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source: trunk/GSASIIplot.py @ 456

Last change on this file since 456 was 456, checked in by toby, 11 years ago
determine path to GSAS files from file; trap & reset focus for tree traversal with arrow keys; move wxinspector to after app creation
Property svn:keywords set to `Date Author Revision URL Id`
File size: 115.5 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2012-01-24 20:31:27 +0000 (Tue, 24 Jan 2012) $
4	# $Author: toby $
5	# $Revision: 456 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 456 2012-01-24 20:31:27Z toby $
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	print 'Matplotlib help on '+Page.GetPageText(pageNo)
173	G2gd.ShowHelp(Page.GetPageText(pageNo),self.TopLevelParent)
174
175	def PlotSngl(self,newPlot=False):
176	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
177	to F, F**2, etc. as requested
178	'''
179	from matplotlib.patches import Circle
180	global HKL,HKLF
181
182	def OnSCMotion(event):
183	xpos = event.xdata
184	if xpos:
185	xpos = round(xpos) #avoid out of frame mouse position
186	ypos = round(event.ydata)
187	zpos = Data['Layer']
188	if '100' in Data['Zone']:
189	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
190	elif '010' in Data['Zone']:
191	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
192	elif '001' in Data['Zone']:
193	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
194	Page.canvas.SetToolTipString(HKLtxt)
195	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
196
197	def OnSCPick(event):
198	zpos = Data['Layer']
199	pos = event.artist.center
200	if '100' in Data['Zone']:
201	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
202	hkl = np.array([zpos,pos[0],pos[1]])
203	elif '010' in Data['Zone']:
204	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
205	hkl = np.array([pos[0],zpos,pos[1]])
206	elif '001' in Data['Zone']:
207	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
208	hkl = np.array([pos[0],pos[1],zpos])
209	h,k,l = hkl
210	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
211	if len(hklf):
212	Fosq,sig,Fcsq = hklf[0]
213	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
214	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
215
216	def OnSCKeyPress(event):
217	print event.key
218
219	try:
220	plotNum = self.G2plotNB.plotList.index('Structure Factors')
221	Page = self.G2plotNB.nb.GetPage(plotNum)
222	if not newPlot:
223	Plot = Page.figure.gca() #get previous powder plot & get limits
224	xylim = Plot.get_xlim(),Plot.get_ylim()
225	Page.figure.clf()
226	Plot = Page.figure.gca() #get a fresh plot after clf()
227	except ValueError:
228	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
229	plotNum = self.G2plotNB.plotList.index('Structure Factors')
230	Page = self.G2plotNB.nb.GetPage(plotNum)
231	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
232	Page.canvas.mpl_connect('pick_event', OnSCPick)
233	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
234	Page.SetFocus()
235
236	Plot.set_aspect(aspect='equal')
237	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
238	Data = self.PatternTree.GetItemPyData( \
239	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
240	Type = Data['Type']
241	scale = Data['Scale']
242	HKLmax = Data['HKLmax']
243	HKLmin = Data['HKLmin']
244	FosqMax = Data['FoMax']
245	FoMax = math.sqrt(FosqMax)
246	ifFc = Data['ifFc']
247	xlabel = ['k, h=','h, k=','h, l=']
248	ylabel = ['l','l','k']
249	zones = ['100','010','001']
250	pzone = [[1,2],[0,2],[0,1]]
251	izone = zones.index(Data['Zone'])
252	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
253	HKL = []
254	HKLF = []
255	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
256	HKL.append(H)
257	HKLF.append([Fosq,sig,Fcsq])
258	if H[izone] == Data['Layer']:
259	B = 0
260	if Type == 'Fosq':
261	A = scale*Fosq/FosqMax
262	B = scale*Fcsq/FosqMax
263	C = abs(A-B)
264	elif Type == 'Fo':
265	A = scale*math.sqrt(max(0,Fosq))/FoMax
266	B = scale*math.sqrt(max(0,Fcsq))/FoMax
267	C = abs(A-B)
268	elif Type == '\|DFsq\|/sig':
269	A = abs(Fosq-Fcsq)/(scale*sig)
270	elif Type == '\|DFsq\|>sig':
271	A = abs(Fosq-Fcsq)/(scale*sig)
272	if A < 1.0: A = 0
273	elif Type == '\|DFsq\|>3sig':
274	A = abs(Fosq-Fcsq)/(scale*sig)
275	if A < 3.0: A = 0
276	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
277	if A > 0.0:
278	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
279	if B:
280	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
281	radius = C
282	if radius > 0:
283	if A > B:
284	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
285	else:
286	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
287	HKL = np.array(HKL,dtype=np.int)
288	HKLF = np.array(HKLF)
289	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
290	Plot.set_ylabel(ylabel[izone],fontsize=12)
291	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
292	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
293	if not newPlot:
294	Page.toolbar.push_current()
295	Plot.set_xlim(xylim[0])
296	Plot.set_ylim(xylim[1])
297	xylim = []
298	Page.toolbar.push_current()
299	Page.toolbar.draw()
300	else:
301	Page.canvas.draw()
302
303	def PlotPatterns(self,newPlot=False):
304	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
305	2-theta or q (future TOF). Can display multiple patterns as "waterfall plots" or contour plots. Log I
306	plotting available.
307	'''
308	global HKL
309
310	def OnKeyBox(event):
311	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('Powder Patterns'):
312	event.key = cb.GetValue()[0]
313	cb.SetValue(' key press')
314	OnPlotKeyPress(event)
315
316	def OnPlotKeyPress(event):
317	newPlot = False
318	if event.key == 'w':
319	if self.Weight:
320	self.Weight = False
321	else:
322	self.Weight = True
323	print 'plot weighting:',self.Weight
324	elif event.key == 'n':
325	if self.Contour:
326	pass
327	else:
328	if self.logPlot:
329	self.logPlot = False
330	else:
331	self.Offset[0] = 0
332	self.logPlot = True
333	elif event.key == 'u':
334	if self.Contour:
335	self.Cmax = min(1.0,self.Cmax*1.2)
336	elif self.logPlot:
337	pass
338	elif self.Offset[0] < 100.:
339	self.Offset[0] += 1.
340	elif event.key == 'd':
341	if self.Contour:
342	self.Cmax = max(0.0,self.Cmax*0.8)
343	elif self.logPlot:
344	pass
345	elif self.Offset[0] > 0.:
346	self.Offset[0] -= 1.
347	elif event.key == 'l':
348	self.Offset[1] -= 1.
349	elif event.key == 'r':
350	self.Offset[1] += 1.
351	elif event.key == 'o':
352	self.Offset = [0,0]
353	elif event.key == 'c':
354	newPlot = True
355	if self.Contour:
356	self.Contour = False
357	else:
358	self.Contour = True
359	self.SinglePlot = False
360	self.Offset = [0.,0.]
361	elif event.key == 'q':
362	newPlot = True
363	if self.qPlot:
364	self.qPlot = False
365	else:
366	self.qPlot = True
367	elif event.key == 's':
368	if self.Contour:
369	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
370	choice.sort()
371	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
372	if dlg.ShowModal() == wx.ID_OK:
373	sel = dlg.GetSelection()
374	self.ContourColor = choice[sel]
375	else:
376	self.ContourColor = 'Paired'
377	dlg.Destroy()
378	else:
379	if self.SinglePlot:
380	self.SinglePlot = False
381	else:
382	self.SinglePlot = True
383	elif event.key == '+':
384	if self.PickId:
385	self.PickId = False
386	elif event.key == 'i': #for smoothing contour plot
387	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
388	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
389	'mitchell','sinc','lanczos']
390	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
391	if dlg.ShowModal() == wx.ID_OK:
392	sel = dlg.GetSelection()
393	self.Interpolate = choice[sel]
394	else:
395	self.Interpolate = 'nearest'
396	dlg.Destroy()
397
398	PlotPatterns(self,newPlot=newPlot)
399
400	def OnMotion(event):
401	xpos = event.xdata
402	if xpos: #avoid out of frame mouse position
403	ypos = event.ydata
404	Page.canvas.SetCursor(wx.CROSS_CURSOR)
405	try:
406	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
407	Parms = dict(zip(Names,Values))
408	try:
409	wave = Parms['Lam']
410	except KeyError:
411	wave = Parms['Lam1']
412	if self.qPlot:
413	xpos = 2.0asind(xposwave/(4*math.pi))
414	dsp = 0.0
415	if abs(xpos) > 0.: #avoid possible singularity at beam center
416	dsp = wave/(2.*sind(abs(xpos)/2.0))
417	if self.Contour:
418	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
419	else:
420	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
421	if self.itemPicked:
422	Page.canvas.SetToolTipString('%9.3f'%(xpos))
423	if self.PickId:
424	found = []
425	if self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists']:
426	if len(HKL):
427	view = Page.toolbar._views.forward()[0][:2]
428	wid = view[1]-view[0]
429	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
430	if len(found):
431	h,k,l = found[0][:3]
432	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
433	else:
434	Page.canvas.SetToolTipString('')
435
436	except TypeError:
437	self.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
438
439	def OnPick(event):
440	if self.itemPicked is not None: return
441	PatternId = self.PatternId
442	try:
443	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
444	except TypeError:
445	return
446	Parms = dict(zip(Names,Values))
447	try:
448	wave = Parms['Lam']
449	except KeyError:
450	wave = Parms['Lam1']
451	PickId = self.PickId
452	pick = event.artist
453	mouse = event.mouseevent
454	xpos = pick.get_xdata()
455	ypos = pick.get_ydata()
456	ind = event.ind
457	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
458	if self.PatternTree.GetItemText(PickId) == 'Peak List':
459	if ind.all() != [0]: #picked a data point
460	if 'C' in Parms['Type']: #CW data - TOF later in an elif
461	ins = [Parms[x] for x in ['U','V','W','X','Y']]
462	if self.qPlot: #qplot - convert back to 2-theta
463	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
464	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
465	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
466	data = self.PatternTree.GetItemPyData(self.PickId)
467	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
468	data.append(XY)
469	G2pdG.UpdatePeakGrid(self,data)
470	PlotPatterns(self)
471	else: #picked a peak list line
472	self.itemPicked = pick
473	elif self.PatternTree.GetItemText(PickId) == 'Limits':
474	if ind.all() != [0]: #picked a data point
475	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
476	data = self.PatternTree.GetItemPyData(LimitId)
477	if 'C' in Parms['Type']: #CW data - TOF later in an elif
478	if self.qPlot: #qplot - convert back to 2-theta
479	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
480	if mouse.button==1:
481	data[1][0] = min(xy[0],data[1][1])
482	if mouse.button==3:
483	data[1][1] = max(xy[0],data[1][0])
484	self.PatternTree.SetItemPyData(LimitId,data)
485	G2pdG.UpdateLimitsGrid(self,data)
486	PlotPatterns(self)
487	else: #picked a limit line
488	self.itemPicked = pick
489	elif self.PatternTree.GetItemText(PickId) == 'Reflection Lists':
490	self.itemPicked = pick
491	pick = str(pick)
492
493	def OnRelease(event):
494	if self.itemPicked is None: return
495	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
496	Parms = dict(zip(Names,Values))
497	try:
498	wave = Parms['Lam']
499	except KeyError:
500	wave = Parms['Lam1']
501	xpos = event.xdata
502	PickId = self.PickId
503	if self.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
504	lines = []
505	for line in self.Lines: lines.append(line.get_xdata()[0])
506	lineNo = lines.index(self.itemPicked.get_xdata()[0])
507	if lineNo in [0,1]:
508	LimitId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Limits')
509	data = self.PatternTree.GetItemPyData(LimitId)
510	if self.qPlot:
511	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
512	else:
513	data[1][lineNo] = xpos
514	self.PatternTree.SetItemPyData(LimitId,data)
515	if self.PatternTree.GetItemText(self.PickId) == 'Limits':
516	G2pdG.UpdateLimitsGrid(self,data)
517	else:
518	PeakId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Peak List')
519	data = self.PatternTree.GetItemPyData(PeakId)
520	# print 'peaks',xpos
521	if event.button == 3:
522	del data[lineNo-2]
523	else:
524	if self.qPlot:
525	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
526	else:
527	data[lineNo-2][0] = xpos
528	self.PatternTree.SetItemPyData(PeakId,data)
529	G2pdG.UpdatePeakGrid(self,data)
530	elif self.PatternTree.GetItemText(PickId) == 'Reflection Lists' and xpos:
531	Phases = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId,'Reflection Lists'))
532	pick = str(self.itemPicked).split('(')[1].strip(')')
533	if 'Line' not in pick: #avoid data points, etc.
534	num = Phases.keys().index(pick)
535	if num:
536	self.refDelt = -(event.ydata-self.refOffset)/(num*Ymax)
537	else: #1st row of refl ticks
538	self.refOffset = event.ydata
539	PlotPatterns(self)
540	self.itemPicked = None
541
542	xylim = []
543	try:
544	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
545	Page = self.G2plotNB.nb.GetPage(plotNum)
546	if not newPlot:
547	Plot = Page.figure.gca() #get previous powder plot & get limits
548	xylim = Plot.get_xlim(),Plot.get_ylim()
549	Page.figure.clf()
550	Plot = Page.figure.gca() #get a fresh plot after clf()
551	except ValueError:
552	newPlot = True
553	self.Cmax = 1.0
554	Plot = self.G2plotNB.addMpl('Powder Patterns').gca()
555	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
556	Page = self.G2plotNB.nb.GetPage(plotNum)
557	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
558	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
559	Page.canvas.mpl_connect('pick_event', OnPick)
560	Page.canvas.mpl_connect('button_release_event', OnRelease)
561	Page.SetFocus()
562	self.G2plotNB.status.DestroyChildren()
563	if self.Contour:
564	Choice = (' key press','d: lower contour max','u: raise contour max',
565	'i: interpolation method','s: color scheme','c: contour off')
566	else:
567	if self.logPlot:
568	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
569	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
570	else:
571	Choice = (' key press','l: offset left','r: offset right','d: offset down',
572	'u: offset up','o: reset offset','n: log(I) on','c: contour on',
573	'q: toggle q plot','s: toggle single plot','+: no selection')
574	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
575	choices=Choice)
576	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
577	cb.SetValue(' key press')
578
579	PickId = self.PickId
580	PatternId = self.PatternId
581	colors=['b','g','r','c','m','k']
582	Lines = []
583	if self.SinglePlot:
584	Pattern = self.PatternTree.GetItemPyData(PatternId)
585	Pattern.append(self.PatternTree.GetItemText(PatternId))
586	PlotList = [Pattern,]
587	ParmList = [self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
588	self.PatternId, 'Instrument Parameters'))[1],]
589	else:
590	PlotList = []
591	ParmList = []
592	item, cookie = self.PatternTree.GetFirstChild(self.root)
593	while item:
594	if 'PWDR' in self.PatternTree.GetItemText(item):
595	Pattern = self.PatternTree.GetItemPyData(item)
596	if len(Pattern) < 3: # put name on end if needed
597	Pattern.append(self.PatternTree.GetItemText(item))
598	PlotList.append(Pattern)
599	ParmList.append(self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
600	item,'Instrument Parameters'))[1])
601	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
602	Ymax = 1.0
603	lenX = 0
604	if self.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
605	Phases = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId,'Reflection Lists'))
606	HKL = []
607	if Phases:
608	for peak in Phases[self.RefList]:
609	HKL.append(peak[:6])
610	HKL = np.array(HKL)
611	else:
612	HKL = np.array(self.HKL)
613	for Pattern in PlotList:
614	xye = Pattern[1]
615	Ymax = max(Ymax,max(xye[1]))
616	offset = self.Offset[0]*Ymax/100.0
617	Title = 'Powder Patterns: '+os.path.split(self.GSASprojectfile)[1]
618	if self.logPlot:
619	Title = 'log('+Title+')'
620	Plot.set_title(Title)
621	if self.qPlot:
622	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
623	else:
624	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
625	Plot.set_ylabel('Intensity',fontsize=12)
626	if self.Contour:
627	ContourZ = []
628	ContourY = []
629	Nseq = 0
630	if len(PlotList) < 2:
631	self.Contour = False
632	for N,Pattern in enumerate(PlotList):
633	Parms = ParmList[N]
634	ifpicked = False
635	LimitId = 0
636	xye = np.array(Pattern[1])
637	if PickId:
638	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
639	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
640	if self.qPlot:
641	Id = G2gd.GetPatternTreeItemId(self,self.root, Pattern[2])
642	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
643	else:
644	X = xye[0]
645	if not lenX:
646	lenX = len(X)
647	Y = xye[1]+offset*N
648	if LimitId:
649	limits = np.array(self.PatternTree.GetItemPyData(LimitId))
650	if self.qPlot:
651	limits = 4np.pinpsind(limits/2.0)/Parms[1]
652	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
653	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
654	if self.Contour:
655
656	if lenX == len(X):
657	ContourY.append(N)
658	ContourZ.append(Y)
659	ContourX = X
660	Nseq += 1
661	Plot.set_ylabel('Data sequence',fontsize=12)
662	else:
663	X += self.Offset[1].005N
664	if ifpicked:
665	Z = xye[3]+offset*N
666	W = xye[4]+offset*N
667	D = xye[5]-Ymax*self.delOffset
668	if self.Weight:
669	W2 = np.sqrt(xye[2])
670	D = W2-Ymaxself.delOffset
671	if self.logPlot:
672	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
673	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
674	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
675	else:
676	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
677	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
678	Plot.plot(X,W,colors[(N+2)%6],picker=False)
679	Plot.plot(X,D,colors[(N+3)%6],picker=False)
680	Plot.axhline(0.,color=wx.BLACK)
681	Page.canvas.SetToolTipString('')
682	if self.PatternTree.GetItemText(PickId) == 'Peak List':
683	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
684	Page.canvas.SetToolTipString(tip)
685	data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List'))
686	for item in data:
687	if self.qPlot:
688	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
689	else:
690	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
691	if self.PatternTree.GetItemText(PickId) == 'Limits':
692	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
693	Page.canvas.SetToolTipString(tip)
694	data = self.LimitsTable.GetData()
695	else:
696	if self.logPlot:
697	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
698	else:
699	Plot.plot(X,Y,colors[N%6],picker=False)
700	if PickId and not self.Contour:
701	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1::2]
702	Parms = dict(zip(Names,Values))
703	try:
704	wave = Parms['Lam']
705	except KeyError:
706	wave = Parms['Lam1']
707	if self.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
708	peaks = np.array((self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))))
709	for peak in peaks:
710	if self.qPlot:
711	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
712	else:
713	Plot.axvline(peak[0],color='b')
714	for hkl in self.HKL:
715	if self.qPlot:
716	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
717	else:
718	Plot.axvline(hkl[5],color='r',dashes=(5,5))
719	elif self.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
720	Phases = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId,'Reflection Lists'))
721	for pId,phase in enumerate(Phases):
722	peaks = Phases[phase]
723	peak = np.array([[peak[4],peak[5]] for peak in peaks])
724	pos = self.refOffset-pIdYmaxself.refDelt*np.ones_like(peak)
725	if self.qPlot:
726	Plot.plot(2*np.pi/peak.T[0],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
727	else:
728	Plot.plot(peak.T[1],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
729	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
730	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
731
732	if self.Contour:
733	acolor = mpl.cm.get_cmap(self.ContourColor)
734	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
735	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
736	Page.figure.colorbar(Img)
737	else:
738	self.Lines = Lines
739	if not newPlot:
740	Page.toolbar.push_current()
741	Plot.set_xlim(xylim[0])
742	Plot.set_ylim(xylim[1])
743	xylim = []
744	Page.toolbar.push_current()
745	Page.toolbar.draw()
746	else:
747	Page.canvas.draw()
748	self.Pwdr = True
749
750	def PlotISFG(self,newPlot=False,type=''):
751	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
752	or multiple plots with waterfall and contour plots as options
753	'''
754	if not type:
755	type = self.G2plotNB.plotList[self.G2plotNB.nb.GetSelection()]
756	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
757	return
758	superMinusOne = unichr(0xaf)+unichr(0xb9)
759
760	def OnPlotKeyPress(event):
761	newPlot = False
762	if event.key == 'u':
763	if self.Contour:
764	self.Cmax = min(1.0,self.Cmax*1.2)
765	elif self.Offset[0] < 100.:
766	self.Offset[0] += 1.
767	elif event.key == 'd':
768	if self.Contour:
769	self.Cmax = max(0.0,self.Cmax*0.8)
770	elif self.Offset[0] > 0.:
771	self.Offset[0] -= 1.
772	elif event.key == 'l':
773	self.Offset[1] -= 1.
774	elif event.key == 'r':
775	self.Offset[1] += 1.
776	elif event.key == 'o':
777	self.Offset = [0,0]
778	elif event.key == 'c':
779	newPlot = True
780	if self.Contour:
781	self.Contour = False
782	else:
783	self.Contour = True
784	self.SinglePlot = False
785	self.Offset = [0.,0.]
786	elif event.key == 's':
787	if self.Contour:
788	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
789	choice.sort()
790	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
791	if dlg.ShowModal() == wx.ID_OK:
792	sel = dlg.GetSelection()
793	self.ContourColor = choice[sel]
794	else:
795	self.ContourColor = 'Paired'
796	dlg.Destroy()
797	else:
798	if self.SinglePlot:
799	self.SinglePlot = False
800	else:
801	self.SinglePlot = True
802	elif event.key == 'i': #for smoothing contour plot
803	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
804	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
805	'mitchell','sinc','lanczos']
806	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
807	if dlg.ShowModal() == wx.ID_OK:
808	sel = dlg.GetSelection()
809	self.Interpolate = choice[sel]
810	else:
811	self.Interpolate = 'nearest'
812	dlg.Destroy()
813	elif event.key == 't' and not self.Contour:
814	if self.Legend:
815	self.Legend = False
816	else:
817	self.Legend = True
818
819
820	PlotISFG(self,newPlot=newPlot,type=type)
821
822	def OnKeyBox(event):
823	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index(type):
824	event.key = cb.GetValue()[0]
825	cb.SetValue(' key press')
826	OnPlotKeyPress(event)
827
828	def OnMotion(event):
829	xpos = event.xdata
830	if xpos: #avoid out of frame mouse position
831	ypos = event.ydata
832	Page.canvas.SetCursor(wx.CROSS_CURSOR)
833	try:
834	if self.Contour:
835	self.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
836	else:
837	self.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
838	except TypeError:
839	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
840
841	xylim = []
842	try:
843	plotNum = self.G2plotNB.plotList.index(type)
844	Page = self.G2plotNB.nb.GetPage(plotNum)
845	if not newPlot:
846	Plot = Page.figure.gca() #get previous plot & get limits
847	xylim = Plot.get_xlim(),Plot.get_ylim()
848	Page.figure.clf()
849	Plot = Page.figure.gca()
850	except ValueError:
851	newPlot = True
852	self.Cmax = 1.0
853	Plot = self.G2plotNB.addMpl(type).gca()
854	plotNum = self.G2plotNB.plotList.index(type)
855	Page = self.G2plotNB.nb.GetPage(plotNum)
856	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
857	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
858
859	Page.SetFocus()
860	self.G2plotNB.status.DestroyChildren()
861	if self.Contour:
862	Choice = (' key press','d: lower contour max','u: raise contour max',
863	'i: interpolation method','s: color scheme','c: contour off')
864	else:
865	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
866	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
867	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
868	choices=Choice)
869	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
870	cb.SetValue(' key press')
871	PatternId = self.PatternId
872	PickId = self.PickId
873	Plot.set_title(type)
874	if type == 'G(R)':
875	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
876	else:
877	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
878	Plot.set_ylabel(r''+type,fontsize=14)
879	colors=['b','g','r','c','m','k']
880	name = self.PatternTree.GetItemText(PatternId)[4:]
881	Pattern = []
882	if self.SinglePlot:
883	name = self.PatternTree.GetItemText(PatternId)
884	name = type+name[4:]
885	Id = G2gd.GetPatternTreeItemId(self,PatternId,name)
886	Pattern = self.PatternTree.GetItemPyData(Id)
887	if Pattern:
888	Pattern.append(name)
889	PlotList = [Pattern,]
890	else:
891	PlotList = []
892	item, cookie = self.PatternTree.GetFirstChild(self.root)
893	while item:
894	if 'PDF' in self.PatternTree.GetItemText(item):
895	name = type+self.PatternTree.GetItemText(item)[4:]
896	Id = G2gd.GetPatternTreeItemId(self,item,name)
897	Pattern = self.PatternTree.GetItemPyData(Id)
898	if Pattern:
899	Pattern.append(name)
900	PlotList.append(Pattern)
901	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
902	PDFdata = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'PDF Controls'))
903	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
904	Xb = [0.,10.]
905	Yb = [0.,-40.np.pinumbDen]
906	Ymax = 1.0
907	lenX = 0
908	for Pattern in PlotList:
909	xye = Pattern[1]
910	Ymax = max(Ymax,max(xye[1]))
911	offset = self.Offset[0]*Ymax/100.0
912	if self.Contour:
913	ContourZ = []
914	ContourY = []
915	Nseq = 0
916	for N,Pattern in enumerate(PlotList):
917	xye = Pattern[1]
918	if PickId:
919	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
920	X = xye[0]
921	if not lenX:
922	lenX = len(X)
923	Y = xye[1]+offset*N
924	if self.Contour:
925	if lenX == len(X):
926	ContourY.append(N)
927	ContourZ.append(Y)
928	ContourX = X
929	Nseq += 1
930	Plot.set_ylabel('Data sequence',fontsize=12)
931	else:
932	X = xye[0]+self.Offset[1].005N
933	if ifpicked:
934	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
935	Page.canvas.SetToolTipString('')
936	else:
937	if self.Legend:
938	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
939	else:
940	Plot.plot(X,Y,colors[N%6],picker=False)
941	if type == 'G(R)':
942	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
943	elif type == 'F(Q)':
944	Plot.axhline(0.,color=wx.BLACK)
945	elif type == 'S(Q)':
946	Plot.axhline(1.,color=wx.BLACK)
947	if self.Contour:
948	acolor = mpl.cm.get_cmap(self.ContourColor)
949	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
950	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
951	Page.figure.colorbar(Img)
952	elif self.Legend:
953	Plot.legend(loc='best')
954	if not newPlot:
955	Page.toolbar.push_current()
956	Plot.set_xlim(xylim[0])
957	Plot.set_ylim(xylim[1])
958	xylim = []
959	Page.toolbar.push_current()
960	Page.toolbar.draw()
961	else:
962	Page.canvas.draw()
963
964	def PlotXY(self,XY,newPlot=False,type=''):
965	'''simple plot of xy data, used for diagnostic purposes
966	'''
967	def OnMotion(event):
968	xpos = event.xdata
969	if xpos: #avoid out of frame mouse position
970	ypos = event.ydata
971	Page.canvas.SetCursor(wx.CROSS_CURSOR)
972	try:
973	self.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
974	except TypeError:
975	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
976
977	try:
978	plotNum = self.G2plotNB.plotList.index(type)
979	Page = self.G2plotNB.nb.GetPage(plotNum)
980	if not newPlot:
981	Plot = Page.figure.gca()
982	xylim = Plot.get_xlim(),Plot.get_ylim()
983	Page.figure.clf()
984	Plot = Page.figure.gca()
985	except ValueError:
986	newPlot = True
987	Plot = self.G2plotNB.addMpl(type).gca()
988	plotNum = self.G2plotNB.plotList.index(type)
989	Page = self.G2plotNB.nb.GetPage(plotNum)
990	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
991
992	Page.SetFocus()
993	self.G2plotNB.status.DestroyChildren()
994	Plot.set_title(type)
995	Plot.set_xlabel(r'X',fontsize=14)
996	Plot.set_ylabel(r''+type,fontsize=14)
997	colors=['b','g','r','c','m','k']
998	Ymax = 1.0
999	lenX = 0
1000	X,Y = XY[:2]
1001	Ymax = max(Ymax,max(Y))
1002	Plot.plot(X,Y,'k',picker=False)
1003	if not newPlot:
1004	Page.toolbar.push_current()
1005	Plot.set_xlim(xylim[0])
1006	Plot.set_ylim(xylim[1])
1007	xylim = []
1008	Page.toolbar.push_current()
1009	Page.toolbar.draw()
1010	else:
1011	Page.canvas.draw()
1012
1013	def PlotPowderLines(self):
1014	''' plotting of powder lines (i.e. no powder pattern) as sticks
1015	'''
1016	global HKL
1017
1018	def OnMotion(event):
1019	xpos = event.xdata
1020	if xpos: #avoid out of frame mouse position
1021	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1022	self.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1023	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
1024	found = []
1025	if len(HKL):
1026	view = Page.toolbar._views.forward()[0][:2]
1027	wid = view[1]-view[0]
1028	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1029	if len(found):
1030	h,k,l = found[0][:3]
1031	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1032	else:
1033	Page.canvas.SetToolTipString('')
1034
1035	try:
1036	plotNum = self.G2plotNB.plotList.index('Powder Lines')
1037	Page = self.G2plotNB.nb.GetPage(plotNum)
1038	Page.figure.clf()
1039	Plot = Page.figure.gca()
1040	except ValueError:
1041	Plot = self.G2plotNB.addMpl('Powder Lines').gca()
1042	plotNum = self.G2plotNB.plotList.index('Powder Lines')
1043	Page = self.G2plotNB.nb.GetPage(plotNum)
1044	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1045
1046	Page.SetFocus()
1047	Plot.set_title('Powder Pattern Lines')
1048	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1049	PickId = self.PickId
1050	PatternId = self.PatternId
1051	peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))
1052	for peak in peaks:
1053	Plot.axvline(peak[0],color='b')
1054	HKL = np.array(self.HKL)
1055	for hkl in self.HKL:
1056	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1057	xmin = peaks[0][0]
1058	xmax = peaks[-1][0]
1059	delt = xmax-xmin
1060	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1061	Plot.set_xlim(xlim)
1062	Page.canvas.draw()
1063	Page.toolbar.push_current()
1064
1065	def PlotPeakWidths(self):
1066	''' Plotting of instrument broadening terms as function of 2-theta (future TOF)
1067	Seen when "Instrument Parameters" chosen from powder pattern data tree
1068	'''
1069	PatternId = self.PatternId
1070	limitID = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
1071	if limitID:
1072	limits = self.PatternTree.GetItemPyData(limitID)
1073	else:
1074	return
1075	instParms = self.PatternTree.GetItemPyData( \
1076	G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))
1077	if instParms[0][0] in ['PXC','PNC']:
1078	lam = instParms[1][1]
1079	if len(instParms[1]) == 13:
1080	GU,GV,GW,LX,LY = instParms[0][6:11]
1081	else:
1082	GU,GV,GW,LX,LY = instParms[0][4:9]
1083	peakID = G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List')
1084	if peakID:
1085	peaks = self.PatternTree.GetItemPyData(peakID)
1086	else:
1087	peaks = []
1088
1089	try:
1090	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1091	Page = self.G2plotNB.nb.GetPage(plotNum)
1092	Page.figure.clf()
1093	Plot = Page.figure.gca()
1094	except ValueError:
1095	Plot = self.G2plotNB.addMpl('Peak Widths').gca()
1096	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1097	Page = self.G2plotNB.nb.GetPage(plotNum)
1098	Page.SetFocus()
1099
1100	Page.canvas.SetToolTipString('')
1101	colors=['b','g','r','c','m','k']
1102	Xmin,Xmax = limits[1]
1103	Xmin = min(0.5,max(Xmin,1))
1104	Xmin /= 2
1105	Xmax /= 2
1106	nPts = 100
1107	delt = (Xmax-Xmin)/nPts
1108	thetas = []
1109	for i in range(nPts):
1110	thetas.append(Xmin+i*delt)
1111	X = []
1112	Y = []
1113	Z = []
1114	W = []
1115	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1116	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1117	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.)
1118	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1119	for theta in thetas:
1120	X.append(4.0math.pisind(theta)/lam) #q
1121	s = sig(theta,GU,GV,GW)
1122	g = gam(theta,LX,LY)
1123	G = gamFW(g,s)
1124	Y.append(s/tand(theta))
1125	Z.append(g/tand(theta))
1126	W.append(G/tand(theta))
1127	Plot.set_title('Instrument and sample peak widths')
1128	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1129	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1130	Plot.plot(X,Y,color='r',label='Gaussian')
1131	Plot.plot(X,Z,color='g',label='Lorentzian')
1132	Plot.plot(X,W,color='b',label='G+L')
1133	X = []
1134	Y = []
1135	Z = []
1136	W = []
1137	V = []
1138	for peak in peaks:
1139	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1140	try:
1141	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1142	except ValueError:
1143	s = 0.01
1144	g = peak[6]*math.pi/18000.
1145	G = gamFW(g,s)
1146	Y.append(s/tand(peak[0]/2.))
1147	Z.append(g/tand(peak[0]/2.))
1148	W.append(G/tand(peak[0]/2.))
1149	Plot.plot(X,Y,'+',color='r',label='G peak')
1150	Plot.plot(X,Z,'+',color='g',label='L peak')
1151	Plot.plot(X,W,'+',color='b',label='G+L peak')
1152	Plot.legend(loc='best')
1153	Page.canvas.draw()
1154
1155	def PlotSizeStrainPO(self,data,Start=False):
1156	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1157	'''
1158
1159	PatternId = self.PatternId
1160	generalData = data['General']
1161	SGData = generalData['SGData']
1162	SGLaue = SGData['SGLaue']
1163	if Start: #initialize the spherical harmonics qlmn arrays
1164	ptx.pyqlmninit()
1165	Start = False
1166	MuStrKeys = G2spc.MustrainNames(SGData)
1167	cell = generalData['Cell'][1:]
1168	A,B = G2lat.cell2AB(cell[:6])
1169	Vol = cell[6]
1170	useList = data['Histograms']
1171	phase = generalData['Name']
1172	plotType = generalData['Data plot type']
1173	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
1174	for ptype in plotDict:
1175	self.G2plotNB.Delete(ptype)
1176
1177	for item in useList:
1178	if useList[item]['Show']:
1179	break
1180	else:
1181	return #nothing to show!!
1182
1183	numPlots = len(useList)
1184
1185	if plotType in ['Mustrain','Size']:
1186	Plot = mp3d.Axes3D(self.G2plotNB.add3D(plotType))
1187	else:
1188	Plot = self.G2plotNB.addMpl(plotType).gca()
1189	plotNum = self.G2plotNB.plotList.index(plotType)
1190	Page = self.G2plotNB.nb.GetPage(plotNum)
1191	Page.SetFocus()
1192	self.G2plotNB.status.SetStatusText('Adjust frame size to get desired aspect ratio',1)
1193	if not Page.IsShown():
1194	Page.Show()
1195
1196	for item in useList:
1197	if useList[item]['Show']:
1198	PHI = np.linspace(0.,360.,30,True)
1199	PSI = np.linspace(0.,180.,30,True)
1200	X = np.outer(npsind(PHI),npsind(PSI))
1201	Y = np.outer(npcosd(PHI),npsind(PSI))
1202	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1203	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
1204	coeff = useList[item][plotDict[plotType]]
1205	except KeyError:
1206	break
1207	if plotType in ['Mustrain','Size']:
1208	if coeff[0] == 'isotropic':
1209	X *= coeff[1][0]
1210	Y *= coeff[1][0]
1211	Z *= coeff[1][0]
1212	elif coeff[0] == 'uniaxial':
1213
1214	def uniaxCalc(xyz,iso,aniso,axes):
1215	Z = np.array(axes)
1216	cp = abs(np.dot(xyz,Z))
1217	sp = np.sqrt(1.-cp**2)
1218	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
1219	return R*xyz
1220
1221	iso,aniso = coeff[1][:2]
1222	axes = np.inner(A,np.array(coeff[3]))
1223	axes /= nl.norm(axes)
1224	Shkl = np.array(coeff[1])
1225	XYZ = np.dstack((X,Y,Z))
1226	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
1227	X,Y,Z = np.dsplit(XYZ,3)
1228	X = X[:,:,0]
1229	Y = Y[:,:,0]
1230	Z = Z[:,:,0]
1231
1232	elif coeff[0] == 'ellipsoidal':
1233
1234	def ellipseCalc(xyz,E,R):
1235	XYZ = xyz*E.T
1236	return np.inner(XYZ.T,R)
1237
1238	S6 = coeff[4]
1239	Sij = G2lat.U6toUij(S6)
1240	E,R = nl.eigh(Sij)
1241	XYZ = np.dstack((X,Y,Z))
1242	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
1243	X,Y,Z = np.dsplit(XYZ,3)
1244	X = X[:,:,0]
1245	Y = Y[:,:,0]
1246	Z = Z[:,:,0]
1247
1248	elif coeff[0] == 'generalized':
1249
1250	def genMustrain(xyz,SGData,A,Shkl):
1251	uvw = np.inner(A.T,xyz)
1252	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1253	sum = np.sum(np.multiply(Shkl,Strm))
1254	sum = np.where(sum > 0.01,sum,0.01)
1255	sum = np.sqrt(sum)*math.pi/0.018 #centidegrees to radians!
1256	return sum*xyz
1257
1258	Shkl = np.array(coeff[4])
1259	if np.any(Shkl):
1260	XYZ = np.dstack((X,Y,Z))
1261	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1262	X,Y,Z = np.dsplit(XYZ,3)
1263	X = X[:,:,0]
1264	Y = Y[:,:,0]
1265	Z = Z[:,:,0]
1266
1267	if np.any(X) and np.any(Y) and np.any(Z):
1268	errFlags = np.seterr(all='ignore')
1269	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1270	np.seterr(all='ignore')
1271	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
1272	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
1273	Plot.set_xlim3d(XYZlim)
1274	Plot.set_ylim3d(XYZlim)
1275	Plot.set_zlim3d(XYZlim)
1276	Plot.set_aspect('equal')
1277	if plotType == 'Size':
1278	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
1279	Plot.set_xlabel(r'X, $\mu$m')
1280	Plot.set_ylabel(r'Y, $\mu$m')
1281	Plot.set_zlabel(r'Z, $\mu$m')
1282	else:
1283	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
1284	Plot.set_xlabel(r'X, $\mu$strain')
1285	Plot.set_ylabel(r'Y, $\mu$strain')
1286	Plot.set_zlabel(r'Z, $\mu$strain')
1287	else:
1288	h,k,l = generalData['POhkl']
1289	if coeff[0] == 'MD':
1290	print 'March-Dollase preferred orientation plot'
1291
1292	else:
1293	PH = np.array(generalData['POhkl'])
1294	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
1295	SHCoef = {}
1296	for item in coeff[5]:
1297	L,N = eval(item.strip('C'))
1298	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
1299	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1300	X = np.linspace(0,90.0,26)
1301	Y = G2lat.polfcal(ODFln,'0',X,0.0)
1302	Plot.plot(X,Y,color='k',label=str(PH))
1303	Plot.legend(loc='best')
1304	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
1305	Plot.set_xlabel(r'$\psi$',fontsize=16)
1306	Plot.set_ylabel('MRD',fontsize=14)
1307	Page.canvas.draw()
1308
1309	def PlotTexture(self,data,newPlot=False,Start=False):
1310	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
1311	plotting.
1312	dict generalData contains all phase info needed which is in data
1313	'''
1314
1315	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1316	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1317	PatternId = self.PatternId
1318	generalData = data['General']
1319	SGData = generalData['SGData']
1320	textureData = generalData['SH Texture']
1321	self.G2plotNB.Delete('Texture')
1322	if not textureData['Order']:
1323	return #no plot!!
1324	SHData = generalData['SH Texture']
1325	SHCoef = SHData['SH Coeff'][1]
1326	cell = generalData['Cell'][1:7]
1327	Amat,Bmat = G2lat.cell2AB(cell)
1328	sq2 = 1.0/math.sqrt(2.0)
1329
1330	def rp2xyz(r,p):
1331	z = npcosd(r)
1332	xy = np.sqrt(1.-z**2)
1333	return xynpsind(p),xynpcosd(p),z
1334
1335	def OnMotion(event):
1336	SHData = data['General']['SH Texture']
1337	if event.xdata and event.ydata: #avoid out of frame errors
1338	xpos = event.xdata
1339	ypos = event.ydata
1340	if 'Inverse' in SHData['PlotType']:
1341	r = xpos2+ypos2
1342	if r <= 1.0:
1343	if 'equal' in self.Projection:
1344	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1345	else:
1346	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1347	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1348	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1349	y,x,z = list(xyz/np.max(np.abs(xyz)))
1350
1351	self.G2plotNB.status.SetFields(['',
1352	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1353
1354	elif 'Axial' in SHData['PlotType']:
1355	pass
1356
1357	else: #ordinary pole figure
1358	z = xpos2+ypos2
1359	if z <= 1.0:
1360	z = np.sqrt(z)
1361	if 'equal' in self.Projection:
1362	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1363	else:
1364	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1365	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1366	self.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1367
1368	if self.Projection == '3D display' and 'Axial' not in SHData['PlotType']:
1369	Plot = mp3d.Axes3D(self.G2plotNB.add3D('Texture'))
1370	else:
1371	Plot = self.G2plotNB.addMpl('Texture').gca()
1372	plotNum = self.G2plotNB.plotList.index('Texture')
1373	Page = self.G2plotNB.nb.GetPage(plotNum)
1374	if self.Projection == '3D display':
1375	pass
1376	else:
1377	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1378
1379	Page.SetFocus()
1380	self.G2plotNB.status.SetFields(['',''])
1381	PH = np.array(SHData['PFhkl'])
1382	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1383	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1384	PX = np.array(SHData['PFxyz'])
1385	gam = atan2d(PX[0],PX[1])
1386	xy = math.sqrt(PX[0]2+PX[1]2)
1387	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1388	psi = asind(xy/xyz)
1389	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1390	if 'Axial' in SHData['PlotType']:
1391	X = np.linspace(0,90.0,26)
1392	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1393	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1394	Plot.legend(loc='best')
1395	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1396	Plot.set_xlabel(r'$\psi$',fontsize=16)
1397	Plot.set_ylabel('MRD',fontsize=14)
1398
1399	else:
1400	npts = 201
1401	if 'Inverse' in SHData['PlotType']:
1402	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1403	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1404	if 'equal' in self.Projection:
1405	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1406	else:
1407	R = np.where(R <= 1.,2.*npatand(R),0.0)
1408	Z = np.zeros_like(R)
1409	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
1410	Z = np.reshape(Z,(npts,npts))
1411	CS = Plot.contour(Y,X,Z,aspect='equal')
1412	Plot.clabel(CS,fontsize=9,inline=1)
1413	try:
1414	Img = Plot.imshow(Z.T,aspect='equal',cmap=self.ContourColor,extent=[-1,1,-1,1])
1415	except ValueError:
1416	pass
1417	if newPlot:
1418	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1419	newPlot = False
1420	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
1421	Plot.set_xlabel(self.Projection.capitalize()+' projection')
1422
1423	else:
1424	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1425	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1426	if 'equal' in self.Projection:
1427	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1428	else:
1429	R = np.where(R <= 1.,2.*npatand(R),0.0)
1430	Z = np.zeros_like(R)
1431	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
1432	Z = np.reshape(Z,(npts,npts))
1433	try:
1434	CS = Plot.contour(Y,X,Z,aspect='equal')
1435	Plot.clabel(CS,fontsize=9,inline=1)
1436	except ValueError:
1437	pass
1438	Img = Plot.imshow(Z.T,aspect='equal',cmap=self.ContourColor,extent=[-1,1,-1,1])
1439	if newPlot:
1440	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1441	newPlot = False
1442	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
1443	Plot.set_xlabel(self.Projection.capitalize()+' projection')
1444	Page.canvas.draw()
1445
1446	def PlotCovariance(self,Data={}):
1447	if not Data:
1448	Data = self.PatternTree.GetItemPyData(
1449	G2gd.GetPatternTreeItemId(self,self.root, 'Covariance'))
1450	if not Data:
1451	print 'No covariance matrix available'
1452	return
1453	varyList = Data['varyList']
1454	values = Data['variables']
1455	Xmax = len(varyList)
1456	covMatrix = Data['covMatrix']
1457	sig = np.sqrt(np.diag(covMatrix))
1458	xvar = np.outer(sig,np.ones_like(sig))
1459	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
1460	title = ' for\n'+Data['title']
1461	newAtomDict = Data['newAtomDict']
1462
1463	def OnPlotKeyPress(event):
1464	newPlot = False
1465	if event.key == 's':
1466	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1467	choice.sort()
1468	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
1469	if dlg.ShowModal() == wx.ID_OK:
1470	sel = dlg.GetSelection()
1471	self.VcovColor = choice[sel]
1472	else:
1473	self.VcovColor = 'RdYlGn'
1474	dlg.Destroy()
1475	PlotCovariance(self)
1476
1477	def OnMotion(event):
1478	if event.button:
1479	ytics = imgAx.get_yticks()
1480	ytics = np.where(ytics<len(varyList),ytics,-1)
1481	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
1482	imgAx.set_yticklabels(ylabs)
1483
1484	if event.xdata and event.ydata: #avoid out of frame errors
1485	xpos = int(event.xdata+.5)
1486	ypos = int(event.ydata+.5)
1487	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
1488	if xpos == ypos:
1489	value = values[xpos]
1490	name = varyList[xpos]
1491	if varyList[xpos] in newAtomDict:
1492	name,value = newAtomDict[name]
1493	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
1494	else:
1495	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
1496	Page.canvas.SetToolTipString(msg)
1497	self.G2plotNB.status.SetFields(['Key: s to change colors',msg])
1498	try:
1499	plotNum = self.G2plotNB.plotList.index('Covariance')
1500	Page = self.G2plotNB.nb.GetPage(plotNum)
1501	Page.figure.clf()
1502	Plot = Page.figure.gca()
1503	if not Page.IsShown():
1504	Page.Show()
1505	except ValueError:
1506	Plot = self.G2plotNB.addMpl('Covariance').gca()
1507	plotNum = self.G2plotNB.plotList.index('Covariance')
1508	Page = self.G2plotNB.nb.GetPage(plotNum)
1509	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1510	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1511
1512	Page.SetFocus()
1513	self.G2plotNB.status.SetFields(['',''])
1514	acolor = mpl.cm.get_cmap(self.VcovColor)
1515	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower')
1516	imgAx = Img.get_axes()
1517	ytics = imgAx.get_yticks()
1518	ylabs = [varyList[int(i)] for i in ytics[:-1]]
1519	imgAx.set_yticklabels(ylabs)
1520	colorBar = Page.figure.colorbar(Img)
1521	Plot.set_title('V-Cov matrix'+title)
1522	Plot.set_xlabel('Variable number')
1523	Plot.set_ylabel('Variable name')
1524	Page.canvas.draw()
1525
1526	def PlotSeq(self,SeqData,SeqSig,SeqNames,sampleParm):
1527
1528	def OnKeyPress(event):
1529	if event.key == 's' and sampleParm:
1530	if self.xAxis:
1531	self.xAxis = False
1532	else:
1533	self.xAxis = True
1534	Draw(False)
1535	try:
1536	plotNum = self.G2plotNB.plotList.index('Sequential refinement')
1537	Page = self.G2plotNB.nb.GetPage(plotNum)
1538	Page.figure.clf()
1539	Plot = Page.figure.gca()
1540	if not Page.IsShown():
1541	Page.Show()
1542	except ValueError:
1543	Plot = self.G2plotNB.addMpl('Sequential refinement').gca()
1544	plotNum = self.G2plotNB.plotList.index('Sequential refinement')
1545	Page = self.G2plotNB.nb.GetPage(plotNum)
1546	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
1547	self.xAxis = False
1548
1549	def Draw(newPlot):
1550	Page.SetFocus()
1551	self.G2plotNB.status.SetFields(['','press s to toggle x-axis = sample environment parameter'])
1552	if len(SeqData):
1553	Plot.clear()
1554	if self.xAxis:
1555	xName = sampleParm.keys()[0]
1556	X = sampleParm[xName]
1557	else:
1558	X = np.arange(0,len(SeqData[0]),1)
1559	xName = 'Data sequence number'
1560	for Y,sig,name in zip(SeqData,SeqSig,SeqNames):
1561	Plot.errorbar(X,Y,yerr=sig,label=name)
1562	Plot.legend(loc='best')
1563	Plot.set_ylabel('Parameter values')
1564	Plot.set_xlabel(xName)
1565	Page.canvas.draw()
1566	Draw(True)
1567
1568	def PlotExposedImage(self,newPlot=False,event=None):
1569	'''General access module for 2D image plotting
1570	'''
1571	plotNo = self.G2plotNB.nb.GetSelection()
1572	if self.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1573	PlotImage(self,newPlot,event,newImage=True)
1574	elif self.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1575	PlotIntegration(self,newPlot,event)
1576
1577	def PlotImage(self,newPlot=False,event=None,newImage=True):
1578	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1579	masks, etc.
1580	'''
1581	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1582	import numpy.ma as ma
1583	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1584	global Data,Masks
1585	colors=['b','g','r','c','m','k']
1586	Data = self.PatternTree.GetItemPyData(
1587	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1588	Masks = self.PatternTree.GetItemPyData(
1589	G2gd.GetPatternTreeItemId(self,self.Image, 'Masks'))
1590
1591	def OnImMotion(event):
1592	Page.canvas.SetToolTipString('')
1593	sizexy = Data['size']
1594	if event.xdata and event.ydata: #avoid out of frame errors
1595	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1596	item = self.itemPicked
1597	pixelSize = Data['pixelSize']
1598	scalex = 1000./pixelSize[0]
1599	scaley = 1000./pixelSize[1]
1600	if item and self.PatternTree.GetItemText(self.PickId) == 'Image Controls':
1601	if 'Text' in str(item):
1602	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1603	else:
1604	xcent,ycent = Data['center']
1605	xpos = event.xdata-xcent
1606	ypos = event.ydata-ycent
1607	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1608	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1609	Page.canvas.SetToolTipString('%6d deg'%(azm))
1610	elif 'line1' in str(item) or 'line2' in str(item):
1611	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1612	else:
1613	xpos = event.xdata
1614	ypos = event.ydata
1615	xpix = xpos*scalex
1616	ypix = ypos*scaley
1617	Int = 0
1618	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1619	Int = self.ImageZ[ypix][xpix]
1620	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1621	Q = 2.*math.pi/dsp
1622	if self.setPoly:
1623	self.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1624	else:
1625	self.G2plotNB.status.SetFields(\
1626	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1627
1628	def OnImPlotKeyPress(event):
1629	try:
1630	PickName = self.PatternTree.GetItemText(self.PickId)
1631	except TypeError:
1632	return
1633	if PickName == 'Masks':
1634	Xpos = event.xdata
1635	if not Xpos: #got point out of frame
1636	return
1637	Ypos = event.ydata
1638	if event.key == 's':
1639	Masks['Points'].append([Xpos,Ypos,1.])
1640	elif event.key == 'r':
1641	tth = G2img.GetTth(Xpos,Ypos,Data)
1642	Masks['Rings'].append([tth,0.1])
1643	elif event.key == 'a':
1644	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1645	azm = int(azm)
1646	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1647	elif event.key == 'p':
1648	self.setPoly = True
1649	Masks['Polygons'].append([])
1650	self.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1651	G2imG.UpdateMasks(self,Masks)
1652	elif PickName == 'Image Controls':
1653	if event.key == 'c':
1654	Xpos = event.xdata
1655	if not Xpos: #got point out of frame
1656	return
1657	Ypos = event.ydata
1658	dlg = wx.MessageDialog(self,'Are you sure you want to change the center?',
1659	'Center change',style=wx.OK\|wx.CANCEL)
1660	try:
1661	if dlg.ShowModal() == wx.ID_OK:
1662	print 'move center to: ',Xpos,Ypos
1663	Data['center'] = [Xpos,Ypos]
1664	G2imG.UpdateImageControls(self,Data,Masks)
1665	finally:
1666	dlg.Destroy()
1667	elif event.key == 'l':
1668	if self.logPlot:
1669	self.logPlot = False
1670	else:
1671	self.logPlot = True
1672	PlotImage(self,newImage=True)
1673
1674	def OnKeyBox(event):
1675	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('2D Powder Image'):
1676	event.key = cb.GetValue()[0]
1677	cb.SetValue(' key press')
1678	if event.key in 'l':
1679	OnImPlotKeyPress(event)
1680
1681	def OnImPick(event):
1682	if self.PatternTree.GetItemText(self.PickId) not in ['Image Controls','Masks']:
1683	return
1684	if self.setPoly:
1685	polygon = Masks['Polygons'][-1]
1686	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1687	if xpos and ypos: #point inside image
1688	if len(polygon) > 2 and event.mouseevent.button == 3:
1689	x0,y0 = polygon[0]
1690	polygon.append([x0,y0])
1691	self.setPoly = False
1692	self.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1693	else:
1694	self.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1695	polygon.append([xpos,ypos])
1696	G2imG.UpdateMasks(self,Masks)
1697	else:
1698	if self.itemPicked is not None: return
1699	self.itemPicked = event.artist
1700	self.mousePicked = event.mouseevent
1701
1702	def OnImRelease(event):
1703	try:
1704	PickName = self.PatternTree.GetItemText(self.PickId)
1705	except TypeError:
1706	return
1707	if PickName not in ['Image Controls','Masks']:
1708	return
1709	pixelSize = Data['pixelSize']
1710	scalex = 1000./pixelSize[0]
1711	scaley = 1000./pixelSize[1]
1712	pixLimit = Data['pixLimit']
1713	if self.itemPicked is None and PickName == 'Image Controls':
1714	# sizexy = Data['size']
1715	Xpos = event.xdata
1716	if not (Xpos and self.ifGetRing): #got point out of frame
1717	return
1718	Ypos = event.ydata
1719	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1720	if event.button == 1:
1721	Xpix = Xpos*scalex
1722	Ypix = Ypos*scaley
1723	xpos,ypos,I,J = G2img.ImageLocalMax(self.ImageZ,pixLimit,Xpix,Ypix)
1724	if I and J:
1725	xpos += .5 #shift to pixel center
1726	ypos += .5
1727	xpos /= scalex #convert to mm
1728	ypos /= scaley
1729	Data['ring'].append([xpos,ypos])
1730	elif event.button == 3:
1731	self.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1732	if G2img.ImageCalibrate(self,Data):
1733	self.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1734	print 'Calibration successful'
1735	else:
1736	self.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1737	print 'Calibration failed'
1738	self.ifGetRing = False
1739	G2imG.UpdateImageControls(self,Data,Masks)
1740	return
1741	PlotImage(self,newImage=False)
1742	return
1743	else:
1744	xpos = event.xdata
1745	if xpos: #avoid out of frame mouse position
1746	ypos = event.ydata
1747	if self.ifGetRing: #delete a calibration ring pick
1748	xypos = [xpos,ypos]
1749	rings = Data['ring']
1750	for ring in rings:
1751	if np.allclose(ring,xypos,.01,0):
1752	rings.remove(ring)
1753	else:
1754	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1755	itemPicked = str(self.itemPicked)
1756	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1757	if 'line1' in itemPicked:
1758	Data['IOtth'][0] = max(tth,0.001)
1759	elif 'line2' in itemPicked:
1760	Data['IOtth'][1] = tth
1761	elif 'line3' in itemPicked:
1762	Data['LRazimuth'][0] = int(azm)
1763	if Data['fullIntegrate']:
1764	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1765	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1766	Data['LRazimuth'][1] = int(azm)
1767
1768	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1769	Data['LRazimuth'][0] -= 360
1770
1771	azLim = np.array(Data['LRazimuth'])
1772	if np.any(azLim>360):
1773	azLim -= 360
1774	Data['LRazimuth'] = list(azLim)
1775
1776	if Data['IOtth'][0] > Data['IOtth'][1]:
1777	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1778
1779	self.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1780	self.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1781	self.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1782	self.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1783	elif 'Circle' in itemPicked and PickName == 'Masks':
1784	spots = Masks['Points']
1785	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1786	newPos = np.array([float(newPos[0]),float(newPos[1])])
1787	for spot in spots:
1788	if np.allclose(np.array([spot[:2]]),newPos):
1789	spot[:2] = xpos,ypos
1790	G2imG.UpdateMasks(self,Masks)
1791	elif 'Line2D' in itemPicked and PickName == 'Masks':
1792	Obj = self.itemPicked.findobj()
1793	rings = Masks['Rings']
1794	arcs = Masks['Arcs']
1795	polygons = Masks['Polygons']
1796	for ring in self.ringList:
1797	if Obj == ring[0]:
1798	rN = ring[1]
1799	if ring[2] == 'o':
1800	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1801	else:
1802	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1803	for arc in self.arcList:
1804	if Obj == arc[0]:
1805	aN = arc[1]
1806	if arc[2] == 'o':
1807	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1808	elif arc[2] == 'i':
1809	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1810	elif arc[2] == 'l':
1811	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1812	else:
1813	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1814	for poly in self.polyList:
1815	if Obj == poly[0]:
1816	ind = self.itemPicked.contains(self.mousePicked)[1]['ind'][0]
1817	oldPos = np.array([self.mousePicked.xdata,self.mousePicked.ydata])
1818	pN = poly[1]
1819	for i,xy in enumerate(polygons[pN]):
1820	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1821	polygons[pN][i] = xpos,ypos
1822	G2imG.UpdateMasks(self,Masks)
1823	# else: #keep for future debugging
1824	# print str(self.itemPicked),event.xdata,event.ydata,event.button
1825	PlotImage(self,newImage=True)
1826	self.itemPicked = None
1827
1828	try:
1829	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1830	Page = self.G2plotNB.nb.GetPage(plotNum)
1831	if not newPlot:
1832	Plot = Page.figure.gca() #get previous powder plot & get limits
1833	xylim = Plot.get_xlim(),Plot.get_ylim()
1834	if newImage:
1835	Page.figure.clf()
1836	Plot = Page.figure.gca() #get a fresh plot after clf()
1837
1838	except ValueError:
1839	Plot = self.G2plotNB.addMpl('2D Powder Image').gca()
1840	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1841	Page = self.G2plotNB.nb.GetPage(plotNum)
1842	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1843	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1844	Page.canvas.mpl_connect('pick_event', OnImPick)
1845	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1846	xylim = []
1847	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1848	Page.SetFocus()
1849	Title = self.PatternTree.GetItemText(self.Image)[4:]
1850	self.G2plotNB.status.DestroyChildren()
1851	if self.logPlot:
1852	Title = 'log('+Title+')'
1853	Plot.set_title(Title)
1854	try:
1855	if self.PatternTree.GetItemText(self.PickId) in ['Image Controls',]:
1856	Choice = (' key press','l: log(I) on',)
1857	if self.logPlot:
1858	Choice[1] = 'l: log(I) off'
1859	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1860	choices=Choice)
1861	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1862	cb.SetValue(' key press')
1863	except TypeError:
1864	pass
1865	size,imagefile = self.PatternTree.GetItemPyData(self.Image)
1866	if imagefile != self.oldImagefile:
1867	imagefile = G2IO.CheckImageFile(self,imagefile)
1868	if not imagefile:
1869	self.G2plotNB.Delete('2D Powder Image')
1870	return
1871	self.PatternTree.SetItemPyData(self.Image,[size,imagefile])
1872	self.ImageZ = G2IO.GetImageData(self,imagefile,imageOnly=True)
1873	# print self.ImageZ.shape,self.ImageZ.size,Data['size'] #might be useful debugging line
1874	self.oldImagefile = imagefile
1875
1876	imScale = 1
1877	if len(self.ImageZ) > 1024:
1878	imScale = len(self.ImageZ)/1024
1879	sizexy = Data['size']
1880	pixelSize = Data['pixelSize']
1881	scalex = 1000./pixelSize[0]
1882	scaley = 1000./pixelSize[1]
1883	Xmax = sizexy[0]*pixelSize[0]/1000.
1884	Ymax = sizexy[1]*pixelSize[1]/1000.
1885	xlim = (0,Xmax)
1886	ylim = (Ymax,0)
1887	Imin,Imax = Data['range'][1]
1888	acolor = mpl.cm.get_cmap(Data['color'])
1889	xcent,ycent = Data['center']
1890	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1891	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1892	#do threshold mask - "real" mask - others are just bondaries
1893	Zlim = Masks['Thresholds'][1]
1894	wx.BeginBusyCursor()
1895	try:
1896
1897	if newImage:
1898	MA = ma.masked_greater(ma.masked_less(self.ImageZ,Zlim[0]),Zlim[1])
1899	MaskA = ma.getmaskarray(MA)
1900	A = G2img.ImageCompress(MA,imScale)
1901	AM = G2img.ImageCompress(MaskA,imScale)
1902	if self.logPlot:
1903	A = np.where(A>0,np.log(A),0)
1904	AM = np.where(AM>0,np.log(AM),0)
1905	Imin,Imax = [np.amin(A),np.amax(A)]
1906	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
1907	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
1908	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
1909	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
1910	if self.setPoly:
1911	Img.set_picker(True)
1912
1913	Plot.plot(xcent,ycent,'x')
1914	if Data['showLines']:
1915	LRAzim = Data['LRazimuth'] #NB: integers
1916	Nazm = Data['outAzimuths']
1917	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
1918	AzmthOff = Data['azmthOff']
1919	IOtth = Data['IOtth']
1920	wave = Data['wavelength']
1921	dspI = wave/(2.0*sind(IOtth[0]/2.0))
1922	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
1923	dspO = wave/(2.0*sind(IOtth[1]/2.0))
1924	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
1925	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
1926	if ellI:
1927	xyI = []
1928	for azm in Azm:
1929	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
1930	xyI = np.array(xyI)
1931	arcxI,arcyI = xyI.T
1932	Plot.plot(arcxI,arcyI,picker=3)
1933	if ellO:
1934	xyO = []
1935	for azm in Azm:
1936	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
1937	xyO = np.array(xyO)
1938	arcxO,arcyO = xyO.T
1939	Plot.plot(arcxO,arcyO,picker=3)
1940	if ellO and ellI:
1941	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
1942	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
1943	for i in range(Nazm):
1944	cake = LRAzim[0]+i*delAzm-AzmthOff
1945	ind = np.searchsorted(Azm,cake)
1946	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
1947
1948	for xring,yring in Data['ring']:
1949	Plot.plot(xring,yring,'r+',picker=3)
1950	if Data['setRings']:
1951	# rings = np.concatenate((Data['rings']),axis=0)
1952	N = 0
1953	for ring in Data['rings']:
1954	xring,yring = np.array(ring).T[:2]
1955	Plot.plot(xring,yring,'+',color=colors[N%6])
1956	N += 1
1957	for ellipse in Data['ellipses']:
1958	cent,phi,[width,height],col = ellipse
1959	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
1960	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
1961	#masks - mask lines numbered after integration limit lines
1962	spots = Masks['Points']
1963	rings = Masks['Rings']
1964	arcs = Masks['Arcs']
1965	polygons = Masks['Polygons']
1966	for x,y,d in spots:
1967	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
1968	self.ringList = []
1969	for iring,(tth,thick) in enumerate(rings):
1970	wave = Data['wavelength']
1971	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
1972	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
1973	self.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1974	self.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1975	self.arcList = []
1976	for iarc,(tth,azm,thick) in enumerate(arcs):
1977	wave = Data['wavelength']
1978	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
1979	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
1980	self.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1981	self.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1982	self.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1983	self.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1984	self.polyList = []
1985	for ipoly,polygon in enumerate(polygons):
1986	x,y = np.hsplit(np.array(polygon),2)
1987	self.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
1988	Plot.plot(x,y,'r')
1989	if newImage:
1990	colorBar = Page.figure.colorbar(Img)
1991	Plot.set_xlim(xlim)
1992	Plot.set_ylim(ylim)
1993	if not newPlot and xylim:
1994	Page.toolbar.push_current()
1995	Plot.set_xlim(xylim[0])
1996	Plot.set_ylim(xylim[1])
1997	xylim = []
1998	Page.toolbar.push_current()
1999	Page.toolbar.draw()
2000	else:
2001	Page.canvas.draw()
2002	finally:
2003	wx.EndBusyCursor()
2004
2005	def PlotIntegration(self,newPlot=False,event=None):
2006	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
2007	'''
2008
2009	def OnMotion(event):
2010	Page.canvas.SetToolTipString('')
2011	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2012	azm = event.ydata
2013	tth = event.xdata
2014	if azm and tth:
2015	self.G2plotNB.status.SetFields(\
2016	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2017
2018	try:
2019	plotNum = self.G2plotNB.plotList.index('2D Integration')
2020	Page = self.G2plotNB.nb.GetPage(plotNum)
2021	if not newPlot:
2022	Plot = Page.figure.gca() #get previous plot & get limits
2023	xylim = Plot.get_xlim(),Plot.get_ylim()
2024	Page.figure.clf()
2025	Plot = Page.figure.gca() #get a fresh plot after clf()
2026
2027	except ValueError:
2028	Plot = self.G2plotNB.addMpl('2D Integration').gca()
2029	plotNum = self.G2plotNB.plotList.index('2D Integration')
2030	Page = self.G2plotNB.nb.GetPage(plotNum)
2031	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2032	Page.views = False
2033	view = False
2034	if not event:
2035	Page.SetFocus()
2036
2037	Data = self.PatternTree.GetItemPyData(
2038	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
2039	image = self.Integrate[0]
2040	xsc = self.Integrate[1]
2041	ysc = self.Integrate[2]
2042	Imin,Imax = Data['range'][1]
2043	acolor = mpl.cm.get_cmap(Data['color'])
2044	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
2045	Plot.set_ylabel('azimuth',fontsize=12)
2046	Plot.set_xlabel('2-theta',fontsize=12)
2047	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
2048	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
2049	colorBar = Page.figure.colorbar(Img)
2050	if Data['ellipses']:
2051	for ellipse in Data['ellipses']:
2052	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2053	x,y = np.hsplit(ring,2)
2054	tth,azm = G2img.GetTthAzm(x,y,Data)
2055	# azm = np.where(azm < 0.,azm+360,azm)
2056	Plot.plot(tth,azm,'b,')
2057	if not newPlot:
2058	Page.toolbar.push_current()
2059	Plot.set_xlim(xylim[0])
2060	Plot.set_ylim(xylim[1])
2061	xylim = []
2062	Page.toolbar.push_current()
2063	Page.toolbar.draw()
2064	else:
2065	Page.canvas.draw()
2066
2067	def PlotTRImage(self,tax,tay,taz,newPlot=False):
2068	'''a test plot routine - not normally used
2069	'''
2070
2071	def OnMotion(event):
2072	Page.canvas.SetToolTipString('')
2073	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2074	azm = event.xdata
2075	tth = event.ydata
2076	if azm and tth:
2077	self.G2plotNB.status.SetFields(\
2078	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2079
2080	try:
2081	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
2082	Page = self.G2plotNB.nb.GetPage(plotNum)
2083	if not newPlot:
2084	Plot = Page.figure.gca() #get previous plot & get limits
2085	xylim = Plot.get_xlim(),Plot.get_ylim()
2086	Page.figure.clf()
2087	Plot = Page.figure.gca() #get a fresh plot after clf()
2088
2089	except ValueError:
2090	Plot = self.G2plotNB.addMpl('2D Transformed Powder Image').gca()
2091	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
2092	Page = self.G2plotNB.nb.GetPage(plotNum)
2093	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2094	Page.views = False
2095	view = False
2096	Page.SetFocus()
2097
2098	Data = self.PatternTree.GetItemPyData(
2099	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
2100	Imin,Imax = Data['range'][1]
2101	step = (Imax-Imin)/5.
2102	V = np.arange(Imin,Imax,step)
2103	acolor = mpl.cm.get_cmap(Data['color'])
2104	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
2105	Plot.set_xlabel('azimuth',fontsize=12)
2106	Plot.set_ylabel('2-theta',fontsize=12)
2107	Plot.contour(tax,tay,taz,V,cmap=acolor)
2108	if Data['showLines']:
2109	IOtth = Data['IOtth']
2110	if Data['fullIntegrate']:
2111	LRAzim = [-180,180]
2112	else:
2113	LRAzim = Data['LRazimuth'] #NB: integers
2114	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
2115	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
2116	if not Data['fullIntegrate']:
2117	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
2118	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
2119	if Data['setRings']:
2120	rings = np.concatenate((Data['rings']),axis=0)
2121	for xring,yring,dsp in rings:
2122	x,y = G2img.GetTthAzm(xring,yring,Data)
2123	Plot.plot(y,x,'r+')
2124	if Data['ellipses']:
2125	for ellipse in Data['ellipses']:
2126	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2127	x,y = np.hsplit(ring,2)
2128	tth,azm = G2img.GetTthAzm(x,y,Data)
2129	Plot.plot(azm,tth,'b,')
2130	if not newPlot:
2131	Page.toolbar.push_current()
2132	Plot.set_xlim(xylim[0])
2133	Plot.set_ylim(xylim[1])
2134	xylim = []
2135	Page.toolbar.push_current()
2136	Page.toolbar.draw()
2137	else:
2138	Page.canvas.draw()
2139
2140	def PlotStructure(self,data):
2141	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
2142	thermal motion ellipsoids and polyhedra
2143	'''
2144	generalData = data['General']
2145	cell = generalData['Cell'][1:7]
2146	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
2147	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2148	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2149	Mydir = generalData['Mydir']
2150	atomData = data['Atoms']
2151	drawingData = data['Drawing']
2152	drawAtoms = drawingData['Atoms']
2153	cx,ct,cs = drawingData['atomPtrs']
2154	Wt = [255,255,255]
2155	Rd = [255,0,0]
2156	Gr = [0,255,0]
2157	Bl = [0,0,255]
2158	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]])
2159	uEdges = np.array([
2160	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
2161	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
2162	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
2163	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
2164	altDown = False
2165	shiftDown = False
2166	ctrlDown = False
2167
2168	def OnKeyBox(event):
2169	import Image
2170	Draw() #make sure plot is fresh!!
2171	mode = cb.GetValue()
2172	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
2173	size = Page.canvas.GetSize()
2174	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
2175	if mode in ['jpeg',]:
2176	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
2177	im = Image.new("RGBA", (size[0],size[1]))
2178	else:
2179	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
2180	im = Image.new("RGB", (size[0],size[1]))
2181	im.fromstring(Pix)
2182	im.save(Fname,mode)
2183	cb.SetValue(' Save as:')
2184	self.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
2185
2186	def GetTruePosition(xy):
2187	View = glGetIntegerv(GL_VIEWPORT)
2188	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
2189	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
2190	Zmax = 1.
2191	for i,atom in enumerate(drawAtoms):
2192	x,y,z = atom[cx:cx+3]
2193	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2194	XY = [int(X),int(View[3]-Y)]
2195	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2196	Zmax = Z
2197	SetSelectedAtoms(i)
2198
2199	def OnMouseDown(event):
2200	xy = event.GetPosition()
2201	if event.ShiftDown():
2202	GetTruePosition(xy)
2203	else:
2204	drawingData['Rotation'][3] = xy
2205	Draw()
2206
2207	def OnMouseMove(event):
2208	newxy = event.GetPosition()
2209	page = getSelection()
2210	if event.ControlDown() and drawingData['showABC']:
2211	if event.LeftIsDown():
2212	SetTestRot(newxy)
2213	elif event.RightIsDown():
2214	SetTestPos(newxy)
2215	elif event.MiddleIsDown():
2216	SetTestRotZ(newxy)
2217	x,y,z = drawingData['testPos'][0]
2218	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2219
2220
2221	if event.Dragging() and not event.ControlDown():
2222	if event.LeftIsDown():
2223	SetRotation(newxy)
2224	angX,angY,angZ = drawingData['Rotation'][:3]
2225	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
2226	elif event.RightIsDown():
2227	SetTranslation(newxy)
2228	Tx,Ty,Tz = drawingData['viewPoint'][0]
2229	self.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2230	elif event.MiddleIsDown():
2231	SetRotationZ(newxy)
2232	angX,angY,angZ = drawingData['Rotation'][:3]
2233	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
2234	Draw()
2235
2236	def OnMouseWheel(event):
2237	drawingData['cameraPos'] += event.GetWheelRotation()/24
2238	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2239	self.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2240	page = getSelection()
2241	if page:
2242	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2243	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2244	names = [child.GetName() for child in panel]
2245	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2246	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2247	Draw()
2248
2249	def getSelection():
2250	try:
2251	return self.dataDisplay.GetSelection()
2252	except AttributeError:
2253	print self.dataDisplay.GetLabel()
2254	self.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2255	return 0
2256
2257	def SetViewPointText(VP):
2258	page = getSelection()
2259	if page:
2260	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2261	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2262	names = [child.GetName() for child in panel]
2263	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
2264
2265	def ClearSelectedAtoms():
2266	page = getSelection()
2267	if page:
2268	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2269	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2270	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2271	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2272
2273	def SetSelectedAtoms(ind):
2274	page = getSelection()
2275	if page:
2276	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2277	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
2278	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2279	Id = drawAtoms[ind][-2]
2280	for i,atom in enumerate(atomData):
2281	if atom[-1] == Id:
2282	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2283
2284	def GetSelectedAtoms():
2285	page = getSelection()
2286	Ind = []
2287	if page:
2288	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2289	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2290	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2291	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2292	return Ind
2293
2294	def OnKey(event): #on key UP!!
2295	keyCode = event.GetKeyCode()
2296	if keyCode > 255:
2297	keyCode = 0
2298	key,xyz = chr(keyCode),event.GetPosition()
2299	indx = drawingData['selectedAtoms']
2300	if key in ['c','C']:
2301	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2302	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
2303	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
2304	SetViewPointText(drawingData['viewPoint'][0])
2305	elif key in ['n','N']:
2306	drawAtoms = drawingData['Atoms']
2307	pI = drawingData['viewPoint'][1]
2308	if indx:
2309	pI[0] = indx[pI[1]]
2310	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2311	pI[1] += 1
2312	if pI[1] >= len(indx):
2313	pI[1] = 0
2314	else:
2315	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2316	pI[0] += 1
2317	if pI[0] >= len(drawAtoms):
2318	pI[0] = 0
2319	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2320	SetViewPointText(drawingData['viewPoint'][0])
2321
2322	elif key in ['p','P']:
2323	drawAtoms = drawingData['Atoms']
2324	pI = drawingData['viewPoint'][1]
2325	if indx:
2326	pI[0] = indx[pI[1]]
2327	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2328	pI[1] -= 1
2329	if pI[1] < 0:
2330	pI[1] = len(indx)-1
2331	else:
2332	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2333	pI[0] -= 1
2334	if pI[0] < 0:
2335	pI[0] = len(drawAtoms)-1
2336	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2337	SetViewPointText(drawingData['viewPoint'][0])
2338	Draw()
2339
2340	def SetBackground():
2341	R,G,B,A = Page.camera['backColor']
2342	glClearColor(R,G,B,A)
2343	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2344
2345	def SetLights():
2346	glEnable(GL_DEPTH_TEST)
2347	glShadeModel(GL_SMOOTH)
2348	glEnable(GL_LIGHTING)
2349	glEnable(GL_LIGHT0)
2350	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2351	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2352	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2353
2354	def SetTranslation(newxy):
2355	Tx,Ty,Tz = drawingData['viewPoint'][0]
2356	anglex,angley,anglez,oldxy = drawingData['Rotation']
2357	Rx = G2lat.rotdMat(anglex,0)
2358	Ry = G2lat.rotdMat(angley,1)
2359	Rz = G2lat.rotdMat(anglez,2)
2360	dxy = list(newxy-oldxy)+[0,]
2361	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
2362	Tx -= dxy[0]*0.01
2363	Ty += dxy[1]*0.01
2364	Tz -= dxy[2]*0.01
2365	drawingData['Rotation'][3] = newxy
2366	drawingData['viewPoint'][0] = Tx,Ty,Tz
2367	SetViewPointText([Tx,Ty,Tz])
2368
2369	def SetTestPos(newxy):
2370	Tx,Ty,Tz = drawingData['testPos'][0]
2371	anglex,angley,anglez,oldxy = drawingData['Rotation']
2372	Rx = G2lat.rotdMat(anglex,0)
2373	Ry = G2lat.rotdMat(angley,1)
2374	Rz = G2lat.rotdMat(anglez,2)
2375	dxy = list(newxy-oldxy)+[0,]
2376	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
2377	Tx += dxy[0]*0.001
2378	Ty -= dxy[1]*0.001
2379	Tz += dxy[2]*0.001
2380	drawingData['Rotation'][3] = newxy
2381	drawingData['testPos'][0] = Tx,Ty,Tz
2382
2383	def SetTestRot(newxy):
2384	Txyz = np.array(drawingData['testPos'][0])
2385	oldxy = drawingData['testPos'][2]
2386	Ax,Ay,Az = drawingData['testPos'][1]
2387	Vxyz = np.array(drawingData['viewPoint'][0])
2388	Dxyz = np.inner(Amat,Txyz-Vxyz)
2389	dxy = list(newxy-oldxy)+[0,]
2390	Ax += dxy[1]*0.01
2391	Ay += dxy[0]*0.01
2392	Rx = G2lat.rotdMat(Ax,0)
2393	Ry = G2lat.rotdMat(Ay,1)
2394	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
2395	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2396	drawingData['testPos'][1] = [Ax,Ay,Az]
2397	drawingData['testPos'][2] = newxy
2398	drawingData['testPos'][0] = Dxyz
2399
2400	def SetTestRotZ(newxy):
2401	Txyz = np.array(drawingData['testPos'][0])
2402	oldxy = drawingData['testPos'][2]
2403	Ax,Ay,Az = drawingData['testPos'][1]
2404	Vxyz = np.array(drawingData['viewPoint'][0])
2405	Dxyz = np.inner(Amat,Txyz-Vxyz)
2406	dxy = list(newxy-oldxy)+[0,]
2407	Az += (dxy[0]+dxy[1])*.01
2408	Rz = G2lat.rotdMat(Az,2)
2409	Dxyz = np.inner(Rz,Dxyz)
2410	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2411	drawingData['testPos'][1] = [Ax,Ay,Az]
2412	drawingData['testPos'][2] = newxy
2413	drawingData['testPos'][0] = Dxyz
2414
2415	def SetRotation(newxy):
2416	anglex,angley,anglez,oldxy = drawingData['Rotation']
2417	dxy = newxy-oldxy
2418	anglex += dxy[1]*.25
2419	angley += dxy[0]*.25
2420	oldxy = newxy
2421	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2422
2423	def SetRotationZ(newxy):
2424	anglex,angley,anglez,oldxy = drawingData['Rotation']
2425	dxy = newxy-oldxy
2426	anglez += (dxy[0]+dxy[1])*.25
2427	oldxy = newxy
2428	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2429
2430	def RenderBox():
2431	glEnable(GL_COLOR_MATERIAL)
2432	glLineWidth(2)
2433	glEnable(GL_BLEND)
2434	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2435	glEnable(GL_LINE_SMOOTH)
2436	glBegin(GL_LINES)
2437	for line,color in zip(uEdges,uColors):
2438	glColor3ubv(color)
2439	glVertex3fv(line[0])
2440	glVertex3fv(line[1])
2441	glEnd()
2442	glColor4ubv([0,0,0,0])
2443	glDisable(GL_LINE_SMOOTH)
2444	glDisable(GL_BLEND)
2445	glDisable(GL_COLOR_MATERIAL)
2446
2447	def RenderUnitVectors(x,y,z):
2448	xyz = np.array([x,y,z])
2449	glEnable(GL_COLOR_MATERIAL)
2450	glLineWidth(1)
2451	glPushMatrix()
2452	glTranslate(x,y,z)
2453	glScalef(1/cell[0],1/cell[1],1/cell[2])
2454	glBegin(GL_LINES)
2455	for line,color in zip(uEdges,uColors)[:3]:
2456	glColor3ubv(color)
2457	glVertex3fv(line[0])
2458	glVertex3fv(line[1])
2459	glEnd()
2460	glPopMatrix()
2461	glColor4ubv([0,0,0,0])
2462	glDisable(GL_COLOR_MATERIAL)
2463
2464	def RenderSphere(x,y,z,radius,color):
2465	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2466	glPushMatrix()
2467	glTranslate(x,y,z)
2468	glMultMatrixf(B4mat.T)
2469	q = gluNewQuadric()
2470	gluSphere(q,radius,20,10)
2471	glPopMatrix()
2472
2473	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2474	s1,s2,s3 = E
2475	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2476	glPushMatrix()
2477	glTranslate(x,y,z)
2478	glMultMatrixf(B4mat.T)
2479	glMultMatrixf(R4.T)
2480	glEnable(GL_NORMALIZE)
2481	glScale(s1,s2,s3)
2482	q = gluNewQuadric()
2483	gluSphere(q,ellipseProb,20,10)
2484	glDisable(GL_NORMALIZE)
2485	glPopMatrix()
2486
2487	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2488	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2489	glPushMatrix()
2490	glTranslate(x,y,z)
2491	glMultMatrixf(B4mat.T)
2492	for bond in Bonds:
2493	glPushMatrix()
2494	Dx = np.inner(Amat,bond)
2495	Z = np.sqrt(np.sum(Dx**2))
2496	azm = atan2d(-Dx[1],-Dx[0])
2497	phi = acosd(Dx[2]/Z)
2498	glRotate(-azm,0,0,1)
2499	glRotate(phi,1,0,0)
2500	q = gluNewQuadric()
2501	gluCylinder(q,radius,radius,Z,slice,2)
2502	glPopMatrix()
2503	glPopMatrix()
2504
2505	def RenderLines(x,y,z,Bonds,color):
2506	xyz = np.array([x,y,z])
2507	glEnable(GL_COLOR_MATERIAL)
2508	glLineWidth(1)
2509	glColor3fv(color)
2510	glPushMatrix()
2511	glBegin(GL_LINES)
2512	for bond in Bonds:
2513	glVertex3fv(xyz)
2514	glVertex3fv(xyz+bond)
2515	glEnd()
2516	glColor4ubv([0,0,0,0])
2517	glPopMatrix()
2518	glDisable(GL_COLOR_MATERIAL)
2519
2520	def RenderPolyhedra(x,y,z,Faces,color):
2521	glPushMatrix()
2522	glTranslate(x,y,z)
2523	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2524	glShadeModel(GL_SMOOTH)
2525	glMultMatrixf(B4mat.T)
2526	for face,norm in Faces:
2527	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2528	glFrontFace(GL_CW)
2529	glNormal3fv(norm)
2530	glBegin(GL_TRIANGLES)
2531	for vert in face:
2532	glVertex3fv(vert)
2533	glEnd()
2534	glPopMatrix()
2535
2536	def RenderBackbone(Backbone,BackboneColor,radius):
2537	glPushMatrix()
2538	glMultMatrixf(B4mat.T)
2539	glEnable(GL_COLOR_MATERIAL)
2540	glShadeModel(GL_SMOOTH)
2541	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2542	glePolyCylinder(Backbone,BackboneColor,radius)
2543	glPopMatrix()
2544	glDisable(GL_COLOR_MATERIAL)
2545
2546	def RenderLabel(x,y,z,label,r):
2547	glPushMatrix()
2548	glTranslate(x,y,z)
2549	glMultMatrixf(B4mat.T)
2550	glDisable(GL_LIGHTING)
2551	glColor3f(0,1.,0)
2552	glRasterPos3f(r,r,r)
2553	for c in list(label):
2554	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2555	glEnable(GL_LIGHTING)
2556	glPopMatrix()
2557
2558	def Draw():
2559	import numpy.linalg as nl
2560	Ind = GetSelectedAtoms()
2561	VS = np.array(Page.canvas.GetSize())
2562	aspect = float(VS[0])/float(VS[1])
2563	cPos = drawingData['cameraPos']
2564	Zclip = drawingData['Zclip']*cPos/200.
2565	anglex,angley,anglez = drawingData['Rotation'][:3]
2566	Tx,Ty,Tz = drawingData['viewPoint'][0]
2567	cx,ct,cs = drawingData['atomPtrs']
2568	bondR = drawingData['bondRadius']
2569	G,g = G2lat.cell2Gmat(cell)
2570	GS = G
2571	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2572	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2573	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2574	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2575
2576	SetBackground()
2577	glInitNames()
2578	glPushName(0)
2579
2580	glMatrixMode(GL_PROJECTION)
2581	glLoadIdentity()
2582	glViewport(0,0,VS[0],VS[1])
2583	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2584	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2585	SetLights()
2586
2587	glMatrixMode(GL_MODELVIEW)
2588	glLoadIdentity()
2589	glRotate(anglez,0,0,1)
2590	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2591	glRotate(angley,sind(anglez),cosd(anglez),0)
2592	glMultMatrixf(A4mat.T)
2593	glTranslate(-Tx,-Ty,-Tz)
2594	if drawingData['unitCellBox']:
2595	RenderBox()
2596	if drawingData['showABC']:
2597	x,y,z = drawingData['testPos'][0]
2598	# if altDown:
2599	# self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2600	# else:
2601	# self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2602	RenderUnitVectors(x,y,z)
2603	Backbone = []
2604	BackboneColor = []
2605	time0 = time.time()
2606	for iat,atom in enumerate(drawingData['Atoms']):
2607	x,y,z = atom[cx:cx+3]
2608	Bonds = atom[-2]
2609	Faces = atom[-1]
2610	try:
2611	atNum = generalData['AtomTypes'].index(atom[ct])
2612	except ValueError:
2613	atNum = -1
2614	CL = atom[cs+2]
2615	color = np.array(CL)/255.
2616	if iat in Ind:
2617	color = np.array(Gr)/255.
2618	radius = 0.5
2619	if atom[cs] != '':
2620	glLoadName(atom[-3])
2621	if 'balls' in atom[cs]:
2622	vdwScale = drawingData['vdwScale']
2623	ballScale = drawingData['ballScale']
2624	if atNum < 0:
2625	radius = 0.2
2626	elif 'H' == atom[ct]:
2627	if drawingData['showHydrogen']:
2628	if 'vdW' in atom[cs] and atNum >= 0:
2629	radius = vdwScale*generalData['vdWRadii'][atNum]
2630	else:
2631	radius = ballScale*drawingData['sizeH']
2632	else:
2633	radius = 0.0
2634	else:
2635	if 'vdW' in atom[cs]:
2636	radius = vdwScale*generalData['vdWRadii'][atNum]
2637	else:
2638	radius = ballScale*generalData['BondRadii'][atNum]
2639	RenderSphere(x,y,z,radius,color)
2640	if 'sticks' in atom[cs]:
2641	RenderBonds(x,y,z,Bonds,bondR,color)
2642	elif 'ellipsoids' in atom[cs]:
2643	RenderBonds(x,y,z,Bonds,bondR,color)
2644	if atom[cs+3] == 'A':
2645	Uij = atom[cs+5:cs+11]
2646	U = np.multiply(G2spc.Uij2U(Uij),GS)
2647	U = np.inner(Amat,np.inner(U,Amat).T)
2648	E,R = nl.eigh(U)
2649	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2650	E = np.sqrt(E)
2651	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2652	pass
2653	else:
2654	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2655	else:
2656	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2657	pass
2658	else:
2659	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2660	RenderSphere(x,y,z,radius,color)
2661	elif 'lines' in atom[cs]:
2662	radius = 0.1
2663	RenderLines(x,y,z,Bonds,color)
2664	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2665	elif atom[cs] == 'sticks':
2666	radius = 0.1
2667	RenderBonds(x,y,z,Bonds,bondR,color)
2668	elif atom[cs] == 'polyhedra':
2669	RenderPolyhedra(x,y,z,Faces,color)
2670	elif atom[cs] == 'backbone':
2671	if atom[ct-1].split()[0] in ['C','N']:
2672	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2673	BackboneColor.append(list(color))
2674
2675	if atom[cs+1] == 'type':
2676	RenderLabel(x,y,z,atom[ct],radius)
2677	elif atom[cs+1] == 'name':
2678	RenderLabel(x,y,z,atom[ct-1],radius)
2679	elif atom[cs+1] == 'number':
2680	RenderLabel(x,y,z,str(iat+1),radius)
2681	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2682	RenderLabel(x,y,z,atom[ct-4],radius)
2683	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2684	RenderLabel(x,y,z,atom[ct-3],radius)
2685	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2686	RenderLabel(x,y,z,atom[ct-2],radius)
2687	if Backbone:
2688	RenderBackbone(Backbone,BackboneColor,bondR)
2689	# print time.time()-time0
2690	Page.canvas.SwapBuffers()
2691
2692	def OnSize(event):
2693	Draw()
2694
2695	def OnFocus(event):
2696	Draw()
2697
2698	try:
2699	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2700	Page = self.G2plotNB.nb.GetPage(plotNum)
2701	except ValueError:
2702	Plot = self.G2plotNB.addOgl(generalData['Name'])
2703	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2704	Page = self.G2plotNB.nb.GetPage(plotNum)
2705	Page.views = False
2706	view = False
2707	altDown = False
2708	Page.SetFocus()
2709	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2710	choices=(' save as:','jpeg','tiff','bmp'))
2711	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2712	cb.SetValue(' save as:')
2713	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2714	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2715	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2716	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2717	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2718	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2719	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2720	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2721	Page.camera['position'] = drawingData['cameraPos']
2722	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2723	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2724	Page.canvas.SetCurrent()
2725	Draw()
2726

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