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source: trunk/GSASIIplot.py @ 1297

Last change on this file since 1297 was 1297, checked in by vondreele, 9 years ago
setup sequential small angle refinements & display includes copy & copy flags over Models stop pattern plots in multiple integrations; now only when done
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File size: 182.5 KB

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1	# -- coding: utf-8 --
2	'''
3	GSASIIplot: plotting routines
4	===============================
5
6	'''
7	########### SVN repository information ###################
8	# $Date: 2014-04-23 21:32:15 +0000 (Wed, 23 Apr 2014) $
9	# $Author: vondreele $
10	# $Revision: 1297 $
11	# $URL: trunk/GSASIIplot.py $
12	# $Id: GSASIIplot.py 1297 2014-04-23 21:32:15Z vondreele $
13	########### SVN repository information ###################
14	import math
15	import time
16	import copy
17	import sys
18	import os.path
19	import numpy as np
20	import numpy.ma as ma
21	import numpy.linalg as nl
22	import wx
23	import wx.aui
24	import wx.glcanvas
25	import matplotlib as mpl
26	import mpl_toolkits.mplot3d.axes3d as mp3d
27	import GSASIIpath
28	GSASIIpath.SetVersionNumber("$Revision: 1297 $")
29	import GSASIIgrid as G2gd
30	import GSASIIimage as G2img
31	import GSASIIpwd as G2pwd
32	import GSASIIIO as G2IO
33	import GSASIIpwdGUI as G2pdG
34	import GSASIIimgGUI as G2imG
35	import GSASIIphsGUI as G2phG
36	import GSASIIlattice as G2lat
37	import GSASIIspc as G2spc
38	import GSASIImath as G2mth
39	import pytexture as ptx
40	from OpenGL.GL import *
41	from OpenGL.GLU import *
42	from OpenGL.GLE import *
43	import gltext
44	from matplotlib.backends.backend_wx import _load_bitmap
45	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
46	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
47
48	# useful degree trig functions
49	sind = lambda x: math.sin(x*math.pi/180.)
50	cosd = lambda x: math.cos(x*math.pi/180.)
51	tand = lambda x: math.tan(x*math.pi/180.)
52	asind = lambda x: 180.*math.asin(x)/math.pi
53	acosd = lambda x: 180.*math.acos(x)/math.pi
54	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
55	atand = lambda x: 180.*math.atan(x)/math.pi
56	# numpy versions
57	npsind = lambda x: np.sin(x*np.pi/180.)
58	npcosd = lambda x: np.cos(x*np.pi/180.)
59	nptand = lambda x: np.tan(x*np.pi/180.)
60	npacosd = lambda x: 180.*np.arccos(x)/np.pi
61	npasind = lambda x: 180.*np.arcsin(x)/np.pi
62	npatand = lambda x: 180.*np.arctan(x)/np.pi
63	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
64
65	class G2PlotMpl(wx.Panel):
66	'needs a doc string'
67	def __init__(self,parent,id=-1,dpi=None,**kwargs):
68	wx.Panel.__init__(self,parent,id=id,**kwargs)
69	mpl.rcParams['legend.fontsize'] = 10
70	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,6))
71	self.canvas = Canvas(self,-1,self.figure)
72	self.toolbar = GSASIItoolbar(self.canvas)
73
74	self.toolbar.Realize()
75
76	sizer=wx.BoxSizer(wx.VERTICAL)
77	sizer.Add(self.canvas,1,wx.EXPAND)
78	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
79	self.SetSizer(sizer)
80
81	class G2PlotOgl(wx.Panel):
82	'needs a doc string'
83	def __init__(self,parent,id=-1,dpi=None,**kwargs):
84	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
85	if 'win' in sys.platform: #Windows already double buffered
86	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
87	else: #fix from Jim Hester for X systems
88	attribs = (wx.glcanvas.WX_GL_DOUBLEBUFFER,)
89	self.canvas = wx.glcanvas.GLCanvas(self,-1,attribList=attribs,**kwargs)
90	self.camera = {}
91	sizer=wx.BoxSizer(wx.VERTICAL)
92	sizer.Add(self.canvas,1,wx.EXPAND)
93	self.SetSizer(sizer)
94
95	class G2Plot3D(wx.Panel):
96	'needs a doc string'
97	def __init__(self,parent,id=-1,dpi=None,**kwargs):
98	wx.Panel.__init__(self,parent,id=id,**kwargs)
99	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
100	self.canvas = Canvas(self,-1,self.figure)
101	self.toolbar = GSASIItoolbar(self.canvas)
102
103	self.toolbar.Realize()
104
105	sizer=wx.BoxSizer(wx.VERTICAL)
106	sizer.Add(self.canvas,1,wx.EXPAND)
107	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
108	self.SetSizer(sizer)
109
110	class G2PlotNoteBook(wx.Panel):
111	'create a tabbed window for plotting'
112	def __init__(self,parent,id=-1):
113	wx.Panel.__init__(self,parent,id=id)
114	#so one can't delete a plot page!!
115	self.nb = wx.aui.AuiNotebook(self, \
116	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
117	sizer = wx.BoxSizer()
118	sizer.Add(self.nb,1,wx.EXPAND)
119	self.SetSizer(sizer)
120	self.status = parent.CreateStatusBar()
121	self.status.SetFieldsCount(2)
122	self.status.SetStatusWidths([150,-1])
123	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
124	self.nb.Bind(wx.EVT_KEY_UP,self.OnNotebookKey)
125
126	self.plotList = []
127
128	def OnNotebookKey(self,event):
129	'''Called when a keystroke event gets picked up by the notebook window
130	rather the child. This is not expected, but somehow it does sometimes
131	on the Mac and perhaps Linux.
132
133	Assume that the page associated with the currently displayed tab
134	has a child, .canvas; give that child the focus and pass it the event.
135	'''
136	try:
137	Page = self.nb.GetPage(self.nb.GetSelection())
138	except ValueError: # occurs with no plot tabs
139	return
140	try:
141	Page.canvas.SetFocus()
142	wx.PostEvent(Page.canvas,event)
143	except AttributeError:
144	pass
145
146	def addMpl(self,name=""):
147	'Add a tabbed page with a matplotlib plot'
148	page = G2PlotMpl(self.nb)
149	self.nb.AddPage(page,name)
150
151	self.plotList.append(name)
152
153	return page.figure
154
155	def add3D(self,name=""):
156	'Add a tabbed page with a 3D plot'
157	page = G2Plot3D(self.nb)
158	self.nb.AddPage(page,name)
159
160	self.plotList.append(name)
161
162	return page.figure
163
164	def addOgl(self,name=""):
165	'Add a tabbed page with an openGL plot'
166	page = G2PlotOgl(self.nb)
167	self.nb.AddPage(page,name)
168
169	self.plotList.append(name)
170
171	return page.figure
172
173	def Delete(self,name):
174	'delete a tabbed page'
175	try:
176	item = self.plotList.index(name)
177	del self.plotList[item]
178	self.nb.DeletePage(item)
179	except ValueError: #no plot of this name - do nothing
180	return
181
182	def clear(self):
183	'clear all pages from plot window'
184	while self.nb.GetPageCount():
185	self.nb.DeletePage(0)
186	self.plotList = []
187	self.status.DestroyChildren()
188
189	def Rename(self,oldName,newName):
190	'rename a tab'
191	try:
192	item = self.plotList.index(oldName)
193	self.plotList[item] = newName
194	self.nb.SetPageText(item,newName)
195	except ValueError: #no plot of this name - do nothing
196	return
197
198	def OnPageChanged(self,event):
199	'respond to someone pressing a tab on the plot window'
200	if self.plotList:
201	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
202	self.status.DestroyChildren() #get rid of special stuff on status bar
203
204	class GSASIItoolbar(Toolbar):
205	'needs a doc string'
206	ON_MPL_HELP = wx.NewId()
207	ON_MPL_KEY = wx.NewId()
208	def __init__(self,plotCanvas):
209	Toolbar.__init__(self,plotCanvas)
210	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6
211	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
212	parent = self.GetParent()
213	key = os.path.join(os.path.split(__file__)[0],'key.ico')
214	self.AddSimpleTool(self.ON_MPL_KEY,_load_bitmap(key),'Key press','Select key press')
215	wx.EVT_TOOL(self,self.ON_MPL_KEY,self.OnKey)
216	help = os.path.join(os.path.split(__file__)[0],'help.ico')
217	self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
218	wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
219	def OnHelp(self,event):
220	'needs a doc string'
221	Page = self.GetParent().GetParent()
222	pageNo = Page.GetSelection()
223	bookmark = Page.GetPageText(pageNo)
224	bookmark = bookmark.strip(')').replace('(','_')
225	G2gd.ShowHelp(bookmark,self.TopLevelParent)
226	def OnKey(self,event):
227	'needs a doc string'
228	parent = self.GetParent()
229	if parent.Choice:
230	dlg = wx.SingleChoiceDialog(parent,'Select','Key press',list(parent.Choice))
231	if dlg.ShowModal() == wx.ID_OK:
232	sel = dlg.GetSelection()
233	event.key = parent.Choice[sel][0]
234	parent.keyPress(event)
235	dlg.Destroy()
236
237	################################################################################
238	##### PlotSngl
239	################################################################################
240
241	def PlotSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=''):
242	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
243	to F, F**2, etc. as requested
244	'''
245	from matplotlib.patches import Circle,CirclePolygon
246	global HKL,HKLF
247
248	def OnSCKeyPress(event):
249	i = zones.index(Data['Zone'])
250	newPlot = False
251	typeChoice = {'1':'\|DFsq\|>sig','3':'\|DFsq\|>3sig','w':'\|DFsq\|/sig','f':'Fo','s':'Fosq'}
252	if event.key == 'h':
253	Data['Zone'] = '100'
254	newPlot = True
255	elif event.key == 'k':
256	Data['Zone'] = '010'
257	newPlot = True
258	elif event.key == 'l':
259	Data['Zone'] = '001'
260	newPlot = True
261	elif event.key == 'u':
262	Data['Scale'] *= 1.1
263	elif event.key == 'd':
264	Data['Scale'] /= 1.1
265	elif event.key == '+':
266	Data['Layer'] = min(Data['Layer']+1,HKLmax[i])
267	elif event.key == '-':
268	Data['Layer'] = max(Data['Layer']-1,HKLmin[i])
269	elif event.key == '0':
270	Data['Layer'] = 0
271	elif event.key in typeChoice and 'HKLF' in Name:
272	Data['Type'] = typeChoice[event.key]
273	newPlot = True
274	PlotSngl(G2frame,newPlot,Data,hklRef,Title)
275
276	def OnSCMotion(event):
277	xpos = event.xdata
278	if xpos:
279	xpos = round(xpos) #avoid out of frame mouse position
280	ypos = round(event.ydata)
281	zpos = Data['Layer']
282	if '100' in Data['Zone']:
283	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
284	elif '010' in Data['Zone']:
285	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
286	elif '001' in Data['Zone']:
287	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
288	Page.canvas.SetToolTipString(HKLtxt)
289	G2frame.G2plotNB.status.SetStatusText('HKL = '+HKLtxt,0)
290	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
291
292	def OnSCPress(event):
293	zpos = Data['Layer']
294	xpos = event.xdata
295	if xpos:
296	pos = int(round(event.xdata)),int(round(event.ydata))
297	if '100' in Data['Zone']:
298	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
299	hkl = np.array([zpos,pos[0],pos[1]])
300	elif '010' in Data['Zone']:
301	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
302	hkl = np.array([pos[0],zpos,pos[1]])
303	elif '001' in Data['Zone']:
304	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
305	hkl = np.array([pos[0],pos[1],zpos])
306	h,k,l = hkl
307	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
308	if len(hklf):
309	Fosq,sig,Fcsq = hklf[0]
310	HKLtxt = '( %.2f %.3f %.2f %.2f)'%(Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
311	G2frame.G2plotNB.status.SetStatusText('Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt,1)
312
313	Name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
314	if not Title:
315	Title = Name
316	try:
317	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
318	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
319	if not newPlot:
320	Plot = Page.figure.gca() #get previous powder plot & get limits
321	xylim = Plot.get_xlim(),Plot.get_ylim()
322	Page.figure.clf()
323	Plot = Page.figure.gca() #get a fresh plot after clf()
324	except ValueError:
325	Plot = G2frame.G2plotNB.addMpl('Structure Factors').gca()
326	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
327	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
328	Page.canvas.mpl_connect('button_press_event', OnSCPress)
329	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
330	Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
331	Page.keyPress = OnSCKeyPress
332	if 'HKLF' in Name:
333	Page.Choice = (' key press','u: increase scale','d: decrease scale',
334	'f: select Fo','s: select Fosq','w: select \|DFsq\|/sig',
335	'1: select \|DFsq\|>sig','3 select \|DFsq\|>3sig',
336	'h: select 100 zone','k: select 010 zone','l: select 001 zone',
337	'+: increase index','-: decrease index','0: zero layer',)
338	else:
339	Page.Choice = (' key press','u: increase scale','d: decrease scale',
340	'h: select 100 zone','k: select 010 zone','l: select 001 zone',
341	'+: increase index','-: decrease index','0: zero layer',)
342	Page.SetFocus()
343
344	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
345	Plot.set_aspect(aspect='equal')
346
347	Type = Data['Type']
348	scale = Data['Scale']
349	HKLmax = Data['HKLmax']
350	HKLmin = Data['HKLmin']
351	FosqMax = Data['FoMax']
352	FoMax = math.sqrt(FosqMax)
353	xlabel = ['k, h=','h, k=','h, l=']
354	ylabel = ['l','l','k']
355	zones = ['100','010','001']
356	pzone = [[1,2],[0,2],[0,1]]
357	izone = zones.index(Data['Zone'])
358	Plot.set_title(Data['Type']+' '+Title)
359	HKL = []
360	HKLF = []
361	time0 = time.time()
362	for refl in hklRef:
363	H = np.array(refl[:3])
364	if 'HKLF' in Name:
365	Fosq,sig,Fcsq = refl[5:8]
366	else:
367	Fosq,sig,Fcsq = refl[8],1.0,refl[9]
368	HKL.append(H)
369	HKLF.append([Fosq,sig,Fcsq])
370	if H[izone] == Data['Layer']:
371	A = 0
372	B = 0
373	if Type == 'Fosq':
374	A = scale*Fosq/FosqMax
375	B = scale*Fcsq/FosqMax
376	C = abs(A-B)
377	elif Type == 'Fo':
378	A = scale*math.sqrt(max(0,Fosq))/FoMax
379	B = scale*math.sqrt(max(0,Fcsq))/FoMax
380	C = abs(A-B)
381	elif Type == '\|DFsq\|/sig':
382	if sig > 0.:
383	A = (Fosq-Fcsq)/(3*sig)
384	B = 0
385	elif Type == '\|DFsq\|>sig':
386	if sig > 0.:
387	A = (Fosq-Fcsq)/(3*sig)
388	if abs(A) < 1.0: A = 0
389	B = 0
390	elif Type == '\|DFsq\|>3sig':
391	if sig > 0.:
392	A = (Fosq-Fcsq)/(3*sig)
393	if abs(A) < 3.0: A = 0
394	B = 0
395	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
396	if Type in ['\|DFsq\|/sig','\|DFsq\|>sig','\|DFsq\|>3sig']:
397	if A > 0.0:
398	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
399	else:
400	Plot.add_artist(Circle(xy,radius=-A,ec='r',fc='w'))
401	else:
402	if A > 0.0 and A > B:
403	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
404	if B:
405	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
406	if A < B:
407	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
408	radius = C
409	if radius > 0:
410	if A > B:
411	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
412	else:
413	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
414	# print 'plot time: %.3f'%(time.time()-time0)
415	HKL = np.array(HKL,dtype=np.int)
416	HKLF = np.array(HKLF)
417	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
418	Plot.set_ylabel(ylabel[izone],fontsize=12)
419	if not newPlot:
420	Page.toolbar.push_current()
421	Plot.set_xlim(xylim[0])
422	Plot.set_ylim(xylim[1])
423	# xylim = []
424	Page.toolbar.push_current()
425	Page.toolbar.draw()
426	else:
427	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
428	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
429	Page.canvas.draw()
430
431	################################################################################
432	##### PlotPatterns
433	################################################################################
434
435	def PlotPatterns(G2frame,newPlot=False,plotType='PWDR'):
436	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
437	2-theta, q or TOF. Can display multiple patterns as "waterfall plots" or contour plots. Log I
438	plotting available.
439	'''
440	global HKL
441	global exclLines
442	plottype = plotType
443	def OnPlotKeyPress(event):
444	newPlot = False
445	if event.key == 'w' and 'PWDR' in plottype:
446	G2frame.ErrorBars = not G2frame.ErrorBars
447	if not G2frame.Weight:
448	G2frame.SinglePlot = True
449	newPlot = True
450	elif event.key == 'e' and 'SASD' in plottype:
451	G2frame.ErrorBars = not G2frame.ErrorBars
452	elif event.key == 'b' and 'PWDR' in plottype:
453	G2frame.SubBack = not G2frame.SubBack
454	if not G2frame.SubBack:
455	G2frame.SinglePlot = True
456	elif event.key == 'n':
457	if G2frame.Contour:
458	pass
459	else:
460	G2frame.logPlot = not G2frame.logPlot
461	if not G2frame.logPlot:
462	G2frame.Offset[0] = 0
463	newPlot = True
464	elif event.key == 'u':
465	if G2frame.Contour:
466	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
467	elif G2frame.Offset[0] < 100.:
468	G2frame.Offset[0] += 1.
469	elif event.key == 'd':
470	if G2frame.Contour:
471	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
472	elif G2frame.Offset[0] > 0.:
473	G2frame.Offset[0] -= 1.
474	elif event.key == 'l':
475	G2frame.Offset[1] -= 1.
476	elif event.key == 'r':
477	G2frame.Offset[1] += 1.
478	elif event.key == 'o':
479	G2frame.Cmax = 1.0
480	G2frame.Offset = [0,0]
481	elif event.key == 'c':
482	newPlot = True
483	G2frame.Contour = not G2frame.Contour
484	if not G2frame.Contour:
485	G2frame.SinglePlot = False
486	G2frame.Offset = [0.,0.]
487	elif event.key == 'q':
488	if 'PWDR' in plottype:
489	newPlot = True
490	G2frame.qPlot = not G2frame.qPlot
491	elif 'SASD' in plottype:
492	newPlot = True
493	G2frame.sqPlot = not G2frame.sqPlot
494	elif event.key == 's':
495	if G2frame.Contour:
496	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
497	choice.sort()
498	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
499	if dlg.ShowModal() == wx.ID_OK:
500	sel = dlg.GetSelection()
501	G2frame.ContourColor = choice[sel]
502	else:
503	G2frame.ContourColor = 'Paired'
504	dlg.Destroy()
505	else:
506	G2frame.SinglePlot = not G2frame.SinglePlot
507	newPlot = True
508	elif event.key == '+':
509	if G2frame.PickId:
510	G2frame.PickId = False
511	elif event.key == 'i' and G2frame.Contour: #for smoothing contour plot
512	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
513	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
514	'mitchell','sinc','lanczos']
515	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
516	if dlg.ShowModal() == wx.ID_OK:
517	sel = dlg.GetSelection()
518	G2frame.Interpolate = choice[sel]
519	else:
520	G2frame.Interpolate = 'nearest'
521	dlg.Destroy()
522
523	wx.CallAfter(PlotPatterns,G2frame,newPlot=newPlot,plotType=plottype)
524
525	def OnMotion(event):
526	xpos = event.xdata
527	if xpos: #avoid out of frame mouse position
528	ypos = event.ydata
529	Page.canvas.SetCursor(wx.CROSS_CURSOR)
530	try:
531	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
532	if 'C' in Parms['Type'][0]:
533	wave = G2mth.getWave(Parms)
534	if G2frame.qPlot and 'PWDR' in plottype:
535	try:
536	xpos = 2.0asind(xposwave/(4*math.pi))
537	except ValueError: #avoid bad value in asin beyond upper limit
538	pass
539	dsp = 0.0
540	if abs(xpos) > 0.:
541	if 'PWDR' in plottype: #avoid possible singularity at beam center
542	dsp = wave/(2.*sind(abs(xpos)/2.0))
543	q = 2.*np.pi/dsp
544	elif 'SASD' in plottype:
545	dsp = 2*np.pi/xpos
546	q = xpos
547	if G2frame.Contour:
548	if 'PWDR' in plottype:
549	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
550	elif 'SASD' in plottype:
551	G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f pattern ID =%5d'%(dsp,q,int(ypos)),1)
552	else:
553	if 'PWDR' in plottype:
554	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
555	elif 'SASD' in plottype:
556	G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f Intensity =%12.5g'%(dsp,q,ypos),1)
557	else: #TOF neutrons
558	dsp = 0.0
559	difC = Parms['difC'][1]
560	dsp = xpos/difC #rough approx.!
561	q = 2.*np.pi/dsp
562	if G2frame.Contour:
563	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
564	else:
565	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
566	if G2frame.itemPicked:
567	Page.canvas.SetToolTipString('%9.5f'%(xpos))
568	if G2frame.PickId:
569	found = []
570	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists'] or \
571	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
572	if len(HKL):
573	view = Page.toolbar._views.forward()[0][:2]
574	wid = view[1]-view[0]
575	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
576	if len(found):
577	h,k,l = found[0][:3]
578	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
579	else:
580	Page.canvas.SetToolTipString('')
581
582	except TypeError:
583	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' powder pattern first',1)
584
585	def OnPress(event): #ugh - this removes a matplotlib error for mouse clicks in log plots
586	olderr = np.seterr(invalid='ignore')
587
588	def OnPick(event):
589	if G2frame.itemPicked is not None: return
590	PatternId = G2frame.PatternId
591	try:
592	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
593	except TypeError:
594	return
595	if 'C' in Parms['Type'][0]:
596	wave = G2mth.getWave(Parms)
597	else:
598	difC = Parms['difC'][1]
599	PickId = G2frame.PickId
600	pick = event.artist
601	mouse = event.mouseevent
602	xpos = pick.get_xdata()
603	ypos = pick.get_ydata()
604	ind = event.ind
605	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
606	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
607	if ind.all() != [0]: #picked a data point
608	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
609	if 'C' in Parms['Type'][0]: #CW data - TOF later in an elif
610	if G2frame.qPlot: #qplot - convert back to 2-theta
611	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
612	XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1])
613	data.append(XY)
614	G2pdG.UpdatePeakGrid(G2frame,data)
615	PlotPatterns(G2frame,plotType=plottype)
616	else: #picked a peak list line
617	G2frame.itemPicked = pick
618	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
619	if ind.all() != [0]: #picked a data point
620	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
621	data = G2frame.PatternTree.GetItemPyData(LimitId)
622	if 'C' in Parms['Type'][0]: #CW data - TOF later in an elif
623	if G2frame.qPlot and 'PWDR' in plottype: #qplot - convert back to 2-theta
624	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
625	if G2frame.ifGetExclude:
626	excl = [0,0]
627	excl[0] = max(data[1][0],min(xy[0],data[1][1]))
628	excl[1] = excl[0]+0.1
629	data.append(excl)
630	G2frame.ifGetExclude = False
631	else:
632	if mouse.button==1:
633	data[1][0] = min(xy[0],data[1][1])
634	if mouse.button==3:
635	data[1][1] = max(xy[0],data[1][0])
636	G2frame.PatternTree.SetItemPyData(LimitId,data)
637	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
638	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
639	else: #picked a limit line
640	G2frame.itemPicked = pick
641	elif G2frame.PatternTree.GetItemText(PickId) == 'Models':
642	if ind.all() != [0]: #picked a data point
643	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
644	data = G2frame.PatternTree.GetItemPyData(LimitId)
645	if mouse.button==1:
646	data[1][0] = min(xy[0],data[1][1])
647	if mouse.button==3:
648	data[1][1] = max(xy[0],data[1][0])
649	G2frame.PatternTree.SetItemPyData(LimitId,data)
650	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
651	else: #picked a limit line
652	G2frame.itemPicked = pick
653	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
654	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
655	G2frame.itemPicked = pick
656	pick = str(pick)
657
658	def OnRelease(event):
659	if G2frame.itemPicked is None: return
660	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
661	if 'C' in Parms['Type'][0]:
662	wave = G2mth.getWave(Parms)
663	else:
664	difC = Parms['difC'][1]
665	xpos = event.xdata
666	PickId = G2frame.PickId
667	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
668	lines = []
669	for line in G2frame.Lines:
670	lines.append(line.get_xdata()[0])
671	try:
672	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
673	except ValueError:
674	lineNo = -1
675	if lineNo in [0,1] or lineNo in exclLines:
676	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
677	data = G2frame.PatternTree.GetItemPyData(LimitId)
678	id = lineNo/2+1
679	id2 = lineNo%2
680	if G2frame.qPlot and 'PWDR' in plottype:
681	if 'C' in Parms['Type'][0]:
682	data[id][id2] = 2.0asind(wavexpos/(4*math.pi))
683	else:
684	data[id][id2] = 2math.piParms['difC'][1]/xpos
685	else:
686	data[id][id2] = xpos
687	if id > 1 and data[id][0] > data[id][1]:
688	data[id].reverse()
689	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
690	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
691	G2frame.PatternTree.SetItemPyData(LimitId,data)
692	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
693	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
694	elif lineNo > 1:
695	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
696	data = G2frame.PatternTree.GetItemPyData(PeakId)
697	if event.button == 3:
698	del data[lineNo-2]
699	else:
700	if G2frame.qPlot:
701	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
702	else:
703	data[lineNo-2][0] = xpos
704	G2frame.PatternTree.SetItemPyData(PeakId,data)
705	G2pdG.UpdatePeakGrid(G2frame,data)
706	elif G2frame.PatternTree.GetItemText(PickId) in ['Models',] and xpos:
707	lines = []
708	for line in G2frame.Lines:
709	lines.append(line.get_xdata()[0])
710	try:
711	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
712	except ValueError:
713	lineNo = -1
714	if lineNo in [0,1]:
715	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
716	data = G2frame.PatternTree.GetItemPyData(LimitId)
717	data[1][lineNo] = xpos
718	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
719	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
720	G2frame.PatternTree.SetItemPyData(LimitId,data)
721	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
722	'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos:
723	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
724	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
725	if 'line' not in pick: #avoid data points, etc.
726	num = Phases.keys().index(pick)
727	if num:
728	G2frame.refDelt = -(event.ydata-G2frame.refOffset)/(num*Ymax)
729	else: #1st row of refl ticks
730	G2frame.refOffset = event.ydata
731	PlotPatterns(G2frame,plotType=plottype)
732	G2frame.itemPicked = None
733
734	try:
735	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
736	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
737	if not newPlot:
738	Plot = Page.figure.gca() #get previous powder plot & get limits
739	xylim = Plot.get_xlim(),Plot.get_ylim()
740	Page.figure.clf()
741	Plot = Page.figure.gca() #get a fresh plot after clf()
742	except ValueError:
743	if plottype == 'SASD':
744	G2frame.logPlot = True
745	G2frame.ErrorBars = True
746	newPlot = True
747	G2frame.Cmax = 1.0
748	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
749	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
750	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
751	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
752	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
753	Page.canvas.mpl_connect('pick_event', OnPick)
754	Page.canvas.mpl_connect('button_release_event', OnRelease)
755	Page.canvas.mpl_connect('button_press_event',OnPress)
756	if plottype == 'PWDR': # avoids a very nasty clash with KILL_FOCUS in SASD TextCtrl?
757	Page.SetFocus()
758	G2frame.G2plotNB.status.DestroyChildren()
759	if G2frame.Contour:
760	Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max',
761	'i: interpolation method','s: color scheme','c: contour off')
762	else:
763	if G2frame.logPlot:
764	if 'PWDR' in plottype:
765	Page.Choice = (' key press','n: log(I) off','l: offset left','r: offset right','o: reset offset',
766	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
767	elif 'SASD' in plottype:
768	Page.Choice = (' key press','c: contour on','n: semilog on',
769	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
770	'q: toggle S(q) plot','s: toggle single plot','+: no selection')
771	else:
772	if 'PWDR' in plottype:
773	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down',
774	'u: offset up','o: reset offset','b: toggle subtract background','n: log(I) on','c: contour on',
775	'q: toggle q plot','s: toggle single plot','w: toggle divide by sig','+: no selection')
776	elif 'SASD' in plottype:
777	Page.Choice = (' key press','c: contour on','n: loglog on','e: toggle error bars',
778	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
779	'q: toggle S(q) plot','s: toggle single plot','+: no selection')
780
781	Page.keyPress = OnPlotKeyPress
782	PickId = G2frame.PickId
783	PatternId = G2frame.PatternId
784	colors=['b','g','r','c','m','k']
785	Lines = []
786	exclLines = []
787	if G2frame.SinglePlot:
788	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
789	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
790	PlotList = [Pattern,]
791	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
792	G2frame.PatternId, 'Instrument Parameters'))
793	Sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters'))
794	ParmList = [Parms,]
795	SampleList = [Sample,]
796	Title = Pattern[-1]
797	else:
798	Title = os.path.split(G2frame.GSASprojectfile)[1]
799	PlotList = []
800	ParmList = []
801	SampleList = []
802	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
803	while item:
804	if plottype in G2frame.PatternTree.GetItemText(item):
805	Pattern = G2frame.PatternTree.GetItemPyData(item)
806	if len(Pattern) < 3: # put name on end if needed
807	Pattern.append(G2frame.PatternTree.GetItemText(item))
808	PlotList.append(Pattern)
809	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
810	item,'Instrument Parameters'))[0])
811	SampleList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
812	item, 'Sample Parameters')))
813	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
814	lenX = 0
815	if PickId:
816	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
817	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
818	HKL = []
819	if Phases:
820	try:
821	for peak in Phases[G2frame.RefList]['RefList']:
822	HKL.append(peak[:6])
823	except TypeError:
824	for peak in Phases[G2frame.RefList]:
825	HKL.append(peak[:6])
826	HKL = np.array(HKL)
827	else:
828	HKL = np.array(G2frame.HKL)
829	Ymax = None
830	for Pattern in PlotList:
831	xye = Pattern[1]
832	if xye[1] is None: continue
833	if Ymax is None: Ymax = max(xye[1])
834	Ymax = max(Ymax,max(xye[1]))
835	if Ymax is None: return # nothing to plot
836	offset = G2frame.Offset[0]*Ymax/100.0
837	if G2frame.logPlot:
838	Title = 'log('+Title+')'
839	Plot.set_title(Title)
840	if G2frame.qPlot or 'SASD' in plottype:
841	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=16)
842	else:
843	if 'C' in ParmList[0]['Type'][0]:
844	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=16)
845	else:
846	Plot.set_xlabel(r'$TOF, \mathsf{\mu}$s',fontsize=16)
847	if G2frame.Weight:
848	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=16)
849	else:
850	if 'C' in ParmList[0]['Type'][0]:
851	if 'PWDR' in plottype:
852	Plot.set_ylabel('$Intensity$',fontsize=16)
853	elif 'SASD' in plottype:
854	if G2frame.sqPlot:
855	Plot.set_ylabel('$S(Q)=I*Q^{4}$',fontsize=16)
856	else:
857	Plot.set_ylabel('$Intensity, cm^{-1}$',fontsize=16)
858	else:
859	Plot.set_ylabel('Normalized intensity',fontsize=16)
860	if G2frame.Contour:
861	ContourZ = []
862	ContourY = []
863	Nseq = 0
864	if len(PlotList) < 2:
865	G2frame.Contour = False
866	for N,Pattern in enumerate(PlotList):
867	Parms = ParmList[N]
868	Sample = SampleList[N]
869	if 'C' in Parms['Type'][0]:
870	wave = G2mth.getWave(Parms)
871	else:
872	difC = Parms['difC'][1]
873	ifpicked = False
874	LimitId = 0
875	if Pattern[1] is None: continue # skip over uncomputed simulations
876	xye = ma.array(ma.getdata(Pattern[1]))
877	Zero = Parms.get('Zero',[0.,0.])[1]
878	if PickId:
879	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
880	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
881	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
882	excls = limits[2:]
883	for excl in excls:
884	xye[0] = ma.masked_inside(xye[0],excl[0],excl[1])
885	if G2frame.qPlot and 'PWDR' in plottype:
886	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
887	if 'C' in Parms['Type'][0]:
888	X = 4np.pinpsind((xye[0]-Zero)/2.0)/wave
889	else:
890	X = 2np.piParms['difC'][1]/(xye[0]-Zero)
891	else:
892	X = xye[0]-Zero
893	if not lenX:
894	lenX = len(X)
895	if 'PWDR' in plottype:
896	Y = xye[1]+offset*N
897	elif 'SASD' in plottype:
898	if G2frame.sqPlot:
899	Y = xye[1]Sample['Scale'][0](1.005)*(offsetN)X*4
900	else:
901	Y = xye[1]Sample['Scale'][0](1.005)*(offsetN)
902	if LimitId and ifpicked:
903	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
904	if G2frame.qPlot and 'PWDR' in plottype:
905	if 'C' in Parms['Type'][0]:
906	limits = 4np.pinpsind(limits/2.0)/wave
907	else:
908	limits = 2np.pidifC/limits
909	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
910	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
911	for i,item in enumerate(limits[2:]):
912	Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))
913	Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.))
914	exclLines += [2i+2,2i+3]
915	if G2frame.Contour:
916
917	if lenX == len(X):
918	ContourY.append(N)
919	ContourZ.append(Y)
920	ContourX = X
921	Nseq += 1
922	Plot.set_ylabel('Data sequence',fontsize=12)
923	else:
924	if 'SASD' in plottype and G2frame.logPlot:
925	X = (1.01)(G2frame.Offset[1]N)
926	else:
927	X += G2frame.Offset[1].005N
928	Xum = ma.getdata(X)
929	if ifpicked:
930	Z = xye[3]+offset*N
931	if 'PWDR' in plottype: #powder background
932	W = xye[4]+offset*N
933	D = xye[5]-Ymax*G2frame.delOffset
934	elif 'SASD' in plottype:
935	if G2frame.sqPlot:
936	D = xye[4]X*4
937	Z = xye[3]X*4
938	else:
939	D = xye[4]
940	Plot.set_yscale("log",nonposy='mask')
941	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
942	if G2frame.logPlot:
943	if 'PWDR' in plottype:
944	Plot.set_yscale("log",nonposy='mask')
945	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
946	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
947	Plot.plot(X,W,colors[(N+2)%6],picker=False)
948	elif 'SASD' in plottype:
949	Plot.set_xscale("log",nonposx='mask')
950	Plot.set_yscale("log",nonposy='mask')
951	if G2frame.ErrorBars:
952	if G2frame.sqPlot:
953	Plot.errorbar(X,Y,yerr=X*4Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
954	ecolor=colors[N%6],picker=3.,clip_on=False)
955	else:
956	Plot.errorbar(X,Y,yerr=Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
957	ecolor=colors[N%6],picker=3.,clip_on=False)
958	else:
959	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
960	Plot.plot(X,D,colors[(N+2)%6],picker=False)
961	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
962	elif G2frame.Weight and 'PWDR' in plottype:
963	DY = xye[1]*np.sqrt(xye[2])
964	DYmax = max(DY)
965	DZ = xye[3]*np.sqrt(xye[2])
966	DS = xye[5]np.sqrt(xye[2])-DYmaxG2frame.delOffset
967	Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False)
968	Plot.plot(X,DZ,colors[(N+1)%6],picker=False)
969	Plot.plot(X,DS,colors[(N+3)%6],picker=False)
970	Plot.axhline(0.,color=wx.BLACK)
971	else:
972	if G2frame.SubBack and 'PWDR' in plottype:
973	Plot.plot(Xum,Y-W,colors[N%6]+'+',picker=3.,clip_on=False)
974	Plot.plot(X,Z-W,colors[(N+1)%6],picker=False)
975	else:
976	Plot.plot(Xum,Y,colors[N%6]+'+',picker=3.,clip_on=False)
977	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
978	if G2frame.logPlot:
979	Plot.set_yscale("log",nonposy='mask')
980	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
981	if 'PWDR' in plottype:
982	Plot.plot(X,W,colors[(N+2)%6],picker=False)
983	Plot.plot(X,D,colors[(N+3)%6],picker=False)
984	Plot.axhline(0.,color=wx.BLACK)
985	Page.canvas.SetToolTipString('')
986	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
987	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
988	Page.canvas.SetToolTipString(tip)
989	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
990	for item in data:
991	if G2frame.qPlot:
992	if 'C' in Parms['Type'][0]:
993	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/wave,color=colors[N%6],picker=2.))
994	else:
995	Lines.append(Plot.axvline(2math.pidifC/item[0],color=colors[N%6],picker=2.))
996	else:
997	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
998	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
999	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
1000	Page.canvas.SetToolTipString(tip)
1001	data = G2frame.LimitsTable.GetData()
1002	else:
1003	if G2frame.logPlot:
1004	if 'PWDR' in plottype:
1005	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1006	elif 'SASD' in plottype:
1007	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1008	else:
1009	if 'PWDR' in plottype:
1010	Plot.plot(X,Y,colors[N%6],picker=False)
1011	elif 'SASD' in plottype:
1012	Plot.loglog(X,Y,colors[N%6],picker=False,nonposy='mask')
1013	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1014	if G2frame.logPlot:
1015	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1016	if PickId and not G2frame.Contour:
1017	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1018	if 'C' in Parms['Type'][0]:
1019	wave = G2mth.getWave(Parms)
1020	else:
1021	difC = Parms['difC'][1]
1022	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
1023	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
1024	for peak in peaks:
1025	if G2frame.qPlot:
1026	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
1027	else:
1028	Plot.axvline(peak[0],color='b')
1029	for hkl in G2frame.HKL:
1030	if G2frame.qPlot:
1031	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
1032	else:
1033	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1034	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
1035	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
1036	refColors=['b','r','c','g','m','k']
1037	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1038	for pId,phase in enumerate(Phases):
1039	try: #patch for old style reflection lists
1040	peaks = Phases[phase]['RefList']
1041	except TypeError:
1042	peaks = Phases[phase]
1043	if not len(peaks):
1044	continue
1045	peak = np.array([[peak[4],peak[5]] for peak in peaks])
1046	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
1047	if G2frame.qPlot:
1048	Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1049	else:
1050	Plot.plot(peak.T[1],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1051	if len(Phases):
1052	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
1053	if handles:
1054	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
1055
1056	if G2frame.Contour:
1057	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1058	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1059	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1060	Page.figure.colorbar(Img)
1061	else:
1062	G2frame.Lines = Lines
1063	if not newPlot:
1064	Page.toolbar.push_current()
1065	Plot.set_xlim(xylim[0])
1066	Plot.set_ylim(xylim[1])
1067	# xylim = []
1068	Page.toolbar.push_current()
1069	Page.toolbar.draw()
1070	else:
1071	Page.canvas.draw()
1072	olderr = np.seterr(invalid='warn') #ugh - this removes a matplotlib error for mouse clicks in log plots
1073	# G2frame.Pwdr = True
1074
1075	################################################################################
1076	##### PlotDeltSig
1077	################################################################################
1078
1079	def PlotDeltSig(G2frame,kind):
1080	'needs a doc string'
1081	try:
1082	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1083	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1084	Page.figure.clf()
1085	Plot = Page.figure.gca() #get a fresh plot after clf()
1086	except ValueError:
1087	newPlot = True
1088	G2frame.Cmax = 1.0
1089	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
1090	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1091	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1092	Page.Choice = None
1093	PatternId = G2frame.PatternId
1094	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
1095	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
1096	wtFactor = Pattern[0]['wtFactor']
1097	if kind == 'PWDR':
1098	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
1099	xye = np.array(Pattern[1])
1100	xmin = np.searchsorted(xye[0],limits[0])
1101	xmax = np.searchsorted(xye[0],limits[1])
1102	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
1103	elif kind == 'HKLF':
1104	refl = Pattern[1]
1105	DS = []
1106	for ref in refl:
1107	if ref[6] > 0.:
1108	DS.append((ref[5]-ref[7])/ref[6])
1109	Page.SetFocus()
1110	G2frame.G2plotNB.status.DestroyChildren()
1111	DS.sort()
1112	EDS = np.zeros_like(DS)
1113	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
1114	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
1115	T = np.sqrt(np.log(1.0/DX**2))
1116	top = 2.515517+0.802853T+0.010328T**2
1117	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
1118	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
1119	low1 = np.searchsorted(EDS,-1.)
1120	hi1 = np.searchsorted(EDS,1.)
1121	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
1122	frac = 100.*(hi1-low1)/len(DS)
1123	G2frame.G2plotNB.status.SetStatusText( \
1124	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
1125	Plot.set_title('Normal probability for '+Pattern[-1])
1126	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
1127	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
1128	Plot.plot(EDS,DS,'r+',label='result')
1129	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
1130	Plot.legend(loc='upper left')
1131	np.seterr(invalid='warn')
1132	Page.canvas.draw()
1133
1134	################################################################################
1135	##### PlotISFG
1136	################################################################################
1137
1138	def PlotISFG(G2frame,newPlot=False,type=''):
1139	''' Plotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
1140	or multiple plots with waterfall and contour plots as options
1141	'''
1142	if not type:
1143	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
1144	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
1145	return
1146	superMinusOne = unichr(0xaf)+unichr(0xb9)
1147
1148	def OnPlotKeyPress(event):
1149	newPlot = False
1150	if event.key == 'u':
1151	if G2frame.Contour:
1152	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
1153	elif G2frame.Offset[0] < 100.:
1154	G2frame.Offset[0] += 1.
1155	elif event.key == 'd':
1156	if G2frame.Contour:
1157	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
1158	elif G2frame.Offset[0] > 0.:
1159	G2frame.Offset[0] -= 1.
1160	elif event.key == 'l':
1161	G2frame.Offset[1] -= 1.
1162	elif event.key == 'r':
1163	G2frame.Offset[1] += 1.
1164	elif event.key == 'o':
1165	G2frame.Offset = [0,0]
1166	elif event.key == 'c':
1167	newPlot = True
1168	G2frame.Contour = not G2frame.Contour
1169	if not G2frame.Contour:
1170	G2frame.SinglePlot = False
1171	G2frame.Offset = [0.,0.]
1172	elif event.key == 's':
1173	if G2frame.Contour:
1174	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1175	choice.sort()
1176	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1177	if dlg.ShowModal() == wx.ID_OK:
1178	sel = dlg.GetSelection()
1179	G2frame.ContourColor = choice[sel]
1180	else:
1181	G2frame.ContourColor = 'Paired'
1182	dlg.Destroy()
1183	else:
1184	G2frame.SinglePlot = not G2frame.SinglePlot
1185	elif event.key == 'i': #for smoothing contour plot
1186	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
1187	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
1188	'mitchell','sinc','lanczos']
1189	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
1190	if dlg.ShowModal() == wx.ID_OK:
1191	sel = dlg.GetSelection()
1192	G2frame.Interpolate = choice[sel]
1193	else:
1194	G2frame.Interpolate = 'nearest'
1195	dlg.Destroy()
1196	elif event.key == 't' and not G2frame.Contour:
1197	G2frame.Legend = not G2frame.Legend
1198	PlotISFG(G2frame,newPlot=newPlot,type=type)
1199
1200	def OnKeyBox(event):
1201	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
1202	event.key = cb.GetValue()[0]
1203	cb.SetValue(' key press')
1204	wx.CallAfter(OnPlotKeyPress,event)
1205	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
1206
1207	def OnMotion(event):
1208	xpos = event.xdata
1209	if xpos: #avoid out of frame mouse position
1210	ypos = event.ydata
1211	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1212	try:
1213	if G2frame.Contour:
1214	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
1215	else:
1216	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
1217	except TypeError:
1218	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1219
1220	xylim = []
1221	try:
1222	plotNum = G2frame.G2plotNB.plotList.index(type)
1223	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1224	if not newPlot:
1225	Plot = Page.figure.gca() #get previous plot & get limits
1226	xylim = Plot.get_xlim(),Plot.get_ylim()
1227	Page.figure.clf()
1228	Plot = Page.figure.gca()
1229	except ValueError:
1230	newPlot = True
1231	G2frame.Cmax = 1.0
1232	Plot = G2frame.G2plotNB.addMpl(type).gca()
1233	plotNum = G2frame.G2plotNB.plotList.index(type)
1234	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1235	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1236	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1237
1238	Page.SetFocus()
1239	G2frame.G2plotNB.status.DestroyChildren()
1240	if G2frame.Contour:
1241	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
1242	'i: interpolation method','s: color scheme','c: contour off')
1243	else:
1244	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
1245	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
1246	Page.keyPress = OnPlotKeyPress
1247	PatternId = G2frame.PatternId
1248	PickId = G2frame.PickId
1249	Plot.set_title(type)
1250	if type == 'G(R)':
1251	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
1252	else:
1253	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
1254	Plot.set_ylabel(r''+type,fontsize=14)
1255	colors=['b','g','r','c','m','k']
1256	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
1257	Pattern = []
1258	if G2frame.SinglePlot:
1259	name = G2frame.PatternTree.GetItemText(PatternId)
1260	name = type+name[4:]
1261	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
1262	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1263	if Pattern:
1264	Pattern.append(name)
1265	PlotList = [Pattern,]
1266	else:
1267	PlotList = []
1268	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1269	while item:
1270	if 'PDF' in G2frame.PatternTree.GetItemText(item):
1271	name = type+G2frame.PatternTree.GetItemText(item)[4:]
1272	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
1273	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1274	if Pattern:
1275	Pattern.append(name)
1276	PlotList.append(Pattern)
1277	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1278	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
1279	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
1280	Xb = [0.,10.]
1281	Yb = [0.,-40.np.pinumbDen]
1282	Ymax = 1.0
1283	lenX = 0
1284	for Pattern in PlotList:
1285	xye = Pattern[1]
1286	Ymax = max(Ymax,max(xye[1]))
1287	offset = G2frame.Offset[0]*Ymax/100.0
1288	if G2frame.Contour:
1289	ContourZ = []
1290	ContourY = []
1291	Nseq = 0
1292	for N,Pattern in enumerate(PlotList):
1293	xye = Pattern[1]
1294	if PickId:
1295	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1296	X = xye[0]
1297	if not lenX:
1298	lenX = len(X)
1299	Y = xye[1]+offset*N
1300	if G2frame.Contour:
1301	if lenX == len(X):
1302	ContourY.append(N)
1303	ContourZ.append(Y)
1304	ContourX = X
1305	Nseq += 1
1306	Plot.set_ylabel('Data sequence',fontsize=12)
1307	else:
1308	X = xye[0]+G2frame.Offset[1].005N
1309	if ifpicked:
1310	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1311	Page.canvas.SetToolTipString('')
1312	else:
1313	if G2frame.Legend:
1314	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1315	else:
1316	Plot.plot(X,Y,colors[N%6],picker=False)
1317	if type == 'G(R)':
1318	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1319	elif type == 'F(Q)':
1320	Plot.axhline(0.,color=wx.BLACK)
1321	elif type == 'S(Q)':
1322	Plot.axhline(1.,color=wx.BLACK)
1323	if G2frame.Contour:
1324	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1325	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1326	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1327	Page.figure.colorbar(Img)
1328	elif G2frame.Legend:
1329	Plot.legend(loc='best')
1330	if not newPlot:
1331	Page.toolbar.push_current()
1332	Plot.set_xlim(xylim[0])
1333	Plot.set_ylim(xylim[1])
1334	xylim = []
1335	Page.toolbar.push_current()
1336	Page.toolbar.draw()
1337	else:
1338	Page.canvas.draw()
1339
1340	################################################################################
1341	##### PlotXY
1342	################################################################################
1343
1344	def PlotXY(G2frame,XY,XY2=None,labelX=None,labelY=None,newPlot=False,type=''):
1345	'''simple plot of xy data, used for diagnostic purposes
1346	'''
1347	def OnMotion(event):
1348	xpos = event.xdata
1349	if xpos: #avoid out of frame mouse position
1350	ypos = event.ydata
1351	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1352	try:
1353	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
1354	except TypeError:
1355	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1356
1357	try:
1358	plotNum = G2frame.G2plotNB.plotList.index(type)
1359	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1360	if not newPlot:
1361	Plot = Page.figure.gca()
1362	xylim = Plot.get_xlim(),Plot.get_ylim()
1363	Page.figure.clf()
1364	Plot = Page.figure.gca()
1365	except ValueError:
1366	newPlot = True
1367	Plot = G2frame.G2plotNB.addMpl(type).gca()
1368	plotNum = G2frame.G2plotNB.plotList.index(type)
1369	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1370	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1371
1372	Page.Choice = None
1373	Page.SetFocus()
1374	G2frame.G2plotNB.status.DestroyChildren()
1375	Plot.set_title(type)
1376	if xLabel:
1377	Plot.set_xlabel(r''+xLabel,fontsize=14)
1378	else:
1379	Plot.set_xlabel(r'X',fontsize=14)
1380	if yLabel:
1381	Plot.set_ylabel(r''+yLabel,fontsize=14)
1382	else:
1383	Plot.set_ylabel(r'Y',fontsize=14)
1384	colors=['b','g','r','c','m','k']
1385	for ixy,xy in enumerate(XY):
1386	X,Y = xy
1387	Plot.plot(X,Y,color(ixy%6)+'+',picker=False)
1388	if len(XY2):
1389	for ixy,xy in enumerate(XY2):
1390	X,Y = xy
1391	Plot.plot(X,Y,color(ixy%6),picker=False)
1392	if not newPlot:
1393	Page.toolbar.push_current()
1394	Plot.set_xlim(xylim[0])
1395	Plot.set_ylim(xylim[1])
1396	xylim = []
1397	Page.toolbar.push_current()
1398	Page.toolbar.draw()
1399	else:
1400	Page.canvas.draw()
1401
1402	################################################################################
1403	##### PlotStrain
1404	################################################################################
1405
1406	def PlotStrain(G2frame,data,newPlot=False):
1407	'''plot of strain data, used for diagnostic purposes
1408	'''
1409	def OnMotion(event):
1410	xpos = event.xdata
1411	if xpos: #avoid out of frame mouse position
1412	ypos = event.ydata
1413	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1414	try:
1415	G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1)
1416	except TypeError:
1417	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
1418
1419	try:
1420	plotNum = G2frame.G2plotNB.plotList.index('Strain')
1421	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1422	if not newPlot:
1423	Plot = Page.figure.gca()
1424	xylim = Plot.get_xlim(),Plot.get_ylim()
1425	Page.figure.clf()
1426	Plot = Page.figure.gca()
1427	except ValueError:
1428	newPlot = True
1429	Plot = G2frame.G2plotNB.addMpl('Strain').gca()
1430	plotNum = G2frame.G2plotNB.plotList.index('Strain')
1431	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1432	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1433
1434	Page.Choice = None
1435	Page.SetFocus()
1436	G2frame.G2plotNB.status.DestroyChildren()
1437	Plot.set_title('Strain')
1438	Plot.set_ylabel(r'd-spacing',fontsize=14)
1439	Plot.set_xlabel(r'Azimuth',fontsize=14)
1440	colors=['b','g','r','c','m','k']
1441	for N,item in enumerate(data['d-zero']):
1442	Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y
1443	Plot.plot(X,Y,colors[N%6]+'+',picker=False)
1444	Y,X = np.array(item['ImtaCalc'])
1445	Plot.plot(X,Y,colors[N%6],picker=False)
1446	if not newPlot:
1447	Page.toolbar.push_current()
1448	Plot.set_xlim(xylim[0])
1449	Plot.set_ylim(xylim[1])
1450	xylim = []
1451	Page.toolbar.push_current()
1452	Page.toolbar.draw()
1453	else:
1454	Page.canvas.draw()
1455
1456	################################################################################
1457	##### PlotSASDSizeDist
1458	################################################################################
1459
1460	def PlotSASDSizeDist(G2frame):
1461
1462	def OnPageChanged(event):
1463	PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection())
1464	if 'Powder' in PlotText:
1465	PlotPatterns(G2frame,plotType='SASD',newPlot=True)
1466	elif 'Size' in PlotText:
1467	PlotSASDSizeDist(G2frame)
1468
1469	def OnMotion(event):
1470	xpos = event.xdata
1471	if xpos: #avoid out of frame mouse position
1472	ypos = event.ydata
1473	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1474	try:
1475	G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1)
1476	except TypeError:
1477	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
1478
1479	try:
1480	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
1481	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1482	Page.figure.clf()
1483	Plot = Page.figure.gca() #get a fresh plot after clf()
1484	except ValueError:
1485	newPlot = True
1486	Plot = G2frame.G2plotNB.addMpl('Size Distribution').gca()
1487	G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged)
1488	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
1489	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1490	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1491	Page.Choice = None
1492	Page.SetFocus()
1493	PatternId = G2frame.PatternId
1494	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Models'))
1495	Bins,Dbins,BinMag = data['Size']['Distribution']
1496	Plot.set_title('Size Distribution')
1497	Plot.set_xlabel(r'$D, \AA$',fontsize=14)
1498	Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14)
1499	if data['Size']['logBins']:
1500	Plot.set_xscale("log",nonposy='mask')
1501	Plot.set_xlim([np.min(2.Bins)/2.,np.max(2.Bins)*2.])
1502	Plot.bar(2.Bins-Dbins,BinMag,2.Dbins,facecolor='white') #plot diameters
1503	if 'Size Calc' in data:
1504	Rbins,Dist = data['Size Calc']
1505	for i in range(len(Rbins)):
1506	if len(Rbins[i]):
1507	Plot.plot(2.*Rbins[i],Dist[i]) #plot diameters
1508	Page.canvas.draw()
1509
1510	################################################################################
1511	##### PlotPowderLines
1512	################################################################################
1513
1514	def PlotPowderLines(G2frame):
1515	''' plotting of powder lines (i.e. no powder pattern) as sticks
1516	'''
1517	global HKL
1518
1519	def OnMotion(event):
1520	xpos = event.xdata
1521	if xpos: #avoid out of frame mouse position
1522	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1523	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1524	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
1525	found = []
1526	if len(HKL):
1527	view = Page.toolbar._views.forward()[0][:2]
1528	wid = view[1]-view[0]
1529	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1530	if len(found):
1531	h,k,l = found[0][:3]
1532	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1533	else:
1534	Page.canvas.SetToolTipString('')
1535
1536	try:
1537	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1538	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1539	Page.figure.clf()
1540	Plot = Page.figure.gca()
1541	except ValueError:
1542	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
1543	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1544	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1545	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1546
1547	Page.Choice = None
1548	Page.SetFocus()
1549	Plot.set_title('Powder Pattern Lines')
1550	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1551	PickId = G2frame.PickId
1552	PatternId = G2frame.PatternId
1553	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
1554	for peak in peaks:
1555	Plot.axvline(peak[0],color='b')
1556	HKL = np.array(G2frame.HKL)
1557	for hkl in G2frame.HKL:
1558	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1559	xmin = peaks[0][0]
1560	xmax = peaks[-1][0]
1561	delt = xmax-xmin
1562	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1563	Plot.set_xlim(xlim)
1564	Page.canvas.draw()
1565	Page.toolbar.push_current()
1566
1567	################################################################################
1568	##### PlotPeakWidths
1569	################################################################################
1570
1571	def PlotPeakWidths(G2frame):
1572	''' Plotting of instrument broadening terms as function of 2-theta
1573	Seen when "Instrument Parameters" chosen from powder pattern data tree
1574	'''
1575	# sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1576	# gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1577	gamFW = lambda s,g: np.exp(np.log(s*5+2.69269s*4g+2.42843s3g*2+4.47163s*2g*3+0.07842sg4+g*5)/5.)
1578	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1579	PatternId = G2frame.PatternId
1580	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1581	if limitID:
1582	limits = G2frame.PatternTree.GetItemPyData(limitID)[:2]
1583	else:
1584	return
1585	Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \
1586	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1587	if 'C' in Parms['Type'][0]:
1588	lam = G2mth.getWave(Parms)
1589	else:
1590	difC = Parms['difC'][0]
1591	peakID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
1592	if peakID:
1593	peaks = G2frame.PatternTree.GetItemPyData(peakID)
1594	else:
1595	peaks = []
1596
1597	try:
1598	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1599	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1600	Page.figure.clf()
1601	Plot = Page.figure.gca()
1602	except ValueError:
1603	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
1604	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1605	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1606	Page.Choice = None
1607	Page.SetFocus()
1608
1609	Page.canvas.SetToolTipString('')
1610	colors=['b','g','r','c','m','k']
1611	X = []
1612	Y = []
1613	Z = []
1614	W = []
1615	if 'C' in Parms['Type'][0]:
1616	Plot.set_title('Instrument and sample peak widths')
1617	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
1618	Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14)
1619	try:
1620	Xmin,Xmax = limits[1]
1621	X = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1622	Q = 4.np.pinpsind(X/2.)/lam
1623	Z = np.ones_like(X)
1624	data = G2mth.setPeakparms(Parms,Parms2,X,Z)
1625	s = 1.17741np.sqrt(data[4])np.pi/18000.
1626	g = data[6]*np.pi/18000.
1627	G = G2pwd.getgamFW(g,s)
1628	Y = s/nptand(X/2.)
1629	Z = g/nptand(X/2.)
1630	W = G/nptand(X/2.)
1631	Plot.plot(Q,Y,color='r',label='Gaussian')
1632	Plot.plot(Q,Z,color='g',label='Lorentzian')
1633	Plot.plot(Q,W,color='b',label='G+L')
1634
1635	fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True)
1636	sf = 1.17741np.sqrt(fit[4])np.pi/18000.
1637	gf = fit[6]*np.pi/18000.
1638	Gf = G2pwd.getgamFW(gf,sf)
1639	Yf = sf/nptand(X/2.)
1640	Zf = gf/nptand(X/2.)
1641	Wf = Gf/nptand(X/2.)
1642	Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit')
1643	Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit')
1644	Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
1645
1646	X = []
1647	Y = []
1648	Z = []
1649	W = []
1650	V = []
1651	for peak in peaks:
1652	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1653	try:
1654	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1655	except ValueError:
1656	s = 0.01
1657	g = peak[6]*math.pi/18000.
1658	G = G2pwd.getgamFW(g,s)
1659	Y.append(s/tand(peak[0]/2.))
1660	Z.append(g/tand(peak[0]/2.))
1661	W.append(G/tand(peak[0]/2.))
1662	if len(peaks):
1663	Plot.plot(X,Y,'+',color='r',label='G peak')
1664	Plot.plot(X,Z,'+',color='g',label='L peak')
1665	Plot.plot(X,W,'+',color='b',label='G+L peak')
1666	Plot.legend(loc='best')
1667	Page.canvas.draw()
1668	except ValueError:
1669	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
1670	'%.3f'%(2*theta)
1671	G2frame.G2plotNB.Delete('Peak Widths')
1672	else:
1673	Plot.set_title('Instrument and sample peak coefficients')
1674	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
1675	Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14)
1676	Xmin,Xmax = limits[1]
1677	T = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1678	Z = np.ones_like(T)
1679	data = G2mth.setPeakparms(Parms,Parms2,T,Z)
1680	ds = T/difC
1681	Q = 2.*np.pi/ds
1682	A = data[4]
1683	B = data[6]
1684	S = 1.17741*np.sqrt(data[8])/T
1685	G = data[10]/T
1686	Plot.plot(Q,A,color='r',label='Alpha')
1687	Plot.plot(Q,B,color='g',label='Beta')
1688	Plot.plot(Q,S,color='b',label='Gaussian')
1689	Plot.plot(Q,G,color='m',label='Lorentzian')
1690
1691	fit = G2mth.setPeakparms(Parms,Parms2,T,Z)
1692	ds = T/difC
1693	Q = 2.*np.pi/ds
1694	Af = fit[4]
1695	Bf = fit[6]
1696	Sf = 1.17741*np.sqrt(fit[8])/T
1697	Gf = fit[10]/T
1698	Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit')
1699	Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit')
1700	Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit')
1701	Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit')
1702
1703	T = []
1704	A = []
1705	B = []
1706	S = []
1707	G = []
1708	W = []
1709	Q = []
1710	V = []
1711	for peak in peaks:
1712	T.append(peak[0])
1713	A.append(peak[4])
1714	B.append(peak[6])
1715	Q.append(2.np.pidifC/peak[0])
1716	S.append(1.17741*np.sqrt(peak[8])/peak[0])
1717	G.append(peak[10]/peak[0])
1718
1719
1720	Plot.plot(Q,A,'+',color='r',label='Alpha peak')
1721	Plot.plot(Q,B,'+',color='g',label='Beta peak')
1722	Plot.plot(Q,S,'+',color='b',label='Gaussian peak')
1723	Plot.plot(Q,G,'+',color='m',label='Lorentzian peak')
1724	Plot.legend(loc='best')
1725	Page.canvas.draw()
1726
1727
1728	################################################################################
1729	##### PlotSizeStrainPO
1730	################################################################################
1731
1732	def PlotSizeStrainPO(G2frame,data,Start=False):
1733	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1734	'''
1735
1736	PatternId = G2frame.PatternId
1737	generalData = data['General']
1738	SGData = generalData['SGData']
1739	SGLaue = SGData['SGLaue']
1740	if Start: #initialize the spherical harmonics qlmn arrays
1741	ptx.pyqlmninit()
1742	Start = False
1743	# MuStrKeys = G2spc.MustrainNames(SGData)
1744	cell = generalData['Cell'][1:]
1745	A,B = G2lat.cell2AB(cell[:6])
1746	Vol = cell[6]
1747	useList = data['Histograms']
1748	phase = generalData['Name']
1749	plotType = generalData['Data plot type']
1750	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
1751	for ptype in plotDict:
1752	G2frame.G2plotNB.Delete(ptype)
1753	if plotType in ['None']:
1754	return
1755
1756	for item in useList:
1757	if useList[item]['Show']:
1758	break
1759	else:
1760	return #nothing to show!!
1761
1762	numPlots = len(useList)
1763
1764	if plotType in ['Mustrain','Size']:
1765	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
1766	else:
1767	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
1768	plotNum = G2frame.G2plotNB.plotList.index(plotType)
1769	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1770	Page.Choice = None
1771	Page.SetFocus()
1772	G2frame.G2plotNB.status.SetStatusText('',1)
1773	if not Page.IsShown():
1774	Page.Show()
1775
1776	for item in useList:
1777	if useList[item]['Show']:
1778	PHI = np.linspace(0.,360.,30,True)
1779	PSI = np.linspace(0.,180.,30,True)
1780	X = np.outer(npsind(PHI),npsind(PSI))
1781	Y = np.outer(npcosd(PHI),npsind(PSI))
1782	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1783	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
1784	coeff = useList[item][plotDict[plotType]]
1785	except KeyError:
1786	break
1787	if plotType in ['Mustrain','Size']:
1788	if coeff[0] == 'isotropic':
1789	X *= coeff[1][0]
1790	Y *= coeff[1][0]
1791	Z *= coeff[1][0]
1792	elif coeff[0] == 'uniaxial':
1793
1794	def uniaxCalc(xyz,iso,aniso,axes):
1795	Z = np.array(axes)
1796	cp = abs(np.dot(xyz,Z))
1797	sp = np.sqrt(1.-cp**2)
1798	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
1799	return R*xyz
1800
1801	iso,aniso = coeff[1][:2]
1802	axes = np.inner(A,np.array(coeff[3]))
1803	axes /= nl.norm(axes)
1804	Shkl = np.array(coeff[1])
1805	XYZ = np.dstack((X,Y,Z))
1806	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
1807	X,Y,Z = np.dsplit(XYZ,3)
1808	X = X[:,:,0]
1809	Y = Y[:,:,0]
1810	Z = Z[:,:,0]
1811
1812	elif coeff[0] == 'ellipsoidal':
1813
1814	def ellipseCalc(xyz,E,R):
1815	XYZ = xyz*E.T
1816	return np.inner(XYZ.T,R)
1817
1818	S6 = coeff[4]
1819	Sij = G2lat.U6toUij(S6)
1820	E,R = nl.eigh(Sij)
1821	XYZ = np.dstack((X,Y,Z))
1822	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
1823	X,Y,Z = np.dsplit(XYZ,3)
1824	X = X[:,:,0]
1825	Y = Y[:,:,0]
1826	Z = Z[:,:,0]
1827
1828	elif coeff[0] == 'generalized':
1829
1830	def genMustrain(xyz,SGData,A,Shkl):
1831	uvw = np.inner(A.T,xyz)
1832	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1833	sum = np.sum(np.multiply(Shkl,Strm))
1834	sum = np.where(sum > 0.01,sum,0.01)
1835	sum = np.sqrt(sum)*math.pi/.18 #centidegrees to radians!
1836	return sum*xyz
1837
1838	Shkl = np.array(coeff[4])
1839	if np.any(Shkl):
1840	XYZ = np.dstack((X,Y,Z))
1841	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1842	X,Y,Z = np.dsplit(XYZ,3)
1843	X = X[:,:,0]
1844	Y = Y[:,:,0]
1845	Z = Z[:,:,0]
1846
1847	if np.any(X) and np.any(Y) and np.any(Z):
1848	errFlags = np.seterr(all='ignore')
1849	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1850	np.seterr(all='ignore')
1851	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
1852	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
1853	Plot.set_xlim3d(XYZlim)
1854	Plot.set_ylim3d(XYZlim)
1855	Plot.set_zlim3d(XYZlim)
1856	Plot.set_aspect('equal')
1857	if plotType == 'Size':
1858	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
1859	Plot.set_xlabel(r'X, $\mu$m')
1860	Plot.set_ylabel(r'Y, $\mu$m')
1861	Plot.set_zlabel(r'Z, $\mu$m')
1862	else:
1863	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
1864	Plot.set_xlabel(r'X, $\mu$strain')
1865	Plot.set_ylabel(r'Y, $\mu$strain')
1866	Plot.set_zlabel(r'Z, $\mu$strain')
1867	else:
1868	h,k,l = generalData['POhkl']
1869	if coeff[0] == 'MD':
1870	print 'March-Dollase preferred orientation plot'
1871
1872	else:
1873	PH = np.array(generalData['POhkl'])
1874	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
1875	SHCoef = {}
1876	for item in coeff[5]:
1877	L,N = eval(item.strip('C'))
1878	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
1879	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1880	X = np.linspace(0,90.0,26)
1881	Y = G2lat.polfcal(ODFln,'0',X,0.0)
1882	Plot.plot(X,Y,color='k',label=str(PH))
1883	Plot.legend(loc='best')
1884	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
1885	Plot.set_xlabel(r'$\psi$',fontsize=16)
1886	Plot.set_ylabel('MRD',fontsize=14)
1887	Page.canvas.draw()
1888
1889	################################################################################
1890	##### PlotTexture
1891	################################################################################
1892
1893	def PlotTexture(G2frame,data,Start=False):
1894	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
1895	plotting.
1896	dict generalData contains all phase info needed which is in data
1897	'''
1898
1899	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1900	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1901	PatternId = G2frame.PatternId
1902	generalData = data['General']
1903	SGData = generalData['SGData']
1904	textureData = generalData['SH Texture']
1905	G2frame.G2plotNB.Delete('Texture')
1906	if not textureData['Order']:
1907	return #no plot!!
1908	SHData = generalData['SH Texture']
1909	SHCoef = SHData['SH Coeff'][1]
1910	cell = generalData['Cell'][1:7]
1911	Amat,Bmat = G2lat.cell2AB(cell)
1912	sq2 = 1.0/math.sqrt(2.0)
1913
1914	def rp2xyz(r,p):
1915	z = npcosd(r)
1916	xy = np.sqrt(1.-z**2)
1917	return xynpsind(p),xynpcosd(p),z
1918
1919	def OnMotion(event):
1920	SHData = data['General']['SH Texture']
1921	if event.xdata and event.ydata: #avoid out of frame errors
1922	xpos = event.xdata
1923	ypos = event.ydata
1924	if 'Inverse' in SHData['PlotType']:
1925	r = xpos2+ypos2
1926	if r <= 1.0:
1927	if 'equal' in G2frame.Projection:
1928	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1929	else:
1930	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1931	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1932	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1933	y,x,z = list(xyz/np.max(np.abs(xyz)))
1934
1935	G2frame.G2plotNB.status.SetFields(['',
1936	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1937
1938	elif 'Axial' in SHData['PlotType']:
1939	pass
1940
1941	else: #ordinary pole figure
1942	z = xpos2+ypos2
1943	if z <= 1.0:
1944	z = np.sqrt(z)
1945	if 'equal' in G2frame.Projection:
1946	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1947	else:
1948	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1949	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1950	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1951
1952	try:
1953	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1954	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1955	Page.figure.clf()
1956	Plot = Page.figure.gca()
1957	if not Page.IsShown():
1958	Page.Show()
1959	except ValueError:
1960	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
1961	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1962	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1963	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1964
1965	Page.Choice = None
1966	Page.SetFocus()
1967	G2frame.G2plotNB.status.SetFields(['',''])
1968	PH = np.array(SHData['PFhkl'])
1969	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1970	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1971	PX = np.array(SHData['PFxyz'])
1972	gam = atan2d(PX[0],PX[1])
1973	xy = math.sqrt(PX[0]2+PX[1]2)
1974	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1975	psi = asind(xy/xyz)
1976	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1977	if 'Axial' in SHData['PlotType']:
1978	X = np.linspace(0,90.0,26)
1979	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1980	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1981	Plot.legend(loc='best')
1982	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1983	Plot.set_xlabel(r'$\psi$',fontsize=16)
1984	Plot.set_ylabel('MRD',fontsize=14)
1985
1986	else:
1987	npts = 201
1988	if 'Inverse' in SHData['PlotType']:
1989	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1990	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1991	if 'equal' in G2frame.Projection:
1992	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1993	else:
1994	R = np.where(R <= 1.,2.*npatand(R),0.0)
1995	Z = np.zeros_like(R)
1996	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
1997	Z = np.reshape(Z,(npts,npts))
1998	CS = Plot.contour(Y,X,Z,aspect='equal')
1999	Plot.clabel(CS,fontsize=9,inline=1)
2000	try:
2001	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2002	except ValueError:
2003	pass
2004	Page.figure.colorbar(Img)
2005	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
2006	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2007
2008	else:
2009	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2010	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2011	if 'equal' in G2frame.Projection:
2012	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2013	else:
2014	R = np.where(R <= 1.,2.*npatand(R),0.0)
2015	Z = np.zeros_like(R)
2016	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
2017	Z = np.reshape(Z,(npts,npts))
2018	try:
2019	CS = Plot.contour(Y,X,Z,aspect='equal')
2020	Plot.clabel(CS,fontsize=9,inline=1)
2021	except ValueError:
2022	pass
2023	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2024	Page.figure.colorbar(Img)
2025	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
2026	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2027	Page.canvas.draw()
2028
2029	################################################################################
2030	##### PlotCovariance
2031	################################################################################
2032
2033	def PlotCovariance(G2frame,Data):
2034	'needs a doc string'
2035	if not Data:
2036	print 'No covariance matrix available'
2037	return
2038	varyList = Data['varyList']
2039	values = Data['variables']
2040	Xmax = len(varyList)
2041	covMatrix = Data['covMatrix']
2042	sig = np.sqrt(np.diag(covMatrix))
2043	xvar = np.outer(sig,np.ones_like(sig))
2044	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
2045	title = ' for\n'+Data['title']
2046	newAtomDict = Data.get('newAtomDict',{})
2047
2048
2049	def OnPlotKeyPress(event):
2050	newPlot = False
2051	if event.key == 's':
2052	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2053	choice.sort()
2054	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2055	if dlg.ShowModal() == wx.ID_OK:
2056	sel = dlg.GetSelection()
2057	G2frame.VcovColor = choice[sel]
2058	else:
2059	G2frame.VcovColor = 'RdYlGn'
2060	dlg.Destroy()
2061	PlotCovariance(G2frame,Data)
2062
2063	def OnMotion(event):
2064	#there is a problem here - reports wrong values
2065	if event.button:
2066	ytics = imgAx.get_yticks()
2067	ytics = np.where(ytics<len(varyList),ytics,-1)
2068	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
2069	imgAx.set_yticklabels(ylabs)
2070	if event.xdata and event.ydata: #avoid out of frame errors
2071	xpos = int(event.xdata+.5)
2072	ypos = int(event.ydata+.5)
2073	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
2074	if xpos == ypos:
2075	value = values[xpos]
2076	name = varyList[xpos]
2077	if varyList[xpos] in newAtomDict:
2078	name,value = newAtomDict[name]
2079	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
2080	else:
2081	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
2082	Page.canvas.SetToolTipString(msg)
2083	G2frame.G2plotNB.status.SetFields(['',msg])
2084
2085	try:
2086	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2087	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2088	Page.figure.clf()
2089	Plot = Page.figure.gca()
2090	if not Page.IsShown():
2091	Page.Show()
2092	except ValueError:
2093	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
2094	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2095	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2096	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2097	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2098	Page.Choice = ['s: to change colors']
2099	Page.keyPress = OnPlotKeyPress
2100	Page.SetFocus()
2101	G2frame.G2plotNB.status.SetFields(['',''])
2102	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
2103	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower',
2104	vmin=-1.,vmax=1.)
2105	imgAx = Img.get_axes()
2106	ytics = imgAx.get_yticks()
2107	ylabs = [varyList[int(i)] for i in ytics[:-1]]
2108	imgAx.set_yticklabels(ylabs)
2109	colorBar = Page.figure.colorbar(Img)
2110	Plot.set_title('V-Cov matrix'+title)
2111	Plot.set_xlabel('Variable number')
2112	Plot.set_ylabel('Variable name')
2113	Page.canvas.draw()
2114
2115	################################################################################
2116	##### PlotTorsion
2117	################################################################################
2118
2119	def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]):
2120	'needs a doc string'
2121
2122	global names
2123	names = Names
2124	sum = np.sum(Torsion)
2125	torsion = np.log(2*Torsion+1.)/sum
2126	tMin = np.min(torsion)
2127	tMax = np.max(torsion)
2128	torsion = 3.*(torsion-tMin)/(tMax-tMin)
2129	X = np.linspace(0.,360.,num=45)
2130
2131	def OnPick(event):
2132	ind = event.ind[0]
2133	msg = 'atoms:'+names[ind]
2134	Page.canvas.SetToolTipString(msg)
2135	try:
2136	page = G2frame.dataDisplay.GetSelection()
2137	except:
2138	return
2139	if G2frame.dataDisplay.GetPageText(page) == 'Torsion restraints':
2140	torGrid = G2frame.dataDisplay.GetPage(page).Torsions
2141	torGrid.ClearSelection()
2142	for row in range(torGrid.GetNumberRows()):
2143	if names[ind] in torGrid.GetCellValue(row,0):
2144	torGrid.SelectRow(row)
2145	torGrid.ForceRefresh()
2146
2147	def OnMotion(event):
2148	if event.xdata and event.ydata: #avoid out of frame errors
2149	xpos = event.xdata
2150	ypos = event.ydata
2151	msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos)
2152	Page.canvas.SetToolTipString(msg)
2153
2154	try:
2155	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
2156	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2157	Page.figure.clf()
2158	Plot = Page.figure.gca()
2159	if not Page.IsShown():
2160	Page.Show()
2161	except ValueError:
2162	Plot = G2frame.G2plotNB.addMpl('Torsion').gca()
2163	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
2164	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2165	Page.canvas.mpl_connect('pick_event', OnPick)
2166	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2167
2168	Page.SetFocus()
2169	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify torsion atoms'])
2170	Plot.plot(X,torsion,'b+')
2171	if len(Coeff):
2172	X2 = np.linspace(0.,360.,45)
2173	Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2])
2174	Plot.plot(X2,Y2,'r')
2175	if len(Angles):
2176	Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles])
2177	Plot.plot(Angles,Eval,'ro',picker=5)
2178	Plot.set_xlim((0.,360.))
2179	Plot.set_title('Torsion angles for '+TorName+' in '+phaseName)
2180	Plot.set_xlabel('angle',fontsize=16)
2181	Plot.set_ylabel('Energy',fontsize=16)
2182	Page.canvas.draw()
2183
2184	################################################################################
2185	##### PlotRama
2186	################################################################################
2187
2188	def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]):
2189	'needs a doc string'
2190
2191	global names
2192	names = Names
2193	rama = np.log(2*Rama+1.)
2194	ramaMax = np.max(rama)
2195	rama = np.reshape(rama,(45,45))
2196	global Phi,Psi
2197	Phi = []
2198	Psi = []
2199
2200	def OnPlotKeyPress(event):
2201	newPlot = False
2202	if event.key == 's':
2203	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2204	choice.sort()
2205	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2206	if dlg.ShowModal() == wx.ID_OK:
2207	sel = dlg.GetSelection()
2208	G2frame.RamaColor = choice[sel]
2209	else:
2210	G2frame.RamaColor = 'RdYlGn'
2211	dlg.Destroy()
2212	PlotRama(G2frame,phaseName,Rama)
2213
2214	def OnPick(event):
2215	ind = event.ind[0]
2216	msg = 'atoms:'+names[ind]
2217	Page.canvas.SetToolTipString(msg)
2218	try:
2219	page = G2frame.dataDisplay.GetSelection()
2220	except:
2221	return
2222	if G2frame.dataDisplay.GetPageText(page) == 'Ramachandran restraints':
2223	ramaGrid = G2frame.dataDisplay.GetPage(page).Ramas
2224	ramaGrid.ClearSelection()
2225	for row in range(ramaGrid.GetNumberRows()):
2226	if names[ind] in ramaGrid.GetCellValue(row,0):
2227	ramaGrid.SelectRow(row)
2228	ramaGrid.ForceRefresh()
2229
2230	def OnMotion(event):
2231	if event.xdata and event.ydata: #avoid out of frame errors
2232	xpos = event.xdata
2233	ypos = event.ydata
2234	msg = 'phi/psi: %5.3f %5.3f'%(xpos,ypos)
2235	Page.canvas.SetToolTipString(msg)
2236
2237	try:
2238	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
2239	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2240	Page.figure.clf()
2241	Plot = Page.figure.gca()
2242	if not Page.IsShown():
2243	Page.Show()
2244	except ValueError:
2245	Plot = G2frame.G2plotNB.addMpl('Ramachandran').gca()
2246	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
2247	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2248	Page.canvas.mpl_connect('pick_event', OnPick)
2249	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2250	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2251
2252	Page.Choice = ['s: to change colors']
2253	Page.keyPress = OnPlotKeyPress
2254	Page.SetFocus()
2255	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify phi/psi atoms'])
2256	acolor = mpl.cm.get_cmap(G2frame.RamaColor)
2257	if RamaName == 'All' or '-1' in RamaName:
2258	if len(Coeff):
2259	X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45))
2260	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
2261	Plot.contour(X,Y,np.reshape(Z,(45,45)))
2262	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
2263	extent=[-180,180,-180,180],origin='lower')
2264	if len(PhiPsi):
2265	Phi,Psi = PhiPsi.T
2266	Phi = np.where(Phi>180.,Phi-360.,Phi)
2267	Psi = np.where(Psi>180.,Psi-360.,Psi)
2268	Plot.plot(Phi,Psi,'ro',picker=5)
2269	Plot.set_xlim((-180.,180.))
2270	Plot.set_ylim((-180.,180.))
2271	else:
2272	if len(Coeff):
2273	X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45))
2274	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
2275	Plot.contour(X,Y,np.reshape(Z,(45,45)))
2276	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
2277	extent=[0,360,0,360],origin='lower')
2278	if len(PhiPsi):
2279	Phi,Psi = PhiPsi.T
2280	Plot.plot(Phi,Psi,'ro',picker=5)
2281	Plot.set_xlim((0.,360.))
2282	Plot.set_ylim((0.,360.))
2283	Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName)
2284	Plot.set_xlabel(r'$\phi$',fontsize=16)
2285	Plot.set_ylabel(r'$\psi$',fontsize=16)
2286	colorBar = Page.figure.colorbar(Img)
2287	Page.canvas.draw()
2288
2289
2290	################################################################################
2291	##### PlotSeq
2292	################################################################################
2293	def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX):
2294	'''Plot a result from a sequential refinement
2295
2296	:param wx.Frame G2frame: The main GSAS-II tree "window"
2297	:param list ColumnList: list of int values corresponding to columns
2298	selected as y values
2299	:param function TableGet: a function that takes a column number
2300	as argument and returns the column label, the values and there ESDs (or None)
2301	:param function SelectX: a function that returns a selected column
2302	number (or None) as the X-axis selection
2303	'''
2304	G2frame.seqYaxisList = ColumnList
2305	G2frame.seqTableGet = TableGet
2306	G2frame.seqXselect = SelectX
2307	try:
2308	G2frame.seqXaxis
2309	except:
2310	G2frame.seqXaxis = None
2311
2312	def OnMotion(event):
2313	if event.xdata and event.ydata: #avoid out of frame errors
2314	xpos = event.xdata
2315	ypos = event.ydata
2316	msg = '%5.3f %.6g'%(xpos,ypos)
2317	Page.canvas.SetToolTipString(msg)
2318
2319	def OnKeyPress(event):
2320	if event.key == 's':
2321	G2frame.seqXaxis = G2frame.seqXselect()
2322	Draw()
2323	try:
2324	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
2325	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2326	Page.figure.clf()
2327	Plot = Page.figure.gca()
2328	if not Page.IsShown():
2329	Page.Show()
2330	except ValueError:
2331	Plot = G2frame.G2plotNB.addMpl('Sequential refinement').gca()
2332	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
2333	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2334	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
2335	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2336	Page.Choice = ['s to select plot x-axis']
2337	Page.keyPress = OnKeyPress
2338
2339	def Draw():
2340	Page.SetFocus()
2341	G2frame.G2plotNB.status.SetFields(['press s to select X axis'])
2342	Plot.clear()
2343	if G2frame.seqXaxis is not None:
2344	xName,X,Xsig = G2frame.seqTableGet(G2frame.seqXaxis)
2345	else:
2346	X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1)
2347	xName = 'Data sequence number'
2348	for col in G2frame.seqYaxisList:
2349	name,Y,sig = G2frame.seqTableGet(col)
2350	if sig:
2351	Plot.errorbar(X,Y,yerr=sig,label=name)
2352	else:
2353	Plot.plot(X,Y)
2354	Plot.plot(X,Y,'o',label=name)
2355	Plot.legend(loc='best')
2356	Plot.set_ylabel('Parameter values')
2357	Plot.set_xlabel(xName)
2358	Page.canvas.draw()
2359	Draw()
2360
2361	################################################################################
2362	##### PlotExposedImage & PlotImage
2363	################################################################################
2364
2365	def PlotExposedImage(G2frame,newPlot=False,event=None):
2366	'''General access module for 2D image plotting
2367	'''
2368	plotNo = G2frame.G2plotNB.nb.GetSelection()
2369	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
2370	PlotImage(G2frame,newPlot,event,newImage=True)
2371	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
2372	PlotIntegration(G2frame,newPlot,event)
2373
2374	def OnStartMask(G2frame):
2375	'''Initiate the start of a Frame or Polygon map
2376
2377	:param wx.Frame G2frame: The main GSAS-II tree "window"
2378	:param str eventkey: a single letter ('f' or 'p') that
2379	determines what type of mask is created.
2380	'''
2381	Masks = G2frame.PatternTree.GetItemPyData(
2382	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
2383	if G2frame.MaskKey == 'f':
2384	Masks['Frames'] = []
2385	elif G2frame.MaskKey == 'p':
2386	Masks['Polygons'].append([])
2387	elif G2frame.MaskKey == 's':
2388	Masks['Points'].append([])
2389	elif G2frame.MaskKey == 'a':
2390	Masks['Arcs'].append([])
2391	elif G2frame.MaskKey == 'r':
2392	Masks['Rings'].append([])
2393	G2imG.UpdateMasks(G2frame,Masks)
2394	PlotImage(G2frame,newImage=True)
2395
2396	def OnStartNewDzero(G2frame):
2397	'''Initiate the start of adding a new d-zero to a strain data set
2398
2399	:param wx.Frame G2frame: The main GSAS-II tree "window"
2400	:param str eventkey: a single letter ('a') that
2401	triggers the addition of a d-zero.
2402	'''
2403	G2frame.dataFrame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value')
2404	StrSta = G2frame.PatternTree.GetItemPyData(
2405	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
2406
2407	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
2408	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
2409	masks, etc.
2410	'''
2411	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
2412	import numpy.ma as ma
2413	Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.))
2414	global Data,Masks
2415	colors=['b','g','r','c','m','k']
2416	Data = G2frame.PatternTree.GetItemPyData(
2417	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2418	# patch
2419	if 'invert_x' not in Data:
2420	Data['invert_x'] = False
2421	Data['invert_y'] = True
2422	# end patch
2423	Masks = G2frame.PatternTree.GetItemPyData(
2424	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
2425	try: #may be absent
2426	StrSta = G2frame.PatternTree.GetItemPyData(
2427	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
2428	except TypeError: #is missing
2429	StrSta = {}
2430
2431	def OnImMotion(event):
2432	Page.canvas.SetToolTipString('')
2433	sizexy = Data['size']
2434	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
2435	Page.canvas.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata))
2436	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2437	item = G2frame.itemPicked
2438	pixelSize = Data['pixelSize']
2439	scalex = 1000./pixelSize[0]
2440	scaley = 1000./pixelSize[1]
2441	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
2442	if 'Text' in str(item):
2443	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
2444	else:
2445	xcent,ycent = Data['center']
2446	xpos = event.xdata-xcent
2447	ypos = event.ydata-ycent
2448	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
2449	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
2450	Page.canvas.SetToolTipString('%6d deg'%(azm))
2451	elif 'line1' in str(item) or 'line2' in str(item):
2452	Page.canvas.SetToolTipString('%8.3f deg'%(tth))
2453	else:
2454	xpos = event.xdata
2455	ypos = event.ydata
2456	xpix = xpos*scalex
2457	ypix = ypos*scaley
2458	Int = 0
2459	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
2460	Int = G2frame.ImageZ[ypix][xpix]
2461	tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
2462	Q = 2.*math.pi/dsp
2463	fields = ['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)]
2464	if G2frame.MaskKey in ['p','f']:
2465	fields[1] = 'Polygon/frame mask pick - LB next point, RB close polygon'
2466	elif G2frame.StrainKey:
2467	fields[0] = 'd-zero pick active'
2468	G2frame.G2plotNB.status.SetFields(fields)
2469
2470	def OnImPlotKeyPress(event):
2471	try:
2472	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
2473	except TypeError:
2474	return
2475	if PickName == 'Masks':
2476	if event.key in ['l','p','f','s','a','r']:
2477	G2frame.MaskKey = event.key
2478	OnStartMask(G2frame)
2479	PlotImage(G2frame,newPlot=False)
2480
2481	elif PickName == 'Stress/Strain':
2482	if event.key in ['a',]:
2483	G2frame.StrainKey = event.key
2484	OnStartNewDzero(G2frame)
2485	PlotImage(G2frame,newPlot=False)
2486
2487	elif PickName == 'Image Controls':
2488	if event.key in ['c',]:
2489	Xpos = event.xdata
2490	if not Xpos: #got point out of frame
2491	return
2492	Ypos = event.ydata
2493	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
2494	'Center change',style=wx.OK\|wx.CANCEL)
2495	try:
2496	if dlg.ShowModal() == wx.ID_OK:
2497	print 'move center to: ',Xpos,Ypos
2498	Data['center'] = [Xpos,Ypos]
2499	G2imG.UpdateImageControls(G2frame,Data,Masks)
2500	PlotImage(G2frame,newPlot=False)
2501	finally:
2502	dlg.Destroy()
2503	return
2504	elif event.key == 'l':
2505	G2frame.logPlot = not G2frame.logPlot
2506	elif event.key in ['x',]:
2507	Data['invert_x'] = not Data['invert_x']
2508	elif event.key in ['y',]:
2509	Data['invert_y'] = not Data['invert_y']
2510	PlotImage(G2frame,newPlot=True)
2511
2512	def OnKeyBox(event):
2513	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
2514	event.key = cb.GetValue()[0]
2515	cb.SetValue(' key press')
2516	if event.key in ['l','s','a','r','p','x','y']:
2517	wx.CallAfter(OnImPlotKeyPress,event)
2518	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
2519
2520	def OnImPick(event):
2521	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
2522	return
2523	if G2frame.itemPicked is not None: return
2524	G2frame.itemPicked = event.artist
2525	G2frame.mousePicked = event.mouseevent
2526
2527	def OnImRelease(event):
2528	try:
2529	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
2530	except TypeError:
2531	return
2532	if PickName not in ['Image Controls','Masks','Stress/Strain']:
2533	return
2534	pixelSize = Data['pixelSize']
2535	scalex = 1000./pixelSize[0]
2536	scaley = 1000./pixelSize[1]
2537	pixLimit = Data['pixLimit']
2538	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
2539	Xpos = event.xdata
2540	if not (Xpos and G2frame.ifGetRing): #got point out of frame
2541	return
2542	Ypos = event.ydata
2543	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
2544	if event.button == 1:
2545	Xpix = Xpos*scalex
2546	Ypix = Ypos*scaley
2547	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix)
2548	if I and J:
2549	xpos += .5 #shift to pixel center
2550	ypos += .5
2551	xpos /= scalex #convert to mm
2552	ypos /= scaley
2553	Data['ring'].append([xpos,ypos])
2554	elif event.button == 3:
2555	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
2556	if G2img.ImageCalibrate(G2frame,Data):
2557	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
2558	print 'Calibration successful'
2559	else:
2560	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
2561	print 'Calibration failed'
2562	G2frame.ifGetRing = False
2563	G2imG.UpdateImageControls(G2frame,Data,Masks)
2564	return
2565	PlotImage(G2frame,newImage=False)
2566	return
2567	elif G2frame.MaskKey and PickName == 'Masks':
2568	Xpos,Ypos = [event.xdata,event.ydata]
2569	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2570	return
2571	if G2frame.MaskKey == 's' and event.button == 1:
2572	Masks['Points'][-1] = [Xpos,Ypos,1.]
2573	G2frame.MaskKey = ''
2574	elif G2frame.MaskKey == 'r' and event.button == 1:
2575	tth = G2img.GetTth(Xpos,Ypos,Data)
2576	Masks['Rings'][-1] = [tth,0.1]
2577	G2frame.MaskKey = ''
2578	elif G2frame.MaskKey == 'a' and event.button == 1:
2579	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
2580	azm = int(azm)
2581	Masks['Arcs'][-1] = [tth,[azm-5,azm+5],0.1]
2582	G2frame.MaskKey = ''
2583	elif G2frame.MaskKey =='p':
2584	polygon = Masks['Polygons'][-1]
2585	if len(polygon) > 2 and event.button == 3:
2586	x0,y0 = polygon[0]
2587	polygon.append([x0,y0])
2588	G2frame.MaskKey = ''
2589	G2frame.G2plotNB.status.SetFields(['','Polygon closed'])
2590	else:
2591	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(Xpos,Ypos)])
2592	polygon.append([Xpos,Ypos])
2593	elif G2frame.MaskKey =='f':
2594	frame = Masks['Frames']
2595	if len(frame) > 2 and event.button == 3:
2596	x0,y0 = frame[0]
2597	frame.append([x0,y0])
2598	G2frame.MaskKey = ''
2599	G2frame.G2plotNB.status.SetFields(['','Frame closed'])
2600	else:
2601	G2frame.G2plotNB.status.SetFields(['','New frame point: %.1f,%.1f'%(Xpos,Ypos)])
2602	frame.append([Xpos,Ypos])
2603	G2imG.UpdateMasks(G2frame,Masks)
2604	PlotImage(G2frame,newImage=False)
2605	elif PickName == 'Stress/Strain' and G2frame.StrainKey:
2606	Xpos,Ypos = [event.xdata,event.ydata]
2607	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2608	return
2609	dsp = G2img.GetDsp(Xpos,Ypos,Data)
2610	StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':1.0,
2611	'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]})
2612	R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ,Data)
2613	if not len(R):
2614	del StrSta['d-zero'][-1]
2615	G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection')
2616	StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True)
2617	G2frame.StrainKey = ''
2618	G2imG.UpdateStressStrain(G2frame,StrSta)
2619	PlotStrain(G2frame,StrSta)
2620	PlotImage(G2frame,newPlot=False)
2621	else:
2622	Xpos,Ypos = [event.xdata,event.ydata]
2623	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2624	return
2625	if G2frame.ifGetRing: #delete a calibration ring pick
2626	xypos = [Xpos,Ypos]
2627	rings = Data['ring']
2628	for ring in rings:
2629	if np.allclose(ring,xypos,.01,0):
2630	rings.remove(ring)
2631	else:
2632	tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3]
2633	itemPicked = str(G2frame.itemPicked)
2634	if 'Line2D' in itemPicked and PickName == 'Image Controls':
2635	if 'line1' in itemPicked:
2636	Data['IOtth'][0] = max(tth,0.001)
2637	elif 'line2' in itemPicked:
2638	Data['IOtth'][1] = tth
2639	elif 'line3' in itemPicked:
2640	Data['LRazimuth'][0] = int(azm)
2641	elif 'line4' in itemPicked and not Data['fullIntegrate']:
2642	Data['LRazimuth'][1] = int(azm)
2643
2644	Data['LRazimuth'][0] %= 360
2645	Data['LRazimuth'][1] %= 360
2646	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
2647	Data['LRazimuth'][1] += 360
2648	if Data['fullIntegrate']:
2649	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
2650
2651	if Data['IOtth'][0] > Data['IOtth'][1]:
2652	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
2653
2654	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
2655	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
2656	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
2657	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
2658	elif 'Circle' in itemPicked and PickName == 'Masks':
2659	spots = Masks['Points']
2660	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
2661	newPos = np.array([float(newPos[0]),float(newPos[1])])
2662	for spot in spots:
2663	if np.allclose(np.array([spot[:2]]),newPos):
2664	spot[:2] = Xpos,Ypos
2665	G2imG.UpdateMasks(G2frame,Masks)
2666	elif 'Line2D' in itemPicked and PickName == 'Masks':
2667	Obj = G2frame.itemPicked.findobj()
2668	rings = Masks['Rings']
2669	arcs = Masks['Arcs']
2670	polygons = Masks['Polygons']
2671	frame = Masks['Frames']
2672	for ring in G2frame.ringList:
2673	if Obj == ring[0]:
2674	rN = ring[1]
2675	if ring[2] == 'o':
2676	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)-rings[rN][1]/2.
2677	else:
2678	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)+rings[rN][1]/2.
2679	for arc in G2frame.arcList:
2680	if Obj == arc[0]:
2681	aN = arc[1]
2682	if arc[2] == 'o':
2683	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)-arcs[aN][2]/2
2684	elif arc[2] == 'i':
2685	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)+arcs[aN][2]/2
2686	elif arc[2] == 'l':
2687	arcs[aN][1][0] = int(G2img.GetAzm(Xpos,Ypos,Data))
2688	else:
2689	arcs[aN][1][1] = int(G2img.GetAzm(Xpos,Ypos,Data))
2690	for poly in G2frame.polyList: #merging points problem here?
2691	if Obj == poly[0]:
2692	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
2693	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
2694	pN = poly[1]
2695	for i,xy in enumerate(polygons[pN]):
2696	if np.allclose(np.array([xy]),oldPos,atol=1.0):
2697	if event.button == 1:
2698	polygons[pN][i] = Xpos,Ypos
2699	elif event.button == 3:
2700	polygons[pN].insert(i,[Xpos,Ypos])
2701	break
2702	if frame:
2703	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
2704	for i,xy in enumerate(frame):
2705	if np.allclose(np.array([xy]),oldPos,atol=1.0):
2706	if event.button == 1:
2707	frame[i] = Xpos,Ypos
2708	elif event.button == 3:
2709	frame.insert(i,[Xpos,Ypos])
2710	break
2711	G2imG.UpdateMasks(G2frame,Masks)
2712	# else: #keep for future debugging
2713	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
2714	PlotImage(G2frame,newImage=True)
2715	G2frame.itemPicked = None
2716
2717	try:
2718	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2719	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2720	if not newPlot:
2721	Plot = Page.figure.gca() #get previous powder plot & get limits
2722	xylim = Plot.get_xlim(),Plot.get_ylim()
2723	if newImage:
2724	Page.figure.clf()
2725	Plot = Page.figure.gca() #get a fresh plot after clf()
2726	except ValueError:
2727	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
2728	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2729	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2730	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
2731	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
2732	Page.canvas.mpl_connect('pick_event', OnImPick)
2733	Page.canvas.mpl_connect('button_release_event', OnImRelease)
2734	xylim = []
2735	Page.Choice = None
2736	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
2737	Page.SetFocus()
2738	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
2739	G2frame.G2plotNB.status.DestroyChildren()
2740	if G2frame.logPlot:
2741	Title = 'log('+Title+')'
2742	Plot.set_title(Title)
2743	try:
2744	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
2745	Page.Choice = (' key press','l: log(I) on','x: flip x','y: flip y',)
2746	if G2frame.logPlot:
2747	Page.Choice[1] = 'l: log(I) off'
2748	Page.keyPress = OnImPlotKeyPress
2749	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Masks',]:
2750	Page.Choice = (' key press','l: log(I) on','s: spot mask','a: arc mask','r: ring mask',
2751	'p: polygon mask','f: frame mask',)
2752	if G2frame.logPlot:
2753	Page.Choice[1] = 'l: log(I) off'
2754	Page.keyPress = OnImPlotKeyPress
2755	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Stress/Strain',]:
2756	Page.Choice = (' key press','a: add new ring',)
2757	Page.keyPress = OnImPlotKeyPress
2758	except TypeError:
2759	pass
2760	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
2761	if imagefile != G2frame.oldImagefile:
2762	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
2763	if not imagefile:
2764	G2frame.G2plotNB.Delete('2D Powder Image')
2765	return
2766	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
2767	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
2768	G2frame.oldImagefile = imagefile
2769
2770	imScale = 1
2771	if len(G2frame.ImageZ) > 1024:
2772	imScale = len(G2frame.ImageZ)/1024
2773	sizexy = Data['size']
2774	pixelSize = Data['pixelSize']
2775	scalex = 1000./pixelSize[0]
2776	scaley = 1000./pixelSize[1]
2777	Xmax = sizexy[0]*pixelSize[0]/1000.
2778	Ymax = sizexy[1]*pixelSize[1]/1000.
2779	xlim = (0,Xmax)
2780	ylim = (Ymax,0)
2781	Imin,Imax = Data['range'][1]
2782	acolor = mpl.cm.get_cmap(Data['color'])
2783	xcent,ycent = Data['center']
2784	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
2785	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
2786	#do threshold mask - "real" mask - others are just bondaries
2787	Zlim = Masks['Thresholds'][1]
2788	wx.BeginBusyCursor()
2789	try:
2790
2791	if newImage:
2792	Imin,Imax = Data['range'][1]
2793	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]),Zlim[1])
2794	MaskA = ma.getmaskarray(MA)
2795	A = G2img.ImageCompress(MA,imScale)
2796	AM = G2img.ImageCompress(MaskA,imScale)
2797	if G2frame.logPlot:
2798	A = np.where(A>Imin,np.where(A<Imax,A,0),0)
2799	A = np.where(A>0,np.log(A),0)
2800	AM = np.where(AM>0,np.log(AM),0)
2801	Imin,Imax = [np.amin(A),np.amax(A)]
2802	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
2803	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
2804	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
2805	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
2806
2807	Plot.plot(xcent,ycent,'x')
2808	#G2frame.PatternTree.GetItemText(item)
2809	if Data['showLines']:
2810	LRAzim = Data['LRazimuth'] #NB: integers
2811	Nazm = Data['outAzimuths']
2812	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
2813	AzmthOff = Data['azmthOff']
2814	IOtth = Data['IOtth']
2815	wave = Data['wavelength']
2816	dspI = wave/(2.0*sind(IOtth[0]/2.0))
2817	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
2818	dspO = wave/(2.0*sind(IOtth[1]/2.0))
2819	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
2820	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
2821	if ellI:
2822	xyI = []
2823	for azm in Azm:
2824	xy = G2img.GetDetectorXY(dspI,azm,Data)
2825	if np.any(xy):
2826	xyI.append(xy)
2827	if len(xyI):
2828	xyI = np.array(xyI)
2829	arcxI,arcyI = xyI.T
2830	Plot.plot(arcxI,arcyI,picker=3)
2831	if ellO:
2832	xyO = []
2833	for azm in Azm:
2834	xy = G2img.GetDetectorXY(dspO,azm,Data)
2835	if np.any(xy):
2836	xyO.append(xy)
2837	if len(xyO):
2838	xyO = np.array(xyO)
2839	arcxO,arcyO = xyO.T
2840	Plot.plot(arcxO,arcyO,picker=3)
2841	if ellO and ellI:
2842	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
2843	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
2844	for i in range(Nazm):
2845	cake = LRAzim[0]+i*delAzm-AzmthOff
2846	if Data['centerAzm']:
2847	cake += delAzm/2.
2848	ind = np.searchsorted(Azm,cake)
2849	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
2850
2851	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
2852	for xring,yring in Data['ring']:
2853	Plot.plot(xring,yring,'r+',picker=3)
2854	if Data['setRings']:
2855	N = 0
2856	for ring in Data['rings']:
2857	xring,yring = np.array(ring).T[:2]
2858	Plot.plot(xring,yring,'.',color=colors[N%6])
2859	N += 1
2860	for ellipse in Data['ellipses']: #what about hyperbola?
2861	cent,phi,[width,height],col = ellipse
2862	if width > 0: #ellipses
2863	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
2864	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
2865	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
2866	for N,ring in enumerate(StrSta['d-zero']):
2867	xring,yring = ring['ImxyObs']
2868	Plot.plot(xring,yring,colors[N%6]+'.')
2869	#masks - mask lines numbered after integration limit lines
2870	spots = Masks['Points']
2871	rings = Masks['Rings']
2872	arcs = Masks['Arcs']
2873	polygons = Masks['Polygons']
2874	if 'Frames' not in Masks:
2875	Masks['Frames'] = []
2876	frame = Masks['Frames']
2877	for spot in spots:
2878	if spot:
2879	x,y,d = spot
2880	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
2881	G2frame.ringList = []
2882	for iring,ring in enumerate(rings):
2883	if ring:
2884	tth,thick = ring
2885	wave = Data['wavelength']
2886	xy1 = []
2887	xy2 = []
2888	Azm = np.linspace(0,362,181)
2889	for azm in Azm:
2890	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
2891	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
2892	x1,y1 = np.array(xy1).T
2893	x2,y2 = np.array(xy2).T
2894	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
2895	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
2896	G2frame.arcList = []
2897	for iarc,arc in enumerate(arcs):
2898	if arc:
2899	tth,azm,thick = arc
2900	wave = Data['wavelength']
2901	xy1 = []
2902	xy2 = []
2903	aR = azm[0],azm[1],azm[1]-azm[0]
2904	if azm[1]-azm[0] > 180:
2905	aR[2] /= 2
2906	Azm = np.linspace(aR[0],aR[1],aR[2])
2907	for azm in Azm:
2908	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
2909	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
2910	x1,y1 = np.array(xy1).T
2911	x2,y2 = np.array(xy2).T
2912	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
2913	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
2914	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
2915	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
2916	G2frame.polyList = []
2917	for ipoly,polygon in enumerate(polygons):
2918	if polygon:
2919	x,y = np.hsplit(np.array(polygon),2)
2920	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
2921	Plot.plot(x,y,'r')
2922	G2frame.frameList = []
2923	if frame:
2924	x,y = np.hsplit(np.array(frame),2)
2925	G2frame.frameList.append([Plot.plot(x,y,'g+',picker=10),0])
2926	Plot.plot(x,y,'g')
2927	if newImage:
2928	colorBar = Page.figure.colorbar(Img)
2929	Plot.set_xlim(xlim)
2930	Plot.set_ylim(ylim)
2931	if Data['invert_x']:
2932	Plot.invert_xaxis()
2933	if Data['invert_y']:
2934	Plot.invert_yaxis()
2935	if not newPlot and xylim:
2936	Page.toolbar.push_current()
2937	Plot.set_xlim(xylim[0])
2938	Plot.set_ylim(xylim[1])
2939	xylim = []
2940	Page.toolbar.push_current()
2941	Page.toolbar.draw()
2942	else:
2943	Page.canvas.draw()
2944	finally:
2945	wx.EndBusyCursor()
2946
2947	################################################################################
2948	##### PlotIntegration
2949	################################################################################
2950
2951	def PlotIntegration(G2frame,newPlot=False,event=None):
2952	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
2953	'''
2954
2955	def OnMotion(event):
2956	Page.canvas.SetToolTipString('')
2957	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2958	azm = event.ydata
2959	tth = event.xdata
2960	if azm and tth:
2961	G2frame.G2plotNB.status.SetFields(\
2962	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2963
2964	try:
2965	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2966	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2967	if not newPlot:
2968	Plot = Page.figure.gca() #get previous plot & get limits
2969	xylim = Plot.get_xlim(),Plot.get_ylim()
2970	Page.figure.clf()
2971	Plot = Page.figure.gca() #get a fresh plot after clf()
2972
2973	except ValueError:
2974	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
2975	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2976	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2977	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2978	Page.views = False
2979	view = False
2980	Page.Choice = None
2981	if not event:
2982	Page.SetFocus()
2983
2984	Data = G2frame.PatternTree.GetItemPyData(
2985	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2986	image = G2frame.Integrate[0]
2987	xsc = G2frame.Integrate[1]
2988	ysc = G2frame.Integrate[2]
2989	Imin,Imax = Data['range'][1]
2990	acolor = mpl.cm.get_cmap(Data['color'])
2991	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
2992	Plot.set_ylabel('azimuth',fontsize=12)
2993	Plot.set_xlabel('2-theta',fontsize=12)
2994	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
2995	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
2996	colorBar = Page.figure.colorbar(Img)
2997	# if Data['ellipses']:
2998	# for ellipse in Data['ellipses']:
2999	# x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3000	# tth,azm = G2img.GetTthAzm(x,y,Data)
3001	## azm = np.where(azm < 0.,azm+360,azm)
3002	# Plot.plot(tth,azm,'b,')
3003	if not newPlot:
3004	Page.toolbar.push_current()
3005	Plot.set_xlim(xylim[0])
3006	Plot.set_ylim(xylim[1])
3007	xylim = []
3008	Page.toolbar.push_current()
3009	Page.toolbar.draw()
3010	else:
3011	Page.canvas.draw()
3012
3013	################################################################################
3014	##### PlotTRImage
3015	################################################################################
3016
3017	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
3018	'''a test plot routine - not normally used
3019	'''
3020
3021	def OnMotion(event):
3022	Page.canvas.SetToolTipString('')
3023	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3024	azm = event.xdata
3025	tth = event.ydata
3026	if azm and tth:
3027	G2frame.G2plotNB.status.SetFields(\
3028	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3029
3030	try:
3031	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3032	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3033	if not newPlot:
3034	Plot = Page.figure.gca() #get previous plot & get limits
3035	xylim = Plot.get_xlim(),Plot.get_ylim()
3036	Page.figure.clf()
3037	Plot = Page.figure.gca() #get a fresh plot after clf()
3038
3039	except ValueError:
3040	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
3041	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3042	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3043	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3044	Page.views = False
3045	view = False
3046	Page.Choice = None
3047	Page.SetFocus()
3048
3049	Data = G2frame.PatternTree.GetItemPyData(
3050	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3051	Imin,Imax = Data['range'][1]
3052	step = (Imax-Imin)/5.
3053	V = np.arange(Imin,Imax,step)
3054	acolor = mpl.cm.get_cmap(Data['color'])
3055	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3056	Plot.set_xlabel('azimuth',fontsize=12)
3057	Plot.set_ylabel('2-theta',fontsize=12)
3058	Plot.contour(tax,tay,taz,V,cmap=acolor)
3059	if Data['showLines']:
3060	IOtth = Data['IOtth']
3061	if Data['fullIntegrate']:
3062	LRAzim = [-180,180]
3063	else:
3064	LRAzim = Data['LRazimuth'] #NB: integers
3065	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
3066	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
3067	if not Data['fullIntegrate']:
3068	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
3069	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
3070	if Data['setRings']:
3071	rings = np.concatenate((Data['rings']),axis=0)
3072	for xring,yring,dsp in rings:
3073	x,y = G2img.GetTthAzm(xring,yring,Data)
3074	Plot.plot(y,x,'r+')
3075	if Data['ellipses']:
3076	for ellipse in Data['ellipses']:
3077	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3078	x,y = np.hsplit(ring,2)
3079	tth,azm = G2img.GetTthAzm(x,y,Data)
3080	Plot.plot(azm,tth,'b,')
3081	if not newPlot:
3082	Page.toolbar.push_current()
3083	Plot.set_xlim(xylim[0])
3084	Plot.set_ylim(xylim[1])
3085	xylim = []
3086	Page.toolbar.push_current()
3087	Page.toolbar.draw()
3088	else:
3089	Page.canvas.draw()
3090
3091	################################################################################
3092	##### PlotStructure
3093	################################################################################
3094
3095	def PlotStructure(G2frame,data):
3096	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
3097	thermal motion ellipsoids and polyhedra
3098	'''
3099
3100	def FindPeaksBonds(XYZ):
3101	rFact = data['Drawing']['radiusFactor']
3102	Bonds = [[] for x in XYZ]
3103	for i,xyz in enumerate(XYZ):
3104	Dx = XYZ-xyz
3105	dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
3106	IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2))
3107	for j in IndB[0]:
3108	Bonds[i].append(Dx[j]/2.)
3109	Bonds[j].append(-Dx[j]/2.)
3110	return Bonds
3111
3112	ForthirdPI = 4.0*math.pi/3.0
3113	generalData = data['General']
3114	cell = generalData['Cell'][1:7]
3115	Vol = generalData['Cell'][7:8][0]
3116	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
3117	Gmat,gmat = G2lat.cell2Gmat(cell)
3118	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3119	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3120	SGData = generalData['SGData']
3121	Mydir = generalData['Mydir']
3122	atomData = data['Atoms']
3123	mapPeaks = []
3124	drawingData = data['Drawing']
3125	if 'Map Peaks' in data:
3126	mapPeaks = np.array(data['Map Peaks'])
3127	peakMax = 100.
3128	if len(mapPeaks):
3129	peakMax = np.max(mapPeaks.T[0])
3130	resRBData = data['RBModels'].get('Residue',[])
3131	vecRBData = data['RBModels'].get('Vector',[])
3132	rbAtmDict = {}
3133	for rbObj in resRBData+vecRBData:
3134	exclList = ['X' for i in range(len(rbObj['Ids']))]
3135	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
3136	testRBObj = data.get('testRBObj',{})
3137	rbObj = testRBObj.get('rbObj',{})
3138	MCSA = data.get('MCSA',{})
3139	mcsaModels = MCSA.get('Models',[])
3140	if mcsaModels:
3141	XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA)
3142	mcsaXYZ = []
3143	mcsaTypes = []
3144	for xyz,atyp in zip(XYZs,Types):
3145	for item in G2spc.GenAtom(xyz,SGData):
3146	mcsaXYZ.append(item[0])
3147	mcsaTypes.append(atyp)
3148	mcsaBonds = FindPeaksBonds(mcsaXYZ)
3149	drawAtoms = drawingData.get('Atoms',[])
3150	mapData = {}
3151	flipData = {}
3152	rhoXYZ = []
3153	showBonds = False
3154	if 'Map' in generalData:
3155	mapData = generalData['Map']
3156	showBonds = mapData.get('Show bonds',False)
3157	if 'Flip' in generalData:
3158	flipData = generalData['Flip']
3159	flipData['mapRoll'] = [0,0,0]
3160	Wt = np.array([255,255,255])
3161	Rd = np.array([255,0,0])
3162	Gr = np.array([0,255,0])
3163	wxGreen = wx.Color(0,255,0)
3164	Bl = np.array([0,0,255])
3165	Or = np.array([255,128,0])
3166	wxOrange = wx.Color(255,128,0)
3167	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]])
3168	uEdges = np.array([
3169	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
3170	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
3171	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
3172	mD = 0.1
3173	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
3174	mapPeakVecs = np.inner(mV,Bmat)
3175
3176	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
3177	altDown = False
3178	shiftDown = False
3179	ctrlDown = False
3180
3181	def OnKeyBox(event):
3182	import Image
3183	# Draw() #make sure plot is fresh!!
3184	mode = cb.GetValue()
3185	if mode in ['jpeg','bmp','tiff',]:
3186	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
3187	size = Page.canvas.GetSize()
3188	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
3189	if mode in ['jpeg',]:
3190	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
3191	im = Image.new("RGBA", (size[0],size[1]))
3192	else:
3193	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
3194	im = Image.new("RGB", (size[0],size[1]))
3195	im.fromstring(Pix)
3196	im.save(Fname,mode)
3197	cb.SetValue(' save as/key:')
3198	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
3199	else:
3200	event.key = cb.GetValue()[0]
3201	cb.SetValue(' save as/key:')
3202	wx.CallAfter(OnKey,event)
3203	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
3204
3205	def OnKey(event): #on key UP!!
3206	# Draw() #make sure plot is fresh!!
3207	try:
3208	keyCode = event.GetKeyCode()
3209	if keyCode > 255:
3210	keyCode = 0
3211	key = chr(keyCode)
3212	except AttributeError: #if from OnKeyBox above
3213	key = str(event.key).upper()
3214	indx = drawingData['selectedAtoms']
3215	cx,ct = drawingData['atomPtrs'][:2]
3216	if key in ['C']:
3217	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
3218	drawingData['viewDir'] = [0,0,1]
3219	drawingData['oldxy'] = []
3220	V0 = np.array([0,0,1])
3221	V = np.inner(Amat,V0)
3222	V /= np.sqrt(np.sum(V**2))
3223	A = np.arccos(np.sum(V*V0))
3224	Q = G2mth.AV2Q(A,[0,1,0])
3225	drawingData['Quaternion'] = Q
3226	SetViewPointText(drawingData['viewPoint'][0])
3227	SetViewDirText(drawingData['viewDir'])
3228	Q = drawingData['Quaternion']
3229	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3230	elif key in ['N']:
3231	drawAtoms = drawingData['Atoms']
3232	if not len(drawAtoms): #no atoms
3233	return
3234	pI = drawingData['viewPoint'][1]
3235	if not len(pI):
3236	pI = [0,0]
3237	if indx:
3238	pI[0] = indx[pI[1]]
3239	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3240	pI[1] += 1
3241	if pI[1] >= len(indx):
3242	pI[1] = 0
3243	else:
3244	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3245	pI[0] += 1
3246	if pI[0] >= len(drawAtoms):
3247	pI[0] = 0
3248	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
3249	SetViewPointText(drawingData['viewPoint'][0])
3250	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
3251
3252	elif key in ['P']:
3253	drawAtoms = drawingData['Atoms']
3254	if not len(drawAtoms): #no atoms
3255	return
3256	pI = drawingData['viewPoint'][1]
3257	if not len(pI):
3258	pI = [0,0]
3259	if indx:
3260	pI[0] = indx[pI[1]]
3261	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3262	pI[1] -= 1
3263	if pI[1] < 0:
3264	pI[1] = len(indx)-1
3265	else:
3266	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3267	pI[0] -= 1
3268	if pI[0] < 0:
3269	pI[0] = len(drawAtoms)-1
3270	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
3271	SetViewPointText(drawingData['viewPoint'][0])
3272	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
3273	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
3274	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
3275	SetMapRoll(dirDict[key])
3276	SetPeakRoll(dirDict[key])
3277	SetMapPeaksText(mapPeaks)
3278	Draw('key')
3279
3280	def GetTruePosition(xy,Add=False):
3281	View = glGetIntegerv(GL_VIEWPORT)
3282	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
3283	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
3284	Zmax = 1.
3285	if Add:
3286	Indx = GetSelectedAtoms()
3287	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
3288	for i,peak in enumerate(mapPeaks):
3289	x,y,z = peak[1:4]
3290	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
3291	XY = [int(X),int(View[3]-Y)]
3292	if np.allclose(xy,XY,atol=10) and Z < Zmax:
3293	Zmax = Z
3294	try:
3295	Indx.remove(i)
3296	ClearSelectedAtoms()
3297	for id in Indx:
3298	SetSelectedAtoms(id,Add)
3299	except:
3300	SetSelectedAtoms(i,Add)
3301	else:
3302	cx = drawingData['atomPtrs'][0]
3303	for i,atom in enumerate(drawAtoms):
3304	x,y,z = atom[cx:cx+3]
3305	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
3306	XY = [int(X),int(View[3]-Y)]
3307	if np.allclose(xy,XY,atol=10) and Z < Zmax:
3308	Zmax = Z
3309	try:
3310	Indx.remove(i)
3311	ClearSelectedAtoms()
3312	for id in Indx:
3313	SetSelectedAtoms(id,Add)
3314	except:
3315	SetSelectedAtoms(i,Add)
3316
3317	def OnMouseDown(event):
3318	xy = event.GetPosition()
3319	if event.ShiftDown():
3320	if event.LeftIsDown():
3321	GetTruePosition(xy)
3322	elif event.RightIsDown():
3323	GetTruePosition(xy,True)
3324	else:
3325	drawingData['oldxy'] = list(xy)
3326
3327	def OnMouseMove(event):
3328	if event.ShiftDown(): #don't want any inadvertant moves when picking
3329	return
3330	newxy = event.GetPosition()
3331
3332	if event.Dragging():
3333	if event.AltDown() and rbObj:
3334	if event.LeftIsDown():
3335	SetRBRotation(newxy)
3336	Q = rbObj['Orient'][0]
3337	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3338	elif event.RightIsDown():
3339	SetRBTranslation(newxy)
3340	Tx,Ty,Tz = rbObj['Orig'][0]
3341	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
3342	elif event.MiddleIsDown():
3343	SetRBRotationZ(newxy)
3344	Q = rbObj['Orient'][0]
3345	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3346	Draw('move')
3347	elif not event.ControlDown():
3348	if event.LeftIsDown():
3349	SetRotation(newxy)
3350	Q = drawingData['Quaternion']
3351	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3352	elif event.RightIsDown():
3353	SetTranslation(newxy)
3354	Tx,Ty,Tz = drawingData['viewPoint'][0]
3355	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
3356	elif event.MiddleIsDown():
3357	SetRotationZ(newxy)
3358	Q = drawingData['Quaternion']
3359	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3360	Draw('move')
3361
3362
3363	def OnMouseWheel(event):
3364	if event.ShiftDown():
3365	return
3366	drawingData['cameraPos'] += event.GetWheelRotation()/24.
3367	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
3368	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
3369	page = getSelection()
3370	if page:
3371	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3372	G2frame.dataDisplay.cameraPosTxt.SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
3373	G2frame.dataDisplay.cameraSlider.SetValue(drawingData['cameraPos'])
3374	Draw('wheel')
3375
3376	def getSelection():
3377	try:
3378	return G2frame.dataDisplay.GetSelection()
3379	except AttributeError:
3380	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!')
3381	return 0
3382
3383	def SetViewPointText(VP):
3384	page = getSelection()
3385	if page:
3386	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3387	G2frame.dataDisplay.viewPoint.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
3388
3389	def SetRBOrigText():
3390	page = getSelection()
3391	if page:
3392	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
3393	for i,sizer in enumerate(testRBObj['Sizers']['Xsizers']):
3394	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orig'][0][i]))
3395
3396	def SetRBOrienText():
3397	page = getSelection()
3398	if page:
3399	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
3400	for i,sizer in enumerate(testRBObj['Sizers']['Osizers']):
3401	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orient'][0][i]))
3402
3403	def SetViewDirText(VD):
3404	page = getSelection()
3405	if page:
3406	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3407	G2frame.dataDisplay.viewDir.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
3408
3409	def SetMapPeaksText(mapPeaks):
3410	page = getSelection()
3411	if page:
3412	if G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3413	G2frame.MapPeaksTable.SetData(mapPeaks)
3414	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
3415	names = [child.GetName() for child in panel]
3416	panel[names.index('grid window')].Refresh()
3417
3418	def ClearSelectedAtoms():
3419	page = getSelection()
3420	if page:
3421	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3422	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
3423	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3424	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
3425	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3426	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
3427
3428
3429	def SetSelectedAtoms(ind,Add=False):
3430	page = getSelection()
3431	if page:
3432	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3433	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
3434	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3435	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add)
3436	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3437	Id = drawAtoms[ind][-3]
3438	for i,atom in enumerate(atomData):
3439	if atom[-1] == Id:
3440	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
3441
3442	def GetSelectedAtoms():
3443	page = getSelection()
3444	Ind = []
3445	if page:
3446	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3447	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
3448	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3449	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows()
3450	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3451	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
3452	return Ind
3453
3454	def SetBackground():
3455	R,G,B,A = Page.camera['backColor']
3456	glClearColor(R,G,B,A)
3457	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
3458
3459	def SetLights():
3460	glEnable(GL_DEPTH_TEST)
3461	glShadeModel(GL_SMOOTH)
3462	glEnable(GL_LIGHTING)
3463	glEnable(GL_LIGHT0)
3464	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
3465	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
3466	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
3467
3468	def GetRoll(newxy,rho):
3469	Q = drawingData['Quaternion']
3470	dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,]))
3471	dxy = np.array(dxy*rho.shape)
3472	roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0))
3473	return roll
3474
3475	def SetMapRoll(newxy):
3476	rho = mapData['rho']
3477	roll = GetRoll(newxy,rho)
3478	mapData['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
3479	drawingData['oldxy'] = list(newxy)
3480
3481	def SetPeakRoll(newxy):
3482	rho = mapData['rho']
3483	roll = GetRoll(newxy,rho)
3484	steps = 1./np.array(rho.shape)
3485	dxy = roll*steps
3486	for peak in mapPeaks:
3487	peak[1:4] += dxy
3488	peak[1:4] %= 1.
3489	peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2))
3490
3491	def SetTranslation(newxy):
3492	#first get translation vector in screen coords.
3493	oldxy = drawingData['oldxy']
3494	if not len(oldxy): oldxy = list(newxy)
3495	dxy = newxy-oldxy
3496	drawingData['oldxy'] = list(newxy)
3497	V = np.array([-dxy[0],dxy[1],0.])
3498	#then transform to rotated crystal coordinates & apply to view point
3499	Q = drawingData['Quaternion']
3500	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
3501	Tx,Ty,Tz = drawingData['viewPoint'][0]
3502	Tx += V[0]*0.01
3503	Ty += V[1]*0.01
3504	Tz += V[2]*0.01
3505	drawingData['viewPoint'][0] = Tx,Ty,Tz
3506	SetViewPointText([Tx,Ty,Tz])
3507
3508	def SetRBTranslation(newxy):
3509	#first get translation vector in screen coords.
3510	oldxy = drawingData['oldxy']
3511	if not len(oldxy): oldxy = list(newxy)
3512	dxy = newxy-oldxy
3513	drawingData['oldxy'] = list(newxy)
3514	V = np.array([-dxy[0],dxy[1],0.])
3515	#then transform to rotated crystal coordinates & apply to RB origin
3516	Q = drawingData['Quaternion']
3517	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
3518	Tx,Ty,Tz = rbObj['Orig'][0]
3519	Tx -= V[0]*0.01
3520	Ty -= V[1]*0.01
3521	Tz -= V[2]*0.01
3522	rbObj['Orig'][0] = Tx,Ty,Tz
3523	SetRBOrigText()
3524
3525	def SetRotation(newxy):
3526	#first get rotation vector in screen coords. & angle increment
3527	oldxy = drawingData['oldxy']
3528	if not len(oldxy): oldxy = list(newxy)
3529	dxy = newxy-oldxy
3530	drawingData['oldxy'] = list(newxy)
3531	V = np.array([dxy[1],dxy[0],0.])
3532	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
3533	# next transform vector back to xtal coordinates via inverse quaternion
3534	# & make new quaternion
3535	Q = drawingData['Quaternion']
3536	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
3537	DQ = G2mth.AVdeg2Q(A,V)
3538	Q = G2mth.prodQQ(Q,DQ)
3539	drawingData['Quaternion'] = Q
3540	# finally get new view vector - last row of rotation matrix
3541	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
3542	VD /= np.sqrt(np.sum(VD**2))
3543	drawingData['viewDir'] = VD
3544	SetViewDirText(VD)
3545
3546	def SetRotationZ(newxy):
3547	#first get rotation vector (= view vector) in screen coords. & angle increment
3548	View = glGetIntegerv(GL_VIEWPORT)
3549	cent = [View[2]/2,View[3]/2]
3550	oldxy = drawingData['oldxy']
3551	if not len(oldxy): oldxy = list(newxy)
3552	dxy = newxy-oldxy
3553	drawingData['oldxy'] = list(newxy)
3554	V = drawingData['viewDir']
3555	A = [0,0]
3556	A[0] = dxy[1]*.25
3557	A[1] = dxy[0]*.25
3558	if newxy[0] > cent[0]:
3559	A[0] *= -1
3560	if newxy[1] < cent[1]:
3561	A[1] *= -1
3562	# next transform vector back to xtal coordinates & make new quaternion
3563	Q = drawingData['Quaternion']
3564	V = np.inner(Amat,V)
3565	Qx = G2mth.AVdeg2Q(A[0],V)
3566	Qy = G2mth.AVdeg2Q(A[1],V)
3567	Q = G2mth.prodQQ(Q,Qx)
3568	Q = G2mth.prodQQ(Q,Qy)
3569	drawingData['Quaternion'] = Q
3570
3571	def SetRBRotation(newxy):
3572	#first get rotation vector in screen coords. & angle increment
3573	oldxy = drawingData['oldxy']
3574	if not len(oldxy): oldxy = list(newxy)
3575	dxy = newxy-oldxy
3576	drawingData['oldxy'] = list(newxy)
3577	V = np.array([dxy[1],dxy[0],0.])
3578	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
3579	# next transform vector back to xtal coordinates via inverse quaternion
3580	# & make new quaternion
3581	Q = rbObj['Orient'][0] #rotate RB to Cart
3582	QC = drawingData['Quaternion'] #rotate Cart to drawing
3583	V = G2mth.prodQVQ(G2mth.invQ(QC),V)
3584	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
3585	DQ = G2mth.AVdeg2Q(A,V)
3586	Q = G2mth.prodQQ(Q,DQ)
3587	rbObj['Orient'][0] = Q
3588	SetRBOrienText()
3589
3590	def SetRBRotationZ(newxy):
3591	#first get rotation vector (= view vector) in screen coords. & angle increment
3592	View = glGetIntegerv(GL_VIEWPORT)
3593	cent = [View[2]/2,View[3]/2]
3594	oldxy = drawingData['oldxy']
3595	if not len(oldxy): oldxy = list(newxy)
3596	dxy = newxy-oldxy
3597	drawingData['oldxy'] = list(newxy)
3598	V = drawingData['viewDir']
3599	A = [0,0]
3600	A[0] = dxy[1]*.25
3601	A[1] = dxy[0]*.25
3602	if newxy[0] < cent[0]:
3603	A[0] *= -1
3604	if newxy[1] > cent[1]:
3605	A[1] *= -1
3606	# next transform vector back to RB coordinates & make new quaternion
3607	Q = rbObj['Orient'][0] #rotate RB to cart
3608	V = np.inner(Amat,V)
3609	V = -G2mth.prodQVQ(G2mth.invQ(Q),V)
3610	Qx = G2mth.AVdeg2Q(A[0],V)
3611	Qy = G2mth.AVdeg2Q(A[1],V)
3612	Q = G2mth.prodQQ(Q,Qx)
3613	Q = G2mth.prodQQ(Q,Qy)
3614	rbObj['Orient'][0] = Q
3615	SetRBOrienText()
3616
3617	def RenderBox():
3618	glEnable(GL_COLOR_MATERIAL)
3619	glLineWidth(2)
3620	glEnable(GL_BLEND)
3621	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
3622	glEnable(GL_LINE_SMOOTH)
3623	glBegin(GL_LINES)
3624	for line,color in zip(uEdges,uColors):
3625	glColor3ubv(color)
3626	glVertex3fv(line[0])
3627	glVertex3fv(line[1])
3628	glEnd()
3629	glColor4ubv([0,0,0,0])
3630	glDisable(GL_LINE_SMOOTH)
3631	glDisable(GL_BLEND)
3632	glDisable(GL_COLOR_MATERIAL)
3633
3634	def RenderUnitVectors(x,y,z):
3635	xyz = np.array([x,y,z])
3636	glEnable(GL_COLOR_MATERIAL)
3637	glLineWidth(1)
3638	glPushMatrix()
3639	glTranslate(x,y,z)
3640	glScalef(1/cell[0],1/cell[1],1/cell[2])
3641	glBegin(GL_LINES)
3642	for line,color in zip(uEdges,uColors)[:3]:
3643	glColor3ubv(color)
3644	glVertex3fv(-line[1]/2.)
3645	glVertex3fv(line[1]/2.)
3646	glEnd()
3647	glPopMatrix()
3648	glColor4ubv([0,0,0,0])
3649	glDisable(GL_COLOR_MATERIAL)
3650
3651	def RenderSphere(x,y,z,radius,color):
3652	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3653	glPushMatrix()
3654	glTranslate(x,y,z)
3655	glMultMatrixf(B4mat.T)
3656	q = gluNewQuadric()
3657	gluSphere(q,radius,20,10)
3658	glPopMatrix()
3659
3660	def RenderDots(XYZ,RC):
3661	glEnable(GL_COLOR_MATERIAL)
3662	XYZ = np.array(XYZ)
3663	glPushMatrix()
3664	for xyz,rc in zip(XYZ,RC):
3665	x,y,z = xyz
3666	r,c = rc
3667	glColor3ubv(c)
3668	glPointSize(r*50)
3669	glBegin(GL_POINTS)
3670	glVertex3fv(xyz)
3671	glEnd()
3672	glPopMatrix()
3673	glColor4ubv([0,0,0,0])
3674	glDisable(GL_COLOR_MATERIAL)
3675
3676	def RenderSmallSphere(x,y,z,radius,color):
3677	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3678	glPushMatrix()
3679	glTranslate(x,y,z)
3680	glMultMatrixf(B4mat.T)
3681	q = gluNewQuadric()
3682	gluSphere(q,radius,4,2)
3683	glPopMatrix()
3684
3685	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
3686	s1,s2,s3 = E
3687	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3688	glPushMatrix()
3689	glTranslate(x,y,z)
3690	glMultMatrixf(B4mat.T)
3691	glMultMatrixf(R4.T)
3692	glEnable(GL_NORMALIZE)
3693	glScale(s1,s2,s3)
3694	q = gluNewQuadric()
3695	gluSphere(q,ellipseProb,20,10)
3696	glDisable(GL_NORMALIZE)
3697	glPopMatrix()
3698
3699	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
3700	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3701	glPushMatrix()
3702	glTranslate(x,y,z)
3703	glMultMatrixf(B4mat.T)
3704	for bond in Bonds:
3705	glPushMatrix()
3706	Dx = np.inner(Amat,bond)
3707	Z = np.sqrt(np.sum(Dx**2))
3708	if Z:
3709	azm = atan2d(-Dx[1],-Dx[0])
3710	phi = acosd(Dx[2]/Z)
3711	glRotate(-azm,0,0,1)
3712	glRotate(phi,1,0,0)
3713	q = gluNewQuadric()
3714	gluCylinder(q,radius,radius,Z,slice,2)
3715	glPopMatrix()
3716	glPopMatrix()
3717
3718	def RenderLines(x,y,z,Bonds,color):
3719	glShadeModel(GL_FLAT)
3720	xyz = np.array([x,y,z])
3721	glEnable(GL_COLOR_MATERIAL)
3722	glLineWidth(1)
3723	glColor3fv(color)
3724	glPushMatrix()
3725	glBegin(GL_LINES)
3726	for bond in Bonds:
3727	glVertex3fv(xyz)
3728	glVertex3fv(xyz+bond)
3729	glEnd()
3730	glColor4ubv([0,0,0,0])
3731	glPopMatrix()
3732	glDisable(GL_COLOR_MATERIAL)
3733	glShadeModel(GL_SMOOTH)
3734
3735	def RenderPolyhedra(x,y,z,Faces,color):
3736	glShadeModel(GL_FLAT)
3737	glPushMatrix()
3738	glTranslate(x,y,z)
3739	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3740	glShadeModel(GL_SMOOTH)
3741	glMultMatrixf(B4mat.T)
3742	for face,norm in Faces:
3743	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
3744	glFrontFace(GL_CW)
3745	glNormal3fv(norm)
3746	glBegin(GL_TRIANGLES)
3747	for vert in face:
3748	glVertex3fv(vert)
3749	glEnd()
3750	glPopMatrix()
3751	glShadeModel(GL_SMOOTH)
3752
3753	def RenderMapPeak(x,y,z,color,den):
3754	glShadeModel(GL_FLAT)
3755	xyz = np.array([x,y,z])
3756	glEnable(GL_COLOR_MATERIAL)
3757	glLineWidth(3)
3758	glColor3fv(color*den/255)
3759	glPushMatrix()
3760	glBegin(GL_LINES)
3761	for vec in mapPeakVecs:
3762	glVertex3fv(vec[0]+xyz)
3763	glVertex3fv(vec[1]+xyz)
3764	glEnd()
3765	glColor4ubv([0,0,0,0])
3766	glPopMatrix()
3767	glDisable(GL_COLOR_MATERIAL)
3768	glShadeModel(GL_SMOOTH)
3769
3770	def RenderBackbone(Backbone,BackboneColor,radius):
3771	glPushMatrix()
3772	glMultMatrixf(B4mat.T)
3773	glEnable(GL_COLOR_MATERIAL)
3774	glShadeModel(GL_SMOOTH)
3775	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
3776	glePolyCylinder(Backbone,BackboneColor,radius)
3777	glPopMatrix()
3778	glDisable(GL_COLOR_MATERIAL)
3779
3780	def RenderLabel(x,y,z,label,r,color,matRot):
3781	'''
3782	color wx.Color object
3783	'''
3784	glPushMatrix()
3785	glTranslate(x,y,z)
3786	glMultMatrixf(B4mat.T)
3787	glDisable(GL_LIGHTING)
3788	glRasterPos3f(0,0,0)
3789	glMultMatrixf(matRot)
3790	glRotate(180,1,0,0) #fix to flip about x-axis
3791	text = gltext.Text(text=label,font=Font,foreground=color)
3792	text.draw_text(scale=0.025)
3793	glEnable(GL_LIGHTING)
3794	glPopMatrix()
3795
3796	def RenderMap(rho,rhoXYZ,indx,Rok):
3797	glShadeModel(GL_FLAT)
3798	cLevel = drawingData['contourLevel']
3799	XYZ = []
3800	RC = []
3801	for i,xyz in enumerate(rhoXYZ):
3802	if not Rok[i]:
3803	x,y,z = xyz
3804	I,J,K = indx[i]
3805	alpha = 1.0
3806	if cLevel < 1.:
3807	alpha = (abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)
3808	if rho[I,J,K] < 0.:
3809	XYZ.append(xyz)
3810	RC.append([0.1*alpha,Rd])
3811	else:
3812	XYZ.append(xyz)
3813	RC.append([0.1*alpha,Gr])
3814	RenderDots(XYZ,RC)
3815	glShadeModel(GL_SMOOTH)
3816
3817	def Draw(caller=''):
3818	#useful debug?
3819	# if caller:
3820	# print caller
3821	# end of useful debug
3822	mapData = generalData['Map']
3823	pageName = ''
3824	page = getSelection()
3825	if page:
3826	pageName = G2frame.dataDisplay.GetPageText(page)
3827	rhoXYZ = []
3828	if len(mapData['rho']):
3829	VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
3830	contLevel = drawingData['contourLevel']*mapData['rhoMax']
3831	if 'delt-F' in mapData['MapType']:
3832	rho = ma.array(mapData['rho'],mask=(np.abs(mapData['rho'])<contLevel))
3833	else:
3834	rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
3835	steps = 1./np.array(rho.shape)
3836	incre = np.where(VP>=0,VP%steps,VP%steps-steps)
3837	Vsteps = -np.array(VP/steps,dtype='i')
3838	rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
3839	indx = np.array(ma.nonzero(rho)).T
3840	rhoXYZ = indx*steps+VP-incre
3841	Nc = len(rhoXYZ)
3842	rcube = 2000.Vol/(ForthirdPINc)
3843	rmax = math.exp(math.log(rcube)/3.)**2
3844	radius = min(drawingData['mapSize']**2,rmax)
3845	view = np.array(drawingData['viewPoint'][0])
3846	Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
3847	Ind = GetSelectedAtoms()
3848	VS = np.array(Page.canvas.GetSize())
3849	aspect = float(VS[0])/float(VS[1])
3850	cPos = drawingData['cameraPos']
3851	Zclip = drawingData['Zclip']*cPos/200.
3852	Q = drawingData['Quaternion']
3853	Tx,Ty,Tz = drawingData['viewPoint'][0]
3854	cx,ct,cs,ci = drawingData['atomPtrs']
3855	bondR = drawingData['bondRadius']
3856	G,g = G2lat.cell2Gmat(cell)
3857	GS = G
3858	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
3859	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
3860	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
3861	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
3862
3863	SetBackground()
3864	glInitNames()
3865	glPushName(0)
3866
3867	glMatrixMode(GL_PROJECTION)
3868	glLoadIdentity()
3869	glViewport(0,0,VS[0],VS[1])
3870	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
3871	gluLookAt(0,0,cPos,0,0,0,0,1,0)
3872	SetLights()
3873
3874	glMatrixMode(GL_MODELVIEW)
3875	glLoadIdentity()
3876	matRot = G2mth.Q2Mat(Q)
3877	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3878	glMultMatrixf(matRot.T)
3879	glMultMatrixf(A4mat.T)
3880	glTranslate(-Tx,-Ty,-Tz)
3881	if drawingData['unitCellBox']:
3882	RenderBox()
3883	if drawingData['showABC']:
3884	x,y,z = drawingData['viewPoint'][0]
3885	RenderUnitVectors(x,y,z)
3886	Backbones = {}
3887	BackboneColor = []
3888	time0 = time.time()
3889	# glEnable(GL_BLEND)
3890	# glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
3891	for iat,atom in enumerate(drawingData['Atoms']):
3892	x,y,z = atom[cx:cx+3]
3893	Bonds = atom[-2]
3894	Faces = atom[-1]
3895	try:
3896	atNum = generalData['AtomTypes'].index(atom[ct])
3897	except ValueError:
3898	atNum = -1
3899	CL = atom[cs+2]
3900	atColor = np.array(CL)/255.
3901	if drawingData['showRigidBodies'] and atom[ci] in rbAtmDict:
3902	bndColor = Or
3903	else:
3904	bndColor = atColor
3905	if iat in Ind and G2frame.dataDisplay.GetPageText(getSelection()) != 'Map peaks':
3906	atColor = np.array(Gr)/255.
3907	# color += [.25,]
3908	radius = 0.5
3909	if atom[cs] != '':
3910	try:
3911	glLoadName(atom[-3])
3912	except: #problem with old files - missing code
3913	pass
3914	if 'balls' in atom[cs]:
3915	vdwScale = drawingData['vdwScale']
3916	ballScale = drawingData['ballScale']
3917	if atNum < 0:
3918	radius = 0.2
3919	elif 'H' == atom[ct]:
3920	if drawingData['showHydrogen']:
3921	if 'vdW' in atom[cs] and atNum >= 0:
3922	radius = vdwScale*generalData['vdWRadii'][atNum]
3923	else:
3924	radius = ballScale*drawingData['sizeH']
3925	else:
3926	radius = 0.0
3927	else:
3928	if 'vdW' in atom[cs]:
3929	radius = vdwScale*generalData['vdWRadii'][atNum]
3930	else:
3931	radius = ballScale*generalData['BondRadii'][atNum]
3932	RenderSphere(x,y,z,radius,atColor)
3933	if 'sticks' in atom[cs]:
3934	RenderBonds(x,y,z,Bonds,bondR,bndColor)
3935	elif 'ellipsoids' in atom[cs]:
3936	RenderBonds(x,y,z,Bonds,bondR,bndColor)
3937	if atom[cs+3] == 'A':
3938	Uij = atom[cs+5:cs+11]
3939	U = np.multiply(G2spc.Uij2U(Uij),GS)
3940	U = np.inner(Amat,np.inner(U,Amat).T)
3941	E,R = nl.eigh(U)
3942	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3943	E = np.sqrt(E)
3944	if atom[ct] == 'H' and not drawingData['showHydrogen']:
3945	pass
3946	else:
3947	RenderEllipsoid(x,y,z,ellipseProb,E,R4,atColor)
3948	else:
3949	if atom[ct] == 'H' and not drawingData['showHydrogen']:
3950	pass
3951	else:
3952	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
3953	RenderSphere(x,y,z,radius,atColor)
3954	elif 'lines' in atom[cs]:
3955	radius = 0.1
3956	RenderLines(x,y,z,Bonds,bndColor)
3957	# RenderBonds(x,y,z,Bonds,0.05,color,6)
3958	elif atom[cs] == 'sticks':
3959	radius = 0.1
3960	RenderBonds(x,y,z,Bonds,bondR,bndColor)
3961	elif atom[cs] == 'polyhedra':
3962	RenderPolyhedra(x,y,z,Faces,atColor)
3963	elif atom[cs] == 'backbone':
3964	if atom[ct-1].split()[0] in ['C','N']:
3965	if atom[2] not in Backbones:
3966	Backbones[atom[2]] = []
3967	Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
3968	BackboneColor.append(list(atColor))
3969
3970	if atom[cs+1] == 'type':
3971	RenderLabel(x,y,z,' '+atom[ct],radius,wxGreen,matRot)
3972	elif atom[cs+1] == 'name':
3973	RenderLabel(x,y,z,' '+atom[ct-1],radius,wxGreen,matRot)
3974	elif atom[cs+1] == 'number':
3975	RenderLabel(x,y,z,' '+str(iat),radius,wxGreen,matRot)
3976	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
3977	RenderLabel(x,y,z,' '+atom[ct-4],radius,wxGreen,matRot)
3978	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
3979	RenderLabel(x,y,z,' '+atom[ct-3],radius,wxGreen,matRot)
3980	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
3981	RenderLabel(x,y,z,' '+atom[ct-2],radius,wxGreen,matRot)
3982	# glDisable(GL_BLEND)
3983	if len(rhoXYZ):
3984	RenderMap(rho,rhoXYZ,indx,Rok)
3985	if len(mapPeaks):
3986	XYZ = mapPeaks.T[1:4].T
3987	mapBonds = FindPeaksBonds(XYZ)
3988	for ind,[mag,x,y,z,d] in enumerate(mapPeaks):
3989	if ind in Ind and pageName == 'Map peaks':
3990	RenderMapPeak(x,y,z,Gr,1.0)
3991	else:
3992	RenderMapPeak(x,y,z,Wt,mag/peakMax)
3993	if showBonds:
3994	RenderLines(x,y,z,mapBonds[ind],Wt)
3995	if len(testRBObj) and pageName == 'RB Models':
3996	XYZ = G2mth.UpdateRBXYZ(Bmat,testRBObj['rbObj'],testRBObj['rbData'],testRBObj['rbType'])[0]
3997	rbBonds = FindPeaksBonds(XYZ)
3998	for ind,[x,y,z] in enumerate(XYZ):
3999	aType = testRBObj['rbAtTypes'][ind]
4000	name = ' '+aType+str(ind)
4001	color = np.array(testRBObj['AtInfo'][aType][1])
4002	RenderSphere(x,y,z,0.2,color/255.)
4003	RenderBonds(x,y,z,rbBonds[ind],0.03,Gr)
4004	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4005	if len(mcsaModels) > 1 and pageName == 'MC/SA': #skip the default MD entry
4006	for ind,[x,y,z] in enumerate(mcsaXYZ):
4007	aType = mcsaTypes[ind]
4008	name = ' '+aType+str(ind)
4009	color = np.array(MCSA['AtInfo'][aType][1])
4010	RenderSphere(x,y,z,0.2,color/255.)
4011	RenderBonds(x,y,z,mcsaBonds[ind],0.03,Gr)
4012	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4013	if Backbones:
4014	for chain in Backbones:
4015	Backbone = Backbones[chain]
4016	RenderBackbone(Backbone,BackboneColor,bondR)
4017	# print time.time()-time0
4018	Page.canvas.SwapBuffers()
4019
4020	def OnSize(event):
4021	Draw('size')
4022
4023	def OnFocus(event): #not needed?? Bind commented out below
4024	Draw('focus')
4025
4026	try:
4027	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
4028	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4029	except ValueError:
4030	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
4031	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
4032	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4033	Page.views = False
4034	view = False
4035	altDown = False
4036	Font = Page.GetFont()
4037	Page.SetFocus()
4038	Page.Choice = None
4039	if mapData['Flip']:
4040	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2',
4041	'u: roll up','d: roll down','l: roll left','r: roll right']
4042	else:
4043	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2','n: next','p: previous']
4044	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
4045	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
4046	cb.SetValue(' save as/key:')
4047	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
4048	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
4049	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
4050	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
4051	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
4052	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
4053	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
4054	# Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
4055	Page.camera['position'] = drawingData['cameraPos']
4056	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
4057	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
4058	try:
4059	Page.canvas.SetCurrent()
4060	except:
4061	pass
4062	Draw('main')
4063
4064	################################################################################
4065	#### Plot Rigid Body
4066	################################################################################
4067
4068	def PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults):
4069	'''RB plotting package. Can show rigid body structures as balls & sticks
4070	'''
4071
4072	def FindBonds(XYZ):
4073	rbTypes = rbData['rbTypes']
4074	Radii = []
4075	for Atype in rbTypes:
4076	Radii.append(AtInfo[Atype][0])
4077	if Atype == 'H':
4078	Radii[-1] = 0.5
4079	Radii = np.array(Radii)
4080	Bonds = [[] for i in range(len(Radii))]
4081	for i,xyz in enumerate(XYZ):
4082	Dx = XYZ-xyz
4083	dist = np.sqrt(np.sum(Dx**2,axis=1))
4084	sumR = Radii[i]+Radii
4085	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
4086	for j in IndB[0]:
4087	Bonds[i].append(Dx[j]*Radii[i]/sumR[j])
4088	Bonds[j].append(-Dx[j]*Radii[j]/sumR[j])
4089	return Bonds
4090
4091	Wt = np.array([255,255,255])
4092	Rd = np.array([255,0,0])
4093	Gr = np.array([0,255,0])
4094	Bl = np.array([0,0,255])
4095	uBox = np.array([[0,0,0],[1,0,0],[0,1,0],[0,0,1]])
4096	uEdges = np.array([[uBox[0],uBox[1]],[uBox[0],uBox[2]],[uBox[0],uBox[3]]])
4097	uColors = [Rd,Gr,Bl]
4098	if rbType == 'Vector':
4099	atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['rbTypes'])]
4100	XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
4101	for imag,mag in enumerate(rbData['VectMag']):
4102	XYZ += mag*rbData['rbVect'][imag]
4103	Bonds = FindBonds(XYZ)
4104	elif rbType == 'Residue':
4105	# atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['atNames'])]
4106	atNames = rbData['atNames']
4107	XYZ = np.copy(rbData['rbXYZ']) #don't mess with original!
4108	Seq = rbData['rbSeq']
4109	for ia,ib,ang,mv in Seq:
4110	va = XYZ[ia]-XYZ[ib]
4111	Q = G2mth.AVdeg2Q(ang,va)
4112	for im in mv:
4113	vb = XYZ[im]-XYZ[ib]
4114	vb = G2mth.prodQVQ(Q,vb)
4115	XYZ[im] = XYZ[ib]+vb
4116	Bonds = FindBonds(XYZ)
4117	elif rbType == 'Z-matrix':
4118	pass
4119
4120	# def SetRBOrigin():
4121	# page = getSelection()
4122	# if page:
4123	# if G2frame.dataDisplay.GetPageText(page) == 'Rigid bodies':
4124	# G2frame.MapPeaksTable.SetData(mapPeaks)
4125	# panel = G2frame.dataDisplay.GetPage(page).GetChildren()
4126	# names = [child.GetName() for child in panel]
4127	# panel[names.index('grid window')].Refresh()
4128
4129	def OnMouseDown(event):
4130	xy = event.GetPosition()
4131	defaults['oldxy'] = list(xy)
4132
4133	def OnMouseMove(event):
4134	newxy = event.GetPosition()
4135
4136	if event.Dragging():
4137	if event.LeftIsDown():
4138	SetRotation(newxy)
4139	Q = defaults['Quaternion']
4140	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4141	# elif event.RightIsDown():
4142	# SetRBOrigin(newxy)
4143	elif event.MiddleIsDown():
4144	SetRotationZ(newxy)
4145	Q = defaults['Quaternion']
4146	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4147	Draw('move')
4148
4149	def OnMouseWheel(event):
4150	defaults['cameraPos'] += event.GetWheelRotation()/24
4151	defaults['cameraPos'] = max(10,min(500,defaults['cameraPos']))
4152	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(defaults['cameraPos']),1)
4153	Draw('wheel')
4154
4155	def SetBackground():
4156	R,G,B,A = Page.camera['backColor']
4157	glClearColor(R,G,B,A)
4158	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
4159
4160	def SetLights():
4161	glEnable(GL_DEPTH_TEST)
4162	glShadeModel(GL_FLAT)
4163	glEnable(GL_LIGHTING)
4164	glEnable(GL_LIGHT0)
4165	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
4166	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
4167	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
4168
4169	# def SetRBOrigin(newxy):
4170	##first get translation vector in screen coords.
4171	# oldxy = defaults['oldxy']
4172	# if not len(oldxy): oldxy = list(newxy)
4173	# dxy = newxy-oldxy
4174	# defaults['oldxy'] = list(newxy)
4175	# V = np.array([dxy[0],-dxy[1],0.])/100.
4176	# Q = defaults['Quaternion']
4177	# V = G2mth.prodQVQ(G2mth.invQ(Q),V)
4178	# rbData['rbXYZ'] += V
4179	# PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults)
4180	#
4181	def SetRotation(newxy):
4182	#first get rotation vector in screen coords. & angle increment
4183	oldxy = defaults['oldxy']
4184	if not len(oldxy): oldxy = list(newxy)
4185	dxy = newxy-oldxy
4186	defaults['oldxy'] = list(newxy)
4187	V = np.array([dxy[1],dxy[0],0.])
4188	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
4189	# next transform vector back to xtal coordinates via inverse quaternion
4190	# & make new quaternion
4191	Q = defaults['Quaternion']
4192	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
4193	DQ = G2mth.AVdeg2Q(A,V)
4194	Q = G2mth.prodQQ(Q,DQ)
4195	defaults['Quaternion'] = Q
4196	# finally get new view vector - last row of rotation matrix
4197	VD = G2mth.Q2Mat(Q)[2]
4198	VD /= np.sqrt(np.sum(VD**2))
4199	defaults['viewDir'] = VD
4200
4201	def SetRotationZ(newxy):
4202	#first get rotation vector (= view vector) in screen coords. & angle increment
4203	View = glGetIntegerv(GL_VIEWPORT)
4204	cent = [View[2]/2,View[3]/2]
4205	oldxy = defaults['oldxy']
4206	if not len(oldxy): oldxy = list(newxy)
4207	dxy = newxy-oldxy
4208	defaults['oldxy'] = list(newxy)
4209	V = defaults['viewDir']
4210	A = [0,0]
4211	A[0] = dxy[1]*.25
4212	A[1] = dxy[0]*.25
4213	if newxy[0] > cent[0]:
4214	A[0] *= -1
4215	if newxy[1] < cent[1]:
4216	A[1] *= -1
4217	# next transform vector back to xtal coordinates & make new quaternion
4218	Q = defaults['Quaternion']
4219	Qx = G2mth.AVdeg2Q(A[0],V)
4220	Qy = G2mth.AVdeg2Q(A[1],V)
4221	Q = G2mth.prodQQ(Q,Qx)
4222	Q = G2mth.prodQQ(Q,Qy)
4223	defaults['Quaternion'] = Q
4224
4225	def RenderUnitVectors(x,y,z):
4226	xyz = np.array([x,y,z])
4227	glEnable(GL_COLOR_MATERIAL)
4228	glLineWidth(1)
4229	glPushMatrix()
4230	glTranslate(x,y,z)
4231	glBegin(GL_LINES)
4232	for line,color in zip(uEdges,uColors):
4233	glColor3ubv(color)
4234	glVertex3fv(-line[1])
4235	glVertex3fv(line[1])
4236	glEnd()
4237	glPopMatrix()
4238	glColor4ubv([0,0,0,0])
4239	glDisable(GL_COLOR_MATERIAL)
4240
4241	def RenderSphere(x,y,z,radius,color):
4242	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4243	glPushMatrix()
4244	glTranslate(x,y,z)
4245	q = gluNewQuadric()
4246	gluSphere(q,radius,20,10)
4247	glPopMatrix()
4248
4249	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
4250	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4251	glPushMatrix()
4252	glTranslate(x,y,z)
4253	for Dx in Bonds:
4254	glPushMatrix()
4255	Z = np.sqrt(np.sum(Dx**2))
4256	if Z:
4257	azm = atan2d(-Dx[1],-Dx[0])
4258	phi = acosd(Dx[2]/Z)
4259	glRotate(-azm,0,0,1)
4260	glRotate(phi,1,0,0)
4261	q = gluNewQuadric()
4262	gluCylinder(q,radius,radius,Z,slice,2)
4263	glPopMatrix()
4264	glPopMatrix()
4265
4266	def RenderLabel(x,y,z,label,matRot):
4267	glPushMatrix()
4268	glTranslate(x,y,z)
4269	glDisable(GL_LIGHTING)
4270	glRasterPos3f(0,0,0)
4271	glMultMatrixf(matRot)
4272	glRotate(180,1,0,0) #fix to flip about x-axis
4273	text = gltext.TextElement(text=label,font=Font,foreground=wx.WHITE)
4274	text.draw_text(scale=0.025)
4275	glEnable(GL_LIGHTING)
4276	glPopMatrix()
4277
4278	def Draw(caller=''):
4279	#useful debug?
4280	# if caller:
4281	# print caller
4282	# end of useful debug
4283	cPos = defaults['cameraPos']
4284	VS = np.array(Page.canvas.GetSize())
4285	aspect = float(VS[0])/float(VS[1])
4286	Zclip = 500.0
4287	Q = defaults['Quaternion']
4288	SetBackground()
4289	glInitNames()
4290	glPushName(0)
4291
4292	glMatrixMode(GL_PROJECTION)
4293	glLoadIdentity()
4294	glViewport(0,0,VS[0],VS[1])
4295	gluPerspective(20.,aspect,1.,500.)
4296	gluLookAt(0,0,cPos,0,0,0,0,1,0)
4297	SetLights()
4298
4299	glMatrixMode(GL_MODELVIEW)
4300	glLoadIdentity()
4301	matRot = G2mth.Q2Mat(Q)
4302	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4303	glMultMatrixf(matRot.T)
4304	RenderUnitVectors(0.,0.,0.)
4305	radius = 0.2
4306	for iat,atom in enumerate(XYZ):
4307	x,y,z = atom
4308	CL = AtInfo[rbData['rbTypes'][iat]][1]
4309	color = np.array(CL)/255.
4310	RenderSphere(x,y,z,radius,color)
4311	RenderBonds(x,y,z,Bonds[iat],0.05,color)
4312	RenderLabel(x,y,z,' '+atNames[iat],matRot)
4313	Page.canvas.SwapBuffers()
4314
4315	def OnSize(event):
4316	Draw('size')
4317
4318	try:
4319	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
4320	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4321	except ValueError:
4322	Plot = G2frame.G2plotNB.addOgl('Rigid body')
4323	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
4324	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4325	Page.views = False
4326	view = False
4327	altDown = False
4328	Page.SetFocus()
4329	Font = Page.GetFont()
4330	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
4331	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
4332	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
4333	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
4334	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
4335	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
4336	Page.camera['position'] = defaults['cameraPos']
4337	Page.camera['backColor'] = np.array([0,0,0,0])
4338	Page.canvas.SetCurrent()
4339	Draw('main')

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