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source: trunk/GSASIIplot.py @ 1300

Last change on this file since 1300 was 1300, checked in by vondreele, 9 years ago
Add additional column to SASD profile - contains fixed background remove contour plotting from SASD data Add background file to SASD models GUI this change breaks old SASD gpx files, they will need to be recreated!
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 182.8 KB

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1	# -- coding: utf-8 --
2	'''
3	GSASIIplot: plotting routines
4	===============================
5
6	'''
7	########### SVN repository information ###################
8	# $Date: 2014-04-25 17:47:06 +0000 (Fri, 25 Apr 2014) $
9	# $Author: vondreele $
10	# $Revision: 1300 $
11	# $URL: trunk/GSASIIplot.py $
12	# $Id: GSASIIplot.py 1300 2014-04-25 17:47:06Z 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: 1300 $")
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':
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' and 'PWDR' in plottype:
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','b: toggle subtract background','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','b: toggle subtract background','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	B = xye[5]
899	if G2frame.sqPlot:
900	Y = xye[1]Sample['Scale'][0](1.005)*(offsetN)X*4
901	else:
902	Y = xye[1]Sample['Scale'][0](1.005)*(offsetN)
903	if LimitId and ifpicked:
904	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
905	if G2frame.qPlot and 'PWDR' in plottype:
906	if 'C' in Parms['Type'][0]:
907	limits = 4np.pinpsind(limits/2.0)/wave
908	else:
909	limits = 2np.pidifC/limits
910	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
911	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
912	for i,item in enumerate(limits[2:]):
913	Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))
914	Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.))
915	exclLines += [2i+2,2i+3]
916	if G2frame.Contour:
917
918	if lenX == len(X):
919	ContourY.append(N)
920	ContourZ.append(Y)
921	ContourX = X
922	Nseq += 1
923	Plot.set_ylabel('Data sequence',fontsize=12)
924	else:
925	if 'SASD' in plottype and G2frame.logPlot:
926	X = (1.01)(G2frame.Offset[1]N)
927	else:
928	X += G2frame.Offset[1].005N
929	Xum = ma.getdata(X)
930	if ifpicked:
931	Z = xye[3]+offset*N
932	if 'PWDR' in plottype: #powder background
933	W = xye[4]+offset*N
934	D = xye[5]-Ymax*G2frame.delOffset
935	elif 'SASD' in plottype:
936	if G2frame.sqPlot:
937	W = xye[4]X*4
938	Z = xye[3]X*4
939	B = BX*4
940	else:
941	W = xye[4]
942	if G2frame.SubBack:
943	YB = Y-B
944	ZB = Z
945	else:
946	YB = Y
947	ZB = Z+B
948	Plot.set_yscale("log",nonposy='mask')
949	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
950	if G2frame.logPlot:
951	if 'PWDR' in plottype:
952	Plot.set_yscale("log",nonposy='mask')
953	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
954	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
955	Plot.plot(X,W,colors[(N+2)%6],picker=False)
956	elif 'SASD' in plottype:
957	Plot.set_xscale("log",nonposx='mask')
958	Plot.set_yscale("log",nonposy='mask')
959	if G2frame.ErrorBars:
960	if G2frame.sqPlot:
961	Plot.errorbar(X,YB,yerr=X*4Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
962	ecolor=colors[N%6],picker=3.,clip_on=False)
963	else:
964	Plot.errorbar(X,YB,yerr=Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
965	ecolor=colors[N%6],picker=3.,clip_on=False)
966	else:
967	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
968	Plot.plot(X,W,colors[(N+2)%6],picker=False)
969	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
970	elif G2frame.Weight and 'PWDR' in plottype:
971	DY = xye[1]*np.sqrt(xye[2])
972	DYmax = max(DY)
973	DZ = xye[3]*np.sqrt(xye[2])
974	DS = xye[5]np.sqrt(xye[2])-DYmaxG2frame.delOffset
975	Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False)
976	Plot.plot(X,DZ,colors[(N+1)%6],picker=False)
977	Plot.plot(X,DS,colors[(N+3)%6],picker=False)
978	Plot.axhline(0.,color=wx.BLACK)
979	else:
980	if G2frame.SubBack:
981	Plot.plot(Xum,Y-W,colors[N%6]+'+',picker=3.,clip_on=False)
982	Plot.plot(X,Z-W,colors[(N+1)%6],picker=False)
983	else:
984	Plot.plot(Xum,Y,colors[N%6]+'+',picker=3.,clip_on=False)
985	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
986	if G2frame.logPlot:
987	Plot.set_yscale("log",nonposy='mask')
988	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
989	if 'PWDR' in plottype:
990	Plot.plot(X,W,colors[(N+2)%6],picker=False)
991	Plot.plot(X,D,colors[(N+3)%6],picker=False)
992	Plot.axhline(0.,color=wx.BLACK)
993	Page.canvas.SetToolTipString('')
994	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
995	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
996	Page.canvas.SetToolTipString(tip)
997	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
998	for item in data:
999	if G2frame.qPlot:
1000	if 'C' in Parms['Type'][0]:
1001	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/wave,color=colors[N%6],picker=2.))
1002	else:
1003	Lines.append(Plot.axvline(2math.pidifC/item[0],color=colors[N%6],picker=2.))
1004	else:
1005	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
1006	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
1007	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
1008	Page.canvas.SetToolTipString(tip)
1009	data = G2frame.LimitsTable.GetData()
1010	else:
1011	if G2frame.logPlot:
1012	if 'PWDR' in plottype:
1013	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1014	elif 'SASD' in plottype:
1015	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1016	else:
1017	if 'PWDR' in plottype:
1018	Plot.plot(X,Y,colors[N%6],picker=False)
1019	elif 'SASD' in plottype:
1020	Plot.loglog(X,Y,colors[N%6],picker=False,nonposy='mask')
1021	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1022	if G2frame.logPlot:
1023	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1024	if PickId and not G2frame.Contour:
1025	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1026	if 'C' in Parms['Type'][0]:
1027	wave = G2mth.getWave(Parms)
1028	else:
1029	difC = Parms['difC'][1]
1030	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
1031	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
1032	for peak in peaks:
1033	if G2frame.qPlot:
1034	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
1035	else:
1036	Plot.axvline(peak[0],color='b')
1037	for hkl in G2frame.HKL:
1038	if G2frame.qPlot:
1039	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
1040	else:
1041	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1042	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
1043	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
1044	refColors=['b','r','c','g','m','k']
1045	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1046	for pId,phase in enumerate(Phases):
1047	try: #patch for old style reflection lists
1048	peaks = Phases[phase]['RefList']
1049	except TypeError:
1050	peaks = Phases[phase]
1051	if not len(peaks):
1052	continue
1053	peak = np.array([[peak[4],peak[5]] for peak in peaks])
1054	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
1055	if G2frame.qPlot:
1056	Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1057	else:
1058	Plot.plot(peak.T[1],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1059	if len(Phases):
1060	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
1061	if handles:
1062	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
1063
1064	if G2frame.Contour:
1065	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1066	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1067	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1068	Page.figure.colorbar(Img)
1069	else:
1070	G2frame.Lines = Lines
1071	if not newPlot:
1072	Page.toolbar.push_current()
1073	Plot.set_xlim(xylim[0])
1074	Plot.set_ylim(xylim[1])
1075	# xylim = []
1076	Page.toolbar.push_current()
1077	Page.toolbar.draw()
1078	else:
1079	Page.canvas.draw()
1080	olderr = np.seterr(invalid='warn') #ugh - this removes a matplotlib error for mouse clicks in log plots
1081	# G2frame.Pwdr = True
1082
1083	################################################################################
1084	##### PlotDeltSig
1085	################################################################################
1086
1087	def PlotDeltSig(G2frame,kind):
1088	'needs a doc string'
1089	try:
1090	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1091	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1092	Page.figure.clf()
1093	Plot = Page.figure.gca() #get a fresh plot after clf()
1094	except ValueError:
1095	newPlot = True
1096	G2frame.Cmax = 1.0
1097	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
1098	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1099	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1100	Page.Choice = None
1101	PatternId = G2frame.PatternId
1102	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
1103	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
1104	wtFactor = Pattern[0]['wtFactor']
1105	if kind == 'PWDR':
1106	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
1107	xye = np.array(Pattern[1])
1108	xmin = np.searchsorted(xye[0],limits[0])
1109	xmax = np.searchsorted(xye[0],limits[1])
1110	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
1111	elif kind == 'HKLF':
1112	refl = Pattern[1]
1113	DS = []
1114	for ref in refl:
1115	if ref[6] > 0.:
1116	DS.append((ref[5]-ref[7])/ref[6])
1117	Page.SetFocus()
1118	G2frame.G2plotNB.status.DestroyChildren()
1119	DS.sort()
1120	EDS = np.zeros_like(DS)
1121	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
1122	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
1123	T = np.sqrt(np.log(1.0/DX**2))
1124	top = 2.515517+0.802853T+0.010328T**2
1125	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
1126	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
1127	low1 = np.searchsorted(EDS,-1.)
1128	hi1 = np.searchsorted(EDS,1.)
1129	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
1130	frac = 100.*(hi1-low1)/len(DS)
1131	G2frame.G2plotNB.status.SetStatusText( \
1132	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
1133	Plot.set_title('Normal probability for '+Pattern[-1])
1134	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
1135	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
1136	Plot.plot(EDS,DS,'r+',label='result')
1137	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
1138	Plot.legend(loc='upper left')
1139	np.seterr(invalid='warn')
1140	Page.canvas.draw()
1141
1142	################################################################################
1143	##### PlotISFG
1144	################################################################################
1145
1146	def PlotISFG(G2frame,newPlot=False,type=''):
1147	''' Plotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
1148	or multiple plots with waterfall and contour plots as options
1149	'''
1150	if not type:
1151	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
1152	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
1153	return
1154	superMinusOne = unichr(0xaf)+unichr(0xb9)
1155
1156	def OnPlotKeyPress(event):
1157	newPlot = False
1158	if event.key == 'u':
1159	if G2frame.Contour:
1160	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
1161	elif G2frame.Offset[0] < 100.:
1162	G2frame.Offset[0] += 1.
1163	elif event.key == 'd':
1164	if G2frame.Contour:
1165	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
1166	elif G2frame.Offset[0] > 0.:
1167	G2frame.Offset[0] -= 1.
1168	elif event.key == 'l':
1169	G2frame.Offset[1] -= 1.
1170	elif event.key == 'r':
1171	G2frame.Offset[1] += 1.
1172	elif event.key == 'o':
1173	G2frame.Offset = [0,0]
1174	elif event.key == 'c':
1175	newPlot = True
1176	G2frame.Contour = not G2frame.Contour
1177	if not G2frame.Contour:
1178	G2frame.SinglePlot = False
1179	G2frame.Offset = [0.,0.]
1180	elif event.key == 's':
1181	if G2frame.Contour:
1182	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1183	choice.sort()
1184	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1185	if dlg.ShowModal() == wx.ID_OK:
1186	sel = dlg.GetSelection()
1187	G2frame.ContourColor = choice[sel]
1188	else:
1189	G2frame.ContourColor = 'Paired'
1190	dlg.Destroy()
1191	else:
1192	G2frame.SinglePlot = not G2frame.SinglePlot
1193	elif event.key == 'i': #for smoothing contour plot
1194	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
1195	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
1196	'mitchell','sinc','lanczos']
1197	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
1198	if dlg.ShowModal() == wx.ID_OK:
1199	sel = dlg.GetSelection()
1200	G2frame.Interpolate = choice[sel]
1201	else:
1202	G2frame.Interpolate = 'nearest'
1203	dlg.Destroy()
1204	elif event.key == 't' and not G2frame.Contour:
1205	G2frame.Legend = not G2frame.Legend
1206	PlotISFG(G2frame,newPlot=newPlot,type=type)
1207
1208	def OnKeyBox(event):
1209	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
1210	event.key = cb.GetValue()[0]
1211	cb.SetValue(' key press')
1212	wx.CallAfter(OnPlotKeyPress,event)
1213	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
1214
1215	def OnMotion(event):
1216	xpos = event.xdata
1217	if xpos: #avoid out of frame mouse position
1218	ypos = event.ydata
1219	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1220	try:
1221	if G2frame.Contour:
1222	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
1223	else:
1224	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
1225	except TypeError:
1226	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1227
1228	xylim = []
1229	try:
1230	plotNum = G2frame.G2plotNB.plotList.index(type)
1231	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1232	if not newPlot:
1233	Plot = Page.figure.gca() #get previous plot & get limits
1234	xylim = Plot.get_xlim(),Plot.get_ylim()
1235	Page.figure.clf()
1236	Plot = Page.figure.gca()
1237	except ValueError:
1238	newPlot = True
1239	G2frame.Cmax = 1.0
1240	Plot = G2frame.G2plotNB.addMpl(type).gca()
1241	plotNum = G2frame.G2plotNB.plotList.index(type)
1242	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1243	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1244	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1245
1246	Page.SetFocus()
1247	G2frame.G2plotNB.status.DestroyChildren()
1248	if G2frame.Contour:
1249	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
1250	'i: interpolation method','s: color scheme','c: contour off')
1251	else:
1252	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
1253	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
1254	Page.keyPress = OnPlotKeyPress
1255	PatternId = G2frame.PatternId
1256	PickId = G2frame.PickId
1257	Plot.set_title(type)
1258	if type == 'G(R)':
1259	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
1260	else:
1261	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
1262	Plot.set_ylabel(r''+type,fontsize=14)
1263	colors=['b','g','r','c','m','k']
1264	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
1265	Pattern = []
1266	if G2frame.SinglePlot:
1267	name = G2frame.PatternTree.GetItemText(PatternId)
1268	name = type+name[4:]
1269	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
1270	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1271	if Pattern:
1272	Pattern.append(name)
1273	PlotList = [Pattern,]
1274	else:
1275	PlotList = []
1276	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1277	while item:
1278	if 'PDF' in G2frame.PatternTree.GetItemText(item):
1279	name = type+G2frame.PatternTree.GetItemText(item)[4:]
1280	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
1281	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1282	if Pattern:
1283	Pattern.append(name)
1284	PlotList.append(Pattern)
1285	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1286	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
1287	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
1288	Xb = [0.,10.]
1289	Yb = [0.,-40.np.pinumbDen]
1290	Ymax = 1.0
1291	lenX = 0
1292	for Pattern in PlotList:
1293	xye = Pattern[1]
1294	Ymax = max(Ymax,max(xye[1]))
1295	offset = G2frame.Offset[0]*Ymax/100.0
1296	if G2frame.Contour:
1297	ContourZ = []
1298	ContourY = []
1299	Nseq = 0
1300	for N,Pattern in enumerate(PlotList):
1301	xye = Pattern[1]
1302	if PickId:
1303	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1304	X = xye[0]
1305	if not lenX:
1306	lenX = len(X)
1307	Y = xye[1]+offset*N
1308	if G2frame.Contour:
1309	if lenX == len(X):
1310	ContourY.append(N)
1311	ContourZ.append(Y)
1312	ContourX = X
1313	Nseq += 1
1314	Plot.set_ylabel('Data sequence',fontsize=12)
1315	else:
1316	X = xye[0]+G2frame.Offset[1].005N
1317	if ifpicked:
1318	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1319	Page.canvas.SetToolTipString('')
1320	else:
1321	if G2frame.Legend:
1322	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1323	else:
1324	Plot.plot(X,Y,colors[N%6],picker=False)
1325	if type == 'G(R)':
1326	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1327	elif type == 'F(Q)':
1328	Plot.axhline(0.,color=wx.BLACK)
1329	elif type == 'S(Q)':
1330	Plot.axhline(1.,color=wx.BLACK)
1331	if G2frame.Contour:
1332	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1333	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1334	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1335	Page.figure.colorbar(Img)
1336	elif G2frame.Legend:
1337	Plot.legend(loc='best')
1338	if not newPlot:
1339	Page.toolbar.push_current()
1340	Plot.set_xlim(xylim[0])
1341	Plot.set_ylim(xylim[1])
1342	xylim = []
1343	Page.toolbar.push_current()
1344	Page.toolbar.draw()
1345	else:
1346	Page.canvas.draw()
1347
1348	################################################################################
1349	##### PlotXY
1350	################################################################################
1351
1352	def PlotXY(G2frame,XY,XY2=None,labelX=None,labelY=None,newPlot=False,type=''):
1353	'''simple plot of xy data, used for diagnostic purposes
1354	'''
1355	def OnMotion(event):
1356	xpos = event.xdata
1357	if xpos: #avoid out of frame mouse position
1358	ypos = event.ydata
1359	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1360	try:
1361	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
1362	except TypeError:
1363	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1364
1365	try:
1366	plotNum = G2frame.G2plotNB.plotList.index(type)
1367	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1368	if not newPlot:
1369	Plot = Page.figure.gca()
1370	xylim = Plot.get_xlim(),Plot.get_ylim()
1371	Page.figure.clf()
1372	Plot = Page.figure.gca()
1373	except ValueError:
1374	newPlot = True
1375	Plot = G2frame.G2plotNB.addMpl(type).gca()
1376	plotNum = G2frame.G2plotNB.plotList.index(type)
1377	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1378	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1379
1380	Page.Choice = None
1381	Page.SetFocus()
1382	G2frame.G2plotNB.status.DestroyChildren()
1383	Plot.set_title(type)
1384	if xLabel:
1385	Plot.set_xlabel(r''+xLabel,fontsize=14)
1386	else:
1387	Plot.set_xlabel(r'X',fontsize=14)
1388	if yLabel:
1389	Plot.set_ylabel(r''+yLabel,fontsize=14)
1390	else:
1391	Plot.set_ylabel(r'Y',fontsize=14)
1392	colors=['b','g','r','c','m','k']
1393	for ixy,xy in enumerate(XY):
1394	X,Y = xy
1395	Plot.plot(X,Y,color(ixy%6)+'+',picker=False)
1396	if len(XY2):
1397	for ixy,xy in enumerate(XY2):
1398	X,Y = xy
1399	Plot.plot(X,Y,color(ixy%6),picker=False)
1400	if not newPlot:
1401	Page.toolbar.push_current()
1402	Plot.set_xlim(xylim[0])
1403	Plot.set_ylim(xylim[1])
1404	xylim = []
1405	Page.toolbar.push_current()
1406	Page.toolbar.draw()
1407	else:
1408	Page.canvas.draw()
1409
1410	################################################################################
1411	##### PlotStrain
1412	################################################################################
1413
1414	def PlotStrain(G2frame,data,newPlot=False):
1415	'''plot of strain data, used for diagnostic purposes
1416	'''
1417	def OnMotion(event):
1418	xpos = event.xdata
1419	if xpos: #avoid out of frame mouse position
1420	ypos = event.ydata
1421	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1422	try:
1423	G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1)
1424	except TypeError:
1425	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
1426
1427	try:
1428	plotNum = G2frame.G2plotNB.plotList.index('Strain')
1429	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1430	if not newPlot:
1431	Plot = Page.figure.gca()
1432	xylim = Plot.get_xlim(),Plot.get_ylim()
1433	Page.figure.clf()
1434	Plot = Page.figure.gca()
1435	except ValueError:
1436	newPlot = True
1437	Plot = G2frame.G2plotNB.addMpl('Strain').gca()
1438	plotNum = G2frame.G2plotNB.plotList.index('Strain')
1439	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1440	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1441
1442	Page.Choice = None
1443	Page.SetFocus()
1444	G2frame.G2plotNB.status.DestroyChildren()
1445	Plot.set_title('Strain')
1446	Plot.set_ylabel(r'd-spacing',fontsize=14)
1447	Plot.set_xlabel(r'Azimuth',fontsize=14)
1448	colors=['b','g','r','c','m','k']
1449	for N,item in enumerate(data['d-zero']):
1450	Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y
1451	Plot.plot(X,Y,colors[N%6]+'+',picker=False)
1452	Y,X = np.array(item['ImtaCalc'])
1453	Plot.plot(X,Y,colors[N%6],picker=False)
1454	if not newPlot:
1455	Page.toolbar.push_current()
1456	Plot.set_xlim(xylim[0])
1457	Plot.set_ylim(xylim[1])
1458	xylim = []
1459	Page.toolbar.push_current()
1460	Page.toolbar.draw()
1461	else:
1462	Page.canvas.draw()
1463
1464	################################################################################
1465	##### PlotSASDSizeDist
1466	################################################################################
1467
1468	def PlotSASDSizeDist(G2frame):
1469
1470	def OnPageChanged(event):
1471	PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection())
1472	if 'Powder' in PlotText:
1473	PlotPatterns(G2frame,plotType='SASD',newPlot=True)
1474	elif 'Size' in PlotText:
1475	PlotSASDSizeDist(G2frame)
1476
1477	def OnMotion(event):
1478	xpos = event.xdata
1479	if xpos: #avoid out of frame mouse position
1480	ypos = event.ydata
1481	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1482	try:
1483	G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1)
1484	except TypeError:
1485	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
1486
1487	try:
1488	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
1489	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1490	Page.figure.clf()
1491	Plot = Page.figure.gca() #get a fresh plot after clf()
1492	except ValueError:
1493	newPlot = True
1494	Plot = G2frame.G2plotNB.addMpl('Size Distribution').gca()
1495	G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged)
1496	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
1497	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1498	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1499	Page.Choice = None
1500	Page.SetFocus()
1501	PatternId = G2frame.PatternId
1502	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Models'))
1503	Bins,Dbins,BinMag = data['Size']['Distribution']
1504	Plot.set_title('Size Distribution')
1505	Plot.set_xlabel(r'$D, \AA$',fontsize=14)
1506	Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14)
1507	if data['Size']['logBins']:
1508	Plot.set_xscale("log",nonposy='mask')
1509	Plot.set_xlim([np.min(2.Bins)/2.,np.max(2.Bins)*2.])
1510	Plot.bar(2.Bins-Dbins,BinMag,2.Dbins,facecolor='white') #plot diameters
1511	if 'Size Calc' in data:
1512	Rbins,Dist = data['Size Calc']
1513	for i in range(len(Rbins)):
1514	if len(Rbins[i]):
1515	Plot.plot(2.*Rbins[i],Dist[i]) #plot diameters
1516	Page.canvas.draw()
1517
1518	################################################################################
1519	##### PlotPowderLines
1520	################################################################################
1521
1522	def PlotPowderLines(G2frame):
1523	''' plotting of powder lines (i.e. no powder pattern) as sticks
1524	'''
1525	global HKL
1526
1527	def OnMotion(event):
1528	xpos = event.xdata
1529	if xpos: #avoid out of frame mouse position
1530	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1531	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1532	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
1533	found = []
1534	if len(HKL):
1535	view = Page.toolbar._views.forward()[0][:2]
1536	wid = view[1]-view[0]
1537	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1538	if len(found):
1539	h,k,l = found[0][:3]
1540	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1541	else:
1542	Page.canvas.SetToolTipString('')
1543
1544	try:
1545	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1546	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1547	Page.figure.clf()
1548	Plot = Page.figure.gca()
1549	except ValueError:
1550	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
1551	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1552	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1553	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1554
1555	Page.Choice = None
1556	Page.SetFocus()
1557	Plot.set_title('Powder Pattern Lines')
1558	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1559	PickId = G2frame.PickId
1560	PatternId = G2frame.PatternId
1561	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
1562	for peak in peaks:
1563	Plot.axvline(peak[0],color='b')
1564	HKL = np.array(G2frame.HKL)
1565	for hkl in G2frame.HKL:
1566	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1567	xmin = peaks[0][0]
1568	xmax = peaks[-1][0]
1569	delt = xmax-xmin
1570	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1571	Plot.set_xlim(xlim)
1572	Page.canvas.draw()
1573	Page.toolbar.push_current()
1574
1575	################################################################################
1576	##### PlotPeakWidths
1577	################################################################################
1578
1579	def PlotPeakWidths(G2frame):
1580	''' Plotting of instrument broadening terms as function of 2-theta
1581	Seen when "Instrument Parameters" chosen from powder pattern data tree
1582	'''
1583	# sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1584	# gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1585	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.)
1586	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1587	PatternId = G2frame.PatternId
1588	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1589	if limitID:
1590	limits = G2frame.PatternTree.GetItemPyData(limitID)[:2]
1591	else:
1592	return
1593	Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \
1594	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1595	if 'C' in Parms['Type'][0]:
1596	lam = G2mth.getWave(Parms)
1597	else:
1598	difC = Parms['difC'][0]
1599	peakID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
1600	if peakID:
1601	peaks = G2frame.PatternTree.GetItemPyData(peakID)
1602	else:
1603	peaks = []
1604
1605	try:
1606	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1607	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1608	Page.figure.clf()
1609	Plot = Page.figure.gca()
1610	except ValueError:
1611	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
1612	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1613	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1614	Page.Choice = None
1615	Page.SetFocus()
1616
1617	Page.canvas.SetToolTipString('')
1618	colors=['b','g','r','c','m','k']
1619	X = []
1620	Y = []
1621	Z = []
1622	W = []
1623	if 'C' in Parms['Type'][0]:
1624	Plot.set_title('Instrument and sample peak widths')
1625	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
1626	Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14)
1627	try:
1628	Xmin,Xmax = limits[1]
1629	X = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1630	Q = 4.np.pinpsind(X/2.)/lam
1631	Z = np.ones_like(X)
1632	data = G2mth.setPeakparms(Parms,Parms2,X,Z)
1633	s = 1.17741np.sqrt(data[4])np.pi/18000.
1634	g = data[6]*np.pi/18000.
1635	G = G2pwd.getgamFW(g,s)
1636	Y = s/nptand(X/2.)
1637	Z = g/nptand(X/2.)
1638	W = G/nptand(X/2.)
1639	Plot.plot(Q,Y,color='r',label='Gaussian')
1640	Plot.plot(Q,Z,color='g',label='Lorentzian')
1641	Plot.plot(Q,W,color='b',label='G+L')
1642
1643	fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True)
1644	sf = 1.17741np.sqrt(fit[4])np.pi/18000.
1645	gf = fit[6]*np.pi/18000.
1646	Gf = G2pwd.getgamFW(gf,sf)
1647	Yf = sf/nptand(X/2.)
1648	Zf = gf/nptand(X/2.)
1649	Wf = Gf/nptand(X/2.)
1650	Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit')
1651	Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit')
1652	Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
1653
1654	X = []
1655	Y = []
1656	Z = []
1657	W = []
1658	V = []
1659	for peak in peaks:
1660	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1661	try:
1662	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1663	except ValueError:
1664	s = 0.01
1665	g = peak[6]*math.pi/18000.
1666	G = G2pwd.getgamFW(g,s)
1667	Y.append(s/tand(peak[0]/2.))
1668	Z.append(g/tand(peak[0]/2.))
1669	W.append(G/tand(peak[0]/2.))
1670	if len(peaks):
1671	Plot.plot(X,Y,'+',color='r',label='G peak')
1672	Plot.plot(X,Z,'+',color='g',label='L peak')
1673	Plot.plot(X,W,'+',color='b',label='G+L peak')
1674	Plot.legend(loc='best')
1675	Page.canvas.draw()
1676	except ValueError:
1677	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
1678	'%.3f'%(2*theta)
1679	G2frame.G2plotNB.Delete('Peak Widths')
1680	else:
1681	Plot.set_title('Instrument and sample peak coefficients')
1682	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
1683	Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14)
1684	Xmin,Xmax = limits[1]
1685	T = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1686	Z = np.ones_like(T)
1687	data = G2mth.setPeakparms(Parms,Parms2,T,Z)
1688	ds = T/difC
1689	Q = 2.*np.pi/ds
1690	A = data[4]
1691	B = data[6]
1692	S = 1.17741*np.sqrt(data[8])/T
1693	G = data[10]/T
1694	Plot.plot(Q,A,color='r',label='Alpha')
1695	Plot.plot(Q,B,color='g',label='Beta')
1696	Plot.plot(Q,S,color='b',label='Gaussian')
1697	Plot.plot(Q,G,color='m',label='Lorentzian')
1698
1699	fit = G2mth.setPeakparms(Parms,Parms2,T,Z)
1700	ds = T/difC
1701	Q = 2.*np.pi/ds
1702	Af = fit[4]
1703	Bf = fit[6]
1704	Sf = 1.17741*np.sqrt(fit[8])/T
1705	Gf = fit[10]/T
1706	Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit')
1707	Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit')
1708	Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit')
1709	Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit')
1710
1711	T = []
1712	A = []
1713	B = []
1714	S = []
1715	G = []
1716	W = []
1717	Q = []
1718	V = []
1719	for peak in peaks:
1720	T.append(peak[0])
1721	A.append(peak[4])
1722	B.append(peak[6])
1723	Q.append(2.np.pidifC/peak[0])
1724	S.append(1.17741*np.sqrt(peak[8])/peak[0])
1725	G.append(peak[10]/peak[0])
1726
1727
1728	Plot.plot(Q,A,'+',color='r',label='Alpha peak')
1729	Plot.plot(Q,B,'+',color='g',label='Beta peak')
1730	Plot.plot(Q,S,'+',color='b',label='Gaussian peak')
1731	Plot.plot(Q,G,'+',color='m',label='Lorentzian peak')
1732	Plot.legend(loc='best')
1733	Page.canvas.draw()
1734
1735
1736	################################################################################
1737	##### PlotSizeStrainPO
1738	################################################################################
1739
1740	def PlotSizeStrainPO(G2frame,data,Start=False):
1741	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1742	'''
1743
1744	PatternId = G2frame.PatternId
1745	generalData = data['General']
1746	SGData = generalData['SGData']
1747	SGLaue = SGData['SGLaue']
1748	if Start: #initialize the spherical harmonics qlmn arrays
1749	ptx.pyqlmninit()
1750	Start = False
1751	# MuStrKeys = G2spc.MustrainNames(SGData)
1752	cell = generalData['Cell'][1:]
1753	A,B = G2lat.cell2AB(cell[:6])
1754	Vol = cell[6]
1755	useList = data['Histograms']
1756	phase = generalData['Name']
1757	plotType = generalData['Data plot type']
1758	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
1759	for ptype in plotDict:
1760	G2frame.G2plotNB.Delete(ptype)
1761	if plotType in ['None']:
1762	return
1763
1764	for item in useList:
1765	if useList[item]['Show']:
1766	break
1767	else:
1768	return #nothing to show!!
1769
1770	numPlots = len(useList)
1771
1772	if plotType in ['Mustrain','Size']:
1773	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
1774	else:
1775	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
1776	plotNum = G2frame.G2plotNB.plotList.index(plotType)
1777	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1778	Page.Choice = None
1779	Page.SetFocus()
1780	G2frame.G2plotNB.status.SetStatusText('',1)
1781	if not Page.IsShown():
1782	Page.Show()
1783
1784	for item in useList:
1785	if useList[item]['Show']:
1786	PHI = np.linspace(0.,360.,30,True)
1787	PSI = np.linspace(0.,180.,30,True)
1788	X = np.outer(npsind(PHI),npsind(PSI))
1789	Y = np.outer(npcosd(PHI),npsind(PSI))
1790	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1791	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
1792	coeff = useList[item][plotDict[plotType]]
1793	except KeyError:
1794	break
1795	if plotType in ['Mustrain','Size']:
1796	if coeff[0] == 'isotropic':
1797	X *= coeff[1][0]
1798	Y *= coeff[1][0]
1799	Z *= coeff[1][0]
1800	elif coeff[0] == 'uniaxial':
1801
1802	def uniaxCalc(xyz,iso,aniso,axes):
1803	Z = np.array(axes)
1804	cp = abs(np.dot(xyz,Z))
1805	sp = np.sqrt(1.-cp**2)
1806	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
1807	return R*xyz
1808
1809	iso,aniso = coeff[1][:2]
1810	axes = np.inner(A,np.array(coeff[3]))
1811	axes /= nl.norm(axes)
1812	Shkl = np.array(coeff[1])
1813	XYZ = np.dstack((X,Y,Z))
1814	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
1815	X,Y,Z = np.dsplit(XYZ,3)
1816	X = X[:,:,0]
1817	Y = Y[:,:,0]
1818	Z = Z[:,:,0]
1819
1820	elif coeff[0] == 'ellipsoidal':
1821
1822	def ellipseCalc(xyz,E,R):
1823	XYZ = xyz*E.T
1824	return np.inner(XYZ.T,R)
1825
1826	S6 = coeff[4]
1827	Sij = G2lat.U6toUij(S6)
1828	E,R = nl.eigh(Sij)
1829	XYZ = np.dstack((X,Y,Z))
1830	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
1831	X,Y,Z = np.dsplit(XYZ,3)
1832	X = X[:,:,0]
1833	Y = Y[:,:,0]
1834	Z = Z[:,:,0]
1835
1836	elif coeff[0] == 'generalized':
1837
1838	def genMustrain(xyz,SGData,A,Shkl):
1839	uvw = np.inner(A.T,xyz)
1840	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1841	sum = np.sum(np.multiply(Shkl,Strm))
1842	sum = np.where(sum > 0.01,sum,0.01)
1843	sum = np.sqrt(sum)*math.pi/.18 #centidegrees to radians!
1844	return sum*xyz
1845
1846	Shkl = np.array(coeff[4])
1847	if np.any(Shkl):
1848	XYZ = np.dstack((X,Y,Z))
1849	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1850	X,Y,Z = np.dsplit(XYZ,3)
1851	X = X[:,:,0]
1852	Y = Y[:,:,0]
1853	Z = Z[:,:,0]
1854
1855	if np.any(X) and np.any(Y) and np.any(Z):
1856	errFlags = np.seterr(all='ignore')
1857	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1858	np.seterr(all='ignore')
1859	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
1860	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
1861	Plot.set_xlim3d(XYZlim)
1862	Plot.set_ylim3d(XYZlim)
1863	Plot.set_zlim3d(XYZlim)
1864	Plot.set_aspect('equal')
1865	if plotType == 'Size':
1866	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
1867	Plot.set_xlabel(r'X, $\mu$m')
1868	Plot.set_ylabel(r'Y, $\mu$m')
1869	Plot.set_zlabel(r'Z, $\mu$m')
1870	else:
1871	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
1872	Plot.set_xlabel(r'X, $\mu$strain')
1873	Plot.set_ylabel(r'Y, $\mu$strain')
1874	Plot.set_zlabel(r'Z, $\mu$strain')
1875	else:
1876	h,k,l = generalData['POhkl']
1877	if coeff[0] == 'MD':
1878	print 'March-Dollase preferred orientation plot'
1879
1880	else:
1881	PH = np.array(generalData['POhkl'])
1882	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
1883	SHCoef = {}
1884	for item in coeff[5]:
1885	L,N = eval(item.strip('C'))
1886	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
1887	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1888	X = np.linspace(0,90.0,26)
1889	Y = G2lat.polfcal(ODFln,'0',X,0.0)
1890	Plot.plot(X,Y,color='k',label=str(PH))
1891	Plot.legend(loc='best')
1892	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
1893	Plot.set_xlabel(r'$\psi$',fontsize=16)
1894	Plot.set_ylabel('MRD',fontsize=14)
1895	Page.canvas.draw()
1896
1897	################################################################################
1898	##### PlotTexture
1899	################################################################################
1900
1901	def PlotTexture(G2frame,data,Start=False):
1902	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
1903	plotting.
1904	dict generalData contains all phase info needed which is in data
1905	'''
1906
1907	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1908	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1909	PatternId = G2frame.PatternId
1910	generalData = data['General']
1911	SGData = generalData['SGData']
1912	textureData = generalData['SH Texture']
1913	G2frame.G2plotNB.Delete('Texture')
1914	if not textureData['Order']:
1915	return #no plot!!
1916	SHData = generalData['SH Texture']
1917	SHCoef = SHData['SH Coeff'][1]
1918	cell = generalData['Cell'][1:7]
1919	Amat,Bmat = G2lat.cell2AB(cell)
1920	sq2 = 1.0/math.sqrt(2.0)
1921
1922	def rp2xyz(r,p):
1923	z = npcosd(r)
1924	xy = np.sqrt(1.-z**2)
1925	return xynpsind(p),xynpcosd(p),z
1926
1927	def OnMotion(event):
1928	SHData = data['General']['SH Texture']
1929	if event.xdata and event.ydata: #avoid out of frame errors
1930	xpos = event.xdata
1931	ypos = event.ydata
1932	if 'Inverse' in SHData['PlotType']:
1933	r = xpos2+ypos2
1934	if r <= 1.0:
1935	if 'equal' in G2frame.Projection:
1936	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1937	else:
1938	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1939	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1940	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1941	y,x,z = list(xyz/np.max(np.abs(xyz)))
1942
1943	G2frame.G2plotNB.status.SetFields(['',
1944	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1945
1946	elif 'Axial' in SHData['PlotType']:
1947	pass
1948
1949	else: #ordinary pole figure
1950	z = xpos2+ypos2
1951	if z <= 1.0:
1952	z = np.sqrt(z)
1953	if 'equal' in G2frame.Projection:
1954	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1955	else:
1956	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1957	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1958	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1959
1960	try:
1961	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1962	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1963	Page.figure.clf()
1964	Plot = Page.figure.gca()
1965	if not Page.IsShown():
1966	Page.Show()
1967	except ValueError:
1968	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
1969	plotNum = G2frame.G2plotNB.plotList.index('Texture')
1970	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1971	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1972
1973	Page.Choice = None
1974	Page.SetFocus()
1975	G2frame.G2plotNB.status.SetFields(['',''])
1976	PH = np.array(SHData['PFhkl'])
1977	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1978	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1979	PX = np.array(SHData['PFxyz'])
1980	gam = atan2d(PX[0],PX[1])
1981	xy = math.sqrt(PX[0]2+PX[1]2)
1982	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1983	psi = asind(xy/xyz)
1984	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1985	if 'Axial' in SHData['PlotType']:
1986	X = np.linspace(0,90.0,26)
1987	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1988	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1989	Plot.legend(loc='best')
1990	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1991	Plot.set_xlabel(r'$\psi$',fontsize=16)
1992	Plot.set_ylabel('MRD',fontsize=14)
1993
1994	else:
1995	npts = 201
1996	if 'Inverse' in SHData['PlotType']:
1997	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1998	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1999	if 'equal' in G2frame.Projection:
2000	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2001	else:
2002	R = np.where(R <= 1.,2.*npatand(R),0.0)
2003	Z = np.zeros_like(R)
2004	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
2005	Z = np.reshape(Z,(npts,npts))
2006	CS = Plot.contour(Y,X,Z,aspect='equal')
2007	Plot.clabel(CS,fontsize=9,inline=1)
2008	try:
2009	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2010	except ValueError:
2011	pass
2012	Page.figure.colorbar(Img)
2013	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
2014	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2015
2016	else:
2017	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2018	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2019	if 'equal' in G2frame.Projection:
2020	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2021	else:
2022	R = np.where(R <= 1.,2.*npatand(R),0.0)
2023	Z = np.zeros_like(R)
2024	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
2025	Z = np.reshape(Z,(npts,npts))
2026	try:
2027	CS = Plot.contour(Y,X,Z,aspect='equal')
2028	Plot.clabel(CS,fontsize=9,inline=1)
2029	except ValueError:
2030	pass
2031	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2032	Page.figure.colorbar(Img)
2033	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
2034	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2035	Page.canvas.draw()
2036
2037	################################################################################
2038	##### PlotCovariance
2039	################################################################################
2040
2041	def PlotCovariance(G2frame,Data):
2042	'needs a doc string'
2043	if not Data:
2044	print 'No covariance matrix available'
2045	return
2046	varyList = Data['varyList']
2047	values = Data['variables']
2048	Xmax = len(varyList)
2049	covMatrix = Data['covMatrix']
2050	sig = np.sqrt(np.diag(covMatrix))
2051	xvar = np.outer(sig,np.ones_like(sig))
2052	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
2053	title = ' for\n'+Data['title']
2054	newAtomDict = Data.get('newAtomDict',{})
2055
2056
2057	def OnPlotKeyPress(event):
2058	newPlot = False
2059	if event.key == 's':
2060	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2061	choice.sort()
2062	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2063	if dlg.ShowModal() == wx.ID_OK:
2064	sel = dlg.GetSelection()
2065	G2frame.VcovColor = choice[sel]
2066	else:
2067	G2frame.VcovColor = 'RdYlGn'
2068	dlg.Destroy()
2069	PlotCovariance(G2frame,Data)
2070
2071	def OnMotion(event):
2072	#there is a problem here - reports wrong values
2073	if event.button:
2074	ytics = imgAx.get_yticks()
2075	ytics = np.where(ytics<len(varyList),ytics,-1)
2076	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
2077	imgAx.set_yticklabels(ylabs)
2078	if event.xdata and event.ydata: #avoid out of frame errors
2079	xpos = int(event.xdata+.5)
2080	ypos = int(event.ydata+.5)
2081	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
2082	if xpos == ypos:
2083	value = values[xpos]
2084	name = varyList[xpos]
2085	if varyList[xpos] in newAtomDict:
2086	name,value = newAtomDict[name]
2087	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
2088	else:
2089	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
2090	Page.canvas.SetToolTipString(msg)
2091	G2frame.G2plotNB.status.SetFields(['',msg])
2092
2093	try:
2094	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2095	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2096	Page.figure.clf()
2097	Plot = Page.figure.gca()
2098	if not Page.IsShown():
2099	Page.Show()
2100	except ValueError:
2101	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
2102	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2103	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2104	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2105	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2106	Page.Choice = ['s: to change colors']
2107	Page.keyPress = OnPlotKeyPress
2108	Page.SetFocus()
2109	G2frame.G2plotNB.status.SetFields(['',''])
2110	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
2111	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower',
2112	vmin=-1.,vmax=1.)
2113	imgAx = Img.get_axes()
2114	ytics = imgAx.get_yticks()
2115	ylabs = [varyList[int(i)] for i in ytics[:-1]]
2116	imgAx.set_yticklabels(ylabs)
2117	colorBar = Page.figure.colorbar(Img)
2118	Plot.set_title('V-Cov matrix'+title)
2119	Plot.set_xlabel('Variable number')
2120	Plot.set_ylabel('Variable name')
2121	Page.canvas.draw()
2122
2123	################################################################################
2124	##### PlotTorsion
2125	################################################################################
2126
2127	def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]):
2128	'needs a doc string'
2129
2130	global names
2131	names = Names
2132	sum = np.sum(Torsion)
2133	torsion = np.log(2*Torsion+1.)/sum
2134	tMin = np.min(torsion)
2135	tMax = np.max(torsion)
2136	torsion = 3.*(torsion-tMin)/(tMax-tMin)
2137	X = np.linspace(0.,360.,num=45)
2138
2139	def OnPick(event):
2140	ind = event.ind[0]
2141	msg = 'atoms:'+names[ind]
2142	Page.canvas.SetToolTipString(msg)
2143	try:
2144	page = G2frame.dataDisplay.GetSelection()
2145	except:
2146	return
2147	if G2frame.dataDisplay.GetPageText(page) == 'Torsion restraints':
2148	torGrid = G2frame.dataDisplay.GetPage(page).Torsions
2149	torGrid.ClearSelection()
2150	for row in range(torGrid.GetNumberRows()):
2151	if names[ind] in torGrid.GetCellValue(row,0):
2152	torGrid.SelectRow(row)
2153	torGrid.ForceRefresh()
2154
2155	def OnMotion(event):
2156	if event.xdata and event.ydata: #avoid out of frame errors
2157	xpos = event.xdata
2158	ypos = event.ydata
2159	msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos)
2160	Page.canvas.SetToolTipString(msg)
2161
2162	try:
2163	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
2164	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2165	Page.figure.clf()
2166	Plot = Page.figure.gca()
2167	if not Page.IsShown():
2168	Page.Show()
2169	except ValueError:
2170	Plot = G2frame.G2plotNB.addMpl('Torsion').gca()
2171	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
2172	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2173	Page.canvas.mpl_connect('pick_event', OnPick)
2174	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2175
2176	Page.SetFocus()
2177	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify torsion atoms'])
2178	Plot.plot(X,torsion,'b+')
2179	if len(Coeff):
2180	X2 = np.linspace(0.,360.,45)
2181	Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2])
2182	Plot.plot(X2,Y2,'r')
2183	if len(Angles):
2184	Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles])
2185	Plot.plot(Angles,Eval,'ro',picker=5)
2186	Plot.set_xlim((0.,360.))
2187	Plot.set_title('Torsion angles for '+TorName+' in '+phaseName)
2188	Plot.set_xlabel('angle',fontsize=16)
2189	Plot.set_ylabel('Energy',fontsize=16)
2190	Page.canvas.draw()
2191
2192	################################################################################
2193	##### PlotRama
2194	################################################################################
2195
2196	def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]):
2197	'needs a doc string'
2198
2199	global names
2200	names = Names
2201	rama = np.log(2*Rama+1.)
2202	ramaMax = np.max(rama)
2203	rama = np.reshape(rama,(45,45))
2204	global Phi,Psi
2205	Phi = []
2206	Psi = []
2207
2208	def OnPlotKeyPress(event):
2209	newPlot = False
2210	if event.key == 's':
2211	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2212	choice.sort()
2213	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2214	if dlg.ShowModal() == wx.ID_OK:
2215	sel = dlg.GetSelection()
2216	G2frame.RamaColor = choice[sel]
2217	else:
2218	G2frame.RamaColor = 'RdYlGn'
2219	dlg.Destroy()
2220	PlotRama(G2frame,phaseName,Rama)
2221
2222	def OnPick(event):
2223	ind = event.ind[0]
2224	msg = 'atoms:'+names[ind]
2225	Page.canvas.SetToolTipString(msg)
2226	try:
2227	page = G2frame.dataDisplay.GetSelection()
2228	except:
2229	return
2230	if G2frame.dataDisplay.GetPageText(page) == 'Ramachandran restraints':
2231	ramaGrid = G2frame.dataDisplay.GetPage(page).Ramas
2232	ramaGrid.ClearSelection()
2233	for row in range(ramaGrid.GetNumberRows()):
2234	if names[ind] in ramaGrid.GetCellValue(row,0):
2235	ramaGrid.SelectRow(row)
2236	ramaGrid.ForceRefresh()
2237
2238	def OnMotion(event):
2239	if event.xdata and event.ydata: #avoid out of frame errors
2240	xpos = event.xdata
2241	ypos = event.ydata
2242	msg = 'phi/psi: %5.3f %5.3f'%(xpos,ypos)
2243	Page.canvas.SetToolTipString(msg)
2244
2245	try:
2246	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
2247	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2248	Page.figure.clf()
2249	Plot = Page.figure.gca()
2250	if not Page.IsShown():
2251	Page.Show()
2252	except ValueError:
2253	Plot = G2frame.G2plotNB.addMpl('Ramachandran').gca()
2254	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
2255	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2256	Page.canvas.mpl_connect('pick_event', OnPick)
2257	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2258	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2259
2260	Page.Choice = ['s: to change colors']
2261	Page.keyPress = OnPlotKeyPress
2262	Page.SetFocus()
2263	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify phi/psi atoms'])
2264	acolor = mpl.cm.get_cmap(G2frame.RamaColor)
2265	if RamaName == 'All' or '-1' in RamaName:
2266	if len(Coeff):
2267	X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45))
2268	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
2269	Plot.contour(X,Y,np.reshape(Z,(45,45)))
2270	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
2271	extent=[-180,180,-180,180],origin='lower')
2272	if len(PhiPsi):
2273	Phi,Psi = PhiPsi.T
2274	Phi = np.where(Phi>180.,Phi-360.,Phi)
2275	Psi = np.where(Psi>180.,Psi-360.,Psi)
2276	Plot.plot(Phi,Psi,'ro',picker=5)
2277	Plot.set_xlim((-180.,180.))
2278	Plot.set_ylim((-180.,180.))
2279	else:
2280	if len(Coeff):
2281	X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45))
2282	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
2283	Plot.contour(X,Y,np.reshape(Z,(45,45)))
2284	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
2285	extent=[0,360,0,360],origin='lower')
2286	if len(PhiPsi):
2287	Phi,Psi = PhiPsi.T
2288	Plot.plot(Phi,Psi,'ro',picker=5)
2289	Plot.set_xlim((0.,360.))
2290	Plot.set_ylim((0.,360.))
2291	Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName)
2292	Plot.set_xlabel(r'$\phi$',fontsize=16)
2293	Plot.set_ylabel(r'$\psi$',fontsize=16)
2294	colorBar = Page.figure.colorbar(Img)
2295	Page.canvas.draw()
2296
2297
2298	################################################################################
2299	##### PlotSeq
2300	################################################################################
2301	def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX):
2302	'''Plot a result from a sequential refinement
2303
2304	:param wx.Frame G2frame: The main GSAS-II tree "window"
2305	:param list ColumnList: list of int values corresponding to columns
2306	selected as y values
2307	:param function TableGet: a function that takes a column number
2308	as argument and returns the column label, the values and there ESDs (or None)
2309	:param function SelectX: a function that returns a selected column
2310	number (or None) as the X-axis selection
2311	'''
2312	G2frame.seqYaxisList = ColumnList
2313	G2frame.seqTableGet = TableGet
2314	G2frame.seqXselect = SelectX
2315	try:
2316	G2frame.seqXaxis
2317	except:
2318	G2frame.seqXaxis = None
2319
2320	def OnMotion(event):
2321	if event.xdata and event.ydata: #avoid out of frame errors
2322	xpos = event.xdata
2323	ypos = event.ydata
2324	msg = '%5.3f %.6g'%(xpos,ypos)
2325	Page.canvas.SetToolTipString(msg)
2326
2327	def OnKeyPress(event):
2328	if event.key == 's':
2329	G2frame.seqXaxis = G2frame.seqXselect()
2330	Draw()
2331	try:
2332	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
2333	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2334	Page.figure.clf()
2335	Plot = Page.figure.gca()
2336	if not Page.IsShown():
2337	Page.Show()
2338	except ValueError:
2339	Plot = G2frame.G2plotNB.addMpl('Sequential refinement').gca()
2340	plotNum = G2frame.G2plotNB.plotList.index('Sequential refinement')
2341	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2342	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
2343	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2344	Page.Choice = ['s to select plot x-axis']
2345	Page.keyPress = OnKeyPress
2346
2347	def Draw():
2348	Page.SetFocus()
2349	G2frame.G2plotNB.status.SetFields(['press s to select X axis'])
2350	Plot.clear()
2351	if G2frame.seqXaxis is not None:
2352	xName,X,Xsig = G2frame.seqTableGet(G2frame.seqXaxis)
2353	else:
2354	X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1)
2355	xName = 'Data sequence number'
2356	for col in G2frame.seqYaxisList:
2357	name,Y,sig = G2frame.seqTableGet(col)
2358	if sig:
2359	Plot.errorbar(X,Y,yerr=sig,label=name)
2360	else:
2361	Plot.plot(X,Y)
2362	Plot.plot(X,Y,'o',label=name)
2363	Plot.legend(loc='best')
2364	Plot.set_ylabel('Parameter values')
2365	Plot.set_xlabel(xName)
2366	Page.canvas.draw()
2367	Draw()
2368
2369	################################################################################
2370	##### PlotExposedImage & PlotImage
2371	################################################################################
2372
2373	def PlotExposedImage(G2frame,newPlot=False,event=None):
2374	'''General access module for 2D image plotting
2375	'''
2376	plotNo = G2frame.G2plotNB.nb.GetSelection()
2377	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
2378	PlotImage(G2frame,newPlot,event,newImage=True)
2379	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
2380	PlotIntegration(G2frame,newPlot,event)
2381
2382	def OnStartMask(G2frame):
2383	'''Initiate the start of a Frame or Polygon map
2384
2385	:param wx.Frame G2frame: The main GSAS-II tree "window"
2386	:param str eventkey: a single letter ('f' or 'p') that
2387	determines what type of mask is created.
2388	'''
2389	Masks = G2frame.PatternTree.GetItemPyData(
2390	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
2391	if G2frame.MaskKey == 'f':
2392	Masks['Frames'] = []
2393	elif G2frame.MaskKey == 'p':
2394	Masks['Polygons'].append([])
2395	elif G2frame.MaskKey == 's':
2396	Masks['Points'].append([])
2397	elif G2frame.MaskKey == 'a':
2398	Masks['Arcs'].append([])
2399	elif G2frame.MaskKey == 'r':
2400	Masks['Rings'].append([])
2401	G2imG.UpdateMasks(G2frame,Masks)
2402	PlotImage(G2frame,newImage=True)
2403
2404	def OnStartNewDzero(G2frame):
2405	'''Initiate the start of adding a new d-zero to a strain data set
2406
2407	:param wx.Frame G2frame: The main GSAS-II tree "window"
2408	:param str eventkey: a single letter ('a') that
2409	triggers the addition of a d-zero.
2410	'''
2411	G2frame.dataFrame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value')
2412	StrSta = G2frame.PatternTree.GetItemPyData(
2413	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
2414
2415	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
2416	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
2417	masks, etc.
2418	'''
2419	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
2420	import numpy.ma as ma
2421	Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.))
2422	global Data,Masks
2423	colors=['b','g','r','c','m','k']
2424	Data = G2frame.PatternTree.GetItemPyData(
2425	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2426	# patch
2427	if 'invert_x' not in Data:
2428	Data['invert_x'] = False
2429	Data['invert_y'] = True
2430	# end patch
2431	Masks = G2frame.PatternTree.GetItemPyData(
2432	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
2433	try: #may be absent
2434	StrSta = G2frame.PatternTree.GetItemPyData(
2435	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
2436	except TypeError: #is missing
2437	StrSta = {}
2438
2439	def OnImMotion(event):
2440	Page.canvas.SetToolTipString('')
2441	sizexy = Data['size']
2442	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
2443	Page.canvas.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata))
2444	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2445	item = G2frame.itemPicked
2446	pixelSize = Data['pixelSize']
2447	scalex = 1000./pixelSize[0]
2448	scaley = 1000./pixelSize[1]
2449	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
2450	if 'Text' in str(item):
2451	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
2452	else:
2453	xcent,ycent = Data['center']
2454	xpos = event.xdata-xcent
2455	ypos = event.ydata-ycent
2456	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
2457	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
2458	Page.canvas.SetToolTipString('%6d deg'%(azm))
2459	elif 'line1' in str(item) or 'line2' in str(item):
2460	Page.canvas.SetToolTipString('%8.3f deg'%(tth))
2461	else:
2462	xpos = event.xdata
2463	ypos = event.ydata
2464	xpix = xpos*scalex
2465	ypix = ypos*scaley
2466	Int = 0
2467	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
2468	Int = G2frame.ImageZ[ypix][xpix]
2469	tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
2470	Q = 2.*math.pi/dsp
2471	fields = ['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)]
2472	if G2frame.MaskKey in ['p','f']:
2473	fields[1] = 'Polygon/frame mask pick - LB next point, RB close polygon'
2474	elif G2frame.StrainKey:
2475	fields[0] = 'd-zero pick active'
2476	G2frame.G2plotNB.status.SetFields(fields)
2477
2478	def OnImPlotKeyPress(event):
2479	try:
2480	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
2481	except TypeError:
2482	return
2483	if PickName == 'Masks':
2484	if event.key in ['l','p','f','s','a','r']:
2485	G2frame.MaskKey = event.key
2486	OnStartMask(G2frame)
2487	PlotImage(G2frame,newPlot=False)
2488
2489	elif PickName == 'Stress/Strain':
2490	if event.key in ['a',]:
2491	G2frame.StrainKey = event.key
2492	OnStartNewDzero(G2frame)
2493	PlotImage(G2frame,newPlot=False)
2494
2495	elif PickName == 'Image Controls':
2496	if event.key in ['c',]:
2497	Xpos = event.xdata
2498	if not Xpos: #got point out of frame
2499	return
2500	Ypos = event.ydata
2501	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
2502	'Center change',style=wx.OK\|wx.CANCEL)
2503	try:
2504	if dlg.ShowModal() == wx.ID_OK:
2505	print 'move center to: ',Xpos,Ypos
2506	Data['center'] = [Xpos,Ypos]
2507	G2imG.UpdateImageControls(G2frame,Data,Masks)
2508	PlotImage(G2frame,newPlot=False)
2509	finally:
2510	dlg.Destroy()
2511	return
2512	elif event.key == 'l':
2513	G2frame.logPlot = not G2frame.logPlot
2514	elif event.key in ['x',]:
2515	Data['invert_x'] = not Data['invert_x']
2516	elif event.key in ['y',]:
2517	Data['invert_y'] = not Data['invert_y']
2518	PlotImage(G2frame,newPlot=True)
2519
2520	def OnKeyBox(event):
2521	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
2522	event.key = cb.GetValue()[0]
2523	cb.SetValue(' key press')
2524	if event.key in ['l','s','a','r','p','x','y']:
2525	wx.CallAfter(OnImPlotKeyPress,event)
2526	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
2527
2528	def OnImPick(event):
2529	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
2530	return
2531	if G2frame.itemPicked is not None: return
2532	G2frame.itemPicked = event.artist
2533	G2frame.mousePicked = event.mouseevent
2534
2535	def OnImRelease(event):
2536	try:
2537	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
2538	except TypeError:
2539	return
2540	if PickName not in ['Image Controls','Masks','Stress/Strain']:
2541	return
2542	pixelSize = Data['pixelSize']
2543	scalex = 1000./pixelSize[0]
2544	scaley = 1000./pixelSize[1]
2545	pixLimit = Data['pixLimit']
2546	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
2547	Xpos = event.xdata
2548	if not (Xpos and G2frame.ifGetRing): #got point out of frame
2549	return
2550	Ypos = event.ydata
2551	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
2552	if event.button == 1:
2553	Xpix = Xpos*scalex
2554	Ypix = Ypos*scaley
2555	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix)
2556	if I and J:
2557	xpos += .5 #shift to pixel center
2558	ypos += .5
2559	xpos /= scalex #convert to mm
2560	ypos /= scaley
2561	Data['ring'].append([xpos,ypos])
2562	elif event.button == 3:
2563	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
2564	if G2img.ImageCalibrate(G2frame,Data):
2565	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
2566	print 'Calibration successful'
2567	else:
2568	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
2569	print 'Calibration failed'
2570	G2frame.ifGetRing = False
2571	G2imG.UpdateImageControls(G2frame,Data,Masks)
2572	return
2573	PlotImage(G2frame,newImage=False)
2574	return
2575	elif G2frame.MaskKey and PickName == 'Masks':
2576	Xpos,Ypos = [event.xdata,event.ydata]
2577	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2578	return
2579	if G2frame.MaskKey == 's' and event.button == 1:
2580	Masks['Points'][-1] = [Xpos,Ypos,1.]
2581	G2frame.MaskKey = ''
2582	elif G2frame.MaskKey == 'r' and event.button == 1:
2583	tth = G2img.GetTth(Xpos,Ypos,Data)
2584	Masks['Rings'][-1] = [tth,0.1]
2585	G2frame.MaskKey = ''
2586	elif G2frame.MaskKey == 'a' and event.button == 1:
2587	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
2588	azm = int(azm)
2589	Masks['Arcs'][-1] = [tth,[azm-5,azm+5],0.1]
2590	G2frame.MaskKey = ''
2591	elif G2frame.MaskKey =='p':
2592	polygon = Masks['Polygons'][-1]
2593	if len(polygon) > 2 and event.button == 3:
2594	x0,y0 = polygon[0]
2595	polygon.append([x0,y0])
2596	G2frame.MaskKey = ''
2597	G2frame.G2plotNB.status.SetFields(['','Polygon closed'])
2598	else:
2599	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(Xpos,Ypos)])
2600	polygon.append([Xpos,Ypos])
2601	elif G2frame.MaskKey =='f':
2602	frame = Masks['Frames']
2603	if len(frame) > 2 and event.button == 3:
2604	x0,y0 = frame[0]
2605	frame.append([x0,y0])
2606	G2frame.MaskKey = ''
2607	G2frame.G2plotNB.status.SetFields(['','Frame closed'])
2608	else:
2609	G2frame.G2plotNB.status.SetFields(['','New frame point: %.1f,%.1f'%(Xpos,Ypos)])
2610	frame.append([Xpos,Ypos])
2611	G2imG.UpdateMasks(G2frame,Masks)
2612	PlotImage(G2frame,newImage=False)
2613	elif PickName == 'Stress/Strain' and G2frame.StrainKey:
2614	Xpos,Ypos = [event.xdata,event.ydata]
2615	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2616	return
2617	dsp = G2img.GetDsp(Xpos,Ypos,Data)
2618	StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':1.0,
2619	'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]})
2620	R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ,Data)
2621	if not len(R):
2622	del StrSta['d-zero'][-1]
2623	G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection')
2624	StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True)
2625	G2frame.StrainKey = ''
2626	G2imG.UpdateStressStrain(G2frame,StrSta)
2627	PlotStrain(G2frame,StrSta)
2628	PlotImage(G2frame,newPlot=False)
2629	else:
2630	Xpos,Ypos = [event.xdata,event.ydata]
2631	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2632	return
2633	if G2frame.ifGetRing: #delete a calibration ring pick
2634	xypos = [Xpos,Ypos]
2635	rings = Data['ring']
2636	for ring in rings:
2637	if np.allclose(ring,xypos,.01,0):
2638	rings.remove(ring)
2639	else:
2640	tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3]
2641	itemPicked = str(G2frame.itemPicked)
2642	if 'Line2D' in itemPicked and PickName == 'Image Controls':
2643	if 'line1' in itemPicked:
2644	Data['IOtth'][0] = max(tth,0.001)
2645	elif 'line2' in itemPicked:
2646	Data['IOtth'][1] = tth
2647	elif 'line3' in itemPicked:
2648	Data['LRazimuth'][0] = int(azm)
2649	elif 'line4' in itemPicked and not Data['fullIntegrate']:
2650	Data['LRazimuth'][1] = int(azm)
2651
2652	Data['LRazimuth'][0] %= 360
2653	Data['LRazimuth'][1] %= 360
2654	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
2655	Data['LRazimuth'][1] += 360
2656	if Data['fullIntegrate']:
2657	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
2658
2659	if Data['IOtth'][0] > Data['IOtth'][1]:
2660	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
2661
2662	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
2663	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
2664	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
2665	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
2666	elif 'Circle' in itemPicked and PickName == 'Masks':
2667	spots = Masks['Points']
2668	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
2669	newPos = np.array([float(newPos[0]),float(newPos[1])])
2670	for spot in spots:
2671	if np.allclose(np.array([spot[:2]]),newPos):
2672	spot[:2] = Xpos,Ypos
2673	G2imG.UpdateMasks(G2frame,Masks)
2674	elif 'Line2D' in itemPicked and PickName == 'Masks':
2675	Obj = G2frame.itemPicked.findobj()
2676	rings = Masks['Rings']
2677	arcs = Masks['Arcs']
2678	polygons = Masks['Polygons']
2679	frame = Masks['Frames']
2680	for ring in G2frame.ringList:
2681	if Obj == ring[0]:
2682	rN = ring[1]
2683	if ring[2] == 'o':
2684	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)-rings[rN][1]/2.
2685	else:
2686	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)+rings[rN][1]/2.
2687	for arc in G2frame.arcList:
2688	if Obj == arc[0]:
2689	aN = arc[1]
2690	if arc[2] == 'o':
2691	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)-arcs[aN][2]/2
2692	elif arc[2] == 'i':
2693	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)+arcs[aN][2]/2
2694	elif arc[2] == 'l':
2695	arcs[aN][1][0] = int(G2img.GetAzm(Xpos,Ypos,Data))
2696	else:
2697	arcs[aN][1][1] = int(G2img.GetAzm(Xpos,Ypos,Data))
2698	for poly in G2frame.polyList: #merging points problem here?
2699	if Obj == poly[0]:
2700	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
2701	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
2702	pN = poly[1]
2703	for i,xy in enumerate(polygons[pN]):
2704	if np.allclose(np.array([xy]),oldPos,atol=1.0):
2705	if event.button == 1:
2706	polygons[pN][i] = Xpos,Ypos
2707	elif event.button == 3:
2708	polygons[pN].insert(i,[Xpos,Ypos])
2709	break
2710	if frame:
2711	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
2712	for i,xy in enumerate(frame):
2713	if np.allclose(np.array([xy]),oldPos,atol=1.0):
2714	if event.button == 1:
2715	frame[i] = Xpos,Ypos
2716	elif event.button == 3:
2717	frame.insert(i,[Xpos,Ypos])
2718	break
2719	G2imG.UpdateMasks(G2frame,Masks)
2720	# else: #keep for future debugging
2721	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
2722	PlotImage(G2frame,newImage=True)
2723	G2frame.itemPicked = None
2724
2725	try:
2726	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2727	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2728	if not newPlot:
2729	Plot = Page.figure.gca() #get previous powder plot & get limits
2730	xylim = Plot.get_xlim(),Plot.get_ylim()
2731	if newImage:
2732	Page.figure.clf()
2733	Plot = Page.figure.gca() #get a fresh plot after clf()
2734	except ValueError:
2735	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
2736	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2737	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2738	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
2739	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
2740	Page.canvas.mpl_connect('pick_event', OnImPick)
2741	Page.canvas.mpl_connect('button_release_event', OnImRelease)
2742	xylim = []
2743	Page.Choice = None
2744	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
2745	Page.SetFocus()
2746	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
2747	G2frame.G2plotNB.status.DestroyChildren()
2748	if G2frame.logPlot:
2749	Title = 'log('+Title+')'
2750	Plot.set_title(Title)
2751	try:
2752	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
2753	Page.Choice = (' key press','l: log(I) on','x: flip x','y: flip y',)
2754	if G2frame.logPlot:
2755	Page.Choice[1] = 'l: log(I) off'
2756	Page.keyPress = OnImPlotKeyPress
2757	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Masks',]:
2758	Page.Choice = (' key press','l: log(I) on','s: spot mask','a: arc mask','r: ring mask',
2759	'p: polygon mask','f: frame mask',)
2760	if G2frame.logPlot:
2761	Page.Choice[1] = 'l: log(I) off'
2762	Page.keyPress = OnImPlotKeyPress
2763	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Stress/Strain',]:
2764	Page.Choice = (' key press','a: add new ring',)
2765	Page.keyPress = OnImPlotKeyPress
2766	except TypeError:
2767	pass
2768	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
2769	if imagefile != G2frame.oldImagefile:
2770	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
2771	if not imagefile:
2772	G2frame.G2plotNB.Delete('2D Powder Image')
2773	return
2774	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
2775	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
2776	G2frame.oldImagefile = imagefile
2777
2778	imScale = 1
2779	if len(G2frame.ImageZ) > 1024:
2780	imScale = len(G2frame.ImageZ)/1024
2781	sizexy = Data['size']
2782	pixelSize = Data['pixelSize']
2783	scalex = 1000./pixelSize[0]
2784	scaley = 1000./pixelSize[1]
2785	Xmax = sizexy[0]*pixelSize[0]/1000.
2786	Ymax = sizexy[1]*pixelSize[1]/1000.
2787	xlim = (0,Xmax)
2788	ylim = (Ymax,0)
2789	Imin,Imax = Data['range'][1]
2790	acolor = mpl.cm.get_cmap(Data['color'])
2791	xcent,ycent = Data['center']
2792	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
2793	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
2794	#do threshold mask - "real" mask - others are just bondaries
2795	Zlim = Masks['Thresholds'][1]
2796	wx.BeginBusyCursor()
2797	try:
2798
2799	if newImage:
2800	Imin,Imax = Data['range'][1]
2801	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]),Zlim[1])
2802	MaskA = ma.getmaskarray(MA)
2803	A = G2img.ImageCompress(MA,imScale)
2804	AM = G2img.ImageCompress(MaskA,imScale)
2805	if G2frame.logPlot:
2806	A = np.where(A>Imin,np.where(A<Imax,A,0),0)
2807	A = np.where(A>0,np.log(A),0)
2808	AM = np.where(AM>0,np.log(AM),0)
2809	Imin,Imax = [np.amin(A),np.amax(A)]
2810	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
2811	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
2812	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
2813	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
2814
2815	Plot.plot(xcent,ycent,'x')
2816	#G2frame.PatternTree.GetItemText(item)
2817	if Data['showLines']:
2818	LRAzim = Data['LRazimuth'] #NB: integers
2819	Nazm = Data['outAzimuths']
2820	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
2821	AzmthOff = Data['azmthOff']
2822	IOtth = Data['IOtth']
2823	wave = Data['wavelength']
2824	dspI = wave/(2.0*sind(IOtth[0]/2.0))
2825	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
2826	dspO = wave/(2.0*sind(IOtth[1]/2.0))
2827	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
2828	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
2829	if ellI:
2830	xyI = []
2831	for azm in Azm:
2832	xy = G2img.GetDetectorXY(dspI,azm,Data)
2833	if np.any(xy):
2834	xyI.append(xy)
2835	if len(xyI):
2836	xyI = np.array(xyI)
2837	arcxI,arcyI = xyI.T
2838	Plot.plot(arcxI,arcyI,picker=3)
2839	if ellO:
2840	xyO = []
2841	for azm in Azm:
2842	xy = G2img.GetDetectorXY(dspO,azm,Data)
2843	if np.any(xy):
2844	xyO.append(xy)
2845	if len(xyO):
2846	xyO = np.array(xyO)
2847	arcxO,arcyO = xyO.T
2848	Plot.plot(arcxO,arcyO,picker=3)
2849	if ellO and ellI:
2850	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
2851	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
2852	for i in range(Nazm):
2853	cake = LRAzim[0]+i*delAzm-AzmthOff
2854	if Data['centerAzm']:
2855	cake += delAzm/2.
2856	ind = np.searchsorted(Azm,cake)
2857	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
2858
2859	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
2860	for xring,yring in Data['ring']:
2861	Plot.plot(xring,yring,'r+',picker=3)
2862	if Data['setRings']:
2863	N = 0
2864	for ring in Data['rings']:
2865	xring,yring = np.array(ring).T[:2]
2866	Plot.plot(xring,yring,'.',color=colors[N%6])
2867	N += 1
2868	for ellipse in Data['ellipses']: #what about hyperbola?
2869	cent,phi,[width,height],col = ellipse
2870	if width > 0: #ellipses
2871	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
2872	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
2873	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
2874	for N,ring in enumerate(StrSta['d-zero']):
2875	xring,yring = ring['ImxyObs']
2876	Plot.plot(xring,yring,colors[N%6]+'.')
2877	#masks - mask lines numbered after integration limit lines
2878	spots = Masks['Points']
2879	rings = Masks['Rings']
2880	arcs = Masks['Arcs']
2881	polygons = Masks['Polygons']
2882	if 'Frames' not in Masks:
2883	Masks['Frames'] = []
2884	frame = Masks['Frames']
2885	for spot in spots:
2886	if spot:
2887	x,y,d = spot
2888	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
2889	G2frame.ringList = []
2890	for iring,ring in enumerate(rings):
2891	if ring:
2892	tth,thick = ring
2893	wave = Data['wavelength']
2894	xy1 = []
2895	xy2 = []
2896	Azm = np.linspace(0,362,181)
2897	for azm in Azm:
2898	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
2899	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
2900	x1,y1 = np.array(xy1).T
2901	x2,y2 = np.array(xy2).T
2902	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
2903	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
2904	G2frame.arcList = []
2905	for iarc,arc in enumerate(arcs):
2906	if arc:
2907	tth,azm,thick = arc
2908	wave = Data['wavelength']
2909	xy1 = []
2910	xy2 = []
2911	aR = azm[0],azm[1],azm[1]-azm[0]
2912	if azm[1]-azm[0] > 180:
2913	aR[2] /= 2
2914	Azm = np.linspace(aR[0],aR[1],aR[2])
2915	for azm in Azm:
2916	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
2917	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
2918	x1,y1 = np.array(xy1).T
2919	x2,y2 = np.array(xy2).T
2920	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
2921	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
2922	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
2923	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
2924	G2frame.polyList = []
2925	for ipoly,polygon in enumerate(polygons):
2926	if polygon:
2927	x,y = np.hsplit(np.array(polygon),2)
2928	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
2929	Plot.plot(x,y,'r')
2930	G2frame.frameList = []
2931	if frame:
2932	x,y = np.hsplit(np.array(frame),2)
2933	G2frame.frameList.append([Plot.plot(x,y,'g+',picker=10),0])
2934	Plot.plot(x,y,'g')
2935	if newImage:
2936	colorBar = Page.figure.colorbar(Img)
2937	Plot.set_xlim(xlim)
2938	Plot.set_ylim(ylim)
2939	if Data['invert_x']:
2940	Plot.invert_xaxis()
2941	if Data['invert_y']:
2942	Plot.invert_yaxis()
2943	if not newPlot and xylim:
2944	Page.toolbar.push_current()
2945	Plot.set_xlim(xylim[0])
2946	Plot.set_ylim(xylim[1])
2947	xylim = []
2948	Page.toolbar.push_current()
2949	Page.toolbar.draw()
2950	else:
2951	Page.canvas.draw()
2952	finally:
2953	wx.EndBusyCursor()
2954
2955	################################################################################
2956	##### PlotIntegration
2957	################################################################################
2958
2959	def PlotIntegration(G2frame,newPlot=False,event=None):
2960	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
2961	'''
2962
2963	def OnMotion(event):
2964	Page.canvas.SetToolTipString('')
2965	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2966	azm = event.ydata
2967	tth = event.xdata
2968	if azm and tth:
2969	G2frame.G2plotNB.status.SetFields(\
2970	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
2971
2972	try:
2973	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2974	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2975	if not newPlot:
2976	Plot = Page.figure.gca() #get previous plot & get limits
2977	xylim = Plot.get_xlim(),Plot.get_ylim()
2978	Page.figure.clf()
2979	Plot = Page.figure.gca() #get a fresh plot after clf()
2980
2981	except ValueError:
2982	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
2983	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
2984	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2985	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2986	Page.views = False
2987	view = False
2988	Page.Choice = None
2989	if not event:
2990	Page.SetFocus()
2991
2992	Data = G2frame.PatternTree.GetItemPyData(
2993	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2994	image = G2frame.Integrate[0]
2995	xsc = G2frame.Integrate[1]
2996	ysc = G2frame.Integrate[2]
2997	Imin,Imax = Data['range'][1]
2998	acolor = mpl.cm.get_cmap(Data['color'])
2999	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3000	Plot.set_ylabel('azimuth',fontsize=12)
3001	Plot.set_xlabel('2-theta',fontsize=12)
3002	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
3003	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
3004	colorBar = Page.figure.colorbar(Img)
3005	# if Data['ellipses']:
3006	# for ellipse in Data['ellipses']:
3007	# x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3008	# tth,azm = G2img.GetTthAzm(x,y,Data)
3009	## azm = np.where(azm < 0.,azm+360,azm)
3010	# Plot.plot(tth,azm,'b,')
3011	if not newPlot:
3012	Page.toolbar.push_current()
3013	Plot.set_xlim(xylim[0])
3014	Plot.set_ylim(xylim[1])
3015	xylim = []
3016	Page.toolbar.push_current()
3017	Page.toolbar.draw()
3018	else:
3019	Page.canvas.draw()
3020
3021	################################################################################
3022	##### PlotTRImage
3023	################################################################################
3024
3025	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
3026	'''a test plot routine - not normally used
3027	'''
3028
3029	def OnMotion(event):
3030	Page.canvas.SetToolTipString('')
3031	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3032	azm = event.xdata
3033	tth = event.ydata
3034	if azm and tth:
3035	G2frame.G2plotNB.status.SetFields(\
3036	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3037
3038	try:
3039	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3040	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3041	if not newPlot:
3042	Plot = Page.figure.gca() #get previous plot & get limits
3043	xylim = Plot.get_xlim(),Plot.get_ylim()
3044	Page.figure.clf()
3045	Plot = Page.figure.gca() #get a fresh plot after clf()
3046
3047	except ValueError:
3048	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
3049	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3050	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3051	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3052	Page.views = False
3053	view = False
3054	Page.Choice = None
3055	Page.SetFocus()
3056
3057	Data = G2frame.PatternTree.GetItemPyData(
3058	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3059	Imin,Imax = Data['range'][1]
3060	step = (Imax-Imin)/5.
3061	V = np.arange(Imin,Imax,step)
3062	acolor = mpl.cm.get_cmap(Data['color'])
3063	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3064	Plot.set_xlabel('azimuth',fontsize=12)
3065	Plot.set_ylabel('2-theta',fontsize=12)
3066	Plot.contour(tax,tay,taz,V,cmap=acolor)
3067	if Data['showLines']:
3068	IOtth = Data['IOtth']
3069	if Data['fullIntegrate']:
3070	LRAzim = [-180,180]
3071	else:
3072	LRAzim = Data['LRazimuth'] #NB: integers
3073	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
3074	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
3075	if not Data['fullIntegrate']:
3076	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
3077	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
3078	if Data['setRings']:
3079	rings = np.concatenate((Data['rings']),axis=0)
3080	for xring,yring,dsp in rings:
3081	x,y = G2img.GetTthAzm(xring,yring,Data)
3082	Plot.plot(y,x,'r+')
3083	if Data['ellipses']:
3084	for ellipse in Data['ellipses']:
3085	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3086	x,y = np.hsplit(ring,2)
3087	tth,azm = G2img.GetTthAzm(x,y,Data)
3088	Plot.plot(azm,tth,'b,')
3089	if not newPlot:
3090	Page.toolbar.push_current()
3091	Plot.set_xlim(xylim[0])
3092	Plot.set_ylim(xylim[1])
3093	xylim = []
3094	Page.toolbar.push_current()
3095	Page.toolbar.draw()
3096	else:
3097	Page.canvas.draw()
3098
3099	################################################################################
3100	##### PlotStructure
3101	################################################################################
3102
3103	def PlotStructure(G2frame,data):
3104	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
3105	thermal motion ellipsoids and polyhedra
3106	'''
3107
3108	def FindPeaksBonds(XYZ):
3109	rFact = data['Drawing']['radiusFactor']
3110	Bonds = [[] for x in XYZ]
3111	for i,xyz in enumerate(XYZ):
3112	Dx = XYZ-xyz
3113	dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
3114	IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2))
3115	for j in IndB[0]:
3116	Bonds[i].append(Dx[j]/2.)
3117	Bonds[j].append(-Dx[j]/2.)
3118	return Bonds
3119
3120	ForthirdPI = 4.0*math.pi/3.0
3121	generalData = data['General']
3122	cell = generalData['Cell'][1:7]
3123	Vol = generalData['Cell'][7:8][0]
3124	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
3125	Gmat,gmat = G2lat.cell2Gmat(cell)
3126	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3127	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3128	SGData = generalData['SGData']
3129	Mydir = generalData['Mydir']
3130	atomData = data['Atoms']
3131	mapPeaks = []
3132	drawingData = data['Drawing']
3133	if 'Map Peaks' in data:
3134	mapPeaks = np.array(data['Map Peaks'])
3135	peakMax = 100.
3136	if len(mapPeaks):
3137	peakMax = np.max(mapPeaks.T[0])
3138	resRBData = data['RBModels'].get('Residue',[])
3139	vecRBData = data['RBModels'].get('Vector',[])
3140	rbAtmDict = {}
3141	for rbObj in resRBData+vecRBData:
3142	exclList = ['X' for i in range(len(rbObj['Ids']))]
3143	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
3144	testRBObj = data.get('testRBObj',{})
3145	rbObj = testRBObj.get('rbObj',{})
3146	MCSA = data.get('MCSA',{})
3147	mcsaModels = MCSA.get('Models',[])
3148	if mcsaModels:
3149	XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA)
3150	mcsaXYZ = []
3151	mcsaTypes = []
3152	for xyz,atyp in zip(XYZs,Types):
3153	for item in G2spc.GenAtom(xyz,SGData):
3154	mcsaXYZ.append(item[0])
3155	mcsaTypes.append(atyp)
3156	mcsaBonds = FindPeaksBonds(mcsaXYZ)
3157	drawAtoms = drawingData.get('Atoms',[])
3158	mapData = {}
3159	flipData = {}
3160	rhoXYZ = []
3161	showBonds = False
3162	if 'Map' in generalData:
3163	mapData = generalData['Map']
3164	showBonds = mapData.get('Show bonds',False)
3165	if 'Flip' in generalData:
3166	flipData = generalData['Flip']
3167	flipData['mapRoll'] = [0,0,0]
3168	Wt = np.array([255,255,255])
3169	Rd = np.array([255,0,0])
3170	Gr = np.array([0,255,0])
3171	wxGreen = wx.Color(0,255,0)
3172	Bl = np.array([0,0,255])
3173	Or = np.array([255,128,0])
3174	wxOrange = wx.Color(255,128,0)
3175	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]])
3176	uEdges = np.array([
3177	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
3178	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
3179	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
3180	mD = 0.1
3181	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
3182	mapPeakVecs = np.inner(mV,Bmat)
3183
3184	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
3185	altDown = False
3186	shiftDown = False
3187	ctrlDown = False
3188
3189	def OnKeyBox(event):
3190	import Image
3191	# Draw() #make sure plot is fresh!!
3192	mode = cb.GetValue()
3193	if mode in ['jpeg','bmp','tiff',]:
3194	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
3195	size = Page.canvas.GetSize()
3196	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
3197	if mode in ['jpeg',]:
3198	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
3199	im = Image.new("RGBA", (size[0],size[1]))
3200	else:
3201	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
3202	im = Image.new("RGB", (size[0],size[1]))
3203	im.fromstring(Pix)
3204	im.save(Fname,mode)
3205	cb.SetValue(' save as/key:')
3206	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
3207	else:
3208	event.key = cb.GetValue()[0]
3209	cb.SetValue(' save as/key:')
3210	wx.CallAfter(OnKey,event)
3211	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
3212
3213	def OnKey(event): #on key UP!!
3214	# Draw() #make sure plot is fresh!!
3215	try:
3216	keyCode = event.GetKeyCode()
3217	if keyCode > 255:
3218	keyCode = 0
3219	key = chr(keyCode)
3220	except AttributeError: #if from OnKeyBox above
3221	key = str(event.key).upper()
3222	indx = drawingData['selectedAtoms']
3223	cx,ct = drawingData['atomPtrs'][:2]
3224	if key in ['C']:
3225	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
3226	drawingData['viewDir'] = [0,0,1]
3227	drawingData['oldxy'] = []
3228	V0 = np.array([0,0,1])
3229	V = np.inner(Amat,V0)
3230	V /= np.sqrt(np.sum(V**2))
3231	A = np.arccos(np.sum(V*V0))
3232	Q = G2mth.AV2Q(A,[0,1,0])
3233	drawingData['Quaternion'] = Q
3234	SetViewPointText(drawingData['viewPoint'][0])
3235	SetViewDirText(drawingData['viewDir'])
3236	Q = drawingData['Quaternion']
3237	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3238	elif key in ['N']:
3239	drawAtoms = drawingData['Atoms']
3240	if not len(drawAtoms): #no atoms
3241	return
3242	pI = drawingData['viewPoint'][1]
3243	if not len(pI):
3244	pI = [0,0]
3245	if indx:
3246	pI[0] = indx[pI[1]]
3247	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3248	pI[1] += 1
3249	if pI[1] >= len(indx):
3250	pI[1] = 0
3251	else:
3252	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3253	pI[0] += 1
3254	if pI[0] >= len(drawAtoms):
3255	pI[0] = 0
3256	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
3257	SetViewPointText(drawingData['viewPoint'][0])
3258	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
3259
3260	elif key in ['P']:
3261	drawAtoms = drawingData['Atoms']
3262	if not len(drawAtoms): #no atoms
3263	return
3264	pI = drawingData['viewPoint'][1]
3265	if not len(pI):
3266	pI = [0,0]
3267	if indx:
3268	pI[0] = indx[pI[1]]
3269	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3270	pI[1] -= 1
3271	if pI[1] < 0:
3272	pI[1] = len(indx)-1
3273	else:
3274	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3275	pI[0] -= 1
3276	if pI[0] < 0:
3277	pI[0] = len(drawAtoms)-1
3278	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
3279	SetViewPointText(drawingData['viewPoint'][0])
3280	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
3281	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
3282	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
3283	SetMapRoll(dirDict[key])
3284	SetPeakRoll(dirDict[key])
3285	SetMapPeaksText(mapPeaks)
3286	Draw('key')
3287
3288	def GetTruePosition(xy,Add=False):
3289	View = glGetIntegerv(GL_VIEWPORT)
3290	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
3291	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
3292	Zmax = 1.
3293	if Add:
3294	Indx = GetSelectedAtoms()
3295	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
3296	for i,peak in enumerate(mapPeaks):
3297	x,y,z = peak[1:4]
3298	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
3299	XY = [int(X),int(View[3]-Y)]
3300	if np.allclose(xy,XY,atol=10) and Z < Zmax:
3301	Zmax = Z
3302	try:
3303	Indx.remove(i)
3304	ClearSelectedAtoms()
3305	for id in Indx:
3306	SetSelectedAtoms(id,Add)
3307	except:
3308	SetSelectedAtoms(i,Add)
3309	else:
3310	cx = drawingData['atomPtrs'][0]
3311	for i,atom in enumerate(drawAtoms):
3312	x,y,z = atom[cx:cx+3]
3313	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
3314	XY = [int(X),int(View[3]-Y)]
3315	if np.allclose(xy,XY,atol=10) and Z < Zmax:
3316	Zmax = Z
3317	try:
3318	Indx.remove(i)
3319	ClearSelectedAtoms()
3320	for id in Indx:
3321	SetSelectedAtoms(id,Add)
3322	except:
3323	SetSelectedAtoms(i,Add)
3324
3325	def OnMouseDown(event):
3326	xy = event.GetPosition()
3327	if event.ShiftDown():
3328	if event.LeftIsDown():
3329	GetTruePosition(xy)
3330	elif event.RightIsDown():
3331	GetTruePosition(xy,True)
3332	else:
3333	drawingData['oldxy'] = list(xy)
3334
3335	def OnMouseMove(event):
3336	if event.ShiftDown(): #don't want any inadvertant moves when picking
3337	return
3338	newxy = event.GetPosition()
3339
3340	if event.Dragging():
3341	if event.AltDown() and rbObj:
3342	if event.LeftIsDown():
3343	SetRBRotation(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	elif event.RightIsDown():
3347	SetRBTranslation(newxy)
3348	Tx,Ty,Tz = rbObj['Orig'][0]
3349	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
3350	elif event.MiddleIsDown():
3351	SetRBRotationZ(newxy)
3352	Q = rbObj['Orient'][0]
3353	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3354	Draw('move')
3355	elif not event.ControlDown():
3356	if event.LeftIsDown():
3357	SetRotation(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	elif event.RightIsDown():
3361	SetTranslation(newxy)
3362	Tx,Ty,Tz = drawingData['viewPoint'][0]
3363	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
3364	elif event.MiddleIsDown():
3365	SetRotationZ(newxy)
3366	Q = drawingData['Quaternion']
3367	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3368	Draw('move')
3369
3370
3371	def OnMouseWheel(event):
3372	if event.ShiftDown():
3373	return
3374	drawingData['cameraPos'] += event.GetWheelRotation()/24.
3375	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
3376	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
3377	page = getSelection()
3378	if page:
3379	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3380	G2frame.dataDisplay.cameraPosTxt.SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
3381	G2frame.dataDisplay.cameraSlider.SetValue(drawingData['cameraPos'])
3382	Draw('wheel')
3383
3384	def getSelection():
3385	try:
3386	return G2frame.dataDisplay.GetSelection()
3387	except AttributeError:
3388	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!')
3389	return 0
3390
3391	def SetViewPointText(VP):
3392	page = getSelection()
3393	if page:
3394	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3395	G2frame.dataDisplay.viewPoint.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
3396
3397	def SetRBOrigText():
3398	page = getSelection()
3399	if page:
3400	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
3401	for i,sizer in enumerate(testRBObj['Sizers']['Xsizers']):
3402	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orig'][0][i]))
3403
3404	def SetRBOrienText():
3405	page = getSelection()
3406	if page:
3407	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
3408	for i,sizer in enumerate(testRBObj['Sizers']['Osizers']):
3409	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orient'][0][i]))
3410
3411	def SetViewDirText(VD):
3412	page = getSelection()
3413	if page:
3414	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3415	G2frame.dataDisplay.viewDir.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
3416
3417	def SetMapPeaksText(mapPeaks):
3418	page = getSelection()
3419	if page:
3420	if G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3421	G2frame.MapPeaksTable.SetData(mapPeaks)
3422	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
3423	names = [child.GetName() for child in panel]
3424	panel[names.index('grid window')].Refresh()
3425
3426	def ClearSelectedAtoms():
3427	page = getSelection()
3428	if page:
3429	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3430	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
3431	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3432	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
3433	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3434	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
3435
3436
3437	def SetSelectedAtoms(ind,Add=False):
3438	page = getSelection()
3439	if page:
3440	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3441	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
3442	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3443	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add)
3444	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3445	Id = drawAtoms[ind][-3]
3446	for i,atom in enumerate(atomData):
3447	if atom[-1] == Id:
3448	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
3449
3450	def GetSelectedAtoms():
3451	page = getSelection()
3452	Ind = []
3453	if page:
3454	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3455	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
3456	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3457	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows()
3458	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3459	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
3460	return Ind
3461
3462	def SetBackground():
3463	R,G,B,A = Page.camera['backColor']
3464	glClearColor(R,G,B,A)
3465	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
3466
3467	def SetLights():
3468	glEnable(GL_DEPTH_TEST)
3469	glShadeModel(GL_SMOOTH)
3470	glEnable(GL_LIGHTING)
3471	glEnable(GL_LIGHT0)
3472	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
3473	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
3474	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
3475
3476	def GetRoll(newxy,rho):
3477	Q = drawingData['Quaternion']
3478	dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,]))
3479	dxy = np.array(dxy*rho.shape)
3480	roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0))
3481	return roll
3482
3483	def SetMapRoll(newxy):
3484	rho = mapData['rho']
3485	roll = GetRoll(newxy,rho)
3486	mapData['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
3487	drawingData['oldxy'] = list(newxy)
3488
3489	def SetPeakRoll(newxy):
3490	rho = mapData['rho']
3491	roll = GetRoll(newxy,rho)
3492	steps = 1./np.array(rho.shape)
3493	dxy = roll*steps
3494	for peak in mapPeaks:
3495	peak[1:4] += dxy
3496	peak[1:4] %= 1.
3497	peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2))
3498
3499	def SetTranslation(newxy):
3500	#first get translation vector in screen coords.
3501	oldxy = drawingData['oldxy']
3502	if not len(oldxy): oldxy = list(newxy)
3503	dxy = newxy-oldxy
3504	drawingData['oldxy'] = list(newxy)
3505	V = np.array([-dxy[0],dxy[1],0.])
3506	#then transform to rotated crystal coordinates & apply to view point
3507	Q = drawingData['Quaternion']
3508	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
3509	Tx,Ty,Tz = drawingData['viewPoint'][0]
3510	Tx += V[0]*0.01
3511	Ty += V[1]*0.01
3512	Tz += V[2]*0.01
3513	drawingData['viewPoint'][0] = Tx,Ty,Tz
3514	SetViewPointText([Tx,Ty,Tz])
3515
3516	def SetRBTranslation(newxy):
3517	#first get translation vector in screen coords.
3518	oldxy = drawingData['oldxy']
3519	if not len(oldxy): oldxy = list(newxy)
3520	dxy = newxy-oldxy
3521	drawingData['oldxy'] = list(newxy)
3522	V = np.array([-dxy[0],dxy[1],0.])
3523	#then transform to rotated crystal coordinates & apply to RB origin
3524	Q = drawingData['Quaternion']
3525	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
3526	Tx,Ty,Tz = rbObj['Orig'][0]
3527	Tx -= V[0]*0.01
3528	Ty -= V[1]*0.01
3529	Tz -= V[2]*0.01
3530	rbObj['Orig'][0] = Tx,Ty,Tz
3531	SetRBOrigText()
3532
3533	def SetRotation(newxy):
3534	#first get rotation vector in screen coords. & angle increment
3535	oldxy = drawingData['oldxy']
3536	if not len(oldxy): oldxy = list(newxy)
3537	dxy = newxy-oldxy
3538	drawingData['oldxy'] = list(newxy)
3539	V = np.array([dxy[1],dxy[0],0.])
3540	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
3541	# next transform vector back to xtal coordinates via inverse quaternion
3542	# & make new quaternion
3543	Q = drawingData['Quaternion']
3544	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
3545	DQ = G2mth.AVdeg2Q(A,V)
3546	Q = G2mth.prodQQ(Q,DQ)
3547	drawingData['Quaternion'] = Q
3548	# finally get new view vector - last row of rotation matrix
3549	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
3550	VD /= np.sqrt(np.sum(VD**2))
3551	drawingData['viewDir'] = VD
3552	SetViewDirText(VD)
3553
3554	def SetRotationZ(newxy):
3555	#first get rotation vector (= view vector) in screen coords. & angle increment
3556	View = glGetIntegerv(GL_VIEWPORT)
3557	cent = [View[2]/2,View[3]/2]
3558	oldxy = drawingData['oldxy']
3559	if not len(oldxy): oldxy = list(newxy)
3560	dxy = newxy-oldxy
3561	drawingData['oldxy'] = list(newxy)
3562	V = drawingData['viewDir']
3563	A = [0,0]
3564	A[0] = dxy[1]*.25
3565	A[1] = dxy[0]*.25
3566	if newxy[0] > cent[0]:
3567	A[0] *= -1
3568	if newxy[1] < cent[1]:
3569	A[1] *= -1
3570	# next transform vector back to xtal coordinates & make new quaternion
3571	Q = drawingData['Quaternion']
3572	V = np.inner(Amat,V)
3573	Qx = G2mth.AVdeg2Q(A[0],V)
3574	Qy = G2mth.AVdeg2Q(A[1],V)
3575	Q = G2mth.prodQQ(Q,Qx)
3576	Q = G2mth.prodQQ(Q,Qy)
3577	drawingData['Quaternion'] = Q
3578
3579	def SetRBRotation(newxy):
3580	#first get rotation vector in screen coords. & angle increment
3581	oldxy = drawingData['oldxy']
3582	if not len(oldxy): oldxy = list(newxy)
3583	dxy = newxy-oldxy
3584	drawingData['oldxy'] = list(newxy)
3585	V = np.array([dxy[1],dxy[0],0.])
3586	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
3587	# next transform vector back to xtal coordinates via inverse quaternion
3588	# & make new quaternion
3589	Q = rbObj['Orient'][0] #rotate RB to Cart
3590	QC = drawingData['Quaternion'] #rotate Cart to drawing
3591	V = G2mth.prodQVQ(G2mth.invQ(QC),V)
3592	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
3593	DQ = G2mth.AVdeg2Q(A,V)
3594	Q = G2mth.prodQQ(Q,DQ)
3595	rbObj['Orient'][0] = Q
3596	SetRBOrienText()
3597
3598	def SetRBRotationZ(newxy):
3599	#first get rotation vector (= view vector) in screen coords. & angle increment
3600	View = glGetIntegerv(GL_VIEWPORT)
3601	cent = [View[2]/2,View[3]/2]
3602	oldxy = drawingData['oldxy']
3603	if not len(oldxy): oldxy = list(newxy)
3604	dxy = newxy-oldxy
3605	drawingData['oldxy'] = list(newxy)
3606	V = drawingData['viewDir']
3607	A = [0,0]
3608	A[0] = dxy[1]*.25
3609	A[1] = dxy[0]*.25
3610	if newxy[0] < cent[0]:
3611	A[0] *= -1
3612	if newxy[1] > cent[1]:
3613	A[1] *= -1
3614	# next transform vector back to RB coordinates & make new quaternion
3615	Q = rbObj['Orient'][0] #rotate RB to cart
3616	V = np.inner(Amat,V)
3617	V = -G2mth.prodQVQ(G2mth.invQ(Q),V)
3618	Qx = G2mth.AVdeg2Q(A[0],V)
3619	Qy = G2mth.AVdeg2Q(A[1],V)
3620	Q = G2mth.prodQQ(Q,Qx)
3621	Q = G2mth.prodQQ(Q,Qy)
3622	rbObj['Orient'][0] = Q
3623	SetRBOrienText()
3624
3625	def RenderBox():
3626	glEnable(GL_COLOR_MATERIAL)
3627	glLineWidth(2)
3628	glEnable(GL_BLEND)
3629	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
3630	glEnable(GL_LINE_SMOOTH)
3631	glBegin(GL_LINES)
3632	for line,color in zip(uEdges,uColors):
3633	glColor3ubv(color)
3634	glVertex3fv(line[0])
3635	glVertex3fv(line[1])
3636	glEnd()
3637	glColor4ubv([0,0,0,0])
3638	glDisable(GL_LINE_SMOOTH)
3639	glDisable(GL_BLEND)
3640	glDisable(GL_COLOR_MATERIAL)
3641
3642	def RenderUnitVectors(x,y,z):
3643	xyz = np.array([x,y,z])
3644	glEnable(GL_COLOR_MATERIAL)
3645	glLineWidth(1)
3646	glPushMatrix()
3647	glTranslate(x,y,z)
3648	glScalef(1/cell[0],1/cell[1],1/cell[2])
3649	glBegin(GL_LINES)
3650	for line,color in zip(uEdges,uColors)[:3]:
3651	glColor3ubv(color)
3652	glVertex3fv(-line[1]/2.)
3653	glVertex3fv(line[1]/2.)
3654	glEnd()
3655	glPopMatrix()
3656	glColor4ubv([0,0,0,0])
3657	glDisable(GL_COLOR_MATERIAL)
3658
3659	def RenderSphere(x,y,z,radius,color):
3660	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3661	glPushMatrix()
3662	glTranslate(x,y,z)
3663	glMultMatrixf(B4mat.T)
3664	q = gluNewQuadric()
3665	gluSphere(q,radius,20,10)
3666	glPopMatrix()
3667
3668	def RenderDots(XYZ,RC):
3669	glEnable(GL_COLOR_MATERIAL)
3670	XYZ = np.array(XYZ)
3671	glPushMatrix()
3672	for xyz,rc in zip(XYZ,RC):
3673	x,y,z = xyz
3674	r,c = rc
3675	glColor3ubv(c)
3676	glPointSize(r*50)
3677	glBegin(GL_POINTS)
3678	glVertex3fv(xyz)
3679	glEnd()
3680	glPopMatrix()
3681	glColor4ubv([0,0,0,0])
3682	glDisable(GL_COLOR_MATERIAL)
3683
3684	def RenderSmallSphere(x,y,z,radius,color):
3685	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3686	glPushMatrix()
3687	glTranslate(x,y,z)
3688	glMultMatrixf(B4mat.T)
3689	q = gluNewQuadric()
3690	gluSphere(q,radius,4,2)
3691	glPopMatrix()
3692
3693	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
3694	s1,s2,s3 = E
3695	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3696	glPushMatrix()
3697	glTranslate(x,y,z)
3698	glMultMatrixf(B4mat.T)
3699	glMultMatrixf(R4.T)
3700	glEnable(GL_NORMALIZE)
3701	glScale(s1,s2,s3)
3702	q = gluNewQuadric()
3703	gluSphere(q,ellipseProb,20,10)
3704	glDisable(GL_NORMALIZE)
3705	glPopMatrix()
3706
3707	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
3708	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3709	glPushMatrix()
3710	glTranslate(x,y,z)
3711	glMultMatrixf(B4mat.T)
3712	for bond in Bonds:
3713	glPushMatrix()
3714	Dx = np.inner(Amat,bond)
3715	Z = np.sqrt(np.sum(Dx**2))
3716	if Z:
3717	azm = atan2d(-Dx[1],-Dx[0])
3718	phi = acosd(Dx[2]/Z)
3719	glRotate(-azm,0,0,1)
3720	glRotate(phi,1,0,0)
3721	q = gluNewQuadric()
3722	gluCylinder(q,radius,radius,Z,slice,2)
3723	glPopMatrix()
3724	glPopMatrix()
3725
3726	def RenderLines(x,y,z,Bonds,color):
3727	glShadeModel(GL_FLAT)
3728	xyz = np.array([x,y,z])
3729	glEnable(GL_COLOR_MATERIAL)
3730	glLineWidth(1)
3731	glColor3fv(color)
3732	glPushMatrix()
3733	glBegin(GL_LINES)
3734	for bond in Bonds:
3735	glVertex3fv(xyz)
3736	glVertex3fv(xyz+bond)
3737	glEnd()
3738	glColor4ubv([0,0,0,0])
3739	glPopMatrix()
3740	glDisable(GL_COLOR_MATERIAL)
3741	glShadeModel(GL_SMOOTH)
3742
3743	def RenderPolyhedra(x,y,z,Faces,color):
3744	glShadeModel(GL_FLAT)
3745	glPushMatrix()
3746	glTranslate(x,y,z)
3747	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3748	glShadeModel(GL_SMOOTH)
3749	glMultMatrixf(B4mat.T)
3750	for face,norm in Faces:
3751	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
3752	glFrontFace(GL_CW)
3753	glNormal3fv(norm)
3754	glBegin(GL_TRIANGLES)
3755	for vert in face:
3756	glVertex3fv(vert)
3757	glEnd()
3758	glPopMatrix()
3759	glShadeModel(GL_SMOOTH)
3760
3761	def RenderMapPeak(x,y,z,color,den):
3762	glShadeModel(GL_FLAT)
3763	xyz = np.array([x,y,z])
3764	glEnable(GL_COLOR_MATERIAL)
3765	glLineWidth(3)
3766	glColor3fv(color*den/255)
3767	glPushMatrix()
3768	glBegin(GL_LINES)
3769	for vec in mapPeakVecs:
3770	glVertex3fv(vec[0]+xyz)
3771	glVertex3fv(vec[1]+xyz)
3772	glEnd()
3773	glColor4ubv([0,0,0,0])
3774	glPopMatrix()
3775	glDisable(GL_COLOR_MATERIAL)
3776	glShadeModel(GL_SMOOTH)
3777
3778	def RenderBackbone(Backbone,BackboneColor,radius):
3779	glPushMatrix()
3780	glMultMatrixf(B4mat.T)
3781	glEnable(GL_COLOR_MATERIAL)
3782	glShadeModel(GL_SMOOTH)
3783	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
3784	glePolyCylinder(Backbone,BackboneColor,radius)
3785	glPopMatrix()
3786	glDisable(GL_COLOR_MATERIAL)
3787
3788	def RenderLabel(x,y,z,label,r,color,matRot):
3789	'''
3790	color wx.Color object
3791	'''
3792	glPushMatrix()
3793	glTranslate(x,y,z)
3794	glMultMatrixf(B4mat.T)
3795	glDisable(GL_LIGHTING)
3796	glRasterPos3f(0,0,0)
3797	glMultMatrixf(matRot)
3798	glRotate(180,1,0,0) #fix to flip about x-axis
3799	text = gltext.Text(text=label,font=Font,foreground=color)
3800	text.draw_text(scale=0.025)
3801	glEnable(GL_LIGHTING)
3802	glPopMatrix()
3803
3804	def RenderMap(rho,rhoXYZ,indx,Rok):
3805	glShadeModel(GL_FLAT)
3806	cLevel = drawingData['contourLevel']
3807	XYZ = []
3808	RC = []
3809	for i,xyz in enumerate(rhoXYZ):
3810	if not Rok[i]:
3811	x,y,z = xyz
3812	I,J,K = indx[i]
3813	alpha = 1.0
3814	if cLevel < 1.:
3815	alpha = (abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)
3816	if rho[I,J,K] < 0.:
3817	XYZ.append(xyz)
3818	RC.append([0.1*alpha,Rd])
3819	else:
3820	XYZ.append(xyz)
3821	RC.append([0.1*alpha,Gr])
3822	RenderDots(XYZ,RC)
3823	glShadeModel(GL_SMOOTH)
3824
3825	def Draw(caller=''):
3826	#useful debug?
3827	# if caller:
3828	# print caller
3829	# end of useful debug
3830	mapData = generalData['Map']
3831	pageName = ''
3832	page = getSelection()
3833	if page:
3834	pageName = G2frame.dataDisplay.GetPageText(page)
3835	rhoXYZ = []
3836	if len(mapData['rho']):
3837	VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
3838	contLevel = drawingData['contourLevel']*mapData['rhoMax']
3839	if 'delt-F' in mapData['MapType']:
3840	rho = ma.array(mapData['rho'],mask=(np.abs(mapData['rho'])<contLevel))
3841	else:
3842	rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
3843	steps = 1./np.array(rho.shape)
3844	incre = np.where(VP>=0,VP%steps,VP%steps-steps)
3845	Vsteps = -np.array(VP/steps,dtype='i')
3846	rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
3847	indx = np.array(ma.nonzero(rho)).T
3848	rhoXYZ = indx*steps+VP-incre
3849	Nc = len(rhoXYZ)
3850	rcube = 2000.Vol/(ForthirdPINc)
3851	rmax = math.exp(math.log(rcube)/3.)**2
3852	radius = min(drawingData['mapSize']**2,rmax)
3853	view = np.array(drawingData['viewPoint'][0])
3854	Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
3855	Ind = GetSelectedAtoms()
3856	VS = np.array(Page.canvas.GetSize())
3857	aspect = float(VS[0])/float(VS[1])
3858	cPos = drawingData['cameraPos']
3859	Zclip = drawingData['Zclip']*cPos/200.
3860	Q = drawingData['Quaternion']
3861	Tx,Ty,Tz = drawingData['viewPoint'][0]
3862	cx,ct,cs,ci = drawingData['atomPtrs']
3863	bondR = drawingData['bondRadius']
3864	G,g = G2lat.cell2Gmat(cell)
3865	GS = G
3866	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
3867	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
3868	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
3869	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
3870
3871	SetBackground()
3872	glInitNames()
3873	glPushName(0)
3874
3875	glMatrixMode(GL_PROJECTION)
3876	glLoadIdentity()
3877	glViewport(0,0,VS[0],VS[1])
3878	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
3879	gluLookAt(0,0,cPos,0,0,0,0,1,0)
3880	SetLights()
3881
3882	glMatrixMode(GL_MODELVIEW)
3883	glLoadIdentity()
3884	matRot = G2mth.Q2Mat(Q)
3885	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3886	glMultMatrixf(matRot.T)
3887	glMultMatrixf(A4mat.T)
3888	glTranslate(-Tx,-Ty,-Tz)
3889	if drawingData['unitCellBox']:
3890	RenderBox()
3891	if drawingData['showABC']:
3892	x,y,z = drawingData['viewPoint'][0]
3893	RenderUnitVectors(x,y,z)
3894	Backbones = {}
3895	BackboneColor = []
3896	time0 = time.time()
3897	# glEnable(GL_BLEND)
3898	# glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
3899	for iat,atom in enumerate(drawingData['Atoms']):
3900	x,y,z = atom[cx:cx+3]
3901	Bonds = atom[-2]
3902	Faces = atom[-1]
3903	try:
3904	atNum = generalData['AtomTypes'].index(atom[ct])
3905	except ValueError:
3906	atNum = -1
3907	CL = atom[cs+2]
3908	atColor = np.array(CL)/255.
3909	if drawingData['showRigidBodies'] and atom[ci] in rbAtmDict:
3910	bndColor = Or
3911	else:
3912	bndColor = atColor
3913	if iat in Ind and G2frame.dataDisplay.GetPageText(getSelection()) != 'Map peaks':
3914	atColor = np.array(Gr)/255.
3915	# color += [.25,]
3916	radius = 0.5
3917	if atom[cs] != '':
3918	try:
3919	glLoadName(atom[-3])
3920	except: #problem with old files - missing code
3921	pass
3922	if 'balls' in atom[cs]:
3923	vdwScale = drawingData['vdwScale']
3924	ballScale = drawingData['ballScale']
3925	if atNum < 0:
3926	radius = 0.2
3927	elif 'H' == atom[ct]:
3928	if drawingData['showHydrogen']:
3929	if 'vdW' in atom[cs] and atNum >= 0:
3930	radius = vdwScale*generalData['vdWRadii'][atNum]
3931	else:
3932	radius = ballScale*drawingData['sizeH']
3933	else:
3934	radius = 0.0
3935	else:
3936	if 'vdW' in atom[cs]:
3937	radius = vdwScale*generalData['vdWRadii'][atNum]
3938	else:
3939	radius = ballScale*generalData['BondRadii'][atNum]
3940	RenderSphere(x,y,z,radius,atColor)
3941	if 'sticks' in atom[cs]:
3942	RenderBonds(x,y,z,Bonds,bondR,bndColor)
3943	elif 'ellipsoids' in atom[cs]:
3944	RenderBonds(x,y,z,Bonds,bondR,bndColor)
3945	if atom[cs+3] == 'A':
3946	Uij = atom[cs+5:cs+11]
3947	U = np.multiply(G2spc.Uij2U(Uij),GS)
3948	U = np.inner(Amat,np.inner(U,Amat).T)
3949	E,R = nl.eigh(U)
3950	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3951	E = np.sqrt(E)
3952	if atom[ct] == 'H' and not drawingData['showHydrogen']:
3953	pass
3954	else:
3955	RenderEllipsoid(x,y,z,ellipseProb,E,R4,atColor)
3956	else:
3957	if atom[ct] == 'H' and not drawingData['showHydrogen']:
3958	pass
3959	else:
3960	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
3961	RenderSphere(x,y,z,radius,atColor)
3962	elif 'lines' in atom[cs]:
3963	radius = 0.1
3964	RenderLines(x,y,z,Bonds,bndColor)
3965	# RenderBonds(x,y,z,Bonds,0.05,color,6)
3966	elif atom[cs] == 'sticks':
3967	radius = 0.1
3968	RenderBonds(x,y,z,Bonds,bondR,bndColor)
3969	elif atom[cs] == 'polyhedra':
3970	RenderPolyhedra(x,y,z,Faces,atColor)
3971	elif atom[cs] == 'backbone':
3972	if atom[ct-1].split()[0] in ['C','N']:
3973	if atom[2] not in Backbones:
3974	Backbones[atom[2]] = []
3975	Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
3976	BackboneColor.append(list(atColor))
3977
3978	if atom[cs+1] == 'type':
3979	RenderLabel(x,y,z,' '+atom[ct],radius,wxGreen,matRot)
3980	elif atom[cs+1] == 'name':
3981	RenderLabel(x,y,z,' '+atom[ct-1],radius,wxGreen,matRot)
3982	elif atom[cs+1] == 'number':
3983	RenderLabel(x,y,z,' '+str(iat),radius,wxGreen,matRot)
3984	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
3985	RenderLabel(x,y,z,' '+atom[ct-4],radius,wxGreen,matRot)
3986	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
3987	RenderLabel(x,y,z,' '+atom[ct-3],radius,wxGreen,matRot)
3988	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
3989	RenderLabel(x,y,z,' '+atom[ct-2],radius,wxGreen,matRot)
3990	# glDisable(GL_BLEND)
3991	if len(rhoXYZ):
3992	RenderMap(rho,rhoXYZ,indx,Rok)
3993	if len(mapPeaks):
3994	XYZ = mapPeaks.T[1:4].T
3995	mapBonds = FindPeaksBonds(XYZ)
3996	for ind,[mag,x,y,z,d] in enumerate(mapPeaks):
3997	if ind in Ind and pageName == 'Map peaks':
3998	RenderMapPeak(x,y,z,Gr,1.0)
3999	else:
4000	RenderMapPeak(x,y,z,Wt,mag/peakMax)
4001	if showBonds:
4002	RenderLines(x,y,z,mapBonds[ind],Wt)
4003	if len(testRBObj) and pageName == 'RB Models':
4004	XYZ = G2mth.UpdateRBXYZ(Bmat,testRBObj['rbObj'],testRBObj['rbData'],testRBObj['rbType'])[0]
4005	rbBonds = FindPeaksBonds(XYZ)
4006	for ind,[x,y,z] in enumerate(XYZ):
4007	aType = testRBObj['rbAtTypes'][ind]
4008	name = ' '+aType+str(ind)
4009	color = np.array(testRBObj['AtInfo'][aType][1])
4010	RenderSphere(x,y,z,0.2,color/255.)
4011	RenderBonds(x,y,z,rbBonds[ind],0.03,Gr)
4012	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4013	if len(mcsaModels) > 1 and pageName == 'MC/SA': #skip the default MD entry
4014	for ind,[x,y,z] in enumerate(mcsaXYZ):
4015	aType = mcsaTypes[ind]
4016	name = ' '+aType+str(ind)
4017	color = np.array(MCSA['AtInfo'][aType][1])
4018	RenderSphere(x,y,z,0.2,color/255.)
4019	RenderBonds(x,y,z,mcsaBonds[ind],0.03,Gr)
4020	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4021	if Backbones:
4022	for chain in Backbones:
4023	Backbone = Backbones[chain]
4024	RenderBackbone(Backbone,BackboneColor,bondR)
4025	# print time.time()-time0
4026	Page.canvas.SwapBuffers()
4027
4028	def OnSize(event):
4029	Draw('size')
4030
4031	def OnFocus(event): #not needed?? Bind commented out below
4032	Draw('focus')
4033
4034	try:
4035	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
4036	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4037	except ValueError:
4038	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
4039	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
4040	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4041	Page.views = False
4042	view = False
4043	altDown = False
4044	Font = Page.GetFont()
4045	Page.SetFocus()
4046	Page.Choice = None
4047	if mapData['Flip']:
4048	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2',
4049	'u: roll up','d: roll down','l: roll left','r: roll right']
4050	else:
4051	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2','n: next','p: previous']
4052	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
4053	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
4054	cb.SetValue(' save as/key:')
4055	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
4056	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
4057	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
4058	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
4059	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
4060	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
4061	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
4062	# Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
4063	Page.camera['position'] = drawingData['cameraPos']
4064	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
4065	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
4066	try:
4067	Page.canvas.SetCurrent()
4068	except:
4069	pass
4070	Draw('main')
4071
4072	################################################################################
4073	#### Plot Rigid Body
4074	################################################################################
4075
4076	def PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults):
4077	'''RB plotting package. Can show rigid body structures as balls & sticks
4078	'''
4079
4080	def FindBonds(XYZ):
4081	rbTypes = rbData['rbTypes']
4082	Radii = []
4083	for Atype in rbTypes:
4084	Radii.append(AtInfo[Atype][0])
4085	if Atype == 'H':
4086	Radii[-1] = 0.5
4087	Radii = np.array(Radii)
4088	Bonds = [[] for i in range(len(Radii))]
4089	for i,xyz in enumerate(XYZ):
4090	Dx = XYZ-xyz
4091	dist = np.sqrt(np.sum(Dx**2,axis=1))
4092	sumR = Radii[i]+Radii
4093	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
4094	for j in IndB[0]:
4095	Bonds[i].append(Dx[j]*Radii[i]/sumR[j])
4096	Bonds[j].append(-Dx[j]*Radii[j]/sumR[j])
4097	return Bonds
4098
4099	Wt = np.array([255,255,255])
4100	Rd = np.array([255,0,0])
4101	Gr = np.array([0,255,0])
4102	Bl = np.array([0,0,255])
4103	uBox = np.array([[0,0,0],[1,0,0],[0,1,0],[0,0,1]])
4104	uEdges = np.array([[uBox[0],uBox[1]],[uBox[0],uBox[2]],[uBox[0],uBox[3]]])
4105	uColors = [Rd,Gr,Bl]
4106	if rbType == 'Vector':
4107	atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['rbTypes'])]
4108	XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
4109	for imag,mag in enumerate(rbData['VectMag']):
4110	XYZ += mag*rbData['rbVect'][imag]
4111	Bonds = FindBonds(XYZ)
4112	elif rbType == 'Residue':
4113	# atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['atNames'])]
4114	atNames = rbData['atNames']
4115	XYZ = np.copy(rbData['rbXYZ']) #don't mess with original!
4116	Seq = rbData['rbSeq']
4117	for ia,ib,ang,mv in Seq:
4118	va = XYZ[ia]-XYZ[ib]
4119	Q = G2mth.AVdeg2Q(ang,va)
4120	for im in mv:
4121	vb = XYZ[im]-XYZ[ib]
4122	vb = G2mth.prodQVQ(Q,vb)
4123	XYZ[im] = XYZ[ib]+vb
4124	Bonds = FindBonds(XYZ)
4125	elif rbType == 'Z-matrix':
4126	pass
4127
4128	# def SetRBOrigin():
4129	# page = getSelection()
4130	# if page:
4131	# if G2frame.dataDisplay.GetPageText(page) == 'Rigid bodies':
4132	# G2frame.MapPeaksTable.SetData(mapPeaks)
4133	# panel = G2frame.dataDisplay.GetPage(page).GetChildren()
4134	# names = [child.GetName() for child in panel]
4135	# panel[names.index('grid window')].Refresh()
4136
4137	def OnMouseDown(event):
4138	xy = event.GetPosition()
4139	defaults['oldxy'] = list(xy)
4140
4141	def OnMouseMove(event):
4142	newxy = event.GetPosition()
4143
4144	if event.Dragging():
4145	if event.LeftIsDown():
4146	SetRotation(newxy)
4147	Q = defaults['Quaternion']
4148	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4149	# elif event.RightIsDown():
4150	# SetRBOrigin(newxy)
4151	elif event.MiddleIsDown():
4152	SetRotationZ(newxy)
4153	Q = defaults['Quaternion']
4154	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4155	Draw('move')
4156
4157	def OnMouseWheel(event):
4158	defaults['cameraPos'] += event.GetWheelRotation()/24
4159	defaults['cameraPos'] = max(10,min(500,defaults['cameraPos']))
4160	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(defaults['cameraPos']),1)
4161	Draw('wheel')
4162
4163	def SetBackground():
4164	R,G,B,A = Page.camera['backColor']
4165	glClearColor(R,G,B,A)
4166	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
4167
4168	def SetLights():
4169	glEnable(GL_DEPTH_TEST)
4170	glShadeModel(GL_FLAT)
4171	glEnable(GL_LIGHTING)
4172	glEnable(GL_LIGHT0)
4173	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
4174	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
4175	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
4176
4177	# def SetRBOrigin(newxy):
4178	##first get translation vector in screen coords.
4179	# oldxy = defaults['oldxy']
4180	# if not len(oldxy): oldxy = list(newxy)
4181	# dxy = newxy-oldxy
4182	# defaults['oldxy'] = list(newxy)
4183	# V = np.array([dxy[0],-dxy[1],0.])/100.
4184	# Q = defaults['Quaternion']
4185	# V = G2mth.prodQVQ(G2mth.invQ(Q),V)
4186	# rbData['rbXYZ'] += V
4187	# PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults)
4188	#
4189	def SetRotation(newxy):
4190	#first get rotation vector in screen coords. & angle increment
4191	oldxy = defaults['oldxy']
4192	if not len(oldxy): oldxy = list(newxy)
4193	dxy = newxy-oldxy
4194	defaults['oldxy'] = list(newxy)
4195	V = np.array([dxy[1],dxy[0],0.])
4196	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
4197	# next transform vector back to xtal coordinates via inverse quaternion
4198	# & make new quaternion
4199	Q = defaults['Quaternion']
4200	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
4201	DQ = G2mth.AVdeg2Q(A,V)
4202	Q = G2mth.prodQQ(Q,DQ)
4203	defaults['Quaternion'] = Q
4204	# finally get new view vector - last row of rotation matrix
4205	VD = G2mth.Q2Mat(Q)[2]
4206	VD /= np.sqrt(np.sum(VD**2))
4207	defaults['viewDir'] = VD
4208
4209	def SetRotationZ(newxy):
4210	#first get rotation vector (= view vector) in screen coords. & angle increment
4211	View = glGetIntegerv(GL_VIEWPORT)
4212	cent = [View[2]/2,View[3]/2]
4213	oldxy = defaults['oldxy']
4214	if not len(oldxy): oldxy = list(newxy)
4215	dxy = newxy-oldxy
4216	defaults['oldxy'] = list(newxy)
4217	V = defaults['viewDir']
4218	A = [0,0]
4219	A[0] = dxy[1]*.25
4220	A[1] = dxy[0]*.25
4221	if newxy[0] > cent[0]:
4222	A[0] *= -1
4223	if newxy[1] < cent[1]:
4224	A[1] *= -1
4225	# next transform vector back to xtal coordinates & make new quaternion
4226	Q = defaults['Quaternion']
4227	Qx = G2mth.AVdeg2Q(A[0],V)
4228	Qy = G2mth.AVdeg2Q(A[1],V)
4229	Q = G2mth.prodQQ(Q,Qx)
4230	Q = G2mth.prodQQ(Q,Qy)
4231	defaults['Quaternion'] = Q
4232
4233	def RenderUnitVectors(x,y,z):
4234	xyz = np.array([x,y,z])
4235	glEnable(GL_COLOR_MATERIAL)
4236	glLineWidth(1)
4237	glPushMatrix()
4238	glTranslate(x,y,z)
4239	glBegin(GL_LINES)
4240	for line,color in zip(uEdges,uColors):
4241	glColor3ubv(color)
4242	glVertex3fv(-line[1])
4243	glVertex3fv(line[1])
4244	glEnd()
4245	glPopMatrix()
4246	glColor4ubv([0,0,0,0])
4247	glDisable(GL_COLOR_MATERIAL)
4248
4249	def RenderSphere(x,y,z,radius,color):
4250	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4251	glPushMatrix()
4252	glTranslate(x,y,z)
4253	q = gluNewQuadric()
4254	gluSphere(q,radius,20,10)
4255	glPopMatrix()
4256
4257	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
4258	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4259	glPushMatrix()
4260	glTranslate(x,y,z)
4261	for Dx in Bonds:
4262	glPushMatrix()
4263	Z = np.sqrt(np.sum(Dx**2))
4264	if Z:
4265	azm = atan2d(-Dx[1],-Dx[0])
4266	phi = acosd(Dx[2]/Z)
4267	glRotate(-azm,0,0,1)
4268	glRotate(phi,1,0,0)
4269	q = gluNewQuadric()
4270	gluCylinder(q,radius,radius,Z,slice,2)
4271	glPopMatrix()
4272	glPopMatrix()
4273
4274	def RenderLabel(x,y,z,label,matRot):
4275	glPushMatrix()
4276	glTranslate(x,y,z)
4277	glDisable(GL_LIGHTING)
4278	glRasterPos3f(0,0,0)
4279	glMultMatrixf(matRot)
4280	glRotate(180,1,0,0) #fix to flip about x-axis
4281	text = gltext.TextElement(text=label,font=Font,foreground=wx.WHITE)
4282	text.draw_text(scale=0.025)
4283	glEnable(GL_LIGHTING)
4284	glPopMatrix()
4285
4286	def Draw(caller=''):
4287	#useful debug?
4288	# if caller:
4289	# print caller
4290	# end of useful debug
4291	cPos = defaults['cameraPos']
4292	VS = np.array(Page.canvas.GetSize())
4293	aspect = float(VS[0])/float(VS[1])
4294	Zclip = 500.0
4295	Q = defaults['Quaternion']
4296	SetBackground()
4297	glInitNames()
4298	glPushName(0)
4299
4300	glMatrixMode(GL_PROJECTION)
4301	glLoadIdentity()
4302	glViewport(0,0,VS[0],VS[1])
4303	gluPerspective(20.,aspect,1.,500.)
4304	gluLookAt(0,0,cPos,0,0,0,0,1,0)
4305	SetLights()
4306
4307	glMatrixMode(GL_MODELVIEW)
4308	glLoadIdentity()
4309	matRot = G2mth.Q2Mat(Q)
4310	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4311	glMultMatrixf(matRot.T)
4312	RenderUnitVectors(0.,0.,0.)
4313	radius = 0.2
4314	for iat,atom in enumerate(XYZ):
4315	x,y,z = atom
4316	CL = AtInfo[rbData['rbTypes'][iat]][1]
4317	color = np.array(CL)/255.
4318	RenderSphere(x,y,z,radius,color)
4319	RenderBonds(x,y,z,Bonds[iat],0.05,color)
4320	RenderLabel(x,y,z,' '+atNames[iat],matRot)
4321	Page.canvas.SwapBuffers()
4322
4323	def OnSize(event):
4324	Draw('size')
4325
4326	try:
4327	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
4328	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4329	except ValueError:
4330	Plot = G2frame.G2plotNB.addOgl('Rigid body')
4331	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
4332	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4333	Page.views = False
4334	view = False
4335	altDown = False
4336	Page.SetFocus()
4337	Font = Page.GetFont()
4338	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
4339	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
4340	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
4341	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
4342	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
4343	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
4344	Page.camera['position'] = defaults['cameraPos']
4345	Page.camera['backColor'] = np.array([0,0,0,0])
4346	Page.canvas.SetCurrent()
4347	Draw('main')

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