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GSASIIplot.py @ 4956

Last change on this file since 4956 was 517, checked in by toby, 13 years ago
make sure that texture is initialized for multiprocessing
Property svn:keywords set to `Date Author Revision URL Id`
File size: 117.8 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2012-03-09 21:10:26 +0000 (Fri, 09 Mar 2012) $
4	# $Author: vondreele $
5	# $Revision: 517 $
6	# $URL: branch/MPbranch/GSASIIplot.py $
7	# $Id: GSASIIplot.py 517 2012-03-09 21:10:26Z vondreele $
8	########### SVN repository information ###################
9	import math
10	import time
11	import copy
12	import os.path
13	import numpy as np
14	import numpy.linalg as nl
15	import wx
16	import wx.aui
17	import wx.glcanvas
18	import matplotlib as mpl
19	import mpl_toolkits.mplot3d.axes3d as mp3d
20	import GSASIIpath
21	import GSASIIgrid as G2gd
22	import GSASIIimage as G2img
23	import GSASIIpwd as G2pwd
24	import GSASIIIO as G2IO
25	import GSASIIpwdGUI as G2pdG
26	import GSASIIimgGUI as G2imG
27	import GSASIIphsGUI as G2phG
28	import GSASIIlattice as G2lat
29	import GSASIIspc as G2spc
30	import pytexture as ptx
31	from OpenGL.GL import *
32	from OpenGL.GLU import *
33	from OpenGL.GLUT import *
34	from OpenGL.GLE import *
35	from matplotlib.backends.backend_wx import _load_bitmap
36	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
37	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
38
39	# useful degree trig functions
40	sind = lambda x: math.sin(x*math.pi/180.)
41	cosd = lambda x: math.cos(x*math.pi/180.)
42	tand = lambda x: math.tan(x*math.pi/180.)
43	asind = lambda x: 180.*math.asin(x)/math.pi
44	acosd = lambda x: 180.*math.acos(x)/math.pi
45	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
46	atand = lambda x: 180.*math.atan(x)/math.pi
47	# numpy versions
48	npsind = lambda x: np.sin(x*np.pi/180.)
49	npcosd = lambda x: np.cos(x*np.pi/180.)
50	npacosd = lambda x: 180.*np.arccos(x)/np.pi
51	npasind = lambda x: 180.*np.arcsin(x)/np.pi
52	npatand = lambda x: 180.*np.arctan(x)/np.pi
53	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
54
55	class G2PlotMpl(wx.Panel):
56	def __init__(self,parent,id=-1,dpi=None,**kwargs):
57	wx.Panel.__init__(self,parent,id=id,**kwargs)
58	mpl.rcParams['legend.fontsize'] = 10
59	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
60	self.canvas = Canvas(self,-1,self.figure)
61	self.toolbar = GSASIItoolbar(self.canvas)
62
63	self.toolbar.Realize()
64
65	sizer=wx.BoxSizer(wx.VERTICAL)
66	sizer.Add(self.canvas,1,wx.EXPAND)
67	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
68	self.SetSizer(sizer)
69
70	class G2PlotOgl(wx.Panel):
71	def __init__(self,parent,id=-1,dpi=None,**kwargs):
72	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
73	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
74	self.camera = {}
75	sizer=wx.BoxSizer(wx.VERTICAL)
76	sizer.Add(self.canvas,1,wx.EXPAND)
77	self.SetSizer(sizer)
78
79	class G2Plot3D(wx.Panel):
80	def __init__(self,parent,id=-1,dpi=None,**kwargs):
81	wx.Panel.__init__(self,parent,id=id,**kwargs)
82	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
83	self.canvas = Canvas(self,-1,self.figure)
84	self.toolbar = GSASIItoolbar(self.canvas)
85
86	self.toolbar.Realize()
87
88	sizer=wx.BoxSizer(wx.VERTICAL)
89	sizer.Add(self.canvas,1,wx.EXPAND)
90	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
91	self.SetSizer(sizer)
92
93	class G2PlotNoteBook(wx.Panel):
94	def __init__(self,parent,id=-1):
95	wx.Panel.__init__(self,parent,id=id)
96	#so one can't delete a plot page!!
97	self.nb = wx.aui.AuiNotebook(self, \
98	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
99	sizer = wx.BoxSizer()
100	sizer.Add(self.nb,1,wx.EXPAND)
101	self.SetSizer(sizer)
102	self.status = parent.CreateStatusBar()
103	self.status.SetFieldsCount(2)
104	self.status.SetStatusWidths([150,-1])
105	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
106
107	self.plotList = []
108
109	def addMpl(self,name=""):
110	page = G2PlotMpl(self.nb)
111	self.nb.AddPage(page,name)
112
113	self.plotList.append(name)
114
115	return page.figure
116
117	def add3D(self,name=""):
118	page = G2Plot3D(self.nb)
119	self.nb.AddPage(page,name)
120
121	self.plotList.append(name)
122
123	return page.figure
124
125	def addOgl(self,name=""):
126	page = G2PlotOgl(self.nb)
127	self.nb.AddPage(page,name)
128
129	self.plotList.append(name)
130
131	return page.figure
132
133	def Delete(self,name):
134	try:
135	item = self.plotList.index(name)
136	del self.plotList[item]
137	self.nb.DeletePage(item)
138	except ValueError: #no plot of this name - do nothing
139	return
140
141	def clear(self):
142	while self.nb.GetPageCount():
143	self.nb.DeletePage(0)
144	self.plotList = []
145	self.status.DestroyChildren()
146
147	def Rename(self,oldName,newName):
148	try:
149	item = self.plotList.index(oldName)
150	self.plotList[item] = newName
151	self.nb.SetPageText(item,newName)
152	except ValueError: #no plot of this name - do nothing
153	return
154
155	def OnPageChanged(self,event):
156	if self.plotList:
157	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
158	self.status.DestroyChildren() #get rid of special stuff on status bar
159
160	class GSASIItoolbar(Toolbar):
161	ON_MPL_HELP = wx.NewId()
162	def __init__(self,plotCanvas):
163	Toolbar.__init__(self,plotCanvas)
164	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6
165	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
166	help = os.path.join(os.path.split(__file__)[0],'help.ico')
167	self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
168	wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
169	def OnHelp(self,event):
170	Page = self.GetParent().GetParent()
171	pageNo = Page.GetSelection()
172	bookmark = Page.GetPageText(pageNo)
173	bookmark = bookmark.strip(')').replace('(','_')
174	G2gd.ShowHelp(bookmark,self.TopLevelParent)
175
176	def PlotSngl(self,newPlot=False):
177	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
178	to F, F**2, etc. as requested
179	'''
180	from matplotlib.patches import Circle
181	global HKL,HKLF
182
183	def OnSCMotion(event):
184	xpos = event.xdata
185	if xpos:
186	xpos = round(xpos) #avoid out of frame mouse position
187	ypos = round(event.ydata)
188	zpos = Data['Layer']
189	if '100' in Data['Zone']:
190	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
191	elif '010' in Data['Zone']:
192	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
193	elif '001' in Data['Zone']:
194	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
195	Page.canvas.SetToolTipString(HKLtxt)
196	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
197
198	def OnSCPick(event):
199	zpos = Data['Layer']
200	pos = event.artist.center
201	if '100' in Data['Zone']:
202	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
203	hkl = np.array([zpos,pos[0],pos[1]])
204	elif '010' in Data['Zone']:
205	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
206	hkl = np.array([pos[0],zpos,pos[1]])
207	elif '001' in Data['Zone']:
208	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
209	hkl = np.array([pos[0],pos[1],zpos])
210	h,k,l = hkl
211	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
212	if len(hklf):
213	Fosq,sig,Fcsq = hklf[0]
214	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
215	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
216
217	def OnSCKeyPress(event):
218	print event.key
219
220	try:
221	plotNum = self.G2plotNB.plotList.index('Structure Factors')
222	Page = self.G2plotNB.nb.GetPage(plotNum)
223	if not newPlot:
224	Plot = Page.figure.gca() #get previous powder plot & get limits
225	xylim = Plot.get_xlim(),Plot.get_ylim()
226	Page.figure.clf()
227	Plot = Page.figure.gca() #get a fresh plot after clf()
228	except ValueError:
229	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
230	plotNum = self.G2plotNB.plotList.index('Structure Factors')
231	Page = self.G2plotNB.nb.GetPage(plotNum)
232	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
233	Page.canvas.mpl_connect('pick_event', OnSCPick)
234	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
235	Page.SetFocus()
236
237	Plot.set_aspect(aspect='equal')
238	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
239	Data = self.PatternTree.GetItemPyData( \
240	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
241	Type = Data['Type']
242	scale = Data['Scale']
243	HKLmax = Data['HKLmax']
244	HKLmin = Data['HKLmin']
245	FosqMax = Data['FoMax']
246	FoMax = math.sqrt(FosqMax)
247	ifFc = Data['ifFc']
248	xlabel = ['k, h=','h, k=','h, l=']
249	ylabel = ['l','l','k']
250	zones = ['100','010','001']
251	pzone = [[1,2],[0,2],[0,1]]
252	izone = zones.index(Data['Zone'])
253	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
254	HKL = []
255	HKLF = []
256	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
257	HKL.append(H)
258	HKLF.append([Fosq,sig,Fcsq])
259	if H[izone] == Data['Layer']:
260	B = 0
261	if Type == 'Fosq':
262	A = scale*Fosq/FosqMax
263	B = scale*Fcsq/FosqMax
264	C = abs(A-B)
265	elif Type == 'Fo':
266	A = scale*math.sqrt(max(0,Fosq))/FoMax
267	B = scale*math.sqrt(max(0,Fcsq))/FoMax
268	C = abs(A-B)
269	elif Type == '\|DFsq\|/sig':
270	A = abs(Fosq-Fcsq)/(scale*sig)
271	elif Type == '\|DFsq\|>sig':
272	A = abs(Fosq-Fcsq)/(scale*sig)
273	if A < 1.0: A = 0
274	elif Type == '\|DFsq\|>3sig':
275	A = abs(Fosq-Fcsq)/(scale*sig)
276	if A < 3.0: A = 0
277	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
278	if A > 0.0:
279	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
280	if B:
281	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
282	radius = C
283	if radius > 0:
284	if A > B:
285	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
286	else:
287	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
288	HKL = np.array(HKL,dtype=np.int)
289	HKLF = np.array(HKLF)
290	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
291	Plot.set_ylabel(ylabel[izone],fontsize=12)
292	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
293	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
294	if not newPlot:
295	Page.toolbar.push_current()
296	Plot.set_xlim(xylim[0])
297	Plot.set_ylim(xylim[1])
298	xylim = []
299	Page.toolbar.push_current()
300	Page.toolbar.draw()
301	else:
302	Page.canvas.draw()
303
304	def PlotPatterns(G2frame,newPlot=False):
305	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
306	2-theta or q (future TOF). Can display multiple patterns as "waterfall plots" or contour plots. Log I
307	plotting available.
308	'''
309	global HKL
310
311	def OnKeyBox(event):
312	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('Powder Patterns'):
313	event.key = cb.GetValue()[0]
314	cb.SetValue(' key press')
315	OnPlotKeyPress(event)
316
317	def OnPlotKeyPress(event):
318	newPlot = False
319	if event.key == 'w':
320	if G2frame.Weight:
321	G2frame.Weight = False
322	else:
323	G2frame.Weight = True
324	print 'plot weighting:',G2frame.Weight
325	elif event.key == 'n':
326	if G2frame.Contour:
327	pass
328	else:
329	if G2frame.logPlot:
330	G2frame.logPlot = False
331	else:
332	G2frame.Offset[0] = 0
333	G2frame.logPlot = True
334	elif event.key == 'u':
335	if G2frame.Contour:
336	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
337	elif G2frame.logPlot:
338	pass
339	elif G2frame.Offset[0] < 100.:
340	G2frame.Offset[0] += 1.
341	elif event.key == 'd':
342	if G2frame.Contour:
343	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
344	elif G2frame.logPlot:
345	pass
346	elif G2frame.Offset[0] > 0.:
347	G2frame.Offset[0] -= 1.
348	elif event.key == 'l':
349	G2frame.Offset[1] -= 1.
350	elif event.key == 'r':
351	G2frame.Offset[1] += 1.
352	elif event.key == 'o':
353	G2frame.Offset = [0,0]
354	elif event.key == 'c':
355	newPlot = True
356	if G2frame.Contour:
357	G2frame.Contour = False
358	else:
359	G2frame.Contour = True
360	G2frame.SinglePlot = False
361	G2frame.Offset = [0.,0.]
362	elif event.key == 'q':
363	newPlot = True
364	if G2frame.qPlot:
365	G2frame.qPlot = False
366	else:
367	G2frame.qPlot = True
368	elif event.key == 's':
369	if G2frame.Contour:
370	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
371	choice.sort()
372	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
373	if dlg.ShowModal() == wx.ID_OK:
374	sel = dlg.GetSelection()
375	G2frame.ContourColor = choice[sel]
376	else:
377	G2frame.ContourColor = 'Paired'
378	dlg.Destroy()
379	else:
380	if G2frame.SinglePlot:
381	G2frame.SinglePlot = False
382	else:
383	G2frame.SinglePlot = True
384	elif event.key == '+':
385	if G2frame.PickId:
386	G2frame.PickId = False
387	elif event.key == 'i': #for smoothing contour plot
388	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
389	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
390	'mitchell','sinc','lanczos']
391	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
392	if dlg.ShowModal() == wx.ID_OK:
393	sel = dlg.GetSelection()
394	G2frame.Interpolate = choice[sel]
395	else:
396	G2frame.Interpolate = 'nearest'
397	dlg.Destroy()
398
399	PlotPatterns(G2frame,newPlot=newPlot)
400
401	def OnMotion(event):
402	xpos = event.xdata
403	if xpos: #avoid out of frame mouse position
404	ypos = event.ydata
405	Page.canvas.SetCursor(wx.CROSS_CURSOR)
406	try:
407	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
408	Parms = dict(zip(Names,Values))
409	try:
410	wave = Parms['Lam']
411	except KeyError:
412	wave = Parms['Lam1']
413	if G2frame.qPlot:
414	xpos = 2.0asind(xposwave/(4*math.pi))
415	dsp = 0.0
416	if abs(xpos) > 0.: #avoid possible singularity at beam center
417	dsp = wave/(2.*sind(abs(xpos)/2.0))
418	if G2frame.Contour:
419	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
420	else:
421	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
422	if G2frame.itemPicked:
423	Page.canvas.SetToolTipString('%9.3f'%(xpos))
424	if G2frame.PickId:
425	found = []
426	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists']:
427	if len(HKL):
428	view = Page.toolbar._views.forward()[0][:2]
429	wid = view[1]-view[0]
430	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
431	if len(found):
432	h,k,l = found[0][:3]
433	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
434	else:
435	Page.canvas.SetToolTipString('')
436
437	except TypeError:
438	G2frame.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
439
440	def OnPick(event):
441	if G2frame.itemPicked is not None: return
442	PatternId = G2frame.PatternId
443	try:
444	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
445	except TypeError:
446	return
447	Parms = dict(zip(Names,Values))
448	try:
449	wave = Parms['Lam']
450	except KeyError:
451	wave = Parms['Lam1']
452	PickId = G2frame.PickId
453	pick = event.artist
454	mouse = event.mouseevent
455	xpos = pick.get_xdata()
456	ypos = pick.get_ydata()
457	ind = event.ind
458	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
459	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
460	if ind.all() != [0]: #picked a data point
461	if 'C' in Parms['Type']: #CW data - TOF later in an elif
462	ins = [Parms[x] for x in ['U','V','W','X','Y']]
463	if G2frame.qPlot: #qplot - convert back to 2-theta
464	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
465	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
466	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
467	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
468	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
469	data.append(XY)
470	G2pdG.UpdatePeakGrid(G2frame,data)
471	PlotPatterns(G2frame)
472	else: #picked a peak list line
473	G2frame.itemPicked = pick
474	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
475	if ind.all() != [0]: #picked a data point
476	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
477	data = G2frame.PatternTree.GetItemPyData(LimitId)
478	if 'C' in Parms['Type']: #CW data - TOF later in an elif
479	if G2frame.qPlot: #qplot - convert back to 2-theta
480	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
481	if mouse.button==1:
482	data[1][0] = min(xy[0],data[1][1])
483	if mouse.button==3:
484	data[1][1] = max(xy[0],data[1][0])
485	G2frame.PatternTree.SetItemPyData(LimitId,data)
486	G2pdG.UpdateLimitsGrid(G2frame,data)
487	PlotPatterns(G2frame)
488	else: #picked a limit line
489	G2frame.itemPicked = pick
490	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists':
491	G2frame.itemPicked = pick
492	pick = str(pick)
493
494	def OnRelease(event):
495	if G2frame.itemPicked is None: return
496	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[1::2]
497	Parms = dict(zip(Names,Values))
498	try:
499	wave = Parms['Lam']
500	except KeyError:
501	wave = Parms['Lam1']
502	xpos = event.xdata
503	PickId = G2frame.PickId
504	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
505	lines = []
506	for line in G2frame.Lines: lines.append(line.get_xdata()[0])
507	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
508	if lineNo in [0,1]:
509	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
510	data = G2frame.PatternTree.GetItemPyData(LimitId)
511	if G2frame.qPlot:
512	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
513	else:
514	data[1][lineNo] = xpos
515	G2frame.PatternTree.SetItemPyData(LimitId,data)
516	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
517	G2pdG.UpdateLimitsGrid(G2frame,data)
518	else:
519	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
520	data = G2frame.PatternTree.GetItemPyData(PeakId)
521	# print 'peaks',xpos
522	if event.button == 3:
523	del data[lineNo-2]
524	else:
525	if G2frame.qPlot:
526	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
527	else:
528	data[lineNo-2][0] = xpos
529	G2frame.PatternTree.SetItemPyData(PeakId,data)
530	G2pdG.UpdatePeakGrid(G2frame,data)
531	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' and xpos:
532	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
533	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
534	if 'Line' not in pick: #avoid data points, etc.
535	num = Phases.keys().index(pick)
536	if num:
537	G2frame.refDelt = -(event.ydata-G2frame.refOffset)/(num*Ymax)
538	else: #1st row of refl ticks
539	G2frame.refOffset = event.ydata
540	PlotPatterns(G2frame)
541	G2frame.itemPicked = None
542
543	xylim = []
544	try:
545	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
546	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
547	if not newPlot:
548	Plot = Page.figure.gca() #get previous powder plot & get limits
549	xylim = Plot.get_xlim(),Plot.get_ylim()
550	Page.figure.clf()
551	Plot = Page.figure.gca() #get a fresh plot after clf()
552	except ValueError:
553	newPlot = True
554	G2frame.Cmax = 1.0
555	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
556	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
557	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
558	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
559	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
560	Page.canvas.mpl_connect('pick_event', OnPick)
561	Page.canvas.mpl_connect('button_release_event', OnRelease)
562	Page.SetFocus()
563	G2frame.G2plotNB.status.DestroyChildren()
564	if G2frame.Contour:
565	Choice = (' key press','d: lower contour max','u: raise contour max',
566	'i: interpolation method','s: color scheme','c: contour off')
567	else:
568	if G2frame.logPlot:
569	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
570	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
571	else:
572	Choice = (' key press','l: offset left','r: offset right','d: offset down',
573	'u: offset up','o: reset offset','n: log(I) on','c: contour on',
574	'q: toggle q plot','s: toggle single plot','+: no selection')
575	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
576	choices=Choice)
577	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
578	cb.SetValue(' key press')
579
580	PickId = G2frame.PickId
581	PatternId = G2frame.PatternId
582	colors=['b','g','r','c','m','k']
583	Lines = []
584	if G2frame.SinglePlot:
585	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
586	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
587	PlotList = [Pattern,]
588	ParmList = [G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
589	G2frame.PatternId, 'Instrument Parameters'))[1],]
590	else:
591	PlotList = []
592	ParmList = []
593	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
594	while item:
595	if 'PWDR' in G2frame.PatternTree.GetItemText(item):
596	Pattern = G2frame.PatternTree.GetItemPyData(item)
597	if len(Pattern) < 3: # put name on end if needed
598	Pattern.append(G2frame.PatternTree.GetItemText(item))
599	PlotList.append(Pattern)
600	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
601	item,'Instrument Parameters'))[1])
602	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
603	Ymax = 1.0
604	lenX = 0
605	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
606	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
607	HKL = []
608	if Phases:
609	for peak in Phases[G2frame.RefList]:
610	HKL.append(peak[:6])
611	HKL = np.array(HKL)
612	else:
613	HKL = np.array(G2frame.HKL)
614	for Pattern in PlotList:
615	xye = Pattern[1]
616	Ymax = max(Ymax,max(xye[1]))
617	offset = G2frame.Offset[0]*Ymax/100.0
618	Title = 'Powder Patterns: '+os.path.split(G2frame.GSASprojectfile)[1]
619	if G2frame.logPlot:
620	Title = 'log('+Title+')'
621	Plot.set_title(Title)
622	if G2frame.qPlot:
623	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
624	else:
625	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
626	Plot.set_ylabel('Intensity',fontsize=12)
627	if G2frame.Contour:
628	ContourZ = []
629	ContourY = []
630	Nseq = 0
631	if len(PlotList) < 2:
632	G2frame.Contour = False
633	for N,Pattern in enumerate(PlotList):
634	Parms = ParmList[N]
635	ifpicked = False
636	LimitId = 0
637	xye = np.array(Pattern[1])
638	if PickId:
639	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
640	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
641	if G2frame.qPlot:
642	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
643	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
644	else:
645	X = xye[0]
646	if not lenX:
647	lenX = len(X)
648	Y = xye[1]+offset*N
649	if LimitId:
650	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
651	if G2frame.qPlot:
652	limits = 4np.pinpsind(limits/2.0)/Parms[1]
653	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
654	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
655	if G2frame.Contour:
656
657	if lenX == len(X):
658	ContourY.append(N)
659	ContourZ.append(Y)
660	ContourX = X
661	Nseq += 1
662	Plot.set_ylabel('Data sequence',fontsize=12)
663	else:
664	X += G2frame.Offset[1].005N
665	if ifpicked:
666	Z = xye[3]+offset*N
667	W = xye[4]+offset*N
668	D = xye[5]-Ymax*G2frame.delOffset
669	if G2frame.Weight:
670	W2 = np.sqrt(xye[2])
671	D = W2-YmaxG2frame.delOffset
672	if G2frame.logPlot:
673	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
674	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
675	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
676	else:
677	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
678	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
679	Plot.plot(X,W,colors[(N+2)%6],picker=False)
680	Plot.plot(X,D,colors[(N+3)%6],picker=False)
681	Plot.axhline(0.,color=wx.BLACK)
682	Page.canvas.SetToolTipString('')
683	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
684	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
685	Page.canvas.SetToolTipString(tip)
686	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
687	for item in data:
688	if G2frame.qPlot:
689	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
690	else:
691	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
692	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
693	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
694	Page.canvas.SetToolTipString(tip)
695	data = G2frame.LimitsTable.GetData()
696	else:
697	if G2frame.logPlot:
698	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
699	else:
700	Plot.plot(X,Y,colors[N%6],picker=False)
701	if PickId and not G2frame.Contour:
702	Values,Names = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))[1::2]
703	Parms = dict(zip(Names,Values))
704	try:
705	wave = Parms['Lam']
706	except KeyError:
707	wave = Parms['Lam1']
708	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
709	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
710	for peak in peaks:
711	if G2frame.qPlot:
712	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
713	else:
714	Plot.axvline(peak[0],color='b')
715	for hkl in G2frame.HKL:
716	if G2frame.qPlot:
717	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
718	else:
719	Plot.axvline(hkl[5],color='r',dashes=(5,5))
720	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
721	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
722	for pId,phase in enumerate(Phases):
723	peaks = Phases[phase]
724	peak = np.array([[peak[4],peak[5]] for peak in peaks])
725	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
726	if G2frame.qPlot:
727	Plot.plot(2*np.pi/peak.T[0],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
728	else:
729	Plot.plot(peak.T[1],pos,colors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
730	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
731	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
732
733	if G2frame.Contour:
734	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
735	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
736	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
737	Page.figure.colorbar(Img)
738	else:
739	G2frame.Lines = Lines
740	if not newPlot:
741	Page.toolbar.push_current()
742	Plot.set_xlim(xylim[0])
743	Plot.set_ylim(xylim[1])
744	xylim = []
745	Page.toolbar.push_current()
746	Page.toolbar.draw()
747	else:
748	Page.canvas.draw()
749	G2frame.Pwdr = True
750
751	def PlotISFG(G2frame,newPlot=False,type=''):
752	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
753	or multiple plots with waterfall and contour plots as options
754	'''
755	if not type:
756	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
757	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
758	return
759	superMinusOne = unichr(0xaf)+unichr(0xb9)
760
761	def OnPlotKeyPress(event):
762	newPlot = False
763	if event.key == 'u':
764	if G2frame.Contour:
765	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
766	elif G2frame.Offset[0] < 100.:
767	G2frame.Offset[0] += 1.
768	elif event.key == 'd':
769	if G2frame.Contour:
770	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
771	elif G2frame.Offset[0] > 0.:
772	G2frame.Offset[0] -= 1.
773	elif event.key == 'l':
774	G2frame.Offset[1] -= 1.
775	elif event.key == 'r':
776	G2frame.Offset[1] += 1.
777	elif event.key == 'o':
778	G2frame.Offset = [0,0]
779	elif event.key == 'c':
780	newPlot = True
781	if G2frame.Contour:
782	G2frame.Contour = False
783	else:
784	G2frame.Contour = True
785	G2frame.SinglePlot = False
786	G2frame.Offset = [0.,0.]
787	elif event.key == 's':
788	if G2frame.Contour:
789	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
790	choice.sort()
791	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
792	if dlg.ShowModal() == wx.ID_OK:
793	sel = dlg.GetSelection()
794	G2frame.ContourColor = choice[sel]
795	else:
796	G2frame.ContourColor = 'Paired'
797	dlg.Destroy()
798	else:
799	if G2frame.SinglePlot:
800	G2frame.SinglePlot = False
801	else:
802	G2frame.SinglePlot = True
803	elif event.key == 'i': #for smoothing contour plot
804	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
805	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
806	'mitchell','sinc','lanczos']
807	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
808	if dlg.ShowModal() == wx.ID_OK:
809	sel = dlg.GetSelection()
810	G2frame.Interpolate = choice[sel]
811	else:
812	G2frame.Interpolate = 'nearest'
813	dlg.Destroy()
814	elif event.key == 't' and not G2frame.Contour:
815	if G2frame.Legend:
816	G2frame.Legend = False
817	else:
818	G2frame.Legend = True
819
820
821	PlotISFG(G2frame,newPlot=newPlot,type=type)
822
823	def OnKeyBox(event):
824	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
825	event.key = cb.GetValue()[0]
826	cb.SetValue(' key press')
827	OnPlotKeyPress(event)
828
829	def OnMotion(event):
830	xpos = event.xdata
831	if xpos: #avoid out of frame mouse position
832	ypos = event.ydata
833	Page.canvas.SetCursor(wx.CROSS_CURSOR)
834	try:
835	if G2frame.Contour:
836	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
837	else:
838	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
839	except TypeError:
840	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
841
842	xylim = []
843	try:
844	plotNum = G2frame.G2plotNB.plotList.index(type)
845	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
846	if not newPlot:
847	Plot = Page.figure.gca() #get previous plot & get limits
848	xylim = Plot.get_xlim(),Plot.get_ylim()
849	Page.figure.clf()
850	Plot = Page.figure.gca()
851	except ValueError:
852	newPlot = True
853	G2frame.Cmax = 1.0
854	Plot = G2frame.G2plotNB.addMpl(type).gca()
855	plotNum = G2frame.G2plotNB.plotList.index(type)
856	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
857	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
858	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
859
860	Page.SetFocus()
861	G2frame.G2plotNB.status.DestroyChildren()
862	if G2frame.Contour:
863	Choice = (' key press','d: lower contour max','u: raise contour max',
864	'i: interpolation method','s: color scheme','c: contour off')
865	else:
866	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
867	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
868	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
869	choices=Choice)
870	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
871	cb.SetValue(' key press')
872	PatternId = G2frame.PatternId
873	PickId = G2frame.PickId
874	Plot.set_title(type)
875	if type == 'G(R)':
876	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
877	else:
878	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
879	Plot.set_ylabel(r''+type,fontsize=14)
880	colors=['b','g','r','c','m','k']
881	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
882	Pattern = []
883	if G2frame.SinglePlot:
884	name = G2frame.PatternTree.GetItemText(PatternId)
885	name = type+name[4:]
886	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
887	Pattern = G2frame.PatternTree.GetItemPyData(Id)
888	if Pattern:
889	Pattern.append(name)
890	PlotList = [Pattern,]
891	else:
892	PlotList = []
893	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
894	while item:
895	if 'PDF' in G2frame.PatternTree.GetItemText(item):
896	name = type+G2frame.PatternTree.GetItemText(item)[4:]
897	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
898	Pattern = G2frame.PatternTree.GetItemPyData(Id)
899	if Pattern:
900	Pattern.append(name)
901	PlotList.append(Pattern)
902	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
903	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
904	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
905	Xb = [0.,10.]
906	Yb = [0.,-40.np.pinumbDen]
907	Ymax = 1.0
908	lenX = 0
909	for Pattern in PlotList:
910	xye = Pattern[1]
911	Ymax = max(Ymax,max(xye[1]))
912	offset = G2frame.Offset[0]*Ymax/100.0
913	if G2frame.Contour:
914	ContourZ = []
915	ContourY = []
916	Nseq = 0
917	for N,Pattern in enumerate(PlotList):
918	xye = Pattern[1]
919	if PickId:
920	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
921	X = xye[0]
922	if not lenX:
923	lenX = len(X)
924	Y = xye[1]+offset*N
925	if G2frame.Contour:
926	if lenX == len(X):
927	ContourY.append(N)
928	ContourZ.append(Y)
929	ContourX = X
930	Nseq += 1
931	Plot.set_ylabel('Data sequence',fontsize=12)
932	else:
933	X = xye[0]+G2frame.Offset[1].005N
934	if ifpicked:
935	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
936	Page.canvas.SetToolTipString('')
937	else:
938	if G2frame.Legend:
939	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
940	else:
941	Plot.plot(X,Y,colors[N%6],picker=False)
942	if type == 'G(R)':
943	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
944	elif type == 'F(Q)':
945	Plot.axhline(0.,color=wx.BLACK)
946	elif type == 'S(Q)':
947	Plot.axhline(1.,color=wx.BLACK)
948	if G2frame.Contour:
949	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
950	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
951	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
952	Page.figure.colorbar(Img)
953	elif G2frame.Legend:
954	Plot.legend(loc='best')
955	if not newPlot:
956	Page.toolbar.push_current()
957	Plot.set_xlim(xylim[0])
958	Plot.set_ylim(xylim[1])
959	xylim = []
960	Page.toolbar.push_current()
961	Page.toolbar.draw()
962	else:
963	Page.canvas.draw()
964
965	def PlotXY(G2frame,XY,newPlot=False,type=''):
966	'''simple plot of xy data, used for diagnostic purposes
967	'''
968	def OnMotion(event):
969	xpos = event.xdata
970	if xpos: #avoid out of frame mouse position
971	ypos = event.ydata
972	Page.canvas.SetCursor(wx.CROSS_CURSOR)
973	try:
974	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
975	except TypeError:
976	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
977
978	try:
979	plotNum = G2frame.G2plotNB.plotList.index(type)
980	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
981	if not newPlot:
982	Plot = Page.figure.gca()
983	xylim = Plot.get_xlim(),Plot.get_ylim()
984	Page.figure.clf()
985	Plot = Page.figure.gca()
986	except ValueError:
987	newPlot = True
988	Plot = G2frame.G2plotNB.addMpl(type).gca()
989	plotNum = G2frame.G2plotNB.plotList.index(type)
990	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
991	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
992
993	Page.SetFocus()
994	G2frame.G2plotNB.status.DestroyChildren()
995	Plot.set_title(type)
996	Plot.set_xlabel(r'X',fontsize=14)
997	Plot.set_ylabel(r''+type,fontsize=14)
998	colors=['b','g','r','c','m','k']
999	Ymax = 1.0
1000	lenX = 0
1001	X,Y = XY[:2]
1002	Ymax = max(Ymax,max(Y))
1003	Plot.plot(X,Y,'k',picker=False)
1004	if not newPlot:
1005	Page.toolbar.push_current()
1006	Plot.set_xlim(xylim[0])
1007	Plot.set_ylim(xylim[1])
1008	xylim = []
1009	Page.toolbar.push_current()
1010	Page.toolbar.draw()
1011	else:
1012	Page.canvas.draw()
1013
1014	def PlotPowderLines(G2frame):
1015	''' plotting of powder lines (i.e. no powder pattern) as sticks
1016	'''
1017	global HKL
1018
1019	def OnMotion(event):
1020	xpos = event.xdata
1021	if xpos: #avoid out of frame mouse position
1022	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1023	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1024	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
1025	found = []
1026	if len(HKL):
1027	view = Page.toolbar._views.forward()[0][:2]
1028	wid = view[1]-view[0]
1029	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1030	if len(found):
1031	h,k,l = found[0][:3]
1032	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1033	else:
1034	Page.canvas.SetToolTipString('')
1035
1036	try:
1037	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1038	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1039	Page.figure.clf()
1040	Plot = Page.figure.gca()
1041	except ValueError:
1042	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
1043	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1044	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1045	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1046
1047	Page.SetFocus()
1048	Plot.set_title('Powder Pattern Lines')
1049	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1050	PickId = G2frame.PickId
1051	PatternId = G2frame.PatternId
1052	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
1053	for peak in peaks:
1054	Plot.axvline(peak[0],color='b')
1055	HKL = np.array(G2frame.HKL)
1056	for hkl in G2frame.HKL:
1057	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1058	xmin = peaks[0][0]
1059	xmax = peaks[-1][0]
1060	delt = xmax-xmin
1061	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1062	Plot.set_xlim(xlim)
1063	Page.canvas.draw()
1064	Page.toolbar.push_current()
1065
1066	def PlotPeakWidths(G2frame):
1067	''' Plotting of instrument broadening terms as function of 2-theta (future TOF)
1068	Seen when "Instrument Parameters" chosen from powder pattern data tree
1069	'''
1070	PatternId = G2frame.PatternId
1071	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1072	if limitID:
1073	limits = G2frame.PatternTree.GetItemPyData(limitID)
1074	else:
1075	return
1076	instParms = G2frame.PatternTree.GetItemPyData( \
1077	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1078	if instParms[0][0] in ['PXC','PNC']:
1079	lam = instParms[1][1]
1080	if len(instParms[1]) == 13:
1081	GU,GV,GW,LX,LY = instParms[0][6:11]
1082	else:
1083	GU,GV,GW,LX,LY = instParms[0][4:9]
1084	peakID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
1085	if peakID:
1086	peaks = G2frame.PatternTree.GetItemPyData(peakID)
1087	else:
1088	peaks = []
1089
1090	try:
1091	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1092	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1093	Page.figure.clf()
1094	Plot = Page.figure.gca()
1095	except ValueError:
1096	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
1097	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1098	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1099	Page.SetFocus()
1100
1101	Page.canvas.SetToolTipString('')
1102	colors=['b','g','r','c','m','k']
1103	Xmin,Xmax = limits[1]
1104	Xmin = min(0.5,max(Xmin,1))
1105	Xmin /= 2
1106	Xmax /= 2
1107	nPts = 100
1108	delt = (Xmax-Xmin)/nPts
1109	thetas = []
1110	for i in range(nPts):
1111	thetas.append(Xmin+i*delt)
1112	X = []
1113	Y = []
1114	Z = []
1115	W = []
1116	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1117	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1118	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.)
1119	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1120	for theta in thetas:
1121	X.append(4.0math.pisind(theta)/lam) #q
1122	s = sig(theta,GU,GV,GW)
1123	g = gam(theta,LX,LY)
1124	G = gamFW(g,s)
1125	Y.append(s/tand(theta))
1126	Z.append(g/tand(theta))
1127	W.append(G/tand(theta))
1128	Plot.set_title('Instrument and sample peak widths')
1129	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1130	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1131	Plot.plot(X,Y,color='r',label='Gaussian')
1132	Plot.plot(X,Z,color='g',label='Lorentzian')
1133	Plot.plot(X,W,color='b',label='G+L')
1134	X = []
1135	Y = []
1136	Z = []
1137	W = []
1138	V = []
1139	for peak in peaks:
1140	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1141	try:
1142	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1143	except ValueError:
1144	s = 0.01
1145	g = peak[6]*math.pi/18000.
1146	G = gamFW(g,s)
1147	Y.append(s/tand(peak[0]/2.))
1148	Z.append(g/tand(peak[0]/2.))
1149	W.append(G/tand(peak[0]/2.))
1150	Plot.plot(X,Y,'+',color='r',label='G peak')
1151	Plot.plot(X,Z,'+',color='g',label='L peak')
1152	Plot.plot(X,W,'+',color='b',label='G+L peak')
1153	Plot.legend(loc='best')
1154	Page.canvas.draw()
1155
1156	def PlotSizeStrainPO(G2frame,data,Start=False):
1157	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1158	'''
1159	# Start is not used -- fix later
1160
1161	PatternId = G2frame.PatternId
1162	generalData = data['General']
1163	SGData = generalData['SGData']
1164	SGLaue = SGData['SGLaue']
1165	G2lat.InitTexture()
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	G2frame.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(G2frame.G2plotNB.add3D(plotType))
1187	else:
1188	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
1189	plotNum = G2frame.G2plotNB.plotList.index(plotType)
1190	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1191	Page.SetFocus()
1192	G2frame.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(G2frame,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 = G2frame.PatternId
1318	generalData = data['General']
1319	SGData = generalData['SGData']
1320	textureData = generalData['SH Texture']
1321	G2frame.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 G2frame.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	G2frame.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 G2frame.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	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1367
1368	if G2frame.Projection == '3D display' and 'Axial' not in SHData['PlotType']:
1369	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D('Texture'))
1370	else:
1371	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
1372	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1373	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1374	if G2frame.Projection == '3D display':
1375	pass
1376	else:
1377	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1378
1379	Page.SetFocus()
1380	G2frame.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 G2frame.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=G2frame.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(G2frame.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 G2frame.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=G2frame.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(G2frame.Projection.capitalize()+' projection')
1444	Page.canvas.draw()
1445
1446	def PlotCovariance(G2frame,Data={}):
1447	if not Data:
1448	Data = G2frame.PatternTree.GetItemPyData(
1449	G2gd.GetPatternTreeItemId(G2frame,G2frame.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(G2frame,'Select','Color scheme',choice)
1469	if dlg.ShowModal() == wx.ID_OK:
1470	sel = dlg.GetSelection()
1471	G2frame.VcovColor = choice[sel]
1472	else:
1473	G2frame.VcovColor = 'RdYlGn'
1474	dlg.Destroy()
1475	PlotCovariance(G2frame)
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	G2frame.G2plotNB.status.SetFields(['Key: s to change colors',msg])
1498	try:
1499	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1500	Page = G2frame.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 = G2frame.G2plotNB.addMpl('Covariance').gca()
1507	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
1508	Page = G2frame.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	G2frame.G2plotNB.status.SetFields(['',''])
1514	acolor = mpl.cm.get_cmap(G2frame.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(G2frame,SeqData,SeqSig,SeqNames,sampleParm):
1527
1528	def OnKeyPress(event):
1529	if event.key == 's' and sampleParm:
1530	if G2frame.xAxis:
1531	G2frame.xAxis = False
1532	else:
1533	G2frame.xAxis = True
1534	Draw(False)
1535	try:
1536	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1537	Page = G2frame.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 = G2frame.G2plotNB.addMpl('Sequential refinement').gca()
1544	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
1545	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1546	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
1547	G2frame.xAxis = False
1548
1549	def Draw(newPlot):
1550	Page.SetFocus()
1551	G2frame.G2plotNB.status.SetFields(['','press s to toggle x-axis = sample environment parameter'])
1552	if len(SeqData):
1553	Plot.clear()
1554	if G2frame.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(G2frame,newPlot=False,event=None):
1569	'''General access module for 2D image plotting
1570	'''
1571	plotNo = G2frame.G2plotNB.nb.GetSelection()
1572	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1573	PlotImage(G2frame,newPlot,event,newImage=True)
1574	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1575	PlotIntegration(G2frame,newPlot,event)
1576
1577	def PlotImage(G2frame,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 = G2frame.PatternTree.GetItemPyData(
1587	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
1588	Masks = G2frame.PatternTree.GetItemPyData(
1589	G2gd.GetPatternTreeItemId(G2frame,G2frame.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 = G2frame.itemPicked
1597	pixelSize = Data['pixelSize']
1598	scalex = 1000./pixelSize[0]
1599	scaley = 1000./pixelSize[1]
1600	if item and G2frame.PatternTree.GetItemText(G2frame.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 = G2frame.ImageZ[ypix][xpix]
1620	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1621	Q = 2.*math.pi/dsp
1622	if G2frame.setPoly:
1623	G2frame.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1624	else:
1625	G2frame.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 = G2frame.PatternTree.GetItemText(G2frame.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	G2frame.setPoly = True
1649	Masks['Polygons'].append([])
1650	G2frame.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1651	G2imG.UpdateMasks(G2frame,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(G2frame,'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(G2frame,Data,Masks)
1665	finally:
1666	dlg.Destroy()
1667	elif event.key == 'l':
1668	if G2frame.logPlot:
1669	G2frame.logPlot = False
1670	else:
1671	G2frame.logPlot = True
1672	PlotImage(G2frame,newImage=True)
1673
1674	def OnKeyBox(event):
1675	if G2frame.G2plotNB.nb.GetSelection() == G2frame.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 G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
1683	return
1684	if G2frame.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	G2frame.setPoly = False
1692	G2frame.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1693	else:
1694	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1695	polygon.append([xpos,ypos])
1696	G2imG.UpdateMasks(G2frame,Masks)
1697	else:
1698	if G2frame.itemPicked is not None: return
1699	G2frame.itemPicked = event.artist
1700	G2frame.mousePicked = event.mouseevent
1701
1702	def OnImRelease(event):
1703	try:
1704	PickName = G2frame.PatternTree.GetItemText(G2frame.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 G2frame.itemPicked is None and PickName == 'Image Controls':
1714	# sizexy = Data['size']
1715	Xpos = event.xdata
1716	if not (Xpos and G2frame.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(G2frame.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	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1732	if G2img.ImageCalibrate(G2frame,Data):
1733	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1734	print 'Calibration successful'
1735	else:
1736	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1737	print 'Calibration failed'
1738	G2frame.ifGetRing = False
1739	G2imG.UpdateImageControls(G2frame,Data,Masks)
1740	return
1741	PlotImage(G2frame,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 G2frame.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(G2frame.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	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1780	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1781	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1782	G2frame.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(G2frame,Masks)
1791	elif 'Line2D' in itemPicked and PickName == 'Masks':
1792	Obj = G2frame.itemPicked.findobj()
1793	rings = Masks['Rings']
1794	arcs = Masks['Arcs']
1795	polygons = Masks['Polygons']
1796	for ring in G2frame.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 G2frame.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 G2frame.polyList:
1815	if Obj == poly[0]:
1816	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
1817	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.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(G2frame,Masks)
1823	# else: #keep for future debugging
1824	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
1825	PlotImage(G2frame,newImage=True)
1826	G2frame.itemPicked = None
1827
1828	try:
1829	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
1830	Page = G2frame.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 = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
1840	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
1841	Page = G2frame.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 = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
1850	G2frame.G2plotNB.status.DestroyChildren()
1851	if G2frame.logPlot:
1852	Title = 'log('+Title+')'
1853	Plot.set_title(Title)
1854	try:
1855	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
1856	Choice = (' key press','l: log(I) on',)
1857	if G2frame.logPlot:
1858	Choice[1] = 'l: log(I) off'
1859	cb = wx.ComboBox(G2frame.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 = G2frame.PatternTree.GetItemPyData(G2frame.Image)
1866	if imagefile != G2frame.oldImagefile:
1867	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
1868	if not imagefile:
1869	G2frame.G2plotNB.Delete('2D Powder Image')
1870	return
1871	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
1872	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
1873	# print G2frame.ImageZ.shape,G2frame.ImageZ.size,Data['size'] #might be useful debugging line
1874	G2frame.oldImagefile = imagefile
1875
1876	imScale = 1
1877	if len(G2frame.ImageZ) > 1024:
1878	imScale = len(G2frame.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(G2frame.ImageZ,Zlim[0]),Zlim[1])
1899	MaskA = ma.getmaskarray(MA)
1900	A = G2img.ImageCompress(MA,imScale)
1901	AM = G2img.ImageCompress(MaskA,imScale)
1902	if G2frame.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 G2frame.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	G2frame.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	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1974	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1975	G2frame.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	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1981	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1982	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1983	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1984	G2frame.polyList = []
1985	for ipoly,polygon in enumerate(polygons):
1986	x,y = np.hsplit(np.array(polygon),2)
1987	G2frame.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	Plot.invert_yaxis()
1994	if not newPlot and xylim:
1995	Page.toolbar.push_current()
1996	Plot.set_xlim(xylim[0])
1997	Plot.set_ylim(xylim[1])
1998	xylim = []
1999	Page.toolbar.push_current()
2000	Page.toolbar.draw()
2001	else:
2002	Page.canvas.draw()
2003	finally:
2004	wx.EndBusyCursor()
2005
2006	def PlotIntegration(G2frame,newPlot=False,event=None):
2007	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
2008	'''
2009
2010	def OnMotion(event):
2011	Page.canvas.SetToolTipString('')
2012	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2013	azm = event.ydata
2014	tth = event.xdata
2015	if azm and tth:
2016	G2frame.G2plotNB.status.SetFields(\
2017	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2018
2019	try:
2020	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2021	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2022	if not newPlot:
2023	Plot = Page.figure.gca() #get previous plot & get limits
2024	xylim = Plot.get_xlim(),Plot.get_ylim()
2025	Page.figure.clf()
2026	Plot = Page.figure.gca() #get a fresh plot after clf()
2027
2028	except ValueError:
2029	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
2030	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2031	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2032	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2033	Page.views = False
2034	view = False
2035	if not event:
2036	Page.SetFocus()
2037
2038	Data = G2frame.PatternTree.GetItemPyData(
2039	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2040	image = G2frame.Integrate[0]
2041	xsc = G2frame.Integrate[1]
2042	ysc = G2frame.Integrate[2]
2043	Imin,Imax = Data['range'][1]
2044	acolor = mpl.cm.get_cmap(Data['color'])
2045	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2046	Plot.set_ylabel('azimuth',fontsize=12)
2047	Plot.set_xlabel('2-theta',fontsize=12)
2048	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
2049	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
2050	colorBar = Page.figure.colorbar(Img)
2051	if Data['ellipses']:
2052	for ellipse in Data['ellipses']:
2053	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2054	x,y = np.hsplit(ring,2)
2055	tth,azm = G2img.GetTthAzm(x,y,Data)
2056	# azm = np.where(azm < 0.,azm+360,azm)
2057	Plot.plot(tth,azm,'b,')
2058	if not newPlot:
2059	Page.toolbar.push_current()
2060	Plot.set_xlim(xylim[0])
2061	Plot.set_ylim(xylim[1])
2062	xylim = []
2063	Page.toolbar.push_current()
2064	Page.toolbar.draw()
2065	else:
2066	Page.canvas.draw()
2067
2068	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
2069	'''a test plot routine - not normally used
2070	'''
2071
2072	def OnMotion(event):
2073	Page.canvas.SetToolTipString('')
2074	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2075	azm = event.xdata
2076	tth = event.ydata
2077	if azm and tth:
2078	G2frame.G2plotNB.status.SetFields(\
2079	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2080
2081	try:
2082	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2083	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2084	if not newPlot:
2085	Plot = Page.figure.gca() #get previous plot & get limits
2086	xylim = Plot.get_xlim(),Plot.get_ylim()
2087	Page.figure.clf()
2088	Plot = Page.figure.gca() #get a fresh plot after clf()
2089
2090	except ValueError:
2091	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
2092	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
2093	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2094	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2095	Page.views = False
2096	view = False
2097	Page.SetFocus()
2098
2099	Data = G2frame.PatternTree.GetItemPyData(
2100	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2101	Imin,Imax = Data['range'][1]
2102	step = (Imax-Imin)/5.
2103	V = np.arange(Imin,Imax,step)
2104	acolor = mpl.cm.get_cmap(Data['color'])
2105	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2106	Plot.set_xlabel('azimuth',fontsize=12)
2107	Plot.set_ylabel('2-theta',fontsize=12)
2108	Plot.contour(tax,tay,taz,V,cmap=acolor)
2109	if Data['showLines']:
2110	IOtth = Data['IOtth']
2111	if Data['fullIntegrate']:
2112	LRAzim = [-180,180]
2113	else:
2114	LRAzim = Data['LRazimuth'] #NB: integers
2115	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
2116	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
2117	if not Data['fullIntegrate']:
2118	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
2119	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
2120	if Data['setRings']:
2121	rings = np.concatenate((Data['rings']),axis=0)
2122	for xring,yring,dsp in rings:
2123	x,y = G2img.GetTthAzm(xring,yring,Data)
2124	Plot.plot(y,x,'r+')
2125	if Data['ellipses']:
2126	for ellipse in Data['ellipses']:
2127	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
2128	x,y = np.hsplit(ring,2)
2129	tth,azm = G2img.GetTthAzm(x,y,Data)
2130	Plot.plot(azm,tth,'b,')
2131	if not newPlot:
2132	Page.toolbar.push_current()
2133	Plot.set_xlim(xylim[0])
2134	Plot.set_ylim(xylim[1])
2135	xylim = []
2136	Page.toolbar.push_current()
2137	Page.toolbar.draw()
2138	else:
2139	Page.canvas.draw()
2140
2141	def PlotStructure(G2frame,data):
2142	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
2143	thermal motion ellipsoids and polyhedra
2144	'''
2145	generalData = data['General']
2146	cell = generalData['Cell'][1:7]
2147	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
2148	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2149	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2150	Mydir = generalData['Mydir']
2151	atomData = data['Atoms']
2152	drawingData = data['Drawing']
2153	drawAtoms = drawingData['Atoms']
2154	cx,ct,cs = drawingData['atomPtrs']
2155	Wt = [255,255,255]
2156	Rd = [255,0,0]
2157	Gr = [0,255,0]
2158	Bl = [0,0,255]
2159	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]])
2160	uEdges = np.array([
2161	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
2162	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
2163	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
2164	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
2165	altDown = False
2166	shiftDown = False
2167	ctrlDown = False
2168
2169	def OnKeyBox(event):
2170	import Image
2171	Draw() #make sure plot is fresh!!
2172	mode = cb.GetValue()
2173	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
2174	size = Page.canvas.GetSize()
2175	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
2176	if mode in ['jpeg',]:
2177	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
2178	im = Image.new("RGBA", (size[0],size[1]))
2179	else:
2180	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
2181	im = Image.new("RGB", (size[0],size[1]))
2182	im.fromstring(Pix)
2183	im.save(Fname,mode)
2184	cb.SetValue(' Save as:')
2185	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
2186
2187	def GetTruePosition(xy,Add=False):
2188	View = glGetIntegerv(GL_VIEWPORT)
2189	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
2190	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
2191	Zmax = 1.
2192	if Add:
2193	Indx = GetSelectedAtoms()
2194	for i,atom in enumerate(drawAtoms):
2195	x,y,z = atom[cx:cx+3]
2196	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
2197	XY = [int(X),int(View[3]-Y)]
2198	if np.allclose(xy,XY,atol=10) and Z < Zmax:
2199	Zmax = Z
2200	try:
2201	Indx.remove(i)
2202	ClearSelectedAtoms()
2203	for id in Indx:
2204	SetSelectedAtoms(id,Add)
2205	except:
2206	SetSelectedAtoms(i,Add)
2207
2208	def OnMouseDown(event):
2209	xy = event.GetPosition()
2210	if event.ShiftDown():
2211	if event.LeftIsDown():
2212	GetTruePosition(xy)
2213	elif event.RightIsDown():
2214	GetTruePosition(xy,True)
2215	else:
2216	drawingData['Rotation'][3] = list(xy)
2217	Draw()
2218
2219	def OnMouseMove(event):
2220	if event.ShiftDown():
2221	return
2222	newxy = event.GetPosition()
2223	page = getSelection()
2224	if event.ControlDown() and drawingData['showABC']:
2225	if event.LeftIsDown():
2226	SetTestRot(newxy)
2227	elif event.RightIsDown():
2228	SetTestPos(newxy)
2229	elif event.MiddleIsDown():
2230	SetTestRotZ(newxy)
2231	x,y,z = drawingData['testPos'][0]
2232	G2frame.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2233	Draw()
2234
2235	if event.Dragging() and not event.ControlDown():
2236	if event.LeftIsDown():
2237	SetRotation(newxy)
2238	angX,angY,angZ = drawingData['Rotation'][:3]
2239	G2frame.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
2240	elif event.RightIsDown():
2241	SetTranslation(newxy)
2242	Tx,Ty,Tz = drawingData['viewPoint'][0]
2243	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2244	elif event.MiddleIsDown():
2245	SetRotationZ(newxy)
2246	angX,angY,angZ = drawingData['Rotation'][:3]
2247	G2frame.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
2248	Draw()
2249
2250	def OnMouseWheel(event):
2251	if event.ShiftDown():
2252	return
2253	drawingData['cameraPos'] += event.GetWheelRotation()/24
2254	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2255	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2256	page = getSelection()
2257	if page:
2258	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2259	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2260	names = [child.GetName() for child in panel]
2261	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2262	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2263	Draw()
2264
2265	def getSelection():
2266	try:
2267	return G2frame.dataDisplay.GetSelection()
2268	except AttributeError:
2269	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2270	return 0
2271
2272	def SetViewPointText(VP):
2273	page = getSelection()
2274	if page:
2275	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
2276	panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2277	names = [child.GetName() for child in panel]
2278	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
2279
2280	def ClearSelectedAtoms():
2281	page = getSelection()
2282	if page:
2283	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2284	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2285	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2286	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2287
2288	def SetSelectedAtoms(ind,Add=False):
2289	page = getSelection()
2290	if page:
2291	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2292	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
2293	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2294	Id = drawAtoms[ind][-2]
2295	for i,atom in enumerate(atomData):
2296	if atom[-1] == Id:
2297	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2298
2299	def GetSelectedAtoms():
2300	page = getSelection()
2301	Ind = []
2302	if page:
2303	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
2304	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2305	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
2306	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2307	return Ind
2308
2309	def OnKey(event): #on key UP!!
2310	keyCode = event.GetKeyCode()
2311	if keyCode > 255:
2312	keyCode = 0
2313	key,xyz = chr(keyCode),event.GetPosition()
2314	indx = drawingData['selectedAtoms']
2315	if key in ['c','C']:
2316	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2317	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
2318	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
2319	SetViewPointText(drawingData['viewPoint'][0])
2320	elif key in ['n','N']:
2321	drawAtoms = drawingData['Atoms']
2322	pI = drawingData['viewPoint'][1]
2323	if indx:
2324	pI[0] = indx[pI[1]]
2325	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2326	pI[1] += 1
2327	if pI[1] >= len(indx):
2328	pI[1] = 0
2329	else:
2330	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2331	pI[0] += 1
2332	if pI[0] >= len(drawAtoms):
2333	pI[0] = 0
2334	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2335	SetViewPointText(drawingData['viewPoint'][0])
2336	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2337
2338	elif key in ['p','P']:
2339	drawAtoms = drawingData['Atoms']
2340	pI = drawingData['viewPoint'][1]
2341	if indx:
2342	pI[0] = indx[pI[1]]
2343	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2344	pI[1] -= 1
2345	if pI[1] < 0:
2346	pI[1] = len(indx)-1
2347	else:
2348	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2349	pI[0] -= 1
2350	if pI[0] < 0:
2351	pI[0] = len(drawAtoms)-1
2352	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2353	SetViewPointText(drawingData['viewPoint'][0])
2354	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
2355	Draw()
2356
2357	def SetBackground():
2358	R,G,B,A = Page.camera['backColor']
2359	glClearColor(R,G,B,A)
2360	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2361
2362	def SetLights():
2363	glEnable(GL_DEPTH_TEST)
2364	glShadeModel(GL_SMOOTH)
2365	glEnable(GL_LIGHTING)
2366	glEnable(GL_LIGHT0)
2367	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2368	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2369	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2370
2371	def SetTranslation(newxy):
2372	Tx,Ty,Tz = drawingData['viewPoint'][0]
2373	anglex,angley,anglez,oldxy = drawingData['Rotation']
2374	Rx = G2lat.rotdMat(anglex,0)
2375	Ry = G2lat.rotdMat(angley,1)
2376	Rz = G2lat.rotdMat(anglez,2)
2377	dxy = list(newxy-oldxy)+[0,]
2378	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
2379	Tx -= dxy[0]*0.01
2380	Ty += dxy[1]*0.01
2381	Tz -= dxy[2]*0.01
2382	drawingData['Rotation'][3] = list(newxy)
2383	drawingData['viewPoint'][0] = Tx,Ty,Tz
2384	SetViewPointText([Tx,Ty,Tz])
2385
2386	def SetTestPos(newxy):
2387	Tx,Ty,Tz = drawingData['testPos'][0]
2388	anglex,angley,anglez,oldxy = drawingData['Rotation']
2389	Rx = G2lat.rotdMat(anglex,0)
2390	Ry = G2lat.rotdMat(angley,1)
2391	Rz = G2lat.rotdMat(anglez,2)
2392	dxy = list(newxy-oldxy)+[0,]
2393	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
2394	Tx += dxy[0]*0.001
2395	Ty -= dxy[1]*0.001
2396	Tz += dxy[2]*0.001
2397	drawingData['Rotation'][3] = list(newxy)
2398	drawingData['testPos'][0] = Tx,Ty,Tz
2399
2400	def SetTestRot(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	Ax += dxy[1]*0.01
2408	Ay += dxy[0]*0.01
2409	Rx = G2lat.rotdMat(Ax,0)
2410	Ry = G2lat.rotdMat(Ay,1)
2411	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
2412	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2413	drawingData['testPos'][1] = [Ax,Ay,Az]
2414	drawingData['testPos'][2] = newxy
2415	drawingData['testPos'][0] = Dxyz
2416
2417	def SetTestRotZ(newxy):
2418	Txyz = np.array(drawingData['testPos'][0])
2419	oldxy = drawingData['testPos'][2]
2420	Ax,Ay,Az = drawingData['testPos'][1]
2421	Vxyz = np.array(drawingData['viewPoint'][0])
2422	Dxyz = np.inner(Amat,Txyz-Vxyz)
2423	dxy = list(newxy-oldxy)+[0,]
2424	Az += (dxy[0]+dxy[1])*.01
2425	Rz = G2lat.rotdMat(Az,2)
2426	Dxyz = np.inner(Rz,Dxyz)
2427	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2428	drawingData['testPos'][1] = [Ax,Ay,Az]
2429	drawingData['testPos'][2] = newxy
2430	drawingData['testPos'][0] = Dxyz
2431
2432	def SetRotation(newxy):
2433	anglex,angley,anglez,oldxy = drawingData['Rotation']
2434	dxy = newxy-oldxy
2435	anglex += dxy[1]*.25
2436	angley += dxy[0]*.25
2437	oldxy = newxy
2438	drawingData['Rotation'] = [anglex,angley,anglez,list(oldxy)]
2439
2440	def SetRotationZ(newxy):
2441	anglex,angley,anglez,oldxy = drawingData['Rotation']
2442	dxy = newxy-oldxy
2443	anglez += (dxy[0]+dxy[1])*.25
2444	oldxy = newxy
2445	drawingData['Rotation'] = [anglex,angley,anglez,list(oldxy)]
2446
2447	def RenderBox():
2448	glEnable(GL_COLOR_MATERIAL)
2449	glLineWidth(2)
2450	glEnable(GL_BLEND)
2451	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2452	glEnable(GL_LINE_SMOOTH)
2453	glBegin(GL_LINES)
2454	for line,color in zip(uEdges,uColors):
2455	glColor3ubv(color)
2456	glVertex3fv(line[0])
2457	glVertex3fv(line[1])
2458	glEnd()
2459	glColor4ubv([0,0,0,0])
2460	glDisable(GL_LINE_SMOOTH)
2461	glDisable(GL_BLEND)
2462	glDisable(GL_COLOR_MATERIAL)
2463
2464	def RenderUnitVectors(x,y,z):
2465	xyz = np.array([x,y,z])
2466	glEnable(GL_COLOR_MATERIAL)
2467	glLineWidth(1)
2468	glPushMatrix()
2469	glTranslate(x,y,z)
2470	glScalef(1/cell[0],1/cell[1],1/cell[2])
2471	glBegin(GL_LINES)
2472	for line,color in zip(uEdges,uColors)[:3]:
2473	glColor3ubv(color)
2474	glVertex3fv(line[0])
2475	glVertex3fv(line[1])
2476	glEnd()
2477	glPopMatrix()
2478	glColor4ubv([0,0,0,0])
2479	glDisable(GL_COLOR_MATERIAL)
2480
2481	def RenderSphere(x,y,z,radius,color):
2482	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2483	glPushMatrix()
2484	glTranslate(x,y,z)
2485	glMultMatrixf(B4mat.T)
2486	q = gluNewQuadric()
2487	gluSphere(q,radius,20,10)
2488	glPopMatrix()
2489
2490	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2491	s1,s2,s3 = E
2492	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2493	glPushMatrix()
2494	glTranslate(x,y,z)
2495	glMultMatrixf(B4mat.T)
2496	glMultMatrixf(R4.T)
2497	glEnable(GL_NORMALIZE)
2498	glScale(s1,s2,s3)
2499	q = gluNewQuadric()
2500	gluSphere(q,ellipseProb,20,10)
2501	glDisable(GL_NORMALIZE)
2502	glPopMatrix()
2503
2504	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2505	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2506	glPushMatrix()
2507	glTranslate(x,y,z)
2508	glMultMatrixf(B4mat.T)
2509	for bond in Bonds:
2510	glPushMatrix()
2511	Dx = np.inner(Amat,bond)
2512	Z = np.sqrt(np.sum(Dx**2))
2513	azm = atan2d(-Dx[1],-Dx[0])
2514	phi = acosd(Dx[2]/Z)
2515	glRotate(-azm,0,0,1)
2516	glRotate(phi,1,0,0)
2517	q = gluNewQuadric()
2518	gluCylinder(q,radius,radius,Z,slice,2)
2519	glPopMatrix()
2520	glPopMatrix()
2521
2522	def RenderLines(x,y,z,Bonds,color):
2523	xyz = np.array([x,y,z])
2524	glEnable(GL_COLOR_MATERIAL)
2525	glLineWidth(1)
2526	glColor3fv(color)
2527	glPushMatrix()
2528	glBegin(GL_LINES)
2529	for bond in Bonds:
2530	glVertex3fv(xyz)
2531	glVertex3fv(xyz+bond)
2532	glEnd()
2533	glColor4ubv([0,0,0,0])
2534	glPopMatrix()
2535	glDisable(GL_COLOR_MATERIAL)
2536
2537	def RenderPolyhedra(x,y,z,Faces,color):
2538	glPushMatrix()
2539	glTranslate(x,y,z)
2540	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2541	glShadeModel(GL_SMOOTH)
2542	glMultMatrixf(B4mat.T)
2543	for face,norm in Faces:
2544	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2545	glFrontFace(GL_CW)
2546	glNormal3fv(norm)
2547	glBegin(GL_TRIANGLES)
2548	for vert in face:
2549	glVertex3fv(vert)
2550	glEnd()
2551	glPopMatrix()
2552
2553	def RenderBackbone(Backbone,BackboneColor,radius):
2554	glPushMatrix()
2555	glMultMatrixf(B4mat.T)
2556	glEnable(GL_COLOR_MATERIAL)
2557	glShadeModel(GL_SMOOTH)
2558	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2559	glePolyCylinder(Backbone,BackboneColor,radius)
2560	glPopMatrix()
2561	glDisable(GL_COLOR_MATERIAL)
2562
2563	def RenderLabel(x,y,z,label,r):
2564	glPushMatrix()
2565	glTranslate(x,y,z)
2566	glMultMatrixf(B4mat.T)
2567	glDisable(GL_LIGHTING)
2568	glColor3f(0,1.,0)
2569	glRasterPos3f(r,r,r)
2570	for c in list(label):
2571	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2572	glEnable(GL_LIGHTING)
2573	glPopMatrix()
2574
2575	def Draw():
2576	Ind = GetSelectedAtoms()
2577	VS = np.array(Page.canvas.GetSize())
2578	aspect = float(VS[0])/float(VS[1])
2579	cPos = drawingData['cameraPos']
2580	Zclip = drawingData['Zclip']*cPos/200.
2581	anglex,angley,anglez = drawingData['Rotation'][:3]
2582	Tx,Ty,Tz = drawingData['viewPoint'][0]
2583	cx,ct,cs = drawingData['atomPtrs']
2584	bondR = drawingData['bondRadius']
2585	G,g = G2lat.cell2Gmat(cell)
2586	GS = G
2587	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2588	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2589	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2590	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2591
2592	SetBackground()
2593	glInitNames()
2594	glPushName(0)
2595
2596	glMatrixMode(GL_PROJECTION)
2597	glLoadIdentity()
2598	glViewport(0,0,VS[0],VS[1])
2599	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2600	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2601	SetLights()
2602
2603	glMatrixMode(GL_MODELVIEW)
2604	glLoadIdentity()
2605	glRotate(anglez,0,0,1)
2606	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2607	glRotate(angley,sind(anglez),cosd(anglez),0)
2608	glMultMatrixf(A4mat.T)
2609	glTranslate(-Tx,-Ty,-Tz)
2610	if drawingData['unitCellBox']:
2611	RenderBox()
2612	if drawingData['showABC']:
2613	x,y,z = drawingData['testPos'][0]
2614	# if altDown:
2615	# G2frame.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2616	# else:
2617	# G2frame.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2618	RenderUnitVectors(x,y,z)
2619	Backbone = []
2620	BackboneColor = []
2621	time0 = time.time()
2622	for iat,atom in enumerate(drawingData['Atoms']):
2623	x,y,z = atom[cx:cx+3]
2624	Bonds = atom[-2]
2625	Faces = atom[-1]
2626	try:
2627	atNum = generalData['AtomTypes'].index(atom[ct])
2628	except ValueError:
2629	atNum = -1
2630	CL = atom[cs+2]
2631	color = np.array(CL)/255.
2632	if iat in Ind:
2633	color = np.array(Gr)/255.
2634	radius = 0.5
2635	if atom[cs] != '':
2636	glLoadName(atom[-3])
2637	if 'balls' in atom[cs]:
2638	vdwScale = drawingData['vdwScale']
2639	ballScale = drawingData['ballScale']
2640	if atNum < 0:
2641	radius = 0.2
2642	elif 'H' == atom[ct]:
2643	if drawingData['showHydrogen']:
2644	if 'vdW' in atom[cs] and atNum >= 0:
2645	radius = vdwScale*generalData['vdWRadii'][atNum]
2646	else:
2647	radius = ballScale*drawingData['sizeH']
2648	else:
2649	radius = 0.0
2650	else:
2651	if 'vdW' in atom[cs]:
2652	radius = vdwScale*generalData['vdWRadii'][atNum]
2653	else:
2654	radius = ballScale*generalData['BondRadii'][atNum]
2655	RenderSphere(x,y,z,radius,color)
2656	if 'sticks' in atom[cs]:
2657	RenderBonds(x,y,z,Bonds,bondR,color)
2658	elif 'ellipsoids' in atom[cs]:
2659	RenderBonds(x,y,z,Bonds,bondR,color)
2660	if atom[cs+3] == 'A':
2661	Uij = atom[cs+5:cs+11]
2662	U = np.multiply(G2spc.Uij2U(Uij),GS)
2663	U = np.inner(Amat,np.inner(U,Amat).T)
2664	E,R = nl.eigh(U)
2665	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2666	E = np.sqrt(E)
2667	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2668	pass
2669	else:
2670	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2671	else:
2672	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2673	pass
2674	else:
2675	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2676	RenderSphere(x,y,z,radius,color)
2677	elif 'lines' in atom[cs]:
2678	radius = 0.1
2679	RenderLines(x,y,z,Bonds,color)
2680	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2681	elif atom[cs] == 'sticks':
2682	radius = 0.1
2683	RenderBonds(x,y,z,Bonds,bondR,color)
2684	elif atom[cs] == 'polyhedra':
2685	RenderPolyhedra(x,y,z,Faces,color)
2686	elif atom[cs] == 'backbone':
2687	if atom[ct-1].split()[0] in ['C','N']:
2688	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2689	BackboneColor.append(list(color))
2690
2691	if atom[cs+1] == 'type':
2692	RenderLabel(x,y,z,atom[ct],radius)
2693	elif atom[cs+1] == 'name':
2694	RenderLabel(x,y,z,atom[ct-1],radius)
2695	elif atom[cs+1] == 'number':
2696	RenderLabel(x,y,z,str(iat),radius)
2697	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2698	RenderLabel(x,y,z,atom[ct-4],radius)
2699	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2700	RenderLabel(x,y,z,atom[ct-3],radius)
2701	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2702	RenderLabel(x,y,z,atom[ct-2],radius)
2703	if Backbone:
2704	RenderBackbone(Backbone,BackboneColor,bondR)
2705	# print time.time()-time0
2706	Page.canvas.SwapBuffers()
2707
2708	def OnSize(event):
2709	Draw()
2710
2711	def OnFocus(event):
2712	Draw()
2713
2714	try:
2715	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
2716	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2717	except ValueError:
2718	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
2719	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
2720	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2721	Page.views = False
2722	view = False
2723	altDown = False
2724	Page.SetFocus()
2725	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2726	choices=(' save as:','jpeg','tiff','bmp'))
2727	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2728	cb.SetValue(' save as:')
2729	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2730	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2731	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2732	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2733	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2734	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2735	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2736	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2737	Page.camera['position'] = drawingData['cameraPos']
2738	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2739	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2740	Page.canvas.SetCurrent()
2741	Draw()
2742

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source: branch/MPbranch/GSASIIplot.py @ 4956

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