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source: trunk/GSASIIplot.py @ 1377

Last change on this file since 1377 was 1377, checked in by vondreele, 9 years ago
set pixLimit to search a 40x40 pixel box for image Calibrate modify image & stress-strain tutorials to reflect this
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 188.6 KB

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1	# -- coding: utf-8 --
2	'''
3	GSASIIplot: plotting routines
4	===============================
5
6	'''
7	########### SVN repository information ###################
8	# $Date: 2014-06-11 17:39:31 +0000 (Wed, 11 Jun 2014) $
9	# $Author: vondreele $
10	# $Revision: 1377 $
11	# $URL: trunk/GSASIIplot.py $
12	# $Id: GSASIIplot.py 1377 2014-06-11 17:39:31Z 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: 1377 $")
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':
446	G2frame.Weight = not G2frame.Weight
447	if not G2frame.Weight and 'PWDR' in plottype:
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 == 's' and 'PWDR' in plottype:
465	if G2frame.Contour:
466	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
467	choice.sort()
468	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
469	if dlg.ShowModal() == wx.ID_OK:
470	sel = dlg.GetSelection()
471	G2frame.ContourColor = choice[sel]
472	else:
473	G2frame.ContourColor = 'Paired'
474	dlg.Destroy()
475	elif G2frame.SinglePlot:
476	G2frame.SqrtPlot = not G2frame.SqrtPlot
477	if G2frame.SqrtPlot:
478	G2frame.delOffset = .002
479	G2frame.refOffset = -10.0
480	G2frame.refDelt = .001
481	else:
482	G2frame.delOffset = .02
483	G2frame.refOffset = -100.0
484	G2frame.refDelt = .01
485	newPlot = True
486	elif event.key == 'u' and (G2frame.Contour or not G2frame.SinglePlot):
487	if G2frame.Contour:
488	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
489	elif G2frame.Offset[0] < 100.:
490	G2frame.Offset[0] += 1.
491	elif event.key == 'd' and (G2frame.Contour or not G2frame.SinglePlot):
492	if G2frame.Contour:
493	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
494	elif G2frame.Offset[0] > 0.:
495	G2frame.Offset[0] -= 1.
496	elif event.key == 'l' and not G2frame.SinglePlot:
497	G2frame.Offset[1] -= 1.
498	elif event.key == 'r' and not G2frame.SinglePlot:
499	G2frame.Offset[1] += 1.
500	elif event.key == 'o' and not G2frame.SinglePlot:
501	G2frame.Cmax = 1.0
502	G2frame.Offset = [0,0]
503	elif event.key == 'c' and 'PWDR' in plottype:
504	newPlot = True
505	if not G2frame.Contour:
506	G2frame.SinglePlot = False
507	G2frame.Offset = [0.,0.]
508	else:
509	G2frame.SinglePlot = True
510	G2frame.Contour = not G2frame.Contour
511	elif event.key == 'q':
512	if 'PWDR' in plottype:
513	newPlot = True
514	G2frame.qPlot = not G2frame.qPlot
515	elif 'SASD' in plottype:
516	newPlot = True
517	G2frame.sqPlot = not G2frame.sqPlot
518	elif event.key == 'm':
519	G2frame.SqrtPlot = False
520	G2frame.SinglePlot = not G2frame.SinglePlot
521	newPlot = True
522	elif event.key == '+':
523	if G2frame.PickId:
524	G2frame.PickId = False
525	elif event.key == 'i' and G2frame.Contour: #for smoothing contour plot
526	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
527	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
528	'mitchell','sinc','lanczos']
529	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
530	if dlg.ShowModal() == wx.ID_OK:
531	sel = dlg.GetSelection()
532	G2frame.Interpolate = choice[sel]
533	else:
534	G2frame.Interpolate = 'nearest'
535	dlg.Destroy()
536
537	wx.CallAfter(PlotPatterns,G2frame,newPlot=newPlot,plotType=plottype)
538
539	def OnMotion(event):
540	xpos = event.xdata
541	if xpos: #avoid out of frame mouse position
542	ypos = event.ydata
543	Page.canvas.SetCursor(wx.CROSS_CURSOR)
544	try:
545	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
546	if 'C' in Parms['Type'][0]:
547	wave = G2mth.getWave(Parms)
548	if G2frame.qPlot and 'PWDR' in plottype:
549	try:
550	xpos = 2.0asind(xposwave/(4*math.pi))
551	except ValueError: #avoid bad value in asin beyond upper limit
552	pass
553	dsp = 0.0
554	if abs(xpos) > 0.: #avoid possible singularity at beam center
555	if 'PWDR' in plottype:
556	dsp = wave/(2.*sind(abs(xpos)/2.0))
557	q = 2.*np.pi/dsp
558	elif 'SASD' in plottype:
559	dsp = 2*np.pi/xpos
560	q = xpos
561	if G2frame.Contour:
562	if 'PWDR' in plottype:
563	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
564	elif 'SASD' in plottype:
565	G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f pattern ID =%5d'%(dsp,q,int(ypos)),1)
566	else:
567	if 'PWDR' in plottype:
568	if G2frame.SqrtPlot:
569	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
570	else:
571	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
572	elif 'SASD' in plottype:
573	G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f Intensity =%12.5g'%(dsp,q,ypos),1)
574	else: #TOF neutrons
575	dsp = 0.0
576	difC = Parms['difC'][1]
577	dsp = xpos/difC #rough approx.!
578	q = 2.*np.pi/dsp
579	if G2frame.Contour:
580	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
581	else:
582	if G2frame.SqrtPlot:
583	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
584	else:
585	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
586	if G2frame.itemPicked:
587	Page.canvas.SetToolTipString('%9.5f'%(xpos))
588	if G2frame.PickId:
589	found = []
590	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List','Reflection Lists'] or \
591	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
592	if len(HKL):
593	view = Page.toolbar._views.forward()[0][:2]
594	wid = view[1]-view[0]
595	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
596	if len(found):
597	h,k,l = found[0][:3]
598	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
599	else:
600	Page.canvas.SetToolTipString('')
601
602	except TypeError:
603	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' powder pattern first',1)
604
605	def OnPress(event): #ugh - this removes a matplotlib error for mouse clicks in log plots
606	olderr = np.seterr(invalid='ignore')
607
608	def OnPick(event):
609	if G2frame.itemPicked is not None: return
610	PatternId = G2frame.PatternId
611	try:
612	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
613	except TypeError:
614	return
615	if 'C' in Parms['Type'][0]:
616	wave = G2mth.getWave(Parms)
617	else:
618	difC = Parms['difC'][1]
619	PickId = G2frame.PickId
620	pick = event.artist
621	mouse = event.mouseevent
622	xpos = pick.get_xdata()
623	ypos = pick.get_ydata()
624	ind = event.ind
625	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
626	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
627	if ind.all() != [0] and ObsLine[0].get_label() in str(pick): #picked a data point
628	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
629	if 'C' in Parms['Type'][0]: #CW data - TOF later in an elif
630	if G2frame.qPlot: #qplot - convert back to 2-theta
631	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
632	XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1])
633	data.append(XY)
634	G2pdG.UpdatePeakGrid(G2frame,data)
635	PlotPatterns(G2frame,plotType=plottype)
636	else: #picked a peak list line
637	G2frame.itemPicked = pick
638	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
639	if ind.all() != [0]: #picked a data point
640	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
641	data = G2frame.PatternTree.GetItemPyData(LimitId)
642	if 'C' in Parms['Type'][0]: #CW data - TOF later in an elif
643	if G2frame.qPlot and 'PWDR' in plottype: #qplot - convert back to 2-theta
644	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
645	if G2frame.ifGetExclude:
646	excl = [0,0]
647	excl[0] = max(data[1][0],min(xy[0],data[1][1]))
648	excl[1] = excl[0]+0.1
649	data.append(excl)
650	G2frame.ifGetExclude = False
651	else:
652	if mouse.button==1:
653	data[1][0] = min(xy[0],data[1][1])
654	if mouse.button==3:
655	data[1][1] = max(xy[0],data[1][0])
656	G2frame.PatternTree.SetItemPyData(LimitId,data)
657	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
658	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
659	else: #picked a limit line
660	G2frame.itemPicked = pick
661	elif G2frame.PatternTree.GetItemText(PickId) == 'Models':
662	if ind.all() != [0]: #picked a data point
663	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
664	data = G2frame.PatternTree.GetItemPyData(LimitId)
665	if mouse.button==1:
666	data[1][0] = min(xy[0],data[1][1])
667	if mouse.button==3:
668	data[1][1] = max(xy[0],data[1][0])
669	G2frame.PatternTree.SetItemPyData(LimitId,data)
670	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
671	else: #picked a limit line
672	G2frame.itemPicked = pick
673	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
674	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
675	G2frame.itemPicked = pick
676	pick = str(pick)
677
678	def OnRelease(event):
679	if G2frame.itemPicked is None: return
680	if DifLine[0] and DifLine[0].get_label() in str(G2frame.itemPicked):
681	ypos = event.ydata
682	G2frame.delOffset = -ypos/Ymax
683	G2frame.itemPicked = None
684	PlotPatterns(G2frame,plotType=plottype)
685	return
686	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
687	if 'C' in Parms['Type'][0]:
688	wave = G2mth.getWave(Parms)
689	else:
690	difC = Parms['difC'][1]
691	xpos = event.xdata
692	PickId = G2frame.PickId
693	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
694	lines = []
695	for line in G2frame.Lines:
696	lines.append(line.get_xdata()[0])
697	try:
698	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
699	except ValueError:
700	lineNo = -1
701	if lineNo in [0,1] or lineNo in exclLines:
702	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
703	data = G2frame.PatternTree.GetItemPyData(LimitId)
704	id = lineNo/2+1
705	id2 = lineNo%2
706	if G2frame.qPlot and 'PWDR' in plottype:
707	if 'C' in Parms['Type'][0]:
708	data[id][id2] = 2.0asind(wavexpos/(4*math.pi))
709	else:
710	data[id][id2] = 2math.piParms['difC'][1]/xpos
711	else:
712	data[id][id2] = xpos
713	if id > 1 and data[id][0] > data[id][1]:
714	data[id].reverse()
715	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
716	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
717	G2frame.PatternTree.SetItemPyData(LimitId,data)
718	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
719	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
720	elif lineNo > 1:
721	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
722	data = G2frame.PatternTree.GetItemPyData(PeakId)
723	if event.button == 3:
724	del data[lineNo-2]
725	else:
726	if G2frame.qPlot:
727	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
728	else:
729	data[lineNo-2][0] = xpos
730	G2frame.PatternTree.SetItemPyData(PeakId,data)
731	G2pdG.UpdatePeakGrid(G2frame,data)
732	elif G2frame.PatternTree.GetItemText(PickId) in ['Models',] and xpos:
733	lines = []
734	for line in G2frame.Lines:
735	lines.append(line.get_xdata()[0])
736	try:
737	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
738	except ValueError:
739	lineNo = -1
740	if lineNo in [0,1]:
741	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
742	data = G2frame.PatternTree.GetItemPyData(LimitId)
743	data[1][lineNo] = xpos
744	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
745	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
746	G2frame.PatternTree.SetItemPyData(LimitId,data)
747	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
748	'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos:
749	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
750	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
751	if 'line' not in pick: #avoid data points, etc.
752	num = Phases.keys().index(pick)
753	if num:
754	G2frame.refDelt = -(event.ydata-G2frame.refOffset)/(num*Ymax)
755	else: #1st row of refl ticks
756	G2frame.refOffset = event.ydata
757	PlotPatterns(G2frame,plotType=plottype)
758	G2frame.itemPicked = None
759
760	try:
761	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
762	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
763	if not newPlot:
764	Plot = Page.figure.gca() #get previous powder plot & get limits
765	xylim = Plot.get_xlim(),Plot.get_ylim()
766	Page.figure.clf()
767	Plot = Page.figure.gca() #get a fresh plot after clf()
768	except ValueError:
769	if plottype == 'SASD':
770	G2frame.logPlot = True
771	G2frame.ErrorBars = True
772	newPlot = True
773	G2frame.Cmax = 1.0
774	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
775	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
776	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
777	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
778	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
779	Page.canvas.mpl_connect('pick_event', OnPick)
780	Page.canvas.mpl_connect('button_release_event', OnRelease)
781	Page.canvas.mpl_connect('button_press_event',OnPress)
782	if plottype == 'PWDR': # avoids a very nasty clash with KILL_FOCUS in SASD TextCtrl?
783	Page.SetFocus()
784	G2frame.G2plotNB.status.DestroyChildren()
785	if G2frame.Contour:
786	Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max',
787	'i: interpolation method','s: color scheme','c: contour off')
788	else:
789	if G2frame.logPlot:
790	if 'PWDR' in plottype:
791	if G2frame.SinglePlot:
792	Page.Choice = (' key press','n: log(I) off',
793	'c: contour on','q: toggle q plot','m: toggle multidata plot','w: toggle divide by sig','+: no selection')
794	else:
795	Page.Choice = (' key press','n: log(I) off',
796	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
797	'c: contour on','q: toggle q plot','m: toggle multidata plot','w: toggle divide by sig','+: no selection')
798	elif 'SASD' in plottype:
799	if G2frame.SinglePlot:
800	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
801	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
802	else:
803	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
804	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
805	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
806	else:
807	if 'PWDR' in plottype:
808	if G2frame.SinglePlot:
809	Page.Choice = (' key press',
810	'b: toggle subtract background','n: log(I) on','s: toggle sqrt plot','c: contour on',
811	'q: toggle q plot','m: toggle multidata plot','w: toggle divide by sig','+: no selection')
812	else:
813	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down',
814	'u: offset up','o: reset offset','b: toggle subtract background','n: log(I) on','c: contour on',
815	'q: toggle q plot','m: toggle multidata plot','w: toggle divide by sig','+: no selection')
816	elif 'SASD' in plottype:
817	if G2frame.SinglePlot:
818	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
819	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
820	else:
821	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
822	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
823	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
824
825	Page.keyPress = OnPlotKeyPress
826	PickId = G2frame.PickId
827	PatternId = G2frame.PatternId
828	colors=['b','g','r','c','m','k']
829	Lines = []
830	exclLines = []
831	if G2frame.SinglePlot:
832	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
833	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
834	PlotList = [Pattern,]
835	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
836	G2frame.PatternId, 'Instrument Parameters'))
837	Sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters'))
838	ParmList = [Parms,]
839	SampleList = [Sample,]
840	Title = Pattern[-1]
841	else:
842	Title = os.path.split(G2frame.GSASprojectfile)[1]
843	PlotList = []
844	ParmList = []
845	SampleList = []
846	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
847	while item:
848	if plottype in G2frame.PatternTree.GetItemText(item):
849	Pattern = G2frame.PatternTree.GetItemPyData(item)
850	if len(Pattern) < 3: # put name on end if needed
851	Pattern.append(G2frame.PatternTree.GetItemText(item))
852	PlotList.append(Pattern)
853	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
854	item,'Instrument Parameters'))[0])
855	SampleList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
856	item, 'Sample Parameters')))
857	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
858	lenX = 0
859	if PickId:
860	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
861	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
862	HKL = []
863	if Phases:
864	try:
865	for peak in Phases[G2frame.RefList]['RefList']:
866	HKL.append(peak[:6])
867	except TypeError:
868	for peak in Phases[G2frame.RefList]:
869	HKL.append(peak[:6])
870	HKL = np.array(HKL)
871	else:
872	HKL = np.array(G2frame.HKL)
873	Ymax = None
874	for Pattern in PlotList:
875	xye = Pattern[1]
876	if xye[1] is None: continue
877	if Ymax is None: Ymax = max(xye[1])
878	Ymax = max(Ymax,max(xye[1]))
879	if Ymax is None: return # nothing to plot
880	offset = G2frame.Offset[0]*Ymax/100.0
881	if G2frame.logPlot:
882	Title = 'log('+Title+')'
883	Plot.set_title(Title)
884	if G2frame.qPlot or 'SASD' in plottype:
885	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=16)
886	else:
887	if 'C' in ParmList[0]['Type'][0]:
888	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=16)
889	else:
890	Plot.set_xlabel(r'$TOF, \mathsf{\mu}$s',fontsize=16)
891	if G2frame.Weight:
892	if 'PWDR' in plottype:
893	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=16)
894	elif 'SASD' in plottype:
895	Plot.set_ylabel(r'$\mathsf{\Delta(I)/\sigma(I)}$',fontsize=16)
896	else:
897	if 'C' in ParmList[0]['Type'][0]:
898	if 'PWDR' in plottype:
899	if G2frame.SqrtPlot:
900	Plot.set_ylabel(r'$\sqrt{Intensity}$',fontsize=16)
901	else:
902	Plot.set_ylabel(r'$Intensity$',fontsize=16)
903	elif 'SASD' in plottype:
904	if G2frame.sqPlot:
905	Plot.set_ylabel(r'$S(Q)=I*Q^{4}$',fontsize=16)
906	else:
907	Plot.set_ylabel(r'$Intensity, cm^{-1}$',fontsize=16)
908	else:
909	if G2frame.SqrtPlot:
910	Plot.set_ylabel(r'$\sqrt{Normalized\ intensity}$',fontsize=16)
911	else:
912	Plot.set_ylabel(r'$Normalized\ intensity$',fontsize=16)
913	if G2frame.Contour:
914	ContourZ = []
915	ContourY = []
916	Nseq = 0
917	for N,Pattern in enumerate(PlotList):
918	Parms = ParmList[N]
919	Sample = SampleList[N]
920	if 'C' in Parms['Type'][0]:
921	wave = G2mth.getWave(Parms)
922	else:
923	difC = Parms['difC'][1]
924	ifpicked = False
925	LimitId = 0
926	if Pattern[1] is None: continue # skip over uncomputed simulations
927	xye = ma.array(ma.getdata(Pattern[1]))
928	Zero = Parms.get('Zero',[0.,0.])[1]
929	if PickId:
930	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
931	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
932	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
933	excls = limits[2:]
934	for excl in excls:
935	xye[0] = ma.masked_inside(xye[0],excl[0],excl[1])
936	if G2frame.qPlot and 'PWDR' in plottype:
937	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
938	if 'C' in Parms['Type'][0]:
939	X = 4np.pinpsind((xye[0]-Zero)/2.0)/wave
940	else:
941	X = 2np.piParms['difC'][1]/(xye[0]-Zero)
942	else:
943	X = xye[0]-Zero
944	if not lenX:
945	lenX = len(X)
946	if 'PWDR' in plottype:
947	if G2frame.SqrtPlot:
948	Y = np.where(xye[1]>=0.,np.sqrt(xye[1]),-np.sqrt(-xye[1]))
949	else:
950	Y = xye[1]+offset*N
951	elif 'SASD' in plottype:
952	B = xye[5]
953	if G2frame.sqPlot:
954	Y = xye[1]Sample['Scale'][0](1.005)*(offsetN)X*4
955	else:
956	Y = xye[1]Sample['Scale'][0](1.005)*(offsetN)
957	if LimitId and ifpicked:
958	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
959	if G2frame.qPlot and 'PWDR' in plottype:
960	if 'C' in Parms['Type'][0]:
961	limits = 4np.pinpsind(limits/2.0)/wave
962	else:
963	limits = 2np.pidifC/limits
964	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
965	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
966	for i,item in enumerate(limits[2:]):
967	Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))
968	Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.))
969	exclLines += [2i+2,2i+3]
970	if G2frame.Contour:
971
972	if lenX == len(X):
973	ContourY.append(N)
974	ContourZ.append(Y)
975	ContourX = X
976	Nseq += 1
977	Plot.set_ylabel('Data sequence',fontsize=12)
978	else:
979	if 'SASD' in plottype and G2frame.logPlot:
980	X = (1.01)(G2frame.Offset[1]N)
981	else:
982	X += G2frame.Offset[1].005N
983	Xum = ma.getdata(X)
984	DifLine = ['']
985	if ifpicked:
986	if G2frame.SqrtPlot:
987	Z = np.where(xye[3]>=0.,np.sqrt(xye[3]),-np.sqrt(-xye[3]))
988	else:
989	Z = xye[3]+offset*N
990	if 'PWDR' in plottype:
991	if G2frame.SqrtPlot:
992	W = np.where(xye[4]>=0.,np.sqrt(xye[4]),-np.sqrt(-xye[4]))
993	D = np.where(xye[5],(Y-Z),0.)-Ymax*G2frame.delOffset
994	else:
995	W = xye[4]+offset*N
996	D = xye[5]-Ymax*G2frame.delOffset #powder background
997	elif 'SASD' in plottype:
998	if G2frame.sqPlot:
999	W = xye[4]X*4
1000	Z = xye[3]X*4
1001	B = BX*4
1002	else:
1003	W = xye[4]
1004	if G2frame.SubBack:
1005	YB = Y-B
1006	ZB = Z
1007	else:
1008	YB = Y
1009	ZB = Z+B
1010	Plot.set_yscale("log",nonposy='mask')
1011	if np.any(W>0.):
1012	Plot.set_ylim(bottom=np.min(np.trim_zeros(W))/2.,top=np.max(Y)*2.)
1013	else:
1014	Plot.set_ylim(bottom=np.min(np.trim_zeros(YB))/2.,top=np.max(Y)*2.)
1015	if G2frame.logPlot:
1016	if 'PWDR' in plottype:
1017	Plot.set_yscale("log",nonposy='mask')
1018	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1019	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
1020	Plot.plot(X,W,colors[(N+2)%6],picker=False) #background
1021	elif 'SASD' in plottype:
1022	Plot.set_xscale("log",nonposx='mask')
1023	Ibeg = np.searchsorted(X,limits[1][0])
1024	Ifin = np.searchsorted(X,limits[1][1])
1025	if G2frame.Weight:
1026	Plot.set_yscale("linear")
1027	DS = (YB-ZB)*np.sqrt(xye[2])
1028	Plot.plot(X[Ibeg:Ifin],DS[Ibeg:Ifin],colors[(N+3)%6],picker=False)
1029	Plot.axhline(0.,color=wx.BLACK)
1030	Plot.set_ylim(bottom=np.min(DS[Ibeg:Ifin])1.2,top=np.max(DS[Ibeg:Ifin])1.2)
1031	else:
1032	Plot.set_yscale("log",nonposy='mask')
1033	if G2frame.ErrorBars:
1034	if G2frame.sqPlot:
1035	Plot.errorbar(X,YB,yerr=X*4Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
1036	ecolor=colors[N%6],picker=3.,clip_on=False)
1037	else:
1038	Plot.errorbar(X,YB,yerr=Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
1039	ecolor=colors[N%6],picker=3.,clip_on=False)
1040	else:
1041	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1042	Plot.plot(X,W,colors[(N+2)%6],picker=False) #const. background
1043	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1044	elif G2frame.Weight and 'PWDR' in plottype:
1045	DY = xye[1]*np.sqrt(xye[2])
1046	Ymax = max(DY)
1047	DZ = xye[3]*np.sqrt(xye[2])
1048	DS = xye[5]np.sqrt(xye[2])-YmaxG2frame.delOffset
1049	ObsLine = Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False) #Io/sig(Io)
1050	Plot.plot(X,DZ,colors[(N+1)%6],picker=False) #Ic/sig(Io)
1051	DifLine = Plot.plot(X,DS,colors[(N+3)%6],picker=1.) #(Io-Ic)/sig(Io)
1052	Plot.axhline(0.,color=wx.BLACK)
1053	else:
1054	if G2frame.SubBack:
1055	if 'PWDR' in plottype:
1056	Plot.plot(Xum,Y-W,colors[N%6]+'+',picker=False,clip_on=False) #Io-Ib
1057	Plot.plot(X,Z-W,colors[(N+1)%6],picker=False) #Ic-Ib
1058	else:
1059	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1060	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1061	else:
1062	if 'PWDR' in plottype:
1063	ObsLine = Plot.plot(Xum,Y,colors[N%6]+'+',picker=3.,clip_on=False) #Io
1064	Plot.plot(X,Z,colors[(N+1)%6],picker=False) #Ic
1065	else:
1066	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1067	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1068	if 'PWDR' in plottype:
1069	Plot.plot(X,W,colors[(N+2)%6],picker=False) #Ib
1070	DifLine = Plot.plot(X,D,colors[(N+3)%6],picker=1.) #Io-Ic
1071	Plot.axhline(0.,color=wx.BLACK)
1072	Page.canvas.SetToolTipString('')
1073	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
1074	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
1075	Page.canvas.SetToolTipString(tip)
1076	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
1077	for item in data:
1078	if G2frame.qPlot:
1079	if 'C' in Parms['Type'][0]:
1080	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/wave,color=colors[N%6],picker=2.))
1081	else:
1082	Lines.append(Plot.axvline(2math.pidifC/item[0],color=colors[N%6],picker=2.))
1083	else:
1084	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
1085	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
1086	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
1087	Page.canvas.SetToolTipString(tip)
1088	data = G2frame.LimitsTable.GetData()
1089
1090	else: #not picked
1091	if G2frame.logPlot:
1092	if 'PWDR' in plottype:
1093	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1094	elif 'SASD' in plottype:
1095	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1096	else:
1097	if 'PWDR' in plottype:
1098	Plot.plot(X,Y,colors[N%6],picker=False)
1099	elif 'SASD' in plottype:
1100	Plot.loglog(X,Y,colors[N%6],picker=False,nonposy='mask')
1101	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1102
1103	if G2frame.logPlot and 'PWDR' in plottype:
1104	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1105	if PickId and not G2frame.Contour:
1106	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1107	if 'C' in Parms['Type'][0]:
1108	wave = G2mth.getWave(Parms)
1109	else:
1110	difC = Parms['difC'][1]
1111	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
1112	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
1113	for peak in peaks:
1114	if G2frame.qPlot:
1115	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
1116	else:
1117	Plot.axvline(peak[0],color='b')
1118	for hkl in G2frame.HKL:
1119	if G2frame.qPlot:
1120	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
1121	else:
1122	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1123	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
1124	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
1125	refColors=['b','r','c','g','m','k']
1126	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1127	for pId,phase in enumerate(Phases):
1128	try: #patch for old style reflection lists
1129	peaks = Phases[phase]['RefList']
1130	except TypeError:
1131	peaks = Phases[phase]
1132	if not len(peaks):
1133	continue
1134	peak = np.array([[peak[4],peak[5]] for peak in peaks])
1135	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
1136	if G2frame.qPlot:
1137	Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1138	else:
1139	Plot.plot(peak.T[1],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1140	if len(Phases):
1141	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
1142	if handles:
1143	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
1144
1145	if G2frame.Contour:
1146	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1147	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1148	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1149	Page.figure.colorbar(Img)
1150	else:
1151	G2frame.Lines = Lines
1152	if not newPlot:
1153	Page.toolbar.push_current()
1154	Plot.set_xlim(xylim[0])
1155	Plot.set_ylim(xylim[1])
1156	# xylim = []
1157	Page.toolbar.push_current()
1158	Page.toolbar.draw()
1159	else:
1160	Page.canvas.draw()
1161	olderr = np.seterr(invalid='ignore') #ugh - this removes a matplotlib error for mouse clicks in log plots
1162	# and sqrt(-ve) in np.where usage
1163	# G2frame.Pwdr = True
1164
1165	################################################################################
1166	##### PlotDeltSig
1167	################################################################################
1168
1169	def PlotDeltSig(G2frame,kind):
1170	'needs a doc string'
1171	try:
1172	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1173	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1174	Page.figure.clf()
1175	Plot = Page.figure.gca() #get a fresh plot after clf()
1176	except ValueError:
1177	newPlot = True
1178	G2frame.Cmax = 1.0
1179	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
1180	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1181	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1182	Page.Choice = None
1183	PatternId = G2frame.PatternId
1184	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
1185	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
1186	wtFactor = Pattern[0]['wtFactor']
1187	if kind == 'PWDR':
1188	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
1189	xye = np.array(Pattern[1])
1190	xmin = np.searchsorted(xye[0],limits[0])
1191	xmax = np.searchsorted(xye[0],limits[1])
1192	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
1193	elif kind == 'HKLF':
1194	refl = Pattern[1]
1195	DS = []
1196	for ref in refl:
1197	if ref[6] > 0.:
1198	DS.append((ref[5]-ref[7])/ref[6])
1199	Page.SetFocus()
1200	G2frame.G2plotNB.status.DestroyChildren()
1201	DS.sort()
1202	EDS = np.zeros_like(DS)
1203	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
1204	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
1205	T = np.sqrt(np.log(1.0/DX**2))
1206	top = 2.515517+0.802853T+0.010328T**2
1207	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
1208	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
1209	low1 = np.searchsorted(EDS,-1.)
1210	hi1 = np.searchsorted(EDS,1.)
1211	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
1212	frac = 100.*(hi1-low1)/len(DS)
1213	G2frame.G2plotNB.status.SetStatusText( \
1214	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
1215	Plot.set_title('Normal probability for '+Pattern[-1])
1216	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
1217	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
1218	Plot.plot(EDS,DS,'r+',label='result')
1219	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
1220	Plot.legend(loc='upper left')
1221	np.seterr(invalid='warn')
1222	Page.canvas.draw()
1223
1224	################################################################################
1225	##### PlotISFG
1226	################################################################################
1227
1228	def PlotISFG(G2frame,newPlot=False,type=''):
1229	''' Plotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
1230	or multiple plots with waterfall and contour plots as options
1231	'''
1232	if not type:
1233	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
1234	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
1235	return
1236	superMinusOne = unichr(0xaf)+unichr(0xb9)
1237
1238	def OnPlotKeyPress(event):
1239	newPlot = False
1240	if event.key == 'u':
1241	if G2frame.Contour:
1242	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
1243	elif G2frame.Offset[0] < 100.:
1244	G2frame.Offset[0] += 1.
1245	elif event.key == 'd':
1246	if G2frame.Contour:
1247	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
1248	elif G2frame.Offset[0] > 0.:
1249	G2frame.Offset[0] -= 1.
1250	elif event.key == 'l':
1251	G2frame.Offset[1] -= 1.
1252	elif event.key == 'r':
1253	G2frame.Offset[1] += 1.
1254	elif event.key == 'o':
1255	G2frame.Offset = [0,0]
1256	elif event.key == 'c':
1257	newPlot = True
1258	G2frame.Contour = not G2frame.Contour
1259	if not G2frame.Contour:
1260	G2frame.SinglePlot = False
1261	G2frame.Offset = [0.,0.]
1262	elif event.key == 's':
1263	if G2frame.Contour:
1264	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1265	choice.sort()
1266	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1267	if dlg.ShowModal() == wx.ID_OK:
1268	sel = dlg.GetSelection()
1269	G2frame.ContourColor = choice[sel]
1270	else:
1271	G2frame.ContourColor = 'Paired'
1272	dlg.Destroy()
1273	else:
1274	G2frame.SinglePlot = not G2frame.SinglePlot
1275	elif event.key == 'i': #for smoothing contour plot
1276	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
1277	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
1278	'mitchell','sinc','lanczos']
1279	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
1280	if dlg.ShowModal() == wx.ID_OK:
1281	sel = dlg.GetSelection()
1282	G2frame.Interpolate = choice[sel]
1283	else:
1284	G2frame.Interpolate = 'nearest'
1285	dlg.Destroy()
1286	elif event.key == 't' and not G2frame.Contour:
1287	G2frame.Legend = not G2frame.Legend
1288	PlotISFG(G2frame,newPlot=newPlot,type=type)
1289
1290	def OnKeyBox(event):
1291	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
1292	event.key = cb.GetValue()[0]
1293	cb.SetValue(' key press')
1294	wx.CallAfter(OnPlotKeyPress,event)
1295	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
1296
1297	def OnMotion(event):
1298	xpos = event.xdata
1299	if xpos: #avoid out of frame mouse position
1300	ypos = event.ydata
1301	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1302	try:
1303	if G2frame.Contour:
1304	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
1305	else:
1306	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
1307	except TypeError:
1308	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1309
1310	xylim = []
1311	try:
1312	plotNum = G2frame.G2plotNB.plotList.index(type)
1313	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1314	if not newPlot:
1315	Plot = Page.figure.gca() #get previous plot & get limits
1316	xylim = Plot.get_xlim(),Plot.get_ylim()
1317	Page.figure.clf()
1318	Plot = Page.figure.gca()
1319	except ValueError:
1320	newPlot = True
1321	G2frame.Cmax = 1.0
1322	Plot = G2frame.G2plotNB.addMpl(type).gca()
1323	plotNum = G2frame.G2plotNB.plotList.index(type)
1324	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1325	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1326	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1327
1328	Page.SetFocus()
1329	G2frame.G2plotNB.status.DestroyChildren()
1330	if G2frame.Contour:
1331	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
1332	'i: interpolation method','s: color scheme','c: contour off')
1333	else:
1334	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
1335	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
1336	Page.keyPress = OnPlotKeyPress
1337	PatternId = G2frame.PatternId
1338	PickId = G2frame.PickId
1339	Plot.set_title(type)
1340	if type == 'G(R)':
1341	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
1342	else:
1343	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
1344	Plot.set_ylabel(r''+type,fontsize=14)
1345	colors=['b','g','r','c','m','k']
1346	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
1347	Pattern = []
1348	if G2frame.SinglePlot:
1349	name = G2frame.PatternTree.GetItemText(PatternId)
1350	name = type+name[4:]
1351	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
1352	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1353	if Pattern:
1354	Pattern.append(name)
1355	PlotList = [Pattern,]
1356	else:
1357	PlotList = []
1358	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1359	while item:
1360	if 'PDF' in G2frame.PatternTree.GetItemText(item):
1361	name = type+G2frame.PatternTree.GetItemText(item)[4:]
1362	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
1363	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1364	if Pattern:
1365	Pattern.append(name)
1366	PlotList.append(Pattern)
1367	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1368	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
1369	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
1370	Xb = [0.,10.]
1371	Yb = [0.,-40.np.pinumbDen]
1372	Ymax = 1.0
1373	lenX = 0
1374	for Pattern in PlotList:
1375	xye = Pattern[1]
1376	Ymax = max(Ymax,max(xye[1]))
1377	offset = G2frame.Offset[0]*Ymax/100.0
1378	if G2frame.Contour:
1379	ContourZ = []
1380	ContourY = []
1381	Nseq = 0
1382	for N,Pattern in enumerate(PlotList):
1383	xye = Pattern[1]
1384	if PickId:
1385	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1386	X = xye[0]
1387	if not lenX:
1388	lenX = len(X)
1389	Y = xye[1]+offset*N
1390	if G2frame.Contour:
1391	if lenX == len(X):
1392	ContourY.append(N)
1393	ContourZ.append(Y)
1394	ContourX = X
1395	Nseq += 1
1396	Plot.set_ylabel('Data sequence',fontsize=12)
1397	else:
1398	X = xye[0]+G2frame.Offset[1].005N
1399	if ifpicked:
1400	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1401	Page.canvas.SetToolTipString('')
1402	else:
1403	if G2frame.Legend:
1404	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1405	else:
1406	Plot.plot(X,Y,colors[N%6],picker=False)
1407	if type == 'G(R)':
1408	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1409	elif type == 'F(Q)':
1410	Plot.axhline(0.,color=wx.BLACK)
1411	elif type == 'S(Q)':
1412	Plot.axhline(1.,color=wx.BLACK)
1413	if G2frame.Contour:
1414	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1415	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1416	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1417	Page.figure.colorbar(Img)
1418	elif G2frame.Legend:
1419	Plot.legend(loc='best')
1420	if not newPlot:
1421	Page.toolbar.push_current()
1422	Plot.set_xlim(xylim[0])
1423	Plot.set_ylim(xylim[1])
1424	xylim = []
1425	Page.toolbar.push_current()
1426	Page.toolbar.draw()
1427	else:
1428	Page.canvas.draw()
1429
1430	################################################################################
1431	##### PlotXY
1432	################################################################################
1433
1434	def PlotXY(G2frame,XY,XY2=None,labelX=None,labelY=None,newPlot=False,type=''):
1435	'''simple plot of xy data, used for diagnostic purposes
1436	'''
1437	def OnMotion(event):
1438	xpos = event.xdata
1439	if xpos: #avoid out of frame mouse position
1440	ypos = event.ydata
1441	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1442	try:
1443	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
1444	except TypeError:
1445	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1446
1447	try:
1448	plotNum = G2frame.G2plotNB.plotList.index(type)
1449	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1450	if not newPlot:
1451	Plot = Page.figure.gca()
1452	xylim = Plot.get_xlim(),Plot.get_ylim()
1453	Page.figure.clf()
1454	Plot = Page.figure.gca()
1455	except ValueError:
1456	newPlot = True
1457	Plot = G2frame.G2plotNB.addMpl(type).gca()
1458	plotNum = G2frame.G2plotNB.plotList.index(type)
1459	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1460	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1461
1462	Page.Choice = None
1463	Page.SetFocus()
1464	G2frame.G2plotNB.status.DestroyChildren()
1465	Plot.set_title(type)
1466	if xLabel:
1467	Plot.set_xlabel(r''+xLabel,fontsize=14)
1468	else:
1469	Plot.set_xlabel(r'X',fontsize=14)
1470	if yLabel:
1471	Plot.set_ylabel(r''+yLabel,fontsize=14)
1472	else:
1473	Plot.set_ylabel(r'Y',fontsize=14)
1474	colors=['b','g','r','c','m','k']
1475	for ixy,xy in enumerate(XY):
1476	X,Y = xy
1477	Plot.plot(X,Y,color(ixy%6)+'+',picker=False)
1478	if len(XY2):
1479	for ixy,xy in enumerate(XY2):
1480	X,Y = xy
1481	Plot.plot(X,Y,color(ixy%6),picker=False)
1482	if not newPlot:
1483	Page.toolbar.push_current()
1484	Plot.set_xlim(xylim[0])
1485	Plot.set_ylim(xylim[1])
1486	xylim = []
1487	Page.toolbar.push_current()
1488	Page.toolbar.draw()
1489	else:
1490	Page.canvas.draw()
1491
1492	################################################################################
1493	##### PlotStrain
1494	################################################################################
1495
1496	def PlotStrain(G2frame,data,newPlot=False):
1497	'''plot of strain data, used for diagnostic purposes
1498	'''
1499	def OnMotion(event):
1500	xpos = event.xdata
1501	if xpos: #avoid out of frame mouse position
1502	ypos = event.ydata
1503	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1504	try:
1505	G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1)
1506	except TypeError:
1507	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
1508
1509	try:
1510	plotNum = G2frame.G2plotNB.plotList.index('Strain')
1511	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1512	if not newPlot:
1513	Plot = Page.figure.gca()
1514	xylim = Plot.get_xlim(),Plot.get_ylim()
1515	Page.figure.clf()
1516	Plot = Page.figure.gca()
1517	except ValueError:
1518	newPlot = True
1519	Plot = G2frame.G2plotNB.addMpl('Strain').gca()
1520	plotNum = G2frame.G2plotNB.plotList.index('Strain')
1521	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1522	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1523
1524	Page.Choice = None
1525	Page.SetFocus()
1526	G2frame.G2plotNB.status.DestroyChildren()
1527	Plot.set_title('Strain')
1528	Plot.set_ylabel(r'd-spacing',fontsize=14)
1529	Plot.set_xlabel(r'Azimuth',fontsize=14)
1530	colors=['b','g','r','c','m','k']
1531	for N,item in enumerate(data['d-zero']):
1532	Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y
1533	Plot.plot(X,Y,colors[N%6]+'+',picker=False)
1534	Y,X = np.array(item['ImtaCalc'])
1535	Plot.plot(X,Y,colors[N%6],picker=False)
1536	if not newPlot:
1537	Page.toolbar.push_current()
1538	Plot.set_xlim(xylim[0])
1539	Plot.set_ylim(xylim[1])
1540	xylim = []
1541	Page.toolbar.push_current()
1542	Page.toolbar.draw()
1543	else:
1544	Page.canvas.draw()
1545
1546	################################################################################
1547	##### PlotSASDSizeDist
1548	################################################################################
1549
1550	def PlotSASDSizeDist(G2frame):
1551
1552	def OnPageChanged(event):
1553	PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection())
1554	if 'Powder' in PlotText:
1555	PlotPatterns(G2frame,plotType='SASD',newPlot=True)
1556	elif 'Size' in PlotText:
1557	PlotSASDSizeDist(G2frame)
1558
1559	def OnMotion(event):
1560	xpos = event.xdata
1561	if xpos: #avoid out of frame mouse position
1562	ypos = event.ydata
1563	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1564	try:
1565	G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1)
1566	except TypeError:
1567	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
1568
1569	try:
1570	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
1571	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1572	Page.figure.clf()
1573	Plot = Page.figure.gca() #get a fresh plot after clf()
1574	except ValueError:
1575	newPlot = True
1576	Plot = G2frame.G2plotNB.addMpl('Size Distribution').gca()
1577	G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged)
1578	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
1579	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1580	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1581	Page.Choice = None
1582	Page.SetFocus()
1583	PatternId = G2frame.PatternId
1584	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Models'))
1585	Bins,Dbins,BinMag = data['Size']['Distribution']
1586	Plot.set_title('Size Distribution')
1587	Plot.set_xlabel(r'$D, \AA$',fontsize=14)
1588	Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14)
1589	if data['Size']['logBins']:
1590	Plot.set_xscale("log",nonposy='mask')
1591	Plot.set_xlim([np.min(2.Bins)/2.,np.max(2.Bins)*2.])
1592	Plot.bar(2.Bins-Dbins,BinMag,2.Dbins,facecolor='white') #plot diameters
1593	if 'Size Calc' in data:
1594	Rbins,Dist = data['Size Calc']
1595	for i in range(len(Rbins)):
1596	if len(Rbins[i]):
1597	Plot.plot(2.*Rbins[i],Dist[i]) #plot diameters
1598	Page.canvas.draw()
1599
1600	################################################################################
1601	##### PlotPowderLines
1602	################################################################################
1603
1604	def PlotPowderLines(G2frame):
1605	''' plotting of powder lines (i.e. no powder pattern) as sticks
1606	'''
1607	global HKL
1608
1609	def OnMotion(event):
1610	xpos = event.xdata
1611	if xpos: #avoid out of frame mouse position
1612	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1613	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
1614	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
1615	found = []
1616	if len(HKL):
1617	view = Page.toolbar._views.forward()[0][:2]
1618	wid = view[1]-view[0]
1619	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
1620	if len(found):
1621	h,k,l = found[0][:3]
1622	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1623	else:
1624	Page.canvas.SetToolTipString('')
1625
1626	try:
1627	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1628	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1629	Page.figure.clf()
1630	Plot = Page.figure.gca()
1631	except ValueError:
1632	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
1633	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
1634	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1635	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1636
1637	Page.Choice = None
1638	Page.SetFocus()
1639	Plot.set_title('Powder Pattern Lines')
1640	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
1641	PickId = G2frame.PickId
1642	PatternId = G2frame.PatternId
1643	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
1644	for peak in peaks:
1645	Plot.axvline(peak[0],color='b')
1646	HKL = np.array(G2frame.HKL)
1647	for hkl in G2frame.HKL:
1648	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1649	xmin = peaks[0][0]
1650	xmax = peaks[-1][0]
1651	delt = xmax-xmin
1652	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1653	Plot.set_xlim(xlim)
1654	Page.canvas.draw()
1655	Page.toolbar.push_current()
1656
1657	################################################################################
1658	##### PlotPeakWidths
1659	################################################################################
1660
1661	def PlotPeakWidths(G2frame):
1662	''' Plotting of instrument broadening terms as function of 2-theta
1663	Seen when "Instrument Parameters" chosen from powder pattern data tree
1664	'''
1665	# sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1666	# gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1667	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.)
1668	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1669	PatternId = G2frame.PatternId
1670	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1671	if limitID:
1672	limits = G2frame.PatternTree.GetItemPyData(limitID)[:2]
1673	else:
1674	return
1675	Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \
1676	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1677	if 'C' in Parms['Type'][0]:
1678	lam = G2mth.getWave(Parms)
1679	else:
1680	difC = Parms['difC'][0]
1681	peakID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
1682	if peakID:
1683	peaks = G2frame.PatternTree.GetItemPyData(peakID)
1684	else:
1685	peaks = []
1686
1687	try:
1688	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1689	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1690	Page.figure.clf()
1691	Plot = Page.figure.gca()
1692	except ValueError:
1693	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
1694	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
1695	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1696	Page.Choice = None
1697	Page.SetFocus()
1698
1699	Page.canvas.SetToolTipString('')
1700	colors=['b','g','r','c','m','k']
1701	X = []
1702	Y = []
1703	Z = []
1704	W = []
1705	if 'C' in Parms['Type'][0]:
1706	Plot.set_title('Instrument and sample peak widths')
1707	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
1708	Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14)
1709	try:
1710	Xmin,Xmax = limits[1]
1711	X = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1712	Q = 4.np.pinpsind(X/2.)/lam
1713	Z = np.ones_like(X)
1714	data = G2mth.setPeakparms(Parms,Parms2,X,Z)
1715	s = 1.17741np.sqrt(data[4])np.pi/18000.
1716	g = data[6]*np.pi/18000.
1717	G = G2pwd.getgamFW(g,s)
1718	Y = s/nptand(X/2.)
1719	Z = g/nptand(X/2.)
1720	W = G/nptand(X/2.)
1721	Plot.plot(Q,Y,color='r',label='Gaussian')
1722	Plot.plot(Q,Z,color='g',label='Lorentzian')
1723	Plot.plot(Q,W,color='b',label='G+L')
1724
1725	fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True)
1726	sf = 1.17741np.sqrt(fit[4])np.pi/18000.
1727	gf = fit[6]*np.pi/18000.
1728	Gf = G2pwd.getgamFW(gf,sf)
1729	Yf = sf/nptand(X/2.)
1730	Zf = gf/nptand(X/2.)
1731	Wf = Gf/nptand(X/2.)
1732	Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit')
1733	Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit')
1734	Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
1735
1736	X = []
1737	Y = []
1738	Z = []
1739	W = []
1740	V = []
1741	for peak in peaks:
1742	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1743	try:
1744	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1745	except ValueError:
1746	s = 0.01
1747	g = peak[6]*math.pi/18000.
1748	G = G2pwd.getgamFW(g,s)
1749	Y.append(s/tand(peak[0]/2.))
1750	Z.append(g/tand(peak[0]/2.))
1751	W.append(G/tand(peak[0]/2.))
1752	if len(peaks):
1753	Plot.plot(X,Y,'+',color='r',label='G peak')
1754	Plot.plot(X,Z,'+',color='g',label='L peak')
1755	Plot.plot(X,W,'+',color='b',label='G+L peak')
1756	Plot.legend(loc='best')
1757	Page.canvas.draw()
1758	except ValueError:
1759	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
1760	'%.3f'%(2*theta)
1761	G2frame.G2plotNB.Delete('Peak Widths')
1762	else:
1763	Plot.set_title('Instrument and sample peak coefficients')
1764	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
1765	Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14)
1766	Xmin,Xmax = limits[1]
1767	T = np.linspace(Xmin,Xmax,num=101,endpoint=True)
1768	Z = np.ones_like(T)
1769	data = G2mth.setPeakparms(Parms,Parms2,T,Z)
1770	ds = T/difC
1771	Q = 2.*np.pi/ds
1772	A = data[4]
1773	B = data[6]
1774	S = 1.17741*np.sqrt(data[8])/T
1775	G = data[10]/T
1776	Plot.plot(Q,A,color='r',label='Alpha')
1777	Plot.plot(Q,B,color='g',label='Beta')
1778	Plot.plot(Q,S,color='b',label='Gaussian')
1779	Plot.plot(Q,G,color='m',label='Lorentzian')
1780
1781	fit = G2mth.setPeakparms(Parms,Parms2,T,Z)
1782	ds = T/difC
1783	Q = 2.*np.pi/ds
1784	Af = fit[4]
1785	Bf = fit[6]
1786	Sf = 1.17741*np.sqrt(fit[8])/T
1787	Gf = fit[10]/T
1788	Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit')
1789	Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit')
1790	Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit')
1791	Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit')
1792
1793	T = []
1794	A = []
1795	B = []
1796	S = []
1797	G = []
1798	W = []
1799	Q = []
1800	V = []
1801	for peak in peaks:
1802	T.append(peak[0])
1803	A.append(peak[4])
1804	B.append(peak[6])
1805	Q.append(2.np.pidifC/peak[0])
1806	S.append(1.17741*np.sqrt(peak[8])/peak[0])
1807	G.append(peak[10]/peak[0])
1808
1809
1810	Plot.plot(Q,A,'+',color='r',label='Alpha peak')
1811	Plot.plot(Q,B,'+',color='g',label='Beta peak')
1812	Plot.plot(Q,S,'+',color='b',label='Gaussian peak')
1813	Plot.plot(Q,G,'+',color='m',label='Lorentzian peak')
1814	Plot.legend(loc='best')
1815	Page.canvas.draw()
1816
1817
1818	################################################################################
1819	##### PlotSizeStrainPO
1820	################################################################################
1821
1822	def PlotSizeStrainPO(G2frame,data,Start=False):
1823	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
1824	'''
1825
1826	PatternId = G2frame.PatternId
1827	generalData = data['General']
1828	SGData = generalData['SGData']
1829	SGLaue = SGData['SGLaue']
1830	if Start: #initialize the spherical harmonics qlmn arrays
1831	ptx.pyqlmninit()
1832	Start = False
1833	# MuStrKeys = G2spc.MustrainNames(SGData)
1834	cell = generalData['Cell'][1:]
1835	A,B = G2lat.cell2AB(cell[:6])
1836	Vol = cell[6]
1837	useList = data['Histograms']
1838	phase = generalData['Name']
1839	plotType = generalData['Data plot type']
1840	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
1841	for ptype in plotDict:
1842	G2frame.G2plotNB.Delete(ptype)
1843	if plotType in ['None']:
1844	return
1845
1846	for item in useList:
1847	if useList[item]['Show']:
1848	break
1849	else:
1850	return #nothing to show!!
1851
1852	numPlots = len(useList)
1853
1854	if plotType in ['Mustrain','Size']:
1855	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
1856	else:
1857	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
1858	plotNum = G2frame.G2plotNB.plotList.index(plotType)
1859	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1860	Page.Choice = None
1861	Page.SetFocus()
1862	G2frame.G2plotNB.status.SetStatusText('',1)
1863	if not Page.IsShown():
1864	Page.Show()
1865
1866	for item in useList:
1867	if useList[item]['Show']:
1868	PHI = np.linspace(0.,360.,30,True)
1869	PSI = np.linspace(0.,180.,30,True)
1870	X = np.outer(npsind(PHI),npsind(PSI))
1871	Y = np.outer(npcosd(PHI),npsind(PSI))
1872	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1873	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
1874	coeff = useList[item][plotDict[plotType]]
1875	except KeyError:
1876	break
1877	if plotType in ['Mustrain','Size']:
1878	if coeff[0] == 'isotropic':
1879	X *= coeff[1][0]
1880	Y *= coeff[1][0]
1881	Z *= coeff[1][0]
1882	elif coeff[0] == 'uniaxial':
1883
1884	def uniaxCalc(xyz,iso,aniso,axes):
1885	Z = np.array(axes)
1886	cp = abs(np.dot(xyz,Z))
1887	sp = np.sqrt(1.-cp**2)
1888	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
1889	return R*xyz
1890
1891	iso,aniso = coeff[1][:2]
1892	axes = np.inner(A,np.array(coeff[3]))
1893	axes /= nl.norm(axes)
1894	Shkl = np.array(coeff[1])
1895	XYZ = np.dstack((X,Y,Z))
1896	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
1897	X,Y,Z = np.dsplit(XYZ,3)
1898	X = X[:,:,0]
1899	Y = Y[:,:,0]
1900	Z = Z[:,:,0]
1901
1902	elif coeff[0] == 'ellipsoidal':
1903
1904	def ellipseCalc(xyz,E,R):
1905	XYZ = xyz*E.T
1906	return np.inner(XYZ.T,R)
1907
1908	S6 = coeff[4]
1909	Sij = G2lat.U6toUij(S6)
1910	E,R = nl.eigh(Sij)
1911	XYZ = np.dstack((X,Y,Z))
1912	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
1913	X,Y,Z = np.dsplit(XYZ,3)
1914	X = X[:,:,0]
1915	Y = Y[:,:,0]
1916	Z = Z[:,:,0]
1917
1918	elif coeff[0] == 'generalized':
1919
1920	def genMustrain(xyz,SGData,A,Shkl):
1921	uvw = np.inner(A.T,xyz)
1922	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1923	sum = np.sum(np.multiply(Shkl,Strm))
1924	sum = np.where(sum > 0.01,sum,0.01)
1925	sum = np.sqrt(sum)*math.pi/.18 #centidegrees to radians!
1926	return sum*xyz
1927
1928	Shkl = np.array(coeff[4])
1929	if np.any(Shkl):
1930	XYZ = np.dstack((X,Y,Z))
1931	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1932	X,Y,Z = np.dsplit(XYZ,3)
1933	X = X[:,:,0]
1934	Y = Y[:,:,0]
1935	Z = Z[:,:,0]
1936
1937	if np.any(X) and np.any(Y) and np.any(Z):
1938	errFlags = np.seterr(all='ignore')
1939	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
1940	np.seterr(all='ignore')
1941	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
1942	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
1943	Plot.set_xlim3d(XYZlim)
1944	Plot.set_ylim3d(XYZlim)
1945	Plot.set_zlim3d(XYZlim)
1946	Plot.set_aspect('equal')
1947	if plotType == 'Size':
1948	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
1949	Plot.set_xlabel(r'X, $\mu$m')
1950	Plot.set_ylabel(r'Y, $\mu$m')
1951	Plot.set_zlabel(r'Z, $\mu$m')
1952	else:
1953	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
1954	Plot.set_xlabel(r'X, $\mu$strain')
1955	Plot.set_ylabel(r'Y, $\mu$strain')
1956	Plot.set_zlabel(r'Z, $\mu$strain')
1957	else:
1958	h,k,l = generalData['POhkl']
1959	if coeff[0] == 'MD':
1960	print 'March-Dollase preferred orientation plot'
1961
1962	else:
1963	PH = np.array(generalData['POhkl'])
1964	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
1965	SHCoef = {}
1966	for item in coeff[5]:
1967	L,N = eval(item.strip('C'))
1968	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
1969	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1970	X = np.linspace(0,90.0,26)
1971	Y = G2lat.polfcal(ODFln,'0',X,0.0)
1972	Plot.plot(X,Y,color='k',label=str(PH))
1973	Plot.legend(loc='best')
1974	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
1975	Plot.set_xlabel(r'$\psi$',fontsize=16)
1976	Plot.set_ylabel('MRD',fontsize=14)
1977	Page.canvas.draw()
1978
1979	################################################################################
1980	##### PlotTexture
1981	################################################################################
1982
1983	def PlotTexture(G2frame,data,Start=False):
1984	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
1985	plotting.
1986	dict generalData contains all phase info needed which is in data
1987	'''
1988
1989	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1990	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1991	PatternId = G2frame.PatternId
1992	generalData = data['General']
1993	SGData = generalData['SGData']
1994	textureData = generalData['SH Texture']
1995	G2frame.G2plotNB.Delete('Texture')
1996	if not textureData['Order']:
1997	return #no plot!!
1998	SHData = generalData['SH Texture']
1999	SHCoef = SHData['SH Coeff'][1]
2000	cell = generalData['Cell'][1:7]
2001	Amat,Bmat = G2lat.cell2AB(cell)
2002	sq2 = 1.0/math.sqrt(2.0)
2003
2004	def rp2xyz(r,p):
2005	z = npcosd(r)
2006	xy = np.sqrt(1.-z**2)
2007	return xynpsind(p),xynpcosd(p),z
2008
2009	def OnMotion(event):
2010	SHData = data['General']['SH Texture']
2011	if event.xdata and event.ydata: #avoid out of frame errors
2012	xpos = event.xdata
2013	ypos = event.ydata
2014	if 'Inverse' in SHData['PlotType']:
2015	r = xpos2+ypos2
2016	if r <= 1.0:
2017	if 'equal' in G2frame.Projection:
2018	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
2019	else:
2020	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
2021	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
2022	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
2023	y,x,z = list(xyz/np.max(np.abs(xyz)))
2024
2025	G2frame.G2plotNB.status.SetFields(['',
2026	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
2027
2028	elif 'Axial' in SHData['PlotType']:
2029	pass
2030
2031	else: #ordinary pole figure
2032	z = xpos2+ypos2
2033	if z <= 1.0:
2034	z = np.sqrt(z)
2035	if 'equal' in G2frame.Projection:
2036	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
2037	else:
2038	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
2039	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
2040	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
2041
2042	try:
2043	plotNum = G2frame.G2plotNB.plotList.index('Texture')
2044	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2045	Page.figure.clf()
2046	Plot = Page.figure.gca()
2047	if not Page.IsShown():
2048	Page.Show()
2049	except ValueError:
2050	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
2051	plotNum = G2frame.G2plotNB.plotList.index('Texture')
2052	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2053	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2054
2055	Page.Choice = None
2056	Page.SetFocus()
2057	G2frame.G2plotNB.status.SetFields(['',''])
2058	PH = np.array(SHData['PFhkl'])
2059	phi,beta = G2lat.CrsAng(PH,cell,SGData)
2060	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
2061	PX = np.array(SHData['PFxyz'])
2062	gam = atan2d(PX[0],PX[1])
2063	xy = math.sqrt(PX[0]2+PX[1]2)
2064	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
2065	psi = asind(xy/xyz)
2066	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
2067	if 'Axial' in SHData['PlotType']:
2068	X = np.linspace(0,90.0,26)
2069	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
2070	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
2071	Plot.legend(loc='best')
2072	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
2073	Plot.set_xlabel(r'$\psi$',fontsize=16)
2074	Plot.set_ylabel('MRD',fontsize=14)
2075
2076	else:
2077	npts = 201
2078	if 'Inverse' in SHData['PlotType']:
2079	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2080	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2081	if 'equal' in G2frame.Projection:
2082	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2083	else:
2084	R = np.where(R <= 1.,2.*npatand(R),0.0)
2085	Z = np.zeros_like(R)
2086	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
2087	Z = np.reshape(Z,(npts,npts))
2088	CS = Plot.contour(Y,X,Z,aspect='equal')
2089	Plot.clabel(CS,fontsize=9,inline=1)
2090	try:
2091	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2092	except ValueError:
2093	pass
2094	Page.figure.colorbar(Img)
2095	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
2096	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2097
2098	else:
2099	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2100	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2101	if 'equal' in G2frame.Projection:
2102	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2103	else:
2104	R = np.where(R <= 1.,2.*npatand(R),0.0)
2105	Z = np.zeros_like(R)
2106	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
2107	Z = np.reshape(Z,(npts,npts))
2108	try:
2109	CS = Plot.contour(Y,X,Z,aspect='equal')
2110	Plot.clabel(CS,fontsize=9,inline=1)
2111	except ValueError:
2112	pass
2113	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2114	Page.figure.colorbar(Img)
2115	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
2116	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2117	Page.canvas.draw()
2118
2119	################################################################################
2120	##### PlotCovariance
2121	################################################################################
2122
2123	def PlotCovariance(G2frame,Data):
2124	'needs a doc string'
2125	if not Data:
2126	print 'No covariance matrix available'
2127	return
2128	varyList = Data['varyList']
2129	values = Data['variables']
2130	Xmax = len(varyList)
2131	covMatrix = Data['covMatrix']
2132	sig = np.sqrt(np.diag(covMatrix))
2133	xvar = np.outer(sig,np.ones_like(sig))
2134	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
2135	title = ' for\n'+Data['title']
2136	newAtomDict = Data.get('newAtomDict',{})
2137
2138
2139	def OnPlotKeyPress(event):
2140	newPlot = False
2141	if event.key == 's':
2142	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2143	choice.sort()
2144	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2145	if dlg.ShowModal() == wx.ID_OK:
2146	sel = dlg.GetSelection()
2147	G2frame.VcovColor = choice[sel]
2148	else:
2149	G2frame.VcovColor = 'RdYlGn'
2150	dlg.Destroy()
2151	PlotCovariance(G2frame,Data)
2152
2153	def OnMotion(event):
2154	#there is a problem here - reports wrong values
2155	if event.button:
2156	ytics = imgAx.get_yticks()
2157	ytics = np.where(ytics<len(varyList),ytics,-1)
2158	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
2159	imgAx.set_yticklabels(ylabs)
2160	if event.xdata and event.ydata: #avoid out of frame errors
2161	xpos = int(event.xdata+.5)
2162	ypos = int(event.ydata+.5)
2163	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
2164	if xpos == ypos:
2165	value = values[xpos]
2166	name = varyList[xpos]
2167	if varyList[xpos] in newAtomDict:
2168	name,value = newAtomDict[name]
2169	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
2170	else:
2171	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
2172	Page.canvas.SetToolTipString(msg)
2173	G2frame.G2plotNB.status.SetFields(['',msg])
2174
2175	try:
2176	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2177	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2178	Page.figure.clf()
2179	Plot = Page.figure.gca()
2180	if not Page.IsShown():
2181	Page.Show()
2182	except ValueError:
2183	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
2184	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2185	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2186	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2187	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2188	Page.Choice = ['s: to change colors']
2189	Page.keyPress = OnPlotKeyPress
2190	Page.SetFocus()
2191	G2frame.G2plotNB.status.SetFields(['',''])
2192	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
2193	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower',
2194	vmin=-1.,vmax=1.)
2195	imgAx = Img.get_axes()
2196	ytics = imgAx.get_yticks()
2197	ylabs = [varyList[int(i)] for i in ytics[:-1]]
2198	imgAx.set_yticklabels(ylabs)
2199	colorBar = Page.figure.colorbar(Img)
2200	Plot.set_title('V-Cov matrix'+title)
2201	Plot.set_xlabel('Variable number')
2202	Plot.set_ylabel('Variable name')
2203	Page.canvas.draw()
2204
2205	################################################################################
2206	##### PlotTorsion
2207	################################################################################
2208
2209	def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]):
2210	'needs a doc string'
2211
2212	global names
2213	names = Names
2214	sum = np.sum(Torsion)
2215	torsion = np.log(2*Torsion+1.)/sum
2216	tMin = np.min(torsion)
2217	tMax = np.max(torsion)
2218	torsion = 3.*(torsion-tMin)/(tMax-tMin)
2219	X = np.linspace(0.,360.,num=45)
2220
2221	def OnPick(event):
2222	ind = event.ind[0]
2223	msg = 'atoms:'+names[ind]
2224	Page.canvas.SetToolTipString(msg)
2225	try:
2226	page = G2frame.dataDisplay.GetSelection()
2227	except:
2228	return
2229	if G2frame.dataDisplay.GetPageText(page) == 'Torsion restraints':
2230	torGrid = G2frame.dataDisplay.GetPage(page).Torsions
2231	torGrid.ClearSelection()
2232	for row in range(torGrid.GetNumberRows()):
2233	if names[ind] in torGrid.GetCellValue(row,0):
2234	torGrid.SelectRow(row)
2235	torGrid.ForceRefresh()
2236
2237	def OnMotion(event):
2238	if event.xdata and event.ydata: #avoid out of frame errors
2239	xpos = event.xdata
2240	ypos = event.ydata
2241	msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos)
2242	Page.canvas.SetToolTipString(msg)
2243
2244	try:
2245	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
2246	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2247	Page.figure.clf()
2248	Plot = Page.figure.gca()
2249	if not Page.IsShown():
2250	Page.Show()
2251	except ValueError:
2252	Plot = G2frame.G2plotNB.addMpl('Torsion').gca()
2253	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
2254	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2255	Page.canvas.mpl_connect('pick_event', OnPick)
2256	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2257
2258	Page.SetFocus()
2259	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify torsion atoms'])
2260	Plot.plot(X,torsion,'b+')
2261	if len(Coeff):
2262	X2 = np.linspace(0.,360.,45)
2263	Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2])
2264	Plot.plot(X2,Y2,'r')
2265	if len(Angles):
2266	Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles])
2267	Plot.plot(Angles,Eval,'ro',picker=5)
2268	Plot.set_xlim((0.,360.))
2269	Plot.set_title('Torsion angles for '+TorName+' in '+phaseName)
2270	Plot.set_xlabel('angle',fontsize=16)
2271	Plot.set_ylabel('Energy',fontsize=16)
2272	Page.canvas.draw()
2273
2274	################################################################################
2275	##### PlotRama
2276	################################################################################
2277
2278	def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]):
2279	'needs a doc string'
2280
2281	global names
2282	names = Names
2283	rama = np.log(2*Rama+1.)
2284	ramaMax = np.max(rama)
2285	rama = np.reshape(rama,(45,45))
2286	global Phi,Psi
2287	Phi = []
2288	Psi = []
2289
2290	def OnPlotKeyPress(event):
2291	newPlot = False
2292	if event.key == 's':
2293	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2294	choice.sort()
2295	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2296	if dlg.ShowModal() == wx.ID_OK:
2297	sel = dlg.GetSelection()
2298	G2frame.RamaColor = choice[sel]
2299	else:
2300	G2frame.RamaColor = 'RdYlGn'
2301	dlg.Destroy()
2302	PlotRama(G2frame,phaseName,Rama)
2303
2304	def OnPick(event):
2305	ind = event.ind[0]
2306	msg = 'atoms:'+names[ind]
2307	Page.canvas.SetToolTipString(msg)
2308	try:
2309	page = G2frame.dataDisplay.GetSelection()
2310	except:
2311	return
2312	if G2frame.dataDisplay.GetPageText(page) == 'Ramachandran restraints':
2313	ramaGrid = G2frame.dataDisplay.GetPage(page).Ramas
2314	ramaGrid.ClearSelection()
2315	for row in range(ramaGrid.GetNumberRows()):
2316	if names[ind] in ramaGrid.GetCellValue(row,0):
2317	ramaGrid.SelectRow(row)
2318	ramaGrid.ForceRefresh()
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 = 'phi/psi: %5.3f %5.3f'%(xpos,ypos)
2325	Page.canvas.SetToolTipString(msg)
2326
2327	try:
2328	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
2329	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2330	Page.figure.clf()
2331	Plot = Page.figure.gca()
2332	if not Page.IsShown():
2333	Page.Show()
2334	except ValueError:
2335	Plot = G2frame.G2plotNB.addMpl('Ramachandran').gca()
2336	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
2337	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2338	Page.canvas.mpl_connect('pick_event', OnPick)
2339	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2340	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2341
2342	Page.Choice = ['s: to change colors']
2343	Page.keyPress = OnPlotKeyPress
2344	Page.SetFocus()
2345	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify phi/psi atoms'])
2346	acolor = mpl.cm.get_cmap(G2frame.RamaColor)
2347	if RamaName == 'All' or '-1' in RamaName:
2348	if len(Coeff):
2349	X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45))
2350	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
2351	Plot.contour(X,Y,np.reshape(Z,(45,45)))
2352	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
2353	extent=[-180,180,-180,180],origin='lower')
2354	if len(PhiPsi):
2355	Phi,Psi = PhiPsi.T
2356	Phi = np.where(Phi>180.,Phi-360.,Phi)
2357	Psi = np.where(Psi>180.,Psi-360.,Psi)
2358	Plot.plot(Phi,Psi,'ro',picker=5)
2359	Plot.set_xlim((-180.,180.))
2360	Plot.set_ylim((-180.,180.))
2361	else:
2362	if len(Coeff):
2363	X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45))
2364	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
2365	Plot.contour(X,Y,np.reshape(Z,(45,45)))
2366	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
2367	extent=[0,360,0,360],origin='lower')
2368	if len(PhiPsi):
2369	Phi,Psi = PhiPsi.T
2370	Plot.plot(Phi,Psi,'ro',picker=5)
2371	Plot.set_xlim((0.,360.))
2372	Plot.set_ylim((0.,360.))
2373	Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName)
2374	Plot.set_xlabel(r'$\phi$',fontsize=16)
2375	Plot.set_ylabel(r'$\psi$',fontsize=16)
2376	colorBar = Page.figure.colorbar(Img)
2377	Page.canvas.draw()
2378
2379
2380	################################################################################
2381	##### PlotSeq
2382	################################################################################
2383	def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX,fitnum=None,fitvals=None):
2384	'''Plot a result from a sequential refinement
2385
2386	:param wx.Frame G2frame: The main GSAS-II tree "window"
2387	:param list ColumnList: list of int values corresponding to columns
2388	selected as y values
2389	:param function TableGet: a function that takes a column number
2390	as argument and returns the column label, the values and there ESDs (or None)
2391	:param function SelectX: a function that returns a selected column
2392	number (or None) as the X-axis selection
2393	'''
2394	G2frame.seqXselect = SelectX
2395	try:
2396	G2frame.seqXaxis
2397	except:
2398	G2frame.seqXaxis = None
2399
2400	def OnMotion(event):
2401	if event.xdata and event.ydata: #avoid out of frame errors
2402	xpos = event.xdata
2403	ypos = event.ydata
2404	msg = '%5.3f %.6g'%(xpos,ypos)
2405	Page.canvas.SetToolTipString(msg)
2406
2407	def OnKeyPress(event):
2408	if event.key == 's':
2409	G2frame.seqXaxis = G2frame.seqXselect()
2410	Draw()
2411
2412	if fitnum is None:
2413	label = 'Sequential refinement'
2414	else:
2415	label = 'Parametric fit #'+str(fitnum+1)
2416	try:
2417	plotNum = G2frame.G2plotNB.plotList.index(label)
2418	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2419	Page.figure.clf()
2420	Plot = Page.figure.gca()
2421	if not Page.IsShown():
2422	Page.Show()
2423	except ValueError:
2424	Plot = G2frame.G2plotNB.addMpl(label).gca()
2425	plotNum = G2frame.G2plotNB.plotList.index(label)
2426	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2427	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
2428	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2429	Page.Choice = ['s to select plot x-axis',]
2430	Page.keyPress = OnKeyPress
2431	Page.seqYaxisList = ColumnList
2432	Page.seqTableGet = TableGet
2433	Page.fitvals = fitvals
2434
2435	def Draw():
2436	Page.SetFocus()
2437	G2frame.G2plotNB.status.SetStatusText('press s to select X axis',1)
2438	Plot.clear()
2439	if G2frame.seqXaxis is not None:
2440	xName,X,Xsig = Page.seqTableGet(G2frame.seqXaxis)
2441	else:
2442	X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1)
2443	xName = 'Data sequence number'
2444	for col in Page.seqYaxisList:
2445	name,Y,sig = Page.seqTableGet(col)
2446	if sig:
2447	if G2frame.seqReverse and not G2frame.seqXaxis:
2448	Y = Y[::-1]
2449	sig = sig[::-1]
2450	Plot.errorbar(X,Y,yerr=sig,label=name)
2451	else:
2452	if G2frame.seqReverse and not G2frame.seqXaxis:
2453	Y = Y[::-1]
2454	Plot.plot(X,Y)
2455	Plot.plot(X,Y,'o',label=name)
2456	if Page.fitvals:
2457	if G2frame.seqReverse and not G2frame.seqXaxis:
2458	Page.fitvals = Page.fitvals[::-1]
2459	Plot.plot(X,Page.fitvals,label='Fit')
2460
2461	Plot.legend(loc='best')
2462	Plot.set_ylabel('Parameter values')
2463	Plot.set_xlabel(xName)
2464	Page.canvas.draw()
2465	Draw()
2466
2467	################################################################################
2468	##### PlotExposedImage & PlotImage
2469	################################################################################
2470
2471	def PlotExposedImage(G2frame,newPlot=False,event=None):
2472	'''General access module for 2D image plotting
2473	'''
2474	plotNo = G2frame.G2plotNB.nb.GetSelection()
2475	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
2476	PlotImage(G2frame,newPlot,event,newImage=True)
2477	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
2478	PlotIntegration(G2frame,newPlot,event)
2479
2480	def OnStartMask(G2frame):
2481	'''Initiate the start of a Frame or Polygon map
2482
2483	:param wx.Frame G2frame: The main GSAS-II tree "window"
2484	:param str eventkey: a single letter ('f' or 'p') that
2485	determines what type of mask is created.
2486	'''
2487	Masks = G2frame.PatternTree.GetItemPyData(
2488	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
2489	if G2frame.MaskKey == 'f':
2490	Masks['Frames'] = []
2491	elif G2frame.MaskKey == 'p':
2492	Masks['Polygons'].append([])
2493	elif G2frame.MaskKey == 's':
2494	Masks['Points'].append([])
2495	elif G2frame.MaskKey == 'a':
2496	Masks['Arcs'].append([])
2497	elif G2frame.MaskKey == 'r':
2498	Masks['Rings'].append([])
2499	G2imG.UpdateMasks(G2frame,Masks)
2500	PlotImage(G2frame,newImage=True)
2501
2502	def OnStartNewDzero(G2frame):
2503	'''Initiate the start of adding a new d-zero to a strain data set
2504
2505	:param wx.Frame G2frame: The main GSAS-II tree "window"
2506	:param str eventkey: a single letter ('a') that
2507	triggers the addition of a d-zero.
2508	'''
2509	G2frame.dataFrame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value',0)
2510	StrSta = G2frame.PatternTree.GetItemPyData(
2511	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
2512
2513	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
2514	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
2515	masks, etc.
2516	'''
2517	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
2518	import numpy.ma as ma
2519	Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.))
2520	global Data,Masks
2521	colors=['b','g','r','c','m','k']
2522	Data = G2frame.PatternTree.GetItemPyData(
2523	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
2524	# patch
2525	if 'invert_x' not in Data:
2526	Data['invert_x'] = False
2527	Data['invert_y'] = True
2528	# end patch
2529	Masks = G2frame.PatternTree.GetItemPyData(
2530	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
2531	try: #may be absent
2532	StrSta = G2frame.PatternTree.GetItemPyData(
2533	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
2534	except TypeError: #is missing
2535	StrSta = {}
2536
2537	def OnImMotion(event):
2538	Page.canvas.SetToolTipString('')
2539	sizexy = Data['size']
2540	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
2541	Page.canvas.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata))
2542	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2543	item = G2frame.itemPicked
2544	pixelSize = Data['pixelSize']
2545	scalex = 1000./pixelSize[0]
2546	scaley = 1000./pixelSize[1]
2547	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
2548	if 'Text' in str(item):
2549	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
2550	else:
2551	xcent,ycent = Data['center']
2552	xpos = event.xdata-xcent
2553	ypos = event.ydata-ycent
2554	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
2555	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
2556	Page.canvas.SetToolTipString('%6d deg'%(azm))
2557	elif 'line1' in str(item) or 'line2' in str(item):
2558	Page.canvas.SetToolTipString('%8.3f deg'%(tth))
2559	else:
2560	xpos = event.xdata
2561	ypos = event.ydata
2562	xpix = xpos*scalex
2563	ypix = ypos*scaley
2564	Int = 0
2565	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
2566	Int = G2frame.ImageZ[ypix][xpix]
2567	tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
2568	Q = 2.*math.pi/dsp
2569	fields = ['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)]
2570	if G2frame.MaskKey in ['p','f']:
2571	fields[1] = 'Polygon/frame mask pick - LB next point, RB close polygon'
2572	elif G2frame.StrainKey:
2573	fields[0] = 'd-zero pick active'
2574	G2frame.G2plotNB.status.SetFields(fields)
2575
2576	def OnImPlotKeyPress(event):
2577	try:
2578	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
2579	except TypeError:
2580	return
2581	if PickName == 'Masks':
2582	if event.key in ['l','p','f','s','a','r']:
2583	G2frame.MaskKey = event.key
2584	OnStartMask(G2frame)
2585	PlotImage(G2frame,newPlot=False)
2586
2587	elif PickName == 'Stress/Strain':
2588	if event.key in ['a',]:
2589	G2frame.StrainKey = event.key
2590	OnStartNewDzero(G2frame)
2591	PlotImage(G2frame,newPlot=False)
2592
2593	elif PickName == 'Image Controls':
2594	if event.key in ['c',]:
2595	Xpos = event.xdata
2596	if not Xpos: #got point out of frame
2597	return
2598	Ypos = event.ydata
2599	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
2600	'Center change',style=wx.OK\|wx.CANCEL)
2601	try:
2602	if dlg.ShowModal() == wx.ID_OK:
2603	print 'move center to: ',Xpos,Ypos
2604	Data['center'] = [Xpos,Ypos]
2605	G2imG.UpdateImageControls(G2frame,Data,Masks)
2606	PlotImage(G2frame,newPlot=False)
2607	finally:
2608	dlg.Destroy()
2609	return
2610	elif event.key == 'l':
2611	G2frame.logPlot = not G2frame.logPlot
2612	elif event.key in ['x',]:
2613	Data['invert_x'] = not Data['invert_x']
2614	elif event.key in ['y',]:
2615	Data['invert_y'] = not Data['invert_y']
2616	PlotImage(G2frame,newPlot=True)
2617
2618	def OnKeyBox(event):
2619	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
2620	event.key = cb.GetValue()[0]
2621	cb.SetValue(' key press')
2622	if event.key in ['l','s','a','r','p','x','y']:
2623	wx.CallAfter(OnImPlotKeyPress,event)
2624	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
2625
2626	def OnImPick(event):
2627	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
2628	return
2629	if G2frame.itemPicked is not None: return
2630	G2frame.itemPicked = event.artist
2631	G2frame.mousePicked = event.mouseevent
2632
2633	def OnImRelease(event):
2634	try:
2635	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
2636	except TypeError:
2637	return
2638	if PickName not in ['Image Controls','Masks','Stress/Strain']:
2639	return
2640	pixelSize = Data['pixelSize']
2641	scalex = 1000./pixelSize[0]
2642	scaley = 1000./pixelSize[1]
2643	# pixLimit = Data['pixLimit'] #can be too tight
2644	pixLimit = 20 #this makes the search box 40x40 pixels
2645	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
2646	Xpos = event.xdata
2647	if not (Xpos and G2frame.ifGetRing): #got point out of frame
2648	return
2649	Ypos = event.ydata
2650	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
2651	if event.button == 1:
2652	Xpix = Xpos*scalex
2653	Ypix = Ypos*scaley
2654	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix)
2655	if I and J:
2656	xpos += .5 #shift to pixel center
2657	ypos += .5
2658	xpos /= scalex #convert to mm
2659	ypos /= scaley
2660	Data['ring'].append([xpos,ypos])
2661	elif event.button == 3:
2662	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...',0)
2663	if G2img.ImageCalibrate(G2frame,Data):
2664	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check',0)
2665	print 'Calibration successful'
2666	else:
2667	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose',0)
2668	print 'Calibration failed'
2669	G2frame.ifGetRing = False
2670	G2imG.UpdateImageControls(G2frame,Data,Masks)
2671	return
2672	PlotImage(G2frame,newImage=False)
2673	return
2674	elif G2frame.MaskKey and PickName == 'Masks':
2675	Xpos,Ypos = [event.xdata,event.ydata]
2676	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2677	return
2678	if G2frame.MaskKey == 's' and event.button == 1:
2679	Masks['Points'][-1] = [Xpos,Ypos,1.]
2680	G2frame.MaskKey = ''
2681	elif G2frame.MaskKey == 'r' and event.button == 1:
2682	tth = G2img.GetTth(Xpos,Ypos,Data)
2683	Masks['Rings'][-1] = [tth,0.1]
2684	G2frame.MaskKey = ''
2685	elif G2frame.MaskKey == 'a' and event.button == 1:
2686	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
2687	azm = int(azm)
2688	Masks['Arcs'][-1] = [tth,[azm-5,azm+5],0.1]
2689	G2frame.MaskKey = ''
2690	elif G2frame.MaskKey =='p':
2691	polygon = Masks['Polygons'][-1]
2692	if len(polygon) > 2 and event.button == 3:
2693	x0,y0 = polygon[0]
2694	polygon.append([x0,y0])
2695	G2frame.MaskKey = ''
2696	G2frame.G2plotNB.status.SetFields(['','Polygon closed'])
2697	else:
2698	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(Xpos,Ypos)])
2699	polygon.append([Xpos,Ypos])
2700	elif G2frame.MaskKey =='f':
2701	frame = Masks['Frames']
2702	if len(frame) > 2 and event.button == 3:
2703	x0,y0 = frame[0]
2704	frame.append([x0,y0])
2705	G2frame.MaskKey = ''
2706	G2frame.G2plotNB.status.SetFields(['','Frame closed'])
2707	else:
2708	G2frame.G2plotNB.status.SetFields(['','New frame point: %.1f,%.1f'%(Xpos,Ypos)])
2709	frame.append([Xpos,Ypos])
2710	G2imG.UpdateMasks(G2frame,Masks)
2711	PlotImage(G2frame,newImage=False)
2712	elif PickName == 'Stress/Strain' and G2frame.StrainKey:
2713	Xpos,Ypos = [event.xdata,event.ydata]
2714	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2715	return
2716	dsp = G2img.GetDsp(Xpos,Ypos,Data)
2717	StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':1.0,
2718	'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]})
2719	R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ,Data)
2720	if not len(R):
2721	del StrSta['d-zero'][-1]
2722	G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection')
2723	StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True)
2724	G2frame.StrainKey = ''
2725	G2imG.UpdateStressStrain(G2frame,StrSta)
2726	PlotStrain(G2frame,StrSta)
2727	PlotImage(G2frame,newPlot=False)
2728	else:
2729	Xpos,Ypos = [event.xdata,event.ydata]
2730	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
2731	return
2732	if G2frame.ifGetRing: #delete a calibration ring pick
2733	xypos = [Xpos,Ypos]
2734	rings = Data['ring']
2735	for ring in rings:
2736	if np.allclose(ring,xypos,.01,0):
2737	rings.remove(ring)
2738	else:
2739	tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3]
2740	itemPicked = str(G2frame.itemPicked)
2741	if 'Line2D' in itemPicked and PickName == 'Image Controls':
2742	if 'line1' in itemPicked:
2743	Data['IOtth'][0] = max(tth,0.001)
2744	elif 'line2' in itemPicked:
2745	Data['IOtth'][1] = tth
2746	elif 'line3' in itemPicked:
2747	Data['LRazimuth'][0] = int(azm)
2748	elif 'line4' in itemPicked and not Data['fullIntegrate']:
2749	Data['LRazimuth'][1] = int(azm)
2750
2751	Data['LRazimuth'][0] %= 360
2752	Data['LRazimuth'][1] %= 360
2753	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
2754	Data['LRazimuth'][1] += 360
2755	if Data['fullIntegrate']:
2756	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
2757
2758	if Data['IOtth'][0] > Data['IOtth'][1]:
2759	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
2760
2761	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
2762	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
2763	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
2764	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
2765	elif 'Circle' in itemPicked and PickName == 'Masks':
2766	spots = Masks['Points']
2767	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
2768	newPos = np.array([float(newPos[0]),float(newPos[1])])
2769	for spot in spots:
2770	if np.allclose(np.array([spot[:2]]),newPos):
2771	spot[:2] = Xpos,Ypos
2772	G2imG.UpdateMasks(G2frame,Masks)
2773	elif 'Line2D' in itemPicked and PickName == 'Masks':
2774	Obj = G2frame.itemPicked.findobj()
2775	rings = Masks['Rings']
2776	arcs = Masks['Arcs']
2777	polygons = Masks['Polygons']
2778	frame = Masks['Frames']
2779	for ring in G2frame.ringList:
2780	if Obj == ring[0]:
2781	rN = ring[1]
2782	if ring[2] == 'o':
2783	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)-rings[rN][1]/2.
2784	else:
2785	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)+rings[rN][1]/2.
2786	for arc in G2frame.arcList:
2787	if Obj == arc[0]:
2788	aN = arc[1]
2789	if arc[2] == 'o':
2790	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)-arcs[aN][2]/2
2791	elif arc[2] == 'i':
2792	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)+arcs[aN][2]/2
2793	elif arc[2] == 'l':
2794	arcs[aN][1][0] = int(G2img.GetAzm(Xpos,Ypos,Data))
2795	else:
2796	arcs[aN][1][1] = int(G2img.GetAzm(Xpos,Ypos,Data))
2797	for poly in G2frame.polyList: #merging points problem here?
2798	if Obj == poly[0]:
2799	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
2800	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
2801	pN = poly[1]
2802	for i,xy in enumerate(polygons[pN]):
2803	if np.allclose(np.array([xy]),oldPos,atol=1.0):
2804	if event.button == 1:
2805	polygons[pN][i] = Xpos,Ypos
2806	elif event.button == 3:
2807	polygons[pN].insert(i,[Xpos,Ypos])
2808	break
2809	if frame:
2810	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
2811	for i,xy in enumerate(frame):
2812	if np.allclose(np.array([xy]),oldPos,atol=1.0):
2813	if event.button == 1:
2814	frame[i] = Xpos,Ypos
2815	elif event.button == 3:
2816	frame.insert(i,[Xpos,Ypos])
2817	break
2818	G2imG.UpdateMasks(G2frame,Masks)
2819	# else: #keep for future debugging
2820	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
2821	PlotImage(G2frame,newImage=True)
2822	G2frame.itemPicked = None
2823
2824	try:
2825	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2826	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2827	if not newPlot:
2828	Plot = Page.figure.gca() #get previous powder plot & get limits
2829	xylim = Plot.get_xlim(),Plot.get_ylim()
2830	if newImage:
2831	Page.figure.clf()
2832	Plot = Page.figure.gca() #get a fresh plot after clf()
2833	except ValueError:
2834	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
2835	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
2836	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2837	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
2838	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
2839	Page.canvas.mpl_connect('pick_event', OnImPick)
2840	Page.canvas.mpl_connect('button_release_event', OnImRelease)
2841	xylim = []
2842	Page.Choice = None
2843	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
2844	Page.SetFocus()
2845	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
2846	G2frame.G2plotNB.status.DestroyChildren()
2847	if G2frame.logPlot:
2848	Title = 'log('+Title+')'
2849	Plot.set_title(Title)
2850	try:
2851	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
2852	Page.Choice = (' key press','l: log(I) on','x: flip x','y: flip y',)
2853	if G2frame.logPlot:
2854	Page.Choice[1] = 'l: log(I) off'
2855	Page.keyPress = OnImPlotKeyPress
2856	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Masks',]:
2857	Page.Choice = (' key press','l: log(I) on','s: spot mask','a: arc mask','r: ring mask',
2858	'p: polygon mask','f: frame mask',)
2859	if G2frame.logPlot:
2860	Page.Choice[1] = 'l: log(I) off'
2861	Page.keyPress = OnImPlotKeyPress
2862	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Stress/Strain',]:
2863	Page.Choice = (' key press','a: add new ring',)
2864	Page.keyPress = OnImPlotKeyPress
2865	except TypeError:
2866	pass
2867	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
2868	if imagefile != G2frame.oldImagefile:
2869	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
2870	if not imagefile:
2871	G2frame.G2plotNB.Delete('2D Powder Image')
2872	return
2873	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
2874	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
2875	G2frame.oldImagefile = imagefile
2876
2877	imScale = 1
2878	if len(G2frame.ImageZ) > 1024:
2879	imScale = len(G2frame.ImageZ)/1024
2880	sizexy = Data['size']
2881	pixelSize = Data['pixelSize']
2882	scalex = 1000./pixelSize[0]
2883	scaley = 1000./pixelSize[1]
2884	Xmax = sizexy[0]*pixelSize[0]/1000.
2885	Ymax = sizexy[1]*pixelSize[1]/1000.
2886	xlim = (0,Xmax)
2887	ylim = (Ymax,0)
2888	Imin,Imax = Data['range'][1]
2889	acolor = mpl.cm.get_cmap(Data['color'])
2890	xcent,ycent = Data['center']
2891	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
2892	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
2893	#do threshold mask - "real" mask - others are just bondaries
2894	Zlim = Masks['Thresholds'][1]
2895	wx.BeginBusyCursor()
2896	try:
2897
2898	if newImage:
2899	Imin,Imax = Data['range'][1]
2900	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]),Zlim[1])
2901	MaskA = ma.getmaskarray(MA)
2902	A = G2img.ImageCompress(MA,imScale)
2903	AM = G2img.ImageCompress(MaskA,imScale)
2904	if G2frame.logPlot:
2905	A = np.where(A>Imin,np.where(A<Imax,A,0),0)
2906	A = np.where(A>0,np.log(A),0)
2907	AM = np.where(AM>0,np.log(AM),0)
2908	Imin,Imax = [np.amin(A),np.amax(A)]
2909	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
2910	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
2911	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
2912	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
2913
2914	Plot.plot(xcent,ycent,'x')
2915	#G2frame.PatternTree.GetItemText(item)
2916	if Data['showLines']:
2917	LRAzim = Data['LRazimuth'] #NB: integers
2918	Nazm = Data['outAzimuths']
2919	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
2920	AzmthOff = Data['azmthOff']
2921	IOtth = Data['IOtth']
2922	wave = Data['wavelength']
2923	dspI = wave/(2.0*sind(IOtth[0]/2.0))
2924	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
2925	dspO = wave/(2.0*sind(IOtth[1]/2.0))
2926	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
2927	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
2928	if ellI:
2929	xyI = []
2930	for azm in Azm:
2931	xy = G2img.GetDetectorXY(dspI,azm,Data)
2932	if np.any(xy):
2933	xyI.append(xy)
2934	if len(xyI):
2935	xyI = np.array(xyI)
2936	arcxI,arcyI = xyI.T
2937	Plot.plot(arcxI,arcyI,picker=3)
2938	if ellO:
2939	xyO = []
2940	for azm in Azm:
2941	xy = G2img.GetDetectorXY(dspO,azm,Data)
2942	if np.any(xy):
2943	xyO.append(xy)
2944	if len(xyO):
2945	xyO = np.array(xyO)
2946	arcxO,arcyO = xyO.T
2947	Plot.plot(arcxO,arcyO,picker=3)
2948	if ellO and ellI:
2949	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
2950	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
2951	for i in range(Nazm):
2952	cake = LRAzim[0]+i*delAzm-AzmthOff
2953	if Data['centerAzm']:
2954	cake += delAzm/2.
2955	ind = np.searchsorted(Azm,cake)
2956	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
2957
2958	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
2959	for xring,yring in Data['ring']:
2960	Plot.plot(xring,yring,'r+',picker=3)
2961	if Data['setRings']:
2962	N = 0
2963	for ring in Data['rings']:
2964	xring,yring = np.array(ring).T[:2]
2965	Plot.plot(xring,yring,'.',color=colors[N%6])
2966	N += 1
2967	for ellipse in Data['ellipses']: #what about hyperbola?
2968	cent,phi,[width,height],col = ellipse
2969	if width > 0: #ellipses
2970	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
2971	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
2972	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
2973	for N,ring in enumerate(StrSta['d-zero']):
2974	xring,yring = ring['ImxyObs']
2975	Plot.plot(xring,yring,colors[N%6]+'.')
2976	#masks - mask lines numbered after integration limit lines
2977	spots = Masks['Points']
2978	rings = Masks['Rings']
2979	arcs = Masks['Arcs']
2980	polygons = Masks['Polygons']
2981	if 'Frames' not in Masks:
2982	Masks['Frames'] = []
2983	frame = Masks['Frames']
2984	for spot in spots:
2985	if spot:
2986	x,y,d = spot
2987	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
2988	G2frame.ringList = []
2989	for iring,ring in enumerate(rings):
2990	if ring:
2991	tth,thick = ring
2992	wave = Data['wavelength']
2993	xy1 = []
2994	xy2 = []
2995	Azm = np.linspace(0,362,181)
2996	for azm in Azm:
2997	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
2998	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
2999	x1,y1 = np.array(xy1).T
3000	x2,y2 = np.array(xy2).T
3001	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
3002	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
3003	G2frame.arcList = []
3004	for iarc,arc in enumerate(arcs):
3005	if arc:
3006	tth,azm,thick = arc
3007	wave = Data['wavelength']
3008	xy1 = []
3009	xy2 = []
3010	aR = azm[0],azm[1],azm[1]-azm[0]
3011	if azm[1]-azm[0] > 180:
3012	aR[2] /= 2
3013	Azm = np.linspace(aR[0],aR[1],aR[2])
3014	for azm in Azm:
3015	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
3016	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
3017	x1,y1 = np.array(xy1).T
3018	x2,y2 = np.array(xy2).T
3019	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
3020	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
3021	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
3022	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
3023	G2frame.polyList = []
3024	for ipoly,polygon in enumerate(polygons):
3025	if polygon:
3026	x,y = np.hsplit(np.array(polygon),2)
3027	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
3028	Plot.plot(x,y,'r')
3029	G2frame.frameList = []
3030	if frame:
3031	x,y = np.hsplit(np.array(frame),2)
3032	G2frame.frameList.append([Plot.plot(x,y,'g+',picker=10),0])
3033	Plot.plot(x,y,'g')
3034	if newImage:
3035	colorBar = Page.figure.colorbar(Img)
3036	Plot.set_xlim(xlim)
3037	Plot.set_ylim(ylim)
3038	if Data['invert_x']:
3039	Plot.invert_xaxis()
3040	if Data['invert_y']:
3041	Plot.invert_yaxis()
3042	if not newPlot and xylim:
3043	Page.toolbar.push_current()
3044	Plot.set_xlim(xylim[0])
3045	Plot.set_ylim(xylim[1])
3046	xylim = []
3047	Page.toolbar.push_current()
3048	Page.toolbar.draw()
3049	else:
3050	Page.canvas.draw()
3051	finally:
3052	wx.EndBusyCursor()
3053
3054	################################################################################
3055	##### PlotIntegration
3056	################################################################################
3057
3058	def PlotIntegration(G2frame,newPlot=False,event=None):
3059	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
3060	'''
3061
3062	def OnMotion(event):
3063	Page.canvas.SetToolTipString('')
3064	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3065	azm = event.ydata
3066	tth = event.xdata
3067	if azm and tth:
3068	G2frame.G2plotNB.status.SetFields(\
3069	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3070
3071	try:
3072	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
3073	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3074	if not newPlot:
3075	Plot = Page.figure.gca() #get previous plot & get limits
3076	xylim = Plot.get_xlim(),Plot.get_ylim()
3077	Page.figure.clf()
3078	Plot = Page.figure.gca() #get a fresh plot after clf()
3079
3080	except ValueError:
3081	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
3082	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
3083	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3084	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3085	Page.views = False
3086	view = False
3087	Page.Choice = None
3088	if not event:
3089	Page.SetFocus()
3090
3091	Data = G2frame.PatternTree.GetItemPyData(
3092	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3093	image = G2frame.Integrate[0]
3094	xsc = G2frame.Integrate[1]
3095	ysc = G2frame.Integrate[2]
3096	Imin,Imax = Data['range'][1]
3097	acolor = mpl.cm.get_cmap(Data['color'])
3098	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3099	Plot.set_ylabel('azimuth',fontsize=12)
3100	Plot.set_xlabel('2-theta',fontsize=12)
3101	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
3102	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
3103	colorBar = Page.figure.colorbar(Img)
3104	# if Data['ellipses']:
3105	# for ellipse in Data['ellipses']:
3106	# x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3107	# tth,azm = G2img.GetTthAzm(x,y,Data)
3108	## azm = np.where(azm < 0.,azm+360,azm)
3109	# Plot.plot(tth,azm,'b,')
3110	if not newPlot:
3111	Page.toolbar.push_current()
3112	Plot.set_xlim(xylim[0])
3113	Plot.set_ylim(xylim[1])
3114	xylim = []
3115	Page.toolbar.push_current()
3116	Page.toolbar.draw()
3117	else:
3118	Page.canvas.draw()
3119
3120	################################################################################
3121	##### PlotTRImage
3122	################################################################################
3123
3124	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
3125	'''a test plot routine - not normally used
3126	'''
3127
3128	def OnMotion(event):
3129	Page.canvas.SetToolTipString('')
3130	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3131	azm = event.xdata
3132	tth = event.ydata
3133	if azm and tth:
3134	G2frame.G2plotNB.status.SetFields(\
3135	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3136
3137	try:
3138	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3139	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3140	if not newPlot:
3141	Plot = Page.figure.gca() #get previous plot & get limits
3142	xylim = Plot.get_xlim(),Plot.get_ylim()
3143	Page.figure.clf()
3144	Plot = Page.figure.gca() #get a fresh plot after clf()
3145
3146	except ValueError:
3147	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
3148	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3149	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3150	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3151	Page.views = False
3152	view = False
3153	Page.Choice = None
3154	Page.SetFocus()
3155
3156	Data = G2frame.PatternTree.GetItemPyData(
3157	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3158	Imin,Imax = Data['range'][1]
3159	step = (Imax-Imin)/5.
3160	V = np.arange(Imin,Imax,step)
3161	acolor = mpl.cm.get_cmap(Data['color'])
3162	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3163	Plot.set_xlabel('azimuth',fontsize=12)
3164	Plot.set_ylabel('2-theta',fontsize=12)
3165	Plot.contour(tax,tay,taz,V,cmap=acolor)
3166	if Data['showLines']:
3167	IOtth = Data['IOtth']
3168	if Data['fullIntegrate']:
3169	LRAzim = [-180,180]
3170	else:
3171	LRAzim = Data['LRazimuth'] #NB: integers
3172	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
3173	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
3174	if not Data['fullIntegrate']:
3175	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
3176	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
3177	if Data['setRings']:
3178	rings = np.concatenate((Data['rings']),axis=0)
3179	for xring,yring,dsp in rings:
3180	x,y = G2img.GetTthAzm(xring,yring,Data)
3181	Plot.plot(y,x,'r+')
3182	if Data['ellipses']:
3183	for ellipse in Data['ellipses']:
3184	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3185	x,y = np.hsplit(ring,2)
3186	tth,azm = G2img.GetTthAzm(x,y,Data)
3187	Plot.plot(azm,tth,'b,')
3188	if not newPlot:
3189	Page.toolbar.push_current()
3190	Plot.set_xlim(xylim[0])
3191	Plot.set_ylim(xylim[1])
3192	xylim = []
3193	Page.toolbar.push_current()
3194	Page.toolbar.draw()
3195	else:
3196	Page.canvas.draw()
3197
3198	################################################################################
3199	##### PlotStructure
3200	################################################################################
3201
3202	def PlotStructure(G2frame,data):
3203	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
3204	thermal motion ellipsoids and polyhedra
3205	'''
3206
3207	def FindPeaksBonds(XYZ):
3208	rFact = data['Drawing']['radiusFactor']
3209	Bonds = [[] for x in XYZ]
3210	for i,xyz in enumerate(XYZ):
3211	Dx = XYZ-xyz
3212	dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
3213	IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2))
3214	for j in IndB[0]:
3215	Bonds[i].append(Dx[j]/2.)
3216	Bonds[j].append(-Dx[j]/2.)
3217	return Bonds
3218
3219	ForthirdPI = 4.0*math.pi/3.0
3220	generalData = data['General']
3221	cell = generalData['Cell'][1:7]
3222	Vol = generalData['Cell'][7:8][0]
3223	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
3224	Gmat,gmat = G2lat.cell2Gmat(cell)
3225	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3226	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3227	SGData = generalData['SGData']
3228	Mydir = generalData['Mydir']
3229	atomData = data['Atoms']
3230	mapPeaks = []
3231	drawingData = data['Drawing']
3232	if 'Map Peaks' in data:
3233	mapPeaks = np.array(data['Map Peaks'])
3234	peakMax = 100.
3235	if len(mapPeaks):
3236	peakMax = np.max(mapPeaks.T[0])
3237	resRBData = data['RBModels'].get('Residue',[])
3238	vecRBData = data['RBModels'].get('Vector',[])
3239	rbAtmDict = {}
3240	for rbObj in resRBData+vecRBData:
3241	exclList = ['X' for i in range(len(rbObj['Ids']))]
3242	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
3243	testRBObj = data.get('testRBObj',{})
3244	rbObj = testRBObj.get('rbObj',{})
3245	MCSA = data.get('MCSA',{})
3246	mcsaModels = MCSA.get('Models',[])
3247	if mcsaModels:
3248	XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA)
3249	mcsaXYZ = []
3250	mcsaTypes = []
3251	for xyz,atyp in zip(XYZs,Types):
3252	for item in G2spc.GenAtom(xyz,SGData):
3253	mcsaXYZ.append(item[0])
3254	mcsaTypes.append(atyp)
3255	mcsaBonds = FindPeaksBonds(mcsaXYZ)
3256	drawAtoms = drawingData.get('Atoms',[])
3257	mapData = {}
3258	flipData = {}
3259	rhoXYZ = []
3260	showBonds = False
3261	if 'Map' in generalData:
3262	mapData = generalData['Map']
3263	showBonds = mapData.get('Show bonds',False)
3264	if 'Flip' in generalData:
3265	flipData = generalData['Flip']
3266	flipData['mapRoll'] = [0,0,0]
3267	Wt = np.array([255,255,255])
3268	Rd = np.array([255,0,0])
3269	Gr = np.array([0,255,0])
3270	wxGreen = wx.Color(0,255,0)
3271	Bl = np.array([0,0,255])
3272	Or = np.array([255,128,0])
3273	wxOrange = wx.Color(255,128,0)
3274	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]])
3275	uEdges = np.array([
3276	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
3277	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
3278	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
3279	mD = 0.1
3280	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
3281	mapPeakVecs = np.inner(mV,Bmat)
3282
3283	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
3284	altDown = False
3285	shiftDown = False
3286	ctrlDown = False
3287
3288	def OnKeyBox(event):
3289	import Image
3290	# Draw() #make sure plot is fresh!!
3291	mode = cb.GetValue()
3292	if mode in ['jpeg','bmp','tiff',]:
3293	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
3294	size = Page.canvas.GetSize()
3295	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
3296	if mode in ['jpeg',]:
3297	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
3298	im = Image.new("RGBA", (size[0],size[1]))
3299	else:
3300	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
3301	im = Image.new("RGB", (size[0],size[1]))
3302	im.fromstring(Pix)
3303	im.save(Fname,mode)
3304	cb.SetValue(' save as/key:')
3305	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
3306	else:
3307	event.key = cb.GetValue()[0]
3308	cb.SetValue(' save as/key:')
3309	wx.CallAfter(OnKey,event)
3310	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
3311
3312	def OnKey(event): #on key UP!!
3313	# Draw() #make sure plot is fresh!!
3314	try:
3315	keyCode = event.GetKeyCode()
3316	if keyCode > 255:
3317	keyCode = 0
3318	key = chr(keyCode)
3319	except AttributeError: #if from OnKeyBox above
3320	key = str(event.key).upper()
3321	indx = drawingData['selectedAtoms']
3322	cx,ct = drawingData['atomPtrs'][:2]
3323	if key in ['C']:
3324	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
3325	drawingData['viewDir'] = [0,0,1]
3326	drawingData['oldxy'] = []
3327	V0 = np.array([0,0,1])
3328	V = np.inner(Amat,V0)
3329	V /= np.sqrt(np.sum(V**2))
3330	A = np.arccos(np.sum(V*V0))
3331	Q = G2mth.AV2Q(A,[0,1,0])
3332	drawingData['Quaternion'] = Q
3333	SetViewPointText(drawingData['viewPoint'][0])
3334	SetViewDirText(drawingData['viewDir'])
3335	Q = drawingData['Quaternion']
3336	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3337	elif key in ['N']:
3338	drawAtoms = drawingData['Atoms']
3339	if not len(drawAtoms): #no atoms
3340	return
3341	pI = drawingData['viewPoint'][1]
3342	if not len(pI):
3343	pI = [0,0]
3344	if indx:
3345	pI[0] = indx[pI[1]]
3346	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3347	pI[1] += 1
3348	if pI[1] >= len(indx):
3349	pI[1] = 0
3350	else:
3351	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3352	pI[0] += 1
3353	if pI[0] >= len(drawAtoms):
3354	pI[0] = 0
3355	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
3356	SetViewPointText(drawingData['viewPoint'][0])
3357	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
3358
3359	elif key in ['P']:
3360	drawAtoms = drawingData['Atoms']
3361	if not len(drawAtoms): #no atoms
3362	return
3363	pI = drawingData['viewPoint'][1]
3364	if not len(pI):
3365	pI = [0,0]
3366	if indx:
3367	pI[0] = indx[pI[1]]
3368	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3369	pI[1] -= 1
3370	if pI[1] < 0:
3371	pI[1] = len(indx)-1
3372	else:
3373	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
3374	pI[0] -= 1
3375	if pI[0] < 0:
3376	pI[0] = len(drawAtoms)-1
3377	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
3378	SetViewPointText(drawingData['viewPoint'][0])
3379	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
3380	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
3381	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
3382	SetMapRoll(dirDict[key])
3383	SetPeakRoll(dirDict[key])
3384	SetMapPeaksText(mapPeaks)
3385	Draw('key')
3386
3387	def GetTruePosition(xy,Add=False):
3388	View = glGetIntegerv(GL_VIEWPORT)
3389	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
3390	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
3391	Zmax = 1.
3392	if Add:
3393	Indx = GetSelectedAtoms()
3394	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
3395	for i,peak in enumerate(mapPeaks):
3396	x,y,z = peak[1:4]
3397	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
3398	XY = [int(X),int(View[3]-Y)]
3399	if np.allclose(xy,XY,atol=10) and Z < Zmax:
3400	Zmax = Z
3401	try:
3402	Indx.remove(i)
3403	ClearSelectedAtoms()
3404	for id in Indx:
3405	SetSelectedAtoms(id,Add)
3406	except:
3407	SetSelectedAtoms(i,Add)
3408	else:
3409	cx = drawingData['atomPtrs'][0]
3410	for i,atom in enumerate(drawAtoms):
3411	x,y,z = atom[cx:cx+3]
3412	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
3413	XY = [int(X),int(View[3]-Y)]
3414	if np.allclose(xy,XY,atol=10) and Z < Zmax:
3415	Zmax = Z
3416	try:
3417	Indx.remove(i)
3418	ClearSelectedAtoms()
3419	for id in Indx:
3420	SetSelectedAtoms(id,Add)
3421	except:
3422	SetSelectedAtoms(i,Add)
3423
3424	def OnMouseDown(event):
3425	xy = event.GetPosition()
3426	if event.ShiftDown():
3427	if event.LeftIsDown():
3428	GetTruePosition(xy)
3429	elif event.RightIsDown():
3430	GetTruePosition(xy,True)
3431	else:
3432	drawingData['oldxy'] = list(xy)
3433
3434	def OnMouseMove(event):
3435	if event.ShiftDown(): #don't want any inadvertant moves when picking
3436	return
3437	newxy = event.GetPosition()
3438
3439	if event.Dragging():
3440	if event.AltDown() and rbObj:
3441	if event.LeftIsDown():
3442	SetRBRotation(newxy)
3443	Q = rbObj['Orient'][0]
3444	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3445	elif event.RightIsDown():
3446	SetRBTranslation(newxy)
3447	Tx,Ty,Tz = rbObj['Orig'][0]
3448	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
3449	elif event.MiddleIsDown():
3450	SetRBRotationZ(newxy)
3451	Q = rbObj['Orient'][0]
3452	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3453	Draw('move')
3454	elif not event.ControlDown():
3455	if event.LeftIsDown():
3456	SetRotation(newxy)
3457	Q = drawingData['Quaternion']
3458	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3459	elif event.RightIsDown():
3460	SetTranslation(newxy)
3461	Tx,Ty,Tz = drawingData['viewPoint'][0]
3462	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
3463	elif event.MiddleIsDown():
3464	SetRotationZ(newxy)
3465	Q = drawingData['Quaternion']
3466	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
3467	Draw('move')
3468
3469
3470	def OnMouseWheel(event):
3471	if event.ShiftDown():
3472	return
3473	drawingData['cameraPos'] += event.GetWheelRotation()/24.
3474	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
3475	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
3476	page = getSelection()
3477	if page:
3478	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3479	G2frame.dataDisplay.cameraPosTxt.SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
3480	G2frame.dataDisplay.cameraSlider.SetValue(drawingData['cameraPos'])
3481	Draw('wheel')
3482
3483	def getSelection():
3484	try:
3485	return G2frame.dataDisplay.GetSelection()
3486	except AttributeError:
3487	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!',1)
3488	return 0
3489
3490	def SetViewPointText(VP):
3491	page = getSelection()
3492	if page:
3493	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3494	G2frame.dataDisplay.viewPoint.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
3495
3496	def SetRBOrigText():
3497	page = getSelection()
3498	if page:
3499	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
3500	for i,sizer in enumerate(testRBObj['Sizers']['Xsizers']):
3501	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orig'][0][i]))
3502
3503	def SetRBOrienText():
3504	page = getSelection()
3505	if page:
3506	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
3507	for i,sizer in enumerate(testRBObj['Sizers']['Osizers']):
3508	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orient'][0][i]))
3509
3510	def SetViewDirText(VD):
3511	page = getSelection()
3512	if page:
3513	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
3514	G2frame.dataDisplay.viewDir.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
3515
3516	def SetMapPeaksText(mapPeaks):
3517	page = getSelection()
3518	if page:
3519	if G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3520	G2frame.MapPeaksTable.SetData(mapPeaks)
3521	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
3522	names = [child.GetName() for child in panel]
3523	panel[names.index('grid window')].Refresh()
3524
3525	def ClearSelectedAtoms():
3526	page = getSelection()
3527	if page:
3528	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3529	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
3530	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3531	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
3532	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3533	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
3534
3535
3536	def SetSelectedAtoms(ind,Add=False):
3537	page = getSelection()
3538	if page:
3539	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3540	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
3541	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3542	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add)
3543	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3544	Id = drawAtoms[ind][-3]
3545	for i,atom in enumerate(atomData):
3546	if atom[-1] == Id:
3547	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
3548
3549	def GetSelectedAtoms():
3550	page = getSelection()
3551	Ind = []
3552	if page:
3553	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
3554	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
3555	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
3556	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows()
3557	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
3558	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
3559	return Ind
3560
3561	def SetBackground():
3562	R,G,B,A = Page.camera['backColor']
3563	glClearColor(R,G,B,A)
3564	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
3565
3566	def SetLights():
3567	glEnable(GL_DEPTH_TEST)
3568	glShadeModel(GL_SMOOTH)
3569	glEnable(GL_LIGHTING)
3570	glEnable(GL_LIGHT0)
3571	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
3572	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
3573	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
3574
3575	def GetRoll(newxy,rho):
3576	Q = drawingData['Quaternion']
3577	dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,]))
3578	dxy = np.array(dxy*rho.shape)
3579	roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0))
3580	return roll
3581
3582	def SetMapRoll(newxy):
3583	rho = mapData['rho']
3584	roll = GetRoll(newxy,rho)
3585	mapData['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
3586	drawingData['oldxy'] = list(newxy)
3587
3588	def SetPeakRoll(newxy):
3589	rho = mapData['rho']
3590	roll = GetRoll(newxy,rho)
3591	steps = 1./np.array(rho.shape)
3592	dxy = roll*steps
3593	for peak in mapPeaks:
3594	peak[1:4] += dxy
3595	peak[1:4] %= 1.
3596	peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2))
3597
3598	def SetTranslation(newxy):
3599	#first get translation vector in screen coords.
3600	oldxy = drawingData['oldxy']
3601	if not len(oldxy): oldxy = list(newxy)
3602	dxy = newxy-oldxy
3603	drawingData['oldxy'] = list(newxy)
3604	V = np.array([-dxy[0],dxy[1],0.])
3605	#then transform to rotated crystal coordinates & apply to view point
3606	Q = drawingData['Quaternion']
3607	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
3608	Tx,Ty,Tz = drawingData['viewPoint'][0]
3609	Tx += V[0]*0.01
3610	Ty += V[1]*0.01
3611	Tz += V[2]*0.01
3612	drawingData['viewPoint'][0] = Tx,Ty,Tz
3613	SetViewPointText([Tx,Ty,Tz])
3614
3615	def SetRBTranslation(newxy):
3616	#first get translation vector in screen coords.
3617	oldxy = drawingData['oldxy']
3618	if not len(oldxy): oldxy = list(newxy)
3619	dxy = newxy-oldxy
3620	drawingData['oldxy'] = list(newxy)
3621	V = np.array([-dxy[0],dxy[1],0.])
3622	#then transform to rotated crystal coordinates & apply to RB origin
3623	Q = drawingData['Quaternion']
3624	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
3625	Tx,Ty,Tz = rbObj['Orig'][0]
3626	Tx -= V[0]*0.01
3627	Ty -= V[1]*0.01
3628	Tz -= V[2]*0.01
3629	rbObj['Orig'][0] = Tx,Ty,Tz
3630	SetRBOrigText()
3631
3632	def SetRotation(newxy):
3633	#first get rotation vector in screen coords. & angle increment
3634	oldxy = drawingData['oldxy']
3635	if not len(oldxy): oldxy = list(newxy)
3636	dxy = newxy-oldxy
3637	drawingData['oldxy'] = list(newxy)
3638	V = np.array([dxy[1],dxy[0],0.])
3639	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
3640	# next transform vector back to xtal coordinates via inverse quaternion
3641	# & make new quaternion
3642	Q = drawingData['Quaternion']
3643	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
3644	DQ = G2mth.AVdeg2Q(A,V)
3645	Q = G2mth.prodQQ(Q,DQ)
3646	drawingData['Quaternion'] = Q
3647	# finally get new view vector - last row of rotation matrix
3648	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
3649	VD /= np.sqrt(np.sum(VD**2))
3650	drawingData['viewDir'] = VD
3651	SetViewDirText(VD)
3652
3653	def SetRotationZ(newxy):
3654	#first get rotation vector (= view vector) in screen coords. & angle increment
3655	View = glGetIntegerv(GL_VIEWPORT)
3656	cent = [View[2]/2,View[3]/2]
3657	oldxy = drawingData['oldxy']
3658	if not len(oldxy): oldxy = list(newxy)
3659	dxy = newxy-oldxy
3660	drawingData['oldxy'] = list(newxy)
3661	V = drawingData['viewDir']
3662	A = [0,0]
3663	A[0] = dxy[1]*.25
3664	A[1] = dxy[0]*.25
3665	if newxy[0] > cent[0]:
3666	A[0] *= -1
3667	if newxy[1] < cent[1]:
3668	A[1] *= -1
3669	# next transform vector back to xtal coordinates & make new quaternion
3670	Q = drawingData['Quaternion']
3671	V = np.inner(Amat,V)
3672	Qx = G2mth.AVdeg2Q(A[0],V)
3673	Qy = G2mth.AVdeg2Q(A[1],V)
3674	Q = G2mth.prodQQ(Q,Qx)
3675	Q = G2mth.prodQQ(Q,Qy)
3676	drawingData['Quaternion'] = Q
3677
3678	def SetRBRotation(newxy):
3679	#first get rotation vector in screen coords. & angle increment
3680	oldxy = drawingData['oldxy']
3681	if not len(oldxy): oldxy = list(newxy)
3682	dxy = newxy-oldxy
3683	drawingData['oldxy'] = list(newxy)
3684	V = np.array([dxy[1],dxy[0],0.])
3685	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
3686	# next transform vector back to xtal coordinates via inverse quaternion
3687	# & make new quaternion
3688	Q = rbObj['Orient'][0] #rotate RB to Cart
3689	QC = drawingData['Quaternion'] #rotate Cart to drawing
3690	V = G2mth.prodQVQ(G2mth.invQ(QC),V)
3691	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
3692	DQ = G2mth.AVdeg2Q(A,V)
3693	Q = G2mth.prodQQ(Q,DQ)
3694	rbObj['Orient'][0] = Q
3695	SetRBOrienText()
3696
3697	def SetRBRotationZ(newxy):
3698	#first get rotation vector (= view vector) in screen coords. & angle increment
3699	View = glGetIntegerv(GL_VIEWPORT)
3700	cent = [View[2]/2,View[3]/2]
3701	oldxy = drawingData['oldxy']
3702	if not len(oldxy): oldxy = list(newxy)
3703	dxy = newxy-oldxy
3704	drawingData['oldxy'] = list(newxy)
3705	V = drawingData['viewDir']
3706	A = [0,0]
3707	A[0] = dxy[1]*.25
3708	A[1] = dxy[0]*.25
3709	if newxy[0] < cent[0]:
3710	A[0] *= -1
3711	if newxy[1] > cent[1]:
3712	A[1] *= -1
3713	# next transform vector back to RB coordinates & make new quaternion
3714	Q = rbObj['Orient'][0] #rotate RB to cart
3715	V = np.inner(Amat,V)
3716	V = -G2mth.prodQVQ(G2mth.invQ(Q),V)
3717	Qx = G2mth.AVdeg2Q(A[0],V)
3718	Qy = G2mth.AVdeg2Q(A[1],V)
3719	Q = G2mth.prodQQ(Q,Qx)
3720	Q = G2mth.prodQQ(Q,Qy)
3721	rbObj['Orient'][0] = Q
3722	SetRBOrienText()
3723
3724	def RenderBox():
3725	glEnable(GL_COLOR_MATERIAL)
3726	glLineWidth(2)
3727	glEnable(GL_BLEND)
3728	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
3729	glEnable(GL_LINE_SMOOTH)
3730	glBegin(GL_LINES)
3731	for line,color in zip(uEdges,uColors):
3732	glColor3ubv(color)
3733	glVertex3fv(line[0])
3734	glVertex3fv(line[1])
3735	glEnd()
3736	glColor4ubv([0,0,0,0])
3737	glDisable(GL_LINE_SMOOTH)
3738	glDisable(GL_BLEND)
3739	glDisable(GL_COLOR_MATERIAL)
3740
3741	def RenderUnitVectors(x,y,z):
3742	xyz = np.array([x,y,z])
3743	glEnable(GL_COLOR_MATERIAL)
3744	glLineWidth(1)
3745	glPushMatrix()
3746	glTranslate(x,y,z)
3747	glScalef(1/cell[0],1/cell[1],1/cell[2])
3748	glBegin(GL_LINES)
3749	for line,color in zip(uEdges,uColors)[:3]:
3750	glColor3ubv(color)
3751	glVertex3fv(-line[1]/2.)
3752	glVertex3fv(line[1]/2.)
3753	glEnd()
3754	glPopMatrix()
3755	glColor4ubv([0,0,0,0])
3756	glDisable(GL_COLOR_MATERIAL)
3757
3758	def RenderSphere(x,y,z,radius,color):
3759	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3760	glPushMatrix()
3761	glTranslate(x,y,z)
3762	glMultMatrixf(B4mat.T)
3763	q = gluNewQuadric()
3764	gluSphere(q,radius,20,10)
3765	glPopMatrix()
3766
3767	def RenderDots(XYZ,RC):
3768	glEnable(GL_COLOR_MATERIAL)
3769	XYZ = np.array(XYZ)
3770	glPushMatrix()
3771	for xyz,rc in zip(XYZ,RC):
3772	x,y,z = xyz
3773	r,c = rc
3774	glColor3ubv(c)
3775	glPointSize(r*50)
3776	glBegin(GL_POINTS)
3777	glVertex3fv(xyz)
3778	glEnd()
3779	glPopMatrix()
3780	glColor4ubv([0,0,0,0])
3781	glDisable(GL_COLOR_MATERIAL)
3782
3783	def RenderSmallSphere(x,y,z,radius,color):
3784	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3785	glPushMatrix()
3786	glTranslate(x,y,z)
3787	glMultMatrixf(B4mat.T)
3788	q = gluNewQuadric()
3789	gluSphere(q,radius,4,2)
3790	glPopMatrix()
3791
3792	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
3793	s1,s2,s3 = E
3794	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3795	glPushMatrix()
3796	glTranslate(x,y,z)
3797	glMultMatrixf(B4mat.T)
3798	glMultMatrixf(R4.T)
3799	glEnable(GL_NORMALIZE)
3800	glScale(s1,s2,s3)
3801	q = gluNewQuadric()
3802	gluSphere(q,ellipseProb,20,10)
3803	glDisable(GL_NORMALIZE)
3804	glPopMatrix()
3805
3806	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
3807	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3808	glPushMatrix()
3809	glTranslate(x,y,z)
3810	glMultMatrixf(B4mat.T)
3811	for bond in Bonds:
3812	glPushMatrix()
3813	Dx = np.inner(Amat,bond)
3814	Z = np.sqrt(np.sum(Dx**2))
3815	if Z:
3816	azm = atan2d(-Dx[1],-Dx[0])
3817	phi = acosd(Dx[2]/Z)
3818	glRotate(-azm,0,0,1)
3819	glRotate(phi,1,0,0)
3820	q = gluNewQuadric()
3821	gluCylinder(q,radius,radius,Z,slice,2)
3822	glPopMatrix()
3823	glPopMatrix()
3824
3825	def RenderLines(x,y,z,Bonds,color):
3826	glShadeModel(GL_FLAT)
3827	xyz = np.array([x,y,z])
3828	glEnable(GL_COLOR_MATERIAL)
3829	glLineWidth(1)
3830	glColor3fv(color)
3831	glPushMatrix()
3832	glBegin(GL_LINES)
3833	for bond in Bonds:
3834	glVertex3fv(xyz)
3835	glVertex3fv(xyz+bond)
3836	glEnd()
3837	glColor4ubv([0,0,0,0])
3838	glPopMatrix()
3839	glDisable(GL_COLOR_MATERIAL)
3840	glShadeModel(GL_SMOOTH)
3841
3842	def RenderPolyhedra(x,y,z,Faces,color):
3843	glShadeModel(GL_FLAT)
3844	glPushMatrix()
3845	glTranslate(x,y,z)
3846	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
3847	glShadeModel(GL_SMOOTH)
3848	glMultMatrixf(B4mat.T)
3849	for face,norm in Faces:
3850	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
3851	glFrontFace(GL_CW)
3852	glNormal3fv(norm)
3853	glBegin(GL_TRIANGLES)
3854	for vert in face:
3855	glVertex3fv(vert)
3856	glEnd()
3857	glPopMatrix()
3858	glShadeModel(GL_SMOOTH)
3859
3860	def RenderMapPeak(x,y,z,color,den):
3861	glShadeModel(GL_FLAT)
3862	xyz = np.array([x,y,z])
3863	glEnable(GL_COLOR_MATERIAL)
3864	glLineWidth(3)
3865	glColor3fv(color*den/255)
3866	glPushMatrix()
3867	glBegin(GL_LINES)
3868	for vec in mapPeakVecs:
3869	glVertex3fv(vec[0]+xyz)
3870	glVertex3fv(vec[1]+xyz)
3871	glEnd()
3872	glColor4ubv([0,0,0,0])
3873	glPopMatrix()
3874	glDisable(GL_COLOR_MATERIAL)
3875	glShadeModel(GL_SMOOTH)
3876
3877	def RenderBackbone(Backbone,BackboneColor,radius):
3878	glPushMatrix()
3879	glMultMatrixf(B4mat.T)
3880	glEnable(GL_COLOR_MATERIAL)
3881	glShadeModel(GL_SMOOTH)
3882	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
3883	glePolyCylinder(Backbone,BackboneColor,radius)
3884	glPopMatrix()
3885	glDisable(GL_COLOR_MATERIAL)
3886
3887	def RenderLabel(x,y,z,label,r,color,matRot):
3888	'''
3889	color wx.Color object
3890	'''
3891	glPushMatrix()
3892	glTranslate(x,y,z)
3893	glMultMatrixf(B4mat.T)
3894	glDisable(GL_LIGHTING)
3895	glRasterPos3f(0,0,0)
3896	glMultMatrixf(matRot)
3897	glRotate(180,1,0,0) #fix to flip about x-axis
3898	text = gltext.Text(text=label,font=Font,foreground=color)
3899	text.draw_text(scale=0.025)
3900	glEnable(GL_LIGHTING)
3901	glPopMatrix()
3902
3903	def RenderMap(rho,rhoXYZ,indx,Rok):
3904	glShadeModel(GL_FLAT)
3905	cLevel = drawingData['contourLevel']
3906	XYZ = []
3907	RC = []
3908	for i,xyz in enumerate(rhoXYZ):
3909	if not Rok[i]:
3910	x,y,z = xyz
3911	I,J,K = indx[i]
3912	alpha = 1.0
3913	if cLevel < 1.:
3914	alpha = (abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)
3915	if rho[I,J,K] < 0.:
3916	XYZ.append(xyz)
3917	RC.append([0.1*alpha,Rd])
3918	else:
3919	XYZ.append(xyz)
3920	RC.append([0.1*alpha,Gr])
3921	RenderDots(XYZ,RC)
3922	glShadeModel(GL_SMOOTH)
3923
3924	def Draw(caller=''):
3925	#useful debug?
3926	# if caller:
3927	# print caller
3928	# end of useful debug
3929	mapData = generalData['Map']
3930	pageName = ''
3931	page = getSelection()
3932	if page:
3933	pageName = G2frame.dataDisplay.GetPageText(page)
3934	rhoXYZ = []
3935	if len(mapData['rho']):
3936	VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
3937	contLevel = drawingData['contourLevel']*mapData['rhoMax']
3938	if 'delt-F' in mapData['MapType']:
3939	rho = ma.array(mapData['rho'],mask=(np.abs(mapData['rho'])<contLevel))
3940	else:
3941	rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
3942	steps = 1./np.array(rho.shape)
3943	incre = np.where(VP>=0,VP%steps,VP%steps-steps)
3944	Vsteps = -np.array(VP/steps,dtype='i')
3945	rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
3946	indx = np.array(ma.nonzero(rho)).T
3947	rhoXYZ = indx*steps+VP-incre
3948	Nc = len(rhoXYZ)
3949	rcube = 2000.Vol/(ForthirdPINc)
3950	rmax = math.exp(math.log(rcube)/3.)**2
3951	radius = min(drawingData['mapSize']**2,rmax)
3952	view = np.array(drawingData['viewPoint'][0])
3953	Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
3954	Ind = GetSelectedAtoms()
3955	VS = np.array(Page.canvas.GetSize())
3956	aspect = float(VS[0])/float(VS[1])
3957	cPos = drawingData['cameraPos']
3958	Zclip = drawingData['Zclip']*cPos/200.
3959	Q = drawingData['Quaternion']
3960	Tx,Ty,Tz = drawingData['viewPoint'][0]
3961	cx,ct,cs,ci = drawingData['atomPtrs']
3962	bondR = drawingData['bondRadius']
3963	G,g = G2lat.cell2Gmat(cell)
3964	GS = G
3965	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
3966	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
3967	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
3968	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
3969
3970	SetBackground()
3971	glInitNames()
3972	glPushName(0)
3973
3974	glMatrixMode(GL_PROJECTION)
3975	glLoadIdentity()
3976	glViewport(0,0,VS[0],VS[1])
3977	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
3978	gluLookAt(0,0,cPos,0,0,0,0,1,0)
3979	SetLights()
3980
3981	glMatrixMode(GL_MODELVIEW)
3982	glLoadIdentity()
3983	matRot = G2mth.Q2Mat(Q)
3984	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
3985	glMultMatrixf(matRot.T)
3986	glMultMatrixf(A4mat.T)
3987	glTranslate(-Tx,-Ty,-Tz)
3988	if drawingData['unitCellBox']:
3989	RenderBox()
3990	if drawingData['showABC']:
3991	x,y,z = drawingData['viewPoint'][0]
3992	RenderUnitVectors(x,y,z)
3993	Backbones = {}
3994	BackboneColor = []
3995	time0 = time.time()
3996	# glEnable(GL_BLEND)
3997	# glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
3998	for iat,atom in enumerate(drawingData['Atoms']):
3999	x,y,z = atom[cx:cx+3]
4000	Bonds = atom[-2]
4001	Faces = atom[-1]
4002	try:
4003	atNum = generalData['AtomTypes'].index(atom[ct])
4004	except ValueError:
4005	atNum = -1
4006	CL = atom[cs+2]
4007	atColor = np.array(CL)/255.
4008	if drawingData['showRigidBodies'] and atom[ci] in rbAtmDict:
4009	bndColor = Or
4010	else:
4011	bndColor = atColor
4012	if iat in Ind and G2frame.dataDisplay.GetPageText(getSelection()) != 'Map peaks':
4013	atColor = np.array(Gr)/255.
4014	# color += [.25,]
4015	radius = 0.5
4016	if atom[cs] != '':
4017	try:
4018	glLoadName(atom[-3])
4019	except: #problem with old files - missing code
4020	pass
4021	if 'balls' in atom[cs]:
4022	vdwScale = drawingData['vdwScale']
4023	ballScale = drawingData['ballScale']
4024	if atNum < 0:
4025	radius = 0.2
4026	elif 'H' == atom[ct]:
4027	if drawingData['showHydrogen']:
4028	if 'vdW' in atom[cs] and atNum >= 0:
4029	radius = vdwScale*generalData['vdWRadii'][atNum]
4030	else:
4031	radius = ballScale*drawingData['sizeH']
4032	else:
4033	radius = 0.0
4034	else:
4035	if 'vdW' in atom[cs]:
4036	radius = vdwScale*generalData['vdWRadii'][atNum]
4037	else:
4038	radius = ballScale*generalData['BondRadii'][atNum]
4039	RenderSphere(x,y,z,radius,atColor)
4040	if 'sticks' in atom[cs]:
4041	RenderBonds(x,y,z,Bonds,bondR,bndColor)
4042	elif 'ellipsoids' in atom[cs]:
4043	RenderBonds(x,y,z,Bonds,bondR,bndColor)
4044	if atom[cs+3] == 'A':
4045	Uij = atom[cs+5:cs+11]
4046	U = np.multiply(G2spc.Uij2U(Uij),GS)
4047	U = np.inner(Amat,np.inner(U,Amat).T)
4048	E,R = nl.eigh(U)
4049	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4050	E = np.sqrt(E)
4051	if atom[ct] == 'H' and not drawingData['showHydrogen']:
4052	pass
4053	else:
4054	RenderEllipsoid(x,y,z,ellipseProb,E,R4,atColor)
4055	else:
4056	if atom[ct] == 'H' and not drawingData['showHydrogen']:
4057	pass
4058	else:
4059	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
4060	RenderSphere(x,y,z,radius,atColor)
4061	elif 'lines' in atom[cs]:
4062	radius = 0.1
4063	RenderLines(x,y,z,Bonds,bndColor)
4064	# RenderBonds(x,y,z,Bonds,0.05,color,6)
4065	elif atom[cs] == 'sticks':
4066	radius = 0.1
4067	RenderBonds(x,y,z,Bonds,bondR,bndColor)
4068	elif atom[cs] == 'polyhedra':
4069	RenderPolyhedra(x,y,z,Faces,atColor)
4070	elif atom[cs] == 'backbone':
4071	if atom[ct-1].split()[0] in ['C','N']:
4072	if atom[2] not in Backbones:
4073	Backbones[atom[2]] = []
4074	Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
4075	BackboneColor.append(list(atColor))
4076
4077	if atom[cs+1] == 'type':
4078	RenderLabel(x,y,z,' '+atom[ct],radius,wxGreen,matRot)
4079	elif atom[cs+1] == 'name':
4080	RenderLabel(x,y,z,' '+atom[ct-1],radius,wxGreen,matRot)
4081	elif atom[cs+1] == 'number':
4082	RenderLabel(x,y,z,' '+str(iat),radius,wxGreen,matRot)
4083	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
4084	RenderLabel(x,y,z,' '+atom[ct-4],radius,wxGreen,matRot)
4085	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
4086	RenderLabel(x,y,z,' '+atom[ct-3],radius,wxGreen,matRot)
4087	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
4088	RenderLabel(x,y,z,' '+atom[ct-2],radius,wxGreen,matRot)
4089	# glDisable(GL_BLEND)
4090	if len(rhoXYZ):
4091	RenderMap(rho,rhoXYZ,indx,Rok)
4092	if len(mapPeaks):
4093	XYZ = mapPeaks.T[1:4].T
4094	mapBonds = FindPeaksBonds(XYZ)
4095	for ind,[mag,x,y,z,d] in enumerate(mapPeaks):
4096	if ind in Ind and pageName == 'Map peaks':
4097	RenderMapPeak(x,y,z,Gr,1.0)
4098	else:
4099	RenderMapPeak(x,y,z,Wt,mag/peakMax)
4100	if showBonds:
4101	RenderLines(x,y,z,mapBonds[ind],Wt)
4102	if len(testRBObj) and pageName == 'RB Models':
4103	XYZ = G2mth.UpdateRBXYZ(Bmat,testRBObj['rbObj'],testRBObj['rbData'],testRBObj['rbType'])[0]
4104	rbBonds = FindPeaksBonds(XYZ)
4105	for ind,[x,y,z] in enumerate(XYZ):
4106	aType = testRBObj['rbAtTypes'][ind]
4107	name = ' '+aType+str(ind)
4108	color = np.array(testRBObj['AtInfo'][aType][1])
4109	RenderSphere(x,y,z,0.2,color/255.)
4110	RenderBonds(x,y,z,rbBonds[ind],0.03,Gr)
4111	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4112	if len(mcsaModels) > 1 and pageName == 'MC/SA': #skip the default MD entry
4113	for ind,[x,y,z] in enumerate(mcsaXYZ):
4114	aType = mcsaTypes[ind]
4115	name = ' '+aType+str(ind)
4116	color = np.array(MCSA['AtInfo'][aType][1])
4117	RenderSphere(x,y,z,0.2,color/255.)
4118	RenderBonds(x,y,z,mcsaBonds[ind],0.03,Gr)
4119	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4120	if Backbones:
4121	for chain in Backbones:
4122	Backbone = Backbones[chain]
4123	RenderBackbone(Backbone,BackboneColor,bondR)
4124	# print time.time()-time0
4125	Page.canvas.SwapBuffers()
4126
4127	def OnSize(event):
4128	Draw('size')
4129
4130	def OnFocus(event): #not needed?? Bind commented out below
4131	Draw('focus')
4132
4133	try:
4134	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
4135	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4136	except ValueError:
4137	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
4138	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
4139	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4140	Page.views = False
4141	view = False
4142	altDown = False
4143	Font = Page.GetFont()
4144	Page.SetFocus()
4145	Page.Choice = None
4146	if mapData['Flip']:
4147	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2',
4148	'u: roll up','d: roll down','l: roll left','r: roll right']
4149	else:
4150	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2','n: next','p: previous']
4151	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
4152	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
4153	cb.SetValue(' save as/key:')
4154	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
4155	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
4156	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
4157	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
4158	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
4159	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
4160	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
4161	# Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
4162	Page.camera['position'] = drawingData['cameraPos']
4163	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
4164	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
4165	try:
4166	Page.canvas.SetCurrent()
4167	except:
4168	pass
4169	Draw('main')
4170
4171	################################################################################
4172	#### Plot Rigid Body
4173	################################################################################
4174
4175	def PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults):
4176	'''RB plotting package. Can show rigid body structures as balls & sticks
4177	'''
4178
4179	def FindBonds(XYZ):
4180	rbTypes = rbData['rbTypes']
4181	Radii = []
4182	for Atype in rbTypes:
4183	Radii.append(AtInfo[Atype][0])
4184	if Atype == 'H':
4185	Radii[-1] = 0.5
4186	Radii = np.array(Radii)
4187	Bonds = [[] for i in range(len(Radii))]
4188	for i,xyz in enumerate(XYZ):
4189	Dx = XYZ-xyz
4190	dist = np.sqrt(np.sum(Dx**2,axis=1))
4191	sumR = Radii[i]+Radii
4192	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
4193	for j in IndB[0]:
4194	Bonds[i].append(Dx[j]*Radii[i]/sumR[j])
4195	Bonds[j].append(-Dx[j]*Radii[j]/sumR[j])
4196	return Bonds
4197
4198	Wt = np.array([255,255,255])
4199	Rd = np.array([255,0,0])
4200	Gr = np.array([0,255,0])
4201	Bl = np.array([0,0,255])
4202	uBox = np.array([[0,0,0],[1,0,0],[0,1,0],[0,0,1]])
4203	uEdges = np.array([[uBox[0],uBox[1]],[uBox[0],uBox[2]],[uBox[0],uBox[3]]])
4204	uColors = [Rd,Gr,Bl]
4205	if rbType == 'Vector':
4206	atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['rbTypes'])]
4207	XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
4208	for imag,mag in enumerate(rbData['VectMag']):
4209	XYZ += mag*rbData['rbVect'][imag]
4210	Bonds = FindBonds(XYZ)
4211	elif rbType == 'Residue':
4212	# atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['atNames'])]
4213	atNames = rbData['atNames']
4214	XYZ = np.copy(rbData['rbXYZ']) #don't mess with original!
4215	Seq = rbData['rbSeq']
4216	for ia,ib,ang,mv in Seq:
4217	va = XYZ[ia]-XYZ[ib]
4218	Q = G2mth.AVdeg2Q(ang,va)
4219	for im in mv:
4220	vb = XYZ[im]-XYZ[ib]
4221	vb = G2mth.prodQVQ(Q,vb)
4222	XYZ[im] = XYZ[ib]+vb
4223	Bonds = FindBonds(XYZ)
4224	elif rbType == 'Z-matrix':
4225	pass
4226
4227	# def SetRBOrigin():
4228	# page = getSelection()
4229	# if page:
4230	# if G2frame.dataDisplay.GetPageText(page) == 'Rigid bodies':
4231	# G2frame.MapPeaksTable.SetData(mapPeaks)
4232	# panel = G2frame.dataDisplay.GetPage(page).GetChildren()
4233	# names = [child.GetName() for child in panel]
4234	# panel[names.index('grid window')].Refresh()
4235
4236	def OnMouseDown(event):
4237	xy = event.GetPosition()
4238	defaults['oldxy'] = list(xy)
4239
4240	def OnMouseMove(event):
4241	newxy = event.GetPosition()
4242
4243	if event.Dragging():
4244	if event.LeftIsDown():
4245	SetRotation(newxy)
4246	Q = defaults['Quaternion']
4247	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4248	# elif event.RightIsDown():
4249	# SetRBOrigin(newxy)
4250	elif event.MiddleIsDown():
4251	SetRotationZ(newxy)
4252	Q = defaults['Quaternion']
4253	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4254	Draw('move')
4255
4256	def OnMouseWheel(event):
4257	defaults['cameraPos'] += event.GetWheelRotation()/24
4258	defaults['cameraPos'] = max(10,min(500,defaults['cameraPos']))
4259	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(defaults['cameraPos']),1)
4260	Draw('wheel')
4261
4262	def SetBackground():
4263	R,G,B,A = Page.camera['backColor']
4264	glClearColor(R,G,B,A)
4265	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
4266
4267	def SetLights():
4268	glEnable(GL_DEPTH_TEST)
4269	glShadeModel(GL_FLAT)
4270	glEnable(GL_LIGHTING)
4271	glEnable(GL_LIGHT0)
4272	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
4273	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
4274	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
4275
4276	# def SetRBOrigin(newxy):
4277	##first get translation vector in screen coords.
4278	# oldxy = defaults['oldxy']
4279	# if not len(oldxy): oldxy = list(newxy)
4280	# dxy = newxy-oldxy
4281	# defaults['oldxy'] = list(newxy)
4282	# V = np.array([dxy[0],-dxy[1],0.])/100.
4283	# Q = defaults['Quaternion']
4284	# V = G2mth.prodQVQ(G2mth.invQ(Q),V)
4285	# rbData['rbXYZ'] += V
4286	# PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults)
4287	#
4288	def SetRotation(newxy):
4289	#first get rotation vector in screen coords. & angle increment
4290	oldxy = defaults['oldxy']
4291	if not len(oldxy): oldxy = list(newxy)
4292	dxy = newxy-oldxy
4293	defaults['oldxy'] = list(newxy)
4294	V = np.array([dxy[1],dxy[0],0.])
4295	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
4296	# next transform vector back to xtal coordinates via inverse quaternion
4297	# & make new quaternion
4298	Q = defaults['Quaternion']
4299	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
4300	DQ = G2mth.AVdeg2Q(A,V)
4301	Q = G2mth.prodQQ(Q,DQ)
4302	defaults['Quaternion'] = Q
4303	# finally get new view vector - last row of rotation matrix
4304	VD = G2mth.Q2Mat(Q)[2]
4305	VD /= np.sqrt(np.sum(VD**2))
4306	defaults['viewDir'] = VD
4307
4308	def SetRotationZ(newxy):
4309	#first get rotation vector (= view vector) in screen coords. & angle increment
4310	View = glGetIntegerv(GL_VIEWPORT)
4311	cent = [View[2]/2,View[3]/2]
4312	oldxy = defaults['oldxy']
4313	if not len(oldxy): oldxy = list(newxy)
4314	dxy = newxy-oldxy
4315	defaults['oldxy'] = list(newxy)
4316	V = defaults['viewDir']
4317	A = [0,0]
4318	A[0] = dxy[1]*.25
4319	A[1] = dxy[0]*.25
4320	if newxy[0] > cent[0]:
4321	A[0] *= -1
4322	if newxy[1] < cent[1]:
4323	A[1] *= -1
4324	# next transform vector back to xtal coordinates & make new quaternion
4325	Q = defaults['Quaternion']
4326	Qx = G2mth.AVdeg2Q(A[0],V)
4327	Qy = G2mth.AVdeg2Q(A[1],V)
4328	Q = G2mth.prodQQ(Q,Qx)
4329	Q = G2mth.prodQQ(Q,Qy)
4330	defaults['Quaternion'] = Q
4331
4332	def RenderUnitVectors(x,y,z):
4333	xyz = np.array([x,y,z])
4334	glEnable(GL_COLOR_MATERIAL)
4335	glLineWidth(1)
4336	glPushMatrix()
4337	glTranslate(x,y,z)
4338	glBegin(GL_LINES)
4339	for line,color in zip(uEdges,uColors):
4340	glColor3ubv(color)
4341	glVertex3fv(-line[1])
4342	glVertex3fv(line[1])
4343	glEnd()
4344	glPopMatrix()
4345	glColor4ubv