(x,y,z,str(iat),radius)
2816	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2817	RenderLabel(x,y,z,atom[ct-4],radius)
2818	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2819	RenderLabel(x,y,z,atom[ct-3],radius)
2820	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2821	RenderLabel(x,y,z,atom[ct-2],radius)
2822	if Backbone:
2823	RenderBackbone(Backbone,BackboneColor,bondR)
2824	# print time.time()-time0
2825	Page.canvas.SwapBuffers()
2826
2827	def OnSize(event):
2828	Draw()
2829
2830	def OnFocus(event):
2831	Draw()
2832
2833	try:
2834	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
2835	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2836	except ValueError:
2837	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
2838	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
2839	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2840	Page.views = False
2841	view = False
2842	altDown = False
2843	Page.SetFocus()
2844	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2845	choices=(' save as:','jpeg','tiff','bmp'))
2846	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2847	cb.SetValue(' save as:')
2848	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2849	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2850	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2851	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2852	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2853	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2854	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2855	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2856	Page.camera['position'] = drawingData['cameraPos']
2857	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2858	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2859	Page.canvas.SetCurrent()
2860	Draw()
2861

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